Query 023713
Match_columns 278
No_of_seqs 165 out of 1073
Neff 8.0
Searched_HMMs 46136
Date Fri Mar 29 06:05:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023713.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023713hhsearch_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 3.8E-63 8.2E-68 449.5 27.2 252 3-265 11-274 (310)
2 KOG1597 Transcription initiati 100.0 3.1E-60 6.7E-65 410.8 24.4 253 4-265 1-258 (308)
3 COG1405 SUA7 Transcription ini 100.0 3.8E-58 8.3E-63 407.8 23.1 245 3-266 1-250 (285)
4 KOG1598 Transcription initiati 100.0 1.1E-36 2.5E-41 283.2 12.3 226 4-272 1-231 (521)
5 PF00382 TFIIB: Transcription 99.8 8.2E-19 1.8E-23 125.4 10.1 71 113-184 1-71 (71)
6 PF08271 TF_Zn_Ribbon: TFIIB z 99.6 1.7E-16 3.7E-21 102.0 3.0 43 4-47 1-43 (43)
7 PRK00423 tfb transcription ini 99.6 1.5E-14 3.4E-19 131.5 12.3 89 109-198 219-307 (310)
8 KOG0834 CDK9 kinase-activating 99.4 2.7E-13 5.9E-18 122.4 8.8 158 107-272 40-217 (323)
9 KOG0835 Cyclin L [General func 99.4 2E-12 4.3E-17 114.6 13.1 152 106-265 23-198 (367)
10 TIGR00569 ccl1 cyclin ccl1. Un 99.4 8.1E-12 1.8E-16 112.9 16.4 154 103-265 52-221 (305)
11 COG1405 SUA7 Transcription ini 99.4 8.7E-13 1.9E-17 117.8 9.6 91 107-198 192-282 (285)
12 KOG1597 Transcription initiati 99.3 5.6E-12 1.2E-16 110.5 10.0 88 108-196 202-289 (308)
13 cd00043 CYCLIN Cyclin box fold 99.2 5.3E-10 1.1E-14 81.3 11.1 83 108-191 4-87 (88)
14 COG5333 CCL1 Cdk activating ki 99.1 9.1E-10 2E-14 97.6 12.4 149 107-263 46-205 (297)
15 smart00385 CYCLIN domain prese 99.1 1.1E-09 2.3E-14 78.9 8.9 80 112-192 2-82 (83)
16 KOG0794 CDK8 kinase-activating 98.8 1E-08 2.2E-13 87.2 8.1 148 108-263 43-207 (264)
17 PF00382 TFIIB: Transcription 98.8 1.4E-08 3.1E-13 72.2 6.7 51 214-266 1-53 (71)
18 KOG0656 G1/S-specific cyclin D 98.8 4.4E-07 9.4E-12 82.5 16.6 151 107-268 79-241 (335)
19 KOG1598 Transcription initiati 98.6 2.3E-08 5E-13 94.5 4.3 91 106-197 163-256 (521)
20 PF00134 Cyclin_N: Cyclin, N-t 98.1 5.3E-05 1.1E-09 59.3 10.9 92 106-198 31-125 (127)
21 cd00043 CYCLIN Cyclin box fold 97.9 2.6E-05 5.6E-10 56.2 5.6 58 208-267 3-62 (88)
22 KOG0653 Cyclin B and related k 97.8 0.00046 1E-08 65.0 13.5 145 105-255 157-306 (391)
23 smart00385 CYCLIN domain prese 97.7 6.8E-05 1.5E-09 53.4 5.3 54 212-267 1-56 (83)
24 COG5024 Cyclin [Cell division 97.7 0.00038 8.3E-09 65.8 11.0 150 109-266 216-369 (440)
25 PF01857 RB_B: Retinoblastoma- 97.7 0.00024 5.1E-09 56.9 8.1 84 106-190 11-96 (135)
26 KOG2496 Cdk activating kinase 97.7 0.0009 1.9E-08 59.7 12.4 142 111-255 61-215 (325)
27 PF11781 RRN7: RNA polymerase 97.1 0.00034 7.4E-09 42.8 2.1 28 4-34 9-36 (36)
28 KOG0835 Cyclin L [General func 96.9 0.005 1.1E-07 55.5 8.7 107 107-222 139-247 (367)
29 PF08792 A2L_zn_ribbon: A2L zi 96.8 0.0011 2.4E-08 39.7 2.6 31 1-33 1-31 (33)
30 PRK00415 rps27e 30S ribosomal 96.6 0.0015 3.3E-08 44.1 2.2 31 4-35 12-42 (59)
31 PRK00420 hypothetical protein; 96.6 0.0017 3.6E-08 50.1 2.6 31 1-34 21-51 (112)
32 PHA00626 hypothetical protein 96.5 0.0025 5.4E-08 42.3 2.7 31 4-35 1-35 (59)
33 COG2051 RPS27A Ribosomal prote 96.4 0.0018 3.9E-08 44.6 1.8 31 4-35 20-50 (67)
34 PF01667 Ribosomal_S27e: Ribos 96.4 0.0015 3.3E-08 43.7 1.4 31 4-35 8-38 (55)
35 PF02984 Cyclin_C: Cyclin, C-t 96.4 0.008 1.7E-07 46.0 5.6 55 209-265 2-58 (118)
36 PF13248 zf-ribbon_3: zinc-rib 96.3 0.0023 5E-08 36.2 1.4 23 3-31 2-24 (26)
37 PF02984 Cyclin_C: Cyclin, C-t 96.2 0.025 5.3E-07 43.2 7.5 87 109-196 3-90 (118)
38 KOG0655 G1/S-specific cyclin E 96.2 0.1 2.2E-06 47.4 12.1 142 107-255 146-304 (408)
39 KOG4164 Cyclin ik3-1/CABLES [C 96.2 0.02 4.4E-07 52.8 7.9 92 107-198 383-478 (497)
40 PRK00398 rpoP DNA-directed RNA 96.2 0.0036 7.9E-08 40.4 2.2 31 1-33 1-31 (46)
41 PF13240 zinc_ribbon_2: zinc-r 96.1 0.0031 6.7E-08 34.6 1.2 22 5-32 1-22 (23)
42 PF14803 Nudix_N_2: Nudix N-te 96.0 0.0023 4.9E-08 38.6 0.4 28 4-33 1-32 (34)
43 PLN00209 ribosomal protein S27 95.9 0.0051 1.1E-07 44.7 2.1 31 4-35 37-67 (86)
44 PTZ00083 40S ribosomal protein 95.9 0.0058 1.3E-07 44.3 2.2 31 4-35 36-66 (85)
45 smart00778 Prim_Zn_Ribbon Zinc 95.7 0.008 1.7E-07 36.9 2.1 28 4-31 4-33 (37)
46 PF02150 RNA_POL_M_15KD: RNA p 95.6 0.01 2.2E-07 36.1 2.2 31 3-34 1-31 (35)
47 COG1645 Uncharacterized Zn-fin 95.5 0.0068 1.5E-07 47.8 1.4 24 3-30 28-51 (131)
48 COG1997 RPL43A Ribosomal prote 95.2 0.017 3.8E-07 42.0 2.7 30 3-34 35-64 (89)
49 PF08274 PhnA_Zn_Ribbon: PhnA 95.1 0.018 3.8E-07 33.7 1.9 27 3-32 2-28 (30)
50 PF09538 FYDLN_acid: Protein o 95.0 0.014 3E-07 44.9 1.9 31 3-36 9-39 (108)
51 TIGR01206 lysW lysine biosynth 95.0 0.013 2.7E-07 39.2 1.4 31 3-34 2-33 (54)
52 PRK00432 30S ribosomal protein 94.9 0.019 4.2E-07 37.8 2.1 27 4-33 21-47 (50)
53 PRK11827 hypothetical protein; 94.9 0.021 4.5E-07 39.0 2.3 28 4-33 9-36 (60)
54 PF10571 UPF0547: Uncharacteri 94.7 0.019 4.1E-07 32.4 1.4 25 4-34 1-25 (26)
55 smart00661 RPOL9 RNA polymeras 94.4 0.031 6.7E-07 36.7 2.1 29 4-34 1-31 (52)
56 PRK10220 hypothetical protein; 94.3 0.12 2.7E-06 39.3 5.5 31 1-34 1-31 (111)
57 PF06677 Auto_anti-p27: Sjogre 94.3 0.041 8.8E-07 34.6 2.4 25 3-30 17-41 (41)
58 PF14354 Lar_restr_allev: Rest 94.2 0.054 1.2E-06 36.9 3.1 29 2-31 2-37 (61)
59 TIGR02300 FYDLN_acid conserved 94.1 0.032 6.9E-07 43.7 1.9 31 3-36 9-39 (129)
60 PF08273 Prim_Zn_Ribbon: Zinc- 94.1 0.042 9.1E-07 34.3 2.1 29 4-32 4-35 (40)
61 PRK00464 nrdR transcriptional 94.0 0.043 9.2E-07 44.9 2.7 30 4-33 1-38 (154)
62 PF03966 Trm112p: Trm112p-like 94.0 0.053 1.1E-06 38.0 2.8 18 17-34 47-64 (68)
63 PF08613 Cyclin: Cyclin; Inte 94.0 1.4 3.1E-05 35.6 11.6 89 109-198 54-148 (149)
64 PF09297 zf-NADH-PPase: NADH p 93.8 0.07 1.5E-06 31.5 2.7 27 4-32 4-30 (32)
65 TIGR02098 MJ0042_CXXC MJ0042 f 93.7 0.026 5.5E-07 34.7 0.6 29 4-34 3-36 (38)
66 COG2835 Uncharacterized conser 93.6 0.049 1.1E-06 37.0 1.9 30 2-33 7-36 (60)
67 PF09862 DUF2089: Protein of u 93.2 0.06 1.3E-06 41.6 2.1 25 6-36 1-25 (113)
68 COG1998 RPS31 Ribosomal protei 93.2 0.052 1.1E-06 35.2 1.4 27 4-32 20-46 (51)
69 KOG4557 Origin recognition com 93.1 5.2 0.00011 34.4 16.3 138 112-265 2-151 (262)
70 COG2824 PhnA Uncharacterized Z 92.6 0.29 6.4E-06 37.0 5.0 33 1-36 1-33 (112)
71 TIGR00244 transcriptional regu 92.5 0.13 2.7E-06 41.5 3.1 30 4-33 1-38 (147)
72 TIGR03655 anti_R_Lar restricti 92.1 0.14 3E-06 34.0 2.5 31 4-35 2-38 (53)
73 TIGR00686 phnA alkylphosphonat 92.0 0.4 8.8E-06 36.5 5.1 30 4-36 3-32 (109)
74 PRK12495 hypothetical protein; 91.9 0.1 2.2E-06 44.7 2.0 32 1-36 40-71 (226)
75 KOG1779 40s ribosomal protein 91.6 0.1 2.3E-06 37.1 1.5 30 4-34 35-64 (84)
76 TIGR01384 TFS_arch transcripti 91.0 0.14 3.1E-06 38.8 1.9 28 4-35 1-28 (104)
77 PRK14892 putative transcriptio 91.0 0.15 3.3E-06 38.5 1.9 41 4-45 22-70 (99)
78 PF03604 DNA_RNApol_7kD: DNA d 90.5 0.16 3.5E-06 30.1 1.4 24 5-31 2-25 (32)
79 PF01780 Ribosomal_L37ae: Ribo 90.3 0.16 3.4E-06 37.6 1.5 32 3-36 35-66 (90)
80 PF00134 Cyclin_N: Cyclin, N-t 90.3 1.3 2.9E-05 34.0 7.0 55 210-266 34-90 (127)
81 PF12760 Zn_Tnp_IS1595: Transp 90.2 0.32 6.9E-06 31.2 2.7 27 4-31 19-45 (46)
82 COG4888 Uncharacterized Zn rib 90.2 0.2 4.3E-06 37.6 1.9 30 4-34 23-57 (104)
83 smart00834 CxxC_CXXC_SSSS Puta 89.9 0.16 3.4E-06 31.5 1.1 31 3-33 5-36 (41)
84 PF05129 Elf1: Transcription e 89.9 0.14 3E-06 37.3 0.9 33 4-36 23-59 (81)
85 cd00350 rubredoxin_like Rubred 89.7 0.25 5.3E-06 29.4 1.7 24 4-31 2-25 (33)
86 smart00342 HTH_ARAC helix_turn 89.5 1.7 3.8E-05 30.2 6.5 71 113-191 4-75 (84)
87 PF07282 OrfB_Zn_ribbon: Putat 89.4 0.25 5.4E-06 34.4 1.9 29 4-34 29-57 (69)
88 smart00659 RPOLCX RNA polymera 89.4 0.29 6.4E-06 31.2 2.0 27 4-33 3-29 (44)
89 COG2888 Predicted Zn-ribbon RN 89.2 0.25 5.4E-06 33.4 1.6 27 4-32 10-36 (61)
90 PF05191 ADK_lid: Adenylate ki 89.1 0.052 1.1E-06 33.1 -1.6 29 5-33 3-31 (36)
91 PF13719 zinc_ribbon_5: zinc-r 88.9 0.17 3.6E-06 31.0 0.6 29 4-33 3-35 (37)
92 smart00440 ZnF_C2C2 C2C2 Zinc 88.9 0.35 7.7E-06 30.1 2.1 27 5-32 2-37 (40)
93 COG1594 RPB9 DNA-directed RNA 88.8 0.34 7.4E-06 37.5 2.4 32 3-36 2-35 (113)
94 PTZ00255 60S ribosomal protein 88.6 0.32 7E-06 35.9 2.0 32 3-36 36-67 (90)
95 KOG4557 Origin recognition com 88.5 1.9 4.1E-05 37.0 6.8 83 112-196 95-182 (262)
96 COG4640 Predicted membrane pro 87.9 0.28 6E-06 45.6 1.6 28 3-36 1-28 (465)
97 PF12773 DZR: Double zinc ribb 87.5 0.31 6.8E-06 31.6 1.3 27 4-33 13-39 (50)
98 PF14255 Cys_rich_CPXG: Cystei 87.4 0.42 9.1E-06 31.7 1.8 29 5-33 2-34 (52)
99 PF03119 DNA_ligase_ZBD: NAD-d 87.3 0.56 1.2E-05 26.9 2.1 22 5-28 1-22 (28)
100 COG4068 Uncharacterized protei 87.3 0.15 3.2E-06 34.3 -0.4 25 4-34 9-34 (64)
101 TIGR00280 L37a ribosomal prote 87.1 0.42 9E-06 35.4 1.8 32 3-36 35-66 (91)
102 PRK06266 transcription initiat 87.0 0.16 3.4E-06 42.6 -0.5 31 4-35 118-148 (178)
103 TIGR00569 ccl1 cyclin ccl1. Un 86.9 14 0.0003 33.7 12.0 72 123-196 180-253 (305)
104 PF00325 Crp: Bacterial regula 86.8 1 2.2E-05 26.7 3.1 28 165-193 1-28 (32)
105 PRK05978 hypothetical protein; 86.6 0.49 1.1E-05 38.4 2.2 35 4-39 34-68 (148)
106 PRK09710 lar restriction allev 86.4 0.82 1.8E-05 31.5 2.9 30 3-33 6-37 (64)
107 COG1656 Uncharacterized conser 86.3 0.38 8.1E-06 39.6 1.4 39 3-48 97-150 (165)
108 PF05460 ORC6: Origin recognit 86.2 0.22 4.8E-06 46.3 0.0 78 121-199 11-89 (353)
109 PF00301 Rubredoxin: Rubredoxi 85.9 0.39 8.6E-06 31.1 1.1 14 24-37 2-15 (47)
110 PRK03976 rpl37ae 50S ribosomal 85.7 0.53 1.2E-05 34.8 1.8 32 3-36 36-67 (90)
111 PRK12286 rpmF 50S ribosomal pr 85.7 0.6 1.3E-05 31.5 1.9 28 4-38 28-55 (57)
112 PRK14890 putative Zn-ribbon RN 85.5 0.71 1.5E-05 31.3 2.2 28 3-32 7-34 (59)
113 PRK09678 DNA-binding transcrip 85.5 0.85 1.8E-05 32.4 2.7 31 3-34 1-40 (72)
114 PF01096 TFIIS_C: Transcriptio 85.2 0.66 1.4E-05 28.7 1.8 28 5-32 2-37 (39)
115 PF14446 Prok-RING_1: Prokaryo 84.9 0.71 1.5E-05 30.8 1.9 28 3-34 5-32 (54)
116 PRK13130 H/ACA RNA-protein com 84.9 0.48 1E-05 31.9 1.1 25 2-34 4-28 (56)
117 COG1996 RPC10 DNA-directed RNA 84.5 0.34 7.3E-06 31.6 0.2 27 4-32 7-33 (49)
118 cd00730 rubredoxin Rubredoxin; 84.4 0.81 1.8E-05 30.0 2.0 11 25-35 3-13 (50)
119 KOG1010 Rb (Retinoblastoma tum 84.0 2.4 5.2E-05 43.3 6.0 84 107-191 678-763 (920)
120 COG3877 Uncharacterized protei 83.9 0.78 1.7E-05 34.8 2.0 27 4-36 7-33 (122)
121 COG5349 Uncharacterized protei 83.8 0.52 1.1E-05 36.6 1.1 39 4-43 22-60 (126)
122 COG1327 Predicted transcriptio 83.6 0.89 1.9E-05 36.8 2.3 30 4-33 1-38 (156)
123 PF01783 Ribosomal_L32p: Ribos 83.6 0.67 1.4E-05 31.1 1.4 24 4-34 27-50 (56)
124 TIGR02443 conserved hypothetic 82.9 1.3 2.7E-05 30.1 2.5 30 4-33 10-41 (59)
125 PF08279 HTH_11: HTH domain; 82.6 3.8 8.3E-05 26.7 4.9 34 161-195 10-43 (55)
126 PF12773 DZR: Double zinc ribb 82.6 0.99 2.1E-05 29.2 1.9 22 3-30 29-50 (50)
127 KOG0794 CDK8 kinase-activating 82.5 8.3 0.00018 33.6 7.9 100 113-222 157-257 (264)
128 PF14122 YokU: YokU-like prote 81.4 1.1 2.3E-05 32.7 1.8 24 20-43 32-55 (87)
129 cd06571 Bac_DnaA_C C-terminal 81.4 6.7 0.00015 28.7 6.3 42 153-197 33-75 (90)
130 PRK02935 hypothetical protein; 81.2 1.1 2.3E-05 34.0 1.8 27 4-34 71-97 (110)
131 TIGR02605 CxxC_CxxC_SSSS putat 81.1 0.76 1.7E-05 30.0 0.9 29 3-31 5-34 (52)
132 PF11672 DUF3268: Protein of u 81.0 1.4 3E-05 33.5 2.5 32 3-35 2-43 (102)
133 PF13545 HTH_Crp_2: Crp-like h 80.9 5.1 0.00011 27.9 5.3 43 151-194 3-55 (76)
134 TIGR02010 IscR iron-sulfur clu 80.8 4.8 0.0001 31.9 5.7 46 147-193 6-51 (135)
135 PF05876 Terminase_GpA: Phage 80.8 0.9 2E-05 44.9 1.8 43 4-46 201-255 (557)
136 TIGR01031 rpmF_bact ribosomal 80.6 1.2 2.6E-05 29.8 1.8 25 4-35 27-51 (55)
137 PF02082 Rrf2: Transcriptional 80.5 3.1 6.6E-05 30.0 4.1 46 148-194 7-52 (83)
138 TIGR03826 YvyF flagellar opero 80.3 0.42 9.2E-06 38.3 -0.6 29 1-34 1-29 (137)
139 KOG1088 Uncharacterized conser 80.3 0.67 1.5E-05 35.7 0.5 18 17-34 92-109 (124)
140 PF09723 Zn-ribbon_8: Zinc rib 80.0 0.88 1.9E-05 28.6 0.9 29 4-32 6-35 (42)
141 PF15616 TerY-C: TerY-C metal 79.7 1 2.2E-05 35.8 1.4 9 4-12 78-86 (131)
142 KOG1010 Rb (Retinoblastoma tum 79.7 14 0.00031 37.9 9.6 62 110-172 35-96 (920)
143 COG1326 Uncharacterized archae 79.4 0.75 1.6E-05 38.8 0.6 31 4-35 7-42 (201)
144 PF07754 DUF1610: Domain of un 79.0 1.5 3.2E-05 24.2 1.5 24 6-31 1-24 (24)
145 PF01325 Fe_dep_repress: Iron 78.9 7.3 0.00016 26.4 5.3 37 155-193 12-48 (60)
146 PRK14559 putative protein seri 78.9 1.2 2.6E-05 44.7 2.0 13 21-33 39-51 (645)
147 PF10058 DUF2296: Predicted in 78.8 0.96 2.1E-05 30.2 0.9 29 4-32 23-53 (54)
148 PF14952 zf-tcix: Putative tre 78.8 1.2 2.7E-05 28.1 1.3 26 4-35 12-39 (44)
149 PF09855 DUF2082: Nucleic-acid 78.7 1.4 3.1E-05 30.4 1.7 9 24-32 37-45 (64)
150 COG3478 Predicted nucleic-acid 78.5 1.5 3.2E-05 30.2 1.7 12 4-16 5-16 (68)
151 PF09862 DUF2089: Protein of u 78.4 3.9 8.5E-05 31.6 4.2 49 168-222 51-99 (113)
152 PRK08402 replication factor A; 78.2 1.7 3.7E-05 40.5 2.6 27 4-32 213-239 (355)
153 PF11023 DUF2614: Protein of u 78.1 0.76 1.6E-05 35.3 0.2 39 4-49 70-108 (114)
154 PHA02942 putative transposase; 77.9 1.3 2.7E-05 41.8 1.7 29 4-35 326-354 (383)
155 PRK08351 DNA-directed RNA poly 77.9 1.2 2.7E-05 30.4 1.2 24 1-32 1-24 (61)
156 PF13717 zinc_ribbon_4: zinc-r 77.7 0.91 2E-05 27.6 0.5 29 4-33 3-35 (36)
157 PF04161 Arv1: Arv1-like famil 77.5 1.1 2.4E-05 38.4 1.1 33 4-36 1-37 (208)
158 PRK10857 DNA-binding transcrip 77.1 6.9 0.00015 32.3 5.7 46 147-193 6-51 (164)
159 cd00729 rubredoxin_SM Rubredox 76.5 2.2 4.7E-05 25.5 1.9 25 4-32 3-27 (34)
160 TIGR03697 NtcA_cyano global ni 76.5 12 0.00025 30.8 7.1 29 165-194 142-170 (193)
161 PRK12336 translation initiatio 75.4 1.9 4.2E-05 36.8 2.0 30 4-33 99-129 (201)
162 cd00092 HTH_CRP helix_turn_hel 75.1 14 0.00031 24.7 6.1 31 163-194 22-52 (67)
163 PRK12380 hydrogenase nickel in 74.5 1.8 4E-05 33.4 1.5 23 5-31 72-94 (113)
164 COG2888 Predicted Zn-ribbon RN 74.3 2 4.4E-05 29.1 1.5 28 4-32 28-59 (61)
165 COG3809 Uncharacterized protei 74.2 3 6.5E-05 29.9 2.4 29 3-33 1-31 (88)
166 KOG2906 RNA polymerase III sub 74.1 2.6 5.7E-05 31.5 2.2 30 3-34 1-32 (105)
167 PF13613 HTH_Tnp_4: Helix-turn 74.1 8.6 0.00019 25.2 4.5 35 163-198 16-50 (53)
168 PF13413 HTH_25: Helix-turn-he 73.6 3.3 7.2E-05 28.3 2.5 57 160-227 4-61 (62)
169 COG1773 Rubredoxin [Energy pro 73.4 2.3 4.9E-05 28.5 1.5 24 3-30 3-26 (55)
170 PF09526 DUF2387: Probable met 73.1 3.5 7.5E-05 29.2 2.5 30 4-33 9-40 (71)
171 PF10122 Mu-like_Com: Mu-like 72.9 1 2.2E-05 29.6 -0.3 31 2-34 3-35 (51)
172 PRK11920 rirA iron-responsive 72.7 11 0.00023 30.7 5.7 45 147-193 6-50 (153)
173 PRK14890 putative Zn-ribbon RN 72.7 2.9 6.2E-05 28.4 1.9 28 4-32 26-57 (59)
174 TIGR00100 hypA hydrogenase nic 72.5 2.3 4.9E-05 33.0 1.6 16 15-30 62-77 (115)
175 PF14353 CpXC: CpXC protein 72.1 3.5 7.5E-05 32.3 2.6 12 23-34 38-49 (128)
176 smart00401 ZnF_GATA zinc finge 71.7 3.5 7.6E-05 27.2 2.1 32 3-34 3-36 (52)
177 PRK00241 nudC NADH pyrophospha 71.7 2.7 5.8E-05 37.4 2.0 29 3-33 99-127 (256)
178 PF08646 Rep_fac-A_C: Replicat 71.6 3.3 7.2E-05 33.2 2.5 27 5-34 20-48 (146)
179 PRK03824 hypA hydrogenase nick 71.4 2.4 5.3E-05 33.8 1.6 21 14-34 61-81 (135)
180 PF06827 zf-FPG_IleRS: Zinc fi 71.3 2.9 6.4E-05 24.0 1.5 28 4-31 2-29 (30)
181 PF12802 MarR_2: MarR family; 70.9 13 0.00028 24.5 5.0 39 154-193 9-47 (62)
182 KOG2593 Transcription initiati 70.9 2 4.3E-05 40.6 1.1 33 3-35 128-165 (436)
183 smart00419 HTH_CRP helix_turn_ 70.8 7.9 0.00017 24.0 3.7 29 164-193 6-34 (48)
184 TIGR03831 YgiT_finger YgiT-typ 70.8 3.1 6.7E-05 26.0 1.7 10 24-33 33-42 (46)
185 smart00550 Zalpha Z-DNA-bindin 70.3 14 0.00031 25.5 5.1 38 156-194 11-49 (68)
186 PRK13719 conjugal transfer tra 70.1 26 0.00057 30.3 7.7 60 165-236 157-216 (217)
187 KOG3134 Predicted membrane pro 70.1 1.4 3E-05 37.8 -0.1 33 4-36 1-37 (225)
188 PF00356 LacI: Bacterial regul 69.9 5 0.00011 25.7 2.5 21 168-189 1-21 (46)
189 COG4530 Uncharacterized protei 69.8 2.5 5.3E-05 32.3 1.2 32 3-37 9-40 (129)
190 PF08613 Cyclin: Cyclin; Inte 69.5 33 0.0007 27.6 7.9 59 205-265 49-114 (149)
191 PF13453 zf-TFIIB: Transcripti 69.3 4.1 8.9E-05 25.3 2.0 28 5-33 1-29 (41)
192 TIGR00738 rrf2_super rrf2 fami 69.1 15 0.00032 28.6 5.6 45 148-193 7-51 (132)
193 TIGR03830 CxxCG_CxxCG_HTH puta 69.0 3.7 7.9E-05 31.8 2.1 21 166-187 78-98 (127)
194 TIGR00155 pqiA_fam integral me 68.7 3.2 6.9E-05 39.4 2.0 30 5-34 15-44 (403)
195 PF01155 HypA: Hydrogenase exp 68.2 1.4 3E-05 34.0 -0.4 24 5-32 72-95 (113)
196 CHL00174 accD acetyl-CoA carbo 68.0 1.1 2.3E-05 40.7 -1.3 30 4-34 39-68 (296)
197 PF06044 DRP: Dam-replacing fa 68.0 2.3 5.1E-05 37.2 0.9 30 4-34 32-64 (254)
198 TIGR00515 accD acetyl-CoA carb 67.9 1.1 2.4E-05 40.4 -1.2 30 4-34 27-56 (285)
199 TIGR02944 suf_reg_Xantho FeS a 67.5 17 0.00038 28.3 5.8 45 147-193 7-51 (130)
200 PF13412 HTH_24: Winged helix- 67.1 20 0.00044 22.5 5.1 29 164-193 15-43 (48)
201 COG2093 DNA-directed RNA polym 65.9 3.6 7.7E-05 28.2 1.2 26 1-32 2-27 (64)
202 COG0333 RpmF Ribosomal protein 65.9 4.7 0.0001 27.2 1.8 27 3-36 27-53 (57)
203 PF00196 GerE: Bacterial regul 65.7 9.4 0.0002 25.3 3.3 33 165-198 17-49 (58)
204 COG1959 Predicted transcriptio 65.6 18 0.00039 29.3 5.6 46 148-194 7-52 (150)
205 PRK03681 hypA hydrogenase nick 65.5 3.7 8E-05 31.8 1.4 7 24-30 88-94 (114)
206 PF06397 Desulfoferrod_N: Desu 65.4 2.6 5.6E-05 25.7 0.4 22 4-26 7-28 (36)
207 PRK11161 fumarate/nitrate redu 65.1 28 0.00062 29.6 7.2 30 165-195 183-212 (235)
208 PRK05508 methionine sulfoxide 64.9 4.2 9.2E-05 31.7 1.7 33 18-50 28-62 (119)
209 PF04606 Ogr_Delta: Ogr/Delta- 64.7 5 0.00011 25.8 1.7 29 5-34 1-38 (47)
210 KOG0834 CDK9 kinase-activating 64.3 5.5 0.00012 36.6 2.6 91 106-197 148-247 (323)
211 PF04216 FdhE: Protein involve 64.2 4 8.7E-05 36.8 1.7 29 4-32 173-206 (290)
212 PF07191 zinc-ribbons_6: zinc- 64.1 4 8.6E-05 28.7 1.2 26 4-33 2-27 (70)
213 PRK14559 putative protein seri 64.1 3.9 8.5E-05 41.2 1.7 14 24-37 28-41 (645)
214 PF13730 HTH_36: Helix-turn-he 63.8 22 0.00049 22.9 4.9 26 167-193 26-51 (55)
215 PF04545 Sigma70_r4: Sigma-70, 63.8 17 0.00036 23.2 4.2 31 164-195 18-48 (50)
216 PRK05654 acetyl-CoA carboxylas 63.7 1.5 3.2E-05 39.8 -1.3 30 4-34 28-57 (292)
217 PF09889 DUF2116: Uncharacteri 63.6 1.4 3.1E-05 29.9 -1.0 27 4-36 4-31 (59)
218 TIGR01384 TFS_arch transcripti 63.6 6.3 0.00014 29.6 2.4 28 4-32 63-99 (104)
219 PRK15103 paraquat-inducible me 63.4 4.5 9.9E-05 38.6 1.9 33 4-36 11-43 (419)
220 PRK06030 hypothetical protein; 63.2 31 0.00067 27.1 6.3 39 154-195 59-97 (124)
221 PF01726 LexA_DNA_bind: LexA D 62.9 14 0.0003 25.5 3.8 33 161-194 20-53 (65)
222 PF14319 Zn_Tnp_IS91: Transpos 62.9 2.9 6.3E-05 32.2 0.4 34 4-39 43-76 (111)
223 KOG3507 DNA-directed RNA polym 62.8 4.4 9.6E-05 27.3 1.2 27 4-33 21-47 (62)
224 PF09339 HTH_IclR: IclR helix- 62.8 15 0.00033 23.7 3.9 36 157-193 9-44 (52)
225 COG0777 AccD Acetyl-CoA carbox 62.6 2.1 4.5E-05 38.2 -0.5 29 4-33 29-57 (294)
226 COG4391 Uncharacterized protei 62.6 4.2 9.2E-05 27.7 1.1 21 14-34 38-59 (62)
227 PRK10219 DNA-binding transcrip 62.5 49 0.0011 24.5 7.3 39 151-191 7-45 (107)
228 PF04079 DUF387: Putative tran 62.3 64 0.0014 26.4 8.3 79 151-236 2-89 (159)
229 PF00165 HTH_AraC: Bacterial r 62.3 13 0.00027 22.8 3.3 26 164-190 6-31 (42)
230 COG3355 Predicted transcriptio 62.3 19 0.00042 28.4 4.9 37 156-193 32-68 (126)
231 PF12172 DUF35_N: Rubredoxin-l 62.0 4.5 9.7E-05 24.4 1.1 21 4-30 12-32 (37)
232 smart00421 HTH_LUXR helix_turn 62.0 17 0.00038 23.0 4.1 32 166-198 18-49 (58)
233 cd04476 RPA1_DBD_C RPA1_DBD_C: 61.9 6.1 0.00013 32.4 2.2 27 4-33 35-61 (166)
234 PRK00222 methionine sulfoxide 61.9 4.9 0.00011 32.4 1.6 34 17-50 37-72 (142)
235 cd06170 LuxR_C_like C-terminal 61.9 33 0.00072 21.7 5.5 32 166-198 15-46 (57)
236 PF13404 HTH_AsnC-type: AsnC-t 61.4 16 0.00034 22.9 3.5 30 162-192 13-42 (42)
237 cd00202 ZnF_GATA Zinc finger D 61.3 3.2 6.9E-05 27.6 0.3 30 5-34 1-32 (54)
238 KOG0402 60S ribosomal protein 61.0 2.8 6.1E-05 30.4 0.1 30 4-35 37-66 (92)
239 PF01599 Ribosomal_S27: Riboso 60.6 10 0.00022 24.5 2.6 26 4-31 19-46 (47)
240 PRK06260 threonine synthase; V 60.4 3.8 8.1E-05 38.7 0.8 30 1-34 1-30 (397)
241 PF04703 FaeA: FaeA-like prote 60.2 21 0.00045 24.5 4.3 36 162-198 11-46 (62)
242 PRK12366 replication factor A; 60.0 4.9 0.00011 40.5 1.6 25 4-32 533-557 (637)
243 TIGR01610 phage_O_Nterm phage 59.8 68 0.0015 23.6 8.4 30 163-193 44-73 (95)
244 PRK10402 DNA-binding transcrip 59.6 32 0.00069 29.4 6.4 46 148-194 151-196 (226)
245 PRK11753 DNA-binding transcrip 59.6 95 0.0021 25.7 9.3 29 165-194 167-195 (211)
246 COG4643 Uncharacterized protei 59.3 5.1 0.00011 36.8 1.4 26 5-30 34-61 (366)
247 PF10080 DUF2318: Predicted me 59.2 5.8 0.00013 30.1 1.5 28 4-34 36-63 (102)
248 PF13790 DUF4182: Domain of un 59.1 4.6 0.0001 24.8 0.8 14 21-34 1-14 (38)
249 PF13463 HTH_27: Winged helix 59.0 22 0.00048 23.9 4.4 32 162-194 14-45 (68)
250 PRK04023 DNA polymerase II lar 58.9 6.8 0.00015 41.0 2.3 12 24-35 664-675 (1121)
251 cd00974 DSRD Desulforedoxin (D 58.9 7.5 0.00016 23.0 1.7 24 3-27 4-27 (34)
252 PRK06450 threonine synthase; V 58.3 14 0.0003 34.1 4.2 29 1-34 1-29 (338)
253 PRK07218 replication factor A; 58.2 4.5 9.7E-05 38.6 0.9 21 4-32 298-318 (423)
254 COG1737 RpiR Transcriptional r 58.0 76 0.0016 28.3 8.8 100 167-274 37-160 (281)
255 TIGR00357 methionine-R-sulfoxi 57.8 6.1 0.00013 31.5 1.5 33 18-50 35-69 (134)
256 PF04967 HTH_10: HTH DNA bindi 57.5 28 0.00061 23.0 4.4 27 167-194 24-50 (53)
257 PF01978 TrmB: Sugar-specific 57.5 15 0.00032 25.1 3.2 30 163-193 19-48 (68)
258 PF03833 PolC_DP2: DNA polymer 57.3 3.5 7.6E-05 42.3 0.0 46 178-225 778-823 (900)
259 PF14206 Cys_rich_CPCC: Cystei 57.1 11 0.00024 27.2 2.5 26 4-32 2-29 (78)
260 PF01485 IBR: IBR domain; Int 57.0 6.8 0.00015 26.1 1.4 28 4-33 19-50 (64)
261 TIGR03829 YokU_near_AblA uncha 57.0 6.1 0.00013 29.2 1.2 38 5-42 1-54 (89)
262 TIGR00613 reco DNA repair prot 56.7 7.7 0.00017 33.6 2.1 28 4-31 148-176 (241)
263 PRK00085 recO DNA repair prote 56.5 7.3 0.00016 33.9 1.9 27 4-30 150-177 (247)
264 PRK11511 DNA-binding transcrip 56.5 65 0.0014 25.0 7.2 42 148-191 8-49 (127)
265 PF09845 DUF2072: Zn-ribbon co 56.1 4.4 9.5E-05 32.1 0.4 24 4-31 2-27 (131)
266 TIGR00310 ZPR1_znf ZPR1 zinc f 56.0 8 0.00017 32.8 2.0 32 5-36 2-43 (192)
267 PRK00564 hypA hydrogenase nick 56.0 4.8 0.0001 31.3 0.6 18 14-31 62-79 (117)
268 COG1510 Predicted transcriptio 55.4 17 0.00036 30.3 3.7 37 156-193 31-67 (177)
269 PF01412 ArfGap: Putative GTPa 55.0 5.1 0.00011 31.0 0.6 31 4-34 14-44 (116)
270 PRK14088 dnaA chromosomal repl 54.9 14 0.00031 35.3 3.8 44 149-195 369-415 (440)
271 PF01857 RB_B: Retinoblastoma- 54.8 33 0.00072 27.3 5.2 53 211-265 15-71 (135)
272 PF13824 zf-Mss51: Zinc-finger 54.7 9.2 0.0002 25.6 1.7 24 5-33 1-24 (55)
273 PF08299 Bac_DnaA_C: Bacterial 54.7 29 0.00063 24.1 4.4 34 155-191 36-70 (70)
274 COG4565 CitB Response regulato 54.7 1.4E+02 0.003 25.9 9.2 87 105-194 113-200 (224)
275 TIGR00319 desulf_FeS4 desulfof 54.6 8.6 0.00019 22.7 1.4 23 4-27 8-30 (34)
276 TIGR00595 priA primosomal prot 54.4 10 0.00022 37.1 2.7 29 4-34 223-251 (505)
277 PF08220 HTH_DeoR: DeoR-like h 54.2 21 0.00046 23.7 3.5 31 164-195 12-42 (57)
278 PRK09391 fixK transcriptional 54.0 67 0.0015 27.5 7.6 29 165-194 178-206 (230)
279 PRK00135 scpB segregation and 53.9 47 0.001 28.1 6.3 68 148-220 5-82 (188)
280 PRK05580 primosome assembly pr 53.6 11 0.00023 38.4 2.7 28 4-33 391-418 (679)
281 PRK06393 rpoE DNA-directed RNA 53.5 5.5 0.00012 27.5 0.5 21 3-31 5-25 (64)
282 PRK14714 DNA polymerase II lar 53.4 7.7 0.00017 41.6 1.8 8 4-11 668-675 (1337)
283 PF08063 PADR1: PADR1 (NUC008) 53.2 8.2 0.00018 25.8 1.3 21 4-27 15-35 (55)
284 PF08281 Sigma70_r4_2: Sigma-7 53.2 27 0.00059 22.4 3.9 29 165-194 25-53 (54)
285 PF14768 RPA_interact_C: Repli 53.2 10 0.00023 27.4 2.0 26 5-34 1-26 (82)
286 PF05344 DUF746: Domain of Unk 53.2 36 0.00078 23.6 4.4 36 160-196 7-42 (65)
287 PRK13918 CRP/FNR family transc 52.9 58 0.0013 26.9 6.8 29 165-194 148-176 (202)
288 smart00345 HTH_GNTR helix_turn 52.9 29 0.00064 22.3 4.1 25 168-193 22-46 (60)
289 PRK11014 transcriptional repre 52.2 37 0.00081 26.9 5.3 45 148-193 7-51 (141)
290 PF14471 DUF4428: Domain of un 52.0 4.8 0.0001 26.5 -0.0 28 5-33 1-30 (51)
291 PF13591 MerR_2: MerR HTH fami 51.6 27 0.00059 25.2 4.0 74 167-241 1-75 (84)
292 PRK01110 rpmF 50S ribosomal pr 51.6 11 0.00023 25.8 1.6 28 4-39 28-55 (60)
293 COG1725 Predicted transcriptio 51.5 22 0.00048 28.0 3.7 27 167-194 36-62 (125)
294 PF01641 SelR: SelR domain; I 51.3 8.2 0.00018 30.4 1.2 32 19-50 33-66 (124)
295 PF13936 HTH_38: Helix-turn-he 50.8 33 0.00072 21.4 3.8 27 163-190 17-43 (44)
296 COG2816 NPY1 NTP pyrophosphohy 50.6 10 0.00022 34.1 1.8 28 4-33 112-139 (279)
297 PHA03074 late transcription fa 50.5 9.4 0.0002 32.5 1.5 30 2-34 3-32 (225)
298 PRK03564 formate dehydrogenase 50.4 14 0.00031 33.7 2.8 9 4-12 188-196 (309)
299 TIGR01562 FdhE formate dehydro 50.0 14 0.0003 33.7 2.7 9 25-33 254-262 (305)
300 COG3364 Zn-ribbon containing p 49.9 4.7 0.0001 30.4 -0.3 25 3-31 2-28 (112)
301 PF01022 HTH_5: Bacterial regu 49.9 45 0.00097 20.9 4.4 31 162-193 11-41 (47)
302 PF10005 DUF2248: Uncharacteri 49.8 9.4 0.0002 35.2 1.5 25 5-35 1-25 (343)
303 PRK15201 fimbriae regulatory p 49.7 57 0.0012 27.5 5.9 33 165-198 147-179 (198)
304 TIGR01562 FdhE formate dehydro 49.4 11 0.00023 34.5 1.8 28 4-31 185-218 (305)
305 COG1779 C4-type Zn-finger prot 49.2 8.2 0.00018 32.8 1.0 36 4-39 15-59 (201)
306 PRK14873 primosome assembly pr 49.0 13 0.00027 37.8 2.4 27 4-32 393-419 (665)
307 COG5333 CCL1 Cdk activating ki 49.0 40 0.00087 30.6 5.4 46 125-170 168-213 (297)
308 PF04502 DUF572: Family of unk 49.0 8.2 0.00018 35.5 1.0 28 4-32 78-105 (324)
309 PF01807 zf-CHC2: CHC2 zinc fi 48.4 16 0.00034 27.3 2.3 28 4-31 34-62 (97)
310 PF08280 HTH_Mga: M protein tr 47.8 27 0.00058 23.3 3.2 33 164-197 17-49 (59)
311 PRK00750 lysK lysyl-tRNA synth 47.6 14 0.0003 36.2 2.5 31 5-36 177-212 (510)
312 PRK06386 replication factor A; 47.6 9.4 0.0002 35.6 1.2 21 4-32 237-257 (358)
313 PF13560 HTH_31: Helix-turn-he 47.5 70 0.0015 21.3 5.4 51 163-228 11-61 (64)
314 smart00647 IBR In Between Ring 47.4 17 0.00038 24.1 2.3 29 3-33 18-50 (64)
315 COG1571 Predicted DNA-binding 47.4 11 0.00024 35.8 1.6 33 4-39 351-383 (421)
316 PF01047 MarR: MarR family; I 47.2 61 0.0013 21.0 4.9 28 165-193 16-43 (59)
317 PF13443 HTH_26: Cro/C1-type H 47.0 62 0.0013 21.3 5.0 45 167-226 11-55 (63)
318 PF10886 DUF2685: Protein of u 46.7 10 0.00022 25.2 0.9 36 3-39 1-39 (54)
319 PF10668 Phage_terminase: Phag 46.7 56 0.0012 22.3 4.6 26 163-189 19-44 (60)
320 PF01381 HTH_3: Helix-turn-hel 46.6 38 0.00083 21.6 3.8 47 164-226 7-53 (55)
321 cd07973 Spt4 Transcription elo 46.5 13 0.00027 28.1 1.5 28 3-33 3-30 (98)
322 PF00320 GATA: GATA zinc finge 46.4 7.2 0.00016 23.5 0.2 27 6-32 1-29 (36)
323 smart00529 HTH_DTXR Helix-turn 46.3 95 0.0021 22.3 6.3 29 113-144 2-30 (96)
324 COG4307 Uncharacterized protei 46.2 8.8 0.00019 34.2 0.7 28 1-34 1-28 (349)
325 smart00105 ArfGap Putative GTP 46.1 11 0.00023 29.0 1.1 31 4-34 4-34 (112)
326 PRK03975 tfx putative transcri 45.9 1.4E+02 0.003 24.0 7.5 31 165-196 20-50 (141)
327 KOG2907 RNA polymerase I trans 45.7 7.5 0.00016 29.9 0.2 31 3-35 7-37 (116)
328 PRK08558 adenine phosphoribosy 45.4 26 0.00057 30.7 3.6 52 159-223 16-68 (238)
329 PF13542 HTH_Tnp_ISL3: Helix-t 45.3 77 0.0017 20.0 5.9 24 167-191 28-51 (52)
330 PHA01976 helix-turn-helix prot 45.2 52 0.0011 22.0 4.5 48 164-227 13-60 (67)
331 PF09082 DUF1922: Domain of un 45.0 14 0.0003 25.8 1.4 26 5-34 5-30 (68)
332 PF13384 HTH_23: Homeodomain-l 44.8 40 0.00086 21.2 3.6 27 166-193 17-43 (50)
333 KOG1921 Endonuclease III [Repl 44.7 2.3E+02 0.0049 25.2 9.5 110 100-223 90-201 (286)
334 smart00418 HTH_ARSR helix_turn 44.6 65 0.0014 20.6 4.8 29 164-193 8-36 (66)
335 COG2260 Predicted Zn-ribbon RN 44.6 12 0.00025 25.3 1.0 23 3-33 5-27 (59)
336 COG3877 Uncharacterized protei 44.4 58 0.0013 24.8 4.7 40 153-198 49-88 (122)
337 PRK08329 threonine synthase; V 44.3 15 0.00032 34.0 2.0 26 3-34 1-26 (347)
338 PF13878 zf-C2H2_3: zinc-finge 44.3 9.4 0.0002 23.8 0.5 17 21-37 11-27 (41)
339 PRK09392 ftrB transcriptional 43.8 1.5E+02 0.0033 25.1 8.2 28 165-193 172-199 (236)
340 PF08006 DUF1700: Protein of u 43.5 51 0.0011 27.3 4.9 40 112-151 6-46 (181)
341 PF01710 HTH_Tnp_IS630: Transp 43.3 1.4E+02 0.0029 23.0 7.0 77 112-196 20-100 (119)
342 smart00354 HTH_LACI helix_turn 43.2 74 0.0016 21.8 5.0 45 168-227 2-48 (70)
343 PF01363 FYVE: FYVE zinc finge 43.1 15 0.00032 25.2 1.4 30 3-36 9-38 (69)
344 cd00674 LysRS_core_class_I cat 42.9 18 0.0004 33.6 2.4 14 162-175 279-292 (353)
345 PF01396 zf-C4_Topoisom: Topoi 42.8 30 0.00065 21.2 2.6 29 4-33 2-34 (39)
346 PRK08197 threonine synthase; V 42.6 11 0.00023 35.6 0.8 26 4-34 8-33 (394)
347 PRK00118 putative DNA-binding 42.3 98 0.0021 23.5 5.9 30 166-196 33-62 (104)
348 smart00351 PAX Paired Box doma 42.2 1.4E+02 0.003 23.2 6.9 61 112-175 35-102 (125)
349 PF04810 zf-Sec23_Sec24: Sec23 41.6 27 0.00058 21.5 2.2 30 3-32 2-33 (40)
350 smart00420 HTH_DEOR helix_turn 41.5 84 0.0018 19.3 5.1 29 165-194 13-41 (53)
351 PF00488 MutS_V: MutS domain V 41.5 32 0.00069 30.0 3.5 27 113-139 208-234 (235)
352 PRK14714 DNA polymerase II lar 41.3 12 0.00027 40.1 1.1 9 4-12 680-688 (1337)
353 COG1426 Predicted transcriptio 41.0 1.2E+02 0.0027 27.2 7.3 56 162-228 12-68 (284)
354 PRK14526 adenylate kinase; Pro 40.6 18 0.00039 31.0 1.8 30 5-34 124-153 (211)
355 PRK03564 formate dehydrogenase 40.5 17 0.00038 33.1 1.8 7 24-30 227-233 (309)
356 smart00290 ZnF_UBP Ubiquitin C 40.2 22 0.00048 22.6 1.8 23 5-35 1-23 (50)
357 smart00064 FYVE Protein presen 39.7 21 0.00045 24.4 1.7 29 4-36 11-39 (68)
358 PF03367 zf-ZPR1: ZPR1 zinc-fi 39.7 23 0.0005 29.1 2.2 31 4-34 2-41 (161)
359 COG0229 Conserved domain frequ 39.7 19 0.0004 28.8 1.6 32 19-50 38-71 (140)
360 smart00344 HTH_ASNC helix_turn 39.6 75 0.0016 23.5 5.0 29 165-194 16-44 (108)
361 PF13913 zf-C2HC_2: zinc-finge 39.5 19 0.0004 19.8 1.1 9 3-11 2-10 (25)
362 cd07377 WHTH_GntR Winged helix 39.4 52 0.0011 21.5 3.7 25 168-193 27-51 (66)
363 PF12840 HTH_20: Helix-turn-he 39.3 56 0.0012 21.7 3.8 31 162-193 20-50 (61)
364 PRK09685 DNA-binding transcrip 39.1 2.7E+02 0.0059 24.5 10.7 42 148-190 196-237 (302)
365 PRK04023 DNA polymerase II lar 39.0 18 0.00038 38.2 1.7 11 23-33 651-661 (1121)
366 PF04216 FdhE: Protein involve 38.6 18 0.00039 32.6 1.6 30 4-33 212-248 (290)
367 PF02796 HTH_7: Helix-turn-hel 38.5 39 0.00085 21.1 2.7 24 165-189 20-43 (45)
368 PF09567 RE_MamI: MamI restric 38.5 13 0.00028 32.8 0.5 37 3-48 82-118 (314)
369 cd00090 HTH_ARSR Arsenical Res 38.4 91 0.002 20.5 4.9 26 167-193 21-46 (78)
370 PF05225 HTH_psq: helix-turn-h 38.4 1E+02 0.0022 19.4 5.2 26 163-190 14-39 (45)
371 cd00131 PAX Paired Box domain 38.4 1.7E+02 0.0037 22.8 7.0 76 112-190 35-126 (128)
372 PF00126 HTH_1: Bacterial regu 38.2 1.1E+02 0.0023 20.2 5.1 31 168-199 15-45 (60)
373 PF03811 Zn_Tnp_IS1: InsA N-te 38.2 33 0.00072 20.8 2.2 13 4-17 6-19 (36)
374 TIGR02392 rpoH_proteo alternat 38.1 70 0.0015 28.3 5.3 31 164-195 234-264 (270)
375 COG3677 Transposase and inacti 38.1 26 0.00056 27.7 2.2 31 3-34 30-64 (129)
376 PF07295 DUF1451: Protein of u 38.0 14 0.00031 29.9 0.7 15 20-34 109-123 (146)
377 smart00346 HTH_ICLR helix_turn 37.9 1.2E+02 0.0025 21.5 5.6 29 165-194 19-47 (91)
378 PRK04217 hypothetical protein; 37.8 57 0.0012 25.1 4.0 28 168-196 60-87 (110)
379 PF03685 UPF0147: Uncharacteri 37.6 1.6E+02 0.0035 21.5 6.3 65 102-181 4-68 (85)
380 COG1198 PriA Primosomal protei 37.1 27 0.00058 35.8 2.6 27 4-32 445-471 (730)
381 PF04552 Sigma54_DBD: Sigma-54 37.0 11 0.00024 30.9 0.0 25 165-190 48-72 (160)
382 PF05066 HARE-HTH: HB1, ASXL, 37.0 37 0.00079 23.5 2.6 32 130-161 20-53 (72)
383 PF09779 Ima1_N: Ima1 N-termin 36.9 23 0.00049 28.1 1.7 29 5-33 2-30 (131)
384 cd04762 HTH_MerR-trunc Helix-T 36.6 47 0.001 20.1 2.9 22 168-190 2-23 (49)
385 TIGR00122 birA_repr_reg BirA b 36.6 90 0.0019 21.2 4.6 30 163-193 10-39 (69)
386 COG0375 HybF Zn finger protein 36.5 18 0.00039 28.0 1.1 20 15-34 62-81 (115)
387 TIGR02642 phage_xxxx uncharact 36.2 23 0.00049 29.9 1.7 23 4-30 100-122 (186)
388 TIGR01889 Staph_reg_Sar staphy 36.1 99 0.0021 23.2 5.1 34 160-194 37-70 (109)
389 PF00392 GntR: Bacterial regul 36.0 63 0.0014 21.6 3.7 29 164-193 21-50 (64)
390 COG5134 Uncharacterized conser 35.9 28 0.0006 30.0 2.1 25 4-28 80-104 (272)
391 PF08772 NOB1_Zn_bind: Nin one 35.5 20 0.00042 25.5 1.0 10 2-11 23-32 (73)
392 COG0177 Nth Predicted EndoIII- 35.5 2.9E+02 0.0063 23.8 8.5 88 139-238 78-167 (211)
393 PF12085 DUF3562: Protein of u 35.4 1.5E+02 0.0033 20.6 5.4 42 168-219 9-50 (66)
394 PF14205 Cys_rich_KTR: Cystein 35.3 33 0.00071 22.9 2.0 32 5-39 6-41 (55)
395 cd00065 FYVE FYVE domain; Zinc 35.2 28 0.00061 22.7 1.7 29 4-36 3-31 (57)
396 PRK07591 threonine synthase; V 34.7 18 0.00039 34.5 1.0 26 4-34 19-44 (421)
397 COG1675 TFA1 Transcription ini 34.7 8.5 0.00018 32.2 -1.1 32 3-36 113-145 (176)
398 TIGR00721 tfx DNA-binding prot 34.6 1.4E+02 0.003 23.9 5.9 32 165-197 20-51 (137)
399 COG1522 Lrp Transcriptional re 34.5 58 0.0013 25.7 3.8 32 162-194 18-49 (154)
400 COG1654 BirA Biotin operon rep 34.4 1.1E+02 0.0023 22.1 4.7 35 162-198 15-49 (79)
401 PRK10840 transcriptional regul 34.1 1.2E+02 0.0025 25.3 5.8 33 165-198 164-196 (216)
402 PRK00149 dnaA chromosomal repl 33.8 87 0.0019 30.0 5.5 41 154-197 392-433 (450)
403 TIGR03001 Sig-70_gmx1 RNA poly 33.8 75 0.0016 27.8 4.7 30 166-196 177-206 (244)
404 PRK13503 transcriptional activ 33.8 73 0.0016 27.8 4.7 39 151-191 173-211 (278)
405 PHA00689 hypothetical protein 33.7 29 0.00064 22.6 1.5 27 21-48 15-41 (62)
406 PRK04179 rpl37e 50S ribosomal 33.6 18 0.00039 24.7 0.6 23 4-31 18-40 (62)
407 PRK10130 transcriptional regul 33.6 3.9E+02 0.0085 24.7 11.0 42 148-191 239-280 (350)
408 PF07022 Phage_CI_repr: Bacter 33.4 49 0.0011 22.6 2.8 43 168-227 14-57 (66)
409 COG1499 NMD3 NMD protein affec 33.4 15 0.00034 34.2 0.3 12 1-12 4-15 (355)
410 PF00376 MerR: MerR family reg 33.4 46 0.00099 20.2 2.3 21 168-189 1-21 (38)
411 PRK04330 hypothetical protein; 33.3 2E+02 0.0043 21.2 6.6 65 102-181 7-71 (88)
412 PRK00762 hypA hydrogenase nick 33.1 18 0.0004 28.3 0.6 18 14-32 61-78 (124)
413 KOG0856 Predicted pilin-like t 33.1 23 0.00051 28.3 1.2 32 19-50 50-83 (146)
414 PF05043 Mga: Mga helix-turn-h 33.0 53 0.0012 23.4 3.1 33 163-196 27-59 (87)
415 cd04761 HTH_MerR-SF Helix-Turn 32.8 54 0.0012 20.3 2.7 21 168-189 2-22 (49)
416 PLN02569 threonine synthase 32.8 24 0.00052 34.4 1.5 26 4-34 50-75 (484)
417 COG5525 Bacteriophage tail ass 32.7 22 0.00048 35.2 1.2 32 5-36 229-272 (611)
418 TIGR00498 lexA SOS regulatory 32.6 70 0.0015 26.7 4.2 34 160-194 19-53 (199)
419 PRK05550 bifunctional methioni 32.5 26 0.00056 31.6 1.5 33 18-50 31-65 (283)
420 smart00530 HTH_XRE Helix-turn- 32.4 1.1E+02 0.0024 18.1 4.8 46 165-226 9-54 (56)
421 PF02591 DUF164: Putative zinc 32.2 25 0.00055 23.2 1.1 31 3-33 22-56 (56)
422 cd06171 Sigma70_r4 Sigma70, re 32.0 92 0.002 18.9 3.8 28 167-195 27-54 (55)
423 COG1321 TroR Mn-dependent tran 32.0 99 0.0022 25.1 4.8 72 155-228 14-97 (154)
424 COG2126 RPL37A Ribosomal prote 31.9 24 0.00053 23.8 0.9 24 4-32 17-40 (61)
425 cd04766 HTH_HspR Helix-Turn-He 31.8 90 0.002 22.6 4.2 71 167-240 2-76 (91)
426 smart00342 HTH_ARAC helix_turn 31.7 74 0.0016 21.5 3.6 25 166-191 1-25 (84)
427 PF01907 Ribosomal_L37e: Ribos 31.7 20 0.00043 23.9 0.5 23 5-32 17-39 (55)
428 smart00347 HTH_MARR helix_turn 31.3 1.2E+02 0.0025 21.5 4.8 28 166-194 24-51 (101)
429 PRK09263 anaerobic ribonucleos 31.2 25 0.00054 36.0 1.3 26 4-31 642-667 (711)
430 KOG0310 Conserved WD40 repeat- 31.2 3.7E+02 0.0081 26.1 9.0 118 113-240 345-462 (487)
431 PRK11032 hypothetical protein; 31.1 22 0.00048 29.3 0.8 15 20-34 121-135 (160)
432 TIGR00354 polC DNA polymerase, 31.1 21 0.00045 37.4 0.7 23 3-33 625-647 (1095)
433 TIGR01764 excise DNA binding d 31.0 65 0.0014 19.6 2.9 22 167-189 2-23 (49)
434 PF12651 RHH_3: Ribbon-helix-h 30.9 1.3E+02 0.0029 18.8 4.2 27 108-134 12-39 (44)
435 PRK11475 DNA-binding transcrip 30.8 1.5E+02 0.0032 25.2 5.9 32 166-198 149-180 (207)
436 PF08221 HTH_9: RNA polymerase 30.7 1.6E+02 0.0034 19.9 4.9 39 153-193 15-53 (62)
437 PRK15121 right oriC-binding tr 30.6 2.1E+02 0.0046 25.3 7.2 80 150-231 6-106 (289)
438 PRK15435 bifunctional DNA-bind 30.6 2.4E+02 0.0051 26.3 7.6 76 150-229 86-181 (353)
439 PRK10870 transcriptional repre 30.5 1.1E+02 0.0023 25.3 4.9 32 161-193 66-97 (176)
440 COG0846 SIR2 NAD-dependent pro 30.3 25 0.00055 31.1 1.1 38 4-41 123-165 (250)
441 PF09334 tRNA-synt_1g: tRNA sy 30.2 28 0.00061 32.8 1.5 26 4-36 137-162 (391)
442 smart00400 ZnF_CHCC zinc finge 30.2 61 0.0013 21.2 2.7 34 4-39 3-37 (55)
443 PRK00481 NAD-dependent deacety 30.1 29 0.00064 30.3 1.5 37 4-41 123-160 (242)
444 TIGR00281 segregation and cond 30.0 1.7E+02 0.0037 24.6 6.0 43 149-196 3-47 (186)
445 PF12728 HTH_17: Helix-turn-he 30.0 65 0.0014 20.3 2.8 22 167-189 2-23 (51)
446 PRK05638 threonine synthase; V 30.0 28 0.00061 33.3 1.4 25 4-34 2-26 (442)
447 PF06689 zf-C4_ClpX: ClpX C4-t 29.9 20 0.00043 22.3 0.3 28 4-31 2-32 (41)
448 PRK09636 RNA polymerase sigma 29.8 1.3E+02 0.0028 26.9 5.6 56 166-223 131-186 (293)
449 cd01411 SIR2H SIR2H: Uncharact 29.8 27 0.00058 30.2 1.1 36 4-41 119-154 (225)
450 PRK11337 DNA-binding transcrip 29.8 3.9E+02 0.0085 23.6 8.8 23 167-190 47-69 (292)
451 PRK13500 transcriptional activ 29.7 4.1E+02 0.0089 23.8 9.7 39 151-191 208-246 (312)
452 PRK10188 DNA-binding transcrip 29.7 1.6E+02 0.0036 25.5 6.1 33 165-198 193-225 (240)
453 PF01371 Trp_repressor: Trp re 29.6 1.1E+02 0.0024 22.4 4.2 31 162-193 45-75 (87)
454 PHA02325 hypothetical protein 29.6 29 0.00063 23.9 1.0 11 1-11 1-11 (72)
455 PF13408 Zn_ribbon_recom: Reco 29.5 27 0.00058 22.7 0.9 14 21-34 3-16 (58)
456 cd01410 SIRT7 SIRT7: Eukaryoti 29.5 28 0.00061 29.7 1.2 38 3-41 95-138 (206)
457 PF10389 CoatB: Bacteriophage 29.5 98 0.0021 19.9 3.4 21 249-269 24-44 (46)
458 PRK08173 DNA topoisomerase III 29.4 33 0.00072 35.9 2.0 27 4-34 625-651 (862)
459 COG5257 GCD11 Translation init 29.4 25 0.00054 32.5 0.9 25 4-33 58-82 (415)
460 PF06676 DUF1178: Protein of u 29.2 30 0.00065 28.1 1.2 39 106-146 83-121 (148)
461 PF14369 zf-RING_3: zinc-finge 29.1 49 0.0011 19.8 1.9 26 4-31 3-29 (35)
462 PF00643 zf-B_box: B-box zinc 29.0 39 0.00085 20.5 1.5 24 2-33 2-25 (42)
463 PF08421 Methyltransf_13: Puta 29.0 28 0.00061 23.6 0.9 17 23-39 40-56 (62)
464 PF14149 YhfH: YhfH-like prote 28.9 11 0.00023 23.1 -1.1 16 21-36 11-26 (37)
465 PF05819 NolX: NolX protein; 28.9 4.1E+02 0.0089 26.1 8.8 126 103-238 363-500 (624)
466 COG2771 CsgD DNA-binding HTH d 28.8 1.5E+02 0.0033 19.1 4.7 32 166-198 19-50 (65)
467 PF10083 DUF2321: Uncharacteri 28.8 32 0.0007 28.1 1.3 27 4-39 29-55 (158)
468 PF12677 DUF3797: Domain of un 28.8 43 0.00093 21.8 1.7 8 4-11 14-21 (49)
469 COG4311 SoxD Sarcosine oxidase 28.6 30 0.00065 25.8 1.1 12 1-12 1-12 (97)
470 cd00021 BBOX B-Box-type zinc f 28.5 49 0.0011 19.4 1.9 25 5-29 2-26 (39)
471 PRK00448 polC DNA polymerase I 28.4 29 0.00062 38.4 1.3 30 4-34 909-944 (1437)
472 PTZ00408 NAD-dependent deacety 28.4 23 0.0005 31.1 0.5 38 4-41 118-157 (242)
473 PF14690 zf-ISL3: zinc-finger 28.4 38 0.00082 21.1 1.4 8 4-11 3-10 (47)
474 PRK04194 hypothetical protein; 28.4 1.5E+02 0.0032 28.2 5.8 37 110-146 75-112 (392)
475 TIGR02947 SigH_actino RNA poly 28.4 1.4E+02 0.0031 24.4 5.4 30 166-196 147-176 (193)
476 COG1107 Archaea-specific RecJ- 28.4 42 0.00091 33.4 2.3 29 3-32 2-30 (715)
477 PRK03573 transcriptional regul 28.4 1.4E+02 0.0029 23.4 5.0 30 163-193 43-72 (144)
478 COG3024 Uncharacterized protei 28.1 32 0.0007 23.7 1.0 28 3-32 7-36 (65)
479 PF14833 NAD_binding_11: NAD-b 28.0 1.8E+02 0.004 22.0 5.6 39 104-142 72-110 (122)
480 PF13518 HTH_28: Helix-turn-he 28.0 1.1E+02 0.0023 19.1 3.6 25 168-193 14-38 (52)
481 PHA02970 hypothetical protein; 28.0 2.2E+02 0.0048 21.5 5.5 74 170-244 29-102 (115)
482 PRK14086 dnaA chromosomal repl 28.0 1.3E+02 0.0028 30.4 5.6 41 154-197 559-599 (617)
483 PRK12469 RNA polymerase factor 27.9 51 0.0011 32.1 2.8 24 165-189 368-391 (481)
484 PRK15411 rcsA colanic acid cap 27.9 97 0.0021 26.2 4.3 33 165-198 151-183 (207)
485 TIGR02844 spore_III_D sporulat 27.7 71 0.0015 23.0 2.9 23 165-188 18-40 (80)
486 COG1110 Reverse gyrase [DNA re 27.7 18 0.0004 38.2 -0.3 24 3-29 8-32 (1187)
487 TIGR02859 spore_sigH RNA polym 27.5 93 0.002 25.5 4.1 32 165-197 164-195 (198)
488 KOG0818 GTPase-activating prot 27.5 29 0.00064 33.7 1.0 30 3-33 8-38 (669)
489 COG2015 Alkyl sulfatase and re 27.5 2.6E+02 0.0057 27.5 7.3 79 159-238 375-466 (655)
490 TIGR02297 HpaA 4-hydroxyphenyl 27.4 4.1E+02 0.009 23.1 9.4 38 152-191 189-226 (287)
491 COG1698 Uncharacterized protei 27.2 2.3E+02 0.0051 20.9 5.4 42 212-255 20-61 (93)
492 PF12793 SgrR_N: Sugar transpo 27.0 1.1E+02 0.0024 23.6 4.0 59 162-221 15-80 (115)
493 PRK11169 leucine-responsive tr 27.0 1E+02 0.0022 25.1 4.1 33 162-195 24-56 (164)
494 PF14502 HTH_41: Helix-turn-he 26.9 1E+02 0.0022 20.0 3.2 28 167-195 7-34 (48)
495 PF14951 DUF4503: Domain of un 26.8 42 0.00092 31.2 1.9 33 5-38 276-309 (389)
496 PRK09978 DNA-binding transcrip 26.8 2.8E+02 0.0062 24.8 7.2 41 148-190 141-181 (274)
497 TIGR02607 antidote_HigA addict 26.8 2.1E+02 0.0046 19.5 5.4 51 162-228 14-64 (78)
498 COG2995 PqiA Uncharacterized p 26.8 33 0.00071 32.4 1.2 31 4-34 19-49 (418)
499 PF01921 tRNA-synt_1f: tRNA sy 26.7 18 0.0004 33.7 -0.4 15 161-175 285-299 (360)
500 TIGR02395 rpoN_sigma RNA polym 26.7 37 0.0008 32.5 1.6 24 165-189 317-340 (429)
No 1
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=100.00 E-value=3.8e-63 Score=449.46 Aligned_cols=252 Identities=31% Similarity=0.554 Sum_probs=233.6
Q ss_pred CCCCCCCCCCCceeEeCCCCceEcCCCcccccccccccccchhhccCCCCCCCCCcccCCCCCcccCCCcceEEecCCCC
Q 023713 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAG 82 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~~~~~~~r~G~~~~~~~~~~~~~t~i~~~~~~ 82 (278)
...||+||+ +++|+|+.+|++||.+||+|++|++||+|||||+|++++ .+|++|+|+|.++++||.|++|.|+++..+
T Consensus 11 ~~~Cp~Cg~-~~iv~d~~~Ge~vC~~CG~Vl~e~~iD~g~EWR~f~~~~-~~~~~RvG~~~~~~~~~~gl~T~I~~~~~~ 88 (310)
T PRK00423 11 KLVCPECGS-DKLIYDYERGEIVCADCGLVIEENIIDQGPEWRAFDPEQ-REKRSRVGAPMTYTIHDKGLSTDIDWRNKD 88 (310)
T ss_pred CCcCcCCCC-CCeeEECCCCeEeecccCCcccccccccCCCccCCCccc-cCCccccCCCCCccccCCCCceEeecCCcc
Confidence 367999998 689999999999999999999999999999999999754 468999999999999999999999977655
Q ss_pred CCccccc-------cccccccccC---CCchhHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHH
Q 023713 83 GSTELLS-------GSLGKLQARS---SHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIV 152 (278)
Q Consensus 83 ~~~~~l~-------~~l~~~~~~~---~~~er~l~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~a 152 (278)
++|..++ .+|++||++. +++||+|..+++.|+++|+.|+||+.++|+|..||+++++.++++||+.++++
T Consensus 89 ~~g~~l~~~~~~~~~rl~~~~~~~~~~~~~er~l~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~ 168 (310)
T PRK00423 89 SYGKSISGKNRAQLYRLRKWQRRIRVSNAAERNLAFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVV 168 (310)
T ss_pred cccccccHHHHHHHHHHHHHhhhcccCChHhHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHH
Confidence 5555443 2477888875 56899999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHHHHHHHH
Q 023713 153 AACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQ 232 (278)
Q Consensus 153 AAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~ 232 (278)
|||||+|||++++|+|++||+.+ +++++++|+++|+.|.+.|+++ +++.+|++||+|||+.|+|++++.+.|.
