Query 025983
Match_columns 245
No_of_seqs 184 out of 1105
Neff 8.5
Searched_HMMs 46136
Date Fri Mar 29 11:48:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025983.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025983hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK00423 tfb transcription ini 100.0 6.2E-59 1.3E-63 405.6 25.4 233 4-245 12-257 (310)
2 KOG1597 Transcription initiati 100.0 6.7E-57 1.5E-61 374.5 22.8 236 4-245 1-241 (308)
3 COG1405 SUA7 Transcription ini 100.0 2E-54 4.3E-59 368.9 22.0 223 4-242 2-227 (285)
4 KOG1598 Transcription initiati 100.0 1.8E-32 3.9E-37 245.2 11.6 199 4-242 1-202 (521)
5 PF00382 TFIIB: Transcription 99.8 5.4E-20 1.2E-24 126.6 10.1 71 112-183 1-71 (71)
6 PRK00423 tfb transcription ini 99.7 6.2E-16 1.3E-20 135.3 12.6 90 107-197 218-307 (310)
7 PF08271 TF_Zn_Ribbon: TFIIB z 99.7 3.2E-17 6.9E-22 101.3 3.2 43 4-47 1-43 (43)
8 COG1405 SUA7 Transcription ini 99.5 2.5E-14 5.5E-19 122.6 10.1 91 106-197 192-282 (285)
9 KOG1597 Transcription initiati 99.5 1.8E-13 4E-18 115.0 10.0 88 107-195 202-289 (308)
10 cd00043 CYCLIN Cyclin box fold 99.3 1.1E-10 2.3E-15 82.1 11.2 83 107-190 4-87 (88)
11 smart00385 CYCLIN domain prese 99.2 3E-10 6.6E-15 78.9 9.0 80 111-191 2-82 (83)
12 KOG0834 CDK9 kinase-activating 99.0 2.7E-09 5.9E-14 92.9 10.0 126 105-236 39-182 (323)
13 TIGR00569 ccl1 cyclin ccl1. Un 98.9 2.5E-08 5.4E-13 86.8 13.8 126 106-238 57-195 (305)
14 KOG1598 Transcription initiati 98.8 4.1E-09 9E-14 95.6 3.1 92 104-196 162-256 (521)
15 KOG0835 Cyclin L [General func 98.6 5.2E-07 1.1E-11 77.4 11.4 124 106-235 24-169 (367)
16 COG5333 CCL1 Cdk activating ki 98.5 1.1E-06 2.3E-11 75.3 10.5 129 106-240 46-183 (297)
17 PF00134 Cyclin_N: Cyclin, N-t 98.1 5.1E-05 1.1E-09 57.2 10.9 92 105-197 31-125 (127)
18 KOG0794 CDK8 kinase-activating 97.9 2.2E-05 4.7E-10 64.6 6.3 128 108-241 44-186 (264)
19 KOG0656 G1/S-specific cyclin D 97.9 0.00035 7.6E-09 61.3 13.7 112 106-223 79-196 (335)
20 PF01857 RB_B: Retinoblastoma- 97.9 7E-05 1.5E-09 57.6 8.1 83 105-188 11-95 (135)
21 PF11781 RRN7: RNA polymerase 97.5 8.3E-05 1.8E-09 43.6 2.1 27 5-34 10-36 (36)
22 KOG2496 Cdk activating kinase 97.4 0.001 2.3E-08 56.9 8.9 87 110-197 61-153 (325)
23 KOG0835 Cyclin L [General func 97.2 0.002 4.3E-08 55.8 8.0 108 105-222 138-248 (367)
24 PF08792 A2L_zn_ribbon: A2L zi 97.1 0.00042 9E-09 39.8 2.6 31 1-33 1-31 (33)
25 PHA00626 hypothetical protein 97.0 0.00054 1.2E-08 43.5 2.6 31 4-35 1-35 (59)
26 PF02984 Cyclin_C: Cyclin, C-t 97.0 0.0047 1E-07 45.6 8.2 87 108-195 3-90 (118)
27 PRK00415 rps27e 30S ribosomal 96.8 0.00079 1.7E-08 43.7 2.1 31 4-35 12-42 (59)
28 PF00382 TFIIB: Transcription 96.8 0.0018 3.9E-08 44.0 4.0 30 213-242 1-30 (71)
29 COG2051 RPS27A Ribosomal prote 96.8 0.00081 1.8E-08 44.4 1.8 31 4-35 20-50 (67)
30 PF01667 Ribosomal_S27e: Ribos 96.7 0.00076 1.7E-08 43.2 1.4 31 4-35 8-38 (55)
31 PRK00420 hypothetical protein; 96.7 0.0013 2.7E-08 48.7 2.6 29 3-34 23-51 (112)
32 PF14803 Nudix_N_2: Nudix N-te 96.6 0.0016 3.6E-08 37.6 2.2 28 4-33 1-32 (34)
33 PF13248 zf-ribbon_3: zinc-rib 96.6 0.0012 2.5E-08 35.8 1.4 24 1-31 1-24 (26)
34 KOG0653 Cyclin B and related k 96.5 0.035 7.6E-07 50.4 11.2 125 106-237 159-287 (391)
35 COG5024 Cyclin [Cell division 96.3 0.028 6E-07 51.4 9.4 119 108-233 216-337 (440)
36 PRK00398 rpoP DNA-directed RNA 96.3 0.0029 6.3E-08 39.2 2.2 31 1-33 1-31 (46)
37 PF13240 zinc_ribbon_2: zinc-r 96.3 0.0021 4.6E-08 33.7 1.3 22 5-32 1-22 (23)
38 PLN00209 ribosomal protein S27 96.3 0.0028 6.1E-08 44.1 2.0 31 4-35 37-67 (86)
39 PTZ00083 40S ribosomal protein 96.2 0.0033 7E-08 43.7 2.1 31 4-35 36-66 (85)
40 PF02150 RNA_POL_M_15KD: RNA p 96.2 0.0041 8.9E-08 36.2 2.2 31 3-34 1-31 (35)
41 COG1645 Uncharacterized Zn-fin 96.2 0.0025 5.3E-08 48.3 1.4 24 3-30 28-51 (131)
42 PF08274 PhnA_Zn_Ribbon: PhnA 95.8 0.008 1.7E-07 33.6 2.0 28 3-33 2-29 (30)
43 smart00778 Prim_Zn_Ribbon Zinc 95.8 0.0091 2E-07 35.1 2.4 28 4-31 4-33 (37)
44 PF09538 FYDLN_acid: Protein o 95.6 0.0074 1.6E-07 44.5 1.9 31 3-36 9-39 (108)
45 COG1997 RPL43A Ribosomal prote 95.5 0.012 2.7E-07 41.0 2.7 30 3-34 35-64 (89)
46 PRK00432 30S ribosomal protein 95.5 0.0099 2.1E-07 37.5 2.0 27 4-33 21-47 (50)
47 PF14354 Lar_restr_allev: Rest 95.3 0.02 4.2E-07 37.6 3.1 29 2-31 2-37 (61)
48 PF10571 UPF0547: Uncharacteri 95.3 0.01 2.3E-07 32.0 1.4 25 4-34 1-25 (26)
49 PF06677 Auto_anti-p27: Sjogre 95.1 0.019 4.1E-07 34.6 2.3 25 3-30 17-41 (41)
50 PRK00464 nrdR transcriptional 95.1 0.017 3.7E-07 45.4 2.7 30 4-33 1-38 (154)
51 TIGR01206 lysW lysine biosynth 95.1 0.012 2.7E-07 37.6 1.5 30 4-34 3-33 (54)
52 PRK11827 hypothetical protein; 95.0 0.016 3.5E-07 37.9 1.8 28 4-33 9-36 (60)
53 TIGR02300 FYDLN_acid conserved 94.8 0.018 3.9E-07 43.3 1.9 31 3-36 9-39 (129)
54 smart00661 RPOL9 RNA polymeras 94.7 0.026 5.7E-07 35.6 2.2 28 5-34 2-31 (52)
55 TIGR02098 MJ0042_CXXC MJ0042 f 94.6 0.016 3.5E-07 34.2 1.0 31 4-34 3-36 (38)
56 TIGR00244 transcriptional regu 94.5 0.04 8.6E-07 42.7 3.1 30 4-33 1-38 (147)
57 PRK10220 hypothetical protein; 94.5 0.034 7.4E-07 40.6 2.6 30 1-33 1-30 (111)
58 TIGR03655 anti_R_Lar restricti 94.3 0.033 7.1E-07 35.6 2.0 32 3-34 1-37 (53)
59 COG1998 RPS31 Ribosomal protei 94.3 0.026 5.7E-07 35.0 1.5 27 4-32 20-46 (51)
60 COG2835 Uncharacterized conser 94.2 0.036 7.7E-07 36.1 2.0 30 2-33 7-36 (60)
61 PF08273 Prim_Zn_Ribbon: Zinc- 94.1 0.042 9.2E-07 32.9 2.1 29 4-32 4-35 (40)
62 PF03966 Trm112p: Trm112p-like 94.1 0.051 1.1E-06 36.6 2.8 17 17-33 47-63 (68)
63 PRK12495 hypothetical protein; 94.0 0.034 7.4E-07 45.7 2.1 32 1-36 40-71 (226)
64 PF09862 DUF2089: Protein of u 94.0 0.039 8.5E-07 40.9 2.2 60 168-233 52-111 (113)
65 PF09297 zf-NADH-PPase: NADH p 93.9 0.066 1.4E-06 30.3 2.6 28 4-33 4-31 (32)
66 PF08613 Cyclin: Cyclin; Inte 93.8 2.2 4.8E-05 33.1 12.0 88 108-196 54-147 (149)
67 COG2824 PhnA Uncharacterized Z 93.4 0.19 4.1E-06 36.5 4.7 33 1-36 1-33 (112)
68 KOG4164 Cyclin ik3-1/CABLES [C 92.7 0.41 8.8E-06 42.8 6.8 60 106-165 383-442 (497)
69 smart00440 ZnF_C2C2 C2C2 Zinc 92.7 0.09 1.9E-06 31.5 1.9 27 5-32 2-37 (40)
70 KOG1779 40s ribosomal protein 92.5 0.048 1E-06 37.2 0.7 30 4-34 35-64 (84)
71 TIGR01384 TFS_arch transcripti 92.4 0.085 1.8E-06 38.5 1.9 28 4-35 1-28 (104)
72 PF12760 Zn_Tnp_IS1595: Transp 92.4 0.15 3.2E-06 31.5 2.7 27 4-31 19-45 (46)
73 PF01780 Ribosomal_L37ae: Ribo 92.3 0.076 1.6E-06 37.6 1.4 30 4-35 36-65 (90)
74 PRK14892 putative transcriptio 92.1 0.11 2.3E-06 37.7 2.0 31 4-35 22-54 (99)
75 TIGR00686 phnA alkylphosphonat 91.9 0.15 3.2E-06 37.3 2.6 31 3-36 2-32 (109)
76 COG4888 Uncharacterized Zn rib 91.7 0.12 2.5E-06 37.2 1.8 30 4-34 23-57 (104)
77 PF07282 OrfB_Zn_ribbon: Putat 91.7 0.14 3E-06 34.3 2.2 29 4-34 29-57 (69)
78 COG1594 RPB9 DNA-directed RNA 91.6 0.15 3.2E-06 38.0 2.4 33 3-36 2-35 (113)
79 COG1327 Predicted transcriptio 91.6 0.13 2.8E-06 39.9 2.0 30 4-33 1-38 (156)
80 PF01096 TFIIS_C: Transcriptio 91.5 0.16 3.5E-06 30.2 2.1 28 5-32 2-37 (39)
81 smart00342 HTH_ARAC helix_turn 91.4 1 2.2E-05 30.3 6.5 71 112-190 4-75 (84)
82 KOG0655 G1/S-specific cyclin E 91.0 0.9 1.9E-05 39.9 6.8 91 107-197 147-240 (408)
83 KOG4557 Origin recognition com 91.0 8.1 0.00018 32.0 12.2 86 111-197 2-91 (262)
84 PF13719 zinc_ribbon_5: zinc-r 91.0 0.098 2.1E-06 30.7 0.7 29 4-33 3-35 (37)
85 PTZ00255 60S ribosomal protein 90.9 0.17 3.7E-06 35.8 2.0 32 3-36 36-67 (90)
86 COG2888 Predicted Zn-ribbon RN 90.9 0.16 3.4E-06 32.9 1.7 24 5-30 11-34 (61)
87 COG4640 Predicted membrane pro 90.8 0.13 2.8E-06 45.9 1.6 28 3-36 1-28 (465)
88 KOG4557 Origin recognition com 90.8 0.98 2.1E-05 37.2 6.5 79 112-192 96-179 (262)
89 PF03604 DNA_RNApol_7kD: DNA d 90.7 0.16 3.4E-06 28.9 1.4 25 5-32 2-26 (32)
90 smart00659 RPOLCX RNA polymera 90.5 0.2 4.2E-06 30.7 1.7 27 4-33 3-29 (44)
91 PRK09710 lar restriction allev 90.5 0.33 7.1E-06 32.0 2.9 30 3-33 6-37 (64)
92 PF05460 ORC6: Origin recognit 90.4 0.082 1.8E-06 47.3 0.0 77 120-197 11-88 (353)
93 PF09862 DUF2089: Protein of u 90.2 0.6 1.3E-05 34.6 4.5 23 6-34 1-23 (113)
94 PF05191 ADK_lid: Adenylate ki 90.1 0.056 1.2E-06 31.6 -0.9 29 5-33 3-31 (36)
95 PRK12286 rpmF 50S ribosomal pr 90.0 0.22 4.7E-06 32.3 1.8 28 4-38 28-55 (57)
96 KOG1010 Rb (Retinoblastoma tum 90.0 0.74 1.6E-05 45.1 6.1 83 107-190 679-763 (920)
97 PF00325 Crp: Bacterial regula 89.7 0.62 1.3E-05 26.4 3.3 27 165-192 2-28 (32)
98 COG3478 Predicted nucleic-acid 89.7 0.24 5.2E-06 32.6 1.8 14 4-18 5-18 (68)
99 smart00834 CxxC_CXXC_SSSS Puta 89.7 0.22 4.7E-06 29.6 1.5 30 4-33 6-36 (41)
100 TIGR00280 L37a ribosomal prote 89.6 0.23 4.9E-06 35.3 1.7 31 3-35 35-65 (91)
101 PF14255 Cys_rich_CPXG: Cystei 89.5 0.25 5.4E-06 31.4 1.7 29 5-33 2-34 (52)
102 PF05129 Elf1: Transcription e 89.4 0.22 4.8E-06 34.8 1.5 32 4-35 23-58 (81)
103 PRK09678 DNA-binding transcrip 89.1 0.44 9.5E-06 32.4 2.8 31 3-34 1-40 (72)
104 PRK13130 H/ACA RNA-protein com 89.0 0.33 7.1E-06 31.3 2.0 25 2-34 4-28 (56)
105 TIGR02443 conserved hypothetic 88.8 0.42 9.1E-06 31.0 2.4 30 4-33 10-41 (59)
106 PF12773 DZR: Double zinc ribb 88.8 0.24 5.2E-06 30.9 1.3 27 4-33 13-39 (50)
107 PRK05978 hypothetical protein; 88.6 0.34 7.4E-06 37.8 2.3 30 4-34 34-63 (148)
108 COG4068 Uncharacterized protei 88.5 0.1 2.2E-06 33.6 -0.5 25 4-34 9-34 (64)
109 PRK03976 rpl37ae 50S ribosomal 88.5 0.3 6.5E-06 34.6 1.8 32 3-36 36-67 (90)
110 cd00350 rubredoxin_like Rubred 87.9 0.4 8.7E-06 27.3 1.7 24 4-31 2-25 (33)
111 PF08279 HTH_11: HTH domain; 87.9 1.7 3.8E-05 27.3 5.0 33 161-194 11-43 (55)
112 PRK06266 transcription initiat 87.8 0.14 3.1E-06 41.3 -0.3 31 4-35 118-148 (178)
113 PF01783 Ribosomal_L32p: Ribos 87.6 0.34 7.5E-06 31.2 1.5 27 4-37 27-53 (56)
114 PF15616 TerY-C: TerY-C metal 87.4 0.32 7E-06 37.0 1.5 21 4-33 78-98 (131)
115 PRK14890 putative Zn-ribbon RN 87.3 0.52 1.1E-05 30.6 2.1 28 3-32 7-34 (59)
116 PF09855 DUF2082: Nucleic-acid 87.3 0.43 9.2E-06 31.7 1.8 9 24-32 37-45 (64)
117 KOG0794 CDK8 kinase-activating 86.9 3.5 7.6E-05 34.5 7.3 82 112-195 157-239 (264)
118 COG5349 Uncharacterized protei 86.8 0.34 7.4E-06 36.1 1.2 38 4-42 22-59 (126)
119 TIGR01031 rpmF_bact ribosomal 86.6 0.48 1E-05 30.5 1.7 27 4-37 27-53 (55)
120 PRK02935 hypothetical protein; 86.4 0.55 1.2E-05 34.1 2.1 27 4-34 71-97 (110)
121 PF13545 HTH_Crp_2: Crp-like h 86.4 2.2 4.7E-05 28.7 5.1 43 150-193 3-55 (76)
122 PF02082 Rrf2: Transcriptional 86.1 1.4 3.1E-05 30.5 4.1 43 149-192 9-51 (83)
123 PF14446 Prok-RING_1: Prokaryo 86.1 0.54 1.2E-05 30.0 1.7 27 4-34 6-32 (54)
124 PF03119 DNA_ligase_ZBD: NAD-d 86.1 0.72 1.6E-05 25.3 2.0 22 5-28 1-22 (28)
125 TIGR00569 ccl1 cyclin ccl1. Un 85.8 9.4 0.0002 33.5 9.9 68 123-192 181-250 (305)
126 COG3877 Uncharacterized protei 85.5 0.63 1.4E-05 33.8 2.0 25 4-34 7-31 (122)
127 PF14952 zf-tcix: Putative tre 85.3 0.54 1.2E-05 28.5 1.4 26 4-35 12-39 (44)
128 PF09526 DUF2387: Probable met 85.1 0.86 1.9E-05 30.9 2.4 30 4-33 9-40 (71)
129 PF11672 DUF3268: Protein of u 85.0 0.82 1.8E-05 33.3 2.5 30 4-34 3-42 (102)
130 PF05876 Terminase_GpA: Phage 85.0 0.5 1.1E-05 45.0 1.7 43 4-46 201-255 (557)
131 PF00165 HTH_AraC: Bacterial r 84.8 3.3 7E-05 24.5 4.8 30 163-196 6-35 (42)
132 COG1996 RPC10 DNA-directed RNA 84.7 0.34 7.3E-06 30.3 0.3 28 4-33 7-34 (49)
133 COG1326 Uncharacterized archae 84.3 0.36 7.8E-06 39.0 0.4 32 4-36 7-43 (201)
134 TIGR02010 IscR iron-sulfur clu 84.1 3.3 7.1E-05 31.6 5.7 45 147-192 7-51 (135)
135 KOG1010 Rb (Retinoblastoma tum 84.1 7.5 0.00016 38.4 9.1 62 109-171 35-96 (920)
136 KOG2906 RNA polymerase III sub 84.0 0.83 1.8E-05 32.7 2.1 31 3-34 1-32 (105)
137 cd00730 rubredoxin Rubredoxin; 83.9 0.91 2E-05 28.6 2.0 11 25-35 3-13 (50)
138 PRK12336 translation initiatio 83.6 0.72 1.6E-05 37.9 1.9 29 5-33 100-129 (201)
139 PF01325 Fe_dep_repress: Iron 83.6 4.8 0.0001 26.2 5.5 37 154-192 12-48 (60)
140 PF04161 Arv1: Arv1-like famil 83.6 0.57 1.2E-05 38.7 1.3 34 4-37 1-38 (208)
141 TIGR03826 YvyF flagellar opero 83.6 0.27 5.9E-06 37.8 -0.6 30 1-35 1-30 (137)
142 cd00043 CYCLIN Cyclin box fold 83.3 2.5 5.4E-05 28.4 4.4 35 207-241 3-37 (88)
143 cd00092 HTH_CRP helix_turn_hel 83.1 5.8 0.00013 25.6 5.9 31 162-193 22-52 (67)
144 PF13717 zinc_ribbon_4: zinc-r 83.1 0.5 1.1E-05 27.5 0.6 29 4-33 3-35 (36)
145 smart00401 ZnF_GATA zinc finge 82.6 1.2 2.6E-05 28.2 2.2 32 3-34 3-36 (52)
146 PF11023 DUF2614: Protein of u 81.8 0.51 1.1E-05 34.7 0.3 39 4-49 70-108 (114)
147 PHA02942 putative transposase; 81.7 1.1 2.3E-05 40.7 2.4 28 4-34 326-353 (383)
148 PF00301 Rubredoxin: Rubredoxi 81.5 0.91 2E-05 28.2 1.3 14 24-37 2-15 (47)
149 TIGR02605 CxxC_CxxC_SSSS putat 81.4 1 2.2E-05 28.2 1.6 28 4-31 6-34 (52)
150 TIGR03697 NtcA_cyano global ni 81.2 8.7 0.00019 30.4 7.4 29 164-193 142-170 (193)
151 PRK10857 DNA-binding transcrip 81.1 4.8 0.0001 31.9 5.7 45 147-192 7-51 (164)
152 PRK14559 putative protein seri 81.1 0.96 2.1E-05 43.7 2.0 11 211-221 295-305 (645)
153 cd06571 Bac_DnaA_C C-terminal 81.0 6.8 0.00015 27.6 5.9 45 149-196 30-75 (90)
154 PRK08402 replication factor A; 80.2 1.4 3E-05 39.5 2.5 27 4-32 213-239 (355)
155 PF00356 LacI: Bacterial regul 80.1 2.2 4.9E-05 26.2 2.8 21 167-188 1-21 (46)
156 PF14122 YokU: YokU-like prote 80.0 1.1 2.3E-05 31.4 1.4 24 20-43 32-55 (87)
157 KOG0834 CDK9 kinase-activating 80.0 1.4 3.1E-05 38.8 2.6 90 105-195 148-246 (323)
158 PF13413 HTH_25: Helix-turn-he 79.5 3.3 7.1E-05 27.2 3.6 56 159-225 4-60 (62)
159 COG4530 Uncharacterized protei 79.3 1 2.2E-05 33.0 1.2 33 3-38 9-41 (129)
160 PF09723 Zn-ribbon_8: Zinc rib 79.3 1.3 2.9E-05 26.6 1.5 28 4-31 6-34 (42)
161 PF00196 GerE: Bacterial regul 79.1 3.6 7.8E-05 26.2 3.7 33 164-197 17-49 (58)
162 smart00385 CYCLIN domain prese 79.1 3.1 6.6E-05 27.6 3.6 29 211-239 1-29 (83)
163 COG1773 Rubredoxin [Energy pro 79.1 1.3 2.9E-05 28.4 1.5 26 1-30 1-26 (55)
164 PF10122 Mu-like_Com: Mu-like 78.9 0.56 1.2E-05 29.5 -0.2 33 2-34 3-35 (51)
165 KOG2593 Transcription initiati 78.9 1 2.2E-05 40.9 1.3 32 4-35 129-165 (436)
166 cd00202 ZnF_GATA Zinc finger D 78.6 0.79 1.7E-05 29.3 0.4 30 5-34 1-32 (54)
167 PRK08351 DNA-directed RNA poly 78.6 1.3 2.8E-05 29.1 1.4 23 1-31 1-23 (61)
168 smart00550 Zalpha Z-DNA-bindin 78.4 7.8 0.00017 25.8 5.3 38 155-193 11-49 (68)
169 PRK05508 methionine sulfoxide 78.3 1.6 3.5E-05 32.7 2.0 32 18-49 28-61 (119)
170 PRK10219 DNA-binding transcrip 78.1 21 0.00046 25.6 8.0 39 150-190 7-45 (107)
171 KOG1088 Uncharacterized conser 78.1 0.89 1.9E-05 33.7 0.6 18 17-34 92-109 (124)
172 TIGR01384 TFS_arch transcripti 77.9 1.9 4E-05 31.3 2.3 28 4-32 63-99 (104)
173 PF10058 DUF2296: Predicted in 77.8 1.4 3E-05 28.2 1.3 29 4-32 23-53 (54)
174 COG1656 Uncharacterized conser 77.5 1.2 2.5E-05 35.3 1.1 29 3-33 97-140 (165)
175 PF13453 zf-TFIIB: Transcripti 77.4 2 4.3E-05 25.6 1.9 28 5-33 1-29 (41)
176 PRK13719 conjugal transfer tra 77.2 15 0.00032 30.6 7.5 61 163-235 156-216 (217)
177 PRK00241 nudC NADH pyrophospha 77.2 1.7 3.6E-05 37.2 2.1 28 4-33 100-127 (256)
178 CHL00174 accD acetyl-CoA carbo 77.2 0.5 1.1E-05 41.1 -1.1 30 4-34 39-68 (296)
179 PRK11920 rirA iron-responsive 77.0 7.9 0.00017 30.3 5.7 44 147-192 7-50 (153)
180 PF13412 HTH_24: Winged helix- 76.9 11 0.00024 22.8 5.3 29 163-192 15-43 (48)
181 smart00419 HTH_CRP helix_turn_ 76.9 5.1 0.00011 24.0 3.8 29 163-192 6-34 (48)
182 TIGR00515 accD acetyl-CoA carb 76.5 0.55 1.2E-05 40.8 -1.0 30 4-34 27-56 (285)
183 PRK03975 tfx putative transcri 76.3 12 0.00026 28.9 6.4 65 164-242 20-92 (141)
184 PF04216 FdhE: Protein involve 76.3 1.5 3.2E-05 38.1 1.6 29 4-32 173-206 (290)
185 COG0333 RpmF Ribosomal protein 76.1 2 4.4E-05 27.8 1.7 28 3-37 27-54 (57)
186 TIGR03830 CxxCG_CxxCG_HTH puta 76.1 2.1 4.4E-05 32.0 2.1 21 165-186 78-98 (127)
187 PF06827 zf-FPG_IleRS: Zinc fi 75.8 1.8 4E-05 23.8 1.3 28 4-31 2-29 (30)
188 PF12802 MarR_2: MarR family; 75.8 9.7 0.00021 24.2 5.1 40 152-192 8-47 (62)
189 COG2816 NPY1 NTP pyrophosphohy 75.8 1.9 4.1E-05 37.1 2.0 27 4-34 112-140 (279)
190 PRK00222 methionine sulfoxide 75.5 2.1 4.5E-05 33.1 2.0 33 18-50 38-72 (142)
191 PF13613 HTH_Tnp_4: Helix-turn 75.1 5.6 0.00012 25.0 3.6 38 158-196 12-49 (53)
192 PF08646 Rep_fac-A_C: Replicat 74.8 2.6 5.5E-05 32.6 2.4 27 5-34 20-48 (146)
193 TIGR00721 tfx DNA-binding prot 74.7 10 0.00023 29.1 5.7 31 164-195 20-50 (137)
194 COG0777 AccD Acetyl-CoA carbox 74.7 0.84 1.8E-05 39.1 -0.4 43 4-48 29-78 (294)
195 PF07754 DUF1610: Domain of un 74.6 2.6 5.6E-05 22.2 1.6 23 6-31 1-24 (24)
196 PRK11511 DNA-binding transcrip 74.5 25 0.00055 26.3 7.8 42 147-190 8-49 (127)
197 PRK05654 acetyl-CoA carboxylas 74.4 0.67 1.5E-05 40.4 -1.1 43 4-48 28-77 (292)
198 cd00729 rubredoxin_SM Rubredox 74.1 2.8 6.2E-05 24.0 1.9 24 4-31 3-26 (34)
199 PRK12380 hydrogenase nickel in 73.8 2 4.3E-05 31.9 1.5 7 5-11 72-78 (113)
200 PF04545 Sigma70_r4: Sigma-70, 73.7 8.9 0.00019 23.5 4.3 31 163-194 18-48 (50)
201 PF14353 CpXC: CpXC protein 73.6 3.1 6.7E-05 31.4 2.5 12 23-34 38-49 (128)
202 COG1959 Predicted transcriptio 73.4 8.1 0.00018 30.1 4.9 44 148-192 8-51 (150)
203 COG1779 C4-type Zn-finger prot 73.3 2.2 4.8E-05 34.7 1.7 37 4-41 15-61 (201)
204 TIGR03831 YgiT_finger YgiT-typ 73.1 2.6 5.7E-05 25.3 1.7 10 24-33 33-42 (46)
205 TIGR00738 rrf2_super rrf2 fami 73.0 11 0.00024 28.2 5.5 44 148-192 8-51 (132)
206 smart00421 HTH_LUXR helix_turn 72.7 10 0.00022 23.2 4.5 32 165-197 18-49 (58)
207 TIGR00357 methionine-R-sulfoxi 72.7 2.6 5.6E-05 32.3 1.9 33 18-50 35-69 (134)
208 PF09339 HTH_IclR: IclR helix- 72.7 8.2 0.00018 24.0 4.0 36 156-192 9-44 (52)
209 TIGR03829 YokU_near_AblA uncha 72.6 2.9 6.3E-05 29.6 2.0 33 5-37 1-49 (89)
210 PF01396 zf-C4_Topoisom: Topoi 72.6 6.2 0.00013 23.3 3.1 29 4-33 2-34 (39)
211 TIGR00100 hypA hydrogenase nic 72.6 2.3 5E-05 31.7 1.6 17 15-31 62-78 (115)
212 PF04703 FaeA: FaeA-like prote 72.1 9.9 0.00022 25.0 4.3 33 163-196 13-45 (62)
213 KOG3134 Predicted membrane pro 72.0 1.2 2.6E-05 36.7 -0.0 34 4-37 1-38 (225)
214 COG2093 DNA-directed RNA polym 71.9 2.3 5E-05 27.9 1.2 26 1-32 2-27 (64)
215 KOG0402 60S ribosomal protein 71.9 1.2 2.7E-05 30.8 -0.0 29 4-34 37-65 (92)
216 cd04476 RPA1_DBD_C RPA1_DBD_C: 71.6 3.1 6.7E-05 32.8 2.2 28 4-34 35-62 (166)
217 PF13730 HTH_36: Helix-turn-he 71.4 15 0.00032 22.9 5.0 25 167-192 27-51 (55)
218 PF06044 DRP: Dam-replacing fa 71.3 1.8 3.9E-05 36.4 0.8 29 4-33 32-63 (254)
219 TIGR02944 suf_reg_Xantho FeS a 71.1 14 0.00031 27.6 5.8 44 147-192 8-51 (130)
220 PRK11161 fumarate/nitrate redu 71.0 22 0.00048 29.2 7.4 29 164-193 183-211 (235)
221 PF13404 HTH_AsnC-type: AsnC-t 70.9 12 0.00027 22.3 4.3 30 161-191 13-42 (42)
222 PRK03824 hypA hydrogenase nick 70.6 2.7 5.8E-05 32.3 1.6 21 14-34 61-81 (135)
223 COG3355 Predicted transcriptio 70.5 12 0.00026 28.3 5.1 36 156-192 33-68 (126)
224 PF04606 Ogr_Delta: Ogr/Delta- 70.1 3.3 7.1E-05 25.5 1.6 28 5-33 1-37 (47)
225 PF13790 DUF4182: Domain of un 69.9 2.2 4.9E-05 25.1 0.8 13 22-34 2-14 (38)
226 TIGR00155 pqiA_fam integral me 69.5 3.2 7E-05 37.9 2.1 30 5-34 15-44 (403)
227 cd06170 LuxR_C_like C-terminal 69.0 14 0.0003 22.6 4.5 32 165-197 15-46 (57)
228 PRK14559 putative protein seri 68.9 2.7 5.8E-05 40.7 1.5 14 21-34 39-52 (645)
229 COG3809 Uncharacterized protei 68.9 4.1 8.9E-05 28.0 2.0 30 3-34 1-32 (88)
230 COG5333 CCL1 Cdk activating ki 68.7 11 0.00023 32.9 4.9 45 124-168 168-212 (297)
231 PRK15201 fimbriae regulatory p 68.5 20 0.00043 29.0 6.1 35 162-197 145-179 (198)
232 PF05344 DUF746: Domain of Unk 68.5 15 0.00032 24.4 4.5 36 159-195 7-42 (65)
233 PF01155 HypA: Hydrogenase exp 68.4 1.3 2.8E-05 32.9 -0.6 24 5-32 72-95 (113)
234 PF07191 zinc-ribbons_6: zinc- 68.3 3 6.5E-05 28.1 1.2 26 4-33 2-27 (70)
235 TIGR00310 ZPR1_znf ZPR1 zinc f 68.2 3.7 8.1E-05 33.5 2.0 32 5-36 2-43 (192)
236 PF14471 DUF4428: Domain of un 68.2 1.7 3.7E-05 27.4 0.0 28 5-33 1-30 (51)
237 PF10080 DUF2318: Predicted me 68.1 4.5 9.7E-05 29.5 2.2 27 5-34 37-63 (102)
238 PF06397 Desulfoferrod_N: Desu 67.7 2.1 4.6E-05 24.9 0.4 22 4-26 7-28 (36)
239 PF01726 LexA_DNA_bind: LexA D 67.6 12 0.00025 24.9 4.0 32 160-192 20-52 (65)
240 PF01381 HTH_3: Helix-turn-hel 66.8 14 0.0003 22.9 4.2 47 163-225 7-53 (55)
241 PRK03564 formate dehydrogenase 66.6 5.3 0.00012 35.1 2.8 9 4-12 188-196 (309)
242 PF01641 SelR: SelR domain; I 66.6 3.4 7.4E-05 31.2 1.4 32 19-50 33-66 (124)
243 PRK04023 DNA polymerase II lar 66.4 4.1 8.9E-05 41.0 2.3 11 24-34 664-674 (1121)
244 PF01978 TrmB: Sugar-specific 66.4 8.8 0.00019 25.2 3.3 36 155-192 13-48 (68)
245 PRK12366 replication factor A; 66.3 3.3 7.1E-05 40.2 1.6 25 4-32 533-557 (637)
246 PF01599 Ribosomal_S27: Riboso 66.2 7.3 0.00016 24.1 2.5 26 4-31 19-46 (47)
247 TIGR01562 FdhE formate dehydro 66.0 5.3 0.00011 35.0 2.6 9 25-33 254-262 (305)
248 TIGR00340 zpr1_rel ZPR1-relate 65.8 4.3 9.3E-05 32.2 1.9 31 6-36 1-41 (163)
249 PF08220 HTH_DeoR: DeoR-like h 65.7 11 0.00024 24.0 3.6 31 162-193 11-41 (57)
250 KOG3507 DNA-directed RNA polym 65.6 4.1 8.9E-05 26.3 1.4 27 4-33 21-47 (62)
251 PF09889 DUF2116: Uncharacteri 65.5 1.8 3.9E-05 28.2 -0.3 25 4-34 4-29 (59)
252 PF03833 PolC_DP2: DNA polymer 65.2 2.1 4.5E-05 42.2 0.0 12 23-34 680-691 (900)
253 PRK11753 DNA-binding transcrip 65.2 40 0.00087 27.0 7.7 29 164-193 167-195 (211)
254 PHA03074 late transcription fa 65.1 3.7 8E-05 33.5 1.4 31 1-34 2-32 (225)
255 COG1510 Predicted transcriptio 65.1 9.8 0.00021 30.4 3.7 38 154-192 30-67 (177)
256 PF00320 GATA: GATA zinc finge 65.0 1.9 4E-05 25.0 -0.2 27 6-32 1-29 (36)
257 PRK15103 paraquat-inducible me 65.0 4.4 9.5E-05 37.2 2.0 32 4-36 11-43 (419)
258 PRK03681 hypA hydrogenase nick 64.9 3.9 8.5E-05 30.4 1.4 14 17-30 64-77 (114)
259 PF13463 HTH_27: Winged helix 64.8 18 0.00038 23.4 4.6 31 161-192 14-44 (68)
260 PF10668 Phage_terminase: Phag 64.5 20 0.00044 23.4 4.6 39 146-188 6-44 (60)
261 cd00974 DSRD Desulforedoxin (D 64.3 5.2 0.00011 22.7 1.6 23 4-27 5-27 (34)
262 smart00345 HTH_GNTR helix_turn 64.2 16 0.00035 22.6 4.2 25 167-192 22-46 (60)
263 PHA01976 helix-turn-helix prot 63.8 28 0.00062 22.4 5.4 47 163-225 13-59 (67)
264 COG1725 Predicted transcriptio 63.8 11 0.00024 28.5 3.7 26 166-192 36-61 (125)
265 PF13936 HTH_38: Helix-turn-he 63.8 16 0.00035 22.0 3.8 26 162-188 17-42 (44)
266 PRK10402 DNA-binding transcrip 63.8 28 0.0006 28.6 6.6 30 163-193 167-196 (226)
267 PRK06030 hypothetical protein; 63.7 24 0.00053 26.6 5.5 39 153-194 59-97 (124)
268 PF12172 DUF35_N: Rubredoxin-l 63.4 3.6 7.8E-05 23.8 0.8 21 4-30 12-32 (37)
269 PF08280 HTH_Mga: M protein tr 63.4 11 0.00024 24.2 3.2 33 163-196 17-49 (59)
270 PRK11014 transcriptional repre 63.3 21 0.00044 27.3 5.3 44 148-192 8-51 (141)
271 PF04216 FdhE: Protein involve 63.1 5.5 0.00012 34.6 2.3 31 4-34 212-249 (290)
272 TIGR00613 reco DNA repair prot 62.9 5.4 0.00012 33.3 2.1 28 4-31 148-176 (241)
273 PF13824 zf-Mss51: Zinc-finger 62.4 5.9 0.00013 25.4 1.7 24 5-33 1-24 (55)
274 PRK00085 recO DNA repair prote 62.4 5.1 0.00011 33.6 1.9 27 4-30 150-177 (247)
275 TIGR00595 priA primosomal prot 62.4 6.4 0.00014 37.1 2.7 29 4-34 223-251 (505)
276 PF14205 Cys_rich_KTR: Cystein 62.3 6.1 0.00013 25.2 1.7 27 5-31 6-36 (55)
277 TIGR01562 FdhE formate dehydro 62.3 5.4 0.00012 35.0 2.0 28 4-31 185-218 (305)
278 PF13542 HTH_Tnp_ISL3: Helix-t 62.1 34 0.00073 20.9 6.0 25 165-190 27-51 (52)
279 PRK01110 rpmF 50S ribosomal pr 62.1 5.7 0.00012 26.0 1.6 28 4-39 28-55 (60)
280 PF08063 PADR1: PADR1 (NUC008) 61.8 4.6 0.0001 25.9 1.1 21 4-27 15-35 (55)
281 PF14768 RPA_interact_C: Repli 61.4 6.7 0.00015 27.3 2.0 26 5-34 1-26 (82)
282 PRK05580 primosome assembly pr 61.4 6.7 0.00015 38.4 2.7 29 4-34 391-419 (679)
283 PRK06386 replication factor A; 61.2 4.4 9.5E-05 36.3 1.3 21 4-32 237-257 (358)
284 PRK07218 replication factor A; 60.9 3.9 8.5E-05 37.5 1.0 21 4-32 298-318 (423)
285 PF04502 DUF572: Family of unk 60.8 4.1 8.8E-05 36.1 1.0 25 4-28 78-102 (324)
286 PRK14714 DNA polymerase II lar 60.7 5.2 0.00011 41.3 1.8 8 4-11 668-675 (1337)
287 COG3877 Uncharacterized protei 60.7 26 0.00056 25.7 4.9 40 152-197 49-88 (122)
288 PF08281 Sigma70_r4_2: Sigma-7 60.7 19 0.0004 22.3 3.9 29 164-193 25-53 (54)
289 PF01412 ArfGap: Putative GTPa 60.6 3.3 7.2E-05 30.8 0.4 31 4-34 14-44 (116)
290 PRK13918 CRP/FNR family transc 60.5 45 0.00098 26.5 7.2 28 164-192 148-175 (202)
291 PF01485 IBR: IBR domain; Int 60.5 5.9 0.00013 25.4 1.5 28 4-33 19-50 (64)
292 COG4643 Uncharacterized protei 60.4 5 0.00011 35.4 1.5 26 5-30 34-61 (366)
293 PF09986 DUF2225: Uncharacteri 60.1 6.1 0.00013 32.8 1.9 27 208-234 183-211 (214)
294 COG0229 Conserved domain frequ 60.1 6.9 0.00015 29.9 2.0 32 18-49 37-70 (140)
295 PRK10130 transcriptional regul 59.9 46 0.00099 29.8 7.6 42 147-190 239-280 (350)
296 PRK00135 scpB segregation and 59.6 36 0.00078 27.6 6.3 45 146-195 4-49 (188)
297 TIGR01610 phage_O_Nterm phage 59.5 60 0.0013 23.0 8.4 30 162-192 44-73 (95)
298 TIGR00319 desulf_FeS4 desulfof 59.4 6.4 0.00014 22.3 1.4 22 4-26 8-29 (34)
299 smart00709 Zpr1 Duplicated dom 59.3 7.9 0.00017 30.6 2.3 31 5-35 2-41 (160)
300 PF03685 UPF0147: Uncharacteri 59.1 60 0.0013 22.8 6.4 53 102-158 5-57 (85)
301 PRK09391 fixK transcriptional 59.1 61 0.0013 26.7 7.9 29 164-193 178-206 (230)
302 PRK03564 formate dehydrogenase 58.5 8.5 0.00018 33.8 2.6 10 24-33 253-262 (309)
303 COG4565 CitB Response regulato 58.4 1.1E+02 0.0024 25.6 9.3 82 109-193 118-200 (224)
304 PF01022 HTH_5: Bacterial regu 58.3 33 0.00071 20.7 4.6 31 161-192 11-41 (47)
305 PF14206 Cys_rich_CPCC: Cystei 58.3 8.1 0.00018 26.7 1.9 27 4-33 2-30 (78)
306 PF13560 HTH_31: Helix-turn-he 58.1 43 0.00094 21.5 5.5 52 161-227 10-61 (64)
307 COG4391 Uncharacterized protei 58.0 5.9 0.00013 25.9 1.1 21 13-33 37-58 (62)
308 PF01807 zf-CHC2: CHC2 zinc fi 57.8 9.1 0.0002 27.4 2.3 27 5-31 35-62 (97)
309 KOG1921 Endonuclease III [Repl 57.8 1.2E+02 0.0025 26.0 8.9 110 99-222 90-201 (286)
310 COG4307 Uncharacterized protei 57.6 4.5 9.7E-05 34.6 0.7 28 1-34 1-28 (349)
311 PF02796 HTH_7: Helix-turn-hel 57.5 14 0.00031 22.3 2.8 25 163-188 19-43 (45)
312 smart00530 HTH_XRE Helix-turn- 57.3 36 0.00078 19.7 5.2 47 163-225 8-54 (56)
313 PF08299 Bac_DnaA_C: Bacterial 57.3 32 0.00069 23.0 4.7 65 109-190 3-70 (70)
314 PRK06450 threonine synthase; V 57.0 5 0.00011 35.7 1.0 29 1-34 1-29 (338)
315 PRK14873 primosome assembly pr 56.9 8.1 0.00018 37.7 2.4 27 4-32 393-419 (665)
316 PRK06260 threonine synthase; V 56.9 5 0.00011 36.5 0.9 30 1-34 1-30 (397)
317 PF10005 DUF2248: Uncharacteri 56.2 6.7 0.00014 34.8 1.6 24 5-34 1-24 (343)
318 PRK00564 hypA hydrogenase nick 56.1 4.9 0.00011 30.0 0.6 19 14-32 62-80 (117)
319 PF00392 GntR: Bacterial regul 56.0 22 0.00048 23.0 3.8 29 163-192 21-50 (64)
320 PF13384 HTH_23: Homeodomain-l 55.7 25 0.00054 21.3 3.8 27 165-192 17-43 (50)
321 PF03811 Zn_Tnp_IS1: InsA N-te 55.7 13 0.00028 21.6 2.2 25 4-29 6-35 (36)
322 PF08772 NOB1_Zn_bind: Nin one 55.2 6.3 0.00014 26.9 1.0 11 1-11 22-32 (73)
323 smart00418 HTH_ARSR helix_turn 55.0 40 0.00086 20.8 4.9 29 163-192 8-36 (66)
324 KOG2907 RNA polymerase I trans 54.9 5 0.00011 29.6 0.5 29 3-34 7-36 (116)
325 PF01047 MarR: MarR family; I 54.9 47 0.001 20.7 5.2 28 164-192 16-43 (59)
326 PF12677 DUF3797: Domain of un 54.8 11 0.00024 23.4 1.9 7 5-11 15-21 (49)
327 PRK14088 dnaA chromosomal repl 54.6 33 0.00072 31.6 6.0 43 149-194 370-415 (440)
328 PF03367 zf-ZPR1: ZPR1 zinc-fi 54.4 9.8 0.00021 30.1 2.1 32 4-35 2-42 (161)
329 PRK00750 lysK lysyl-tRNA synth 54.1 10 0.00022 35.8 2.5 32 5-37 177-213 (510)
330 TIGR02297 HpaA 4-hydroxyphenyl 54.1 1E+02 0.0022 26.1 8.6 38 151-190 189-226 (287)
331 PF13443 HTH_26: Cro/C1-type H 54.0 13 0.00028 23.8 2.4 46 165-225 10-55 (63)
332 PF04967 HTH_10: HTH DNA bindi 53.6 34 0.00074 21.7 4.1 27 165-192 23-49 (53)
333 smart00647 IBR In Between Ring 53.6 13 0.00027 23.8 2.3 28 4-33 19-50 (64)
334 PF04810 zf-Sec23_Sec24: Sec23 53.4 15 0.00034 21.6 2.4 30 3-32 2-33 (40)
335 smart00105 ArfGap Putative GTP 53.3 7.1 0.00015 28.8 1.1 31 4-34 4-34 (112)
336 COG3677 Transposase and inacti 53.1 11 0.00024 28.7 2.1 31 3-34 30-64 (129)
337 PRK08197 threonine synthase; V 53.0 6.3 0.00014 35.8 1.0 26 4-34 8-33 (394)
338 PF08006 DUF1700: Protein of u 53.0 32 0.00069 27.5 5.0 40 111-150 6-46 (181)
339 PRK08329 threonine synthase; V 52.9 9.5 0.00021 34.0 2.0 26 3-34 1-26 (347)
340 KOG0856 Predicted pilin-like t 52.8 10 0.00022 29.1 1.9 34 17-50 48-83 (146)
341 COG4311 SoxD Sarcosine oxidase 52.8 7.5 0.00016 27.7 1.1 12 1-12 1-12 (97)
342 smart00290 ZnF_UBP Ubiquitin C 52.7 11 0.00024 23.0 1.8 22 5-34 1-22 (50)
343 PRK06393 rpoE DNA-directed RNA 52.6 6.7 0.00014 26.0 0.8 21 3-31 5-25 (64)
344 smart00354 HTH_LACI helix_turn 52.4 57 0.0012 21.5 5.4 45 167-226 2-48 (70)
345 COG1654 BirA Biotin operon rep 52.2 43 0.00094 23.1 4.8 35 161-197 15-49 (79)
346 PF13913 zf-C2HC_2: zinc-finge 52.2 9.1 0.0002 20.2 1.1 9 3-11 2-10 (25)
347 PF01921 tRNA-synt_1f: tRNA sy 52.1 5.4 0.00012 35.8 0.4 12 162-173 287-298 (360)
348 PF14319 Zn_Tnp_IS91: Transpos 51.9 5.5 0.00012 29.5 0.3 33 4-38 43-75 (111)
349 PRK15435 bifunctional DNA-bind 51.5 95 0.0021 27.8 8.2 38 149-190 86-123 (353)
350 TIGR02392 rpoH_proteo alternat 51.3 37 0.0008 29.0 5.4 29 163-192 234-262 (270)
351 TIGR00122 birA_repr_reg BirA b 50.8 44 0.00096 21.8 4.7 31 161-192 9-39 (69)
352 PRK04330 hypothetical protein; 50.5 88 0.0019 22.1 6.4 53 101-157 7-59 (88)
353 TIGR03070 couple_hipB transcri 50.4 56 0.0012 19.9 5.0 45 163-223 13-57 (58)
354 PF07295 DUF1451: Protein of u 50.3 7.4 0.00016 30.3 0.8 15 20-34 109-123 (146)
355 cd00674 LysRS_core_class_I cat 50.2 13 0.00028 33.4 2.4 13 162-174 280-292 (353)
356 PRK04217 hypothetical protein; 50.2 31 0.00067 25.5 4.1 27 167-194 60-86 (110)
357 COG1571 Predicted DNA-binding 50.1 9.9 0.00021 34.8 1.7 33 4-39 351-383 (421)
358 PRK05550 bifunctional methioni 50.0 11 0.00023 32.7 1.8 33 18-50 31-65 (283)
359 cd07377 WHTH_GntR Winged helix 49.8 32 0.00069 21.7 3.8 25 167-192 27-51 (66)
360 PRK09685 DNA-binding transcrip 49.6 1.5E+02 0.0033 25.2 9.1 42 147-189 196-237 (302)
361 TIGR02607 antidote_HigA addict 49.4 65 0.0014 21.3 5.5 51 161-227 14-64 (78)
362 PRK04179 rpl37e 50S ribosomal 49.1 7.7 0.00017 25.4 0.6 23 4-31 18-40 (62)
363 smart00064 FYVE Protein presen 49.1 13 0.00027 24.5 1.7 30 4-37 11-40 (68)
364 PF01363 FYVE: FYVE zinc finge 49.0 11 0.00024 24.9 1.4 30 4-37 10-39 (69)
365 COG1198 PriA Primosomal protei 48.8 14 0.00031 36.4 2.6 27 4-32 445-471 (730)
366 PRK09392 ftrB transcriptional 48.6 68 0.0015 26.3 6.5 28 164-192 172-199 (236)
367 PF09334 tRNA-synt_1g: tRNA sy 48.6 8.3 0.00018 35.1 1.0 24 4-34 137-160 (391)
368 PF06689 zf-C4_ClpX: ClpX C4-t 48.3 6.6 0.00014 23.4 0.2 28 4-31 2-32 (41)
369 PF05225 HTH_psq: helix-turn-h 48.2 60 0.0013 19.6 5.4 26 162-189 14-39 (45)
370 PF01710 HTH_Tnp_IS630: Transp 48.2 1.1E+02 0.0024 22.6 7.1 77 111-195 20-100 (119)
371 PRK14714 DNA polymerase II lar 48.1 8.9 0.00019 39.7 1.2 23 4-33 680-702 (1337)
372 cd00065 FYVE FYVE domain; Zinc 47.9 14 0.00031 23.2 1.8 30 4-37 3-32 (57)
373 PRK10572 DNA-binding transcrip 47.9 1.3E+02 0.0027 25.6 8.2 17 17-33 69-85 (290)
374 cd07973 Spt4 Transcription elo 47.8 14 0.00029 26.8 1.8 29 3-34 3-31 (98)
375 PRK15121 right oriC-binding tr 47.4 1.1E+02 0.0023 26.3 7.7 40 149-190 6-45 (289)
376 PF01907 Ribosomal_L37e: Ribos 47.4 8.3 0.00018 24.7 0.6 24 5-33 17-40 (55)
377 smart00420 HTH_DEOR helix_turn 47.3 60 0.0013 19.3 5.2 29 164-193 13-41 (53)
378 COG2126 RPL37A Ribosomal prote 47.0 10 0.00022 24.5 0.9 24 5-33 18-41 (61)
379 PF09082 DUF1922: Domain of un 47.0 14 0.00031 24.7 1.7 27 4-34 4-30 (68)
380 PF14502 HTH_41: Helix-turn-he 46.9 39 0.00085 21.0 3.5 27 166-193 7-33 (48)
381 COG2771 CsgD DNA-binding HTH d 46.3 70 0.0015 20.0 5.0 33 164-197 18-50 (65)
382 cd00090 HTH_ARSR Arsenical Res 46.2 67 0.0015 20.3 5.1 26 166-192 21-46 (78)
383 PRK11475 DNA-binding transcrip 46.0 73 0.0016 26.1 6.1 33 164-197 148-180 (207)
384 PF13878 zf-C2H2_3: zinc-finge 45.2 4.8 0.0001 24.1 -0.8 17 21-37 11-27 (41)
385 PRK15411 rcsA colanic acid cap 44.7 42 0.00092 27.3 4.6 33 164-197 151-183 (207)
386 PF12844 HTH_19: Helix-turn-he 44.7 58 0.0013 20.7 4.4 48 162-225 9-56 (64)
387 COG5525 Bacteriophage tail ass 44.7 11 0.00025 35.8 1.3 32 5-36 229-272 (611)
388 PRK10371 DNA-binding transcrip 44.4 1.1E+02 0.0024 26.4 7.4 40 149-190 192-231 (302)
389 smart00344 HTH_ASNC helix_turn 44.3 51 0.0011 23.5 4.5 30 163-193 15-44 (108)
390 PF12840 HTH_20: Helix-turn-he 44.3 47 0.001 21.1 3.9 31 161-192 20-50 (61)
391 PRK10840 transcriptional regul 44.2 45 0.00097 26.9 4.7 33 164-197 164-196 (216)
392 PF13591 MerR_2: MerR HTH fami 44.0 52 0.0011 22.8 4.3 69 166-240 1-75 (84)
393 TIGR02844 spore_III_D sporulat 44.0 29 0.00063 24.1 2.9 23 164-187 18-40 (80)
394 PF00488 MutS_V: MutS domain V 43.4 29 0.00064 29.1 3.5 27 112-138 208-234 (235)
395 smart00342 HTH_ARAC helix_turn 43.3 40 0.00087 22.1 3.7 25 165-190 1-25 (84)
396 cd04762 HTH_MerR-trunc Helix-T 43.2 36 0.00077 19.9 3.0 22 167-189 2-23 (49)
397 COG1522 Lrp Transcriptional re 43.0 38 0.00083 25.8 3.9 31 161-192 18-48 (154)
398 COG2260 Predicted Zn-ribbon RN 43.0 14 0.0003 24.0 1.1 24 3-34 5-28 (59)
399 cd06171 Sigma70_r4 Sigma70, re 42.9 59 0.0013 19.0 4.1 28 166-194 27-54 (55)
400 PRK14526 adenylate kinase; Pro 42.9 17 0.00036 30.0 1.9 29 5-33 124-152 (211)
401 cd04766 HTH_HspR Helix-Turn-He 42.5 62 0.0013 22.6 4.6 68 166-239 2-76 (91)
402 PRK05638 threonine synthase; V 42.2 14 0.00031 34.0 1.5 25 4-34 2-26 (442)
403 PF14149 YhfH: YhfH-like prote 42.1 4 8.7E-05 23.9 -1.3 16 21-36 11-26 (37)
404 PRK15320 transcriptional activ 41.8 49 0.0011 27.3 4.3 37 160-197 174-210 (251)
405 PLN02569 threonine synthase 41.5 15 0.00033 34.4 1.6 26 4-34 50-75 (484)
406 PF05043 Mga: Mga helix-turn-h 41.4 39 0.00085 23.2 3.4 33 162-195 27-59 (87)
407 PRK13503 transcriptional activ 41.1 60 0.0013 27.3 5.2 39 150-190 173-211 (278)
408 smart00351 PAX Paired Box doma 41.1 1.5E+02 0.0032 22.1 7.1 60 112-174 36-102 (125)
409 TIGR00617 rpa1 replication fac 41.0 20 0.00043 34.7 2.3 28 4-34 475-504 (608)
410 COG2197 CitB Response regulato 40.9 51 0.0011 27.0 4.5 37 160-197 158-194 (211)
411 PRK11032 hypothetical protein; 40.9 13 0.00028 29.4 0.9 15 20-34 121-135 (160)
412 PF04079 DUF387: Putative tran 40.9 83 0.0018 24.8 5.5 80 150-236 2-90 (159)
413 TIGR03001 Sig-70_gmx1 RNA poly 40.7 30 0.00065 29.2 3.2 27 165-192 177-203 (244)
414 TIGR01764 excise DNA binding d 40.6 40 0.00088 19.7 3.0 22 166-188 2-23 (49)
415 cd04761 HTH_MerR-SF Helix-Turn 40.6 38 0.00082 20.1 2.9 21 167-188 2-22 (49)
416 PRK09393 ftrA transcriptional 40.6 1.3E+02 0.0027 26.2 7.2 40 149-190 219-258 (322)
417 smart00400 ZnF_CHCC zinc finge 40.6 36 0.00077 21.4 2.8 27 4-30 3-30 (55)
418 smart00346 HTH_ICLR helix_turn 40.5 1.2E+02 0.0025 20.6 5.8 28 164-192 19-46 (91)
419 PF01371 Trp_repressor: Trp re 40.3 67 0.0014 22.6 4.3 31 161-192 45-75 (87)
420 PRK08173 DNA topoisomerase III 40.1 18 0.00039 36.5 1.9 27 4-34 625-651 (862)
421 COG1321 TroR Mn-dependent tran 40.1 69 0.0015 25.1 4.9 71 154-227 14-97 (154)
422 PRK09430 djlA Dna-J like membr 40.0 2.4E+02 0.0052 24.2 10.6 101 109-239 151-255 (267)
423 PRK14018 trifunctional thiored 40.0 19 0.0004 34.1 1.9 31 19-49 414-446 (521)
424 PF09779 Ima1_N: Ima1 N-termin 39.9 21 0.00046 27.1 1.9 29 5-33 2-30 (131)
425 PRK04023 DNA polymerase II lar 39.9 18 0.0004 36.7 1.9 12 23-34 651-662 (1121)
426 PRK11169 leucine-responsive tr 39.6 64 0.0014 25.3 4.7 31 161-192 24-54 (164)
427 TIGR02947 SigH_actino RNA poly 39.4 64 0.0014 25.6 4.8 29 165-194 147-175 (193)
428 PF06676 DUF1178: Protein of u 39.2 16 0.00035 28.5 1.2 26 120-145 96-121 (148)
429 PF13408 Zn_ribbon_recom: Reco 39.1 16 0.00034 22.9 0.9 14 21-34 3-16 (58)
430 PF02787 CPSase_L_D3: Carbamoy 38.8 1.5E+02 0.0032 22.2 6.3 56 165-227 23-78 (123)
431 PF07022 Phage_CI_repr: Bacter 38.7 36 0.00078 22.3 2.7 43 167-225 14-56 (66)
432 COG3388 Predicted transcriptio 38.6 85 0.0018 22.5 4.6 74 161-238 24-97 (101)
433 PF12728 HTH_17: Helix-turn-he 38.6 43 0.00094 20.3 2.9 22 166-188 2-23 (51)
434 COG1499 NMD3 NMD protein affec 38.5 11 0.00025 33.7 0.3 13 1-13 4-16 (355)
435 PRK13500 transcriptional activ 38.5 2.6E+02 0.0057 24.2 10.2 40 149-190 207-246 (312)
436 PRK08558 adenine phosphoribosy 38.4 61 0.0013 27.3 4.7 30 158-188 16-45 (238)
437 PF00376 MerR: MerR family reg 38.4 38 0.00082 19.7 2.4 20 167-187 1-20 (38)
438 PF14369 zf-RING_3: zinc-finge 38.2 29 0.00062 19.9 1.8 27 3-31 2-29 (35)
439 PF09567 RE_MamI: MamI restric 38.1 13 0.00028 31.5 0.5 37 3-48 82-118 (314)
440 PHA02325 hypothetical protein 38.1 18 0.00038 23.9 1.0 11 1-11 1-11 (72)
441 TIGR02642 phage_xxxx uncharact 38.0 20 0.00043 29.1 1.5 23 4-30 100-122 (186)
442 TIGR01889 Staph_reg_Sar staphy 37.9 1E+02 0.0022 22.2 5.2 33 159-192 37-69 (109)
443 PF00126 HTH_1: Bacterial regu 37.9 1.1E+02 0.0023 19.4 5.3 30 167-197 15-44 (60)
444 PF07900 DUF1670: Protein of u 37.7 75 0.0016 26.5 4.9 61 112-196 75-135 (220)
445 PRK07591 threonine synthase; V 37.7 14 0.0003 34.0 0.7 26 4-34 19-44 (421)
446 PF12085 DUF3562: Protein of u 37.7 1.2E+02 0.0027 20.2 5.2 42 167-218 9-50 (66)
447 PF04552 Sigma54_DBD: Sigma-54 37.7 11 0.00024 29.8 0.0 24 164-188 48-71 (160)
448 PRK00118 putative DNA-binding 37.6 65 0.0014 23.5 4.1 29 165-194 33-61 (104)
449 PF14951 DUF4503: Domain of un 37.5 22 0.00048 31.8 1.8 34 5-39 276-310 (389)
450 PF10083 DUF2321: Uncharacteri 37.4 21 0.00045 28.0 1.5 26 5-39 30-55 (158)
451 PF00440 TetR_N: Bacterial reg 37.1 93 0.002 18.6 4.4 34 154-188 5-38 (47)
452 PF05066 HARE-HTH: HB1, ASXL, 37.1 32 0.00069 22.9 2.3 31 130-160 21-53 (72)
453 PRK10188 DNA-binding transcrip 37.1 61 0.0013 27.2 4.5 33 164-197 193-225 (240)
454 PF14690 zf-ISL3: zinc-finger 37.0 21 0.00046 21.4 1.3 8 4-11 3-10 (47)
455 TIGR00354 polC DNA polymerase, 36.9 15 0.00032 37.0 0.8 23 3-33 625-647 (1095)
456 PRK15340 transcriptional regul 36.9 1.4E+02 0.003 24.9 6.4 55 122-190 95-149 (216)
457 TIGR00498 lexA SOS regulatory 36.9 60 0.0013 26.1 4.3 32 160-192 20-52 (199)
458 COG1675 TFA1 Transcription ini 36.8 8.6 0.00019 30.9 -0.7 30 4-35 114-144 (176)
459 TIGR00281 segregation and cond 36.8 1.3E+02 0.0027 24.4 6.0 42 148-194 3-46 (186)
460 PHA02591 hypothetical protein; 36.8 69 0.0015 22.1 3.7 31 157-188 51-81 (83)
461 KOG1070 rRNA processing protei 36.6 4.9E+02 0.011 28.2 11.1 33 108-142 1458-1490(1710)
462 PF08221 HTH_9: RNA polymerase 36.4 1.2E+02 0.0026 19.6 5.1 39 152-192 15-53 (62)
463 COG2390 DeoR Transcriptional r 36.4 1.3E+02 0.0028 26.7 6.5 67 149-223 15-81 (321)
464 PF01552 Pico_P2B: Picornaviru 36.3 40 0.00087 24.4 2.7 14 155-168 52-65 (99)
465 COG5257 GCD11 Translation init 36.1 17 0.00038 32.3 1.0 25 4-33 58-82 (415)
466 COG1107 Archaea-specific RecJ- 35.8 27 0.00058 33.4 2.2 28 4-32 3-30 (715)
467 PRK11179 DNA-binding transcrip 35.7 85 0.0018 24.2 4.8 32 161-193 19-50 (153)
468 PHA03082 DNA-dependent RNA pol 35.7 14 0.00031 23.8 0.3 13 23-35 4-16 (63)
469 PF05864 Chordopox_RPO7: Chord 35.6 15 0.00032 23.7 0.3 13 23-35 4-16 (63)
470 PRK10572 DNA-binding transcrip 35.5 1.5E+02 0.0033 25.1 6.8 39 150-190 185-223 (290)
471 PF01418 HTH_6: Helix-turn-hel 35.5 39 0.00084 22.9 2.5 24 164-188 33-56 (77)
472 smart00347 HTH_MARR helix_turn 35.2 1.1E+02 0.0025 20.8 5.1 28 165-193 24-51 (101)
473 TIGR02859 spore_sigH RNA polym 35.2 63 0.0014 25.6 4.1 31 164-195 164-194 (198)
474 PHA02970 hypothetical protein; 35.1 1.7E+02 0.0037 21.2 5.7 73 169-242 29-101 (115)
475 TIGR02937 sigma70-ECF RNA poly 35.0 70 0.0015 23.5 4.2 30 165-195 126-155 (158)
476 PF10543 ORF6N: ORF6N domain; 34.9 62 0.0013 22.6 3.5 29 166-195 13-41 (88)
477 PRK09483 response regulator; P 34.9 78 0.0017 25.0 4.7 33 164-197 162-194 (217)
478 cd00021 BBOX B-Box-type zinc f 34.8 33 0.00072 19.4 1.8 25 5-29 2-26 (39)
479 PF01475 FUR: Ferric uptake re 34.7 19 0.0004 26.6 0.9 13 22-34 79-91 (120)
480 TIGR00467 lysS_arch lysyl-tRNA 34.7 24 0.00053 33.3 1.8 32 5-37 170-204 (515)
481 PRK09636 RNA polymerase sigma 34.6 87 0.0019 26.9 5.2 57 165-223 131-187 (293)
482 PRK13870 transcriptional regul 34.6 62 0.0013 27.1 4.1 33 164-197 187-219 (234)
483 PF05269 Phage_CII: Bacterioph 34.6 1.1E+02 0.0023 21.9 4.6 22 165-187 23-44 (91)
484 COG0375 HybF Zn finger protein 34.3 21 0.00045 26.6 1.0 20 15-34 62-81 (115)
485 PF08421 Methyltransf_13: Puta 34.2 21 0.00046 23.3 1.0 16 24-39 41-56 (62)
486 PF04855 SNF5: SNF5 / SMARCB1 34.1 66 0.0014 27.3 4.2 24 204-227 139-162 (244)
487 PRK10870 transcriptional repre 34.1 96 0.0021 24.6 5.0 36 156-192 62-97 (176)
488 PF04855 SNF5: SNF5 / SMARCB1 34.1 74 0.0016 27.0 4.4 36 204-239 34-71 (244)
489 PRK09462 fur ferric uptake reg 34.1 19 0.00041 27.7 0.9 12 23-34 90-101 (148)
490 PRK09706 transcriptional repre 34.0 94 0.002 23.3 4.7 23 163-186 16-38 (135)
491 PRK13501 transcriptional activ 33.9 2.9E+02 0.0064 23.4 9.3 30 160-190 187-216 (290)
492 PTZ00073 60S ribosomal protein 33.9 19 0.00042 25.4 0.7 23 4-31 17-39 (91)
493 PRK04194 hypothetical protein; 33.8 1.1E+02 0.0023 28.0 5.7 30 110-139 76-105 (392)
494 PF07638 Sigma70_ECF: ECF sigm 33.7 69 0.0015 25.5 4.1 30 165-195 151-180 (185)
495 PRK04016 DNA-directed RNA poly 33.7 18 0.0004 23.7 0.6 12 24-35 5-16 (62)
496 PF12793 SgrR_N: Sugar transpo 33.6 78 0.0017 23.4 4.1 30 162-192 16-45 (115)
497 PRK13502 transcriptional activ 33.6 2.1E+02 0.0046 24.0 7.4 41 147-189 175-215 (282)
498 COG1885 Uncharacterized protei 33.2 32 0.00069 25.1 1.8 9 4-12 50-58 (115)
499 TIGR01391 dnaG DNA primase, ca 33.2 40 0.00086 30.9 2.9 27 5-31 36-63 (415)
500 PF02591 DUF164: Putative zinc 33.0 25 0.00054 22.3 1.1 30 4-33 23-56 (56)
No 1
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=100.00 E-value=6.2e-59 Score=405.58 Aligned_cols=233 Identities=34% Similarity=0.655 Sum_probs=214.7
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcccccccccccCcccccccCCCCCCCCCcccCCCCccccCCCceeEEecCC-CC
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPLLADGGLSTVIAKPN-GA 82 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e~~id~~~ewr~f~~~~~~~~~~r~G~~~~~~~~~~~l~t~i~~~~-~~ 82 (245)
..||+||+ +++++|+.+|++||.+||+|++|++||+|||||+|++++ .++++|+|+|.++++||.|++|.|+++. +.
