Query 009187
Match_columns 540
No_of_seqs 263 out of 1115
Neff 6.3
Searched_HMMs 46136
Date Thu Mar 28 21:29:10 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/009187.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/009187hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1598 Transcription initiati 100.0 5.7E-76 1.2E-80 621.4 24.2 452 2-522 1-493 (521)
2 PRK00423 tfb transcription ini 100.0 1.4E-51 3E-56 425.4 26.9 244 2-254 12-296 (310)
3 COG1405 SUA7 Transcription ini 100.0 4.8E-51 1E-55 413.5 24.9 245 1-254 1-271 (285)
4 KOG1597 Transcription initiati 100.0 8.9E-46 1.9E-50 366.6 23.9 246 2-254 1-280 (308)
5 PF07741 BRF1: Brf1-like TBP-b 100.0 6.2E-30 1.3E-34 221.1 1.7 96 396-516 1-97 (97)
6 PF00382 TFIIB: Transcription 99.7 1.4E-16 3E-21 129.9 9.7 71 78-150 1-71 (71)
7 KOG0835 Cyclin L [General func 99.6 4E-14 8.6E-19 143.1 17.7 182 66-254 18-221 (367)
8 PF00382 TFIIB: Transcription 99.5 4.4E-14 9.6E-19 115.2 8.3 71 179-251 1-71 (71)
9 TIGR00569 ccl1 cyclin ccl1. Un 99.5 6.5E-13 1.4E-17 137.0 17.9 171 68-246 52-234 (305)
10 KOG0834 CDK9 kinase-activating 99.5 4.9E-13 1.1E-17 138.1 12.5 177 71-254 39-237 (323)
11 PRK00423 tfb transcription ini 99.3 5.4E-12 1.2E-16 131.0 12.0 89 74-164 219-307 (310)
12 PF08271 TF_Zn_Ribbon: TFIIB z 99.3 2.2E-12 4.7E-17 95.3 2.7 43 2-44 1-43 (43)
13 COG5333 CCL1 Cdk activating ki 99.2 1.2E-10 2.5E-15 118.1 13.4 159 72-237 46-212 (297)
14 COG1405 SUA7 Transcription ini 99.0 1.1E-09 2.4E-14 112.0 10.2 91 73-165 193-283 (285)
15 KOG1598 Transcription initiati 98.9 1.8E-09 4E-14 116.3 6.6 164 76-318 168-340 (521)
16 cd00043 CYCLIN Cyclin box fold 98.9 1.7E-08 3.8E-13 82.7 11.1 83 73-157 4-87 (88)
17 KOG1597 Transcription initiati 98.9 1.2E-08 2.6E-13 102.7 10.4 87 74-162 203-289 (308)
18 KOG0794 CDK8 kinase-activating 98.8 2E-08 4.2E-13 98.0 10.4 155 74-236 44-213 (264)
19 smart00385 CYCLIN domain prese 98.8 3.2E-08 6.9E-13 80.4 8.8 80 77-158 2-82 (83)
20 KOG0656 G1/S-specific cyclin D 98.5 2.5E-06 5.4E-11 88.8 15.8 151 72-229 79-238 (335)
21 cd00043 CYCLIN Cyclin box fold 98.5 8.2E-07 1.8E-11 72.7 9.0 80 173-254 3-83 (88)
22 smart00385 CYCLIN domain prese 98.4 1.4E-06 3.1E-11 70.6 7.8 76 177-254 1-77 (83)
23 KOG2496 Cdk activating kinase 97.8 0.0002 4.2E-09 73.1 12.5 137 86-229 73-220 (325)
24 PF00134 Cyclin_N: Cyclin, N-t 97.7 0.00033 7.1E-09 62.3 10.6 93 70-164 30-125 (127)
25 KOG0653 Cyclin B and related k 97.4 0.0015 3.2E-08 70.3 13.0 153 74-235 161-317 (391)
26 PF01857 RB_B: Retinoblastoma- 97.4 0.001 2.2E-08 61.2 9.5 84 70-155 10-95 (135)
27 KOG4557 Origin recognition com 97.4 0.0052 1.1E-07 60.0 14.7 160 77-249 2-168 (262)
28 COG5024 Cyclin [Cell division 96.8 0.0074 1.6E-07 65.5 10.7 149 75-233 217-369 (440)
29 PF11781 RRN7: RNA polymerase 96.5 0.0017 3.8E-08 46.1 2.0 27 3-31 10-36 (36)
30 PF02984 Cyclin_C: Cyclin, C-t 96.3 0.0083 1.8E-07 52.3 5.9 78 174-253 2-80 (118)
31 KOG0835 Cyclin L [General func 95.5 0.088 1.9E-06 54.7 10.0 106 74-187 141-247 (367)
32 PF09862 DUF2089: Protein of u 95.5 0.22 4.8E-06 44.5 11.2 55 135-193 51-106 (113)
33 PRK00415 rps27e 30S ribosomal 95.2 0.011 2.4E-07 46.5 1.7 31 2-32 12-42 (59)
34 PF01667 Ribosomal_S27e: Ribos 95.1 0.011 2.3E-07 46.1 1.3 31 2-32 8-38 (55)
35 COG2051 RPS27A Ribosomal prote 95.1 0.013 2.7E-07 47.0 1.7 32 2-33 20-51 (67)
36 PF02150 RNA_POL_M_15KD: RNA p 94.8 0.019 4E-07 40.6 1.9 31 1-31 1-31 (35)
37 KOG0655 G1/S-specific cyclin E 94.7 0.36 7.9E-06 50.3 11.7 106 74-186 148-257 (408)
38 PTZ00083 40S ribosomal protein 94.6 0.025 5.5E-07 47.5 2.5 32 2-33 36-67 (85)
39 PF02984 Cyclin_C: Cyclin, C-t 94.6 0.19 4.2E-06 43.6 8.2 86 75-162 4-90 (118)
40 PLN00209 ribosomal protein S27 94.4 0.025 5.3E-07 47.7 1.9 32 2-33 37-68 (86)
41 PF14803 Nudix_N_2: Nudix N-te 94.3 0.019 4.1E-07 40.4 1.0 28 3-30 2-32 (34)
42 PHA00626 hypothetical protein 94.3 0.035 7.5E-07 43.1 2.4 31 2-32 1-35 (59)
43 PF13248 zf-ribbon_3: zinc-rib 94.2 0.025 5.4E-07 37.2 1.3 23 1-28 2-24 (26)
44 TIGR01206 lysW lysine biosynth 94.1 0.032 6.9E-07 43.3 2.0 31 1-31 2-33 (54)
45 PF13240 zinc_ribbon_2: zinc-r 93.7 0.034 7.3E-07 35.6 1.2 22 3-29 1-22 (23)
46 PRK00420 hypothetical protein; 93.3 0.058 1.3E-06 48.1 2.5 27 3-31 25-51 (112)
47 PF08792 A2L_zn_ribbon: A2L zi 93.3 0.066 1.4E-06 37.4 2.2 27 3-30 5-31 (33)
48 PF08274 PhnA_Zn_Ribbon: PhnA 92.3 0.11 2.3E-06 35.5 2.1 28 1-30 2-29 (30)
49 COG1645 Uncharacterized Zn-fin 91.6 0.11 2.5E-06 47.3 2.2 23 3-28 30-52 (131)
50 TIGR00569 ccl1 cyclin ccl1. Un 91.6 0.49 1.1E-05 49.4 7.1 71 176-246 60-130 (305)
51 TIGR02098 MJ0042_CXXC MJ0042 f 91.4 0.11 2.3E-06 37.0 1.4 30 2-31 3-36 (38)
52 smart00661 RPOL9 RNA polymeras 91.2 0.16 3.4E-06 38.4 2.2 30 3-32 2-32 (52)
53 PRK00432 30S ribosomal protein 90.9 0.16 3.5E-06 38.8 2.1 26 3-30 22-47 (50)
54 smart00778 Prim_Zn_Ribbon Zinc 90.7 0.2 4.4E-06 35.9 2.2 27 2-28 4-33 (37)
55 PF14354 Lar_restr_allev: Rest 90.6 0.2 4.4E-06 39.3 2.5 27 2-28 4-37 (61)
56 COG1997 RPL43A Ribosomal prote 90.6 0.18 4E-06 42.7 2.3 29 3-32 37-65 (89)
57 PF08613 Cyclin: Cyclin; Inte 90.4 4.1 8.9E-05 37.9 11.5 89 74-164 54-148 (149)
58 PF03966 Trm112p: Trm112p-like 90.2 0.23 5.1E-06 40.1 2.6 17 14-30 47-63 (68)
59 KOG4164 Cyclin ik3-1/CABLES [C 89.6 1 2.2E-05 48.0 7.3 90 75-166 386-480 (497)
60 PRK11827 hypothetical protein; 89.6 0.27 5.9E-06 39.0 2.3 27 3-30 10-36 (60)
61 PRK00398 rpoP DNA-directed RNA 89.2 0.3 6.5E-06 36.3 2.3 27 3-30 5-31 (46)
62 PF00134 Cyclin_N: Cyclin, N-t 89.2 1.4 3E-05 38.8 7.0 67 176-244 35-102 (127)
63 PRK00464 nrdR transcriptional 89.1 0.27 5.9E-06 46.3 2.5 29 2-30 1-38 (154)
64 TIGR03655 anti_R_Lar restricti 88.0 0.39 8.5E-06 36.9 2.3 31 2-32 2-38 (53)
65 PF05460 ORC6: Origin recognit 87.1 0.19 4E-06 53.6 0.0 86 80-165 3-89 (353)
66 COG2835 Uncharacterized conser 87.0 0.43 9.4E-06 37.7 2.0 28 2-30 9-36 (60)
67 COG1594 RPB9 DNA-directed RNA 86.9 0.42 9.2E-06 42.7 2.1 33 1-33 2-35 (113)
68 COG1998 RPS31 Ribosomal protei 85.8 0.46 1E-05 36.1 1.5 26 3-29 21-46 (51)
69 PF10571 UPF0547: Uncharacteri 85.7 0.45 9.7E-06 31.4 1.3 24 3-31 2-25 (26)
70 PF09538 FYDLN_acid: Protein o 85.6 0.44 9.6E-06 42.3 1.6 29 3-33 11-39 (108)
71 PF13719 zinc_ribbon_5: zinc-r 85.6 0.45 9.9E-06 33.9 1.3 28 3-30 4-35 (37)
72 PF09297 zf-NADH-PPase: NADH p 85.2 0.78 1.7E-05 31.5 2.3 26 3-29 5-30 (32)
73 KOG1779 40s ribosomal protein 84.4 0.5 1.1E-05 39.2 1.3 30 2-31 35-64 (84)
74 smart00342 HTH_ARAC helix_turn 84.4 4.2 9.1E-05 32.3 6.8 71 78-157 4-75 (84)
75 PRK09678 DNA-binding transcrip 84.2 0.85 1.8E-05 37.6 2.5 30 1-30 1-39 (72)
76 COG4640 Predicted membrane pro 84.0 0.54 1.2E-05 50.1 1.6 26 1-31 1-26 (465)
77 PF08273 Prim_Zn_Ribbon: Zinc- 83.6 0.72 1.6E-05 33.6 1.7 27 3-29 5-35 (40)
78 PF06677 Auto_anti-p27: Sjogre 83.5 0.85 1.9E-05 33.4 2.0 23 3-27 19-41 (41)
79 COG4888 Uncharacterized Zn rib 83.3 0.67 1.5E-05 40.3 1.6 29 3-31 24-57 (104)
80 PRK14892 putative transcriptio 83.0 0.81 1.8E-05 40.0 2.1 30 3-32 23-54 (99)
81 PF07282 OrfB_Zn_ribbon: Putat 82.8 0.88 1.9E-05 36.5 2.1 29 3-32 30-58 (69)
82 PRK00135 scpB segregation and 82.3 21 0.00046 34.8 11.8 151 115-312 5-168 (188)
83 PF12760 Zn_Tnp_IS1595: Transp 82.3 1.3 2.7E-05 33.0 2.6 26 3-28 20-45 (46)
84 KOG4557 Origin recognition com 82.1 4.4 9.4E-05 40.1 6.8 80 77-159 95-179 (262)
85 TIGR02300 FYDLN_acid conserved 81.7 0.86 1.9E-05 41.4 1.8 29 3-33 11-39 (129)
86 smart00440 ZnF_C2C2 C2C2 Zinc 81.7 1 2.2E-05 32.7 1.8 27 3-29 2-37 (40)
87 PRK09710 lar restriction allev 81.5 1.2 2.5E-05 35.8 2.3 28 3-30 8-37 (64)
88 KOG1010 Rb (Retinoblastoma tum 80.8 4.3 9.2E-05 47.4 7.3 84 72-157 678-763 (920)
89 PF05191 ADK_lid: Adenylate ki 80.4 0.46 9.9E-06 33.8 -0.3 28 3-30 3-31 (36)
90 PF01780 Ribosomal_L37ae: Ribo 80.3 0.92 2E-05 38.9 1.4 31 3-34 37-67 (90)
91 TIGR00244 transcriptional regu 80.2 1.4 3.1E-05 41.0 2.8 28 2-29 1-37 (147)
92 KOG2906 RNA polymerase III sub 80.2 1.2 2.5E-05 38.7 2.0 31 1-31 1-32 (105)
93 KOG0834 CDK9 kinase-activating 79.3 3.5 7.5E-05 43.5 5.6 66 177-244 44-109 (323)
94 PF12773 DZR: Double zinc ribb 79.0 1.1 2.3E-05 33.7 1.3 12 19-30 28-39 (50)
95 PRK06266 transcription initiat 78.8 0.62 1.4E-05 44.9 -0.1 30 3-32 119-148 (178)
96 PF05876 Terminase_GpA: Phage 78.5 1 2.2E-05 51.0 1.4 33 2-34 201-243 (557)
97 PRK12495 hypothetical protein; 78.4 1.3 2.8E-05 43.9 2.0 27 3-32 44-70 (226)
98 TIGR00686 phnA alkylphosphonat 78.2 3.1 6.8E-05 36.8 4.1 30 2-33 3-32 (109)
99 COG2888 Predicted Zn-ribbon RN 78.1 1.3 2.7E-05 35.1 1.4 9 20-28 50-58 (61)
100 PRK14559 putative protein seri 77.2 1.3 2.7E-05 51.0 1.8 25 1-30 1-25 (645)
101 PTZ00255 60S ribosomal protein 76.1 1.9 4E-05 37.1 2.1 31 3-34 38-68 (90)
102 PRK10220 hypothetical protein; 75.8 2.1 4.5E-05 37.9 2.3 29 3-33 5-33 (111)
103 PF15616 TerY-C: TerY-C metal 74.1 1.8 4E-05 39.7 1.6 19 3-29 79-97 (131)
104 TIGR01384 TFS_arch transcripti 73.7 2.1 4.5E-05 37.3 1.8 27 3-32 2-28 (104)
105 cd06571 Bac_DnaA_C C-terminal 73.1 13 0.00027 31.6 6.5 42 120-163 33-75 (90)
106 COG3809 Uncharacterized protei 72.7 2.7 5.8E-05 35.1 2.1 30 1-30 1-31 (88)
107 PF13717 zinc_ribbon_4: zinc-r 72.7 2.2 4.8E-05 30.2 1.4 28 3-30 4-35 (36)
108 PF01096 TFIIS_C: Transcriptio 72.0 2.5 5.5E-05 30.5 1.6 27 3-29 2-37 (39)
109 TIGR02010 IscR iron-sulfur clu 72.0 8.7 0.00019 35.0 5.6 47 114-160 6-52 (135)
110 TIGR00280 L37a ribosomal prote 71.8 2.6 5.6E-05 36.3 1.9 31 3-34 37-67 (91)
111 PRK13130 H/ACA RNA-protein com 71.2 1.8 3.9E-05 34.0 0.7 34 1-44 5-38 (56)
112 KOG2496 Cdk activating kinase 70.7 14 0.0003 38.5 7.2 71 175-245 59-129 (325)
113 PF11672 DUF3268: Protein of u 70.2 3.5 7.6E-05 36.3 2.4 31 2-32 3-43 (102)
114 PF04079 DUF387: Putative tran 70.2 28 0.00061 33.0 8.7 135 118-295 2-148 (159)
115 PRK12286 rpmF 50S ribosomal pr 69.9 2.8 6E-05 33.0 1.6 27 2-34 28-54 (57)
116 PF09986 DUF2225: Uncharacteri 69.6 17 0.00037 36.0 7.5 48 78-126 78-125 (214)
117 PRK14890 putative Zn-ribbon RN 69.1 3.3 7.2E-05 32.7 1.8 25 4-29 10-34 (59)
118 PF01783 Ribosomal_L32p: Ribos 68.5 2.1 4.5E-05 33.4 0.6 25 2-32 27-51 (56)
119 smart00834 CxxC_CXXC_SSSS Puta 68.2 3.2 7E-05 29.5 1.5 28 3-30 7-36 (41)
120 PF02082 Rrf2: Transcriptional 67.2 9 0.0002 31.8 4.3 45 116-160 8-52 (83)
121 PRK03976 rpl37ae 50S ribosomal 67.1 3.6 7.9E-05 35.3 1.8 32 3-35 38-69 (90)
122 COG1327 Predicted transcriptio 66.9 3.6 7.9E-05 38.5 1.9 28 2-29 1-37 (156)
123 smart00659 RPOLCX RNA polymera 66.8 3.7 8.1E-05 30.5 1.6 25 3-29 4-28 (44)
124 PF00325 Crp: Bacterial regula 66.4 7.9 0.00017 26.9 3.0 27 133-159 2-28 (32)
125 COG3478 Predicted nucleic-acid 66.4 3.5 7.6E-05 33.1 1.5 14 2-15 5-18 (68)
126 TIGR01031 rpmF_bact ribosomal 66.1 4.1 8.8E-05 31.8 1.8 25 2-32 27-51 (55)
127 PF01857 RB_B: Retinoblastoma- 66.0 22 0.00047 32.8 6.9 66 179-246 18-85 (135)
128 TIGR03697 NtcA_cyano global ni 65.6 28 0.00061 32.6 7.9 29 132-160 142-170 (193)
129 PF12773 DZR: Double zinc ribb 65.5 4.3 9.4E-05 30.3 1.8 21 2-27 30-50 (50)
130 COG1326 Uncharacterized archae 65.4 2.9 6.3E-05 40.7 1.0 29 3-32 8-42 (201)
131 PF08613 Cyclin: Cyclin; Inte 65.1 40 0.00087 31.2 8.6 80 172-253 51-136 (149)
132 PF05129 Elf1: Transcription e 64.8 3.7 8E-05 34.6 1.4 31 3-33 24-59 (81)
133 PF03604 DNA_RNApol_7kD: DNA d 64.2 4.5 9.7E-05 28.1 1.5 24 3-28 2-25 (32)
134 PRK10857 DNA-binding transcrip 63.2 16 0.00035 34.7 5.6 47 114-160 6-52 (164)
135 PF14353 CpXC: CpXC protein 62.1 5.1 0.00011 36.1 2.0 11 20-30 38-48 (128)
136 PF13545 HTH_Crp_2: Crp-like h 61.8 20 0.00043 28.6 5.2 43 118-160 3-55 (76)
137 PRK11920 rirA iron-responsive 61.5 19 0.00041 33.7 5.7 46 114-160 6-51 (153)
138 PF09855 DUF2082: Nucleic-acid 61.3 5.9 0.00013 31.9 1.9 27 3-29 2-45 (64)
139 PF10122 Mu-like_Com: Mu-like 61.2 2.5 5.4E-05 32.4 -0.2 29 2-30 5-34 (51)
140 cd00350 rubredoxin_like Rubred 60.8 6.3 0.00014 27.3 1.8 23 3-28 3-25 (33)
141 COG1656 Uncharacterized conser 60.1 4 8.6E-05 38.9 0.9 29 2-30 98-140 (165)
142 COG1386 scpB Chromosome segreg 60.0 1.7E+02 0.0037 28.5 12.1 150 116-313 10-171 (184)
143 PF14255 Cys_rich_CPXG: Cystei 59.5 6.1 0.00013 30.5 1.7 30 2-31 1-35 (52)
144 COG2824 PhnA Uncharacterized Z 58.7 12 0.00026 33.1 3.5 31 2-34 4-34 (112)
145 TIGR00281 segregation and cond 58.3 1.8E+02 0.0038 28.4 11.9 149 116-312 3-165 (186)
146 PF01325 Fe_dep_repress: Iron 58.0 30 0.00065 27.2 5.4 38 122-160 12-49 (60)
147 PF06044 DRP: Dam-replacing fa 57.9 4.5 9.7E-05 40.8 0.9 29 2-30 32-63 (254)
148 PF03119 DNA_ligase_ZBD: NAD-d 56.7 7.7 0.00017 26.0 1.6 22 3-25 1-22 (28)
149 COG0777 AccD Acetyl-CoA carbox 56.5 3.4 7.3E-05 42.4 -0.3 30 1-30 28-57 (294)
150 PF14446 Prok-RING_1: Prokaryo 56.4 7.3 0.00016 30.4 1.6 26 3-31 7-32 (54)
151 COG0333 RpmF Ribosomal protein 56.3 7.2 0.00016 30.7 1.6 27 1-33 27-53 (57)
152 PRK05654 acetyl-CoA carboxylas 56.2 3.1 6.7E-05 43.3 -0.6 29 2-30 28-56 (292)
153 COG5333 CCL1 Cdk activating ki 56.0 9.1 0.0002 39.8 2.8 55 176-232 49-103 (297)
154 TIGR00515 accD acetyl-CoA carb 55.9 3.2 7E-05 43.0 -0.5 29 2-30 27-55 (285)
155 CHL00174 accD acetyl-CoA carbo 55.1 3.3 7.1E-05 43.1 -0.6 29 2-30 39-67 (296)
156 PF11023 DUF2614: Protein of u 54.3 4.7 0.0001 35.9 0.3 39 2-43 70-108 (114)
157 PF14122 YokU: YokU-like prote 54.2 7.4 0.00016 33.0 1.5 23 18-40 33-55 (87)
158 PF13613 HTH_Tnp_4: Helix-turn 54.2 24 0.00051 26.8 4.2 34 131-164 17-50 (53)
159 TIGR02605 CxxC_CxxC_SSSS putat 54.2 7.4 0.00016 29.3 1.4 26 3-28 7-34 (52)
160 KOG0794 CDK8 kinase-activating 54.0 22 0.00047 35.8 4.9 57 176-234 45-101 (264)
161 PRK00241 nudC NADH pyrophospha 52.9 10 0.00022 38.7 2.5 29 2-31 100-128 (256)
162 PRK12380 hydrogenase nickel in 52.9 7.9 0.00017 34.5 1.5 36 2-42 71-106 (113)
163 PRK05978 hypothetical protein; 52.8 10 0.00022 35.7 2.3 30 2-31 34-63 (148)
164 cd00092 HTH_CRP helix_turn_hel 52.8 53 0.0011 25.2 6.2 31 130-160 22-52 (67)
165 COG1996 RPC10 DNA-directed RNA 52.7 6.9 0.00015 29.9 1.0 26 3-29 8-33 (49)
166 PF10668 Phage_terminase: Phag 52.4 33 0.00072 27.3 4.8 38 214-254 5-42 (60)
167 PF08279 HTH_11: HTH domain; 52.3 34 0.00074 25.6 4.8 34 128-161 10-43 (55)
168 TIGR00738 rrf2_super rrf2 fami 52.0 33 0.00072 30.5 5.5 45 115-159 7-51 (132)
169 cd00202 ZnF_GATA Zinc finger D 51.9 5.6 0.00012 30.8 0.4 29 3-31 1-32 (54)
170 PRK12336 translation initiatio 51.8 7.4 0.00016 38.3 1.3 29 2-30 99-129 (201)
171 PRK11161 fumarate/nitrate redu 51.5 61 0.0013 31.6 7.8 29 132-160 183-211 (235)
172 PF00301 Rubredoxin: Rubredoxi 51.4 8.8 0.00019 29.0 1.4 13 21-33 2-14 (47)
173 PRK09210 RNA polymerase sigma 51.0 3.4E+02 0.0074 29.0 16.7 90 66-155 130-254 (367)
174 PF07754 DUF1610: Domain of un 50.7 12 0.00026 24.4 1.6 24 4-28 1-24 (24)
175 PRK10572 DNA-binding transcrip 50.5 72 0.0016 32.3 8.4 26 132-157 247-273 (290)
176 PRK08402 replication factor A; 50.4 9.8 0.00021 40.7 2.0 26 3-29 214-239 (355)
177 PF00165 HTH_AraC: Bacterial r 50.3 24 0.00051 25.2 3.5 27 131-157 6-32 (42)
178 smart00401 ZnF_GATA zinc finge 50.2 11 0.00023 29.0 1.7 28 3-30 5-35 (52)
179 KOG2593 Transcription initiati 49.9 7.3 0.00016 42.3 1.0 30 3-32 130-165 (436)
180 COG3877 Uncharacterized protei 49.7 94 0.002 27.6 7.5 67 123-202 52-120 (122)
181 COG3877 Uncharacterized protei 49.5 12 0.00026 33.0 2.1 27 3-34 8-34 (122)
182 TIGR02944 suf_reg_Xantho FeS a 49.1 42 0.00092 30.0 5.7 45 114-159 7-51 (130)
183 PRK11511 DNA-binding transcrip 48.9 68 0.0015 28.8 7.0 42 115-157 8-49 (127)
184 PF00356 LacI: Bacterial regul 48.7 21 0.00045 26.7 3.0 19 135-153 1-19 (46)
185 TIGR02443 conserved hypothetic 48.6 14 0.00031 29.2 2.2 28 2-29 10-40 (59)
186 COG2093 DNA-directed RNA polym 48.2 10 0.00022 30.4 1.3 21 3-28 6-26 (64)
187 PF01485 IBR: IBR domain; Int 48.2 14 0.00029 28.5 2.0 28 2-30 19-50 (64)
188 KOG0402 60S ribosomal protein 48.2 6.7 0.00015 33.1 0.3 30 3-33 38-67 (92)
189 COG5349 Uncharacterized protei 47.7 9.9 0.00021 34.4 1.3 29 3-32 23-52 (126)
190 PF04216 FdhE: Protein involve 47.6 9.7 0.00021 39.3 1.5 28 3-30 174-207 (290)
191 PF01396 zf-C4_Topoisom: Topoi 47.4 23 0.00049 25.5 2.9 30 2-31 2-35 (39)
192 PF09526 DUF2387: Probable met 47.3 14 0.00031 30.3 2.1 29 3-31 10-41 (71)
193 PF12833 HTH_18: Helix-turn-he 47.2 80 0.0017 25.4 6.6 67 81-157 1-70 (81)
194 smart00647 IBR In Between Ring 46.8 17 0.00036 28.0 2.4 29 2-30 19-50 (64)
195 PRK02935 hypothetical protein; 46.8 12 0.00027 33.0 1.7 38 2-42 71-108 (110)
196 cd00730 rubredoxin Rubredoxin; 46.6 14 0.00031 28.2 1.9 13 21-33 2-14 (50)
197 TIGR03831 YgiT_finger YgiT-typ 46.5 15 0.00032 26.5 1.9 10 21-30 33-42 (46)
198 TIGR03830 CxxCG_CxxCG_HTH puta 46.3 15 0.00032 32.5 2.3 20 133-152 78-97 (127)
199 PF09723 Zn-ribbon_8: Zinc rib 45.1 13 0.00028 27.2 1.4 26 3-28 7-34 (42)
200 TIGR00100 hypA hydrogenase nic 45.1 13 0.00027 33.3 1.6 34 3-41 72-105 (115)
201 PF13936 HTH_38: Helix-turn-he 44.8 25 0.00053 25.8 2.8 28 227-254 13-40 (44)
202 PRK03824 hypA hydrogenase nick 44.3 13 0.00028 34.2 1.6 11 19-29 106-116 (135)
203 PRK10219 DNA-binding transcrip 44.1 1.1E+02 0.0023 26.3 7.3 39 118-157 7-45 (107)
204 PRK08351 DNA-directed RNA poly 44.1 14 0.0003 29.6 1.5 20 3-29 5-24 (61)
205 KOG0654 G2/Mitotic-specific cy 44.1 1.7E+02 0.0036 31.6 9.9 164 75-254 148-315 (359)
206 PF06397 Desulfoferrod_N: Desu 44.0 11 0.00024 26.9 0.8 21 3-23 8-28 (36)
207 PRK08329 threonine synthase; V 43.8 15 0.00032 39.0 2.1 26 1-31 1-26 (347)
208 COG1959 Predicted transcriptio 43.5 54 0.0012 30.6 5.7 45 116-160 8-52 (150)
209 smart00419 HTH_CRP helix_turn_ 43.4 38 0.00083 24.1 3.7 30 131-160 6-35 (48)
210 PF13824 zf-Mss51: Zinc-finger 43.3 16 0.00035 28.6 1.7 24 3-30 1-24 (55)
211 COG3677 Transposase and inacti 43.1 16 0.00034 33.5 1.9 31 1-31 30-64 (129)
212 PF08646 Rep_fac-A_C: Replicat 42.9 18 0.00038 33.3 2.3 28 3-32 20-49 (146)
213 PF13542 HTH_Tnp_ISL3: Helix-t 42.8 80 0.0017 23.3 5.5 23 134-156 28-50 (52)
214 COG4068 Uncharacterized protei 42.6 5.5 0.00012 31.4 -1.0 24 3-31 10-34 (64)
215 PF04606 Ogr_Delta: Ogr/Delta- 42.5 16 0.00034 27.3 1.5 28 3-30 1-37 (47)
216 PF10080 DUF2318: Predicted me 42.4 15 0.00033 32.3 1.7 31 3-35 37-67 (102)
217 PRK03681 hypA hydrogenase nick 42.3 15 0.00032 32.9 1.5 35 3-41 72-106 (114)
218 PRK10402 DNA-binding transcrip 42.2 76 0.0016 31.0 6.8 46 115-160 151-196 (226)
219 KOG3915 Transcription regulato 42.2 77 0.0017 35.0 7.1 18 412-433 530-547 (641)
220 PRK11753 DNA-binding transcrip 41.8 1.1E+02 0.0024 29.1 7.7 29 132-160 167-195 (211)
221 COG1779 C4-type Zn-finger prot 41.4 12 0.00026 36.7 0.9 34 2-35 15-58 (201)
222 PF04161 Arv1: Arv1-like famil 41.4 13 0.00028 36.6 1.2 32 2-33 1-37 (208)