T Consensus 169 AAclYiACR~~~~prtl~eI~~~-~~v~~k~i~~~~~~l~k~L~~~------~~~~~p~~~i~r~~~~L~L~~~v~~~A~ 241 (310)
T PRK00423 169 AAALYAACRRCKVPRTLDEIAEV-SRVSRKEIGRCYRFLLRELNLK------LPPTDPIDYVPRFASELGLSGEVQKKAI 241 (310)
T ss_pred HHHHHHHHHHcCCCcCHHHHHHH-hCCCHHHHHHHHHHHHHHhCCC------CCCCCHHHHHHHHHHHcCCCHHHHHHHH
Confidence 99999999999999999999995 8999999999999999999987 7889999999999999999999999999
Q ss_pred HHHHHhhhcC--CCCChhHHHHHHHHHHHHHHHHH
Q 023713 233 EAVQKSEDLD--IRLILVFFSLFLVETHIQLIVWA 265 (278)
Q Consensus 233 ~i~~~~~~~~--~Gr~P~~iaaA~v~~~~~~~~~~ 265 (278)
+|++++.+.| .||+|.+||||+| ||++.+..
T Consensus 242 ~i~~~a~~~~l~~Gr~P~sIAAAaI--YlA~~~~g 274 (310)
T PRK00423 242 EILQKAKEKGLTSGKGPTGLAAAAI--YIASLLLG 274 (310)
T ss_pred HHHHHHHhcCcccCCCHHHHHHHHH--HHHHHHhC
Confidence 9999999888 6999999999999 99998764
No 2
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=3.1e-60 Score=410.80 Aligned_cols=253 Identities=53% Similarity=0.812 Sum_probs=230.7
Q ss_pred CCCCCCCCCCc-eeEeCCCCceEcCCCcccccccccccccchhhccCCCCCCCCCcccCCCCCcccCCCcceEEecCCCC
Q 023713 4 SYCADCKRLTE-VVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAG 82 (278)
Q Consensus 4 ~~Cp~Cg~~~~-vv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~~~~~~~r~G~~~~~~~~~~~~~t~i~~~~~~ 82 (278)
+.||+|+..+. +|+|+.+|++||..||+|+++++||+++|||+|+++.++.||+|||+|.||+|.+++++|+|+++. +
T Consensus 1 ~~c~~C~~~~~~~V~d~~~gdtvC~~CGlVl~~r~Id~~sEwrtfsnd~~~~DPsrvG~~sNPlL~~g~L~T~I~~g~-g 79 (308)
T KOG1597|consen 1 MTCPDCKRHPENLVEDHSAGDTVCSECGLVLEDRIIDEGSEWRTFSNDDSDADPSRVGASSNPLLDGGDLSTFISKGT-G 79 (308)
T ss_pred CCCCCCCCCCCCeeeeccCCceecccCCeeeccccccccccccccccCCCCCCccccCCCCCCCCCCCCcceeeecCC-C
Confidence 47999998766 999999999999999999999999999999999998888999999999999999999999999987 5
Q ss_pred CCccccccccccccccC--CCchhHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHH
Q 023713 83 GSTELLSGSLGKLQARS--SHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIAC 160 (278)
Q Consensus 83 ~~~~~l~~~l~~~~~~~--~~~er~l~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~ac 160 (278)
.++..++ .+.++|++. +++|+.+..+|..|..||+.++||..+.++|.++||++.+.+.++||+.++++|||||+||
T Consensus 80 ~~s~~~s-~l~~~Q~~~sm~~~d~~~~~a~~~I~~m~d~~~Lp~~I~d~A~~ifk~v~~~k~lrGks~eai~AAclyiAC 158 (308)
T KOG1597|consen 80 TSSSFAS-SLGKAQNRNSMSNSDRVLKAAFKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIAC 158 (308)
T ss_pred CCHHHHH-HHHHHhcccccCCccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHH
Confidence 5544343 488899854 6789999999999999999999999999999999999999999999999999999999999
Q ss_pred HhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh
Q 023713 161 RQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED 240 (278)
Q Consensus 161 R~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~ 240 (278)
|+++.|||++||+.+ .+|++++|+|.+|.|.+.|+... ++..++..+||+|||+.|+|+++++.+|.++++++..
T Consensus 159 Rq~~~pRT~kEI~~~-anv~kKEIgr~~K~i~~~l~~s~----~~~s~~t~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~ 233 (308)
T KOG1597|consen 159 RQEDVPRTFKEISAV-ANVSKKEIGRCVKLIGEALETSV----DLISISTGDFMPRFCSNLGLPKSAQEAATEIAEKAEE 233 (308)
T ss_pred HhcCCCchHHHHHHH-HcCCHHHHHHHHHHHHHHHhccc----hhhhhhHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHH
Confidence 999999999999996 78999999999999999998651 2334568999999999999999999999999999999
Q ss_pred cC--CCCChhHHHHHHHHHHHHHHHHH
Q 023713 241 LD--IRLILVFFSLFLVETHIQLIVWA 265 (278)
Q Consensus 241 ~~--~Gr~P~~iaaA~v~~~~~~~~~~ 265 (278)
++ .||+|.+||||+| |++..+-.
T Consensus 234 ~~~~~gRsPiSIAAa~I--Ymisqls~ 258 (308)
T KOG1597|consen 234 MDIRAGRSPISIAAAAI--YMISQLSD 258 (308)
T ss_pred hccccCCCchhHHHHHH--HHHHHhcc
Confidence 88 5899999999999 87766543
No 3
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=3.8e-58 Score=407.79 Aligned_cols=245 Identities=34% Similarity=0.612 Sum_probs=226.7
Q ss_pred CCCCCCCCCCCceeEeCCCCceEcCCCcccccccccccccchhhccCCCCCCCCCcccCCCCCcccCCCcceEEecCCCC
Q 023713 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAG 82 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~~~~~~~r~G~~~~~~~~~~~~~t~i~~~~~~ 82 (278)
++.||+||+ ++++.|+++|++||.+||+|++|..||.|||||.|+ + ...+ |+|.|.++.+||.|++|.|+++...
T Consensus 1 ~~~CpeCg~-~~~~~d~~~ge~VC~~CG~Vi~~~~id~gpewr~f~--e-~~~~-r~g~P~t~~~~d~~l~t~i~~~~~~ 75 (285)
T COG1405 1 VMSCPECGS-TNIITDYERGEIVCADCGLVLEDSLIDPGPEWRAFD--E-RHER-RVGAPLTPSIHDKGLSTIIGWGDKD 75 (285)
T ss_pred CCCCCCCCC-ccceeeccCCeEEeccCCEEeccccccCCCCccccc--c-cccc-cccCCCccccCccchhhhcccchhH
Confidence 368999999 699999999999999999999999999999999993 2 2234 9999999999999999999987532
Q ss_pred CCccccccccccccccC---CCchhHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHH
Q 023713 83 GSTELLSGSLGKLQARS---SHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIA 159 (278)
Q Consensus 83 ~~~~~l~~~l~~~~~~~---~~~er~l~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~a 159 (278)
...+|++||.+. +..||++..++.+|.++++.|+||.++.|+|..||++++++++++||+.++++|||+|+|
T Consensus 76 -----~~~rlr~~~~~~~v~~~~ernl~~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~a 150 (285)
T COG1405 76 -----KMYRLRKWQIRIRVSSAKERNLITALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAA 150 (285)
T ss_pred -----HHHHHHHHHhccccccchhhHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHH
Confidence 234588898654 468999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhh
Q 023713 160 CRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSE 239 (278)
Q Consensus 160 cR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~ 239 (278)
||+++.|+|+.||+.. +++++++|+++|+.+.+.|++. +++.+|.+||+|||+.|+|++++.+.|.+|+++++
T Consensus 151 cR~~~~prtl~eIa~a-~~V~~kei~rtyr~~~~~L~l~------~~~~~p~~yi~rf~s~L~l~~~v~~~a~ei~~~~~ 223 (285)
T COG1405 151 CRINGVPRTLDEIAKA-LGVSKKEIGRTYRLLVRELKLK------IPPVDPSDYIPRFASKLGLSDEVRRKAIEIVKKAK 223 (285)
T ss_pred HHHcCCCccHHHHHHH-HCCCHHHHHHHHHHHHHhcCCC------CCCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHHH
Confidence 9999999999999995 8999999999999999999997 78899999999999999999999999999999999
Q ss_pred hcC--CCCChhHHHHHHHHHHHHHHHHHH
Q 023713 240 DLD--IRLILVFFSLFLVETHIQLIVWAF 266 (278)
Q Consensus 240 ~~~--~Gr~P~~iaaA~v~~~~~~~~~~~ 266 (278)
+.+ .||+|.++|||+| ||+.++.+.
T Consensus 224 ~~g~~~Gk~P~glAaaai--y~as~l~~~ 250 (285)
T COG1405 224 RAGLTAGKSPAGLAAAAI--YLASLLLGE 250 (285)
T ss_pred HhCcccCCCchhHHHHHH--HHHHHHhCC
Confidence 988 6999999999999 999998763
No 4
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=100.00 E-value=1.1e-36 Score=283.18 Aligned_cols=226 Identities=21% Similarity=0.314 Sum_probs=196.1
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcccccccccccccchhhccCCCCCCCCCcccCCCCCcccCCCcceEEecCCCCC
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAGG 83 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~~~~~~~r~G~~~~~~~~~~~~~t~i~~~~~~~ 83 (278)
++|++||+ +++..|+.+|..+|+.||+|++++.|.. | .+|.+.. -|+.|+....+.
T Consensus 1 ~~C~~C~~-s~fe~d~a~g~~~C~~CG~v~E~~~ivs--e-v~F~e~~--------------------~G~~v~~~~~g~ 56 (521)
T KOG1598|consen 1 MVCKNCGG-SNFERDEATGNLYCTACGTVLEYNNIVA--E-VTFVEGA--------------------QGQFVRVGQSGA 56 (521)
T ss_pred CcCCCCCC-CCcccccccCCceeccccceeeccceeE--E-eeeeccc--------------------ceeEEeccccCC
Confidence 47999999 7899999999999999999999999984 4 4787421 123443222111
Q ss_pred CccccccccccccccCCCchhHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhc
Q 023713 84 STELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQE 163 (278)
Q Consensus 84 ~~~~l~~~l~~~~~~~~~~er~l~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~ 163 (278)
.. ...++++++.++...|.+++..|+|++ +++.|..+|+.+.+.++++||+...++|+|+|++||++
T Consensus 57 ~~------------s~e~r~~t~~n~r~~i~~~~~~l~l~~-~~~~a~~~~k~a~~~nftkGr~~~~vvasClY~vcR~e 123 (521)
T KOG1598|consen 57 GS------------SLESREKTIYNARRLIEELTERLNLGN-KTEVAFNFFKLAPDRNFTKGRRSTEVVAACLYLVCRLE 123 (521)
T ss_pred cc------------chHHHHHHHHHHHhHHHHHHHhcCcch-HHHHHHHHHHHHhhCCCCCCcchHHHHHHHHHHHHHhh
Confidence 10 124678999999999999999999999 99999999999999999999999999999999999999
Q ss_pred CCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCC---HHHHHHHHHHHHHhhh
Q 023713 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMT---NQAVKAAQEAVQKSED 240 (278)
Q Consensus 164 ~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~---~~v~~~A~~i~~~~~~ 240 (278)
+.++.+.|++++ ++|++++||+.|++|.+.|.+... -.|.+||..||+||...|.+. ++|+..|.+|++.|++
T Consensus 124 ~t~hlliDfS~~-Lqv~Vy~LG~~~l~l~~~L~i~en---~~plvDpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkr 199 (521)
T KOG1598|consen 124 KTDHLLIDFSSY-LQVSVYDLGSNFLEVTDSLSIGEN---VSPLVDPSLYIVRFSCRLLFGDKTEDVAKTATRLAQRMKR 199 (521)
T ss_pred CCceEEEEeccc-eEEehhhhhHHHHHHHHHhccccc---cccccCcceeeechhHhhhcCCchHHHHHHHHHHHHHHHH
Confidence 999999999995 999999999999999999988521 168899999999999999775 4689999999999999
Q ss_pred cC--CCCChhHHHHHHHHHHHHHHHHHHHhcccc
Q 023713 241 LD--IRLILVFFSLFLVETHIQLIVWAFMRCIYT 272 (278)
Q Consensus 241 ~~--~Gr~P~~iaaA~v~~~~~~~~~~~~~~~~~ 272 (278)
.| +||+|.+|++||| +|++++.+|++.++-
T Consensus 200 dwm~tGRRPsglcGAaL--liAar~h~~~rsi~d 231 (521)
T KOG1598|consen 200 DWMQTGRRPSGLCGAAL--LIAARMHGFRRTIGD 231 (521)
T ss_pred HHHHhCCCccchhHHHH--HHHHHHcCccccHHH
Confidence 99 7999999999999 999999999987754
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=99.79 E-value=8.2e-19 Score=125.43 Aligned_cols=71 Identities=44% Similarity=0.836 Sum_probs=65.9
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHH
Q 023713 113 ISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEI 184 (278)
Q Consensus 113 I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i 184 (278)
|+++|+.|+||+.+.++|.++|+++.+.++.+||++.+++|||||+|||+++.|+|++||+++ ++|++++|
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~-~~Vs~~tI 71 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEA-AGVSEKTI 71 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHH-CTSSHHHH
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHH-hCCCCCcC
Confidence 689999999999999999999999999999999999999999999999999999999999995 99999986
No 6
>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=99.63 E-value=1.7e-16 Score=102.03 Aligned_cols=43 Identities=47% Similarity=1.025 Sum_probs=38.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcccccccccccccchhhc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIF 47 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f 47 (278)
++||+||+ +.+++|+.+|++||++||.|++|+.++.++|||+|
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 67999999999999999999999999999999998
No 7
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.58 E-value=1.5e-14 Score=131.51 Aligned_cols=89 Identities=22% Similarity=0.382 Sum_probs=85.5
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHH
Q 023713 109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAK 188 (278)
Q Consensus 109 ~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~ 188 (278)
..++|.++|+.|+||..+.+.|.+|++++.+.+++.||+|.++||||||+||+.++.|+|++||+.+ .+|++.+|++.|
T Consensus 219 p~~~i~r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v-~~Vs~~tI~~~y 297 (310)
T PRK00423 219 PIDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEV-AGVTEVTVRNRY 297 (310)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHH-cCCCHHHHHHHH
Confidence 5689999999999999999999999999999999999999999999999999999999999999996 999999999999
Q ss_pred HHHHHHhhhh
Q 023713 189 EFIVKHLEAE 198 (278)
Q Consensus 189 ~~l~~~L~~~ 198 (278)
++|.+.|++.
T Consensus 298 kel~~~l~~~ 307 (310)
T PRK00423 298 KELAEKLDIK 307 (310)
T ss_pred HHHHHHhCcc
Confidence 9999999864
No 8
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=99.44 E-value=2.7e-13 Score=122.43 Aligned_cols=158 Identities=16% Similarity=0.225 Sum_probs=130.7
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcC-CCH--HH
Q 023713 107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANG-TTK--KE 183 (278)
Q Consensus 107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~-v~~--~~ 183 (278)
..+..+|.+++.+|++|...+.+|..+|.+++-...++.-.+..+|++|+|+|++.++.|+.++||..+... ..+ .+
T Consensus 40 ~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s~~~~~~~~~~ 119 (323)
T KOG0834|consen 40 QEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVSYRYLNPKDLE 119 (323)
T ss_pred HHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHHHHHcCccccc
Confidence 678999999999999999999999999999999888888889999999999999999999999999765221 122 12
Q ss_pred HHHH-----------HHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHH----HHHHHHHHHHHhhhcC--CCCC
Q 023713 184 IGRA-----------KEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQ----AVKAAQEAVQKSEDLD--IRLI 246 (278)
Q Consensus 184 i~~~-----------~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~----v~~~A~~i~~~~~~~~--~Gr~ 246 (278)
.... .+.|.+.|+++ +...+|..|+.+|+..|+.... +...|+.+++...... .--.
T Consensus 120 ~~~~~~~~~~~Iv~~E~~lL~tl~Fd------l~v~hPy~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL~y~ 193 (323)
T KOG0834|consen 120 LEEVYWELKERIVQLELLLLETLGFD------LNVEHPYKYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLCLQYS 193 (323)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHccCc------eeccCchHHHHHHHHHhhhhhhccccHHHHHHHHhchhheeeeeEeec
Confidence 3333 34445566665 7778999999999999998875 8899999999988754 5779
Q ss_pred hhHHHHHHHHHHHHHHHHHHHhcccc
Q 023713 247 LVFFSLFLVETHIQLIVWAFMRCIYT 272 (278)
Q Consensus 247 P~~iaaA~v~~~~~~~~~~~~~~~~~ 272 (278)
|..||.|+| |||+.+.+..-+..+
T Consensus 194 p~~IAva~i--~lA~~~~~~~~~~~~ 217 (323)
T KOG0834|consen 194 PHSIAVACI--HLAAKLLGVELPSDT 217 (323)
T ss_pred CcEEEeehh--hHHHHHcCCCCCCCc
Confidence 999999999 999999877554443
No 9
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=99.43 E-value=2e-12 Score=114.61 Aligned_cols=152 Identities=17% Similarity=0.211 Sum_probs=133.1
Q ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCC------
Q 023713 106 LIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT------ 179 (278)
Q Consensus 106 l~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v------ 179 (278)
..=+..+|++.|-.|+||+...-++..+|++....+.+.+.+.+.++.|||.+|.+.+..|++++||..|+..+
T Consensus 23 ~~LG~e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiEE~Prr~rdVinVFh~L~~r~~~ 102 (367)
T KOG0835|consen 23 RILGCELIQEAGILLNLPQVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIEEEPRRIRDVINVFHYLEQRRES 102 (367)
T ss_pred HHHhHHHHHhhhHhhcCcHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhccccccHhHHHHHHHHHHHHHhc
Confidence 34578999999999999999999999999999998888899999999999999999999999999998763221
Q ss_pred --------------CHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHHH--HHHHHHHHHHhhhcC-
Q 023713 180 --------------TKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQA--VKAAQEAVQKSEDLD- 242 (278)
Q Consensus 180 --------------~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v--~~~A~~i~~~~~~~~- 242 (278)
-+..+.++..+|.+.||+. +...+|+.+|--|.+-|++++.. .+.+|.+.+.+.+.+
T Consensus 103 ~~~~~~~~~~~~~~lk~~~ir~e~~ILr~LGF~------~Hv~hPhklii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v 176 (367)
T KOG0835|consen 103 EAAEHLILARLYINLKMQVIRAERRILRELGFD------VHVEHPHKLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDV 176 (367)
T ss_pred cCcchhhhhhHHhhhhhHHHHHHHHHHHHhCCe------eeeeccHHHHHHHHHHhcCCCchhHHHHHHHhhhhccccce
Confidence 1334557778899999987 77889999999999999998764 899999999998876
Q ss_pred -CCCChhHHHHHHHHHHHHHHHHH
Q 023713 243 -IRLILVFFSLFLVETHIQLIVWA 265 (278)
Q Consensus 243 -~Gr~P~~iaaA~v~~~~~~~~~~ 265 (278)
..-.|.+||+|+| |+++...+
T Consensus 177 ~vry~pe~iACaci--yLaAR~~e 198 (367)
T KOG0835|consen 177 FVRYSPESIACACI--YLAARNLE 198 (367)
T ss_pred eeecCHHHHHHHHH--HHHHhhhc
Confidence 5889999999999 99888766
No 10
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=99.42 E-value=8.1e-12 Score=112.89 Aligned_cols=154 Identities=12% Similarity=0.139 Sum_probs=129.5
Q ss_pred hhHH-HHHHHHHHHHHHhcC--CCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCC
Q 023713 103 DRNL-IQAFKSISAMSDRLG--LVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT 179 (278)
Q Consensus 103 er~l-~~~~~~I~~i~~~L~--Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v 179 (278)
|+.+ ......|.++|..|+ ||+.++-+|..+|++.+-.+.+.-..+..++++|||+||+.+..|+++.+++.. ..-
T Consensus 52 E~~l~~~y~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~-~~~ 130 (305)
T TIGR00569 52 ELDLVKYYEKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGN-LKE 130 (305)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhh-ccC
Confidence 3444 466889999999999 999999999999999999888877899999999999999999999999999874 333
Q ss_pred C----HHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcC-------CCHHHHHHHHHHHHHhhhcC--CCCC
Q 023713 180 T----KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLG-------MTNQAVKAAQEAVQKSEDLD--IRLI 246 (278)
Q Consensus 180 ~----~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~-------l~~~v~~~A~~i~~~~~~~~--~Gr~ 246 (278)
+ ...|......|.+.|++. +...+|..++..|...|+ -.+.+.+.|+.+++.+...+ .=-.
T Consensus 131 ~~~~~~~~Il~~E~~lL~~L~F~------L~V~hPyr~L~~~l~dl~~~l~~~~~~~~l~q~a~~~lndsl~Td~~L~y~ 204 (305)
T TIGR00569 131 TPLKALEQVLEYELLLIQQLNFH------LIVHNPYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYT 204 (305)
T ss_pred CchhhHHHHHHHHHHHHHHCCCc------EEeeCccHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHcCCceecCC
Confidence 2 478999999999999987 667789998888886543 22457788999999888766 5689
Q ss_pred hhHHHHHHHHHHHHHHHHH
Q 023713 247 LVFFSLFLVETHIQLIVWA 265 (278)
Q Consensus 247 P~~iaaA~v~~~~~~~~~~ 265 (278)
|.-||+||| |+++....
T Consensus 205 Ps~IAlAAI--~lA~~~~~ 221 (305)
T TIGR00569 205 PSQIALAAI--LHTASRAG 221 (305)
T ss_pred HHHHHHHHH--HHHHHHhC
Confidence 999999999 99886543
No 11
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=99.41 E-value=8.7e-13 Score=117.80 Aligned_cols=91 Identities=26% Similarity=0.379 Sum_probs=87.2
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHH
Q 023713 107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGR 186 (278)
Q Consensus 107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~ 186 (278)
.+..++|.+||+.|+||+.+...|.+|.+++.+.+.+.||+|..+||||||+|+++++.++|.+||+.+ +++++.+|++
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 366789999999999999999999999999999999999999999999999999999999999999996 9999999999
Q ss_pred HHHHHHHHhhhh
Q 023713 187 AKEFIVKHLEAE 198 (278)
Q Consensus 187 ~~~~l~~~L~~~ 198 (278)
.|++|.+.+++.
T Consensus 271 rykel~~~~~i~ 282 (285)
T COG1405 271 RYKELADALDIE 282 (285)
T ss_pred HHHHHHHhhccc
Confidence 999999999874
No 12
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=99.34 E-value=5.6e-12 Score=110.48 Aligned_cols=88 Identities=24% Similarity=0.348 Sum_probs=83.8
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHH
Q 023713 108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA 187 (278)
Q Consensus 108 ~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~ 187 (278)
+.-++|.+||+.|+||.++++.|.++.+++.+.+...||+|.++|||.||+++++...++|++||..+ +||.+.+|+..
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 36789999999999999999999999999999999999999999999999999999999999999996 99999999999
Q ss_pred HHHHHHHhh
Q 023713 188 KEFIVKHLE 196 (278)
Q Consensus 188 ~~~l~~~L~ 196 (278)
||.|..++.
T Consensus 281 YK~Lyp~~~ 289 (308)
T KOG1597|consen 281 YKDLYPHAD 289 (308)
T ss_pred HHHHhhchh
Confidence 999987764
No 13
>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=99.16 E-value=5.3e-10 Score=81.33 Aligned_cols=83 Identities=24% Similarity=0.378 Sum_probs=77.7
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCC-CHHHHHH
Q 023713 108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT-TKKEIGR 186 (278)
Q Consensus 108 ~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v-~~~~i~~ 186 (278)
.+.++|.+++..+++|..+...|..+++++...+.+.++++..+++||+|+||+.++.|.+++|+... .+. +..+|.+
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 888 9999999
Q ss_pred HHHHH
Q 023713 187 AKEFI 191 (278)
Q Consensus 187 ~~~~l 191 (278)
.++.|
T Consensus 83 ~e~~i 87 (88)
T cd00043 83 MEKLL 87 (88)
T ss_pred HHHHh
Confidence 88875
No 14
>COG5333 CCL1 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=99.12 E-value=9.1e-10 Score=97.63 Aligned_cols=149 Identities=19% Similarity=0.280 Sum_probs=125.9
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHH-------cCC
Q 023713 107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVA-------NGT 179 (278)
Q Consensus 107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~-------~~v 179 (278)
...+..|..+|.+|+||..+..+|..+|++.+-+....+.+...++++|||+|||.++.|+-+.-.+-.+ ..-
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 4568999999999999999999999999999998889999999999999999999999765544332221 123
Q ss_pred CHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCH--HHHHHHHHHHHHhhhcC--CCCChhHHHHHHH
Q 023713 180 TKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTN--QAVKAAQEAVQKSEDLD--IRLILVFFSLFLV 255 (278)
Q Consensus 180 ~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~--~v~~~A~~i~~~~~~~~--~Gr~P~~iaaA~v 255 (278)
+.+.|-....++.+.|+.. .-..+|..++.-|...+.+.. +..+.|+.+++.+.+.. .=-.|-.||.|++
T Consensus 126 sr~~Il~~E~~lLEaL~fd------~~V~hPy~~l~~f~~~~q~~~~~~~~~~aw~~inDa~~t~~~llypphiIA~a~l 199 (297)
T COG5333 126 SRERILEYEFELLEALDFD------LHVHHPYKYLEGFLKDLQEKDKYKLLQIAWKIINDALRTDLCLLYPPHIIALAAL 199 (297)
T ss_pred cHHHHHHHHHHHHHHcccc------eEeccccHHHHHHHHHHHhccHHHHHHHHHHHHHhhhhceeeeecChHHHHHHHH
Confidence 5788888888999999987 677889999999999987764 48999999999998866 4567999999999
Q ss_pred HHHHHHHH
Q 023713 256 ETHIQLIV 263 (278)
Q Consensus 256 ~~~~~~~~ 263 (278)
+|++-+
T Consensus 200 --~ia~~~ 205 (297)
T COG5333 200 --LIACEV 205 (297)
T ss_pred --HHHHHh
Confidence 888765
No 15
>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=99.06 E-value=1.1e-09 Score=78.88 Aligned_cols=80 Identities=23% Similarity=0.303 Sum_probs=71.9
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCC-CHHHHHHHHHH
Q 023713 112 SISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT-TKKEIGRAKEF 190 (278)
Q Consensus 112 ~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v-~~~~i~~~~~~ 190 (278)
+|.++++.+++|+.+...|..+++++.....+.++++..+++||+|+|||.++.+++..++... ++. +..+|.+.++.
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 6889999999999999999999999988433445999999999999999999999999999885 888 99999999988
Q ss_pred HH
Q 023713 191 IV 192 (278)
Q Consensus 191 l~ 192 (278)
|.
T Consensus 81 il 82 (83)
T smart00385 81 LL 82 (83)
T ss_pred Hh
Confidence 74
No 16
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=98.85 E-value=1e-08 Score=87.22 Aligned_cols=148 Identities=18% Similarity=0.275 Sum_probs=116.7
Q ss_pred HHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCH-HHHHHHH----------
Q 023713 108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTV-KEFCSVA---------- 176 (278)
Q Consensus 108 ~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl-~eia~~~---------- 176 (278)
.....|..+++.|+|-+.++-+|.-++++.+-++.+++-.+..+|.-|||+||+.+..|++. +-+...+
T Consensus 43 ~~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L~~~f~~~ 122 (264)
T KOG0794|consen 43 FMANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECPIVHIRLLVNEAKVLKTRFSYW 122 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHhhhcccc
Confidence 45678999999999999999999999999999888999999999999999999999998222 2222110
Q ss_pred ---cCCCHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCC-CHHHHHHHHHHHHHhhhcC--CCCChhHH
Q 023713 177 ---NGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGM-TNQAVKAAQEAVQKSEDLD--IRLILVFF 250 (278)
Q Consensus 177 ---~~v~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l-~~~v~~~A~~i~~~~~~~~--~Gr~P~~i 250 (278)
...+.+.|-...-.|.+.|+-- +-..+|..=+..+++.+|+ +......++.|++..-+.+ .=-.|--|
T Consensus 123 ~e~~~~~~~~I~e~Ef~llE~Ld~~------LIVhHPYrsL~q~~qd~gi~d~~~l~~~W~ivNDSyr~Dl~Ll~PPh~I 196 (264)
T KOG0794|consen 123 PEKFPYERKDILEMEFYLLEALDCY------LIVHHPYRSLLQFVQDMGINDQKLLQLAWSIVNDSYRMDLCLLYPPHQI 196 (264)
T ss_pred hhhcCCCcCcchhhhhhHHhhhcee------EEEecCCccHHHHHHHhcccchhhhhhhHhhhcchhhcceeeecCHHHH
Confidence 1123344555555666666643 3445677779999999999 5558999999999999877 57899999
Q ss_pred HHHHHHHHHHHHH
Q 023713 251 SLFLVETHIQLIV 263 (278)
Q Consensus 251 aaA~v~~~~~~~~ 263 (278)
|-|+| ||+.-+
T Consensus 197 alAcl--~Ia~~~ 207 (264)
T KOG0794|consen 197 ALACL--YIACVI 207 (264)
T ss_pred HHHHH--HHHHhh
Confidence 99999 998753
No 17
>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=98.81 E-value=1.4e-08 Score=72.25 Aligned_cols=51 Identities=16% Similarity=0.206 Sum_probs=43.8
Q ss_pred HHHHHhhcCCCHHHHHHHHHHHHHhhhcC--CCCChhHHHHHHHHHHHHHHHHHH
Q 023713 214 LRRFCSNLGMTNQAVKAAQEAVQKSEDLD--IRLILVFFSLFLVETHIQLIVWAF 266 (278)
Q Consensus 214 i~r~~~~L~l~~~v~~~A~~i~~~~~~~~--~Gr~P~~iaaA~v~~~~~~~~~~~ 266 (278)
|+|||+.|+|++++.+.|.+|++.+.+.+ .||+|.++|||+| |+++...+.
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~i--Y~acr~~~~ 53 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACI--YLACRLNGV 53 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHH--HHHHHHTTS
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHH--HHHHHHcCC
Confidence 68999999999999999999999999887 5999999999999 999876543
No 18
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=98.77 E-value=4.4e-07 Score=82.49 Aligned_cols=151 Identities=15% Similarity=0.169 Sum_probs=116.9
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCC-CCCCC--cHHHHHHHHHHHHHHhcCC--CCCHHHHHHH-HcCCC
Q 023713 107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQK-PLRGR--NQEAIVAACLYIACRQENK--PRTVKEFCSV-ANGTT 180 (278)
Q Consensus 107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~-~~~gr--~~~~~aAAclY~acR~~~~--p~tl~eia~~-~~~v~ 180 (278)
.+|+++|-+.|...+..+.+.=.|.+++.+..... +.+++ -...+|+||+.+|.+.+.. |.++.-.... ..-..
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 57999999999999999999999999999977644 33443 3789999999999999886 5444322221 13467
Q ss_pred HHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCC----HHHHHHHHH-HHHHhhhcC-CCCChhHHHHHH
Q 023713 181 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMT----NQAVKAAQE-AVQKSEDLD-IRLILVFFSLFL 254 (278)
Q Consensus 181 ~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~----~~v~~~A~~-i~~~~~~~~-~Gr~P~~iaaA~ 254 (278)
.++|.|....+...|+=+ +..+.|.+|+.-|++++++. ..+...+.. ++..+++.. .+-.|..||+|+
T Consensus 159 aktI~rmELLVLstL~Wr------l~aVTP~sF~~~fl~ki~~~~~~~~~~~~~~s~~ll~~~~d~~Fl~y~pSviAaa~ 232 (335)
T KOG0656|consen 159 AKTIQRMELLVLSTLKWR------LRAVTPFSFIDHFLSKISQKDHNKHLFLKHASLFLLSVITDIKFLEYPPSVIAAAA 232 (335)
T ss_pred HHHHHHHHHHHHhhcccc------ccCCCchHHHHHHHHHcCcccchHHHHHHHHHHHHHHHhhhhhhhcCChHHHHHHH
Confidence 999999999999999877 77889999999999999985 334555554 444445444 689999999998
Q ss_pred HHHHHHHHHHHHHh
Q 023713 255 VETHIQLIVWAFMR 268 (278)
Q Consensus 255 v~~~~~~~~~~~~~ 268 (278)
+ +++++.+.
T Consensus 233 ~-----~~v~~~~~ 241 (335)
T KOG0656|consen 233 I-----LSVSASVD 241 (335)
T ss_pred H-----HHHHHhhc
Confidence 8 56665554
No 19
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=98.64 E-value=2.3e-08 Score=94.54 Aligned_cols=91 Identities=19% Similarity=0.212 Sum_probs=75.0
Q ss_pred HHHHHHHHHHHHHhcC-CCH--HHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHH
Q 023713 106 LIQAFKSISAMSDRLG-LVT--TIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKK 182 (278)
Q Consensus 106 l~~~~~~I~~i~~~L~-Lp~--~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~ 182 (278)
|.+..-+|.+++..|- .|. .++.+|..+..++.......||+|..+++||||+|||.+|+++|..||+.+ ..|+..
T Consensus 163 lvDpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~~rsi~dIv~v-vhV~e~ 241 (521)
T KOG1598|consen 163 LVDPSLYIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGFRRTIGDIAKV-VHVCES 241 (521)
T ss_pred ccCcceeeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCccccHHHHHHH-HHHhHH
Confidence 3445557777777763 343 477777777777766667789999999999999999999999999999996 899999
Q ss_pred HHHHHHHHHHHHhhh
Q 023713 183 EIGRAKEFIVKHLEA 197 (278)
Q Consensus 183 ~i~~~~~~l~~~L~~ 197 (278)
+|.+.|+++.+.+..
T Consensus 242 Tl~kRl~Ef~~T~s~ 256 (521)
T KOG1598|consen 242 TLSKRLKEFSDTLSG 256 (521)
T ss_pred HHHHHHHHHhccccc
Confidence 999999999876654
No 20
>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=98.09 E-value=5.3e-05 Score=59.34 Aligned_cols=92 Identities=21% Similarity=0.342 Sum_probs=77.1
Q ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCC-CCCHHHHHHHHc--CCCHH
Q 023713 106 LIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVAN--GTTKK 182 (278)
Q Consensus 106 l~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~-p~tl~eia~~~~--~v~~~ 182 (278)
-....++|..++..++++..+.-.|..++.+..........+...++++|+++||+.+.. +.++.++... . ..+.+
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 356789999999999999999999999999998887777788999999999999999887 7888998774 3 35789
Q ss_pred HHHHHHHHHHHHhhhh
Q 023713 183 EIGRAKEFIVKHLEAE 198 (278)
Q Consensus 183 ~i~~~~~~l~~~L~~~ 198 (278)
+|....+.+.+.|+.+
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 9999999999988864
No 21
>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=97.91 E-value=2.6e-05 Score=56.19 Aligned_cols=58 Identities=14% Similarity=0.089 Sum_probs=53.1
Q ss_pred CCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhhcC--CCCChhHHHHHHHHHHHHHHHHHHH
Q 023713 208 IHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLD--IRLILVFFSLFLVETHIQLIVWAFM 267 (278)
Q Consensus 208 ~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~--~Gr~P~~iaaA~v~~~~~~~~~~~~ 267 (278)
..|.+||.++++.+++++++...|..++++..... .+++|..+|+|+| |||..+....
T Consensus 3 ~~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l--~lA~k~~~~~ 62 (88)
T cd00043 3 PTPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAAL--YLAAKVEEIP 62 (88)
T ss_pred chHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHH--HHHHHHcCCC
Confidence 46889999999999999999999999999998765 6999999999999 9999988773
No 22
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=97.80 E-value=0.00046 Score=65.00 Aligned_cols=145 Identities=14% Similarity=0.163 Sum_probs=115.1
Q ss_pred HHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHH-HHHHhcCCC-CCHHHHHHHH-cCCCH
Q 023713 105 NLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLY-IACRQENKP-RTVKEFCSVA-NGTTK 181 (278)
Q Consensus 105 ~l~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY-~acR~~~~p-~tl~eia~~~-~~v~~ 181 (278)
....-.+++-++-.+++|..++.-.|..|+.+.........+....+..+|++ +||+.+... -++.|+.-+. -..+.
T Consensus 157 mR~iLvdwlvevh~~F~L~~ETL~LaVnliDRfL~~~~v~~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd~~~s~ 236 (391)
T KOG0653|consen 157 MRAILVDWLVEVHEKFGLSPETLYLAVNLIDRFLSKVKVPLKKLQLVGVSALLSIACKYEEISLPSVEDLVLITDGAYSR 236 (391)
T ss_pred HHHHHHHHHHHhhhhcCcCHHHHHHHHHHHHHHHHHhcccHHHhhHHhHHHHHHHHHhhhhccCCccceeEeeeCCccch
Confidence 33456789999999999999999999999999988766777777777777756 999965544 3356654321 23689
Q ss_pred HHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhhcC--CCCChhHHHHHHH
Q 023713 182 KEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLD--IRLILVFFSLFLV 255 (278)
Q Consensus 182 ~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~--~Gr~P~~iaaA~v 255 (278)
.+|.++.+.+...|+.. +....|..|+.||........+....+..+++...-.- +...|..+|||+.
T Consensus 237 ~~il~mE~~il~~L~f~------l~~p~~~~FLrr~~ka~~~d~~~~~~~k~~~El~l~d~~~~~~~~s~~aaa~~ 306 (391)
T KOG0653|consen 237 EEILRMEKYILNVLEFD------LSVPTPLSFLRRFLKAADYDIKTRTLVKYLLELSLCDYSMLSIPPSSSAAASF 306 (391)
T ss_pred HHHHHHHHHHHhccCee------ecCCchHHHHHHHHHhhhcchhHHHHHHHHHHHHHhhhHHhccCcHHHHHHHH
Confidence 99999999999999886 67778999999999999977777888888888776432 6788888888888
No 23
>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=97.73 E-value=6.8e-05 Score=53.40 Aligned_cols=54 Identities=13% Similarity=0.218 Sum_probs=48.6
Q ss_pred HHHHHHHhhcCCCHHHHHHHHHHHHHhhhc-C-CCCChhHHHHHHHHHHHHHHHHHHH
Q 023713 212 DYLRRFCSNLGMTNQAVKAAQEAVQKSEDL-D-IRLILVFFSLFLVETHIQLIVWAFM 267 (278)
Q Consensus 212 ~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~-~-~Gr~P~~iaaA~v~~~~~~~~~~~~ 267 (278)
+||.++++.+++++++...|..++++.... . .+++|..+|+|+| |||..+.+.-
T Consensus 1 ~~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l--~lA~k~~~~~ 56 (83)
T smart00385 1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAAL--YLAAKTEEIP 56 (83)
T ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHH--HHHHHHhcCC
Confidence 489999999999999999999999999873 3 6899999999999 9999988754
No 24
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=97.69 E-value=0.00038 Score=65.78 Aligned_cols=150 Identities=13% Similarity=0.156 Sum_probs=120.3
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCC-CCHHHHHHHH-cCCCHHHHHH
Q 023713 109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKP-RTVKEFCSVA-NGTTKKEIGR 186 (278)
Q Consensus 109 ~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p-~tl~eia~~~-~~v~~~~i~~ 186 (278)
..++|.++=.+|+|-+.+...|..|..+.+..+...=.+...+++.|+|+||+-+.+. .++++++-+. ...+.++|.+
T Consensus 216 Lv~wlvevH~~F~llpeTL~lainiiDrfLs~~~v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~t~~~i~~ 295 (440)
T COG5024 216 LVDWLVEVHGKFGLLPETLFLAINIIDRFLSSRVVSLEKYQLVGISALFIASKYEEVNCPSIKDLVYATDGAFTRDDIIR 295 (440)
T ss_pred HHHHHHHhcccccccchHHHHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccccHHHHHH
Confidence 4678888888999988999999999999999887776678899999999999988754 5567775532 3568999999
Q ss_pred HHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhhcC--CCCChhHHHHHHHHHHHHHHHH
Q 023713 187 AKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLD--IRLILVFFSLFLVETHIQLIVW 264 (278)
Q Consensus 187 ~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~--~Gr~P~~iaaA~v~~~~~~~~~ 264 (278)
+.+.+...|+.. +....|..|+.|+-....-+......+..+.+...-.- .+-.|..+|||+- |++..+.
T Consensus 296 aE~~ml~~l~f~------is~P~P~sFLRriSka~dyd~~srt~~k~~~e~s~~~~~f~~~~~S~~~aaa~--~~s~~~~ 367 (440)
T COG5024 296 AERYMLEVLDFN------ISWPSPMSFLRRISKASDYDIFSRTPAKFSSEISPVDYKFIQISPSWCAAAAM--YLSRKIL 367 (440)
T ss_pred HHHHHhhhcccc------cCCCChHHHHHHHHhhcccchhhhhhHhhhCCchHhhhhhccCCchHHHHHHH--HHHHhhh
Confidence 999999999987 77778999988888877777777777777766655432 3344888999988 9888776
Q ss_pred HH
Q 023713 265 AF 266 (278)
Q Consensus 265 ~~ 266 (278)
+-
T Consensus 368 ~~ 369 (440)
T COG5024 368 SQ 369 (440)
T ss_pred cc
Confidence 53
No 25
>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=97.68 E-value=0.00024 Score=56.91 Aligned_cols=84 Identities=11% Similarity=0.245 Sum_probs=63.8
Q ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhh--CCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHH
Q 023713 106 LIQAFKSISAMSDRLGLVTTIKDRANEIYKKVED--QKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKE 183 (278)
Q Consensus 106 l~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~--~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~ 183 (278)
+.-|..+|+.+|++|+|++.+.+....+|+.+.. -.++++|..+.+..+|+|..||..+.++|++||-.. ..-.+..
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 YKLAAVRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDIIKA-YRKQPQA 89 (135)
T ss_dssp HHHHHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHHHH-HTTSTT-
T ss_pred HHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHHHH-HHhcccc
Confidence 3457889999999999999999999999988764 457899999999999999999999999999999774 4444444
Q ss_pred HHHHHHH
Q 023713 184 IGRAKEF 190 (278)
Q Consensus 184 i~~~~~~ 190 (278)
-..+|+.