T Consensus 12 ~~Cp~Cg~-~~iv~d~~~Ge~vC~~CG~Vl~e~~iD~g~EWR~f~~~~-~~~~~RvG~~~~~~~~~~gl~T~I~~~~~~~ 89 (310)
T PRK00423 12 LVCPECGS-DKLIYDYERGEIVCADCGLVIEENIIDQGPEWRAFDPEQ-REKRSRVGAPMTYTIHDKGLSTDIDWRNKDS 89 (310)
T ss_pred CcCcCCCC-CCeeEECCCCeEeecccCCcccccccccCCCccCCCccc-cCCccccCCCCCccccCCCCceEeecCCccc
Confidence 57999998 789999999999999999999999999999999999754 4689999999999999999999999655 34
Q ss_pred Cccccc-------hhhhhcccCC---CCCchhHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHH
Q 025983 83 SGEFLS-------SSLGRWQNRG---SNPDRGLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLA 152 (245)
Q Consensus 83 ~~~~l~-------~~l~~~~~~~---~~~e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaA 152 (245)
.|..++ .+|++||++. ++.||+|.+++.+|+++|+.|+||+.++++|..||+++++.++++|++.++++|
T Consensus 90 ~g~~l~~~~~~~~~rl~~~~~~~~~~~~~er~l~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~A 169 (310)
T PRK00423 90 YGKSISGKNRAQLYRLRKWQRRIRVSNAAERNLAFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVA 169 (310)
T ss_pred ccccccHHHHHHHHHHHHHhhhcccCChHhHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHH
Confidence 455554 2478898865 567999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCccCCccccCCCCHHhHHHHHhhhcCCCHHHHHHHHH
Q 025983 153 ACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMNNQAVKAAQE 232 (245)
Q Consensus 153 A~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~ 232 (245)
||||+|||+++.|+|++||+++ +++++++|+++|+.|.+.|+++ +|+.+|++||+|||+.|+|++++.+.|.+
T Consensus 170 AclYiACR~~~~prtl~eI~~~-~~v~~k~i~~~~~~l~k~L~~~------~~~~~p~~~i~r~~~~L~L~~~v~~~A~~ 242 (310)
T PRK00423 170 AALYAACRRCKVPRTLDEIAEV-SRVSRKEIGRCYRFLLRELNLK------LPPTDPIDYVPRFASELGLSGEVQKKAIE 242 (310)
T ss_pred HHHHHHHHHcCCCcCHHHHHHH-hCCCHHHHHHHHHHHHHHhCCC------CCCCCHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 9999999999999999999995 8999999999999999999987 78899999999999999999999999999
Q ss_pred HHHHhhhccc--CCC
Q 025983 233 AVQKSEEFDI--RYS 245 (245)
Q Consensus 233 i~~~~~~~~~--~~~ 245 (245)
|++.+.+.++ ||+
T Consensus 243 i~~~a~~~~l~~Gr~ 257 (310)
T PRK00423 243 ILQKAKEKGLTSGKG 257 (310)
T ss_pred HHHHHHhcCcccCCC
Confidence 9999999887 553
No 2
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=6.7e-57 Score=374.53 Aligned_cols=236 Identities=60% Similarity=0.904 Sum_probs=216.8
Q ss_pred CCCCCCCCCCc-eeeeCCCCceEccCCcccccccccccCcccccccCCCCCCCCCcccCCCCccccCCCceeEEecCCCC
Q 025983 4 AFCSDCKKHTE-VVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPLLADGGLSTVIAKPNGA 82 (245)
Q Consensus 4 ~~Cp~Cg~~~~-iv~d~~~G~~vC~~CG~V~~e~~id~~~ewr~f~~~~~~~~~~r~G~~~~~~~~~~~l~t~i~~~~~~ 82 (245)
++||+|+.++. +|+|+.+|++||..||+|+++++||.++|||+|+++.++.||+|||++.+|++.+++|+|.|+++.+.
T Consensus 1 ~~c~~C~~~~~~~V~d~~~gdtvC~~CGlVl~~r~Id~~sEwrtfsnd~~~~DPsrvG~~sNPlL~~g~L~T~I~~g~g~ 80 (308)
T KOG1597|consen 1 MTCPDCKRHPENLVEDHSAGDTVCSECGLVLEDRIIDEGSEWRTFSNDDSDADPSRVGASSNPLLDGGDLSTFISKGTGT 80 (308)
T ss_pred CCCCCCCCCCCCeeeeccCCceecccCCeeeccccccccccccccccCCCCCCccccCCCCCCCCCCCCcceeeecCCCC
Confidence 47999998766 99999999999999999999999999999999999888899999999999999999999999998877
Q ss_pred CccccchhhhhcccC--CCCCchhHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHH
Q 025983 83 SGEFLSSSLGRWQNR--GSNPDRGLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACR 160 (245)
Q Consensus 83 ~~~~l~~~l~~~~~~--~~~~e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY~acR 160 (245)
++..+++ |.+||++ +++.|+.+..++..|..||+.|+||..+.++|.++|+++.+.+.++||+.++++|||||+|||
T Consensus 81 ~s~~~s~-l~~~Q~~~sm~~~d~~~~~a~~~I~~m~d~~~Lp~~I~d~A~~ifk~v~~~k~lrGks~eai~AAclyiACR 159 (308)
T KOG1597|consen 81 SSSFASS-LGKAQNRNSMSNSDRVLKAAFKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIACR 159 (308)
T ss_pred CHHHHHH-HHHHhcccccCCccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHHH
Confidence 6655543 8889874 367899999999999999999999999999999999999999999999999999999999999
Q ss_pred hCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCccCCccccCCCCHHhHHHHHhhhcCCCHHHHHHHHHHHHHhhhc
Q 025983 161 QEDKPRTVKEICSVANGATKKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMNNQAVKAAQEAVQKSEEF 240 (245)
Q Consensus 161 ~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~ 240 (245)
+++.|||++||+.+ ++|+.++|+++++.|.+.|+... .+..+...+||+|||+.|+|++.++++|.++++++.++
T Consensus 160 q~~~pRT~kEI~~~-anv~kKEIgr~~K~i~~~l~~s~----~~~s~~t~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~~ 234 (308)
T KOG1597|consen 160 QEDVPRTFKEISAV-ANVSKKEIGRCVKLIGEALETSV----DLISISTGDFMPRFCSNLGLPKSAQEAATEIAEKAEEM 234 (308)
T ss_pred hcCCCchHHHHHHH-HcCCHHHHHHHHHHHHHHHhccc----hhhhhhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHh
Confidence 99999999999996 78999999999999999998651 12345689999999999999999999999999999999
Q ss_pred cc--CCC
Q 025983 241 DI--RYS 245 (245)
Q Consensus 241 ~~--~~~ 245 (245)
++ |||
T Consensus 235 ~~~~gRs 241 (308)
T KOG1597|consen 235 DIRAGRS 241 (308)
T ss_pred ccccCCC
Confidence 98 465
No 3
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=2e-54 Score=368.94 Aligned_cols=223 Identities=37% Similarity=0.699 Sum_probs=206.6
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcccccccccccCcccccccCCCCCCCCCcccCCCCccccCCCceeEEecCCCCC
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPLLADGGLSTVIAKPNGAS 83 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e~~id~~~ewr~f~~~~~~~~~~r~G~~~~~~~~~~~l~t~i~~~~~~~ 83 (245)
+.||+||+ +++++|++.|++||.+||+|++|..||.|||||.|++ . ..+ |+|+|.++.+||.+++|.|+++...
T Consensus 2 ~~CpeCg~-~~~~~d~~~ge~VC~~CG~Vi~~~~id~gpewr~f~e--~-~~~-r~g~P~t~~~~d~~l~t~i~~~~~~- 75 (285)
T COG1405 2 MSCPECGS-TNIITDYERGEIVCADCGLVLEDSLIDPGPEWRAFDE--R-HER-RVGAPLTPSIHDKGLSTIIGWGDKD- 75 (285)
T ss_pred CCCCCCCC-ccceeeccCCeEEeccCCEEeccccccCCCCcccccc--c-ccc-cccCCCccccCccchhhhcccchhH-
Confidence 67999999 6999999999999999999999999999999999932 2 234 9999999999999999999986532
Q ss_pred ccccchhhhhcccCC---CCCchhHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHH
Q 025983 84 GEFLSSSLGRWQNRG---SNPDRGLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACR 160 (245)
Q Consensus 84 ~~~l~~~l~~~~~~~---~~~e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY~acR 160 (245)
...+|++||.+. +..|+++..++.+|.++++.|+||..+.++|..||++++++++++||+.++++|||+|+|||
T Consensus 76 ---~~~rlr~~~~~~~v~~~~ernl~~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~acR 152 (285)
T COG1405 76 ---KMYRLRKWQIRIRVSSAKERNLITALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAACR 152 (285)
T ss_pred ---HHHHHHHHHhccccccchhhHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHHH
Confidence 224588888653 46899999999999999999999999999999999999999999999999999999999999
Q ss_pred hCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCccCCccccCCCCHHhHHHHHhhhcCCCHHHHHHHHHHHHHhhhc
Q 025983 161 QEDKPRTVKEICSVANGATKKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMNNQAVKAAQEAVQKSEEF 240 (245)
Q Consensus 161 ~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~ 240 (245)
+++.|+||.||+. ++++++++|+++|+.+.+.|++. +++.+|.+||+|||+.|+|++++.+.|.+|+++++++
T Consensus 153 ~~~~prtl~eIa~-a~~V~~kei~rtyr~~~~~L~l~------~~~~~p~~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~ 225 (285)
T COG1405 153 INGVPRTLDEIAK-ALGVSKKEIGRTYRLLVRELKLK------IPPVDPSDYIPRFASKLGLSDEVRRKAIEIVKKAKRA 225 (285)
T ss_pred HcCCCccHHHHHH-HHCCCHHHHHHHHHHHHHhcCCC------CCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHh
Confidence 9999999999999 59999999999999999999997 7889999999999999999999999999999999999
Q ss_pred cc
Q 025983 241 DI 242 (245)
Q Consensus 241 ~~ 242 (245)
|+
T Consensus 226 g~ 227 (285)
T COG1405 226 GL 227 (285)
T ss_pred Cc
Confidence 97
No 4
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=99.98 E-value=1.8e-32 Score=245.16 Aligned_cols=199 Identities=22% Similarity=0.388 Sum_probs=171.8
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcccccccccccCcccccccCCCCCCCCCcccCCCCccccCCCceeEEecCCCCC
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPTNPLLADGGLSTVIAKPNGAS 83 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e~~id~~~ewr~f~~~~~~~~~~r~G~~~~~~~~~~~l~t~i~~~~~~~ 83 (245)
++|++||+ +++..|+.+|..+|+.||+|+++++|. +| .+|.+.. .|+.|+.+..+.
T Consensus 1 ~~C~~C~~-s~fe~d~a~g~~~C~~CG~v~E~~~iv--se-v~F~e~~--------------------~G~~v~~~~~g~ 56 (521)
T KOG1598|consen 1 MVCKNCGG-SNFERDEATGNLYCTACGTVLEYNNIV--AE-VTFVEGA--------------------QGQFVRVGQSGA 56 (521)
T ss_pred CcCCCCCC-CCcccccccCCceeccccceeecccee--EE-eeeeccc--------------------ceeEEeccccCC
Confidence 47999999 799999999999999999999999998 55 5887531 112232211111
Q ss_pred ccccchhhhhcccCCCCCchhHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhCC
Q 025983 84 GEFLSSSLGRWQNRGSNPDRGLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQED 163 (245)
Q Consensus 84 ~~~l~~~l~~~~~~~~~~e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY~acR~~~ 163 (245)
+. ..+++++++.++.+.|..++.+|+|++ +++.|..+|+.+.+.++.+||+...++|+|+|++||+++
T Consensus 57 ~~-----------s~e~r~~t~~n~r~~i~~~~~~l~l~~-~~~~a~~~~k~a~~~nftkGr~~~~vvasClY~vcR~e~ 124 (521)
T KOG1598|consen 57 GS-----------SLESREKTIYNARRLIEELTERLNLGN-KTEVAFNFFKLAPDRNFTKGRRSTEVVAACLYLVCRLEK 124 (521)
T ss_pred cc-----------chHHHHHHHHHHHhHHHHHHHhcCcch-HHHHHHHHHHHHhhCCCCCCcchHHHHHHHHHHHHHhhC
Confidence 10 014678999999999999999999999 999999999999999999999999999999999999999
Q ss_pred CCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCccCCccccCCCCHHhHHHHHhhhcCCC---HHHHHHHHHHHHHhhhc
Q 025983 164 KPRTVKEICSVANGATKKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMN---NQAVKAAQEAVQKSEEF 240 (245)
Q Consensus 164 ~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~---~~v~~~A~~i~~~~~~~ 240 (245)
.++.+.|++++ ++|+++.||+.|++|.+.|.+.. ++ .|.+||..||+||...|.+. ++|...|.+|+++|++.
T Consensus 125 t~hlliDfS~~-Lqv~Vy~LG~~~l~l~~~L~i~e--n~-~plvDpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrd 200 (521)
T KOG1598|consen 125 TDHLLIDFSSY-LQVSVYDLGSNFLEVTDSLSIGE--NV-SPLVDPSLYIVRFSCRLLFGDKTEDVAKTATRLAQRMKRD 200 (521)
T ss_pred CceEEEEeccc-eEEehhhhhHHHHHHHHHhcccc--cc-ccccCcceeeechhHhhhcCCchHHHHHHHHHHHHHHHHH
Confidence 99999999996 99999999999999999999863 23 78999999999999999886 56899999999999999
Q ss_pred cc
Q 025983 241 DI 242 (245)
Q Consensus 241 ~~ 242 (245)
|+
T Consensus 201 wm 202 (521)
T KOG1598|consen 201 WM 202 (521)
T ss_pred HH
Confidence 87
No 5
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=99.83 E-value=5.4e-20 Score=126.57 Aligned_cols=71 Identities=42% Similarity=0.819 Sum_probs=65.9
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHH
Q 025983 112 IATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKEICSVANGATKKEI 183 (245)
Q Consensus 112 I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i 183 (245)
|+++|+.|+||+.+.+.|.++|+.+.+.++.+||+|.+++|||||+|||+++.|+|++||++ +++|++++|
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~-~~~Vs~~tI 71 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAE-AAGVSEKTI 71 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHH-HCTSSHHHH
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHH-HhCCCCCcC
Confidence 68999999999999999999999999999999999999999999999999999999999999 499999987
No 6
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.67 E-value=6.2e-16 Score=135.25 Aligned_cols=90 Identities=23% Similarity=0.403 Sum_probs=86.2
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHH
Q 025983 107 LAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRA 186 (245)
Q Consensus 107 ~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~ 186 (245)
.+..+|.++|+.|+||..+.+.|..|++++.+.+++.||+|.++||||||+||+++|.|+|++||+++ ++|++.+|++.
T Consensus 218 ~p~~~i~r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v-~~Vs~~tI~~~ 296 (310)
T PRK00423 218 DPIDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEV-AGVTEVTVRNR 296 (310)
T ss_pred CHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHH-cCCCHHHHHHH
Confidence 36799999999999999999999999999999999999999999999999999999999999999995 89999999999
Q ss_pred HHHHHHHhCCc
Q 025983 187 KEYIVKQLGLE 197 (245)
Q Consensus 187 ~~~l~~~l~~~ 197 (245)
|++|.+.|++.
T Consensus 297 ykel~~~l~~~ 307 (310)
T PRK00423 297 YKELAEKLDIK 307 (310)
T ss_pred HHHHHHHhCcc
Confidence 99999999864
No 7
>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=99.67 E-value=3.2e-17 Score=101.31 Aligned_cols=43 Identities=51% Similarity=1.076 Sum_probs=38.8
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcccccccccccCcccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTF 47 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e~~id~~~ewr~f 47 (245)
++||+||+ +.+++|+.+|++||++||.|++|+.++.++|||+|
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 57999999999999999999999999999999987
No 8
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=99.55 E-value=2.5e-14 Score=122.64 Aligned_cols=91 Identities=27% Similarity=0.391 Sum_probs=87.7
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHH
Q 025983 106 ILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKEICSVANGATKKEIGR 185 (245)
Q Consensus 106 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~ 185 (245)
.++..+|.+||+.|+||+.+...|.+|.+++.+.+.+.||+|..+||||||+|+++++.++|++||+.+ ++|++.+|++
T Consensus 192 ~~p~~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~~~~~tq~eva~v-~~vtevTIrn 270 (285)
T COG1405 192 VDPSDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGERRTQKEVAKV-AGVTEVTIRN 270 (285)
T ss_pred CCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhCCchHHHHHHHH-hCCeeeHHHH
Confidence 468899999999999999999999999999999999999999999999999999999999999999996 8999999999
Q ss_pred HHHHHHHHhCCc
Q 025983 186 AKEYIVKQLGLE 197 (245)
Q Consensus 186 ~~~~l~~~l~~~ 197 (245)
.|++|.+.+++.
T Consensus 271 rykel~~~~~i~ 282 (285)
T COG1405 271 RYKELADALDIE 282 (285)
T ss_pred HHHHHHHhhccc
Confidence 999999999875
No 9
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=99.49 E-value=1.8e-13 Score=115.03 Aligned_cols=88 Identities=24% Similarity=0.337 Sum_probs=84.0
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHH
Q 025983 107 LAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRA 186 (245)
Q Consensus 107 ~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~ 186 (245)
+..++|.+||+.|+||.++++.|.++.+++.+..+..||+|.++|||.||+++++...++|++||.++ +||.+.+|+..
T Consensus 202 ~t~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~~v-tgVaE~TIr~s 280 (308)
T KOG1597|consen 202 STGDFMPRFCSNLGLPKSAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQLSDEKKTQKEIGEV-TGVAEVTIRNS 280 (308)
T ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHhccCcccHHHHHHH-hhhhHHHHHHH
Confidence 36789999999999999999999999999999999999999999999999999999999999999995 89999999999
Q ss_pred HHHHHHHhC
Q 025983 187 KEYIVKQLG 195 (245)
Q Consensus 187 ~~~l~~~l~ 195 (245)
|+.|..++.
T Consensus 281 YK~Lyp~~~ 289 (308)
T KOG1597|consen 281 YKDLYPHAD 289 (308)
T ss_pred HHHHhhchh
Confidence 999998775
No 10
>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=99.26 E-value=1.1e-10 Score=82.10 Aligned_cols=83 Identities=25% Similarity=0.364 Sum_probs=77.7
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhCCCCcCHHHHHHHHhCC-CHHHHHH
Q 025983 107 LAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKEICSVANGA-TKKEIGR 185 (245)
Q Consensus 107 ~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY~acR~~~~~~tl~dia~~~~~v-~~~~i~~ 185 (245)
.+.++|.+++..+++|+.+...|..+++++.....+.++++..+++||+|+||+.++.|.+++++... .+. +..+|.+
T Consensus 4 ~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~-~~~~~~~~i~~ 82 (88)
T cd00043 4 TPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHV-TGYATEEEILR 82 (88)
T ss_pred hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHH-hCCCCHHHHHH
Confidence 46789999999999999999999999999999888889999999999999999999999999999995 899 9999999
Q ss_pred HHHHH
Q 025983 186 AKEYI 190 (245)
Q Consensus 186 ~~~~l 190 (245)
.++.|
T Consensus 83 ~e~~i 87 (88)
T cd00043 83 MEKLL 87 (88)
T ss_pred HHHHh
Confidence 88865
No 11
>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=99.15 E-value=3e-10 Score=78.95 Aligned_cols=80 Identities=21% Similarity=0.281 Sum_probs=71.9
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhCCCCcCHHHHHHHHhCC-CHHHHHHHHHH
Q 025983 111 TIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKEICSVANGA-TKKEIGRAKEY 189 (245)
Q Consensus 111 ~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY~acR~~~~~~tl~dia~~~~~v-~~~~i~~~~~~ 189 (245)
+|.++++.+++|+.+...|..+++++.....+.++++..+|+||+|+||+.++.+.+..++... .+. +..+|.+.++.
T Consensus 2 ~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~-~~~~~~~~i~~~~~~ 80 (83)
T smart00385 2 FLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIPPWTKELVHY-TGYFTEEEILRMEKL 80 (83)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCCCCchhHhHh-hCCCCHHHHHHHHHH
Confidence 6889999999999999999999999987433445999999999999999999999999999995 899 99999999887
Q ss_pred HH
Q 025983 190 IV 191 (245)
Q Consensus 190 l~ 191 (245)
|.
T Consensus 81 il 82 (83)
T smart00385 81 LL 82 (83)
T ss_pred Hh
Confidence 74
No 12
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=98.99 E-value=2.7e-09 Score=92.87 Aligned_cols=126 Identities=19% Similarity=0.271 Sum_probs=100.2
Q ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhCCCCcCHHHHHHHHhCC-CH--H
Q 025983 105 LILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKEICSVANGA-TK--K 181 (245)
Q Consensus 105 l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY~acR~~~~~~tl~dia~~~~~v-~~--~ 181 (245)
-.++..+|.+++.+|++|...+.+|..||.+++-...++.-.+..+|++|+|+|++.++.|+.++||..++... .+ .
T Consensus 39 r~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s~~~~~~~~~ 118 (323)
T KOG0834|consen 39 RQEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVSYRYLNPKDL 118 (323)
T ss_pred HHHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHHHHHcCcccc
Confidence 35689999999999999999999999999999998888888889999999999999999999999998753211 11 1
Q ss_pred HHHHHHHH-----------HHHHhCCccCCccccCCCCHHhHHHHHhhhcCCCHH----HHHHHHHHHHH
Q 025983 182 EIGRAKEY-----------IVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMNNQ----AVKAAQEAVQK 236 (245)
Q Consensus 182 ~i~~~~~~-----------l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~----v~~~A~~i~~~ 236 (245)
+....|.+ |.+.|+++ +...+|..||.+|+..|+.... +.+.|--.++-
T Consensus 119 ~~~~~~~~~~~~Iv~~E~~lL~tl~Fd------l~v~hPy~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD 182 (323)
T KOG0834|consen 119 ELEEVYWELKERIVQLELLLLETLGFD------LNVEHPYKYLLKYLKKLKADENLKQPLAQAAWNFVND 182 (323)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHccCc------eeccCchHHHHHHHHHhhhhhhccccHHHHHHHHhch
Confidence 33344433 34566665 6778899999999999999875 55555544443
No 13
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=98.94 E-value=2.5e-08 Score=86.81 Aligned_cols=126 Identities=11% Similarity=0.182 Sum_probs=102.4
Q ss_pred HHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhCCCCcCHHHHHHHHhCCC----
Q 025983 106 ILAFKTIATMSDRLG--LVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKEICSVANGAT---- 179 (245)
Q Consensus 106 ~~~~~~I~~~~~~L~--Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY~acR~~~~~~tl~dia~~~~~v~---- 179 (245)
......|.++|..|+ ||+.++-+|..+|++++-.+.+.-.++..++++|+|+||+.+..|+++.+++.. ..-+
T Consensus 57 ~~y~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~-~~~~~~~~ 135 (305)
T TIGR00569 57 KYYEKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGN-LKETPLKA 135 (305)
T ss_pred HHHHHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhh-ccCCchhh
Confidence 345688999999999 999999999999999998887777899999999999999999999999999874 4333
Q ss_pred HHHHHHHHHHHHHHhCCccCCccccCCCCHHhHHHHHhhhcC-----C--CHHHHHHHHHHHHHhh
Q 025983 180 KKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLG-----M--NNQAVKAAQEAVQKSE 238 (245)
Q Consensus 180 ~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~-----l--~~~v~~~A~~i~~~~~ 238 (245)
...|...-..|.+.|++. +....|..++..|...|+ + .+.+.+.|...++.+-
T Consensus 136 ~~~Il~~E~~lL~~L~F~------L~V~hPyr~L~~~l~dl~~~l~~~~~~~~l~q~a~~~lndsl 195 (305)
T TIGR00569 136 LEQVLEYELLLIQQLNFH------LIVHNPYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLNRTL 195 (305)
T ss_pred HHHHHHHHHHHHHHCCCc------EEeeCccHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHH
Confidence 377888888899999987 667789888888875443 1 2446666666665543
No 14
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=98.76 E-value=4.1e-09 Score=95.63 Aligned_cols=92 Identities=21% Similarity=0.221 Sum_probs=77.6
Q ss_pred hHHHHHHHHHHHHHhcCC-CH--HHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCH
Q 025983 104 GLILAFKTIATMSDRLGL-VA--TIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKEICSVANGATK 180 (245)
Q Consensus 104 ~l~~~~~~I~~~~~~L~L-p~--~v~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~ 180 (245)
.+.++.-+|.+++..|-. |. .++.+|.++..+....+...||+|..+++||||+|||++|+++|..||+.+ .+|++
T Consensus 162 plvDpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~~rsi~dIv~v-vhV~e 240 (521)
T KOG1598|consen 162 PLVDPSLYIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGFRRTIGDIAKV-VHVCE 240 (521)
T ss_pred cccCcceeeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCccccHHHHHHH-HHHhH
Confidence 345566678888777744 33 478888888888777777889999999999999999999999999999996 89999
Q ss_pred HHHHHHHHHHHHHhCC
Q 025983 181 KEIGRAKEYIVKQLGL 196 (245)
Q Consensus 181 ~~i~~~~~~l~~~l~~ 196 (245)
.+|.+.|+++.+.+..
T Consensus 241 ~Tl~kRl~Ef~~T~s~ 256 (521)
T KOG1598|consen 241 STLSKRLKEFSDTLSG 256 (521)
T ss_pred HHHHHHHHHHhccccc
Confidence 9999999999876653
No 15
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=98.61 E-value=5.2e-07 Score=77.44 Aligned_cols=124 Identities=19% Similarity=0.326 Sum_probs=102.0
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhCCCCcCHHHHHHHHhCCC------
Q 025983 106 ILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKEICSVANGAT------ 179 (245)
Q Consensus 106 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY~acR~~~~~~tl~dia~~~~~v~------ 179 (245)
.=+..+|++.|-.|+||+...-++.-+|++.+....+.+.+.+.++.|||.+|.+.+..|++++||..|...+.
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 34678999999999999999999999999999888888999999999999999999999999999987522111
Q ss_pred --------------HHHHHHHHHHHHHHhCCccCCccccCCCCHHhHHHHHhhhcCCCHHH--HHHHHHHHH
Q 025983 180 --------------KKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMNNQA--VKAAQEAVQ 235 (245)
Q Consensus 180 --------------~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v--~~~A~~i~~ 235 (245)
+..+-++..++.+.||+. +...+|+.+|--|..-|++++.. .+++--..+
T Consensus 104 ~~~~~~~~~~~~~lk~~~ir~e~~ILr~LGF~------~Hv~hPhklii~YLqtL~~~~~~~l~Q~~wNfmN 169 (367)
T KOG0835|consen 104 AAEHLILARLYINLKMQVIRAERRILRELGFD------VHVEHPHKLIIMYLQTLQLPPNLKLLQAAWNFMN 169 (367)
T ss_pred CcchhhhhhHHhhhhhHHHHHHHHHHHHhCCe------eeeeccHHHHHHHHHHhcCCCchhHHHHHHHhhh
Confidence 123445667888999987 88899999999999999998654 444443333
No 16
>COG5333 CCL1 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=98.51 E-value=1.1e-06 Score=75.25 Aligned_cols=129 Identities=19% Similarity=0.312 Sum_probs=104.0
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhCCCCcCHHHHHHHH-------hCC
Q 025983 106 ILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKEICSVA-------NGA 178 (245)
Q Consensus 106 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY~acR~~~~~~tl~dia~~~-------~~v 178 (245)
......|..+|.+|+||..+..+|..+|++.+-+...++.++..+|++|||+||+.++.|+-+.-.+-.+ .--
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 4567899999999999999999999999999988888999999999999999999999765544333321 124
Q ss_pred CHHHHHHHHHHHHHHhCCccCCccccCCCCHHhHHHHHhhhcCCCHH--HHHHHHHHHHHhhhc
Q 025983 179 TKKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMNNQ--AVKAAQEAVQKSEEF 240 (245)
Q Consensus 179 ~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~--v~~~A~~i~~~~~~~ 240 (245)
+.+.|-..-.++.+.|... ..+.+|..++..|...+.+... .-+.|-.+++-+-+.
T Consensus 126 sr~~Il~~E~~lLEaL~fd------~~V~hPy~~l~~f~~~~q~~~~~~~~~~aw~~inDa~~t 183 (297)
T COG5333 126 SRERILEYEFELLEALDFD------LHVHHPYKYLEGFLKDLQEKDKYKLLQIAWKIINDALRT 183 (297)
T ss_pred cHHHHHHHHHHHHHHcccc------eEeccccHHHHHHHHHHHhccHHHHHHHHHHHHHhhhhc
Confidence 5677888888888999876 6677899999999988887655 777777776655443
No 17
>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=98.12 E-value=5.1e-05 Score=57.23 Aligned_cols=92 Identities=18% Similarity=0.344 Sum_probs=76.3
Q ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhCCC-CcCHHHHHHHHh--CCCHH
Q 025983 105 LILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDK-PRTVKEICSVAN--GATKK 181 (245)
Q Consensus 105 l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY~acR~~~~-~~tl~dia~~~~--~v~~~ 181 (245)
.....++|..++..++++..+...|..++.+..........+...++++|+|+||+.+.. +.++.++... . ..+..
T Consensus 31 r~~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~-~~~~~~~~ 109 (127)
T PF00134_consen 31 RQIIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRI-SDNTFTKK 109 (127)
T ss_dssp HHHHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHH-TTTSSHHH
T ss_pred HHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHH-HcCCCCHH
Confidence 355788999999999999999999999999998887777788999999999999999987 7888998774 4 35788
Q ss_pred HHHHHHHHHHHHhCCc
Q 025983 182 EIGRAKEYIVKQLGLE 197 (245)
Q Consensus 182 ~i~~~~~~l~~~l~~~ 197 (245)
+|...-+.+...|+.+
T Consensus 110 ~i~~~E~~iL~~L~f~ 125 (127)
T PF00134_consen 110 DILEMEREILSALNFD 125 (127)
T ss_dssp HHHHHHHHHHHHTTT-
T ss_pred HHHHHHHHHHHHCCCC
Confidence 9999988898888764
No 18
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=97.95 E-value=2.2e-05 Score=64.58 Aligned_cols=128 Identities=20% Similarity=0.319 Sum_probs=89.4
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhCCCCcC-HHHHHHHH--h--------
Q 025983 108 AFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRT-VKEICSVA--N-------- 176 (245)
Q Consensus 108 ~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY~acR~~~~~~t-l~dia~~~--~-------- 176 (245)
-.+.|..+++.|+|.+.++.+|.-+|++.+-+..+++-.|..+|+.|+|+||+.+..|+. .+-++..+ +
T Consensus 44 ~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L~~~f~~~~ 123 (264)
T KOG0794|consen 44 MANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECPIVHIRLLVNEAKVLKTRFSYWP 123 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHhhhcccch
Confidence 457899999999999999999999999999888899999999999999999999999832 22222211 1
Q ss_pred ---CCCHHHHHHHHHHHHHHhCCccCCccccCCCCHHhHHHHHhhhcCC-CHHHHHHHHHHHHHhhhcc
Q 025983 177 ---GATKKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGM-NNQAVKAAQEAVQKSEEFD 241 (245)
Q Consensus 177 ---~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l-~~~v~~~A~~i~~~~~~~~ 241 (245)
.-+.+.|-..-..|.+.|+-= +-+-+|..-+..+....|+ +.+..+.+-.|++-.-+++
T Consensus 124 e~~~~~~~~I~e~Ef~llE~Ld~~------LIVhHPYrsL~q~~qd~gi~d~~~l~~~W~ivNDSyr~D 186 (264)
T KOG0794|consen 124 EKFPYERKDILEMEFYLLEALDCY------LIVHHPYRSLLQFVQDMGINDQKLLQLAWSIVNDSYRMD 186 (264)
T ss_pred hhcCCCcCcchhhhhhHHhhhcee------EEEecCCccHHHHHHHhcccchhhhhhhHhhhcchhhcc
Confidence 111222333333444555422 2334566668888888888 4447777777777665554
No 19
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=97.92 E-value=0.00035 Score=61.30 Aligned_cols=112 Identities=16% Similarity=0.190 Sum_probs=90.7
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCC---HHHHHHHHHHHHHHhCCC--CcCHHHHHHH-HhCCC
Q 025983 106 ILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRN---QDALLAACLYIACRQEDK--PRTVKEICSV-ANGAT 179 (245)
Q Consensus 106 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~---~~~iaAA~lY~acR~~~~--~~tl~dia~~-~~~v~ 179 (245)
.+|.++|-++|+..+..+.+.--|..++.+...-.-+..-+ ...+|+||+.+|++.+.. |.++.-.... ..-..
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 57999999999999999999999999999986644333333 789999999999999986 5544322221 12356
Q ss_pred HHHHHHHHHHHHHHhCCccCCccccCCCCHHhHHHHHhhhcCCC
Q 025983 180 KKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMN 223 (245)
Q Consensus 180 ~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~ 223 (245)
.++|.+.-..+...|+=+ +..+.|.+|+.-|+.+++..
T Consensus 159 aktI~rmELLVLstL~Wr------l~aVTP~sF~~~fl~ki~~~ 196 (335)
T KOG0656|consen 159 AKTIQRMELLVLSTLKWR------LRAVTPFSFIDHFLSKISQK 196 (335)
T ss_pred HHHHHHHHHHHHhhcccc------ccCCCchHHHHHHHHHcCcc
Confidence 899999999999999877 78899999999999999985
No 20
>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=97.90 E-value=7e-05 Score=57.60 Aligned_cols=83 Identities=14% Similarity=0.283 Sum_probs=63.7
Q ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhh--CCCCCCCCHHHHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHH
Q 025983 105 LILAFKTIATMSDRLGLVATIKDRANEIYKKVED--QKSSRGRNQDALLAACLYIACRQEDKPRTVKEICSVANGATKKE 182 (245)
Q Consensus 105 l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~--~~~~~gr~~~~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~ 182 (245)
..-|..+|+.+|++|+|++.+.+....+|..+.. ..++++|..+.+.-+|+|..||..+.+++++||-. +..-.+..
T Consensus 11 y~la~~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~Ii~-~Yr~qpq~ 89 (135)
T PF01857_consen 11 YKLAAVRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDIIK-AYRKQPQA 89 (135)
T ss_dssp HHHHHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHHH-HHTTSTT-
T ss_pred HHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHHH-HHHhcccc
Confidence 3447889999999999999999999999988764 45789999999999999999999999999999988 45444444
Q ss_pred HHHHHH
Q 025983 183 IGRAKE 188 (245)
Q Consensus 183 i~~~~~ 188 (245)
-..+|+
T Consensus 90 ~~~Vyr 95 (135)
T PF01857_consen 90 SSHVYR 95 (135)
T ss_dssp -THHHH
T ss_pred cccceE
Confidence 444444
No 21
>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=97.46 E-value=8.3e-05 Score=43.63 Aligned_cols=27 Identities=30% Similarity=0.554 Sum_probs=23.6
Q ss_pred CCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 5 ~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
.|+.||+ . .+...+|..+|..||+|++
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 3 6778999999999999974
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=97.41 E-value=0.001 Score=56.95 Aligned_cols=87 Identities=14% Similarity=0.297 Sum_probs=66.4
Q ss_pred HHHHHHHHhc--CCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhCCCCcCHHHHHHHHhC----CCHHHH
Q 025983 110 KTIATMSDRL--GLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKEICSVANG----ATKKEI 183 (245)
Q Consensus 110 ~~I~~~~~~L--~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY~acR~~~~~~tl~dia~~~~~----v~~~~i 183 (245)
..+-.+|.++ +||.+|+-+|..+|++++=.+...--+|..|.++|+|+||+.+..-++..+|+.- .. -+...|
T Consensus 61 ~~l~~f~~k~~p~lp~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~ISieqFvkn-~~~~~~k~~e~v 139 (325)
T KOG2496|consen 61 LSLVNFYSKFKPNLPTSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFYISIEQFVKN-MNGRKWKTHEIV 139 (325)
T ss_pred HHHHHHHHHhcCCCchHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhheecHHHHHhh-ccCcccccHHHH
Confidence 3455666665 7899999999999999988777777899999999999999999999999999874 43 223333
Q ss_pred HHHHHHHHHHhCCc
Q 025983 184 GRAKEYIVKQLGLE 197 (245)
Q Consensus 184 ~~~~~~l~~~l~~~ 197 (245)
-+.-..+.+.|+..
T Consensus 140 Lk~E~~llqsL~f~ 153 (325)
T KOG2496|consen 140 LKYEFLLLQSLKFS 153 (325)
T ss_pred HhchHHHHHhhhhh
Confidence 33334555555543
No 23
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=97.16 E-value=0.002 Score=55.80 Aligned_cols=108 Identities=17% Similarity=0.187 Sum_probs=76.1
Q ss_pred HHHHHHHHHHHHHhcCCCHHH--HHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhCCCCcCHH-HHHHHHhCCCHH
Q 025983 105 LILAFKTIATMSDRLGLVATI--KDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVK-EICSVANGATKK 181 (245)
Q Consensus 105 l~~~~~~I~~~~~~L~Lp~~v--~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY~acR~~~~~~tl~-dia~~~~~v~~~ 181 (245)
+.++...|-.+..-|++|++. ...+..+.....--.++.-.+|++||+||+|+|+|..++|.+.. .--. +++.++.
T Consensus 138 v~hPhklii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~vry~pe~iACaciyLaAR~~eIpLp~~P~Wf~-~Fd~~k~ 216 (367)
T KOG0835|consen 138 VEHPHKLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVFVRYSPESIACACIYLAARNLEIPLPFQPHWFK-AFDTTKR 216 (367)
T ss_pred eeccHHHHHHHHHHhcCCCchhHHHHHHHhhhhccccceeeecCHHHHHHHHHHHHHhhhcCCCCCCccHHH-HcCCcHH
Confidence 356778899999999999755 55566666666555566667899999999999999999886643 4445 5788998
Q ss_pred HHHHHHHHHHHHhCCccCCccccCCCCHHhHHHHHhhhcCC
Q 025983 182 EIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGM 222 (245)
Q Consensus 182 ~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l 222 (245)
+|-..-..+....... .| -..+|.-|++.+..
T Consensus 217 eid~ic~~l~~lY~~~------~p---~~~li~~~vd~~k~ 248 (367)
T KOG0835|consen 217 EIDEICYRLIPLYKRA------KP---DETLIEAFVDRLKR 248 (367)
T ss_pred HHHHHHHHHHHHHHhc------cc---CHHHHHHHHHHhhH
Confidence 8887665555544322 12 14567777766654
No 24
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=97.14 E-value=0.00042 Score=39.80 Aligned_cols=31 Identities=23% Similarity=0.446 Sum_probs=25.3
Q ss_pred CCCCCCCCCCCCCceeeeCCCCceEccCCcccc
Q 025983 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (245)
Q Consensus 1 ~~~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~ 33 (245)
|....|+.||+ + .++..+.+..+|..||.+.
T Consensus 1 ~~~~~C~~C~~-~-~i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 1 SNLKKCSKCGG-N-GIVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred CCceEcCCCCC-C-eEEEecCCeEEcccCCcEe
Confidence 56688999998 3 4555789999999999875
No 25
>PHA00626 hypothetical protein
Probab=97.05 E-value=0.00054 Score=43.54 Aligned_cols=31 Identities=23% Similarity=0.549 Sum_probs=23.7
Q ss_pred CCCCCCCCCCceeee----CCCCceEccCCcccccc
Q 025983 4 AFCSDCKKHTEVVFD----HSAGDTVCSECGLVLES 35 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d----~~~G~~vC~~CG~V~~e 35 (245)
+.||.||+ .+++.- ..+..++|.+||+-...
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 46999998 566643 23789999999998753
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=97.03 E-value=0.0047 Score=45.56 Aligned_cols=87 Identities=13% Similarity=0.113 Sum_probs=63.6
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhCCC-CcCHHHHHHHHhCCCHHHHHHH
Q 025983 108 AFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDK-PRTVKEICSVANGATKKEIGRA 186 (245)
Q Consensus 108 ~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY~acR~~~~-~~tl~dia~~~~~v~~~~i~~~ 186 (245)
+..+|+.+....+....+...|..+.....-...+-.-+|..+||||+|+|.+..+. +.--..+... .+++..+|..+
T Consensus 3 p~~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~-t~~~~~~l~~c 81 (118)
T PF02984_consen 3 PYDFLRRFLKISNADQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEKL-TGYDKEDLKEC 81 (118)
T ss_dssp HHHHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHH-HTS-HHHHHHH
T ss_pred HHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchhh-cCCCHHHHHHH
Confidence 456778885555556678888888887765544456788999999999999999765 3334445563 78999999999
Q ss_pred HHHHHHHhC
Q 025983 187 KEYIVKQLG 195 (245)
Q Consensus 187 ~~~l~~~l~ 195 (245)
++.|.+.+.
T Consensus 82 ~~~i~~~~~ 90 (118)
T PF02984_consen 82 IELIQELLS 90 (118)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 999987664
No 27
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=96.84 E-value=0.00079 Score=43.67 Aligned_cols=31 Identities=35% Similarity=0.757 Sum_probs=28.2
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLES 35 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e 35 (245)
.+||.|+. ..+||++.+-...|..||.+|.+
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 47999998 68999999999999999999963
No 28
>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=96.83 E-value=0.0018 Score=43.98 Aligned_cols=30 Identities=30% Similarity=0.570 Sum_probs=26.7
Q ss_pred HHHHhhhcCCCHHHHHHHHHHHHHhhhccc
Q 025983 213 MRRFCSNLGMNNQAVKAAQEAVQKSEEFDI 242 (245)
Q Consensus 213 i~r~~~~L~l~~~v~~~A~~i~~~~~~~~~ 242 (245)
|+|||+.|+|++.+.+.|.++++.+.+.++
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~ 30 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQERGL 30 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHTTT
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHcCC
Confidence 689999999999999999999999999887
No 29
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=96.77 E-value=0.00081 Score=44.39 Aligned_cols=31 Identities=35% Similarity=0.778 Sum_probs=28.0
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLES 35 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e 35 (245)
.+||.||. ..++|++.+-.+.|..||.+|-+
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 36999998 68999999999999999999964
No 30
>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=96.73 E-value=0.00076 Score=43.25 Aligned_cols=31 Identities=32% Similarity=0.701 Sum_probs=23.3
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLES 35 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e 35 (245)
.+||.|+. ..+||++.+-.+.|..||.+|-+
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 57999998 68999999999999999999953
No 31
>PRK00420 hypothetical protein; Validated
Probab=96.70 E-value=0.0013 Score=48.73 Aligned_cols=29 Identities=28% Similarity=0.600 Sum_probs=23.6
Q ss_pred CCCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 3 ~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
...||.||.+ .+...+|..+|..||.++.
T Consensus 23 ~~~CP~Cg~p---Lf~lk~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 23 SKHCPVCGLP---LFELKDGEVVCPVHGKVYI 51 (112)
T ss_pred cCCCCCCCCc---ceecCCCceECCCCCCeee
Confidence 4689999973 4444899999999999874
No 32
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=96.62 E-value=0.0016 Score=37.56 Aligned_cols=28 Identities=25% Similarity=0.666 Sum_probs=15.7
Q ss_pred CCCCCCCCCCceeeeC----CCCceEccCCcccc
Q 025983 4 AFCSDCKKHTEVVFDH----SAGDTVCSECGLVL 33 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~----~~G~~vC~~CG~V~ 33 (245)
..||.||.. +.... ..--.||..||.|.
T Consensus 1 kfC~~CG~~--l~~~ip~gd~r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 1 KFCPQCGGP--LERRIPEGDDRERLVCPACGFIH 32 (34)
T ss_dssp -B-TTT--B---EEE--TT-SS-EEEETTTTEEE
T ss_pred CccccccCh--hhhhcCCCCCccceECCCCCCEE
Confidence 369999984 33332 34459999999984
No 33
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=96.60 E-value=0.0012 Score=35.84 Aligned_cols=24 Identities=29% Similarity=0.952 Sum_probs=18.7
Q ss_pred CCCCCCCCCCCCCceeeeCCCCceEccCCcc
Q 025983 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (245)
Q Consensus 1 ~~~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~ 31 (245)
|+ +.||+||.. + ..+..+|..||.
T Consensus 1 m~-~~Cp~Cg~~--~----~~~~~fC~~CG~ 24 (26)
T PF13248_consen 1 ME-MFCPNCGAE--I----DPDAKFCPNCGA 24 (26)
T ss_pred Cc-CCCcccCCc--C----CcccccChhhCC
Confidence 44 789999972 2 356899999996
No 34
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=96.52 E-value=0.035 Score=50.38 Aligned_cols=125 Identities=16% Similarity=0.270 Sum_probs=96.5
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHH-HHHHhCCCCcC-HHHHHHHHh--CCCHH
Q 025983 106 ILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLY-IACRQEDKPRT-VKEICSVAN--GATKK 181 (245)
Q Consensus 106 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY-~acR~~~~~~t-l~dia~~~~--~v~~~ 181 (245)
..-.+++-++-.+++|..+..-.|..|+.++........++...+..+|++ +||+.+....+ +.|+.-+ . ..+..
T Consensus 159 ~iLvdwlvevh~~F~L~~ETL~LaVnliDRfL~~~~v~~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv~i-sd~~~s~~ 237 (391)
T KOG0653|consen 159 AILVDWLVEVHEKFGLSPETLYLAVNLIDRFLSKVKVPLKKLQLVGVSALLSIACKYEEISLPSVEDLVLI-TDGAYSRE 237 (391)
T ss_pred HHHHHHHHHhhhhcCcCHHHHHHHHHHHHHHHHHhcccHHHhhHHhHHHHHHHHHhhhhccCCccceeEee-eCCccchH
Confidence 345688999999999999999999999999887765666777777777755 99997554333 5555432 2 36789
Q ss_pred HHHHHHHHHHHHhCCccCCccccCCCCHHhHHHHHhhhcCCCHHHHHHHHHHHHHh
Q 025983 182 EIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMNNQAVKAAQEAVQKS 237 (245)
Q Consensus 182 ~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~ 237 (245)
+|.+.-+.+...|+.. +....|..|+.||........+....+..+++..
T Consensus 238 ~il~mE~~il~~L~f~------l~~p~~~~FLrr~~ka~~~d~~~~~~~k~~~El~ 287 (391)
T KOG0653|consen 238 EILRMEKYILNVLEFD------LSVPTPLSFLRRFLKAADYDIKTRTLVKYLLELS 287 (391)
T ss_pred HHHHHHHHHHhccCee------ecCCchHHHHHHHHHhhhcchhHHHHHHHHHHHH
Confidence 9999999999988876 6667899999999999886666666666665543
No 35
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=96.34 E-value=0.028 Score=51.38 Aligned_cols=119 Identities=16% Similarity=0.222 Sum_probs=94.4
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhCCC-CcCHHHHHHHHh--CCCHHHHH
Q 025983 108 AFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDK-PRTVKEICSVAN--GATKKEIG 184 (245)
Q Consensus 108 ~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY~acR~~~~-~~tl~dia~~~~--~v~~~~i~ 184 (245)
..++|.++=.+++|-++....|..|..+.+..+...=.+...+++.|+||||+.+.+ +.++++++-+ + ..+.+.|.
T Consensus 216 Lv~wlvevH~~F~llpeTL~lainiiDrfLs~~~v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~-t~g~~t~~~i~ 294 (440)
T COG5024 216 LVDWLVEVHGKFGLLPETLFLAINIIDRFLSSRVVSLEKYQLVGISALFIASKYEEVNCPSIKDLVYA-TDGAFTRDDII 294 (440)
T ss_pred HHHHHHHhcccccccchHHHHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHH-HcccccHHHHH
Confidence 356788888889998899999999999998887766667889999999999998875 4457777653 3 56799999
Q ss_pred HHHHHHHHHhCCccCCccccCCCCHHhHHHHHhhhcCCCHHHHHHHHHH
Q 025983 185 RAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMNNQAVKAAQEA 233 (245)
Q Consensus 185 ~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i 233 (245)
++.+.+...|+.. +.-..|..|+.|+.....-+......+..+
T Consensus 295 ~aE~~ml~~l~f~------is~P~P~sFLRriSka~dyd~~srt~~k~~ 337 (440)
T COG5024 295 RAERYMLEVLDFN------ISWPSPMSFLRRISKASDYDIFSRTPAKFS 337 (440)
T ss_pred HHHHHHhhhcccc------cCCCChHHHHHHHHhhcccchhhhhhHhhh
Confidence 9999999999876 666678899888777766665555555444
No 36
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=96.33 E-value=0.0029 Score=39.22 Aligned_cols=31 Identities=29% Similarity=0.682 Sum_probs=25.0
Q ss_pred CCCCCCCCCCCCCceeeeCCCCceEccCCcccc
Q 025983 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (245)
Q Consensus 1 ~~~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~ 33 (245)
|....||+||. .+.+|+..+.+.|..||.-+
T Consensus 1 ~~~y~C~~CG~--~~~~~~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 1 MAEYKCARCGR--EVELDEYGTGVRCPYCGYRI 31 (46)
T ss_pred CCEEECCCCCC--EEEECCCCCceECCCCCCeE
Confidence 56688999997 46777777799999999644
No 37
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=96.32 E-value=0.0021 Score=33.73 Aligned_cols=22 Identities=23% Similarity=0.915 Sum_probs=17.0
Q ss_pred CCCCCCCCCceeeeCCCCceEccCCccc
Q 025983 5 FCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (245)
Q Consensus 5 ~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V 32 (245)
+||+||.. + ..+..+|..||.-
T Consensus 1 ~Cp~CG~~--~----~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAE--I----EDDAKFCPNCGTP 22 (23)
T ss_pred CCcccCCC--C----CCcCcchhhhCCc
Confidence 59999984 2 2468889999974
No 38
>PLN00209 ribosomal protein S27; Provisional
Probab=96.27 E-value=0.0028 Score=44.14 Aligned_cols=31 Identities=35% Similarity=0.657 Sum_probs=28.2
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLES 35 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e 35 (245)
.+||.|+. ..+||++.+-.+.|..||.+|.+
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 47999998 68999999999999999999953
No 39
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=96.20 E-value=0.0033 Score=43.72 Aligned_cols=31 Identities=26% Similarity=0.618 Sum_probs=28.1
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLES 35 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e 35 (245)
.+||.|+. ..+||++.+-.+.|..||.+|-+
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 47999998 68999999999999999999953
No 40
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=96.19 E-value=0.0041 Score=36.21 Aligned_cols=31 Identities=19% Similarity=0.484 Sum_probs=19.5
Q ss_pred CCCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 3 ~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
+..||+||+ --+......+...|..||++.+
T Consensus 1 m~FCp~C~n-lL~p~~~~~~~~~C~~C~Y~~~ 31 (35)
T PF02150_consen 1 MRFCPECGN-LLYPKEDKEKRVACRTCGYEEP 31 (35)
T ss_dssp --BETTTTS-BEEEEEETTTTEEESSSS-EEE
T ss_pred CeeCCCCCc-cceEcCCCccCcCCCCCCCccC
Confidence 468999997 3333334445457999999864
No 41
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=96.16 E-value=0.0025 Score=48.30 Aligned_cols=24 Identities=29% Similarity=0.927 Sum_probs=20.1
Q ss_pred CCCCCCCCCCCceeeeCCCCceEccCCc
Q 025983 3 DAFCSDCKKHTEVVFDHSAGDTVCSECG 30 (245)
Q Consensus 3 ~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG 30 (245)
...||.||.+ .|- .+|+++|..||
T Consensus 28 ~~hCp~Cg~P---LF~-KdG~v~CPvC~ 51 (131)
T COG1645 28 AKHCPKCGTP---LFR-KDGEVFCPVCG 51 (131)
T ss_pred HhhCcccCCc---cee-eCCeEECCCCC
Confidence 4579999984 444 89999999999
No 42
>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=95.78 E-value=0.008 Score=33.63 Aligned_cols=28 Identities=25% Similarity=0.427 Sum_probs=14.8
Q ss_pred CCCCCCCCCCCceeeeCCCCceEccCCcccc
Q 025983 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (245)
Q Consensus 3 ~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~ 33 (245)
.-+||.|++. ..- .+...+||.+||.-.