223 PRK06030 hypothetical protein; 40.8 86 0.0019 28.6 6.3 39 121-161 59-97 (124)
224 PF13022 HTH_Tnp_1_2: Helix-tu 40.7 35 0.00076 31.8 3.8 36 219-254 16-54 (142)
225 PF04810 zf-Sec23_Sec24: Sec23 40.5 23 0.00051 25.5 2.1 28 2-29 3-33 (40)
226 TIGR00595 priA primosomal prot 40.5 20 0.00042 40.2 2.6 29 2-31 223-251 (505)
227 KOG1088 Uncharacterized conser 40.4 12 0.00027 33.6 0.8 18 14-31 92-109 (124)
228 PF04545 Sigma70_r4: Sigma-70, 40.2 58 0.0012 24.0 4.3 31 131-161 18-48 (50)
229 PF14206 Cys_rich_CPCC: Cystei 39.6 22 0.00048 29.8 2.1 28 2-29 2-29 (78)
230 PRK05657 RNA polymerase sigma 39.3 4.8E+02 0.01 27.4 15.5 22 233-254 281-302 (325)
231 PF12802 MarR_2: MarR family; 39.1 75 0.0016 24.1 5.0 41 120-160 8-48 (62)
232 PF13453 zf-TFIIB: Transcripti 38.7 25 0.00053 25.4 2.0 27 3-29 1-28 (41)
233 COG1318 Predicted transcriptio 38.7 39 0.00085 32.5 3.8 25 231-255 58-82 (182)
234 PF00196 GerE: Bacterial regul 38.6 45 0.00098 25.5 3.6 33 133-165 18-50 (58)
235 PF01155 HypA: Hydrogenase exp 38.4 7.8 0.00017 34.5 -0.8 34 3-41 72-105 (113)
236 TIGR00155 pqiA_fam integral me 38.3 19 0.00042 39.2 2.0 29 3-31 15-44 (403)
237 TIGR02297 HpaA 4-hydroxyphenyl 38.1 1.7E+02 0.0037 29.3 8.8 38 119-157 189-226 (287)
238 PF04967 HTH_10: HTH DNA bindi 37.7 56 0.0012 25.3 3.9 30 225-254 9-43 (53)
239 PRK03564 formate dehydrogenase 37.3 23 0.00049 37.3 2.3 27 3-29 189-221 (309)
240 PF05344 DUF746: Domain of Unk 36.9 80 0.0017 25.6 4.8 45 127-180 7-51 (65)
241 PRK09391 fixK transcriptional 36.6 1.6E+02 0.0035 28.9 8.1 29 132-160 178-206 (230)
242 PF13412 HTH_24: Winged helix- 36.5 1.1E+02 0.0023 22.3 5.2 28 132-159 16-43 (48)
243 PRK05580 primosome assembly pr 36.1 25 0.00053 40.9 2.5 29 2-31 391-419 (679)
244 PRK05901 RNA polymerase sigma 36.0 6.9E+02 0.015 28.3 16.1 89 65-153 271-394 (509)
245 PRK14873 primosome assembly pr 35.9 23 0.0005 41.1 2.2 27 2-29 393-419 (665)
246 PRK13918 CRP/FNR family transc 35.6 1.5E+02 0.0033 27.9 7.6 29 132-160 148-176 (202)
247 PRK01110 rpmF 50S ribosomal pr 35.4 19 0.00041 28.6 1.0 27 2-35 28-54 (60)
248 KOG1010 Rb (Retinoblastoma tum 35.3 83 0.0018 37.3 6.4 58 75-135 35-92 (920)
249 smart00421 HTH_LUXR helix_turn 35.0 72 0.0016 23.1 4.2 31 134-164 19-49 (58)
250 PF00320 GATA: GATA zinc finge 35.0 11 0.00024 26.6 -0.3 25 4-28 1-28 (36)
251 PRK10130 transcriptional regul 34.9 3.3E+02 0.0072 29.0 10.7 53 116-182 240-292 (350)
252 PRK14559 putative protein seri 34.8 21 0.00045 41.2 1.7 25 3-32 29-53 (645)
253 PRK14088 dnaA chromosomal repl 34.8 57 0.0012 35.8 5.0 68 91-161 345-415 (440)
254 PRK14086 dnaA chromosomal repl 34.7 96 0.0021 35.8 6.8 71 91-163 527-599 (617)
255 smart00550 Zalpha Z-DNA-bindin 34.7 1E+02 0.0022 24.6 5.3 38 123-160 11-49 (68)
256 cd04476 RPA1_DBD_C RPA1_DBD_C: 34.7 26 0.00056 32.9 2.0 27 3-31 36-62 (166)
257 cd00729 rubredoxin_SM Rubredox 33.6 32 0.00069 24.0 1.8 24 3-29 4-27 (34)
258 PF04703 FaeA: FaeA-like prote 33.6 71 0.0015 25.5 4.0 34 131-164 13-46 (62)
259 TIGR00319 desulf_FeS4 desulfof 33.5 26 0.00056 24.2 1.3 20 4-23 10-29 (34)
260 TIGR00310 ZPR1_znf ZPR1 zinc f 33.4 27 0.00059 34.2 2.0 30 3-32 2-42 (192)
261 TIGR01562 FdhE formate dehydro 33.4 28 0.0006 36.6 2.2 9 20-28 224-232 (305)
262 PF12116 SpoIIID: Stage III sp 33.2 33 0.00072 28.9 2.1 30 225-254 10-39 (82)
263 PRK06393 rpoE DNA-directed RNA 33.1 24 0.00053 28.4 1.3 19 3-28 7-25 (64)
264 PRK00564 hypA hydrogenase nick 33.0 21 0.00046 32.0 1.1 35 3-41 73-107 (117)
265 PRK13501 transcriptional activ 32.9 1.6E+02 0.0034 29.8 7.7 34 124-157 231-266 (290)
266 PRK13503 transcriptional activ 32.9 2.2E+02 0.0047 28.3 8.6 36 122-157 224-261 (278)
267 PF13404 HTH_AsnC-type: AsnC-t 32.8 62 0.0013 23.6 3.3 26 229-254 12-37 (42)
268 PF10083 DUF2321: Uncharacteri 32.8 18 0.00039 34.1 0.6 15 22-36 41-55 (158)
269 PRK03564 formate dehydrogenase 32.7 31 0.00067 36.3 2.4 11 21-31 253-263 (309)
270 PRK15103 paraquat-inducible me 32.6 25 0.00054 38.5 1.8 30 3-32 12-42 (419)
271 PF14768 RPA_interact_C: Repli 32.6 35 0.00075 28.6 2.2 26 3-31 1-26 (82)
272 cd00974 DSRD Desulforedoxin (D 32.4 28 0.0006 24.1 1.4 22 3-24 6-27 (34)
273 cd06170 LuxR_C_like C-terminal 32.3 89 0.0019 22.7 4.3 32 133-164 15-46 (57)
274 PF13790 DUF4182: Domain of un 32.0 23 0.0005 25.6 0.9 14 19-32 2-15 (38)
275 PF01599 Ribosomal_S27: Riboso 32.0 42 0.00091 25.4 2.3 25 3-28 20-46 (47)
276 PF10668 Phage_terminase: Phag 31.8 1.3E+02 0.0027 24.1 5.1 24 130-153 19-42 (60)
277 PRK11014 transcriptional repre 31.7 96 0.0021 28.3 5.3 46 115-160 7-52 (141)
278 PF04967 HTH_10: HTH DNA bindi 31.7 2.1E+02 0.0045 22.1 6.2 44 98-159 6-49 (53)
279 PRK15121 right oriC-binding tr 31.7 1.2E+02 0.0025 31.0 6.5 41 116-157 5-45 (289)
280 PF10058 DUF2296: Predicted in 31.4 25 0.00054 27.3 1.1 27 3-29 24-53 (54)
281 PF09339 HTH_IclR: IclR helix- 31.4 88 0.0019 23.4 4.1 36 124-159 9-44 (52)
282 PRK09978 DNA-binding transcrip 30.9 1.7E+02 0.0038 30.2 7.5 86 78-188 161-249 (274)
283 TIGR01562 FdhE formate dehydro 30.8 28 0.00061 36.5 1.7 28 3-30 186-220 (305)
284 PF08220 HTH_DeoR: DeoR-like h 30.4 34 0.00074 26.4 1.7 20 234-253 14-33 (57)
285 PF06827 zf-FPG_IleRS: Zinc fi 30.4 24 0.00053 23.6 0.8 26 3-28 3-29 (30)
286 PHA03074 late transcription fa 30.3 27 0.00058 34.4 1.3 27 3-31 6-32 (225)
287 PRK09393 ftrA transcriptional 30.1 1.7E+02 0.0036 30.3 7.4 83 78-182 237-320 (322)
288 PF01710 HTH_Tnp_IS630: Transp 30.1 3.5E+02 0.0077 23.9 8.5 72 77-157 20-95 (119)
289 COG2816 NPY1 NTP pyrophosphohy 29.9 31 0.00067 35.7 1.8 29 3-32 113-141 (279)
290 PF06676 DUF1178: Protein of u 29.5 27 0.00058 32.9 1.1 26 86-113 96-121 (148)
291 PF08299 Bac_DnaA_C: Bacterial 29.3 1.4E+02 0.003 24.1 5.2 35 121-157 35-70 (70)
292 PF04502 DUF572: Family of unk 29.2 25 0.00054 37.1 1.0 9 22-30 79-87 (324)
293 KOG3507 DNA-directed RNA polym 29.2 32 0.00069 27.3 1.3 24 3-28 22-45 (62)
294 PHA00689 hypothetical protein 28.9 32 0.00069 26.3 1.3 9 20-28 17-25 (62)
295 COG4391 Uncharacterized protei 28.6 31 0.00067 27.6 1.2 14 17-30 45-58 (62)
296 PRK05932 RNA polymerase factor 28.4 4.8E+02 0.01 29.0 10.8 78 77-162 140-236 (455)
297 PF02796 HTH_7: Helix-turn-hel 28.4 46 0.001 24.3 2.1 26 229-254 16-41 (45)
298 TIGR02297 HpaA 4-hydroxyphenyl 28.3 2.1E+02 0.0045 28.7 7.6 69 78-157 205-276 (287)
299 PRK00085 recO DNA repair prote 28.2 33 0.00072 34.1 1.7 25 3-27 151-177 (247)
300 PF13463 HTH_27: Winged helix 28.1 1.2E+02 0.0025 23.4 4.5 32 129-160 14-45 (68)
301 PRK10219 DNA-binding transcrip 28.1 2.7E+02 0.0058 23.7 7.2 71 78-157 24-95 (107)
302 TIGR02393 RpoD_Cterm RNA polym 28.0 5.9E+02 0.013 25.1 17.6 22 233-254 195-216 (238)
303 PF04545 Sigma70_r4: Sigma-70, 28.0 80 0.0017 23.2 3.4 24 231-254 17-40 (50)
304 PRK09685 DNA-binding transcrip 27.9 3.1E+02 0.0068 27.7 8.9 41 115-155 196-236 (302)
305 PRK12366 replication factor A; 27.8 28 0.00061 40.2 1.2 24 3-29 534-557 (637)
306 PF01807 zf-CHC2: CHC2 zinc fi 27.6 33 0.00071 29.6 1.3 27 2-28 34-62 (97)
307 PF14471 DUF4428: Domain of un 27.5 22 0.00047 27.3 0.2 27 3-30 1-30 (51)
308 PF14319 Zn_Tnp_IS91: Transpos 27.4 34 0.00073 30.4 1.4 32 3-35 44-75 (111)
309 PRK11511 DNA-binding transcrip 27.4 2.5E+02 0.0054 25.0 7.1 71 78-157 28-99 (127)
310 COG1110 Reverse gyrase [DNA re 27.3 25 0.00055 42.3 0.7 43 481-523 891-933 (1187)
311 PRK09392 ftrB transcriptional 27.2 1.9E+02 0.004 28.2 6.8 29 132-160 172-200 (236)
312 PRK07218 replication factor A; 27.0 31 0.00068 37.8 1.3 31 3-42 299-329 (423)
313 PF08281 Sigma70_r4_2: Sigma-7 27.0 1E+02 0.0022 22.9 3.8 27 134-160 27-53 (54)
314 PRK00149 dnaA chromosomal repl 27.0 1.2E+02 0.0026 33.2 5.9 71 91-163 360-433 (450)
315 TIGR03829 YokU_near_AblA uncha 26.7 45 0.00098 28.7 1.9 14 20-33 35-48 (89)
316 smart00345 HTH_GNTR helix_turn 26.6 1.2E+02 0.0025 22.4 4.2 26 135-160 22-47 (60)
317 PF07191 zinc-ribbons_6: zinc- 26.4 35 0.00075 28.1 1.2 26 2-30 2-27 (70)
318 PF01978 TrmB: Sugar-specific 26.3 80 0.0017 24.8 3.3 37 123-160 13-49 (68)
319 TIGR00613 reco DNA repair prot 26.3 41 0.0009 33.3 2.0 26 3-28 149-176 (241)
320 PF01047 MarR: MarR family; I 26.1 1.8E+02 0.0039 21.8 5.1 37 122-160 8-44 (59)
321 PRK08197 threonine synthase; V 26.0 36 0.00077 36.7 1.5 25 3-31 9-33 (394)
322 COG1773 Rubredoxin [Energy pro 25.8 42 0.00092 26.3 1.5 21 4-27 6-26 (55)
323 PRK15340 transcriptional regul 25.7 3E+02 0.0065 27.5 7.8 71 78-157 128-199 (216)
324 PF01412 ArfGap: Putative GTPa 25.7 21 0.00046 31.7 -0.2 29 3-31 15-44 (116)
325 PF04216 FdhE: Protein involve 25.3 34 0.00074 35.3 1.2 29 3-31 213-249 (290)
326 PF01726 LexA_DNA_bind: LexA D 25.3 1.1E+02 0.0025 24.4 4.0 32 128-159 20-52 (65)
327 COG1571 Predicted DNA-binding 25.3 40 0.00087 36.8 1.7 32 3-36 352-383 (421)
328 PF09889 DUF2116: Uncharacteri 25.2 25 0.00054 27.9 0.1 24 3-31 5-29 (59)
329 PF02042 RWP-RK: RWP-RK domain 25.1 1.1E+02 0.0025 23.6 3.7 31 133-167 15-45 (52)
330 PF07295 DUF1451: Protein of u 25.1 34 0.00074 32.0 1.0 15 17-31 109-123 (146)
331 PF08279 HTH_11: HTH domain; 24.7 78 0.0017 23.6 2.8 24 231-254 12-35 (55)
332 COG1198 PriA Primosomal protei 24.6 50 0.0011 38.8 2.4 26 3-29 446-471 (730)
333 smart00290 ZnF_UBP Ubiquitin C 24.6 50 0.0011 24.4 1.7 23 3-32 1-23 (50)
334 PRK15435 bifunctional DNA-bind 24.6 1.9E+02 0.0042 30.8 6.7 50 116-181 85-134 (353)
335 PRK09685 DNA-binding transcrip 24.6 2.3E+02 0.005 28.6 7.2 25 133-157 264-289 (302)
336 PRK13500 transcriptional activ 24.5 5.8E+02 0.013 26.2 10.2 39 118-157 208-246 (312)
337 PF13384 HTH_23: Homeodomain-l 24.2 1.1E+02 0.0023 22.4 3.5 21 234-254 17-37 (50)
338 PF13913 zf-C2HC_2: zinc-finge 24.2 39 0.00083 21.9 0.8 10 1-10 2-11 (25)
339 smart00351 PAX Paired Box doma 24.1 4E+02 0.0086 23.9 7.7 62 77-143 35-103 (125)
340 PRK14088 dnaA chromosomal repl 23.9 5.9E+02 0.013 28.0 10.5 46 207-254 359-407 (440)
341 TIGR03879 near_KaiC_dom probab 23.8 1.7E+02 0.0036 24.3 4.7 23 233-255 31-53 (73)
342 PRK13502 transcriptional activ 23.8 3.5E+02 0.0076 27.1 8.2 37 121-157 228-266 (282)
343 PRK06260 threonine synthase; V 23.7 41 0.00089 36.3 1.5 26 3-31 5-30 (397)
344 PF14369 zf-RING_3: zinc-finge 23.7 50 0.0011 23.3 1.4 26 3-28 4-29 (35)
345 COG4565 CitB Response regulato 23.6 5.6E+02 0.012 25.8 9.1 89 68-160 111-200 (224)
346 PF13730 HTH_36: Helix-turn-he 23.5 2E+02 0.0042 21.4 4.8 25 135-159 27-51 (55)
347 COG3355 Predicted transcriptio 23.4 1.7E+02 0.0036 26.9 5.0 38 123-160 32-69 (126)
348 cd00674 LysRS_core_class_I cat 23.3 49 0.0011 35.4 1.9 29 2-31 170-203 (353)
349 PF07022 Phage_CI_repr: Bacter 23.1 80 0.0017 25.0 2.7 51 135-216 14-64 (66)
350 PF08063 PADR1: PADR1 (NUC008) 23.0 37 0.0008 26.4 0.7 20 3-24 16-35 (55)
351 PF13413 HTH_25: Helix-turn-he 23.0 1.5E+02 0.0032 23.4 4.2 54 127-188 4-57 (62)
352 PRK13502 transcriptional activ 22.8 2.8E+02 0.0062 27.7 7.4 41 116-157 176-216 (282)
353 PRK08173 DNA topoisomerase III 22.8 47 0.001 39.8 1.8 25 3-30 626-650 (862)
354 PF13542 HTH_Tnp_ISL3: Helix-t 22.8 2.2E+02 0.0048 20.8 5.0 20 235-254 28-47 (52)
355 COG1725 Predicted transcriptio 22.6 97 0.0021 28.3 3.4 26 135-160 37-62 (125)
356 PF13404 HTH_AsnC-type: AsnC-t 22.6 1.8E+02 0.0039 21.2 4.2 29 129-157 13-41 (42)
357 TIGR00155 pqiA_fam integral me 22.4 49 0.0011 36.0 1.8 25 3-31 217-241 (403)
358 PRK00118 putative DNA-binding 22.3 3.1E+02 0.0066 24.2 6.4 59 133-205 33-91 (104)
359 PRK00750 lysK lysyl-tRNA synth 22.3 52 0.0011 36.9 2.0 29 2-31 176-210 (510)
360 PF14952 zf-tcix: Putative tre 22.3 47 0.001 24.8 1.0 24 3-31 13-38 (44)
361 COG1675 TFA1 Transcription ini 22.2 25 0.00054 34.0 -0.5 30 3-33 115-145 (176)
362 PF01846 FF: FF domain; Inter 22.2 1.1E+02 0.0024 22.6 3.2 36 490-525 2-37 (51)
363 TIGR02885 spore_sigF RNA polym 22.2 7.3E+02 0.016 24.1 15.6 23 232-254 197-219 (231)
364 TIGR00340 zpr1_rel ZPR1-relate 22.1 56 0.0012 31.2 1.8 29 4-32 1-40 (163)
365 PRK04023 DNA polymerase II lar 22.0 51 0.0011 39.8 1.9 6 4-9 629-634 (1121)
366 smart00342 HTH_ARAC helix_turn 21.8 1.3E+02 0.0028 23.4 3.8 25 133-157 1-25 (84)
367 PF12172 DUF35_N: Rubredoxin-l 21.6 50 0.0011 23.1 1.1 20 3-27 13-32 (37)
368 TIGR01610 phage_O_Nterm phage 21.5 5.1E+02 0.011 22.0 8.3 31 130-160 44-74 (95)
369 smart00760 Bac_DnaA_C Bacteria 21.5 1.7E+02 0.0037 22.6 4.2 22 121-144 35-56 (60)
370 PF01022 HTH_5: Bacterial regu 21.4 2.4E+02 0.0053 20.5 4.9 31 129-159 11-41 (47)
371 COG4753 Response regulator con 21.4 4.1E+02 0.0088 29.8 8.5 32 128-159 383-414 (475)
372 KOG2907 RNA polymerase I trans 21.3 30 0.00066 30.9 -0.1 32 3-35 9-40 (116)
373 PF13936 HTH_38: Helix-turn-he 21.3 1.6E+02 0.0035 21.4 3.8 25 131-155 18-42 (44)
374 PF05605 zf-Di19: Drought indu 21.3 49 0.0011 25.2 1.1 26 2-28 3-39 (54)
375 PRK15320 transcriptional activ 21.2 2E+02 0.0043 28.7 5.4 36 132-167 178-213 (251)
376 PLN02569 threonine synthase 21.1 52 0.0011 36.7 1.6 25 3-31 51-75 (484)
377 PF03367 zf-ZPR1: ZPR1 zinc-fi 21.0 51 0.0011 31.3 1.3 30 2-31 2-41 (161)
378 PRK13503 transcriptional activ 21.0 1.4E+02 0.0029 29.8 4.6 40 117-157 172-211 (278)
379 PRK06386 replication factor A; 20.9 46 0.001 35.7 1.1 20 3-29 238-257 (358)
380 cd00569 HTH_Hin_like Helix-tur 20.8 1.2E+02 0.0027 18.9 2.9 21 234-254 21-41 (42)
381 PRK15340 transcriptional regul 20.8 7E+02 0.015 24.9 9.4 54 91-157 96-149 (216)
382 smart00418 HTH_ARSR helix_turn 20.8 2.4E+02 0.0051 20.6 4.9 30 131-160 8-37 (66)
383 COG2260 Predicted Zn-ribbon RN 20.8 47 0.001 26.3 0.8 33 1-43 5-37 (59)
384 PF12677 DUF3797: Domain of un 20.7 68 0.0015 24.5 1.6 10 3-12 15-24 (49)
385 PRK09401 reverse gyrase; Revie 20.7 37 0.00081 42.0 0.4 25 3-28 9-33 (1176)
386 PF14951 DUF4503: Domain of un 20.7 58 0.0013 34.9 1.8 33 3-35 276-309 (389)
387 KOG1921 Endonuclease III [Repl 20.5 7.6E+02 0.017 25.4 9.4 61 130-199 152-216 (286)
388 PF00628 PHD: PHD-finger; Int 20.4 75 0.0016 23.4 1.9 26 3-32 1-26 (51)
389 smart00709 Zpr1 Duplicated dom 20.3 74 0.0016 30.2 2.3 31 2-32 1-41 (160)
390 PRK07591 threonine synthase; V 20.2 53 0.0012 35.8 1.5 25 3-31 20-44 (421)
391 PRK14714 DNA polymerase II lar 20.1 60 0.0013 40.1 2.0 25 3-33 681-705 (1337)
392 TIGR02642 phage_xxxx uncharact 20.0 62 0.0013 31.6 1.7 23 2-27 100-122 (186)
No 1
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=100.00 E-value=5.7e-76 Score=621.43 Aligned_cols=452 Identities=32% Similarity=0.463 Sum_probs=357.1
Q ss_pred CCCCCCCCCCeeeecCCCceecCcccceeccccccccccccccCCCCccccCccceeeccc---ccchHHHHHHHHHHHH
Q 009187 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFVKNAAGQSQLSGNFVRTIQSE---YGASRERLMEKAFDDM 78 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~~Ids~~ef~~~s~G~s~v~G~~v~~~~~~---~~~srer~L~~a~~~I 78 (540)
++|++||++++..|+++|.++|+.||+|+|+++|+++++|.+. ++|+||+..|.+ ..++|+++++++++.|
T Consensus 1 ~~C~~C~~s~fe~d~a~g~~~C~~CG~v~E~~~ivsev~F~e~------~~G~~v~~~~~g~~~s~e~r~~t~~n~r~~i 74 (521)
T KOG1598|consen 1 MVCKNCGGSNFERDEATGNLYCTACGTVLEYNNIVAEVTFVEG------AQGQFVRVGQSGAGSSLESREKTIYNARRLI 74 (521)
T ss_pred CcCCCCCCCCcccccccCCceeccccceeeccceeEEeeeecc------cceeEEeccccCCccchHHHHHHHHHHHhHH
Confidence 5799999999999999999999999999999999999999986 679999877654 3489999999999999
Q ss_pred HHHHHHhCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHH
Q 009187 79 RQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLC 158 (540)
Q Consensus 79 ~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~ 158 (540)
..++.+|+|+ + ++++|.+||++|.++||++||+...|+|+|+|++||+++++|+|+||+++++|++|.||++|++|+
T Consensus 75 ~~~~~~l~l~--~-~~~~a~~~~k~a~~~nftkGr~~~~vvasClY~vcR~e~t~hlliDfS~~Lqv~Vy~LG~~~l~l~ 151 (521)
T KOG1598|consen 75 EELTERLNLG--N-KTEVAFNFFKLAPDRNFTKGRRSTEVVAACLYLVCRLEKTDHLLIDFSSYLQVSVYDLGSNFLEVT 151 (521)
T ss_pred HHHHHhcCcc--h-HHHHHHHHHHHHhhCCCCCCcchHHHHHHHHHHHHHhhCCceEEEEeccceEEehhhhhHHHHHHH
Confidence 9999999999 7 999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhccccccccccCChhhHHHHHHHhhC-CCCCHHHHHHHHHHHHhhcccccccCCChhhHHHHHHHHHHHhcCCCCCH
Q 009187 159 QVLYIADESNVLKQVDPSIFLHKFTDRLL-PGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSK 237 (540)
Q Consensus 159 ~~L~i~~~p~~~~~~dP~~~I~Rf~~~L~-~~~~~~V~~~A~~Iv~~m~~~~i~tGR~P~~IAaAALylAa~~~g~~~t~ 237 (540)
+.|.|+. |+.+++||+.||+||+..|. ++.+++|+++|.+|+++|++|||++||+|+||||||||+|||+||+++|+
T Consensus 152 ~~L~i~e--n~~plvDpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~~rsi 229 (521)
T KOG1598|consen 152 DSLSIGE--NVSPLVDPSLYIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGFRRTI 229 (521)
T ss_pred HHhcccc--ccccccCcceeeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCccccH
Confidence 9999985 24568999999999999995 88889999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHcccHHHHhhhh-cCCCCCCCCCCCCccchhhccccCCCCccccchhhhHHHHhhhccccCCCCCChhhHHHHH
Q 009187 238 SDIIEDFMARKKELHEGV-AANLPNNGPKVSGMNEVLCKHKDTGKPFACGLCRSCYEEFMTISEGLEGGADPPAFQVAER 316 (540)
Q Consensus 238 ~eI~~~~~~~~~ti~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~ef~~~~~~l~~~~dpPaf~~~~~ 316 (540)
.||+.++.|++.||++|+ +|..|+++.+ ++++|+.+ |++.++|||+|+..++
T Consensus 230 ~dIv~vvhV~e~Tl~kRl~Ef~~T~s~~L-------------------------ti~ef~~~--d~e~~~~ppsft~~~~ 282 (521)
T KOG1598|consen 230 GDIAKVVHVCESTLSKRLKEFSDTLSGDL-------------------------TIDELAEI--DLEYESDPPSFTASPS 282 (521)
T ss_pred HHHHHHHHHhHHHHHHHHHHHhccccccc-------------------------cHHHHHhh--hhhhccCcchhhcccc
Confidence 999999999999999995 9999988874 78999999 9999999999998775
Q ss_pred H-HHHHHHhhh------hc--ccc----cccCCcccccc---cc-cCCCCCCccCCC----CCCccccccCC------C-
Q 009187 317 E-RMVKASAEE------NS--SFE----RESDSPFMSRV---DK-VQSPEPESIGVP----KNCTTQTASNE------G- 368 (540)
Q Consensus 317 ~-~~~~~~~~~------~~--~~~----~~~~~~~~~~~---~~-~~~~~~~~~~~~----~~~~~~~~~~~------~- 368 (540)
+ ++.....++ .. .+. .....+..... .. .+.+.+...... ....-+...+. |
T Consensus 283 ~~~k~~~~~k~~l~~~~~~~e~~~~~~~~~~~~~~~~~~~~l~~~~q~~~~~~~~~e~~~~~~~e~~~ssE~~dk~~~g~ 362 (521)
T KOG1598|consen 283 KEAKYVEDKKKMLSRTMQLVELANETWLVTLRHSLPVITGGLFLAWQDLQPRDRLVESYDDLASECPLSSEDEDKPASGR 362 (521)
T ss_pred hhhhhhhhhhhhhhhhhhhhhcccchhhhccccCCcccchhhhcccccchhhhhhhhhhhhhhhcCcccccccCCcCccc
Confidence 3 221111111 00 000 00000000000 00 000000000000 00000000000 0
Q ss_pred ----CCCCCC----CCCCCCCCcCCCCCCCCCCCChHHHhhcCCCHHHHHHHHHHHhhhCHHHHHHHHHHHHHHHHHHHH
Q 009187 369 ----EGDHTK----TPGVDATTEASDGSDNFSDIDDFEVDGYLHNEEEKHYKKIIWEEMNREYLEEQAAKEAAAAAAKAA 440 (540)
Q Consensus 369 ----~~~~~~----~~~~~~~~~~~~~~~~lsdiDD~Eid~yil~eeE~~~K~~lW~~~N~eyl~eq~~Ke~~~~~~~~~ 440 (540)
...... ...........++...++++||++++.++|++++.+.++.+ | +|++||.||..+.++++++++.