T Consensus 90 ~~~Vyr~ 96 (135)
T PF01857_consen 90 SSHVYRS 96 (135)
T ss_dssp -THHHHS
T ss_pred cccceEE
Confidence 4444543
No 26
>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=97.67 E-value=0.0009 Score=59.65 Aligned_cols=142 Identities=14% Similarity=0.229 Sum_probs=95.6
Q ss_pred HHHHHHHHhc--CCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcC----CCHHHH
Q 023713 111 KSISAMSDRL--GLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANG----TTKKEI 184 (278)
Q Consensus 111 ~~I~~i~~~L--~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~----v~~~~i 184 (278)
..+-++++++ .||.+|+-+|..+|++++=.+...--+++.+.++|+|+||+.+..-+|..+|+.- .. -+...|
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 3445555555 7899999999999999987777777889999999999999999999999999874 43 334555
Q ss_pred HHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCC--CHHHH---HHHHHHHHHhhhcC--CCCChhHHHHHHH
Q 023713 185 GRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGM--TNQAV---KAAQEAVQKSEDLD--IRLILVFFSLFLV 255 (278)
Q Consensus 185 ~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l--~~~v~---~~A~~i~~~~~~~~--~Gr~P~~iaaA~v 255 (278)
-+.-..+.+.|+... .+..|.-..+-|+..+-..|.. +++.. ....+.++.+.-.+ .=-.|.=||-|+|
T Consensus 140 Lk~E~~llqsL~f~L--~vh~PyRPleGFl~D~kt~l~~~~n~d~~~~~~d~~~fl~~~lltDa~lLytPsQIALaAi 215 (325)
T KOG2496|consen 140 LKYEFLLLQSLKFSL--TVHNPYRPLEGFLLDMKTRLPALENPDILRKHDDSKKFLDRALLTDAYLLYTPSQIALAAI 215 (325)
T ss_pred HhchHHHHHhhhhhh--eecCCCCchHHHHHHHHHHHHhccCHHHHhhhhhHHHHHHHHHHhccceecChHHHHHHHH
Confidence 555557777777652 1112322334455444444321 22221 22235556555544 4578999999999
No 27
>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=97.11 E-value=0.00034 Score=42.80 Aligned_cols=28 Identities=29% Similarity=0.545 Sum_probs=23.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
..|+.||+ . .+...+|..+|..||.|.+
T Consensus 9 ~~C~~C~~-~--~~~~~dG~~yC~~cG~~~E 36 (36)
T PF11781_consen 9 EPCPVCGS-R--WFYSDDGFYYCDRCGHQSE 36 (36)
T ss_pred CcCCCCCC-e--EeEccCCEEEhhhCceEcC
Confidence 34999998 3 7778999999999999974
No 28
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=96.93 E-value=0.005 Score=55.52 Aligned_cols=107 Identities=20% Similarity=0.207 Sum_probs=77.4
Q ss_pred HHHHHHHHHHHHhcCCCHHH--HHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHH
Q 023713 107 IQAFKSISAMSDRLGLVTTI--KDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEI 184 (278)
Q Consensus 107 ~~~~~~I~~i~~~L~Lp~~v--~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i 184 (278)
.+....|-.+.+.|+||++. ...+.++......-.+..--+++.+|+||+|+|.|..++|.+..-..-.+++.++.+|
T Consensus 139 ~hPhklii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~vry~pe~iACaciyLaAR~~eIpLp~~P~Wf~~Fd~~k~ei 218 (367)
T KOG0835|consen 139 EHPHKLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVFVRYSPESIACACIYLAARNLEIPLPFQPHWFKAFDTTKREI 218 (367)
T ss_pred eccHHHHHHHHHHhcCCCchhHHHHHHHhhhhccccceeeecCHHHHHHHHHHHHHhhhcCCCCCCccHHHHcCCcHHHH
Confidence 44567788889999999754 6777777776665566666789999999999999999988665533222578899988
Q ss_pred HHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcC
Q 023713 185 GRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLG 222 (278)
Q Consensus 185 ~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~ 222 (278)
-..-..+....... .| -..+|.-|+..+.
T Consensus 219 d~ic~~l~~lY~~~------~p---~~~li~~~vd~~k 247 (367)
T KOG0835|consen 219 DEICYRLIPLYKRA------KP---DETLIEAFVDRLK 247 (367)
T ss_pred HHHHHHHHHHHHhc------cc---CHHHHHHHHHHhh
Confidence 87776666655542 11 2467777777664
No 29
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=96.83 E-value=0.0011 Score=39.71 Aligned_cols=31 Identities=16% Similarity=0.442 Sum_probs=25.4
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713 1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (278)
Q Consensus 1 ~~~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl 33 (278)
|....|+.||+ + .++....+..+|.+||.+.
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 45678999998 3 4555789999999999885
No 30
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=96.58 E-value=0.0015 Score=44.14 Aligned_cols=31 Identities=35% Similarity=0.745 Sum_probs=28.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e 35 (278)
.+||.|+. ..+||++.+-.+.|..||.+|.+
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 58999999999999999999963
No 31
>PRK00420 hypothetical protein; Validated
Probab=96.56 E-value=0.0017 Score=50.08 Aligned_cols=31 Identities=26% Similarity=0.560 Sum_probs=24.4
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 1 ~~~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
|-...||.||.+ .+-..+|+.+|..||.++.
T Consensus 21 ml~~~CP~Cg~p---Lf~lk~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 21 MLSKHCPVCGLP---LFELKDGEVVCPVHGKVYI 51 (112)
T ss_pred HccCCCCCCCCc---ceecCCCceECCCCCCeee
Confidence 344789999983 3434899999999999874
No 32
>PHA00626 hypothetical protein
Probab=96.49 E-value=0.0025 Score=42.33 Aligned_cols=31 Identities=19% Similarity=0.538 Sum_probs=23.7
Q ss_pred CCCCCCCCCCceeEe----CCCCceEcCCCcccccc
Q 023713 4 SYCADCKRLTEVVFD----HSAGDTICSECGLVLEA 35 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D----~~~G~~vC~~CG~Vl~e 35 (278)
+.||.||+ .+++.. -.+..++|.+||.-...
T Consensus 1 m~CP~CGS-~~Ivrcg~cr~~snrYkCkdCGY~ft~ 35 (59)
T PHA00626 1 MSCPKCGS-GNIAKEKTMRGWSDDYVCCDCGYNDSK 35 (59)
T ss_pred CCCCCCCC-ceeeeeceecccCcceEcCCCCCeech
Confidence 47999999 466643 23789999999998753
No 33
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=96.44 E-value=0.0018 Score=44.61 Aligned_cols=31 Identities=35% Similarity=0.764 Sum_probs=28.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e 35 (278)
..||.||. ..++|++.+-.+.|..||.+|-+
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 46999998 57999999999999999999963
No 34
>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=96.42 E-value=0.0015 Score=43.65 Aligned_cols=31 Identities=32% Similarity=0.687 Sum_probs=23.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e 35 (278)
.+||.|+. ..+||++.+-.+.|..||.+|.+
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 68999999999999999999963
No 35
>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This is the C-terminal domain of cyclins.; GO: 0005634 nucleus; PDB: 3QHR_D 3QHW_B 1W98_B 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D 2IW9_D ....
Probab=96.39 E-value=0.008 Score=45.97 Aligned_cols=55 Identities=13% Similarity=0.064 Sum_probs=45.0
Q ss_pred CHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhhcC--CCCChhHHHHHHHHHHHHHHHHH
Q 023713 209 HASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLD--IRLILVFFSLFLVETHIQLIVWA 265 (278)
Q Consensus 209 ~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~--~Gr~P~~iaaA~v~~~~~~~~~~ 265 (278)
.|.+|+.+|....+.+.++...|+.+++.+.-.. .+-+|..||||+| +++..+..
T Consensus 2 Tp~~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai--~lA~~~~~ 58 (118)
T PF02984_consen 2 TPYDFLRRFLKISNADQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAI--LLARKILG 58 (118)
T ss_dssp -HHHHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHH--HHHHHHHH
T ss_pred cHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHH--HHHHHHhC
Confidence 5899999997766677889999999999876543 7999999999999 88887754
No 36
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=96.27 E-value=0.0023 Score=36.16 Aligned_cols=23 Identities=22% Similarity=0.897 Sum_probs=18.4
Q ss_pred CCCCCCCCCCCceeEeCCCCceEcCCCcc
Q 023713 3 DSYCADCKRLTEVVFDHSAGDTICSECGL 31 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~ 31 (278)
+..||+||.. + ..+..+|.+||.
T Consensus 2 ~~~Cp~Cg~~--~----~~~~~fC~~CG~ 24 (26)
T PF13248_consen 2 EMFCPNCGAE--I----DPDAKFCPNCGA 24 (26)
T ss_pred cCCCcccCCc--C----CcccccChhhCC
Confidence 3899999983 2 356999999996
No 37
>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This is the C-terminal domain of cyclins.; GO: 0005634 nucleus; PDB: 3QHR_D 3QHW_B 1W98_B 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D 2IW9_D ....
Probab=96.24 E-value=0.025 Score=43.22 Aligned_cols=87 Identities=14% Similarity=0.129 Sum_probs=62.0
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCC-CCCHHHHHHHHcCCCHHHHHHH
Q 023713 109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVANGTTKKEIGRA 187 (278)
Q Consensus 109 ~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~-p~tl~eia~~~~~v~~~~i~~~ 187 (278)
.+.+|+.+....+....+...|..+.....-...+-.-++..+||||+|+|.+..+. +.--..+.. .++++..+|..+
T Consensus 3 p~~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~-~t~~~~~~l~~c 81 (118)
T PF02984_consen 3 PYDFLRRFLKISNADQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEK-LTGYDKEDLKEC 81 (118)
T ss_dssp HHHHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHH-HHTS-HHHHHHH
T ss_pred HHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchh-hcCCCHHHHHHH
Confidence 456777775544555677788888877755443355678999999999999998765 333344555 478999999999
Q ss_pred HHHHHHHhh
Q 023713 188 KEFIVKHLE 196 (278)
Q Consensus 188 ~~~l~~~L~ 196 (278)
++.|.+.+.
T Consensus 82 ~~~i~~~~~ 90 (118)
T PF02984_consen 82 IELIQELLS 90 (118)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 999988775
No 38
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=96.22 E-value=0.1 Score=47.42 Aligned_cols=142 Identities=15% Similarity=0.226 Sum_probs=104.1
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCC-CCCCCcHHHHHHHHHHHHHHhcC-CCCCHHHHHHHH-cCCCHHH
Q 023713 107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQK-PLRGRNQEAIVAACLYIACRQEN-KPRTVKEFCSVA-NGTTKKE 183 (278)
Q Consensus 107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~-~~~gr~~~~~aAAclY~acR~~~-~p~tl~eia~~~-~~v~~~~ 183 (278)
.-.++++-++|+-.+|...+.-.|..+|.+...-. -...-....+--+|+|+|.+.+. .|--+.|||.+. .-.+..+
T Consensus 146 aILlDWlmEVCEvykLHRETFyLAvDy~DRyl~t~~~v~kt~lQLIGitsLFIAAK~EEIYpPKl~eFAyvTDgAcs~dd 225 (408)
T KOG0655|consen 146 AILLDWLMEVCEVYKLHRETFYLAVDYFDRYLETQVEVSKTNLQLIGITSLFIAAKLEEIYPPKLIEFAYVTDGACSEDD 225 (408)
T ss_pred HHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHhhccCccccceeeeccCccchHH
Confidence 34589999999999999999999999999975422 12223456777899999999876 578889998762 3468999
Q ss_pred HHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCH-----------H-HHHHHHHHHHHh-hhcC-CCCChhH
Q 023713 184 IGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTN-----------Q-AVKAAQEAVQKS-EDLD-IRLILVF 249 (278)
Q Consensus 184 i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~-----------~-v~~~A~~i~~~~-~~~~-~Gr~P~~ 249 (278)
|.+....|.+.|+-+ +.++.....+.-|.+-+.+++ + ..+.| +|++.. .+.+ .-.+...
T Consensus 226 IltmE~iilkal~W~------l~PiTii~WL~vylQv~~~n~~~k~l~Pq~~~~efiqia-qlLDlc~ldids~~fsYri 298 (408)
T KOG0655|consen 226 ILTMELIILKALKWE------LSPITIISWLNVYLQVDALNDAPKVLLPQYSQEEFIQIA-QLLDLCILDIDSLEFSYRI 298 (408)
T ss_pred HHHHHHHHHHHhccc------ccceehHHHHHHHHHHHhcCCCCceeccccchHHHHHHH-HHHHHHHhccccccchHHH
Confidence 999999999999987 677788888888887765541 1 22222 233322 2223 4677788
Q ss_pred HHHHHH
Q 023713 250 FSLFLV 255 (278)
Q Consensus 250 iaaA~v 255 (278)
+|||||
T Consensus 299 laAAal 304 (408)
T KOG0655|consen 299 LAAAAL 304 (408)
T ss_pred HHHHHH
Confidence 888888
No 39
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=96.21 E-value=0.02 Score=52.82 Aligned_cols=92 Identities=12% Similarity=0.147 Sum_probs=64.2
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCC----CCHHHHHHHHcCCCHH
Q 023713 107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKP----RTVKEFCSVANGTTKK 182 (278)
Q Consensus 107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p----~tl~eia~~~~~v~~~ 182 (278)
.-..+++.+++..-+|...++.+|-.+|.++.=++++...++..+|+|||.+|.+.++.. .++.|=.+..+..+..
T Consensus 383 rSlKREMr~l~~d~~id~~TVa~AyVYFEKliLkglisK~NRKlcAGAclLlaaKmnD~Kks~vKslIek~Ee~fR~nrr 462 (497)
T KOG4164|consen 383 RSLKREMRELGEDCGIDVVTVAMAYVYFEKLILKGLISKQNRKLCAGACLLLAAKMNDLKKSTVKSLIEKLEEQFRLNRR 462 (497)
T ss_pred HHHHHHHHHhhhccCccceeehhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhcccHH
Confidence 334567777777788888899999999999887788877788999999999999988765 2333333323455555
Q ss_pred HHHHHHHHHHHHhhhh
Q 023713 183 EIGRAKEFIVKHLEAE 198 (278)
Q Consensus 183 ~i~~~~~~l~~~L~~~ 198 (278)
+|-...--+.-.|.+.
T Consensus 463 dLia~Ef~VlvaLefa 478 (497)
T KOG4164|consen 463 DLIAFEFPVLVALEFA 478 (497)
T ss_pred hhhhhhhhHHHhhhhh
Confidence 5555444444444443
No 40
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=96.20 E-value=0.0036 Score=40.39 Aligned_cols=31 Identities=39% Similarity=0.748 Sum_probs=25.3
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713 1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (278)
Q Consensus 1 ~~~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl 33 (278)
|....||+||. .+.+|+..+...|..||.-+
T Consensus 1 ~~~y~C~~CG~--~~~~~~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 1 MAEYKCARCGR--EVELDEYGTGVRCPYCGYRI 31 (46)
T ss_pred CCEEECCCCCC--EEEECCCCCceECCCCCCeE
Confidence 56689999997 47778777799999999643
No 41
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=96.09 E-value=0.0031 Score=34.57 Aligned_cols=22 Identities=27% Similarity=0.916 Sum_probs=17.1
Q ss_pred CCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713 5 YCADCKRLTEVVFDHSAGDTICSECGLV 32 (278)
Q Consensus 5 ~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V 32 (278)
.||+||.+ + ..+..+|++||.-
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 42
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=95.96 E-value=0.0023 Score=38.60 Aligned_cols=28 Identities=18% Similarity=0.662 Sum_probs=15.9
Q ss_pred CCCCCCCCCCceeEe----CCCCceEcCCCcccc
Q 023713 4 SYCADCKRLTEVVFD----HSAGDTICSECGLVL 33 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D----~~~G~~vC~~CG~Vl 33 (278)
..||.||++ +... ...-..||+.||.|-
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 4333 355568999999983
No 43
>PLN00209 ribosomal protein S27; Provisional
Probab=95.92 E-value=0.0051 Score=44.68 Aligned_cols=31 Identities=32% Similarity=0.641 Sum_probs=28.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e 35 (278)
..||.|+. ..+||++++-.+.|..||.+|.+
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 58999999999999999999963
No 44
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=95.86 E-value=0.0058 Score=44.27 Aligned_cols=31 Identities=26% Similarity=0.624 Sum_probs=28.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e 35 (278)
..||.|+. ..+||++++-.+.|..||.+|.+
T Consensus 36 VkCp~C~n-~q~VFShA~t~V~C~~Cg~~L~~ 66 (85)
T PTZ00083 36 VKCPGCSQ-ITTVFSHAQTVVLCGGCSSQLCQ 66 (85)
T ss_pred EECCCCCC-eeEEEecCceEEEccccCCEeec
Confidence 57999998 68999999999999999999953
No 45
>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=95.74 E-value=0.008 Score=36.90 Aligned_cols=28 Identities=32% Similarity=0.736 Sum_probs=22.0
Q ss_pred CCCCCCCCCCceeEeC--CCCceEcCCCcc
Q 023713 4 SYCADCKRLTEVVFDH--SAGDTICSECGL 31 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~--~~G~~vC~~CG~ 31 (278)
..||.||+....-+|. .+|..+|..||.
T Consensus 4 ~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred cCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 5799999865555665 559999999984
No 46
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=95.63 E-value=0.01 Score=36.07 Aligned_cols=31 Identities=16% Similarity=0.452 Sum_probs=19.5
Q ss_pred CCCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
|..||+||. --+......+...|..||.+.+
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 3334444555557999999864
No 47
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=95.46 E-value=0.0068 Score=47.83 Aligned_cols=24 Identities=29% Similarity=0.895 Sum_probs=20.0
Q ss_pred CCCCCCCCCCCceeEeCCCCceEcCCCc
Q 023713 3 DSYCADCKRLTEVVFDHSAGDTICSECG 30 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG 30 (278)
...||.||.+ + |- .+|+++|+.||
T Consensus 28 ~~hCp~Cg~P--L-F~-KdG~v~CPvC~ 51 (131)
T COG1645 28 AKHCPKCGTP--L-FR-KDGEVFCPVCG 51 (131)
T ss_pred HhhCcccCCc--c-ee-eCCeEECCCCC
Confidence 3679999984 3 43 89999999999
No 48
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=95.20 E-value=0.017 Score=42.05 Aligned_cols=30 Identities=30% Similarity=0.560 Sum_probs=25.9
Q ss_pred CCCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
...||.||+ + .|.-..+|-+.|..||.++.
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 467999998 4 57778999999999999875
No 49
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=95.05 E-value=0.018 Score=33.67 Aligned_cols=27 Identities=22% Similarity=0.367 Sum_probs=14.6
Q ss_pred CCCCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713 3 DSYCADCKRLTEVVFDHSAGDTICSECGLV 32 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V 32 (278)
.-.||.|+++ ..-. +...+||.+||.-
T Consensus 2 ~p~Cp~C~se-~~y~--D~~~~vCp~C~~e 28 (30)
T PF08274_consen 2 LPKCPLCGSE-YTYE--DGELLVCPECGHE 28 (30)
T ss_dssp S---TTT------EE---SSSEEETTTTEE
T ss_pred CCCCCCCCCc-ceec--cCCEEeCCccccc
Confidence 3579999995 3333 4789999999964
No 50
>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=95.02 E-value=0.014 Score=44.87 Aligned_cols=31 Identities=19% Similarity=0.602 Sum_probs=26.4
Q ss_pred CCCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY 36 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~ 36 (278)
.+.||.||.. .||-..--+||..||.++...
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 4789999984 788888889999999998644
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=95.01 E-value=0.013 Score=39.24 Aligned_cols=31 Identities=39% Similarity=0.768 Sum_probs=21.2
Q ss_pred CCCCCCCCCCCceeEeCCCCc-eEcCCCccccc
Q 023713 3 DSYCADCKRLTEVVFDHSAGD-TICSECGLVLE 34 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~-~vC~~CG~Vl~ 34 (278)
+..||.||..-+ +.|...|+ +.|.+||.-++
T Consensus 2 ~~~CP~CG~~ie-v~~~~~GeiV~Cp~CGaele 33 (54)
T TIGR01206 2 QFECPDCGAEIE-LENPELGELVICDECGAELE 33 (54)
T ss_pred ccCCCCCCCEEe-cCCCccCCEEeCCCCCCEEE
Confidence 368999998422 23333355 56999999885
No 52
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=94.92 E-value=0.019 Score=37.76 Aligned_cols=27 Identities=19% Similarity=0.605 Sum_probs=21.1
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl 33 (278)
..||.||+ + +..+ ..+...|..||...
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 53
>PRK11827 hypothetical protein; Provisional
Probab=94.90 E-value=0.021 Score=38.98 Aligned_cols=28 Identities=18% Similarity=0.494 Sum_probs=24.6
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl 33 (278)
..||.|++ .+.+|....+++|..||.+.
T Consensus 9 LaCP~ckg--~L~~~~~~~~Lic~~~~laY 36 (60)
T PRK11827 9 IACPVCNG--KLWYNQEKQELICKLDNLAF 36 (60)
T ss_pred eECCCCCC--cCeEcCCCCeEECCccCeec
Confidence 57999997 48888888899999999986
No 54
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=94.74 E-value=0.019 Score=32.42 Aligned_cols=25 Identities=28% Similarity=0.771 Sum_probs=19.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
..||+|+.. | ......|..||.++.
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 356889999999864
No 55
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=94.35 E-value=0.031 Score=36.72 Aligned_cols=29 Identities=17% Similarity=0.612 Sum_probs=19.9
Q ss_pred CCCCCCCCCCceeEeCCC--CceEcCCCccccc
Q 023713 4 SYCADCKRLTEVVFDHSA--GDTICSECGLVLE 34 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~--G~~vC~~CG~Vl~ 34 (278)
..||.||. .+...... ...+|+.||.+..
T Consensus 1 ~FCp~Cg~--~l~~~~~~~~~~~vC~~Cg~~~~ 31 (52)
T smart00661 1 KFCPKCGN--MLIPKEGKEKRRFVCRKCGYEEP 31 (52)
T ss_pred CCCCCCCC--ccccccCCCCCEEECCcCCCeEE
Confidence 36999997 23333222 3899999998764
No 56
>PRK10220 hypothetical protein; Provisional
Probab=94.34 E-value=0.12 Score=39.27 Aligned_cols=31 Identities=26% Similarity=0.467 Sum_probs=23.1
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 1 ~~~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
|..-.||.|+++ -.-. ....+||.+||.--.
T Consensus 1 m~lP~CP~C~se-ytY~--d~~~~vCpeC~hEW~ 31 (111)
T PRK10220 1 MSLPHCPKCNSE-YTYE--DNGMYICPECAHEWN 31 (111)
T ss_pred CCCCcCCCCCCc-ceEc--CCCeEECCcccCcCC
Confidence 677889999984 3333 356799999997553
No 57
>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=94.28 E-value=0.041 Score=34.61 Aligned_cols=25 Identities=32% Similarity=0.828 Sum_probs=19.7
Q ss_pred CCCCCCCCCCCceeEeCCCCceEcCCCc
Q 023713 3 DSYCADCKRLTEVVFDHSAGDTICSECG 30 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG 30 (278)
...||.||.+ +.. ..+|+++|..|+
T Consensus 17 ~~~Cp~C~~P--L~~-~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 17 DEHCPDCGTP--LMR-DKDGKIYCVSCG 41 (41)
T ss_pred cCccCCCCCe--eEE-ecCCCEECCCCC
Confidence 4689999863 444 579999999996
No 58
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=94.23 E-value=0.054 Score=36.89 Aligned_cols=29 Identities=24% Similarity=0.634 Sum_probs=21.2
Q ss_pred CCCCCCCCCCCCceeEeCCCC-------ceEcCCCcc
Q 023713 2 ADSYCADCKRLTEVVFDHSAG-------DTICSECGL 31 (278)
Q Consensus 2 ~~~~Cp~Cg~~~~vv~D~~~G-------~~vC~~CG~ 31 (278)
+...||-||+ ..+.++...+ .+.|.+||.
T Consensus 2 ~LkPCPFCG~-~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGS-ADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCC-cceEeecccCCCCCCEEEEEcCCCCC
Confidence 3568999998 5666665544 366999999
No 59
>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=94.07 E-value=0.032 Score=43.69 Aligned_cols=31 Identities=10% Similarity=0.203 Sum_probs=26.6
Q ss_pred CCCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY 36 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~ 36 (278)
.+.||.||.. .||-..--+||..||.++...
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 4789999984 788888999999999998644
No 60
>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=94.06 E-value=0.042 Score=34.34 Aligned_cols=29 Identities=31% Similarity=0.620 Sum_probs=16.4
Q ss_pred CCCCCCCCCCcee-EeC--CCCceEcCCCccc
Q 023713 4 SYCADCKRLTEVV-FDH--SAGDTICSECGLV 32 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv-~D~--~~G~~vC~~CG~V 32 (278)
..||.||+....- +|. .+|..+|..|+-+
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 4699999855544 553 5699999999434
No 61
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=94.04 E-value=0.043 Score=44.92 Aligned_cols=30 Identities=27% Similarity=0.569 Sum_probs=20.6
Q ss_pred CCCCCCCCCCceeEeCC---CCce-----EcCCCcccc
Q 023713 4 SYCADCKRLTEVVFDHS---AGDT-----ICSECGLVL 33 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~---~G~~-----vC~~CG~Vl 33 (278)
+.||+||++.+-+.|.. .|.. -|++||.-.
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence 57999998533566643 4543 499999765
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=94.03 E-value=0.053 Score=37.99 Aligned_cols=18 Identities=33% Similarity=0.752 Sum_probs=16.0
Q ss_pred EeCCCCceEcCCCccccc
Q 023713 17 FDHSAGDTICSECGLVLE 34 (278)
Q Consensus 17 ~D~~~G~~vC~~CG~Vl~ 34 (278)
++..+|.++|.+||.+..
T Consensus 47 ~~i~eg~L~Cp~c~r~YP 64 (68)
T PF03966_consen 47 VEIVEGELICPECGREYP 64 (68)
T ss_dssp EETTTTEEEETTTTEEEE
T ss_pred ccccCCEEEcCCCCCEEe
Confidence 688999999999999863
No 63
>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=93.99 E-value=1.4 Score=35.63 Aligned_cols=89 Identities=15% Similarity=0.154 Sum_probs=65.9
Q ss_pred HHHHHHHHHHhcCCCHHHHHHHHHHHHHHhh---CCC--CCCCcHHHHHHHHHHHHHH-hcCCCCCHHHHHHHHcCCCHH
Q 023713 109 AFKSISAMSDRLGLVTTIKDRANEIYKKVED---QKP--LRGRNQEAIVAACLYIACR-QENKPRTVKEFCSVANGTTKK 182 (278)
Q Consensus 109 ~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~---~~~--~~gr~~~~~aAAclY~acR-~~~~p~tl~eia~~~~~v~~~ 182 (278)
..+++.++....+++..+.-.|..+..++.. ... +...+..-+..+|+-+|.+ ..+...+.+..+.+ .|++.+
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 5778999999999999999999999999877 222 3345666677777777877 56788999999996 899999
Q ss_pred HHHHHHHHHHHHhhhh
Q 023713 183 EIGRAKEFIVKHLEAE 198 (278)
Q Consensus 183 ~i~~~~~~l~~~L~~~ 198 (278)
+|++..+.+...++.+
T Consensus 133 eln~lE~~fL~~l~~~ 148 (149)
T PF08613_consen 133 ELNELEREFLKLLDYN 148 (149)
T ss_dssp HHHHHHHHHHHHTTT-
T ss_pred HHHHHHHHHHHHCCCc
Confidence 9999999999888753
No 64
>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=93.83 E-value=0.07 Score=31.53 Aligned_cols=27 Identities=19% Similarity=0.465 Sum_probs=16.6
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLV 32 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V 32 (278)
..|+.||++ .+.....-..+|++||..
T Consensus 4 rfC~~CG~~--t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 4 RFCGRCGAP--TKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp SB-TTT--B--EEE-SSSS-EEESSSS-E
T ss_pred cccCcCCcc--ccCCCCcCEeECCCCcCE
Confidence 689999984 455566788999999975
No 65
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=93.65 E-value=0.026 Score=34.70 Aligned_cols=29 Identities=28% Similarity=0.607 Sum_probs=20.7
Q ss_pred CCCCCCCCCCceeEe-----CCCCceEcCCCccccc
Q 023713 4 SYCADCKRLTEVVFD-----HSAGDTICSECGLVLE 34 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D-----~~~G~~vC~~CG~Vl~ 34 (278)
..||+||.. ..++ ...+.+.|++||.++.
T Consensus 3 ~~CP~C~~~--~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTS--FRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCE--EEeCHHHcCCCCCEEECCCCCCEEE
Confidence 579999983 2222 2345799999999874
No 66
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=93.65 E-value=0.049 Score=36.96 Aligned_cols=30 Identities=30% Similarity=0.651 Sum_probs=26.5
Q ss_pred CCCCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713 2 ADSYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (278)
Q Consensus 2 ~~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl 33 (278)
+...||.|.+. +.+|.+.++++|..||...
T Consensus 7 eiLaCP~~kg~--L~~~~~~~~L~c~~~~~aY 36 (60)
T COG2835 7 EILACPVCKGP--LVYDEEKQELICPRCKLAY 36 (60)
T ss_pred eeeeccCcCCc--ceEeccCCEEEecccCcee
Confidence 45679999983 9999999999999999986
No 67
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=93.22 E-value=0.06 Score=41.59 Aligned_cols=25 Identities=32% Similarity=0.634 Sum_probs=20.4
Q ss_pred CCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713 6 CADCKRLTEVVFDHSAGDTICSECGLVLEAY 36 (278)
Q Consensus 6 Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~ 36 (278)
||.||+ .-+|. .+-|.+||+.++.+
T Consensus 1 CPvCg~-~l~vt-----~l~C~~C~t~i~G~ 25 (113)
T PF09862_consen 1 CPVCGG-ELVVT-----RLKCPSCGTEIEGE 25 (113)
T ss_pred CCCCCC-ceEEE-----EEEcCCCCCEEEee
Confidence 999998 44454 89999999999643
No 68
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=93.17 E-value=0.052 Score=35.21 Aligned_cols=27 Identities=26% Similarity=0.733 Sum_probs=22.1
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLV 32 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V 32 (278)
..||.||. ..+..|+.. .+.|..||..
T Consensus 20 ~~CPrCG~-gvfmA~H~d-R~~CGkCgyT 46 (51)
T COG1998 20 RFCPRCGP-GVFMADHKD-RWACGKCGYT 46 (51)
T ss_pred ccCCCCCC-cchhhhcCc-eeEeccccce
Confidence 57999996 566777766 8999999986
No 69
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=93.12 E-value=5.2 Score=34.43 Aligned_cols=138 Identities=17% Similarity=0.219 Sum_probs=95.8
Q ss_pred HHHHHHHhcCCC--HHHHHHHHHHHHHHhh--CCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHH
Q 023713 112 SISAMSDRLGLV--TTIKDRANEIYKKVED--QKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA 187 (278)
Q Consensus 112 ~I~~i~~~L~Lp--~~v~e~A~~i~k~~~~--~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~ 187 (278)
.|.+++.+|||. +.+.+.|.+|.+...- .+..-|-.-..-|.-|+=+|.-.-++|..-.-... ..|.++++-.+.
T Consensus 2 lI~~l~~klgL~~ep~~lrKa~E~~RL~~~~~~~~~~~v~E~~kaV~CldlAa~~l~i~fDr~~avK-LSGl~k~~Y~~~ 80 (262)
T KOG4557|consen 2 LISDLGRKLGLDNEPLLLRKAAEIRRLCDAQFDSSIIGVGEICKAVICLDLAATRLQIIFDRQAAVK-LSGLSKKAYSRS 80 (262)
T ss_pred cHHHHHHhcCCccChHHHHHHHHHHHHHHhhccCccccccchhHHHHhHHHHHHHhcccccHHHHHH-hccccHHHHHHH
Confidence 478899999993 5789999999887643 23334445566777888888888888877666667 489999999999
Q ss_pred HHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh-------cCC-CCChhHHHHHHHHHHH
Q 023713 188 KEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED-------LDI-RLILVFFSLFLVETHI 259 (278)
Q Consensus 188 ~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~-------~~~-Gr~P~~iaaA~v~~~~ 259 (278)
++.+...||+. . ..+ |..+|=+||. .++++.|.+++..-+. .+. =.+|. .++||+ |.
T Consensus 81 ~~sfe~llgln------~-~~~----VrdlaVQfgc-~evi~~a~~vl~syk~~lpaT~~~~~D~SrP~-ft~aA~--~~ 145 (262)
T KOG4557|consen 81 FNSFENLLGLN------I-KLN----VRDLAVQFGC-VEVIKSAQNVLSSYKERLPATRRANADFSRPV-FTAAAF--YL 145 (262)
T ss_pred HHHHHHHhcch------h-hcC----HHHHHHHHhH-HHHHHHHHHHHHHHHhcCchhhhcCCcccchH-HHHHHH--HH
Confidence 99999999986 1 122 3445555554 3566677777765544 122 22454 556667 78
Q ss_pred HHHHHH
Q 023713 260 QLIVWA 265 (278)
Q Consensus 260 ~~~~~~ 265 (278)
++.+..
T Consensus 146 ack~lK 151 (262)
T KOG4557|consen 146 ACKKLK 151 (262)
T ss_pred HHHHHH
Confidence 877653
No 70
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=92.63 E-value=0.29 Score=37.04 Aligned_cols=33 Identities=24% Similarity=0.614 Sum_probs=24.5
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713 1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY 36 (278)
Q Consensus 1 ~~~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~ 36 (278)
|.+-.||.|.++ -+++ ..+.++|++|+.--.+.
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 566789999983 4554 45599999999876544
No 71
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=92.47 E-value=0.13 Score=41.53 Aligned_cols=30 Identities=30% Similarity=0.633 Sum_probs=23.5
Q ss_pred CCCCCCCCCCceeEeC---CCCceE-----cCCCcccc
Q 023713 4 SYCADCKRLTEVVFDH---SAGDTI-----CSECGLVL 33 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~---~~G~~v-----C~~CG~Vl 33 (278)
|.||.||...+-|.|. ..|..| |.+||.=.
T Consensus 1 M~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RF 38 (147)
T TIGR00244 1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERF 38 (147)
T ss_pred CCCCCCCCCCCEeeeccccCCCCeeeecccCCccCCcc
Confidence 5799999866668886 667666 99999754
No 72
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=92.12 E-value=0.14 Score=34.04 Aligned_cols=31 Identities=26% Similarity=0.382 Sum_probs=20.9
Q ss_pred CCCCCCCCCCce-eE---eC--CCCceEcCCCcccccc
Q 023713 4 SYCADCKRLTEV-VF---DH--SAGDTICSECGLVLEA 35 (278)
Q Consensus 4 ~~Cp~Cg~~~~v-v~---D~--~~G~~vC~~CG~Vl~e 35 (278)
..||.||+. +. +. |. ..|-..|.+||.....
T Consensus 2 kPCPfCGg~-~~~~~~~~~~~~~~~~~~C~~Cga~~~~ 38 (53)
T TIGR03655 2 KPCPFCGGA-DVYLRRGFDPLDLSHYFECSTCGASGPV 38 (53)
T ss_pred CCCCCCCCc-ceeeEeccCCCCCEEEEECCCCCCCccc
Confidence 579999994 44 32 32 3444579999998653
No 73
>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=91.99 E-value=0.4 Score=36.47 Aligned_cols=30 Identities=20% Similarity=0.432 Sum_probs=21.6
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAY 36 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~ 36 (278)
-.||.|+++ -.-.| ...+||++||.--.+.
T Consensus 3 p~CP~C~se-ytY~d--g~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 3 PPCPKCNSE-YTYHD--GTQLICPSCLYEWNEN 32 (109)
T ss_pred CcCCcCCCc-ceEec--CCeeECcccccccccc
Confidence 479999984 33433 5579999999876544
No 74
>PRK12495 hypothetical protein; Provisional
Probab=91.89 E-value=0.1 Score=44.75 Aligned_cols=32 Identities=22% Similarity=0.668 Sum_probs=25.8
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713 1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY 36 (278)
Q Consensus 1 ~~~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~ 36 (278)
|....|+.||.+ |+ ...|..+|..|+.++.+.
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 456789999984 44 458999999999998753
No 75
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=91.59 E-value=0.1 Score=37.15 Aligned_cols=30 Identities=27% Similarity=0.683 Sum_probs=27.1
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
.+||.|-. .+.+|.+++..++|.+|++|+=
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 57999997 6889999999999999999973
No 76
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=90.98 E-value=0.14 Score=38.78 Aligned_cols=28 Identities=29% Similarity=0.789 Sum_probs=21.8
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e 35 (278)
..||.||+. +.+..+.++|..||.+...
T Consensus 1 ~fC~~Cg~~----l~~~~~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 1 KFCPKCGSL----MTPKNGVYVCPSCGYEKEK 28 (104)
T ss_pred CCCcccCcc----cccCCCeEECcCCCCcccc
Confidence 379999972 3456789999999998653
No 77
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=90.96 E-value=0.15 Score=38.49 Aligned_cols=41 Identities=22% Similarity=0.467 Sum_probs=28.1
Q ss_pred CCCCCCCCCCce--eEeCCCCceEcCCCccccccc------ccccccchh
Q 023713 4 SYCADCKRLTEV--VFDHSAGDTICSECGLVLEAY------SVDETSEWR 45 (278)
Q Consensus 4 ~~Cp~Cg~~~~v--v~D~~~G~~vC~~CG~Vl~e~------~id~~~ewr 45 (278)
..||+||. ..+ -.|...+..+|..||..-+-. .||-..+|.
T Consensus 22 f~CP~Cge-~~v~v~~~k~~~h~~C~~CG~y~~~~V~~l~epIDVY~~wi 70 (99)
T PRK14892 22 FECPRCGK-VSISVKIKKNIAIITCGNCGLYTEFEVPSVYDEVDVYNKFI 70 (99)
T ss_pred eECCCCCC-eEeeeecCCCcceEECCCCCCccCEECCccccchhhHHHHH
Confidence 46999996 333 355677899999999986432 245455564
No 78
>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=90.52 E-value=0.16 Score=30.11 Aligned_cols=24 Identities=29% Similarity=0.641 Sum_probs=17.4
Q ss_pred CCCCCCCCCceeEeCCCCceEcCCCcc
Q 023713 5 YCADCKRLTEVVFDHSAGDTICSECGL 31 (278)
Q Consensus 5 ~Cp~Cg~~~~vv~D~~~G~~vC~~CG~ 31 (278)
.|.+||.+ +.+.....+-|.+||.
T Consensus 2 ~C~~Cg~~---~~~~~~~~irC~~CG~ 25 (32)
T PF03604_consen 2 ICGECGAE---VELKPGDPIRCPECGH 25 (32)
T ss_dssp BESSSSSS---E-BSTSSTSSBSSSS-
T ss_pred CCCcCCCe---eEcCCCCcEECCcCCC
Confidence 58999984 3356677889999996
No 79
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=90.35 E-value=0.16 Score=37.58 Aligned_cols=32 Identities=25% Similarity=0.440 Sum_probs=25.3
Q ss_pred CCCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY 36 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~ 36 (278)
...||.||. .. +.-...|-+-|..||.++...
T Consensus 35 ky~Cp~Cgk-~~-vkR~a~GIW~C~~C~~~~AGG 66 (90)
T PF01780_consen 35 KYTCPFCGK-TS-VKRVATGIWKCKKCGKKFAGG 66 (90)
T ss_dssp -BEESSSSS-SE-EEEEETTEEEETTTTEEEE-B
T ss_pred CCcCCCCCC-ce-eEEeeeEEeecCCCCCEEeCC
Confidence 357999998 44 666799999999999998643
No 80
>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=90.33 E-value=1.3 Score=33.99 Aligned_cols=55 Identities=13% Similarity=0.129 Sum_probs=46.8
Q ss_pred HHHHHHHHHhhcCCCHHHHHHHHHHHHHhhhcC--CCCChhHHHHHHHHHHHHHHHHHH
Q 023713 210 ASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLD--IRLILVFFSLFLVETHIQLIVWAF 266 (278)
Q Consensus 210 p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~--~Gr~P~~iaaA~v~~~~~~~~~~~ 266 (278)
..+||.+.+..+++++++...|..+.++..... ...++.-+++|++ +||..++..
T Consensus 34 ~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl--~lA~K~~e~ 90 (127)
T PF00134_consen 34 IIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACL--FLASKMEED 90 (127)
T ss_dssp HHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHH--HHHHHHHTS
T ss_pred HHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHH--HHhhhhhcc
Confidence 457899999999999999999999999887654 4678889999999 999999865
No 81
>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=90.24 E-value=0.32 Score=31.21 Aligned_cols=27 Identities=22% Similarity=0.438 Sum_probs=20.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGL 31 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~ 31 (278)
..||.||+ ..+..-...+..-|.+|+.
T Consensus 19 ~~CP~Cg~-~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGS-TKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCC-eeeEEeCCCCeEECCCCCC
Confidence 56999998 4555555579999999974
No 82
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=90.16 E-value=0.2 Score=37.55 Aligned_cols=30 Identities=30% Similarity=0.746 Sum_probs=23.2
Q ss_pred CCCCCCCCCCcee---Ee--CCCCceEcCCCccccc
Q 023713 4 SYCADCKRLTEVV---FD--HSAGDTICSECGLVLE 34 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv---~D--~~~G~~vC~~CG~Vl~ 34 (278)
..||.||+. .++ +| ..-|..+|.+||.-.+
T Consensus 23 FtCp~Cghe-~vs~ctvkk~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 23 FTCPRCGHE-KVSSCTVKKTVNIGTAVCGNCGLSFE 57 (104)
T ss_pred EecCccCCe-eeeEEEEEecCceeEEEcccCcceEE
Confidence 469999984 555 55 3678999999998764
No 83
>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=89.95 E-value=0.16 Score=31.47 Aligned_cols=31 Identities=32% Similarity=0.555 Sum_probs=20.4
Q ss_pred CCCCCCCCCCCceeEeCC-CCceEcCCCcccc
Q 023713 3 DSYCADCKRLTEVVFDHS-AGDTICSECGLVL 33 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~-~G~~vC~~CG~Vl 33 (278)
...|++||..-++..... .....|.+||.-+
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~ 36 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISDDPLATCPECGGDV 36 (41)
T ss_pred EEEcCCCCCEEEEEEecCCCCCCCCCCCCCcc
Confidence 357999997323333322 5577899999844
No 84
>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=89.90 E-value=0.14 Score=37.25 Aligned_cols=33 Identities=24% Similarity=0.466 Sum_probs=18.1
Q ss_pred CCCCCCCCCCcee--EeC--CCCceEcCCCccccccc
Q 023713 4 SYCADCKRLTEVV--FDH--SAGDTICSECGLVLEAY 36 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv--~D~--~~G~~vC~~CG~Vl~e~ 36 (278)
..||.|+...+|. .|. ..|.+.|..||...+-.
T Consensus 23 F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~ 59 (81)
T PF05129_consen 23 FDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTK 59 (81)
T ss_dssp ---TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE
T ss_pred EcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEc
Confidence 4699999545553 343 57899999999987543
No 85
>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=89.67 E-value=0.25 Score=29.41 Aligned_cols=24 Identities=25% Similarity=0.729 Sum_probs=18.8
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGL 31 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~ 31 (278)
..|+.||- ++|.......|..||.
T Consensus 2 ~~C~~CGy----~y~~~~~~~~CP~Cg~ 25 (33)
T cd00350 2 YVCPVCGY----IYDGEEAPWVCPVCGA 25 (33)
T ss_pred EECCCCCC----EECCCcCCCcCcCCCC
Confidence 46888885 5677777888999886
No 86
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=89.52 E-value=1.7 Score=30.21 Aligned_cols=71 Identities=17% Similarity=0.216 Sum_probs=44.0
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCC-CHHHHHHHHHHH
Q 023713 113 ISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT-TKKEIGRAKEFI 191 (278)
Q Consensus 113 I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v-~~~~i~~~~~~l 191 (278)
|.+++..++++.....+ +|+.........-.....+.-|.-|+.- .+.++.|||.. .|. +...+.+.+++.
T Consensus 4 ~~~la~~~~~s~~~l~~---~f~~~~~~s~~~~~~~~r~~~a~~~l~~----~~~~~~~ia~~-~g~~s~~~f~r~Fk~~ 75 (84)
T smart00342 4 LEDLAEALGMSPRHLQR---LFKKETGTTPKQYLRDRRLERARRLLRD----TDLSVTEIALR-VGFSSQSYFSRAFKKL 75 (84)
T ss_pred HHHHHHHhCCCHHHHHH---HHHHHhCcCHHHHHHHHHHHHHHHHHHc----CCCCHHHHHHH-hCCCChHHHHHHHHHH
Confidence 67888999998655444 4444432211110112233444444431 28999999995 999 999999998764
No 87
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=89.41 E-value=0.25 Score=34.39 Aligned_cols=29 Identities=21% Similarity=0.540 Sum_probs=21.8
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
..||.||... ..+......+|..||...+
T Consensus 29 q~C~~CG~~~--~~~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 29 QTCPRCGHRN--KKRRSGRVFTCPNCGFEMD 57 (69)
T ss_pred cCccCccccc--ccccccceEEcCCCCCEEC
Confidence 6799999731 2246777899999999864
No 88
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=89.41 E-value=0.29 Score=31.22 Aligned_cols=27 Identities=30% Similarity=0.645 Sum_probs=20.1
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl 33 (278)
..|.+||.+ +..+ ..+.+-|++||.=+
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 679999984 3333 57889999999643
No 89
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=89.22 E-value=0.25 Score=33.39 Aligned_cols=27 Identities=30% Similarity=0.641 Sum_probs=15.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLV 32 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V 32 (278)
..|..||.. |-.+..--...|.+||.|
T Consensus 10 ~~CtSCg~~--i~p~e~~v~F~CPnCGe~ 36 (61)
T COG2888 10 PVCTSCGRE--IAPGETAVKFPCPNCGEV 36 (61)
T ss_pred ceeccCCCE--eccCCceeEeeCCCCCce
Confidence 367777752 324444445667777743
No 90
>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=89.08 E-value=0.052 Score=33.12 Aligned_cols=29 Identities=28% Similarity=0.775 Sum_probs=21.0
Q ss_pred CCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713 5 YCADCKRLTEVVFDHSAGDTICSECGLVL 33 (278)
Q Consensus 5 ~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl 33 (278)
.||.||+.=++.+++..-+.+|..||.-|
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 68999974466777778888999998754
No 91
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=88.94 E-value=0.17 Score=31.02 Aligned_cols=29 Identities=28% Similarity=0.636 Sum_probs=20.9
Q ss_pred CCCCCCCCCCceeEe----CCCCceEcCCCcccc
Q 023713 4 SYCADCKRLTEVVFD----HSAGDTICSECGLVL 33 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D----~~~G~~vC~~CG~Vl 33 (278)
..||+|+..-. |.| ...+.+-|+.||.+.
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 57999997322 222 357789999999886
No 92
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=88.93 E-value=0.35 Score=30.14 Aligned_cols=27 Identities=26% Similarity=0.541 Sum_probs=18.9
Q ss_pred CCCCCCCCCceeEe---------CCCCceEcCCCccc
Q 023713 5 YCADCKRLTEVVFD---------HSAGDTICSECGLV 32 (278)
Q Consensus 5 ~Cp~Cg~~~~vv~D---------~~~G~~vC~~CG~V 32 (278)
.||.||.. +.++= +.+-..+|.+||..
T Consensus 2 ~Cp~C~~~-~a~~~q~Q~RsaDE~mT~fy~C~~C~~~ 37 (40)
T smart00440 2 PCPKCGNR-EATFFQLQTRSADEPMTVFYVCTKCGHR 37 (40)
T ss_pred cCCCCCCC-eEEEEEEcccCCCCCCeEEEEeCCCCCE
Confidence 69999984 44431 23447899999964
No 93
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=88.85 E-value=0.34 Score=37.54 Aligned_cols=32 Identities=31% Similarity=0.729 Sum_probs=24.3
Q ss_pred CCCCCCCCCCCceeE--eCCCCceEcCCCccccccc
Q 023713 3 DSYCADCKRLTEVVF--DHSAGDTICSECGLVLEAY 36 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~--D~~~G~~vC~~CG~Vl~e~ 36 (278)
|..||.||+- ++. |...+.++|..||...+-.
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 6799999982 333 3367799999999987644
No 94
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=88.63 E-value=0.32 Score=35.94 Aligned_cols=32 Identities=19% Similarity=0.421 Sum_probs=25.7
Q ss_pred CCCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY 36 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~ 36 (278)
...||.||. .. +.-...|-+.|..||.++...
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 468999997 44 455688999999999998644
No 95
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=88.49 E-value=1.9 Score=37.01 Aligned_cols=83 Identities=14% Similarity=0.312 Sum_probs=58.2
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHhhC-CCC----CCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHH
Q 023713 112 SISAMSDRLGLVTTIKDRANEIYKKVEDQ-KPL----RGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGR 186 (278)
Q Consensus 112 ~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~-~~~----~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~ 186 (278)
-|+++|=.||+-+ ++..|.++.+...+. ..+ .-.+.-..++|++|.|||..+..+.-..+..+ .|+++.++..
T Consensus 95 ~VrdlaVQfgc~e-vi~~a~~vl~syk~~lpaT~~~~~D~SrP~ft~aA~~~ack~lKlKVdK~kli~~-sg~~~s~F~~ 172 (262)
T KOG4557|consen 95 NVRDLAVQFGCVE-VIKSAQNVLSSYKERLPATRRANADFSRPVFTAAAFYLACKKLKLKVDKLKLIEV-SGTSESEFSC 172 (262)
T ss_pred CHHHHHHHHhHHH-HHHHHHHHHHHHHhcCchhhhcCCcccchHHHHHHHHHHHHHHHHhhhHhhcccc-cCCCHHHHHH
Confidence 4566666666654 667777777766542 111 12345679999999999999988877766664 8999988887
Q ss_pred HHHHHHHHhh
Q 023713 187 AKEFIVKHLE 196 (278)
Q Consensus 187 ~~~~l~~~L~ 196 (278)
.-+.+.+...
T Consensus 173 l~kqler~~~ 182 (262)
T KOG4557|consen 173 LSKQLERNYK 182 (262)
T ss_pred HHHHHHHHHH
Confidence 7777766553
No 96
>COG4640 Predicted membrane protein [Function unknown]
Probab=87.91 E-value=0.28 Score=45.59 Aligned_cols=28 Identities=21% Similarity=0.692 Sum_probs=21.5
Q ss_pred CCCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY 36 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~ 36 (278)
|..||.||+. -.+++.-|+.||.=+...
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 6789999973 235677799999887644
No 97
>PF12773 DZR: Double zinc ribbon
Probab=87.48 E-value=0.31 Score=31.62 Aligned_cols=27 Identities=22% Similarity=0.662 Sum_probs=12.0
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl 33 (278)
..||.||.. +. .......+|..||..+
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 445555542 11 2223345555555544
No 98
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=87.38 E-value=0.42 Score=31.66 Aligned_cols=29 Identities=34% Similarity=0.673 Sum_probs=20.9
Q ss_pred CCCCCCCCCceeEeCCCCce----EcCCCcccc
Q 023713 5 YCADCKRLTEVVFDHSAGDT----ICSECGLVL 33 (278)
Q Consensus 5 ~Cp~Cg~~~~vv~D~~~G~~----vC~~CG~Vl 33 (278)
.||+||....+..|.+.|.- =|.-|-.=+
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~PI 34 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCCRPI 34 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhcCCcc
Confidence 69999987788999888842 255555443
No 99
>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=87.35 E-value=0.56 Score=26.86 Aligned_cols=22 Identities=23% Similarity=0.533 Sum_probs=12.1
Q ss_pred CCCCCCCCCceeEeCCCCceEcCC
Q 023713 5 YCADCKRLTEVVFDHSAGDTICSE 28 (278)
Q Consensus 5 ~Cp~Cg~~~~vv~D~~~G~~vC~~ 28 (278)
.||.||+ .++.+..+-.+.|.+
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 4999998 477776777788875
No 100
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=87.32 E-value=0.15 Score=34.32 Aligned_cols=25 Identities=32% Similarity=0.883 Sum_probs=19.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCC-Cccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSE-CGLVLE 34 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~-CG~Vl~ 34 (278)
..|+.||.+ +- .++.+|++ ||.+++
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 579999984 33 56999996 999885
No 101
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=87.05 E-value=0.42 Score=35.40 Aligned_cols=32 Identities=25% Similarity=0.459 Sum_probs=25.9
Q ss_pred CCCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY 36 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~ 36 (278)
...||.||. .. +.-...|-+.|..||.++...
T Consensus 35 ~y~CpfCgk-~~-vkR~a~GIW~C~~C~~~~AGG 66 (91)
T TIGR00280 35 KYVCPFCGK-KT-VKRGSTGIWTCRKCGAKFAGG 66 (91)
T ss_pred CccCCCCCC-Cc-eEEEeeEEEEcCCCCCEEeCC
Confidence 468999997 44 556789999999999998643
No 102
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=87.04 E-value=0.16 Score=42.64 Aligned_cols=31 Identities=23% Similarity=0.491 Sum_probs=23.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e 35 (278)
..||.|+.. =...|.-+....|+.||.+|.+
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 569999973 2234456678999999999974
No 103
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=86.90 E-value=14 Score=33.74 Aligned_cols=72 Identities=6% Similarity=-0.009 Sum_probs=47.3
Q ss_pred CHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCC--CHHHHHHHHHHHHHHhh
Q 023713 123 VTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT--TKKEIGRAKEFIVKHLE 196 (278)
Q Consensus 123 p~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v--~~~~i~~~~~~l~~~L~ 196 (278)
++.+...|..+...+.--...--..|..+|+||||+|+|..++...-.+- ++ .++ +..+++..+..+++...
T Consensus 180 ~~~l~q~a~~~lndsl~Td~~L~y~Ps~IAlAAI~lA~~~~~~~l~~~~~-e~-~~~~~~~~~~~~l~~~~~~~~~ 253 (305)
T TIGR00569 180 PEYLRKHADKFLNRTLLTDAYLLYTPSQIALAAILHTASRAGLNMESYLT-EQ-LSVPGNREELPQLIDIMRELRI 253 (305)
T ss_pred hHHHHHHHHHHHHHHHcCCceecCCHHHHHHHHHHHHHHHhCCCCcccch-hh-hcccccHHHHHHHHHHHHHHHH
Confidence 34567777777776554333223678999999999999999876544332 32 344 66777777666655443
No 104
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=86.81 E-value=1 Score=26.66 Aligned_cols=28 Identities=18% Similarity=0.297 Sum_probs=22.1
Q ss_pred CCCCHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 165 ~p~tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
.|.|-.|||+. +|.+..++.|.++++.+
T Consensus 1 l~mtr~diA~~-lG~t~ETVSR~l~~l~~ 28 (32)
T PF00325_consen 1 LPMTRQDIADY-LGLTRETVSRILKKLER 28 (32)
T ss_dssp EE--HHHHHHH-HTS-HHHHHHHHHHHHH
T ss_pred CCcCHHHHHHH-hCCcHHHHHHHHHHHHH
Confidence 36788999994 99999999999999875
No 105
>PRK05978 hypothetical protein; Provisional
Probab=86.57 E-value=0.49 Score=38.39 Aligned_cols=35 Identities=17% Similarity=0.369 Sum_probs=23.6
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcccccccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVD 39 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~~id 39 (278)
.+||+||. ..+..-+-.=..-|..||.-++-..-|
T Consensus 34 grCP~CG~-G~LF~g~Lkv~~~C~~CG~~~~~~~a~ 68 (148)
T PRK05978 34 GRCPACGE-GKLFRAFLKPVDHCAACGEDFTHHRAD 68 (148)
T ss_pred CcCCCCCC-CcccccccccCCCccccCCccccCCcc
Confidence 68999997 555333333456799999988644333
No 106
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=86.44 E-value=0.82 Score=31.49 Aligned_cols=30 Identities=20% Similarity=0.353 Sum_probs=20.4
Q ss_pred CCCCCCCCCCCceeEeCCCC--ceEcCCCcccc
Q 023713 3 DSYCADCKRLTEVVFDHSAG--DTICSECGLVL 33 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G--~~vC~~CG~Vl 33 (278)
...||.||.. ++..-...| ..+|..||...