T Consensus 2 ~p~Cp~C~se-~~y--~D~~~~vCp~C~~ew 29 (30)
T PF08274_consen 2 LPKCPLCGSE-YTY--EDGELLVCPECGHEW 29 (30)
T ss_dssp S---TTT------E--E-SSSEEETTTTEEE
T ss_pred CCCCCCCCCc-cee--ccCCEEeCCcccccC
Confidence 3579999994 333 346789999999743
No 43
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=95.78 E-value=0.0091 Score=35.13 Aligned_cols=28 Identities=32% Similarity=0.741 Sum_probs=21.3
Q ss_pred CCCCCCCCCCceeeeC--CCCceEccCCcc
Q 025983 4 AFCSDCKKHTEVVFDH--SAGDTVCSECGL 31 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~--~~G~~vC~~CG~ 31 (245)
..||.||+....-+|. .+|..+|..||.
T Consensus 4 ~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred cCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 5699999865554554 459999999984
No 44
>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=95.59 E-value=0.0074 Score=44.51 Aligned_cols=31 Identities=23% Similarity=0.664 Sum_probs=26.4
Q ss_pred CCCCCCCCCCCceeeeCCCCceEccCCccccccc
Q 025983 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (245)
Q Consensus 3 ~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e~ 36 (245)
++.||.||.. .||-..--+||..||.++.-.
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 4689999984 789888889999999998644
No 45
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=95.51 E-value=0.012 Score=41.04 Aligned_cols=30 Identities=27% Similarity=0.550 Sum_probs=25.8
Q ss_pred CCCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 3 ~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
...||.||+ + .+....+|-..|..||.+..
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 357999998 4 67788999999999999875
No 46
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=95.51 E-value=0.0099 Score=37.54 Aligned_cols=27 Identities=22% Similarity=0.630 Sum_probs=20.9
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~ 33 (245)
..||.||+ + +..+ ..+...|..||...
T Consensus 21 ~fCP~Cg~-~-~m~~-~~~r~~C~~Cgyt~ 47 (50)
T PRK00432 21 KFCPRCGS-G-FMAE-HLDRWHCGKCGYTE 47 (50)
T ss_pred CcCcCCCc-c-hhec-cCCcEECCCcCCEE
Confidence 57999998 4 4444 45899999999864
No 47
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=95.34 E-value=0.02 Score=37.57 Aligned_cols=29 Identities=24% Similarity=0.633 Sum_probs=21.1
Q ss_pred CCCCCCCCCCCCceeeeCCCC-------ceEccCCcc
Q 025983 2 TDAFCSDCKKHTEVVFDHSAG-------DTVCSECGL 31 (245)
Q Consensus 2 ~~~~Cp~Cg~~~~iv~d~~~G-------~~vC~~CG~ 31 (245)
++..||-||+ ..+.++...+ .+.|.+||.
T Consensus 2 ~LkPCPFCG~-~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGS-ADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCC-cceEeecccCCCCCCEEEEEcCCCCC
Confidence 3568999997 5666665444 266999999
No 48
>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=95.34 E-value=0.01 Score=32.05 Aligned_cols=25 Identities=28% Similarity=0.794 Sum_probs=19.2
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
..||+|+.. | ......|..||++..
T Consensus 1 K~CP~C~~~--V----~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 1 KTCPECGAE--V----PESAKFCPHCGYDFE 25 (26)
T ss_pred CcCCCCcCC--c----hhhcCcCCCCCCCCc
Confidence 369999983 2 355789999999863
No 49
>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=95.15 E-value=0.019 Score=34.60 Aligned_cols=25 Identities=32% Similarity=0.907 Sum_probs=19.6
Q ss_pred CCCCCCCCCCCceeeeCCCCceEccCCc
Q 025983 3 DAFCSDCKKHTEVVFDHSAGDTVCSECG 30 (245)
Q Consensus 3 ~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG 30 (245)
...||.||.+ .+...+|.++|..|+
T Consensus 17 ~~~Cp~C~~P---L~~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDCGTP---LMRDKDGKIYCVSCG 41 (41)
T ss_pred cCccCCCCCe---eEEecCCCEECCCCC
Confidence 4689999862 344679999999996
No 50
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=95.13 E-value=0.017 Score=45.39 Aligned_cols=30 Identities=27% Similarity=0.576 Sum_probs=20.1
Q ss_pred CCCCCCCCCCceeeeCC---CCc-----eEccCCcccc
Q 025983 4 AFCSDCKKHTEVVFDHS---AGD-----TVCSECGLVL 33 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~---~G~-----~vC~~CG~V~ 33 (245)
|+||+||++.+-+.|.. .|. .-|.+||.-.
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence 57999998533455543 454 4499998765
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=95.10 E-value=0.012 Score=37.63 Aligned_cols=30 Identities=37% Similarity=0.804 Sum_probs=21.5
Q ss_pred CCCCCCCCCCceeeeCCCCc-eEccCCccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGD-TVCSECGLVLE 34 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~-~vC~~CG~V~~ 34 (245)
..||.||..-+ +.|...|+ +.|..||.-++
T Consensus 3 ~~CP~CG~~ie-v~~~~~GeiV~Cp~CGaele 33 (54)
T TIGR01206 3 FECPDCGAEIE-LENPELGELVICDECGAELE 33 (54)
T ss_pred cCCCCCCCEEe-cCCCccCCEEeCCCCCCEEE
Confidence 58999998422 33444466 67999999885
No 52
>PRK11827 hypothetical protein; Provisional
Probab=94.98 E-value=0.016 Score=37.92 Aligned_cols=28 Identities=14% Similarity=0.494 Sum_probs=24.1
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~ 33 (245)
..||.|++ .+.+|....+++|..||.+.
T Consensus 9 LaCP~ckg--~L~~~~~~~~Lic~~~~laY 36 (60)
T PRK11827 9 IACPVCNG--KLWYNQEKQELICKLDNLAF 36 (60)
T ss_pred eECCCCCC--cCeEcCCCCeEECCccCeec
Confidence 57999996 47888888899999999886
No 53
>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=94.82 E-value=0.018 Score=43.27 Aligned_cols=31 Identities=13% Similarity=0.288 Sum_probs=26.5
Q ss_pred CCCCCCCCCCCceeeeCCCCceEccCCccccccc
Q 025983 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (245)
Q Consensus 3 ~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e~ 36 (245)
++.||.||+. .+|-..--+||..||.++...
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 4689999984 789888999999999998644
No 54
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=94.66 E-value=0.026 Score=35.60 Aligned_cols=28 Identities=25% Similarity=0.679 Sum_probs=19.3
Q ss_pred CCCCCCCCCceeeeCC-C-CceEccCCccccc
Q 025983 5 FCSDCKKHTEVVFDHS-A-GDTVCSECGLVLE 34 (245)
Q Consensus 5 ~Cp~Cg~~~~iv~d~~-~-G~~vC~~CG~V~~ 34 (245)
.||.||+- +..... . ...+|..||.+..
T Consensus 2 FCp~Cg~~--l~~~~~~~~~~~vC~~Cg~~~~ 31 (52)
T smart00661 2 FCPKCGNM--LIPKEGKEKRRFVCRKCGYEEP 31 (52)
T ss_pred CCCCCCCc--cccccCCCCCEEECCcCCCeEE
Confidence 69999972 333222 2 3799999998764
No 55
>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=94.59 E-value=0.016 Score=34.16 Aligned_cols=31 Identities=32% Similarity=0.659 Sum_probs=20.5
Q ss_pred CCCCCCCCCCceeee---CCCCceEccCCccccc
Q 025983 4 AFCSDCKKHTEVVFD---HSAGDTVCSECGLVLE 34 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d---~~~G~~vC~~CG~V~~ 34 (245)
..||+|+..-.+-.| ...+.+.|..||.++.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 579999973222111 2345799999999874
No 56
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=94.46 E-value=0.04 Score=42.65 Aligned_cols=30 Identities=30% Similarity=0.742 Sum_probs=23.3
Q ss_pred CCCCCCCCCCceeeeC---CCCceE-----ccCCcccc
Q 025983 4 AFCSDCKKHTEVVFDH---SAGDTV-----CSECGLVL 33 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~---~~G~~v-----C~~CG~V~ 33 (245)
|+||.||...+-|.|. +.|..| |..||.=.
T Consensus 1 M~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RF 38 (147)
T TIGR00244 1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERF 38 (147)
T ss_pred CCCCCCCCCCCEeeeccccCCCCeeeecccCCccCCcc
Confidence 5799999876678885 667665 99998654
No 57
>PRK10220 hypothetical protein; Provisional
Probab=94.45 E-value=0.034 Score=40.56 Aligned_cols=30 Identities=23% Similarity=0.528 Sum_probs=22.4
Q ss_pred CCCCCCCCCCCCCceeeeCCCCceEccCCcccc
Q 025983 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (245)
Q Consensus 1 ~~~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~ 33 (245)
|+.-.||.|++. ..-. ....+||.+||.--
T Consensus 1 m~lP~CP~C~se-ytY~--d~~~~vCpeC~hEW 30 (111)
T PRK10220 1 MSLPHCPKCNSE-YTYE--DNGMYICPECAHEW 30 (111)
T ss_pred CCCCcCCCCCCc-ceEc--CCCeEECCcccCcC
Confidence 788899999983 3333 35569999999754
No 58
>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=94.32 E-value=0.033 Score=35.57 Aligned_cols=32 Identities=22% Similarity=0.233 Sum_probs=20.9
Q ss_pred CCCCCCCCCCCceee---eC--CCCceEccCCccccc
Q 025983 3 DAFCSDCKKHTEVVF---DH--SAGDTVCSECGLVLE 34 (245)
Q Consensus 3 ~~~Cp~Cg~~~~iv~---d~--~~G~~vC~~CG~V~~ 34 (245)
+..||.||+....+. |. ..|...|..||....
T Consensus 1 LkPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~ 37 (53)
T TIGR03655 1 LKPCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGP 37 (53)
T ss_pred CCCCCCCCCcceeeEeccCCCCCEEEEECCCCCCCcc
Confidence 357999998533132 32 334457999999865
No 59
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=94.31 E-value=0.026 Score=35.02 Aligned_cols=27 Identities=30% Similarity=0.768 Sum_probs=21.7
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V 32 (245)
..||.||. ..+..|+.+ -+.|..||..
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 46999996 566667655 8999999986
No 60
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=94.17 E-value=0.036 Score=36.07 Aligned_cols=30 Identities=27% Similarity=0.669 Sum_probs=26.3
Q ss_pred CCCCCCCCCCCCceeeeCCCCceEccCCcccc
Q 025983 2 TDAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (245)
Q Consensus 2 ~~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~ 33 (245)
+...||.|.. .+.+|.+.++++|..||...
T Consensus 7 eiLaCP~~kg--~L~~~~~~~~L~c~~~~~aY 36 (60)
T COG2835 7 EILACPVCKG--PLVYDEEKQELICPRCKLAY 36 (60)
T ss_pred eeeeccCcCC--cceEeccCCEEEecccCcee
Confidence 4567999997 38999999999999999986
No 61
>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=94.15 E-value=0.042 Score=32.91 Aligned_cols=29 Identities=28% Similarity=0.634 Sum_probs=16.1
Q ss_pred CCCCCCCCCCcee-eeC--CCCceEccCCccc
Q 025983 4 AFCSDCKKHTEVV-FDH--SAGDTVCSECGLV 32 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv-~d~--~~G~~vC~~CG~V 32 (245)
..||.||+....- ++. .+|..+|..|+-+
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 3599999864443 443 4699999999434
No 62
>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=94.11 E-value=0.051 Score=36.57 Aligned_cols=17 Identities=29% Similarity=0.788 Sum_probs=15.5
Q ss_pred eeCCCCceEccCCcccc
Q 025983 17 FDHSAGDTVCSECGLVL 33 (245)
Q Consensus 17 ~d~~~G~~vC~~CG~V~ 33 (245)
++..+|.++|.+||.+.
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 68899999999999986
No 63
>PRK12495 hypothetical protein; Provisional
Probab=94.01 E-value=0.034 Score=45.71 Aligned_cols=32 Identities=28% Similarity=0.778 Sum_probs=25.9
Q ss_pred CCCCCCCCCCCCCceeeeCCCCceEccCCccccccc
Q 025983 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (245)
Q Consensus 1 ~~~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e~ 36 (245)
|....|+.||.+ |+ ...|.++|..|+.++.+.
T Consensus 40 msa~hC~~CG~P---Ip-a~pG~~~Cp~CQ~~~~~~ 71 (226)
T PRK12495 40 MTNAHCDECGDP---IF-RHDGQEFCPTCQQPVTED 71 (226)
T ss_pred cchhhcccccCc---cc-CCCCeeECCCCCCccccc
Confidence 566789999984 44 458999999999998653
No 64
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=93.99 E-value=0.039 Score=40.91 Aligned_cols=60 Identities=20% Similarity=0.216 Sum_probs=34.4
Q ss_pred HHHHHHHHhCCCHHHHHHHHHHHHHHhCCccCCccccCCCCHHhHHHHHhhhcCCCHHHHHHHHHH
Q 025983 168 VKEICSVANGATKKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMNNQAVKAAQEA 233 (245)
Q Consensus 168 l~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i 233 (245)
|+|++.. +|||.-|++..+.+|.+.|+... .+..........+.++|.-+.=....|.++
T Consensus 52 lKe~e~~-lgiSYPTvR~rLd~ii~~lg~~~-----~~~~~~~~~~~~IL~~L~~GeIs~eeA~~~ 111 (113)
T PF09862_consen 52 LKEMEKE-LGISYPTVRNRLDKIIEKLGYEE-----DEEEEEEDERKEILDKLEKGEISVEEALEI 111 (113)
T ss_pred HHHHHHH-HCCCcHHHHHHHHHHHHHhCCCC-----CcccccchhHHHHHHHHHcCCCCHHHHHHH
Confidence 6777774 77777777777777777777621 222333455555556655444333444433
No 65
>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=93.91 E-value=0.066 Score=30.33 Aligned_cols=28 Identities=21% Similarity=0.463 Sum_probs=16.0
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~ 33 (245)
..|+.||++ . ......-..+|.+||...
T Consensus 4 rfC~~CG~~-t-~~~~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 4 RFCGRCGAP-T-KPAPGGWARRCPSCGHEH 31 (32)
T ss_dssp SB-TTT--B-E-EE-SSSS-EEESSSS-EE
T ss_pred cccCcCCcc-c-cCCCCcCEeECCCCcCEe
Confidence 679999984 3 344556679999999753
No 66
>PF08613 Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This entry includes cyclin PHO80 and other cyclins that partner with the cyclin-dependent kinase (CDK) PHO85. The PHO80/PHO85 cyclin-cdk complex is used for a regulatory process other than cell-cycle control []. This entry also includes other PHO80-like cyclins that are involved in the cell-cycle control. They belong to the P/U family and interact preferentially with CDKA1 [].; GO: 0019901 protein kinase binding, 0000079 regulation of cyclin-dependent protein kinase activity; PDB: 2PK9_D 2PMI_D.
Probab=93.82 E-value=2.2 Score=33.13 Aligned_cols=88 Identities=15% Similarity=0.137 Sum_probs=64.8
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHhh---CCC--CCCCCHHHHHHHHHHHHHHh-CCCCcCHHHHHHHHhCCCHH
Q 025983 108 AFKTIATMSDRLGLVATIKDRANEIYKKVED---QKS--SRGRNQDALLAACLYIACRQ-EDKPRTVKEICSVANGATKK 181 (245)
Q Consensus 108 ~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~---~~~--~~gr~~~~iaAA~lY~acR~-~~~~~tl~dia~~~~~v~~~ 181 (245)
..+++.++....+++..+.-.|..+..++.. ... +...+..-+..+|+-+|.+. .+...+.+..|.+ .|++.+
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 IRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKV-GGISLK 132 (149)
T ss_dssp HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHH-HTS-HH
T ss_pred HHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhh-cCCCHH
Confidence 5678999999999999999999999988877 222 33456666777777777775 4578899999996 899999
Q ss_pred HHHHHHHHHHHHhCC
Q 025983 182 EIGRAKEYIVKQLGL 196 (245)
Q Consensus 182 ~i~~~~~~l~~~l~~ 196 (245)
+|++.-+.+...|+.
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 999999999888875
No 67
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=93.38 E-value=0.19 Score=36.52 Aligned_cols=33 Identities=21% Similarity=0.665 Sum_probs=24.3
Q ss_pred CCCCCCCCCCCCCceeeeCCCCceEccCCccccccc
Q 025983 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (245)
Q Consensus 1 ~~~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e~ 36 (245)
|++..||.|++. .+++ +.+.++|.+|+.--.+.
T Consensus 1 ~~lp~cp~c~sE--ytYe-d~~~~~cpec~~ew~~~ 33 (112)
T COG2824 1 MSLPPCPKCNSE--YTYE-DGGQLICPECAHEWNEN 33 (112)
T ss_pred CCCCCCCccCCc--eEEe-cCceEeCchhccccccc
Confidence 567889999983 4554 35589999999866543
No 68
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=92.74 E-value=0.41 Score=42.85 Aligned_cols=60 Identities=15% Similarity=0.180 Sum_probs=50.5
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhCCCC
Q 025983 106 ILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKP 165 (245)
Q Consensus 106 ~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY~acR~~~~~ 165 (245)
.-..+++.+++...+|..-.+.+|..||.++.=++++...+...+|+|||.+|.++++..
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 334567888888888888899999999999888888877788999999999999988654
No 69
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=92.68 E-value=0.09 Score=31.49 Aligned_cols=27 Identities=30% Similarity=0.578 Sum_probs=18.7
Q ss_pred CCCCCCCCCceeee---------CCCCceEccCCccc
Q 025983 5 FCSDCKKHTEVVFD---------HSAGDTVCSECGLV 32 (245)
Q Consensus 5 ~Cp~Cg~~~~iv~d---------~~~G~~vC~~CG~V 32 (245)
.||.||.. +.++= +.+-..+|.+||..
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 69999974 45431 23446899999964
No 70
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=92.55 E-value=0.048 Score=37.22 Aligned_cols=30 Identities=33% Similarity=0.692 Sum_probs=26.9
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
.+||.|-. .+.++.+.+..++|.+|++|+=
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 6789999999999999999983
No 71
>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=92.44 E-value=0.085 Score=38.51 Aligned_cols=28 Identities=32% Similarity=0.750 Sum_probs=21.8
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLES 35 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e 35 (245)
+.||.||+. +.+..+.++|..||.+.+.
T Consensus 1 ~fC~~Cg~~----l~~~~~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 1 KFCPKCGSL----MTPKNGVYVCPSCGYEKEK 28 (104)
T ss_pred CCCcccCcc----cccCCCeEECcCCCCcccc
Confidence 369999972 3456789999999998653
No 72
>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=92.41 E-value=0.15 Score=31.46 Aligned_cols=27 Identities=22% Similarity=0.469 Sum_probs=20.8
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~ 31 (245)
..||.||+ ..+..-...+..-|.+|+.
T Consensus 19 ~~CP~Cg~-~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGS-TKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCC-eeeEEeCCCCeEECCCCCC
Confidence 46999998 4555555579999999984
No 73
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=92.27 E-value=0.076 Score=37.64 Aligned_cols=30 Identities=30% Similarity=0.511 Sum_probs=25.0
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLES 35 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e 35 (245)
..||.||. .. +.-...|-..|..||.++.-
T Consensus 36 y~Cp~Cgk-~~-vkR~a~GIW~C~~C~~~~AG 65 (90)
T PF01780_consen 36 YTCPFCGK-TS-VKRVATGIWKCKKCGKKFAG 65 (90)
T ss_dssp BEESSSSS-SE-EEEEETTEEEETTTTEEEE-
T ss_pred CcCCCCCC-ce-eEEeeeEEeecCCCCCEEeC
Confidence 57999998 44 66788999999999999863
No 74
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=92.06 E-value=0.11 Score=37.73 Aligned_cols=31 Identities=26% Similarity=0.562 Sum_probs=23.2
Q ss_pred CCCCCCCCCCce--eeeCCCCceEccCCcccccc
Q 025983 4 AFCSDCKKHTEV--VFDHSAGDTVCSECGLVLES 35 (245)
Q Consensus 4 ~~Cp~Cg~~~~i--v~d~~~G~~vC~~CG~V~~e 35 (245)
..||+||. ..+ -.|...+..+|..||+.-+-
T Consensus 22 f~CP~Cge-~~v~v~~~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 22 FECPRCGK-VSISVKIKKNIAIITCGNCGLYTEF 54 (99)
T ss_pred eECCCCCC-eEeeeecCCCcceEECCCCCCccCE
Confidence 46999996 333 34556789999999998753
No 75
>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=91.92 E-value=0.15 Score=37.26 Aligned_cols=31 Identities=16% Similarity=0.426 Sum_probs=21.4
Q ss_pred CCCCCCCCCCCceeeeCCCCceEccCCccccccc
Q 025983 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (245)
Q Consensus 3 ~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e~ 36 (245)
.-.||.|++. -.-.| ...+||.+||.--...
T Consensus 2 lp~CP~C~se-ytY~d--g~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 2 LPPCPKCNSE-YTYHD--GTQLICPSCLYEWNEN 32 (109)
T ss_pred CCcCCcCCCc-ceEec--CCeeECcccccccccc
Confidence 3579999983 33333 4569999999876433
No 76
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=91.74 E-value=0.12 Score=37.23 Aligned_cols=30 Identities=33% Similarity=0.782 Sum_probs=22.9
Q ss_pred CCCCCCCCCCcee---ee--CCCCceEccCCccccc
Q 025983 4 AFCSDCKKHTEVV---FD--HSAGDTVCSECGLVLE 34 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv---~d--~~~G~~vC~~CG~V~~ 34 (245)
..||.||. ..++ .+ ..-|.++|..||+-.+
T Consensus 23 FtCp~Cgh-e~vs~ctvkk~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 23 FTCPRCGH-EKVSSCTVKKTVNIGTAVCGNCGLSFE 57 (104)
T ss_pred EecCccCC-eeeeEEEEEecCceeEEEcccCcceEE
Confidence 36999998 4555 44 3678899999998764
No 77
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=91.69 E-value=0.14 Score=34.31 Aligned_cols=29 Identities=21% Similarity=0.576 Sum_probs=21.1
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
+.||.||.. . ......-..+|..||...+
T Consensus 29 q~C~~CG~~-~-~~~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 29 QTCPRCGHR-N-KKRRSGRVFTCPNCGFEMD 57 (69)
T ss_pred cCccCcccc-c-ccccccceEEcCCCCCEEC
Confidence 679999973 2 1235667799999999864
No 78
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=91.56 E-value=0.15 Score=38.00 Aligned_cols=33 Identities=30% Similarity=0.616 Sum_probs=23.9
Q ss_pred CCCCCCCCCCCce-eeeCCCCceEccCCccccccc
Q 025983 3 DAFCSDCKKHTEV-VFDHSAGDTVCSECGLVLESH 36 (245)
Q Consensus 3 ~~~Cp~Cg~~~~i-v~d~~~G~~vC~~CG~V~~e~ 36 (245)
|+.||.||+- -+ -.|...+.++|..||...+-.
T Consensus 2 m~FCp~Cgsl-l~p~~~~~~~~l~C~kCgye~~~~ 35 (113)
T COG1594 2 MRFCPKCGSL-LYPKKDDEGGKLVCRKCGYEEEAS 35 (113)
T ss_pred ccccCCccCe-eEEeEcCCCcEEECCCCCcchhcc
Confidence 5789999973 22 123367799999999987544
No 79
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=91.56 E-value=0.13 Score=39.92 Aligned_cols=30 Identities=30% Similarity=0.644 Sum_probs=22.1
Q ss_pred CCCCCCCCCCceeeeC---CCCce-----EccCCcccc
Q 025983 4 AFCSDCKKHTEVVFDH---SAGDT-----VCSECGLVL 33 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~---~~G~~-----vC~~CG~V~ 33 (245)
|+||.|+.+.+-|.|. +.|.. .|.+||.=.
T Consensus 1 M~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RF 38 (156)
T COG1327 1 MKCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERF 38 (156)
T ss_pred CCCCCCCCCCCeeeecccccccchhhhhhccccccccc
Confidence 6799999876667784 45543 599998654
No 80
>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=91.54 E-value=0.16 Score=30.16 Aligned_cols=28 Identities=29% Similarity=0.583 Sum_probs=15.3
Q ss_pred CCCCCCCCCceeeeC--------CCCceEccCCccc
Q 025983 5 FCSDCKKHTEVVFDH--------SAGDTVCSECGLV 32 (245)
Q Consensus 5 ~Cp~Cg~~~~iv~d~--------~~G~~vC~~CG~V 32 (245)
.||.||....+.+.. .+-..+|.+||..
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 699999853333321 2234789999964
No 81
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=91.44 E-value=1 Score=30.30 Aligned_cols=71 Identities=20% Similarity=0.248 Sum_probs=43.1
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhCCCCcCHHHHHHHHhCC-CHHHHHHHHHHH
Q 025983 112 IATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKEICSVANGA-TKKEIGRAKEYI 190 (245)
Q Consensus 112 I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY~acR~~~~~~tl~dia~~~~~v-~~~~i~~~~~~l 190 (245)
|.+++..++++.....+ +|+.........-....-+.-|+-|+. ..+.++.|+|.. +|. +...+.+.|++.
T Consensus 4 ~~~la~~~~~s~~~l~~---~f~~~~~~s~~~~~~~~r~~~a~~~l~----~~~~~~~~ia~~-~g~~s~~~f~r~Fk~~ 75 (84)
T smart00342 4 LEDLAEALGMSPRHLQR---LFKKETGTTPKQYLRDRRLERARRLLR----DTDLSVTEIALR-VGFSSQSYFSRAFKKL 75 (84)
T ss_pred HHHHHHHhCCCHHHHHH---HHHHHhCcCHHHHHHHHHHHHHHHHHH----cCCCCHHHHHHH-hCCCChHHHHHHHHHH
Confidence 67888999998755444 444433221110011122333444443 228999999995 899 999999988754
No 82
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=90.99 E-value=0.9 Score=39.89 Aligned_cols=91 Identities=16% Similarity=0.222 Sum_probs=71.1
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCC-CCCCCCHHHHHHHHHHHHHHhCCC-CcCHHHHHHHHh-CCCHHHH
Q 025983 107 LAFKTIATMSDRLGLVATIKDRANEIYKKVEDQK-SSRGRNQDALLAACLYIACRQEDK-PRTVKEICSVAN-GATKKEI 183 (245)
Q Consensus 107 ~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~-~~~gr~~~~iaAA~lY~acR~~~~-~~tl~dia~~~~-~v~~~~i 183 (245)
--++++-++|+--+|-.+..-.|..+|.+...-. -...-....+--+|+|+|++.+.+ |--+.|||.++- ..+..+|
T Consensus 147 ILlDWlmEVCEvykLHRETFyLAvDy~DRyl~t~~~v~kt~lQLIGitsLFIAAK~EEIYpPKl~eFAyvTDgAcs~ddI 226 (408)
T KOG0655|consen 147 ILLDWLMEVCEVYKLHRETFYLAVDYFDRYLETQVEVSKTNLQLIGITSLFIAAKLEEIYPPKLIEFAYVTDGACSEDDI 226 (408)
T ss_pred HHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHhhccCccccceeeeccCccchHHH
Confidence 3578999999999999999999999998876432 122335677888999999999885 777889987532 3568889
Q ss_pred HHHHHHHHHHhCCc
Q 025983 184 GRAKEYIVKQLGLE 197 (245)
Q Consensus 184 ~~~~~~l~~~l~~~ 197 (245)
...-..|.+.|+-.
T Consensus 227 ltmE~iilkal~W~ 240 (408)
T KOG0655|consen 227 LTMELIILKALKWE 240 (408)
T ss_pred HHHHHHHHHHhccc
Confidence 98888888888765
No 83
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=90.96 E-value=8.1 Score=31.98 Aligned_cols=86 Identities=22% Similarity=0.281 Sum_probs=68.4
Q ss_pred HHHHHHHhcCCC--HHHHHHHHHHHHHHhh--CCCCCCCCHHHHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHH
Q 025983 111 TIATMSDRLGLV--ATIKDRANEIYKKVED--QKSSRGRNQDALLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRA 186 (245)
Q Consensus 111 ~I~~~~~~L~Lp--~~v~~~A~~i~~~~~~--~~~~~gr~~~~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~ 186 (245)
.|.+++.+|||. +.+.+.|.+|.+...- .+..-|-.-..-|.-|+=+|.-..+++..-...... .|.++++-.+.
T Consensus 2 lI~~l~~klgL~~ep~~lrKa~E~~RL~~~~~~~~~~~v~E~~kaV~CldlAa~~l~i~fDr~~avKL-SGl~k~~Y~~~ 80 (262)
T KOG4557|consen 2 LISDLGRKLGLDNEPLLLRKAAEIRRLCDAQFDSSIIGVGEICKAVICLDLAATRLQIIFDRQAAVKL-SGLSKKAYSRS 80 (262)
T ss_pred cHHHHHHhcCCccChHHHHHHHHHHHHHHhhccCccccccchhHHHHhHHHHHHHhcccccHHHHHHh-ccccHHHHHHH
Confidence 488899999993 5799999999887632 233334455667788888888888898887777674 89999999999
Q ss_pred HHHHHHHhCCc
Q 025983 187 KEYIVKQLGLE 197 (245)
Q Consensus 187 ~~~l~~~l~~~ 197 (245)
++.+...||++
T Consensus 81 ~~sfe~llgln 91 (262)
T KOG4557|consen 81 FNSFENLLGLN 91 (262)
T ss_pred HHHHHHHhcch
Confidence 99999999986
No 84
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=90.95 E-value=0.098 Score=30.74 Aligned_cols=29 Identities=28% Similarity=0.685 Sum_probs=20.5
Q ss_pred CCCCCCCCCCceeee----CCCCceEccCCcccc
Q 025983 4 AFCSDCKKHTEVVFD----HSAGDTVCSECGLVL 33 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d----~~~G~~vC~~CG~V~ 33 (245)
..||+|+..-. +.| ...+.+-|..||.+.
T Consensus 3 i~CP~C~~~f~-v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTRFR-VPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCCCCceEE-cCHHHcccCCcEEECCCCCcEe
Confidence 46999997322 222 346678999999986
No 85
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=90.91 E-value=0.17 Score=35.84 Aligned_cols=32 Identities=25% Similarity=0.474 Sum_probs=25.7
Q ss_pred CCCCCCCCCCCceeeeCCCCceEccCCccccccc
Q 025983 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (245)
Q Consensus 3 ~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e~ 36 (245)
...||.||. +. +.-...|-..|..||.++.-.
T Consensus 36 ~y~CpfCgk-~~-vkR~a~GIW~C~~C~~~~AGG 67 (90)
T PTZ00255 36 KYFCPFCGK-HA-VKRQAVGIWRCKGCKKTVAGG 67 (90)
T ss_pred CccCCCCCC-Cc-eeeeeeEEEEcCCCCCEEeCC
Confidence 357999997 45 456788999999999998643
No 86
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=90.90 E-value=0.16 Score=32.93 Aligned_cols=24 Identities=25% Similarity=0.764 Sum_probs=10.8
Q ss_pred CCCCCCCCCceeeeCCCCceEccCCc
Q 025983 5 FCSDCKKHTEVVFDHSAGDTVCSECG 30 (245)
Q Consensus 5 ~Cp~Cg~~~~iv~d~~~G~~vC~~CG 30 (245)
.|..||.. |..+..--...|.+||
T Consensus 11 ~CtSCg~~--i~p~e~~v~F~CPnCG 34 (61)
T COG2888 11 VCTSCGRE--IAPGETAVKFPCPNCG 34 (61)
T ss_pred eeccCCCE--eccCCceeEeeCCCCC
Confidence 45556541 2122222335566666
No 87
>COG4640 Predicted membrane protein [Function unknown]
Probab=90.77 E-value=0.13 Score=45.87 Aligned_cols=28 Identities=29% Similarity=0.793 Sum_probs=21.1
Q ss_pred CCCCCCCCCCCceeeeCCCCceEccCCccccccc
Q 025983 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (245)
Q Consensus 3 ~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e~ 36 (245)
|..||.||+. -.+++.-|+.||.=+...
T Consensus 1 M~fC~kcG~q------k~Ed~~qC~qCG~~~t~~ 28 (465)
T COG4640 1 MKFCPKCGSQ------KAEDDVQCTQCGHKFTSR 28 (465)
T ss_pred CCcccccccc------cccccccccccCCcCCch
Confidence 5789999983 235566799999887643
No 88
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=90.77 E-value=0.98 Score=37.21 Aligned_cols=79 Identities=14% Similarity=0.318 Sum_probs=54.7
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHHHHhhCC-CC----CCCCHHHHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHH
Q 025983 112 IATMSDRLGLVATIKDRANEIYKKVEDQK-SS----RGRNQDALLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRA 186 (245)
Q Consensus 112 I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~-~~----~gr~~~~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~ 186 (245)
|+++|-+||+-+ ++..|.++.+...+.- -+ ..-+....++|++|.|||..+..+.-..+..+ .|+++..+...
T Consensus 96 VrdlaVQfgc~e-vi~~a~~vl~syk~~lpaT~~~~~D~SrP~ft~aA~~~ack~lKlKVdK~kli~~-sg~~~s~F~~l 173 (262)
T KOG4557|consen 96 VRDLAVQFGCVE-VIKSAQNVLSSYKERLPATRRANADFSRPVFTAAAFYLACKKLKLKVDKLKLIEV-SGTSESEFSCL 173 (262)
T ss_pred HHHHHHHHhHHH-HHHHHHHHHHHHHhcCchhhhcCCcccchHHHHHHHHHHHHHHHHhhhHhhcccc-cCCCHHHHHHH
Confidence 667777777754 7777887777654421 01 12345678999999999999988776666674 78888777766
Q ss_pred HHHHHH
Q 025983 187 KEYIVK 192 (245)
Q Consensus 187 ~~~l~~ 192 (245)
-+.+-+
T Consensus 174 ~kqler 179 (262)
T KOG4557|consen 174 SKQLER 179 (262)
T ss_pred HHHHHH
Confidence 555544
No 89
>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=90.69 E-value=0.16 Score=28.88 Aligned_cols=25 Identities=28% Similarity=0.660 Sum_probs=17.2
Q ss_pred CCCCCCCCCceeeeCCCCceEccCCccc
Q 025983 5 FCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (245)
Q Consensus 5 ~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V 32 (245)
.|..||.. +.+.....+-|.+||.=
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 58999974 23455667899999963
No 90
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=90.45 E-value=0.2 Score=30.71 Aligned_cols=27 Identities=26% Similarity=0.680 Sum_probs=19.9
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~ 33 (245)
..|..||.. +..+ ..+.+-|.+||.=+
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 679999973 2223 56789999999744
No 91
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=90.45 E-value=0.33 Score=32.04 Aligned_cols=30 Identities=20% Similarity=0.325 Sum_probs=20.5
Q ss_pred CCCCCCCCCCCceeeeCCCCc--eEccCCcccc
Q 025983 3 DAFCSDCKKHTEVVFDHSAGD--TVCSECGLVL 33 (245)
Q Consensus 3 ~~~Cp~Cg~~~~iv~d~~~G~--~vC~~CG~V~ 33 (245)
...||.||.. .+..-...|- .+|..||...
T Consensus 6 lKPCPFCG~~-~~~v~~~~g~~~v~C~~CgA~~ 37 (64)
T PRK09710 6 VKPCPFCGCP-SVTVKAISGYYRAKCNGCESRT 37 (64)
T ss_pred ccCCCCCCCc-eeEEEecCceEEEEcCCCCcCc
Confidence 4679999984 4433333443 6899999964
No 92
>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=90.35 E-value=0.082 Score=47.31 Aligned_cols=77 Identities=17% Similarity=0.214 Sum_probs=0.0
Q ss_pred CCCHHHHHHHHHHHHHHh-hCCCCCCCCHHHHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCc
Q 025983 120 GLVATIKDRANEIYKKVE-DQKSSRGRNQDALLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYIVKQLGLE 197 (245)
Q Consensus 120 ~Lp~~v~~~A~~i~~~~~-~~~~~~gr~~~~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~ 197 (245)
++|+.++..|..+|+... ....+++..-.+-+.+|+|+||...+.+..+...... .++.++...+.|..|...|+..
T Consensus 11 ~~~~~ll~~a~~L~~ls~~~~~~l~~~~EiaR~~iCa~lA~~~l~~~~dl~~~~~~-~pl~pk~y~~l~~~~~~~L~~~ 88 (353)
T PF05460_consen 11 GLPPKLLSKASELYRLSRQKKSSLKPEEEIARAHICAELACERLKEKLDLPYAIKR-SPLPPKVYKKLLNTFENLLGNS 88 (353)
T ss_dssp -------------------------------------------------------------------------------
T ss_pred CCCHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhCCccCchhhcCC-CCCCHHHHHHHHHHHHHHHhCC
Confidence 456789999999999987 4445666666677899999999999999988887774 8999999999999999988875
No 93
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=90.22 E-value=0.6 Score=34.65 Aligned_cols=23 Identities=35% Similarity=0.726 Sum_probs=19.6
Q ss_pred CCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 6 CSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 6 Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
||.||. .-.|+ .+-|.+||+.++
T Consensus 1 CPvCg~-~l~vt-----~l~C~~C~t~i~ 23 (113)
T PF09862_consen 1 CPVCGG-ELVVT-----RLKCPSCGTEIE 23 (113)
T ss_pred CCCCCC-ceEEE-----EEEcCCCCCEEE
Confidence 999998 45555 899999999996
No 94
>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=90.08 E-value=0.056 Score=31.62 Aligned_cols=29 Identities=28% Similarity=0.718 Sum_probs=21.3
Q ss_pred CCCCCCCCCceeeeCCCCceEccCCcccc
Q 025983 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (245)
Q Consensus 5 ~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~ 33 (245)
.||.||..=++.+++..-+.+|..||.-|
T Consensus 3 ~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L 31 (36)
T PF05191_consen 3 ICPKCGRIYHIEFNPPKVEGVCDNCGGEL 31 (36)
T ss_dssp EETTTTEEEETTTB--SSTTBCTTTTEBE
T ss_pred CcCCCCCccccccCCCCCCCccCCCCCee
Confidence 58999975567777777888999999754
No 95
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=90.05 E-value=0.22 Score=32.30 Aligned_cols=28 Identities=21% Similarity=0.611 Sum_probs=20.2
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccccccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSI 38 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e~~i 38 (245)
..||+||.. . .-..+|..||+--+..++
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 469999973 1 347899999987655443
No 96
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=90.03 E-value=0.74 Score=45.08 Aligned_cols=83 Identities=17% Similarity=0.279 Sum_probs=69.6
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhC--CCCCCCCHHHHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHH
Q 025983 107 LAFKTIATMSDRLGLVATIKDRANEIYKKVEDQ--KSSRGRNQDALLAACLYIACRQEDKPRTVKEICSVANGATKKEIG 184 (245)
Q Consensus 107 ~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~--~~~~gr~~~~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~ 184 (245)
-|..+|+.+|++|.|.+...+....+|.-..-. .+++.|..+.+.-+|+|+.||..+...++.+|.. +..-...-..
T Consensus 679 LAavRL~~Lc~rL~l~~e~r~~IWtlFehsl~~et~Lm~dRHLDQillCaiy~i~KV~~~~ltF~eIm~-~YR~QPqa~~ 757 (920)
T KOG1010|consen 679 LAAVRLNDLCERLSLSDELREQIWTLFEHSLTNETELMRDRHLDQILLCAIYGIAKVKKEDLTFSEIMR-AYRRQPQAVS 757 (920)
T ss_pred HHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHhccHHHHHhhhHHHHHHHHHHhheehhcccchHHHHHH-HHhcCchhhh
Confidence 367889999999999999999988888765433 4678899999999999999999999999999988 4666666666
Q ss_pred HHHHHH
Q 025983 185 RAKEYI 190 (245)
Q Consensus 185 ~~~~~l 190 (245)
.+|+..
T Consensus 758 ~vyRsV 763 (920)
T KOG1010|consen 758 LVYRSV 763 (920)
T ss_pred hhhhhe
Confidence 777754
No 97
>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=89.72 E-value=0.62 Score=26.42 Aligned_cols=27 Identities=22% Similarity=0.386 Sum_probs=21.8
Q ss_pred CcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 165 PRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 165 ~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
|.|-.|||+. +|.+..++.|.+++|.+
T Consensus 2 ~mtr~diA~~-lG~t~ETVSR~l~~l~~ 28 (32)
T PF00325_consen 2 PMTRQDIADY-LGLTRETVSRILKKLER 28 (32)
T ss_dssp E--HHHHHHH-HTS-HHHHHHHHHHHHH
T ss_pred CcCHHHHHHH-hCCcHHHHHHHHHHHHH
Confidence 6788999995 99999999999999875
No 98
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=89.70 E-value=0.24 Score=32.60 Aligned_cols=14 Identities=21% Similarity=0.358 Sum_probs=9.4
Q ss_pred CCCCCCCCCCceeee
Q 025983 4 AFCSDCKKHTEVVFD 18 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d 18 (245)
.+||.||. ++...+
T Consensus 5 ~kCpKCgn-~~~~ek 18 (68)
T COG3478 5 FKCPKCGN-TNYEEK 18 (68)
T ss_pred ccCCCcCC-cchhhc
Confidence 35999997 454443
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=89.66 E-value=0.22 Score=29.56 Aligned_cols=30 Identities=33% Similarity=0.545 Sum_probs=19.8
Q ss_pred CCCCCCCCCCceeeeCC-CCceEccCCcccc
Q 025983 4 AFCSDCKKHTEVVFDHS-AGDTVCSECGLVL 33 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~-~G~~vC~~CG~V~ 33 (245)
..|+.||..-++..... .....|.+||.-+
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~ 36 (41)
T smart00834 6 YRCEDCGHTFEVLQKISDDPLATCPECGGDV 36 (41)
T ss_pred EEcCCCCCEEEEEEecCCCCCCCCCCCCCcc
Confidence 47999997423333322 4567899999844
No 100
>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=89.58 E-value=0.23 Score=35.29 Aligned_cols=31 Identities=29% Similarity=0.538 Sum_probs=25.6
Q ss_pred CCCCCCCCCCCceeeeCCCCceEccCCcccccc
Q 025983 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLES 35 (245)
Q Consensus 3 ~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e 35 (245)
...||.||. +. +.-...|-..|..||.++.-
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 357999997 44 56678999999999999864
No 101
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=89.48 E-value=0.25 Score=31.38 Aligned_cols=29 Identities=34% Similarity=0.696 Sum_probs=21.3
Q ss_pred CCCCCCCCCceeeeCCCCc----eEccCCcccc
Q 025983 5 FCSDCKKHTEVVFDHSAGD----TVCSECGLVL 33 (245)
Q Consensus 5 ~Cp~Cg~~~~iv~d~~~G~----~vC~~CG~V~ 33 (245)
.||+||....+..|.+.|. -=|.-|-.=+
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~PI 34 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCCRPI 34 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhcCCcc
Confidence 5999998778888988885 2366665544
No 102
>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=89.37 E-value=0.22 Score=34.75 Aligned_cols=32 Identities=25% Similarity=0.534 Sum_probs=17.3
Q ss_pred CCCCCCCCCCce--eeeC--CCCceEccCCcccccc
Q 025983 4 AFCSDCKKHTEV--VFDH--SAGDTVCSECGLVLES 35 (245)
Q Consensus 4 ~~Cp~Cg~~~~i--v~d~--~~G~~vC~~CG~V~~e 35 (245)
..||.|+...++ ..|. ..|.+.|..||...+-
T Consensus 23 F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~ 58 (81)
T PF05129_consen 23 FDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQT 58 (81)
T ss_dssp ---TTT--SS-EEEEEETTTTEEEEEESSS--EEEE
T ss_pred EcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEE
Confidence 469999954444 3443 5778999999988753
No 103
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=89.14 E-value=0.44 Score=32.42 Aligned_cols=31 Identities=13% Similarity=0.305 Sum_probs=21.4
Q ss_pred CCCCCCCCCCCceeeeCC-------CCceEcc--CCccccc
Q 025983 3 DAFCSDCKKHTEVVFDHS-------AGDTVCS--ECGLVLE 34 (245)
Q Consensus 3 ~~~Cp~Cg~~~~iv~d~~-------~G~~vC~--~CG~V~~ 34 (245)
|+.||.||. ...|.+.. +=-..|+ +||....
T Consensus 1 mm~CP~Cg~-~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF~ 40 (72)
T PRK09678 1 MFHCPLCQH-AAHARTSRYITDTTKERYHQCQNVNCSATFI 40 (72)
T ss_pred CccCCCCCC-ccEEEEChhcChhhheeeeecCCCCCCCEEE
Confidence 578999998 45666631 1225688 8998764
No 104
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=88.98 E-value=0.33 Score=31.34 Aligned_cols=25 Identities=20% Similarity=0.517 Sum_probs=19.3
Q ss_pred CCCCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 2 TDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 2 ~~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
-+.+|+.||. -++ ..+|..||....
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 3578999997 333 679999998864
No 105
>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=88.83 E-value=0.42 Score=31.00 Aligned_cols=30 Identities=23% Similarity=0.530 Sum_probs=20.1
Q ss_pred CCCCCCCCCCceeeeCCCC--ceEccCCcccc
Q 025983 4 AFCSDCKKHTEVVFDHSAG--DTVCSECGLVL 33 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G--~~vC~~CG~V~ 33 (245)
-.||.|+.-..+..=.+.| ..-|..||+--
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~ 41 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGYQE 41 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCCcc
Confidence 3699999855553322333 37899999863
No 106
>PF12773 DZR: Double zinc ribbon
Probab=88.81 E-value=0.24 Score=30.87 Aligned_cols=27 Identities=22% Similarity=0.688 Sum_probs=12.2
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~ 33 (245)
..||+||.. +. .......+|..||..+
T Consensus 13 ~fC~~CG~~--l~-~~~~~~~~C~~Cg~~~ 39 (50)
T PF12773_consen 13 KFCPHCGTP--LP-PPDQSKKICPNCGAEN 39 (50)
T ss_pred cCChhhcCC--hh-hccCCCCCCcCCcCCC
Confidence 345555542 11 2223345555555554
No 107
>PRK05978 hypothetical protein; Provisional
Probab=88.59 E-value=0.34 Score=37.77 Aligned_cols=30 Identities=17% Similarity=0.410 Sum_probs=21.8
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
.+||.||. ..+..-+-.=..-|..||.-++
T Consensus 34 grCP~CG~-G~LF~g~Lkv~~~C~~CG~~~~ 63 (148)
T PRK05978 34 GRCPACGE-GKLFRAFLKPVDHCAACGEDFT 63 (148)
T ss_pred CcCCCCCC-CcccccccccCCCccccCCccc
Confidence 57999998 5664333444568999998875
No 108
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=88.53 E-value=0.1 Score=33.57 Aligned_cols=25 Identities=40% Similarity=0.907 Sum_probs=19.5
Q ss_pred CCCCCCCCCCceeeeCCCCceEccC-Cccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSE-CGLVLE 34 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~-CG~V~~ 34 (245)
..|+.||.+ |- .|+.+|++ ||.+++
T Consensus 9 ~HC~VCg~a--Ip----~de~~CSe~C~eil~ 34 (64)
T COG4068 9 RHCVVCGKA--IP----PDEQVCSEECGEILN 34 (64)
T ss_pred ccccccCCc--CC----CccchHHHHHHHHHH
Confidence 579999974 33 46899986 998885
No 109
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=88.51 E-value=0.3 Score=34.62 Aligned_cols=32 Identities=22% Similarity=0.502 Sum_probs=25.7
Q ss_pred CCCCCCCCCCCceeeeCCCCceEccCCccccccc
Q 025983 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESH 36 (245)
Q Consensus 3 ~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e~ 36 (245)
...||.||. +. +.-...|-.-|..||.++.-.
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 357999997 44 456789999999999998643
No 110
>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=87.92 E-value=0.4 Score=27.30 Aligned_cols=24 Identities=29% Similarity=0.743 Sum_probs=16.9
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~ 31 (245)
..|+.||- ++|+......|..||.
T Consensus 2 ~~C~~CGy----~y~~~~~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGY----IYDGEEAPWVCPVCGA 25 (33)
T ss_pred EECCCCCC----EECCCcCCCcCcCCCC
Confidence 35888884 4566666778888876
No 111
>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=87.87 E-value=1.7 Score=27.29 Aligned_cols=33 Identities=21% Similarity=0.295 Sum_probs=27.8
Q ss_pred hCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHHHh
Q 025983 161 QEDKPRTVKEICSVANGATKKEIGRAKEYIVKQL 194 (245)
Q Consensus 161 ~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l 194 (245)
.++.|+|..++|+. ++||..+|.+.++.|.+.+
T Consensus 11 ~~~~~it~~eLa~~-l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 11 ESKEPITAKELAEE-LGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HTTTSBEHHHHHHH-CTS-HHHHHHHHHHHHHTT
T ss_pred HcCCCcCHHHHHHH-hCCCHHHHHHHHHHHHHCC
Confidence 45667999999995 9999999999999997665
No 112
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=87.76 E-value=0.14 Score=41.26 Aligned_cols=31 Identities=26% Similarity=0.558 Sum_probs=22.7
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLES 35 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e 35 (245)
..||.|+.. =...|..+....|..||.++.+
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 2233456678999999999964
No 113
>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=87.59 E-value=0.34 Score=31.23 Aligned_cols=27 Identities=22% Similarity=0.599 Sum_probs=18.8
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcccccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHS 37 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e~~ 37 (245)
..||+||.. .....+|.+||+.=...+
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 469999962 135789999997654433
No 114
>PF15616 TerY-C: TerY-C metal binding domain
Probab=87.40 E-value=0.32 Score=37.04 Aligned_cols=21 Identities=29% Similarity=0.763 Sum_probs=13.6
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~ 33 (245)
--||+||+. .+..+| .||.|.
T Consensus 78 PgCP~CGn~--------~~fa~C-~CGkl~ 98 (131)
T PF15616_consen 78 PGCPHCGNQ--------YAFAVC-GCGKLF 98 (131)
T ss_pred CCCCCCcCh--------hcEEEe-cCCCEE
Confidence 469999974 244555 566664
No 115
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=87.33 E-value=0.52 Score=30.59 Aligned_cols=28 Identities=25% Similarity=0.581 Sum_probs=14.9
Q ss_pred CCCCCCCCCCCceeeeCCCCceEccCCccc
Q 025983 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (245)
Q Consensus 3 ~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V 32 (245)
..+|..||.. |..-..--...|.+||.+
T Consensus 7 ~~~CtSCg~~--i~~~~~~~~F~CPnCG~~ 34 (59)
T PRK14890 7 PPKCTSCGIE--IAPREKAVKFLCPNCGEV 34 (59)
T ss_pred CccccCCCCc--ccCCCccCEeeCCCCCCe
Confidence 3457777752 221111234667777766
No 116
>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=87.32 E-value=0.43 Score=31.72 Aligned_cols=9 Identities=33% Similarity=1.147 Sum_probs=7.3
Q ss_pred eEccCCccc
Q 025983 24 TVCSECGLV 32 (245)
Q Consensus 24 ~vC~~CG~V 32 (245)
++|++||..
T Consensus 37 v~C~~CGYT 45 (64)
T PF09855_consen 37 VSCTNCGYT 45 (64)
T ss_pred EECCCCCCE
Confidence 578888876
No 117
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=86.88 E-value=3.5 Score=34.50 Aligned_cols=82 Identities=16% Similarity=0.177 Sum_probs=57.2
Q ss_pred HHHHHHhcCC-CHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHH
Q 025983 112 IATMSDRLGL-VATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYI 190 (245)
Q Consensus 112 I~~~~~~L~L-p~~v~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l 190 (245)
+.++.+.+|+ +....+-+..|...-+...+.-=..|..+|-||+|+||-..+.+.+-.=+++ +.++...+..+.++|
T Consensus 157 L~q~~qd~gi~d~~~l~~~W~ivNDSyr~Dl~Ll~PPh~IalAcl~Ia~~~~~k~~~~~w~~e--l~vD~ekV~~~v~~I 234 (264)
T KOG0794|consen 157 LLQFVQDMGINDQKLLQLAWSIVNDSYRMDLCLLYPPHQIALACLYIACVIDEKDIPKAWFAE--LSVDMEKVKDIVQEI 234 (264)
T ss_pred HHHHHHHhcccchhhhhhhHhhhcchhhcceeeecCHHHHHHHHHHHHHhhcCCChHHHHHHH--HhccHHHHHHHHHHH
Confidence 5555555666 3446666666665555444333457899999999999999988876444555 468988888888888
Q ss_pred HHHhC
Q 025983 191 VKQLG 195 (245)
Q Consensus 191 ~~~l~ 195 (245)
.+...
T Consensus 235 ~~lYe 239 (264)
T KOG0794|consen 235 LKLYE 239 (264)
T ss_pred HHHHH
Confidence 76544
No 118
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=86.76 E-value=0.34 Score=36.12 Aligned_cols=38 Identities=18% Similarity=0.378 Sum_probs=24.1
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcccccccccccCc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETS 42 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e~~id~~~ 42 (245)
..||+||. ..+.--.-.=--.|..||.=...+--|++|
T Consensus 22 grCP~CGe-GrLF~gFLK~~p~C~aCG~dyg~~~a~DgP 59 (126)
T COG5349 22 GRCPRCGE-GRLFRGFLKVVPACEACGLDYGFADADDGP 59 (126)
T ss_pred CCCCCCCC-chhhhhhcccCchhhhccccccCCcccCCC
Confidence 36999997 555322334456899999877544444443
No 119
>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=86.58 E-value=0.48 Score=30.45 Aligned_cols=27 Identities=22% Similarity=0.653 Sum_probs=18.7
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcccccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHS 37 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e~~ 37 (245)
..||+||.. ..-.-||..||+--+..+
T Consensus 27 ~~C~~cG~~-------~~~H~vc~~cG~Y~gr~v 53 (55)
T TIGR01031 27 VVCPNCGEF-------KLPHRVCPSCGYYKGRQV 53 (55)
T ss_pred eECCCCCCc-------ccCeeECCccCeECCEEc
Confidence 469999972 134789999997655443
No 120
>PRK02935 hypothetical protein; Provisional
Probab=86.38 E-value=0.55 Score=34.10 Aligned_cols=27 Identities=26% Similarity=0.609 Sum_probs=19.5
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
..||+|++.+...= -...|-.|+.-+.
T Consensus 71 V~CP~C~K~TKmLG----rvD~CM~C~~PLT 97 (110)
T PRK02935 71 VICPSCEKPTKMLG----RVDACMHCNQPLT 97 (110)
T ss_pred eECCCCCchhhhcc----ceeecCcCCCcCC
Confidence 46999998644332 1458999999885
No 121
>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=86.36 E-value=2.2 Score=28.65 Aligned_cols=43 Identities=23% Similarity=0.278 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHhCC----------CCcCHHHHHHHHhCCCHHHHHHHHHHHHHH
Q 025983 150 LLAACLYIACRQED----------KPRTVKEICSVANGATKKEIGRAKEYIVKQ 193 (245)
Q Consensus 150 iaAA~lY~acR~~~----------~~~tl~dia~~~~~v~~~~i~~~~~~l~~~ 193 (245)
+|...++++.+... .|.+..+||+. +|++..++.+.+++|.+.
T Consensus 3 la~~Ll~l~~~~~~~~~~~~~~~~~~lt~~~iA~~-~g~sr~tv~r~l~~l~~~ 55 (76)
T PF13545_consen 3 LARFLLELAERFGRRQDGDGIRIPLPLTQEEIADM-LGVSRETVSRILKRLKDE 55 (76)
T ss_dssp HHHHHHHHHHHHEEEEETTEEEEEEESSHHHHHHH-HTSCHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHCCCCCCCCceEEecCCHHHHHHH-HCCCHHHHHHHHHHHHHC
Confidence 45566666666442 57899999995 999999999999999863
No 122
>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=86.07 E-value=1.4 Score=30.52 Aligned_cols=43 Identities=26% Similarity=0.320 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 149 ALLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 149 ~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
.-.-+.+|+|-...+.|.+..|||+. .+++...+.+....|.+
T Consensus 9 ~Al~~l~~la~~~~~~~~s~~eiA~~-~~i~~~~l~kil~~L~~ 51 (83)
T PF02082_consen 9 YALRILLYLARHPDGKPVSSKEIAER-LGISPSYLRKILQKLKK 51 (83)
T ss_dssp HHHHHHHHHHCTTTSC-BEHHHHHHH-HTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHhCCCCCCCCHHHHHHH-HCcCHHHHHHHHHHHhh
Confidence 34456677777666678999999994 99999999999999986
No 123
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=86.07 E-value=0.54 Score=30.04 Aligned_cols=27 Identities=30% Similarity=0.645 Sum_probs=20.1
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
.+|+.||.. + -+..--+||..||.+.=
T Consensus 6 ~~C~~Cg~~---~-~~~dDiVvCp~CgapyH 32 (54)
T PF14446_consen 6 CKCPVCGKK---F-KDGDDIVVCPECGAPYH 32 (54)
T ss_pred ccChhhCCc---c-cCCCCEEECCCCCCccc
Confidence 579999973 2 23445799999999873
No 124
>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=86.05 E-value=0.72 Score=25.26 Aligned_cols=22 Identities=23% Similarity=0.540 Sum_probs=11.2
Q ss_pred CCCCCCCCCceeeeCCCCceEccC
Q 025983 5 FCSDCKKHTEVVFDHSAGDTVCSE 28 (245)
Q Consensus 5 ~Cp~Cg~~~~iv~d~~~G~~vC~~ 28 (245)
.||.||+ .++.++.+=.+.|.+
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 4999997 366666666777764
No 125
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=85.83 E-value=9.4 Score=33.51 Aligned_cols=68 Identities=4% Similarity=0.015 Sum_probs=43.5
Q ss_pred HHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhCCCCcCHHHHHHHHhCC--CHHHHHHHHHHHHH
Q 025983 123 ATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKEICSVANGA--TKKEIGRAKEYIVK 192 (245)
Q Consensus 123 ~~v~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY~acR~~~~~~tl~dia~~~~~v--~~~~i~~~~~~l~~ 192 (245)
+.+...|..+...+.--...--..|..||+||||+|++..+....-.+- ++ ..+ +..+++..+..+++
T Consensus 181 ~~l~q~a~~~lndsl~Td~~L~y~Ps~IAlAAI~lA~~~~~~~l~~~~~-e~-~~~~~~~~~~~~l~~~~~~ 250 (305)
T TIGR00569 181 EYLRKHADKFLNRTLLTDAYLLYTPSQIALAAILHTASRAGLNMESYLT-EQ-LSVPGNREELPQLIDIMRE 250 (305)
T ss_pred HHHHHHHHHHHHHHHcCCceecCCHHHHHHHHHHHHHHHhCCCCcccch-hh-hcccccHHHHHHHHHHHHH
Confidence 4566667766665543332223679999999999999999875543332 42 445 66666666555544
No 126
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=85.45 E-value=0.63 Score=33.82 Aligned_cols=25 Identities=24% Similarity=0.615 Sum_probs=21.4
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
..||.||. ..+|+ ++-|.+||+-+.