T Consensus 363 ~~~~~~~~sd~~~~~~~~~~~~~~~d~~~~~~~~~~~~l~r~~l~~~a~~~a~~~-~-~n~e~l~E~~~~~~~~ak~~~~ 440 (521)
T KOG1598|consen 363 LAELLAVLSDMAEQLASVWLRVLTLDKRSGVKHIDDLLLERQLLEESAGRDATEP-M-ENAETLVEERPGKAKAAKEREE 440 (521)
T ss_pred cchhhhcccccchhhhhcchhhhhccccccccccCHHHHHHHHhhhHHhhhcchh-h-hhHHHHHhhchhhhhhhHhhhh
Confidence 000000 00001223345677889999999999999999999999999 7 9999999999998877653221
Q ss_pred HHhhhcCCccchHHHHHHHHHHHHHHhhhhHHHHhhhHhhhccCCCCCCHHHHHHHHHHhcccccccCHHHHhhhhCCCC
Q 009187 441 LEASYKNCPEGLQAAQELAAAAAAAVAKSRKEKQQKRAAEAKNSGPAQTALEATRRMLTKKRLSSKINYDVLEKLFDDSV 520 (540)
Q Consensus 441 ~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~k~k~~k~~~~~~~~~~a~ta~EA~~~ml~~K~~S~KINYdvl~~L~~~~~ 520 (540)
++ .. ++++..+.++++++.||.||+++|++++++|++|||++|+.|||...
T Consensus 441 ------------------------g~-~~----~~~k~~~r~~s~~~~t~~eavk~~~~i~~~s~~in~~~L~~i~d~~~ 491 (521)
T KOG1598|consen 441 ------------------------GI-NS----LSKKVGERRNSPELLTAPEAVKSMKEIKPVSSVINYSVLENISDAEI 491 (521)
T ss_pred ------------------------cc-cc----cccccccccCCCcccccHHHHHHHHhccccccchHHHHHHHHhhhhc
Confidence 11 01 22344455789999999999999999999999999999999998866
Q ss_pred cc
Q 009187 521 CL 522 (540)
Q Consensus 521 ~~ 522 (540)
..
T Consensus 492 e~ 493 (521)
T KOG1598|consen 492 EQ 493 (521)
T ss_pred cc
Confidence 53
No 2
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=100.00 E-value=1.4e-51 Score=425.37 Aligned_cols=244 Identities=22% Similarity=0.372 Sum_probs=222.6
Q ss_pred CCCCCCCCCCeeeecCCCceecCcccceeccccccccccccccCC----CCccccCcc----------------------
Q 009187 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFVKNAA----GQSQLSGNF---------------------- 55 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~~Ids~~ef~~~s~----G~s~v~G~~---------------------- 55 (540)
..||+||+..+++|+.+|++||++||+||+|++||++|||+.+++ ..+|+++..
T Consensus 12 ~~Cp~Cg~~~iv~d~~~Ge~vC~~CG~Vl~e~~iD~g~EWR~f~~~~~~~~~RvG~~~~~~~~~~gl~T~I~~~~~~~~g 91 (310)
T PRK00423 12 LVCPECGSDKLIYDYERGEIVCADCGLVIEENIIDQGPEWRAFDPEQREKRSRVGAPMTYTIHDKGLSTDIDWRNKDSYG 91 (310)
T ss_pred CcCcCCCCCCeeEECCCCeEeecccCCcccccccccCCCccCCCccccCCccccCCCCCccccCCCCceEeecCCccccc
Confidence 369999998899999999999999999999999999999987653 123332211
Q ss_pred --ce-----------eeccc--ccchHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHH
Q 009187 56 --VR-----------TIQSE--YGASRERLMEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQA 120 (540)
Q Consensus 56 --v~-----------~~~~~--~~~srer~L~~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaA 120 (540)
++ .||.+ ..++.||+|..|++.|+++|+.|+|| +.|+++|..||+++++.++++||+.+.++|
T Consensus 92 ~~l~~~~~~~~~rl~~~~~~~~~~~~~er~l~~a~~~I~~~~~~L~Lp--~~v~e~A~~iyk~~~~~~~~rgrs~~~i~A 169 (310)
T PRK00423 92 KSISGKNRAQLYRLRKWQRRIRVSNAAERNLAFALSELDRIASQLGLP--RSVREEAAVIYRKAVEKGLIRGRSIEGVVA 169 (310)
T ss_pred ccccHHHHHHHHHHHHHhhhcccCChHhHHHHHHHHHHHHHHHHcCCC--HHHHHHHHHHHHHHHhcCcccCCCHHHHHH
Confidence 10 22222 23778999999999999999999999 999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHHHhhccccccccccCChhhHHHHHHHhhCCCCCHHHHHHHHH
Q 009187 121 SCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARD 200 (540)
Q Consensus 121 ACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~L~i~~~p~~~~~~dP~~~I~Rf~~~L~~~~~~~V~~~A~~ 200 (540)
||||+|||++++|+||+||+.++++++++|+++|+.|.+.|+++.++ ++|+.||+|||+.|++ +..|.+.|.+
T Consensus 170 AclYiACR~~~~prtl~eI~~~~~v~~k~i~~~~~~l~k~L~~~~~~-----~~p~~~i~r~~~~L~L--~~~v~~~A~~ 242 (310)
T PRK00423 170 AALYAACRRCKVPRTLDEIAEVSRVSRKEIGRCYRFLLRELNLKLPP-----TDPIDYVPRFASELGL--SGEVQKKAIE 242 (310)
T ss_pred HHHHHHHHHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCCC-----CCHHHHHHHHHHHcCC--CHHHHHHHHH
Confidence 99999999999999999999999999999999999999999998766 8999999999999985 7899999999
Q ss_pred HHHhhcccccccCCChhhHHHHHHHHHHHhcCCCCCHHHHHHHHcccHHHHhhh
Q 009187 201 ILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIIEDFMARKKELHEG 254 (540)
Q Consensus 201 Iv~~m~~~~i~tGR~P~~IAaAALylAa~~~g~~~t~~eI~~~~~~~~~ti~~~ 254 (540)
|++.+.+.|++.||+|.+|||||||+||+++|+++|+++|+.++++++.||+++
T Consensus 243 i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~~Vs~~tI~~~ 296 (310)
T PRK00423 243 ILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNR 296 (310)
T ss_pred HHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999998
No 3
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=4.8e-51 Score=413.54 Aligned_cols=245 Identities=24% Similarity=0.444 Sum_probs=224.2
Q ss_pred CCCCCCCCCCCeeeecCCCceecCcccceeccccccccccccccCC-CCccccCc------------c-----------c
Q 009187 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFVKNAA-GQSQLSGN------------F-----------V 56 (540)
Q Consensus 1 m~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~~Ids~~ef~~~s~-G~s~v~G~------------~-----------v 56 (540)
|+.||+||+..+++|+.+|++||.+||.|++++.||.+|+|+-+.. +..++++. + +
T Consensus 1 ~~~CpeCg~~~~~~d~~~ge~VC~~CG~Vi~~~~id~gpewr~f~e~~~~r~g~P~t~~~~d~~l~t~i~~~~~~~~~rl 80 (285)
T COG1405 1 VMSCPECGSTNIITDYERGEIVCADCGLVLEDSLIDPGPEWRAFDERHERRVGAPLTPSIHDKGLSTIIGWGDKDKMYRL 80 (285)
T ss_pred CCCCCCCCCccceeeccCCeEEeccCCEEeccccccCCCCcccccccccccccCCCccccCccchhhhcccchhHHHHHH
Confidence 5689999999999999999999999999999999999999994310 00022211 1 1
Q ss_pred eeeccc--ccchHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCC
Q 009187 57 RTIQSE--YGASRERLMEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPF 134 (540)
Q Consensus 57 ~~~~~~--~~~srer~L~~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~pr 134 (540)
+.||.+ .++++|+++..++.+|.+++.+|+|| .++.++|..||++++++++++||+.+.++|||||+|||+++.||
T Consensus 81 r~~~~~~~v~~~~ernl~~a~~~l~~~~~~l~LP--~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~acR~~~~pr 158 (285)
T COG1405 81 RKWQIRIRVSSAKERNLITALEELERIASALGLP--ESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAACRINGVPR 158 (285)
T ss_pred HHHHhccccccchhhHHHHHHHHHHHHHHHhCCC--chHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHHHHcCCCc
Confidence 234432 45689999999999999999999999 99999999999999999999999999999999999999999999
Q ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHhhccccccccccCChhhHHHHHHHhhCCCCCHHHHHHHHHHHHhhcccccccCC
Q 009187 135 LLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGR 214 (540)
Q Consensus 135 tL~DIs~vl~V~~~~Lgr~~~~L~~~L~i~~~p~~~~~~dP~~~I~Rf~~~L~~~~~~~V~~~A~~Iv~~m~~~~i~tGR 214 (540)
||.||+.+++|++++|+++|+.+.+.|++..+| +||..||+|||+.|++ +++|.+.|.+|++.+.+.+++.||
T Consensus 159 tl~eIa~a~~V~~kei~rtyr~~~~~L~l~~~~-----~~p~~yi~rf~s~L~l--~~~v~~~a~ei~~~~~~~g~~~Gk 231 (285)
T COG1405 159 TLDEIAKALGVSKKEIGRTYRLLVRELKLKIPP-----VDPSDYIPRFASKLGL--SDEVRRKAIEIVKKAKRAGLTAGK 231 (285)
T ss_pred cHHHHHHHHCCCHHHHHHHHHHHHHhcCCCCCC-----CCHHHHHHHHHHHcCC--CHHHHHHHHHHHHHHHHhCcccCC
Confidence 999999999999999999999999999998877 9999999999999996 799999999999999999999999
Q ss_pred ChhhHHHHHHHHHHHhcCCCCCHHHHHHHHcccHHHHhhh
Q 009187 215 KPSGLCGAALYVSALTHGLKFSKSDIIEDFMARKKELHEG 254 (540)
Q Consensus 215 ~P~~IAaAALylAa~~~g~~~t~~eI~~~~~~~~~ti~~~ 254 (540)
+|.||||||||+|++++|+++||++|+.++++|+.||||+
T Consensus 232 ~P~glAaaaiy~as~l~~~~~tq~eva~v~~vtevTIrnr 271 (285)
T COG1405 232 SPAGLAAAAIYLASLLLGERRTQKEVAKVAGVTEVTIRNR 271 (285)
T ss_pred CchhHHHHHHHHHHHHhCCchHHHHHHHHhCCeeeHHHHH
Confidence 9999999999999999999999999999999999999999
No 4
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=8.9e-46 Score=366.56 Aligned_cols=246 Identities=21% Similarity=0.363 Sum_probs=221.0
Q ss_pred CCCCCCCCC--CeeeecCCCceecCcccceeccccccccccccccCC-----CCccccC---------ccce--------
Q 009187 2 VWCSSCARH--VTGHRPYDSQLCCDRCGKVLEDHNFSTEATFVKNAA-----GQSQLSG---------NFVR-------- 57 (540)
Q Consensus 2 ~~Cp~Cgs~--~iv~D~~~G~~VCt~CG~Vlee~~Ids~~ef~~~s~-----G~s~v~G---------~~v~-------- 57 (540)
++|++|+.. .+++|+.+|++||..||.|+++++||.+.+|+.+++ .+|+|++ ++.+
T Consensus 1 ~~c~~C~~~~~~~V~d~~~gdtvC~~CGlVl~~r~Id~~sEwrtfsnd~~~~DPsrvG~~sNPlL~~g~L~T~I~~g~g~ 80 (308)
T KOG1597|consen 1 MTCPDCKRHPENLVEDHSAGDTVCSECGLVLEDRIIDEGSEWRTFSNDDSDADPSRVGASSNPLLDGGDLSTFISKGTGT 80 (308)
T ss_pred CCCCCCCCCCCCeeeeccCCceecccCCeeeccccccccccccccccCCCCCCccccCCCCCCCCCCCCcceeeecCCCC
Confidence 479999986 489999999999999999999999998888886553 2456542 1111
Q ss_pred ---------eeccc-ccchHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHH
Q 009187 58 ---------TIQSE-YGASRERLMEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLAC 127 (540)
Q Consensus 58 ---------~~~~~-~~~srer~L~~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiAC 127 (540)
.+|.+ ..++.++.+..|+..|..|++.|+|| ..|.++|.++|+++.+.+.+|||+.++++|||||+||
T Consensus 81 ~s~~~s~l~~~Q~~~sm~~~d~~~~~a~~~I~~m~d~~~Lp--~~I~d~A~~ifk~v~~~k~lrGks~eai~AAclyiAC 158 (308)
T KOG1597|consen 81 SSSFASSLGKAQNRNSMSNSDRVLKAAFKEITAMCDRLSLP--ATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIAC 158 (308)
T ss_pred CHHHHHHHHHHhcccccCCccHHHHHHHHHHHHHHHHhCCc--hHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHH
Confidence 23432 24677899999999999999999999 9999999999999999999999999999999999999
Q ss_pred HhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHHHhhccccccccccCChhhHHHHHHHhhCCCCCHHHHHHHHHHHHhhcc
Q 009187 128 RQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKR 207 (540)
Q Consensus 128 R~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~L~i~~~p~~~~~~dP~~~I~Rf~~~L~~~~~~~V~~~A~~Iv~~m~~ 207 (540)
|++++|||++||+.+.+|+.++||+.++.|.+.|++.++.+ .+...+||+|||+.|.+ ++.+++.|.++++++..
T Consensus 159 Rq~~~pRT~kEI~~~anv~kKEIgr~~K~i~~~l~~s~~~~---s~~t~~~m~RFCs~L~L--~~~~q~aA~e~a~ka~~ 233 (308)
T KOG1597|consen 159 RQEDVPRTFKEISAVANVSKKEIGRCVKLIGEALETSVDLI---SISTGDFMPRFCSNLGL--PKSAQEAATEIAEKAEE 233 (308)
T ss_pred HhcCCCchHHHHHHHHcCCHHHHHHHHHHHHHHHhccchhh---hhhHHHHHHHHHHhcCC--CHHHHHHHHHHHHHHHH
Confidence 99999999999999999999999999999999999876542 35688999999999985 89999999999999999
Q ss_pred cccccCCChhhHHHHHHHHHHHhcCCCCCHHHHHHHHcccHHHHhhh
Q 009187 208 DWITTGRKPSGLCGAALYVSALTHGLKFSKSDIIEDFMARKKELHEG 254 (540)
Q Consensus 208 ~~i~tGR~P~~IAaAALylAa~~~g~~~t~~eI~~~~~~~~~ti~~~ 254 (540)
..+..||+|.+||||+|||++++...++|+++|.++.+|+|.|||+.
T Consensus 234 ~~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~~vtgVaE~TIr~s 280 (308)
T KOG1597|consen 234 MDIRAGRSPISIAAAAIYMISQLSDEKKTQKEIGEVTGVAEVTIRNS 280 (308)
T ss_pred hccccCCCchhHHHHHHHHHHHhccCcccHHHHHHHhhhhHHHHHHH
Confidence 99999999999999999999999999999999999999999999998
No 5
>PF07741 BRF1: Brf1-like TBP-binding domain; InterPro: IPR011665 The Vaccinia virus has an infection-induced host cell cycle control mechanism. p53 and Rb, which are associated with the is inactivated Rb, which are associated with the RNA polymerase III transcription factor B (TFIIIB) subunits, TBP and Brf1, are inactivated [, ]. TFIIB, Brf1, and Brf2 share related N-terminal zinc ribbon and core domains. TFIIB bridges RNA polymerase II (Pol II) with the promoter-bound pre-initiation complex, whereas Brf1 and Brf2 are involved in the recruitment of Pol III. Brf1 and Brf2 both have a C-terminal extension absent in TFIIB, but their C-terminal extensions are unrelated. In yeast Brf1, the C-terminal extension interacts with the TBP/TATA box complex and contributes to the recruitment of Bdp1 []. It is suggested that the structure of the TBP-DNA complex may be altered upon entry of Brf1 and Bdp1 into the complex. Entry of Brf1 and Bdp1 into the complex imposes a strict sequence preference for the downstream half of the TATA box []. This region covers both the Brf homology II and III regions []. ; GO: 0008270 zinc ion binding, 0045893 positive regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1NGM_J.
Probab=99.95 E-value=6.2e-30 Score=221.08 Aligned_cols=96 Identities=54% Similarity=0.796 Sum_probs=34.5
Q ss_pred hHHHhhcCCCHHHHHHHHHHHhhhCHHHHHHHHHHHHHHHHHHHHHHhhhcCCccchHHHHHHHHHHHHHHhhhhHHHHh
Q 009187 396 DFEVDGYLHNEEEKHYKKIIWEEMNREYLEEQAAKEAAAAAAKAALEASYKNCPEGLQAAQELAAAAAAAVAKSRKEKQQ 475 (540)
Q Consensus 396 D~Eid~yil~eeE~~~K~~lW~~~N~eyl~eq~~Ke~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~k~k~~ 475 (540)
|+|||.|||||+|+++|++||+++|+|||++|++|+++.+++.+ .++ +++|++++
T Consensus 1 DdEid~~il~eeE~~~K~~iW~~~NkdyL~~~~~K~~~~~~~~~----------------------~~~---~~~k~k~~ 55 (97)
T PF07741_consen 1 DDEIDNYILSEEEVKIKERIWMEMNKDYLEEQEEKELKAKAEEE----------------------AGA---KSRKKKKK 55 (97)
T ss_dssp -HHHHTTC--HHHHHHHHHHHHHHTHHHHHHHHHCCCCT-----------------------------------------
T ss_pred ChHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh----------------------hcc---CCCccccc
Confidence 56999999999999999999999999999999999976554211 111 22333333
Q ss_pred hhHhhhcc-CCCCCCHHHHHHHHHHhcccccccCHHHHhhhh
Q 009187 476 KRAAEAKN-SGPAQTALEATRRMLTKKRLSSKINYDVLEKLF 516 (540)
Q Consensus 476 k~~~~~~~-~~~a~ta~EA~~~ml~~K~~S~KINYdvl~~L~ 516 (540)
+++...++ .+||.||+||+++||++|+||+|||||+|++||
T Consensus 56 rk~~~~~~~~~~a~ta~EA~~~ml~~k~~S~KINYd~L~~LF 97 (97)
T PF07741_consen 56 RKRRKKKNQAPPAETAAEAARKMLKKKKFSKKINYDALESLF 97 (97)
T ss_dssp ------------------------------------------
T ss_pred cccccccCCCCCCCCHHHHHHHHHHhcCcccccCHHHHHhhC
Confidence 34444455 899999999999999999999999999999998
No 6
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=99.69 E-value=1.4e-16 Score=129.92 Aligned_cols=71 Identities=27% Similarity=0.516 Sum_probs=66.3
Q ss_pred HHHHHHHhCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHH
Q 009187 78 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYEL 150 (540)
Q Consensus 78 I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~prtL~DIs~vl~V~~~~L 150 (540)
|+++|+.|+|| .++.+.|..||+.+.+.++++||++..++|||||+|||+++.|+|++||+++++|++++|
T Consensus 1 I~r~~~~L~L~--~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~~~Vs~~tI 71 (71)
T PF00382_consen 1 IPRICSKLGLP--EDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEAAGVSEKTI 71 (71)
T ss_dssp HHHHHHHTT----HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHHCTSSHHHH
T ss_pred ChHHHhHcCCC--HHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCCCcC
Confidence 68999999999 999999999999999999999999999999999999999999999999999999999876
No 7
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=99.59 E-value=4e-14 Score=143.12 Aligned_cols=182 Identities=15% Similarity=0.170 Sum_probs=159.3
Q ss_pred hHHHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCCHHHHHHHhCc
Q 009187 66 SRERLMEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNI 145 (540)
Q Consensus 66 srer~L~~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~prtL~DIs~vl~V 145 (540)
..+-...-|...|++-|-.|+|| +...-+++.+|++.+....+.+...++++.|||.+|.+.+..|++++||..|++-
T Consensus 18 ~e~el~~LG~e~Iqea~ILL~L~--q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiEE~Prr~rdVinVFh~ 95 (367)
T KOG0835|consen 18 TEEELRILGCELIQEAGILLNLP--QVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIEEEPRRIRDVINVFHY 95 (367)
T ss_pred hHHHHHHHhHHHHHhhhHhhcCc--HHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhccccccHhHHHHHHHH
Confidence 33444556889999999999999 9999999999999999999999999999999999999999999999999988742
Q ss_pred ----------C-----------HHHHHHHHHHHHHHhhccccccccccCChhhHHHHHHHhhCCCCCHHHHHHHHHHHHh
Q 009187 146 ----------N-----------VYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILAS 204 (540)
Q Consensus 146 ----------~-----------~~~Lgr~~~~L~~~L~i~~~p~~~~~~dP~~~I~Rf~~~L~~~~~~~V~~~A~~Iv~~ 204 (540)
. .-.+.++.++|++.||+..+. .+|+.+|-.|...|++..+.++.+.+|.+.+.
T Consensus 96 L~~r~~~~~~~~~~~~~~~~~lk~~~ir~e~~ILr~LGF~~Hv-----~hPhklii~YLqtL~~~~~~~l~Q~~wNfmND 170 (367)
T KOG0835|consen 96 LEQRRESEAAEHLILARLYINLKMQVIRAERRILRELGFDVHV-----EHPHKLIIMYLQTLQLPPNLKLLQAAWNFMND 170 (367)
T ss_pred HHHHHhccCcchhhhhhHHhhhhhHHHHHHHHHHHHhCCeeee-----eccHHHHHHHHHHhcCCCchhHHHHHHHhhhh
Confidence 0 112456778999999999887 89999999999999875566799999999999
Q ss_pred hcccccccCCChhhHHHHHHHHHHHhcCCCCC-HHHHHHHHcccHHHHhhh
Q 009187 205 MKRDWITTGRKPSGLCGAALYVSALTHGLKFS-KSDIIEDFMARKKELHEG 254 (540)
Q Consensus 205 m~~~~i~tGR~P~~IAaAALylAa~~~g~~~t-~~eI~~~~~~~~~ti~~~ 254 (540)
..+..+..-..|.+||+|+||||||-.+++++ +-.+...|+.+...|...
T Consensus 171 slRT~v~vry~pe~iACaciyLaAR~~eIpLp~~P~Wf~~Fd~~k~eid~i 221 (367)
T KOG0835|consen 171 SLRTDVFVRYSPESIACACIYLAARNLEIPLPFQPHWFKAFDTTKREIDEI 221 (367)
T ss_pred ccccceeeecCHHHHHHHHHHHHHhhhcCCCCCCccHHHHcCCcHHHHHHH
Confidence 99999999999999999999999999998754 447899999998876665
No 8
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=99.51 E-value=4.4e-14 Score=115.17 Aligned_cols=71 Identities=18% Similarity=0.341 Sum_probs=66.2
Q ss_pred HHHHHHhhCCCCCHHHHHHHHHHHHhhcccccccCCChhhHHHHHHHHHHHhcCCCCCHHHHHHHHcccHHHH
Q 009187 179 LHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIIEDFMARKKEL 251 (540)
Q Consensus 179 I~Rf~~~L~~~~~~~V~~~A~~Iv~~m~~~~i~tGR~P~~IAaAALylAa~~~g~~~t~~eI~~~~~~~~~ti 251 (540)
|+|||+.|++ ++.|...|.+|++.+.+.|+..||+|.+||||+||+||+.+|.++|++||++.+++++.||
T Consensus 1 I~r~~~~L~L--~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~~~Vs~~tI 71 (71)
T PF00382_consen 1 IPRICSKLGL--PEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEAAGVSEKTI 71 (71)
T ss_dssp HHHHHHHTT----HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHHCTSSHHHH
T ss_pred ChHHHhHcCC--CHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHHhCCCCCcC
Confidence 6899999985 8899999999999999999999999999999999999999999999999999999999886
No 9
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=99.50 E-value=6.5e-13 Score=137.02 Aligned_cols=171 Identities=16% Similarity=0.106 Sum_probs=143.7
Q ss_pred HHHHH-HHHHHHHHHHHHhC--CCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCCHHHHHHHhC
Q 009187 68 ERLME-KAFDDMRQMKNALN--IGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLN 144 (540)
Q Consensus 68 er~L~-~a~~~I~~ia~~L~--Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~prtL~DIs~vl~ 144 (540)
|+.+. .....|.++|..|+ || +.++.+|..||++++-.+.+.-..+..|+++|||+||+.+..|+++.+|+..+.