T Consensus 6 lKPCPFCG~~-~~~v~~~~g~~~v~C~~CgA~~ 37 (64)
T PRK09710 6 VKPCPFCGCP-SVTVKAISGYYRAKCNGCESRT 37 (64)
T ss_pred ccCCCCCCCc-eeEEEecCceEEEEcCCCCcCc
Confidence 3679999984 443333344 36899999964
No 107
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=86.34 E-value=0.38 Score=39.56 Aligned_cols=39 Identities=23% Similarity=0.438 Sum_probs=26.0
Q ss_pred CCCCCCCCCCCceeEe---------------CCCCceEcCCCcccccccccccccchhhcc
Q 023713 3 DSYCADCKRLTEVVFD---------------HSAGDTICSECGLVLEAYSVDETSEWRIFA 48 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D---------------~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~ 48 (278)
...||+|+++ ++.- ..+-..+|++||.+.- -|+.|+...
T Consensus 97 ~~RCp~CN~~--L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW-----~GsHw~~m~ 150 (165)
T COG1656 97 FSRCPECNGE--LEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYW-----KGSHWRRMV 150 (165)
T ss_pred cccCcccCCE--eccCcHHHHhhccchhhhhcccceeECCCCccccc-----CchHHHHHH
Confidence 5789999973 3222 2233677999999986 456776543
No 108
>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=86.18 E-value=0.22 Score=46.31 Aligned_cols=78 Identities=15% Similarity=0.210 Sum_probs=0.0
Q ss_pred CCCHHHHHHHHHHHHHHh-hCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhhc
Q 023713 121 GLVTTIKDRANEIYKKVE-DQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEM 199 (278)
Q Consensus 121 ~Lp~~v~e~A~~i~k~~~-~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~~ 199 (278)
++|+.++..|.++|+... ....+++..-.+-+.+|+|+||...+.+..+..... ..+++++...+.|..|.+.|+...
T Consensus 11 ~~~~~ll~~a~~L~~ls~~~~~~l~~~~EiaR~~iCa~lA~~~l~~~~dl~~~~~-~~pl~pk~y~~l~~~~~~~L~~~s 89 (353)
T PF05460_consen 11 GLPPKLLSKASELYRLSRQKKSSLKPEEEIARAHICAELACERLKEKLDLPYAIK-RSPLPPKVYKKLLNTFENLLGNSS 89 (353)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred CCCHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhCCccCchhhcC-CCCCCHHHHHHHHHHHHHHHhCCC
Confidence 456889999999999887 455667766678889999999999999998888666 489999999999999999888763
No 109
>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=85.89 E-value=0.39 Score=31.09 Aligned_cols=14 Identities=29% Similarity=0.669 Sum_probs=7.3
Q ss_pred eEcCCCcccccccc
Q 023713 24 TICSECGLVLEAYS 37 (278)
Q Consensus 24 ~vC~~CG~Vl~e~~ 37 (278)
..|..||.|.++..
T Consensus 2 y~C~~CgyvYd~~~ 15 (47)
T PF00301_consen 2 YQCPVCGYVYDPEK 15 (47)
T ss_dssp EEETTTSBEEETTT
T ss_pred cCCCCCCEEEcCCc
Confidence 34555555555443
No 110
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=85.67 E-value=0.53 Score=34.80 Aligned_cols=32 Identities=25% Similarity=0.481 Sum_probs=25.7
Q ss_pred CCCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY 36 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~ 36 (278)
...||.||. .. +.-...|-+-|..||.++...
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 468999997 34 555789999999999998644
No 111
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=85.65 E-value=0.6 Score=31.53 Aligned_cols=28 Identities=21% Similarity=0.533 Sum_probs=19.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccccccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSV 38 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~~i 38 (278)
..||+||.. ..-..||.+||+--+..++
T Consensus 28 ~~C~~CG~~-------~~~H~vC~~CG~Y~gr~v~ 55 (57)
T PRK12286 28 VECPNCGEP-------KLPHRVCPSCGYYKGREVV 55 (57)
T ss_pred eECCCCCCc-------cCCeEECCCCCcCCCEEee
Confidence 469999973 2348899999987654443
No 112
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=85.53 E-value=0.71 Score=31.27 Aligned_cols=28 Identities=25% Similarity=0.557 Sum_probs=16.6
Q ss_pred CCCCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713 3 DSYCADCKRLTEVVFDHSAGDTICSECGLV 32 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V 32 (278)
...|..||.. |..-...-...|.+||.+
T Consensus 7 ~~~CtSCg~~--i~~~~~~~~F~CPnCG~~ 34 (59)
T PRK14890 7 PPKCTSCGIE--IAPREKAVKFLCPNCGEV 34 (59)
T ss_pred CccccCCCCc--ccCCCccCEeeCCCCCCe
Confidence 3568888862 221112345678888876
No 113
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=85.51 E-value=0.85 Score=32.35 Aligned_cols=31 Identities=13% Similarity=0.275 Sum_probs=22.3
Q ss_pred CCCCCCCCCCCceeEeC-------CCCceEcC--CCccccc
Q 023713 3 DSYCADCKRLTEVVFDH-------SAGDTICS--ECGLVLE 34 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~-------~~G~~vC~--~CG~Vl~ 34 (278)
|+.||.||+ .+.|.+. .+--..|+ +||....
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 579999998 4666664 23345788 8998874
No 114
>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=85.24 E-value=0.66 Score=28.71 Aligned_cols=28 Identities=25% Similarity=0.555 Sum_probs=15.5
Q ss_pred CCCCCCCCCceeEe--------CCCCceEcCCCccc
Q 023713 5 YCADCKRLTEVVFD--------HSAGDTICSECGLV 32 (278)
Q Consensus 5 ~Cp~Cg~~~~vv~D--------~~~G~~vC~~CG~V 32 (278)
.||.||+...+.+. +.+-..+|.+||..
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 69999985333332 12335789999964
No 115
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=84.91 E-value=0.71 Score=30.75 Aligned_cols=28 Identities=21% Similarity=0.545 Sum_probs=20.7
Q ss_pred CCCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
..+|+.||.. +. ...--+||.+||++.-
T Consensus 5 ~~~C~~Cg~~---~~-~~dDiVvCp~CgapyH 32 (54)
T PF14446_consen 5 GCKCPVCGKK---FK-DGDDIVVCPECGAPYH 32 (54)
T ss_pred CccChhhCCc---cc-CCCCEEECCCCCCccc
Confidence 3689999973 22 3445789999999973
No 116
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=84.86 E-value=0.48 Score=31.87 Aligned_cols=25 Identities=24% Similarity=0.538 Sum_probs=19.2
Q ss_pred CCCCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 2 ADSYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 2 ~~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
-+..|+.||. -++ ..+|..||....
T Consensus 4 ~mr~C~~Cgv-YTL-------k~~CP~CG~~t~ 28 (56)
T PRK13130 4 KIRKCPKCGV-YTL-------KEICPVCGGKTK 28 (56)
T ss_pred cceECCCCCC-EEc-------cccCcCCCCCCC
Confidence 4678999997 333 678999998753
No 117
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=84.49 E-value=0.34 Score=31.63 Aligned_cols=27 Identities=33% Similarity=0.635 Sum_probs=21.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLV 32 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V 32 (278)
..|-.||.. +..|.....+.|+.||.=
T Consensus 7 Y~C~~Cg~~--~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 7 YKCARCGRE--VELDQETRGIRCPYCGSR 33 (49)
T ss_pred EEhhhcCCe--eehhhccCceeCCCCCcE
Confidence 579999983 445678889999999963
No 118
>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=84.36 E-value=0.81 Score=30.03 Aligned_cols=11 Identities=27% Similarity=0.911 Sum_probs=5.9
Q ss_pred EcCCCcccccc
Q 023713 25 ICSECGLVLEA 35 (278)
Q Consensus 25 vC~~CG~Vl~e 35 (278)
+|+.||.|.++
T Consensus 3 ~C~~CgyiYd~ 13 (50)
T cd00730 3 ECRICGYIYDP 13 (50)
T ss_pred CCCCCCeEECC
Confidence 45555555543
No 119
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=84.01 E-value=2.4 Score=43.31 Aligned_cols=84 Identities=12% Similarity=0.229 Sum_probs=68.7
Q ss_pred HHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhh--CCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHH
Q 023713 107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVED--QKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEI 184 (278)
Q Consensus 107 ~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~--~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i 184 (278)
.-|..+|+.+|++|.|.+.+.+...-+|.-... -.+++.|..+.+.-+|+|+.+|..+...|+.||-.. ..-.....
T Consensus 678 ~LAavRL~~Lc~rL~l~~e~r~~IWtlFehsl~~et~Lm~dRHLDQillCaiy~i~KV~~~~ltF~eIm~~-YR~QPqa~ 756 (920)
T KOG1010|consen 678 HLAAVRLNDLCERLSLSDELREQIWTLFEHSLTNETELMRDRHLDQILLCAIYGIAKVKKEDLTFSEIMRA-YRRQPQAV 756 (920)
T ss_pred HHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHhccHHHHHhhhHHHHHHHHHHhheehhcccchHHHHHHH-HhcCchhh
Confidence 346788999999999999999998888876543 346788999999999999999999999999999763 55556666
Q ss_pred HHHHHHH
Q 023713 185 GRAKEFI 191 (278)
Q Consensus 185 ~~~~~~l 191 (278)
..+|+.+
T Consensus 757 ~~vyRsV 763 (920)
T KOG1010|consen 757 SLVYRSV 763 (920)
T ss_pred hhhhhhe
Confidence 6666654
No 120
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=83.94 E-value=0.78 Score=34.76 Aligned_cols=27 Identities=26% Similarity=0.609 Sum_probs=22.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAY 36 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~ 36 (278)
..||.||. ..+|+ ++-|.+||+-++.+
T Consensus 7 ~~cPvcg~-~~iVT-----eL~c~~~etTVrg~ 33 (122)
T COG3877 7 NRCPVCGR-KLIVT-----ELKCSNCETTVRGN 33 (122)
T ss_pred CCCCcccc-cceeE-----EEecCCCCceEecc
Confidence 68999998 46776 89999999998633
No 121
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=83.82 E-value=0.52 Score=36.62 Aligned_cols=39 Identities=18% Similarity=0.364 Sum_probs=25.6
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcccccccccccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSE 43 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~~id~~~e 43 (278)
..||+||. ..+..-.-.=.-.|..||.=+..+--|++|-
T Consensus 22 grCP~CGe-GrLF~gFLK~~p~C~aCG~dyg~~~a~DgPa 60 (126)
T COG5349 22 GRCPRCGE-GRLFRGFLKVVPACEACGLDYGFADADDGPA 60 (126)
T ss_pred CCCCCCCC-chhhhhhcccCchhhhccccccCCcccCCCc
Confidence 57999997 5543223333558999998876665555543
No 122
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=83.60 E-value=0.89 Score=36.79 Aligned_cols=30 Identities=30% Similarity=0.604 Sum_probs=21.6
Q ss_pred CCCCCCCCCCceeEeC---CCCce-----EcCCCcccc
Q 023713 4 SYCADCKRLTEVVFDH---SAGDT-----ICSECGLVL 33 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~---~~G~~-----vC~~CG~Vl 33 (278)
|.||.|+++.+=|.|+ ..|.. .|.+||.=.
T Consensus 1 M~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RF 38 (156)
T COG1327 1 MKCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERF 38 (156)
T ss_pred CCCCCCCCCCCeeeecccccccchhhhhhccccccccc
Confidence 5799999865667785 44543 599998654
No 123
>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=83.57 E-value=0.67 Score=31.14 Aligned_cols=24 Identities=21% Similarity=0.642 Sum_probs=17.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
..||+||.. .....+|.+||+.=.
T Consensus 27 ~~c~~cg~~-------~~~H~vc~~cG~y~~ 50 (56)
T PF01783_consen 27 VKCPNCGEP-------KLPHRVCPSCGYYKG 50 (56)
T ss_dssp EESSSSSSE-------ESTTSBCTTTBBSSS
T ss_pred eeeccCCCE-------ecccEeeCCCCeECC
Confidence 469999962 245789999996644
No 124
>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=82.88 E-value=1.3 Score=30.07 Aligned_cols=30 Identities=20% Similarity=0.459 Sum_probs=20.2
Q ss_pred CCCCCCCCCCceeEeCCCC--ceEcCCCcccc
Q 023713 4 SYCADCKRLTEVVFDHSAG--DTICSECGLVL 33 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G--~~vC~~CG~Vl 33 (278)
-.||.|+.-..++.=.++| ..-|.+||.--
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~ 41 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGYQE 41 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCCcc
Confidence 4799999854554323333 37799999863
No 125
>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=82.64 E-value=3.8 Score=26.73 Aligned_cols=34 Identities=21% Similarity=0.265 Sum_probs=28.3
Q ss_pred HhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHh
Q 023713 161 RQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHL 195 (278)
Q Consensus 161 R~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L 195 (278)
..++-|+|..|+|+. ++|+..+|.+.++.|.+.+
T Consensus 10 ~~~~~~it~~eLa~~-l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 10 LESKEPITAKELAEE-LGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHTTTSBEHHHHHHH-CTS-HHHHHHHHHHHHHTT
T ss_pred HHcCCCcCHHHHHHH-hCCCHHHHHHHHHHHHHCC
Confidence 345667999999995 9999999999999997665
No 126
>PF12773 DZR: Double zinc ribbon
Probab=82.59 E-value=0.99 Score=29.20 Aligned_cols=22 Identities=23% Similarity=0.832 Sum_probs=16.5
Q ss_pred CCCCCCCCCCCceeEeCCCCceEcCCCc
Q 023713 3 DSYCADCKRLTEVVFDHSAGDTICSECG 30 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG 30 (278)
...||.||.. ...+..+|..||
T Consensus 29 ~~~C~~Cg~~------~~~~~~fC~~CG 50 (50)
T PF12773_consen 29 KKICPNCGAE------NPPNAKFCPNCG 50 (50)
T ss_pred CCCCcCCcCC------CcCCcCccCccc
Confidence 3579999973 235688999998
No 127
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=82.46 E-value=8.3 Score=33.64 Aligned_cols=100 Identities=18% Similarity=0.195 Sum_probs=63.3
Q ss_pred HHHHHHhcCC-CHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHH
Q 023713 113 ISAMSDRLGL-VTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFI 191 (278)
Q Consensus 113 I~~i~~~L~L-p~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l 191 (278)
+.++-+.+|+ +....+-+..|...-+...+.-=-.|..+|-||+|+||-..+.+.+-.=+++ +.+|...+....++|
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 3444444555 3446666666655544444333356889999999999998887775444444 468888888888888
Q ss_pred HHHhhhhcccccccCCCCHHHHHHHHHhhcC
Q 023713 192 VKHLEAEMGQSVEMGTIHASDYLRRFCSNLG 222 (278)
Q Consensus 192 ~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~ 222 (278)
.+....- ...+-.. |....++|-
T Consensus 235 ~~lYe~w-------k~~~E~~-v~~ll~kl~ 257 (264)
T KOG0794|consen 235 LKLYELW-------KIFDEKK-VKKLLSKLP 257 (264)
T ss_pred HHHHHHH-------hhhhHHH-HHHHHHhcc
Confidence 8777653 1223333 555555554
No 128
>PF14122 YokU: YokU-like protein
Probab=81.41 E-value=1.1 Score=32.74 Aligned_cols=24 Identities=33% Similarity=0.595 Sum_probs=18.0
Q ss_pred CCCceEcCCCcccccccccccccc
Q 023713 20 SAGDTICSECGLVLEAYSVDETSE 43 (278)
Q Consensus 20 ~~G~~vC~~CG~Vl~e~~id~~~e 43 (278)
.+=.++|.+||.|..+..+...-|
T Consensus 32 ~tP~i~C~~CgmvYq~d~vi~EIE 55 (87)
T PF14122_consen 32 DTPAIICSNCGMVYQDDEVIKEIE 55 (87)
T ss_pred CCceeeecCCCcEEehhHHHHHHh
Confidence 344589999999998877665554
No 129
>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=81.38 E-value=6.7 Score=28.74 Aligned_cols=42 Identities=19% Similarity=0.186 Sum_probs=34.1
Q ss_pred HHHHHHHHHhcCCCCCHHHHHHHHcC-CCHHHHHHHHHHHHHHhhh
Q 023713 153 AACLYIACRQENKPRTVKEFCSVANG-TTKKEIGRAKEFIVKHLEA 197 (278)
Q Consensus 153 AAclY~acR~~~~p~tl~eia~~~~~-v~~~~i~~~~~~l~~~L~~ 197 (278)
..++|++-+.. ..|+.+|+.. +| .+..++..+++++.+.+..
T Consensus 33 ~ia~yl~~~~~--~~s~~~Ig~~-fg~r~hStV~~a~~ri~~~~~~ 75 (90)
T cd06571 33 QIAMYLARELT--GLSLPEIGRA-FGGRDHSTVLHAVRKIEELLEE 75 (90)
T ss_pred HHHHHHHHHHh--CCCHHHHHHH-hCCCCHhHHHHHHHHHHHHHHh
Confidence 35677775544 5689999995 77 9999999999999998864
No 130
>PRK02935 hypothetical protein; Provisional
Probab=81.19 E-value=1.1 Score=34.03 Aligned_cols=27 Identities=22% Similarity=0.541 Sum_probs=19.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
..||+|+.++...= -...|..|+.-+.
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 46999998654332 2458999998875
No 131
>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=81.06 E-value=0.76 Score=30.04 Aligned_cols=29 Identities=28% Similarity=0.549 Sum_probs=17.9
Q ss_pred CCCCCCCCCCCceeEe-CCCCceEcCCCcc
Q 023713 3 DSYCADCKRLTEVVFD-HSAGDTICSECGL 31 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D-~~~G~~vC~~CG~ 31 (278)
..+|++||..-++... .+.....|..||.
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 3579999973222221 2245678999997
No 132
>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=81.05 E-value=1.4 Score=33.46 Aligned_cols=32 Identities=19% Similarity=0.451 Sum_probs=20.9
Q ss_pred CCCCCCCCCCCceeEe------CC--C-Cc-eEcCCCcccccc
Q 023713 3 DSYCADCKRLTEVVFD------HS--A-GD-TICSECGLVLEA 35 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D------~~--~-G~-~vC~~CG~Vl~e 35 (278)
...||+||.. ....+ .. . .. ++|+.|+.-|.=
T Consensus 2 p~~CpYCg~~-~~l~~~~~iYg~~~~~~~~~y~C~~C~AyVG~ 43 (102)
T PF11672_consen 2 PIICPYCGGP-AELVDGSEIYGHRYDDGPYLYVCTPCDAYVGC 43 (102)
T ss_pred CcccCCCCCe-eEEcccchhcCccCCCCceeEECCCCCceeee
Confidence 3689999984 34333 11 2 32 799999888763
No 133
>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=80.88 E-value=5.1 Score=27.86 Aligned_cols=43 Identities=19% Similarity=0.238 Sum_probs=33.9
Q ss_pred HHHHHHHHHHHhcC----------CCCCHHHHHHHHcCCCHHHHHHHHHHHHHH
Q 023713 151 IVAACLYIACRQEN----------KPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (278)
Q Consensus 151 ~aAAclY~acR~~~----------~p~tl~eia~~~~~v~~~~i~~~~~~l~~~ 194 (278)
+|...++++-+... .|.|..|||+. +|++..++.+.+++|.+.
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 45556666665442 57899999994 999999999999999874
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=80.78 E-value=4.8 Score=31.86 Aligned_cols=46 Identities=20% Similarity=0.186 Sum_probs=39.3
Q ss_pred cHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 147 NQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 147 ~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
+.+.-..+++|+|-...+.|.+..|||+. .+++...+.+....|.+
T Consensus 6 ~~~YAl~~l~~La~~~~~~~~s~~~ia~~-~~ip~~~l~kil~~L~~ 51 (135)
T TIGR02010 6 KGRYAVTAMLDLALNAETGPVTLADISER-QGISLSYLEQLFAKLRK 51 (135)
T ss_pred HHHHHHHHHHHHHhCCCCCcCcHHHHHHH-HCcCHHHHHHHHHHHHH
Confidence 45666778899997766778999999995 99999999999999976
No 135
>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=80.78 E-value=0.9 Score=44.92 Aligned_cols=43 Identities=19% Similarity=0.515 Sum_probs=29.7
Q ss_pred CCCCCCCCCCcee-----Ee----CCCCceEcCCCcccccccc---cccccchhh
Q 023713 4 SYCADCKRLTEVV-----FD----HSAGDTICSECGLVLEAYS---VDETSEWRI 46 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv-----~D----~~~G~~vC~~CG~Vl~e~~---id~~~ewr~ 46 (278)
..||+||....+. +| +.+-.++|..||..++|+. ....-+|+.
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 4799999754433 22 4567899999999998863 223456755
No 136
>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=80.63 E-value=1.2 Score=29.85 Aligned_cols=25 Identities=20% Similarity=0.679 Sum_probs=17.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e 35 (278)
..||+||.. ..-.-||..||.--+.
T Consensus 27 ~~C~~cG~~-------~~~H~vc~~cG~Y~gr 51 (55)
T TIGR01031 27 VVCPNCGEF-------KLPHRVCPSCGYYKGR 51 (55)
T ss_pred eECCCCCCc-------ccCeeECCccCeECCE
Confidence 469999972 2347899999976543
No 137
>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=80.46 E-value=3.1 Score=29.97 Aligned_cols=46 Identities=20% Similarity=0.273 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHH
Q 023713 148 QEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (278)
Q Consensus 148 ~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~ 194 (278)
.+.-.-+.+|++-...+.|.|..|||+. .+++...+.+....|.+.
T Consensus 7 ~~~Al~~l~~la~~~~~~~~s~~eiA~~-~~i~~~~l~kil~~L~~~ 52 (83)
T PF02082_consen 7 TDYALRILLYLARHPDGKPVSSKEIAER-LGISPSYLRKILQKLKKA 52 (83)
T ss_dssp HHHHHHHHHHHHCTTTSC-BEHHHHHHH-HTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHhCCCCCCCCHHHHHHH-HCcCHHHHHHHHHHHhhC
Confidence 3455567788887777778999999995 999999999999999873
No 138
>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=80.30 E-value=0.42 Score=38.29 Aligned_cols=29 Identities=31% Similarity=0.685 Sum_probs=23.6
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 1 ~~~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
|+...||.||+ +|-. +|..+|.+|....+
T Consensus 1 m~l~nC~~Cgk----lF~~-~~~~iCp~C~~~~e 29 (137)
T TIGR03826 1 MELANCPKCGR----LFVK-TGRDVCPSCYEEEE 29 (137)
T ss_pred CCCccccccch----hhhh-cCCccCHHHhHHHH
Confidence 77899999998 2444 48999999998864
No 139
>KOG1088 consensus Uncharacterized conserved protein [Function unknown]
Probab=80.26 E-value=0.67 Score=35.75 Aligned_cols=18 Identities=33% Similarity=0.691 Sum_probs=15.3
Q ss_pred EeCCCCceEcCCCccccc
Q 023713 17 FDHSAGDTICSECGLVLE 34 (278)
Q Consensus 17 ~D~~~G~~vC~~CG~Vl~ 34 (278)
.|-.+|+++|.+||.|..
T Consensus 92 ~~v~EG~l~CpetG~vfp 109 (124)
T KOG1088|consen 92 IDVIEGELVCPETGRVFP 109 (124)
T ss_pred hhhccceEecCCCCcEee
Confidence 455789999999999974
No 140
>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=80.04 E-value=0.88 Score=28.59 Aligned_cols=29 Identities=28% Similarity=0.566 Sum_probs=18.4
Q ss_pred CCCCCCCCCCceeEeC-CCCceEcCCCccc
Q 023713 4 SYCADCKRLTEVVFDH-SAGDTICSECGLV 32 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~-~~G~~vC~~CG~V 32 (278)
..|+.||..-++..-. +.....|..||..
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~ 35 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISEDDPVPCPECGST 35 (42)
T ss_pred EEeCCCCCEEEEEEEcCCCCCCcCCCCCCC
Confidence 5789998632333222 2467889999873
No 141
>PF15616 TerY-C: TerY-C metal binding domain
Probab=79.73 E-value=1 Score=35.75 Aligned_cols=9 Identities=22% Similarity=0.656 Sum_probs=7.1
Q ss_pred CCCCCCCCC
Q 023713 4 SYCADCKRL 12 (278)
Q Consensus 4 ~~Cp~Cg~~ 12 (278)
--||+||..
T Consensus 78 PgCP~CGn~ 86 (131)
T PF15616_consen 78 PGCPHCGNQ 86 (131)
T ss_pred CCCCCCcCh
Confidence 469999974
No 142
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=79.69 E-value=14 Score=37.93 Aligned_cols=62 Identities=23% Similarity=0.366 Sum_probs=48.7
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHH
Q 023713 110 FKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEF 172 (278)
Q Consensus 110 ~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~ei 172 (278)
.+.....|..|++++....+|.+.|..+...-.+-| +-..+-|.++|.+||...+|.--+-+
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 345677899999999999999999988876554444 46789999999999999877544444
No 143
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=79.44 E-value=0.75 Score=38.75 Aligned_cols=31 Identities=35% Similarity=0.565 Sum_probs=20.2
Q ss_pred CCCCCCCCCCce--eEeCCCC---ceEcCCCcccccc
Q 023713 4 SYCADCKRLTEV--VFDHSAG---DTICSECGLVLEA 35 (278)
Q Consensus 4 ~~Cp~Cg~~~~v--v~D~~~G---~~vC~~CG~Vl~e 35 (278)
..||.||+. ++ ..--..| .+-|.+||+|-.+
T Consensus 7 ~~Cp~Cg~e-ev~hEVik~~g~~~lvrC~eCG~V~~~ 42 (201)
T COG1326 7 IECPSCGSE-EVSHEVIKERGREPLVRCEECGTVHPA 42 (201)
T ss_pred EECCCCCcc-hhhHHHHHhcCCceEEEccCCCcEeec
Confidence 469999953 33 1111233 4789999999854
No 144
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=79.03 E-value=1.5 Score=24.18 Aligned_cols=24 Identities=29% Similarity=0.717 Sum_probs=14.0
Q ss_pred CCCCCCCCceeEeCCCCceEcCCCcc
Q 023713 6 CADCKRLTEVVFDHSAGDTICSECGL 31 (278)
Q Consensus 6 Cp~Cg~~~~vv~D~~~G~~vC~~CG~ 31 (278)
|..||.. |.--...-...|.+||.
T Consensus 1 C~sC~~~--i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRP--IAPREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCc--ccCcccCceEeCCCCCC
Confidence 6778762 22212244678999984
No 145
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=78.94 E-value=7.3 Score=26.38 Aligned_cols=37 Identities=14% Similarity=0.246 Sum_probs=30.1
Q ss_pred HHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 155 CLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 155 clY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
+||.... .+.+.+..|||.. +++++.++..++++|.+
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 3555554 8889999999994 99999999999999875
No 146
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=78.89 E-value=1.2 Score=44.74 Aligned_cols=13 Identities=23% Similarity=0.713 Sum_probs=6.6
Q ss_pred CCceEcCCCcccc
Q 023713 21 AGDTICSECGLVL 33 (278)
Q Consensus 21 ~G~~vC~~CG~Vl 33 (278)
.|..+|.+||.-+
T Consensus 39 ~~~~fC~~CG~~~ 51 (645)
T PRK14559 39 VDEAHCPNCGAET 51 (645)
T ss_pred cccccccccCCcc
Confidence 3445555555544
No 147
>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=78.84 E-value=0.96 Score=30.20 Aligned_cols=29 Identities=17% Similarity=0.425 Sum_probs=21.9
Q ss_pred CCCCCCCCCCcee--EeCCCCceEcCCCccc
Q 023713 4 SYCADCKRLTEVV--FDHSAGDTICSECGLV 32 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv--~D~~~G~~vC~~CG~V 32 (278)
.+|++|.+.+-+. .+.+.-..+|..||..
T Consensus 23 LIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 23 LICSKCFSHNGLAPKEEFEEIQYRCPYCGAL 53 (54)
T ss_pred EECcccchhhcccccccCCceEEEcCCCCCc
Confidence 5799998764444 6677778999999963
No 148
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=78.76 E-value=1.2 Score=28.13 Aligned_cols=26 Identities=23% Similarity=0.740 Sum_probs=18.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCC--Ccccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSE--CGLVLEA 35 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~--CG~Vl~e 35 (278)
..||.||. ++-.+| +.|.+ |+.|+..
T Consensus 12 rkCp~CGt-----~NG~R~-~~CKN~~C~~~~~~ 39 (44)
T PF14952_consen 12 RKCPKCGT-----YNGTRG-LSCKNKSCPQVFNV 39 (44)
T ss_pred ccCCcCcC-----ccCccc-ccccCCccchhhhc
Confidence 57999996 233344 77875 9988753
No 149
>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=78.70 E-value=1.4 Score=30.45 Aligned_cols=9 Identities=33% Similarity=1.117 Sum_probs=7.4
Q ss_pred eEcCCCccc
Q 023713 24 TICSECGLV 32 (278)
Q Consensus 24 ~vC~~CG~V 32 (278)
++|++||..
T Consensus 37 v~C~~CGYT 45 (64)
T PF09855_consen 37 VSCTNCGYT 45 (64)
T ss_pred EECCCCCCE
Confidence 579999986
No 150
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=78.48 E-value=1.5 Score=30.17 Aligned_cols=12 Identities=25% Similarity=0.515 Sum_probs=8.3
Q ss_pred CCCCCCCCCCcee
Q 023713 4 SYCADCKRLTEVV 16 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv 16 (278)
..||.||. ++..
T Consensus 5 ~kCpKCgn-~~~~ 16 (68)
T COG3478 5 FKCPKCGN-TNYE 16 (68)
T ss_pred ccCCCcCC-cchh
Confidence 45999997 4433
No 151
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=78.38 E-value=3.9 Score=31.61 Aligned_cols=49 Identities=16% Similarity=0.132 Sum_probs=37.7
Q ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcC
Q 023713 168 TVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLG 222 (278)
Q Consensus 168 tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~ 222 (278)
+++|++.. +||+-.+++..+..|.+.|+... .+..........+.++|.
T Consensus 51 nlKe~e~~-lgiSYPTvR~rLd~ii~~lg~~~-----~~~~~~~~~~~~IL~~L~ 99 (113)
T PF09862_consen 51 NLKEMEKE-LGISYPTVRNRLDKIIEKLGYEE-----DEEEEEEDERKEILDKLE 99 (113)
T ss_pred CHHHHHHH-HCCCcHHHHHHHHHHHHHhCCCC-----CcccccchhHHHHHHHHH
Confidence 49999995 99999999999999999999831 233344556666666664
No 152
>PRK08402 replication factor A; Reviewed
Probab=78.17 E-value=1.7 Score=40.49 Aligned_cols=27 Identities=37% Similarity=0.812 Sum_probs=22.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLV 32 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V 32 (278)
..||.|.. .++.|...|.+.|.+||.|
T Consensus 213 ~aCp~CnK--kv~~~~~~~~~~Ce~~~~v 239 (355)
T PRK08402 213 DACPECRR--KVDYDPATDTWICPEHGEV 239 (355)
T ss_pred ecCCCCCe--EEEEecCCCCEeCCCCCCc
Confidence 47999997 3556888999999999975
No 153
>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=78.12 E-value=0.76 Score=35.25 Aligned_cols=39 Identities=23% Similarity=0.491 Sum_probs=24.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcccccccccccccchhhccC
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFAN 49 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~ 49 (278)
..||+|+..+- +.- -+.-|..|+.-+. +|...|=.+|++
T Consensus 70 V~CP~C~K~TK-mLG---r~D~CM~C~~pLT---Ld~~legkef~~ 108 (114)
T PF11023_consen 70 VECPNCGKQTK-MLG---RVDACMHCKEPLT---LDPSLEGKEFDE 108 (114)
T ss_pred eECCCCCChHh-hhc---hhhccCcCCCcCc---cCchhhcchhhH
Confidence 46999998532 221 1248999998875 444444445664
No 154
>PHA02942 putative transposase; Provisional
Probab=77.94 E-value=1.3 Score=41.79 Aligned_cols=29 Identities=17% Similarity=0.420 Sum_probs=21.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e 35 (278)
..||.||.. . .+.......|.+||.+.+.
T Consensus 326 q~Cs~CG~~-~--~~l~~r~f~C~~CG~~~dr 354 (383)
T PHA02942 326 VSCPKCGHK-M--VEIAHRYFHCPSCGYENDR 354 (383)
T ss_pred ccCCCCCCc-c--CcCCCCEEECCCCCCEeCc
Confidence 579999973 2 2344568999999999753
No 155
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=77.87 E-value=1.2 Score=30.44 Aligned_cols=24 Identities=25% Similarity=0.753 Sum_probs=16.8
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713 1 MADSYCADCKRLTEVVFDHSAGDTICSECGLV 32 (278)
Q Consensus 1 ~~~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V 32 (278)
|....|.+|+.- + + ...|.+||..
T Consensus 1 M~~kAC~~C~~i---~-~----~~~CP~Cgs~ 24 (61)
T PRK08351 1 MTEKACRHCHYI---T-T----EDRCPVCGSR 24 (61)
T ss_pred CchhhhhhCCcc---c-C----CCcCCCCcCC
Confidence 556789999972 3 3 2269999983
No 156
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=77.68 E-value=0.91 Score=27.56 Aligned_cols=29 Identities=28% Similarity=0.603 Sum_probs=19.7
Q ss_pred CCCCCCCCCCceeEe----CCCCceEcCCCcccc
Q 023713 4 SYCADCKRLTEVVFD----HSAGDTICSECGLVL 33 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D----~~~G~~vC~~CG~Vl 33 (278)
..||+|+.. --|-| .....+-|+.||.+.
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 579999973 22222 345568899999874
No 157
>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=77.50 E-value=1.1 Score=38.44 Aligned_cols=33 Identities=30% Similarity=0.700 Sum_probs=23.8
Q ss_pred CCCCCCCCC-CceeEeCCCCc---eEcCCCccccccc
Q 023713 4 SYCADCKRL-TEVVFDHSAGD---TICSECGLVLEAY 36 (278)
Q Consensus 4 ~~Cp~Cg~~-~~vv~D~~~G~---~vC~~CG~Vl~e~ 36 (278)
+.|-+||.+ +.+-.+++.|. ..|.+||.|.|.-
T Consensus 1 miCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~vaDkY 37 (208)
T PF04161_consen 1 MICIECGHPVKSLYRQYSPGNIRLTKCPNCGKVADKY 37 (208)
T ss_pred CEeccCCCcchhhhhccCCCcEEEeeccccCCcccce
Confidence 479999985 23455666553 7899999998644
No 158
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=77.14 E-value=6.9 Score=32.26 Aligned_cols=46 Identities=17% Similarity=0.180 Sum_probs=38.7
Q ss_pred cHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 147 NQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 147 ~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
+.+.-..+++|+|-...+.|.+..+||+ ..+++..-+.+.+..|.+
T Consensus 6 ~~~yAl~~l~~lA~~~~~~~vs~~eIA~-~~~ip~~~l~kIl~~L~~ 51 (164)
T PRK10857 6 KGRYAVTAMLDVALNSEAGPVPLADISE-RQGISLSYLEQLFSRLRK 51 (164)
T ss_pred HHHHHHHHHHHHHhCCCCCcCcHHHHHH-HHCcCHHHHHHHHHHHHH
Confidence 4566777888888555567899999999 499999999999999986
No 159
>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=76.53 E-value=2.2 Score=25.54 Aligned_cols=25 Identities=20% Similarity=0.527 Sum_probs=14.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLV 32 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V 32 (278)
..|+.||- +++...-..+|..||.-
T Consensus 3 ~~C~~CG~----i~~g~~~p~~CP~Cg~~ 27 (34)
T cd00729 3 WVCPVCGY----IHEGEEAPEKCPICGAP 27 (34)
T ss_pred EECCCCCC----EeECCcCCCcCcCCCCc
Confidence 46777775 23333334577777763
No 160
>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=76.47 E-value=12 Score=30.80 Aligned_cols=29 Identities=21% Similarity=0.142 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHHcCCCHHHHHHHHHHHHHH
Q 023713 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (278)
Q Consensus 165 ~p~tl~eia~~~~~v~~~~i~~~~~~l~~~ 194 (278)
.|.|..|||+ .+|++..++.|.+++|.+.
T Consensus 142 ~~~t~~~iA~-~lG~tretvsR~l~~l~~~ 170 (193)
T TIGR03697 142 LRLSHQAIAE-AIGSTRVTITRLLGDLRKK 170 (193)
T ss_pred CCCCHHHHHH-HhCCcHHHHHHHHHHHHHC
Confidence 7899999999 5999999999999999874
No 161
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=75.39 E-value=1.9 Score=36.84 Aligned_cols=30 Identities=23% Similarity=0.455 Sum_probs=21.7
Q ss_pred CCCCCCCCC-CceeEeCCCCceEcCCCcccc
Q 023713 4 SYCADCKRL-TEVVFDHSAGDTICSECGLVL 33 (278)
Q Consensus 4 ~~Cp~Cg~~-~~vv~D~~~G~~vC~~CG~Vl 33 (278)
..||.|+++ +.++.|...=.+.|..||..-
T Consensus 99 V~C~~C~~pdT~l~k~~~~~~l~C~aCGa~~ 129 (201)
T PRK12336 99 VICSECGLPDTRLVKEDRVLMLRCDACGAHR 129 (201)
T ss_pred EECCCCCCCCcEEEEcCCeEEEEcccCCCCc
Confidence 469999995 455555444456899999874
No 162
>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=75.06 E-value=14 Score=24.68 Aligned_cols=31 Identities=19% Similarity=0.257 Sum_probs=26.8
Q ss_pred cCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHH
Q 023713 163 ENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (278)
Q Consensus 163 ~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~ 194 (278)
...+.+..|+++. ++++..++.+.++.|.+.
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 999999999999998764
No 163
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=74.47 E-value=1.8 Score=33.40 Aligned_cols=23 Identities=26% Similarity=0.751 Sum_probs=10.5
Q ss_pred CCCCCCCCCceeEeCCCCceEcCCCcc
Q 023713 5 YCADCKRLTEVVFDHSAGDTICSECGL 31 (278)
Q Consensus 5 ~Cp~Cg~~~~vv~D~~~G~~vC~~CG~ 31 (278)
+|+.||.. +....-...|+.||.
T Consensus 72 ~C~~Cg~~----~~~~~~~~~CP~Cgs 94 (113)
T PRK12380 72 WCWDCSQV----VEIHQHDAQCPHCHG 94 (113)
T ss_pred EcccCCCE----EecCCcCccCcCCCC
Confidence 46666641 222223344666663
No 164
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=74.25 E-value=2 Score=29.06 Aligned_cols=28 Identities=21% Similarity=0.505 Sum_probs=15.6
Q ss_pred CCCCCCCCCCceeEeC----CCCceEcCCCccc
Q 023713 4 SYCADCKRLTEVVFDH----SAGDTICSECGLV 32 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~----~~G~~vC~~CG~V 32 (278)
..||+||. ..|.... ..-.++|.+||..
T Consensus 28 F~CPnCGe-~~I~Rc~~CRk~g~~Y~Cp~CGF~ 59 (61)
T COG2888 28 FPCPNCGE-VEIYRCAKCRKLGNPYRCPKCGFE 59 (61)
T ss_pred eeCCCCCc-eeeehhhhHHHcCCceECCCcCcc
Confidence 35777775 2333221 3446777777753
No 165
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=74.25 E-value=3 Score=29.91 Aligned_cols=29 Identities=28% Similarity=0.520 Sum_probs=19.4
Q ss_pred CCCCCCCCCCCceeEeCCCCc--eEcCCCcccc
Q 023713 3 DSYCADCKRLTEVVFDHSAGD--TICSECGLVL 33 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~--~vC~~CG~Vl 33 (278)
+..||.|+. +++.....|. -.|+.|+=|-
T Consensus 1 ~llCP~C~v--~l~~~~rs~vEiD~CPrCrGVW 31 (88)
T COG3809 1 MLLCPICGV--ELVMSVRSGVEIDYCPRCRGVW 31 (88)
T ss_pred CcccCcCCc--eeeeeeecCceeeeCCccccEe
Confidence 467999996 3444333443 4699998875
No 166
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=74.14 E-value=2.6 Score=31.50 Aligned_cols=30 Identities=17% Similarity=0.565 Sum_probs=20.7
Q ss_pred CCCCCCCCCCCceeEeC-C-CCceEcCCCccccc
Q 023713 3 DSYCADCKRLTEVVFDH-S-AGDTICSECGLVLE 34 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~-~-~G~~vC~~CG~Vl~ 34 (278)
|..||.||. .+++.. . --...|..|++|..
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 468999997 344432 2 24578999999964
No 167
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=74.13 E-value=8.6 Score=25.17 Aligned_cols=35 Identities=11% Similarity=0.023 Sum_probs=29.7
Q ss_pred cCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhh
Q 023713 163 ENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (278)
Q Consensus 163 ~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~ 198 (278)
-+...+..++|.. +||+..++.+.++.+...|...
T Consensus 16 LR~~~~~~~La~~-FgIs~stvsri~~~~~~~L~~~ 50 (53)
T PF13613_consen 16 LRLNLTFQDLAYR-FGISQSTVSRIFHEWIPLLYQV 50 (53)
T ss_pred HHcCCcHhHHhhh-eeecHHHHHHHHHHHHHHHHHh
Confidence 3466789999995 9999999999999999888654
No 168
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=73.60 E-value=3.3 Score=28.30 Aligned_cols=57 Identities=14% Similarity=0.267 Sum_probs=32.5
Q ss_pred HHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhhcccccccCC-CCHHHHHHHHHhhcCCCHHH
Q 023713 160 CRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGT-IHASDYLRRFCSNLGMTNQA 227 (278)
Q Consensus 160 cR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~~~~~~~~~~-~~p~~~i~r~~~~L~l~~~v 227 (278)
-.++....|+.|++.. ++++...|.... .=+++ .+|. +-...||..|++.|||+++-
T Consensus 4 ~~R~~~glsl~~va~~-t~I~~~~l~aiE-----~~~~~-----~lp~~~y~rg~lr~Ya~~Lgld~~~ 61 (62)
T PF13413_consen 4 EAREAKGLSLEDVAEE-TKISVSYLEAIE-----NGDFD-----SLPSPVYARGYLRKYARFLGLDPDE 61 (62)
T ss_dssp HHHHCTT--HHHHHHH-CS--HHHHHHHH-----CT-GC-----CSSSHHHHHHHHHHHHHHTT--HHH
T ss_pred HHHHHcCCCHHHHHHH-hCCCHHHHHHHH-----CcChh-----hCCcHHHHHHHHHHHHHHhCcCccc
Confidence 3456677999999995 899888774331 11121 1332 22467999999999998763
No 169
>COG1773 Rubredoxin [Energy production and conversion]
Probab=73.44 E-value=2.3 Score=28.49 Aligned_cols=24 Identities=29% Similarity=0.582 Sum_probs=12.5
Q ss_pred CCCCCCCCCCCceeEeCCCCceEcCCCc
Q 023713 3 DSYCADCKRLTEVVFDHSAGDTICSECG 30 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG 30 (278)
...|..||= |+|++.|+-.|..|+
T Consensus 3 ~~~C~~CG~----vYd~e~Gdp~~gi~p 26 (55)
T COG1773 3 RWRCSVCGY----VYDPEKGDPRCGIAP 26 (55)
T ss_pred ceEecCCce----EeccccCCccCCCCC
Confidence 345555553 455555555554443
No 170
>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=73.12 E-value=3.5 Score=29.17 Aligned_cols=30 Identities=20% Similarity=0.627 Sum_probs=21.4
Q ss_pred CCCCCCCCCCcee--EeCCCCceEcCCCcccc
Q 023713 4 SYCADCKRLTEVV--FDHSAGDTICSECGLVL 33 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv--~D~~~G~~vC~~CG~Vl 33 (278)
-.||.|++-..|. .+...-..-|.+||..-
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 4799999854443 34445566799999984
No 171
>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=72.90 E-value=1 Score=29.58 Aligned_cols=31 Identities=16% Similarity=0.465 Sum_probs=22.8
Q ss_pred CCCCCCCCCCCCcee--EeCCCCceEcCCCccccc
Q 023713 2 ADSYCADCKRLTEVV--FDHSAGDTICSECGLVLE 34 (278)
Q Consensus 2 ~~~~Cp~Cg~~~~vv--~D~~~G~~vC~~CG~Vl~ 34 (278)
.+.+|+.|+.- +. -+..+.++-|..||++-.
T Consensus 3 ~eiRC~~Cnkl--La~~g~~~~leIKCpRC~tiN~ 35 (51)
T PF10122_consen 3 KEIRCGHCNKL--LAKAGEVIELEIKCPRCKTINH 35 (51)
T ss_pred cceeccchhHH--HhhhcCccEEEEECCCCCccce
Confidence 45789999962 21 245578999999999953
No 172
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=72.72 E-value=11 Score=30.67 Aligned_cols=45 Identities=13% Similarity=0.207 Sum_probs=37.3
Q ss_pred cHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 147 NQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 147 ~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
..+.-+-+.+|+|- ..+.+.+.+|||+. .+++..-|.+.+..|++
T Consensus 6 ~~~YAlr~L~~LA~-~~~~~~s~~eIA~~-~~is~~~L~kIl~~L~~ 50 (153)
T PRK11920 6 QTNYAIRMLMYCAA-NDGKLSRIPEIARA-YGVSELFLFKILQPLVE 50 (153)
T ss_pred HHhHHHHHHHHHHh-CCCCcCcHHHHHHH-HCcCHHHHHHHHHHHHH
Confidence 34566678899994 45668899999994 89999999999999987
No 173
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=72.67 E-value=2.9 Score=28.36 Aligned_cols=28 Identities=18% Similarity=0.540 Sum_probs=16.1
Q ss_pred CCCCCCCCCCceeEe----CCCCceEcCCCccc
Q 023713 4 SYCADCKRLTEVVFD----HSAGDTICSECGLV 32 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D----~~~G~~vC~~CG~V 32 (278)
..||+||. ..|..- ...-.+.|.+||..
T Consensus 26 F~CPnCG~-~~I~RC~~CRk~~~~Y~CP~CGF~ 57 (59)
T PRK14890 26 FLCPNCGE-VIIYRCEKCRKQSNPYTCPKCGFE 57 (59)
T ss_pred eeCCCCCC-eeEeechhHHhcCCceECCCCCCc
Confidence 35888886 223222 14456778888764
No 174
>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=72.50 E-value=2.3 Score=32.99 Aligned_cols=16 Identities=13% Similarity=0.557 Sum_probs=7.8
Q ss_pred eeEeCCCCceEcCCCc
Q 023713 15 VVFDHSAGDTICSECG 30 (278)
Q Consensus 15 vv~D~~~G~~vC~~CG 30 (278)
+..+..-+...|.+||
T Consensus 62 L~I~~~p~~~~C~~Cg 77 (115)
T TIGR00100 62 LNIEDEPVECECEDCS 77 (115)
T ss_pred EEEEeeCcEEEcccCC
Confidence 4444444455555555
No 175
>PF14353 CpXC: CpXC protein
Probab=72.09 E-value=3.5 Score=32.32 Aligned_cols=12 Identities=25% Similarity=0.742 Sum_probs=10.0
Q ss_pred ceEcCCCccccc
Q 023713 23 DTICSECGLVLE 34 (278)
Q Consensus 23 ~~vC~~CG~Vl~ 34 (278)
..+|.+||....
T Consensus 38 ~~~CP~Cg~~~~ 49 (128)
T PF14353_consen 38 SFTCPSCGHKFR 49 (128)
T ss_pred EEECCCCCCcee
Confidence 679999998763
No 176
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=71.69 E-value=3.5 Score=27.16 Aligned_cols=32 Identities=25% Similarity=0.767 Sum_probs=21.9
Q ss_pred CCCCCCCCCCCceeE-eCCCCc-eEcCCCccccc
Q 023713 3 DSYCADCKRLTEVVF-DHSAGD-TICSECGLVLE 34 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~-D~~~G~-~vC~~CG~Vl~ 34 (278)
...|.+|+...+.++ +...|. .+|..||+-..
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~ 36 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGLYYK 36 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccHHHH
Confidence 467999987544444 335565 89999998764
No 177
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=71.65 E-value=2.7 Score=37.36 Aligned_cols=29 Identities=14% Similarity=0.432 Sum_probs=21.0
Q ss_pred CCCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl 33 (278)
...||.||+. +......-...|..||.+.
T Consensus 99 ~~fC~~CG~~--~~~~~~~~~~~C~~c~~~~ 127 (256)
T PRK00241 99 HRFCGYCGHP--MHPSKTEWAMLCPHCRERY 127 (256)
T ss_pred CccccccCCC--CeecCCceeEECCCCCCEE
Confidence 3689999984 3334455668899999764
No 178
>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=71.57 E-value=3.3 Score=33.16 Aligned_cols=27 Identities=26% Similarity=0.728 Sum_probs=19.6
Q ss_pred CCC--CCCCCCceeEeCCCCceEcCCCccccc
Q 023713 5 YCA--DCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 5 ~Cp--~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
.|| .|++ .+..+ .+|.+.|..||..++
T Consensus 20 aC~~~~C~k--Kv~~~-~~~~y~C~~C~~~~~ 48 (146)
T PF08646_consen 20 ACPNEKCNK--KVTEN-GDGSYRCEKCNKTVE 48 (146)
T ss_dssp E-TSTTTS---B-EEE-TTTEEEETTTTEEES
T ss_pred CCCCccCCC--EeecC-CCcEEECCCCCCcCC
Confidence 599 9997 35555 779999999998874
No 179
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=71.44 E-value=2.4 Score=33.80 Aligned_cols=21 Identities=24% Similarity=0.623 Sum_probs=13.9
Q ss_pred ceeEeCCCCceEcCCCccccc
Q 023713 14 EVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 14 ~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
.+..+...+...|.+||.+..
T Consensus 61 ~L~i~~~p~~~~C~~CG~~~~ 81 (135)
T PRK03824 61 EIIFEEEEAVLKCRNCGNEWS 81 (135)
T ss_pred EEEEEecceEEECCCCCCEEe
Confidence 455556667777777776653
No 180
>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=71.25 E-value=2.9 Score=23.98 Aligned_cols=28 Identities=18% Similarity=0.419 Sum_probs=16.1
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGL 31 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~ 31 (278)
..||.|+....-+........+|..|--
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 5799999743334445777899998854
No 181
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=70.90 E-value=13 Score=24.55 Aligned_cols=39 Identities=21% Similarity=0.232 Sum_probs=28.9
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 154 ACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 154 AclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
.++++.....+.+.|+.||++. +++++.++.+.++.|.+
T Consensus 9 ~vL~~l~~~~~~~~t~~~la~~-l~~~~~~vs~~v~~L~~ 47 (62)
T PF12802_consen 9 RVLMALARHPGEELTQSELAER-LGISKSTVSRIVKRLEK 47 (62)
T ss_dssp HHHHHHHHSTTSGEEHHHHHHH-HTS-HHHHHHHHHHHHH
T ss_pred HHHHHHHHCCCCCcCHHHHHHH-HCcCHHHHHHHHHHHHH
Confidence 3444444444445899999995 99999999999999875
No 182
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=70.88 E-value=2 Score=40.57 Aligned_cols=33 Identities=27% Similarity=0.718 Sum_probs=24.8
Q ss_pred CCCCCCCCCC-Cce----eEeCCCCceEcCCCcccccc
Q 023713 3 DSYCADCKRL-TEV----VFDHSAGDTICSECGLVLEA 35 (278)
Q Consensus 3 ~~~Cp~Cg~~-~~v----v~D~~~G~~vC~~CG~Vl~e 35 (278)
...||.|++. +.+ .+|..+|...|..||.=|.+
T Consensus 128 ~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelve 165 (436)
T KOG2593|consen 128 GYVCPNCQKKYTSLEALQLLDNETGEFHCENCGGELVE 165 (436)
T ss_pred cccCCccccchhhhHHHHhhcccCceEEEecCCCchhc
Confidence 3679999973 222 56788999999999976543
No 183
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=70.77 E-value=7.9 Score=24.03 Aligned_cols=29 Identities=24% Similarity=0.347 Sum_probs=25.6
Q ss_pred CCCCCHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 164 ~~p~tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
..|.+..|+++. ++++..++.+.++.|.+
T Consensus 6 ~~~~s~~~la~~-l~~s~~tv~~~l~~L~~ 34 (48)
T smart00419 6 RLPLTRQEIAEL-LGLTRETVSRTLKRLEK 34 (48)
T ss_pred EeccCHHHHHHH-HCCCHHHHHHHHHHHHH
Confidence 367899999994 99999999999999876
No 184
>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=70.76 E-value=3.1 Score=26.02 Aligned_cols=10 Identities=30% Similarity=0.959 Sum_probs=7.4
Q ss_pred eEcCCCcccc
Q 023713 24 TICSECGLVL 33 (278)
Q Consensus 24 ~vC~~CG~Vl 33 (278)
.+|.+||..+
T Consensus 33 ~~C~~CGE~~ 42 (46)
T TIGR03831 33 LVCPQCGEEY 42 (46)
T ss_pred cccccCCCEe
Confidence 3588888765
No 185
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=70.27 E-value=14 Score=25.52 Aligned_cols=38 Identities=18% Similarity=0.184 Sum_probs=29.9
Q ss_pred HHHHHHhcCC-CCCHHHHHHHHcCCCHHHHHHHHHHHHHH
Q 023713 156 LYIACRQENK-PRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (278)
Q Consensus 156 lY~acR~~~~-p~tl~eia~~~~~v~~~~i~~~~~~l~~~ 194 (278)
|+...+..+- +.++.|||. .+|++..++++....|.+.
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 3444555665 499999999 4999999999998888764
No 186
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=70.06 E-value=26 Score=30.30 Aligned_cols=60 Identities=12% Similarity=-0.024 Sum_probs=46.0
Q ss_pred CCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHH
Q 023713 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQ 236 (278)
Q Consensus 165 ~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~ 236 (278)
...|-+|||.. ++++++++.+....|.+.||++ +-.+.+ +++-+.++-..+.+.+.+|++
T Consensus 157 ~G~SnkEIA~~-L~IS~~TVk~hvs~I~~KLgv~----------sR~eLv-~~A~~~gli~~~~~~~~~ii~ 216 (217)
T PRK13719 157 FGFSHEYIAQL-LNITVGSSKNKISEILKFFGIS----------SRDELL-IILHTSEMIFYLYKKVFEIIN 216 (217)
T ss_pred CCCCHHHHHHH-hCCCHHHHHHHHHHHHHHhCCC----------CHHHHH-HHHHHcCChHHHHHHHHHHhc
Confidence 56889999995 9999999999999999999975 223333 455566777777777777654
No 187
>KOG3134 consensus Predicted membrane protein [Function unknown]
Probab=70.06 E-value=1.4 Score=37.82 Aligned_cols=33 Identities=27% Similarity=0.574 Sum_probs=26.3
Q ss_pred CCCCCCCCC-CceeEeCCCC---ceEcCCCccccccc
Q 023713 4 SYCADCKRL-TEVVFDHSAG---DTICSECGLVLEAY 36 (278)
Q Consensus 4 ~~Cp~Cg~~-~~vv~D~~~G---~~vC~~CG~Vl~e~ 36 (278)
++|-+||++ .++-.++..| -.-|.+|+.|+++-
T Consensus 1 ~~CVeCg~~vksLy~~Ys~g~irlt~C~nC~e~vDkY 37 (225)
T KOG3134|consen 1 YRCVECGSEVKSLYTQYSPGNIRLTKCPNCQEVVDKY 37 (225)
T ss_pred CcccccCchHHHHHHhcCCCcEEEeeCCchhhHHHhH
Confidence 479999985 4667788888 56899999998644
No 188
>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=69.92 E-value=5 Score=25.72 Aligned_cols=21 Identities=24% Similarity=0.461 Sum_probs=18.0
Q ss_pred CHHHHHHHHcCCCHHHHHHHHH
Q 023713 168 TVKEFCSVANGTTKKEIGRAKE 189 (278)
Q Consensus 168 tl~eia~~~~~v~~~~i~~~~~ 189 (278)
|++|||.. +|++..++.+++.