T Consensus 7 ~~cPvcg~-~~iVT-----eL~c~~~etTVr 31 (122)
T COG3877 7 NRCPVCGR-KLIVT-----ELKCSNCETTVR 31 (122)
T ss_pred CCCCcccc-cceeE-----EEecCCCCceEe
Confidence 57999998 56776 799999999985
No 127
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=85.34 E-value=0.54 Score=28.48 Aligned_cols=26 Identities=23% Similarity=0.627 Sum_probs=18.3
Q ss_pred CCCCCCCCCCceeeeCCCCceEccC--Ccccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSE--CGLVLES 35 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~--CG~V~~e 35 (245)
.+||.||.- .-.+| +.|.+ |+.|...
T Consensus 12 rkCp~CGt~-----NG~R~-~~CKN~~C~~~~~~ 39 (44)
T PF14952_consen 12 RKCPKCGTY-----NGTRG-LSCKNKSCPQVFNV 39 (44)
T ss_pred ccCCcCcCc-----cCccc-ccccCCccchhhhc
Confidence 689999962 33444 77875 9998753
No 128
>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=85.07 E-value=0.86 Score=30.94 Aligned_cols=30 Identities=23% Similarity=0.621 Sum_probs=21.3
Q ss_pred CCCCCCCCCCcee--eeCCCCceEccCCcccc
Q 025983 4 AFCSDCKKHTEVV--FDHSAGDTVCSECGLVL 33 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv--~d~~~G~~vC~~CG~V~ 33 (245)
-.||.|++-..+. .+...-..-|..||+.-
T Consensus 9 a~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e 40 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRENGVEYVECVECGYTE 40 (71)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEecCCCCee
Confidence 3699999855553 23444557899999985
No 129
>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=84.99 E-value=0.82 Score=33.32 Aligned_cols=30 Identities=23% Similarity=0.537 Sum_probs=20.0
Q ss_pred CCCCCCCCCCceeee------C--CC-Cc-eEccCCccccc
Q 025983 4 AFCSDCKKHTEVVFD------H--SA-GD-TVCSECGLVLE 34 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d------~--~~-G~-~vC~~CG~V~~ 34 (245)
..||+||.. ....+ . .. .. .+|+.|+.-|.
T Consensus 3 ~~CpYCg~~-~~l~~~~~iYg~~~~~~~~~y~C~~C~AyVG 42 (102)
T PF11672_consen 3 IICPYCGGP-AELVDGSEIYGHRYDDGPYLYVCTPCDAYVG 42 (102)
T ss_pred cccCCCCCe-eEEcccchhcCccCCCCceeEECCCCCceee
Confidence 579999984 33333 1 12 22 78999988886
No 130
>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=84.98 E-value=0.5 Score=44.96 Aligned_cols=43 Identities=23% Similarity=0.635 Sum_probs=28.8
Q ss_pred CCCCCCCCCCcee-----ee----CCCCceEccCCcccccccc---cccCccccc
Q 025983 4 AFCSDCKKHTEVV-----FD----HSAGDTVCSECGLVLESHS---IDETSEWRT 46 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv-----~d----~~~G~~vC~~CG~V~~e~~---id~~~ewr~ 46 (245)
..||+||....+. +| +.+-.++|..||..++|+. ....-+|+.
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 3699999753332 22 4456799999999998863 223456764
No 131
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=84.81 E-value=3.3 Score=24.54 Aligned_cols=30 Identities=20% Similarity=0.325 Sum_probs=21.1
Q ss_pred CCCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Q 025983 163 DKPRTVKEICSVANGATKKEIGRAKEYIVKQLGL 196 (245)
Q Consensus 163 ~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~ 196 (245)
..+.++.|||+. +|++...+.+.|+ +.+|+
T Consensus 6 ~~~~~l~~iA~~-~g~S~~~f~r~Fk---~~~g~ 35 (42)
T PF00165_consen 6 QQKLTLEDIAEQ-AGFSPSYFSRLFK---KETGM 35 (42)
T ss_dssp -SS--HHHHHHH-HTS-HHHHHHHHH---HHTSS
T ss_pred cCCCCHHHHHHH-HCCCHHHHHHHHH---HHHCc
Confidence 457899999995 8999999988877 45554
No 132
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=84.68 E-value=0.34 Score=30.30 Aligned_cols=28 Identities=25% Similarity=0.631 Sum_probs=21.1
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~ 33 (245)
..|-.||.. +..|.....+-|..||.=+
T Consensus 7 Y~C~~Cg~~--~~~~~~~~~irCp~Cg~rI 34 (49)
T COG1996 7 YKCARCGRE--VELDQETRGIRCPYCGSRI 34 (49)
T ss_pred EEhhhcCCe--eehhhccCceeCCCCCcEE
Confidence 579999973 4446678889999999643
No 133
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=84.29 E-value=0.36 Score=39.01 Aligned_cols=32 Identities=31% Similarity=0.546 Sum_probs=20.5
Q ss_pred CCCCCCCCCCce--eeeCCCC---ceEccCCccccccc
Q 025983 4 AFCSDCKKHTEV--VFDHSAG---DTVCSECGLVLESH 36 (245)
Q Consensus 4 ~~Cp~Cg~~~~i--v~d~~~G---~~vC~~CG~V~~e~ 36 (245)
..||.||. .++ ..--..| .+-|.+||+|-.+.
T Consensus 7 ~~Cp~Cg~-eev~hEVik~~g~~~lvrC~eCG~V~~~~ 43 (201)
T COG1326 7 IECPSCGS-EEVSHEVIKERGREPLVRCEECGTVHPAI 43 (201)
T ss_pred EECCCCCc-chhhHHHHHhcCCceEEEccCCCcEeece
Confidence 46999995 333 1111234 47799999998553
No 134
>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=84.08 E-value=3.3 Score=31.56 Aligned_cols=45 Identities=20% Similarity=0.190 Sum_probs=37.9
Q ss_pred HHHHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 147 QDALLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 147 ~~~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
.+.-..+++|+|-+..+.|.+..+||+. .+++...+.+....|.+
T Consensus 7 ~~YAl~~l~~La~~~~~~~~s~~~ia~~-~~ip~~~l~kil~~L~~ 51 (135)
T TIGR02010 7 GRYAVTAMLDLALNAETGPVTLADISER-QGISLSYLEQLFAKLRK 51 (135)
T ss_pred HHHHHHHHHHHHhCCCCCcCcHHHHHHH-HCcCHHHHHHHHHHHHH
Confidence 4455678888887766678999999994 99999999999999976
No 135
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=84.06 E-value=7.5 Score=38.42 Aligned_cols=62 Identities=26% Similarity=0.370 Sum_probs=48.6
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhCCCCcCHHHH
Q 025983 109 FKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKEI 171 (245)
Q Consensus 109 ~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY~acR~~~~~~tl~di 171 (245)
.+.....|..|++++.....|.+.|..+...-.+.| +-..+-|.++|.+||...+|.-.+-+
T Consensus 35 ~q~~~~~c~~lnld~~~~~ea~d~yta~~q~~sleg-s~~hW~~cAlY~~~r~S~~~~v~~~~ 96 (920)
T KOG1010|consen 35 EQDSDELCRPLNLDEQTETEAWDTYTAVSQRLSLEG-SESHWLACALYTACRRSSVPTVGGGI 96 (920)
T ss_pred hhhhhhhhhhhcccchhhhhhHHHHHHHHhHhCCCc-cHHHHHHHHHHHHHHhccCCccCcce
Confidence 345778899999999999999999998866544444 36688999999999999776544444
No 136
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=84.03 E-value=0.83 Score=32.73 Aligned_cols=31 Identities=23% Similarity=0.521 Sum_probs=20.8
Q ss_pred CCCCCCCCCCCceeeeCCC-CceEccCCccccc
Q 025983 3 DAFCSDCKKHTEVVFDHSA-GDTVCSECGLVLE 34 (245)
Q Consensus 3 ~~~Cp~Cg~~~~iv~d~~~-G~~vC~~CG~V~~ 34 (245)
|..||.||+ .=+|....+ ....|..|++|..
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 458999997 233332222 4578999999974
No 137
>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=83.89 E-value=0.91 Score=28.56 Aligned_cols=11 Identities=27% Similarity=0.939 Sum_probs=6.1
Q ss_pred EccCCcccccc
Q 025983 25 VCSECGLVLES 35 (245)
Q Consensus 25 vC~~CG~V~~e 35 (245)
+|..||.|.++
T Consensus 3 ~C~~CgyiYd~ 13 (50)
T cd00730 3 ECRICGYIYDP 13 (50)
T ss_pred CCCCCCeEECC
Confidence 45555655544
No 138
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=83.64 E-value=0.72 Score=37.93 Aligned_cols=29 Identities=28% Similarity=0.534 Sum_probs=20.6
Q ss_pred CCCCCCCC-CceeeeCCCCceEccCCcccc
Q 025983 5 FCSDCKKH-TEVVFDHSAGDTVCSECGLVL 33 (245)
Q Consensus 5 ~Cp~Cg~~-~~iv~d~~~G~~vC~~CG~V~ 33 (245)
.||.|+++ +.++.+...=.+.|..||..-
T Consensus 100 ~C~~C~~pdT~l~k~~~~~~l~C~aCGa~~ 129 (201)
T PRK12336 100 ICSECGLPDTRLVKEDRVLMLRCDACGAHR 129 (201)
T ss_pred ECCCCCCCCcEEEEcCCeEEEEcccCCCCc
Confidence 59999995 344544444457899999874
No 139
>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=83.62 E-value=4.8 Score=26.17 Aligned_cols=37 Identities=16% Similarity=0.284 Sum_probs=30.3
Q ss_pred HHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 154 CLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 154 ~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
+||.... .+.+.+..|||+. ++++..++....++|.+
T Consensus 12 ~Iy~l~~-~~~~v~~~~iA~~-L~vs~~tvt~ml~~L~~ 48 (60)
T PF01325_consen 12 AIYELSE-EGGPVRTKDIAER-LGVSPPTVTEMLKRLAE 48 (60)
T ss_dssp HHHHHHH-CTSSBBHHHHHHH-HTS-HHHHHHHHHHHHH
T ss_pred HHHHHHc-CCCCccHHHHHHH-HCCChHHHHHHHHHHHH
Confidence 4555555 8899999999994 99999999999999875
No 140
>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=83.60 E-value=0.57 Score=38.69 Aligned_cols=34 Identities=26% Similarity=0.599 Sum_probs=24.5
Q ss_pred CCCCCCCCC-CceeeeCCCCc---eEccCCcccccccc
Q 025983 4 AFCSDCKKH-TEVVFDHSAGD---TVCSECGLVLESHS 37 (245)
Q Consensus 4 ~~Cp~Cg~~-~~iv~d~~~G~---~vC~~CG~V~~e~~ 37 (245)
+.|-+||.+ +++..++..|. ..|.+||.|.|.-+
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 469999985 23445565553 89999999996543
No 141
>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=83.58 E-value=0.27 Score=37.83 Aligned_cols=30 Identities=33% Similarity=0.637 Sum_probs=24.1
Q ss_pred CCCCCCCCCCCCCceeeeCCCCceEccCCcccccc
Q 025983 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLES 35 (245)
Q Consensus 1 ~~~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e 35 (245)
|++..||.||+ +|-. +|..+|.+|....++
T Consensus 1 m~l~nC~~Cgk----lF~~-~~~~iCp~C~~~~e~ 30 (137)
T TIGR03826 1 MELANCPKCGR----LFVK-TGRDVCPSCYEEEER 30 (137)
T ss_pred CCCccccccch----hhhh-cCCccCHHHhHHHHH
Confidence 78889999998 2444 489999999988753
No 142
>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=83.29 E-value=2.5 Score=28.41 Aligned_cols=35 Identities=20% Similarity=0.230 Sum_probs=30.7
Q ss_pred CCHHhHHHHHhhhcCCCHHHHHHHHHHHHHhhhcc
Q 025983 207 IHAGDFMRRFCSNLGMNNQAVKAAQEAVQKSEEFD 241 (245)
Q Consensus 207 ~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~ 241 (245)
..|.+|+.++++.+++++++...|..++++....+
T Consensus 3 ~~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~ 37 (88)
T cd00043 3 PTPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDY 37 (88)
T ss_pred chHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhc
Confidence 35789999999999999999999999999886643
No 143
>cd00092 HTH_CRP helix_turn_helix, cAMP Regulatory protein C-terminus; DNA binding domain of prokaryotic regulatory proteins belonging to the catabolite activator protein family.
Probab=83.13 E-value=5.8 Score=25.62 Aligned_cols=31 Identities=23% Similarity=0.319 Sum_probs=26.8
Q ss_pred CCCCcCHHHHHHHHhCCCHHHHHHHHHHHHHH
Q 025983 162 EDKPRTVKEICSVANGATKKEIGRAKEYIVKQ 193 (245)
Q Consensus 162 ~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~ 193 (245)
...+.+..|+|+. ++++..++.+.++.|.+.
T Consensus 22 ~~~~~s~~ela~~-~g~s~~tv~r~l~~L~~~ 52 (67)
T cd00092 22 VQLPLTRQEIADY-LGLTRETVSRTLKELEEE 52 (67)
T ss_pred ccCCcCHHHHHHH-HCCCHHHHHHHHHHHHHC
Confidence 3467999999994 999999999999999763
No 144
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=83.09 E-value=0.5 Score=27.52 Aligned_cols=29 Identities=28% Similarity=0.650 Sum_probs=19.4
Q ss_pred CCCCCCCCCCceeee----CCCCceEccCCcccc
Q 025983 4 AFCSDCKKHTEVVFD----HSAGDTVCSECGLVL 33 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d----~~~G~~vC~~CG~V~ 33 (245)
..||+|+.. --|-| +....+-|+.||.+.
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 469999973 22222 234558899999874
No 145
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=82.57 E-value=1.2 Score=28.20 Aligned_cols=32 Identities=28% Similarity=0.768 Sum_probs=22.3
Q ss_pred CCCCCCCCCCCceeee-CCCCc-eEccCCccccc
Q 025983 3 DAFCSDCKKHTEVVFD-HSAGD-TVCSECGLVLE 34 (245)
Q Consensus 3 ~~~Cp~Cg~~~~iv~d-~~~G~-~vC~~CG~V~~ 34 (245)
...|.+|+...+.++. ...|. ++|..||+-..
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~ 36 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYK 36 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccHHHH
Confidence 3679999975444443 35565 99999998764
No 146
>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=81.84 E-value=0.51 Score=34.74 Aligned_cols=39 Identities=26% Similarity=0.516 Sum_probs=24.0
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcccccccccccCcccccccC
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFAN 49 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e~~id~~~ewr~f~~ 49 (245)
..||+|+..+-..=. ...|..|+.-+. +|.+-|-.+|++
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 469999985322211 248999999885 343334345654
No 147
>PHA02942 putative transposase; Provisional
Probab=81.67 E-value=1.1 Score=40.71 Aligned_cols=28 Identities=18% Similarity=0.480 Sum_probs=20.7
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
+.||.||.. . .+.......|..||.+.+
T Consensus 326 q~Cs~CG~~-~--~~l~~r~f~C~~CG~~~d 353 (383)
T PHA02942 326 VSCPKCGHK-M--VEIAHRYFHCPSCGYEND 353 (383)
T ss_pred ccCCCCCCc-c--CcCCCCEEECCCCCCEeC
Confidence 679999973 2 233455799999999975
No 148
>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=81.49 E-value=0.91 Score=28.17 Aligned_cols=14 Identities=29% Similarity=0.755 Sum_probs=7.5
Q ss_pred eEccCCcccccccc
Q 025983 24 TVCSECGLVLESHS 37 (245)
Q Consensus 24 ~vC~~CG~V~~e~~ 37 (245)
..|..||.|.++..
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 149
>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=81.36 E-value=1 Score=28.22 Aligned_cols=28 Identities=29% Similarity=0.567 Sum_probs=16.8
Q ss_pred CCCCCCCCCCceeee-CCCCceEccCCcc
Q 025983 4 AFCSDCKKHTEVVFD-HSAGDTVCSECGL 31 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d-~~~G~~vC~~CG~ 31 (245)
.+|+.||..-++... .+...+.|..||.
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 478888863222221 2245677888887
No 150
>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=81.17 E-value=8.7 Score=30.44 Aligned_cols=29 Identities=21% Similarity=0.176 Sum_probs=26.4
Q ss_pred CCcCHHHHHHHHhCCCHHHHHHHHHHHHHH
Q 025983 164 KPRTVKEICSVANGATKKEIGRAKEYIVKQ 193 (245)
Q Consensus 164 ~~~tl~dia~~~~~v~~~~i~~~~~~l~~~ 193 (245)
.|.|..|||+. +|++..++.|.+++|.+.
T Consensus 142 ~~~t~~~iA~~-lG~tretvsR~l~~l~~~ 170 (193)
T TIGR03697 142 LRLSHQAIAEA-IGSTRVTITRLLGDLRKK 170 (193)
T ss_pred CCCCHHHHHHH-hCCcHHHHHHHHHHHHHC
Confidence 68999999995 999999999999999864
No 151
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=81.13 E-value=4.8 Score=31.93 Aligned_cols=45 Identities=18% Similarity=0.189 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 147 QDALLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 147 ~~~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
.+.-..+++|+|-...+.|.+..+||+ ..+++..-+.+.+..|.+
T Consensus 7 ~~yAl~~l~~lA~~~~~~~vs~~eIA~-~~~ip~~~l~kIl~~L~~ 51 (164)
T PRK10857 7 GRYAVTAMLDVALNSEAGPVPLADISE-RQGISLSYLEQLFSRLRK 51 (164)
T ss_pred HHHHHHHHHHHHhCCCCCcCcHHHHHH-HHCcCHHHHHHHHHHHHH
Confidence 455667788888555567999999999 599999999999999975
No 152
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=81.10 E-value=0.96 Score=43.73 Aligned_cols=11 Identities=9% Similarity=0.162 Sum_probs=5.2
Q ss_pred hHHHHHhhhcC
Q 025983 211 DFMRRFCSNLG 221 (245)
Q Consensus 211 ~~i~r~~~~L~ 221 (245)
.++..++..|.
T Consensus 295 ~~l~~l~~~l~ 305 (645)
T PRK14559 295 ESLIPLLQDLQ 305 (645)
T ss_pred HHHHHHHHHHH
Confidence 34445555543
No 153
>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=81.05 E-value=6.8 Score=27.59 Aligned_cols=45 Identities=18% Similarity=0.117 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHHhCCCCcCHHHHHHHHhC-CCHHHHHHHHHHHHHHhCC
Q 025983 149 ALLAACLYIACRQEDKPRTVKEICSVANG-ATKKEIGRAKEYIVKQLGL 196 (245)
Q Consensus 149 ~iaAA~lY~acR~~~~~~tl~dia~~~~~-v~~~~i~~~~~~l~~~l~~ 196 (245)
..=..++|++-+.. ..|+.+|+.. +| .+..++..+++++.+.+..
T Consensus 30 ~aR~ia~yl~~~~~--~~s~~~Ig~~-fg~r~hStV~~a~~ri~~~~~~ 75 (90)
T cd06571 30 LARQIAMYLARELT--GLSLPEIGRA-FGGRDHSTVLHAVRKIEELLEE 75 (90)
T ss_pred hHHHHHHHHHHHHh--CCCHHHHHHH-hCCCCHhHHHHHHHHHHHHHHh
Confidence 33446778776654 5679999995 88 9999999999999988864
No 154
>PRK08402 replication factor A; Reviewed
Probab=80.15 E-value=1.4 Score=39.55 Aligned_cols=27 Identities=30% Similarity=0.767 Sum_probs=22.1
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V 32 (245)
..||.|+. .++.|...|...|..||.|
T Consensus 213 ~aCp~CnK--kv~~~~~~~~~~Ce~~~~v 239 (355)
T PRK08402 213 DACPECRR--KVDYDPATDTWICPEHGEV 239 (355)
T ss_pred ecCCCCCe--EEEEecCCCCEeCCCCCCc
Confidence 46999997 3555888899999999975
No 155
>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=80.14 E-value=2.2 Score=26.23 Aligned_cols=21 Identities=29% Similarity=0.510 Sum_probs=18.4
Q ss_pred CHHHHHHHHhCCCHHHHHHHHH
Q 025983 167 TVKEICSVANGATKKEIGRAKE 188 (245)
Q Consensus 167 tl~dia~~~~~v~~~~i~~~~~ 188 (245)
|++|||.. +|++..++.+++.
T Consensus 1 Ti~dIA~~-agvS~~TVSr~ln 21 (46)
T PF00356_consen 1 TIKDIARE-AGVSKSTVSRVLN 21 (46)
T ss_dssp CHHHHHHH-HTSSHHHHHHHHT
T ss_pred CHHHHHHH-HCcCHHHHHHHHh
Confidence 78999995 8999999988865
No 156
>PF14122 YokU: YokU-like protein
Probab=80.01 E-value=1.1 Score=31.36 Aligned_cols=24 Identities=25% Similarity=0.634 Sum_probs=17.0
Q ss_pred CCCceEccCCcccccccccccCcc
Q 025983 20 SAGDTVCSECGLVLESHSIDETSE 43 (245)
Q Consensus 20 ~~G~~vC~~CG~V~~e~~id~~~e 43 (245)
++=.++|.+||.|-.+..+...-|
T Consensus 32 ~tP~i~C~~CgmvYq~d~vi~EIE 55 (87)
T PF14122_consen 32 DTPAIICSNCGMVYQDDEVIKEIE 55 (87)
T ss_pred CCceeeecCCCcEEehhHHHHHHh
Confidence 344489999999997766554444
No 157
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=80.01 E-value=1.4 Score=38.80 Aligned_cols=90 Identities=8% Similarity=0.023 Sum_probs=56.3
Q ss_pred HHHHHHHHHHHHHhcCCCHH----HHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhCCCCcCHHHH---HHHHhC
Q 025983 105 LILAFKTIATMSDRLGLVAT----IKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKEI---CSVANG 177 (245)
Q Consensus 105 l~~~~~~I~~~~~~L~Lp~~----v~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY~acR~~~~~~tl~di---a~~~~~ 177 (245)
+..+..++-+++..|+-..+ +...|..+.....--.+.---.+..||+||||+||...+.+.....- -.. ++
T Consensus 148 v~hPy~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL~y~p~~IAva~i~lA~~~~~~~~~~~~~~~w~~~-~d 226 (323)
T KOG0834|consen 148 VEHPYKYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLCLQYSPHSIAVACIHLAAKLLGVELPSDTDKRWWRE-FD 226 (323)
T ss_pred ccCchHHHHHHHHHhhhhhhccccHHHHHHHHhchhheeeeeEeecCcEEEeehhhHHHHHcCCCCCCCcccchhhh-hc
Confidence 34566667777776665543 44555555444433222223478899999999999999975443321 221 34
Q ss_pred --CCHHHHHHHHHHHHHHhC
Q 025983 178 --ATKKEIGRAKEYIVKQLG 195 (245)
Q Consensus 178 --v~~~~i~~~~~~l~~~l~ 195 (245)
++...|.....++...+.
T Consensus 227 ~~vt~e~l~~i~~~~l~~y~ 246 (323)
T KOG0834|consen 227 ETVTNELLDDICHEFLDLYE 246 (323)
T ss_pred ccCCHHHHHHHHHHHHHHHh
Confidence 888888888777776554
No 158
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=79.51 E-value=3.3 Score=27.18 Aligned_cols=56 Identities=11% Similarity=0.282 Sum_probs=32.6
Q ss_pred HHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCccCCccccCC-CCHHhHHHHHhhhcCCCHH
Q 025983 159 CRQEDKPRTVKEICSVANGATKKEIGRAKEYIVKQLGLETGQSVEMGT-IHAGDFMRRFCSNLGMNNQ 225 (245)
Q Consensus 159 cR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~-~~p~~~i~r~~~~L~l~~~ 225 (245)
-.++....|+.|++.. ++++...|...-. =+++ .+|. +-...||..||+.||++++
T Consensus 4 ~~R~~~glsl~~va~~-t~I~~~~l~aiE~-----~~~~-----~lp~~~y~rg~lr~Ya~~Lgld~~ 60 (62)
T PF13413_consen 4 EAREAKGLSLEDVAEE-TKISVSYLEAIEN-----GDFD-----SLPSPVYARGYLRKYARFLGLDPD 60 (62)
T ss_dssp HHHHCTT--HHHHHHH-CS--HHHHHHHHC-----T-GC-----CSSSHHHHHHHHHHHHHHTT--HH
T ss_pred HHHHHcCCCHHHHHHH-hCCCHHHHHHHHC-----cChh-----hCCcHHHHHHHHHHHHHHhCcCcc
Confidence 3456778999999995 8999887754322 1111 1332 2346799999999999875
No 159
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=79.34 E-value=1 Score=32.95 Aligned_cols=33 Identities=12% Similarity=0.128 Sum_probs=26.5
Q ss_pred CCCCCCCCCCCceeeeCCCCceEccCCccccccccc
Q 025983 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSI 38 (245)
Q Consensus 3 ~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e~~i 38 (245)
++.||+||+. .+|-.+--+||..||.-.....+
T Consensus 9 KridPetg~K---FYDLNrdPiVsPytG~s~P~s~f 41 (129)
T COG4530 9 KRIDPETGKK---FYDLNRDPIVSPYTGKSYPRSYF 41 (129)
T ss_pred cccCccccch---hhccCCCccccCcccccchHHHH
Confidence 4689999984 78888999999999987644433
No 160
>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=79.28 E-value=1.3 Score=26.62 Aligned_cols=28 Identities=29% Similarity=0.616 Sum_probs=17.2
Q ss_pred CCCCCCCCCCceeeeC-CCCceEccCCcc
Q 025983 4 AFCSDCKKHTEVVFDH-SAGDTVCSECGL 31 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~-~~G~~vC~~CG~ 31 (245)
.+|+.||..-++..-. +.....|..||.
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 4688888532333222 245688888887
No 161
>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=79.15 E-value=3.6 Score=26.23 Aligned_cols=33 Identities=27% Similarity=0.424 Sum_probs=28.3
Q ss_pred CCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCc
Q 025983 164 KPRTVKEICSVANGATKKEIGRAKEYIVKQLGLE 197 (245)
Q Consensus 164 ~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~ 197 (245)
...+.++||+. +++++.+|....+.+.+.|+..
T Consensus 17 ~G~~~~eIA~~-l~is~~tV~~~~~~i~~Kl~~~ 49 (58)
T PF00196_consen 17 QGMSNKEIAEE-LGISEKTVKSHRRRIMKKLGVK 49 (58)
T ss_dssp TTS-HHHHHHH-HTSHHHHHHHHHHHHHHHHT-S
T ss_pred hcCCcchhHHh-cCcchhhHHHHHHHHHHHhCCC
Confidence 56789999995 9999999999999999999975
No 162
>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=79.09 E-value=3.1 Score=27.64 Aligned_cols=29 Identities=24% Similarity=0.554 Sum_probs=26.0
Q ss_pred hHHHHHhhhcCCCHHHHHHHHHHHHHhhh
Q 025983 211 DFMRRFCSNLGMNNQAVKAAQEAVQKSEE 239 (245)
Q Consensus 211 ~~i~r~~~~L~l~~~v~~~A~~i~~~~~~ 239 (245)
+||.++++.+++++++...|..++++...
T Consensus 1 ~~l~~~~~~~~~~~~~~~~a~~~~~~~l~ 29 (83)
T smart00385 1 DFLRRVCKALNLDPETLNLAVNLLDRFLS 29 (83)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 48899999999999999999999998866
No 163
>COG1773 Rubredoxin [Energy production and conversion]
Probab=79.08 E-value=1.3 Score=28.36 Aligned_cols=26 Identities=35% Similarity=0.588 Sum_probs=15.2
Q ss_pred CCCCCCCCCCCCCceeeeCCCCceEccCCc
Q 025983 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECG 30 (245)
Q Consensus 1 ~~~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG 30 (245)
|....|..||= |+|++.|+-.|.-|+
T Consensus 1 m~~~~C~~CG~----vYd~e~Gdp~~gi~p 26 (55)
T COG1773 1 MKRWRCSVCGY----VYDPEKGDPRCGIAP 26 (55)
T ss_pred CCceEecCCce----EeccccCCccCCCCC
Confidence 44455666663 566666666655554
No 164
>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=78.90 E-value=0.56 Score=29.46 Aligned_cols=33 Identities=15% Similarity=0.339 Sum_probs=22.7
Q ss_pred CCCCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 2 TDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 2 ~~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
.+..|++|+.--.-.-+....++-|..||++-.
T Consensus 3 ~eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~ 35 (51)
T PF10122_consen 3 KEIRCGHCNKLLAKAGEVIELEIKCPRCKTINH 35 (51)
T ss_pred cceeccchhHHHhhhcCccEEEEECCCCCccce
Confidence 457899999621101245568999999999963
No 165
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=78.87 E-value=1 Score=40.87 Aligned_cols=32 Identities=31% Similarity=0.787 Sum_probs=24.1
Q ss_pred CCCCCCCCC-Cce----eeeCCCCceEccCCcccccc
Q 025983 4 AFCSDCKKH-TEV----VFDHSAGDTVCSECGLVLES 35 (245)
Q Consensus 4 ~~Cp~Cg~~-~~i----v~d~~~G~~vC~~CG~V~~e 35 (245)
..||.|++. +.+ .+|..+|...|..||.=|.+
T Consensus 129 Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelve 165 (436)
T KOG2593|consen 129 YVCPNCQKKYTSLEALQLLDNETGEFHCENCGGELVE 165 (436)
T ss_pred ccCCccccchhhhHHHHhhcccCceEEEecCCCchhc
Confidence 579999984 111 55788999999999975533
No 166
>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=78.60 E-value=0.79 Score=29.33 Aligned_cols=30 Identities=37% Similarity=0.849 Sum_probs=20.1
Q ss_pred CCCCCCCCCceeee--CCCCceEccCCccccc
Q 025983 5 FCSDCKKHTEVVFD--HSAGDTVCSECGLVLE 34 (245)
Q Consensus 5 ~Cp~Cg~~~~iv~d--~~~G~~vC~~CG~V~~ 34 (245)
.|.+|+...+..+. +..+..+|..||+-..
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~ 32 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWK 32 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHH
Confidence 48888875444443 3467788888888764
No 167
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=78.58 E-value=1.3 Score=29.09 Aligned_cols=23 Identities=30% Similarity=0.768 Sum_probs=16.2
Q ss_pred CCCCCCCCCCCCCceeeeCCCCceEccCCcc
Q 025983 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (245)
Q Consensus 1 ~~~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~ 31 (245)
|....|.+|+.- + + ...|..||.
T Consensus 1 M~~kAC~~C~~i---~-~----~~~CP~Cgs 23 (61)
T PRK08351 1 MTEKACRHCHYI---T-T----EDRCPVCGS 23 (61)
T ss_pred CchhhhhhCCcc---c-C----CCcCCCCcC
Confidence 666789999962 2 2 226999997
No 168
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=78.43 E-value=7.8 Score=25.78 Aligned_cols=38 Identities=18% Similarity=0.204 Sum_probs=29.8
Q ss_pred HHHHHHhCCC-CcCHHHHHHHHhCCCHHHHHHHHHHHHHH
Q 025983 155 LYIACRQEDK-PRTVKEICSVANGATKKEIGRAKEYIVKQ 193 (245)
Q Consensus 155 lY~acR~~~~-~~tl~dia~~~~~v~~~~i~~~~~~l~~~ 193 (245)
|+...+..+- +.++.|||. .+|++..++++....|.+.
T Consensus 11 IL~~L~~~g~~~~ta~eLa~-~lgl~~~~v~r~L~~L~~~ 49 (68)
T smart00550 11 ILEFLENSGDETSTALQLAK-NLGLPKKEVNRVLYSLEKK 49 (68)
T ss_pred HHHHHHHCCCCCcCHHHHHH-HHCCCHHHHHHHHHHHHHC
Confidence 3444455565 499999999 5999999999998888754
No 169
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=78.29 E-value=1.6 Score=32.66 Aligned_cols=32 Identities=25% Similarity=0.628 Sum_probs=27.8
Q ss_pred eCCCCceEccCCcccc--cccccccCcccccccC
Q 025983 18 DHSAGDTVCSECGLVL--ESHSIDETSEWRTFAN 49 (245)
Q Consensus 18 d~~~G~~vC~~CG~V~--~e~~id~~~ewr~f~~ 49 (245)
..+.|.++|..||.-| .+.-+|.|.-|.+|.+
T Consensus 28 ~~~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPSF~~ 61 (119)
T PRK05508 28 FFEKGTYVCKQCGAPLYRSEDKFKSGCGWPSFDD 61 (119)
T ss_pred cCCCeEEEecCCCCccccccccccCCCCCcccCc
Confidence 3589999999999988 5667899999999985
No 170
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=78.13 E-value=21 Score=25.57 Aligned_cols=39 Identities=15% Similarity=0.213 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHH
Q 025983 150 LLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYI 190 (245)
Q Consensus 150 iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l 190 (245)
+..+.-|+... ...|.++.++|+. ++++...+.+.+++.
T Consensus 7 ~~~~~~~i~~~-~~~~~~~~~lA~~-~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 7 IQTLIAWIDEH-IDQPLNIDVVAKK-SGYSKWYLQRMFRTV 45 (107)
T ss_pred HHHHHHHHHHh-cCCCCCHHHHHHH-HCCCHHHHHHHHHHH
Confidence 44455555554 4567999999995 899999999887754
No 171
>KOG1088 consensus Uncharacterized conserved protein [Function unknown]
Probab=78.12 E-value=0.89 Score=33.68 Aligned_cols=18 Identities=39% Similarity=0.696 Sum_probs=15.2
Q ss_pred eeCCCCceEccCCccccc
Q 025983 17 FDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 17 ~d~~~G~~vC~~CG~V~~ 34 (245)
.|-.+|+++|.+||.|..
T Consensus 92 ~~v~EG~l~CpetG~vfp 109 (124)
T KOG1088|consen 92 IDVIEGELVCPETGRVFP 109 (124)
T ss_pred hhhccceEecCCCCcEee
Confidence 355789999999999974
No 172
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=77.94 E-value=1.9 Score=31.32 Aligned_cols=28 Identities=25% Similarity=0.584 Sum_probs=19.1
Q ss_pred CCCCCCCCCCceeee---------CCCCceEccCCccc
Q 025983 4 AFCSDCKKHTEVVFD---------HSAGDTVCSECGLV 32 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d---------~~~G~~vC~~CG~V 32 (245)
..||.||.. ..++- +.+=..+|.+||..
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 54332 23335899999964
No 173
>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=77.83 E-value=1.4 Score=28.21 Aligned_cols=29 Identities=24% Similarity=0.566 Sum_probs=20.8
Q ss_pred CCCCCCCCCCcee--eeCCCCceEccCCccc
Q 025983 4 AFCSDCKKHTEVV--FDHSAGDTVCSECGLV 32 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv--~d~~~G~~vC~~CG~V 32 (245)
..|++|..++-.. .+.+.-..+|..||..
T Consensus 23 LIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 23 LICSKCFSHNGLAPKEEFEEIQYRCPYCGAL 53 (54)
T ss_pred EECcccchhhcccccccCCceEEEcCCCCCc
Confidence 4699999764443 5666668899999863
No 174
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=77.50 E-value=1.2 Score=35.26 Aligned_cols=29 Identities=17% Similarity=0.440 Sum_probs=18.6
Q ss_pred CCCCCCCCCCCceee---------------eCCCCceEccCCcccc
Q 025983 3 DAFCSDCKKHTEVVF---------------DHSAGDTVCSECGLVL 33 (245)
Q Consensus 3 ~~~Cp~Cg~~~~iv~---------------d~~~G~~vC~~CG~V~ 33 (245)
...||+|+.. ++. -..+-...|..||.+.
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 3579999963 221 1223356799999886
No 175
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=77.37 E-value=2 Score=25.61 Aligned_cols=28 Identities=21% Similarity=0.456 Sum_probs=16.3
Q ss_pred CCCCCCCCCceeeeC-CCCceEccCCcccc
Q 025983 5 FCSDCKKHTEVVFDH-SAGDTVCSECGLVL 33 (245)
Q Consensus 5 ~Cp~Cg~~~~iv~d~-~~G~~vC~~CG~V~ 33 (245)
+||.|+.. -..... .---.+|..||=+-
T Consensus 1 ~CP~C~~~-l~~~~~~~~~id~C~~C~G~W 29 (41)
T PF13453_consen 1 KCPRCGTE-LEPVRLGDVEIDVCPSCGGIW 29 (41)
T ss_pred CcCCCCcc-cceEEECCEEEEECCCCCeEE
Confidence 59999973 222221 11225699998764
No 176
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=77.25 E-value=15 Score=30.62 Aligned_cols=61 Identities=13% Similarity=0.033 Sum_probs=46.6
Q ss_pred CCCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCccCCccccCCCCHHhHHHHHhhhcCCCHHHHHHHHHHHH
Q 025983 163 DKPRTVKEICSVANGATKKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMNNQAVKAAQEAVQ 235 (245)
Q Consensus 163 ~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~ 235 (245)
....+.+|||+. +++++.++......|.+.|++. ..+ +.+ +++-+.++-..+-+.+.+|+.
T Consensus 156 a~G~SnkEIA~~-L~IS~~TVk~hvs~I~~KLgv~---------sR~-eLv-~~A~~~gli~~~~~~~~~ii~ 216 (217)
T PRK13719 156 SFGFSHEYIAQL-LNITVGSSKNKISEILKFFGIS---------SRD-ELL-IILHTSEMIFYLYKKVFEIIN 216 (217)
T ss_pred HCCCCHHHHHHH-hCCCHHHHHHHHHHHHHHhCCC---------CHH-HHH-HHHHHcCChHHHHHHHHHHhc
Confidence 357889999995 9999999999999999999975 122 222 455566787777777777764
No 177
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=77.24 E-value=1.7 Score=37.18 Aligned_cols=28 Identities=18% Similarity=0.419 Sum_probs=20.1
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~ 33 (245)
+.||.||+. . ......-...|..||.+.
T Consensus 100 ~fC~~CG~~-~-~~~~~~~~~~C~~c~~~~ 127 (256)
T PRK00241 100 RFCGYCGHP-M-HPSKTEWAMLCPHCRERY 127 (256)
T ss_pred ccccccCCC-C-eecCCceeEECCCCCCEE
Confidence 689999984 3 333444558999999765
No 178
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=77.17 E-value=0.5 Score=41.13 Aligned_cols=30 Identities=20% Similarity=0.470 Sum_probs=22.1
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
.+||.|+. .-...|-.....||..||.-..
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 47999997 3333445677899999999763
No 179
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=77.00 E-value=7.9 Score=30.26 Aligned_cols=44 Identities=18% Similarity=0.252 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 147 QDALLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 147 ~~~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
.+.-.-+.+|+|.. .+.+.+.++||+ ..+++..-+.+.+..|++
T Consensus 7 ~~YAlr~L~~LA~~-~~~~~s~~eIA~-~~~is~~~L~kIl~~L~~ 50 (153)
T PRK11920 7 TNYAIRMLMYCAAN-DGKLSRIPEIAR-AYGVSELFLFKILQPLVE 50 (153)
T ss_pred HhHHHHHHHHHHhC-CCCcCcHHHHHH-HHCcCHHHHHHHHHHHHH
Confidence 34455678888844 566889999999 499999999999999986
No 180
>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=76.94 E-value=11 Score=22.83 Aligned_cols=29 Identities=17% Similarity=0.232 Sum_probs=23.4
Q ss_pred CCCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 163 DKPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 163 ~~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
+-+.|..|+|.. ++++..++.+.+++|.+
T Consensus 15 ~~~~t~~ela~~-~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 15 NPRITQKELAEK-LGISRSTVNRYLKKLEE 43 (48)
T ss_dssp CTTS-HHHHHHH-HTS-HHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHH-hCCCHHHHHHHHHHHHH
Confidence 445999999995 99999999999998875
No 181
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=76.85 E-value=5.1 Score=23.95 Aligned_cols=29 Identities=28% Similarity=0.358 Sum_probs=25.6
Q ss_pred CCCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 163 DKPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 163 ~~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
..|.+..|+|+ .++++..++.+.++.|.+
T Consensus 6 ~~~~s~~~la~-~l~~s~~tv~~~l~~L~~ 34 (48)
T smart00419 6 RLPLTRQEIAE-LLGLTRETVSRTLKRLEK 34 (48)
T ss_pred EeccCHHHHHH-HHCCCHHHHHHHHHHHHH
Confidence 35789999999 499999999999998876
No 182
>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=76.53 E-value=0.55 Score=40.75 Aligned_cols=30 Identities=17% Similarity=0.429 Sum_probs=21.4
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
.+||.|+. .-...|-.....||..||.-..
T Consensus 27 ~~c~~c~~-~~~~~~l~~~~~vc~~c~~h~r 56 (285)
T TIGR00515 27 TKCPKCGQ-VLYTKELERNLEVCPKCDHHMR 56 (285)
T ss_pred eECCCCcc-hhhHHHHHhhCCCCCCCCCcCc
Confidence 47999997 2223344566799999999763
No 183
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=76.35 E-value=12 Score=28.95 Aligned_cols=65 Identities=12% Similarity=0.260 Sum_probs=42.7
Q ss_pred CCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCccCCccccCCCCHHhHHHHHhhhcCC--------CHHHHHHHHHHHH
Q 025983 164 KPRTVKEICSVANGATKKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGM--------NNQAVKAAQEAVQ 235 (245)
Q Consensus 164 ~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l--------~~~v~~~A~~i~~ 235 (245)
...|..|||+. +|++..+|.+..+...+.|.-. ..-+ +|...|+- +.++..+...+.+
T Consensus 20 ~GlTq~EIAe~-LGiS~~tVs~ie~ra~kkLr~~------------~~tl-~~~~~l~a~~~v~~~~G~d~~~ip~~v~~ 85 (141)
T PRK03975 20 RGLTQQEIADI-LGTSRANVSSIEKRARENIEKA------------RETL-AFAETLNAPVRVTIPAGTDLFDIPKRIYK 85 (141)
T ss_pred cCCCHHHHHHH-HCCCHHHHHHHHHHHHHHHHHH------------HHHH-HHHHHcCCCeEEEecCCCcHHHhHHHHHH
Confidence 56899999995 9999999888877666655421 0111 44444443 3566666666666
Q ss_pred Hhhhccc
Q 025983 236 KSEEFDI 242 (245)
Q Consensus 236 ~~~~~~~ 242 (245)
.+.+.||
T Consensus 86 ~~d~~~i 92 (141)
T PRK03975 86 EADEAGI 92 (141)
T ss_pred HhhHcCC
Confidence 6666665
No 184
>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=76.28 E-value=1.5 Score=38.12 Aligned_cols=29 Identities=28% Similarity=0.663 Sum_probs=12.6
Q ss_pred CCCCCCCCCCce-eeeCCC--Cc--eEccCCccc
Q 025983 4 AFCSDCKKHTEV-VFDHSA--GD--TVCSECGLV 32 (245)
Q Consensus 4 ~~Cp~Cg~~~~i-v~d~~~--G~--~vC~~CG~V 32 (245)
..||.||+.+.+ +..... |. +.|.-||+-
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 579999986433 333333 54 889999864
No 185
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=76.11 E-value=2 Score=27.76 Aligned_cols=28 Identities=21% Similarity=0.565 Sum_probs=18.9
Q ss_pred CCCCCCCCCCCceeeeCCCCceEccCCcccccccc
Q 025983 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHS 37 (245)
Q Consensus 3 ~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e~~ 37 (245)
+..||.||.. - --.-||.+||+--+..+
T Consensus 27 ~~~c~~cG~~-~------l~Hrvc~~cg~Y~g~~v 54 (57)
T COG0333 27 LSVCPNCGEY-K------LPHRVCLKCGYYKGRQV 54 (57)
T ss_pred ceeccCCCCc-c------cCceEcCCCCCccCeEe
Confidence 3579999962 2 23689999997655433
No 186
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=76.06 E-value=2.1 Score=32.00 Aligned_cols=21 Identities=14% Similarity=0.164 Sum_probs=11.2
Q ss_pred CcCHHHHHHHHhCCCHHHHHHH
Q 025983 165 PRTVKEICSVANGATKKEIGRA 186 (245)
Q Consensus 165 ~~tl~dia~~~~~v~~~~i~~~ 186 (245)
.++..++|.. +|++..+|.+.
T Consensus 78 gltq~~lA~~-lg~~~~tis~~ 98 (127)
T TIGR03830 78 GLSQREAAEL-LGGGVNAFSRY 98 (127)
T ss_pred CCCHHHHHHH-hCCCHHHHHHH
Confidence 4455566663 56665555443
No 187
>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=75.79 E-value=1.8 Score=23.80 Aligned_cols=28 Identities=18% Similarity=0.372 Sum_probs=15.3
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~ 31 (245)
.+||.|+....-+.....+..+|..|-.
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 4799999742223345667789998854
No 188
>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=75.79 E-value=9.7 Score=24.19 Aligned_cols=40 Identities=20% Similarity=0.221 Sum_probs=29.7
Q ss_pred HHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 152 AACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 152 AA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
..++++.....+.+.++.||++. ++++..++.+..+.|.+
T Consensus 8 ~~vL~~l~~~~~~~~t~~~la~~-l~~~~~~vs~~v~~L~~ 47 (62)
T PF12802_consen 8 FRVLMALARHPGEELTQSELAER-LGISKSTVSRIVKRLEK 47 (62)
T ss_dssp HHHHHHHHHSTTSGEEHHHHHHH-HTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHHCCCCCcCHHHHHHH-HCcCHHHHHHHHHHHHH
Confidence 34455554544445899999995 99999999999999865
No 189
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=75.77 E-value=1.9 Score=37.12 Aligned_cols=27 Identities=30% Similarity=0.696 Sum_probs=19.5
Q ss_pred CCCCCCCCCCceeeeCCCCc--eEccCCccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGD--TVCSECGLVLE 34 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~--~vC~~CG~V~~ 34 (245)
+.|+.||.. + .+..|. .+|.+||...=
T Consensus 112 RFCg~CG~~-~---~~~~~g~~~~C~~cg~~~f 140 (279)
T COG2816 112 RFCGRCGTK-T---YPREGGWARVCPKCGHEHF 140 (279)
T ss_pred cCCCCCCCc-C---ccccCceeeeCCCCCCccC
Confidence 579999984 2 233343 79999999874
No 190
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=75.49 E-value=2.1 Score=33.10 Aligned_cols=33 Identities=27% Similarity=0.602 Sum_probs=28.1
Q ss_pred eCCCCceEccCCcccc--cccccccCcccccccCC
Q 025983 18 DHSAGDTVCSECGLVL--ESHSIDETSEWRTFANE 50 (245)
Q Consensus 18 d~~~G~~vC~~CG~V~--~e~~id~~~ewr~f~~~ 50 (245)
..+.|.++|..||.-| .+.-+|.|.-|..|.+.
T Consensus 38 ~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~ 72 (142)
T PRK00222 38 NKEKGIYVCIVCGEPLFSSDTKFDSGCGWPSFTKP 72 (142)
T ss_pred CCCCeEEEecCCCchhcCCcccccCCCCCcCcCcc
Confidence 3689999999999998 55678999999999853
No 191
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=75.15 E-value=5.6 Score=25.03 Aligned_cols=38 Identities=11% Similarity=-0.010 Sum_probs=30.4
Q ss_pred HHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Q 025983 158 ACRQEDKPRTVKEICSVANGATKKEIGRAKEYIVKQLGL 196 (245)
Q Consensus 158 acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~ 196 (245)
+.-......+..++|.. +||+..++.+.+..+...|..
T Consensus 12 ~L~~LR~~~~~~~La~~-FgIs~stvsri~~~~~~~L~~ 49 (53)
T PF13613_consen 12 TLMYLRLNLTFQDLAYR-FGISQSTVSRIFHEWIPLLYQ 49 (53)
T ss_pred HHHHHHcCCcHhHHhhh-eeecHHHHHHHHHHHHHHHHH
Confidence 33334566789999995 999999999999999887754
No 192
>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=74.84 E-value=2.6 Score=32.56 Aligned_cols=27 Identities=30% Similarity=0.732 Sum_probs=19.5
Q ss_pred CCC--CCCCCCceeeeCCCCceEccCCccccc
Q 025983 5 FCS--DCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 5 ~Cp--~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
.|| .|++. +..+ .+|...|..||..++
T Consensus 20 aC~~~~C~kK--v~~~-~~~~y~C~~C~~~~~ 48 (146)
T PF08646_consen 20 ACPNEKCNKK--VTEN-GDGSYRCEKCNKTVE 48 (146)
T ss_dssp E-TSTTTS-B---EEE-TTTEEEETTTTEEES
T ss_pred CCCCccCCCE--eecC-CCcEEECCCCCCcCC
Confidence 599 99983 4444 679999999998874
No 193
>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=74.70 E-value=10 Score=29.15 Aligned_cols=31 Identities=16% Similarity=0.201 Sum_probs=26.5
Q ss_pred CCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhC
Q 025983 164 KPRTVKEICSVANGATKKEIGRAKEYIVKQLG 195 (245)
Q Consensus 164 ~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~ 195 (245)
...|..|||+. +|++..++.+..+...+.|.
T Consensus 20 ~GlTq~EIAe~-LgiS~stV~~~e~ra~kkLr 50 (137)
T TIGR00721 20 KGLSQKEIAKE-LKTTRANVSAIEKRAMENIE 50 (137)
T ss_pred cCCCHHHHHHH-HCcCHHHHHHHHHhHHHHHH
Confidence 56699999995 99999999988888777775
No 194
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=74.68 E-value=0.84 Score=39.08 Aligned_cols=43 Identities=21% Similarity=0.459 Sum_probs=28.4
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccccc-------ccccccCccccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE-------SHSIDETSEWRTFA 48 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~-------e~~id~~~ewr~f~ 48 (245)
.+||.||. .-..-|-.+...||..||.-.. +..+|.|+ |+.+.
T Consensus 29 ~KCp~c~~-~~y~~eL~~n~~vcp~c~~h~ri~A~~Ri~~llD~gs-f~el~ 78 (294)
T COG0777 29 TKCPSCGE-MLYRKELESNLKVCPKCGHHMRISARERLEALLDEGS-FEELD 78 (294)
T ss_pred eECCCccc-eeeHHHHHhhhhcccccCcccccCHHHHHHHhhCCCc-ceecc
Confidence 47999997 3334455677899999998752 23456553 45554
No 195
>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=74.64 E-value=2.6 Score=22.22 Aligned_cols=23 Identities=26% Similarity=0.778 Sum_probs=13.0
Q ss_pred CCCCCCCCceeeeCC-CCceEccCCcc
Q 025983 6 CSDCKKHTEVVFDHS-AGDTVCSECGL 31 (245)
Q Consensus 6 Cp~Cg~~~~iv~d~~-~G~~vC~~CG~ 31 (245)
|..||.. + .... .-...|.+||.
T Consensus 1 C~sC~~~--i-~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRP--I-APREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCc--c-cCcccCceEeCCCCCC
Confidence 6677752 2 2222 34577888883
No 196
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=74.52 E-value=25 Score=26.28 Aligned_cols=42 Identities=12% Similarity=0.137 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHH
Q 025983 147 QDALLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYI 190 (245)
Q Consensus 147 ~~~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l 190 (245)
...+..+.-|+--.. ..+.++.++|+. +|+++..+.+.+++.
T Consensus 8 ~~~i~~~~~~I~~~~-~~~~sl~~lA~~-~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 8 AITIHSILDWIEDNL-ESPLSLEKVSER-SGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHHHHHHHHHHhc-CCCCCHHHHHHH-HCcCHHHHHHHHHHH
Confidence 445555666666554 457999999995 899999998887754
No 197
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=74.40 E-value=0.67 Score=40.37 Aligned_cols=43 Identities=23% Similarity=0.454 Sum_probs=27.5
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccccc-------ccccccCccccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE-------SHSIDETSEWRTFA 48 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~-------e~~id~~~ewr~f~ 48 (245)
.+||.|+. .-...|-.....||..||.-.. +.++|.++ |..+.
T Consensus 28 ~~c~~c~~-~~~~~~l~~~~~vc~~c~~h~rl~areRi~~L~D~gs-F~E~~ 77 (292)
T PRK05654 28 TKCPSCGQ-VLYRKELEANLNVCPKCGHHMRISARERLDLLLDEGS-FVELD 77 (292)
T ss_pred eECCCccc-hhhHHHHHhcCCCCCCCCCCeeCCHHHHHHHHccCCc-cEEec
Confidence 47999997 3333344556789999999763 12466554 44443
No 198
>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=74.10 E-value=2.8 Score=23.97 Aligned_cols=24 Identities=21% Similarity=0.589 Sum_probs=13.0
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~ 31 (245)
..|+.||- +++...-..+|..||.
T Consensus 3 ~~C~~CG~----i~~g~~~p~~CP~Cg~ 26 (34)
T cd00729 3 WVCPVCGY----IHEGEEAPEKCPICGA 26 (34)
T ss_pred EECCCCCC----EeECCcCCCcCcCCCC
Confidence 45777774 2333233357777775
No 199
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=73.78 E-value=2 Score=31.90 Aligned_cols=7 Identities=43% Similarity=1.407 Sum_probs=4.0
Q ss_pred CCCCCCC
Q 025983 5 FCSDCKK 11 (245)
Q Consensus 5 ~Cp~Cg~ 11 (245)
+|+.||.
T Consensus 72 ~C~~Cg~ 78 (113)
T PRK12380 72 WCWDCSQ 78 (113)
T ss_pred EcccCCC
Confidence 4666664
No 200
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=73.67 E-value=8.9 Score=23.51 Aligned_cols=31 Identities=23% Similarity=0.267 Sum_probs=24.7
Q ss_pred CCCcCHHHHHHHHhCCCHHHHHHHHHHHHHHh
Q 025983 163 DKPRTVKEICSVANGATKKEIGRAKEYIVKQL 194 (245)
Q Consensus 163 ~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l 194 (245)
..+.|+.|||.. +|++..++.+..+...+.|
T Consensus 18 ~~~~t~~eIa~~-lg~s~~~V~~~~~~al~kL 48 (50)
T PF04545_consen 18 FEGLTLEEIAER-LGISRSTVRRILKRALKKL 48 (50)
T ss_dssp TST-SHHHHHHH-HTSCHHHHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHH-HCCcHHHHHHHHHHHHHHh
Confidence 678899999995 9999999998877665544
No 201
>PF14353 CpXC: CpXC protein
Probab=73.64 E-value=3.1 Score=31.37 Aligned_cols=12 Identities=25% Similarity=0.758 Sum_probs=9.9
Q ss_pred ceEccCCccccc
Q 025983 23 DTVCSECGLVLE 34 (245)
Q Consensus 23 ~~vC~~CG~V~~ 34 (245)
..+|..||....
T Consensus 38 ~~~CP~Cg~~~~ 49 (128)
T PF14353_consen 38 SFTCPSCGHKFR 49 (128)
T ss_pred EEECCCCCCcee
Confidence 479999998873
No 202
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=73.40 E-value=8.1 Score=30.13 Aligned_cols=44 Identities=23% Similarity=0.271 Sum_probs=37.7
Q ss_pred HHHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 148 DALLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 148 ~~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
+.-.-+.+|+|....+.|.+..+||+. .++++.-+.+.+..|++
T Consensus 8 ~yal~~L~~LA~~~~~~~~s~~~IA~~-~~is~~~L~kil~~L~k 51 (150)
T COG1959 8 EYALRALLYLALLPGGGPVSSAEIAER-QGISPSYLEKILSKLRK 51 (150)
T ss_pred hHHHHHHHHHHhCCCCCcccHHHHHHH-hCcCHHHHHHHHHHHHH
Confidence 455667889998777779999999995 99999999999999986
No 203
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=73.33 E-value=2.2 Score=34.73 Aligned_cols=37 Identities=24% Similarity=0.448 Sum_probs=24.1
Q ss_pred CCCCCCCCCCce----eee-CCCCc-----eEccCCcccccccccccC
Q 025983 4 AFCSDCKKHTEV----VFD-HSAGD-----TVCSECGLVLESHSIDET 41 (245)
Q Consensus 4 ~~Cp~Cg~~~~i----v~d-~~~G~-----~vC~~CG~V~~e~~id~~ 41 (245)
..||.||+. -. .+| |--|+ ++|..||+=..|-...+.
T Consensus 15 ~~CPvCg~~-l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~DV~~~e~ 61 (201)
T COG1779 15 IDCPVCGGT-LKAHMYLYDIPYFGEVLISTGVCERCGYRSTDVKTLEE 61 (201)
T ss_pred ecCCcccce-eeEEEeeecCCccceEEEEEEEccccCCcccceeeccc
Confidence 469999973 11 122 45565 689999998876554433
No 204
>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=73.11 E-value=2.6 Score=25.29 Aligned_cols=10 Identities=40% Similarity=0.969 Sum_probs=7.4
Q ss_pred eEccCCcccc
Q 025983 24 TVCSECGLVL 33 (245)
Q Consensus 24 ~vC~~CG~V~ 33 (245)
.+|.+||..+
T Consensus 33 ~~C~~CGE~~ 42 (46)
T TIGR03831 33 LVCPQCGEEY 42 (46)
T ss_pred cccccCCCEe
Confidence 3588888765
No 205
>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=72.98 E-value=11 Score=28.20 Aligned_cols=44 Identities=23% Similarity=0.341 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 148 DALLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 148 ~~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
+.-..+.+|++-...+.|.+..+|++. ++++...+++....|.+
T Consensus 8 ~~al~~l~~la~~~~~~~~s~~eia~~-~~i~~~~v~~il~~L~~ 51 (132)
T TIGR00738 8 EYALRALLDLALNPDEGPVSVKEIAER-QGISRSYLEKILRTLRR 51 (132)
T ss_pred HHHHHHHHHHHhCCCCCcCcHHHHHHH-HCcCHHHHHHHHHHHHH
Confidence 344555666663322459999999994 99999999999999986
No 206
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=72.75 E-value=10 Score=23.17 Aligned_cols=32 Identities=28% Similarity=0.365 Sum_probs=28.4
Q ss_pred CcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCc
Q 025983 165 PRTVKEICSVANGATKKEIGRAKEYIVKQLGLE 197 (245)
Q Consensus 165 ~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~ 197 (245)
..+..+||.. ++++..++.+....+.+.|+.+
T Consensus 18 g~s~~eia~~-l~is~~tv~~~~~~~~~kl~~~ 49 (58)
T smart00421 18 GLTNKEIAER-LGISEKTVKTHLSNIMRKLGVR 49 (58)
T ss_pred CCCHHHHHHH-HCCCHHHHHHHHHHHHHHHCCC
Confidence 3589999995 9999999999999999998865
No 207
>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=72.70 E-value=2.6 Score=32.29 Aligned_cols=33 Identities=24% Similarity=0.452 Sum_probs=27.9
Q ss_pred eCCCCceEccCCcccc--cccccccCcccccccCC
Q 025983 18 DHSAGDTVCSECGLVL--ESHSIDETSEWRTFANE 50 (245)
Q Consensus 18 d~~~G~~vC~~CG~V~--~e~~id~~~ewr~f~~~ 50 (245)
..+.|.++|..||.-| .+.-+|.|.-|.+|.+.