T Consensus 52 E~~l~~~y~~~i~~~~~~lkp~Lp--q~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~~ 129 (305)
T TIGR00569 52 ELDLVKYYEKRLLDFCSAFKPTMP--TSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLK 129 (305)
T ss_pred HHHHHHHHHHHHHHHHHHhcCCCC--chHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhhcc
Confidence 55554 45589999999999 99 999999999999999999888889999999999999999999999999998765
Q ss_pred cC----HHHHHHHHHHHHHHhhccccccccccCChhhHHHHHHHhhC-----CCCCHHHHHHHHHHHHhhcccccccCCC
Q 009187 145 IN----VYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLL-----PGGNKKVCDTARDILASMKRDWITTGRK 215 (540)
Q Consensus 145 V~----~~~Lgr~~~~L~~~L~i~~~p~~~~~~dP~~~I~Rf~~~L~-----~~~~~~V~~~A~~Iv~~m~~~~i~tGR~ 215 (540)
-+ ...|...-..|++.|+++... ..|..++..|...|. ......+.+.|+.+++.+....+.--..
T Consensus 130 ~~~~~~~~~Il~~E~~lL~~L~F~L~V-----~hPyr~L~~~l~dl~~~l~~~~~~~~l~q~a~~~lndsl~Td~~L~y~ 204 (305)
T TIGR00569 130 ETPLKALEQVLEYELLLIQQLNFHLIV-----HNPYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYT 204 (305)
T ss_pred CCchhhHHHHHHHHHHHHHHCCCcEEe-----eCccHHHHHHHHHHHHhhccccchHHHHHHHHHHHHHHHcCCceecCC
Confidence 43 377889999999999998765 789998888886552 2234568899999999887776666699
Q ss_pred hhhHHHHHHHHHHHhcCCCCCHHHHHHHHcc
Q 009187 216 PSGLCGAALYVSALTHGLKFSKSDIIEDFMA 246 (540)
Q Consensus 216 P~~IAaAALylAa~~~g~~~t~~eI~~~~~~ 246 (540)
|+-||.||||+|++.+|++....+. +.+++
T Consensus 205 Ps~IAlAAI~lA~~~~~~~l~~~~~-e~~~~ 234 (305)
T TIGR00569 205 PSQIALAAILHTASRAGLNMESYLT-EQLSV 234 (305)
T ss_pred HHHHHHHHHHHHHHHhCCCCcccch-hhhcc
Confidence 9999999999999999997766553 45554
No 10
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=99.45 E-value=4.9e-13 Score=138.09 Aligned_cols=177 Identities=17% Similarity=0.188 Sum_probs=145.3
Q ss_pred HHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCCHHHHHHHhC--cCH-
Q 009187 71 MEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLN--INV- 147 (540)
Q Consensus 71 L~~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~prtL~DIs~vl~--V~~- 147 (540)
-..+.+.|.+++.+|++| +..+.+|..||++++-...++.-....+|++|||+|++.+++|+.++||..+.. .++
T Consensus 39 r~~~~~fI~elg~~L~~~--~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s~~~~~~~ 116 (323)
T KOG0834|consen 39 RQEGAKFIQELGVRLKMP--QKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVSYRYLNPK 116 (323)
T ss_pred HHHHHHHHHHHHHHcCCC--ccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHHHHHcCcc
Confidence 357889999999999999 888999999999999999999888889999999999999999999999988752 232
Q ss_pred ------------HHHHHHHHHHHHHhhccccccccccCChhhHHHHHHHhhCCCCC--HHHHHHHHHHHHhhcccccccC
Q 009187 148 ------------YELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGN--KKVCDTARDILASMKRDWITTG 213 (540)
Q Consensus 148 ------------~~Lgr~~~~L~~~L~i~~~p~~~~~~dP~~~I~Rf~~~L~~~~~--~~V~~~A~~Iv~~m~~~~i~tG 213 (540)
..|-..-+.|++.|+++... -.|+.|+.+|+..|..+.+ ..++..||.+++......++--
T Consensus 117 ~~~~~~~~~~~~~~Iv~~E~~lL~tl~Fdl~v-----~hPy~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL~ 191 (323)
T KOG0834|consen 117 DLELEEVYWELKERIVQLELLLLETLGFDLNV-----EHPYKYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLCLQ 191 (323)
T ss_pred cccHHHHHHHHHHHHHHHHHHHHHHccCceec-----cCchHHHHHHHHHhhhhhhccccHHHHHHHHhchhheeeeeEe
Confidence 12333346677778887654 7799999999999974333 2599999999999888777778
Q ss_pred CChhhHHHHHHHHHHHhcCCCCCHH---HHHHHHc--ccHHHHhhh
Q 009187 214 RKPSGLCGAALYVSALTHGLKFSKS---DIIEDFM--ARKKELHEG 254 (540)
Q Consensus 214 R~P~~IAaAALylAa~~~g~~~t~~---eI~~~~~--~~~~ti~~~ 254 (540)
..|..||.|+||||+.++|+..+.. .++++|+ +|...|++-
T Consensus 192 y~p~~IAva~i~lA~~~~~~~~~~~~~~~w~~~~d~~vt~e~l~~i 237 (323)
T KOG0834|consen 192 YSPHSIAVACIHLAAKLLGVELPSDTDKRWWREFDETVTNELLDDI 237 (323)
T ss_pred ecCcEEEeehhhHHHHHcCCCCCCCcccchhhhhcccCCHHHHHHH
Confidence 9999999999999999999864422 3678888 776655444
No 11
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.34 E-value=5.4e-12 Score=131.00 Aligned_cols=89 Identities=16% Similarity=0.227 Sum_probs=85.7
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHH
Q 009187 74 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAV 153 (540)
Q Consensus 74 a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~ 153 (540)
...+|.++|+.|+|| ..+.++|..+++.+.+.+++.||++..++|||||+|||.+|.|+|++||+++.+|+..+|++.
T Consensus 219 p~~~i~r~~~~L~L~--~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v~~Vs~~tI~~~ 296 (310)
T PRK00423 219 PIDYVPRFASELGLS--GEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEVAGVTEVTVRNR 296 (310)
T ss_pred HHHHHHHHHHHcCCC--HHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHHcCCCHHHHHHH
Confidence 458899999999999 999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhhcc
Q 009187 154 YLQLCQVLYIA 164 (540)
Q Consensus 154 ~~~L~~~L~i~ 164 (540)
|+.|.+.|++.
T Consensus 297 ykel~~~l~~~ 307 (310)
T PRK00423 297 YKELAEKLDIK 307 (310)
T ss_pred HHHHHHHhCcc
Confidence 99999999864
No 12
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=99.27 E-value=2.2e-12 Score=95.27 Aligned_cols=43 Identities=23% Similarity=0.524 Sum_probs=38.3
Q ss_pred CCCCCCCCCCeeeecCCCceecCcccceecccccccccccccc
Q 009187 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFVKN 44 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~~Ids~~ef~~~ 44 (540)
++||+||+..+++|+.+|++||+.||.||++++|+++++|+++
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl~e~~i~~~~e~r~f 43 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGLVLEENIIDEGPEWREF 43 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-BBEE-TTBSCCCSCCHC
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCCEeecccccCCcccccC
Confidence 4699999998999999999999999999999999999999864
No 13
>COG5333 CCL1 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=99.22 E-value=1.2e-10 Score=118.13 Aligned_cols=159 Identities=18% Similarity=0.168 Sum_probs=136.9
Q ss_pred HHHHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCCHHHHHHHh--------
Q 009187 72 EKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYL-------- 143 (540)
Q Consensus 72 ~~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~prtL~DIs~vl-------- 143 (540)
..++..|..+|.+|+|| ..+..+|..+|++.+-++..++-+...|+++|||+||+.+++|+-+.-.+-..
T Consensus 46 i~~~k~i~~l~~~L~lp--~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed~~~~I~i~~~~~~~~~se~~ 123 (297)
T COG5333 46 IYYLKLIMDLCTRLNLP--QTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDISIESFEARDLWSEEP 123 (297)
T ss_pred HHHHHHHHHHHHhcCCC--cchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeecccccchhhHHHHHhhccccccc
Confidence 46779999999999999 99999999999999999999999999999999999999999865554333333
Q ss_pred CcCHHHHHHHHHHHHHHhhccccccccccCChhhHHHHHHHhhCCCCCHHHHHHHHHHHHhhcccccccCCChhhHHHHH
Q 009187 144 NINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAA 223 (540)
Q Consensus 144 ~V~~~~Lgr~~~~L~~~L~i~~~p~~~~~~dP~~~I~Rf~~~L~~~~~~~V~~~A~~Iv~~m~~~~i~tGR~P~~IAaAA 223 (540)
.-+...|-..-..+++.|+++.+. ..|..++..|...+......++.+.||.+++.+-+..++-=..|..||.||
T Consensus 124 ~~sr~~Il~~E~~lLEaL~fd~~V-----~hPy~~l~~f~~~~q~~~~~~~~~~aw~~inDa~~t~~~llypphiIA~a~ 198 (297)
T COG5333 124 KSSRERILEYEFELLEALDFDLHV-----HHPYKYLEGFLKDLQEKDKYKLLQIAWKIINDALRTDLCLLYPPHIIALAA 198 (297)
T ss_pred cccHHHHHHHHHHHHHHcccceEe-----ccccHHHHHHHHHHHhccHHHHHHHHHHHHHhhhhceeeeecChHHHHHHH
Confidence 246677888888999999998776 789999999999996322357999999999999999988899999999999
Q ss_pred HHHHHHhcCCCCCH
Q 009187 224 LYVSALTHGLKFSK 237 (540)
Q Consensus 224 LylAa~~~g~~~t~ 237 (540)
|++|+...|.+...
T Consensus 199 l~ia~~~~~~~~~~ 212 (297)
T COG5333 199 LLIACEVLGMPIIK 212 (297)
T ss_pred HHHHHHhcCCccch
Confidence 99999998876543
No 14
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=99.02 E-value=1.1e-09 Score=112.00 Aligned_cols=91 Identities=18% Similarity=0.212 Sum_probs=86.9
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHH
Q 009187 73 KAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGA 152 (540)
Q Consensus 73 ~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr 152 (540)
+...+|.++|+.|+|| +.+...|.+|.+++...|.+-||++..+||||||+|+++++.++|.++|+.+++|.+-+|..
T Consensus 193 ~p~~yi~rf~s~L~l~--~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~~~~~tq~eva~v~~vtevTIrn 270 (285)
T COG1405 193 DPSDYIPRFASKLGLS--DEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGERRTQKEVAKVAGVTEVTIRN 270 (285)
T ss_pred CHHHHHHHHHHHcCCC--HHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhCCchHHHHHHHHhCCeeeHHHH
Confidence 3467899999999999 99999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhhccc
Q 009187 153 VYLQLCQVLYIAD 165 (540)
Q Consensus 153 ~~~~L~~~L~i~~ 165 (540)
.|+.|...+++..
T Consensus 271 rykel~~~~~i~~ 283 (285)
T COG1405 271 RYKELADALDIEV 283 (285)
T ss_pred HHHHHHHhhcccc
Confidence 9999999998754
No 15
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=98.90 E-value=1.8e-09 Score=116.26 Aligned_cols=164 Identities=12% Similarity=0.044 Sum_probs=118.7
Q ss_pred HHHHHHHHHhCCCCc-hHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHH
Q 009187 76 DDMRQMKNALNIGES-DEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVY 154 (540)
Q Consensus 76 ~~I~~ia~~L~Lp~~-~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~ 154 (540)
-+|.+++..|-..++ ..|+.+|.++..++...++..||++..+++||||||||+||+++|+.||+.+++|+..+|.+.|
T Consensus 168 L~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~~rsi~dIv~vvhV~e~Tl~kRl 247 (521)
T KOG1598|consen 168 LYIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGFRRTIGDIAKVVHVCESTLSKRL 247 (521)
T ss_pred eeeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCccccHHHHHHHHHHhHHHHHHHH
Confidence 356677777755433 4688899999888888889999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhhccccccccccCChhhHHHHHHHhhCCCCCHHHHHHHHHHHHhhcccccccCCChhhHHHHHHHHHHHhcCCC
Q 009187 155 LQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLK 234 (540)
Q Consensus 155 ~~L~~~L~i~~~p~~~~~~dP~~~I~Rf~~~L~~~~~~~V~~~A~~Iv~~m~~~~i~tGR~P~~IAaAALylAa~~~g~~ 234 (540)
..+...+....+. .-| ..+
T Consensus 248 ~Ef~~T~s~~Lti------------~ef-~~~------------------------------------------------ 266 (521)
T KOG1598|consen 248 KEFSDTLSGDLTI------------DEL-AEI------------------------------------------------ 266 (521)
T ss_pred HHHhccccccccH------------HHH-Hhh------------------------------------------------
Confidence 8887766543211 111 000
Q ss_pred CCHHHHHHHHcccHHHHhhhhcCCCCCCCCCC--------CCccchhhccccCCCCccccchhhhHHHHhhhccccCCCC
Q 009187 235 FSKSDIIEDFMARKKELHEGVAANLPNNGPKV--------SGMNEVLCKHKDTGKPFACGLCRSCYEEFMTISEGLEGGA 306 (540)
Q Consensus 235 ~t~~eI~~~~~~~~~ti~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~~~~~~g~~~~~~~ef~~~~~~l~~~~ 306 (540)
.+..+ ++||.|+... ...+.+.|.|.+.. ++..++|..++..|..+++++++..
T Consensus 267 ---------------d~e~~--~~ppsft~~~~~~~k~~~~~k~~l~~~~~~~e-~~~~~~~~~~~~~~~~~~~~l~~~~ 328 (521)
T KOG1598|consen 267 ---------------DLEYE--SDPPSFTASPSKEAKYVEDKKKMLSRTMQLVE-LANETWLVTLRHSLPVITGGLFLAW 328 (521)
T ss_pred ---------------hhhhc--cCcchhhcccchhhhhhhhhhhhhhhhhhhhh-cccchhhhccccCCcccchhhhccc
Confidence 01111 2222222110 11334555555433 6778888889999999999999999
Q ss_pred CChhhHHHHHHH
Q 009187 307 DPPAFQVAERER 318 (540)
Q Consensus 307 dpPaf~~~~~~~ 318 (540)
.||.|+....++
T Consensus 329 q~~~~~~~~~e~ 340 (521)
T KOG1598|consen 329 QDLQPRDRLVES 340 (521)
T ss_pred ccchhhhhhhhh
Confidence 999999877664
No 16
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=98.90 E-value=1.7e-08 Score=82.70 Aligned_cols=83 Identities=23% Similarity=0.257 Sum_probs=78.1
Q ss_pred HHHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCCHHHHHHHhCc-CHHHHH
Q 009187 73 KAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNI-NVYELG 151 (540)
Q Consensus 73 ~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~prtL~DIs~vl~V-~~~~Lg 151 (540)
.+...|.+++..++++ ..+...|..+++++...+.+.++++..+++||||+||+.++.|.++.+|..+.+. +..+|.
T Consensus 4 ~~~~~l~~~~~~~~~~--~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~ 81 (88)
T cd00043 4 TPLDFLRRVAKALGLS--PETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGYATEEEIL 81 (88)
T ss_pred hHHHHHHHHHHHcCCC--HHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCCCCHHHHH
Confidence 4678999999999999 9999999999999999999999999999999999999999999999999999999 999998
Q ss_pred HHHHHH
Q 009187 152 AVYLQL 157 (540)
Q Consensus 152 r~~~~L 157 (540)
+.++.|
T Consensus 82 ~~e~~i 87 (88)
T cd00043 82 RMEKLL 87 (88)
T ss_pred HHHHHh
Confidence 887765
No 17
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=98.86 E-value=1.2e-08 Score=102.74 Aligned_cols=87 Identities=13% Similarity=0.128 Sum_probs=83.3
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHH
Q 009187 74 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAV 153 (540)
Q Consensus 74 a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~ 153 (540)
.-.+|.++|+.|+|| ..+++.|.++.+.+.+..+..||++..|+||.+|+++++...+++++||..++||..-+|..+
T Consensus 203 t~~~m~RFCs~L~L~--~~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~~vtgVaE~TIr~s 280 (308)
T KOG1597|consen 203 TGDFMPRFCSNLGLP--KSAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQLSDEKKTQKEIGEVTGVAEVTIRNS 280 (308)
T ss_pred HHHHHHHHHHhcCCC--HHHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHhccCcccHHHHHHHhhhhHHHHHHH
Confidence 557899999999999 999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHhh
Q 009187 154 YLQLCQVLY 162 (540)
Q Consensus 154 ~~~L~~~L~ 162 (540)
|+.|...+.
T Consensus 281 YK~Lyp~~~ 289 (308)
T KOG1597|consen 281 YKDLYPHAD 289 (308)
T ss_pred HHHHhhchh
Confidence 999987764
No 18
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=98.83 E-value=2e-08 Score=98.01 Aligned_cols=155 Identities=17% Similarity=0.224 Sum_probs=120.3
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCC----CCHHHHHHHh------
Q 009187 74 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKP----FLLIDFSNYL------ 143 (540)
Q Consensus 74 a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p----rtL~DIs~vl------ 143 (540)
..+.|+.++..|+|. +.++.||..+|++.+-++.+++-.+..+|+.|||+||+.+..| |+|.--+.++
T Consensus 44 ~~n~I~~lg~~lklR--Q~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~i~~~r~l~~~a~~L~~~f~~ 121 (264)
T KOG0794|consen 44 MANVIQKLGQHLKLR--QRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECPIVHIRLLVNEAKVLKTRFSY 121 (264)
T ss_pred HHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcchHHHHHHHHHHHHHhhhccc
Confidence 347899999999999 9999999999999999999999999999999999999999998 2222222222
Q ss_pred -----CcCHHHHHHHHHHHHHHhhccccccccccCChhhHHHHHHHhhCCCCCHHHHHHHHHHHHhhcccccccCCChhh
Q 009187 144 -----NINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSG 218 (540)
Q Consensus 144 -----~V~~~~Lgr~~~~L~~~L~i~~~p~~~~~~dP~~~I~Rf~~~L~~~~~~~V~~~A~~Iv~~m~~~~i~tGR~P~~ 218 (540)
......|...-..|+..|+-=.- +-.|..-+..|...++. .+.+....+|.|++..-+..++-=..|.-
T Consensus 122 ~~e~~~~~~~~I~e~Ef~llE~Ld~~LI-----VhHPYrsL~q~~qd~gi-~d~~~l~~~W~ivNDSyr~Dl~Ll~PPh~ 195 (264)
T KOG0794|consen 122 WPEKFPYERKDILEMEFYLLEALDCYLI-----VHHPYRSLLQFVQDMGI-NDQKLLQLAWSIVNDSYRMDLCLLYPPHQ 195 (264)
T ss_pred chhhcCCCcCcchhhhhhHHhhhceeEE-----EecCCccHHHHHHHhcc-cchhhhhhhHhhhcchhhcceeeecCHHH
Confidence 11222233333455565552211 24577778889888874 36778899999999999988888899999
Q ss_pred HHHHHHHHHHHhcCCCCC
Q 009187 219 LCGAALYVSALTHGLKFS 236 (540)
Q Consensus 219 IAaAALylAa~~~g~~~t 236 (540)
||-||||+|+-.++-..+
T Consensus 196 IalAcl~Ia~~~~~k~~~ 213 (264)
T KOG0794|consen 196 IALACLYIACVIDEKDIP 213 (264)
T ss_pred HHHHHHHHHHhhcCCChH
Confidence 999999999998876654
No 19
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=98.78 E-value=3.2e-08 Score=80.36 Aligned_cols=80 Identities=19% Similarity=0.191 Sum_probs=72.0
Q ss_pred HHHHHHHHhCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCCHHHHHHHhCc-CHHHHHHHHH
Q 009187 77 DMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNI-NVYELGAVYL 155 (540)
Q Consensus 77 ~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~prtL~DIs~vl~V-~~~~Lgr~~~ 155 (540)
.|.+++..+++| ..+...|..+++++.....+.++++..++|||||+|||.++.+.+..++...+++ +..+|.+.++
T Consensus 2 ~l~~~~~~~~~~--~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~~~~ 79 (83)
T smart00385 2 FLRRVCKALNLD--PETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIPPWTKELVHYTGYFTEEEILRMEK 79 (83)
T ss_pred HHHHHHHHcCCC--HHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCCCCHHHHHHHHH
Confidence 588999999999 9999999999999998433344999999999999999999999999999999999 9999998888
Q ss_pred HHH
Q 009187 156 QLC 158 (540)
Q Consensus 156 ~L~ 158 (540)
.|.
T Consensus 80 ~il 82 (83)
T smart00385 80 LLL 82 (83)
T ss_pred HHh
Confidence 764
No 20
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=98.52 E-value=2.5e-06 Score=88.80 Aligned_cols=151 Identities=17% Similarity=0.203 Sum_probs=122.6
Q ss_pred HHHHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhCc-ccCCC--chhHHHHHHHHHHHHhcCC--CCCHHHHHHHh--C
Q 009187 72 EKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARN-FTKGR--RTEQVQASCLYLACRQKSK--PFLLIDFSNYL--N 144 (540)
Q Consensus 72 ~~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~-~~rGR--~~~~vaAACLYiACR~e~~--prtL~DIs~vl--~ 144 (540)
..|...|-++|...+.. ..+.=-|.+++.+.+.-. +-+++ -...+++|||.+|.+.+.+ |.++.-..... -
T Consensus 79 ~~A~~WIl~V~~~~~~~--~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlAvaCLsLAsKmeE~~vPll~dl~v~~~~~~ 156 (335)
T KOG0656|consen 79 KQALDWILKVCEEYNFE--PLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLAVACLSLASKMEETDVPLLADLQVEYTDNV 156 (335)
T ss_pred HHHHHHHHHHHHHhCCc--hHHHHHHHHHHHHhhcccccCCCchHHHHHHHHHHHHHHHhhcCcCCchhhhhhhcccccc
Confidence 46889999999999999 899999999999988644 44443 2688999999999999887 65554444442 3
Q ss_pred cCHHHHHHHHHHHHHHhhccccccccccCChhhHHHHHHHhhCC--CCCHHHHHHHHHHHHhhcccccccCCChhhHHHH
Q 009187 145 INVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLP--GGNKKVCDTARDILASMKRDWITTGRKPSGLCGA 222 (540)
Q Consensus 145 V~~~~Lgr~~~~L~~~L~i~~~p~~~~~~dP~~~I~Rf~~~L~~--~~~~~V~~~A~~Iv~~m~~~~i~tGR~P~~IAaA 222 (540)
+..++|.+.-+.++..|+-...+ +.|..||..|+.++++ ...+.+...+..++-....+.-..+..|+.||||
T Consensus 157 feaktI~rmELLVLstL~Wrl~a-----VTP~sF~~~fl~ki~~~~~~~~~~~~~~s~~ll~~~~d~~Fl~y~pSviAaa 231 (335)
T KOG0656|consen 157 FEAKTIQRMELLVLSTLKWRLRA-----VTPFSFIDHFLSKISQKDHNKHLFLKHASLFLLSVITDIKFLEYPPSVIAAA 231 (335)
T ss_pred ccHHHHHHHHHHHHhhccccccC-----CCchHHHHHHHHHcCcccchHHHHHHHHHHHHHHHhhhhhhhcCChHHHHHH
Confidence 68899999999999999998876 9999999999999963 3346677778777777666776789999999999
Q ss_pred HHHHHHH
Q 009187 223 ALYVSAL 229 (540)
Q Consensus 223 ALylAa~ 229 (540)
++..++.
T Consensus 232 ~~~~v~~ 238 (335)
T KOG0656|consen 232 AILSVSA 238 (335)
T ss_pred HHHHHHH
Confidence 8876654
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=98.48 E-value=8.2e-07 Score=72.66 Aligned_cols=80 Identities=23% Similarity=0.246 Sum_probs=73.6
Q ss_pred CChhhHHHHHHHhhCCCCCHHHHHHHHHHHHhhcccccccCCChhhHHHHHHHHHHHhcCCCCCHHHHHHHHcc-cHHHH
Q 009187 173 VDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIIEDFMA-RKKEL 251 (540)
Q Consensus 173 ~dP~~~I~Rf~~~L~~~~~~~V~~~A~~Iv~~m~~~~i~tGR~P~~IAaAALylAa~~~g~~~t~~eI~~~~~~-~~~ti 251 (540)
..|..||.+++..++. +..+...|..+++++...+...|++|..||+||||+|+++.+...+.++++...+. +..+|
T Consensus 3 ~~~~~~l~~~~~~~~~--~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i 80 (88)
T cd00043 3 PTPLDFLRRVAKALGL--SPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHVTGYATEEEI 80 (88)
T ss_pred chHHHHHHHHHHHcCC--CHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHHhCCCCHHHH
Confidence 4578999999999974 89999999999999988888899999999999999999999999999999999999 88887
Q ss_pred hhh
Q 009187 252 HEG 254 (540)
Q Consensus 252 ~~~ 254 (540)
.+.
T Consensus 81 ~~~ 83 (88)
T cd00043 81 LRM 83 (88)
T ss_pred HHH
Confidence 754
No 22
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=98.37 E-value=1.4e-06 Score=70.58 Aligned_cols=76 Identities=20% Similarity=0.211 Sum_probs=67.6
Q ss_pred hHHHHHHHhhCCCCCHHHHHHHHHHHHhhcccccccCCChhhHHHHHHHHHHHhcCCCCCHHHHHHHHcc-cHHHHhhh
Q 009187 177 IFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIIEDFMA-RKKELHEG 254 (540)
Q Consensus 177 ~~I~Rf~~~L~~~~~~~V~~~A~~Iv~~m~~~~i~tGR~P~~IAaAALylAa~~~g~~~t~~eI~~~~~~-~~~ti~~~ 254 (540)
.||.+|++.++. ++++...|..+++++....-..+++|..||+||||+|+++.+.+++..++...++. +..+|.+.
T Consensus 1 ~~l~~~~~~~~~--~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~~~~~~~~~i~~~ 77 (83)
T smart00385 1 DFLRRVCKALNL--DPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIPPWTKELVHYTGYFTEEEILRM 77 (83)
T ss_pred CHHHHHHHHcCC--CHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCCCCchhHhHhhCCCCHHHHHHH
Confidence 489999999985 78999999999999987544456999999999999999999999999999999999 88887765
No 23
>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=97.85 E-value=0.0002 Score=73.06 Aligned_cols=137 Identities=20% Similarity=0.175 Sum_probs=98.1
Q ss_pred CCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCCHHHHHHHhC----cCHHHHHHHHHHHHHHh
Q 009187 86 NIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLN----INVYELGAVYLQLCQVL 161 (540)
Q Consensus 86 ~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~prtL~DIs~vl~----V~~~~Lgr~~~~L~~~L 161 (540)
+|| .+|+.+|..+|++++=.+...--++..|+++|+|+||+.+..-+++-+|+.-.. -....|-+.-..+++.|
T Consensus 73 ~lp--~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~ISieqFvkn~~~~~~k~~e~vLk~E~~llqsL 150 (325)
T KOG2496|consen 73 NLP--TSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFYISIEQFVKNMNGRKWKTHEIVLKYEFLLLQSL 150 (325)
T ss_pred CCc--hHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhheecHHHHHhhccCcccccHHHHHhchHHHHHhh
Confidence 788 999999999999999999998899999999999999999999999999998876 55566666667778888
Q ss_pred hccccccccccCChh----hHHHHHHHhhCCCCCHHHH-HHH--HHHHHhhcccccccCCChhhHHHHHHHHHHH
Q 009187 162 YIADESNVLKQVDPS----IFLHKFTDRLLPGGNKKVC-DTA--RDILASMKRDWITTGRKPSGLCGAALYVSAL 229 (540)
Q Consensus 162 ~i~~~p~~~~~~dP~----~~I~Rf~~~L~~~~~~~V~-~~A--~~Iv~~m~~~~i~tGR~P~~IAaAALylAa~ 229 (540)
.+.... -.|. .|+..+-..|-+-.+.+.. ... .+.++++.-....-=..|+-||-|||+.|+-
T Consensus 151 ~f~L~v-----h~PyRPleGFl~D~kt~l~~~~n~d~~~~~~d~~~fl~~~lltDa~lLytPsQIALaAil~a~~ 220 (325)
T KOG2496|consen 151 KFSLTV-----HNPYRPLEGFLLDMKTRLPALENPDILRKHDDSKKFLDRALLTDAYLLYTPSQIALAAILHAAG 220 (325)
T ss_pred hhhhee-----cCCCCchHHHHHHHHHHHHhccCHHHHhhhhhHHHHHHHHHHhccceecChHHHHHHHHHHHhc
Confidence 766432 2333 4444444443211133322 122 2455554444445568899999999966544
No 24
>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. Cyclins contain two domains of similar all-alpha fold, of which this entry is associated with the N-terminal domain.; PDB: 2W2H_B 3RGF_B 1KXU_A 1JKW_A 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D ....