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 9999999988754
No 189
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=69.80 E-value=2.5 Score=32.34 Aligned_cols=32 Identities=6% Similarity=0.049 Sum_probs=25.8
Q ss_pred CCCCCCCCCCCceeEeCCCCceEcCCCcccccccc
Q 023713 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYS 37 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~~ 37 (278)
.++||+||+. .+|-.+--+||..||.-.....
T Consensus 9 KridPetg~K---FYDLNrdPiVsPytG~s~P~s~ 40 (129)
T COG4530 9 KRIDPETGKK---FYDLNRDPIVSPYTGKSYPRSY 40 (129)
T ss_pred cccCccccch---hhccCCCccccCcccccchHHH
Confidence 3789999984 6888888999999998764433
No 190
>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=69.55 E-value=33 Score=27.58 Aligned_cols=59 Identities=10% Similarity=0.020 Sum_probs=42.7
Q ss_pred cCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh---cC----CCCChhHHHHHHHHHHHHHHHHH
Q 023713 205 MGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED---LD----IRLILVFFSLFLVETHIQLIVWA 265 (278)
Q Consensus 205 ~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~---~~----~Gr~P~~iaaA~v~~~~~~~~~~ 265 (278)
+|..+..+|+.|+.....+++++.-.|.-.++++.. .. ...++.-+-.+++ .||.++|.
T Consensus 49 ~p~i~i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~al--ilA~K~~~ 114 (149)
T PF08613_consen 49 VPSISIRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTAL--ILASKFLD 114 (149)
T ss_dssp --SS-HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHH--HHHHHHH-
T ss_pred CCCCcHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHH--HHHHhhcc
Confidence 577889999999999999999999999988888877 22 2456666777777 77877774
No 191
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=69.28 E-value=4.1 Score=25.27 Aligned_cols=28 Identities=18% Similarity=0.424 Sum_probs=15.9
Q ss_pred CCCCCCCCCceeEeC-CCCceEcCCCcccc
Q 023713 5 YCADCKRLTEVVFDH-SAGDTICSECGLVL 33 (278)
Q Consensus 5 ~Cp~Cg~~~~vv~D~-~~G~~vC~~CG~Vl 33 (278)
.||.|+.. -..... .---.+|.+||=+-
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 211111 12234699998664
No 192
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=69.08 E-value=15 Score=28.60 Aligned_cols=45 Identities=20% Similarity=0.290 Sum_probs=35.0
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 148 QEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 148 ~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
.+....+.+|++-...+.|.+..||++. ++++...+.+....|.+
T Consensus 7 ~~~al~~l~~la~~~~~~~~s~~eia~~-~~i~~~~v~~il~~L~~ 51 (132)
T TIGR00738 7 TEYALRALLDLALNPDEGPVSVKEIAER-QGISRSYLEKILRTLRR 51 (132)
T ss_pred HHHHHHHHHHHHhCCCCCcCcHHHHHHH-HCcCHHHHHHHHHHHHH
Confidence 3455566677764333458999999995 99999999999999986
No 193
>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=68.98 E-value=3.7 Score=31.80 Aligned_cols=21 Identities=14% Similarity=0.115 Sum_probs=10.9
Q ss_pred CCCHHHHHHHHcCCCHHHHHHH
Q 023713 166 PRTVKEFCSVANGTTKKEIGRA 187 (278)
Q Consensus 166 p~tl~eia~~~~~v~~~~i~~~ 187 (278)
..|..++|.. +|++..+|.+.
T Consensus 78 gltq~~lA~~-lg~~~~tis~~ 98 (127)
T TIGR03830 78 GLSQREAAEL-LGGGVNAFSRY 98 (127)
T ss_pred CCCHHHHHHH-hCCCHHHHHHH
Confidence 4455555553 55555555443
No 194
>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=68.73 E-value=3.2 Score=39.38 Aligned_cols=30 Identities=27% Similarity=0.625 Sum_probs=19.2
Q ss_pred CCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 5 YCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 5 ~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
.||+||....+..-...+...|+.||.++.
T Consensus 15 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~ 44 (403)
T TIGR00155 15 LCSQCDMLVALPRIESGQKAACPRCGTTLT 44 (403)
T ss_pred eCCCCCCcccccCCCCCCeeECCCCCCCCc
Confidence 589998632222223445678999998885
No 195
>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=68.16 E-value=1.4 Score=34.03 Aligned_cols=24 Identities=33% Similarity=0.737 Sum_probs=12.3
Q ss_pred CCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713 5 YCADCKRLTEVVFDHSAGDTICSECGLV 32 (278)
Q Consensus 5 ~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V 32 (278)
+|+.||.. ++.......|+.||.-
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 46677652 3444444667777654
No 196
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=68.05 E-value=1.1 Score=40.69 Aligned_cols=30 Identities=23% Similarity=0.476 Sum_probs=21.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
.+||.|+. .-...|-.....||.+||.-..
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 57999997 3233344567899999998764
No 197
>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=68.04 E-value=2.3 Score=37.16 Aligned_cols=30 Identities=23% Similarity=0.600 Sum_probs=10.8
Q ss_pred CCCCCCCCCCce---eEeCCCCceEcCCCccccc
Q 023713 4 SYCADCKRLTEV---VFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 4 ~~Cp~Cg~~~~v---v~D~~~G~~vC~~CG~Vl~ 34 (278)
..||+||+. .+ --...-.+..|.+|+.-.+
T Consensus 32 ~yCP~Cg~~-~L~~f~NN~PVaDF~C~~C~eeyE 64 (254)
T PF06044_consen 32 MYCPNCGSK-PLSKFENNRPVADFYCPNCNEEYE 64 (254)
T ss_dssp ---TTT--S-S-EE--------EEE-TTT--EEE
T ss_pred CcCCCCCCh-hHhhccCCCccceeECCCCchHHh
Confidence 579999984 22 2223557899999987553
No 198
>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=67.94 E-value=1.1 Score=40.45 Aligned_cols=30 Identities=13% Similarity=0.448 Sum_probs=21.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
.+||.|+. .-...|-.....||.+||.-..
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 57999997 2222334566789999998763
No 199
>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=67.50 E-value=17 Score=28.26 Aligned_cols=45 Identities=9% Similarity=0.129 Sum_probs=36.6
Q ss_pred cHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 147 NQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 147 ~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
..+....+.+|++- ..+-+.+..||++. .+++...+.+..+.|.+
T Consensus 7 ~~~yal~~l~~la~-~~~~~~s~~eia~~-l~is~~~v~~~l~~L~~ 51 (130)
T TIGR02944 7 LTDYATLVLTTLAQ-NDSQPYSAAEIAEQ-TGLNAPTVSKILKQLSL 51 (130)
T ss_pred HHhHHHHHHHHHHh-CCCCCccHHHHHHH-HCcCHHHHHHHHHHHHH
Confidence 34566677888874 34568999999994 99999999999999986
No 200
>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=67.14 E-value=20 Score=22.49 Aligned_cols=29 Identities=21% Similarity=0.229 Sum_probs=23.1
Q ss_pred CCCCCHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 164 ~~p~tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
+-+.|..|+|.. ++++..++.+.+++|.+
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 334999999995 99999999999999865
No 201
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=65.90 E-value=3.6 Score=28.18 Aligned_cols=26 Identities=35% Similarity=0.857 Sum_probs=17.7
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713 1 MADSYCADCKRLTEVVFDHSAGDTICSECGLV 32 (278)
Q Consensus 1 ~~~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V 32 (278)
|....|.+|+.- + .+..-+|+.||.=
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 345679999872 2 2456789999864
No 202
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=65.89 E-value=4.7 Score=27.22 Aligned_cols=27 Identities=22% Similarity=0.545 Sum_probs=18.2
Q ss_pred CCCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY 36 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~ 36 (278)
+..||+||. .- --.-||.+||.--+..
T Consensus 27 ~~~c~~cG~-~~------l~Hrvc~~cg~Y~g~~ 53 (57)
T COG0333 27 LSVCPNCGE-YK------LPHRVCLKCGYYKGRQ 53 (57)
T ss_pred ceeccCCCC-cc------cCceEcCCCCCccCeE
Confidence 357999996 21 2367999999765433
No 203
>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=65.70 E-value=9.4 Score=25.26 Aligned_cols=33 Identities=21% Similarity=0.281 Sum_probs=28.0
Q ss_pred CCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhh
Q 023713 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (278)
Q Consensus 165 ~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~ 198 (278)
...+.+|||.. .++++++|....+.|.+.||+.
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 9999999999999999999875
No 204
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=65.64 E-value=18 Score=29.32 Aligned_cols=46 Identities=20% Similarity=0.213 Sum_probs=39.7
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHH
Q 023713 148 QEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (278)
Q Consensus 148 ~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~ 194 (278)
.+...-|.+|+|....+-|.+..+||.. .++++.-+.+.+..|++.
T Consensus 7 ~~yal~~L~~LA~~~~~~~~s~~~IA~~-~~is~~~L~kil~~L~ka 52 (150)
T COG1959 7 GEYALRALLYLALLPGGGPVSSAEIAER-QGISPSYLEKILSKLRKA 52 (150)
T ss_pred HhHHHHHHHHHHhCCCCCcccHHHHHHH-hCcCHHHHHHHHHHHHHc
Confidence 4566778899998877779999999994 999999999999999873
No 205
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=65.47 E-value=3.7 Score=31.77 Aligned_cols=7 Identities=29% Similarity=1.004 Sum_probs=3.6
Q ss_pred eEcCCCc
Q 023713 24 TICSECG 30 (278)
Q Consensus 24 ~vC~~CG 30 (278)
..|+.||
T Consensus 88 ~~CP~Cg 94 (114)
T PRK03681 88 RRCPQCH 94 (114)
T ss_pred CcCcCcC
Confidence 3455555
No 206
>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=65.37 E-value=2.6 Score=25.67 Aligned_cols=22 Identities=23% Similarity=0.585 Sum_probs=10.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTIC 26 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC 26 (278)
.+|..||. ---+.+...|.++|
T Consensus 7 YkC~~CGn-iVev~~~g~g~lvC 28 (36)
T PF06397_consen 7 YKCEHCGN-IVEVVHDGGGPLVC 28 (36)
T ss_dssp EE-TTT---EEEEEE--SS-EEE
T ss_pred EEccCCCC-EEEEEECCCCCEEe
Confidence 56888886 33356667778888
No 207
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=65.11 E-value=28 Score=29.65 Aligned_cols=30 Identities=20% Similarity=0.005 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHHcCCCHHHHHHHHHHHHHHh
Q 023713 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHL 195 (278)
Q Consensus 165 ~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L 195 (278)
.|.|..+||+ .+|++..++.|..++|.+.=
T Consensus 183 ~~lt~~~iA~-~lG~sr~tvsR~l~~l~~~g 212 (235)
T PRK11161 183 LTMTRGDIGN-YLGLTVETISRLLGRFQKSG 212 (235)
T ss_pred ccccHHHHHH-HhCCcHHHHHHHHHHHHHCC
Confidence 6899999999 59999999999999987643
No 208
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=64.93 E-value=4.2 Score=31.69 Aligned_cols=33 Identities=24% Similarity=0.565 Sum_probs=28.0
Q ss_pred eCCCCceEcCCCcccc--cccccccccchhhccCC
Q 023713 18 DHSAGDTICSECGLVL--EAYSVDETSEWRIFANE 50 (278)
Q Consensus 18 D~~~G~~vC~~CG~Vl--~e~~id~~~ewr~f~~~ 50 (278)
..+.|.++|..||.-| .+.-+|.|.-|.+|.+.
T Consensus 28 ~~~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPSF~~~ 62 (119)
T PRK05508 28 FFEKGTYVCKQCGAPLYRSEDKFKSGCGWPSFDDE 62 (119)
T ss_pred cCCCeEEEecCCCCccccccccccCCCCCcccCcc
Confidence 3589999999999988 55678999999999853
No 209
>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=64.75 E-value=5 Score=25.76 Aligned_cols=29 Identities=17% Similarity=0.421 Sum_probs=18.2
Q ss_pred CCCCCCCCCceeEe-------CCCCceEcCC--Cccccc
Q 023713 5 YCADCKRLTEVVFD-------HSAGDTICSE--CGLVLE 34 (278)
Q Consensus 5 ~Cp~Cg~~~~vv~D-------~~~G~~vC~~--CG~Vl~ 34 (278)
.||.||+. ..+.- ..+--..|+| ||.-..
T Consensus 1 ~CP~Cg~~-a~ir~S~~~s~~~~~~Y~qC~N~~Cg~tfv 38 (47)
T PF04606_consen 1 RCPHCGSK-ARIRTSRQLSPLTRELYCQCTNPECGHTFV 38 (47)
T ss_pred CcCCCCCe-eEEEEchhhCcceEEEEEEECCCcCCCEEE
Confidence 59999984 44432 2333457887 987653
No 210
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=64.34 E-value=5.5 Score=36.58 Aligned_cols=91 Identities=10% Similarity=0.039 Sum_probs=56.4
Q ss_pred HHHHHHHHHHHHHhcCCCHH----HHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHH---HHHHcC
Q 023713 106 LIQAFKSISAMSDRLGLVTT----IKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEF---CSVANG 178 (278)
Q Consensus 106 l~~~~~~I~~i~~~L~Lp~~----v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~ei---a~~~~~ 178 (278)
+.+...++-+++..|+-..+ +...|..+.....--.+.---.+..+|+||||+||...+++.....- ... ++
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 34445566666666655443 45555555554433222222468899999999999999886554322 221 34
Q ss_pred --CCHHHHHHHHHHHHHHhhh
Q 023713 179 --TTKKEIGRAKEFIVKHLEA 197 (278)
Q Consensus 179 --v~~~~i~~~~~~l~~~L~~ 197 (278)
++...|......+...+..
T Consensus 227 ~~vt~e~l~~i~~~~l~~y~~ 247 (323)
T KOG0834|consen 227 ETVTNELLDDICHEFLDLYEQ 247 (323)
T ss_pred ccCCHHHHHHHHHHHHHHHhh
Confidence 7888888887777776643
No 211
>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=64.19 E-value=4 Score=36.81 Aligned_cols=29 Identities=31% Similarity=0.635 Sum_probs=12.8
Q ss_pred CCCCCCCCCCce-eEeCCC--C--ceEcCCCccc
Q 023713 4 SYCADCKRLTEV-VFDHSA--G--DTICSECGLV 32 (278)
Q Consensus 4 ~~Cp~Cg~~~~v-v~D~~~--G--~~vC~~CG~V 32 (278)
..||.||+...+ +.+... | .+.|+-||+-
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 689999985333 333332 4 5789988864
No 212
>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=64.08 E-value=4 Score=28.72 Aligned_cols=26 Identities=19% Similarity=0.607 Sum_probs=15.6
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl 33 (278)
..||.|+.+ +.. ..|...|..|+.-+
T Consensus 2 ~~CP~C~~~--L~~--~~~~~~C~~C~~~~ 27 (70)
T PF07191_consen 2 NTCPKCQQE--LEW--QGGHYHCEACQKDY 27 (70)
T ss_dssp -B-SSS-SB--EEE--ETTEEEETTT--EE
T ss_pred CcCCCCCCc--cEE--eCCEEECccccccc
Confidence 579999973 444 45899999998755
No 213
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=64.05 E-value=3.9 Score=41.17 Aligned_cols=14 Identities=21% Similarity=0.591 Sum_probs=10.8
Q ss_pred eEcCCCcccccccc
Q 023713 24 TICSECGLVLEAYS 37 (278)
Q Consensus 24 ~vC~~CG~Vl~e~~ 37 (278)
..|.+||.-+.+..
T Consensus 28 ~~Cp~CG~~~~~~~ 41 (645)
T PRK14559 28 KPCPQCGTEVPVDE 41 (645)
T ss_pred CcCCCCCCCCCccc
Confidence 57999999986543
No 214
>PF13730 HTH_36: Helix-turn-helix domain
Probab=63.84 E-value=22 Score=22.93 Aligned_cols=26 Identities=12% Similarity=0.217 Sum_probs=23.2
Q ss_pred CCHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 167 RTVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 167 ~tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
.+..+|++. +|++..+|.++.++|.+
T Consensus 26 pS~~~la~~-~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 26 PSQETLAKD-LGVSRRTVQRAIKELEE 51 (55)
T ss_pred cCHHHHHHH-HCcCHHHHHHHHHHHHH
Confidence 389999995 99999999999999875
No 215
>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=63.75 E-value=17 Score=23.19 Aligned_cols=31 Identities=19% Similarity=0.228 Sum_probs=25.0
Q ss_pred CCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHh
Q 023713 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKHL 195 (278)
Q Consensus 164 ~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L 195 (278)
..+.|+.|||.. +|++..++.+..+...+.|
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 567899999995 9999999998887766554
No 216
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=63.69 E-value=1.5 Score=39.79 Aligned_cols=30 Identities=20% Similarity=0.537 Sum_probs=21.1
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
.+||.|+. .-...|-.....||..||.-..
T Consensus 28 ~~c~~c~~-~~~~~~l~~~~~vc~~c~~h~r 57 (292)
T PRK05654 28 TKCPSCGQ-VLYRKELEANLNVCPKCGHHMR 57 (292)
T ss_pred eECCCccc-hhhHHHHHhcCCCCCCCCCCee
Confidence 57999997 2223334455689999998763
No 217
>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=63.62 E-value=1.4 Score=29.91 Aligned_cols=27 Identities=19% Similarity=0.486 Sum_probs=19.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEcC-CCccccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICS-ECGLVLEAY 36 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~-~CG~Vl~e~ 36 (278)
..||+||.+ +-. .+..|+ +|+.....+
T Consensus 4 kHC~~CG~~--Ip~----~~~fCS~~C~~~~~k~ 31 (59)
T PF09889_consen 4 KHCPVCGKP--IPP----DESFCSPKCREEYRKR 31 (59)
T ss_pred CcCCcCCCc--CCc----chhhhCHHHHHHHHHH
Confidence 579999973 333 489996 899887543
No 218
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=63.61 E-value=6.3 Score=29.63 Aligned_cols=28 Identities=25% Similarity=0.547 Sum_probs=19.5
Q ss_pred CCCCCCCCCCceeEe---------CCCCceEcCCCccc
Q 023713 4 SYCADCKRLTEVVFD---------HSAGDTICSECGLV 32 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D---------~~~G~~vC~~CG~V 32 (278)
..||.||+. ..++= +.+=..+|.+||..
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 54442 24447889999974
No 219
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=63.39 E-value=4.5 Score=38.56 Aligned_cols=33 Identities=21% Similarity=0.499 Sum_probs=20.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAY 36 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~ 36 (278)
..||+||....+......+...|..||.++..+
T Consensus 11 ~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~~~ 43 (419)
T PRK15103 11 ILCPQCDMLVALPRLEHGQKAACPRCGTTLTVR 43 (419)
T ss_pred ccCCCCCceeecCCCCCCCeeECCCCCCCCcCC
Confidence 459999973221211234457799999999533
No 220
>PRK06030 hypothetical protein; Provisional
Probab=63.18 E-value=31 Score=27.12 Aligned_cols=39 Identities=15% Similarity=0.205 Sum_probs=31.5
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHh
Q 023713 154 ACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHL 195 (278)
Q Consensus 154 AclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L 195 (278)
.++|++-.. ...|+.+|+.. +|-+..++..+++.+.+.+
T Consensus 59 IAMYL~r~~--~~~sl~~IG~~-FGRDHSTV~haikkIe~~~ 97 (124)
T PRK06030 59 IAMYVAHVS--LGWPMNEVALA-FGRDRTTVGHACHTVEDLR 97 (124)
T ss_pred HHHHHHHHH--cCCCHHHHHHH-HCCChhHHHHHHHHHHHHh
Confidence 467877555 44589999995 7899999999999887765
No 221
>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=62.88 E-value=14 Score=25.49 Aligned_cols=33 Identities=18% Similarity=0.320 Sum_probs=24.9
Q ss_pred HhcCCCCCHHHHHHHHcCCC-HHHHHHHHHHHHHH
Q 023713 161 RQENKPRTVKEFCSVANGTT-KKEIGRAKEFIVKH 194 (278)
Q Consensus 161 R~~~~p~tl~eia~~~~~v~-~~~i~~~~~~l~~~ 194 (278)
..+|.|-|++||++. +|++ ..++.+.++.|.+.
T Consensus 20 ~~~G~~Pt~rEIa~~-~g~~S~~tv~~~L~~Le~k 53 (65)
T PF01726_consen 20 EENGYPPTVREIAEA-LGLKSTSTVQRHLKALERK 53 (65)
T ss_dssp HHHSS---HHHHHHH-HTSSSHHHHHHHHHHHHHT
T ss_pred HHcCCCCCHHHHHHH-hCCCChHHHHHHHHHHHHC
Confidence 478999999999994 8997 88998888888653
No 222
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=62.87 E-value=2.9 Score=32.20 Aligned_cols=34 Identities=18% Similarity=0.540 Sum_probs=26.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcccccccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVD 39 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~~id 39 (278)
..|++||. ..++....... .|+.||..-.+..++
T Consensus 43 ~~C~~Cg~-~~~~~~SCk~R-~CP~C~~~~~~~W~~ 76 (111)
T PF14319_consen 43 YRCEDCGH-EKIVYNSCKNR-HCPSCQAKATEQWIE 76 (111)
T ss_pred eecCCCCc-eEEecCcccCc-CCCCCCChHHHHHHH
Confidence 57999998 57777766666 999999998755443
No 223
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=62.82 E-value=4.4 Score=27.34 Aligned_cols=27 Identities=26% Similarity=0.672 Sum_probs=16.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl 33 (278)
..|-+||+++ .+ ...-.+-|.+||.=+
T Consensus 21 YiCgdC~~en-~l--k~~D~irCReCG~RI 47 (62)
T KOG3507|consen 21 YICGDCGQEN-TL--KRGDVIRCRECGYRI 47 (62)
T ss_pred EEeccccccc-cc--cCCCcEehhhcchHH
Confidence 4688899853 22 123345699998643
No 224
>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=62.81 E-value=15 Score=23.68 Aligned_cols=36 Identities=22% Similarity=0.272 Sum_probs=27.8
Q ss_pred HHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 157 YIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 157 Y~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
.-+-..++.|.++.||+.. +++++.++.+..+.|.+
T Consensus 9 L~~l~~~~~~~t~~eia~~-~gl~~stv~r~L~tL~~ 44 (52)
T PF09339_consen 9 LEALAESGGPLTLSEIARA-LGLPKSTVHRLLQTLVE 44 (52)
T ss_dssp HHCHHCTBSCEEHHHHHHH-HTS-HHHHHHHHHHHHH
T ss_pred HHHHHcCCCCCCHHHHHHH-HCcCHHHHHHHHHHHHH
Confidence 3344556777899999995 99999999998888764
No 225
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=62.65 E-value=2.1 Score=38.21 Aligned_cols=29 Identities=17% Similarity=0.512 Sum_probs=21.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl 33 (278)
.+||.||. .-..-|-.....||.+||.-.
T Consensus 29 ~KCp~c~~-~~y~~eL~~n~~vcp~c~~h~ 57 (294)
T COG0777 29 TKCPSCGE-MLYRKELESNLKVCPKCGHHM 57 (294)
T ss_pred eECCCccc-eeeHHHHHhhhhcccccCccc
Confidence 57999997 333334567789999999875
No 226
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=62.61 E-value=4.2 Score=27.71 Aligned_cols=21 Identities=24% Similarity=0.640 Sum_probs=16.3
Q ss_pred ceeEe-CCCCceEcCCCccccc
Q 023713 14 EVVFD-HSAGDTICSECGLVLE 34 (278)
Q Consensus 14 ~vv~D-~~~G~~vC~~CG~Vl~ 34 (278)
.|..| -.+|+++|.-||++..
T Consensus 38 rV~L~mg~~gev~CPYC~t~y~ 59 (62)
T COG4391 38 RVFLDMGDEGEVVCPYCSTRYR 59 (62)
T ss_pred EEEEEcCCCCcEecCccccEEE
Confidence 44444 4899999999999864
No 227
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=62.54 E-value=49 Score=24.53 Aligned_cols=39 Identities=15% Similarity=0.177 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHH
Q 023713 151 IVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFI 191 (278)
Q Consensus 151 ~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l 191 (278)
+..+.-|+-.. -..|.++.|+|.. ++++...+.+.+++.
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 33444454444 4567999999995 899999999988874
No 228
>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=62.34 E-value=64 Score=26.43 Aligned_cols=79 Identities=18% Similarity=0.280 Sum_probs=48.8
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhhcc---------cccccCCCCHHHHHHHHHhhc
Q 023713 151 IVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMG---------QSVEMGTIHASDYLRRFCSNL 221 (278)
Q Consensus 151 ~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~~~---------~~~~~~~~~p~~~i~r~~~~L 221 (278)
++=|.||. .+-|+++.+++++ ++ +..++.....+|.+.++-... .+.-....+-..|+.++...
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 4668999999996 89 999999999999998843221 11111223567788888877
Q ss_pred CCCHHHHHHHHHHHH
Q 023713 222 GMTNQAVKAAQEAVQ 236 (278)
Q Consensus 222 ~l~~~v~~~A~~i~~ 236 (278)
.-.....+.|.+.+-
T Consensus 75 ~~~~~LS~aalEtLA 89 (159)
T PF04079_consen 75 PKPPKLSQAALETLA 89 (159)
T ss_dssp CCCHHHHHHHHHHHH
T ss_pred CccCCCCHHHHHHHH
Confidence 224555555555433
No 229
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=62.32 E-value=13 Score=22.85 Aligned_cols=26 Identities=12% Similarity=0.126 Sum_probs=19.0
Q ss_pred CCCCCHHHHHHHHcCCCHHHHHHHHHH
Q 023713 164 NKPRTVKEFCSVANGTTKKEIGRAKEF 190 (278)
Q Consensus 164 ~~p~tl~eia~~~~~v~~~~i~~~~~~ 190 (278)
..+.++.|||+. .|++...+.+.+++
T Consensus 6 ~~~~~l~~iA~~-~g~S~~~f~r~Fk~ 31 (42)
T PF00165_consen 6 QQKLTLEDIAEQ-AGFSPSYFSRLFKK 31 (42)
T ss_dssp -SS--HHHHHHH-HTS-HHHHHHHHHH
T ss_pred cCCCCHHHHHHH-HCCCHHHHHHHHHH
Confidence 457899999995 89999999888876
No 230
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=62.28 E-value=19 Score=28.38 Aligned_cols=37 Identities=24% Similarity=0.398 Sum_probs=30.4
Q ss_pred HHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 156 LYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 156 lY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
+|++.=..+-|.|..|||+. ++.+..++.++.+.|..
T Consensus 32 v~~~LL~~~~~~tvdelae~-lnr~rStv~rsl~~L~~ 68 (126)
T COG3355 32 VYKALLEENGPLTVDELAEI-LNRSRSTVYRSLQNLLE 68 (126)
T ss_pred HHHHHHhhcCCcCHHHHHHH-HCccHHHHHHHHHHHHH
Confidence 34444446789999999995 99999999999999875
No 231
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=62.03 E-value=4.5 Score=24.42 Aligned_cols=21 Identities=43% Similarity=1.102 Sum_probs=10.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECG 30 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG 30 (278)
.+|+.||. +.+-+ ..+|..||
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 34422 27888887
No 232
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=62.00 E-value=17 Score=22.95 Aligned_cols=32 Identities=22% Similarity=0.214 Sum_probs=28.0
Q ss_pred CCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhh
Q 023713 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (278)
Q Consensus 166 p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~ 198 (278)
..+..|||.. ++++..++.+..+.+.+.|+.+
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 9999999999999998888764
No 233
>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=61.95 E-value=6.1 Score=32.36 Aligned_cols=27 Identities=26% Similarity=0.726 Sum_probs=20.8
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl 33 (278)
..||.|++. ++ +...|.+.|..|+..+
T Consensus 35 ~aC~~C~kk--v~-~~~~~~~~C~~C~~~~ 61 (166)
T cd04476 35 PACPGCNKK--VV-EEGNGTYRCEKCNKSV 61 (166)
T ss_pred ccccccCcc--cE-eCCCCcEECCCCCCcC
Confidence 469999983 33 4344999999999887
No 234
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=61.93 E-value=4.9 Score=32.35 Aligned_cols=34 Identities=24% Similarity=0.473 Sum_probs=28.3
Q ss_pred EeCCCCceEcCCCcccc--cccccccccchhhccCC
Q 023713 17 FDHSAGDTICSECGLVL--EAYSVDETSEWRIFANE 50 (278)
Q Consensus 17 ~D~~~G~~vC~~CG~Vl--~e~~id~~~ewr~f~~~ 50 (278)
...+.|.++|..||.-| .+.-+|.|.-|.+|.+.
T Consensus 37 ~~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~ 72 (142)
T PRK00222 37 DNKEKGIYVCIVCGEPLFSSDTKFDSGCGWPSFTKP 72 (142)
T ss_pred CCCCCeEEEecCCCchhcCCcccccCCCCCcCcCcc
Confidence 34589999999999988 55678999999999854
No 235
>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=61.89 E-value=33 Score=21.67 Aligned_cols=32 Identities=22% Similarity=0.332 Sum_probs=28.2
Q ss_pred CCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhh
Q 023713 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (278)
Q Consensus 166 p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~ 198 (278)
..+.+|||.. ++++..++.+..+++.+.++..
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 9999999999999999888764
No 236
>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=61.43 E-value=16 Score=22.86 Aligned_cols=30 Identities=20% Similarity=0.255 Sum_probs=22.8
Q ss_pred hcCCCCCHHHHHHHHcCCCHHHHHHHHHHHH
Q 023713 162 QENKPRTVKEFCSVANGTTKKEIGRAKEFIV 192 (278)
Q Consensus 162 ~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~ 192 (278)
+.+-..++.+||.. .|++..++.+.+++|.
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 34567899999995 9999999999988873
No 237
>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=61.32 E-value=3.2 Score=27.64 Aligned_cols=30 Identities=33% Similarity=0.834 Sum_probs=18.4
Q ss_pred CCCCCCCCCceeEe--CCCCceEcCCCccccc
Q 023713 5 YCADCKRLTEVVFD--HSAGDTICSECGLVLE 34 (278)
Q Consensus 5 ~Cp~Cg~~~~vv~D--~~~G~~vC~~CG~Vl~ 34 (278)
.|.+||...+..+- +..+..+|..||+-..
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~ 32 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWK 32 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHH
Confidence 47778764333332 3367778888887764
No 238
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=61.05 E-value=2.8 Score=30.36 Aligned_cols=30 Identities=23% Similarity=0.448 Sum_probs=24.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e 35 (278)
..|+-||.. -+--...|-+-|..|..|+..
T Consensus 37 y~CsfCGK~--~vKR~AvGiW~C~~C~kv~ag 66 (92)
T KOG0402|consen 37 YTCSFCGKK--TVKRKAVGIWKCGSCKKVVAG 66 (92)
T ss_pred hhhhhcchh--hhhhhceeEEecCCccceecc
Confidence 579999983 355678899999999999863
No 239
>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=60.64 E-value=10 Score=24.52 Aligned_cols=26 Identities=23% Similarity=0.691 Sum_probs=17.5
Q ss_pred CCCC--CCCCCCceeEeCCCCceEcCCCcc
Q 023713 4 SYCA--DCKRLTEVVFDHSAGDTICSECGL 31 (278)
Q Consensus 4 ~~Cp--~Cg~~~~vv~D~~~G~~vC~~CG~ 31 (278)
..|| .||. .-..-++. ....|..||+
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 8997 44455554 4889999986
No 240
>PRK06260 threonine synthase; Validated
Probab=60.43 E-value=3.8 Score=38.70 Aligned_cols=30 Identities=33% Similarity=0.594 Sum_probs=23.1
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 1 ~~~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
|....|+.||.. ++...-...|..||-.++
T Consensus 1 ~~~~~C~~cg~~----~~~~~~~~~Cp~cg~~l~ 30 (397)
T PRK06260 1 MYWLKCIECGKE----YDPDEIIYTCPECGGLLE 30 (397)
T ss_pred CCEEEECCCCCC----CCCCCccccCCCCCCeEE
Confidence 667899999983 555555688999998764
No 241
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=60.23 E-value=21 Score=24.46 Aligned_cols=36 Identities=22% Similarity=0.196 Sum_probs=28.1
Q ss_pred hcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhh
Q 023713 162 QENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (278)
Q Consensus 162 ~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~ 198 (278)
..+.|.+-.|||+ +++++..++++....|.+.=.++
T Consensus 11 ~~~~p~~T~eiA~-~~gls~~~aR~yL~~Le~eG~V~ 46 (62)
T PF04703_consen 11 EQNGPLKTREIAD-ALGLSIYQARYYLEKLEKEGKVE 46 (62)
T ss_dssp HHTS-EEHHHHHH-HHTS-HHHHHHHHHHHHHCTSEE
T ss_pred HcCCCCCHHHHHH-HhCCCHHHHHHHHHHHHHCCCEE
Confidence 3378999999999 59999999999999988765443
No 242
>PRK12366 replication factor A; Reviewed
Probab=60.03 E-value=4.9 Score=40.48 Aligned_cols=25 Identities=36% Similarity=0.901 Sum_probs=20.1
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLV 32 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V 32 (278)
..||.|+.. ++ + ..|.+.|..||.+
T Consensus 533 ~aCp~CnkK--v~-~-~~g~~~C~~c~~~ 557 (637)
T PRK12366 533 YLCPNCRKR--VE-E-VDGEYICEFCGEV 557 (637)
T ss_pred ecccccCeE--eE-c-CCCcEECCCCCCC
Confidence 479999872 33 3 5799999999988
No 243
>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=59.82 E-value=68 Score=23.63 Aligned_cols=30 Identities=10% Similarity=0.244 Sum_probs=26.9
Q ss_pred cCCCCCHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 163 ENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 163 ~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
...+.|..|||+. .+++..++.++++.|.+
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 5678999999994 99999999999999875
No 244
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=59.59 E-value=32 Score=29.37 Aligned_cols=46 Identities=9% Similarity=0.042 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHH
Q 023713 148 QEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (278)
Q Consensus 148 ~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~ 194 (278)
.+.-.|..|+........|.|..|||+ .+|++..++.|.+++|.+.
T Consensus 151 ~~~Rla~~L~~~~~~~~~~~t~~~lA~-~lG~sretvsR~L~~L~~~ 196 (226)
T PRK10402 151 LENRLAAFILLTQEGDLYHEKHTQAAE-YLGVSYRHLLYVLAQFIQD 196 (226)
T ss_pred HHHHHHHHHHhcccCCcccchHHHHHH-HHCCcHHHHHHHHHHHHHC
Confidence 333444444433333345678999999 5999999999999999874
No 245
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=59.55 E-value=95 Score=25.69 Aligned_cols=29 Identities=17% Similarity=0.273 Sum_probs=25.9
Q ss_pred CCCCHHHHHHHHcCCCHHHHHHHHHHHHHH
Q 023713 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (278)
Q Consensus 165 ~p~tl~eia~~~~~v~~~~i~~~~~~l~~~ 194 (278)
.|.|.+|||+ .+|++..+++|.+++|.+.
T Consensus 167 ~~~t~~~lA~-~lG~tr~tvsR~l~~l~~~ 195 (211)
T PRK11753 167 IKITRQEIGR-IVGCSREMVGRVLKMLEDQ 195 (211)
T ss_pred cCCCHHHHHH-HhCCCHHHHHHHHHHHHHC
Confidence 5899999999 4999999999999998764
No 246
>COG4643 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=59.29 E-value=5.1 Score=36.76 Aligned_cols=26 Identities=31% Similarity=0.707 Sum_probs=21.5
Q ss_pred CCCCCCCCCceeEeC-C-CCceEcCCCc
Q 023713 5 YCADCKRLTEVVFDH-S-AGDTICSECG 30 (278)
Q Consensus 5 ~Cp~Cg~~~~vv~D~-~-~G~~vC~~CG 30 (278)
.||.||....+-+|. + .|..+|-.||
T Consensus 34 ~cpvcg~k~RFr~dD~kGrGtw~c~y~~ 61 (366)
T COG4643 34 PCPVCGGKDRFRFDDRKGRGTWFCNYCG 61 (366)
T ss_pred CCCccCCccccccCCccCCccEEEEeec
Confidence 799999866776665 3 6999999999
No 247
>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=59.17 E-value=5.8 Score=30.10 Aligned_cols=28 Identities=18% Similarity=0.656 Sum_probs=21.6
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
..|--||. .. +-.+.+++||..||++..
T Consensus 36 daCeiC~~-~G--Y~q~g~~lvC~~C~~~~~ 63 (102)
T PF10080_consen 36 DACEICGP-KG--YYQEGDQLVCKNCGVRFN 63 (102)
T ss_pred EeccccCC-Cc--eEEECCEEEEecCCCEEe
Confidence 36889986 33 335688999999999985
No 248
>PF13790 DUF4182: Domain of unknown function (DUF4182)
Probab=59.10 E-value=4.6 Score=24.82 Aligned_cols=14 Identities=21% Similarity=0.835 Sum_probs=12.3
Q ss_pred CCceEcCCCccccc
Q 023713 21 AGDTICSECGLVLE 34 (278)
Q Consensus 21 ~G~~vC~~CG~Vl~ 34 (278)
.|.+||+.|+.+++
T Consensus 1 MGtIvCq~C~~~Id 14 (38)
T PF13790_consen 1 MGTIVCQHCNETID 14 (38)
T ss_pred CCEEEeccccceee
Confidence 38899999999985
No 249
>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=58.99 E-value=22 Score=23.85 Aligned_cols=32 Identities=16% Similarity=0.278 Sum_probs=24.0
Q ss_pred hcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHH
Q 023713 162 QENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (278)
Q Consensus 162 ~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~ 194 (278)
..+-+.++.+|++. ++++..++.+.+++|.+.
T Consensus 14 ~~~~~~t~~~l~~~-~~~~~~~vs~~i~~L~~~ 45 (68)
T PF13463_consen 14 HSDGPMTQSDLAER-LGISKSTVSRIIKKLEEK 45 (68)
T ss_dssp --TS-BEHHHHHHH-TT--HHHHHHHHHHHHHT
T ss_pred ccCCCcCHHHHHHH-HCcCHHHHHHHHHHHHHC
Confidence 67888999999995 999999999999998753
No 250
>PRK04023 DNA polymerase II large subunit; Validated
Probab=58.89 E-value=6.8 Score=41.04 Aligned_cols=12 Identities=25% Similarity=0.614 Sum_probs=7.1
Q ss_pred eEcCCCcccccc
Q 023713 24 TICSECGLVLEA 35 (278)
Q Consensus 24 ~vC~~CG~Vl~e 35 (278)
..|.+||..+..
T Consensus 664 y~CPKCG~El~~ 675 (1121)
T PRK04023 664 DECEKCGREPTP 675 (1121)
T ss_pred CcCCCCCCCCCc
Confidence 456666666643
No 251
>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=58.87 E-value=7.5 Score=23.01 Aligned_cols=24 Identities=21% Similarity=0.468 Sum_probs=13.6
Q ss_pred CCCCCCCCCCCceeEeCCCCceEcC
Q 023713 3 DSYCADCKRLTEVVFDHSAGDTICS 27 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~ 27 (278)
..+|..||. --.+.+...|+++|-
T Consensus 4 ~ykC~~CGn-iv~v~~~~~~~l~Cc 27 (34)
T cd00974 4 VYKCEICGN-IVEVLNVGGGTLVCC 27 (34)
T ss_pred EEEcCCCCc-EEEEEECCCcceeec
Confidence 346777775 233445556666664
No 252
>PRK06450 threonine synthase; Validated
Probab=58.29 E-value=14 Score=34.12 Aligned_cols=29 Identities=24% Similarity=0.576 Sum_probs=21.2
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 1 ~~~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
|+...|+.||.. ++. .-...|..||-.++
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 566799999983 333 33578999997764
No 253
>PRK07218 replication factor A; Provisional
Probab=58.24 E-value=4.5 Score=38.61 Aligned_cols=21 Identities=29% Similarity=0.798 Sum_probs=16.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLV 32 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V 32 (278)
.+||.|+.. + + ...|..||.|
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 579999983 2 2 3799999988
No 254
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=57.99 E-value=76 Score=28.33 Aligned_cols=100 Identities=14% Similarity=0.120 Sum_probs=55.6
Q ss_pred CCHHHHHHHHcCCCHHHHHHHHHH--------HHHHhhhhccc----ccc--cCCCCHHHHHHHHHhh----c-----CC
Q 023713 167 RTVKEFCSVANGTTKKEIGRAKEF--------IVKHLEAEMGQ----SVE--MGTIHASDYLRRFCSN----L-----GM 223 (278)
Q Consensus 167 ~tl~eia~~~~~v~~~~i~~~~~~--------l~~~L~~~~~~----~~~--~~~~~p~~~i~r~~~~----L-----~l 223 (278)
.|..|+|.. ++|++.+|-|..++ ++..|...... ... ....++..+..++.+. | .+
T Consensus 37 ~si~elA~~-a~VS~aTv~Rf~~kLGf~Gf~efk~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~t~~~l 115 (281)
T COG1737 37 LSIAELAER-AGVSPATVVRFARKLGFEGFSEFKLALAQELAEGRAQLLREIAEDDGPESILEKLLAANIAALERTLNLL 115 (281)
T ss_pred HHHHHHHHH-hCCCHHHHHHHHHHcCCCCHHHHHHHHHHHHhhccchhhcccCCCCCHHHHHHHHHHHHHHHHHHHHHhc
Confidence 567899984 89999999887443 33333222100 000 1223444444444433 3 34
Q ss_pred CHHHHHHHHHHHHHhhhcC-CCCChhHHHHHHHHHHHHHHHHHHHhcccccc
Q 023713 224 TNQAVKAAQEAVQKSEDLD-IRLILVFFSLFLVETHIQLIVWAFMRCIYTFR 274 (278)
Q Consensus 224 ~~~v~~~A~~i~~~~~~~~-~Gr~P~~iaaA~v~~~~~~~~~~~~~~~~~~~ 274 (278)
+++....|-+++..+++.. .|.. .+-..|-- +.|.|+|-+.+-.
T Consensus 116 ~~~~l~~av~~L~~A~rI~~~G~g-~S~~vA~~------~~~~l~~ig~~~~ 160 (281)
T COG1737 116 DEEALERAVELLAKARRIYFFGLG-SSGLVASD------LAYKLMRIGLNVV 160 (281)
T ss_pred CHHHHHHHHHHHHcCCeEEEEEec-hhHHHHHH------HHHHHHHcCCcee
Confidence 5666777777777777755 5633 33333333 5777777766544
No 255
>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=57.83 E-value=6.1 Score=31.51 Aligned_cols=33 Identities=21% Similarity=0.372 Sum_probs=27.7
Q ss_pred eCCCCceEcCCCcccc--cccccccccchhhccCC
Q 023713 18 DHSAGDTICSECGLVL--EAYSVDETSEWRIFANE 50 (278)
Q Consensus 18 D~~~G~~vC~~CG~Vl--~e~~id~~~ewr~f~~~ 50 (278)
..+.|.++|..||.-| .+.-+|.|.-|.+|.+.
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 55578999999999854
No 256
>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=57.49 E-value=28 Score=23.01 Aligned_cols=27 Identities=15% Similarity=0.175 Sum_probs=21.8
Q ss_pred CCHHHHHHHHcCCCHHHHHHHHHHHHHH
Q 023713 167 RTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (278)
Q Consensus 167 ~tl~eia~~~~~v~~~~i~~~~~~l~~~ 194 (278)
.++.|+|+. +||+..++...++.-.+.
T Consensus 24 ~tl~elA~~-lgis~st~~~~LRrae~k 50 (53)
T PF04967_consen 24 ITLEELAEE-LGISKSTVSEHLRRAERK 50 (53)
T ss_pred CCHHHHHHH-hCCCHHHHHHHHHHHHHH
Confidence 789999995 999999888777765443
No 257
>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=57.45 E-value=15 Score=25.13 Aligned_cols=30 Identities=23% Similarity=0.334 Sum_probs=26.4
Q ss_pred cCCCCCHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 163 ENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 163 ~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
..-+.|..||+.. ++++..++.+..+.|.+
T Consensus 19 ~~~~~t~~eIa~~-l~i~~~~v~~~L~~L~~ 48 (68)
T PF01978_consen 19 KNGPATAEEIAEE-LGISRSTVYRALKSLEE 48 (68)
T ss_dssp HHCHEEHHHHHHH-HTSSHHHHHHHHHHHHH
T ss_pred HcCCCCHHHHHHH-HCcCHHHHHHHHHHHHH
Confidence 5567999999995 99999999999999875
No 258
>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=57.27 E-value=3.5 Score=42.28 Aligned_cols=46 Identities=11% Similarity=0.031 Sum_probs=0.0
Q ss_pred CCCHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCH
Q 023713 178 GTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTN 225 (278)
Q Consensus 178 ~v~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~ 225 (278)
+...++|+-...+|+ .||... ...+-|..++.+.++=-++..=||.
T Consensus 778 HfrP~EIgvsvEkLr-ELGY~~-Di~G~pL~~~dQivELk~QDIils~ 823 (900)
T PF03833_consen 778 HFRPREIGVSVEKLR-ELGYTH-DIYGKPLESDDQIVELKVQDIILSE 823 (900)
T ss_dssp ------------------------------------------------
T ss_pred cccHHhcCCCHHHHH-HhCccc-cccCCccCCccceeEeehhcEecch
Confidence 334445555544443 444321 1112344455555555555554443
No 259
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=57.15 E-value=11 Score=27.16 Aligned_cols=26 Identities=19% Similarity=0.407 Sum_probs=19.2
Q ss_pred CCCCCCCCCCceeEeCCCC--ceEcCCCccc
Q 023713 4 SYCADCKRLTEVVFDHSAG--DTICSECGLV 32 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G--~~vC~~CG~V 32 (278)
..||-||.. +++...+ ..||.-|+.-
T Consensus 2 ~~CPCCg~~---Tl~~~~~~~ydIC~VC~WE 29 (78)
T PF14206_consen 2 YPCPCCGYY---TLEERGEGTYDICPVCFWE 29 (78)
T ss_pred ccCCCCCcE---EeccCCCcCceECCCCCcc
Confidence 479999983 3444444 8899999986
No 260
>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=56.99 E-value=6.8 Score=26.12 Aligned_cols=28 Identities=21% Similarity=0.706 Sum_probs=15.8
Q ss_pred CCCCC--CCCCCceeEeCCCCc--eEcCCCcccc
Q 023713 4 SYCAD--CKRLTEVVFDHSAGD--TICSECGLVL 33 (278)
Q Consensus 4 ~~Cp~--Cg~~~~vv~D~~~G~--~vC~~CG~Vl 33 (278)
..||. |+. -+..+..... +.|..||...
T Consensus 19 ~~Cp~~~C~~--~~~~~~~~~~~~~~C~~C~~~f 50 (64)
T PF01485_consen 19 RWCPNPDCEY--IIEKDDGCNSPIVTCPSCGTEF 50 (64)
T ss_dssp C--TTSST-----ECS-SSTTS--CCTTSCCSEE
T ss_pred cCCCCCCCcc--cEEecCCCCCCeeECCCCCCcC
Confidence 58988 997 2555555555 8899998764
No 261
>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=56.96 E-value=6.1 Score=29.18 Aligned_cols=38 Identities=24% Similarity=0.518 Sum_probs=24.4
Q ss_pred CCCCCCC------CCceeEeCCCC----------ceEcCCCccccccccccccc
Q 023713 5 YCADCKR------LTEVVFDHSAG----------DTICSECGLVLEAYSVDETS 42 (278)
Q Consensus 5 ~Cp~Cg~------~~~vv~D~~~G----------~~vC~~CG~Vl~e~~id~~~ 42 (278)
.|+-|++ .+++.+|...| -++|.+||.+.-+..+-..-
T Consensus 1 ~C~~C~~~~~~~~~tTv~~el~~G~~~IvIknVPa~~C~~CGe~y~~dev~~eI 54 (89)
T TIGR03829 1 KCRWCEEEKAIARTTTVYWELPDGTKAIEIKETPSISCSHCGMEYQDDTTVKEI 54 (89)
T ss_pred CCcccCCCceecceEEEEEEecCCceEEEEecCCcccccCCCcEeecHHHHHHH
Confidence 4888953 13456666555 46899999988655544333
No 262
>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=56.68 E-value=7.7 Score=33.63 Aligned_cols=28 Identities=29% Similarity=0.720 Sum_probs=21.8
Q ss_pred CCCCCCCCCC-ceeEeCCCCceEcCCCcc
Q 023713 4 SYCADCKRLT-EVVFDHSAGDTICSECGL 31 (278)
Q Consensus 4 ~~Cp~Cg~~~-~vv~D~~~G~~vC~~CG~ 31 (278)
..|..||... ...++...|..+|.+|+.
T Consensus 148 ~~C~~cg~~~~~~~fs~~~gg~~C~~c~~ 176 (241)
T TIGR00613 148 DKCAVCGSKEDLIYFSMTYGGALCRQCGE 176 (241)
T ss_pred CccCCCCCcCCCceEchhcCeEEChhhCc
Confidence 5799998622 357888999999999965
No 263
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=56.54 E-value=7.3 Score=33.92 Aligned_cols=27 Identities=37% Similarity=0.806 Sum_probs=22.3
Q ss_pred CCCCCCCCCC-ceeEeCCCCceEcCCCc
Q 023713 4 SYCADCKRLT-EVVFDHSAGDTICSECG 30 (278)
Q Consensus 4 ~~Cp~Cg~~~-~vv~D~~~G~~vC~~CG 30 (278)
..|-.||+.. ...++..+|..+|.+|+
T Consensus 150 ~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 150 DHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred hhHhcCCCCCCceEEecccCCccccccc
Confidence 4799999742 35788999999999998
No 264
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=56.51 E-value=65 Score=25.00 Aligned_cols=42 Identities=14% Similarity=0.109 Sum_probs=30.4
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHH
Q 023713 148 QEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFI 191 (278)
Q Consensus 148 ~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l 191 (278)
...+..+.-|+--.. ..+.++.|+|+. +++++..+.+.+++.
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 344555555555444 457999999995 899999999887764
No 265
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=56.14 E-value=4.4 Score=32.09 Aligned_cols=24 Identities=38% Similarity=0.812 Sum_probs=13.2
Q ss_pred CCCCCCCCCCceeEeCCC--CceEcCCCcc
Q 023713 4 SYCADCKRLTEVVFDHSA--GDTICSECGL 31 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~--G~~vC~~CG~ 31 (278)
..|..||. +|+..+ =.-=|.+||-
T Consensus 2 H~Ct~Cg~----~f~dgs~eil~GCP~CGg 27 (131)
T PF09845_consen 2 HQCTKCGR----VFEDGSKEILSGCPECGG 27 (131)
T ss_pred cccCcCCC----CcCCCcHHHHccCcccCC
Confidence 57888886 233111 1123788874
No 266
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=55.98 E-value=8 Score=32.83 Aligned_cols=32 Identities=28% Similarity=0.578 Sum_probs=18.7
Q ss_pred CCCCCCCCCce---eEe--CCCC-----ceEcCCCccccccc
Q 023713 5 YCADCKRLTEV---VFD--HSAG-----DTICSECGLVLEAY 36 (278)
Q Consensus 5 ~Cp~Cg~~~~v---v~D--~~~G-----~~vC~~CG~Vl~e~ 36 (278)
.||+||..... .++ +--| ...|..||.=-.|-
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 59999964221 111 2233 35799999875433
No 267
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=55.95 E-value=4.8 Score=31.29 Aligned_cols=18 Identities=11% Similarity=0.265 Sum_probs=10.0
Q ss_pred ceeEeCCCCceEcCCCcc
Q 023713 14 EVVFDHSAGDTICSECGL 31 (278)
Q Consensus 14 ~vv~D~~~G~~vC~~CG~ 31 (278)
.+..+..-+...|.+||.
T Consensus 62 ~L~Ie~vp~~~~C~~Cg~ 79 (117)
T PRK00564 62 ILDIVDEKVELECKDCSH 79 (117)
T ss_pred EEEEEecCCEEEhhhCCC
Confidence 455555555566666663
No 268
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=55.37 E-value=17 Score=30.30 Aligned_cols=37 Identities=22% Similarity=0.277 Sum_probs=30.7
Q ss_pred HHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 156 LYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 156 lY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
||-..-..+-|.|+.||++ ++|++...++-+.++|..
T Consensus 31 iYgilyls~~Pmtl~Ei~E-~lg~Sks~vS~~lkkL~~ 67 (177)
T COG1510 31 IYGILYLSRKPLTLDEIAE-ALGMSKSNVSMGLKKLQD 67 (177)
T ss_pred HhhhheecCCCccHHHHHH-HHCCCcchHHHHHHHHHh
Confidence 3444445789999999999 599999999999999865
No 269
>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=55.04 E-value=5.1 Score=30.97 Aligned_cols=31 Identities=26% Similarity=0.464 Sum_probs=20.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
..|-+||+....-.+..-|..+|..|.-|-.
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 5799999854445556789999999998864
No 270
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=54.91 E-value=14 Score=35.34 Aligned_cols=44 Identities=9% Similarity=0.088 Sum_probs=35.2
Q ss_pred HHHHHH---HHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHh
Q 023713 149 EAIVAA---CLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHL 195 (278)
Q Consensus 149 ~~~aAA---clY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L 195 (278)
..++-| +.|++-+ ....|+.+|+.. +|.+..++.++++++.+.+
T Consensus 369 ~~i~~aR~iamyl~r~--~~~~s~~~Ig~~-fgr~hstV~~a~~~i~~~~ 415 (440)
T PRK14088 369 VKALLARRIGMYVAKN--YLGSSLRTIAEK-FNRSHPVVVDSVKKVKDSL 415 (440)
T ss_pred ccccHHHHHHHHHHHH--HhCCCHHHHHHH-hCCCHHHHHHHHHHHHHHH
Confidence 345555 8888843 556699999995 7999999999999998866
No 271
>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=54.81 E-value=33 Score=27.35 Aligned_cols=53 Identities=13% Similarity=0.028 Sum_probs=43.0
Q ss_pred HHHHHHHHhhcCCCHHHHHHHHHHHHHhhhcC----CCCChhHHHHHHHHHHHHHHHHH
Q 023713 211 SDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLD----IRLILVFFSLFLVETHIQLIVWA 265 (278)
Q Consensus 211 ~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~----~Gr~P~~iaaA~v~~~~~~~~~~ 265 (278)
..=+..+|++|++++++....+.+.+.+.... -+|+-.-+...+| |+-+++-+
T Consensus 15 ~~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCai--Y~i~Kv~~ 71 (135)
T PF01857_consen 15 AVRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAI--YGICKVSK 71 (135)
T ss_dssp HHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHH--HHHHHHTT
T ss_pred HHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHH--HHHHHhhc
Confidence 34567799999999999889999888876533 5999999999999 99887654
No 272
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=54.72 E-value=9.2 Score=25.60 Aligned_cols=24 Identities=25% Similarity=0.648 Sum_probs=18.4
Q ss_pred CCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713 5 YCADCKRLTEVVFDHSAGDTICSECGLVL 33 (278)
Q Consensus 5 ~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl 33 (278)
.||.|+... ...-...|++||...