T Consensus 35 ~~~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPSF~~~ 69 (134)
T TIGR00357 35 NKEEGIYVDITCGEPLFSSEDKFDSGCGWPSFYKP 69 (134)
T ss_pred CCCCeEEEccCCCCccccccchhcCCCCCcCcCcc
Confidence 3589999999999988 55678999999999753
No 208
>PF09339 HTH_IclR: IclR helix-turn-helix domain; InterPro: IPR005471 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium. These proteins have a Helix-Turn-Helix motif at the N terminus that is similar to that of other DNA-binding proteins [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1MKM_A 3MQ0_A 3R4K_A 2G7U_C 2O0Y_C 2XRO_F 2XRN_B 2IA2_D.
Probab=72.66 E-value=8.2 Score=23.99 Aligned_cols=36 Identities=28% Similarity=0.322 Sum_probs=27.9
Q ss_pred HHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 156 YIACRQEDKPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 156 Y~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
.-+-...+.+.++.||++ .+|++..++.+..+.|.+
T Consensus 9 L~~l~~~~~~~t~~eia~-~~gl~~stv~r~L~tL~~ 44 (52)
T PF09339_consen 9 LEALAESGGPLTLSEIAR-ALGLPKSTVHRLLQTLVE 44 (52)
T ss_dssp HHCHHCTBSCEEHHHHHH-HHTS-HHHHHHHHHHHHH
T ss_pred HHHHHcCCCCCCHHHHHH-HHCcCHHHHHHHHHHHHH
Confidence 334445677789999999 599999999999888865
No 209
>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=72.62 E-value=2.9 Score=29.62 Aligned_cols=33 Identities=27% Similarity=0.697 Sum_probs=21.5
Q ss_pred CCCCCCCC------CceeeeCCCC----------ceEccCCcccccccc
Q 025983 5 FCSDCKKH------TEVVFDHSAG----------DTVCSECGLVLESHS 37 (245)
Q Consensus 5 ~Cp~Cg~~------~~iv~d~~~G----------~~vC~~CG~V~~e~~ 37 (245)
.|+-|+.. +++.+|...| -++|.+||.+.-+.-
T Consensus 1 ~C~~C~~~~~~~~~tTv~~el~~G~~~IvIknVPa~~C~~CGe~y~~de 49 (89)
T TIGR03829 1 KCRWCEEEKAIARTTTVYWELPDGTKAIEIKETPSISCSHCGMEYQDDT 49 (89)
T ss_pred CCcccCCCceecceEEEEEEecCCceEEEEecCCcccccCCCcEeecHH
Confidence 48999541 3445555555 378999998875443
No 210
>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=72.61 E-value=6.2 Score=23.30 Aligned_cols=29 Identities=24% Similarity=0.465 Sum_probs=19.5
Q ss_pred CCCCCCCCCCceeeeCCCCc-eEccC---Ccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGD-TVCSE---CGLVL 33 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~-~vC~~---CG~V~ 33 (245)
..||.||+ .-++.....|. +.|++ |....
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 45555555554 57876 76654
No 211
>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=72.60 E-value=2.3 Score=31.67 Aligned_cols=17 Identities=12% Similarity=0.485 Sum_probs=8.2
Q ss_pred eeeeCCCCceEccCCcc
Q 025983 15 VVFDHSAGDTVCSECGL 31 (245)
Q Consensus 15 iv~d~~~G~~vC~~CG~ 31 (245)
+..+...+...|.+||.
T Consensus 62 L~I~~~p~~~~C~~Cg~ 78 (115)
T TIGR00100 62 LNIEDEPVECECEDCSE 78 (115)
T ss_pred EEEEeeCcEEEcccCCC
Confidence 34444445555555553
No 212
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=72.11 E-value=9.9 Score=25.00 Aligned_cols=33 Identities=21% Similarity=0.178 Sum_probs=26.6
Q ss_pred CCCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Q 025983 163 DKPRTVKEICSVANGATKKEIGRAKEYIVKQLGL 196 (245)
Q Consensus 163 ~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~ 196 (245)
+.|.+-.|||+ +++++..++++....|.+.=.+
T Consensus 13 ~~p~~T~eiA~-~~gls~~~aR~yL~~Le~eG~V 45 (62)
T PF04703_consen 13 NGPLKTREIAD-ALGLSIYQARYYLEKLEKEGKV 45 (62)
T ss_dssp TS-EEHHHHHH-HHTS-HHHHHHHHHHHHHCTSE
T ss_pred CCCCCHHHHHH-HhCCCHHHHHHHHHHHHHCCCE
Confidence 78999999999 5999999999999988775433
No 213
>KOG3134 consensus Predicted membrane protein [Function unknown]
Probab=71.99 E-value=1.2 Score=36.70 Aligned_cols=34 Identities=24% Similarity=0.518 Sum_probs=26.9
Q ss_pred CCCCCCCCC-CceeeeCCCCc---eEccCCcccccccc
Q 025983 4 AFCSDCKKH-TEVVFDHSAGD---TVCSECGLVLESHS 37 (245)
Q Consensus 4 ~~Cp~Cg~~-~~iv~d~~~G~---~vC~~CG~V~~e~~ 37 (245)
+.|-+||.. .++-.++..|. +-|.+|+.|+++-+
T Consensus 1 ~~CVeCg~~vksLy~~Ys~g~irlt~C~nC~e~vDkYi 38 (225)
T KOG3134|consen 1 YRCVECGSEVKSLYTQYSPGNIRLTKCPNCQEVVDKYI 38 (225)
T ss_pred CcccccCchHHHHHHhcCCCcEEEeeCCchhhHHHhHe
Confidence 469999975 46677888884 78999999997543
No 214
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=71.90 E-value=2.3 Score=27.87 Aligned_cols=26 Identities=27% Similarity=0.768 Sum_probs=16.8
Q ss_pred CCCCCCCCCCCCCceeeeCCCCceEccCCccc
Q 025983 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (245)
Q Consensus 1 ~~~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V 32 (245)
|....|.+|+.- + ....-+|..||.=
T Consensus 2 ~~~kAC~~Ck~l---~---~~d~e~CP~Cgs~ 27 (64)
T COG2093 2 STEKACKNCKRL---T---PEDTEICPVCGST 27 (64)
T ss_pred chhHHHhhcccc---C---CCCCccCCCCCCc
Confidence 345678889862 2 1345689999853
No 215
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=71.90 E-value=1.2 Score=30.84 Aligned_cols=29 Identities=31% Similarity=0.504 Sum_probs=24.2
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
..|+.||.. -+-....|..-|..|..|+.
T Consensus 37 y~CsfCGK~--~vKR~AvGiW~C~~C~kv~a 65 (92)
T KOG0402|consen 37 YTCSFCGKK--TVKRKAVGIWKCGSCKKVVA 65 (92)
T ss_pred hhhhhcchh--hhhhhceeEEecCCccceec
Confidence 569999983 35567899999999999986
No 216
>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=71.57 E-value=3.1 Score=32.81 Aligned_cols=28 Identities=25% Similarity=0.697 Sum_probs=21.2
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
..||.|++. + .+...|...|..|+..++
T Consensus 35 ~aC~~C~kk--v-~~~~~~~~~C~~C~~~~~ 62 (166)
T cd04476 35 PACPGCNKK--V-VEEGNGTYRCEKCNKSVP 62 (166)
T ss_pred ccccccCcc--c-EeCCCCcEECCCCCCcCC
Confidence 369999983 3 344448999999998873
No 217
>PF13730 HTH_36: Helix-turn-helix domain
Probab=71.38 E-value=15 Score=22.88 Aligned_cols=25 Identities=12% Similarity=0.266 Sum_probs=22.8
Q ss_pred CHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 167 TVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 167 tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
+...|++. +|++..+|.++.++|.+
T Consensus 27 S~~~la~~-~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 27 SQETLAKD-LGVSRRTVQRAIKELEE 51 (55)
T ss_pred CHHHHHHH-HCcCHHHHHHHHHHHHH
Confidence 89999995 99999999999999875
No 218
>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=71.26 E-value=1.8 Score=36.38 Aligned_cols=29 Identities=17% Similarity=0.596 Sum_probs=10.5
Q ss_pred CCCCCCCCCCceee---eCCCCceEccCCcccc
Q 025983 4 AFCSDCKKHTEVVF---DHSAGDTVCSECGLVL 33 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~---d~~~G~~vC~~CG~V~ 33 (245)
+.||+||+. .+-. ..--.+..|.+|+.-.
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 579999984 2311 1234578999998654
No 219
>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=71.11 E-value=14 Score=27.64 Aligned_cols=44 Identities=14% Similarity=0.184 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 147 QDALLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 147 ~~~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
.+.-..+.+|++- ..+.+.+..||++. ++++...+.+..+.|.+
T Consensus 8 ~~yal~~l~~la~-~~~~~~s~~eia~~-l~is~~~v~~~l~~L~~ 51 (130)
T TIGR02944 8 TDYATLVLTTLAQ-NDSQPYSAAEIAEQ-TGLNAPTVSKILKQLSL 51 (130)
T ss_pred HhHHHHHHHHHHh-CCCCCccHHHHHHH-HCcCHHHHHHHHHHHHH
Confidence 3455666778774 34578999999994 99999999999999976
No 220
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=71.03 E-value=22 Score=29.19 Aligned_cols=29 Identities=24% Similarity=0.124 Sum_probs=26.0
Q ss_pred CCcCHHHHHHHHhCCCHHHHHHHHHHHHHH
Q 025983 164 KPRTVKEICSVANGATKKEIGRAKEYIVKQ 193 (245)
Q Consensus 164 ~~~tl~dia~~~~~v~~~~i~~~~~~l~~~ 193 (245)
.|+|..+||+. +|++..++.|..++|.+.
T Consensus 183 ~~lt~~~iA~~-lG~sr~tvsR~l~~l~~~ 211 (235)
T PRK11161 183 LTMTRGDIGNY-LGLTVETISRLLGRFQKS 211 (235)
T ss_pred ccccHHHHHHH-hCCcHHHHHHHHHHHHHC
Confidence 58999999995 999999999999988763
No 221
>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=70.87 E-value=12 Score=22.34 Aligned_cols=30 Identities=23% Similarity=0.308 Sum_probs=22.8
Q ss_pred hCCCCcCHHHHHHHHhCCCHHHHHHHHHHHH
Q 025983 161 QEDKPRTVKEICSVANGATKKEIGRAKEYIV 191 (245)
Q Consensus 161 ~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~ 191 (245)
+.+-..+..+||.. +|++..++.+.+++|.
T Consensus 13 q~d~r~s~~~la~~-lglS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 13 QEDGRRSYAELAEE-LGLSESTVRRRIRRLE 42 (42)
T ss_dssp HH-TTS-HHHHHHH-HTS-HHHHHHHHHHHH
T ss_pred HHcCCccHHHHHHH-HCcCHHHHHHHHHHhC
Confidence 45577899999995 9999999999988763
No 222
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=70.58 E-value=2.7 Score=32.27 Aligned_cols=21 Identities=24% Similarity=0.629 Sum_probs=13.6
Q ss_pred ceeeeCCCCceEccCCccccc
Q 025983 14 EVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 14 ~iv~d~~~G~~vC~~CG~V~~ 34 (245)
.+..+.......|.+||.+..
T Consensus 61 ~L~i~~~p~~~~C~~CG~~~~ 81 (135)
T PRK03824 61 EIIFEEEEAVLKCRNCGNEWS 81 (135)
T ss_pred EEEEEecceEEECCCCCCEEe
Confidence 445555667777888876653
No 223
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=70.50 E-value=12 Score=28.32 Aligned_cols=36 Identities=22% Similarity=0.397 Sum_probs=30.1
Q ss_pred HHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 156 YIACRQEDKPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 156 Y~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
|.+.-..+-|.|..|||+. ++.+..++.++.+.|..
T Consensus 33 ~~~LL~~~~~~tvdelae~-lnr~rStv~rsl~~L~~ 68 (126)
T COG3355 33 YKALLEENGPLTVDELAEI-LNRSRSTVYRSLQNLLE 68 (126)
T ss_pred HHHHHhhcCCcCHHHHHHH-HCccHHHHHHHHHHHHH
Confidence 4454446789999999996 99999999999998874
No 224
>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=70.09 E-value=3.3 Score=25.54 Aligned_cols=28 Identities=18% Similarity=0.484 Sum_probs=17.3
Q ss_pred CCCCCCCCCceeeeC-------CCCceEccC--Ccccc
Q 025983 5 FCSDCKKHTEVVFDH-------SAGDTVCSE--CGLVL 33 (245)
Q Consensus 5 ~Cp~Cg~~~~iv~d~-------~~G~~vC~~--CG~V~ 33 (245)
.||+||+. ..+... .+--..|++ ||.-.
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 59999983 444331 222356777 88765
No 225
>PF13790 DUF4182: Domain of unknown function (DUF4182)
Probab=69.86 E-value=2.2 Score=25.07 Aligned_cols=13 Identities=31% Similarity=0.925 Sum_probs=11.9
Q ss_pred CceEccCCccccc
Q 025983 22 GDTVCSECGLVLE 34 (245)
Q Consensus 22 G~~vC~~CG~V~~ 34 (245)
|.+||+.|+.+++
T Consensus 2 GtIvCq~C~~~Id 14 (38)
T PF13790_consen 2 GTIVCQHCNETID 14 (38)
T ss_pred CEEEeccccceee
Confidence 7899999999995
No 226
>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=69.49 E-value=3.2 Score=37.88 Aligned_cols=30 Identities=27% Similarity=0.607 Sum_probs=17.9
Q ss_pred CCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 5 ~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
.||+|+.-.++..-...+...|..||.++.
T Consensus 15 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~ 44 (403)
T TIGR00155 15 LCSQCDMLVALPRIESGQKAACPRCGTTLT 44 (403)
T ss_pred eCCCCCCcccccCCCCCCeeECCCCCCCCc
Confidence 488888632221112334567888888884
No 227
>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=68.96 E-value=14 Score=22.62 Aligned_cols=32 Identities=28% Similarity=0.482 Sum_probs=28.5
Q ss_pred CcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCc
Q 025983 165 PRTVKEICSVANGATKKEIGRAKEYIVKQLGLE 197 (245)
Q Consensus 165 ~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~ 197 (245)
..+.++||.. ++++..++.+...++.+.++..
T Consensus 15 ~~s~~eia~~-l~~s~~tv~~~~~~~~~~l~~~ 46 (57)
T cd06170 15 GKTNKEIADI-LGISEKTVKTHLRNIMRKLGVK 46 (57)
T ss_pred CCCHHHHHHH-HCCCHHHHHHHHHHHHHHhCCC
Confidence 4699999995 9999999999999999988864
No 228
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=68.90 E-value=2.7 Score=40.75 Aligned_cols=14 Identities=21% Similarity=0.648 Sum_probs=9.1
Q ss_pred CCceEccCCccccc
Q 025983 21 AGDTVCSECGLVLE 34 (245)
Q Consensus 21 ~G~~vC~~CG~V~~ 34 (245)
.|...|.+||.-+.
T Consensus 39 ~~~~fC~~CG~~~~ 52 (645)
T PRK14559 39 VDEAHCPNCGAETG 52 (645)
T ss_pred cccccccccCCccc
Confidence 45667777776554
No 229
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=68.86 E-value=4.1 Score=28.01 Aligned_cols=30 Identities=23% Similarity=0.459 Sum_probs=19.8
Q ss_pred CCCCCCCCCCCceeeeCCCC--ceEccCCccccc
Q 025983 3 DAFCSDCKKHTEVVFDHSAG--DTVCSECGLVLE 34 (245)
Q Consensus 3 ~~~Cp~Cg~~~~iv~d~~~G--~~vC~~CG~V~~ 34 (245)
++.||.|+.. ++.....| ...|..|+-|-=
T Consensus 1 ~llCP~C~v~--l~~~~rs~vEiD~CPrCrGVWL 32 (88)
T COG3809 1 MLLCPICGVE--LVMSVRSGVEIDYCPRCRGVWL 32 (88)
T ss_pred CcccCcCCce--eeeeeecCceeeeCCccccEee
Confidence 3579999963 44333333 357999988853
No 230
>COG5333 CCL1 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=68.66 E-value=11 Score=32.93 Aligned_cols=45 Identities=18% Similarity=0.094 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhCCCCcCH
Q 025983 124 TIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTV 168 (245)
Q Consensus 124 ~v~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY~acR~~~~~~tl 168 (245)
+..+.|..+...+..-.+.---.|..+|.||+++||+..+.|.-.
T Consensus 168 ~~~~~aw~~inDa~~t~~~llypphiIA~a~l~ia~~~~~~~~~~ 212 (297)
T COG5333 168 KLLQIAWKIINDALRTDLCLLYPPHIIALAALLIACEVLGMPIIK 212 (297)
T ss_pred HHHHHHHHHHHhhhhceeeeecChHHHHHHHHHHHHHhcCCccch
Confidence 467777777777766554444678999999999999999987543
No 231
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=68.52 E-value=20 Score=29.02 Aligned_cols=35 Identities=9% Similarity=0.164 Sum_probs=30.6
Q ss_pred CCCCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCc
Q 025983 162 EDKPRTVKEICSVANGATKKEIGRAKEYIVKQLGLE 197 (245)
Q Consensus 162 ~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~ 197 (245)
-....+.+|||+. +++++.++......+.+.|+..
T Consensus 145 LAqGkTnKEIAe~-L~IS~rTVkth~srImkKLgV~ 179 (198)
T PRK15201 145 IASGYHLSETAAL-LSLSEEQTKSLRRSIMRKLHVK 179 (198)
T ss_pred HHCCCCHHHHHHH-hCCCHHHHHHHHHHHHHHhCCC
Confidence 3457889999995 9999999999999999999975
No 232
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=68.48 E-value=15 Score=24.41 Aligned_cols=36 Identities=14% Similarity=0.044 Sum_probs=31.5
Q ss_pred HHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhC
Q 025983 159 CRQEDKPRTVKEICSVANGATKKEIGRAKEYIVKQLG 195 (245)
Q Consensus 159 cR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~ 195 (245)
.|+.+.|+++.+.|+. +|++...+.+....+++.+-
T Consensus 7 IrlLs~~~s~~~Aa~~-lG~~~~~v~~wv~~fR~wll 42 (65)
T PF05344_consen 7 IRLLSQQISVAQAADR-LGTDPGTVRRWVRMFRQWLL 42 (65)
T ss_pred HHHhcccccHHHHHHH-HCcCHHHHHHHHHHHHHHHH
Confidence 3678999999999995 99999999999998888663
No 233
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=68.35 E-value=1.3 Score=32.90 Aligned_cols=24 Identities=33% Similarity=0.779 Sum_probs=12.3
Q ss_pred CCCCCCCCCceeeeCCCCceEccCCccc
Q 025983 5 FCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (245)
Q Consensus 5 ~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V 32 (245)
+|+.||.. +++......|..||.-
T Consensus 72 ~C~~Cg~~----~~~~~~~~~CP~Cgs~ 95 (113)
T PF01155_consen 72 RCRDCGHE----FEPDEFDFSCPRCGSP 95 (113)
T ss_dssp EETTTS-E----EECHHCCHH-SSSSSS
T ss_pred ECCCCCCE----EecCCCCCCCcCCcCC
Confidence 57777752 3333444667777754
No 234
>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=68.28 E-value=3 Score=28.14 Aligned_cols=26 Identities=19% Similarity=0.635 Sum_probs=15.7
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~ 33 (245)
..||.|+.+ + +...|.+.|..|+.-+
T Consensus 2 ~~CP~C~~~--L--~~~~~~~~C~~C~~~~ 27 (70)
T PF07191_consen 2 NTCPKCQQE--L--EWQGGHYHCEACQKDY 27 (70)
T ss_dssp -B-SSS-SB--E--EEETTEEEETTT--EE
T ss_pred CcCCCCCCc--c--EEeCCEEECccccccc
Confidence 469999972 4 4456899999998755
No 235
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=68.18 E-value=3.7 Score=33.49 Aligned_cols=32 Identities=25% Similarity=0.606 Sum_probs=19.3
Q ss_pred CCCCCCCCCce---eee--CCCCc-----eEccCCccccccc
Q 025983 5 FCSDCKKHTEV---VFD--HSAGD-----TVCSECGLVLESH 36 (245)
Q Consensus 5 ~Cp~Cg~~~~i---v~d--~~~G~-----~vC~~CG~V~~e~ 36 (245)
.||+||..... .++ |--|+ ..|.+||+=-.|-
T Consensus 2 ~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~ev 43 (192)
T TIGR00310 2 DCPSCGGECETVMKTVNDIPYFGEVLETSTICEHCGYRSNDV 43 (192)
T ss_pred cCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCCCcccee
Confidence 59999964222 111 22343 6799999876443
No 236
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=68.18 E-value=1.7 Score=27.43 Aligned_cols=28 Identities=29% Similarity=0.652 Sum_probs=18.9
Q ss_pred CCCCCCCCCcee--eeCCCCceEccCCcccc
Q 025983 5 FCSDCKKHTEVV--FDHSAGDTVCSECGLVL 33 (245)
Q Consensus 5 ~Cp~Cg~~~~iv--~d~~~G~~vC~~CG~V~ 33 (245)
.|+-||..-.+. +..++| +||.+|--=+
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 499999742221 235778 8999998554
No 237
>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=68.07 E-value=4.5 Score=29.51 Aligned_cols=27 Identities=22% Similarity=0.628 Sum_probs=21.0
Q ss_pred CCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 5 ~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
.|--|+. .... .+.+++||..||+++.
T Consensus 37 aCeiC~~-~GY~--q~g~~lvC~~C~~~~~ 63 (102)
T PF10080_consen 37 ACEICGP-KGYY--QEGDQLVCKNCGVRFN 63 (102)
T ss_pred eccccCC-CceE--EECCEEEEecCCCEEe
Confidence 5889986 3433 4578899999999985
No 238
>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=67.69 E-value=2.1 Score=24.93 Aligned_cols=22 Identities=27% Similarity=0.554 Sum_probs=9.6
Q ss_pred CCCCCCCCCCceeeeCCCCceEc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVC 26 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC 26 (245)
.+|..||.. --+.+...|.++|
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 468888863 2234556677777
No 239
>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=67.57 E-value=12 Score=24.85 Aligned_cols=32 Identities=25% Similarity=0.377 Sum_probs=24.5
Q ss_pred HhCCCCcCHHHHHHHHhCCC-HHHHHHHHHHHHH
Q 025983 160 RQEDKPRTVKEICSVANGAT-KKEIGRAKEYIVK 192 (245)
Q Consensus 160 R~~~~~~tl~dia~~~~~v~-~~~i~~~~~~l~~ 192 (245)
..+|.|-|++||++ .+|++ ..++.+..+.|.+
T Consensus 20 ~~~G~~Pt~rEIa~-~~g~~S~~tv~~~L~~Le~ 52 (65)
T PF01726_consen 20 EENGYPPTVREIAE-ALGLKSTSTVQRHLKALER 52 (65)
T ss_dssp HHHSS---HHHHHH-HHTSSSHHHHHHHHHHHHH
T ss_pred HHcCCCCCHHHHHH-HhCCCChHHHHHHHHHHHH
Confidence 36899999999999 59997 8999888888864
No 240
>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=66.83 E-value=14 Score=22.86 Aligned_cols=47 Identities=19% Similarity=0.297 Sum_probs=32.6
Q ss_pred CCCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCccCCccccCCCCHHhHHHHHhhhcCCCHH
Q 025983 163 DKPRTVKEICSVANGATKKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMNNQ 225 (245)
Q Consensus 163 ~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~ 225 (245)
....|+.|+|+. +|++..+|.+..+- .. . -+.+.+.++++.|+++.+
T Consensus 7 ~~gls~~~la~~-~gis~~~i~~~~~g------~~------~---~~~~~~~~ia~~l~~~~~ 53 (55)
T PF01381_consen 7 EKGLSQKELAEK-LGISRSTISRIENG------KR------N---PSLDTLKKIAKALGVSPE 53 (55)
T ss_dssp HTTS-HHHHHHH-HTS-HHHHHHHHTT------SS------T---SBHHHHHHHHHHHTSEHH
T ss_pred HcCCCHHHHHHH-hCCCcchhHHHhcC------CC------C---CCHHHHHHHHHHHCCCHH
Confidence 455788999994 89999999877552 11 1 234788899999998765
No 241
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=66.63 E-value=5.3 Score=35.07 Aligned_cols=9 Identities=33% Similarity=0.925 Sum_probs=5.3
Q ss_pred CCCCCCCCC
Q 025983 4 AFCSDCKKH 12 (245)
Q Consensus 4 ~~Cp~Cg~~ 12 (245)
..||.||+.
T Consensus 188 ~~CPvCGs~ 196 (309)
T PRK03564 188 QFCPVCGSM 196 (309)
T ss_pred CCCCCCCCc
Confidence 456666664
No 242
>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=66.61 E-value=3.4 Score=31.22 Aligned_cols=32 Identities=28% Similarity=0.603 Sum_probs=26.1
Q ss_pred CCCCceEccCCcccc--cccccccCcccccccCC
Q 025983 19 HSAGDTVCSECGLVL--ESHSIDETSEWRTFANE 50 (245)
Q Consensus 19 ~~~G~~vC~~CG~V~--~e~~id~~~ewr~f~~~ 50 (245)
.+.|.++|..||.-| .+.-++.+.-|.+|.+.
T Consensus 33 ~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~ 66 (124)
T PF01641_consen 33 KEEGIYVCAVCGTPLFSSDTKFDSGCGWPSFWQP 66 (124)
T ss_dssp TSSEEEEETTTS-EEEEGGGEETSSSSSSEESSC
T ss_pred CCCEEEEcCCCCCccccCcccccCCcCCccccCc
Confidence 578999999999998 55567889999999853
No 243
>PRK04023 DNA polymerase II large subunit; Validated
Probab=66.44 E-value=4.1 Score=41.03 Aligned_cols=11 Identities=27% Similarity=0.685 Sum_probs=6.3
Q ss_pred eEccCCccccc
Q 025983 24 TVCSECGLVLE 34 (245)
Q Consensus 24 ~vC~~CG~V~~ 34 (245)
..|..||..+.
T Consensus 664 y~CPKCG~El~ 674 (1121)
T PRK04023 664 DECEKCGREPT 674 (1121)
T ss_pred CcCCCCCCCCC
Confidence 44666666653
No 244
>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=66.38 E-value=8.8 Score=25.22 Aligned_cols=36 Identities=25% Similarity=0.400 Sum_probs=28.8
Q ss_pred HHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 155 LYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 155 lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
+|.+.- ..-+.|..||++. ++++..++.+..+.|.+
T Consensus 13 vy~~Ll-~~~~~t~~eIa~~-l~i~~~~v~~~L~~L~~ 48 (68)
T PF01978_consen 13 VYLALL-KNGPATAEEIAEE-LGISRSTVYRALKSLEE 48 (68)
T ss_dssp HHHHHH-HHCHEEHHHHHHH-HTSSHHHHHHHHHHHHH
T ss_pred HHHHHH-HcCCCCHHHHHHH-HCcCHHHHHHHHHHHHH
Confidence 344433 5567999999995 99999999999999875
No 245
>PRK12366 replication factor A; Reviewed
Probab=66.35 E-value=3.3 Score=40.16 Aligned_cols=25 Identities=36% Similarity=0.930 Sum_probs=20.0
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V 32 (245)
..||.|++. + .+ ..|...|..||.+
T Consensus 533 ~aCp~CnkK--v-~~-~~g~~~C~~c~~~ 557 (637)
T PRK12366 533 YLCPNCRKR--V-EE-VDGEYICEFCGEV 557 (637)
T ss_pred ecccccCeE--e-Ec-CCCcEECCCCCCC
Confidence 469999873 3 33 5799999999988
No 246
>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=66.15 E-value=7.3 Score=24.14 Aligned_cols=26 Identities=23% Similarity=0.668 Sum_probs=17.4
Q ss_pred CCCC--CCCCCCceeeeCCCCceEccCCcc
Q 025983 4 AFCS--DCKKHTEVVFDHSAGDTVCSECGL 31 (245)
Q Consensus 4 ~~Cp--~Cg~~~~iv~d~~~G~~vC~~CG~ 31 (245)
..|| .||. .-+.-++. ....|..||+
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 9997 44555553 4789999986
No 247
>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=65.99 E-value=5.3 Score=35.05 Aligned_cols=9 Identities=33% Similarity=0.785 Sum_probs=5.7
Q ss_pred EccCCcccc
Q 025983 25 VCSECGLVL 33 (245)
Q Consensus 25 vC~~CG~V~ 33 (245)
+|.+|+.-+
T Consensus 254 ~C~~C~~Yl 262 (305)
T TIGR01562 254 TCDSCQGYL 262 (305)
T ss_pred eccccccch
Confidence 666666655
No 248
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=65.79 E-value=4.3 Score=32.24 Aligned_cols=31 Identities=26% Similarity=0.606 Sum_probs=19.0
Q ss_pred CCCCCCCCcee----ee-CCCCc-----eEccCCccccccc
Q 025983 6 CSDCKKHTEVV----FD-HSAGD-----TVCSECGLVLESH 36 (245)
Q Consensus 6 Cp~Cg~~~~iv----~d-~~~G~-----~vC~~CG~V~~e~ 36 (245)
||.||..+... ++ |--|+ ..|.+||+=-.|-
T Consensus 1 CP~Cg~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~ev 41 (163)
T TIGR00340 1 CPVCGSRTLKAVTYDYDIPYFGKIMLSTYICEKCGYRSTDV 41 (163)
T ss_pred CCCCCCcceEeeeEeccCCCcceEEEEEEECCCCCCchhhe
Confidence 99999741111 11 33444 5799999976543
No 249
>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=65.68 E-value=11 Score=24.02 Aligned_cols=31 Identities=29% Similarity=0.318 Sum_probs=26.6
Q ss_pred CCCCcCHHHHHHHHhCCCHHHHHHHHHHHHHH
Q 025983 162 EDKPRTVKEICSVANGATKKEIGRAKEYIVKQ 193 (245)
Q Consensus 162 ~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~ 193 (245)
.+-..++.|+++. ++||..+|++-+..|.+.
T Consensus 11 ~~~~~s~~ela~~-~~VS~~TiRRDl~~L~~~ 41 (57)
T PF08220_consen 11 EKGKVSVKELAEE-FGVSEMTIRRDLNKLEKQ 41 (57)
T ss_pred HcCCEEHHHHHHH-HCcCHHHHHHHHHHHHHC
Confidence 3457899999995 999999999999988754
No 250
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=65.64 E-value=4.1 Score=26.34 Aligned_cols=27 Identities=26% Similarity=0.737 Sum_probs=16.1
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~ 33 (245)
..|-+||.. +.+ ....-+-|.+||.=+
T Consensus 21 YiCgdC~~e-n~l--k~~D~irCReCG~RI 47 (62)
T KOG3507|consen 21 YICGDCGQE-NTL--KRGDVIRCRECGYRI 47 (62)
T ss_pred EEecccccc-ccc--cCCCcEehhhcchHH
Confidence 358888874 332 123346688888644
No 251
>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=65.51 E-value=1.8 Score=28.25 Aligned_cols=25 Identities=24% Similarity=0.642 Sum_probs=18.3
Q ss_pred CCCCCCCCCCceeeeCCCCceEcc-CCccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCS-ECGLVLE 34 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~-~CG~V~~ 34 (245)
..||+||.+ |- ..+..|+ +|+....
T Consensus 4 kHC~~CG~~--Ip----~~~~fCS~~C~~~~~ 29 (59)
T PF09889_consen 4 KHCPVCGKP--IP----PDESFCSPKCREEYR 29 (59)
T ss_pred CcCCcCCCc--CC----cchhhhCHHHHHHHH
Confidence 579999974 32 2489995 7987764
No 252
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=65.19 E-value=2.1 Score=42.24 Aligned_cols=12 Identities=42% Similarity=1.043 Sum_probs=0.0
Q ss_pred ceEccCCccccc
Q 025983 23 DTVCSECGLVLE 34 (245)
Q Consensus 23 ~~vC~~CG~V~~ 34 (245)
..+|..||..++
T Consensus 680 ~~~Cp~C~~~~~ 691 (900)
T PF03833_consen 680 VYVCPDCGIEVE 691 (900)
T ss_dssp ------------
T ss_pred ceeccccccccC
Confidence 356777776664
No 253
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=65.17 E-value=40 Score=27.01 Aligned_cols=29 Identities=24% Similarity=0.360 Sum_probs=25.9
Q ss_pred CCcCHHHHHHHHhCCCHHHHHHHHHHHHHH
Q 025983 164 KPRTVKEICSVANGATKKEIGRAKEYIVKQ 193 (245)
Q Consensus 164 ~~~tl~dia~~~~~v~~~~i~~~~~~l~~~ 193 (245)
.|.|.++||+. +|++..++.|.+++|.+.
T Consensus 167 ~~~t~~~lA~~-lG~tr~tvsR~l~~l~~~ 195 (211)
T PRK11753 167 IKITRQEIGRI-VGCSREMVGRVLKMLEDQ 195 (211)
T ss_pred cCCCHHHHHHH-hCCCHHHHHHHHHHHHHC
Confidence 48899999995 999999999999998763
No 254
>PHA03074 late transcription factor VLTF-3; Provisional
Probab=65.11 E-value=3.7 Score=33.50 Aligned_cols=31 Identities=26% Similarity=0.570 Sum_probs=25.3
Q ss_pred CCCCCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 1 ~~~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
|....|.+|++ ..++. +.|-..|..|+.|..
T Consensus 2 ~~l~~C~~C~~-ngiv~--~k~~efC~fC~~~f~ 32 (225)
T PHA03074 2 MNLKLCSGCRH-NGIVS--EKDYEFCIFCESVFQ 32 (225)
T ss_pred cchhhcCCCCC-CCeee--ecCEEEeecHHHHHh
Confidence 34578999998 57775 478999999999985
No 255
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=65.05 E-value=9.8 Score=30.40 Aligned_cols=38 Identities=24% Similarity=0.280 Sum_probs=31.4
Q ss_pred HHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 154 CLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 154 ~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
-||-+.-+.+.|.|+.||++ ++|+|...+.-..++|..
T Consensus 30 ~iYgilyls~~Pmtl~Ei~E-~lg~Sks~vS~~lkkL~~ 67 (177)
T COG1510 30 QIYGILYLSRKPLTLDEIAE-ALGMSKSNVSMGLKKLQD 67 (177)
T ss_pred HHhhhheecCCCccHHHHHH-HHCCCcchHHHHHHHHHh
Confidence 34555556789999999999 599999999999998864
No 256
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=65.03 E-value=1.9 Score=25.04 Aligned_cols=27 Identities=30% Similarity=0.844 Sum_probs=14.7
Q ss_pred CCCCCCCCceeee-CCCCce-EccCCccc
Q 025983 6 CSDCKKHTEVVFD-HSAGDT-VCSECGLV 32 (245)
Q Consensus 6 Cp~Cg~~~~iv~d-~~~G~~-vC~~CG~V 32 (245)
|.+|+...+...- ...|.. +|..||.-
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~ 29 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLY 29 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHH
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHH
Confidence 7788864333333 346776 89988864
No 257
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=64.97 E-value=4.4 Score=37.23 Aligned_cols=32 Identities=22% Similarity=0.608 Sum_probs=20.1
Q ss_pred CCCCCCCCCCceeeeCCCC-ceEccCCccccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAG-DTVCSECGLVLESH 36 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G-~~vC~~CG~V~~e~ 36 (245)
..||+|+.-.. +.+-..| ...|..||.++..+
T Consensus 11 ~~C~~Cd~l~~-~~~l~~g~~a~CpRCg~~L~~~ 43 (419)
T PRK15103 11 ILCPQCDMLVA-LPRLEHGQKAACPRCGTTLTVR 43 (419)
T ss_pred ccCCCCCceee-cCCCCCCCeeECCCCCCCCcCC
Confidence 35999997311 1222334 47799999999533
No 258
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=64.87 E-value=3.9 Score=30.38 Aligned_cols=14 Identities=14% Similarity=0.655 Sum_probs=6.1
Q ss_pred eeCCCCceEccCCc
Q 025983 17 FDHSAGDTVCSECG 30 (245)
Q Consensus 17 ~d~~~G~~vC~~CG 30 (245)
.+..-+...|.+||
T Consensus 64 i~~~p~~~~C~~Cg 77 (114)
T PRK03681 64 LEEQEAECWCETCQ 77 (114)
T ss_pred EEeeCcEEEcccCC
Confidence 33334444444444
No 259
>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=64.83 E-value=18 Score=23.38 Aligned_cols=31 Identities=19% Similarity=0.326 Sum_probs=23.7
Q ss_pred hCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 161 QEDKPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 161 ~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
..+.+.++.+|++. ++++..++.+..++|.+
T Consensus 14 ~~~~~~t~~~l~~~-~~~~~~~vs~~i~~L~~ 44 (68)
T PF13463_consen 14 HSDGPMTQSDLAER-LGISKSTVSRIIKKLEE 44 (68)
T ss_dssp --TS-BEHHHHHHH-TT--HHHHHHHHHHHHH
T ss_pred ccCCCcCHHHHHHH-HCcCHHHHHHHHHHHHH
Confidence 56788999999995 99999999999999875
No 260
>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=64.49 E-value=20 Score=23.39 Aligned_cols=39 Identities=18% Similarity=0.211 Sum_probs=26.8
Q ss_pred CHHHHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHH
Q 025983 146 NQDALLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKE 188 (245)
Q Consensus 146 ~~~~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~ 188 (245)
+|.-=-|-=+|. .++-.++++|||+. ++|+..+|++--.
T Consensus 6 sp~rdkA~e~y~---~~~g~i~lkdIA~~-Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 6 SPNRDKAFEIYK---ESNGKIKLKDIAEK-LGVSESTIRKWKS 44 (60)
T ss_pred CcCHHHHHHHHH---HhCCCccHHHHHHH-HCCCHHHHHHHhh
Confidence 333333444553 35567899999995 9999999987543
No 261
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=64.34 E-value=5.2 Score=22.72 Aligned_cols=23 Identities=26% Similarity=0.499 Sum_probs=11.5
Q ss_pred CCCCCCCCCCceeeeCCCCceEcc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCS 27 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~ 27 (245)
.+|..||.. -.+.+...|.++|-
T Consensus 5 ykC~~CGni-v~v~~~~~~~l~Cc 27 (34)
T cd00974 5 YKCEICGNI-VEVLNVGGGTLVCC 27 (34)
T ss_pred EEcCCCCcE-EEEEECCCcceeec
Confidence 456666652 22334445555554
No 262
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=64.22 E-value=16 Score=22.63 Aligned_cols=25 Identities=12% Similarity=0.247 Sum_probs=23.2
Q ss_pred CHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 167 TVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 167 tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
+..++++. ++++..+++++++.|.+
T Consensus 22 s~~~la~~-~~vs~~tv~~~l~~L~~ 46 (60)
T smart00345 22 SERELAAQ-LGVSRTTVREALSRLEA 46 (60)
T ss_pred CHHHHHHH-HCCCHHHHHHHHHHHHH
Confidence 89999995 99999999999999986
No 263
>PHA01976 helix-turn-helix protein
Probab=63.83 E-value=28 Score=22.44 Aligned_cols=47 Identities=13% Similarity=0.150 Sum_probs=34.0
Q ss_pred CCCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCccCCccccCCCCHHhHHHHHhhhcCCCHH
Q 025983 163 DKPRTVKEICSVANGATKKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMNNQ 225 (245)
Q Consensus 163 ~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~ 225 (245)
....|+.++|+. ++++..+|.+..+ +.. .| +.+.+.+++..|+++.+
T Consensus 13 ~~glt~~~lA~~-~gvs~~~v~~~e~------g~~------~p---~~~~l~~ia~~l~v~~~ 59 (67)
T PHA01976 13 ARAWSAPELSRR-AGVRHSLIYDFEA------DKR------LP---NLKTLLRLADALGVTLD 59 (67)
T ss_pred HcCCCHHHHHHH-hCCCHHHHHHHHc------CCC------CC---CHHHHHHHHHHHCcCHH
Confidence 345789999995 8999988876532 211 22 34788999999999866
No 264
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=63.82 E-value=11 Score=28.51 Aligned_cols=26 Identities=19% Similarity=0.319 Sum_probs=23.5
Q ss_pred cCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 166 RTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 166 ~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
-|.+++|.. ++|++.|+.|+|+.|.+
T Consensus 36 PSvRelA~~-~~VNpnTv~raY~eLE~ 61 (125)
T COG1725 36 PSVRELAKD-LGVNPNTVQRAYQELER 61 (125)
T ss_pred CcHHHHHHH-hCCCHHHHHHHHHHHHH
Confidence 568999995 99999999999999976
No 265
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=63.80 E-value=16 Score=21.96 Aligned_cols=26 Identities=15% Similarity=0.336 Sum_probs=17.4
Q ss_pred CCCCcCHHHHHHHHhCCCHHHHHHHHH
Q 025983 162 EDKPRTVKEICSVANGATKKEIGRAKE 188 (245)
Q Consensus 162 ~~~~~tl~dia~~~~~v~~~~i~~~~~ 188 (245)
.....++.+||.. +|++..+|.+.++
T Consensus 17 ~~~G~s~~~IA~~-lg~s~sTV~relk 42 (44)
T PF13936_consen 17 LEQGMSIREIAKR-LGRSRSTVSRELK 42 (44)
T ss_dssp HCS---HHHHHHH-TT--HHHHHHHHH
T ss_pred HHcCCCHHHHHHH-HCcCcHHHHHHHh
Confidence 4466899999995 9999999988765
No 266
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=63.80 E-value=28 Score=28.63 Aligned_cols=30 Identities=3% Similarity=-0.025 Sum_probs=26.2
Q ss_pred CCCcCHHHHHHHHhCCCHHHHHHHHHHHHHH
Q 025983 163 DKPRTVKEICSVANGATKKEIGRAKEYIVKQ 193 (245)
Q Consensus 163 ~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~ 193 (245)
..|.+..|||+. +|++..++.|.+++|.+.
T Consensus 167 ~~~~t~~~lA~~-lG~sretvsR~L~~L~~~ 196 (226)
T PRK10402 167 LYHEKHTQAAEY-LGVSYRHLLYVLAQFIQD 196 (226)
T ss_pred cccchHHHHHHH-HCCcHHHHHHHHHHHHHC
Confidence 356789999995 999999999999999874
No 267
>PRK06030 hypothetical protein; Provisional
Probab=63.68 E-value=24 Score=26.63 Aligned_cols=39 Identities=15% Similarity=0.241 Sum_probs=31.7
Q ss_pred HHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHHHh
Q 025983 153 ACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYIVKQL 194 (245)
Q Consensus 153 A~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l 194 (245)
.++|++-...+ .++.+|+.. +|-+-.++..+++.+.+.+
T Consensus 59 IAMYL~r~~~~--~sl~~IG~~-FGRDHSTV~haikkIe~~~ 97 (124)
T PRK06030 59 IAMYVAHVSLG--WPMNEVALA-FGRDRTTVGHACHTVEDLR 97 (124)
T ss_pred HHHHHHHHHcC--CCHHHHHHH-HCCChhHHHHHHHHHHHHh
Confidence 57888866544 589999995 8999999999999887765
No 268
>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=63.39 E-value=3.6 Score=23.79 Aligned_cols=21 Identities=43% Similarity=1.053 Sum_probs=10.7
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECG 30 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG 30 (245)
++|+.||. +.+-+ ..+|..||
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 23433 37788887
No 269
>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=63.38 E-value=11 Score=24.21 Aligned_cols=33 Identities=15% Similarity=0.088 Sum_probs=26.2
Q ss_pred CCCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Q 025983 163 DKPRTVKEICSVANGATKKEIGRAKEYIVKQLGL 196 (245)
Q Consensus 163 ~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~ 196 (245)
+-..++.|+|.. ++++..+|.+....|...++-
T Consensus 17 ~~~~~~~ela~~-l~~S~rti~~~i~~L~~~f~~ 49 (59)
T PF08280_consen 17 NKWITLKELAKK-LNISERTIKNDINELNEFFPE 49 (59)
T ss_dssp HTSBBHHHHHHH-CTS-HHHHHHHHHHHHTT--T
T ss_pred CCCCcHHHHHHH-HCCCHHHHHHHHHHHHHHhhh
Confidence 456799999995 999999999999999877764
No 270
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=63.31 E-value=21 Score=27.30 Aligned_cols=44 Identities=18% Similarity=0.335 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 148 DALLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 148 ~~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
+.-.-+.+|++-...+.+.+..+||+ ..+++...++++++.|.+
T Consensus 8 ~YAl~~~i~la~~~~g~~~s~~~ia~-~~~is~~~vrk~l~~L~~ 51 (141)
T PRK11014 8 DYGLRALIYMASLPEGRMTSISEVTE-VYGVSRNHMVKIINQLSR 51 (141)
T ss_pred hHHHHHHHHHhcCCCCCccCHHHHHH-HHCcCHHHHHHHHHHHHh
Confidence 34455566777555677889999999 499999999999999986
No 271
>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=63.14 E-value=5.5 Score=34.55 Aligned_cols=31 Identities=26% Similarity=0.573 Sum_probs=15.2
Q ss_pred CCCCCCCCCCceeeeC--CCC-----ceEccCCccccc
Q 025983 4 AFCSDCKKHTEVVFDH--SAG-----DTVCSECGLVLE 34 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~--~~G-----~~vC~~CG~V~~ 34 (245)
..||+||.....-+.+ .+| -.+|.+||.-+.
T Consensus 212 ~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK 249 (290)
T PF04216_consen 212 IKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLK 249 (290)
T ss_dssp TS-TTT---SS-EEE--------SEEEEEETTTTEEEE
T ss_pred CCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHH
Confidence 4799999753322221 122 279999999883
No 272
>TIGR00613 reco DNA repair protein RecO. All proteins in this family for which functions are known are DNA binding proteins that are involved in the initiation of recombination or recombinational repair.
Probab=62.88 E-value=5.4 Score=33.35 Aligned_cols=28 Identities=25% Similarity=0.706 Sum_probs=21.2
Q ss_pred CCCCCCCCC-CceeeeCCCCceEccCCcc
Q 025983 4 AFCSDCKKH-TEVVFDHSAGDTVCSECGL 31 (245)
Q Consensus 4 ~~Cp~Cg~~-~~iv~d~~~G~~vC~~CG~ 31 (245)
..|..||.. ....+++..|..+|.+|+.
T Consensus 148 ~~C~~cg~~~~~~~fs~~~gg~~C~~c~~ 176 (241)
T TIGR00613 148 DKCAVCGSKEDLIYFSMTYGGALCRQCGE 176 (241)
T ss_pred CccCCCCCcCCCceEchhcCeEEChhhCc
Confidence 468899862 2256788899999999965
No 273
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=62.39 E-value=5.9 Score=25.40 Aligned_cols=24 Identities=29% Similarity=0.735 Sum_probs=18.3
Q ss_pred CCCCCCCCCceeeeCCCCceEccCCcccc
Q 025983 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (245)
Q Consensus 5 ~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~ 33 (245)
.||.|+.. - +..-...|.+||...
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 49999973 1 445578899999987
No 274
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=62.37 E-value=5.1 Score=33.61 Aligned_cols=27 Identities=37% Similarity=0.827 Sum_probs=21.9
Q ss_pred CCCCCCCCCC-ceeeeCCCCceEccCCc
Q 025983 4 AFCSDCKKHT-EVVFDHSAGDTVCSECG 30 (245)
Q Consensus 4 ~~Cp~Cg~~~-~iv~d~~~G~~vC~~CG 30 (245)
..|-.||... ...+++.+|..+|..|+
T Consensus 150 ~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 150 DHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred hhHhcCCCCCCceEEecccCCccccccc
Confidence 4699999742 25678899999999998
No 275
>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=62.36 E-value=6.4 Score=37.06 Aligned_cols=29 Identities=21% Similarity=0.647 Sum_probs=22.8
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
..||+|+. .+.+-..++.+.|..||....
T Consensus 223 ~~C~~C~~--~l~~h~~~~~l~Ch~Cg~~~~ 251 (505)
T TIGR00595 223 LCCPNCDV--SLTYHKKEGKLRCHYCGYQEP 251 (505)
T ss_pred cCCCCCCC--ceEEecCCCeEEcCCCcCcCC
Confidence 46999986 356666788999999998764
No 276
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=62.34 E-value=6.1 Score=25.18 Aligned_cols=27 Identities=19% Similarity=0.487 Sum_probs=15.6
Q ss_pred CCCCCCCCCceeeeC----CCCceEccCCcc
Q 025983 5 FCSDCKKHTEVVFDH----SAGDTVCSECGL 31 (245)
Q Consensus 5 ~Cp~Cg~~~~iv~d~----~~G~~vC~~CG~ 31 (245)
.||.||+.+.+-.-+ .+=-+.|..|-.
T Consensus 6 ~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~ 36 (55)
T PF14205_consen 6 LCPICGNKTRLKIREDTVLKNFPLYCPKCKQ 36 (55)
T ss_pred ECCCCCCccceeeecCceeccccccCCCCCc
Confidence 599999754332222 222377888853
No 277
>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=62.27 E-value=5.4 Score=35.01 Aligned_cols=28 Identities=25% Similarity=0.560 Sum_probs=17.9
Q ss_pred CCCCCCCCCCc--eeeeC--CCC--ceEccCCcc
Q 025983 4 AFCSDCKKHTE--VVFDH--SAG--DTVCSECGL 31 (245)
Q Consensus 4 ~~Cp~Cg~~~~--iv~d~--~~G--~~vC~~CG~ 31 (245)
..||.||+.+. ++... .+| .+.|.-|++
T Consensus 185 ~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~t 218 (305)
T TIGR01562 185 TLCPACGSPPVASMVRQGGKETGLRYLSCSLCAT 218 (305)
T ss_pred CcCCCCCChhhhhhhcccCCCCCceEEEcCCCCC
Confidence 37999998542 23331 456 478888864
No 278
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=62.12 E-value=34 Score=20.88 Aligned_cols=25 Identities=16% Similarity=0.251 Sum_probs=21.8
Q ss_pred CcCHHHHHHHHhCCCHHHHHHHHHHH
Q 025983 165 PRTVKEICSVANGATKKEIGRAKEYI 190 (245)
Q Consensus 165 ~~tl~dia~~~~~v~~~~i~~~~~~l 190 (245)
..|+++||.. +|++..++++.++..
T Consensus 27 ~~s~~~vA~~-~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 27 SRSFKDVARE-LGVSWSTVRRIFDRY 51 (52)
T ss_pred cCCHHHHHHH-HCCCHHHHHHHHHhh
Confidence 3899999995 999999999998753
No 279
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=62.05 E-value=5.7 Score=25.96 Aligned_cols=28 Identities=7% Similarity=-0.031 Sum_probs=19.1
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcccccccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSID 39 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e~~id 39 (245)
..||+||.. . .-.-||. ||+.-+..+++
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 469999962 1 2367899 99887665554
No 280
>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=61.77 E-value=4.6 Score=25.89 Aligned_cols=21 Identities=33% Similarity=0.722 Sum_probs=14.1
Q ss_pred CCCCCCCCCCceeeeCCCCceEcc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCS 27 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~ 27 (245)
..||.|+. ..+++|.. .++|+
T Consensus 15 ~~Cp~C~~-~~l~~~~~--~Y~C~ 35 (55)
T PF08063_consen 15 EPCPKCKG-GQLYFDGS--GYKCT 35 (55)
T ss_dssp ---SSSSE--EEEEETT--EEEEE
T ss_pred CCCCCCCC-CeEEecCC--ccEeC
Confidence 57999998 68888755 78887
No 281
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=61.45 E-value=6.7 Score=27.26 Aligned_cols=26 Identities=31% Similarity=0.724 Sum_probs=19.4
Q ss_pred CCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 5 ~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
.||.|.. .++.. ..+.+.| .||+-+.
T Consensus 1 iCPVC~~-~~L~~--~~~~i~C-~Cgl~l~ 26 (82)
T PF14768_consen 1 ICPVCQK-GNLRE--NSNVISC-SCGLRLN 26 (82)
T ss_pred CCCccCC-Ccccc--cCCeEEC-CCccEEe
Confidence 5999998 56654 5778888 7786664
No 282
>PRK05580 primosome assembly protein PriA; Validated
Probab=61.44 E-value=6.7 Score=38.35 Aligned_cols=29 Identities=21% Similarity=0.516 Sum_probs=23.1
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
..||+|+. .+++....+.+.|..||....
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 46999996 467777788999999998753
No 283
>PRK06386 replication factor A; Reviewed
Probab=61.23 E-value=4.4 Score=36.34 Aligned_cols=21 Identities=33% Similarity=0.705 Sum_probs=15.0
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V 32 (245)
..||+|+.. + + .| .|.+||.|
T Consensus 237 ~rCP~C~R~---l-~--~g--~C~~HG~v 257 (358)
T PRK06386 237 TKCSVCNKI---I-E--DG--VCKDHPDA 257 (358)
T ss_pred ecCcCCCeE---c-c--CC--cCCCCCCC
Confidence 479999972 2 2 23 89999975
No 284
>PRK07218 replication factor A; Provisional
Probab=60.94 E-value=3.9 Score=37.54 Aligned_cols=21 Identities=24% Similarity=0.689 Sum_probs=16.3
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V 32 (245)
..||.|+.. + + ...|..||.|
T Consensus 298 ~rCP~C~r~---v-~----~~~C~~hG~v 318 (423)
T PRK07218 298 ERCPECGRV---I-Q----KGQCRSHGAV 318 (423)
T ss_pred ecCcCcccc---c-c----CCcCCCCCCc
Confidence 479999973 2 2 3699999988
No 285
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=60.80 E-value=4.1 Score=36.08 Aligned_cols=25 Identities=24% Similarity=0.380 Sum_probs=18.4
Q ss_pred CCCCCCCCCCceeeeCCCCceEccC
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSE 28 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~ 28 (245)
++||.|++.=.+-+||.+++++|..
T Consensus 78 ~kC~~C~~~i~~kTDPkn~dY~~~~ 102 (324)
T PF04502_consen 78 IKCPRCSNEIEFKTDPKNTDYVVES 102 (324)
T ss_pred EEcCCCCCEEeeecCCCCCCeeeec
Confidence 4688888755667788887777765
No 286
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=60.74 E-value=5.2 Score=41.32 Aligned_cols=8 Identities=25% Similarity=0.796 Sum_probs=4.6
Q ss_pred CCCCCCCC
Q 025983 4 AFCSDCKK 11 (245)
Q Consensus 4 ~~Cp~Cg~ 11 (245)
.+||.||.
T Consensus 668 rkCPkCG~ 675 (1337)
T PRK14714 668 RRCPSCGT 675 (1337)
T ss_pred EECCCCCC
Confidence 35666664
No 287
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.73 E-value=26 Score=25.66 Aligned_cols=40 Identities=18% Similarity=0.393 Sum_probs=33.1
Q ss_pred HHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCc
Q 025983 152 AACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYIVKQLGLE 197 (245)
Q Consensus 152 AA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~ 197 (245)
-.-+|+-||= .|+||-.. +|++..+++..+.++.+.+|.+
T Consensus 49 Fv~lf~r~RG-----nlKEvEr~-lg~sYptvR~kld~vlramgy~ 88 (122)
T COG3877 49 FVELFLRCRG-----NLKEVERE-LGISYPTVRTKLDEVLRAMGYN 88 (122)
T ss_pred HHHHHHHHcc-----CHHHHHHH-HCCccHHHHHHHHHHHHHcCCC
Confidence 3446666663 38999885 9999999999999999999987
No 288
>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=60.72 E-value=19 Score=22.30 Aligned_cols=29 Identities=17% Similarity=0.227 Sum_probs=20.5
Q ss_pred CCcCHHHHHHHHhCCCHHHHHHHHHHHHHH
Q 025983 164 KPRTVKEICSVANGATKKEIGRAKEYIVKQ 193 (245)
Q Consensus 164 ~~~tl~dia~~~~~v~~~~i~~~~~~l~~~ 193 (245)
...+..|||+. +|+++.++...+.+-.+.
T Consensus 25 ~g~s~~eIa~~-l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 25 QGMSYAEIAEI-LGISESTVKRRLRRARKK 53 (54)
T ss_dssp S---HHHHHHH-CTS-HHHHHHHHHHHHHH
T ss_pred HCcCHHHHHHH-HCcCHHHHHHHHHHHHhh
Confidence 34678999995 999999999888776554
No 289
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=60.62 E-value=3.3 Score=30.77 Aligned_cols=31 Identities=23% Similarity=0.462 Sum_probs=20.1
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
..|-+||+....-.+..-|..+|..|.-|..
T Consensus 14 ~~CaDCg~~~p~w~s~~~GiflC~~Cag~HR 44 (116)
T PF01412_consen 14 KVCADCGAPNPTWASLNYGIFLCLECAGIHR 44 (116)
T ss_dssp TB-TTT-SBS--EEETTTTEEE-HHHHHHHH
T ss_pred CcCCCCCCCCCCEEEeecChhhhHHHHHHHH
Confidence 5799999853344556789999999998864
No 290
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=60.51 E-value=45 Score=26.51 Aligned_cols=28 Identities=11% Similarity=0.196 Sum_probs=25.9
Q ss_pred CCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 164 KPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 164 ~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
.|.|..+||+. +|++..++.|.+++|.+
T Consensus 148 ~~~t~~~iA~~-lG~tretvsR~l~~l~~ 175 (202)
T PRK13918 148 IYATHDELAAA-VGSVRETVTKVIGELSR 175 (202)
T ss_pred ecCCHHHHHHH-hCccHHHHHHHHHHHHH
Confidence 68899999995 99999999999999986
No 291
>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=60.50 E-value=5.9 Score=25.41 Aligned_cols=28 Identities=21% Similarity=0.706 Sum_probs=15.7
Q ss_pred CCCCC--CCCCCceeeeCCCCc--eEccCCcccc
Q 025983 4 AFCSD--CKKHTEVVFDHSAGD--TVCSECGLVL 33 (245)
Q Consensus 4 ~~Cp~--Cg~~~~iv~d~~~G~--~vC~~CG~V~ 33 (245)
..||. |+.. +..+..... +.|..||...