Probab=97.71 E-value=0.00033 Score=62.32 Aligned_cols=93 Identities=13% Similarity=0.250 Sum_probs=77.8
Q ss_pred HHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCC-CCCHHHHHHHhC--cC
Q 009187 70 LMEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSK-PFLLIDFSNYLN--IN 146 (540)
Q Consensus 70 ~L~~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~-prtL~DIs~vl~--V~ 146 (540)
......+.|..++..++++ ..+.-.|..+|.+..............+++||+|+||+.+.. +.++.++....+ .+
T Consensus 30 ~r~~~~~~i~~~~~~~~l~--~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~~~~~~ 107 (127)
T PF00134_consen 30 MRQIIIDWIIELCQRLKLS--PETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRISDNTFT 107 (127)
T ss_dssp HHHHHHHHHHHHHHHTT-B--HHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHTTTSSH
T ss_pred HHHHHHHHHHHHHHhcccc--hhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHHcCCCC
Confidence 3456778999999999999 999999999999999888778888889999999999999877 888999988874 67
Q ss_pred HHHHHHHHHHHHHHhhcc
Q 009187 147 VYELGAVYLQLCQVLYIA 164 (540)
Q Consensus 147 ~~~Lgr~~~~L~~~L~i~ 164 (540)
..+|...-+.++..|+.+
T Consensus 108 ~~~i~~~E~~iL~~L~f~ 125 (127)
T PF00134_consen 108 KKDILEMEREILSALNFD 125 (127)
T ss_dssp HHHHHHHHHHHHHHTTT-
T ss_pred HHHHHHHHHHHHHHCCCC
Confidence 888999999999988865
No 25
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=97.44 E-value=0.0015 Score=70.34 Aligned_cols=153 Identities=14% Similarity=0.093 Sum_probs=122.7
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHH-HHHHhcCC-CCCHHHHHHHhC--cCHHH
Q 009187 74 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLY-LACRQKSK-PFLLIDFSNYLN--INVYE 149 (540)
Q Consensus 74 a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLY-iACR~e~~-prtL~DIs~vl~--V~~~~ 149 (540)
-.+.+-++-..++|. ....-.|..|+.+.+....+..++...|..+||+ |||+.+.. +-++.|+.-+.+ .+..+
T Consensus 161 Lvdwlvevh~~F~L~--~ETL~LaVnliDRfL~~~~v~~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd~~~s~~~ 238 (391)
T KOG0653|consen 161 LVDWLVEVHEKFGLS--PETLYLAVNLIDRFLSKVKVPLKKLQLVGVSALLSIACKYEEISLPSVEDLVLITDGAYSREE 238 (391)
T ss_pred HHHHHHHhhhhcCcC--HHHHHHHHHHHHHHHHHhcccHHHhhHHhHHHHHHHHHhhhhccCCccceeEeeeCCccchHH
Confidence 357888899999999 8999999999999998866777777778778855 99996444 444777776654 78899
Q ss_pred HHHHHHHHHHHhhccccccccccCChhhHHHHHHHhhCCCCCHHHHHHHHHHHHhhcccccccCCChhhHHHHHHHHHHH
Q 009187 150 LGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSAL 229 (540)
Q Consensus 150 Lgr~~~~L~~~L~i~~~p~~~~~~dP~~~I~Rf~~~L~~~~~~~V~~~A~~Iv~~m~~~~i~tGR~P~~IAaAALylAa~ 229 (540)
|.+.-+.+...|++.... ..|..|+.||.....- +......+..++....-+.-.....|+.+|||+.+++.+
T Consensus 239 il~mE~~il~~L~f~l~~-----p~~~~FLrr~~ka~~~--d~~~~~~~k~~~El~l~d~~~~~~~~s~~aaa~~~~~~~ 311 (391)
T KOG0653|consen 239 ILRMEKYILNVLEFDLSV-----PTPLSFLRRFLKAADY--DIKTRTLVKYLLELSLCDYSMLSIPPSSSAAASFTLALR 311 (391)
T ss_pred HHHHHHHHHhccCeeecC-----CchHHHHHHHHHhhhc--chhHHHHHHHHHHHHHhhhHHhccCcHHHHHHHHHHHHH
Confidence 999999999999887654 7899999999988862 455566666677766666667789999999999999998
Q ss_pred hcCCCC
Q 009187 230 THGLKF 235 (540)
Q Consensus 230 ~~g~~~ 235 (540)
+.+.+.
T Consensus 312 ~~~~~~ 317 (391)
T KOG0653|consen 312 MLSKGD 317 (391)
T ss_pred HhccCC
Confidence 876654
No 26
>PF01857 RB_B: Retinoblastoma-associated protein B domain; InterPro: IPR002719 Retinoblastoma-like and retinoblastoma-associated proteins may have a function in cell cycle regulation. They form a complex with adenovirus E1A and SV40 large T antigen, and may bind and modulate the function of certain cellular proteins with which T and E1A compete for pocket binding. The proteins may act as tumor suppressors, and are potent inhibitors of E2F-mediated trans-activation. This domain has the cyclin fold []. The crystal structure of the Rb pocket bound to a nine-residue E7 peptide containing the LxCxE motif, shared by other Rb-binding viral and cellular proteins, shows that the LxCxE peptide binds a highly conserved groove on the B-box portion of the pocket; the A-box portion (see IPR002720 from INTERPRO) appears to be required for the stable folding of the B box. Also highly conserved is the extensive A-B interface, suggesting that it may be an additional protein-binding site. The A and B boxes each contain the cyclin-fold structural motif, with the LxCxE-binding site on the B-box cyclin fold being similar to a Cdk2-binding site of cyclin A and to a TBP-binding site of TFIIB []. The A and B boxes are found at the C-terminal end of the protein; the B-box is on C-terminal side of the A-box.; GO: 0051726 regulation of cell cycle, 0005634 nucleus; PDB: 1GUX_B 3POM_A 1GH6_B 1N4M_A 1O9K_H 4ELL_B 2R7G_C 4ELJ_A.
Probab=97.40 E-value=0.001 Score=61.24 Aligned_cols=84 Identities=12% Similarity=0.216 Sum_probs=65.3
Q ss_pred HHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHh--CcccCCCchhHHHHHHHHHHHHhcCCCCCHHHHHHHhCcCH
Q 009187 70 LMEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVA--RNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINV 147 (540)
Q Consensus 70 ~L~~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~--~~~~rGR~~~~vaAACLYiACR~e~~prtL~DIs~vl~V~~ 147 (540)
.+.-|..+|+.+|..|+|+ +.+.+....+|.-+.. ..++++|...+++.+|+|+.||..+.+.+++||-....-.+
T Consensus 10 vy~la~~Rl~~LC~~L~l~--~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~Ii~~Yr~qp 87 (135)
T PF01857_consen 10 VYKLAAVRLQDLCERLDLS--SDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDIIKAYRKQP 87 (135)
T ss_dssp HHHHHHHHHHHHHHHHTTS--TTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHHHHHTTST
T ss_pred HHHHHHHHHHHHHHHcCCc--HHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHhcc
Confidence 3445778999999999999 8899999999988774 45789999999999999999999999999999998876544
Q ss_pred HHHHHHHH
Q 009187 148 YELGAVYL 155 (540)
Q Consensus 148 ~~Lgr~~~ 155 (540)
..-..+|+
T Consensus 88 q~~~~Vyr 95 (135)
T PF01857_consen 88 QASSHVYR 95 (135)
T ss_dssp T--THHHH
T ss_pred cccccceE
Confidence 44444444
No 27
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=97.40 E-value=0.0052 Score=59.96 Aligned_cols=160 Identities=14% Similarity=0.112 Sum_probs=123.4
Q ss_pred HHHHHHHHhCCCCchHHHHHHHHHHHHHHhC--cccCCCchhHHHHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHH
Q 009187 77 DMRQMKNALNIGESDEIVHVAKRFYGIAVAR--NFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVY 154 (540)
Q Consensus 77 ~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~--~~~rGR~~~~vaAACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~ 154 (540)
.|.+++.+|||..+..++..|.+|.++..-+ ++.-|-.-..-+.-|+=+|.-.-++|..-.-.....|.+.....+.|
T Consensus 2 lI~~l~~klgL~~ep~~lrKa~E~~RL~~~~~~~~~~~v~E~~kaV~CldlAa~~l~i~fDr~~avKLSGl~k~~Y~~~~ 81 (262)
T KOG4557|consen 2 LISDLGRKLGLDNEPLLLRKAAEIRRLCDAQFDSSIIGVGEICKAVICLDLAATRLQIIFDRQAAVKLSGLSKKAYSRSF 81 (262)
T ss_pred cHHHHHHhcCCccChHHHHHHHHHHHHHHhhccCccccccchhHHHHhHHHHHHHhcccccHHHHHHhccccHHHHHHHH
Confidence 4889999999965579999999998886532 33344444556778998888888898887777788899999999999
Q ss_pred HHHHHHhhccccccccccCChhhHHHHHHHhhCCCCCHHHHHHHHHHHHhhccc-----ccccCCChhhHHHHHHHHHHH
Q 009187 155 LQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRD-----WITTGRKPSGLCGAALYVSAL 229 (540)
Q Consensus 155 ~~L~~~L~i~~~p~~~~~~dP~~~I~Rf~~~L~~~~~~~V~~~A~~Iv~~m~~~-----~i~tGR~P~~IAaAALylAa~ 229 (540)
+.+-..||++... -|..+|-+|+ -.+|++.|..|+...+.. .+.+-..-.-.++||+|+||+
T Consensus 82 ~sfe~llgln~~~----------~VrdlaVQfg---c~evi~~a~~vl~syk~~lpaT~~~~~D~SrP~ft~aA~~~ack 148 (262)
T KOG4557|consen 82 NSFENLLGLNIKL----------NVRDLAVQFG---CVEVIKSAQNVLSSYKERLPATRRANADFSRPVFTAAAFYLACK 148 (262)
T ss_pred HHHHHHhcchhhc----------CHHHHHHHHh---HHHHHHHHHHHHHHHHhcCchhhhcCCcccchHHHHHHHHHHHH
Confidence 9999999987543 2556677787 478999999998876642 122222333468899999999
Q ss_pred hcCCCCCHHHHHHHHcccHH
Q 009187 230 THGLKFSKSDIIEDFMARKK 249 (540)
Q Consensus 230 ~~g~~~t~~eI~~~~~~~~~ 249 (540)
....+++....+.+.|++++
T Consensus 149 ~lKlKVdK~kli~~sg~~~s 168 (262)
T KOG4557|consen 149 KLKLKVDKLKLIEVSGTSES 168 (262)
T ss_pred HHHHhhhHhhcccccCCCHH
Confidence 99999998888888888765
No 28
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=96.82 E-value=0.0074 Score=65.49 Aligned_cols=149 Identities=14% Similarity=0.056 Sum_probs=110.7
Q ss_pred HHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCC-CCCHHHHHHHhC--cCHHHHH
Q 009187 75 FDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSK-PFLLIDFSNYLN--INVYELG 151 (540)
Q Consensus 75 ~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~-prtL~DIs~vl~--V~~~~Lg 151 (540)
.+.|.++-..+++- ......|..|..+.+..+.+.=-+...|++.||||||+-+.+ +.+++++.-++. .+...|.
T Consensus 217 v~wlvevH~~F~ll--peTL~lainiiDrfLs~~~v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~t~~~i~ 294 (440)
T COG5024 217 VDWLVEVHGKFGLL--PETLFLAINIIDRFLSSRVVSLEKYQLVGISALFIASKYEEVNCPSIKDLVYATDGAFTRDDII 294 (440)
T ss_pred HHHHHHhccccccc--chHHHHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccccHHHHH
Confidence 36677788888987 788889999999999888877777888999999999998776 556888888874 7899999
Q ss_pred HHHHHHHHHhhccccccccccCChhhHHHHHHHhhCCCCCHHHHHHHHHHHHhhccc-ccccCCChhhHHHHHHHHHHHh
Q 009187 152 AVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRD-WITTGRKPSGLCGAALYVSALT 230 (540)
Q Consensus 152 r~~~~L~~~L~i~~~p~~~~~~dP~~~I~Rf~~~L~~~~~~~V~~~A~~Iv~~m~~~-~i~tGR~P~~IAaAALylAa~~ 230 (540)
++.+.+...|+.++-. ..|.-|+.|+.....- +......+..+...+.-+ .+.... |+.+++||-|++-.+
T Consensus 295 ~aE~~ml~~l~f~is~-----P~P~sFLRriSka~dy--d~~srt~~k~~~e~s~~~~~f~~~~-~S~~~aaa~~~s~~~ 366 (440)
T COG5024 295 RAERYMLEVLDFNISW-----PSPMSFLRRISKASDY--DIFSRTPAKFSSEISPVDYKFIQIS-PSWCAAAAMYLSRKI 366 (440)
T ss_pred HHHHHHhhhcccccCC-----CChHHHHHHHHhhccc--chhhhhhHhhhCCchHhhhhhccCC-chHHHHHHHHHHHhh
Confidence 9999999999987643 7799998777666542 222222333333332222 233445 999999999998776
Q ss_pred cCC
Q 009187 231 HGL 233 (540)
Q Consensus 231 ~g~ 233 (540)
.+-
T Consensus 367 ~~~ 369 (440)
T COG5024 367 LSQ 369 (440)
T ss_pred hcc
Confidence 543
No 29
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=96.48 E-value=0.0017 Score=46.12 Aligned_cols=27 Identities=33% Similarity=0.637 Sum_probs=23.4
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceec
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vle 31 (540)
.|+.||+. .+...+|..+|..||+|++
T Consensus 10 ~C~~C~~~--~~~~~dG~~yC~~cG~~~E 36 (36)
T PF11781_consen 10 PCPVCGSR--WFYSDDGFYYCDRCGHQSE 36 (36)
T ss_pred cCCCCCCe--EeEccCCEEEhhhCceEcC
Confidence 49999997 5667799999999999975
No 30
>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=96.31 E-value=0.0083 Score=52.27 Aligned_cols=78 Identities=22% Similarity=0.180 Sum_probs=55.9
Q ss_pred ChhhHHHHHHHhhCCCCCHHHHHHHHHHHHhhcccccccCCChhhHHHHHHHHHHHhcCC-CCCHHHHHHHHcccHHHHh
Q 009187 174 DPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGL-KFSKSDIIEDFMARKKELH 252 (540)
Q Consensus 174 dP~~~I~Rf~~~L~~~~~~~V~~~A~~Iv~~m~~~~i~tGR~P~~IAaAALylAa~~~g~-~~t~~eI~~~~~~~~~ti~ 252 (540)
.|..|+.+|....+ .+.++...|..|++.+.-+.-..+.+|+.||+||||+|..+++. ..-...+...++....+|+
T Consensus 2 Tp~~Fl~~~~~~~~--~~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t~~~~~~l~ 79 (118)
T PF02984_consen 2 TPYDFLRRFLKISN--ADQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEKLTGYDKEDLK 79 (118)
T ss_dssp -HHHHHHHHHTSSS--HHHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHHTS-HHHHH
T ss_pred cHHHHHHHHHHHcC--CcHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchhhcCCCHHHHH
Confidence 47889999944333 25678889999999888777788999999999999999999875 3333445555566555444
Q ss_pred h
Q 009187 253 E 253 (540)
Q Consensus 253 ~ 253 (540)
+
T Consensus 80 ~ 80 (118)
T PF02984_consen 80 E 80 (118)
T ss_dssp H
T ss_pred H
Confidence 3
No 31
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=95.54 E-value=0.088 Score=54.67 Aligned_cols=106 Identities=16% Similarity=0.275 Sum_probs=78.0
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCCHH-HHHHHhCcCHHHHHH
Q 009187 74 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLI-DFSNYLNINVYELGA 152 (540)
Q Consensus 74 a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~prtL~-DIs~vl~V~~~~Lgr 152 (540)
-.+.|-.+.+.|++|++..+...+.+|......-.++.--+++.||+||+|+|.|..++|.+.. .--.+++++..+|-.
T Consensus 141 Phklii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~vry~pe~iACaciyLaAR~~eIpLp~~P~Wf~~Fd~~k~eid~ 220 (367)
T KOG0835|consen 141 PHKLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVFVRYSPESIACACIYLAARNLEIPLPFQPHWFKAFDTTKREIDE 220 (367)
T ss_pred cHHHHHHHHHHhcCCCchhHHHHHHHhhhhccccceeeecCHHHHHHHHHHHHHhhhcCCCCCCccHHHHcCCcHHHHHH
Confidence 3466888899999996566788888888888777777778899999999999999999876654 344567788888877
Q ss_pred HHHHHHHHhhccccccccccCChhhHHHHHHHhhC
Q 009187 153 VYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLL 187 (540)
Q Consensus 153 ~~~~L~~~L~i~~~p~~~~~~dP~~~I~Rf~~~L~ 187 (540)
...++........ | -..+|.-|++.+.
T Consensus 221 ic~~l~~lY~~~~-p-------~~~li~~~vd~~k 247 (367)
T KOG0835|consen 221 ICYRLIPLYKRAK-P-------DETLIEAFVDRLK 247 (367)
T ss_pred HHHHHHHHHHhcc-c-------CHHHHHHHHHHhh
Confidence 6666655443321 1 1346777777663
No 32
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=95.49 E-value=0.22 Score=44.50 Aligned_cols=55 Identities=11% Similarity=0.033 Sum_probs=42.6
Q ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHhhccccccccccCChhhHHHHHHHhhC-CCCCHH
Q 009187 135 LLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLL-PGGNKK 193 (540)
Q Consensus 135 tL~DIs~vl~V~~~~Lgr~~~~L~~~L~i~~~p~~~~~~dP~~~I~Rf~~~L~-~~~~~~ 193 (540)
.|++++..+||+--++...+..|.+.|+....+ ..........+.++|. |+.+.+
T Consensus 51 nlKe~e~~lgiSYPTvR~rLd~ii~~lg~~~~~----~~~~~~~~~~IL~~L~~GeIs~e 106 (113)
T PF09862_consen 51 NLKEMEKELGISYPTVRNRLDKIIEKLGYEEDE----EEEEEDERKEILDKLEKGEISVE 106 (113)
T ss_pred CHHHHHHHHCCCcHHHHHHHHHHHHHhCCCCCc----ccccchhHHHHHHHHHcCCCCHH
Confidence 689999999999999999999999999983332 2445677888888884 555443
No 33
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=95.17 E-value=0.011 Score=46.47 Aligned_cols=31 Identities=26% Similarity=0.541 Sum_probs=28.8
Q ss_pred CCCCCCCCCCeeeecCCCceecCcccceecc
Q 009187 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee 32 (540)
++||.|+...+++++++-.+.|..||.+|.+
T Consensus 12 VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~~ 42 (59)
T PRK00415 12 VKCPDCGNEQVVFSHASTVVRCLVCGKTLAE 42 (59)
T ss_pred EECCCCCCeEEEEecCCcEEECcccCCCccc
Confidence 4799999999999999999999999999974
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=95.06 E-value=0.011 Score=46.07 Aligned_cols=31 Identities=29% Similarity=0.503 Sum_probs=23.9
Q ss_pred CCCCCCCCCCeeeecCCCceecCcccceecc
Q 009187 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee 32 (540)
++||.|+...+++++++-.+.|..||+||-+
T Consensus 8 VkCp~C~~~q~vFSha~t~V~C~~Cg~~L~~ 38 (55)
T PF01667_consen 8 VKCPGCYNIQTVFSHAQTVVKCVVCGTVLAQ 38 (55)
T ss_dssp EE-TTT-SEEEEETT-SS-EE-SSSTSEEEE
T ss_pred EECCCCCCeeEEEecCCeEEEcccCCCEecC
Confidence 4799999999999999999999999999974
No 35
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=95.05 E-value=0.013 Score=47.04 Aligned_cols=32 Identities=22% Similarity=0.494 Sum_probs=29.2
Q ss_pred CCCCCCCCCCeeeecCCCceecCcccceeccc
Q 009187 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDH 33 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~ 33 (540)
++||.||...+++++.+-.+.|-.||.+|-+.
T Consensus 20 VkCpdC~N~q~vFshast~V~C~~CG~~l~~P 51 (67)
T COG2051 20 VKCPDCGNEQVVFSHASTVVTCLICGTTLAEP 51 (67)
T ss_pred EECCCCCCEEEEeccCceEEEecccccEEEec
Confidence 47999999999999999999999999999753
No 36
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=94.82 E-value=0.019 Score=40.62 Aligned_cols=31 Identities=19% Similarity=0.574 Sum_probs=20.6
Q ss_pred CCCCCCCCCCCeeeecCCCceecCcccceec
Q 009187 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (540)
Q Consensus 1 m~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vle 31 (540)
|..||.||.-.+......+..+|..||.+.+
T Consensus 1 m~FCp~C~nlL~p~~~~~~~~~C~~C~Y~~~ 31 (35)
T PF02150_consen 1 MRFCPECGNLLYPKEDKEKRVACRTCGYEEP 31 (35)
T ss_dssp --BETTTTSBEEEEEETTTTEEESSSS-EEE
T ss_pred CeeCCCCCccceEcCCCccCcCCCCCCCccC
Confidence 7789999986544444455558999999854
No 37
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=94.73 E-value=0.36 Score=50.32 Aligned_cols=106 Identities=11% Similarity=0.170 Sum_probs=81.4
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhCcccCCC-chhHHHHHHHHHHHHhcCC-CCCHHHHHHHhC--cCHHH
Q 009187 74 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGR-RTEQVQASCLYLACRQKSK-PFLLIDFSNYLN--INVYE 149 (540)
Q Consensus 74 a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR-~~~~vaAACLYiACR~e~~-prtL~DIs~vl~--V~~~~ 149 (540)
-++.+-++|.-..|. ....--|..||.+.+.-..--.+ ....|--+|||||.+.+.+ |--++|||-++. ++..+
T Consensus 148 LlDWlmEVCEvykLH--RETFyLAvDy~DRyl~t~~~v~kt~lQLIGitsLFIAAK~EEIYpPKl~eFAyvTDgAcs~dd 225 (408)
T KOG0655|consen 148 LLDWLMEVCEVYKLH--RETFYLAVDYFDRYLETQVEVSKTNLQLIGITSLFIAAKLEEIYPPKLIEFAYVTDGACSEDD 225 (408)
T ss_pred HHHHHHHHHHHHHHh--hhHHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHhhccCccccceeeeccCccchHH
Confidence 357889999999999 88888899999887653211122 2344556999999999887 889999999875 78999
Q ss_pred HHHHHHHHHHHhhccccccccccCChhhHHHHHHHhh
Q 009187 150 LGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRL 186 (540)
Q Consensus 150 Lgr~~~~L~~~L~i~~~p~~~~~~dP~~~I~Rf~~~L 186 (540)
|...-+.|++.|+...-| +....++.-|..-+
T Consensus 226 IltmE~iilkal~W~l~P-----iTii~WL~vylQv~ 257 (408)
T KOG0655|consen 226 ILTMELIILKALKWELSP-----ITIISWLNVYLQVD 257 (408)
T ss_pred HHHHHHHHHHHhcccccc-----eehHHHHHHHHHHH
Confidence 999999999999988766 54555666665555
No 38
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=94.59 E-value=0.025 Score=47.53 Aligned_cols=32 Identities=22% Similarity=0.447 Sum_probs=29.3
Q ss_pred CCCCCCCCCCeeeecCCCceecCcccceeccc
Q 009187 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDH 33 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~ 33 (540)
+.||.|+...+++++++-.+.|..||++|-+.
T Consensus 36 VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~P 67 (85)
T PTZ00083 36 VKCPGCSQITTVFSHAQTVVLCGGCSSQLCQP 67 (85)
T ss_pred EECCCCCCeeEEEecCceEEEccccCCEeecc
Confidence 47999999999999999999999999999653
No 39
>PF02984 Cyclin_C: Cyclin, C-terminal domain; InterPro: IPR004367 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This is the C-terminal domain of cyclins.; GO: 0005634 nucleus; PDB: 3QHR_D 3QHW_B 1W98_B 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D 2IW9_D ....
Probab=94.55 E-value=0.19 Score=43.56 Aligned_cols=86 Identities=14% Similarity=0.150 Sum_probs=64.6
Q ss_pred HHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCC-CCCHHHHHHHhCcCHHHHHHH
Q 009187 75 FDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSK-PFLLIDFSNYLNINVYELGAV 153 (540)
Q Consensus 75 ~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~-prtL~DIs~vl~V~~~~Lgr~ 153 (540)
+.+|+.+....+.. ..+...|..+...+.-...+-+-++..+||||+|+|.+..+. +.--..+....+++...|...
T Consensus 4 ~~Fl~~~~~~~~~~--~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~~t~~~~~~l~~c 81 (118)
T PF02984_consen 4 YDFLRRFLKISNAD--QEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEKLTGYDKEDLKEC 81 (118)
T ss_dssp HHHHHHHHTSSSHH--HHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHHHcCCc--HHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchhhcCCCHHHHHHH
Confidence 45666664443444 678888888888877666667788899999999999998765 455566777789999999999
Q ss_pred HHHHHHHhh
Q 009187 154 YLQLCQVLY 162 (540)
Q Consensus 154 ~~~L~~~L~ 162 (540)
+..|...+.
T Consensus 82 ~~~i~~~~~ 90 (118)
T PF02984_consen 82 IELIQELLS 90 (118)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 988888765
No 40
>PLN00209 ribosomal protein S27; Provisional
Probab=94.36 E-value=0.025 Score=47.70 Aligned_cols=32 Identities=25% Similarity=0.460 Sum_probs=29.3
Q ss_pred CCCCCCCCCCeeeecCCCceecCcccceeccc
Q 009187 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDH 33 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~ 33 (540)
++||.|+...+++++++-.+.|..||++|-+.