T Consensus 1 ~Cpv~~~~~-----~~~v~~~Cp~cGipt 24 (55)
T PF13824_consen 1 LCPVCKKDL-----PAHVNFECPDCGIPT 24 (55)
T ss_pred CCCCCcccc-----ccccCCcCCCCCCcC
Confidence 499999731 445578899999986
No 273
>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=54.72 E-value=29 Score=24.13 Aligned_cols=34 Identities=18% Similarity=0.180 Sum_probs=24.1
Q ss_pred HHHHHHHhcCCCCCHHHHHHHHcC-CCHHHHHHHHHHH
Q 023713 155 CLYIACRQENKPRTVKEFCSVANG-TTKKEIGRAKEFI 191 (278)
Q Consensus 155 clY~acR~~~~p~tl~eia~~~~~-v~~~~i~~~~~~l 191 (278)
+.|++-... +.++.||+.. +| -|..++..+++++
T Consensus 36 a~yL~r~~~--~~sl~~Ig~~-fg~rdHstV~~a~~ki 70 (70)
T PF08299_consen 36 AMYLARELT--GLSLSEIGRY-FGGRDHSTVIHAIRKI 70 (70)
T ss_dssp HHHHHHHHS-----HHHHHHH-CTSSTHHHHHHHHHHH
T ss_pred HHHHHHHHh--CCCHHHHHHH-hCCCCHHHHHHHHHhC
Confidence 456664444 5789999995 77 9999999988864
No 274
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=54.67 E-value=1.4e+02 Score=25.94 Aligned_cols=87 Identities=16% Similarity=0.173 Sum_probs=63.8
Q ss_pred HHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHh-hCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHH
Q 023713 105 NLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVE-DQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKE 183 (278)
Q Consensus 105 ~l~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~-~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~ 183 (278)
.|..-.++-..+.+.=.+++.-+|+......+.. ...+.+|-+...+=..+-.+. ..+.+.|..|+|. +.|++..+
T Consensus 113 aL~~y~~~r~~l~~~~~~sQ~~lD~l~~~~~k~~~~~~LPkGi~~~Tl~~i~~~~~--~~~~~~Taeela~-~~giSRvT 189 (224)
T COG4565 113 ALTRYRQKRHALESHQQLSQKELDQLFNIQSKEQPPDDLPKGLDELTLQKVREALK--EPDQELTAEELAQ-ALGISRVT 189 (224)
T ss_pred HHHHHHHHHHHHhhhcccCHHHHHHHHhccccccCcccCCCCcCHHHHHHHHHHHh--CcCCccCHHHHHH-HhCccHHH
Confidence 3444445555566666888888998887775522 244667877766666555555 6789999999999 59999999
Q ss_pred HHHHHHHHHHH
Q 023713 184 IGRAKEFIVKH 194 (278)
Q Consensus 184 i~~~~~~l~~~ 194 (278)
.+|.+..+...
T Consensus 190 aRRYLeyl~~~ 200 (224)
T COG4565 190 ARRYLEYLVSN 200 (224)
T ss_pred HHHHHHHHHhc
Confidence 99998888764
No 275
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=54.65 E-value=8.6 Score=22.72 Aligned_cols=23 Identities=22% Similarity=0.547 Sum_probs=11.8
Q ss_pred CCCCCCCCCCceeEeCCCCceEcC
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICS 27 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~ 27 (278)
.+|..||. --.+.+...|+++|-
T Consensus 8 ykC~~Cgn-iv~v~~~~~~~l~Cc 30 (34)
T TIGR00319 8 YKCEVCGN-IVEVLHAGGGQLVCC 30 (34)
T ss_pred EEcCCCCc-EEEEEECCCcceecc
Confidence 45666665 223444455555554
No 276
>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=54.37 E-value=10 Score=37.07 Aligned_cols=29 Identities=21% Similarity=0.631 Sum_probs=23.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
..||+|+. .+++....+.+.|..||....
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 477777889999999998753
No 277
>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=54.19 E-value=21 Score=23.68 Aligned_cols=31 Identities=23% Similarity=0.197 Sum_probs=26.5
Q ss_pred CCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHh
Q 023713 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKHL 195 (278)
Q Consensus 164 ~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L 195 (278)
+-..++.|+++. ++|+..+|++-+..|.+.-
T Consensus 12 ~~~~s~~ela~~-~~VS~~TiRRDl~~L~~~g 42 (57)
T PF08220_consen 12 KGKVSVKELAEE-FGVSEMTIRRDLNKLEKQG 42 (57)
T ss_pred cCCEEHHHHHHH-HCcCHHHHHHHHHHHHHCC
Confidence 456899999995 9999999999999987643
No 278
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=53.96 E-value=67 Score=27.48 Aligned_cols=29 Identities=17% Similarity=0.241 Sum_probs=26.2
Q ss_pred CCCCHHHHHHHHcCCCHHHHHHHHHHHHHH
Q 023713 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (278)
Q Consensus 165 ~p~tl~eia~~~~~v~~~~i~~~~~~l~~~ 194 (278)
.|.|..|||+ .+|++..++.|..++|.+.
T Consensus 178 i~lt~~~IA~-~lGisretlsR~L~~L~~~ 206 (230)
T PRK09391 178 LPMSRRDIAD-YLGLTIETVSRALSQLQDR 206 (230)
T ss_pred ecCCHHHHHH-HHCCCHHHHHHHHHHHHHC
Confidence 6789999999 5999999999999999864
No 279
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=53.92 E-value=47 Score=28.06 Aligned_cols=68 Identities=13% Similarity=0.292 Sum_probs=47.4
Q ss_pred HHHHHHHHHHHHHHhcCCC-CCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhhcc--------ccccc-CCCCHHHHHHHH
Q 023713 148 QEAIVAACLYIACRQENKP-RTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMG--------QSVEM-GTIHASDYLRRF 217 (278)
Q Consensus 148 ~~~~aAAclY~acR~~~~p-~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~~~--------~~~~~-~~~~p~~~i~r~ 217 (278)
...++=|+||. .+-| +++.+++.+ ++++..++..+...|.+.+.-... ..+.+ ...+-.+++.+|
T Consensus 5 ~~~~iEA~LF~----sg~pgls~~~La~~-l~~~~~~v~~~l~~L~~~y~~~~~gi~i~~~~~~y~l~tk~e~~~~v~~~ 79 (188)
T PRK00135 5 YKSIIEALLFV----SGEEGLSLEQLAEI-LELEPTEVQQLLEELQEKYEGDDRGLKLIEFNDVYKLVTKEENADYLQKL 79 (188)
T ss_pred HHHHHHHHHHH----cCCCCCCHHHHHHH-HCCCHHHHHHHHHHHHHHHhhCCCCEEEEEECCEEEEEEcHHHHHHHHHH
Confidence 45677788886 5676 999999995 899999999999999888753210 11111 122455688887
Q ss_pred Hhh
Q 023713 218 CSN 220 (278)
Q Consensus 218 ~~~ 220 (278)
...
T Consensus 80 ~~~ 82 (188)
T PRK00135 80 VKT 82 (188)
T ss_pred hcc
Confidence 654
No 280
>PRK05580 primosome assembly protein PriA; Validated
Probab=53.64 E-value=11 Score=38.42 Aligned_cols=28 Identities=18% Similarity=0.530 Sum_probs=23.1
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl 33 (278)
..||+|+. .+++....+.+.|..||...
T Consensus 391 ~~C~~C~~--~l~~h~~~~~l~Ch~Cg~~~ 418 (679)
T PRK05580 391 AECPHCDA--SLTLHRFQRRLRCHHCGYQE 418 (679)
T ss_pred cCCCCCCC--ceeEECCCCeEECCCCcCCC
Confidence 46999987 47887788999999999875
No 281
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=53.53 E-value=5.5 Score=27.50 Aligned_cols=21 Identities=29% Similarity=0.642 Sum_probs=14.5
Q ss_pred CCCCCCCCCCCceeEeCCCCceEcCCCcc
Q 023713 3 DSYCADCKRLTEVVFDHSAGDTICSECGL 31 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~ 31 (278)
...|.+|+. ++ + ..+|..||.
T Consensus 5 ~~AC~~C~~---i~-~----~~~Cp~Cgs 25 (64)
T PRK06393 5 YRACKKCKR---LT-P----EKTCPVHGD 25 (64)
T ss_pred hhhHhhCCc---cc-C----CCcCCCCCC
Confidence 467889987 23 2 238999987
No 282
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=53.44 E-value=7.7 Score=41.60 Aligned_cols=8 Identities=25% Similarity=0.854 Sum_probs=4.7
Q ss_pred CCCCCCCC
Q 023713 4 SYCADCKR 11 (278)
Q Consensus 4 ~~Cp~Cg~ 11 (278)
.+||.||.
T Consensus 668 rkCPkCG~ 675 (1337)
T PRK14714 668 RRCPSCGT 675 (1337)
T ss_pred EECCCCCC
Confidence 45666665
No 283
>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=53.21 E-value=8.2 Score=25.80 Aligned_cols=21 Identities=33% Similarity=0.730 Sum_probs=14.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEcC
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICS 27 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~ 27 (278)
..||.|++ ..+++|.. .++|+
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 67888855 78887
No 284
>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=53.19 E-value=27 Score=22.42 Aligned_cols=29 Identities=14% Similarity=0.169 Sum_probs=20.6
Q ss_pred CCCCHHHHHHHHcCCCHHHHHHHHHHHHHH
Q 023713 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (278)
Q Consensus 165 ~p~tl~eia~~~~~v~~~~i~~~~~~l~~~ 194 (278)
...|..|||.. +|+++.++...+..-.+.
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 999999999888776654
No 285
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=53.17 E-value=10 Score=27.38 Aligned_cols=26 Identities=27% Similarity=0.685 Sum_probs=19.6
Q ss_pred CCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 5 YCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 5 ~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
.||.|.. ..+.. ..+.+.| .||.-+.
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 56665 5788888 7886664
No 286
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=53.15 E-value=36 Score=23.58 Aligned_cols=36 Identities=17% Similarity=0.100 Sum_probs=31.5
Q ss_pred HHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhh
Q 023713 160 CRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLE 196 (278)
Q Consensus 160 cR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~ 196 (278)
.|.-+.|+++.+.++. +|+++..+.+.++.+++.+-
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 3677899999999995 99999999999999988663
No 287
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=52.93 E-value=58 Score=26.86 Aligned_cols=29 Identities=14% Similarity=0.202 Sum_probs=26.3
Q ss_pred CCCCHHHHHHHHcCCCHHHHHHHHHHHHHH
Q 023713 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (278)
Q Consensus 165 ~p~tl~eia~~~~~v~~~~i~~~~~~l~~~ 194 (278)
.|.|..|||+ .+|++..++.|.+++|.+.
T Consensus 148 ~~~t~~~iA~-~lG~tretvsR~l~~l~~~ 176 (202)
T PRK13918 148 IYATHDELAA-AVGSVRETVTKVIGELSRE 176 (202)
T ss_pred ecCCHHHHHH-HhCccHHHHHHHHHHHHHC
Confidence 6789999999 5999999999999999863
No 288
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=52.92 E-value=29 Score=22.25 Aligned_cols=25 Identities=12% Similarity=0.216 Sum_probs=23.2
Q ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 168 TVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 168 tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
|..|+++. ++++..++.++++.|.+
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 289
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=52.22 E-value=37 Score=26.86 Aligned_cols=45 Identities=16% Similarity=0.293 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 148 QEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 148 ~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
.+.-.-+.+|++-...+.+.+..+||+. .+++...++++++.|.+
T Consensus 7 ~~YAl~~~i~la~~~~g~~~s~~~ia~~-~~is~~~vrk~l~~L~~ 51 (141)
T PRK11014 7 TDYGLRALIYMASLPEGRMTSISEVTEV-YGVSRNHMVKIINQLSR 51 (141)
T ss_pred HhHHHHHHHHHhcCCCCCccCHHHHHHH-HCcCHHHHHHHHHHHHh
Confidence 4455566777776566778999999995 99999999999999987
No 290
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=51.95 E-value=4.8 Score=26.46 Aligned_cols=28 Identities=32% Similarity=0.654 Sum_probs=18.7
Q ss_pred CCCCCCCCCcee--EeCCCCceEcCCCcccc
Q 023713 5 YCADCKRLTEVV--FDHSAGDTICSECGLVL 33 (278)
Q Consensus 5 ~Cp~Cg~~~~vv--~D~~~G~~vC~~CG~Vl 33 (278)
.|+-||..-.+. +..+.| +||.+|--=+
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 335778 8999997544
No 291
>PF13591 MerR_2: MerR HTH family regulatory protein
Probab=51.58 E-value=27 Score=25.22 Aligned_cols=74 Identities=16% Similarity=0.263 Sum_probs=42.2
Q ss_pred CCHHHHHHHHcCCCHHHHHHHHHH-HHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhhc
Q 023713 167 RTVKEFCSVANGTTKKEIGRAKEF-IVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDL 241 (278)
Q Consensus 167 ~tl~eia~~~~~v~~~~i~~~~~~-l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~ 241 (278)
+|+.|++.. .+++...|...+.. +..-.+......++.....--..+.|+-..|+++.+-...+.++++++..+
T Consensus 1 is~~e~~~~-~~i~~~~l~~lve~Gli~p~~~~~~~~f~~~~l~rl~~~~rL~~Dl~in~~gi~lil~LLd~i~~L 75 (84)
T PF13591_consen 1 ISLEEFCEA-CGIEPEFLRELVEEGLIEPEGEEEEWYFSEEDLARLRRIRRLHRDLGINLEGIALILDLLDRIEQL 75 (84)
T ss_pred CCHHHHHHH-HCcCHHHHHHHHHCCCeeecCCCCeeeECHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHH
Confidence 478899884 89998888655431 111111000001111111122356777888888888888888888777653
No 292
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=51.55 E-value=11 Score=25.76 Aligned_cols=28 Identities=7% Similarity=-0.073 Sum_probs=18.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcccccccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVD 39 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~~id 39 (278)
..||+||.. . .-.-||. ||+--+..+++
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 468899862 2 2367899 99876655543
No 293
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=51.51 E-value=22 Score=28.02 Aligned_cols=27 Identities=19% Similarity=0.287 Sum_probs=24.2
Q ss_pred CCHHHHHHHHcCCCHHHHHHHHHHHHHH
Q 023713 167 RTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (278)
Q Consensus 167 ~tl~eia~~~~~v~~~~i~~~~~~l~~~ 194 (278)
-|.+|+|.. ++|+..++.|+|++|.+.
T Consensus 36 PSvRelA~~-~~VNpnTv~raY~eLE~e 62 (125)
T COG1725 36 PSVRELAKD-LGVNPNTVQRAYQELERE 62 (125)
T ss_pred CcHHHHHHH-hCCCHHHHHHHHHHHHHC
Confidence 578999994 999999999999999863
No 294
>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=51.34 E-value=8.2 Score=30.39 Aligned_cols=32 Identities=25% Similarity=0.531 Sum_probs=26.0
Q ss_pred CCCCceEcCCCcccc--cccccccccchhhccCC
Q 023713 19 HSAGDTICSECGLVL--EAYSVDETSEWRIFANE 50 (278)
Q Consensus 19 ~~~G~~vC~~CG~Vl--~e~~id~~~ewr~f~~~ 50 (278)
.+.|.++|..||.-| .+.-+|.+.-|.+|.+.
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 578999999999988 55567889999999853
No 295
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=50.81 E-value=33 Score=21.43 Aligned_cols=27 Identities=11% Similarity=0.230 Sum_probs=17.7
Q ss_pred cCCCCCHHHHHHHHcCCCHHHHHHHHHH
Q 023713 163 ENKPRTVKEFCSVANGTTKKEIGRAKEF 190 (278)
Q Consensus 163 ~~~p~tl~eia~~~~~v~~~~i~~~~~~ 190 (278)
.....|+.+||.. +|++..+|.+.++.
T Consensus 17 ~~~G~s~~~IA~~-lg~s~sTV~relkR 43 (44)
T PF13936_consen 17 LEQGMSIREIAKR-LGRSRSTVSRELKR 43 (44)
T ss_dssp HCS---HHHHHHH-TT--HHHHHHHHHH
T ss_pred HHcCCCHHHHHHH-HCcCcHHHHHHHhc
Confidence 3455899999995 99999999987763
No 296
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=50.61 E-value=10 Score=34.08 Aligned_cols=28 Identities=21% Similarity=0.589 Sum_probs=19.1
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl 33 (278)
+.|+.||+++ .. -...=-.+|++||...
T Consensus 112 RFCg~CG~~~-~~-~~~g~~~~C~~cg~~~ 139 (279)
T COG2816 112 RFCGRCGTKT-YP-REGGWARVCPKCGHEH 139 (279)
T ss_pred cCCCCCCCcC-cc-ccCceeeeCCCCCCcc
Confidence 6799999852 22 1233356899999876
No 297
>PHA03074 late transcription factor VLTF-3; Provisional
Probab=50.46 E-value=9.4 Score=32.49 Aligned_cols=30 Identities=20% Similarity=0.514 Sum_probs=25.1
Q ss_pred CCCCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 2 ADSYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 2 ~~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
....|..|++ ..+|. +.|-..|-.|+.|..
T Consensus 3 ~l~~C~~C~~-ngiv~--~k~~efC~fC~~~f~ 32 (225)
T PHA03074 3 NLKLCSGCRH-NGIVS--EKDYEFCIFCESVFQ 32 (225)
T ss_pred chhhcCCCCC-CCeee--ecCEEEeecHHHHHh
Confidence 3468999999 67775 489999999999985
No 298
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=50.40 E-value=14 Score=33.69 Aligned_cols=9 Identities=22% Similarity=1.006 Sum_probs=5.8
Q ss_pred CCCCCCCCC
Q 023713 4 SYCADCKRL 12 (278)
Q Consensus 4 ~~Cp~Cg~~ 12 (278)
..||.||+.
T Consensus 188 ~~CPvCGs~ 196 (309)
T PRK03564 188 QFCPVCGSM 196 (309)
T ss_pred CCCCCCCCc
Confidence 467777764
No 299
>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=50.03 E-value=14 Score=33.72 Aligned_cols=9 Identities=33% Similarity=0.763 Sum_probs=4.8
Q ss_pred EcCCCcccc
Q 023713 25 ICSECGLVL 33 (278)
Q Consensus 25 vC~~CG~Vl 33 (278)
+|.+|+.-+
T Consensus 254 ~C~~C~~Yl 262 (305)
T TIGR01562 254 TCDSCQGYL 262 (305)
T ss_pred eccccccch
Confidence 555555544
No 300
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=49.89 E-value=4.7 Score=30.43 Aligned_cols=25 Identities=32% Similarity=0.721 Sum_probs=15.3
Q ss_pred CCCCCCCCCCCceeEeCC--CCceEcCCCcc
Q 023713 3 DSYCADCKRLTEVVFDHS--AGDTICSECGL 31 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~--~G~~vC~~CG~ 31 (278)
+..|..||. +||.. .=.-=|.+||.
T Consensus 2 pH~CtrCG~----vf~~g~~~il~GCp~CG~ 28 (112)
T COG3364 2 PHQCTRCGE----VFDDGSEEILSGCPKCGC 28 (112)
T ss_pred Cceeccccc----ccccccHHHHccCccccc
Confidence 378999996 34421 11224889985
No 301
>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=49.88 E-value=45 Score=20.95 Aligned_cols=31 Identities=16% Similarity=0.223 Sum_probs=25.7
Q ss_pred hcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 162 QENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 162 ~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
..+-|.+..||++. ++++..++.+-.+.|.+
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 44588999999995 99999999999988864
No 302
>PF10005 DUF2248: Uncharacterized protein conserved in bacteria (DUF2248); InterPro: IPR011201 This is a family of uncharacterised bacterial proteins.
Probab=49.82 E-value=9.4 Score=35.24 Aligned_cols=25 Identities=36% Similarity=0.874 Sum_probs=20.3
Q ss_pred CCCCCCCCCceeEeCCCCceEcCCCcccccc
Q 023713 5 YCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (278)
Q Consensus 5 ~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e 35 (278)
.|+.||. .|-|+ ...|..||.-|.-
T Consensus 1 ~C~~Cg~--~v~Fe----Nt~C~~Cg~~LGf 25 (343)
T PF10005_consen 1 SCPNCGQ--PVFFE----NTRCLSCGSALGF 25 (343)
T ss_pred CCCCCCC--cceeC----CCccccCCccccC
Confidence 5999997 36775 7899999998863
No 303
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=49.73 E-value=57 Score=27.53 Aligned_cols=33 Identities=9% Similarity=0.170 Sum_probs=28.9
Q ss_pred CCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhh
Q 023713 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (278)
Q Consensus 165 ~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~ 198 (278)
...|.+|||.. ++++.+++......+.+.|+..
T Consensus 147 qGkTnKEIAe~-L~IS~rTVkth~srImkKLgV~ 179 (198)
T PRK15201 147 SGYHLSETAAL-LSLSEEQTKSLRRSIMRKLHVK 179 (198)
T ss_pred CCCCHHHHHHH-hCCCHHHHHHHHHHHHHHhCCC
Confidence 57889999995 8999999999999999999875
No 304
>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=49.37 E-value=11 Score=34.45 Aligned_cols=28 Identities=25% Similarity=0.519 Sum_probs=17.4
Q ss_pred CCCCCCCCCCc--eeEeC--CCC--ceEcCCCcc
Q 023713 4 SYCADCKRLTE--VVFDH--SAG--DTICSECGL 31 (278)
Q Consensus 4 ~~Cp~Cg~~~~--vv~D~--~~G--~~vC~~CG~ 31 (278)
..||.||+.+. ++... .+| .+.|.-|++
T Consensus 185 ~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~t 218 (305)
T TIGR01562 185 TLCPACGSPPVASMVRQGGKETGLRYLSCSLCAT 218 (305)
T ss_pred CcCCCCCChhhhhhhcccCCCCCceEEEcCCCCC
Confidence 48999998532 23321 344 577887765
No 305
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=49.19 E-value=8.2 Score=32.77 Aligned_cols=36 Identities=19% Similarity=0.415 Sum_probs=22.3
Q ss_pred CCCCCCCCCC-ce--eEe-CCCC-----ceEcCCCcccccccccc
Q 023713 4 SYCADCKRLT-EV--VFD-HSAG-----DTICSECGLVLEAYSVD 39 (278)
Q Consensus 4 ~~Cp~Cg~~~-~v--v~D-~~~G-----~~vC~~CG~Vl~e~~id 39 (278)
..||.||+.= .+ .+| +-.| .++|..||+=..|-...
T Consensus 15 ~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~DV~~~ 59 (201)
T COG1779 15 IDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGYRSTDVKTL 59 (201)
T ss_pred ecCCcccceeeEEEeeecCCccceEEEEEEEccccCCcccceeec
Confidence 5799999720 11 111 2334 46899999987665543
No 306
>PRK14873 primosome assembly protein PriA; Provisional
Probab=49.02 E-value=13 Score=37.79 Aligned_cols=27 Identities=22% Similarity=0.608 Sum_probs=20.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLV 32 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V 32 (278)
..||+|+. .+++-...+.+.|..||.-
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 56889986 3666556778889999974
No 307
>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=49.01 E-value=40 Score=30.55 Aligned_cols=46 Identities=20% Similarity=0.084 Sum_probs=33.0
Q ss_pred HHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHH
Q 023713 125 TIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVK 170 (278)
Q Consensus 125 ~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~ 170 (278)
...+.|..+...+....+.---.+..+|.||+++||+..+.|.-..
T Consensus 168 ~~~~~aw~~inDa~~t~~~llypphiIA~a~l~ia~~~~~~~~~~~ 213 (297)
T COG5333 168 KLLQIAWKIINDALRTDLCLLYPPHIIALAALLIACEVLGMPIIKL 213 (297)
T ss_pred HHHHHHHHHHHhhhhceeeeecChHHHHHHHHHHHHHhcCCccchh
Confidence 3666677776666554433334688999999999999999885443
No 308
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=48.99 E-value=8.2 Score=35.49 Aligned_cols=28 Identities=21% Similarity=0.334 Sum_probs=21.6
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLV 32 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V 32 (278)
++||.|++.-.+-+||.++++||.. |..
T Consensus 78 ~kC~~C~~~i~~kTDPkn~dY~~~~-Ga~ 105 (324)
T PF04502_consen 78 IKCPRCSNEIEFKTDPKNTDYVVES-GAR 105 (324)
T ss_pred EEcCCCCCEEeeecCCCCCCeeeec-Cee
Confidence 4699998866778899998888876 443
No 309
>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=48.39 E-value=16 Score=27.26 Aligned_cols=28 Identities=14% Similarity=0.305 Sum_probs=17.5
Q ss_pred CCCCCCCCC-CceeEeCCCCceEcCCCcc
Q 023713 4 SYCADCKRL-TEVVFDHSAGDTICSECGL 31 (278)
Q Consensus 4 ~~Cp~Cg~~-~~vv~D~~~G~~vC~~CG~ 31 (278)
..||-|+.. +++.++...|...|-.||.
T Consensus 34 ~~CPfH~d~~pS~~i~~~k~~~~Cf~Cg~ 62 (97)
T PF01807_consen 34 CLCPFHDDKTPSFSINPDKNRFKCFGCGK 62 (97)
T ss_dssp E--SSS--SS--EEEETTTTEEEETTT--
T ss_pred EECcCCCCCCCceEEECCCCeEEECCCCC
Confidence 359999853 4678889999999999994
No 310
>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=47.75 E-value=27 Score=23.34 Aligned_cols=33 Identities=18% Similarity=0.150 Sum_probs=25.9
Q ss_pred CCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhh
Q 023713 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEA 197 (278)
Q Consensus 164 ~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~ 197 (278)
+-..++.|+|.. ++++..+|.+.+..|...|+-
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 345799999995 999999999999999887764
No 311
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=47.61 E-value=14 Score=36.20 Aligned_cols=31 Identities=32% Similarity=0.660 Sum_probs=20.6
Q ss_pred CCCCCCCCCcee---EeCCCC--ceEcCCCccccccc
Q 023713 5 YCADCKRLTEVV---FDHSAG--DTICSECGLVLEAY 36 (278)
Q Consensus 5 ~Cp~Cg~~~~vv---~D~~~G--~~vC~~CG~Vl~e~ 36 (278)
.||+||....++ +|...| .+.| +||.--+-.
T Consensus 177 ic~~cg~~~~~~~~~~d~~~~~v~y~~-~cG~~~~~~ 212 (510)
T PRK00750 177 ICPKCGKVLTTPVISYDAEAGTVTYDC-ECGHEGEVP 212 (510)
T ss_pred eCCCCCccceEEEEEEeCCCCEEEEEc-CCCCEEEEe
Confidence 699999864332 577777 4455 599876433
No 312
>PRK06386 replication factor A; Reviewed
Probab=47.56 E-value=9.4 Score=35.61 Aligned_cols=21 Identities=14% Similarity=0.632 Sum_probs=15.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLV 32 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V 32 (278)
.+||+|+.. .+ . ..|.+||.|
T Consensus 237 ~rCP~C~R~----l~--~--g~C~~HG~v 257 (358)
T PRK06386 237 TKCSVCNKI----IE--D--GVCKDHPDA 257 (358)
T ss_pred ecCcCCCeE----cc--C--CcCCCCCCC
Confidence 579999972 22 2 399999985
No 313
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=47.53 E-value=70 Score=21.33 Aligned_cols=51 Identities=16% Similarity=0.238 Sum_probs=33.3
Q ss_pred cCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHHHH
Q 023713 163 ENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAV 228 (278)
Q Consensus 163 ~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~ 228 (278)
+....|..++|.. +|++..+|.+..+ |- .+ ..+.+.+.+++..|+++++..
T Consensus 11 ~~~gls~~~lA~~-~g~s~s~v~~iE~------G~-------~~-~p~~~~l~~l~~~l~~~~~~~ 61 (64)
T PF13560_consen 11 ERAGLSQAQLADR-LGVSQSTVSRIER------GR-------RP-RPSPDTLQRLARALGVPPDER 61 (64)
T ss_dssp HCHTS-HHHHHHH-HTS-HHHHHHHHT------TS-------SS-S-BHHHHHHHHHHTT--HHHH
T ss_pred HHcCCCHHHHHHH-HCcCHHHHHHHHC------CC-------CC-CCCHHHHHHHHHHHCcCHHHH
Confidence 3446899999994 9999998876633 21 11 234689999999999987654
No 314
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=47.39 E-value=17 Score=24.09 Aligned_cols=29 Identities=21% Similarity=0.779 Sum_probs=20.3
Q ss_pred CCCCC--CCCCCCceeEe--CCCCceEcCCCcccc
Q 023713 3 DSYCA--DCKRLTEVVFD--HSAGDTICSECGLVL 33 (278)
Q Consensus 3 ~~~Cp--~Cg~~~~vv~D--~~~G~~vC~~CG~Vl 33 (278)
...|| .|+.. +..+ .....+.|..||...
T Consensus 18 ~~~CP~~~C~~~--~~~~~~~~~~~v~C~~C~~~f 50 (64)
T smart00647 18 LKWCPAPDCSAA--IIVTEEEGCNRVTCPKCGFSF 50 (64)
T ss_pred ccCCCCCCCcce--EEecCCCCCCeeECCCCCCeE
Confidence 35799 89862 3332 367788999998765
No 315
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=47.39 E-value=11 Score=35.81 Aligned_cols=33 Identities=15% Similarity=0.350 Sum_probs=23.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcccccccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVD 39 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~~id 39 (278)
-.||.||.. . ...-.+..-|..||+-..+..+-
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 379999983 2 22334469999999998766554
No 316
>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=47.15 E-value=61 Score=21.01 Aligned_cols=28 Identities=18% Similarity=0.181 Sum_probs=23.6
Q ss_pred CCCCHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 165 ~p~tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
-+.++.||++ .++++...+.+.++.|.+
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 499999999999999875
No 317
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=46.98 E-value=62 Score=21.32 Aligned_cols=45 Identities=16% Similarity=0.191 Sum_probs=27.0
Q ss_pred CCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHH
Q 023713 167 RTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQ 226 (278)
Q Consensus 167 ~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~ 226 (278)
+|..++|.. .|++..+|.+.++.= . ..-..+-+.++|..|+.+++
T Consensus 11 it~~~La~~-~gis~~tl~~~~~~~-------------~-~~~~~~~l~~ia~~l~~~~~ 55 (63)
T PF13443_consen 11 ITQKDLARK-TGISRSTLSRILNGK-------------P-SNPSLDTLEKIAKALNCSPE 55 (63)
T ss_dssp --HHHHHHH-HT--HHHHHHHHTTT-------------------HHHHHHHHHHHT--HH
T ss_pred CCHHHHHHH-HCcCHHHHHHHHhcc-------------c-ccccHHHHHHHHHHcCCCHH
Confidence 489999994 899999988776521 1 11235788999999998764
No 318
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=46.74 E-value=10 Score=25.23 Aligned_cols=36 Identities=25% Similarity=0.532 Sum_probs=25.9
Q ss_pred CCCCCCCCCC--CceeEeCCCCceEcCC-Ccccccccccc
Q 023713 3 DSYCADCKRL--TEVVFDHSAGDTICSE-CGLVLEAYSVD 39 (278)
Q Consensus 3 ~~~Cp~Cg~~--~~vv~D~~~G~~vC~~-CG~Vl~e~~id 39 (278)
|.+|..|+.+ ..++++...| .||.. |-.-++|..+.
T Consensus 1 m~~CvVCKqpi~~a~~v~T~~G-~VH~g~C~~y~~e~~~S 39 (54)
T PF10886_consen 1 MEICVVCKQPIDDALVVETESG-PVHPGVCAQYLEELPVS 39 (54)
T ss_pred CCeeeeeCCccCcceEEEcCCC-ccCcHHHHHHHHhcccc
Confidence 4689999975 3467777777 77765 77777777654
No 319
>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=46.72 E-value=56 Score=22.27 Aligned_cols=26 Identities=19% Similarity=0.252 Sum_probs=21.5
Q ss_pred cCCCCCHHHHHHHHcCCCHHHHHHHHH
Q 023713 163 ENKPRTVKEFCSVANGTTKKEIGRAKE 189 (278)
Q Consensus 163 ~~~p~tl~eia~~~~~v~~~~i~~~~~ 189 (278)
++-.++++|||+. ++|+..+|++.-.
T Consensus 19 ~~g~i~lkdIA~~-Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 19 SNGKIKLKDIAEK-LGVSESTIRKWKS 44 (60)
T ss_pred hCCCccHHHHHHH-HCCCHHHHHHHhh
Confidence 4556889999995 9999999997744
No 320
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=46.60 E-value=38 Score=21.62 Aligned_cols=47 Identities=21% Similarity=0.318 Sum_probs=32.7
Q ss_pred CCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHH
Q 023713 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQ 226 (278)
Q Consensus 164 ~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~ 226 (278)
....|+.|+|.. .|++..+|.+..+- + ...+.+.+.++++.|+++.+
T Consensus 7 ~~gls~~~la~~-~gis~~~i~~~~~g-------~--------~~~~~~~~~~ia~~l~~~~~ 53 (55)
T PF01381_consen 7 EKGLSQKELAEK-LGISRSTISRIENG-------K--------RNPSLDTLKKIAKALGVSPE 53 (55)
T ss_dssp HTTS-HHHHHHH-HTS-HHHHHHHHTT-------S--------STSBHHHHHHHHHHHTSEHH
T ss_pred HcCCCHHHHHHH-hCCCcchhHHHhcC-------C--------CCCCHHHHHHHHHHHCCCHH
Confidence 345788999994 89999999876443 1 11245788999999998765
No 321
>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=46.51 E-value=13 Score=28.06 Aligned_cols=28 Identities=18% Similarity=0.310 Sum_probs=18.8
Q ss_pred CCCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl 33 (278)
...|..|+- |..+.+--...|.+||.++
T Consensus 3 lrAC~~C~~---I~~~~qf~~~gCpnC~~~l 30 (98)
T cd07973 3 LRACLLCSL---IKTEDQFERDGCPNCEGYL 30 (98)
T ss_pred CchhccCCc---ccccccccCCCCCCCcchh
Confidence 467999986 3333333457899998776
No 322
>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=46.37 E-value=7.2 Score=23.51 Aligned_cols=27 Identities=26% Similarity=0.730 Sum_probs=14.4
Q ss_pred CCCCCCCCce-eEeCCCCce-EcCCCccc
Q 023713 6 CADCKRLTEV-VFDHSAGDT-ICSECGLV 32 (278)
Q Consensus 6 Cp~Cg~~~~v-v~D~~~G~~-vC~~CG~V 32 (278)
|-+|+...+. -.....|.. +|..||.-
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 6778864222 223346777 89888864
No 323
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=46.28 E-value=95 Score=22.31 Aligned_cols=29 Identities=21% Similarity=0.366 Sum_probs=20.9
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCC
Q 023713 113 ISAMSDRLGLVTTIKDRANEIYKKVEDQKPLR 144 (278)
Q Consensus 113 I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~ 144 (278)
+.++++.|+++.+.+.. +++.+.+.+++.
T Consensus 2 ~~ela~~l~is~stvs~---~l~~L~~~glI~ 30 (96)
T smart00529 2 TSEIAERLNVSPPTVTQ---MLKKLEKDGLVE 30 (96)
T ss_pred HHHHHHHhCCChHHHHH---HHHHHHHCCCEE
Confidence 56889999999766555 566666677664
No 324
>COG4307 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.15 E-value=8.8 Score=34.16 Aligned_cols=28 Identities=36% Similarity=0.891 Sum_probs=22.8
Q ss_pred CCCCCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 1 ~~~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
|-...||+||. .+-|| ...|-.||.-+.
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 45678999997 47776 678999999886
No 325
>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=46.15 E-value=11 Score=28.97 Aligned_cols=31 Identities=23% Similarity=0.425 Sum_probs=22.8
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
..|-+||+...--....-|..+|.+|.-|-.
T Consensus 4 ~~CaDC~~~~p~w~s~~~GifvC~~CsgiHR 34 (112)
T smart00105 4 KKCFDCGAPNPTWASVNLGVFLCIECSGIHR 34 (112)
T ss_pred CcccCCCCCCCCcEEeccceeEhHHhHHHHH
Confidence 5799999843223344679999999998875
No 326
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=45.93 E-value=1.4e+02 Score=24.02 Aligned_cols=31 Identities=16% Similarity=0.309 Sum_probs=25.6
Q ss_pred CCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhh
Q 023713 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHLE 196 (278)
Q Consensus 165 ~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~ 196 (278)
...|..|||+. ++++..+|++..+...+.|.
T Consensus 20 ~GlTq~EIAe~-LGiS~~tVs~ie~ra~kkLr 50 (141)
T PRK03975 20 RGLTQQEIADI-LGTSRANVSSIEKRARENIE 50 (141)
T ss_pred cCCCHHHHHHH-HCCCHHHHHHHHHHHHHHHH
Confidence 55899999995 99999999988877666654
No 327
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=45.68 E-value=7.5 Score=29.88 Aligned_cols=31 Identities=19% Similarity=0.574 Sum_probs=21.3
Q ss_pred CCCCCCCCCCCceeEeCCCCceEcCCCcccccc
Q 023713 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e 35 (278)
...|+.||+- +..-...+..+|..|+.+..-
T Consensus 7 ~~FC~~CG~l--l~~~~~~~~~~C~~Ck~~~~v 37 (116)
T KOG2907|consen 7 LDFCSDCGSL--LEEPSAQSTVLCIRCKIEYPV 37 (116)
T ss_pred cchhhhhhhh--cccccccCceEeccccccCCH
Confidence 3679999972 333346677779999988753
No 328
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=45.44 E-value=26 Score=30.68 Aligned_cols=52 Identities=15% Similarity=0.220 Sum_probs=34.4
Q ss_pred HHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhhcccccccCC-CCHHHHHHHHHhhcCC
Q 023713 159 ACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGT-IHASDYLRRFCSNLGM 223 (278)
Q Consensus 159 acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~~~~~~~~~~-~~p~~~i~r~~~~L~l 223 (278)
..|..+.-+|.+|+++. +|++...|+|..+- .. +|. .+..+++..++..+.+
T Consensus 16 ~lr~lk~~~ty~el~~~-~g~p~~~l~RYv~g-----~~-------~P~~~~a~~~~~~l~~~~~~ 68 (238)
T PRK08558 16 VLRSLKKTYTYEELSSI-TGLPESVLNRYVNG-----HV-------LPSVERAREIVEKLGPYYNL 68 (238)
T ss_pred HHHHHhcccCHHHHHHH-HCCCHHHHHHHHcC-----Cc-------CCCHHHHHHHHHHHHHhhhh
Confidence 34566666899999995 99999999987541 10 232 2355666666666644
No 329
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=45.32 E-value=77 Score=19.99 Aligned_cols=24 Identities=17% Similarity=0.194 Sum_probs=21.3
Q ss_pred CCHHHHHHHHcCCCHHHHHHHHHHH
Q 023713 167 RTVKEFCSVANGTTKKEIGRAKEFI 191 (278)
Q Consensus 167 ~tl~eia~~~~~v~~~~i~~~~~~l 191 (278)
.|+++||.. +|++..++++.++..
T Consensus 28 ~s~~~vA~~-~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 28 RSFKDVARE-LGVSWSTVRRIFDRY 51 (52)
T ss_pred CCHHHHHHH-HCCCHHHHHHHHHhh
Confidence 899999995 999999999988753
No 330
>PHA01976 helix-turn-helix protein
Probab=45.18 E-value=52 Score=22.02 Aligned_cols=48 Identities=17% Similarity=0.189 Sum_probs=34.5
Q ss_pred CCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHHH
Q 023713 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQA 227 (278)
Q Consensus 164 ~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v 227 (278)
....|..|+|.. .+++..+|.+..+ +.. . .+.+.+.++++.|+++.+.
T Consensus 13 ~~glt~~~lA~~-~gvs~~~v~~~e~------g~~------~---p~~~~l~~ia~~l~v~~~~ 60 (67)
T PHA01976 13 ARAWSAPELSRR-AGVRHSLIYDFEA------DKR------L---PNLKTLLRLADALGVTLDW 60 (67)
T ss_pred HcCCCHHHHHHH-hCCCHHHHHHHHc------CCC------C---CCHHHHHHHHHHHCcCHHH
Confidence 345789999995 8999988876532 111 1 2357889999999998763
No 331
>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=45.03 E-value=14 Score=25.83 Aligned_cols=26 Identities=35% Similarity=0.726 Sum_probs=19.6
Q ss_pred CCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 5 YCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 5 ~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
+| .||. .+..|...-.--| .||..+.
T Consensus 5 rC-~Cgr--~lya~e~~kTkkC-~CG~~l~ 30 (68)
T PF09082_consen 5 RC-DCGR--YLYAKEGAKTKKC-VCGKTLK 30 (68)
T ss_dssp EE-TTS----EEEETT-SEEEE-TTTEEEE
T ss_pred Ee-cCCC--EEEecCCcceeEe-cCCCeee
Confidence 68 7997 4788888888999 9999984
No 332
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=44.84 E-value=40 Score=21.19 Aligned_cols=27 Identities=11% Similarity=0.122 Sum_probs=18.3
Q ss_pred CCCHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 166 PRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 166 p~tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
..|..+||.. +|++..++.+..+...+
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 99999999999887653
No 333
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=44.73 E-value=2.3e+02 Score=25.22 Aligned_cols=110 Identities=15% Similarity=0.138 Sum_probs=60.2
Q ss_pred CCchhHHHHHHHHHHHHHHhcCCCHHHHHHH--HHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHc
Q 023713 100 SHPDRNLIQAFKSISAMSDRLGLVTTIKDRA--NEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVAN 177 (278)
Q Consensus 100 ~~~er~l~~~~~~I~~i~~~L~Lp~~v~e~A--~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~ 177 (278)
+.+|.....|...|.+.+ +|...-+..+ ..|-+.++.-++.+.+-....-.|-|..-=-..++|.++.|+.+. -
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 345666667777777666 5543222221 122233334444433322222233333333344899999999884 7
Q ss_pred CCCHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCC
Q 023713 178 GTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGM 223 (278)
Q Consensus 178 ~v~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l 223 (278)
||-.+- ++..|....|. +..+--...+.|+|+.|+.
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 887753 34444445543 2233446789999999986
No 334
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=44.64 E-value=65 Score=20.56 Aligned_cols=29 Identities=10% Similarity=0.152 Sum_probs=25.5
Q ss_pred CCCCCHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 164 ~~p~tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
+-|.++.||+.. ++++..++.+.++.|.+
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 89999999999998875
No 335
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=44.63 E-value=12 Score=25.33 Aligned_cols=23 Identities=26% Similarity=0.564 Sum_probs=17.1
Q ss_pred CCCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl 33 (278)
+..||.||. =++ ...|+.||-+.
T Consensus 5 ~rkC~~cg~-YTL-------ke~Cp~CG~~t 27 (59)
T COG2260 5 IRKCPKCGR-YTL-------KEKCPVCGGDT 27 (59)
T ss_pred hhcCcCCCc-eee-------cccCCCCCCcc
Confidence 478999997 222 25899999875
No 336
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.37 E-value=58 Score=24.85 Aligned_cols=40 Identities=15% Similarity=0.275 Sum_probs=33.2
Q ss_pred HHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhh
Q 023713 153 AACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (278)
Q Consensus 153 AAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~ 198 (278)
-.-+|+-||- .|+||-.. +|++-.+++.-+.++.+.+|.+
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 39999885 9999999999999999999987
No 337
>PRK08329 threonine synthase; Validated
Probab=44.33 E-value=15 Score=34.05 Aligned_cols=26 Identities=27% Similarity=0.639 Sum_probs=18.1
Q ss_pred CCCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
|..|+.||.. ++.... ..| .||-.|+
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 3789999983 333333 789 8997764
No 338
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=44.27 E-value=9.4 Score=23.79 Aligned_cols=17 Identities=35% Similarity=0.767 Sum_probs=13.4
Q ss_pred CCceEcCCCcccccccc
Q 023713 21 AGDTICSECGLVLEAYS 37 (278)
Q Consensus 21 ~G~~vC~~CG~Vl~e~~ 37 (278)
-|...|..||.+.....
T Consensus 11 ~~~~~C~~CgM~Y~~~~ 27 (41)
T PF13878_consen 11 FGATTCPTCGMLYSPGS 27 (41)
T ss_pred cCCcCCCCCCCEECCCC
Confidence 36789999999986553
No 339
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=43.83 E-value=1.5e+02 Score=25.11 Aligned_cols=28 Identities=21% Similarity=0.239 Sum_probs=24.7
Q ss_pred CCCCHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 165 ~p~tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
+|.+..|||+ .+|++..++.|..++|.+
T Consensus 172 i~~t~~~iA~-~lG~tretvsR~l~~L~~ 199 (236)
T PRK09392 172 LPYEKRVLAS-YLGMTPENLSRAFAALAS 199 (236)
T ss_pred eeCCHHHHHH-HhCCChhHHHHHHHHHHh
Confidence 4677899999 599999999999999865
No 340
>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=43.45 E-value=51 Score=27.30 Aligned_cols=40 Identities=20% Similarity=0.298 Sum_probs=30.6
Q ss_pred HHHHHHHhc-CCCHHHHHHHHHHHHHHhhCCCCCCCcHHHH
Q 023713 112 SISAMSDRL-GLVTTIKDRANEIYKKVEDQKPLRGRNQEAI 151 (278)
Q Consensus 112 ~I~~i~~~L-~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~ 151 (278)
+++++-..| +||++-++++.+.|+...+...-.|++-+.+
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 455555555 4899999999999999988777778776643
No 341
>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=43.32 E-value=1.4e+02 Score=22.95 Aligned_cols=77 Identities=26% Similarity=0.253 Sum_probs=45.4
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCC----CCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHH
Q 023713 112 SISAMSDRLGLVTTIKDRANEIYKKVEDQKPL----RGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA 187 (278)
Q Consensus 112 ~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~----~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~ 187 (278)
.+.++|..++++...+.. .+++. +.+.+ +|+. .+- .=-+.+.-.+.--.|+.|++.. ++|+..+|+++
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---WLKRK-ETGDLEPKPRGRK--KID-RDELKALVEENPDATLRELAER-LGVSPSTIWRA 91 (119)
T ss_pred hHHHHHHHhCcHHHHHHH---HHHhc-ccccccccccccc--ccc-HHHHHHHHHHCCCcCHHHHHHH-cCCCHHHHHHH
Confidence 577888889988655554 44422 22222 2321 110 1112222233444899999995 89999999999
Q ss_pred HHHHHHHhh
Q 023713 188 KEFIVKHLE 196 (278)
Q Consensus 188 ~~~l~~~L~ 196 (278)
.+++--...
T Consensus 92 Lkrlg~t~K 100 (119)
T PF01710_consen 92 LKRLGITRK 100 (119)
T ss_pred HHHcCchhc
Confidence 887654443
No 342
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=43.18 E-value=74 Score=21.84 Aligned_cols=45 Identities=18% Similarity=0.359 Sum_probs=30.4
Q ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHHhhhhcccccccCCCCH--HHHHHHHHhhcCCCHHH
Q 023713 168 TVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHA--SDYLRRFCSNLGMTNQA 227 (278)
Q Consensus 168 tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p--~~~i~r~~~~L~l~~~v 227 (278)
|+.|||.. +|++..++.+++ +-+ +.+.| .+-|.+++.+||..+..
T Consensus 2 t~~~iA~~-~gvS~~TVSr~l-------n~~-------~~v~~~t~~~i~~~~~~~gy~~~~ 48 (70)
T smart00354 2 TIKDVARL-AGVSKATVSRVL-------NGN-------GRVSEETREKVLAAMEELGYIPNR 48 (70)
T ss_pred CHHHHHHH-HCCCHHHHHHHH-------CCC-------CCCCHHHHHHHHHHHHHhCCCCCH
Confidence 68899994 999999998754 221 22233 34577788888876543
No 343
>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=43.08 E-value=15 Score=25.23 Aligned_cols=30 Identities=27% Similarity=0.516 Sum_probs=15.5
Q ss_pred CCCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY 36 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~ 36 (278)
...|..|+.. |..-...--|..||.|+=..
T Consensus 9 ~~~C~~C~~~----F~~~~rrhhCr~CG~~vC~~ 38 (69)
T PF01363_consen 9 ASNCMICGKK----FSLFRRRHHCRNCGRVVCSS 38 (69)
T ss_dssp -SB-TTT--B-----BSSS-EEE-TTT--EEECC
T ss_pred CCcCcCcCCc----CCCceeeEccCCCCCEECCc
Confidence 3679999973 45567888899999888533
No 344
>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=42.88 E-value=18 Score=33.65 Aligned_cols=14 Identities=14% Similarity=0.183 Sum_probs=9.3
Q ss_pred hcCCCCCHHHHHHH
Q 023713 162 QENKPRTVKEFCSV 175 (278)
Q Consensus 162 ~~~~p~tl~eia~~ 175 (278)
..|..+++.|+.+.
T Consensus 279 SkGnvI~~~dll~~ 292 (353)
T cd00674 279 SKGNVITPSDWLEV 292 (353)
T ss_pred CCCCcCCHHHHHHH
Confidence 34666777777663
No 345
>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=42.83 E-value=30 Score=21.21 Aligned_cols=29 Identities=24% Similarity=0.410 Sum_probs=18.1
Q ss_pred CCCCCCCCCCceeEeCCCC-ceEcCC---Ccccc
Q 023713 4 SYCADCKRLTEVVFDHSAG-DTICSE---CGLVL 33 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G-~~vC~~---CG~Vl 33 (278)
..||.||+ ..++.....| .+.|++ |....
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 4555544444 346765 66554
No 346
>PRK08197 threonine synthase; Validated
Probab=42.57 E-value=11 Score=35.57 Aligned_cols=26 Identities=27% Similarity=0.713 Sum_probs=19.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
.+|+.||.. ++.......| .||-.++
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 679999983 4555557889 8997764
No 347
>PRK00118 putative DNA-binding protein; Validated
Probab=42.35 E-value=98 Score=23.50 Aligned_cols=30 Identities=13% Similarity=0.079 Sum_probs=24.8
Q ss_pred CCCHHHHHHHHcCCCHHHHHHHHHHHHHHhh
Q 023713 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKHLE 196 (278)
Q Consensus 166 p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~ 196 (278)
..|..|||.. +|++..++.+.+.+..+.+.
T Consensus 33 g~S~~EIAe~-lGIS~~TV~r~L~RArkkLr 62 (104)
T PRK00118 33 DYSLGEIAEE-FNVSRQAVYDNIKRTEKLLE 62 (104)
T ss_pred CCCHHHHHHH-HCcCHHHHHHHHHHHHHHHH
Confidence 5789999995 99999999988877766664
No 348
>smart00351 PAX Paired Box domain.
Probab=42.17 E-value=1.4e+02 Score=23.22 Aligned_cols=61 Identities=16% Similarity=0.143 Sum_probs=34.9
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCC-----CCcHHHHH-HHHHHH-HHHhcCCCCCHHHHHHH
Q 023713 112 SISAMSDRLGLVTTIKDRANEIYKKVEDQKPLR-----GRNQEAIV-AACLYI-ACRQENKPRTVKEFCSV 175 (278)
Q Consensus 112 ~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~-----gr~~~~~a-AAclY~-acR~~~~p~tl~eia~~ 175 (278)
-..++|..|+++..++.. +.+++.+.+.+. |+++..+. ....++ ....++-..|+.|++..
T Consensus 35 s~~~iA~~~gvs~~tV~k---wi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~p~~t~~el~~~ 102 (125)
T smart00351 35 RPCDISRQLCVSHGCVSK---ILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQENPGIFAWEIRDR 102 (125)
T ss_pred CHHHHHHHHCcCHHHHHH---HHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHCCCCCHHHHHHH
Confidence 467899999999766665 445544444332 32332221 222232 24556666899998764
No 349
>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=41.57 E-value=27 Score=21.48 Aligned_cols=30 Identities=27% Similarity=0.572 Sum_probs=18.2
Q ss_pred CCCCCCCCCC--CceeEeCCCCceEcCCCccc
Q 023713 3 DSYCADCKRL--TEVVFDHSAGDTICSECGLV 32 (278)
Q Consensus 3 ~~~Cp~Cg~~--~~vv~D~~~G~~vC~~CG~V 32 (278)
..+|..|++- .-..+|......+|.-||..
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 3579999862 34477877889999999985
No 350
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=41.53 E-value=84 Score=19.34 Aligned_cols=29 Identities=17% Similarity=0.249 Sum_probs=25.1
Q ss_pred CCCCHHHHHHHHcCCCHHHHHHHHHHHHHH
Q 023713 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (278)
Q Consensus 165 ~p~tl~eia~~~~~v~~~~i~~~~~~l~~~ 194 (278)
.+.+..+++.. ++++..++.+.++.|.+.
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 46899999995 899999999999888764
No 351
>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=41.52 E-value=32 Score=29.99 Aligned_cols=27 Identities=33% Similarity=0.490 Sum_probs=21.2
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHHHHhh
Q 023713 113 ISAMSDRLGLVTTIKDRANEIYKKVED 139 (278)
Q Consensus 113 I~~i~~~L~Lp~~v~e~A~~i~k~~~~ 139 (278)
=-+++..+|+|++++++|.++++.+.+
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 345788899999999999999998754
No 352
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=41.34 E-value=12 Score=40.13 Aligned_cols=9 Identities=33% Similarity=0.885 Sum_probs=6.0
Q ss_pred CCCCCCCCC
Q 023713 4 SYCADCKRL 12 (278)
Q Consensus 4 ~~Cp~Cg~~ 12 (278)
..||.||+.
T Consensus 680 ~fCP~CGs~ 688 (1337)
T PRK14714 680 NRCPDCGTH 688 (1337)
T ss_pred ccCcccCCc
Confidence 467777764
No 353
>COG1426 Predicted transcriptional regulator contains Xre-like HTH domain [Function unknown]
Probab=40.99 E-value=1.2e+02 Score=27.22 Aligned_cols=56 Identities=13% Similarity=0.275 Sum_probs=35.4
Q ss_pred hcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhhcccccccCC-CCHHHHHHHHHhhcCCCHHHH
Q 023713 162 QENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGT-IHASDYLRRFCSNLGMTNQAV 228 (278)
Q Consensus 162 ~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~~~~~~~~~~-~~p~~~i~r~~~~L~l~~~v~ 228 (278)
++...+||.|++.. ++|...-|... ++=+++ .+|. +=..-||..|+.-|+|+.+..
T Consensus 12 Re~~gLsL~dva~~-t~I~~~~L~ai-----Eeg~~~-----~lp~~~y~rG~ir~YA~~l~ld~~~l 68 (284)
T COG1426 12 REEKGLSLEDVAAR-TKIRKSYLRAL-----EEGNFD-----KLPGPVYIRGYIRSYAKFLGLDEDEL 68 (284)
T ss_pred HHHcCCCHHHHHHH-hCccHHHHHHH-----hcCccc-----cccchHHHHHHHHHHHHHhCCCHHHH
Confidence 45567899999884 77776655332 111222 1232 224569999999999997743
No 354
>PRK14526 adenylate kinase; Provisional
Probab=40.56 E-value=18 Score=31.00 Aligned_cols=30 Identities=20% Similarity=0.422 Sum_probs=18.8
Q ss_pred CCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 5 YCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 5 ~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
.||.||..-++.+++..-..+|..||.-+.
T Consensus 124 ~~~~~g~~y~~~~~pp~~~~~~~~~~~~l~ 153 (211)
T PRK14526 124 ICKSCNNIFNIYTLPTKEKGICDVCKGDLY 153 (211)
T ss_pred cccccCCccccccCCCCccCcCCCCCCeee
Confidence 477777654556666555667777765443
No 355
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=40.51 E-value=17 Score=33.15 Aligned_cols=7 Identities=43% Similarity=1.103 Sum_probs=3.1
Q ss_pred eEcCCCc
Q 023713 24 TICSECG 30 (278)
Q Consensus 24 ~vC~~CG 30 (278)
+-|+.||
T Consensus 227 ~~C~~Cg 233 (309)
T PRK03564 227 VKCSNCE 233 (309)
T ss_pred ccCCCCC
Confidence 3444444
No 356
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=40.19 E-value=22 Score=22.60 Aligned_cols=23 Identities=26% Similarity=0.563 Sum_probs=17.4
Q ss_pred CCCCCCCCCceeEeCCCCceEcCCCcccccc
Q 023713 5 YCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (278)
Q Consensus 5 ~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e 35 (278)
+|..|+... ...+|..||.|.-.