T Consensus 19 ~~Cp~~~C~~~--~~~~~~~~~~~~~C~~C~~~f 50 (64)
T PF01485_consen 19 RWCPNPDCEYI--IEKDDGCNSPIVTCPSCGTEF 50 (64)
T ss_dssp C--TTSST-----ECS-SSTTS--CCTTSCCSEE
T ss_pred cCCCCCCCccc--EEecCCCCCCeeECCCCCCcC
Confidence 58988 9962 445555555 8999999775
No 292
>COG4643 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=60.42 E-value=5 Score=35.42 Aligned_cols=26 Identities=31% Similarity=0.721 Sum_probs=21.5
Q ss_pred CCCCCCCCCceeeeC-C-CCceEccCCc
Q 025983 5 FCSDCKKHTEVVFDH-S-AGDTVCSECG 30 (245)
Q Consensus 5 ~Cp~Cg~~~~iv~d~-~-~G~~vC~~CG 30 (245)
.||.||....+-+|. + .|..+|..||
T Consensus 34 ~cpvcg~k~RFr~dD~kGrGtw~c~y~~ 61 (366)
T COG4643 34 PCPVCGGKDRFRFDDRKGRGTWFCNYCG 61 (366)
T ss_pred CCCccCCccccccCCccCCccEEEEeec
Confidence 699999876776664 3 6999999999
No 293
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=60.07 E-value=6.1 Score=32.77 Aligned_cols=27 Identities=11% Similarity=0.143 Sum_probs=16.2
Q ss_pred CHHhHHHHHhhhcCCCH--HHHHHHHHHH
Q 025983 208 HAGDFMRRFCSNLGMNN--QAVKAAQEAV 234 (245)
Q Consensus 208 ~p~~~i~r~~~~L~l~~--~v~~~A~~i~ 234 (245)
+...++.|++..=+.+. .+.+.|++.-
T Consensus 183 eA~~~fs~vi~~~~~s~~~~l~~~AR~~w 211 (214)
T PF09986_consen 183 EAKRWFSRVIGSKKASKEPKLKDMARDQW 211 (214)
T ss_pred HHHHHHHHHHcCCCCCCcHHHHHHHHHHH
Confidence 34556666666666665 5666666543
No 294
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=60.06 E-value=6.9 Score=29.95 Aligned_cols=32 Identities=28% Similarity=0.630 Sum_probs=27.2
Q ss_pred eCCCCceEccCCcccc--cccccccCcccccccC
Q 025983 18 DHSAGDTVCSECGLVL--ESHSIDETSEWRTFAN 49 (245)
Q Consensus 18 d~~~G~~vC~~CG~V~--~e~~id~~~ewr~f~~ 49 (245)
..+.|.++|..||.-| .+.-+|+|--|.+|.+
T Consensus 37 ~~~~GiY~c~~cg~pLF~S~~KfdSgcGWPSF~~ 70 (140)
T COG0229 37 NKEKGIYVCIVCGEPLFSSEDKFDSGCGWPSFTK 70 (140)
T ss_pred ccCCceEEeecCCCccccccccccCCCCCccccc
Confidence 3588999999999987 5567899999999985
No 295
>PRK10130 transcriptional regulator EutR; Provisional
Probab=59.90 E-value=46 Score=29.77 Aligned_cols=42 Identities=21% Similarity=0.296 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHH
Q 025983 147 QDALLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYI 190 (245)
Q Consensus 147 ~~~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l 190 (245)
...+..+.=|+--. ...|+++.|||.. +++|..+|.+.|++.
T Consensus 239 ~~~v~~~~~~i~~~-~~~~ltv~~lA~~-~gvS~r~L~r~Fk~~ 280 (350)
T PRK10130 239 RRLLSRAREYVLEN-MSEPVTVLDLCNQ-LHVSRRTLQNAFHAI 280 (350)
T ss_pred HHHHHHHHHHHHhh-hcCCCCHHHHHHH-HCCCHHHHHHHHHHH
Confidence 44556666676644 4568999999995 999999999998754
No 296
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=59.59 E-value=36 Score=27.64 Aligned_cols=45 Identities=11% Similarity=0.271 Sum_probs=37.4
Q ss_pred CHHHHHHHHHHHHHHhCCCC-cCHHHHHHHHhCCCHHHHHHHHHHHHHHhC
Q 025983 146 NQDALLAACLYIACRQEDKP-RTVKEICSVANGATKKEIGRAKEYIVKQLG 195 (245)
Q Consensus 146 ~~~~iaAA~lY~acR~~~~~-~tl~dia~~~~~v~~~~i~~~~~~l~~~l~ 195 (245)
+...++=|+||+ .+.| +++.+++.+ ++++..++..+...|.+...
T Consensus 4 ~~~~~iEA~LF~----sg~pgls~~~La~~-l~~~~~~v~~~l~~L~~~y~ 49 (188)
T PRK00135 4 NYKSIIEALLFV----SGEEGLSLEQLAEI-LELEPTEVQQLLEELQEKYE 49 (188)
T ss_pred cHHHHHHHHHHH----cCCCCCCHHHHHHH-HCCCHHHHHHHHHHHHHHHh
Confidence 345677788886 5777 999999996 89999999999999988764
No 297
>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=59.50 E-value=60 Score=22.96 Aligned_cols=30 Identities=13% Similarity=0.290 Sum_probs=26.9
Q ss_pred CCCCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 162 EDKPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 162 ~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
...+++..|||+. +|++..++.+++++|.+
T Consensus 44 ~~~~is~~eLa~~-~g~sr~tVsr~L~~Le~ 73 (95)
T TIGR01610 44 KQDRVTATVIAEL-TGLSRTHVSDAIKSLAR 73 (95)
T ss_pred cCCccCHHHHHHH-HCcCHHHHHHHHHHHHH
Confidence 5678999999995 99999999999999875
No 298
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=59.43 E-value=6.4 Score=22.29 Aligned_cols=22 Identities=27% Similarity=0.539 Sum_probs=9.8
Q ss_pred CCCCCCCCCCceeeeCCCCceEc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVC 26 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC 26 (245)
.+|..||.. -.+.+...|.++|
T Consensus 8 ykC~~Cgni-v~v~~~~~~~l~C 29 (34)
T TIGR00319 8 YKCEVCGNI-VEVLHAGGGQLVC 29 (34)
T ss_pred EEcCCCCcE-EEEEECCCcceec
Confidence 345555542 2233334445555
No 299
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=59.26 E-value=7.9 Score=30.62 Aligned_cols=31 Identities=16% Similarity=0.387 Sum_probs=19.0
Q ss_pred CCCCCCCCCce---eee-CCCCc-----eEccCCcccccc
Q 025983 5 FCSDCKKHTEV---VFD-HSAGD-----TVCSECGLVLES 35 (245)
Q Consensus 5 ~Cp~Cg~~~~i---v~d-~~~G~-----~vC~~CG~V~~e 35 (245)
.||.||..... .++ |.-|+ ..|.+||+=-.|
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 59999964221 111 33444 579999987544
No 300
>PF03685 UPF0147: Uncharacterised protein family (UPF0147); InterPro: IPR005354 The proteins in this entry are functionally uncharacterised.; PDB: 2QZG_C 2QSB_A.
Probab=59.15 E-value=60 Score=22.80 Aligned_cols=53 Identities=11% Similarity=0.199 Sum_probs=40.3
Q ss_pred chhHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHH
Q 025983 102 DRGLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIA 158 (245)
Q Consensus 102 e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY~a 158 (245)
+..+.++...++++.+.-.+|.++...|.+....+.+.+ .++..=||.++++-
T Consensus 5 e~~i~~~~~~L~~I~~D~sVPRNIRr~a~ea~~~L~~e~----~~~~vRaataIs~L 57 (85)
T PF03685_consen 5 EEKIKQAIQMLERIINDTSVPRNIRRAAEEAKEILNNEE----ESPGVRAATAISIL 57 (85)
T ss_dssp HHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHCT-TT----S-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHhCCC----cchhHhHHHHHHHH
Confidence 567888999999999999999999999999888876543 55666788887764
No 301
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=59.11 E-value=61 Score=26.71 Aligned_cols=29 Identities=21% Similarity=0.310 Sum_probs=26.0
Q ss_pred CCcCHHHHHHHHhCCCHHHHHHHHHHHHHH
Q 025983 164 KPRTVKEICSVANGATKKEIGRAKEYIVKQ 193 (245)
Q Consensus 164 ~~~tl~dia~~~~~v~~~~i~~~~~~l~~~ 193 (245)
.|.|..+||+. +|++..++.|..++|.+.
T Consensus 178 i~lt~~~IA~~-lGisretlsR~L~~L~~~ 206 (230)
T PRK09391 178 LPMSRRDIADY-LGLTIETVSRALSQLQDR 206 (230)
T ss_pred ecCCHHHHHHH-HCCCHHHHHHHHHHHHHC
Confidence 57899999995 999999999999999863
No 302
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=58.52 E-value=8.5 Score=33.83 Aligned_cols=10 Identities=40% Similarity=1.105 Sum_probs=4.9
Q ss_pred eEccCCcccc
Q 025983 24 TVCSECGLVL 33 (245)
Q Consensus 24 ~vC~~CG~V~ 33 (245)
.+|.+|+.-+
T Consensus 253 e~C~~C~~Yl 262 (309)
T PRK03564 253 ESCGDCGTYL 262 (309)
T ss_pred eecccccccc
Confidence 3455555554
No 303
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=58.38 E-value=1.1e+02 Score=25.56 Aligned_cols=82 Identities=18% Similarity=0.187 Sum_probs=59.2
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHHH-hhCCCCCCCCHHHHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHH
Q 025983 109 FKTIATMSDRLGLVATIKDRANEIYKKV-EDQKSSRGRNQDALLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRAK 187 (245)
Q Consensus 109 ~~~I~~~~~~L~Lp~~v~~~A~~i~~~~-~~~~~~~gr~~~~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~ 187 (245)
.++-..+.+.=.+++.-++.......+. -...+.+|-+...+-..+-.+. ..+.+.|..|+|. +.|+|..+.+|.+
T Consensus 118 ~~~r~~l~~~~~~sQ~~lD~l~~~~~k~~~~~~LPkGi~~~Tl~~i~~~~~--~~~~~~Taeela~-~~giSRvTaRRYL 194 (224)
T COG4565 118 RQKRHALESHQQLSQKELDQLFNIQSKEQPPDDLPKGLDELTLQKVREALK--EPDQELTAEELAQ-ALGISRVTARRYL 194 (224)
T ss_pred HHHHHHHhhhcccCHHHHHHHHhccccccCcccCCCCcCHHHHHHHHHHHh--CcCCccCHHHHHH-HhCccHHHHHHHH
Confidence 3444445555578888888877776442 2344667877766666555555 6779999999999 5999999999998
Q ss_pred HHHHHH
Q 025983 188 EYIVKQ 193 (245)
Q Consensus 188 ~~l~~~ 193 (245)
..+...
T Consensus 195 eyl~~~ 200 (224)
T COG4565 195 EYLVSN 200 (224)
T ss_pred HHHHhc
Confidence 888753
No 304
>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=58.35 E-value=33 Score=20.70 Aligned_cols=31 Identities=16% Similarity=0.265 Sum_probs=25.7
Q ss_pred hCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 161 QEDKPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 161 ~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
+..-|.+..||++. ++++..++.+-.+.|.+
T Consensus 11 L~~~~~~~~el~~~-l~~s~~~vs~hL~~L~~ 41 (47)
T PF01022_consen 11 LSEGPLTVSELAEE-LGLSQSTVSHHLKKLRE 41 (47)
T ss_dssp HTTSSEEHHHHHHH-HTS-HHHHHHHHHHHHH
T ss_pred HHhCCCchhhHHHh-ccccchHHHHHHHHHHH
Confidence 45588999999995 99999999999988864
No 305
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=58.27 E-value=8.1 Score=26.70 Aligned_cols=27 Identities=15% Similarity=0.293 Sum_probs=19.3
Q ss_pred CCCCCCCCCCceeeeCCCC--ceEccCCcccc
Q 025983 4 AFCSDCKKHTEVVFDHSAG--DTVCSECGLVL 33 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G--~~vC~~CG~V~ 33 (245)
..||-||- .+ ++...+ ..||.-|+.--
T Consensus 2 ~~CPCCg~-~T--l~~~~~~~ydIC~VC~WEd 30 (78)
T PF14206_consen 2 YPCPCCGY-YT--LEERGEGTYDICPVCFWED 30 (78)
T ss_pred ccCCCCCc-EE--eccCCCcCceECCCCCccc
Confidence 57999997 33 343333 78999999863
No 306
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=58.10 E-value=43 Score=21.48 Aligned_cols=52 Identities=15% Similarity=0.263 Sum_probs=33.7
Q ss_pred hCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCccCCccccCCCCHHhHHHHHhhhcCCCHHHH
Q 025983 161 QEDKPRTVKEICSVANGATKKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMNNQAV 227 (245)
Q Consensus 161 ~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~ 227 (245)
+.....|..++|+ .+|++..+|.+.-+ |- .+ ..+.+.+.+++..|+++.+..
T Consensus 10 R~~~gls~~~lA~-~~g~s~s~v~~iE~------G~-------~~-~p~~~~l~~l~~~l~~~~~~~ 61 (64)
T PF13560_consen 10 RERAGLSQAQLAD-RLGVSQSTVSRIER------GR-------RP-RPSPDTLQRLARALGVPPDER 61 (64)
T ss_dssp HHCHTS-HHHHHH-HHTS-HHHHHHHHT------TS-------SS-S-BHHHHHHHHHHTT--HHHH
T ss_pred HHHcCCCHHHHHH-HHCcCHHHHHHHHC------CC-------CC-CCCHHHHHHHHHHHCcCHHHH
Confidence 3445689999999 49999998877643 21 11 124579999999999987643
No 307
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=57.96 E-value=5.9 Score=25.91 Aligned_cols=21 Identities=29% Similarity=0.640 Sum_probs=16.4
Q ss_pred Cceeee-CCCCceEccCCcccc
Q 025983 13 TEVVFD-HSAGDTVCSECGLVL 33 (245)
Q Consensus 13 ~~iv~d-~~~G~~vC~~CG~V~ 33 (245)
+.+..| ..+|+.+|.-||++.
T Consensus 37 PrV~L~mg~~gev~CPYC~t~y 58 (62)
T COG4391 37 PRVFLDMGDEGEVVCPYCSTRY 58 (62)
T ss_pred CEEEEEcCCCCcEecCccccEE
Confidence 445555 489999999999985
No 308
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=57.79 E-value=9.1 Score=27.43 Aligned_cols=27 Identities=15% Similarity=0.389 Sum_probs=16.9
Q ss_pred CCCCCCCC-CceeeeCCCCceEccCCcc
Q 025983 5 FCSDCKKH-TEVVFDHSAGDTVCSECGL 31 (245)
Q Consensus 5 ~Cp~Cg~~-~~iv~d~~~G~~vC~~CG~ 31 (245)
.||.|+.. +++.+++..|...|-.||.
T Consensus 35 ~CPfH~d~~pS~~i~~~k~~~~Cf~Cg~ 62 (97)
T PF01807_consen 35 LCPFHDDKTPSFSINPDKNRFKCFGCGK 62 (97)
T ss_dssp --SSS--SS--EEEETTTTEEEETTT--
T ss_pred ECcCCCCCCCceEEECCCCeEEECCCCC
Confidence 59999953 4678888999999999984
No 309
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=57.77 E-value=1.2e+02 Score=25.96 Aligned_cols=110 Identities=16% Similarity=0.139 Sum_probs=60.3
Q ss_pred CCCchhHHHHHHHHHHHHHhcCCCHHHHHHH--HHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhCCCCcCHHHHHHHHh
Q 025983 99 SNPDRGLILAFKTIATMSDRLGLVATIKDRA--NEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKEICSVAN 176 (245)
Q Consensus 99 ~~~e~~l~~~~~~I~~~~~~L~Lp~~v~~~A--~~i~~~~~~~~~~~gr~~~~iaAA~lY~acR~~~~~~tl~dia~~~~ 176 (245)
+.+|.....|...|.+.| +|...-+..+ ..|-..++.-+|.+.+-....-.|-|..-=-..++|.++.|+... -
T Consensus 90 QTKDevt~~Am~rL~~~~---gLT~e~v~~~de~~l~~LI~~VgFy~rKA~ylkkta~IL~d~f~gDIP~~v~dLlsL-P 165 (286)
T KOG1921|consen 90 QTKDEVTAAAMLRLKEYG---GLTLEAVLKIDEPTLNELIYPVGFYTRKAKYLKKTAKILQDKFDGDIPDTVEDLLSL-P 165 (286)
T ss_pred chHHHHHHHHHHHHHHhc---CCCHHHHhccChHhHHhhhhhccchHHHHHHHHHHHHHHHHHhCCCCchhHHHHhcC-C
Confidence 345666677777777776 6654333222 223334444455432211112222222222234799999999884 7
Q ss_pred CCCHHHHHHHHHHHHHHhCCccCCccccCCCCHHhHHHHHhhhcCC
Q 025983 177 GATKKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGM 222 (245)
Q Consensus 177 ~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l 222 (245)
||-.+- +|.-|....|. +.-+.....|+|+|++|+.
T Consensus 166 GVGPKM---a~L~m~~AWn~-------i~GI~VDtHVHRi~nrlgW 201 (286)
T KOG1921|consen 166 GVGPKM---AHLTMQVAWNK-------IVGICVDTHVHRICNRLGW 201 (286)
T ss_pred CCchHH---HHHHHHHHhcc-------ceeEEeehHHHHHHHHhcc
Confidence 888763 23334444443 2223345689999999997
No 310
>COG4307 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=57.56 E-value=4.5 Score=34.56 Aligned_cols=28 Identities=36% Similarity=0.940 Sum_probs=22.3
Q ss_pred CCCCCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 1 ~~~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
|-...||.||- .+.++ ...|..||.-+.
T Consensus 1 mk~FhC~~CgQ--~v~Fe----N~~C~~Cg~~Lg 28 (349)
T COG4307 1 MKDFHCPNCGQ--RVAFE----NSACLSCGSALG 28 (349)
T ss_pred CCcccCCCCCC--eeeec----chHHHhhhhHhh
Confidence 55678999995 46666 678999998886
No 311
>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=57.50 E-value=14 Score=22.25 Aligned_cols=25 Identities=16% Similarity=0.225 Sum_probs=17.4
Q ss_pred CCCcCHHHHHHHHhCCCHHHHHHHHH
Q 025983 163 DKPRTVKEICSVANGATKKEIGRAKE 188 (245)
Q Consensus 163 ~~~~tl~dia~~~~~v~~~~i~~~~~ 188 (245)
....+..+||.. +||+..+|.+..+
T Consensus 19 ~~G~si~~IA~~-~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 19 AEGMSIAEIAKQ-FGVSRSTVYRYLN 43 (45)
T ss_dssp HTT--HHHHHHH-TTS-HHHHHHHHC
T ss_pred HCCCCHHHHHHH-HCcCHHHHHHHHh
Confidence 344889999995 9999999977653
No 312
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=57.29 E-value=36 Score=19.69 Aligned_cols=47 Identities=17% Similarity=0.354 Sum_probs=32.6
Q ss_pred CCCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCccCCccccCCCCHHhHHHHHhhhcCCCHH
Q 025983 163 DKPRTVKEICSVANGATKKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMNNQ 225 (245)
Q Consensus 163 ~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~ 225 (245)
...++..+++. ..+++..+|.+... + . . ..+...+.+++..|+++.+
T Consensus 8 ~~~~s~~~la~-~~~i~~~~i~~~~~------~-~------~--~~~~~~~~~i~~~~~~~~~ 54 (56)
T smart00530 8 EKGLTQEELAE-KLGVSRSTLSRIEN------G-K------R--KPSLETLKKLAKALGVSLD 54 (56)
T ss_pred HcCCCHHHHHH-HhCCCHHHHHHHHC------C-C------C--CCCHHHHHHHHHHhCCChh
Confidence 34578999999 48999888865321 1 1 1 1156788999999998764
No 313
>PF08299 Bac_DnaA_C: Bacterial dnaA protein helix-turn-helix; InterPro: IPR013159 This entry represents the C-terminal domain of bacterial DnaA proteins [, , ] that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC). DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) [].; GO: 0005524 ATP binding, 0043565 sequence-specific DNA binding, 0006270 DNA-dependent DNA replication initiation, 0006275 regulation of DNA replication; PDB: 2HCB_B 3R8F_C 1L8Q_A 3PVP_B 3PVV_A 1J1V_A.
Probab=57.26 E-value=32 Score=22.97 Aligned_cols=65 Identities=17% Similarity=0.212 Sum_probs=36.0
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHH--HHHHHHHHHHhCCCCcCHHHHHHHHhC-CCHHHHHH
Q 025983 109 FKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDAL--LAACLYIACRQEDKPRTVKEICSVANG-ATKKEIGR 185 (245)
Q Consensus 109 ~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~i--aAA~lY~acR~~~~~~tl~dia~~~~~-v~~~~i~~ 185 (245)
...++.+|+.+++|..-+. .++|....+ =-.+.|++-... ..++.+|+.. +| -+-.++..
T Consensus 3 ~~Ii~~Va~~~~v~~~~i~--------------s~~R~~~i~~aR~va~yL~r~~~--~~sl~~Ig~~-fg~rdHstV~~ 65 (70)
T PF08299_consen 3 EDIIEAVAEYFGVSVEDIR--------------SKSRKRKIVEARQVAMYLARELT--GLSLSEIGRY-FGGRDHSTVIH 65 (70)
T ss_dssp HHHHHHHHHHTT--HHHHH--------------SS---HHHHHHHHHHHHHHHHHS-----HHHHHHH-CTSSTHHHHHH
T ss_pred HHHHHHHHHHHCCCHHHHh--------------CCCCChhhcchHHHHHHHHHHHh--CCCHHHHHHH-hCCCCHHHHHH
Confidence 3456677777777753221 122332211 223457665554 5789999995 87 99999998
Q ss_pred HHHHH
Q 025983 186 AKEYI 190 (245)
Q Consensus 186 ~~~~l 190 (245)
+++++
T Consensus 66 a~~ki 70 (70)
T PF08299_consen 66 AIRKI 70 (70)
T ss_dssp HHHHH
T ss_pred HHHhC
Confidence 88764
No 314
>PRK06450 threonine synthase; Validated
Probab=57.00 E-value=5 Score=35.67 Aligned_cols=29 Identities=28% Similarity=0.626 Sum_probs=21.0
Q ss_pred CCCCCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 1 ~~~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
|+..+|+.||.. ++. .-...|..||-.++
T Consensus 1 ~~~~~C~~Cg~~----~~~-~~~~~C~~cg~~l~ 29 (338)
T PRK06450 1 MVKEVCMKCGKE----RES-IYEIRCKKCGGPFE 29 (338)
T ss_pred CceeEECCcCCc----CCC-cccccCCcCCCEeE
Confidence 666799999973 233 33578999997764
No 315
>PRK14873 primosome assembly protein PriA; Provisional
Probab=56.90 E-value=8.1 Score=37.70 Aligned_cols=27 Identities=26% Similarity=0.615 Sum_probs=20.3
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V 32 (245)
..||+|+. .+.+-...+.+.|..||.-
T Consensus 393 ~~C~~C~~--~L~~h~~~~~l~Ch~CG~~ 419 (665)
T PRK14873 393 ARCRHCTG--PLGLPSAGGTPRCRWCGRA 419 (665)
T ss_pred eECCCCCC--ceeEecCCCeeECCCCcCC
Confidence 46999986 3555556778999999984
No 316
>PRK06260 threonine synthase; Validated
Probab=56.90 E-value=5 Score=36.46 Aligned_cols=30 Identities=37% Similarity=0.630 Sum_probs=22.3
Q ss_pred CCCCCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 1 MTDAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 1 ~~~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
|-..+|+.||.. ++...-...|..||-.++
T Consensus 1 ~~~~~C~~cg~~----~~~~~~~~~Cp~cg~~l~ 30 (397)
T PRK06260 1 MYWLKCIECGKE----YDPDEIIYTCPECGGLLE 30 (397)
T ss_pred CCEEEECCCCCC----CCCCCccccCCCCCCeEE
Confidence 556789999973 455555678999998764
No 317
>PF10005 DUF2248: Uncharacterized protein conserved in bacteria (DUF2248); InterPro: IPR011201 This is a family of uncharacterised bacterial proteins.
Probab=56.20 E-value=6.7 Score=34.83 Aligned_cols=24 Identities=38% Similarity=0.937 Sum_probs=19.5
Q ss_pred CCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 5 ~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
.|+.||. .+.|+ ...|..||.-|.
T Consensus 1 ~C~~Cg~--~v~Fe----Nt~C~~Cg~~LG 24 (343)
T PF10005_consen 1 SCPNCGQ--PVFFE----NTRCLSCGSALG 24 (343)
T ss_pred CCCCCCC--cceeC----CCccccCCcccc
Confidence 4999996 36665 789999999885
No 318
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=56.07 E-value=4.9 Score=30.00 Aligned_cols=19 Identities=16% Similarity=0.324 Sum_probs=10.5
Q ss_pred ceeeeCCCCceEccCCccc
Q 025983 14 EVVFDHSAGDTVCSECGLV 32 (245)
Q Consensus 14 ~iv~d~~~G~~vC~~CG~V 32 (245)
.+..+..-+...|.+||..
T Consensus 62 ~L~Ie~vp~~~~C~~Cg~~ 80 (117)
T PRK00564 62 ILDIVDEKVELECKDCSHV 80 (117)
T ss_pred EEEEEecCCEEEhhhCCCc
Confidence 4445555566666666633
No 319
>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=55.98 E-value=22 Score=22.98 Aligned_cols=29 Identities=10% Similarity=0.189 Sum_probs=23.5
Q ss_pred CCCc-CHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 163 DKPR-TVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 163 ~~~~-tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
|..+ +..++++. ++++..+++++++.|..
T Consensus 21 g~~lps~~~la~~-~~vsr~tvr~al~~L~~ 50 (64)
T PF00392_consen 21 GDRLPSERELAER-YGVSRTTVREALRRLEA 50 (64)
T ss_dssp TSBE--HHHHHHH-HTS-HHHHHHHHHHHHH
T ss_pred CCEeCCHHHHHHH-hccCCcHHHHHHHHHHH
Confidence 4567 89999995 99999999999998875
No 320
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=55.69 E-value=25 Score=21.28 Aligned_cols=27 Identities=15% Similarity=0.177 Sum_probs=18.2
Q ss_pred CcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 165 PRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 165 ~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
..+..+||.. +|++..++.+..+...+
T Consensus 17 G~s~~~ia~~-lgvs~~Tv~~w~kr~~~ 43 (50)
T PF13384_consen 17 GWSIREIAKR-LGVSRSTVYRWIKRYRE 43 (50)
T ss_dssp T--HHHHHHH-HTS-HHHHHHHHT----
T ss_pred CCCHHHHHHH-HCcCHHHHHHHHHHccc
Confidence 7789999995 99999999998887653
No 321
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=55.65 E-value=13 Score=21.63 Aligned_cols=25 Identities=32% Similarity=0.805 Sum_probs=15.2
Q ss_pred CCCCCCCCCCc-eeeeC--CCCc--eEccCC
Q 025983 4 AFCSDCKKHTE-VVFDH--SAGD--TVCSEC 29 (245)
Q Consensus 4 ~~Cp~Cg~~~~-iv~d~--~~G~--~vC~~C 29 (245)
..||.|++ +. ++-.- ..|. +-|.+|
T Consensus 6 v~CP~C~s-~~~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 6 VHCPRCQS-TEGVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eeCCCCCC-CCcceeCCCCCCCCEeEecCcC
Confidence 57999998 45 54331 2332 567666
No 322
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=55.22 E-value=6.3 Score=26.87 Aligned_cols=11 Identities=45% Similarity=1.141 Sum_probs=4.1
Q ss_pred CCCCCCCCCCC
Q 025983 1 MTDAFCSDCKK 11 (245)
Q Consensus 1 ~~~~~Cp~Cg~ 11 (245)
|....||.||.
T Consensus 22 ~~k~FCp~CGn 32 (73)
T PF08772_consen 22 MTKQFCPKCGN 32 (73)
T ss_dssp SS--S-SSS--
T ss_pred CCceeCcccCC
Confidence 45567888886
No 323
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=54.97 E-value=40 Score=20.80 Aligned_cols=29 Identities=10% Similarity=0.196 Sum_probs=25.8
Q ss_pred CCCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 163 DKPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 163 ~~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
+.+.++.+|++. ++++..++.+..+.|.+
T Consensus 8 ~~~~~~~~i~~~-l~is~~~v~~~l~~L~~ 36 (66)
T smart00418 8 EGELCVCELAEI-LGLSQSTVSHHLKKLRE 36 (66)
T ss_pred cCCccHHHHHHH-HCCCHHHHHHHHHHHHH
Confidence 567899999995 99999999999998875
No 324
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=54.94 E-value=5 Score=29.61 Aligned_cols=29 Identities=24% Similarity=0.665 Sum_probs=20.1
Q ss_pred CCCCCCCCCCCceeee-CCCCceEccCCccccc
Q 025983 3 DAFCSDCKKHTEVVFD-HSAGDTVCSECGLVLE 34 (245)
Q Consensus 3 ~~~Cp~Cg~~~~iv~d-~~~G~~vC~~CG~V~~ 34 (245)
...|+.||+ +... ...+..+|..|+.+..
T Consensus 7 ~~FC~~CG~---ll~~~~~~~~~~C~~Ck~~~~ 36 (116)
T KOG2907|consen 7 LDFCSDCGS---LLEEPSAQSTVLCIRCKIEYP 36 (116)
T ss_pred cchhhhhhh---hcccccccCceEeccccccCC
Confidence 357999996 2333 3566677999988774
No 325
>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=54.90 E-value=47 Score=20.70 Aligned_cols=28 Identities=18% Similarity=0.204 Sum_probs=23.6
Q ss_pred CCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 164 KPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 164 ~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
-+.++.++++ .++++..++.+..+.|.+
T Consensus 16 ~~~~~~~la~-~~~~~~~~~t~~i~~L~~ 43 (59)
T PF01047_consen 16 GGITQSELAE-KLGISRSTVTRIIKRLEK 43 (59)
T ss_dssp SSEEHHHHHH-HHTS-HHHHHHHHHHHHH
T ss_pred CCCCHHHHHH-HHCCChhHHHHHHHHHHH
Confidence 3489999999 499999999999998875
No 326
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=54.84 E-value=11 Score=23.38 Aligned_cols=7 Identities=29% Similarity=0.966 Sum_probs=6.3
Q ss_pred CCCCCCC
Q 025983 5 FCSDCKK 11 (245)
Q Consensus 5 ~Cp~Cg~ 11 (245)
.||.||.
T Consensus 15 ~Cp~CGN 21 (49)
T PF12677_consen 15 KCPKCGN 21 (49)
T ss_pred cCcccCC
Confidence 6999997
No 327
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=54.63 E-value=33 Score=31.64 Aligned_cols=43 Identities=14% Similarity=0.140 Sum_probs=34.4
Q ss_pred HHHHH---HHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHHHh
Q 025983 149 ALLAA---CLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYIVKQL 194 (245)
Q Consensus 149 ~iaAA---~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l 194 (245)
.++-| ++|++-+ -...++.+|+.. +|.+..++..+++++.+.+
T Consensus 370 ~i~~aR~iamyl~r~--~~~~s~~~Ig~~-fgr~hstV~~a~~~i~~~~ 415 (440)
T PRK14088 370 KALLARRIGMYVAKN--YLGSSLRTIAEK-FNRSHPVVVDSVKKVKDSL 415 (440)
T ss_pred cccHHHHHHHHHHHH--HhCCCHHHHHHH-hCCCHHHHHHHHHHHHHHH
Confidence 44445 8888844 455699999995 8999999999999998865
No 328
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 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 ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=54.41 E-value=9.8 Score=30.11 Aligned_cols=32 Identities=16% Similarity=0.453 Sum_probs=16.3
Q ss_pred CCCCCCCCCCce---ee-eCCCCc-----eEccCCcccccc
Q 025983 4 AFCSDCKKHTEV---VF-DHSAGD-----TVCSECGLVLES 35 (245)
Q Consensus 4 ~~Cp~Cg~~~~i---v~-d~~~G~-----~vC~~CG~V~~e 35 (245)
..||.||..... .+ .|--|+ ..|.+||+=-.|
T Consensus 2 s~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~e 42 (161)
T PF03367_consen 2 SLCPNCGENGTTRILLTDIPYFKEVIIMSFECEHCGYKNNE 42 (161)
T ss_dssp EE-TTTSSCCEEEEEEEEETTTEEEEEEEEE-TTT--EEEE
T ss_pred CcCCCCCCCcEEEEEEEcCCCCceEEEEEeECCCCCCEeee
Confidence 469999985321 11 244555 479999986543
No 329
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=54.06 E-value=10 Score=35.78 Aligned_cols=32 Identities=34% Similarity=0.633 Sum_probs=21.0
Q ss_pred CCCCCCCCCcee---eeCCCC--ceEccCCcccccccc
Q 025983 5 FCSDCKKHTEVV---FDHSAG--DTVCSECGLVLESHS 37 (245)
Q Consensus 5 ~Cp~Cg~~~~iv---~d~~~G--~~vC~~CG~V~~e~~ 37 (245)
.||+||....++ +|.+.| .+.| .||.-.+-.+
T Consensus 177 ic~~cg~~~~~~~~~~d~~~~~v~y~~-~cG~~~~~~~ 213 (510)
T PRK00750 177 ICPKCGKVLTTPVISYDAEAGTVTYDC-ECGHEGEVPV 213 (510)
T ss_pred eCCCCCccceEEEEEEeCCCCEEEEEc-CCCCEEEEec
Confidence 699999864332 477776 4556 4998765433
No 330
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=54.05 E-value=1e+02 Score=26.10 Aligned_cols=38 Identities=8% Similarity=0.006 Sum_probs=29.1
Q ss_pred HHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHH
Q 025983 151 LAACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYI 190 (245)
Q Consensus 151 aAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l 190 (245)
..+.-|+.... ..++++.++|+. +++|+..+.+.+++.
T Consensus 189 ~~~~~~I~~~~-~~~~sl~~lA~~-~~~S~~~l~r~Fk~~ 226 (287)
T TIGR02297 189 NRFNFLIEENY-KQHLRLPEYADR-LGISESRLNDICRRF 226 (287)
T ss_pred HHHHHHHHHhh-ccCCCHHHHHHH-HCCCHHHHHHHHHHH
Confidence 44555666443 458999999995 999999999988853
No 331
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=54.04 E-value=13 Score=23.80 Aligned_cols=46 Identities=13% Similarity=0.149 Sum_probs=27.4
Q ss_pred CcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCccCCccccCCCCHHhHHHHHhhhcCCCHH
Q 025983 165 PRTVKEICSVANGATKKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMNNQ 225 (245)
Q Consensus 165 ~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~ 225 (245)
.++..++|.. .|++..+|.+.++.= .. .-..+.+.++|..|+.+.+
T Consensus 10 ~it~~~La~~-~gis~~tl~~~~~~~-------------~~-~~~~~~l~~ia~~l~~~~~ 55 (63)
T PF13443_consen 10 GITQKDLARK-TGISRSTLSRILNGK-------------PS-NPSLDTLEKIAKALNCSPE 55 (63)
T ss_dssp T--HHHHHHH-HT--HHHHHHHHTTT-------------------HHHHHHHHHHHT--HH
T ss_pred CCCHHHHHHH-HCcCHHHHHHHHhcc-------------cc-cccHHHHHHHHHHcCCCHH
Confidence 3489999995 899999988776611 01 1234788999999998754
No 332
>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=53.58 E-value=34 Score=21.69 Aligned_cols=27 Identities=15% Similarity=0.181 Sum_probs=21.3
Q ss_pred CcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 165 PRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 165 ~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
..++.|+|+. +||+..++...++.-.+
T Consensus 23 ~~tl~elA~~-lgis~st~~~~LRrae~ 49 (53)
T PF04967_consen 23 RITLEELAEE-LGISKSTVSEHLRRAER 49 (53)
T ss_pred cCCHHHHHHH-hCCCHHHHHHHHHHHHH
Confidence 3789999995 99999888877665543
No 333
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=53.57 E-value=13 Score=23.83 Aligned_cols=28 Identities=21% Similarity=0.858 Sum_probs=19.8
Q ss_pred CCCC--CCCCCCceeee--CCCCceEccCCcccc
Q 025983 4 AFCS--DCKKHTEVVFD--HSAGDTVCSECGLVL 33 (245)
Q Consensus 4 ~~Cp--~Cg~~~~iv~d--~~~G~~vC~~CG~V~ 33 (245)
.+|| .|+.. +..+ .....+.|..||...
T Consensus 19 ~~CP~~~C~~~--~~~~~~~~~~~v~C~~C~~~f 50 (64)
T smart00647 19 KWCPAPDCSAA--IIVTEEEGCNRVTCPKCGFSF 50 (64)
T ss_pred cCCCCCCCcce--EEecCCCCCCeeECCCCCCeE
Confidence 5799 89862 3332 366779999999766
No 334
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=53.38 E-value=15 Score=21.63 Aligned_cols=30 Identities=23% Similarity=0.541 Sum_probs=17.6
Q ss_pred CCCCCCCCCC--CceeeeCCCCceEccCCccc
Q 025983 3 DAFCSDCKKH--TEVVFDHSAGDTVCSECGLV 32 (245)
Q Consensus 3 ~~~Cp~Cg~~--~~iv~d~~~G~~vC~~CG~V 32 (245)
..+|..|++- +-..+|......+|.-||..
T Consensus 2 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp S-B-TTT--BS-TTSEEETTTTEEEETTT--E
T ss_pred ccccCCCCCEECCcceEcCCCCEEECcCCCCc
Confidence 3579999962 34467777778999999985
No 335
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=53.28 E-value=7.1 Score=28.79 Aligned_cols=31 Identities=23% Similarity=0.405 Sum_probs=22.9
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
..|-.||+...--....-|..+|..|.-|..
T Consensus 4 ~~CaDC~~~~p~w~s~~~GifvC~~CsgiHR 34 (112)
T smart00105 4 KKCFDCGAPNPTWASVNLGVFLCIECSGIHR 34 (112)
T ss_pred CcccCCCCCCCCcEEeccceeEhHHhHHHHH
Confidence 4699999842223345679999999999875
No 336
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=53.14 E-value=11 Score=28.67 Aligned_cols=31 Identities=29% Similarity=0.605 Sum_probs=20.0
Q ss_pred CCCCCCCCCCCceeee-C-CCC--ceEccCCccccc
Q 025983 3 DAFCSDCKKHTEVVFD-H-SAG--DTVCSECGLVLE 34 (245)
Q Consensus 3 ~~~Cp~Cg~~~~iv~d-~-~~G--~~vC~~CG~V~~ 34 (245)
+..||.|++ .+++.- . ..| -..|.+||.-..
T Consensus 30 ~~~cP~C~s-~~~~k~g~~~~~~qRyrC~~C~~tf~ 64 (129)
T COG3677 30 KVNCPRCKS-SNVVKIGGIRRGHQRYKCKSCGSTFT 64 (129)
T ss_pred cCcCCCCCc-cceeeECCccccccccccCCcCccee
Confidence 468999998 453322 1 222 478999987664
No 337
>PRK08197 threonine synthase; Validated
Probab=53.02 E-value=6.3 Score=35.75 Aligned_cols=26 Identities=31% Similarity=0.733 Sum_probs=19.2
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
.+|+.||.. ++...-...| .||-.++
T Consensus 8 ~~C~~Cg~~----~~~~~~~~~C-~cg~~l~ 33 (394)
T PRK08197 8 LECSKCGET----YDADQVHNLC-KCGKPLL 33 (394)
T ss_pred EEECCCCCC----CCCCCcceec-CCCCeeE
Confidence 579999973 4445557889 8997764
No 338
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=52.98 E-value=32 Score=27.45 Aligned_cols=40 Identities=15% Similarity=0.317 Sum_probs=28.4
Q ss_pred HHHHHHHhc-CCCHHHHHHHHHHHHHHhhCCCCCCCCHHHH
Q 025983 111 TIATMSDRL-GLVATIKDRANEIYKKVEDQKSSRGRNQDAL 150 (245)
Q Consensus 111 ~I~~~~~~L-~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~i 150 (245)
+++++-..| +||++-.+++.++|+...+.+.-.|++-+.+
T Consensus 6 fL~~L~~~L~~lp~~e~~e~l~~Y~e~f~d~~~~G~sEeei 46 (181)
T PF08006_consen 6 FLNELEKYLKKLPEEEREEILEYYEEYFDDAGEEGKSEEEI 46 (181)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhCCCCHHHH
Confidence 444444444 4888888889999988888776677766544
No 339
>PRK08329 threonine synthase; Validated
Probab=52.91 E-value=9.5 Score=33.99 Aligned_cols=26 Identities=23% Similarity=0.636 Sum_probs=17.8
Q ss_pred CCCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 3 ~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
|.+|+.||.. ++.... ..| .||-.++
T Consensus 1 ~l~C~~Cg~~----~~~~~~-~~C-~c~~~l~ 26 (347)
T PRK08329 1 MLRCTKCGRT----YEEKFK-LRC-DCGGTLL 26 (347)
T ss_pred CcCcCCCCCC----cCCCCc-eec-CCCCcEE
Confidence 3689999973 333333 789 8997763
No 340
>KOG0856 consensus Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones]
Probab=52.83 E-value=10 Score=29.08 Aligned_cols=34 Identities=26% Similarity=0.572 Sum_probs=28.1
Q ss_pred eeCCCCceEccCCcccc--cccccccCcccccccCC
Q 025983 17 FDHSAGDTVCSECGLVL--ESHSIDETSEWRTFANE 50 (245)
Q Consensus 17 ~d~~~G~~vC~~CG~V~--~e~~id~~~ewr~f~~~ 50 (245)
--.+.|-++|..||.-| .+.-+|.|--|.+|.+.
T Consensus 48 ~~~e~GvY~C~~C~~pLykS~tKfdsgcGWPAF~e~ 83 (146)
T KOG0856|consen 48 KHFEEGVYVCAGCGTPLYKSTTKFDSGCGWPAFFEA 83 (146)
T ss_pred cccCCceEEEeecCCccccccccccCCCCCchhhhc
Confidence 33589999999999988 45578999999999864
No 341
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=52.75 E-value=7.5 Score=27.72 Aligned_cols=12 Identities=25% Similarity=0.437 Sum_probs=9.7
Q ss_pred CCCCCCCCCCCC
Q 025983 1 MTDAFCSDCKKH 12 (245)
Q Consensus 1 ~~~~~Cp~Cg~~ 12 (245)
|....||+||.-
T Consensus 1 mlLI~CP~Cg~R 12 (97)
T COG4311 1 MLLIPCPYCGER 12 (97)
T ss_pred CceecCCCCCCC
Confidence 677889999963
No 342
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=52.67 E-value=11 Score=23.03 Aligned_cols=22 Identities=32% Similarity=0.490 Sum_probs=17.0
Q ss_pred CCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 5 ~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
+|..|+... ...+|..||.|.-
T Consensus 1 ~C~~C~~~~--------~l~~CL~C~~~~c 22 (50)
T smart00290 1 RCSVCGTIE--------NLWLCLTCGQVGC 22 (50)
T ss_pred CcccCCCcC--------CeEEecCCCCccc
Confidence 589999732 2679999999975
No 343
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=52.64 E-value=6.7 Score=25.98 Aligned_cols=21 Identities=24% Similarity=0.561 Sum_probs=13.6
Q ss_pred CCCCCCCCCCCceeeeCCCCceEccCCcc
Q 025983 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (245)
Q Consensus 3 ~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~ 31 (245)
.+.|.+|+.- + + ..+|..||.
T Consensus 5 ~~AC~~C~~i---~-~----~~~Cp~Cgs 25 (64)
T PRK06393 5 YRACKKCKRL---T-P----EKTCPVHGD 25 (64)
T ss_pred hhhHhhCCcc---c-C----CCcCCCCCC
Confidence 3568888862 2 2 228888886
No 344
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=52.43 E-value=57 Score=21.54 Aligned_cols=45 Identities=18% Similarity=0.270 Sum_probs=32.1
Q ss_pred CHHHHHHHHhCCCHHHHHHHHHHHHHHhCCccCCccccCCCCHH--hHHHHHhhhcCCCHHH
Q 025983 167 TVKEICSVANGATKKEIGRAKEYIVKQLGLETGQSVEMGTIHAG--DFMRRFCSNLGMNNQA 226 (245)
Q Consensus 167 tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~--~~i~r~~~~L~l~~~v 226 (245)
++.|||. .+|++..++.++++ - -+.+.|+ .-|.+++.+||..+..
T Consensus 2 t~~~iA~-~~gvS~~TVSr~ln-------~-------~~~v~~~t~~~i~~~~~~~gy~~~~ 48 (70)
T smart00354 2 TIKDVAR-LAGVSKATVSRVLN-------G-------NGRVSEETREKVLAAMEELGYIPNR 48 (70)
T ss_pred CHHHHHH-HHCCCHHHHHHHHC-------C-------CCCCCHHHHHHHHHHHHHhCCCCCH
Confidence 6889999 49999999988653 1 1223343 4588899999986554
No 345
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=52.20 E-value=43 Score=23.14 Aligned_cols=35 Identities=6% Similarity=0.138 Sum_probs=29.4
Q ss_pred hCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCc
Q 025983 161 QEDKPRTVKEICSVANGATKKEIGRAKEYIVKQLGLE 197 (245)
Q Consensus 161 ~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~ 197 (245)
..+.+++-.++++ .+|++...|++.++.|+ .-|++
T Consensus 15 ~~~~~~SGe~La~-~LgiSRtaVwK~Iq~Lr-~~G~~ 49 (79)
T COG1654 15 LTGNFVSGEKLAE-ELGISRTAVWKHIQQLR-EEGVD 49 (79)
T ss_pred cCCCcccHHHHHH-HHCccHHHHHHHHHHHH-HhCCc
Confidence 4567999999999 59999999999999998 44543
No 346
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=52.18 E-value=9.1 Score=20.15 Aligned_cols=9 Identities=22% Similarity=0.501 Sum_probs=7.0
Q ss_pred CCCCCCCCC
Q 025983 3 DAFCSDCKK 11 (245)
Q Consensus 3 ~~~Cp~Cg~ 11 (245)
+..||.||.
T Consensus 2 l~~C~~CgR 10 (25)
T PF13913_consen 2 LVPCPICGR 10 (25)
T ss_pred CCcCCCCCC
Confidence 567888886
No 347
>PF01921 tRNA-synt_1f: tRNA synthetases class I (K); InterPro: IPR002904 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and in a number of bacterial groups that include the alphaproteobacteria and spirochaetes[]. A refined crystal structures shows that the active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [].; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IRX_A.
Probab=52.11 E-value=5.4 Score=35.77 Aligned_cols=12 Identities=17% Similarity=0.016 Sum_probs=3.7
Q ss_pred CCCCcCHHHHHH
Q 025983 162 EDKPRTVKEICS 173 (245)
Q Consensus 162 ~~~~~tl~dia~ 173 (245)
.|.-+|+.|+.+
T Consensus 287 kG~~~t~~e~L~ 298 (360)
T PF01921_consen 287 KGNGITPEEWLE 298 (360)
T ss_dssp ------HHHHHT
T ss_pred CCCccCHHHHHH
Confidence 455666776644
No 348
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=51.90 E-value=5.5 Score=29.46 Aligned_cols=33 Identities=21% Similarity=0.556 Sum_probs=24.2
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccccccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSI 38 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e~~i 38 (245)
..|+.||. ..++...-.+- .|..||..-.+..+
T Consensus 43 ~~C~~Cg~-~~~~~~SCk~R-~CP~C~~~~~~~W~ 75 (111)
T PF14319_consen 43 YRCEDCGH-EKIVYNSCKNR-HCPSCQAKATEQWI 75 (111)
T ss_pred eecCCCCc-eEEecCcccCc-CCCCCCChHHHHHH
Confidence 46999997 56666554444 99999999875443
No 349
>PRK15435 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional
Probab=51.47 E-value=95 Score=27.80 Aligned_cols=38 Identities=13% Similarity=0.214 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHH
Q 025983 149 ALLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYI 190 (245)
Q Consensus 149 ~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l 190 (245)
.+..++-|+-- +.+.++.++|.. +|++...+.+.|++.
T Consensus 86 ~i~~a~~~I~~---~~~lsl~eLA~~-lG~S~~~L~R~Fkk~ 123 (353)
T PRK15435 86 KITHACRLLEQ---ETPVTLEALADQ-VAMSPFHLHRLFKAT 123 (353)
T ss_pred HHHHHHHHHHh---CCCCCHHHHHHH-HCCCHHHHHHHHHHH
Confidence 45555556532 567899999995 899999999888754
No 350
>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=51.32 E-value=37 Score=28.97 Aligned_cols=29 Identities=21% Similarity=0.358 Sum_probs=22.4
Q ss_pred CCCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 163 DKPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 163 ~~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
..+.|++|||.. +||+..++.+..++..+
T Consensus 234 ~~~~t~~eIA~~-lgvS~~~V~q~~~~Al~ 262 (270)
T TIGR02392 234 DDKLTLQELAAE-YGVSAERIRQIEKNAMK 262 (270)
T ss_pred CCCcCHHHHHHH-HCCCHHHHHHHHHHHHH
Confidence 348999999995 99999999955444433
No 351
>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=50.82 E-value=44 Score=21.84 Aligned_cols=31 Identities=13% Similarity=0.266 Sum_probs=26.1
Q ss_pred hCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 161 QEDKPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 161 ~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
+.+.+.+..+++. .++++..+|++..+.|.+
T Consensus 9 L~~~~~~~~eLa~-~l~vS~~tv~~~l~~L~~ 39 (69)
T TIGR00122 9 LADNPFSGEKLGE-ALGMSRTAVNKHIQTLRE 39 (69)
T ss_pred HHcCCcCHHHHHH-HHCCCHHHHHHHHHHHHH
Confidence 3345678999999 599999999999999864
No 352
>PRK04330 hypothetical protein; Provisional
Probab=50.49 E-value=88 Score=22.12 Aligned_cols=53 Identities=11% Similarity=0.176 Sum_probs=43.8
Q ss_pred CchhHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHH
Q 025983 101 PDRGLILAFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYI 157 (245)
Q Consensus 101 ~e~~l~~~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY~ 157 (245)
.+..+.++...++++.+.-.+|.++...|.+....+.+.+ .++..=||.+|++
T Consensus 7 ~e~~ik~~~~~L~~I~~D~sVPRNIRraa~ea~~~L~~e~----~~~~vRaA~AIs~ 59 (88)
T PRK04330 7 NEEKIKQAIQMLEEIINDTSVPRNIRRAATEAKEILLNEE----ESPGVRAATAISI 59 (88)
T ss_pred hHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHhCcC----cchhHHHHHHHHH
Confidence 4678899999999999999999999999999988887654 4555667777775
No 353
>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=50.39 E-value=56 Score=19.87 Aligned_cols=45 Identities=18% Similarity=0.175 Sum_probs=30.9
Q ss_pred CCCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCccCCccccCCCCHHhHHHHHhhhcCCC
Q 025983 163 DKPRTVKEICSVANGATKKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMN 223 (245)
Q Consensus 163 ~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~ 223 (245)
....++.++|.. ++++..+|.+..+ +.. .| +...+.+++..|+++
T Consensus 13 ~~gltq~~lA~~-~gvs~~~vs~~e~------g~~------~~---~~~~~~~i~~~lgv~ 57 (58)
T TIGR03070 13 ALGLTQADLADL-AGVGLRFIRDVEN------GKP------TV---RLDKVLRVLDALGLE 57 (58)
T ss_pred HcCCCHHHHHHH-hCCCHHHHHHHHC------CCC------CC---CHHHHHHHHHHcCCC
Confidence 356789999995 8999888876642 110 11 345778888888864
No 354
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=50.29 E-value=7.4 Score=30.30 Aligned_cols=15 Identities=40% Similarity=0.926 Sum_probs=13.1
Q ss_pred CCCceEccCCccccc
Q 025983 20 SAGDTVCSECGLVLE 34 (245)
Q Consensus 20 ~~G~~vC~~CG~V~~ 34 (245)
.-|.++|.+||..+.
T Consensus 109 g~G~l~C~~Cg~~~~ 123 (146)
T PF07295_consen 109 GPGTLVCENCGHEVE 123 (146)
T ss_pred cCceEecccCCCEEE
Confidence 579999999999874
No 355
>cd00674 LysRS_core_class_I catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity.
Probab=50.22 E-value=13 Score=33.40 Aligned_cols=13 Identities=15% Similarity=0.046 Sum_probs=8.9
Q ss_pred CCCCcCHHHHHHH
Q 025983 162 EDKPRTVKEICSV 174 (245)
Q Consensus 162 ~~~~~tl~dia~~ 174 (245)
.|..+++.|+.+.
T Consensus 280 kGnvI~~~dll~~ 292 (353)
T cd00674 280 KGNVITPSDWLEV 292 (353)
T ss_pred CCCcCCHHHHHHH
Confidence 4667777777663
No 356
>PRK04217 hypothetical protein; Provisional
Probab=50.21 E-value=31 Score=25.47 Aligned_cols=27 Identities=22% Similarity=0.180 Sum_probs=22.4
Q ss_pred CHHHHHHHHhCCCHHHHHHHHHHHHHHh
Q 025983 167 TVKEICSVANGATKKEIGRAKEYIVKQL 194 (245)
Q Consensus 167 tl~dia~~~~~v~~~~i~~~~~~l~~~l 194 (245)
++.|||+. ++++..+|.+.+....+.|
T Consensus 60 S~~EIAk~-LGIS~sTV~r~L~RArkkL 86 (110)
T PRK04217 60 TQEEAGKR-MGVSRGTVWRALTSARKKV 86 (110)
T ss_pred CHHHHHHH-HCcCHHHHHHHHHHHHHHH
Confidence 89999995 9999999988877666555
No 357
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=50.12 E-value=9.9 Score=34.76 Aligned_cols=33 Identities=18% Similarity=0.420 Sum_probs=23.3
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcccccccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSID 39 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e~~id 39 (245)
-.||.||.. . ...-.+..-|..||+-..+..+-
T Consensus 351 p~Cp~Cg~~-m--~S~G~~g~rC~kCg~~~~~~~~~ 383 (421)
T COG1571 351 PVCPRCGGR-M--KSAGRNGFRCKKCGTRARETLIK 383 (421)
T ss_pred CCCCccCCc-h--hhcCCCCcccccccccCCccccc
Confidence 479999973 1 22333368999999999766554
No 358
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=50.02 E-value=11 Score=32.75 Aligned_cols=33 Identities=24% Similarity=0.655 Sum_probs=27.9
Q ss_pred eCCCCceEccCCcccc--cccccccCcccccccCC
Q 025983 18 DHSAGDTVCSECGLVL--ESHSIDETSEWRTFANE 50 (245)
Q Consensus 18 d~~~G~~vC~~CG~V~--~e~~id~~~ewr~f~~~ 50 (245)
..+.|.++|..||.-| .+.-+|+|.-|.+|.+.
T Consensus 31 ~~~~G~y~c~~c~~~LF~s~~Kf~sg~GWPsF~~~ 65 (283)
T PRK05550 31 HDEKGVYLCRRCGAPLFRSEDKFNSGCGWPSFDDE 65 (283)
T ss_pred CCCCcEEEcCCCCchhcCChhhccCCCCCcCcCcc
Confidence 3689999999999998 55678999999999853
No 359
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=49.80 E-value=32 Score=21.70 Aligned_cols=25 Identities=12% Similarity=0.221 Sum_probs=22.7
Q ss_pred CHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 167 TVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 167 tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
+..++++. ++++..++++.++.|.+
T Consensus 27 ~~~~la~~-~~is~~~v~~~l~~L~~ 51 (66)
T cd07377 27 SERELAEE-LGVSRTTVREALRELEA 51 (66)
T ss_pred CHHHHHHH-HCCCHHHHHHHHHHHHH
Confidence 69999995 89999999999999875
No 360
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=49.58 E-value=1.5e+02 Score=25.19 Aligned_cols=42 Identities=10% Similarity=0.016 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHH
Q 025983 147 QDALLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEY 189 (245)
Q Consensus 147 ~~~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~ 189 (245)
...+..+.-|+.-.......++.+||. ++++|+..|.+.|++
T Consensus 196 ~~~l~~~~~~I~~~l~~~~ls~~~lA~-~~giS~r~L~r~Fk~ 237 (302)
T PRK09685 196 ERQFQKVVALIDQSIQEEILRPEWIAG-ELGISVRSLYRLFAE 237 (302)
T ss_pred HHHHHHHHHHHHHhcCCCCCCHHHHHH-HHCCCHHHHHHHHHH
Confidence 444556667777665555599999999 599999999988873
No 361
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=49.40 E-value=65 Score=21.32 Aligned_cols=51 Identities=18% Similarity=0.296 Sum_probs=36.1
Q ss_pred hCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCccCCccccCCCCHHhHHHHHhhhcCCCHHHH
Q 025983 161 QEDKPRTVKEICSVANGATKKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMNNQAV 227 (245)
Q Consensus 161 ~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~ 227 (245)
+.....|+.++|.. +|++..+|.+..+ +- ... +...+.+++..|+.+.+.-
T Consensus 14 ~~~~~~t~~~lA~~-~gis~~tis~~~~------g~--------~~~-~~~~~~~l~~~l~v~~~~l 64 (78)
T TIGR02607 14 LEPLGLSIRALAKA-LGVSRSTLSRIVN------GR--------RGI-TADMALRLAKALGTSPEFW 64 (78)
T ss_pred HHHcCCCHHHHHHH-hCCCHHHHHHHHc------CC--------CCC-CHHHHHHHHHHcCCCHHHH
Confidence 34566789999995 8999888877533 11 112 3468889999999987643
No 362
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=49.15 E-value=7.7 Score=25.41 Aligned_cols=23 Identities=26% Similarity=0.787 Sum_probs=14.1
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~ 31 (245)
..|..||.. +.- .=...|..||.
T Consensus 18 t~CrRCG~~-syh----~qK~~CasCGy 40 (62)
T PRK04179 18 IRCRRCGRH-SYN----VRKKYCAACGF 40 (62)
T ss_pred chhcccCcc-ccc----ccccchhhcCC
Confidence 357788863 322 22567888886
No 363
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 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. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=49.00 E-value=11 Score=24.88 Aligned_cols=30 Identities=30% Similarity=0.551 Sum_probs=16.1
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcccccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHS 37 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e~~ 37 (245)
..|..|+.. |..-.-.--|..||.|+=..-
T Consensus 10 ~~C~~C~~~----F~~~~rrhhCr~CG~~vC~~C 39 (69)
T PF01363_consen 10 SNCMICGKK----FSLFRRRHHCRNCGRVVCSSC 39 (69)
T ss_dssp SB-TTT--B-----BSSS-EEE-TTT--EEECCC
T ss_pred CcCcCcCCc----CCCceeeEccCCCCCEECCch
Confidence 579999973 455577889999999986443
No 365
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=48.82 E-value=14 Score=36.39 Aligned_cols=27 Identities=26% Similarity=0.742 Sum_probs=21.5
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V 32 (245)
..||+|.. .+++-..+|.+.|-.||..