T Consensus 37 VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~P 68 (86)
T PLN00209 37 VKCQGCFNITTVFSHSQTVVVCGSCQTVLCQP 68 (86)
T ss_pred EECCCCCCeeEEEecCceEEEccccCCEeecc
Confidence 47999999999999999999999999999753
No 41
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=94.30 E-value=0.019 Score=40.35 Aligned_cols=28 Identities=21% Similarity=0.628 Sum_probs=15.8
Q ss_pred CCCCCCCCC---eeeecCCCceecCccccee
Q 009187 3 WCSSCARHV---TGHRPYDSQLCCDRCGKVL 30 (540)
Q Consensus 3 ~Cp~Cgs~~---iv~D~~~G~~VCt~CG~Vl 30 (540)
.||.||+.. +..+...--.||+.||.|-
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACGFIH 32 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTTEEE
T ss_pred ccccccChhhhhcCCCCCccceECCCCCCEE
Confidence 699999972 2222346679999999983
No 42
>PHA00626 hypothetical protein
Probab=94.28 E-value=0.035 Score=43.07 Aligned_cols=31 Identities=16% Similarity=0.456 Sum_probs=23.1
Q ss_pred CCCCCCCCCCeeee----cCCCceecCcccceecc
Q 009187 2 VWCSSCARHVTGHR----PYDSQLCCDRCGKVLED 32 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D----~~~G~~VCt~CG~Vlee 32 (540)
+.||.||+..++-. ..+..++|.+||.-..-
T Consensus 1 m~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~ 35 (59)
T PHA00626 1 MSCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSK 35 (59)
T ss_pred CCCCCCCCceeeeeceecccCcceEcCCCCCeech
Confidence 46999999766542 22689999999986543
No 43
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=94.18 E-value=0.025 Score=37.21 Aligned_cols=23 Identities=22% Similarity=0.723 Sum_probs=18.4
Q ss_pred CCCCCCCCCCCeeeecCCCceecCcccc
Q 009187 1 MVWCSSCARHVTGHRPYDSQLCCDRCGK 28 (540)
Q Consensus 1 m~~Cp~Cgs~~iv~D~~~G~~VCt~CG~ 28 (540)
++.||+||.. + ..+..+|..||.
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 4579999984 2 357899999996
No 44
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=94.14 E-value=0.032 Score=43.32 Aligned_cols=31 Identities=29% Similarity=0.632 Sum_probs=22.8
Q ss_pred CCCCCCCCCCCeeeecCCC-ceecCcccceec
Q 009187 1 MVWCSSCARHVTGHRPYDS-QLCCDRCGKVLE 31 (540)
Q Consensus 1 m~~Cp~Cgs~~iv~D~~~G-~~VCt~CG~Vle 31 (540)
|..||.||...-+-|...| .+.|..||.-++
T Consensus 2 ~~~CP~CG~~iev~~~~~GeiV~Cp~CGaele 33 (54)
T TIGR01206 2 QFECPDCGAEIELENPELGELVICDECGAELE 33 (54)
T ss_pred ccCCCCCCCEEecCCCccCCEEeCCCCCCEEE
Confidence 3479999997434444446 567999999887
No 45
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=93.69 E-value=0.034 Score=35.64 Aligned_cols=22 Identities=27% Similarity=0.889 Sum_probs=17.7
Q ss_pred CCCCCCCCCeeeecCCCceecCcccce
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~V 29 (540)
+||+||... ..+..+|..||+-
T Consensus 1 ~Cp~CG~~~-----~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEI-----EDDAKFCPNCGTP 22 (23)
T ss_pred CCcccCCCC-----CCcCcchhhhCCc
Confidence 599999873 2478899999974
No 46
>PRK00420 hypothetical protein; Validated
Probab=93.34 E-value=0.058 Score=48.09 Aligned_cols=27 Identities=26% Similarity=0.492 Sum_probs=21.9
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceec
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vle 31 (540)
.||.||...+- ..+|..+|..||.++.
T Consensus 25 ~CP~Cg~pLf~--lk~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 25 HCPVCGLPLFE--LKDGEVVCPVHGKVYI 51 (112)
T ss_pred CCCCCCCccee--cCCCceECCCCCCeee
Confidence 69999987433 2589999999999865
No 47
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=93.33 E-value=0.066 Score=37.39 Aligned_cols=27 Identities=26% Similarity=0.465 Sum_probs=22.5
Q ss_pred CCCCCCCCCeeeecCCCceecCccccee
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vl 30 (540)
.|+.||+..++. ...+..||..||.+-
T Consensus 5 ~C~~C~~~~i~~-~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 5 KCSKCGGNGIVN-KEDDYEVCIFCGSSF 31 (33)
T ss_pred EcCCCCCCeEEE-ecCCeEEcccCCcEe
Confidence 699999986553 568999999999874
No 48
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=92.29 E-value=0.11 Score=35.53 Aligned_cols=28 Identities=25% Similarity=0.531 Sum_probs=15.1
Q ss_pred CCCCCCCCCCCeeeecCCCceecCccccee
Q 009187 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (540)
Q Consensus 1 m~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vl 30 (540)
+..||.|++...-. +...+||..||.-.
T Consensus 2 ~p~Cp~C~se~~y~--D~~~~vCp~C~~ew 29 (30)
T PF08274_consen 2 LPKCPLCGSEYTYE--DGELLVCPECGHEW 29 (30)
T ss_dssp S---TTT-----EE---SSSEEETTTTEEE
T ss_pred CCCCCCCCCcceec--cCCEEeCCcccccC
Confidence 35799999985443 46899999999753
No 49
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=91.62 E-value=0.11 Score=47.32 Aligned_cols=23 Identities=26% Similarity=0.739 Sum_probs=19.6
Q ss_pred CCCCCCCCCeeeecCCCceecCcccc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGK 28 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~ 28 (540)
.||.||...+- .+|.++|..||+
T Consensus 30 hCp~Cg~PLF~---KdG~v~CPvC~~ 52 (131)
T COG1645 30 HCPKCGTPLFR---KDGEVFCPVCGY 52 (131)
T ss_pred hCcccCCccee---eCCeEECCCCCc
Confidence 59999998554 579999999993
No 50
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=91.59 E-value=0.49 Score=49.44 Aligned_cols=71 Identities=11% Similarity=0.103 Sum_probs=55.5
Q ss_pred hhHHHHHHHhhCCCCCHHHHHHHHHHHHhhcccccccCCChhhHHHHHHHHHHHhcCCCCCHHHHHHHHcc
Q 009187 176 SIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIIEDFMA 246 (540)
Q Consensus 176 ~~~I~Rf~~~L~~~~~~~V~~~A~~Iv~~m~~~~i~tGR~P~~IAaAALylAa~~~g~~~t~~eI~~~~~~ 246 (540)
+.+|..++..|.-..++.|.-+|.-+.++.--.+-..-..|.-|+++||||||..-++.++..+++..+..
T Consensus 60 ~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~~~~ 130 (305)
T TIGR00569 60 EKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGNLKE 130 (305)
T ss_pred HHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhhccC
Confidence 34566777777611388999999999988654444456899999999999999999999999998876543
No 51
>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=91.42 E-value=0.11 Score=37.03 Aligned_cols=30 Identities=20% Similarity=0.575 Sum_probs=21.0
Q ss_pred CCCCCCCCCCeeee----cCCCceecCcccceec
Q 009187 2 VWCSSCARHVTGHR----PYDSQLCCDRCGKVLE 31 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D----~~~G~~VCt~CG~Vle 31 (540)
..||+||...-+-+ ...+.+.|..||.++.
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 46999998632222 1345799999999874
No 52
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=91.16 E-value=0.16 Score=38.44 Aligned_cols=30 Identities=17% Similarity=0.561 Sum_probs=20.8
Q ss_pred CCCCCCCCCeeeecCC-CceecCcccceecc
Q 009187 3 WCSSCARHVTGHRPYD-SQLCCDRCGKVLED 32 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~-G~~VCt~CG~Vlee 32 (540)
.||.||.-....+... ..++|..||.+...
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~~ 32 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEEPI 32 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCeEEC
Confidence 6999998543332222 38999999998643
No 53
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=90.91 E-value=0.16 Score=38.77 Aligned_cols=26 Identities=19% Similarity=0.539 Sum_probs=20.7
Q ss_pred CCCCCCCCCeeeecCCCceecCccccee
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vl 30 (540)
.||.||+. +..++ .+...|..||...
T Consensus 22 fCP~Cg~~-~m~~~-~~r~~C~~Cgyt~ 47 (50)
T PRK00432 22 FCPRCGSG-FMAEH-LDRWHCGKCGYTE 47 (50)
T ss_pred cCcCCCcc-hhecc-CCcEECCCcCCEE
Confidence 69999997 54443 5899999999863
No 54
>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=90.66 E-value=0.2 Score=35.89 Aligned_cols=27 Identities=19% Similarity=0.388 Sum_probs=20.3
Q ss_pred CCCCCCCCC-Ceeeec--CCCceecCcccc
Q 009187 2 VWCSSCARH-VTGHRP--YDSQLCCDRCGK 28 (540)
Q Consensus 2 ~~Cp~Cgs~-~iv~D~--~~G~~VCt~CG~ 28 (540)
..||.||+. .+-+|. ..|..+|..||.
T Consensus 4 ~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred cCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 369999986 333554 469999999985
No 55
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=90.65 E-value=0.2 Score=39.27 Aligned_cols=27 Identities=22% Similarity=0.429 Sum_probs=20.1
Q ss_pred CCCCCCCCCCeeeecCCC-------ceecCcccc
Q 009187 2 VWCSSCARHVTGHRPYDS-------QLCCDRCGK 28 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G-------~~VCt~CG~ 28 (540)
..||.||+..+.++...+ .+.|+.||.
T Consensus 4 kPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 4 KPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred cCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 369999988766655443 366999999
No 56
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=90.63 E-value=0.18 Score=42.69 Aligned_cols=29 Identities=28% Similarity=0.571 Sum_probs=25.2
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceecc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee 32 (540)
.||.||+. .+-...+|-..|..||.+..-
T Consensus 37 ~Cp~C~~~-~VkR~a~GIW~C~kCg~~fAG 65 (89)
T COG1997 37 VCPFCGRT-TVKRIATGIWKCRKCGAKFAG 65 (89)
T ss_pred cCCCCCCc-ceeeeccCeEEcCCCCCeecc
Confidence 59999998 667788999999999998753
No 57
>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=90.42 E-value=4.1 Score=37.86 Aligned_cols=89 Identities=11% Similarity=0.093 Sum_probs=66.5
Q ss_pred HHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHh---Ccc--cCCCchhHHHHHHHHHHHHh-cCCCCCHHHHHHHhCcCH
Q 009187 74 AFDDMRQMKNALNIGESDEIVHVAKRFYGIAVA---RNF--TKGRRTEQVQASCLYLACRQ-KSKPFLLIDFSNYLNINV 147 (540)
Q Consensus 74 a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~---~~~--~rGR~~~~vaAACLYiACR~-e~~prtL~DIs~vl~V~~ 147 (540)
..++|.++....+++ ..+.-.|..+..+... ... +.......+..+||-+|.+. .+...+.+.+|.+.|++.
T Consensus 54 i~~fl~ri~~~~~~s--~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~gis~ 131 (149)
T PF08613_consen 54 IRDFLSRILKYTQCS--PECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGGISL 131 (149)
T ss_dssp HHHHHHHHHHHTT----HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHTS-H
T ss_pred HHHHHHHHHHHcCCC--hHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcCCCH
Confidence 457788889999999 8899899988888877 221 23455667899999999994 788999999999999999
Q ss_pred HHHHHHHHHHHHHhhcc
Q 009187 148 YELGAVYLQLCQVLYIA 164 (540)
Q Consensus 148 ~~Lgr~~~~L~~~L~i~ 164 (540)
.+|.+.-+.++..|+.+
T Consensus 132 ~eln~lE~~fL~~l~~~ 148 (149)
T PF08613_consen 132 KELNELEREFLKLLDYN 148 (149)
T ss_dssp HHHHHHHHHHHHHTTT-
T ss_pred HHHHHHHHHHHHHCCCc
Confidence 99999999998888754
No 58
>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=90.24 E-value=0.23 Score=40.10 Aligned_cols=17 Identities=24% Similarity=0.638 Sum_probs=14.8
Q ss_pred eecCCCceecCccccee
Q 009187 14 HRPYDSQLCCDRCGKVL 30 (540)
Q Consensus 14 ~D~~~G~~VCt~CG~Vl 30 (540)
++..+|.++|.+||.+.
T Consensus 47 ~~i~eg~L~Cp~c~r~Y 63 (68)
T PF03966_consen 47 VEIVEGELICPECGREY 63 (68)
T ss_dssp EETTTTEEEETTTTEEE
T ss_pred ccccCCEEEcCCCCCEE
Confidence 56779999999999985
No 59
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=89.60 E-value=1 Score=48.01 Aligned_cols=90 Identities=16% Similarity=0.207 Sum_probs=65.3
Q ss_pred HHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCC-CCHHHH----HHHhCcCHHH
Q 009187 75 FDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKP-FLLIDF----SNYLNINVYE 149 (540)
Q Consensus 75 ~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~p-rtL~DI----s~vl~V~~~~ 149 (540)
.+++++++.--+|. ...+.+|..||.+..=+|++.-.+...+|+|||.+|.+.+..- .+++-+ -+.+..+..+
T Consensus 386 KREMr~l~~d~~id--~~TVa~AyVYFEKliLkglisK~NRKlcAGAclLlaaKmnD~Kks~vKslIek~Ee~fR~nrrd 463 (497)
T KOG4164|consen 386 KREMRELGEDCGID--VVTVAMAYVYFEKLILKGLISKQNRKLCAGACLLLAAKMNDLKKSTVKSLIEKLEEQFRLNRRD 463 (497)
T ss_pred HHHHHHhhhccCcc--ceeehhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHhcccHHh
Confidence 45677777777887 7899999999999888888877777889999999999988652 233333 3345677777
Q ss_pred HHHHHHHHHHHhhcccc
Q 009187 150 LGAVYLQLCQVLYIADE 166 (540)
Q Consensus 150 Lgr~~~~L~~~L~i~~~ 166 (540)
|-..-.-++-.|.+..+
T Consensus 464 Lia~Ef~VlvaLefaL~ 480 (497)
T KOG4164|consen 464 LIAFEFPVLVALEFALH 480 (497)
T ss_pred hhhhhhhHHHhhhhhcc
Confidence 66555555555655544
No 60
>PRK11827 hypothetical protein; Provisional
Probab=89.55 E-value=0.27 Score=39.02 Aligned_cols=27 Identities=15% Similarity=0.252 Sum_probs=23.0
Q ss_pred CCCCCCCCCeeeecCCCceecCccccee
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vl 30 (540)
.||.|++. +.+|.....+||..||.+.
T Consensus 10 aCP~ckg~-L~~~~~~~~Lic~~~~laY 36 (60)
T PRK11827 10 ACPVCNGK-LWYNQEKQELICKLDNLAF 36 (60)
T ss_pred ECCCCCCc-CeEcCCCCeEECCccCeec
Confidence 69999986 5677777899999999885
No 61
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=89.25 E-value=0.3 Score=36.34 Aligned_cols=27 Identities=26% Similarity=0.695 Sum_probs=21.6
Q ss_pred CCCCCCCCCeeeecCCCceecCccccee
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vl 30 (540)
.|++||.. +.+|+..+.+.|..||.-+
T Consensus 5 ~C~~CG~~-~~~~~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 5 KCARCGRE-VELDEYGTGVRCPYCGYRI 31 (46)
T ss_pred ECCCCCCE-EEECCCCCceECCCCCCeE
Confidence 69999986 5566666699999999743
No 62
>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=89.16 E-value=1.4 Score=38.85 Aligned_cols=67 Identities=15% Similarity=0.051 Sum_probs=51.7
Q ss_pred hhHHHHHHHhhCCCCCHHHHHHHHHHHHhhcccccccCCChhhHHHHHHHHHHHhcCC-CCCHHHHHHHH
Q 009187 176 SIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGL-KFSKSDIIEDF 244 (540)
Q Consensus 176 ~~~I~Rf~~~L~~~~~~~V~~~A~~Iv~~m~~~~i~tGR~P~~IAaAALylAa~~~g~-~~t~~eI~~~~ 244 (540)
..||...+..+++ +..+.-.|..++.++..........+.-|++||+++|+.+.+. ..+..+++...
T Consensus 35 ~~~i~~~~~~~~l--~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~~ 102 (127)
T PF00134_consen 35 IDWIIELCQRLKL--SPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRIS 102 (127)
T ss_dssp HHHHHHHHHHTT---BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHHT
T ss_pred HHHHHHHHHhccc--chhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHHH
Confidence 4567777777764 8899999999999986666677899999999999999999887 45566665554
No 63
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=89.12 E-value=0.27 Score=46.31 Aligned_cols=29 Identities=24% Similarity=0.484 Sum_probs=19.9
Q ss_pred CCCCCCCCCC-eeeecC---CCcee-----cCccccee
Q 009187 2 VWCSSCARHV-TGHRPY---DSQLC-----CDRCGKVL 30 (540)
Q Consensus 2 ~~Cp~Cgs~~-iv~D~~---~G~~V-----Ct~CG~Vl 30 (540)
|.||+||+.. .+.|.. .|..| |..||.-.
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence 5799999864 455543 45444 99999753
No 64
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=88.04 E-value=0.39 Score=36.90 Aligned_cols=31 Identities=19% Similarity=0.332 Sum_probs=21.4
Q ss_pred CCCCCCCCCCe-e---eec--CCCceecCcccceecc
Q 009187 2 VWCSSCARHVT-G---HRP--YDSQLCCDRCGKVLED 32 (540)
Q Consensus 2 ~~Cp~Cgs~~i-v---~D~--~~G~~VCt~CG~Vlee 32 (540)
..||.||+... + ++. ..|...|+.||.....
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~~ 38 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGPV 38 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECCCCCCCccc
Confidence 46999999854 2 221 3455689999998653
No 65
>PF05460 ORC6: Origin recognition complex subunit 6 (ORC6); InterPro: IPR008721 The Origin Recognition Complex (ORC) is a six-subunit ATP-dependent DNA-binding complex encoded in yeast by ORC1-6 []. ORC is a central component for eukaryotic DNA replication, and binds chromatin at replication origins throughout the cell cycle []. ORC directs DNA replication throughout the genome and is required for its initiation [, , ]. ORC bound at replication origins serves as the foundation for assembly of the pre-replicative complex (pre-RC), which includes Cdc6, Tah11 (aka Cdt1), and the Mcm2-7 complex [, , ]. Pre-RC assembly during G1 is required for replication licensing of chromosomes prior to DNA synthesis during S phase [, , ]. Cell cycle-regulated phosphorylation of Orc2, Orc6, Cdc6, and MCM by the cyclin-dependent protein kinase Cdc28 regulates initiation of DNA replication, including blocking reinitiation in G2/M phase [, , , ]. In yeast, ORC also plays a role in the establishment of silencing at the mating-type loci Hidden MAT Left (HML) and Hidden MAT Right (HMR) [, , ]. ORC participates in the assembly of transcriptionally silent chromatin at HML and HMR by recruiting the Sir1 silencing protein to the HML and HMR silencers [, , ]. Both Orc1 and Orc5 bind ATP, though only Orc1 has ATPase activity []. The binding of ATP by Orc1 is required for ORC binding to DNA and is essential for cell viability []. The ATPase activity of Orc1 is involved in formation of the pre-RC [, , ]. ATP binding by Orc5 is crucial for the stability of ORC as a whole. Only the Orc1-5 subunits are required for origin binding; Orc6 is essential for maintenance of pre-RCs once formed []. Interactions within ORC suggest that Orc2-3-6 may form a core complex []. ORC homologues have been found in various eukaryotes, including fission yeast, insects, amphibians, and humans []. This entry represents subunit 6, which directs DNA replication by binding to replication origins and is also involved in transcriptional silencing; interacts with Spp1 and with trimethylated histone H3; phosphorylated by Cdc28 [, ]. In Saccharomyces cerevisiae (Baker's yeast), both ends of the Orc6 interact with Cdt1 [] and the N terminus mediates an interaction with the S-phase cyclin Clb5 []. ; GO: 0003677 DNA binding, 0006260 DNA replication, 0005664 nuclear origin of replication recognition complex; PDB: 3M03_B.
Probab=87.10 E-value=0.19 Score=53.62 Aligned_cols=86 Identities=13% Similarity=0.092 Sum_probs=0.0
Q ss_pred HHHHHhCCCCchHHHHHHHHHHHHHH-hCcccCCCchhHHHHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHH
Q 009187 80 QMKNALNIGESDEIVHVAKRFYGIAV-ARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLC 158 (540)
Q Consensus 80 ~ia~~L~Lp~~~~i~e~A~~iyk~a~-~~~~~rGR~~~~vaAACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~ 158 (540)
+|+-.++++.+..++..|..||++.. ....+++..-..-+.+|+||||...+.++-+..+....+++++...+.|..|.
T Consensus 3 ~l~p~~~~~~~~~ll~~a~~L~~ls~~~~~~l~~~~EiaR~~iCa~lA~~~l~~~~dl~~~~~~~pl~pk~y~~l~~~~~ 82 (353)
T PF05460_consen 3 DLIPKLGGGLPPKLLSKASELYRLSRQKKSSLKPEEEIARAHICAELACERLKEKLDLPYAIKRSPLPPKVYKKLLNTFE 82 (353)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred hhhhccCCCCCHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhCCccCchhhcCCCCCCHHHHHHHHHHHH
Confidence 34445554433899999999999988 45667777667778899999999999999888888888999988888888888
Q ss_pred HHhhccc
Q 009187 159 QVLYIAD 165 (540)
Q Consensus 159 ~~L~i~~ 165 (540)
+.|+...
T Consensus 83 ~~L~~~s 89 (353)
T PF05460_consen 83 NLLGNSS 89 (353)
T ss_dssp -------
T ss_pred HHHhCCC
Confidence 8887654
No 66
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=86.96 E-value=0.43 Score=37.74 Aligned_cols=28 Identities=21% Similarity=0.442 Sum_probs=25.1
Q ss_pred CCCCCCCCCCeeeecCCCceecCccccee
Q 009187 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vl 30 (540)
..||.|.+. +.+|.+.+.+||..||...
T Consensus 9 LaCP~~kg~-L~~~~~~~~L~c~~~~~aY 36 (60)
T COG2835 9 LACPVCKGP-LVYDEEKQELICPRCKLAY 36 (60)
T ss_pred eeccCcCCc-ceEeccCCEEEecccCcee
Confidence 469999998 7888899999999999875
No 67
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=86.86 E-value=0.42 Score=42.73 Aligned_cols=33 Identities=24% Similarity=0.579 Sum_probs=25.2
Q ss_pred CCCCCCCCCCCee-eecCCCceecCcccceeccc
Q 009187 1 MVWCSSCARHVTG-HRPYDSQLCCDRCGKVLEDH 33 (540)
Q Consensus 1 m~~Cp~Cgs~~iv-~D~~~G~~VCt~CG~Vlee~ 33 (540)
|..||.||+-.+. -|...+.++|..||...+-.
T Consensus 2 m~FCp~Cgsll~p~~~~~~~~l~C~kCgye~~~~ 35 (113)
T COG1594 2 MRFCPKCGSLLYPKKDDEGGKLVCRKCGYEEEAS 35 (113)
T ss_pred ccccCCccCeeEEeEcCCCcEEECCCCCcchhcc
Confidence 6789999996433 34457799999999987644
No 68
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=85.82 E-value=0.46 Score=36.05 Aligned_cols=26 Identities=27% Similarity=0.701 Sum_probs=20.9
Q ss_pred CCCCCCCCCeeeecCCCceecCcccce
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~V 29 (540)
.||.||-..+--|+.+ -+.|..||..
T Consensus 21 ~CPrCG~gvfmA~H~d-R~~CGkCgyT 46 (51)
T COG1998 21 FCPRCGPGVFMADHKD-RWACGKCGYT 46 (51)
T ss_pred cCCCCCCcchhhhcCc-eeEeccccce
Confidence 5999997666666644 8999999986
No 69
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=85.69 E-value=0.45 Score=31.43 Aligned_cols=24 Identities=33% Similarity=0.731 Sum_probs=19.0
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceec
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vle 31 (540)
.||+|+... ......|..||.+..
T Consensus 2 ~CP~C~~~V-----~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAEV-----PESAKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCCc-----hhhcCcCCCCCCCCc
Confidence 699999873 257789999998753
No 70
>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=85.63 E-value=0.44 Score=42.28 Aligned_cols=29 Identities=21% Similarity=0.527 Sum_probs=23.5
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceeccc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDH 33 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~ 33 (540)
.||+||.. -||-..--+||..||++....
T Consensus 11 ~Cp~CG~k--FYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 11 TCPSCGAK--FYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cCCCCcch--hccCCCCCccCCCCCCccCcc
Confidence 69999987 366666779999999998754
No 71
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=85.57 E-value=0.45 Score=33.90 Aligned_cols=28 Identities=21% Similarity=0.609 Sum_probs=20.9
Q ss_pred CCCCCCCCCeeee----cCCCceecCccccee
Q 009187 3 WCSSCARHVTGHR----PYDSQLCCDRCGKVL 30 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D----~~~G~~VCt~CG~Vl 30 (540)
.||+|+..--+-| ...+.+-|+.||.|.
T Consensus 4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred ECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 6999998732223 346799999999985
No 72
>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=85.16 E-value=0.78 Score=31.48 Aligned_cols=26 Identities=23% Similarity=0.606 Sum_probs=15.0
Q ss_pred CCCCCCCCCeeeecCCCceecCcccce
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~V 29 (540)
.|+.||+... .....-..+|..||..
T Consensus 5 fC~~CG~~t~-~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 5 FCGRCGAPTK-PAPGGWARRCPSCGHE 30 (32)
T ss_dssp B-TTT--BEE-E-SSSS-EEESSSS-E
T ss_pred ccCcCCcccc-CCCCcCEeECCCCcCE
Confidence 6999999743 3334568999999986
No 73
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=84.38 E-value=0.5 Score=39.20 Aligned_cols=30 Identities=23% Similarity=0.551 Sum_probs=27.2
Q ss_pred CCCCCCCCCCeeeecCCCceecCcccceec
Q 009187 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vle 31 (540)
++||.|-....++.++...+||.+|++|+=
T Consensus 35 VkC~gc~~iT~vfSHaqtvVvc~~c~~il~ 64 (84)
T KOG1779|consen 35 VKCPGCFKITTVFSHAQTVVVCEGCSTILC 64 (84)
T ss_pred EEcCCceEEEEEeecCceEEEcCCCceEEE
Confidence 479999988889999999999999999974
No 74
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=84.37 E-value=4.2 Score=32.32 Aligned_cols=71 Identities=7% Similarity=0.128 Sum_probs=44.4
Q ss_pred HHHHHHHhCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCCHHHHHHHhCc-CHHHHHHHHHH
Q 009187 78 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNI-NVYELGAVYLQ 156 (540)
Q Consensus 78 I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~prtL~DIs~vl~V-~~~~Lgr~~~~ 156 (540)
|.++|..+|++ ...... +|+.........-.....+.-|+-|+.-. +.++.|||..+|. +...+.+.|++
T Consensus 4 ~~~la~~~~~s--~~~l~~---~f~~~~~~s~~~~~~~~r~~~a~~~l~~~----~~~~~~ia~~~g~~s~~~f~r~Fk~ 74 (84)
T smart00342 4 LEDLAEALGMS--PRHLQR---LFKKETGTTPKQYLRDRRLERARRLLRDT----DLSVTEIALRVGFSSQSYFSRAFKK 74 (84)
T ss_pred HHHHHHHhCCC--HHHHHH---HHHHHhCcCHHHHHHHHHHHHHHHHHHcC----CCCHHHHHHHhCCCChHHHHHHHHH
Confidence 67889999998 443332 33333222221111222344455555422 8999999999999 99999988876
Q ss_pred H
Q 009187 157 L 157 (540)
Q Consensus 157 L 157 (540)
.
T Consensus 75 ~ 75 (84)
T smart00342 75 L 75 (84)
T ss_pred H
Confidence 5
No 75
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=84.21 E-value=0.85 Score=37.59 Aligned_cols=30 Identities=17% Similarity=0.514 Sum_probs=22.3
Q ss_pred CCCCCCCCCCCeeeec-------CCCceecC--ccccee
Q 009187 1 MVWCSSCARHVTGHRP-------YDSQLCCD--RCGKVL 30 (540)
Q Consensus 1 m~~Cp~Cgs~~iv~D~-------~~G~~VCt--~CG~Vl 30 (540)
|+.||.||+...+.+. .+-...|+ +||...