T Consensus 1 ~C~~C~~~~--------~l~~CL~C~~~~c~ 23 (50)
T smart00290 1 RCSVCGTIE--------NLWLCLTCGQVGCG 23 (50)
T ss_pred CcccCCCcC--------CeEEecCCCCcccC
Confidence 588999731 27799999999753
No 357
>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 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=39.68 E-value=23 Score=29.12 Aligned_cols=31 Identities=19% Similarity=0.393 Sum_probs=15.3
Q ss_pred CCCCCCCCCCce---eE-eCCCCc-----eEcCCCccccc
Q 023713 4 SYCADCKRLTEV---VF-DHSAGD-----TICSECGLVLE 34 (278)
Q Consensus 4 ~~Cp~Cg~~~~v---v~-D~~~G~-----~vC~~CG~Vl~ 34 (278)
..||+||..... .+ .+--|+ ..|.+||.=-.
T Consensus 2 s~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~ 41 (161)
T PF03367_consen 2 SLCPNCGENGTTRILLTDIPYFKEVIIMSFECEHCGYKNN 41 (161)
T ss_dssp EE-TTTSSCCEEEEEEEEETTTEEEEEEEEE-TTT--EEE
T ss_pred CcCCCCCCCcEEEEEEEcCCCCceEEEEEeECCCCCCEee
Confidence 469999985221 11 233444 37999998653
No 359
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=39.66 E-value=19 Score=28.79 Aligned_cols=32 Identities=25% Similarity=0.520 Sum_probs=27.0
Q ss_pred CCCCceEcCCCcccc--cccccccccchhhccCC
Q 023713 19 HSAGDTICSECGLVL--EAYSVDETSEWRIFANE 50 (278)
Q Consensus 19 ~~~G~~vC~~CG~Vl--~e~~id~~~ewr~f~~~ 50 (278)
.+.|.++|.-||.-| .+.-+|.|--|.+|.+-
T Consensus 38 ~~~GiY~c~~cg~pLF~S~~KfdSgcGWPSF~~p 71 (140)
T COG0229 38 KEKGIYVCIVCGEPLFSSEDKFDSGCGWPSFTKP 71 (140)
T ss_pred cCCceEEeecCCCccccccccccCCCCCcccccc
Confidence 589999999999887 55668999999999853
No 360
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=39.59 E-value=75 Score=23.49 Aligned_cols=29 Identities=7% Similarity=0.093 Sum_probs=25.8
Q ss_pred CCCCHHHHHHHHcCCCHHHHHHHHHHHHHH
Q 023713 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (278)
Q Consensus 165 ~p~tl~eia~~~~~v~~~~i~~~~~~l~~~ 194 (278)
-+.|..++++. ++++..++.+.++.|.+.
T Consensus 16 ~~~~~~~la~~-l~~s~~tv~~~l~~L~~~ 44 (108)
T smart00344 16 ARISLAELAKK-VGLSPSTVHNRVKRLEEE 44 (108)
T ss_pred CCCCHHHHHHH-HCcCHHHHHHHHHHHHHC
Confidence 46899999995 999999999999999874
No 361
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=39.45 E-value=19 Score=19.81 Aligned_cols=9 Identities=33% Similarity=0.556 Sum_probs=6.8
Q ss_pred CCCCCCCCC
Q 023713 3 DSYCADCKR 11 (278)
Q Consensus 3 ~~~Cp~Cg~ 11 (278)
+..||.||.
T Consensus 2 l~~C~~CgR 10 (25)
T PF13913_consen 2 LVPCPICGR 10 (25)
T ss_pred CCcCCCCCC
Confidence 567888886
No 362
>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=39.36 E-value=52 Score=21.50 Aligned_cols=25 Identities=12% Similarity=0.193 Sum_probs=22.6
Q ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 168 TVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 168 tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
+..|+++. ++++..++++.++.|.+
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 363
>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=39.28 E-value=56 Score=21.66 Aligned_cols=31 Identities=19% Similarity=0.258 Sum_probs=26.6
Q ss_pred hcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 162 QENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 162 ~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
..+-|.|..||++. ++++..++.+.++.|.+
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 99999999999998875
No 364
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=39.10 E-value=2.7e+02 Score=24.51 Aligned_cols=42 Identities=7% Similarity=-0.046 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHH
Q 023713 148 QEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEF 190 (278)
Q Consensus 148 ~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~ 190 (278)
...+..+.-|+.-....-..|+.+||.. +++++..|.+.+++
T Consensus 196 ~~~l~~~~~~I~~~l~~~~ls~~~lA~~-~giS~r~L~r~Fk~ 237 (302)
T PRK09685 196 ERQFQKVVALIDQSIQEEILRPEWIAGE-LGISVRSLYRLFAE 237 (302)
T ss_pred HHHHHHHHHHHHHhcCCCCCCHHHHHHH-HCCCHHHHHHHHHH
Confidence 3445566666665554445899999995 99999999998874
No 365
>PRK04023 DNA polymerase II large subunit; Validated
Probab=39.03 E-value=18 Score=38.15 Aligned_cols=11 Identities=27% Similarity=0.785 Sum_probs=5.6
Q ss_pred ceEcCCCcccc
Q 023713 23 DTICSECGLVL 33 (278)
Q Consensus 23 ~~vC~~CG~Vl 33 (278)
...|..||...
T Consensus 651 i~fCP~CG~~~ 661 (1121)
T PRK04023 651 VYRCPRCGIEV 661 (1121)
T ss_pred ceeCccccCcC
Confidence 34555555554
No 366
>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=38.64 E-value=18 Score=32.58 Aligned_cols=30 Identities=20% Similarity=0.486 Sum_probs=15.8
Q ss_pred CCCCCCCCCCceeEe-------CCCCceEcCCCcccc
Q 023713 4 SYCADCKRLTEVVFD-------HSAGDTICSECGLVL 33 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D-------~~~G~~vC~~CG~Vl 33 (278)
..||+||.....-+. +...-.+|.+||.-+
T Consensus 212 ~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~Yl 248 (290)
T PF04216_consen 212 IKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYL 248 (290)
T ss_dssp TS-TTT---SS-EEE--------SEEEEEETTTTEEE
T ss_pred CCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchH
Confidence 579999974322111 223346899999987
No 367
>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=38.54 E-value=39 Score=21.12 Aligned_cols=24 Identities=13% Similarity=0.195 Sum_probs=16.9
Q ss_pred CCCCHHHHHHHHcCCCHHHHHHHHH
Q 023713 165 KPRTVKEFCSVANGTTKKEIGRAKE 189 (278)
Q Consensus 165 ~p~tl~eia~~~~~v~~~~i~~~~~ 189 (278)
...|..+||.. ++|+..+|.|..+
T Consensus 20 ~G~si~~IA~~-~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 20 EGMSIAEIAKQ-FGVSRSTVYRYLN 43 (45)
T ss_dssp TT--HHHHHHH-TTS-HHHHHHHHC
T ss_pred CCCCHHHHHHH-HCcCHHHHHHHHh
Confidence 33889999995 9999999987653
No 368
>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=38.46 E-value=13 Score=32.82 Aligned_cols=37 Identities=24% Similarity=0.604 Sum_probs=23.2
Q ss_pred CCCCCCCCCCCceeEeCCCCceEcCCCcccccccccccccchhhcc
Q 023713 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFA 48 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~ 48 (278)
..+|.+||+. |. .=+.-|++||.-= -.-++.+.| -|.
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 4689999983 21 2367899999752 222455777 444
No 369
>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=38.42 E-value=91 Score=20.47 Aligned_cols=26 Identities=19% Similarity=0.242 Sum_probs=23.3
Q ss_pred CCHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 167 RTVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 167 ~tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
.+..||+.. ++++..++.+.++.|.+
T Consensus 21 ~~~~ei~~~-~~i~~~~i~~~l~~L~~ 46 (78)
T cd00090 21 LTVSELAER-LGLSQSTVSRHLKKLEE 46 (78)
T ss_pred cCHHHHHHH-HCcCHhHHHHHHHHHHH
Confidence 899999995 89999999999998865
No 370
>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=38.42 E-value=1e+02 Score=19.39 Aligned_cols=26 Identities=12% Similarity=0.193 Sum_probs=18.4
Q ss_pred cCCCCCHHHHHHHHcCCCHHHHHHHHHH
Q 023713 163 ENKPRTVKEFCSVANGTTKKEIGRAKEF 190 (278)
Q Consensus 163 ~~~p~tl~eia~~~~~v~~~~i~~~~~~ 190 (278)
+|. .++.+.|.. .||+..+|.+.++.
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 444 999999995 99999999976653
No 371
>cd00131 PAX Paired Box domain
Probab=38.37 E-value=1.7e+02 Score=22.84 Aligned_cols=76 Identities=14% Similarity=0.059 Sum_probs=42.9
Q ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCC----C-CCcHHH-HH-HHHHHHHHHhcCCCCCHHHHHHHHc--CC---
Q 023713 112 SISAMSDRLGLVTTIKDRANEIYKKVEDQKPL----R-GRNQEA-IV-AACLYIACRQENKPRTVKEFCSVAN--GT--- 179 (278)
Q Consensus 112 ~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~----~-gr~~~~-~a-AAclY~acR~~~~p~tl~eia~~~~--~v--- 179 (278)
...+++..|+++..++.....=|+. .+.+ . |+++.. .. ..........++-..|+.|+++... ++
T Consensus 35 s~~~iA~~~~Vs~~tV~r~i~r~~e---~G~v~pk~~gg~rpr~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~ 111 (128)
T cd00131 35 RPCDISRQLRVSHGCVSKILNRYYE---TGSIRPGAIGGSKPRVATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDK 111 (128)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHH---cCCcCCCCCCCCCCCcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCccc
Confidence 4667899999998777665544443 2221 1 322222 11 2232333334555589999977411 44
Q ss_pred ----CHHHHHHHHHH
Q 023713 180 ----TKKEIGRAKEF 190 (278)
Q Consensus 180 ----~~~~i~~~~~~ 190 (278)
++.+|++.++.
T Consensus 112 ~~~~s~stI~R~L~~ 126 (128)
T cd00131 112 SNVPSVSSINRILRN 126 (128)
T ss_pred CCCCCHHHHHHHHHh
Confidence 78888887553
No 372
>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=38.18 E-value=1.1e+02 Score=20.21 Aligned_cols=31 Identities=10% Similarity=0.216 Sum_probs=26.9
Q ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHHhhhhc
Q 023713 168 TVKEFCSVANGTTKKEIGRAKEFIVKHLEAEM 199 (278)
Q Consensus 168 tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~~ 199 (278)
++...|+. ++++...|.+.++.|.+.+|.+.
T Consensus 15 s~~~AA~~-l~is~~~vs~~i~~LE~~lg~~L 45 (60)
T PF00126_consen 15 SISAAAEE-LGISQSAVSRQIKQLEEELGVPL 45 (60)
T ss_dssp SHHHHHHH-CTSSHHHHHHHHHHHHHHHTS-S
T ss_pred CHHHHHHH-hhccchHHHHHHHHHHHHhCCeE
Confidence 57888884 99999999999999999999763
No 373
>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=38.16 E-value=33 Score=20.75 Aligned_cols=13 Identities=38% Similarity=0.657 Sum_probs=9.3
Q ss_pred CCCCCCCCCCc-eeE
Q 023713 4 SYCADCKRLTE-VVF 17 (278)
Q Consensus 4 ~~Cp~Cg~~~~-vv~ 17 (278)
..||.|++ +. |+-
T Consensus 6 v~CP~C~s-~~~v~k 19 (36)
T PF03811_consen 6 VHCPRCQS-TEGVKK 19 (36)
T ss_pred eeCCCCCC-CCccee
Confidence 57999998 45 443
No 374
>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=38.11 E-value=70 Score=28.30 Aligned_cols=31 Identities=19% Similarity=0.329 Sum_probs=23.5
Q ss_pred CCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHh
Q 023713 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKHL 195 (278)
Q Consensus 164 ~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L 195 (278)
+.+.|++|||.. +|++...+.+..++..+.|
T Consensus 234 ~~~~t~~eIA~~-lgvS~~~V~q~~~~Al~kL 264 (270)
T TIGR02392 234 DDKLTLQELAAE-YGVSAERIRQIEKNAMKKL 264 (270)
T ss_pred CCCcCHHHHHHH-HCCCHHHHHHHHHHHHHHH
Confidence 348999999995 9999999995555444443
No 375
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=38.09 E-value=26 Score=27.72 Aligned_cols=31 Identities=26% Similarity=0.487 Sum_probs=20.3
Q ss_pred CCCCCCCCCCCceeEeC----CCCceEcCCCccccc
Q 023713 3 DSYCADCKRLTEVVFDH----SAGDTICSECGLVLE 34 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~----~~G~~vC~~CG~Vl~ 34 (278)
+..||.|++. .++.-. ..-...|.+||.-..
T Consensus 30 ~~~cP~C~s~-~~~k~g~~~~~~qRyrC~~C~~tf~ 64 (129)
T COG3677 30 KVNCPRCKSS-NVVKIGGIRRGHQRYKCKSCGSTFT 64 (129)
T ss_pred cCcCCCCCcc-ceeeECCccccccccccCCcCccee
Confidence 4689999984 533221 233578999997653
No 376
>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=38.01 E-value=14 Score=29.86 Aligned_cols=15 Identities=33% Similarity=0.919 Sum_probs=13.1
Q ss_pred CCCceEcCCCccccc
Q 023713 20 SAGDTICSECGLVLE 34 (278)
Q Consensus 20 ~~G~~vC~~CG~Vl~ 34 (278)
.-|.++|.+||..+.
T Consensus 109 g~G~l~C~~Cg~~~~ 123 (146)
T PF07295_consen 109 GPGTLVCENCGHEVE 123 (146)
T ss_pred cCceEecccCCCEEE
Confidence 579999999999874
No 377
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=37.93 E-value=1.2e+02 Score=21.48 Aligned_cols=29 Identities=17% Similarity=0.103 Sum_probs=25.7
Q ss_pred CCCCHHHHHHHHcCCCHHHHHHHHHHHHHH
Q 023713 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (278)
Q Consensus 165 ~p~tl~eia~~~~~v~~~~i~~~~~~l~~~ 194 (278)
-|.++.||+.. ++++..++.+..+.|.+.
T Consensus 19 ~~~t~~~ia~~-l~i~~~tv~r~l~~L~~~ 47 (91)
T smart00346 19 GGLTLAELAER-LGLSKSTAHRLLNTLQEL 47 (91)
T ss_pred CCcCHHHHHHH-hCCCHHHHHHHHHHHHHC
Confidence 48999999995 999999999999998763
No 378
>PRK04217 hypothetical protein; Provisional
Probab=37.79 E-value=57 Score=25.06 Aligned_cols=28 Identities=21% Similarity=0.133 Sum_probs=23.6
Q ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHHhh
Q 023713 168 TVKEFCSVANGTTKKEIGRAKEFIVKHLE 196 (278)
Q Consensus 168 tl~eia~~~~~v~~~~i~~~~~~l~~~L~ 196 (278)
|+.|||.. ++++..+|.+.+....+.|.
T Consensus 60 S~~EIAk~-LGIS~sTV~r~L~RArkkLr 87 (110)
T PRK04217 60 TQEEAGKR-MGVSRGTVWRALTSARKKVA 87 (110)
T ss_pred CHHHHHHH-HCcCHHHHHHHHHHHHHHHH
Confidence 89999995 99999999988877766664
No 379
>PF03685 UPF0147: Uncharacterised protein family (UPF0147); InterPro: IPR005354 The proteins in this entry are functionally uncharacterised.; PDB: 2QZG_C 2QSB_A.
Probab=37.57 E-value=1.6e+02 Score=21.51 Aligned_cols=65 Identities=12% Similarity=0.228 Sum_probs=44.6
Q ss_pred chhHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCH
Q 023713 102 PDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTK 181 (278)
Q Consensus 102 ~er~l~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~ 181 (278)
.+..+.++...++++.+.-.+|.++...|.+....+.+.+ .++-.-||.++++ |.||+. .-+++.
T Consensus 4 ~e~~i~~~~~~L~~I~~D~sVPRNIRr~a~ea~~~L~~e~----~~~~vRaataIs~----------LdeIsn-DPNmP~ 68 (85)
T PF03685_consen 4 NEEKIKQAIQMLERIINDTSVPRNIRRAAEEAKEILNNEE----ESPGVRAATAISI----------LDEISN-DPNMPS 68 (85)
T ss_dssp HHHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHCT-TT----S-HHHHHHHHHHH----------HHHHCT--TTS-H
T ss_pred HHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHhCCC----cchhHhHHHHHHH----------HHHhhc-CCCCch
Confidence 3567889999999999999999999999998888776544 4455666666665 566655 255543
No 380
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=37.11 E-value=27 Score=35.82 Aligned_cols=27 Identities=22% Similarity=0.731 Sum_probs=21.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLV 32 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V 32 (278)
..||+|.. .+++--.+|.+.|-.||..
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 3677778899999999987
No 381
>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=37.05 E-value=11 Score=30.94 Aligned_cols=25 Identities=28% Similarity=0.387 Sum_probs=0.0
Q ss_pred CCCCHHHHHHHHcCCCHHHHHHHHHH
Q 023713 165 KPRTVKEFCSVANGTTKKEIGRAKEF 190 (278)
Q Consensus 165 ~p~tl~eia~~~~~v~~~~i~~~~~~ 190 (278)
.|.|++|||+. +|+++.+|.|+++-
T Consensus 48 ~PLt~~~iA~~-lgl~~STVSRav~~ 72 (160)
T PF04552_consen 48 KPLTMKDIADE-LGLHESTVSRAVKN 72 (160)
T ss_dssp --------------------------
T ss_pred cCCCHHHHHHH-hCCCHhHHHHHHcC
Confidence 68999999995 99999999999773
No 382
>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=37.01 E-value=37 Score=23.51 Aligned_cols=32 Identities=28% Similarity=0.562 Sum_probs=23.8
Q ss_pred HHHHHHHHhhCCCCC--CCcHHHHHHHHHHHHHH
Q 023713 130 ANEIYKKVEDQKPLR--GRNQEAIVAACLYIACR 161 (278)
Q Consensus 130 A~~i~k~~~~~~~~~--gr~~~~~aAAclY~acR 161 (278)
..+|++++.+.++.. |+.|...++|.+|.-++
T Consensus 20 ~~eI~~~i~~~~~~~~~~k~p~~~i~a~ly~~~~ 53 (72)
T PF05066_consen 20 FKEIWEEIQERGLYKKSGKTPEATIAAQLYTDIK 53 (72)
T ss_dssp HHHHHHHHHHHHTS---GGGGGHHHH-HHHHHHH
T ss_pred HHHHHHHHHHhCCCCcccCCHHHHHHHHHHHHcc
Confidence 345677777766666 89999999999998887
No 383
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=36.88 E-value=23 Score=28.07 Aligned_cols=29 Identities=21% Similarity=0.478 Sum_probs=22.9
Q ss_pred CCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713 5 YCADCKRLTEVVFDHSAGDTICSECGLVL 33 (278)
Q Consensus 5 ~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl 33 (278)
.|-.||..+.+-++...-...|..|+.+=
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 58999986666666666679999999873
No 384
>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=36.64 E-value=47 Score=20.13 Aligned_cols=22 Identities=23% Similarity=0.191 Sum_probs=18.8
Q ss_pred CHHHHHHHHcCCCHHHHHHHHHH
Q 023713 168 TVKEFCSVANGTTKKEIGRAKEF 190 (278)
Q Consensus 168 tl~eia~~~~~v~~~~i~~~~~~ 190 (278)
++.|+|+. ++++..+|.+..+.
T Consensus 2 s~~e~a~~-lgvs~~tl~~~~~~ 23 (49)
T cd04762 2 TTKEAAEL-LGVSPSTLRRWVKE 23 (49)
T ss_pred CHHHHHHH-HCcCHHHHHHHHHc
Confidence 67899995 99999999988764
No 385
>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=36.59 E-value=90 Score=21.17 Aligned_cols=30 Identities=7% Similarity=0.228 Sum_probs=25.6
Q ss_pred cCCCCCHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 163 ENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 163 ~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
.+-+.+..|++.. ++++..++++..+.|.+
T Consensus 10 ~~~~~~~~eLa~~-l~vS~~tv~~~l~~L~~ 39 (69)
T TIGR00122 10 ADNPFSGEKLGEA-LGMSRTAVNKHIQTLRE 39 (69)
T ss_pred HcCCcCHHHHHHH-HCCCHHHHHHHHHHHHH
Confidence 3446789999994 99999999999999965
No 386
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=36.47 E-value=18 Score=28.04 Aligned_cols=20 Identities=20% Similarity=0.624 Sum_probs=10.5
Q ss_pred eeEeCCCCceEcCCCccccc
Q 023713 15 VVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 15 vv~D~~~G~~vC~~CG~Vl~ 34 (278)
+......++.-|.+||.++.
T Consensus 62 l~Ie~~p~~~~C~~C~~~~~ 81 (115)
T COG0375 62 LHIEEEPAECWCLDCGQEVE 81 (115)
T ss_pred EEEEEeccEEEeccCCCeec
Confidence 44444555555666654443
No 387
>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=36.20 E-value=23 Score=29.93 Aligned_cols=23 Identities=17% Similarity=0.627 Sum_probs=14.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECG 30 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG 30 (278)
..||.|++.. .+.. +.-.|..|+
T Consensus 100 ~~C~~C~G~G-~~i~---~~~~C~~C~ 122 (186)
T TIGR02642 100 CKCPRCRGTG-LIQR---RQRECDTCA 122 (186)
T ss_pred CcCCCCCCee-EEec---CCCCCCCCC
Confidence 6899998833 3332 125688884
No 388
>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=36.05 E-value=99 Score=23.17 Aligned_cols=34 Identities=12% Similarity=0.036 Sum_probs=29.2
Q ss_pred HHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHH
Q 023713 160 CRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (278)
Q Consensus 160 cR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~ 194 (278)
+...+-+.++.|++.. ++++..++.+.++.|.+.
T Consensus 37 ~~~~~~~~t~~eL~~~-l~~~~stvs~~i~~Le~k 70 (109)
T TIGR01889 37 LENNEGKLTLKEIIKE-ILIKQSALVKIIKKLSKK 70 (109)
T ss_pred hhccCCcCcHHHHHHH-HCCCHHHHHHHHHHHHHC
Confidence 4566678999999995 999999999999999753
No 389
>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=35.95 E-value=63 Score=21.61 Aligned_cols=29 Identities=10% Similarity=0.166 Sum_probs=23.0
Q ss_pred CCCC-CHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 164 NKPR-TVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 164 ~~p~-tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
|... +..++++. ++++..+++++++.|..
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 3456 88999995 99999999999999875
No 390
>COG5134 Uncharacterized conserved protein [Function unknown]
Probab=35.85 E-value=28 Score=29.99 Aligned_cols=25 Identities=16% Similarity=0.272 Sum_probs=20.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCC
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSE 28 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~ 28 (278)
..||.|+.+-.+-+|+.+|++|=..
T Consensus 80 I~C~~C~n~i~~RTDPkN~~YV~Es 104 (272)
T COG5134 80 IKCHLCSNPIDVRTDPKNTEYVVES 104 (272)
T ss_pred EEccCCCCceeeecCCCCceEEEec
Confidence 3699999866788899999988655
No 391
>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=35.54 E-value=20 Score=25.51 Aligned_cols=10 Identities=20% Similarity=0.979 Sum_probs=3.0
Q ss_pred CCCCCCCCCC
Q 023713 2 ADSYCADCKR 11 (278)
Q Consensus 2 ~~~~Cp~Cg~ 11 (278)
....||.||.
T Consensus 23 ~k~FCp~CGn 32 (73)
T PF08772_consen 23 TKQFCPKCGN 32 (73)
T ss_dssp S--S-SSS--
T ss_pred CceeCcccCC
Confidence 3455666665
No 392
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=35.51 E-value=2.9e+02 Score=23.80 Aligned_cols=88 Identities=14% Similarity=0.168 Sum_probs=50.5
Q ss_pred hCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHH
Q 023713 139 DQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFC 218 (278)
Q Consensus 139 ~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~ 218 (278)
..|+.+.|....+..|=+.+-=-.-.+|.+..|+.+. -||-.|+-.=+ |...+| .|.+--+..|.|++
T Consensus 78 ~iGlyr~KAk~I~~~~~~l~e~~~g~vP~~~~eL~~L-PGVGrKTAnvV---L~~a~g--------~p~i~VDTHV~Rvs 145 (211)
T COG0177 78 SIGLYRNKAKNIKELARILLEKFGGEVPDTREELLSL-PGVGRKTANVV---LSFAFG--------IPAIAVDTHVHRVS 145 (211)
T ss_pred hcCCcHHHHHHHHHHHHHHHHHcCCCCCchHHHHHhC-CCcchHHHHHH---HHhhcC--------CCcccccchHHHHH
Confidence 4555554433333333332222223689999999884 89988876433 223344 33444566899999
Q ss_pred hhcCCCH--HHHHHHHHHHHHh
Q 023713 219 SNLGMTN--QAVKAAQEAVQKS 238 (278)
Q Consensus 219 ~~L~l~~--~v~~~A~~i~~~~ 238 (278)
+++||.+ .....-+.+.+.+
T Consensus 146 ~R~gl~~~~~p~~ve~~L~~~i 167 (211)
T COG0177 146 NRLGLVPGKTPEEVEEALMKLI 167 (211)
T ss_pred HHhCCCCCCCHHHHHHHHHHHC
Confidence 9999974 2333333444444
No 393
>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=35.44 E-value=1.5e+02 Score=20.57 Aligned_cols=42 Identities=19% Similarity=0.385 Sum_probs=33.9
Q ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHh
Q 023713 168 TVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCS 219 (278)
Q Consensus 168 tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~ 219 (278)
.+++||+. .+++..++.+.|..-...|.- .....|||+=|+.
T Consensus 9 ~i~~iA~~-t~~P~e~V~~my~dt~~~l~~---------~ARV~DYl~lfaa 50 (66)
T PF12085_consen 9 VIRSIAEE-TGTPAETVRRMYDDTMRELSS---------GARVHDYLPLFAA 50 (66)
T ss_pred HHHHHHHH-HCCCHHHHHHHHHHHHHHHHc---------CCchhhhHHHHHH
Confidence 46789985 899999999999988888753 3567899988764
No 394
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=35.29 E-value=33 Score=22.88 Aligned_cols=32 Identities=22% Similarity=0.394 Sum_probs=18.1
Q ss_pred CCCCCCCCCcee--EeC--CCCceEcCCCcccccccccc
Q 023713 5 YCADCKRLTEVV--FDH--SAGDTICSECGLVLEAYSVD 39 (278)
Q Consensus 5 ~Cp~Cg~~~~vv--~D~--~~G~~vC~~CG~Vl~e~~id 39 (278)
.||.||+.+.+- .|. .+=-+.|..|-. |.+|+
T Consensus 6 ~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~---EtlI~ 41 (55)
T PF14205_consen 6 LCPICGNKTRLKIREDTVLKNFPLYCPKCKQ---ETLID 41 (55)
T ss_pred ECCCCCCccceeeecCceeccccccCCCCCc---eEEEE
Confidence 599999744332 221 344567888863 44444
No 395
>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=35.21 E-value=28 Score=22.67 Aligned_cols=29 Identities=24% Similarity=0.614 Sum_probs=22.3
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAY 36 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~ 36 (278)
..|+.|+.. ++.-....-|..||.|+=..
T Consensus 3 ~~C~~C~~~----F~~~~rk~~Cr~Cg~~~C~~ 31 (57)
T cd00065 3 SSCMGCGKP----FTLTRRRHHCRNCGRIFCSK 31 (57)
T ss_pred CcCcccCcc----ccCCccccccCcCcCCcChH
Confidence 579999973 55567788999999998543
No 396
>PRK07591 threonine synthase; Validated
Probab=34.74 E-value=18 Score=34.45 Aligned_cols=26 Identities=27% Similarity=0.525 Sum_probs=19.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
.+|+.||.. ++...- ..|.+||-.|+
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 579999983 444333 88999998775
No 397
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=34.72 E-value=8.5 Score=32.20 Aligned_cols=32 Identities=31% Similarity=0.611 Sum_probs=22.1
Q ss_pred CCCCCCCCCCCceeEeC-CCCceEcCCCccccccc
Q 023713 3 DSYCADCKRLTEVVFDH-SAGDTICSECGLVLEAY 36 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~-~~G~~vC~~CG~Vl~e~ 36 (278)
...||.|... .-+|. -+-+..|+.||.+|++.
T Consensus 113 ~y~C~~~~~r--~sfdeA~~~~F~Cp~Cg~~L~~~ 145 (176)
T COG1675 113 YYVCPNCHVK--YSFDEAMELGFTCPKCGEDLEEY 145 (176)
T ss_pred ceeCCCCCCc--ccHHHHHHhCCCCCCCCchhhhc
Confidence 3579998863 44553 23348999999999643
No 398
>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=34.59 E-value=1.4e+02 Score=23.86 Aligned_cols=32 Identities=19% Similarity=0.215 Sum_probs=27.0
Q ss_pred CCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhh
Q 023713 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEA 197 (278)
Q Consensus 165 ~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~ 197 (278)
...|..|||+. ++++..++.+..+...+.|..
T Consensus 20 ~GlTq~EIAe~-LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 20 KGLSQKEIAKE-LKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCHHHHHHH-HCcCHHHHHHHHHhHHHHHHH
Confidence 55699999995 999999999888887777763
No 399
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=34.47 E-value=58 Score=25.71 Aligned_cols=32 Identities=16% Similarity=0.140 Sum_probs=27.5
Q ss_pred hcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHH
Q 023713 162 QENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (278)
Q Consensus 162 ~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~ 194 (278)
+.+.+.++.+||+. .|++..++.+.+++|.+.
T Consensus 18 ~~d~r~~~~eia~~-lglS~~~v~~Ri~~L~~~ 49 (154)
T COG1522 18 QEDARISNAELAER-VGLSPSTVLRRIKRLEEE 49 (154)
T ss_pred HHhCCCCHHHHHHH-HCCCHHHHHHHHHHHHHC
Confidence 44556999999995 999999999999999863
No 400
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=34.37 E-value=1.1e+02 Score=22.06 Aligned_cols=35 Identities=3% Similarity=0.010 Sum_probs=29.4
Q ss_pred hcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhh
Q 023713 162 QENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (278)
Q Consensus 162 ~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~ 198 (278)
..+.+++-.++++. +|++...|++.++.|+ .-|++
T Consensus 15 ~~~~~~SGe~La~~-LgiSRtaVwK~Iq~Lr-~~G~~ 49 (79)
T COG1654 15 LTGNFVSGEKLAEE-LGISRTAVWKHIQQLR-EEGVD 49 (79)
T ss_pred cCCCcccHHHHHHH-HCccHHHHHHHHHHHH-HhCCc
Confidence 45678999999995 9999999999999997 44544
No 401
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=34.07 E-value=1.2e+02 Score=25.32 Aligned_cols=33 Identities=21% Similarity=0.146 Sum_probs=27.0
Q ss_pred CCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhh
Q 023713 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (278)
Q Consensus 165 ~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~ 198 (278)
...|-+|||.. ++++..++....+.|.+.||.+
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 55788888885 8888888888888888888864
No 402
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=33.77 E-value=87 Score=29.97 Aligned_cols=41 Identities=22% Similarity=0.212 Sum_probs=32.7
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHHc-CCCHHHHHHHHHHHHHHhhh
Q 023713 154 ACLYIACRQENKPRTVKEFCSVAN-GTTKKEIGRAKEFIVKHLEA 197 (278)
Q Consensus 154 AclY~acR~~~~p~tl~eia~~~~-~v~~~~i~~~~~~l~~~L~~ 197 (278)
.+.|++-+. ...|+.+|+.. + +-+..++.++++++.+.+..
T Consensus 392 iamyl~~~~--~~~s~~~Ig~~-fg~rdhstV~~a~~~i~~~~~~ 433 (450)
T PRK00149 392 IAMYLAKEL--TDLSLPEIGRA-FGGRDHTTVLHAVRKIEKLLEE 433 (450)
T ss_pred HHHHHHHHh--cCCCHHHHHHH-cCCCCHhHHHHHHHHHHHHHHh
Confidence 466777554 44589999995 6 69999999999999998754
No 403
>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=33.77 E-value=75 Score=27.77 Aligned_cols=30 Identities=7% Similarity=0.029 Sum_probs=22.3
Q ss_pred CCCHHHHHHHHcCCCHHHHHHHHHHHHHHhh
Q 023713 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKHLE 196 (278)
Q Consensus 166 p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~ 196 (278)
..|.+|||.. +|+++.++...+..-++.|.
T Consensus 177 g~S~~EIA~~-Lgis~~TVk~rl~RAr~~Lr 206 (244)
T TIGR03001 177 GLSMDRIGAM-YQVHRSTVSRWVAQARERLL 206 (244)
T ss_pred CCCHHHHHHH-HCcCHHHHHHHHHHHHHHHH
Confidence 4679999995 99999888766665555443
No 404
>PRK13503 transcriptional activator RhaS; Provisional
Probab=33.76 E-value=73 Score=27.75 Aligned_cols=39 Identities=3% Similarity=-0.015 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHH
Q 023713 151 IVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFI 191 (278)
Q Consensus 151 ~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l 191 (278)
+-.+.=|+- ..-..++|+.|+|+. +++++..+.+.+++.
T Consensus 173 i~~~~~~I~-~~~~~~~tl~~lA~~-~~lS~~~l~r~Fk~~ 211 (278)
T PRK13503 173 LNQLLAWLE-DHFAEEVNWEALADQ-FSLSLRTLHRQLKQQ 211 (278)
T ss_pred HHHHHHHHH-HhhcCCCCHHHHHHH-HCCCHHHHHHHHHHH
Confidence 334444443 334568999999995 999999999988753
No 405
>PHA00689 hypothetical protein
Probab=33.72 E-value=29 Score=22.55 Aligned_cols=27 Identities=22% Similarity=0.548 Sum_probs=17.1
Q ss_pred CCceEcCCCcccccccccccccchhhcc
Q 023713 21 AGDTICSECGLVLEAYSVDETSEWRIFA 48 (278)
Q Consensus 21 ~G~~vC~~CG~Vl~e~~id~~~ewr~f~ 48 (278)
---+.|..||.- .-+.-|+|.||.-..
T Consensus 15 pravtckrcgkt-glrweddggewvlme 41 (62)
T PHA00689 15 PRAVTCKRCGKT-GLRWEDDGGEWVLME 41 (62)
T ss_pred cceeehhhcccc-CceeecCCCcEEEEe
Confidence 345678888765 345667777885543
No 406
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=33.64 E-value=18 Score=24.72 Aligned_cols=23 Identities=26% Similarity=0.707 Sum_probs=14.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGL 31 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~ 31 (278)
..|..||.. +.- --...|..||.
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 458888873 221 22567888886
No 407
>PRK10130 transcriptional regulator EutR; Provisional
Probab=33.62 E-value=3.9e+02 Score=24.73 Aligned_cols=42 Identities=19% Similarity=0.296 Sum_probs=31.8
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHH
Q 023713 148 QEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFI 191 (278)
Q Consensus 148 ~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l 191 (278)
...+..+.=|+--. -..|+|+.|||.. ++++..+|.+.|++.
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 34455666666543 4568999999995 999999999998864
No 408
>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=33.44 E-value=49 Score=22.55 Aligned_cols=43 Identities=16% Similarity=0.198 Sum_probs=26.6
Q ss_pred CHHHHHHHHcCCCHHHHH-HHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHHH
Q 023713 168 TVKEFCSVANGTTKKEIG-RAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQA 227 (278)
Q Consensus 168 tl~eia~~~~~v~~~~i~-~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v 227 (278)
+.+|+|+. ++++..+|. ...++ ..-|.+++.+++..++++-+-
T Consensus 14 ~~~~lA~~-lgis~st~s~~~~~r----------------~~~P~~~l~~ia~~~gvsl~W 57 (66)
T PF07022_consen 14 SDKELAER-LGISKSTLSNNWKKR----------------GSIPAEWLIKIALETGVSLDW 57 (66)
T ss_dssp SCHHHHCC-TT--HHHHH-HHHHS----------------SS--HHHHHHHHHHH---HHH
T ss_pred CHHHHHHH-hCcCHHHhhHHHHhC----------------CCCCHHHHHHHHHHHCcCHHH
Confidence 66799994 999999998 44321 123689999999999987653
No 409
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=33.41 E-value=15 Score=34.16 Aligned_cols=12 Identities=25% Similarity=0.636 Sum_probs=9.1
Q ss_pred CCCCCCCCCCCC
Q 023713 1 MADSYCADCKRL 12 (278)
Q Consensus 1 ~~~~~Cp~Cg~~ 12 (278)
|.++.|+.||.+
T Consensus 4 ~~~~~C~~CGr~ 15 (355)
T COG1499 4 ASTILCVRCGRS 15 (355)
T ss_pred CcccEeccCCCc
Confidence 346789999974
No 410
>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=33.36 E-value=46 Score=20.23 Aligned_cols=21 Identities=14% Similarity=0.273 Sum_probs=15.9
Q ss_pred CHHHHHHHHcCCCHHHHHHHHH
Q 023713 168 TVKEFCSVANGTTKKEIGRAKE 189 (278)
Q Consensus 168 tl~eia~~~~~v~~~~i~~~~~ 189 (278)
|+.|+|+. +||++.+|+..-+
T Consensus 1 ti~e~A~~-~gvs~~tlR~ye~ 21 (38)
T PF00376_consen 1 TIGEVAKL-LGVSPRTLRYYER 21 (38)
T ss_dssp EHHHHHHH-HTS-HHHHHHHHH
T ss_pred CHHHHHHH-HCCCHHHHHHHHH
Confidence 46899995 9999999977643
No 411
>PRK04330 hypothetical protein; Provisional
Probab=33.26 E-value=2e+02 Score=21.21 Aligned_cols=65 Identities=12% Similarity=0.199 Sum_probs=49.7
Q ss_pred chhHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCH
Q 023713 102 PDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTK 181 (278)
Q Consensus 102 ~er~l~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~ 181 (278)
.+..+.++...++++.+--.+|.++...|.+....+.+.+ .++..-||.++++ |.||+. .-+++.
T Consensus 7 ~e~~ik~~~~~L~~I~~D~sVPRNIRraa~ea~~~L~~e~----~~~~vRaA~AIs~----------LdeIs~-DPNmP~ 71 (88)
T PRK04330 7 NEEKIKQAIQMLEEIINDTSVPRNIRRAATEAKEILLNEE----ESPGVRAATAISI----------LDEISN-DPNMPL 71 (88)
T ss_pred hHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHhCcC----cchhHHHHHHHHH----------HHHhhc-CCCCCh
Confidence 4677889999999999999999999999999988887665 3344566666664 566765 355554
No 412
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=33.13 E-value=18 Score=28.31 Aligned_cols=18 Identities=22% Similarity=0.648 Sum_probs=9.8
Q ss_pred ceeEeCCCCceEcCCCccc
Q 023713 14 EVVFDHSAGDTICSECGLV 32 (278)
Q Consensus 14 ~vv~D~~~G~~vC~~CG~V 32 (278)
.+......+...| +||..
T Consensus 61 ~L~I~~vp~~~~C-~Cg~~ 78 (124)
T PRK00762 61 DLIVEMIPVEIEC-ECGYE 78 (124)
T ss_pred EEEEEecCeeEEe-eCcCc
Confidence 4555555556666 66633
No 413
>KOG0856 consensus Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones]
Probab=33.11 E-value=23 Score=28.31 Aligned_cols=32 Identities=25% Similarity=0.585 Sum_probs=27.1
Q ss_pred CCCCceEcCCCcccc--cccccccccchhhccCC
Q 023713 19 HSAGDTICSECGLVL--EAYSVDETSEWRIFANE 50 (278)
Q Consensus 19 ~~~G~~vC~~CG~Vl--~e~~id~~~ewr~f~~~ 50 (278)
.+.|.++|..||.-| .+.-+|.|--|.+|.+.
T Consensus 50 ~e~GvY~C~~C~~pLykS~tKfdsgcGWPAF~e~ 83 (146)
T KOG0856|consen 50 FEEGVYVCAGCGTPLYKSTTKFDSGCGWPAFFEA 83 (146)
T ss_pred cCCceEEEeecCCccccccccccCCCCCchhhhc
Confidence 489999999999987 45568999999999864
No 414
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=32.99 E-value=53 Score=23.41 Aligned_cols=33 Identities=15% Similarity=0.128 Sum_probs=26.9
Q ss_pred cCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhh
Q 023713 163 ENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLE 196 (278)
Q Consensus 163 ~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~ 196 (278)
.+-+.++.++|+. ..++..++.+..+.+.+.|.
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 5678899999995 99999999999999998775
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=32.83 E-value=54 Score=20.26 Aligned_cols=21 Identities=14% Similarity=0.317 Sum_probs=17.7
Q ss_pred CHHHHHHHHcCCCHHHHHHHHH
Q 023713 168 TVKEFCSVANGTTKKEIGRAKE 189 (278)
Q Consensus 168 tl~eia~~~~~v~~~~i~~~~~ 189 (278)
++.|+|.. +|++..+|+...+
T Consensus 2 ~~~e~a~~-~gv~~~tlr~~~~ 22 (49)
T cd04761 2 TIGELAKL-TGVSPSTLRYYER 22 (49)
T ss_pred cHHHHHHH-HCcCHHHHHHHHH
Confidence 67899995 9999999987754
No 416
>PLN02569 threonine synthase
Probab=32.80 E-value=24 Score=34.39 Aligned_cols=26 Identities=12% Similarity=0.073 Sum_probs=20.8
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
..|+.||.. ++...-...| .||-.|+
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 679999973 6666778899 7998884
No 417
>COG5525 Bacteriophage tail assembly protein [General function prediction only]
Probab=32.69 E-value=22 Score=35.21 Aligned_cols=32 Identities=25% Similarity=0.583 Sum_probs=22.8
Q ss_pred CCCCCCCCCceeEeCC------------CCceEcCCCccccccc
Q 023713 5 YCADCKRLTEVVFDHS------------AGDTICSECGLVLEAY 36 (278)
Q Consensus 5 ~Cp~Cg~~~~vv~D~~------------~G~~vC~~CG~Vl~e~ 36 (278)
.||+||...-+.++.. .-.+.|..|+.++.+.
T Consensus 229 pCPHCGe~q~l~~~e~~~~~g~~~~~~~~~~~~c~h~~~~i~~~ 272 (611)
T COG5525 229 PCPHCGEEQQLKFGEKSGPRGLKDTPAEAAFIQCEHCGCVIRPK 272 (611)
T ss_pred eCCCCCchhhccccccCCCcCcccchhhhhhhhccccCceeeee
Confidence 5999997655555322 2346899999999873
No 418
>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=32.64 E-value=70 Score=26.72 Aligned_cols=34 Identities=12% Similarity=0.202 Sum_probs=29.4
Q ss_pred HHhcCCCCCHHHHHHHHcCCC-HHHHHHHHHHHHHH
Q 023713 160 CRQENKPRTVKEFCSVANGTT-KKEIGRAKEFIVKH 194 (278)
Q Consensus 160 cR~~~~p~tl~eia~~~~~v~-~~~i~~~~~~l~~~ 194 (278)
.+.++.|.|++|||. .++++ ..++.+.++.|.+.
T Consensus 19 ~~~~~~~~~~~ela~-~~~~~s~~tv~~~l~~L~~~ 53 (199)
T TIGR00498 19 IESTGYPPSIREIAR-AVGLRSPSAAEEHLKALERK 53 (199)
T ss_pred HHhcCCCCcHHHHHH-HhCCCChHHHHHHHHHHHHC
Confidence 366889999999999 49998 99999999998763
No 419
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=32.45 E-value=26 Score=31.61 Aligned_cols=33 Identities=24% Similarity=0.588 Sum_probs=27.8
Q ss_pred eCCCCceEcCCCcccc--cccccccccchhhccCC
Q 023713 18 DHSAGDTICSECGLVL--EAYSVDETSEWRIFANE 50 (278)
Q Consensus 18 D~~~G~~vC~~CG~Vl--~e~~id~~~ewr~f~~~ 50 (278)
..+.|..+|..||.-| .+.-+|.|.-|.+|.+.
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 3589999999999988 55578999999999853
No 420
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=32.45 E-value=1.1e+02 Score=18.08 Aligned_cols=46 Identities=17% Similarity=0.308 Sum_probs=32.4
Q ss_pred CCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHH
Q 023713 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQ 226 (278)
Q Consensus 165 ~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~ 226 (278)
...+..+++.. .+++...|.+.. .- ....+.+.+.+++..|+++.+
T Consensus 9 ~~~s~~~la~~-~~i~~~~i~~~~-------~~--------~~~~~~~~~~~i~~~~~~~~~ 54 (56)
T smart00530 9 KGLTQEELAEK-LGVSRSTLSRIE-------NG--------KRKPSLETLKKLAKALGVSLD 54 (56)
T ss_pred cCCCHHHHHHH-hCCCHHHHHHHH-------CC--------CCCCCHHHHHHHHHHhCCChh
Confidence 45788999984 899988886531 11 111267888999999998764
No 421
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=32.23 E-value=25 Score=23.20 Aligned_cols=31 Identities=19% Similarity=0.542 Sum_probs=19.0
Q ss_pred CCCCCCCCCC--CceeEeC--CCCceEcCCCcccc
Q 023713 3 DSYCADCKRL--TEVVFDH--SAGDTICSECGLVL 33 (278)
Q Consensus 3 ~~~Cp~Cg~~--~~vv~D~--~~G~~vC~~CG~Vl 33 (278)
...|..|+-. +..+-+- ..+.+.|.+||.+|
T Consensus 22 ~~~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 22 GGTCSGCHMELPPQELNEIRKGDEIVFCPNCGRIL 56 (56)
T ss_pred CCccCCCCEEcCHHHHHHHHcCCCeEECcCCCccC
Confidence 3678888842 1111121 34679999999875
No 422
>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=32.04 E-value=92 Score=18.87 Aligned_cols=28 Identities=14% Similarity=0.262 Sum_probs=22.9
Q ss_pred CCHHHHHHHHcCCCHHHHHHHHHHHHHHh
Q 023713 167 RTVKEFCSVANGTTKKEIGRAKEFIVKHL 195 (278)
Q Consensus 167 ~tl~eia~~~~~v~~~~i~~~~~~l~~~L 195 (278)
.+..+||.. ++++..+|.+......+.+
T Consensus 27 ~~~~~ia~~-~~~s~~~i~~~~~~~~~~l 54 (55)
T cd06171 27 LSYEEIAEI-LGISRSTVRQRLHRALKKL 54 (55)
T ss_pred CCHHHHHHH-HCcCHHHHHHHHHHHHHHc
Confidence 678999995 8999999988887776554
No 423
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=31.98 E-value=99 Score=25.13 Aligned_cols=72 Identities=13% Similarity=0.078 Sum_probs=46.6
Q ss_pred HHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhhcccccc-----------cCCCCHHHHHHHHHh-hcC
Q 023713 155 CLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVE-----------MGTIHASDYLRRFCS-NLG 222 (278)
Q Consensus 155 clY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~~~~~~~-----------~~~~~p~~~i~r~~~-~L~ 222 (278)
+||..-+ .+.+...+|||.. ++|+..++..++++|.+.==++-.++.. .....-...+.+|.. .||
T Consensus 14 ~Iy~l~~-~~~~~~~~diA~~-L~Vsp~sVt~ml~rL~~~GlV~~~~y~gi~LT~~G~~~a~~~~r~hrlle~fL~~~lg 91 (154)
T COG1321 14 TIYELLE-EKGFARTKDIAER-LKVSPPSVTEMLKRLERLGLVEYEPYGGVTLTEKGREKAKELLRKHRLLERFLVDVLG 91 (154)
T ss_pred HHHHHHh-ccCcccHHHHHHH-hCCCcHHHHHHHHHHHHCCCeEEecCCCeEEChhhHHHHHHHHHHHHHHHHHHHHHhC
Confidence 4665555 7778899999995 9999999999999997521111001110 111234557777777 589
Q ss_pred CCHHHH
Q 023713 223 MTNQAV 228 (278)
Q Consensus 223 l~~~v~ 228 (278)
++.+..
T Consensus 92 ~~~~~~ 97 (154)
T COG1321 92 LDWEEA 97 (154)
T ss_pred CCHHHH
Confidence 886643
No 424
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=31.94 E-value=24 Score=23.81 Aligned_cols=24 Identities=25% Similarity=0.631 Sum_probs=14.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLV 32 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V 32 (278)
..|..||.. +.- .-.-.|..||.=
T Consensus 17 ~~CRRCGr~-syh----v~k~~CaaCGfg 40 (61)
T COG2126 17 IRCRRCGRR-SYH----VRKKYCAACGFG 40 (61)
T ss_pred ehhhhccch-hee----eccceecccCCC
Confidence 358888873 221 225578888875
No 425
>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=31.80 E-value=90 Score=22.59 Aligned_cols=71 Identities=14% Similarity=0.182 Sum_probs=40.3
Q ss_pred CCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhhc--cc--ccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh
Q 023713 167 RTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEM--GQ--SVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED 240 (278)
Q Consensus 167 ~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~~--~~--~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~ 240 (278)
.++.|+|.. +|+++.+|+...+. ..+.-.. +. .++.....--.+|.++.+.+|++-+.......+.+.+..
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~~~~~~ 76 (91)
T cd04766 2 YVISVAAEL-SGMHPQTLRLYERL--GLLSPSRTDGGTRRYSERDIERLRRIQRLTQELGVNLAGVKRILELEEELAE 76 (91)
T ss_pred cCHHHHHHH-HCcCHHHHHHHHHC--CCcCCCcCCCCCeeECHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHH
Confidence 578999995 99999999888542 1111000 00 000001112235666667788887766666666665543
No 426
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=31.74 E-value=74 Score=21.55 Aligned_cols=25 Identities=16% Similarity=0.276 Sum_probs=20.7
Q ss_pred CCCHHHHHHHHcCCCHHHHHHHHHHH
Q 023713 166 PRTVKEFCSVANGTTKKEIGRAKEFI 191 (278)
Q Consensus 166 p~tl~eia~~~~~v~~~~i~~~~~~l 191 (278)
|.++.++|.. ++++...+.+.++..
T Consensus 1 ~~~~~~la~~-~~~s~~~l~~~f~~~ 25 (84)
T smart00342 1 PLTLEDLAEA-LGMSPRHLQRLFKKE 25 (84)
T ss_pred CCCHHHHHHH-hCCCHHHHHHHHHHH
Confidence 5789999995 899999988887754
No 427
>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=31.73 E-value=20 Score=23.94 Aligned_cols=23 Identities=26% Similarity=0.819 Sum_probs=13.5
Q ss_pred CCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713 5 YCADCKRLTEVVFDHSAGDTICSECGLV 32 (278)
Q Consensus 5 ~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V 32 (278)
.|..||+. + +- --.-.|..||.=
T Consensus 17 ~CrRCG~~-s--yH--~qK~~CasCGyp 39 (55)
T PF01907_consen 17 LCRRCGRR-S--YH--IQKKTCASCGYP 39 (55)
T ss_dssp E-TTTSSE-E--EE--TTTTEETTTBTT
T ss_pred eecccCCe-e--ee--cCCCcccccCCC
Confidence 47888872 2 22 235678888864
No 428
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=31.31 E-value=1.2e+02 Score=21.51 Aligned_cols=28 Identities=21% Similarity=0.335 Sum_probs=25.2
Q ss_pred CCCHHHHHHHHcCCCHHHHHHHHHHHHHH
Q 023713 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (278)
Q Consensus 166 p~tl~eia~~~~~v~~~~i~~~~~~l~~~ 194 (278)
+.+..+|+.. ++++..+|.+.++.|.+.
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 429
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=31.18 E-value=25 Score=35.99 Aligned_cols=26 Identities=27% Similarity=0.608 Sum_probs=15.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGL 31 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~ 31 (278)
..|++||-...+..+ ..| ..|+.||-
T Consensus 642 ~~C~~CG~~Ge~~~~-~~~-~~CP~CG~ 667 (711)
T PRK09263 642 DECYECGFTGEFECT-EKG-FTCPKCGN 667 (711)
T ss_pred cccCCCCCCccccCC-CCC-CcCcCCCC
Confidence 579999963222121 223 68999985
No 430
>KOG0310 consensus Conserved WD40 repeat-containing protein [Function unknown]
Probab=31.16 E-value=3.7e+02 Score=26.06 Aligned_cols=118 Identities=19% Similarity=0.115 Sum_probs=74.5
Q ss_pred HHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHH
Q 023713 113 ISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIV 192 (278)
Q Consensus 113 I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~ 192 (278)
|.+=..+++|+.-=...-..=++++.+.-+-.++.++.++|+.-++.-|- -+.....|-++++|...+..|.
T Consensus 345 v~n~~~r~~L~~~Dk~Lk~F~~kkALd~vl~~~~~pelvvavl~eL~~Rg--------~l~~AL~grde~eL~~lLnfl~ 416 (487)
T KOG0310|consen 345 VVNEVKRLKLTYFDKRLKQFKHKKALDHVLEPKKDPELVVAVLSELVHRG--------GLRRALAGRDESELAPLLNFLV 416 (487)
T ss_pred EeccccccCCchHHHHHhhhhHHHHHHHHhcccCChhHHHHHHHHHHHhh--------HHHHHhcCccHHHHHHHHHHHH
Confidence 33444456776422222233344554443333788999999999988662 1223346889999999999999
Q ss_pred HHhhhhcccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhh
Q 023713 193 KHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSED 240 (278)
Q Consensus 193 ~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~ 240 (278)
+.+.... ...+-..-...++.-|...++.++.+.++-+.|-..+.+
T Consensus 417 ~~l~~~r--f~~~L~~~~~~iLd~Y~~~i~~s~~l~k~i~~L~~~V~~ 462 (487)
T KOG0310|consen 417 KNLTVVR--FASILMEVVSVILDLYARDIEGSPMLAKLIQALRGKVEQ 462 (487)
T ss_pred hhccchh--hHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHHHHH
Confidence 9887542 111111224567788888899999888777777666554
No 431
>PRK11032 hypothetical protein; Provisional
Probab=31.10 E-value=22 Score=29.27 Aligned_cols=15 Identities=27% Similarity=0.731 Sum_probs=12.8
Q ss_pred CCCceEcCCCccccc
Q 023713 20 SAGDTICSECGLVLE 34 (278)
Q Consensus 20 ~~G~~vC~~CG~Vl~ 34 (278)
.-|.+||.+||.-+.
T Consensus 121 g~G~LvC~~Cg~~~~ 135 (160)
T PRK11032 121 GLGNLVCEKCHHHLA 135 (160)
T ss_pred ecceEEecCCCCEEE
Confidence 479999999998863
No 432
>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=31.08 E-value=21 Score=37.44 Aligned_cols=23 Identities=22% Similarity=0.423 Sum_probs=17.3
Q ss_pred CCCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl 33 (278)
..+||.||.. + =...|.+||.-.