T Consensus 445 ~~Cp~Cd~--~lt~H~~~~~L~CH~Cg~~ 471 (730)
T COG1198 445 AECPNCDS--PLTLHKATGQLRCHYCGYQ 471 (730)
T ss_pred ccCCCCCc--ceEEecCCCeeEeCCCCCC
Confidence 46888886 3566667899999999988
No 366
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=48.62 E-value=68 Score=26.30 Aligned_cols=28 Identities=21% Similarity=0.261 Sum_probs=24.6
Q ss_pred CCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 164 KPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 164 ~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
.|.+..|||+. +|++..++.|..++|.+
T Consensus 172 i~~t~~~iA~~-lG~tretvsR~l~~L~~ 199 (236)
T PRK09392 172 LPYEKRVLASY-LGMTPENLSRAFAALAS 199 (236)
T ss_pred eeCCHHHHHHH-hCCChhHHHHHHHHHHh
Confidence 46778999995 99999999999999865
No 367
>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....
Probab=48.58 E-value=8.3 Score=35.06 Aligned_cols=24 Identities=33% Similarity=0.816 Sum_probs=14.7
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
..||+||.. ...| ..|..||..++
T Consensus 137 g~CP~C~~~------~a~g-~~Ce~cG~~~~ 160 (391)
T PF09334_consen 137 GTCPYCGSD------KARG-DQCENCGRPLE 160 (391)
T ss_dssp CEETTT--S------SCTT-TEETTTSSBEE
T ss_pred ccccCcCcc------ccCC-CcccCCCCCcc
Confidence 468888852 2233 56888988886
No 368
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=48.34 E-value=6.6 Score=23.44 Aligned_cols=28 Identities=25% Similarity=0.539 Sum_probs=14.4
Q ss_pred CCCCCCCCCC---ceeeeCCCCceEccCCcc
Q 025983 4 AFCSDCKKHT---EVVFDHSAGDTVCSECGL 31 (245)
Q Consensus 4 ~~Cp~Cg~~~---~iv~d~~~G~~vC~~CG~ 31 (245)
.+|.-||.+. .....-..|-.||.+|=.
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~ 32 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPNGAYICDECVE 32 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES-SEEEEHHHHH
T ss_pred CCccCCCCCHHHHhceecCCCCcEECHHHHH
Confidence 5799999742 123344557889988743
No 369
>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=48.23 E-value=60 Score=19.59 Aligned_cols=26 Identities=12% Similarity=0.225 Sum_probs=18.5
Q ss_pred CCCCcCHHHHHHHHhCCCHHHHHHHHHH
Q 025983 162 EDKPRTVKEICSVANGATKKEIGRAKEY 189 (245)
Q Consensus 162 ~~~~~tl~dia~~~~~v~~~~i~~~~~~ 189 (245)
+|. .++...|.. +||+..+|.+.++.
T Consensus 14 ~g~-~S~r~AA~~-ygVp~sTL~~r~~g 39 (45)
T PF05225_consen 14 NGK-MSIRKAAKK-YGVPRSTLRRRLRG 39 (45)
T ss_dssp TTS-S-HHHHHHH-HT--HHHHHHHHHH
T ss_pred hCC-CCHHHHHHH-HCcCHHHHHHHHcC
Confidence 555 999999995 99999999976653
No 370
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=48.19 E-value=1.1e+02 Score=22.56 Aligned_cols=77 Identities=21% Similarity=0.222 Sum_probs=44.9
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCC----CCCCHHHHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHH
Q 025983 111 TIATMSDRLGLVATIKDRANEIYKKVEDQKSS----RGRNQDALLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRA 186 (245)
Q Consensus 111 ~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~----~gr~~~~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~ 186 (245)
-+.++|..++++...+.. ++++ .+.+.+ +|++ .+- .=-+.+.-.++--.|+.|+|.. ++|+..+|.++
T Consensus 20 s~~eaa~~F~VS~~Tv~~---W~k~-~~~G~~~~k~r~~~--Kid-~~~L~~~v~~~pd~tl~Ela~~-l~Vs~~ti~~~ 91 (119)
T PF01710_consen 20 SIREAAKRFGVSRNTVYR---WLKR-KETGDLEPKPRGRK--KID-RDELKALVEENPDATLRELAER-LGVSPSTIWRA 91 (119)
T ss_pred hHHHHHHHhCcHHHHHHH---HHHh-cccccccccccccc--ccc-HHHHHHHHHHCCCcCHHHHHHH-cCCCHHHHHHH
Confidence 477888889988655544 4442 222222 2221 110 1112222234455899999995 99999999998
Q ss_pred HHHHHHHhC
Q 025983 187 KEYIVKQLG 195 (245)
Q Consensus 187 ~~~l~~~l~ 195 (245)
+++|--...
T Consensus 92 Lkrlg~t~K 100 (119)
T PF01710_consen 92 LKRLGITRK 100 (119)
T ss_pred HHHcCchhc
Confidence 886644443
No 371
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=48.13 E-value=8.9 Score=39.69 Aligned_cols=23 Identities=43% Similarity=0.925 Sum_probs=12.5
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~ 33 (245)
..||.||+.++. ...|.+||.-+
T Consensus 680 ~fCP~CGs~te~-------vy~CPsCGaev 702 (1337)
T PRK14714 680 NRCPDCGTHTEP-------VYVCPDCGAEV 702 (1337)
T ss_pred ccCcccCCcCCC-------ceeCccCCCcc
Confidence 367777764221 23566666644
No 372
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=47.92 E-value=14 Score=23.18 Aligned_cols=30 Identities=27% Similarity=0.628 Sum_probs=22.8
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcccccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHS 37 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e~~ 37 (245)
..|+.|+.. +.......-|..||.|+=..-
T Consensus 3 ~~C~~C~~~----F~~~~rk~~Cr~Cg~~~C~~C 32 (57)
T cd00065 3 SSCMGCGKP----FTLTRRRHHCRNCGRIFCSKC 32 (57)
T ss_pred CcCcccCcc----ccCCccccccCcCcCCcChHH
Confidence 579999973 444577889999999986543
No 373
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=47.87 E-value=1.3e+02 Score=25.63 Aligned_cols=17 Identities=24% Similarity=0.233 Sum_probs=11.1
Q ss_pred eeCCCCceEccCCcccc
Q 025983 17 FDHSAGDTVCSECGLVL 33 (245)
Q Consensus 17 ~d~~~G~~vC~~CG~V~ 33 (245)
+....|++++-..|.+.
T Consensus 69 ~~~~~g~~i~i~p~~~h 85 (290)
T PRK10572 69 FVCRPGDLLLFPPGEIH 85 (290)
T ss_pred EecCCCCEEEECCCCce
Confidence 34466777777777765
No 374
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=47.77 E-value=14 Score=26.78 Aligned_cols=29 Identities=17% Similarity=0.329 Sum_probs=18.0
Q ss_pred CCCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 3 ~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
...|..|+- |..+..--...|.+||.++.
T Consensus 3 lrAC~~C~~---I~~~~qf~~~gCpnC~~~l~ 31 (98)
T cd07973 3 LRACLLCSL---IKTEDQFERDGCPNCEGYLD 31 (98)
T ss_pred CchhccCCc---ccccccccCCCCCCCcchhc
Confidence 456888886 23332233567999987763
No 375
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=47.42 E-value=1.1e+02 Score=26.26 Aligned_cols=40 Identities=13% Similarity=0.272 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHH
Q 025983 149 ALLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYI 190 (245)
Q Consensus 149 ~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l 190 (245)
.+..++-|+-... ..+.++.++|+. +++|...+.|.|+..
T Consensus 6 ~i~~~~~~i~~~~-~~~~~l~~lA~~-~~~S~~~l~r~F~~~ 45 (289)
T PRK15121 6 IIRDLLIWLEGHL-DQPLSLDNVAAK-AGYSKWHLQRMFKDV 45 (289)
T ss_pred HHHHHHHHHHhcc-cCCCCHHHHHHH-HCcCHHHHHHHHHHH
Confidence 4556667766553 468999999995 899999999988865
No 376
>PF01907 Ribosomal_L37e: Ribosomal protein L37e; InterPro: IPR001569 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 consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A19_A 4A1D_A 4A18_A 4A1B_A 1S1I_Y 3O5H_d 3IZS_l 3O58_d 2ZKR_2 3IZR_l ....
Probab=47.41 E-value=8.3 Score=24.68 Aligned_cols=24 Identities=21% Similarity=0.690 Sum_probs=13.9
Q ss_pred CCCCCCCCCceeeeCCCCceEccCCcccc
Q 025983 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (245)
Q Consensus 5 ~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~ 33 (245)
.|..||+ .+.- --.-.|..||+=-
T Consensus 17 ~CrRCG~-~syH----~qK~~CasCGyp~ 40 (55)
T PF01907_consen 17 LCRRCGR-RSYH----IQKKTCASCGYPA 40 (55)
T ss_dssp E-TTTSS-EEEE----TTTTEETTTBTTT
T ss_pred eecccCC-eeee----cCCCcccccCCCc
Confidence 4778886 3322 2356788888643
No 377
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=47.26 E-value=60 Score=19.26 Aligned_cols=29 Identities=21% Similarity=0.290 Sum_probs=25.2
Q ss_pred CCcCHHHHHHHHhCCCHHHHHHHHHHHHHH
Q 025983 164 KPRTVKEICSVANGATKKEIGRAKEYIVKQ 193 (245)
Q Consensus 164 ~~~tl~dia~~~~~v~~~~i~~~~~~l~~~ 193 (245)
.+.+..+++.. ++++..++.+..+.|.+.
T Consensus 13 ~~~s~~~l~~~-l~~s~~tv~~~l~~L~~~ 41 (53)
T smart00420 13 GKVSVEELAEL-LGVSEMTIRRDLNKLEEQ 41 (53)
T ss_pred CCcCHHHHHHH-HCCCHHHHHHHHHHHHHC
Confidence 46899999994 899999999999888764
No 378
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=47.02 E-value=10 Score=24.50 Aligned_cols=24 Identities=21% Similarity=0.606 Sum_probs=15.0
Q ss_pred CCCCCCCCCceeeeCCCCceEccCCcccc
Q 025983 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (245)
Q Consensus 5 ~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~ 33 (245)
.|-.||. .+.-. -.-.|..||.=-
T Consensus 18 ~CRRCGr-~syhv----~k~~CaaCGfgr 41 (61)
T COG2126 18 RCRRCGR-RSYHV----RKKYCAACGFGR 41 (61)
T ss_pred hhhhccc-hheee----ccceecccCCCC
Confidence 5888887 33322 256788888753
No 379
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=47.02 E-value=14 Score=24.69 Aligned_cols=27 Identities=30% Similarity=0.634 Sum_probs=19.5
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
..| .||. .+..|...-..-| .||..+.
T Consensus 4 frC-~Cgr--~lya~e~~kTkkC-~CG~~l~ 30 (68)
T PF09082_consen 4 FRC-DCGR--YLYAKEGAKTKKC-VCGKTLK 30 (68)
T ss_dssp EEE-TTS----EEEETT-SEEEE-TTTEEEE
T ss_pred EEe-cCCC--EEEecCCcceeEe-cCCCeee
Confidence 358 7997 3677888888999 9999984
No 380
>PF14502 HTH_41: Helix-turn-helix domain
Probab=46.94 E-value=39 Score=21.00 Aligned_cols=27 Identities=19% Similarity=0.318 Sum_probs=23.7
Q ss_pred cCHHHHHHHHhCCCHHHHHHHHHHHHHH
Q 025983 166 RTVKEICSVANGATKKEIGRAKEYIVKQ 193 (245)
Q Consensus 166 ~tl~dia~~~~~v~~~~i~~~~~~l~~~ 193 (245)
.|+.|.++. ++++.-+|+++++.|.+.
T Consensus 7 ~tI~e~~~~-~~vs~GtiQ~Alk~Le~~ 33 (48)
T PF14502_consen 7 PTISEYSEK-FGVSRGTIQNALKFLEEN 33 (48)
T ss_pred CCHHHHHHH-hCcchhHHHHHHHHHHHC
Confidence 578999995 999999999999988764
No 381
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=46.27 E-value=70 Score=20.04 Aligned_cols=33 Identities=21% Similarity=0.418 Sum_probs=28.8
Q ss_pred CCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCc
Q 025983 164 KPRTVKEICSVANGATKKEIGRAKEYIVKQLGLE 197 (245)
Q Consensus 164 ~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~ 197 (245)
...+..+|+.. ++++..++....+.+.+.++..
T Consensus 18 ~G~s~~eia~~-l~is~~tV~~h~~~i~~Kl~~~ 50 (65)
T COG2771 18 QGKSNKEIARI-LGISEETVKTHLRNIYRKLGVK 50 (65)
T ss_pred CCCCHHHHHHH-HCCCHHHHHHHHHHHHHHHCCC
Confidence 34889999995 9999999999999999988864
No 382
>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=46.19 E-value=67 Score=20.35 Aligned_cols=26 Identities=19% Similarity=0.268 Sum_probs=23.4
Q ss_pred cCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 166 RTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 166 ~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
.+..||++. ++++..++.+.++.|.+
T Consensus 21 ~~~~ei~~~-~~i~~~~i~~~l~~L~~ 46 (78)
T cd00090 21 LTVSELAER-LGLSQSTVSRHLKKLEE 46 (78)
T ss_pred cCHHHHHHH-HCcCHhHHHHHHHHHHH
Confidence 889999995 89999999999998865
No 383
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=45.96 E-value=73 Score=26.08 Aligned_cols=33 Identities=18% Similarity=0.226 Sum_probs=25.9
Q ss_pred CCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCc
Q 025983 164 KPRTVKEICSVANGATKKEIGRAKEYIVKQLGLE 197 (245)
Q Consensus 164 ~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~ 197 (245)
...|-++||+. ++++++|+......|.+.|+..
T Consensus 148 ~G~snkeIA~~-L~iS~~TV~~h~~~I~~KLgv~ 180 (207)
T PRK11475 148 RGYSMPQIAEQ-LERNIKTIRAHKFNVMSKLGVS 180 (207)
T ss_pred CCCCHHHHHHH-HCCCHHHHHHHHHHHHHHcCCC
Confidence 45778888884 8888888888888888888764
No 384
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=45.23 E-value=4.8 Score=24.10 Aligned_cols=17 Identities=35% Similarity=0.831 Sum_probs=13.3
Q ss_pred CCceEccCCcccccccc
Q 025983 21 AGDTVCSECGLVLESHS 37 (245)
Q Consensus 21 ~G~~vC~~CG~V~~e~~ 37 (245)
-|...|..||.+-....
T Consensus 11 ~~~~~C~~CgM~Y~~~~ 27 (41)
T PF13878_consen 11 FGATTCPTCGMLYSPGS 27 (41)
T ss_pred cCCcCCCCCCCEECCCC
Confidence 36789999999986544
No 385
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=44.72 E-value=42 Score=27.33 Aligned_cols=33 Identities=12% Similarity=0.124 Sum_probs=27.6
Q ss_pred CCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCc
Q 025983 164 KPRTVKEICSVANGATKKEIGRAKEYIVKQLGLE 197 (245)
Q Consensus 164 ~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~ 197 (245)
...|-++||+. ++++++++....+.|.+.|+..
T Consensus 151 ~G~snkeIA~~-L~iS~~TVk~h~~~I~~KL~v~ 183 (207)
T PRK15411 151 AGQGTIQISDQ-MNIKAKTVSSHKGNIKRKIKTH 183 (207)
T ss_pred cCCCHHHHHHH-cCCCHHHHHHHHHHHHHHhCCC
Confidence 46778899984 8999999999998898888865
No 386
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=44.70 E-value=58 Score=20.67 Aligned_cols=48 Identities=19% Similarity=0.354 Sum_probs=28.7
Q ss_pred CCCCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCccCCccccCCCCHHhHHHHHhhhcCCCHH
Q 025983 162 EDKPRTVKEICSVANGATKKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMNNQ 225 (245)
Q Consensus 162 ~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~ 225 (245)
.....|+.++|. .++++...|.+..+ | + . ..+...+..+|..|+++.+
T Consensus 9 ~~~~lt~~~~a~-~~~i~~~~i~~~e~------g-~------~--~~~~~~l~~i~~~~~v~~~ 56 (64)
T PF12844_consen 9 EEKGLTQKDLAE-KLGISRSTISKIEN------G-K------R--KPSVSTLKKIAEALGVSLD 56 (64)
T ss_dssp HHCT--HHHHHH-HHTS-HHHHHHHHT------T-S------S----BHHHHHHHHHHHTS-HH
T ss_pred HHcCCCHHHHHH-HHCcCHHHHHHHHC------C-C------c--CCCHHHHHHHHHHhCCCHH
Confidence 344678999999 48998776655432 1 1 1 1124678899999998865
No 387
>COG5525 Bacteriophage tail assembly protein [General function prediction only]
Probab=44.65 E-value=11 Score=35.77 Aligned_cols=32 Identities=22% Similarity=0.638 Sum_probs=22.1
Q ss_pred CCCCCCCCCceeeeCCC------------CceEccCCccccccc
Q 025983 5 FCSDCKKHTEVVFDHSA------------GDTVCSECGLVLESH 36 (245)
Q Consensus 5 ~Cp~Cg~~~~iv~d~~~------------G~~vC~~CG~V~~e~ 36 (245)
.||+||...-+.++..+ -.+.|..|+.++.+.
T Consensus 229 pCPHCGe~q~l~~~e~~~~~g~~~~~~~~~~~~c~h~~~~i~~~ 272 (611)
T COG5525 229 PCPHCGEEQQLKFGEKSGPRGLKDTPAEAAFIQCEHCGCVIRPK 272 (611)
T ss_pred eCCCCCchhhccccccCCCcCcccchhhhhhhhccccCceeeee
Confidence 59999975444443222 236899999999873
No 388
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=44.40 E-value=1.1e+02 Score=26.44 Aligned_cols=40 Identities=8% Similarity=-0.012 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHH
Q 025983 149 ALLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYI 190 (245)
Q Consensus 149 ~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l 190 (245)
.+..++-|+..... .+.++.++|+. +++++..+.+.+++.
T Consensus 192 ~i~~~~~~i~~~~~-~~~tl~~lA~~-~~~S~~~l~r~Fk~~ 231 (302)
T PRK10371 192 YVSQMLGFIAENYD-QALTINDVAEH-VKLNANYAMGIFQRV 231 (302)
T ss_pred HHHHHHHHHHHhhc-CCCCHHHHHHH-HCcCHHHHHHHHHHH
Confidence 35666667766644 68999999995 899999999888763
No 389
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=44.33 E-value=51 Score=23.50 Aligned_cols=30 Identities=10% Similarity=0.182 Sum_probs=26.2
Q ss_pred CCCcCHHHHHHHHhCCCHHHHHHHHHHHHHH
Q 025983 163 DKPRTVKEICSVANGATKKEIGRAKEYIVKQ 193 (245)
Q Consensus 163 ~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~ 193 (245)
+-+.+..++++. +|++..++.+.++.|.+.
T Consensus 15 ~~~~~~~~la~~-l~~s~~tv~~~l~~L~~~ 44 (108)
T smart00344 15 DARISLAELAKK-VGLSPSTVHNRVKRLEEE 44 (108)
T ss_pred hCCCCHHHHHHH-HCcCHHHHHHHHHHHHHC
Confidence 347899999995 999999999999999763
No 390
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=44.31 E-value=47 Score=21.15 Aligned_cols=31 Identities=16% Similarity=0.260 Sum_probs=26.5
Q ss_pred hCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 161 QEDKPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 161 ~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
..+-|.+..+|++. ++++..++.+.++.|.+
T Consensus 20 ~~~~~~t~~ela~~-l~~~~~t~s~hL~~L~~ 50 (61)
T PF12840_consen 20 ASNGPMTVSELAEE-LGISQSTVSYHLKKLEE 50 (61)
T ss_dssp HHCSTBEHHHHHHH-HTS-HHHHHHHHHHHHH
T ss_pred hcCCCCCHHHHHHH-HCCCHHHHHHHHHHHHH
Confidence 46789999999995 99999999999998865
No 391
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=44.19 E-value=45 Score=26.88 Aligned_cols=33 Identities=27% Similarity=0.282 Sum_probs=29.1
Q ss_pred CCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCc
Q 025983 164 KPRTVKEICSVANGATKKEIGRAKEYIVKQLGLE 197 (245)
Q Consensus 164 ~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~ 197 (245)
...|-++||+. ++++..|+....+.|.+.|+..
T Consensus 164 ~G~s~~eIA~~-l~iS~~TV~~h~~~i~~Kl~v~ 196 (216)
T PRK10840 164 EGFLVTEIAKK-LNRSIKTISSQKKSAMMKLGVE 196 (216)
T ss_pred CCCCHHHHHHH-HCCCHHHHHHHHHHHHHHcCCC
Confidence 56889999995 8999999999999999999875
No 392
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=44.02 E-value=52 Score=22.77 Aligned_cols=69 Identities=20% Similarity=0.285 Sum_probs=44.6
Q ss_pred cCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCccCCc-cccCCCCH-----HhHHHHHhhhcCCCHHHHHHHHHHHHHhhh
Q 025983 166 RTVKEICSVANGATKKEIGRAKEYIVKQLGLETGQS-VEMGTIHA-----GDFMRRFCSNLGMNNQAVKAAQEAVQKSEE 239 (245)
Q Consensus 166 ~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~-~~~~~~~p-----~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~ 239 (245)
+|+.|++. .++++...|..... .|+-.... -.-+..++ -..+.|+...|+++.+-..++.+++++...
T Consensus 1 is~~e~~~-~~~i~~~~l~~lve-----~Gli~p~~~~~~~~f~~~~l~rl~~~~rL~~Dl~in~~gi~lil~LLd~i~~ 74 (84)
T PF13591_consen 1 ISLEEFCE-ACGIEPEFLRELVE-----EGLIEPEGEEEEWYFSEEDLARLRRIRRLHRDLGINLEGIALILDLLDRIEQ 74 (84)
T ss_pred CCHHHHHH-HHCcCHHHHHHHHH-----CCCeeecCCCCeeeECHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 47889999 48999888765432 23210000 00011222 246778889999999999999999988876
Q ss_pred c
Q 025983 240 F 240 (245)
Q Consensus 240 ~ 240 (245)
+
T Consensus 75 L 75 (84)
T PF13591_consen 75 L 75 (84)
T ss_pred H
Confidence 4
No 393
>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=44.00 E-value=29 Score=24.06 Aligned_cols=23 Identities=26% Similarity=0.367 Sum_probs=19.9
Q ss_pred CCcCHHHHHHHHhCCCHHHHHHHH
Q 025983 164 KPRTVKEICSVANGATKKEIGRAK 187 (245)
Q Consensus 164 ~~~tl~dia~~~~~v~~~~i~~~~ 187 (245)
-..++.|||.. +|++..++.+.+
T Consensus 18 ~~~ti~dvA~~-~gvS~~TVsr~L 40 (80)
T TIGR02844 18 TKATVRETAKV-FGVSKSTVHKDV 40 (80)
T ss_pred CCCCHHHHHHH-hCCCHHHHHHHh
Confidence 55789999995 999999999954
No 394
>PF00488 MutS_V: MutS domain V C-terminus.; InterPro: IPR000432 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the C-terminal domain found in proteins in the MutS family of DNA mismatch repair proteins. The C-terminal region of MutS is comprised of the ATPase domain and the HTH (helix-turn-helix) domain, the latter being involved in dimer contacts. Yeast MSH3 [], bacterial proteins involved in DNA mismatch repair, and the predicted protein product of the Rep-3 gene of mouse share extensive sequence similarity. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. ; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1FW6_A 1EWQ_A 1EWR_B 1NNE_B 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B ....
Probab=43.44 E-value=29 Score=29.07 Aligned_cols=27 Identities=33% Similarity=0.502 Sum_probs=20.8
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHHHHhh
Q 025983 112 IATMSDRLGLVATIKDRANEIYKKVED 138 (245)
Q Consensus 112 I~~~~~~L~Lp~~v~~~A~~i~~~~~~ 138 (245)
=-+++..+|+|++++++|.++++.+.+
T Consensus 208 ai~iA~~~g~p~~II~rA~~i~~~l~~ 234 (235)
T PF00488_consen 208 AIEIAKLAGLPEEIIERAKEILKQLEE 234 (235)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHT
T ss_pred HHHHHHHhCcCHHHHHHHHHHHHHHhc
Confidence 345778889999999999999998753
No 395
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=43.33 E-value=40 Score=22.06 Aligned_cols=25 Identities=16% Similarity=0.302 Sum_probs=20.5
Q ss_pred CcCHHHHHHHHhCCCHHHHHHHHHHH
Q 025983 165 PRTVKEICSVANGATKKEIGRAKEYI 190 (245)
Q Consensus 165 ~~tl~dia~~~~~v~~~~i~~~~~~l 190 (245)
|.++.++|.. ++++...+.+.+++.
T Consensus 1 ~~~~~~la~~-~~~s~~~l~~~f~~~ 25 (84)
T smart00342 1 PLTLEDLAEA-LGMSPRHLQRLFKKE 25 (84)
T ss_pred CCCHHHHHHH-hCCCHHHHHHHHHHH
Confidence 5689999994 899999988887754
No 396
>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=43.19 E-value=36 Score=19.87 Aligned_cols=22 Identities=23% Similarity=0.234 Sum_probs=18.5
Q ss_pred CHHHHHHHHhCCCHHHHHHHHHH
Q 025983 167 TVKEICSVANGATKKEIGRAKEY 189 (245)
Q Consensus 167 tl~dia~~~~~v~~~~i~~~~~~ 189 (245)
++.|+|+. ++|+..+|.+..+.
T Consensus 2 s~~e~a~~-lgvs~~tl~~~~~~ 23 (49)
T cd04762 2 TTKEAAEL-LGVSPSTLRRWVKE 23 (49)
T ss_pred CHHHHHHH-HCcCHHHHHHHHHc
Confidence 67899995 99999999887663
No 397
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=43.04 E-value=38 Score=25.80 Aligned_cols=31 Identities=19% Similarity=0.206 Sum_probs=26.9
Q ss_pred hCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 161 QEDKPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 161 ~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
+.+.+.++.++|+ .+|+|..++.+..++|.+
T Consensus 18 ~~d~r~~~~eia~-~lglS~~~v~~Ri~~L~~ 48 (154)
T COG1522 18 QEDARISNAELAE-RVGLSPSTVLRRIKRLEE 48 (154)
T ss_pred HHhCCCCHHHHHH-HHCCCHHHHHHHHHHHHH
Confidence 4556699999999 499999999999999975
No 398
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=42.96 E-value=14 Score=23.95 Aligned_cols=24 Identities=21% Similarity=0.515 Sum_probs=17.5
Q ss_pred CCCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 3 ~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
+.+||.||. =++ .-.|..||-+..
T Consensus 5 ~rkC~~cg~-YTL-------ke~Cp~CG~~t~ 28 (59)
T COG2260 5 IRKCPKCGR-YTL-------KEKCPVCGGDTK 28 (59)
T ss_pred hhcCcCCCc-eee-------cccCCCCCCccc
Confidence 368999996 222 358999998764
No 399
>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=42.89 E-value=59 Score=19.04 Aligned_cols=28 Identities=18% Similarity=0.323 Sum_probs=23.1
Q ss_pred cCHHHHHHHHhCCCHHHHHHHHHHHHHHh
Q 025983 166 RTVKEICSVANGATKKEIGRAKEYIVKQL 194 (245)
Q Consensus 166 ~tl~dia~~~~~v~~~~i~~~~~~l~~~l 194 (245)
.+..+||+. +|++..+|.+........|
T Consensus 27 ~~~~~ia~~-~~~s~~~i~~~~~~~~~~l 54 (55)
T cd06171 27 LSYEEIAEI-LGISRSTVRQRLHRALKKL 54 (55)
T ss_pred CCHHHHHHH-HCcCHHHHHHHHHHHHHHc
Confidence 678999995 9999999998888776654
No 400
>PRK14526 adenylate kinase; Provisional
Probab=42.88 E-value=17 Score=30.04 Aligned_cols=29 Identities=17% Similarity=0.431 Sum_probs=18.4
Q ss_pred CCCCCCCCCceeeeCCCCceEccCCcccc
Q 025983 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (245)
Q Consensus 5 ~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~ 33 (245)
.||.||..-++.+++.....+|..||.-+
T Consensus 124 ~~~~~g~~y~~~~~pp~~~~~~~~~~~~l 152 (211)
T PRK14526 124 ICKSCNNIFNIYTLPTKEKGICDVCKGDL 152 (211)
T ss_pred cccccCCccccccCCCCccCcCCCCCCee
Confidence 47777765455666655566777776544
No 401
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=42.55 E-value=62 Score=22.57 Aligned_cols=68 Identities=18% Similarity=0.218 Sum_probs=41.0
Q ss_pred cCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCccC-Cc-cccCCCCHH-----hHHHHHhhhcCCCHHHHHHHHHHHHHhh
Q 025983 166 RTVKEICSVANGATKKEIGRAKEYIVKQLGLETG-QS-VEMGTIHAG-----DFMRRFCSNLGMNNQAVKAAQEAVQKSE 238 (245)
Q Consensus 166 ~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~-~~-~~~~~~~p~-----~~i~r~~~~L~l~~~v~~~A~~i~~~~~ 238 (245)
.++.++|.. +||++.+|+...+ .|+-.. .. -+.-..++. .+|.++.+.+|++-+..+....+.+.+.
T Consensus 2 ~~i~e~A~~-~gvs~~tLr~ye~-----~Gli~p~r~~~g~R~y~~~dv~~l~~i~~L~~d~g~~l~~i~~~l~l~~~~~ 75 (91)
T cd04766 2 YVISVAAEL-SGMHPQTLRLYER-----LGLLSPSRTDGGTRRYSERDIERLRRIQRLTQELGVNLAGVKRILELEEELA 75 (91)
T ss_pred cCHHHHHHH-HCcCHHHHHHHHH-----CCCcCCCcCCCCCeeECHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHH
Confidence 578999995 9999999987743 232100 00 000011222 3566666679999877777766666655
Q ss_pred h
Q 025983 239 E 239 (245)
Q Consensus 239 ~ 239 (245)
.
T Consensus 76 ~ 76 (91)
T cd04766 76 E 76 (91)
T ss_pred H
Confidence 4
No 402
>PRK05638 threonine synthase; Validated
Probab=42.24 E-value=14 Score=34.01 Aligned_cols=25 Identities=28% Similarity=0.741 Sum_probs=17.4
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
.+|+.||.. ++.. -...| .||-.++
T Consensus 2 l~C~~Cg~~----~~~~-~~~~C-~c~~~l~ 26 (442)
T PRK05638 2 MKCPKCGRE----YNSY-IPPFC-ICGELLE 26 (442)
T ss_pred eEeCCCCCC----CCCC-Cceec-CCCCcEE
Confidence 579999973 3322 23889 8997774
No 403
>PF14149 YhfH: YhfH-like protein
Probab=42.13 E-value=4 Score=23.89 Aligned_cols=16 Identities=31% Similarity=0.696 Sum_probs=12.7
Q ss_pred CCceEccCCccccccc
Q 025983 21 AGDTVCSECGLVLESH 36 (245)
Q Consensus 21 ~G~~vC~~CG~V~~e~ 36 (245)
-+...|+.||..++|.
T Consensus 11 Lp~K~C~~CG~~i~EQ 26 (37)
T PF14149_consen 11 LPPKKCTECGKEIEEQ 26 (37)
T ss_pred CCCcccHHHHHHHHHH
Confidence 4567899999998765
No 404
>PRK15320 transcriptional activator SprB; Provisional
Probab=41.81 E-value=49 Score=27.34 Aligned_cols=37 Identities=14% Similarity=0.196 Sum_probs=31.9
Q ss_pred HhCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCc
Q 025983 160 RQEDKPRTVKEICSVANGATKKEIGRAKEYIVKQLGLE 197 (245)
Q Consensus 160 R~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~ 197 (245)
++.-...+.+|||+. ++++.++|.....+|.+.|+.+
T Consensus 174 ~LLAkG~SNKEIAek-L~LS~KTVSTYKnRLLeKLgAk 210 (251)
T PRK15320 174 ILLSSGHPAIELAKK-FGLGTKTVSIYRKKVMYRLGMD 210 (251)
T ss_pred HHHHcCCCHHHHHHH-hccchhhHHHHHHHHHHHcCCC
Confidence 334467889999995 8999999999999999999986
No 405
>PLN02569 threonine synthase
Probab=41.55 E-value=15 Score=34.41 Aligned_cols=26 Identities=12% Similarity=0.120 Sum_probs=20.4
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
..|+.||.. ++...-...| .||-.++
T Consensus 50 l~C~~Cg~~----y~~~~~~~~C-~cgg~l~ 75 (484)
T PLN02569 50 LECPLTGEK----YSLDEVVYRS-KSGGLLD 75 (484)
T ss_pred cEeCCCCCc----CCCccccccC-CCCCeEE
Confidence 579999973 5666677899 8998884
No 406
>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=41.43 E-value=39 Score=23.18 Aligned_cols=33 Identities=12% Similarity=0.112 Sum_probs=26.8
Q ss_pred CCCCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhC
Q 025983 162 EDKPRTVKEICSVANGATKKEIGRAKEYIVKQLG 195 (245)
Q Consensus 162 ~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~ 195 (245)
.+.+.++.++|+. ..+|..++.+..+.+.+.|.
T Consensus 27 ~~~~~s~~~la~~-~~iS~sti~~~i~~l~~~l~ 59 (87)
T PF05043_consen 27 NNEYVSIEDLAEE-LFISRSTIYRDIKKLNKYLK 59 (87)
T ss_dssp H-SEEEHHHHHHH-HT--HHHHHHHHHHHHHHHH
T ss_pred cCCCcCHHHHHHH-HCCCHHHHHHHHHHHHHHHH
Confidence 6788999999995 99999999999999988774
No 407
>PRK13503 transcriptional activator RhaS; Provisional
Probab=41.11 E-value=60 Score=27.27 Aligned_cols=39 Identities=5% Similarity=-0.021 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHH
Q 025983 150 LLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYI 190 (245)
Q Consensus 150 iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l 190 (245)
+-.+.=|+-- .-..++|+.|+|+. +++++..+.+.+++.
T Consensus 173 i~~~~~~I~~-~~~~~~tl~~lA~~-~~lS~~~l~r~Fk~~ 211 (278)
T PRK13503 173 LNQLLAWLED-HFAEEVNWEALADQ-FSLSLRTLHRQLKQQ 211 (278)
T ss_pred HHHHHHHHHH-hhcCCCCHHHHHHH-HCCCHHHHHHHHHHH
Confidence 4444445443 34568999999995 999999999988743
No 408
>smart00351 PAX Paired Box domain.
Probab=41.06 E-value=1.5e+02 Score=22.09 Aligned_cols=60 Identities=18% Similarity=0.100 Sum_probs=34.1
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCC-----CCCHHHH-HHHHHHH-HHHhCCCCcCHHHHHHH
Q 025983 112 IATMSDRLGLVATIKDRANEIYKKVEDQKSSR-----GRNQDAL-LAACLYI-ACRQEDKPRTVKEICSV 174 (245)
Q Consensus 112 I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~-----gr~~~~i-aAA~lY~-acR~~~~~~tl~dia~~ 174 (245)
..++|..|+++...+..-..-| .+.+.+. |+++..+ .....|+ ....++-..|+.|+++.
T Consensus 36 ~~~iA~~~gvs~~tV~kwi~r~---~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~p~~t~~el~~~ 102 (125)
T smart00351 36 PCDISRQLCVSHGCVSKILGRY---YETGSIRPGAIGGSKPKVATPKVVKKIADYKQENPGIFAWEIRDR 102 (125)
T ss_pred HHHHHHHHCcCHHHHHHHHHHH---HHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHCCCCCHHHHHHH
Confidence 6789999999987666544444 3333321 3233222 2222233 24556666889888774
No 409
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=40.98 E-value=20 Score=34.66 Aligned_cols=28 Identities=29% Similarity=0.718 Sum_probs=21.5
Q ss_pred CCCCC--CCCCCceeeeCCCCceEccCCccccc
Q 025983 4 AFCSD--CKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 4 ~~Cp~--Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
..||. |.+. +.+...|.+.|..|+....
T Consensus 475 ~ACp~~~CnKK---V~~~~~g~~~CekC~~~~~ 504 (608)
T TIGR00617 475 RACPSEDCNKK---VVDQGDGTYRCEKCNKNFA 504 (608)
T ss_pred ccCChhhCCCc---cccCCCCCEECCCCCCCCC
Confidence 35987 9873 4466679999999998764
No 410
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=40.90 E-value=51 Score=27.03 Aligned_cols=37 Identities=22% Similarity=0.265 Sum_probs=28.9
Q ss_pred HhCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCc
Q 025983 160 RQEDKPRTVKEICSVANGATKKEIGRAKEYIVKQLGLE 197 (245)
Q Consensus 160 R~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~ 197 (245)
++-....+-+|||+. ++++++|+......|.+.|++.
T Consensus 158 ~lla~G~snkeIA~~-L~iS~~TVk~h~~~i~~KL~v~ 194 (211)
T COG2197 158 RLLAEGLSNKEIAEE-LNLSEKTVKTHVSNILRKLGVR 194 (211)
T ss_pred HHHHCCCCHHHHHHH-HCCCHhHHHHHHHHHHHHcCCC
Confidence 344457788889884 8899999888888888888865
No 411
>PRK11032 hypothetical protein; Provisional
Probab=40.86 E-value=13 Score=29.43 Aligned_cols=15 Identities=33% Similarity=0.738 Sum_probs=12.7
Q ss_pred CCCceEccCCccccc
Q 025983 20 SAGDTVCSECGLVLE 34 (245)
Q Consensus 20 ~~G~~vC~~CG~V~~ 34 (245)
.-|.+||.+||.-+.
T Consensus 121 g~G~LvC~~Cg~~~~ 135 (160)
T PRK11032 121 GLGNLVCEKCHHHLA 135 (160)
T ss_pred ecceEEecCCCCEEE
Confidence 478999999999873
No 412
>PF04079 DUF387: Putative transcriptional regulators (Ypuh-like); InterPro: IPR005234 This family represents ScpB, which along with ScpA (IPR003768 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [, ]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [], where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes []. ; GO: 0051304 chromosome separation; PDB: 1T6S_B 2Z99_A.
Probab=40.85 E-value=83 Score=24.78 Aligned_cols=80 Identities=16% Similarity=0.312 Sum_probs=49.7
Q ss_pred HHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCcc--------CCccc-cCCCCHHhHHHHHhhhc
Q 025983 150 LLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYIVKQLGLET--------GQSVE-MGTIHAGDFMRRFCSNL 220 (245)
Q Consensus 150 iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~--------~~~~~-~~~~~p~~~i~r~~~~L 220 (245)
++=|.||. .+.|+++.+++++ ++ +...+.....+|.+.+.-.. +..+. ....+-..|+.++...
T Consensus 2 ~iEAlLF~----s~~pvs~~~La~~-l~-~~~~v~~~l~~L~~~y~~~~~gl~l~~~~~~y~l~tk~~~~~~v~~~~~~- 74 (159)
T PF04079_consen 2 IIEALLFA----SGEPVSIEELAEI-LG-SEDEVEEALEELQEEYNEEDRGLELVEVGGGYRLQTKPEYAEYVEKLFKK- 74 (159)
T ss_dssp HHHHHHHH-----SS-B-HHHHHHH-CT--HHHHHHHHHHHHHHHHHCT-SEEEEEETTEEEEEE-GGGHHHHHHHHCT-
T ss_pred hhHhhHHH----cCCCCCHHHHHHH-hC-CHHHHHHHHHHHHHHhccCCCCEEEEEECCEEEEEEhHHHHHHHHHHhcc-
Confidence 34567775 4679999999996 89 99999999999998872111 01111 1123456788888877
Q ss_pred CCCHHHHHHHHHHHHH
Q 025983 221 GMNNQAVKAAQEAVQK 236 (245)
Q Consensus 221 ~l~~~v~~~A~~i~~~ 236 (245)
.......+.|.+.+..
T Consensus 75 ~~~~~LS~aalEtLAi 90 (159)
T PF04079_consen 75 PKPPKLSQAALETLAI 90 (159)
T ss_dssp CCCHHHHHHHHHHHHH
T ss_pred CccCCCCHHHHHHHHH
Confidence 3356666666655543
No 413
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=40.71 E-value=30 Score=29.16 Aligned_cols=27 Identities=7% Similarity=0.059 Sum_probs=20.1
Q ss_pred CcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 165 PRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 165 ~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
..+.+|||.. +|+++.++...+.+-++
T Consensus 177 g~S~~EIA~~-Lgis~~TVk~rl~RAr~ 203 (244)
T TIGR03001 177 GLSMDRIGAM-YQVHRSTVSRWVAQARE 203 (244)
T ss_pred CCCHHHHHHH-HCcCHHHHHHHHHHHHH
Confidence 4679999995 99999888755544443
No 414
>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=40.64 E-value=40 Score=19.74 Aligned_cols=22 Identities=27% Similarity=0.259 Sum_probs=18.2
Q ss_pred cCHHHHHHHHhCCCHHHHHHHHH
Q 025983 166 RTVKEICSVANGATKKEIGRAKE 188 (245)
Q Consensus 166 ~tl~dia~~~~~v~~~~i~~~~~ 188 (245)
.|+.|+|+. +|++..+|.+..+
T Consensus 2 lt~~e~a~~-lgis~~ti~~~~~ 23 (49)
T TIGR01764 2 LTVEEAAEY-LGVSKDTVYRLIH 23 (49)
T ss_pred CCHHHHHHH-HCCCHHHHHHHHH
Confidence 478999996 9999999977654
No 415
>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=40.60 E-value=38 Score=20.15 Aligned_cols=21 Identities=14% Similarity=0.332 Sum_probs=17.6
Q ss_pred CHHHHHHHHhCCCHHHHHHHHH
Q 025983 167 TVKEICSVANGATKKEIGRAKE 188 (245)
Q Consensus 167 tl~dia~~~~~v~~~~i~~~~~ 188 (245)
++.|+|+. +||+..+|+...+
T Consensus 2 ~~~e~a~~-~gv~~~tlr~~~~ 22 (49)
T cd04761 2 TIGELAKL-TGVSPSTLRYYER 22 (49)
T ss_pred cHHHHHHH-HCcCHHHHHHHHH
Confidence 67899995 9999999987643
No 416
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=40.57 E-value=1.3e+02 Score=26.22 Aligned_cols=40 Identities=15% Similarity=0.136 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHH
Q 025983 149 ALLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYI 190 (245)
Q Consensus 149 ~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l 190 (245)
.+..+.-|+-- ....++++.++|+. +++++.++.+.+++.
T Consensus 219 ~~~~~~~~i~~-~~~~~~sl~~lA~~-~~~S~~~l~r~fk~~ 258 (322)
T PRK09393 219 RLGPLIDWMRA-HLAEPHTVASLAAR-AAMSPRTFLRRFEAA 258 (322)
T ss_pred HHHHHHHHHHh-ccCCCCCHHHHHHH-HCcCHHHHHHHHHHH
Confidence 34444555543 34568999999995 999999999887754
No 417
>smart00400 ZnF_CHCC zinc finger.
Probab=40.56 E-value=36 Score=21.39 Aligned_cols=27 Identities=15% Similarity=0.305 Sum_probs=21.2
Q ss_pred CCCCCCCCC-CceeeeCCCCceEccCCc
Q 025983 4 AFCSDCKKH-TEVVFDHSAGDTVCSECG 30 (245)
Q Consensus 4 ~~Cp~Cg~~-~~iv~d~~~G~~vC~~CG 30 (245)
..||-+... ++...++..+...|-.||
T Consensus 3 ~~cPfh~d~~pSf~v~~~kn~~~Cf~cg 30 (55)
T smart00400 3 GLCPFHGEKTPSFSVSPDKQFFHCFGCG 30 (55)
T ss_pred ccCcCCCCCCCCEEEECCCCEEEEeCCC
Confidence 359998853 567778888889999997
No 418
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=40.47 E-value=1.2e+02 Score=20.65 Aligned_cols=28 Identities=18% Similarity=0.144 Sum_probs=25.4
Q ss_pred CCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 164 KPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 164 ~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
.|.++.||++. ++++..++.+....|.+
T Consensus 19 ~~~t~~~ia~~-l~i~~~tv~r~l~~L~~ 46 (91)
T smart00346 19 GGLTLAELAER-LGLSKSTAHRLLNTLQE 46 (91)
T ss_pred CCcCHHHHHHH-hCCCHHHHHHHHHHHHH
Confidence 48999999995 99999999999999876
No 419
>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=40.31 E-value=67 Score=22.64 Aligned_cols=31 Identities=19% Similarity=0.269 Sum_probs=26.8
Q ss_pred hCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 161 QEDKPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 161 ~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
+.....|.++|+.. +|+|.-+|.|.-+.|..
T Consensus 45 lL~~g~syreIa~~-tgvS~aTItRvsr~Lk~ 75 (87)
T PF01371_consen 45 LLDEGKSYREIAEE-TGVSIATITRVSRCLKY 75 (87)
T ss_dssp HHHTTSSHHHHHHH-HTSTHHHHHHHHHHHHH
T ss_pred HHHCCCCHHHHHHH-hCCCHHHHHHHHHHHHc
Confidence 66677899999995 99999999999888764
No 420
>PRK08173 DNA topoisomerase III; Validated
Probab=40.09 E-value=18 Score=36.49 Aligned_cols=27 Identities=19% Similarity=0.561 Sum_probs=19.0
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
..||.||+. ++ ...+.+.|++|+..+.
T Consensus 625 ~~CP~Cg~~--~~--~~~~~~~Cs~C~f~~~ 651 (862)
T PRK08173 625 TPCPNCGGV--VK--ENYRRFACTKCDFSIS 651 (862)
T ss_pred ccCCccccc--cc--ccCceeEcCCCCcccc
Confidence 469999973 32 1233499999998873
No 421
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=40.05 E-value=69 Score=25.07 Aligned_cols=71 Identities=17% Similarity=0.237 Sum_probs=45.6
Q ss_pred HHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCcc---CCccccC---------CCCHHhHHHHHhh-hc
Q 025983 154 CLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYIVKQLGLET---GQSVEMG---------TIHAGDFMRRFCS-NL 220 (245)
Q Consensus 154 ~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~---~~~~~~~---------~~~p~~~i~r~~~-~L 220 (245)
+||..-+ .+.+...+|||+. ++|+..++....++|.+ .|+-. ...+.+. ...-...+.+|.. .|
T Consensus 14 ~Iy~l~~-~~~~~~~~diA~~-L~Vsp~sVt~ml~rL~~-~GlV~~~~y~gi~LT~~G~~~a~~~~r~hrlle~fL~~~l 90 (154)
T COG1321 14 TIYELLE-EKGFARTKDIAER-LKVSPPSVTEMLKRLER-LGLVEYEPYGGVTLTEKGREKAKELLRKHRLLERFLVDVL 90 (154)
T ss_pred HHHHHHh-ccCcccHHHHHHH-hCCCcHHHHHHHHHHHH-CCCeEEecCCCeEEChhhHHHHHHHHHHHHHHHHHHHHHh
Confidence 5665655 7778889999995 99999999999999975 22211 1111111 1123345666766 59
Q ss_pred CCCHHHH
Q 025983 221 GMNNQAV 227 (245)
Q Consensus 221 ~l~~~v~ 227 (245)
|++.+..
T Consensus 91 g~~~~~~ 97 (154)
T COG1321 91 GLDWEEA 97 (154)
T ss_pred CCCHHHH
Confidence 9986644
No 422
>PRK09430 djlA Dna-J like membrane chaperone protein; Provisional
Probab=40.04 E-value=2.4e+02 Score=24.15 Aligned_cols=101 Identities=17% Similarity=0.267 Sum_probs=0.0
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhCCCCcCHHHHHHHHhCCC----HHHHH
Q 025983 109 FKTIATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKEICSVANGAT----KKEIG 184 (245)
Q Consensus 109 ~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY~acR~~~~~~tl~dia~~~~~v~----~~~i~ 184 (245)
...|.++|..|+++..-.+.....+.......--.+... | +....+.++.+.-.+ ++++ ..+|.
T Consensus 151 ~~~L~~Ia~~Lgis~~df~~~~~~~~~~~~f~~~~~~~~--------~---~~~~~~~~~~~ay~v-Lgv~~~as~~eIk 218 (267)
T PRK09430 151 RQVLYVIAEELGFSRFQFDQLLRMMQAGFRFQQQQGGGG--------Y---QQAQRGPTLEDAYKV-LGVSESDDDQEIK 218 (267)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcccccccc--------c---ccccCCCcHHhHHHH-cCCCCCCCHHHHH
Q ss_pred HHHHHHHHHhCCccCCccccCCCCHHhHHHHHhhhcCCCHHHHHHHHHHHHHhhh
Q 025983 185 RAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMNNQAVKAAQEAVQKSEE 239 (245)
Q Consensus 185 ~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~ 239 (245)
++|++|.+... |..+. .-+++++....|.+-.+.+.+
T Consensus 219 ~aYr~L~~~~H-------------PDk~~-----~~g~~~~~~~~a~ek~~~I~~ 255 (267)
T PRK09430 219 RAYRKLMSEHH-------------PDKLV-----AKGLPPEMMEMAKEKAQEIQA 255 (267)
T ss_pred HHHHHHHHHhC-------------cCCCC-----CCCCChhhHHHHHHHHHHHHH
No 423
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=40.00 E-value=19 Score=34.14 Aligned_cols=31 Identities=23% Similarity=0.340 Sum_probs=27.2
Q ss_pred CCCCceEccCCcccc--cccccccCcccccccC
Q 025983 19 HSAGDTVCSECGLVL--ESHSIDETSEWRTFAN 49 (245)
Q Consensus 19 ~~~G~~vC~~CG~V~--~e~~id~~~ewr~f~~ 49 (245)
.+.|.++|..||.-| .+.-+|.|.-|.+|.+
T Consensus 414 ~~~G~y~c~~c~~pLf~s~~Kf~sg~GWPsF~~ 446 (521)
T PRK14018 414 FKPGIYVDVVSGEPLFSSADKYDSGCGWPSFTR 446 (521)
T ss_pred CCCEEEEecCCCCccccCcccccCCCCCcccCc
Confidence 589999999999988 5567899999999985
No 424
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=39.93 E-value=21 Score=27.12 Aligned_cols=29 Identities=21% Similarity=0.517 Sum_probs=21.6
Q ss_pred CCCCCCCCCceeeeCCCCceEccCCcccc
Q 025983 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (245)
Q Consensus 5 ~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~ 33 (245)
.|-.||..+.+-++...-...|..|+.+=
T Consensus 2 ~C~fC~~~s~~~~~~~~~~w~C~~C~q~N 30 (131)
T PF09779_consen 2 NCWFCGQNSKVPYDNRNSNWTCPHCEQYN 30 (131)
T ss_pred eeccCCCCCCCCCCCCCCeeECCCCCCcc
Confidence 59999986555555545569999999874
No 425
>PRK04023 DNA polymerase II large subunit; Validated
Probab=39.86 E-value=18 Score=36.66 Aligned_cols=12 Identities=33% Similarity=0.830 Sum_probs=6.3
Q ss_pred ceEccCCccccc
Q 025983 23 DTVCSECGLVLE 34 (245)
Q Consensus 23 ~~vC~~CG~V~~ 34 (245)
...|..||....
T Consensus 651 i~fCP~CG~~~~ 662 (1121)
T PRK04023 651 VYRCPRCGIEVE 662 (1121)
T ss_pred ceeCccccCcCC
Confidence 345555555543
No 426
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=39.60 E-value=64 Score=25.26 Aligned_cols=31 Identities=13% Similarity=0.055 Sum_probs=27.3
Q ss_pred hCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 161 QEDKPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 161 ~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
+.+-..+..|||+. +|++..++.+.+++|.+
T Consensus 24 q~d~R~s~~eiA~~-lglS~~tv~~Ri~rL~~ 54 (164)
T PRK11169 24 QKDGRISNVELSKR-VGLSPTPCLERVRRLER 54 (164)
T ss_pred ccCCCCCHHHHHHH-HCcCHHHHHHHHHHHHH
Confidence 46667889999995 99999999999999986
No 427
>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=39.35 E-value=64 Score=25.65 Aligned_cols=29 Identities=24% Similarity=0.115 Sum_probs=22.4
Q ss_pred CcCHHHHHHHHhCCCHHHHHHHHHHHHHHh
Q 025983 165 PRTVKEICSVANGATKKEIGRAKEYIVKQL 194 (245)
Q Consensus 165 ~~tl~dia~~~~~v~~~~i~~~~~~l~~~l 194 (245)
..+.+|||.. +|+++.++...+.+-++.|
T Consensus 147 g~s~~EIA~~-lgis~~tVk~~l~Rar~~L 175 (193)
T TIGR02947 147 GFAYKEIAEI-MGTPIGTVMSRLHRGRKQL 175 (193)
T ss_pred CCCHHHHHHH-HCCCHHHHHHHHHHHHHHH
Confidence 4679999995 9999998887666555544
No 428
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=39.17 E-value=16 Score=28.46 Aligned_cols=26 Identities=12% Similarity=0.173 Sum_probs=17.3
Q ss_pred CCCHHHHHHHHHHHHHHhhCCCCCCC
Q 025983 120 GLVATIKDRANEIYKKVEDQKSSRGR 145 (245)
Q Consensus 120 ~Lp~~v~~~A~~i~~~~~~~~~~~gr 145 (245)
.+.+...++|..|..--.+...++|.
T Consensus 96 ~VG~~FAeEAR~iHyGea~~R~I~G~ 121 (148)
T PF06676_consen 96 DVGDRFAEEARKIHYGEAEERGIYGE 121 (148)
T ss_pred chhHHHHHHHHHHHcCCCccccCcCc
Confidence 45567788888877655555556665
No 429
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=39.11 E-value=16 Score=22.94 Aligned_cols=14 Identities=29% Similarity=0.707 Sum_probs=12.1
Q ss_pred CCceEccCCccccc
Q 025983 21 AGDTVCSECGLVLE 34 (245)
Q Consensus 21 ~G~~vC~~CG~V~~ 34 (245)
+|.++|..||.-+-
T Consensus 3 ~g~l~C~~CG~~m~ 16 (58)
T PF13408_consen 3 SGLLRCGHCGSKMT 16 (58)
T ss_pred CCcEEcccCCcEeE
Confidence 68999999998874
No 430
>PF02787 CPSase_L_D3: Carbamoyl-phosphate synthetase large chain, oligomerisation domain; InterPro: IPR005480 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the oligomerisation domain found in the large subunit of carbamoyl phosphate synthases as well as in certain other carboxy phsophate domain-containing enzymes.; GO: 0006807 nitrogen compound metabolic process; PDB: 1M6V_C 1CS0_C 1C30_E 1C3O_G 1BXR_A 1T36_E 1A9X_A 1KEE_G 1CE8_A 1JDB_H ....
Probab=38.82 E-value=1.5e+02 Score=22.24 Aligned_cols=56 Identities=14% Similarity=0.209 Sum_probs=26.9
Q ss_pred CcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCccCCccccCCCCHHhHHHHHhhhcCCCHHHH
Q 025983 165 PRTVKEICSVANGATKKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMNNQAV 227 (245)
Q Consensus 165 ~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~ 227 (245)
..++.+|.++ ++|+..=|.+....+.-.-.+... ....+++ +.+-+.++||++...
T Consensus 23 G~sveeI~e~-T~ID~wFL~~i~~Iv~~e~~L~~~----~~~~~~~--~L~~aK~~GFsD~~I 78 (123)
T PF02787_consen 23 GYSVEEIHEL-TKIDPWFLEQIKNIVDMEKELKEY----LNELDPE--LLRKAKRLGFSDRQI 78 (123)
T ss_dssp TB-HHHHHHH-H---HHHHHHHHHHHHHHHHHHHH----GGG--HH--HHHHHHHTT--HHHH
T ss_pred CCCHHHHHHH-HCccHHHHHHHHHHHHHHHHHHHh----hccchHH--HHHHHHHcCCCHHHH
Confidence 5689999995 899987666554333221111100 1123444 557889999997643
No 431
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=38.65 E-value=36 Score=22.31 Aligned_cols=43 Identities=14% Similarity=0.244 Sum_probs=25.8
Q ss_pred CHHHHHHHHhCCCHHHHHHHHHHHHHHhCCccCCccccCCCCHHhHHHHHhhhcCCCHH
Q 025983 167 TVKEICSVANGATKKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMNNQ 225 (245)
Q Consensus 167 tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~ 225 (245)
+.+|+|+ .++|+..+|.+.++. -+ .-|.+++.+++..++++-+
T Consensus 14 ~~~~lA~-~lgis~st~s~~~~~----r~-----------~~P~~~l~~ia~~~gvsl~ 56 (66)
T PF07022_consen 14 SDKELAE-RLGISKSTLSNNWKK----RG-----------SIPAEWLIKIALETGVSLD 56 (66)
T ss_dssp SCHHHHC-CTT--HHHHH-HHHH----SS-----------S--HHHHHHHHHHH---HH
T ss_pred CHHHHHH-HhCcCHHHhhHHHHh----CC-----------CCCHHHHHHHHHHHCcCHH
Confidence 5679999 499999999843321 11 2368999999999998865
No 432
>COG3388 Predicted transcriptional regulator [Transcription]
Probab=38.58 E-value=85 Score=22.51 Aligned_cols=74 Identities=9% Similarity=0.172 Sum_probs=45.8
Q ss_pred hCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCccCCccccCCCCHHhHHHHHhhhcCCCHHHHHHHHHHHHHhh
Q 025983 161 QEDKPRTVKEICSVANGATKKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMNNQAVKAAQEAVQKSE 238 (245)
Q Consensus 161 ~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~ 238 (245)
.+..|+-+..++++ +|.....++-..+-|-+.-=+...+...++..+..+|+..+..+| .++...+..|.+..+
T Consensus 24 ~eeqPiGI~klS~~-TGmp~HKVRYSLRVLEq~~iI~PS~~GAi~td~~~e~ie~i~~dl---~ei~e~~~~i~e~~~ 97 (101)
T COG3388 24 LEEQPIGIIKLSDE-TGMPEHKVRYSLRVLEQENIISPSRQGAILTDDFPEFIEEIIGDL---SEINEEAENIEEDVA 97 (101)
T ss_pred HHhCCceeEeechh-cCCchhhhhhhhhhhhhcCccCccccCCccCccHHHHHHHHHHHH---HHHHHHHHHHHHHHH
Confidence 46688888889996 899999998877766543222222222244445567777777766 445555555544443
No 433
>PF12728 HTH_17: Helix-turn-helix domain
Probab=38.56 E-value=43 Score=20.33 Aligned_cols=22 Identities=27% Similarity=0.270 Sum_probs=17.8
Q ss_pred cCHHHHHHHHhCCCHHHHHHHHH
Q 025983 166 RTVKEICSVANGATKKEIGRAKE 188 (245)
Q Consensus 166 ~tl~dia~~~~~v~~~~i~~~~~ 188 (245)
.|..|+|+. ++++..+|.+..+
T Consensus 2 lt~~e~a~~-l~is~~tv~~~~~ 23 (51)
T PF12728_consen 2 LTVKEAAEL-LGISRSTVYRWIR 23 (51)
T ss_pred CCHHHHHHH-HCcCHHHHHHHHH
Confidence 478999995 9999999876543
No 434
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=38.55 E-value=11 Score=33.71 Aligned_cols=13 Identities=15% Similarity=0.644 Sum_probs=9.5
Q ss_pred CCCCCCCCCCCCC
Q 025983 1 MTDAFCSDCKKHT 13 (245)
Q Consensus 1 ~~~~~Cp~Cg~~~ 13 (245)
|.++.|+.||.+.