T Consensus 1 mm~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF 39 (72)
T PRK09678 1 MFHCPLCQHAAHARTSRYITDTTKERYHQCQNVNCSATF 39 (72)
T ss_pred CccCCCCCCccEEEEChhcChhhheeeeecCCCCCCCEE
Confidence 8999999998765553 23456798 999864
No 76
>COG4640 Predicted membrane protein [Function unknown]
Probab=83.99 E-value=0.54 Score=50.06 Aligned_cols=26 Identities=23% Similarity=0.804 Sum_probs=20.6
Q ss_pred CCCCCCCCCCCeeeecCCCceecCcccceec
Q 009187 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (540)
Q Consensus 1 m~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vle 31 (540)
|..||.||+.. .+|+.-|+.||.-+.
T Consensus 1 M~fC~kcG~qk-----~Ed~~qC~qCG~~~t 26 (465)
T COG4640 1 MKFCPKCGSQK-----AEDDVQCTQCGHKFT 26 (465)
T ss_pred CCccccccccc-----ccccccccccCCcCC
Confidence 88999999863 356677999998654
No 77
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=83.61 E-value=0.72 Score=33.64 Aligned_cols=27 Identities=19% Similarity=0.336 Sum_probs=15.3
Q ss_pred CCCCCCCCC-e-eeec--CCCceecCcccce
Q 009187 3 WCSSCARHV-T-GHRP--YDSQLCCDRCGKV 29 (540)
Q Consensus 3 ~Cp~Cgs~~-i-v~D~--~~G~~VCt~CG~V 29 (540)
.||.||++. . +++. .+|..+|..||.+
T Consensus 5 pCP~CGG~DrFri~~d~~~~G~~~C~~C~~~ 35 (40)
T PF08273_consen 5 PCPICGGKDRFRIFDDKDGRGTWICRQCGGD 35 (40)
T ss_dssp --TTTT-TTTEEEETT----S-EEETTTTBE
T ss_pred CCCCCcCccccccCcCcccCCCEECCCCCCc
Confidence 599999973 3 3553 4699999999434
No 78
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=83.50 E-value=0.85 Score=33.44 Aligned_cols=23 Identities=30% Similarity=0.871 Sum_probs=18.1
Q ss_pred CCCCCCCCCeeeecCCCceecCccc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCG 27 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG 27 (540)
.||.||... +...+|.++|..||
T Consensus 19 ~Cp~C~~PL--~~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 19 HCPDCGTPL--MRDKDGKIYCVSCG 41 (41)
T ss_pred ccCCCCCee--EEecCCCEECCCCC
Confidence 699997653 33468999999997
No 79
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=83.30 E-value=0.67 Score=40.32 Aligned_cols=29 Identities=21% Similarity=0.535 Sum_probs=22.8
Q ss_pred CCCCCCCCCee---eec--CCCceecCcccceec
Q 009187 3 WCSSCARHVTG---HRP--YDSQLCCDRCGKVLE 31 (540)
Q Consensus 3 ~Cp~Cgs~~iv---~D~--~~G~~VCt~CG~Vle 31 (540)
.||.||+..++ ++- .-|.++|..||.-.+
T Consensus 24 tCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 24 TCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFE 57 (104)
T ss_pred ecCccCCeeeeEEEEEecCceeEEEcccCcceEE
Confidence 59999997655 553 468999999998654
No 80
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=83.01 E-value=0.81 Score=39.99 Aligned_cols=30 Identities=20% Similarity=0.426 Sum_probs=22.8
Q ss_pred CCCCCCCCCe--eeecCCCceecCcccceecc
Q 009187 3 WCSSCARHVT--GHRPYDSQLCCDRCGKVLED 32 (540)
Q Consensus 3 ~Cp~Cgs~~i--v~D~~~G~~VCt~CG~Vlee 32 (540)
.||+||...+ ..|...+.++|..||+.-+-
T Consensus 23 ~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 23 ECPRCGKVSISVKIKKNIAIITCGNCGLYTEF 54 (99)
T ss_pred ECCCCCCeEeeeecCCCcceEECCCCCCccCE
Confidence 6999996422 34556789999999998664
No 81
>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=82.85 E-value=0.88 Score=36.49 Aligned_cols=29 Identities=21% Similarity=0.566 Sum_probs=21.0
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceecc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee 32 (540)
.||.||..... .......+|..||.+.+-
T Consensus 30 ~C~~CG~~~~~-~~~~r~~~C~~Cg~~~~r 58 (69)
T PF07282_consen 30 TCPRCGHRNKK-RRSGRVFTCPNCGFEMDR 58 (69)
T ss_pred CccCccccccc-ccccceEEcCCCCCEECc
Confidence 59999986432 345668899999988653
No 82
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=82.31 E-value=21 Score=34.75 Aligned_cols=151 Identities=13% Similarity=0.203 Sum_probs=84.8
Q ss_pred hhHHHHHHHHHHHHhcCCC-CCHHHHHHHhCcCHHHHHHHHHHHHHHhhccccc--------cccccCCh--hhHHHHHH
Q 009187 115 TEQVQASCLYLACRQKSKP-FLLIDFSNYLNINVYELGAVYLQLCQVLYIADES--------NVLKQVDP--SIFLHKFT 183 (540)
Q Consensus 115 ~~~vaAACLYiACR~e~~p-rtL~DIs~vl~V~~~~Lgr~~~~L~~~L~i~~~p--------~~~~~~dP--~~~I~Rf~ 183 (540)
...++=|.||+ .+-| .++.+|+.+++++...+..+...|.....-.... .|.-.+.| ..||.+|.
T Consensus 5 ~~~~iEA~LF~----sg~pgls~~~La~~l~~~~~~v~~~l~~L~~~y~~~~~gi~i~~~~~~y~l~tk~e~~~~v~~~~ 80 (188)
T PRK00135 5 YKSIIEALLFV----SGEEGLSLEQLAEILELEPTEVQQLLEELQEKYEGDDRGLKLIEFNDVYKLVTKEENADYLQKLV 80 (188)
T ss_pred HHHHHHHHHHH----cCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhhCCCCEEEEEECCEEEEEEcHHHHHHHHHHh
Confidence 45677788887 4777 9999999999999988988888888876422111 01111222 23344432
Q ss_pred HhhCCCCCHHHHHHHHHHHHhhcccccccCCChhhHHHHHHHHHHHhcCCCCCHHHHHHHHcccHHHHhhh-hcCCC-CC
Q 009187 184 DRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIIEDFMARKKELHEG-VAANL-PN 261 (540)
Q Consensus 184 ~~L~~~~~~~V~~~A~~Iv~~m~~~~i~tGR~P~~IAaAALylAa~~~g~~~t~~eI~~~~~~~~~ti~~~-~~~~~-~~ 261 (540)
..- ......+.|+++ ||...++-++|..+|.+..|++...+-+. .+-.. ..
T Consensus 81 ~~~---~~~~LS~aaLEt------------------------LaiIay~qPiTr~eI~~irGv~~~~ii~~L~~~gLI~e 133 (188)
T PRK00135 81 KTP---IKQSLSQAALEV------------------------LAIIAYKQPITRIEIDEIRGVNSDGALQTLLAKGLIKE 133 (188)
T ss_pred ccc---ccCCCCHHHHHH------------------------HHHHHHcCCcCHHHHHHHHCCCHHHHHHHHHHCCCeEE
Confidence 221 011233333333 33444678999999999999976544333 22222 00
Q ss_pred CCCCCCCccchhhccccCCCCccccchhhhHHHHhhhccccCCCCCChhhH
Q 009187 262 NGPKVSGMNEVLCKHKDTGKPFACGLCRSCYEEFMTISEGLEGGADPPAFQ 312 (540)
Q Consensus 262 ~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~ef~~~~~~l~~~~dpPaf~ 312 (540)
.+ .....++|..+++... |...- |+.+-.|=|-+.
T Consensus 134 ~g-----------r~~~~Grp~ly~tT~~----F~~~f-Gi~sl~dLP~~~ 168 (188)
T PRK00135 134 VG-----------RKEVPGRPILYGTTDE----FLDYF-GINSLDELPKLS 168 (188)
T ss_pred cC-----------cCCCCCCCeeeehhHH----HHHHc-CCCChhhCCCch
Confidence 00 1111345666655444 44432 666666656554
No 83
>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=82.27 E-value=1.3 Score=33.04 Aligned_cols=26 Identities=19% Similarity=0.450 Sum_probs=19.5
Q ss_pred CCCCCCCCCeeeecCCCceecCcccc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGK 28 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~ 28 (540)
.||+||+.....-...+..-|..|+.
T Consensus 20 ~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 20 VCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 59999997443334469999999984
No 84
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=82.08 E-value=4.4 Score=40.14 Aligned_cols=80 Identities=15% Similarity=0.194 Sum_probs=52.1
Q ss_pred HHHHHHHHhCCCCchHHHHHHHHHHHHHHhC-----cccCCCchhHHHHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHH
Q 009187 77 DMRQMKNALNIGESDEIVHVAKRFYGIAVAR-----NFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELG 151 (540)
Q Consensus 77 ~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~-----~~~rGR~~~~vaAACLYiACR~e~~prtL~DIs~vl~V~~~~Lg 151 (540)
.|+++|-+||+. .++..|.++.+...++ ..-..-+.....+|++|.|||..+.-..-.-+..+.|+.+..+.
T Consensus 95 ~VrdlaVQfgc~---evi~~a~~vl~syk~~lpaT~~~~~D~SrP~ft~aA~~~ack~lKlKVdK~kli~~sg~~~s~F~ 171 (262)
T KOG4557|consen 95 NVRDLAVQFGCV---EVIKSAQNVLSSYKERLPATRRANADFSRPVFTAAAFYLACKKLKLKVDKLKLIEVSGTSESEFS 171 (262)
T ss_pred CHHHHHHHHhHH---HHHHHHHHHHHHHHhcCchhhhcCCcccchHHHHHHHHHHHHHHHHhhhHhhcccccCCCHHHHH
Confidence 478888888887 7888888888776552 11112344678999999999987655444444445566665555
Q ss_pred HHHHHHHH
Q 009187 152 AVYLQLCQ 159 (540)
Q Consensus 152 r~~~~L~~ 159 (540)
...+++-+
T Consensus 172 ~l~kqler 179 (262)
T KOG4557|consen 172 CLSKQLER 179 (262)
T ss_pred HHHHHHHH
Confidence 44444443
No 85
>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=81.66 E-value=0.86 Score=41.42 Aligned_cols=29 Identities=7% Similarity=0.033 Sum_probs=23.6
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceeccc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDH 33 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~ 33 (540)
.||+||.. -||-..--+||..||.+....
T Consensus 11 ~Cp~cg~k--FYDLnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 11 ICPNTGSK--FYDLNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred cCCCcCcc--ccccCCCCccCCCcCCccCcc
Confidence 59999987 366667889999999997644
No 86
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=81.65 E-value=1 Score=32.74 Aligned_cols=27 Identities=22% Similarity=0.604 Sum_probs=19.6
Q ss_pred CCCCCCCCCeeee---------cCCCceecCcccce
Q 009187 3 WCSSCARHVTGHR---------PYDSQLCCDRCGKV 29 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D---------~~~G~~VCt~CG~V 29 (540)
.||.||+...++= +.+-.++|.+||..
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~ 37 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHR 37 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCE
Confidence 6999998865441 22448999999964
No 87
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=81.50 E-value=1.2 Score=35.81 Aligned_cols=28 Identities=14% Similarity=0.354 Sum_probs=21.3
Q ss_pred CCCCCCCCCeeeecCCC--ceecCccccee
Q 009187 3 WCSSCARHVTGHRPYDS--QLCCDRCGKVL 30 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G--~~VCt~CG~Vl 30 (540)
.||.||...+..-...| .++|-.||...
T Consensus 8 PCPFCG~~~~~v~~~~g~~~v~C~~CgA~~ 37 (64)
T PRK09710 8 PCPFCGCPSVTVKAISGYYRAKCNGCESRT 37 (64)
T ss_pred CCCCCCCceeEEEecCceEEEEcCCCCcCc
Confidence 59999998665554455 57999999963
No 88
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=80.79 E-value=4.3 Score=47.36 Aligned_cols=84 Identities=12% Similarity=0.213 Sum_probs=69.0
Q ss_pred HHHHHHHHHHHHHhCCCCchHHHHHHHHHHHHHHh--CcccCCCchhHHHHHHHHHHHHhcCCCCCHHHHHHHhCcCHHH
Q 009187 72 EKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAVA--RNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYE 149 (540)
Q Consensus 72 ~~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~--~~~~rGR~~~~vaAACLYiACR~e~~prtL~DIs~vl~V~~~~ 149 (540)
.-|..+|+.+|.+|.|. +.+.+.-..+|.-... -.+++.|...++.-+|+|+.||..+...++.+|-..+.-.+.-
T Consensus 678 ~LAavRL~~Lc~rL~l~--~e~r~~IWtlFehsl~~et~Lm~dRHLDQillCaiy~i~KV~~~~ltF~eIm~~YR~QPqa 755 (920)
T KOG1010|consen 678 HLAAVRLNDLCERLSLS--DELREQIWTLFEHSLTNETELMRDRHLDQILLCAIYGIAKVKKEDLTFSEIMRAYRRQPQA 755 (920)
T ss_pred HHHHHHHHHHHHHhhhh--hHHHHHHHHHHHHHHhccHHHHHhhhHHHHHHHHHHhheehhcccchHHHHHHHHhcCchh
Confidence 34668899999999999 8888888888876554 3577899999999999999999999999999998887665555
Q ss_pred HHHHHHHH
Q 009187 150 LGAVYLQL 157 (540)
Q Consensus 150 Lgr~~~~L 157 (540)
...+|+.+
T Consensus 756 ~~~vyRsV 763 (920)
T KOG1010|consen 756 VSLVYRSV 763 (920)
T ss_pred hhhhhhhe
Confidence 55666543
No 89
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=80.40 E-value=0.46 Score=33.82 Aligned_cols=28 Identities=32% Similarity=0.695 Sum_probs=21.3
Q ss_pred CCCCCCCC-CeeeecCCCceecCccccee
Q 009187 3 WCSSCARH-VTGHRPYDSQLCCDRCGKVL 30 (540)
Q Consensus 3 ~Cp~Cgs~-~iv~D~~~G~~VCt~CG~Vl 30 (540)
.||.||.. ++.+++-.-..+|..||.-|
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 59999986 67778777888999999754
No 90
>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=80.31 E-value=0.92 Score=38.91 Aligned_cols=31 Identities=23% Similarity=0.503 Sum_probs=25.1
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceecccc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHN 34 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~~ 34 (540)
.||.||... +.....|-..|..||.++.-..
T Consensus 37 ~Cp~Cgk~~-vkR~a~GIW~C~~C~~~~AGGA 67 (90)
T PF01780_consen 37 TCPFCGKTS-VKRVATGIWKCKKCGKKFAGGA 67 (90)
T ss_dssp EESSSSSSE-EEEEETTEEEETTTTEEEE-BS
T ss_pred cCCCCCCce-eEEeeeEEeecCCCCCEEeCCC
Confidence 599999986 4566799999999999987543
No 91
>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=80.24 E-value=1.4 Score=41.02 Aligned_cols=28 Identities=25% Similarity=0.496 Sum_probs=21.2
Q ss_pred CCCCCCCCC-Ceeeec---CCCcee-----cCcccce
Q 009187 2 VWCSSCARH-VTGHRP---YDSQLC-----CDRCGKV 29 (540)
Q Consensus 2 ~~Cp~Cgs~-~iv~D~---~~G~~V-----Ct~CG~V 29 (540)
|.||.||.. .-|.|+ ..|..| |..||.=
T Consensus 1 M~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~R 37 (147)
T TIGR00244 1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHER 37 (147)
T ss_pred CCCCCCCCCCCEeeeccccCCCCeeeecccCCccCCc
Confidence 579999996 456675 467776 9999974
No 92
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=80.19 E-value=1.2 Score=38.72 Aligned_cols=31 Identities=19% Similarity=0.569 Sum_probs=23.5
Q ss_pred CCCCCCCCCCCeeeecC-CCceecCcccceec
Q 009187 1 MVWCSSCARHVTGHRPY-DSQLCCDRCGKVLE 31 (540)
Q Consensus 1 m~~Cp~Cgs~~iv~D~~-~G~~VCt~CG~Vle 31 (540)
|..||.||.-.++.... -....|..|+.|..
T Consensus 1 m~FCP~Cgn~Live~g~~~~rf~C~tCpY~~~ 32 (105)
T KOG2906|consen 1 MLFCPTCGNMLIVESGESCNRFSCRTCPYVFP 32 (105)
T ss_pred CcccCCCCCEEEEecCCeEeeEEcCCCCceee
Confidence 78999999875554333 36789999999954
No 93
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=79.31 E-value=3.5 Score=43.50 Aligned_cols=66 Identities=18% Similarity=0.125 Sum_probs=47.9
Q ss_pred hHHHHHHHhhCCCCCHHHHHHHHHHHHhhcccccccCCChhhHHHHHHHHHHHhcCCCCCHHHHHHHH
Q 009187 177 IFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIIEDF 244 (540)
Q Consensus 177 ~~I~Rf~~~L~~~~~~~V~~~A~~Iv~~m~~~~i~tGR~P~~IAaAALylAa~~~g~~~t~~eI~~~~ 244 (540)
.||...+.+|+. +.....+|.-|.++.--......-.|..||++|||||+...+..+..++|+.+.
T Consensus 44 ~fI~elg~~L~~--~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s 109 (323)
T KOG0834|consen 44 KFIQELGVRLKM--PQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVS 109 (323)
T ss_pred HHHHHHHHHcCC--CccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHH
Confidence 456666666652 333455555555655444556678889999999999999999999999997664
No 94
>PF12773 DZR: Double zinc ribbon
Probab=79.00 E-value=1.1 Score=33.65 Aligned_cols=12 Identities=33% Similarity=0.678 Sum_probs=5.9
Q ss_pred CceecCccccee
Q 009187 19 SQLCCDRCGKVL 30 (540)
Q Consensus 19 G~~VCt~CG~Vl 30 (540)
...+|..||..+
T Consensus 28 ~~~~C~~Cg~~~ 39 (50)
T PF12773_consen 28 SKKICPNCGAEN 39 (50)
T ss_pred CCCCCcCCcCCC
Confidence 344555555543
No 95
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=78.76 E-value=0.62 Score=44.92 Aligned_cols=30 Identities=27% Similarity=0.741 Sum_probs=23.7
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceecc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee 32 (540)
.||.|+..-...|..+....|..||.+|.+
T Consensus 119 ~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 119 FCPNCHIRFTFDEAMEYGFRCPQCGEMLEE 148 (178)
T ss_pred ECCCCCcEEeHHHHhhcCCcCCCCCCCCee
Confidence 599999764444555788999999999985
No 96
>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=78.47 E-value=1 Score=50.97 Aligned_cols=33 Identities=27% Similarity=0.682 Sum_probs=25.1
Q ss_pred CCCCCCCCCC------eeee----cCCCceecCcccceecccc
Q 009187 2 VWCSSCARHV------TGHR----PYDSQLCCDRCGKVLEDHN 34 (540)
Q Consensus 2 ~~Cp~Cgs~~------iv~D----~~~G~~VCt~CG~Vlee~~ 34 (540)
+.||+||... +.++ +..-.++|..||..++|..
T Consensus 201 vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e~~ 243 (557)
T PF05876_consen 201 VPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEEHD 243 (557)
T ss_pred ccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCHHH
Confidence 5799999852 3333 3467899999999999853
No 97
>PRK12495 hypothetical protein; Provisional
Probab=78.40 E-value=1.3 Score=43.88 Aligned_cols=27 Identities=22% Similarity=0.608 Sum_probs=22.8
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceecc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee 32 (540)
.|+.||...+ ...|.++|..|+.++.+
T Consensus 44 hC~~CG~PIp---a~pG~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 44 HCDECGDPIF---RHDGQEFCPTCQQPVTE 70 (226)
T ss_pred hcccccCccc---CCCCeeECCCCCCcccc
Confidence 6999999855 23799999999999875
No 98
>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=78.17 E-value=3.1 Score=36.77 Aligned_cols=30 Identities=27% Similarity=0.498 Sum_probs=22.8
Q ss_pred CCCCCCCCCCeeeecCCCceecCcccceeccc
Q 009187 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDH 33 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~ 33 (540)
..||.|++.-.-.| ...+||..||.--...
T Consensus 3 p~CP~C~seytY~d--g~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 3 PPCPKCNSEYTYHD--GTQLICPSCLYEWNEN 32 (109)
T ss_pred CcCCcCCCcceEec--CCeeECcccccccccc
Confidence 46999999854433 4689999999977544
No 99
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=78.11 E-value=1.3 Score=35.06 Aligned_cols=9 Identities=33% Similarity=0.958 Sum_probs=4.2
Q ss_pred ceecCcccc
Q 009187 20 QLCCDRCGK 28 (540)
Q Consensus 20 ~~VCt~CG~ 28 (540)
.++|.+||.
T Consensus 50 ~Y~Cp~CGF 58 (61)
T COG2888 50 PYRCPKCGF 58 (61)
T ss_pred ceECCCcCc
Confidence 444444443
No 100
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=77.19 E-value=1.3 Score=50.96 Aligned_cols=25 Identities=28% Similarity=0.756 Sum_probs=13.0
Q ss_pred CCCCCCCCCCCeeeecCCCceecCccccee
Q 009187 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (540)
Q Consensus 1 m~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vl 30 (540)
|..||+||..+ ..|.-+|..||.-+
T Consensus 1 M~~Cp~Cg~~n-----~~~akFC~~CG~~l 25 (645)
T PRK14559 1 MLICPQCQFEN-----PNNNRFCQKCGTSL 25 (645)
T ss_pred CCcCCCCCCcC-----CCCCccccccCCCC
Confidence 66677777652 13444444444443
No 101
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=76.05 E-value=1.9 Score=37.06 Aligned_cols=31 Identities=23% Similarity=0.580 Sum_probs=25.1
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceecccc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHN 34 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~~ 34 (540)
.||.||...+ .....|-..|..||.++.-..
T Consensus 38 ~CpfCgk~~v-kR~a~GIW~C~~C~~~~AGGA 68 (90)
T PTZ00255 38 FCPFCGKHAV-KRQAVGIWRCKGCKKTVAGGA 68 (90)
T ss_pred cCCCCCCCce-eeeeeEEEEcCCCCCEEeCCc
Confidence 5999998754 556689999999999987543
No 102
>PRK10220 hypothetical protein; Provisional
Probab=75.80 E-value=2.1 Score=37.88 Aligned_cols=29 Identities=21% Similarity=0.536 Sum_probs=21.7
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceeccc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDH 33 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~ 33 (540)
.||.|++.-.-.| ...+||..||.--...
T Consensus 5 ~CP~C~seytY~d--~~~~vCpeC~hEW~~~ 33 (111)
T PRK10220 5 HCPKCNSEYTYED--NGMYICPECAHEWNDA 33 (111)
T ss_pred cCCCCCCcceEcC--CCeEECCcccCcCCcc
Confidence 6999999854333 5689999999865433
No 103
>PF15616 TerY-C: TerY-C metal binding domain
Probab=74.12 E-value=1.8 Score=39.67 Aligned_cols=19 Identities=32% Similarity=0.864 Sum_probs=12.2
Q ss_pred CCCCCCCCCeeeecCCCceecCcccce
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~V 29 (540)
.||+||.. .|.++| .||.|
T Consensus 79 gCP~CGn~-------~~fa~C-~CGkl 97 (131)
T PF15616_consen 79 GCPHCGNQ-------YAFAVC-GCGKL 97 (131)
T ss_pred CCCCCcCh-------hcEEEe-cCCCE
Confidence 59999985 345555 45555
No 104
>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=73.68 E-value=2.1 Score=37.25 Aligned_cols=27 Identities=26% Similarity=0.743 Sum_probs=21.4
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceecc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee 32 (540)
.||.||.-. .+..|.++|..||.+...
T Consensus 2 fC~~Cg~~l---~~~~~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 2 FCPKCGSLM---TPKNGVYVCPSCGYEKEK 28 (104)
T ss_pred CCcccCccc---ccCCCeEECcCCCCcccc
Confidence 699999863 244689999999998653
No 105
>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=73.11 E-value=13 Score=31.57 Aligned_cols=42 Identities=12% Similarity=0.074 Sum_probs=35.2
Q ss_pred HHHHHHHHHhcCCCCCHHHHHHHhC-cCHHHHHHHHHHHHHHhhc
Q 009187 120 ASCLYLACRQKSKPFLLIDFSNYLN-INVYELGAVYLQLCQVLYI 163 (540)
Q Consensus 120 AACLYiACR~e~~prtL~DIs~vl~-V~~~~Lgr~~~~L~~~L~i 163 (540)
..|.|++-+.. ..++.+|+..++ .+..++...++++.+.+.-
T Consensus 33 ~ia~yl~~~~~--~~s~~~Ig~~fg~r~hStV~~a~~ri~~~~~~ 75 (90)
T cd06571 33 QIAMYLARELT--GLSLPEIGRAFGGRDHSTVLHAVRKIEELLEE 75 (90)
T ss_pred HHHHHHHHHHh--CCCHHHHHHHhCCCCHhHHHHHHHHHHHHHHh
Confidence 36788886665 467899999999 9999999999999998764
No 106
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=72.69 E-value=2.7 Score=35.07 Aligned_cols=30 Identities=27% Similarity=0.509 Sum_probs=20.1
Q ss_pred CCCCCCCCCCCe-eeecCCCceecCccccee
Q 009187 1 MVWCSSCARHVT-GHRPYDSQLCCDRCGKVL 30 (540)
Q Consensus 1 m~~Cp~Cgs~~i-v~D~~~G~~VCt~CG~Vl 30 (540)
|+.||.|+...+ ...+.--.-.|..|+-|-
T Consensus 1 ~llCP~C~v~l~~~~rs~vEiD~CPrCrGVW 31 (88)
T COG3809 1 MLLCPICGVELVMSVRSGVEIDYCPRCRGVW 31 (88)
T ss_pred CcccCcCCceeeeeeecCceeeeCCccccEe
Confidence 778999998732 222222355799998884
No 107
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=72.67 E-value=2.2 Score=30.25 Aligned_cols=28 Identities=25% Similarity=0.718 Sum_probs=19.9
Q ss_pred CCCCCCCCCeeee----cCCCceecCccccee
Q 009187 3 WCSSCARHVTGHR----PYDSQLCCDRCGKVL 30 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D----~~~G~~VCt~CG~Vl 30 (540)
.||+|+..--+-| +....+-|+.||.+.
T Consensus 4 ~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 6999998632222 234578999999874
No 108
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=71.98 E-value=2.5 Score=30.45 Aligned_cols=27 Identities=22% Similarity=0.524 Sum_probs=16.4
Q ss_pred CCCCCCCCCeeee---------cCCCceecCcccce
Q 009187 3 WCSSCARHVTGHR---------PYDSQLCCDRCGKV 29 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D---------~~~G~~VCt~CG~V 29 (540)
.||.||+...++- +.+-.++|.+||..
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 6999999854332 12447899999964
No 109
>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=71.96 E-value=8.7 Score=34.98 Aligned_cols=47 Identities=21% Similarity=0.275 Sum_probs=38.5
Q ss_pred chhHHHHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 009187 114 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (540)
Q Consensus 114 ~~~~vaAACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~ 160 (540)
+.+.-+.+++|+|-+..+.|.+..+||..++++...+.+...+|.+.
T Consensus 6 ~~~YAl~~l~~La~~~~~~~~s~~~ia~~~~ip~~~l~kil~~L~~~ 52 (135)
T TIGR02010 6 KGRYAVTAMLDLALNAETGPVTLADISERQGISLSYLEQLFAKLRKA 52 (135)
T ss_pred HHHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 34556778999998766779999999999999999998877777663
No 110
>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=71.84 E-value=2.6 Score=36.29 Aligned_cols=31 Identities=19% Similarity=0.516 Sum_probs=25.3
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceecccc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHN 34 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~~ 34 (540)
.||.||... +.....|-..|..||.++.-..