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 3689999983 2 267899999763
No 433
>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=31.02 E-value=65 Score=19.59 Aligned_cols=22 Identities=27% Similarity=0.235 Sum_probs=18.3
Q ss_pred CCHHHHHHHHcCCCHHHHHHHHH
Q 023713 167 RTVKEFCSVANGTTKKEIGRAKE 189 (278)
Q Consensus 167 ~tl~eia~~~~~v~~~~i~~~~~ 189 (278)
.|+.|+|.. +|++..+|.+..+
T Consensus 2 lt~~e~a~~-lgis~~ti~~~~~ 23 (49)
T TIGR01764 2 LTVEEAAEY-LGVSKDTVYRLIH 23 (49)
T ss_pred CCHHHHHHH-HCCCHHHHHHHHH
Confidence 478999995 9999999987764
No 434
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=30.91 E-value=1.3e+02 Score=18.80 Aligned_cols=27 Identities=19% Similarity=0.399 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHhcCCCH-HHHHHHHHHH
Q 023713 108 QAFKSISAMSDRLGLVT-TIKDRANEIY 134 (278)
Q Consensus 108 ~~~~~I~~i~~~L~Lp~-~v~e~A~~i~ 134 (278)
+....+..++...++|. .++++|.+.|
T Consensus 12 el~~~L~~ls~~t~i~~S~Ll~eAle~~ 39 (44)
T PF12651_consen 12 ELYEKLKELSEETGIPKSKLLREALEDY 39 (44)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHH
Confidence 35678999999999995 7788887766
No 435
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=30.80 E-value=1.5e+02 Score=25.16 Aligned_cols=32 Identities=13% Similarity=0.057 Sum_probs=19.8
Q ss_pred CCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhh
Q 023713 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (278)
Q Consensus 166 p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~ 198 (278)
..|-+|||+. ++++++++......|.+.||.+
T Consensus 149 G~snkeIA~~-L~iS~~TV~~h~~~I~~KLgv~ 180 (207)
T PRK11475 149 GYSMPQIAEQ-LERNIKTIRAHKFNVMSKLGVS 180 (207)
T ss_pred CCCHHHHHHH-HCCCHHHHHHHHHHHHHHcCCC
Confidence 4566666663 6666666666666666666543
No 436
>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=30.72 E-value=1.6e+02 Score=19.90 Aligned_cols=39 Identities=15% Similarity=0.191 Sum_probs=25.6
Q ss_pred HHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 153 AACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 153 AAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
++-|+-..-..| +.|+.+|.. .++++.+.+.++.-.|.+
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 334443433344 688999999 489999999999877765
No 437
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=30.61 E-value=2.1e+02 Score=25.31 Aligned_cols=80 Identities=10% Similarity=0.168 Sum_probs=52.1
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHH--------HHhhhhc--------ccc-----cccCCC
Q 023713 150 AIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIV--------KHLEAEM--------GQS-----VEMGTI 208 (278)
Q Consensus 150 ~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~--------~~L~~~~--------~~~-----~~~~~~ 208 (278)
.+..++-|+-... ..+.++.++|.. ++++...+.|.++... +.+.+.. +.+ ....-.
T Consensus 6 ~i~~~~~~i~~~~-~~~~~l~~lA~~-~~~S~~~l~r~F~~~~g~s~~~yi~~~Rl~~A~~~L~~~~~~i~~iA~~~Gf~ 83 (289)
T PRK15121 6 IIRDLLIWLEGHL-DQPLSLDNVAAK-AGYSKWHLQRMFKDVTGHAIGAYIRARRLSKAAVALRLTSRPILDIALQYRFD 83 (289)
T ss_pred HHHHHHHHHHhcc-cCCCCHHHHHHH-HCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHCCC
Confidence 4555666666443 467999999995 8999999999887652 1111110 000 123445
Q ss_pred CHHHHHHHHHhhcCCCHHHHHHH
Q 023713 209 HASDYLRRFCSNLGMTNQAVKAA 231 (278)
Q Consensus 209 ~p~~~i~r~~~~L~l~~~v~~~A 231 (278)
++..|-..|-...|+++...+..
T Consensus 84 s~~~f~r~Fk~~~g~sP~~~r~~ 106 (289)
T PRK15121 84 SQQTFTRAFKKQFAQTPALYRRS 106 (289)
T ss_pred CHHHHHHHHHHHHCcCHHHHHhc
Confidence 78888888889999988765543
No 438
>PRK15435 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional
Probab=30.55 E-value=2.4e+02 Score=26.25 Aligned_cols=76 Identities=22% Similarity=0.322 Sum_probs=46.6
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHH--------Hhhh-------hcccc-----cccCCCC
Q 023713 150 AIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVK--------HLEA-------EMGQS-----VEMGTIH 209 (278)
Q Consensus 150 ~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~--------~L~~-------~~~~~-----~~~~~~~ 209 (278)
.+..++-|+-- +.+.++.++|.. ++++...+.+.|++... .+.+ ..+.+ ....-.+
T Consensus 86 ~i~~a~~~I~~---~~~lsl~eLA~~-lG~S~~~L~R~Fkk~~G~TP~~yl~~~Rl~~A~~lL~~~~sI~eIA~~~Gf~s 161 (353)
T PRK15435 86 KITHACRLLEQ---ETPVTLEALADQ-VAMSPFHLHRLFKATTGMTPKAWQQAWRARRLREALAKGESVTTSILNAGFPD 161 (353)
T ss_pred HHHHHHHHHHh---CCCCCHHHHHHH-HCCCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCCC
Confidence 45555555532 467899999984 89999999888876421 0000 00000 1133357
Q ss_pred HHHHHHHHHhhcCCCHHHHH
Q 023713 210 ASDYLRRFCSNLGMTNQAVK 229 (278)
Q Consensus 210 p~~~i~r~~~~L~l~~~v~~ 229 (278)
+..|...|-..+|++|...+
T Consensus 162 ~s~F~~~Fkk~~G~TPs~yR 181 (353)
T PRK15435 162 SSSYYRKADETLGMTAKQFR 181 (353)
T ss_pred hHHHHHHHHHHHCcCchhHH
Confidence 77788888888888776554
No 439
>PRK10870 transcriptional repressor MprA; Provisional
Probab=30.52 E-value=1.1e+02 Score=25.31 Aligned_cols=32 Identities=22% Similarity=0.288 Sum_probs=27.7
Q ss_pred HhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 161 RQENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 161 R~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
+..+-+.+..||++. ++++..++.+.+++|.+
T Consensus 66 ~~~~~~it~~eLa~~-l~l~~~tvsr~v~rLe~ 97 (176)
T PRK10870 66 SQENHSIQPSELSCA-LGSSRTNATRIADELEK 97 (176)
T ss_pred cCCCCCcCHHHHHHH-HCCCHHHHHHHHHHHHH
Confidence 445677999999995 99999999999999975
No 440
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=30.31 E-value=25 Score=31.10 Aligned_cols=38 Identities=26% Similarity=0.317 Sum_probs=24.1
Q ss_pred CCCCCCCCCCc---eeEeCCCC-ceEcCCCcc-cccccccccc
Q 023713 4 SYCADCKRLTE---VVFDHSAG-DTICSECGL-VLEAYSVDET 41 (278)
Q Consensus 4 ~~Cp~Cg~~~~---vv~D~~~G-~~vC~~CG~-Vl~e~~id~~ 41 (278)
..|..||.... +......+ -..|..||. ++..+++-.|
T Consensus 123 ~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~~lrP~VV~fG 165 (250)
T COG0846 123 VRCSKCGNQYYDEDVIKFIEDGLIPRCPKCGGPVLRPDVVWFG 165 (250)
T ss_pred eEeCCCcCccchhhhhhhcccCCCCcCccCCCccccCCEEEeC
Confidence 57999986311 11112222 467999999 9988876554
No 441
>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=30.24 E-value=28 Score=32.85 Aligned_cols=26 Identities=31% Similarity=0.659 Sum_probs=15.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAY 36 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~ 36 (278)
..||.||.. ...| ..|.+||..++..
T Consensus 137 g~CP~C~~~------~a~g-~~Ce~cG~~~~~~ 162 (391)
T PF09334_consen 137 GTCPYCGSD------KARG-DQCENCGRPLEPE 162 (391)
T ss_dssp CEETTT--S------SCTT-TEETTTSSBEECC
T ss_pred ccccCcCcc------ccCC-CcccCCCCCcccc
Confidence 568888852 2233 5678888888633
No 442
>smart00400 ZnF_CHCC zinc finger.
Probab=30.17 E-value=61 Score=21.15 Aligned_cols=34 Identities=12% Similarity=0.182 Sum_probs=24.8
Q ss_pred CCCCCCCCC-CceeEeCCCCceEcCCCcccccccccc
Q 023713 4 SYCADCKRL-TEVVFDHSAGDTICSECGLVLEAYSVD 39 (278)
Q Consensus 4 ~~Cp~Cg~~-~~vv~D~~~G~~vC~~CG~Vl~e~~id 39 (278)
..||-++.. +++.++...+...|-.||. ..++|+
T Consensus 3 ~~cPfh~d~~pSf~v~~~kn~~~Cf~cg~--gGd~i~ 37 (55)
T smart00400 3 GLCPFHGEKTPSFSVSPDKQFFHCFGCGA--GGNVIS 37 (55)
T ss_pred ccCcCCCCCCCCEEEECCCCEEEEeCCCC--CCCHHH
Confidence 469999753 4677888889999999983 344554
No 443
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=30.11 E-value=29 Score=30.26 Aligned_cols=37 Identities=19% Similarity=0.388 Sum_probs=21.4
Q ss_pred CCCCCCCCCCceeEeC-CCCceEcCCCcccccccccccc
Q 023713 4 SYCADCKRLTEVVFDH-SAGDTICSECGLVLEAYSVDET 41 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~-~~G~~vC~~CG~Vl~e~~id~~ 41 (278)
..|..|+..-. ..+. ......|..||-++..+++-.|
T Consensus 123 ~~C~~C~~~~~-~~~~~~~~~p~C~~Cgg~lrP~Vv~fg 160 (242)
T PRK00481 123 ARCTKCGQTYD-LDEYLKPEPPRCPKCGGILRPDVVLFG 160 (242)
T ss_pred eeeCCCCCCcC-hhhhccCCCCCCCCCCCccCCCeEECC
Confidence 56999975211 0111 1123349999998888876443
No 444
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=30.03 E-value=1.7e+02 Score=24.63 Aligned_cols=43 Identities=23% Similarity=0.462 Sum_probs=31.6
Q ss_pred HHHHHHHHHHHHHhcCCC-CCHHHHHHHHcCCC-HHHHHHHHHHHHHHhh
Q 023713 149 EAIVAACLYIACRQENKP-RTVKEFCSVANGTT-KKEIGRAKEFIVKHLE 196 (278)
Q Consensus 149 ~~~aAAclY~acR~~~~p-~tl~eia~~~~~v~-~~~i~~~~~~l~~~L~ 196 (278)
..++=|.||++ +-| +|+.+|+.+ ++++ ...+......|.+...
T Consensus 3 ~~~iEAlLF~s----g~pgls~~~La~i-l~~~~~~~~~~~l~~l~~~~~ 47 (186)
T TIGR00281 3 KAIIEALLFVS----GEPGVTLAELVRI-LGKEKAEKLNAIMELLEDYLS 47 (186)
T ss_pred HHHHHHHHHHc----CCCCCCHHHHHHH-hCCCchHHHHHHHHHHHHHHh
Confidence 45677888876 788 999999996 8888 4466666666666543
No 445
>PF12728 HTH_17: Helix-turn-helix domain
Probab=30.03 E-value=65 Score=20.32 Aligned_cols=22 Identities=27% Similarity=0.250 Sum_probs=18.0
Q ss_pred CCHHHHHHHHcCCCHHHHHHHHH
Q 023713 167 RTVKEFCSVANGTTKKEIGRAKE 189 (278)
Q Consensus 167 ~tl~eia~~~~~v~~~~i~~~~~ 189 (278)
.|..|+|+. ++++..+|.+..+
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 9999999877654
No 446
>PRK05638 threonine synthase; Validated
Probab=29.96 E-value=28 Score=33.33 Aligned_cols=25 Identities=32% Similarity=0.743 Sum_probs=17.5
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
..|+.||.. ++.. -...| +||-.++
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 579999983 3322 33889 8997774
No 447
>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=29.90 E-value=20 Score=22.27 Aligned_cols=28 Identities=29% Similarity=0.568 Sum_probs=14.5
Q ss_pred CCCCCCCCCC---ceeEeCCCCceEcCCCcc
Q 023713 4 SYCADCKRLT---EVVFDHSAGDTICSECGL 31 (278)
Q Consensus 4 ~~Cp~Cg~~~---~vv~D~~~G~~vC~~CG~ 31 (278)
.+|.-||.+. ...+.-..|-.||.+|=.
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 5799999741 123344557899988843
No 448
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=29.79 E-value=1.3e+02 Score=26.87 Aligned_cols=56 Identities=14% Similarity=0.165 Sum_probs=38.5
Q ss_pred CCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCC
Q 023713 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGM 223 (278)
Q Consensus 166 p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l 223 (278)
..+.+|||+. +|+++.++...+.+-++.|.-.. +....++......+.+|...++-
T Consensus 131 g~s~~EIA~~-lg~s~~tVk~~l~RAr~~Lr~~~-~~~~~~~~~~~~~v~~f~~A~~~ 186 (293)
T PRK09636 131 GVPFDEIAST-LGRSPAACRQLASRARKHVRAAR-PRFPVSDEEGAELVEAFFAALAS 186 (293)
T ss_pred CCCHHHHHHH-HCCCHHHHHHHHHHHHHHHHhhC-CCCCCCchHHHHHHHHHHHHHHh
Confidence 4789999996 99999888877776666665431 11113344566788888888864
No 449
>cd01411 SIR2H SIR2H: Uncharacterized prokaryotic Sir2 homologs from several gram positive bacterial species and Fusobacteria; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=29.79 E-value=27 Score=30.24 Aligned_cols=36 Identities=22% Similarity=0.404 Sum_probs=23.4
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcccccccccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDET 41 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~~id~~ 41 (278)
..|..|+.. ...+.......|..||-++..+++..|
T Consensus 119 ~~C~~C~~~--~~~~~~~~~p~C~~Cgg~lrP~vv~fg 154 (225)
T cd01411 119 IYCTVCGKT--VDWEEYLKSPYHAKCGGVIRPDIVLYE 154 (225)
T ss_pred eEeCCCCCc--cchhhcCCCCCCCCCCCEeCCCEEEcC
Confidence 569999762 212222224679999999988887544
No 450
>PRK11337 DNA-binding transcriptional repressor RpiR; Provisional
Probab=29.79 E-value=3.9e+02 Score=23.56 Aligned_cols=23 Identities=9% Similarity=0.128 Sum_probs=18.3
Q ss_pred CCHHHHHHHHcCCCHHHHHHHHHH
Q 023713 167 RTVKEFCSVANGTTKKEIGRAKEF 190 (278)
Q Consensus 167 ~tl~eia~~~~~v~~~~i~~~~~~ 190 (278)
.|+.|+|+. ++++..+|.|..++
T Consensus 47 ~si~~lA~~-~~vS~aTi~Rf~kk 69 (292)
T PRK11337 47 TALKDIAEA-LAVSEAMIVKVAKK 69 (292)
T ss_pred cCHHHHHHH-hCCChHHHHHHHHH
Confidence 578899984 89999999887443
No 451
>PRK13500 transcriptional activator RhaR; Provisional
Probab=29.74 E-value=4.1e+02 Score=23.78 Aligned_cols=39 Identities=10% Similarity=0.185 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHH
Q 023713 151 IVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFI 191 (278)
Q Consensus 151 ~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l 191 (278)
+...+-|+- +.-..++++.++|+. +++++..+.+.+|+.
T Consensus 208 l~~i~~yI~-~~~~e~isl~~lA~~-~~iS~~~L~r~FK~~ 246 (312)
T PRK13500 208 LDKLITRLA-ASLKSPFALDKFCDE-ASCSERVLRQQFRQQ 246 (312)
T ss_pred HHHHHHHHH-HcccCCCCHHHHHHH-HCcCHHHHHHHHHHH
Confidence 333444433 334567999999995 999999999998864
No 452
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=29.66 E-value=1.6e+02 Score=25.52 Aligned_cols=33 Identities=12% Similarity=0.195 Sum_probs=28.5
Q ss_pred CCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhh
Q 023713 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (278)
Q Consensus 165 ~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~ 198 (278)
...|-+|||.+ +++++.++....+.+.+.|+..
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 55889999996 8999999999999999988864
No 453
>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=29.61 E-value=1.1e+02 Score=22.40 Aligned_cols=31 Identities=13% Similarity=0.206 Sum_probs=26.1
Q ss_pred hcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 162 QENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 162 ~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
.-....|.+||+.. +|++.-+|.|.-+.|..
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 55566889999995 99999999999888764
No 454
>PHA02325 hypothetical protein
Probab=29.60 E-value=29 Score=23.91 Aligned_cols=11 Identities=27% Similarity=0.773 Sum_probs=7.8
Q ss_pred CCCCCCCCCCC
Q 023713 1 MADSYCADCKR 11 (278)
Q Consensus 1 ~~~~~Cp~Cg~ 11 (278)
|....||.||.
T Consensus 1 m~~k~CPkC~A 11 (72)
T PHA02325 1 MDTKICPKCGA 11 (72)
T ss_pred CCccccCccCC
Confidence 55677788876
No 455
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=29.51 E-value=27 Score=22.71 Aligned_cols=14 Identities=29% Similarity=0.698 Sum_probs=12.1
Q ss_pred CCceEcCCCccccc
Q 023713 21 AGDTICSECGLVLE 34 (278)
Q Consensus 21 ~G~~vC~~CG~Vl~ 34 (278)
.|.++|..||.-+.
T Consensus 3 ~g~l~C~~CG~~m~ 16 (58)
T PF13408_consen 3 SGLLRCGHCGSKMT 16 (58)
T ss_pred CCcEEcccCCcEeE
Confidence 68899999998874
No 456
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=29.48 E-value=28 Score=29.69 Aligned_cols=38 Identities=26% Similarity=0.347 Sum_probs=23.9
Q ss_pred CCCCCCCCCCCceeEeC------CCCceEcCCCcccccccccccc
Q 023713 3 DSYCADCKRLTEVVFDH------SAGDTICSECGLVLEAYSVDET 41 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~------~~G~~vC~~CG~Vl~e~~id~~ 41 (278)
...|+.|+.. --..+. ......|..||-++..+++..|
T Consensus 95 ~~~C~~C~~~-~~~~~~~~~~~~~~~~p~C~~Cgg~lrP~VV~Fg 138 (206)
T cd01410 95 IEVCKSCGPE-YVRDDVVETRGDKETGRRCHACGGILKDTIVDFG 138 (206)
T ss_pred cccCCCCCCc-cchHHHHHHhhcCCCCCcCCCCcCccCCcEEECC
Confidence 3579999963 111111 1123569999999988887655
No 457
>PF10389 CoatB: Bacteriophage coat protein B ; InterPro: IPR008020 The major coat protein in the capsid of filamentous bacteriophage forms a helical assembly of about 7000 identical protomers, with each protomer comprised of 46 amino acids, after the cleavage of the signal peptide. Each protomer forms a slightly curved helix that combines to form a tubular structure that encapsulates the viral DNA [].; PDB: 2IFO_A.
Probab=29.48 E-value=98 Score=19.91 Aligned_cols=21 Identities=10% Similarity=0.207 Sum_probs=16.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhc
Q 023713 249 FFSLFLVETHIQLIVWAFMRC 269 (278)
Q Consensus 249 ~iaaA~v~~~~~~~~~~~~~~ 269 (278)
.|++|.|-..+...+|+++|.
T Consensus 24 ~ig~avL~v~V~i~v~kwiRr 44 (46)
T PF10389_consen 24 TIGGAVLGVIVGIAVYKWIRR 44 (46)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHh
Confidence 566777767889999999985
No 458
>PRK08173 DNA topoisomerase III; Validated
Probab=29.44 E-value=33 Score=35.91 Aligned_cols=27 Identities=19% Similarity=0.563 Sum_probs=19.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
..||.||+. ++. ..+.+.|++|+..+.
T Consensus 625 ~~CP~Cg~~--~~~--~~~~~~Cs~C~f~~~ 651 (862)
T PRK08173 625 TPCPNCGGV--VKE--NYRRFACTKCDFSIS 651 (862)
T ss_pred ccCCccccc--ccc--cCceeEcCCCCcccc
Confidence 469999973 322 234499999998874
No 459
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=29.43 E-value=25 Score=32.53 Aligned_cols=25 Identities=28% Similarity=0.687 Sum_probs=18.2
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl 33 (278)
.+||+|+.+ +-. .-+..|.+||.-.
T Consensus 58 ~kC~~c~~~-~~y----~~~~~C~~cg~~~ 82 (415)
T COG5257 58 YKCPECYRP-ECY----TTEPKCPNCGAET 82 (415)
T ss_pred EeCCCCCCC-ccc----ccCCCCCCCCCCc
Confidence 579999973 323 3478999999754
No 460
>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=29.21 E-value=30 Score=28.11 Aligned_cols=39 Identities=13% Similarity=0.198 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCC
Q 023713 106 LIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGR 146 (278)
Q Consensus 106 l~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr 146 (278)
|.+..++|..=++ .+-+.-.++|..|..--.+...++|.
T Consensus 83 l~~~~~~v~~n~e--~VG~~FAeEAR~iHyGea~~R~I~G~ 121 (148)
T PF06676_consen 83 LRKLRRHVEKNSE--DVGDRFAEEARKIHYGEAEERGIYGE 121 (148)
T ss_pred HHHHHHHHHHhCc--chhHHHHHHHHHHHcCCCccccCcCc
Confidence 3344444444333 44456678887776544444556665
No 461
>PF14369 zf-RING_3: zinc-finger
Probab=29.08 E-value=49 Score=19.81 Aligned_cols=26 Identities=27% Similarity=0.732 Sum_probs=15.3
Q ss_pred CCCCCCCCCCceeEe-CCCCceEcCCCcc
Q 023713 4 SYCADCKRLTEVVFD-HSAGDTICSECGL 31 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D-~~~G~~vC~~CG~ 31 (278)
.+|=.|... |... ....++.|+.|+-
T Consensus 3 ywCh~C~~~--V~~~~~~~~~~~CP~C~~ 29 (35)
T PF14369_consen 3 YWCHQCNRF--VRIAPSPDSDVACPRCHG 29 (35)
T ss_pred EeCccCCCE--eEeCcCCCCCcCCcCCCC
Confidence 568888862 3332 2334445999973
No 462
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=29.04 E-value=39 Score=20.50 Aligned_cols=24 Identities=17% Similarity=0.531 Sum_probs=13.9
Q ss_pred CCCCCCCCCCCCceeEeCCCCceEcCCCcccc
Q 023713 2 ADSYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (278)
Q Consensus 2 ~~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl 33 (278)
++..|+.|+.. .+ .++|.+|+..+
T Consensus 2 ~~~~C~~H~~~-~~-------~~~C~~C~~~~ 25 (42)
T PF00643_consen 2 QEPKCPEHPEE-PL-------SLFCEDCNEPL 25 (42)
T ss_dssp SSSB-SSTTTS-BE-------EEEETTTTEEE
T ss_pred cCccCccCCcc-ce-------EEEecCCCCcc
Confidence 46789999973 22 34566665544
No 463
>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=28.95 E-value=28 Score=23.64 Aligned_cols=17 Identities=35% Similarity=0.622 Sum_probs=10.0
Q ss_pred ceEcCCCcccccccccc
Q 023713 23 DTICSECGLVLEAYSVD 39 (278)
Q Consensus 23 ~~vC~~CG~Vl~e~~id 39 (278)
..+|.+||+|.-++.++
T Consensus 40 l~~C~~CglvQl~~~v~ 56 (62)
T PF08421_consen 40 LYVCEDCGLVQLEEVVP 56 (62)
T ss_dssp EEEETTT--EEESS---
T ss_pred EEECCCCCchhcCCcCC
Confidence 46899999998777665
No 464
>PF14149 YhfH: YhfH-like protein
Probab=28.86 E-value=11 Score=23.11 Aligned_cols=16 Identities=31% Similarity=0.623 Sum_probs=12.0
Q ss_pred CCceEcCCCccccccc
Q 023713 21 AGDTICSECGLVLEAY 36 (278)
Q Consensus 21 ~G~~vC~~CG~Vl~e~ 36 (278)
-+.-.|++||-.++|.
T Consensus 11 Lp~K~C~~CG~~i~EQ 26 (37)
T PF14149_consen 11 LPPKKCTECGKEIEEQ 26 (37)
T ss_pred CCCcccHHHHHHHHHH
Confidence 3456899999988765
No 465
>PF05819 NolX: NolX protein; InterPro: IPR008718 This family consists of Rhizobium NolX and Xanthomonas HrpF proteins. The interaction between the plant pathogen Xanthomonas campestris pv. vesicatoria (strain 85-10) and its host plants is controlled by hrp genes (hypersensitive reaction and pathogenicity), which encode a type III protein secretion system. Among type III-secreted proteins are avirulence proteins, effectors involved in the induction of plant defence reactions. HrpF is dispensable for protein secretion but required for AvrBs3 recognition in planta, is thought to function as a translocator of effector proteins into the host cell []. NolX, a Glycine max (Soybean) cultivar specificity protein, is secreted by a type III secretion system (TTSS) and shows homology to HrpF. It is not known whether NolX functions at the bacterium-plant interface or acts inside the host cell. NolX is expressed in planta only during the early stages of nodule development [].; GO: 0009877 nodulation
Probab=28.86 E-value=4.1e+02 Score=26.11 Aligned_cols=126 Identities=18% Similarity=0.250 Sum_probs=78.2
Q ss_pred hhHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCCCCCCcHHHHHHHHHHHHHHhcC---------CCCCHHHHH
Q 023713 103 DRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQEN---------KPRTVKEFC 173 (278)
Q Consensus 103 er~l~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~gr~~~~~aAAclY~acR~~~---------~p~tl~eia 173 (278)
.-+..+|++++=++.+. ||..+- .+-|+++++...-.|+-+-.++||+=|++---.. -++.-.++.
T Consensus 363 vMT~nDA~RELYrYSdy--LPK~L~---~~~f~~IVdG~s~tgKcPPQViAAAqyF~~hpd~W~~l~~g~~~~v~k~dfl 437 (624)
T PF05819_consen 363 VMTENDAMRELYRYSDY--LPKNLS---LEDFKQIVDGDSKTGKCPPQVIAAAQYFVDHPDEWKQLYGGPSDKVSKEDFL 437 (624)
T ss_pred ccchhHHHHHHHHhhhc--cccccC---HHHHHhHhcCccccCCCCHHHHHHHHHHHhChHHHHHhcCCCccccchhHHH
Confidence 34667888989888884 564433 3468899998888899888888888888742211 223334444
Q ss_pred HH---HcCCCHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHh
Q 023713 174 SV---ANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKS 238 (278)
Q Consensus 174 ~~---~~~v~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~ 238 (278)
.+ ....+..++ ++++-|..+...-.+ -...-..+=+..+++.=.++++|.++|..|+..-
T Consensus 438 q~ass~m~LT~~El-kTL~Tin~nqd~FFg----~G~~ltrdKLa~ma~D~~~~p~Vr~AA~qLl~dp 500 (624)
T PF05819_consen 438 QVASSSMHLTAPEL-KTLDTINSNQDAFFG----DGKELTRDKLASMADDKSLDPEVREAAKQLLSDP 500 (624)
T ss_pred HHHHhhcccChHHH-HHHHHhhhchhhhhC----CccccCHHHHHHhhcCcccCHHHHHHHHHHhccc
Confidence 32 122333333 334444444433211 1111234667788888889999999999988743
No 466
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=28.78 E-value=1.5e+02 Score=19.13 Aligned_cols=32 Identities=16% Similarity=0.265 Sum_probs=27.6
Q ss_pred CCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhh
Q 023713 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (278)
Q Consensus 166 p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~ 198 (278)
..+..||+.. ++++..++....+.+.+.++..
T Consensus 19 G~s~~eia~~-l~is~~tV~~h~~~i~~Kl~~~ 50 (65)
T COG2771 19 GKSNKEIARI-LGISEETVKTHLRNIYRKLGVK 50 (65)
T ss_pred CCCHHHHHHH-HCCCHHHHHHHHHHHHHHHCCC
Confidence 3889999995 8999999999999998888764
No 467
>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=28.77 E-value=32 Score=28.08 Aligned_cols=27 Identities=19% Similarity=0.561 Sum_probs=16.9
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCcccccccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVD 39 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~e~~id 39 (278)
..|..||+. . | ..|++|+.=++.....
T Consensus 29 ~fC~kCG~~-t-I-------~~Cp~C~~~IrG~y~v 55 (158)
T PF10083_consen 29 KFCSKCGAK-T-I-------TSCPNCSTPIRGDYHV 55 (158)
T ss_pred HHHHHhhHH-H-H-------HHCcCCCCCCCCceec
Confidence 457788863 2 2 3588888777655444
No 468
>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=28.76 E-value=43 Score=21.76 Aligned_cols=8 Identities=25% Similarity=0.874 Sum_probs=6.8
Q ss_pred CCCCCCCC
Q 023713 4 SYCADCKR 11 (278)
Q Consensus 4 ~~Cp~Cg~ 11 (278)
..||.||.
T Consensus 14 ~~Cp~CGN 21 (49)
T PF12677_consen 14 CKCPKCGN 21 (49)
T ss_pred ccCcccCC
Confidence 46999997
No 469
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=28.62 E-value=30 Score=25.75 Aligned_cols=12 Identities=25% Similarity=0.329 Sum_probs=9.3
Q ss_pred CCCCCCCCCCCC
Q 023713 1 MADSYCADCKRL 12 (278)
Q Consensus 1 ~~~~~Cp~Cg~~ 12 (278)
|....||+||..
T Consensus 1 mlLI~CP~Cg~R 12 (97)
T COG4311 1 MLLIPCPYCGER 12 (97)
T ss_pred CceecCCCCCCC
Confidence 566789999963
No 470
>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=28.46 E-value=49 Score=19.45 Aligned_cols=25 Identities=16% Similarity=0.501 Sum_probs=13.5
Q ss_pred CCCCCCCCCceeEeCCCCceEcCCC
Q 023713 5 YCADCKRLTEVVFDHSAGDTICSEC 29 (278)
Q Consensus 5 ~Cp~Cg~~~~vv~D~~~G~~vC~~C 29 (278)
.|+.++.+...++=...+..+|..|
T Consensus 2 ~C~~H~~~~~~~fC~~~~~~iC~~C 26 (39)
T cd00021 2 LCDEHGEEPLSLFCETDRALLCVDC 26 (39)
T ss_pred CCCccCCcceEEEeCccChhhhhhc
Confidence 5888876322333344455555555
No 471
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=28.44 E-value=29 Score=38.43 Aligned_cols=30 Identities=40% Similarity=0.817 Sum_probs=23.1
Q ss_pred CCCCCCCCCCceeEeCCCC------ceEcCCCccccc
Q 023713 4 SYCADCKRLTEVVFDHSAG------DTICSECGLVLE 34 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G------~~vC~~CG~Vl~ 34 (278)
..||+|.- .+.+.|.+-| +-.|+.||.-+.
T Consensus 909 y~C~~C~~-~ef~~~~~~~sG~Dlpdk~Cp~Cg~~~~ 944 (1437)
T PRK00448 909 YVCPNCKY-SEFFTDGSVGSGFDLPDKDCPKCGTKLK 944 (1437)
T ss_pred ccCccccc-ccccccccccccccCccccCcccccccc
Confidence 47999997 6777775555 456999999874
No 472
>PTZ00408 NAD-dependent deacetylase; Provisional
Probab=28.44 E-value=23 Score=31.09 Aligned_cols=38 Identities=21% Similarity=0.239 Sum_probs=22.7
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCc--ccccccccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECG--LVLEAYSVDET 41 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG--~Vl~e~~id~~ 41 (278)
..|..|+..-+...+...+...|..|| -++..+++-.|
T Consensus 118 ~~C~~C~~~~~~~~~~~~~~p~C~~Cg~~g~lrP~vV~FG 157 (242)
T PTZ00408 118 VRCTATGHVFDWTEDVVHGSSRCKCCGCVGTLRPHIVWFG 157 (242)
T ss_pred EEECCCCcccCchhhhhcCCCccccCCCCCCCCCCEEEcC
Confidence 579999963111111223446799998 56777776544
No 473
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=28.39 E-value=38 Score=21.14 Aligned_cols=8 Identities=25% Similarity=0.874 Sum_probs=5.1
Q ss_pred CCCCCCCC
Q 023713 4 SYCADCKR 11 (278)
Q Consensus 4 ~~Cp~Cg~ 11 (278)
..||.||+
T Consensus 3 ~~Cp~Cg~ 10 (47)
T PF14690_consen 3 PRCPHCGS 10 (47)
T ss_pred ccCCCcCC
Confidence 45777775
No 474
>PRK04194 hypothetical protein; Provisional
Probab=28.39 E-value=1.5e+02 Score=28.20 Aligned_cols=37 Identities=19% Similarity=0.434 Sum_probs=26.9
Q ss_pred HHHHHHHHHhcCCCHHHHHHHHHHHHHHhhC-CCCCCC
Q 023713 110 FKSISAMSDRLGLVTTIKDRANEIYKKVEDQ-KPLRGR 146 (278)
Q Consensus 110 ~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~-~~~~gr 146 (278)
+..|.++.+..+||+.+++.|..+|+++-+. ....|.
T Consensus 75 ~~~I~~ii~~s~l~~~vk~~a~~iF~~lA~AEa~VHG~ 112 (392)
T PRK04194 75 LSEIKALIENSDLPEKVKERALAVFERLAEAEAKVHGI 112 (392)
T ss_pred HHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 3456666678899999999999999986543 233444
No 475
>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=28.38 E-value=1.4e+02 Score=24.44 Aligned_cols=30 Identities=20% Similarity=0.071 Sum_probs=22.7
Q ss_pred CCCHHHHHHHHcCCCHHHHHHHHHHHHHHhh
Q 023713 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKHLE 196 (278)
Q Consensus 166 p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~ 196 (278)
..+.+|||.. +|++..++...+.+-++.|.
T Consensus 147 g~s~~EIA~~-lgis~~tVk~~l~Rar~~Lr 176 (193)
T TIGR02947 147 GFAYKEIAEI-MGTPIGTVMSRLHRGRKQLR 176 (193)
T ss_pred CCCHHHHHHH-HCCCHHHHHHHHHHHHHHHH
Confidence 3679999995 99999888877665555553
No 476
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=28.36 E-value=42 Score=33.36 Aligned_cols=29 Identities=17% Similarity=0.441 Sum_probs=15.1
Q ss_pred CCCCCCCCCCCceeEeCCCCceEcCCCccc
Q 023713 3 DSYCADCKRLTEVVFDHSAGDTICSECGLV 32 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~V 32 (278)
+..||.||+..-++. ..+-..+|..-|.+
T Consensus 2 ~~~C~~C~g~G~i~v-~~e~c~vc~gtG~~ 30 (715)
T COG1107 2 IKKCPECGGKGKIVV-GEEECPVCHGTGFS 30 (715)
T ss_pred CccccccCCCceEee-eeeecccccccccc
Confidence 367888887444333 22223344444555
No 477
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=28.35 E-value=1.4e+02 Score=23.42 Aligned_cols=30 Identities=7% Similarity=0.092 Sum_probs=25.7
Q ss_pred cCCCCCHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 163 ENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 163 ~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
.+-+.|+.||++. ++++..++.+.++.|.+
T Consensus 43 ~~~~~t~~eLa~~-l~~~~~tvt~~v~~Le~ 72 (144)
T PRK03573 43 LPPEQSQIQLAKA-IGIEQPSLVRTLDQLEE 72 (144)
T ss_pred cCCCCCHHHHHHH-hCCChhhHHHHHHHHHH
Confidence 3445789999995 99999999999999976
No 478
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.12 E-value=32 Score=23.70 Aligned_cols=28 Identities=32% Similarity=0.744 Sum_probs=16.2
Q ss_pred CCCCCCCCCCCceeE-eCCCCceEcCC-Cccc
Q 023713 3 DSYCADCKRLTEVVF-DHSAGDTICSE-CGLV 32 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~-D~~~G~~vC~~-CG~V 32 (278)
...||.||.+ ++. +...=.-+|+. |-.|
T Consensus 7 ~v~CP~Cgkp--v~w~~~s~frPFCSkRCklI 36 (65)
T COG3024 7 TVPCPTCGKP--VVWGEESPFRPFCSKRCKLI 36 (65)
T ss_pred cccCCCCCCc--ccccccCCcCcchhHhhhhc
Confidence 3679999983 333 23334456654 6544
No 479
>PF14833 NAD_binding_11: NAD-binding of NADP-dependent 3-hydroxyisobutyrate dehydrogenase; PDB: 3OBB_A 3Q3C_A 2UYY_D 3G0O_A 1WP4_A 2CVZ_B 1YB4_A 3PDU_G 2I9P_D 2GF2_D ....
Probab=28.04 E-value=1.8e+02 Score=21.99 Aligned_cols=39 Identities=10% Similarity=0.185 Sum_probs=30.5
Q ss_pred hHHHHHHHHHHHHHHhcCCCHHHHHHHHHHHHHHhhCCC
Q 023713 104 RNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKP 142 (278)
Q Consensus 104 r~l~~~~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~ 142 (278)
....+=.+.+.+.+...++|..+.+.+.++|+.+.+.+.
T Consensus 72 ~~~~KDl~l~~~~a~~~g~~~p~~~~~~~~~~~a~~~g~ 110 (122)
T PF14833_consen 72 DLARKDLRLALDLAKEAGVPLPLGSAARQLYQAAKAQGG 110 (122)
T ss_dssp HHHHHHHHHHHHHHHHTT---HHHHHHHHHHHHHHHTTT
T ss_pred HhhccHHHHHHHHHHHcCCCCHHHHHHHHHHHHHHhcCC
Confidence 344556788899999999999999999999999998864
No 480
>PF13518 HTH_28: Helix-turn-helix domain
Probab=27.98 E-value=1.1e+02 Score=19.10 Aligned_cols=25 Identities=16% Similarity=0.166 Sum_probs=22.3
Q ss_pred CHHHHHHHHcCCCHHHHHHHHHHHHH
Q 023713 168 TVKEFCSVANGTTKKEIGRAKEFIVK 193 (278)
Q Consensus 168 tl~eia~~~~~v~~~~i~~~~~~l~~ 193 (278)
|+.++|.. ++|+..+|.+.++....
T Consensus 14 s~~~~a~~-~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 14 SVREIARE-FGISRSTVYRWIKRYRE 38 (52)
T ss_pred CHHHHHHH-HCCCHhHHHHHHHHHHh
Confidence 99999995 99999999999888765
No 481
>PHA02970 hypothetical protein; Provisional
Probab=27.98 E-value=2.2e+02 Score=21.51 Aligned_cols=74 Identities=11% Similarity=0.071 Sum_probs=40.6
Q ss_pred HHHHHHHcCCCHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHHHHHHHHHHHHHhhhcCCC
Q 023713 170 KEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDIR 244 (278)
Q Consensus 170 ~eia~~~~~v~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~~G 244 (278)
.|+++. ---++++|...|-.+.+.-.+.......+.-......|.-|..-|.+-+...-.-..|.+++...++|
T Consensus 29 ~D~sey-~~YN~~EIn~lY~~FLk~h~L~sid~~kL~d~~idHIiyHFiEyl~~Lkntil~r~~IcKRiLnKD~g 102 (115)
T PHA02970 29 HDLSEY-EVYNPKEINSLYISFLKHHNLLSIDDRKLNDDAIDHIIYHFIEYLQKLKNTILTRNNICKRILNKDTG 102 (115)
T ss_pred ccHHHH-hcCCHHHHHHHHHHHHHHcccccccccccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhc
Confidence 366553 44689999999998887666542111222222344566667766665555443333444444433333
No 482
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=27.97 E-value=1.3e+02 Score=30.37 Aligned_cols=41 Identities=10% Similarity=0.118 Sum_probs=32.9
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhh
Q 023713 154 ACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEA 197 (278)
Q Consensus 154 AclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~ 197 (278)
.|+|++-+ -...|+.+|+.. +|-+..++..++++|.+.+..
T Consensus 559 iAMYL~r~--lt~~Sl~~IG~~-FgRdHSTV~~A~~kI~~~~~~ 599 (617)
T PRK14086 559 IAMYLCRE--LTDLSLPKIGQQ-FGRDHTTVMHADRKIRALMAE 599 (617)
T ss_pred HHHHHHHH--HcCCCHHHHHHH-hCCChhHHHHHHHHHHHHHHh
Confidence 56776644 455789999995 789999999999999988764
No 483
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=27.88 E-value=51 Score=32.10 Aligned_cols=24 Identities=25% Similarity=0.400 Sum_probs=21.9
Q ss_pred CCCCHHHHHHHHcCCCHHHHHHHHH
Q 023713 165 KPRTVKEFCSVANGTTKKEIGRAKE 189 (278)
Q Consensus 165 ~p~tl~eia~~~~~v~~~~i~~~~~ 189 (278)
.|.+++|||+. .|+.+.||+|+..
T Consensus 368 kPLtlkdVAe~-lglHeSTVSRa~~ 391 (481)
T PRK12469 368 KPLVLRDVAEE-LGLHESTISRATG 391 (481)
T ss_pred cCCcHHHHHHH-hCCCcchhhHHhc
Confidence 68999999995 9999999999965
No 484
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=27.88 E-value=97 Score=26.17 Aligned_cols=33 Identities=9% Similarity=0.112 Sum_probs=21.9
Q ss_pred CCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhh
Q 023713 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (278)
Q Consensus 165 ~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~ 198 (278)
...|-+|||.. ++++++++....+.|.+.|+.+
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 34566777773 6777777777777777666654
No 485
>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=27.74 E-value=71 Score=23.04 Aligned_cols=23 Identities=26% Similarity=0.342 Sum_probs=19.6
Q ss_pred CCCCHHHHHHHHcCCCHHHHHHHH
Q 023713 165 KPRTVKEFCSVANGTTKKEIGRAK 188 (278)
Q Consensus 165 ~p~tl~eia~~~~~v~~~~i~~~~ 188 (278)
-..|++|||.. +|++..++++.+
T Consensus 18 ~~~ti~dvA~~-~gvS~~TVsr~L 40 (80)
T TIGR02844 18 TKATVRETAKV-FGVSKSTVHKDV 40 (80)
T ss_pred CCCCHHHHHHH-hCCCHHHHHHHh
Confidence 45799999995 999999999854
No 486
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=27.66 E-value=18 Score=38.17 Aligned_cols=24 Identities=25% Similarity=0.674 Sum_probs=15.4
Q ss_pred CCCCCCCCCCCceeEeC-CCCceEcCCC
Q 023713 3 DSYCADCKRLTEVVFDH-SAGDTICSEC 29 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~D~-~~G~~vC~~C 29 (278)
...||+||++ +--|. ..|.. |..|
T Consensus 8 ~~~CpNCGG~--isseRL~~glp-Ce~C 32 (1187)
T COG1110 8 GSSCPNCGGD--ISSERLEKGLP-CERC 32 (1187)
T ss_pred hccCCCCCCc--CcHHHHhcCCC-chhc
Confidence 5789999984 33332 44544 8877
No 487
>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=27.52 E-value=93 Score=25.53 Aligned_cols=32 Identities=19% Similarity=0.205 Sum_probs=27.1
Q ss_pred CCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhh
Q 023713 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEA 197 (278)
Q Consensus 165 ~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~ 197 (278)
...|..|||.. +|+++.++...+.+.++.|..
T Consensus 164 ~~~s~~eIA~~-l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 164 DGKSYQEIACD-LNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred cCCCHHHHHHH-HCCCHHHHHHHHHHHHHHHHH
Confidence 36789999995 999999999988888887753
No 488
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=27.50 E-value=29 Score=33.69 Aligned_cols=30 Identities=30% Similarity=0.699 Sum_probs=23.2
Q ss_pred CCCCCCCCCCCceeE-eCCCCceEcCCCcccc
Q 023713 3 DSYCADCKRLTEVVF-DHSAGDTICSECGLVL 33 (278)
Q Consensus 3 ~~~Cp~Cg~~~~vv~-D~~~G~~vC~~CG~Vl 33 (278)
...|-.||+ .+.-+ .-..|.++|.+|=.|-
T Consensus 8 ~evC~DC~~-~dp~WASvnrGt~lC~eCcsvH 38 (669)
T KOG0818|consen 8 SEVCADCSG-PDPSWASVNRGTFLCDECCSVH 38 (669)
T ss_pred hhhhcccCC-CCCcceeecCceEehHhhhHHH
Confidence 467999998 44433 3479999999998885
No 489
>COG2015 Alkyl sulfatase and related hydrolases [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=27.48 E-value=2.6e+02 Score=27.47 Aligned_cols=79 Identities=16% Similarity=0.164 Sum_probs=54.9
Q ss_pred HHHhcCCCCCHHHHHHHHcCCCHHHHHHHH------------H-HHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCH
Q 023713 159 ACRQENKPRTVKEFCSVANGTTKKEIGRAK------------E-FIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTN 225 (278)
Q Consensus 159 acR~~~~p~tl~eia~~~~~v~~~~i~~~~------------~-~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~ 225 (278)
..|+.+...|..||++ .++++..--+..+ | .+.+.||--++..-.+.|..|.++-+||+..+|-..
T Consensus 375 TLrL~NqG~T~~eI~~-~~~lPpaL~~~W~~rGYyGSvshNarAVy~rYlG~yD~NPa~L~P~~p~d~a~ryV~amGGad 453 (655)
T COG2015 375 TLRLANQGYTGNEIAD-MIQLPPALAREWYTRGYYGSVSHNARAVYNRYLGYYDGNPANLHPLPPVDSAKRYVEAMGGAD 453 (655)
T ss_pred HHHHHhcCccHHHHHH-HhcCChHHHHhHhhcCccccccccHHHHHHHHhccccCCccccCCCChhHhHHHHHHHhccHH
Confidence 5688899999999999 4888765444332 1 223444433333334667889999999999999888
Q ss_pred HHHHHHHHHHHHh
Q 023713 226 QAVKAAQEAVQKS 238 (278)
Q Consensus 226 ~v~~~A~~i~~~~ 238 (278)
.|...|.+..++.
T Consensus 454 rVl~la~ea~~kG 466 (655)
T COG2015 454 RVLELAREAFDKG 466 (655)
T ss_pred HHHHHHHHHHhcc
Confidence 8887777765443
No 490
>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=27.36 E-value=4.1e+02 Score=23.05 Aligned_cols=38 Identities=8% Similarity=0.047 Sum_probs=28.8
Q ss_pred HHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHHH
Q 023713 152 VAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFI 191 (278)
Q Consensus 152 aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~l 191 (278)
..+.-|+... -..++|+.++|+. +++++..+.+.+++.
T Consensus 189 ~~~~~~I~~~-~~~~~sl~~lA~~-~~~S~~~l~r~Fk~~ 226 (287)
T TIGR02297 189 NRFNFLIEEN-YKQHLRLPEYADR-LGISESRLNDICRRF 226 (287)
T ss_pred HHHHHHHHHh-hccCCCHHHHHHH-HCCCHHHHHHHHHHH
Confidence 3444565544 3458999999995 999999999998874
No 491
>COG1698 Uncharacterized protein conserved in archaea [Function unknown]
Probab=27.24 E-value=2.3e+02 Score=20.94 Aligned_cols=42 Identities=12% Similarity=0.055 Sum_probs=31.1
Q ss_pred HHHHHHHhhcCCCHHHHHHHHHHHHHhhhcCCCCChhHHHHHHH
Q 023713 212 DYLRRFCSNLGMTNQAVKAAQEAVQKSEDLDIRLILVFFSLFLV 255 (278)
Q Consensus 212 ~~i~r~~~~L~l~~~v~~~A~~i~~~~~~~~~Gr~P~~iaaA~v 255 (278)
..+.++.+.-..|..+.++|.++.+.+.+ .|..|.-=||.+|
T Consensus 20 ~lL~~Ii~DttVPRNIRraA~~a~e~L~~--e~e~p~vRaAtaI 61 (93)
T COG1698 20 QLLDEIIQDTTVPRNIRRAAEEAKEALNN--EGESPAVRAATAI 61 (93)
T ss_pred HHHHHHHccccccHHHHHHHHHHHHHHhC--CCCCchhHHHHHH
Confidence 34455666667788888888888887765 4688888788777
No 492
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=27.03 E-value=1.1e+02 Score=23.60 Aligned_cols=59 Identities=8% Similarity=0.035 Sum_probs=38.4
Q ss_pred hcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHh--hhhcccccc----c-CCCCHHHHHHHHHhhc
Q 023713 162 QENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHL--EAEMGQSVE----M-GTIHASDYLRRFCSNL 221 (278)
Q Consensus 162 ~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L--~~~~~~~~~----~-~~~~p~~~i~r~~~~L 221 (278)
....++|+.|+|++ +.++........+++.+.= .-.++...+ + =..+|++.+...+.++
T Consensus 15 ~~~~~vtl~elA~~-l~cS~Rn~r~lLkkm~~~gWi~W~pg~GRG~~S~L~~l~~~~~~~~~~~~~~ 80 (115)
T PF12793_consen 15 GQPVEVTLDELAEL-LFCSRRNARTLLKKMQEEGWITWQPGRGRGNRSQLTFLKSPEELLEQQAEEL 80 (115)
T ss_pred CCCcceeHHHHHHH-hCCCHHHHHHHHHHHHHCCCeeeeCCCCCCCCCeeEEeeCHHHHHHHHHHHH
Confidence 34567899999995 8999999999999987632 222211111 1 1246777776666554
No 493
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=26.96 E-value=1e+02 Score=25.09 Aligned_cols=33 Identities=9% Similarity=-0.029 Sum_probs=28.2
Q ss_pred hcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHh
Q 023713 162 QENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHL 195 (278)
Q Consensus 162 ~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L 195 (278)
+.+-..|..|||+. .|++..++.+.+++|.+.=
T Consensus 24 q~d~R~s~~eiA~~-lglS~~tv~~Ri~rL~~~G 56 (164)
T PRK11169 24 QKDGRISNVELSKR-VGLSPTPCLERVRRLERQG 56 (164)
T ss_pred ccCCCCCHHHHHHH-HCcCHHHHHHHHHHHHHCC
Confidence 45667889999995 9999999999999998743
No 494
>PF14502 HTH_41: Helix-turn-helix domain
Probab=26.93 E-value=1e+02 Score=19.99 Aligned_cols=28 Identities=21% Similarity=0.350 Sum_probs=24.1
Q ss_pred CCHHHHHHHHcCCCHHHHHHHHHHHHHHh
Q 023713 167 RTVKEFCSVANGTTKKEIGRAKEFIVKHL 195 (278)
Q Consensus 167 ~tl~eia~~~~~v~~~~i~~~~~~l~~~L 195 (278)
.|+.|.++. ++++.-+|.++++.|.+.=
T Consensus 7 ~tI~e~~~~-~~vs~GtiQ~Alk~Le~~g 34 (48)
T PF14502_consen 7 PTISEYSEK-FGVSRGTIQNALKFLEENG 34 (48)
T ss_pred CCHHHHHHH-hCcchhHHHHHHHHHHHCC
Confidence 578899995 8999999999999997643
No 495
>PF14951 DUF4503: Domain of unknown function (DUF4503)
Probab=26.84 E-value=42 Score=31.21 Aligned_cols=33 Identities=18% Similarity=0.475 Sum_probs=25.9
Q ss_pred CCCCCCCCCceeEeC-CCCceEcCCCccccccccc
Q 023713 5 YCADCKRLTEVVFDH-SAGDTICSECGLVLEAYSV 38 (278)
Q Consensus 5 ~Cp~Cg~~~~vv~D~-~~G~~vC~~CG~Vl~e~~i 38 (278)
.|..||+ ..+...+ .+|-.-|.+|-.|+.+..+
T Consensus 276 vCd~CGn-~rLe~~pe~rg~~~C~~Cs~~V~sP~~ 309 (389)
T PF14951_consen 276 VCDRCGN-GRLEQSPEDRGAFSCGDCSRVVTSPVL 309 (389)
T ss_pred cccccCC-ccceeCccCCCceeccchhhhccCcce
Confidence 5999998 6777554 5777999999999976554
No 496
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=26.81 E-value=2.8e+02 Score=24.83 Aligned_cols=41 Identities=10% Similarity=-0.002 Sum_probs=30.8
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHHcCCCHHHHHHHHHH
Q 023713 148 QEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEF 190 (278)
Q Consensus 148 ~~~~aAAclY~acR~~~~p~tl~eia~~~~~v~~~~i~~~~~~ 190 (278)
...+.-++-|+-... ..|.++.++|.. +++++..+.|.+++
T Consensus 141 ~~~~~~v~~yI~~~~-~~~lsl~~lA~~-~g~S~~~L~R~Fk~ 181 (274)
T PRK09978 141 PNMRTRVCTVINNNI-AHEWTLARIASE-LLMSPSLLKKKLRE 181 (274)
T ss_pred HHHHHHHHHHHHhcc-cCCCCHHHHHHH-HCcCHHHHHHHHHh
Confidence 344555666666554 448999999995 99999999998864
No 497
>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=26.80 E-value=2.1e+02 Score=19.49 Aligned_cols=51 Identities=16% Similarity=0.250 Sum_probs=35.9
Q ss_pred hcCCCCCHHHHHHHHcCCCHHHHHHHHHHHHHHhhhhcccccccCCCCHHHHHHHHHhhcCCCHHHH
Q 023713 162 QENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLRRFCSNLGMTNQAV 228 (278)
Q Consensus 162 ~~~~p~tl~eia~~~~~v~~~~i~~~~~~l~~~L~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~ 228 (278)
......|..|+|.. +|++..+|.+..+ | . ... +.+.+.+++..|+.+.+..
T Consensus 14 ~~~~~~t~~~lA~~-~gis~~tis~~~~------g-~-------~~~-~~~~~~~l~~~l~v~~~~l 64 (78)
T TIGR02607 14 LEPLGLSIRALAKA-LGVSRSTLSRIVN------G-R-------RGI-TADMALRLAKALGTSPEFW 64 (78)
T ss_pred HHHcCCCHHHHHHH-hCCCHHHHHHHHc------C-C-------CCC-CHHHHHHHHHHcCCCHHHH
Confidence 34456789999994 8999888877532 1 1 112 3478889999999987743
No 498
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=26.76 E-value=33 Score=32.35 Aligned_cols=31 Identities=26% Similarity=0.591 Sum_probs=21.1
Q ss_pred CCCCCCCCCCceeEeCCCCceEcCCCccccc
Q 023713 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (278)
Q Consensus 4 ~~Cp~Cg~~~~vv~D~~~G~~vC~~CG~Vl~ 34 (278)
..||+|+-..++-.=...-.-.|..||..+.
T Consensus 19 ~~C~eCd~~~~~P~l~~~q~A~CPRC~~~l~ 49 (418)
T COG2995 19 ILCPECDMLVSLPRLDSGQSAYCPRCGHTLT 49 (418)
T ss_pred ecCCCCCceeccccCCCCCcccCCCCCCccc
Confidence 4699999743333333455678999999885
No 499
>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=26.74 E-value=18 Score=33.69 Aligned_cols=15 Identities=13% Similarity=0.115 Sum_probs=4.7
Q ss_pred HhcCCCCCHHHHHHH
Q 023713 161 RQENKPRTVKEFCSV 175 (278)
Q Consensus 161 R~~~~p~tl~eia~~ 175 (278)
...|.-+|+.|..++
T Consensus 285 sSkG~~~t~~e~L~~ 299 (360)
T PF01921_consen 285 SSKGNGITPEEWLEY 299 (360)
T ss_dssp --------HHHHHTT
T ss_pred cCCCCccCHHHHHHh
Confidence 345666777777653
No 500
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=26.68 E-value=37 Score=32.52 Aligned_cols=24 Identities=33% Similarity=0.440 Sum_probs=22.2
Q ss_pred CCCCHHHHHHHHcCCCHHHHHHHHH
Q 023713 165 KPRTVKEFCSVANGTTKKEIGRAKE 189 (278)
Q Consensus 165 ~p~tl~eia~~~~~v~~~~i~~~~~ 189 (278)
.|.|++|||+. +|+++.||+|+.+
T Consensus 317 kPLtlkdiA~~-lglheSTVSRav~ 340 (429)
T TIGR02395 317 KPLTLREVAEE-LGLHESTISRAIN 340 (429)
T ss_pred cCCcHHHHHHH-hCCCccchhhhhc
Confidence 78999999995 9999999999976
Done!