T Consensus 4 ~~~~~C~~CGr~~ 16 (355)
T COG1499 4 ASTILCVRCGRSV 16 (355)
T ss_pred CcccEeccCCCcC
Confidence 3457899999853
No 435
>PRK13500 transcriptional activator RhaR; Provisional
Probab=38.49 E-value=2.6e+02 Score=24.16 Aligned_cols=40 Identities=10% Similarity=0.144 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHH
Q 025983 149 ALLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYI 190 (245)
Q Consensus 149 ~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l 190 (245)
.+...+-|+-- ....++++.++|+. +++++..+.+.+++.
T Consensus 207 ~l~~i~~yI~~-~~~e~isl~~lA~~-~~iS~~~L~r~FK~~ 246 (312)
T PRK13500 207 LLDKLITRLAA-SLKSPFALDKFCDE-ASCSERVLRQQFRQQ 246 (312)
T ss_pred HHHHHHHHHHH-cccCCCCHHHHHHH-HCcCHHHHHHHHHHH
Confidence 34444445443 34567999999995 999999999998854
No 436
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=38.43 E-value=61 Score=27.29 Aligned_cols=30 Identities=23% Similarity=0.306 Sum_probs=23.9
Q ss_pred HHHhCCCCcCHHHHHHHHhCCCHHHHHHHHH
Q 025983 158 ACRQEDKPRTVKEICSVANGATKKEIGRAKE 188 (245)
Q Consensus 158 acR~~~~~~tl~dia~~~~~v~~~~i~~~~~ 188 (245)
..|..+.-.|.+|++++ +|++...|+|..+
T Consensus 16 ~lr~lk~~~ty~el~~~-~g~p~~~l~RYv~ 45 (238)
T PRK08558 16 VLRSLKKTYTYEELSSI-TGLPESVLNRYVN 45 (238)
T ss_pred HHHHHhcccCHHHHHHH-HCCCHHHHHHHHc
Confidence 34666667899999995 9999999988754
No 437
>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=38.41 E-value=38 Score=19.72 Aligned_cols=20 Identities=15% Similarity=0.331 Sum_probs=15.3
Q ss_pred CHHHHHHHHhCCCHHHHHHHH
Q 025983 167 TVKEICSVANGATKKEIGRAK 187 (245)
Q Consensus 167 tl~dia~~~~~v~~~~i~~~~ 187 (245)
++.|+|+. +||+..+|+..-
T Consensus 1 ti~e~A~~-~gvs~~tlR~ye 20 (38)
T PF00376_consen 1 TIGEVAKL-LGVSPRTLRYYE 20 (38)
T ss_dssp EHHHHHHH-HTS-HHHHHHHH
T ss_pred CHHHHHHH-HCCCHHHHHHHH
Confidence 46799995 899999997653
No 438
>PF14369 zf-RING_3: zinc-finger
Probab=38.21 E-value=29 Score=19.94 Aligned_cols=27 Identities=22% Similarity=0.660 Sum_probs=15.7
Q ss_pred CCCCCCCCCCCceeee-CCCCceEccCCcc
Q 025983 3 DAFCSDCKKHTEVVFD-HSAGDTVCSECGL 31 (245)
Q Consensus 3 ~~~Cp~Cg~~~~iv~d-~~~G~~vC~~CG~ 31 (245)
..+|=.|... |... ..+....|..|+-
T Consensus 2 ~ywCh~C~~~--V~~~~~~~~~~~CP~C~~ 29 (35)
T PF14369_consen 2 RYWCHQCNRF--VRIAPSPDSDVACPRCHG 29 (35)
T ss_pred CEeCccCCCE--eEeCcCCCCCcCCcCCCC
Confidence 3578889863 3222 2334445999973
No 439
>PF09567 RE_MamI: MamI restriction endonuclease; InterPro: IPR019067 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the MamI restriction endonuclease which recognises and cleaves GATNN^NNATC. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=38.10 E-value=13 Score=31.50 Aligned_cols=37 Identities=24% Similarity=0.582 Sum_probs=22.3
Q ss_pred CCCCCCCCCCCceeeeCCCCceEccCCcccccccccccCccccccc
Q 025983 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSIDETSEWRTFA 48 (245)
Q Consensus 3 ~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e~~id~~~ewr~f~ 48 (245)
..+|.+||+. |. .=+.-|.+||.-= -.-++.+-| -|.
T Consensus 82 l~~C~~CGa~---V~---~~e~~Cp~C~Stn--I~r~DdSkW-l~~ 118 (314)
T PF09567_consen 82 LGKCNNCGAN---VS---RLEESCPNCGSTN--IKRKDDSKW-LFG 118 (314)
T ss_pred hhhhccccce---ee---ehhhcCCCCCccc--ccccCCcce-ecc
Confidence 3579999973 21 2367899998642 222334677 454
No 440
>PHA02325 hypothetical protein
Probab=38.05 E-value=18 Score=23.89 Aligned_cols=11 Identities=27% Similarity=0.827 Sum_probs=8.1
Q ss_pred CCCCCCCCCCC
Q 025983 1 MTDAFCSDCKK 11 (245)
Q Consensus 1 ~~~~~Cp~Cg~ 11 (245)
|....||.||+
T Consensus 1 m~~k~CPkC~A 11 (72)
T PHA02325 1 MDTKICPKCGA 11 (72)
T ss_pred CCccccCccCC
Confidence 56677888886
No 441
>TIGR02642 phage_xxxx uncharacterized phage protein. This uncharacterized protein is found in prophage regions of Shewanella oneidensis MR-1, Vibrio vulnificus YJ016, Yersinia pseudotuberculosis IP 32953, and Aeromonas hydrophila ATCC7966. It appears to have regions of sequence similarity to phage lambda antitermination protein Q.
Probab=38.01 E-value=20 Score=29.12 Aligned_cols=23 Identities=17% Similarity=0.548 Sum_probs=14.7
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECG 30 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG 30 (245)
..||.|+....++. +...|..|+
T Consensus 100 ~~C~~C~G~G~~i~----~~~~C~~C~ 122 (186)
T TIGR02642 100 CKCPRCRGTGLIQR----RQRECDTCA 122 (186)
T ss_pred CcCCCCCCeeEEec----CCCCCCCCC
Confidence 67999998433332 125688885
No 442
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=37.93 E-value=1e+02 Score=22.25 Aligned_cols=33 Identities=15% Similarity=0.089 Sum_probs=28.7
Q ss_pred HHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 159 CRQEDKPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 159 cR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
|...+-+.++.+++.. ++++..++.+.++.|.+
T Consensus 37 ~~~~~~~~t~~eL~~~-l~~~~stvs~~i~~Le~ 69 (109)
T TIGR01889 37 LENNEGKLTLKEIIKE-ILIKQSALVKIIKKLSK 69 (109)
T ss_pred hhccCCcCcHHHHHHH-HCCCHHHHHHHHHHHHH
Confidence 4556678999999995 99999999999999875
No 443
>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=37.90 E-value=1.1e+02 Score=19.42 Aligned_cols=30 Identities=13% Similarity=0.352 Sum_probs=26.4
Q ss_pred CHHHHHHHHhCCCHHHHHHHHHHHHHHhCCc
Q 025983 167 TVKEICSVANGATKKEIGRAKEYIVKQLGLE 197 (245)
Q Consensus 167 tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~ 197 (245)
++...|+ .++++...|.+.++.|-+.++.+
T Consensus 15 s~~~AA~-~l~is~~~vs~~i~~LE~~lg~~ 44 (60)
T PF00126_consen 15 SISAAAE-ELGISQSAVSRQIKQLEEELGVP 44 (60)
T ss_dssp SHHHHHH-HCTSSHHHHHHHHHHHHHHHTS-
T ss_pred CHHHHHH-HhhccchHHHHHHHHHHHHhCCe
Confidence 5788888 49999999999999999999975
No 444
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=37.71 E-value=75 Score=26.46 Aligned_cols=61 Identities=20% Similarity=0.263 Sum_probs=44.6
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHHH
Q 025983 112 IATMSDRLGLVATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYIV 191 (245)
Q Consensus 112 I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~ 191 (245)
++...+..++..--..+..+++..|++.+ --.|..|++.+ +++|..+|++-.+.+.
T Consensus 75 ~e~~~~~~~~~elr~~rIvRl~~EAy~Qg-----------------------glLT~~Dla~L-L~~S~~TI~~~i~~yq 130 (220)
T PF07900_consen 75 IEMRNEKYGLSELRKHRIVRLTNEAYDQG-----------------------GLLTQEDLAML-LGISPRTISKDIKEYQ 130 (220)
T ss_pred HHHHHhhcCHHHHHHHHHHHHHHHHHHcC-----------------------CcccHHHHHHH-HCCCHHHHHHHHHHHH
Confidence 44455555665555666677777766543 44688999985 9999999999999999
Q ss_pred HHhCC
Q 025983 192 KQLGL 196 (245)
Q Consensus 192 ~~l~~ 196 (245)
+.-|+
T Consensus 131 ~e~g~ 135 (220)
T PF07900_consen 131 KEHGV 135 (220)
T ss_pred HHcCc
Confidence 87554
No 445
>PRK07591 threonine synthase; Validated
Probab=37.70 E-value=14 Score=33.96 Aligned_cols=26 Identities=31% Similarity=0.574 Sum_probs=19.1
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~ 34 (245)
.+|+.||.. ++...- ..|.+||-.++
T Consensus 19 l~C~~Cg~~----~~~~~~-~~C~~cg~~l~ 44 (421)
T PRK07591 19 LKCRECGAE----YPLGPI-HVCEECFGPLE 44 (421)
T ss_pred EEeCCCCCc----CCCCCC-ccCCCCCCeEE
Confidence 579999973 344333 88999998774
No 446
>PF12085 DUF3562: Protein of unknown function (DUF3562); InterPro: IPR021945 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 62 to 84 amino acids in length. This protein has two completely conserved residues (A and Y) that may be functionally important.
Probab=37.68 E-value=1.2e+02 Score=20.15 Aligned_cols=42 Identities=14% Similarity=0.356 Sum_probs=33.4
Q ss_pred CHHHHHHHHhCCCHHHHHHHHHHHHHHhCCccCCccccCCCCHHhHHHHHhh
Q 025983 167 TVKEICSVANGATKKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCS 218 (245)
Q Consensus 167 tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~ 218 (245)
.++.||+. .+++..++.+.|..-...|.-. ....+||+=|+.
T Consensus 9 ~i~~iA~~-t~~P~e~V~~my~dt~~~l~~~---------ARV~DYl~lfaa 50 (66)
T PF12085_consen 9 VIRSIAEE-TGTPAETVRRMYDDTMRELSSG---------ARVHDYLPLFAA 50 (66)
T ss_pred HHHHHHHH-HCCCHHHHHHHHHHHHHHHHcC---------CchhhhHHHHHH
Confidence 47889995 8999999999999888877533 456789887763
No 447
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=37.68 E-value=11 Score=29.83 Aligned_cols=24 Identities=33% Similarity=0.515 Sum_probs=0.0
Q ss_pred CCcCHHHHHHHHhCCCHHHHHHHHH
Q 025983 164 KPRTVKEICSVANGATKKEIGRAKE 188 (245)
Q Consensus 164 ~~~tl~dia~~~~~v~~~~i~~~~~ 188 (245)
.|.|++|||+ .+|+++.||.|+.+
T Consensus 48 ~PLt~~~iA~-~lgl~~STVSRav~ 71 (160)
T PF04552_consen 48 KPLTMKDIAD-ELGLHESTVSRAVK 71 (160)
T ss_dssp -------------------------
T ss_pred cCCCHHHHHH-HhCCCHhHHHHHHc
Confidence 6899999999 49999999999876
No 448
>PRK00118 putative DNA-binding protein; Validated
Probab=37.64 E-value=65 Score=23.51 Aligned_cols=29 Identities=14% Similarity=0.095 Sum_probs=23.3
Q ss_pred CcCHHHHHHHHhCCCHHHHHHHHHHHHHHh
Q 025983 165 PRTVKEICSVANGATKKEIGRAKEYIVKQL 194 (245)
Q Consensus 165 ~~tl~dia~~~~~v~~~~i~~~~~~l~~~l 194 (245)
..|..|||+. +|++..++.+.+.+..+.+
T Consensus 33 g~S~~EIAe~-lGIS~~TV~r~L~RArkkL 61 (104)
T PRK00118 33 DYSLGEIAEE-FNVSRQAVYDNIKRTEKLL 61 (104)
T ss_pred CCCHHHHHHH-HCcCHHHHHHHHHHHHHHH
Confidence 5678999996 9999999988877665544
No 449
>PF14951 DUF4503: Domain of unknown function (DUF4503)
Probab=37.51 E-value=22 Score=31.77 Aligned_cols=34 Identities=21% Similarity=0.530 Sum_probs=26.7
Q ss_pred CCCCCCCCCceeeeC-CCCceEccCCcccccccccc
Q 025983 5 FCSDCKKHTEVVFDH-SAGDTVCSECGLVLESHSID 39 (245)
Q Consensus 5 ~Cp~Cg~~~~iv~d~-~~G~~vC~~CG~V~~e~~id 39 (245)
.|..||+ +.+...+ ++|...|.+|-.|+.+..+-
T Consensus 276 vCd~CGn-~rLe~~pe~rg~~~C~~Cs~~V~sP~~r 310 (389)
T PF14951_consen 276 VCDRCGN-GRLEQSPEDRGAFSCGDCSRVVTSPVLR 310 (389)
T ss_pred cccccCC-ccceeCccCCCceeccchhhhccCccee
Confidence 5999998 6777654 56779999999999765543
No 450
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=37.43 E-value=21 Score=28.03 Aligned_cols=26 Identities=27% Similarity=0.704 Sum_probs=15.8
Q ss_pred CCCCCCCCCceeeeCCCCceEccCCcccccccccc
Q 025983 5 FCSDCKKHTEVVFDHSAGDTVCSECGLVLESHSID 39 (245)
Q Consensus 5 ~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~~e~~id 39 (245)
.|..||+. .| ..|.+|+.=+.-....
T Consensus 30 fC~kCG~~-tI--------~~Cp~C~~~IrG~y~v 55 (158)
T PF10083_consen 30 FCSKCGAK-TI--------TSCPNCSTPIRGDYHV 55 (158)
T ss_pred HHHHhhHH-HH--------HHCcCCCCCCCCceec
Confidence 57778863 22 3588888777544333
No 451
>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=37.12 E-value=93 Score=18.56 Aligned_cols=34 Identities=15% Similarity=0.200 Sum_probs=24.0
Q ss_pred HHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHH
Q 025983 154 CLYIACRQEDKPRTVKEICSVANGATKKEIGRAKE 188 (245)
Q Consensus 154 ~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~ 188 (245)
++-+.-+.-=...|+.+|++ .+++++..|-+.|.
T Consensus 5 a~~l~~~~G~~~~s~~~Ia~-~~gvs~~~~y~~f~ 38 (47)
T PF00440_consen 5 ALELFAEKGYEAVSIRDIAR-RAGVSKGSFYRYFP 38 (47)
T ss_dssp HHHHHHHHHTTTSSHHHHHH-HHTSCHHHHHHHCS
T ss_pred HHHHHHHhCHHhCCHHHHHH-HHccchhhHHHHcC
Confidence 33333343345689999999 48999999877654
No 452
>PF05066 HARE-HTH: HB1, ASXL, restriction endonuclease HTH domain; InterPro: IPR007759 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. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling []. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich C-terminal region [].; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent; PDB: 2KRC_A.
Probab=37.10 E-value=32 Score=22.86 Aligned_cols=31 Identities=26% Similarity=0.566 Sum_probs=22.8
Q ss_pred HHHHHHHhhCCCCC--CCCHHHHHHHHHHHHHH
Q 025983 130 NEIYKKVEDQKSSR--GRNQDALLAACLYIACR 160 (245)
Q Consensus 130 ~~i~~~~~~~~~~~--gr~~~~iaAA~lY~acR 160 (245)
.+|++.+.+.+... |+.|....++.+|--++
T Consensus 21 ~eI~~~i~~~~~~~~~~k~p~~~i~a~ly~~~~ 53 (72)
T PF05066_consen 21 KEIWEEIQERGLYKKSGKTPEATIAAQLYTDIK 53 (72)
T ss_dssp HHHHHHHHHHHTS---GGGGGHHHH-HHHHHHH
T ss_pred HHHHHHHHHhCCCCcccCCHHHHHHHHHHHHcc
Confidence 44666666666666 88999999999998887
No 453
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=37.07 E-value=61 Score=27.20 Aligned_cols=33 Identities=12% Similarity=0.208 Sum_probs=28.7
Q ss_pred CCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCc
Q 025983 164 KPRTVKEICSVANGATKKEIGRAKEYIVKQLGLE 197 (245)
Q Consensus 164 ~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~ 197 (245)
...|-.|||.+ +++++.++....+.+.+.|+..
T Consensus 193 ~G~t~~eIa~~-l~is~~TV~~h~~~~~~KL~~~ 225 (240)
T PRK10188 193 EGKTSAEIAMI-LSISENTVNFHQKNMQKKFNAP 225 (240)
T ss_pred cCCCHHHHHHH-hCCCHHHHHHHHHHHHHHhCCC
Confidence 56889999996 8999999999999999998864
No 454
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=37.00 E-value=21 Score=21.40 Aligned_cols=8 Identities=25% Similarity=0.829 Sum_probs=5.9
Q ss_pred CCCCCCCC
Q 025983 4 AFCSDCKK 11 (245)
Q Consensus 4 ~~Cp~Cg~ 11 (245)
..||+||+
T Consensus 3 ~~Cp~Cg~ 10 (47)
T PF14690_consen 3 PRCPHCGS 10 (47)
T ss_pred ccCCCcCC
Confidence 46888886
No 455
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=36.91 E-value=15 Score=37.05 Aligned_cols=23 Identities=26% Similarity=0.460 Sum_probs=17.3
Q ss_pred CCCCCCCCCCCceeeeCCCCceEccCCcccc
Q 025983 3 DAFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (245)
Q Consensus 3 ~~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~ 33 (245)
..+||.||.. + =...|..||.-.
T Consensus 625 ~RKCPkCG~y-T-------lk~rCP~CG~~T 647 (1095)
T TIGR00354 625 IRKCPQCGKE-S-------FWLKCPVCGELT 647 (1095)
T ss_pred EEECCCCCcc-c-------ccccCCCCCCcc
Confidence 3689999973 2 267899999764
No 456
>PRK15340 transcriptional regulator InvF; Provisional
Probab=36.90 E-value=1.4e+02 Score=24.87 Aligned_cols=55 Identities=13% Similarity=0.093 Sum_probs=34.6
Q ss_pred CHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHH
Q 025983 122 VATIKDRANEIYKKVEDQKSSRGRNQDALLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYI 190 (245)
Q Consensus 122 p~~v~~~A~~i~~~~~~~~~~~gr~~~~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l 190 (245)
|+...+.+..+.++...-+ ..-|+ ......+.++.++|+. +|+++..+.+.|++.
T Consensus 95 ~d~~~~~~~~~~r~~e~y~------------l~~~L-l~~~~~~~sleeLA~~-~gvS~r~f~RlFk~~ 149 (216)
T PRK15340 95 PSPAFNKVLALLRKSESYW------------LVGYL-LAQSTSGNTMRMLGED-YGVSYTHFRRLCSRA 149 (216)
T ss_pred CChhHHHHHHHHHHHHHHH------------HHHHH-HhCccCCCCHHHHHHH-HCcCHHHHHHHHHHH
Confidence 5567777777777653211 11222 2333456788888885 888888888877643
No 457
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=36.85 E-value=60 Score=26.15 Aligned_cols=32 Identities=16% Similarity=0.250 Sum_probs=28.5
Q ss_pred HhCCCCcCHHHHHHHHhCCC-HHHHHHHHHHHHH
Q 025983 160 RQEDKPRTVKEICSVANGAT-KKEIGRAKEYIVK 192 (245)
Q Consensus 160 R~~~~~~tl~dia~~~~~v~-~~~i~~~~~~l~~ 192 (245)
+..+.|.+++|||+ .++++ ..++.+.++.|.+
T Consensus 20 ~~~~~~~~~~ela~-~~~~~s~~tv~~~l~~L~~ 52 (199)
T TIGR00498 20 ESTGYPPSIREIAR-AVGLRSPSAAEEHLKALER 52 (199)
T ss_pred HhcCCCCcHHHHHH-HhCCCChHHHHHHHHHHHH
Confidence 56789999999999 59998 9999999998875
No 458
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=36.85 E-value=8.6 Score=30.90 Aligned_cols=30 Identities=30% Similarity=0.649 Sum_probs=20.5
Q ss_pred CCCCCCCCCCceeeeC-CCCceEccCCcccccc
Q 025983 4 AFCSDCKKHTEVVFDH-SAGDTVCSECGLVLES 35 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~-~~G~~vC~~CG~V~~e 35 (245)
..||.|... .-+|. -.-+..|..||.++++
T Consensus 114 y~C~~~~~r--~sfdeA~~~~F~Cp~Cg~~L~~ 144 (176)
T COG1675 114 YVCPNCHVK--YSFDEAMELGFTCPKCGEDLEE 144 (176)
T ss_pred eeCCCCCCc--ccHHHHHHhCCCCCCCCchhhh
Confidence 469988863 34453 2334889999999964
No 459
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=36.82 E-value=1.3e+02 Score=24.44 Aligned_cols=42 Identities=24% Similarity=0.471 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHHhCCCC-cCHHHHHHHHhCCCH-HHHHHHHHHHHHHh
Q 025983 148 DALLAACLYIACRQEDKP-RTVKEICSVANGATK-KEIGRAKEYIVKQL 194 (245)
Q Consensus 148 ~~iaAA~lY~acR~~~~~-~tl~dia~~~~~v~~-~~i~~~~~~l~~~l 194 (245)
..++=|+||++ +.| +++.+++.+ ++++. ..+......|.+..
T Consensus 3 ~~~iEAlLF~s----g~pgls~~~La~i-l~~~~~~~~~~~l~~l~~~~ 46 (186)
T TIGR00281 3 KAIIEALLFVS----GEPGVTLAELVRI-LGKEKAEKLNAIMELLEDYL 46 (186)
T ss_pred HHHHHHHHHHc----CCCCCCHHHHHHH-hCCCchHHHHHHHHHHHHHH
Confidence 45677888876 788 999999996 88884 46666666665554
No 460
>PHA02591 hypothetical protein; Provisional
Probab=36.79 E-value=69 Score=22.13 Aligned_cols=31 Identities=26% Similarity=0.320 Sum_probs=24.3
Q ss_pred HHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHH
Q 025983 157 IACRQEDKPRTVKEICSVANGATKKEIGRAKE 188 (245)
Q Consensus 157 ~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~ 188 (245)
+|-++.....|+.+||.. +|++..++++..+
T Consensus 51 vA~eL~eqGlSqeqIA~~-LGVsqetVrKYL~ 81 (83)
T PHA02591 51 VTHELARKGFTVEKIASL-LGVSVRKVRRYLE 81 (83)
T ss_pred HHHHHHHcCCCHHHHHHH-hCCCHHHHHHHHh
Confidence 344566677899999995 9999999987654
No 461
>KOG1070 consensus rRNA processing protein Rrp5 [RNA processing and modification]
Probab=36.63 E-value=4.9e+02 Score=28.21 Aligned_cols=33 Identities=18% Similarity=0.127 Sum_probs=27.1
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCC
Q 025983 108 AFKTIATMSDRLGLVATIKDRANEIYKKVEDQKSS 142 (245)
Q Consensus 108 ~~~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~~~~ 142 (245)
++-+|+-|+-.|.+++ ++.|..++.+|...--+
T Consensus 1458 Si~WI~YMaf~LelsE--iekAR~iaerAL~tIN~ 1490 (1710)
T KOG1070|consen 1458 SILWIRYMAFHLELSE--IEKARKIAERALKTINF 1490 (1710)
T ss_pred chHHHHHHHHHhhhhh--hHHHHHHHHHHhhhCCc
Confidence 5779999999999986 88999999998765433
No 462
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=36.37 E-value=1.2e+02 Score=19.62 Aligned_cols=39 Identities=18% Similarity=0.204 Sum_probs=25.6
Q ss_pred HHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 152 AACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 152 AA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
++.|+-..-..| +.|+.+|.. ..+++.+.++++.-.|.+
T Consensus 15 ~~~V~~~Ll~~G-~ltl~~i~~-~t~l~~~~Vk~~L~~LiQ 53 (62)
T PF08221_consen 15 VAKVGEVLLSRG-RLTLREIVR-RTGLSPKQVKKALVVLIQ 53 (62)
T ss_dssp HHHHHHHHHHC--SEEHHHHHH-HHT--HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHcC-CcCHHHHHH-HhCCCHHHHHHHHHHHHH
Confidence 333443333344 778999999 489999999999887765
No 463
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=36.35 E-value=1.3e+02 Score=26.67 Aligned_cols=67 Identities=18% Similarity=0.181 Sum_probs=42.4
Q ss_pred HHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCccCCccccCCCCHHhHHHHHhhhcCCC
Q 025983 149 ALLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMN 223 (245)
Q Consensus 149 ~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~ 223 (245)
..-+|-+|+. .+.|..|||+. +|++..+++|...+-++ -|+-.+ .+..+...-.++=.++-++++|.
T Consensus 15 ~~~~A~lYY~-----~gltQ~eIA~~-LgiSR~~v~rlL~~Ar~-~GiV~I-~i~~~~~~~~~Le~~L~~~fgL~ 81 (321)
T COG2390 15 LARAAWLYYV-----EGLTQSEIAER-LGISRATVSRLLAKARE-EGIVKI-SINSPVEGCLELEQQLKERFGLK 81 (321)
T ss_pred HHHHHHHHHh-----cCCCHHHHHHH-hCCCHHHHHHHHHHHHH-CCeEEE-EeCCCCcchHHHHHHHHHhcCCC
Confidence 3445556654 78999999995 99999999998887654 332111 11122222223446677888885
No 464
>PF01552 Pico_P2B: Picornavirus 2B protein; InterPro: IPR002527 Poliovirus infection leads to drastic alterations in membrane permeability late during infection. Proteins 2B and 2BC enhance membrane permeability [, ].; GO: 0000166 nucleotide binding, 0003968 RNA-directed RNA polymerase activity, 0005198 structural molecule activity, 0008233 peptidase activity, 0008234 cysteine-type peptidase activity, 0016740 transferase activity, 0016779 nucleotidyltransferase activity, 0016787 hydrolase activity, 0018144 RNA-protein covalent cross-linking, 0019012 virion
Probab=36.30 E-value=40 Score=24.41 Aligned_cols=14 Identities=43% Similarity=0.442 Sum_probs=7.3
Q ss_pred HHHHHHhCCCCcCH
Q 025983 155 LYIACRQEDKPRTV 168 (245)
Q Consensus 155 lY~acR~~~~~~tl 168 (245)
+-+.+|....+.|+
T Consensus 52 lvIi~Rn~~D~~Tv 65 (99)
T PF01552_consen 52 LVIIIRNSDDLPTV 65 (99)
T ss_pred heeeeecCCchHHH
Confidence 34455665555544
No 465
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=36.15 E-value=17 Score=32.28 Aligned_cols=25 Identities=24% Similarity=0.635 Sum_probs=18.4
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLVL 33 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V~ 33 (245)
.+||+|..+ + ..+-+..|.+||.-.
T Consensus 58 ~kC~~c~~~-~----~y~~~~~C~~cg~~~ 82 (415)
T COG5257 58 YKCPECYRP-E----CYTTEPKCPNCGAET 82 (415)
T ss_pred EeCCCCCCC-c----ccccCCCCCCCCCCc
Confidence 579999973 2 223478999999765
No 466
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=35.80 E-value=27 Score=33.39 Aligned_cols=28 Identities=21% Similarity=0.517 Sum_probs=15.4
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCccc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGLV 32 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~V 32 (245)
+.||.|++..-++. ...-..+|..-|.+
T Consensus 3 ~~C~~C~g~G~i~v-~~e~c~vc~gtG~~ 30 (715)
T COG1107 3 KKCPECGGKGKIVV-GEEECPVCHGTGFS 30 (715)
T ss_pred ccccccCCCceEee-eeeecccccccccc
Confidence 67999998544443 22223444444555
No 467
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=35.75 E-value=85 Score=24.19 Aligned_cols=32 Identities=16% Similarity=0.133 Sum_probs=27.6
Q ss_pred hCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHHH
Q 025983 161 QEDKPRTVKEICSVANGATKKEIGRAKEYIVKQ 193 (245)
Q Consensus 161 ~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~~ 193 (245)
+.+-..+..+||+. +|+++.++.+.+++|.+.
T Consensus 19 q~d~R~s~~eiA~~-lglS~~tV~~Ri~rL~~~ 50 (153)
T PRK11179 19 MENARTPYAELAKQ-FGVSPGTIHVRVEKMKQA 50 (153)
T ss_pred HHcCCCCHHHHHHH-HCcCHHHHHHHHHHHHHC
Confidence 45567889999995 999999999999999863
No 468
>PHA03082 DNA-dependent RNA polymerase subunit; Provisional
Probab=35.73 E-value=14 Score=23.77 Aligned_cols=13 Identities=46% Similarity=0.871 Sum_probs=10.5
Q ss_pred ceEccCCcccccc
Q 025983 23 DTVCSECGLVLES 35 (245)
Q Consensus 23 ~~vC~~CG~V~~e 35 (245)
.+||+.||.=+.|
T Consensus 4 ~lVCsTCGrDlSe 16 (63)
T PHA03082 4 QLVCSTCGRDLSE 16 (63)
T ss_pred eeeecccCcchhH
Confidence 5899999987754
No 469
>PF05864 Chordopox_RPO7: Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide (RPO7); InterPro: IPR008448 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several Chordopoxvirus DNA-directed RNA polymerase 7 kDa polypeptide sequences. DNA-dependent RNA polymerase catalyses the transcription of DNA into RNA [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent
Probab=35.63 E-value=15 Score=23.71 Aligned_cols=13 Identities=46% Similarity=0.871 Sum_probs=10.4
Q ss_pred ceEccCCcccccc
Q 025983 23 DTVCSECGLVLES 35 (245)
Q Consensus 23 ~~vC~~CG~V~~e 35 (245)
.+||+.||.=+.|
T Consensus 4 ~lvCSTCGrDlSe 16 (63)
T PF05864_consen 4 QLVCSTCGRDLSE 16 (63)
T ss_pred eeeecccCCcchH
Confidence 5899999987754
No 470
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=35.46 E-value=1.5e+02 Score=25.10 Aligned_cols=39 Identities=10% Similarity=0.122 Sum_probs=29.9
Q ss_pred HHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHH
Q 025983 150 LLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYI 190 (245)
Q Consensus 150 iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l 190 (245)
+.-++-|+.-. ...++++.++|+. +++|...+.+.+++.
T Consensus 185 i~~~~~~i~~~-~~~~isl~~lA~~-~~lS~~~l~r~Fk~~ 223 (290)
T PRK10572 185 VREACQYISDH-LASEFDIESVAQH-VCLSPSRLAHLFRQQ 223 (290)
T ss_pred HHHHHHHHHhc-ccCCCCHHHHHHH-HCCCHHHHHHHHHHH
Confidence 44555566443 4479999999995 899999999988754
No 471
>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=35.45 E-value=39 Score=22.85 Aligned_cols=24 Identities=17% Similarity=0.201 Sum_probs=14.8
Q ss_pred CCcCHHHHHHHHhCCCHHHHHHHHH
Q 025983 164 KPRTVKEICSVANGATKKEIGRAKE 188 (245)
Q Consensus 164 ~~~tl~dia~~~~~v~~~~i~~~~~ 188 (245)
...++.|||+ .++|+..+|.|..+
T Consensus 33 ~~~si~elA~-~~~vS~sti~Rf~k 56 (77)
T PF01418_consen 33 AFMSISELAE-KAGVSPSTIVRFCK 56 (77)
T ss_dssp CT--HHHHHH-HCTS-HHHHHHHHH
T ss_pred HHccHHHHHH-HcCCCHHHHHHHHH
Confidence 3467888888 48888888766544
No 472
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=35.22 E-value=1.1e+02 Score=20.77 Aligned_cols=28 Identities=21% Similarity=0.373 Sum_probs=25.2
Q ss_pred CcCHHHHHHHHhCCCHHHHHHHHHHHHHH
Q 025983 165 PRTVKEICSVANGATKKEIGRAKEYIVKQ 193 (245)
Q Consensus 165 ~~tl~dia~~~~~v~~~~i~~~~~~l~~~ 193 (245)
+.+..+++.. ++++..+|.+.++.|.+.
T Consensus 24 ~~~~~~la~~-~~~s~~~i~~~l~~L~~~ 51 (101)
T smart00347 24 PLSVSELAKR-LGVSPSTVTRVLDRLEKK 51 (101)
T ss_pred CcCHHHHHHH-HCCCchhHHHHHHHHHHC
Confidence 6899999995 899999999999999874
No 473
>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=35.21 E-value=63 Score=25.62 Aligned_cols=31 Identities=19% Similarity=0.221 Sum_probs=26.5
Q ss_pred CCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhC
Q 025983 164 KPRTVKEICSVANGATKKEIGRAKEYIVKQLG 195 (245)
Q Consensus 164 ~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~ 195 (245)
...+.+|||+. +|+++.++...+.+.++.|.
T Consensus 164 ~~~s~~eIA~~-l~~s~~tV~~~l~r~r~~L~ 194 (198)
T TIGR02859 164 DGKSYQEIACD-LNRHVKSIDNALQRVKRKLE 194 (198)
T ss_pred cCCCHHHHHHH-HCCCHHHHHHHHHHHHHHHH
Confidence 36789999995 99999999988888887764
No 474
>PHA02970 hypothetical protein; Provisional
Probab=35.05 E-value=1.7e+02 Score=21.20 Aligned_cols=73 Identities=11% Similarity=0.081 Sum_probs=40.8
Q ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHhCCccCCccccCCCCHHhHHHHHhhhcCCCHHHHHHHHHHHHHhhhccc
Q 025983 169 KEICSVANGATKKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMNNQAVKAAQEAVQKSEEFDI 242 (245)
Q Consensus 169 ~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~~ 242 (245)
.|+++. ---++++|...|-.+.+.-.+.......+........|.-|.+-|++-+...-.-.-|.++.-..++
T Consensus 29 ~D~sey-~~YN~~EIn~lY~~FLk~h~L~sid~~kL~d~~idHIiyHFiEyl~~Lkntil~r~~IcKRiLnKD~ 101 (115)
T PHA02970 29 HDLSEY-EVYNPKEINSLYISFLKHHNLLSIDDRKLNDDAIDHIIYHFIEYLQKLKNTILTRNNICKRILNKDT 101 (115)
T ss_pred ccHHHH-hcCCHHHHHHHHHHHHHHcccccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 466664 3467999999999988876654321111221122345666777776655544333445555544444
No 475
>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=34.96 E-value=70 Score=23.45 Aligned_cols=30 Identities=23% Similarity=0.234 Sum_probs=25.6
Q ss_pred CcCHHHHHHHHhCCCHHHHHHHHHHHHHHhC
Q 025983 165 PRTVKEICSVANGATKKEIGRAKEYIVKQLG 195 (245)
Q Consensus 165 ~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~ 195 (245)
..+..|||.. +|+++.+|.+...+..+.|.
T Consensus 126 g~s~~eIA~~-l~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 126 GLSYKEIAEI-LGISVGTVKRRLKRARKKLR 155 (158)
T ss_pred CCCHHHHHHH-HCCCHHHHHHHHHHHHHHHH
Confidence 5789999995 99999999999888876653
No 476
>PF10543 ORF6N: ORF6N domain; InterPro: IPR018873 This entry represents an N-terminal DNA-binding domain found in a wide range of proteins from bacterial and eukaryotic DNA viruses and there bacterial homologues, they include the poxvirus D6R/N1R and baculoviral Bro protein families. The KilA-N domain is considered to be homologous to the fungal DNA-binding APSES domain. Both the KilA-N and APSES domains share a common fold with the nucleic acid-binding modules of the LAGLIDADG nucleases and the amino-terminal domains of the tRNA endonuclease []. This entry represents the amino-terminal domain of the Enterobacteria phage P22 antirepressor ((P03037 from SWISSPROT) []. It is found associated with IPR018876 from INTERPRO.
Probab=34.90 E-value=62 Score=22.64 Aligned_cols=29 Identities=17% Similarity=0.179 Sum_probs=26.5
Q ss_pred cCHHHHHHHHhCCCHHHHHHHHHHHHHHhC
Q 025983 166 RTVKEICSVANGATKKEIGRAKEYIVKQLG 195 (245)
Q Consensus 166 ~tl~dia~~~~~v~~~~i~~~~~~l~~~l~ 195 (245)
+|..+||++ .+++..+|.+.++.-.+.+.
T Consensus 13 ~t~~~lA~~-yg~~~~~i~~~~~rN~~rF~ 41 (88)
T PF10543_consen 13 MTDEDLAEL-YGVETKTINRNFKRNKDRFI 41 (88)
T ss_pred EEHHHHHHH-hCcCHHHHHHHHHHHHHhCC
Confidence 678999995 99999999999999988886
No 477
>PRK09483 response regulator; Provisional
Probab=34.87 E-value=78 Score=24.96 Aligned_cols=33 Identities=18% Similarity=0.253 Sum_probs=28.1
Q ss_pred CCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCc
Q 025983 164 KPRTVKEICSVANGATKKEIGRAKEYIVKQLGLE 197 (245)
Q Consensus 164 ~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~ 197 (245)
...+.++||+. ++++..++....+.|.+.|+..
T Consensus 162 ~G~~~~~Ia~~-l~is~~TV~~~~~~i~~Kl~v~ 194 (217)
T PRK09483 162 KGQKVNEISEQ-LNLSPKTVNSYRYRMFSKLNIS 194 (217)
T ss_pred CCCCHHHHHHH-hCCCHHHHHHHHHHHHHHcCCC
Confidence 44678899995 8999999999999999998864
No 478
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=34.83 E-value=33 Score=19.36 Aligned_cols=25 Identities=16% Similarity=0.578 Sum_probs=13.0
Q ss_pred CCCCCCCCCceeeeCCCCceEccCC
Q 025983 5 FCSDCKKHTEVVFDHSAGDTVCSEC 29 (245)
Q Consensus 5 ~Cp~Cg~~~~iv~d~~~G~~vC~~C 29 (245)
.|+.++..+-.++=.+.+..+|..|
T Consensus 2 ~C~~H~~~~~~~fC~~~~~~iC~~C 26 (39)
T cd00021 2 LCDEHGEEPLSLFCETDRALLCVDC 26 (39)
T ss_pred CCCccCCcceEEEeCccChhhhhhc
Confidence 5888876322233334445555555
No 479
>PF01475 FUR: Ferric uptake regulator family; InterPro: IPR002481 The Ferric uptake regulator (FUR) family includes metal ion uptake regulator proteins. These are responsible for controlling the intracellular concentration of iron in many bacteria. Although iron is essential for most organisms, high concentrations can be toxic because of the formation of hydroxyl radicals []. FURs can also control zinc homeostasis [] and is the subject of research on the pathogenesis of mycobacteria.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1MZB_A 2RGV_B 2FE3_B 3F8N_B 3EYY_B 2W57_A 2FU4_A 2O03_A 3MWM_B 2XIG_B ....
Probab=34.73 E-value=19 Score=26.56 Aligned_cols=13 Identities=31% Similarity=1.012 Sum_probs=10.2
Q ss_pred CceEccCCccccc
Q 025983 22 GDTVCSECGLVLE 34 (245)
Q Consensus 22 G~~vC~~CG~V~~ 34 (245)
...+|..||.|.+
T Consensus 79 ~h~iC~~Cg~v~~ 91 (120)
T PF01475_consen 79 HHFICTQCGKVID 91 (120)
T ss_dssp EEEEETTTS-EEE
T ss_pred eEEEECCCCCEEE
Confidence 4599999999985
No 480
>TIGR00467 lysS_arch lysyl-tRNA synthetase, archaeal and spirochete. This model represents the lysyl-tRNA synthetases that are class I amino-acyl tRNA synthetases. It includes archaeal and spirochete examples of the enzyme. All other known examples are class IIc amino-acyl tRNA synthetases and seem to form a separate orthologous set.
Probab=34.73 E-value=24 Score=33.32 Aligned_cols=32 Identities=28% Similarity=0.602 Sum_probs=20.0
Q ss_pred CCCCCCCCCceeeeCC---CCceEccCCcccccccc
Q 025983 5 FCSDCKKHTEVVFDHS---AGDTVCSECGLVLESHS 37 (245)
Q Consensus 5 ~Cp~Cg~~~~iv~d~~---~G~~vC~~CG~V~~e~~ 37 (245)
.||.||.....+++.. +=.+.| +||.-.+-.+
T Consensus 170 ic~~cGrv~~~~~~~~~~~~v~Y~c-~cG~~g~~~~ 204 (515)
T TIGR00467 170 FCENCGRDTTTVNNYDNEYSIEYSC-ECGNQESVDI 204 (515)
T ss_pred ecCCcCccCceEEEecCCceEEEEc-CCCCEEEEee
Confidence 6999998533333433 345678 4998765433
No 481
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=34.63 E-value=87 Score=26.90 Aligned_cols=57 Identities=12% Similarity=0.138 Sum_probs=37.3
Q ss_pred CcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCccCCccccCCCCHHhHHHHHhhhcCCC
Q 025983 165 PRTVKEICSVANGATKKEIGRAKEYIVKQLGLETGQSVEMGTIHAGDFMRRFCSNLGMN 223 (245)
Q Consensus 165 ~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~ 223 (245)
..+.+|||++ +|+++.++...+.+-++.|.-... ....++......+.+|...++-+
T Consensus 131 g~s~~EIA~~-lg~s~~tVk~~l~RAr~~Lr~~~~-~~~~~~~~~~~~v~~f~~A~~~g 187 (293)
T PRK09636 131 GVPFDEIAST-LGRSPAACRQLASRARKHVRAARP-RFPVSDEEGAELVEAFFAALASG 187 (293)
T ss_pred CCCHHHHHHH-HCCCHHHHHHHHHHHHHHHHhhCC-CCCCCchHHHHHHHHHHHHHHhC
Confidence 4789999996 999998888776665555543210 01133344566788888877654
No 482
>PRK13870 transcriptional regulator TraR; Provisional
Probab=34.58 E-value=62 Score=27.06 Aligned_cols=33 Identities=18% Similarity=0.288 Sum_probs=25.3
Q ss_pred CCcCHHHHHHHHhCCCHHHHHHHHHHHHHHhCCc
Q 025983 164 KPRTVKEICSVANGATKKEIGRAKEYIVKQLGLE 197 (245)
Q Consensus 164 ~~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~~~ 197 (245)
..+|-.|||.+ ++|++.++....+..++.|+-.
T Consensus 187 ~GKT~~EIa~I-LgISe~TV~~Hl~na~~KLga~ 219 (234)
T PRK13870 187 VGKTMEEIADV-EGVKYNSVRVKLREAMKRFDVR 219 (234)
T ss_pred cCCCHHHHHHH-HCCCHHHHHHHHHHHHHHcCCC
Confidence 46778888886 7888888888888777777743
No 483
>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=34.58 E-value=1.1e+02 Score=21.88 Aligned_cols=22 Identities=27% Similarity=0.317 Sum_probs=17.5
Q ss_pred CcCHHHHHHHHhCCCHHHHHHHH
Q 025983 165 PRTVKEICSVANGATKKEIGRAK 187 (245)
Q Consensus 165 ~~tl~dia~~~~~v~~~~i~~~~ 187 (245)
.++.+.+|+ +.|+++.+|.|..
T Consensus 23 ~~gq~~vA~-~~Gv~eStISR~k 44 (91)
T PF05269_consen 23 SVGQKKVAE-AMGVDESTISRWK 44 (91)
T ss_dssp HHHHHHHHH-HHTSSTTTHHHHH
T ss_pred HHhhHHHHH-HhCCCHHHHHHHH
Confidence 356788999 5899999998874
No 484
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=34.33 E-value=21 Score=26.61 Aligned_cols=20 Identities=20% Similarity=0.611 Sum_probs=12.8
Q ss_pred eeeeCCCCceEccCCccccc
Q 025983 15 VVFDHSAGDTVCSECGLVLE 34 (245)
Q Consensus 15 iv~d~~~G~~vC~~CG~V~~ 34 (245)
+.....-++.-|.+||.++.
T Consensus 62 l~Ie~~p~~~~C~~C~~~~~ 81 (115)
T COG0375 62 LHIEEEPAECWCLDCGQEVE 81 (115)
T ss_pred EEEEEeccEEEeccCCCeec
Confidence 44555667777777766654
No 485
>PF08421 Methyltransf_13: Putative zinc binding domain; InterPro: IPR013630 This domain is found at the N terminus of bacterial methyltransferases. ; PDB: 4E2X_A 3NDJ_A 3NDI_A 4E32_A 4E33_A 4E31_A 4E2Y_A 4E2W_A 4E2Z_A 4E30_A.
Probab=34.20 E-value=21 Score=23.26 Aligned_cols=16 Identities=38% Similarity=0.812 Sum_probs=9.6
Q ss_pred eEccCCcccccccccc
Q 025983 24 TVCSECGLVLESHSID 39 (245)
Q Consensus 24 ~vC~~CG~V~~e~~id 39 (245)
.+|.+||+|.-++.++
T Consensus 41 ~~C~~CglvQl~~~v~ 56 (62)
T PF08421_consen 41 YVCEDCGLVQLEEVVP 56 (62)
T ss_dssp EEETTT--EEESS---
T ss_pred EECCCCCchhcCCcCC
Confidence 7899999998776655
No 486
>PF04855 SNF5: SNF5 / SMARCB1 / INI1; InterPro: IPR006939 SNF5 is a component of the yeast SWI/SNF complex, which is an ATP-dependent nucleosome-remodelling complex that regulates the transcription of a subset of yeast genes. SNF5 is a key component of all SWI/SNF-class complexes characterised so far []. This family consists of the conserved region of SNF5, including a direct repeat motif. SNF5 is essential for the assembly promoter targeting and chromatin remodelling activity of the SWI-SNF complex []. SNF5 is also known as SMARCB1, for SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily b, member 1, and also INI1 for integrase interactor 1. Loss-of function mutations in SNF5 are thought to contribute to oncogenesis in malignant rhabdoid tumours (MRTs) [].; GO: 0006338 chromatin remodeling, 0000228 nuclear chromosome
Probab=34.12 E-value=66 Score=27.26 Aligned_cols=24 Identities=25% Similarity=0.515 Sum_probs=20.2
Q ss_pred cCCCCHHhHHHHHhhhcCCCHHHH
Q 025983 204 MGTIHAGDFMRRFCSNLGMNNQAV 227 (245)
Q Consensus 204 ~~~~~p~~~i~r~~~~L~l~~~v~ 227 (245)
-+..+|+.|-..+|..|||+.+..
T Consensus 139 ~~~~~PE~FA~~~c~dLgL~~Ef~ 162 (244)
T PF04855_consen 139 NPPNSPEEFARVLCADLGLPGEFV 162 (244)
T ss_pred CCCCCHHHHHHHHHHHcCCcHHHH
Confidence 356889999999999999996633
No 487
>PRK10870 transcriptional repressor MprA; Provisional
Probab=34.08 E-value=96 Score=24.63 Aligned_cols=36 Identities=17% Similarity=0.206 Sum_probs=29.1
Q ss_pred HHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 156 YIACRQEDKPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 156 Y~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
+......+.+.+..||++. ++++..++.+...+|.+
T Consensus 62 ~~L~~~~~~~it~~eLa~~-l~l~~~tvsr~v~rLe~ 97 (176)
T PRK10870 62 ITLESQENHSIQPSELSCA-LGSSRTNATRIADELEK 97 (176)
T ss_pred HHHhcCCCCCcCHHHHHHH-HCCCHHHHHHHHHHHHH
Confidence 3333445678999999995 99999999999999975
No 488
>PF04855 SNF5: SNF5 / SMARCB1 / INI1; InterPro: IPR006939 SNF5 is a component of the yeast SWI/SNF complex, which is an ATP-dependent nucleosome-remodelling complex that regulates the transcription of a subset of yeast genes. SNF5 is a key component of all SWI/SNF-class complexes characterised so far []. This family consists of the conserved region of SNF5, including a direct repeat motif. SNF5 is essential for the assembly promoter targeting and chromatin remodelling activity of the SWI-SNF complex []. SNF5 is also known as SMARCB1, for SWI/SNF-related, matrix-associated, actin-dependent regulator of chromatin, subfamily b, member 1, and also INI1 for integrase interactor 1. Loss-of function mutations in SNF5 are thought to contribute to oncogenesis in malignant rhabdoid tumours (MRTs) [].; GO: 0006338 chromatin remodeling, 0000228 nuclear chromosome
Probab=34.06 E-value=74 Score=27.00 Aligned_cols=36 Identities=19% Similarity=0.302 Sum_probs=27.0
Q ss_pred cCCCCHHhHHHHHhhhcCCCHHH--HHHHHHHHHHhhh
Q 025983 204 MGTIHAGDFMRRFCSNLGMNNQA--VKAAQEAVQKSEE 239 (245)
Q Consensus 204 ~~~~~p~~~i~r~~~~L~l~~~v--~~~A~~i~~~~~~ 239 (245)
-+.++|+.|...+|..|+|++.. .+++..|-+.+.+
T Consensus 34 e~~itpe~FA~~lc~Dl~lp~~~~~~~I~~sI~~Qi~e 71 (244)
T PF04855_consen 34 EPLITPEEFAEILCEDLDLPPSFFVQQIANSIREQIEE 71 (244)
T ss_pred CCCCCHHHHHHHHHHHHCCCcHHHHHHHHHHHHHHHHH
Confidence 35688999999999999999774 5556655555443
No 489
>PRK09462 fur ferric uptake regulator; Provisional
Probab=34.06 E-value=19 Score=27.73 Aligned_cols=12 Identities=42% Similarity=1.113 Sum_probs=10.9
Q ss_pred ceEccCCccccc
Q 025983 23 DTVCSECGLVLE 34 (245)
Q Consensus 23 ~~vC~~CG~V~~ 34 (245)
.++|..||.|++
T Consensus 90 H~iC~~Cg~i~~ 101 (148)
T PRK09462 90 HLICLDCGKVIE 101 (148)
T ss_pred ceEECCCCCEEE
Confidence 599999999986
No 490
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=33.95 E-value=94 Score=23.35 Aligned_cols=23 Identities=4% Similarity=0.033 Sum_probs=15.1
Q ss_pred CCCcCHHHHHHHHhCCCHHHHHHH
Q 025983 163 DKPRTVKEICSVANGATKKEIGRA 186 (245)
Q Consensus 163 ~~~~tl~dia~~~~~v~~~~i~~~ 186 (245)
....|..++|.. +||+..+|++.
T Consensus 16 ~~gltq~~lA~~-~gvs~~~is~~ 38 (135)
T PRK09706 16 QLKLSQRSLAKA-VKVSHVSISQW 38 (135)
T ss_pred HcCCCHHHHHHH-hCCCHHHHHHH
Confidence 345667777774 77777777654
No 491
>PRK13501 transcriptional activator RhaR; Provisional
Probab=33.89 E-value=2.9e+02 Score=23.37 Aligned_cols=30 Identities=7% Similarity=0.091 Sum_probs=24.7
Q ss_pred HhCCCCcCHHHHHHHHhCCCHHHHHHHHHHH
Q 025983 160 RQEDKPRTVKEICSVANGATKKEIGRAKEYI 190 (245)
Q Consensus 160 R~~~~~~tl~dia~~~~~v~~~~i~~~~~~l 190 (245)
.....++++.++|+. +++++..+.+.+++.
T Consensus 187 ~~~~e~~sl~~lA~~-~~lS~~~l~r~Fk~~ 216 (290)
T PRK13501 187 QSLGAYFDMADFCHK-NQLVERSLKQLFRQQ 216 (290)
T ss_pred HhhccCCCHHHHHHH-HCcCHHHHHHHHHHH
Confidence 345678999999995 899999999987743
No 492
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=33.87 E-value=19 Score=25.45 Aligned_cols=23 Identities=26% Similarity=0.781 Sum_probs=15.9
Q ss_pred CCCCCCCCCCceeeeCCCCceEccCCcc
Q 025983 4 AFCSDCKKHTEVVFDHSAGDTVCSECGL 31 (245)
Q Consensus 4 ~~Cp~Cg~~~~iv~d~~~G~~vC~~CG~ 31 (245)
..|..||. .+.-. -...|..||.
T Consensus 17 tlCrRCG~-~syH~----qK~~CasCGy 39 (91)
T PTZ00073 17 TLCRRCGK-RSFHV----QKKRCASCGY 39 (91)
T ss_pred chhcccCc-ccccc----ccccchhcCC
Confidence 35999997 34332 2567999999
No 493
>PRK04194 hypothetical protein; Provisional
Probab=33.80 E-value=1.1e+02 Score=27.99 Aligned_cols=30 Identities=17% Similarity=0.423 Sum_probs=24.8
Q ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHHHhhC
Q 025983 110 KTIATMSDRLGLVATIKDRANEIYKKVEDQ 139 (245)
Q Consensus 110 ~~I~~~~~~L~Lp~~v~~~A~~i~~~~~~~ 139 (245)
..|..+.+..+||+.+.+.|..+|+.+.+.
T Consensus 76 ~~I~~ii~~s~l~~~vk~~a~~iF~~lA~A 105 (392)
T PRK04194 76 SEIKALIENSDLPEKVKERALAVFERLAEA 105 (392)
T ss_pred HHHHHHHHhCCCCHHHHHHHHHHHHHHHHH
Confidence 456666688899999999999999987653
No 494
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=33.72 E-value=69 Score=25.52 Aligned_cols=30 Identities=20% Similarity=0.185 Sum_probs=25.6
Q ss_pred CcCHHHHHHHHhCCCHHHHHHHHHHHHHHhC
Q 025983 165 PRTVKEICSVANGATKKEIGRAKEYIVKQLG 195 (245)
Q Consensus 165 ~~tl~dia~~~~~v~~~~i~~~~~~l~~~l~ 195 (245)
..|..|||.. +|+|+.++.+.++.++..|.
T Consensus 151 Gls~~EIA~~-lgiS~~tV~r~l~~aR~~l~ 180 (185)
T PF07638_consen 151 GLSVEEIAER-LGISERTVRRRLRRARAWLR 180 (185)
T ss_pred CCCHHHHHHH-HCcCHHHHHHHHHHHHHHHH
Confidence 3599999995 99999999999998876653
No 495
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=33.67 E-value=18 Score=23.74 Aligned_cols=12 Identities=33% Similarity=0.805 Sum_probs=10.4
Q ss_pred eEccCCcccccc
Q 025983 24 TVCSECGLVLES 35 (245)
Q Consensus 24 ~vC~~CG~V~~e 35 (245)
+.|-.||.|+.+
T Consensus 5 vRCFTCGkvi~~ 16 (62)
T PRK04016 5 VRCFTCGKVIAE 16 (62)
T ss_pred eEecCCCCChHH
Confidence 679999999974
No 496
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=33.61 E-value=78 Score=23.43 Aligned_cols=30 Identities=7% Similarity=0.076 Sum_probs=26.1
Q ss_pred CCCCcCHHHHHHHHhCCCHHHHHHHHHHHHH
Q 025983 162 EDKPRTVKEICSVANGATKKEIGRAKEYIVK 192 (245)
Q Consensus 162 ~~~~~tl~dia~~~~~v~~~~i~~~~~~l~~ 192 (245)
...++|+.|+|++ +.+|....+...+++.+
T Consensus 16 ~~~~vtl~elA~~-l~cS~Rn~r~lLkkm~~ 45 (115)
T PF12793_consen 16 QPVEVTLDELAEL-LFCSRRNARTLLKKMQE 45 (115)
T ss_pred CCcceeHHHHHHH-hCCCHHHHHHHHHHHHH
Confidence 3467899999995 99999999999999875
No 497
>PRK13502 transcriptional activator RhaR; Provisional
Probab=33.55 E-value=2.1e+02 Score=24.04 Aligned_cols=41 Identities=10% Similarity=0.124 Sum_probs=31.4
Q ss_pred HHHHHHHHHHHHHHhCCCCcCHHHHHHHHhCCCHHHHHHHHHH
Q 025983 147 QDALLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEY 189 (245)
Q Consensus 147 ~~~iaAA~lY~acR~~~~~~tl~dia~~~~~v~~~~i~~~~~~ 189 (245)
...+....-|+.-. ...+.++.++|.. +++++..+.+.+++
T Consensus 175 ~~~~~~~~~~I~~~-~~~~~~~~~lA~~-~~iS~~~L~r~fk~ 215 (282)
T PRK13502 175 ETLLDKLITALANS-LECPFALDAFCQQ-EQCSERVLRQQFRA 215 (282)
T ss_pred HHHHHHHHHHHHhc-ccCCCCHHHHHHH-HCcCHHHHHHHHHH
Confidence 34456666777644 3457999999994 99999999998875
No 498
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=33.24 E-value=32 Score=25.06 Aligned_cols=9 Identities=22% Similarity=0.767 Sum_probs=5.0
Q ss_pred CCCCCCCCC
Q 025983 4 AFCSDCKKH 12 (245)
Q Consensus 4 ~~Cp~Cg~~ 12 (245)
..||.||.+
T Consensus 50 t~CP~Cg~~ 58 (115)
T COG1885 50 TSCPKCGEP 58 (115)
T ss_pred ccCCCCCCc
Confidence 346666653
No 499
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=33.17 E-value=40 Score=30.90 Aligned_cols=27 Identities=15% Similarity=0.305 Sum_probs=22.9
Q ss_pred CCCCCCCC-CceeeeCCCCceEccCCcc
Q 025983 5 FCSDCKKH-TEVVFDHSAGDTVCSECGL 31 (245)
Q Consensus 5 ~Cp~Cg~~-~~iv~d~~~G~~vC~~CG~ 31 (245)
.||-|+.. +++.+++..|..-|-.||.
T Consensus 36 ~CPfh~ek~pSf~v~~~k~~~~Cf~Cg~ 63 (415)
T TIGR01391 36 LCPFHHEKTPSFSVSPEKQFYHCFGCGA 63 (415)
T ss_pred eCCCCCCCCCeEEEEcCCCcEEECCCCC
Confidence 59999863 4778889999999999986
No 500
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=33.03 E-value=25 Score=22.28 Aligned_cols=30 Identities=23% Similarity=0.597 Sum_probs=18.6
Q ss_pred CCCCCCCCC--CceeeeC--CCCceEccCCcccc
Q 025983 4 AFCSDCKKH--TEVVFDH--SAGDTVCSECGLVL 33 (245)
Q Consensus 4 ~~Cp~Cg~~--~~iv~d~--~~G~~vC~~CG~V~ 33 (245)
..|..|+-. +..+-+- ..+...|.+||.++
T Consensus 23 ~~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 23 GTCSGCHMELPPQELNEIRKGDEIVFCPNCGRIL 56 (56)
T ss_pred CccCCCCEEcCHHHHHHHHcCCCeEECcCCCccC
Confidence 578888842 1222222 24579999999875
Done!