T Consensus 37 ~CpfCgk~~-vkR~a~GIW~C~~C~~~~AGGA 67 (91)
T TIGR00280 37 VCPFCGKKT-VKRGSTGIWTCRKCGAKFAGGA 67 (91)
T ss_pred cCCCCCCCc-eEEEeeEEEEcCCCCCEEeCCc
Confidence 599999875 4556789999999999987543
No 111
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=71.20 E-value=1.8 Score=33.96 Aligned_cols=34 Identities=18% Similarity=0.393 Sum_probs=23.5
Q ss_pred CCCCCCCCCCCeeeecCCCceecCcccceecccccccccccccc
Q 009187 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFVKN 44 (540)
Q Consensus 1 m~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~~Ids~~ef~~~ 44 (540)
|..|+.||...+ ..+|..||.... +.+-+-|+-+
T Consensus 5 mr~C~~CgvYTL-------k~~CP~CG~~t~---~~~P~rfSp~ 38 (56)
T PRK13130 5 IRKCPKCGVYTL-------KEICPVCGGKTK---NPHPPRFSPE 38 (56)
T ss_pred ceECCCCCCEEc-------cccCcCCCCCCC---CCCCCCCCCC
Confidence 568999998643 568999998743 3344456544
No 112
>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=70.65 E-value=14 Score=38.48 Aligned_cols=71 Identities=11% Similarity=0.183 Sum_probs=61.2
Q ss_pred hhhHHHHHHHhhCCCCCHHHHHHHHHHHHhhcccccccCCChhhHHHHHHHHHHHhcCCCCCHHHHHHHHc
Q 009187 175 PSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIIEDFM 245 (540)
Q Consensus 175 P~~~I~Rf~~~L~~~~~~~V~~~A~~Iv~~m~~~~i~tGR~P~~IAaAALylAa~~~g~~~t~~eI~~~~~ 245 (540)
-...+-.|++.+.-.++..|+.+|...-.++--.|-..--.|-.|.++++|+|+...++.+|..+++.-..
T Consensus 59 ~E~~l~~f~~k~~p~lp~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~ISieqFvkn~~ 129 (325)
T KOG2496|consen 59 EELSLVNFYSKFKPNLPTSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFYISIEQFVKNMN 129 (325)
T ss_pred HHHHHHHHHHHhcCCCchHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhheecHHHHHhhcc
Confidence 35567788888864568999999999888887778888899999999999999999999999999887665
No 113
>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=70.25 E-value=3.5 Score=36.26 Aligned_cols=31 Identities=16% Similarity=0.329 Sum_probs=21.5
Q ss_pred CCCCCCCCCCeeee--------cCC-Cc-eecCcccceecc
Q 009187 2 VWCSSCARHVTGHR--------PYD-SQ-LCCDRCGKVLED 32 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D--------~~~-G~-~VCt~CG~Vlee 32 (540)
..||+||+.....+ +.. +. .+|+.|+.-|.=
T Consensus 3 ~~CpYCg~~~~l~~~~~iYg~~~~~~~~~y~C~~C~AyVG~ 43 (102)
T PF11672_consen 3 IICPYCGGPAELVDGSEIYGHRYDDGPYLYVCTPCDAYVGC 43 (102)
T ss_pred cccCCCCCeeEEcccchhcCccCCCCceeEECCCCCceeee
Confidence 47999999744433 112 33 899999998773
No 114
>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=70.17 E-value=28 Score=32.96 Aligned_cols=135 Identities=15% Similarity=0.206 Sum_probs=74.7
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHHHhhccccc--------ccc--ccCChhhHHHHHHHhhC
Q 009187 118 VQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADES--------NVL--KQVDPSIFLHKFTDRLL 187 (540)
Q Consensus 118 vaAACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~L~i~~~p--------~~~--~~~dP~~~I~Rf~~~L~ 187 (540)
++=|.||.+ +-|.++.+++++++ +...+......|.+.+.-.... .|+ ...+-..||.+|...-
T Consensus 2 ~iEAlLF~s----~~pvs~~~La~~l~-~~~~v~~~l~~L~~~y~~~~~gl~l~~~~~~y~l~tk~~~~~~v~~~~~~~- 75 (159)
T PF04079_consen 2 IIEALLFAS----GEPVSIEELAEILG-SEDEVEEALEELQEEYNEEDRGLELVEVGGGYRLQTKPEYAEYVEKLFKKP- 75 (159)
T ss_dssp HHHHHHHH-----SS-B-HHHHHHHCT--HHHHHHHHHHHHHHHHHCT-SEEEEEETTEEEEEE-GGGHHHHHHHHCTC-
T ss_pred hhHhhHHHc----CCCCCHHHHHHHhC-CHHHHHHHHHHHHHHhccCCCCEEEEEECCEEEEEEhHHHHHHHHHHhccC-
Confidence 455778875 66999999999999 9999999999999888322111 111 1123344555554442
Q ss_pred CCCCHHHHHHHHHHHHhhcccccccCCChhhHHHHHHHHHHHhcCCCCCHHHHHHHHcccHH-HHhhhhcCCCCCCCCCC
Q 009187 188 PGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIIEDFMARKK-ELHEGVAANLPNNGPKV 266 (540)
Q Consensus 188 ~~~~~~V~~~A~~Iv~~m~~~~i~tGR~P~~IAaAALylAa~~~g~~~t~~eI~~~~~~~~~-ti~~~~~~~~~~~~~~~ 266 (540)
......+.|++.+ |...++.++|..+|-+.-|+... .|++..+-..-
T Consensus 76 --~~~~LS~aalEtL------------------------AiIAY~QPiTr~eIe~IRGv~s~~~i~~L~e~glI------ 123 (159)
T PF04079_consen 76 --KPPKLSQAALETL------------------------AIIAYKQPITRAEIEEIRGVNSDSVIKTLLERGLI------ 123 (159)
T ss_dssp --CCHHHHHHHHHHH------------------------HHHHHH-SEEHHHHHHHHTS--HCHHHHHHHTTSE------
T ss_pred --ccCCCCHHHHHHH------------------------HHHHhcCCcCHHHHHHHcCCChHHHHHHHHHCCCE------
Confidence 2456666666544 33446789999999999887643 33333222220
Q ss_pred CCccchhhcccc-CCCCccccchhhhHHHH
Q 009187 267 SGMNEVLCKHKD-TGKPFACGLCRSCYEEF 295 (540)
Q Consensus 267 ~~~~~~~~~~~~-~~~~~~~g~~~~~~~ef 295 (540)
. ..-+++ .|+|+.+|....-++.|
T Consensus 124 ---~--~~gr~~~~Grp~ly~tT~~Fl~~F 148 (159)
T PF04079_consen 124 ---E--EVGRKDTPGRPILYGTTDKFLEYF 148 (159)
T ss_dssp ---E--EEEE-TTTT--EEEEE-HHHHHHC
T ss_pred ---E--ecCcCCCCCCCeEeehhHHHHHHc
Confidence 0 011222 46788887766655555
No 115
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=69.92 E-value=2.8 Score=32.98 Aligned_cols=27 Identities=22% Similarity=0.463 Sum_probs=19.9
Q ss_pred CCCCCCCCCCeeeecCCCceecCcccceecccc
Q 009187 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHN 34 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~~ 34 (540)
+.||+||... .--.||..||+--+..+
T Consensus 28 ~~C~~CG~~~------~~H~vC~~CG~Y~gr~v 54 (57)
T PRK12286 28 VECPNCGEPK------LPHRVCPSCGYYKGREV 54 (57)
T ss_pred eECCCCCCcc------CCeEECCCCCcCCCEEe
Confidence 4699999863 35689999998655433
No 116
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=69.64 E-value=17 Score=36.03 Aligned_cols=48 Identities=17% Similarity=0.211 Sum_probs=29.2
Q ss_pred HHHHHHHhCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHH
Q 009187 78 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLA 126 (540)
Q Consensus 78 I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiA 126 (540)
|...-....+++ .-..+.|..-|++|.-....++-+...+|..||=+|
T Consensus 78 i~~~~~~~~~~~-~Rt~~~ai~~YkLAll~~~~~~~~~s~~A~l~LrlA 125 (214)
T PF09986_consen 78 ISSRWKPRDFSG-ERTLEEAIESYKLALLCAQIKKEKPSKKAGLCLRLA 125 (214)
T ss_pred HHhhcccCCCCC-CCCHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHH
Confidence 333333335553 456677888888887666666655556666666555
No 117
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=69.09 E-value=3.3 Score=32.72 Aligned_cols=25 Identities=28% Similarity=0.809 Sum_probs=11.2
Q ss_pred CCCCCCCCeeeecCCCceecCcccce
Q 009187 4 CSSCARHVTGHRPYDSQLCCDRCGKV 29 (540)
Q Consensus 4 Cp~Cgs~~iv~D~~~G~~VCt~CG~V 29 (540)
|..||......+ ..-...|.+||.+
T Consensus 10 CtSCg~~i~~~~-~~~~F~CPnCG~~ 34 (59)
T PRK14890 10 CTSCGIEIAPRE-KAVKFLCPNCGEV 34 (59)
T ss_pred ccCCCCcccCCC-ccCEeeCCCCCCe
Confidence 556655421111 1234556666654
No 118
>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=68.55 E-value=2.1 Score=33.40 Aligned_cols=25 Identities=24% Similarity=0.529 Sum_probs=18.3
Q ss_pred CCCCCCCCCCeeeecCCCceecCcccceecc
Q 009187 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee 32 (540)
+.||+||.. ...-.||..||+.=.-
T Consensus 27 ~~c~~cg~~------~~~H~vc~~cG~y~~r 51 (56)
T PF01783_consen 27 VKCPNCGEP------KLPHRVCPSCGYYKGR 51 (56)
T ss_dssp EESSSSSSE------ESTTSBCTTTBBSSSS
T ss_pred eeeccCCCE------ecccEeeCCCCeECCE
Confidence 469999963 2466899999976443
No 119
>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=68.23 E-value=3.2 Score=29.49 Aligned_cols=28 Identities=21% Similarity=0.525 Sum_probs=19.0
Q ss_pred CCCCCCCC-Ceeeec-CCCceecCccccee
Q 009187 3 WCSSCARH-VTGHRP-YDSQLCCDRCGKVL 30 (540)
Q Consensus 3 ~Cp~Cgs~-~iv~D~-~~G~~VCt~CG~Vl 30 (540)
.|+.||.. .+.... ....+.|..||.-+
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~ 36 (41)
T smart00834 7 RCEDCGHTFEVLQKISDDPLATCPECGGDV 36 (41)
T ss_pred EcCCCCCEEEEEEecCCCCCCCCCCCCCcc
Confidence 59999985 232222 25678899999844
No 120
>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=67.20 E-value=9 Score=31.78 Aligned_cols=45 Identities=22% Similarity=0.244 Sum_probs=36.3
Q ss_pred hHHHHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 009187 116 EQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (540)
Q Consensus 116 ~~vaAACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~ 160 (540)
..-+-+.+|+|-...+.|.+..+||+.++++...+.+....|.+.
T Consensus 8 ~~Al~~l~~la~~~~~~~~s~~eiA~~~~i~~~~l~kil~~L~~~ 52 (83)
T PF02082_consen 8 DYALRILLYLARHPDGKPVSSKEIAERLGISPSYLRKILQKLKKA 52 (83)
T ss_dssp HHHHHHHHHHHCTTTSC-BEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHhCCCCCCCCHHHHHHHHCcCHHHHHHHHHHHhhC
Confidence 344557788888777788999999999999999999998888874
No 121
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=67.10 E-value=3.6 Score=35.31 Aligned_cols=32 Identities=22% Similarity=0.541 Sum_probs=25.5
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceeccccc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNF 35 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~~I 35 (540)
.||.||...+ -....|-.-|..||.++.-..+
T Consensus 38 ~CpfCgk~~v-kR~a~GIW~C~~C~~~~AGGAy 69 (90)
T PRK03976 38 VCPVCGRPKV-KRVGTGIWECRKCGAKFAGGAY 69 (90)
T ss_pred cCCCCCCCce-EEEEEEEEEcCCCCCEEeCCcc
Confidence 5999987754 4567899999999999875543
No 122
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=66.95 E-value=3.6 Score=38.51 Aligned_cols=28 Identities=18% Similarity=0.442 Sum_probs=19.7
Q ss_pred CCCCCCCCC-Ceeeec---CCCce-----ecCcccce
Q 009187 2 VWCSSCARH-VTGHRP---YDSQL-----CCDRCGKV 29 (540)
Q Consensus 2 ~~Cp~Cgs~-~iv~D~---~~G~~-----VCt~CG~V 29 (540)
|.||.|++. .-|.|+ ..|.. .|.+||.=
T Consensus 1 M~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~R 37 (156)
T COG1327 1 MKCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGER 37 (156)
T ss_pred CCCCCCCCCCCeeeecccccccchhhhhhcccccccc
Confidence 579999997 345664 35654 49999864
No 123
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=66.83 E-value=3.7 Score=30.52 Aligned_cols=25 Identities=24% Similarity=0.636 Sum_probs=18.9
Q ss_pred CCCCCCCCCeeeecCCCceecCcccce
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~V 29 (540)
.|..||... ..+ ..+.+-|..||.=
T Consensus 4 ~C~~Cg~~~-~~~-~~~~irC~~CG~r 28 (44)
T smart00659 4 ICGECGREN-EIK-SKDVVRCRECGYR 28 (44)
T ss_pred ECCCCCCEe-ecC-CCCceECCCCCce
Confidence 599999863 233 4688999999973
No 124
>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=66.40 E-value=7.9 Score=26.88 Aligned_cols=27 Identities=19% Similarity=0.373 Sum_probs=21.9
Q ss_pred CCCHHHHHHHhCcCHHHHHHHHHHHHH
Q 009187 133 PFLLIDFSNYLNINVYELGAVYLQLCQ 159 (540)
Q Consensus 133 prtL~DIs~vl~V~~~~Lgr~~~~L~~ 159 (540)
|.+-.|||+.+|++..++.|.+.+|.+
T Consensus 2 ~mtr~diA~~lG~t~ETVSR~l~~l~~ 28 (32)
T PF00325_consen 2 PMTRQDIADYLGLTRETVSRILKKLER 28 (32)
T ss_dssp E--HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CcCHHHHHHHhCCcHHHHHHHHHHHHH
Confidence 677899999999999999999988876
No 125
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=66.39 E-value=3.5 Score=33.11 Aligned_cols=14 Identities=14% Similarity=0.449 Sum_probs=10.1
Q ss_pred CCCCCCCCCCeeee
Q 009187 2 VWCSSCARHVTGHR 15 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D 15 (540)
..||.||..+...+
T Consensus 5 ~kCpKCgn~~~~ek 18 (68)
T COG3478 5 FKCPKCGNTNYEEK 18 (68)
T ss_pred ccCCCcCCcchhhc
Confidence 46999998765444
No 126
>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=66.15 E-value=4.1 Score=31.78 Aligned_cols=25 Identities=24% Similarity=0.559 Sum_probs=18.5
Q ss_pred CCCCCCCCCCeeeecCCCceecCcccceecc
Q 009187 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee 32 (540)
+.||+||... .---||..||+--+-
T Consensus 27 ~~C~~cG~~~------~~H~vc~~cG~Y~gr 51 (55)
T TIGR01031 27 VVCPNCGEFK------LPHRVCPSCGYYKGR 51 (55)
T ss_pred eECCCCCCcc------cCeeECCccCeECCE
Confidence 4699999853 356799999976543
No 127
>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=66.00 E-value=22 Score=32.83 Aligned_cols=66 Identities=15% Similarity=0.159 Sum_probs=50.4
Q ss_pred HHHHHHhhCCCCCHHHHHHHHHHHHhhc--ccccccCCChhhHHHHHHHHHHHhcCCCCCHHHHHHHHcc
Q 009187 179 LHKFTDRLLPGGNKKVCDTARDILASMK--RDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIIEDFMA 246 (540)
Q Consensus 179 I~Rf~~~L~~~~~~~V~~~A~~Iv~~m~--~~~i~tGR~P~~IAaAALylAa~~~g~~~t~~eI~~~~~~ 246 (540)
|..+|+.|++ +.++....|.+.+.+. ..++.-+|+---|.-.|||..|++++..+|-++|.+....
T Consensus 18 l~~LC~~L~l--~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~Ii~~Yr~ 85 (135)
T PF01857_consen 18 LQDLCERLDL--SSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDIIKAYRK 85 (135)
T ss_dssp HHHHHHHHTT--STTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHHHHHTT
T ss_pred HHHHHHHcCC--cHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHHHHHHh
Confidence 5567888874 5567777777777653 5689999999999999999999999999999999887743
No 128
>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=65.55 E-value=28 Score=32.64 Aligned_cols=29 Identities=3% Similarity=-0.074 Sum_probs=27.1
Q ss_pred CCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 009187 132 KPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (540)
Q Consensus 132 ~prtL~DIs~vl~V~~~~Lgr~~~~L~~~ 160 (540)
.|.|..|||+.+|++..++.|++++|.+.
T Consensus 142 ~~~t~~~iA~~lG~tretvsR~l~~l~~~ 170 (193)
T TIGR03697 142 LRLSHQAIAEAIGSTRVTITRLLGDLRKK 170 (193)
T ss_pred CCCCHHHHHHHhCCcHHHHHHHHHHHHHC
Confidence 68899999999999999999999999886
No 129
>PF12773 DZR: Double zinc ribbon
Probab=65.52 E-value=4.3 Score=30.32 Aligned_cols=21 Identities=24% Similarity=0.689 Sum_probs=14.9
Q ss_pred CCCCCCCCCCeeeecCCCceecCccc
Q 009187 2 VWCSSCARHVTGHRPYDSQLCCDRCG 27 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VCt~CG 27 (540)
..||.||.. ...+..+|..||
T Consensus 30 ~~C~~Cg~~-----~~~~~~fC~~CG 50 (50)
T PF12773_consen 30 KICPNCGAE-----NPPNAKFCPNCG 50 (50)
T ss_pred CCCcCCcCC-----CcCCcCccCccc
Confidence 457888775 135778888888
No 130
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=65.37 E-value=2.9 Score=40.68 Aligned_cols=29 Identities=24% Similarity=0.557 Sum_probs=19.8
Q ss_pred CCCCCCCCCe---eeecCCC---ceecCcccceecc
Q 009187 3 WCSSCARHVT---GHRPYDS---QLCCDRCGKVLED 32 (540)
Q Consensus 3 ~Cp~Cgs~~i---v~D~~~G---~~VCt~CG~Vlee 32 (540)
.||.||+..+ +.-. .| .+=|.+||+|-.+
T Consensus 8 ~Cp~Cg~eev~hEVik~-~g~~~lvrC~eCG~V~~~ 42 (201)
T COG1326 8 ECPSCGSEEVSHEVIKE-RGREPLVRCEECGTVHPA 42 (201)
T ss_pred ECCCCCcchhhHHHHHh-cCCceEEEccCCCcEeec
Confidence 5999996443 1222 23 5789999999854
No 131
>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=65.09 E-value=40 Score=31.20 Aligned_cols=80 Identities=15% Similarity=0.023 Sum_probs=55.7
Q ss_pred cCChhhHHHHHHHhhCCCCCHHHHHHHHHHHHhhcc---c--ccccCCChhhHHHHHHHHHHHhcC-CCCCHHHHHHHHc
Q 009187 172 QVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKR---D--WITTGRKPSGLCGAALYVSALTHG-LKFSKSDIIEDFM 245 (540)
Q Consensus 172 ~~dP~~~I~Rf~~~L~~~~~~~V~~~A~~Iv~~m~~---~--~i~tGR~P~~IAaAALylAa~~~g-~~~t~~eI~~~~~ 245 (540)
.++-..|+.|+...... +..+.-.|+-++.++.. . ...+...+.-+-.+||.+|+.+++ ...+.+.+++++|
T Consensus 51 ~i~i~~fl~ri~~~~~~--s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v~g 128 (149)
T PF08613_consen 51 SISIRDFLSRILKYTQC--SPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKVGG 128 (149)
T ss_dssp SS-HHHHHHHHHHHTT----HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHHHT
T ss_pred CCcHHHHHHHHHHHcCC--ChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhhcC
Confidence 36777888888887764 78888899999998877 1 223456777899999999998865 5688999999999
Q ss_pred ccHHHHhh
Q 009187 246 ARKKELHE 253 (540)
Q Consensus 246 ~~~~ti~~ 253 (540)
++..+|-.
T Consensus 129 is~~eln~ 136 (149)
T PF08613_consen 129 ISLKELNE 136 (149)
T ss_dssp S-HHHHHH
T ss_pred CCHHHHHH
Confidence 98765533
No 132
>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=64.81 E-value=3.7 Score=34.55 Aligned_cols=31 Identities=19% Similarity=0.404 Sum_probs=17.9
Q ss_pred CCCCCCCC---Ceeeec--CCCceecCcccceeccc
Q 009187 3 WCSSCARH---VTGHRP--YDSQLCCDRCGKVLEDH 33 (540)
Q Consensus 3 ~Cp~Cgs~---~iv~D~--~~G~~VCt~CG~Vlee~ 33 (540)
.||.||.. .+..|. ..|.+.|..||...+-.
T Consensus 24 ~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~ 59 (81)
T PF05129_consen 24 DCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTK 59 (81)
T ss_dssp --TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE
T ss_pred cCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEc
Confidence 59999954 334454 46899999999987644
No 133
>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=64.17 E-value=4.5 Score=28.10 Aligned_cols=24 Identities=25% Similarity=0.700 Sum_probs=16.7
Q ss_pred CCCCCCCCCeeeecCCCceecCcccc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGK 28 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~ 28 (540)
.|..||.... ......+-|..||.
T Consensus 2 ~C~~Cg~~~~--~~~~~~irC~~CG~ 25 (32)
T PF03604_consen 2 ICGECGAEVE--LKPGDPIRCPECGH 25 (32)
T ss_dssp BESSSSSSE---BSTSSTSSBSSSS-
T ss_pred CCCcCCCeeE--cCCCCcEECCcCCC
Confidence 4889998732 34456789999996
No 134
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=63.19 E-value=16 Score=34.68 Aligned_cols=47 Identities=19% Similarity=0.230 Sum_probs=38.0
Q ss_pred chhHHHHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 009187 114 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (540)
Q Consensus 114 ~~~~vaAACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~ 160 (540)
+.+.-+.+++|+|-...+-|.++.+||+.++++...|.+....|.+.
T Consensus 6 ~~~yAl~~l~~lA~~~~~~~vs~~eIA~~~~ip~~~l~kIl~~L~~a 52 (164)
T PRK10857 6 KGRYAVTAMLDVALNSEAGPVPLADISERQGISLSYLEQLFSRLRKN 52 (164)
T ss_pred HHHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 34566778899996556679999999999999999998877777663
No 135
>PF14353 CpXC: CpXC protein
Probab=62.12 E-value=5.1 Score=36.11 Aligned_cols=11 Identities=27% Similarity=0.948 Sum_probs=9.5
Q ss_pred ceecCccccee
Q 009187 20 QLCCDRCGKVL 30 (540)
Q Consensus 20 ~~VCt~CG~Vl 30 (540)
..+|..||...
T Consensus 38 ~~~CP~Cg~~~ 48 (128)
T PF14353_consen 38 SFTCPSCGHKF 48 (128)
T ss_pred EEECCCCCCce
Confidence 67999999875
No 136
>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=61.77 E-value=20 Score=28.63 Aligned_cols=43 Identities=16% Similarity=0.148 Sum_probs=34.2
Q ss_pred HHHHHHHHHHHhcC----------CCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 009187 118 VQASCLYLACRQKS----------KPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (540)
Q Consensus 118 vaAACLYiACR~e~----------~prtL~DIs~vl~V~~~~Lgr~~~~L~~~ 160 (540)
++.-.++++.+... .|.+..+||+.+|++..++.++++.|.+.
T Consensus 3 la~~Ll~l~~~~~~~~~~~~~~~~~~lt~~~iA~~~g~sr~tv~r~l~~l~~~ 55 (76)
T PF13545_consen 3 LARFLLELAERFGRRQDGDGIRIPLPLTQEEIADMLGVSRETVSRILKRLKDE 55 (76)
T ss_dssp HHHHHHHHHHHHEEEEETTEEEEEEESSHHHHHHHHTSCHHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHCCCCCCCCceEEecCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 45555566655432 58899999999999999999999999886
No 137
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=61.54 E-value=19 Score=33.73 Aligned_cols=46 Identities=13% Similarity=0.105 Sum_probs=36.9
Q ss_pred chhHHHHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 009187 114 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (540)
Q Consensus 114 ~~~~vaAACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~ 160 (540)
+.+.-+-+.+|+|-. .+.+.+..+||+..+++...|.+.+..|.+.
T Consensus 6 ~~~YAlr~L~~LA~~-~~~~~s~~eIA~~~~is~~~L~kIl~~L~~a 51 (153)
T PRK11920 6 QTNYAIRMLMYCAAN-DGKLSRIPEIARAYGVSELFLFKILQPLVEA 51 (153)
T ss_pred HHhHHHHHHHHHHhC-CCCcCcHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 345556688999944 5568899999999999999998888877774
No 138
>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=61.33 E-value=5.9 Score=31.93 Aligned_cols=27 Identities=19% Similarity=0.534 Sum_probs=17.6
Q ss_pred CCCCCCCCCeeeec---CCC--------------ceecCcccce
Q 009187 3 WCSSCARHVTGHRP---YDS--------------QLCCDRCGKV 29 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~---~~G--------------~~VCt~CG~V 29 (540)
.||.||+.....+. ..| .++|++||..
T Consensus 2 ~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~CGYT 45 (64)
T PF09855_consen 2 KCPKCGNEEYESGEVRATGGGLSKIFDVQNKKFTTVSCTNCGYT 45 (64)
T ss_pred CCCCCCCcceecceEEccCCeeEEEEEecCcEEEEEECCCCCCE
Confidence 59999987543332 111 3589999986
No 139
>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=61.17 E-value=2.5 Score=32.42 Aligned_cols=29 Identities=17% Similarity=0.591 Sum_probs=21.7
Q ss_pred CCCCCCCCCCee-eecCCCceecCccccee
Q 009187 2 VWCSSCARHVTG-HRPYDSQLCCDRCGKVL 30 (540)
Q Consensus 2 ~~Cp~Cgs~~iv-~D~~~G~~VCt~CG~Vl 30 (540)
..|++|+.-... -+....++-|..||+|-
T Consensus 5 iRC~~CnklLa~~g~~~~leIKCpRC~tiN 34 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVIELEIKCPRCKTIN 34 (51)
T ss_pred eeccchhHHHhhhcCccEEEEECCCCCccc
Confidence 479999986333 24456899999999983
No 140
>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=60.80 E-value=6.3 Score=27.25 Aligned_cols=23 Identities=22% Similarity=0.531 Sum_probs=17.3
Q ss_pred CCCCCCCCCeeeecCCCceecCcccc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGK 28 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~ 28 (540)
.|+.||- ++|.......|..||.
T Consensus 3 ~C~~CGy---~y~~~~~~~~CP~Cg~ 25 (33)
T cd00350 3 VCPVCGY---IYDGEEAPWVCPVCGA 25 (33)
T ss_pred ECCCCCC---EECCCcCCCcCcCCCC
Confidence 5888885 4566667788888886
No 141
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=60.13 E-value=4 Score=38.85 Aligned_cols=29 Identities=28% Similarity=0.762 Sum_probs=18.9
Q ss_pred CCCCCCCCCCeee--------------ecCCCceecCccccee
Q 009187 2 VWCSSCARHVTGH--------------RPYDSQLCCDRCGKVL 30 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~--------------D~~~G~~VCt~CG~Vl 30 (540)
+.||.|++...-. -..+-..+|+.||.|.
T Consensus 98 ~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiY 140 (165)
T COG1656 98 SRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIY 140 (165)
T ss_pred ccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccc
Confidence 5799999862211 2233467799999873
No 142
>COG1386 scpB Chromosome segregation and condensation protein B [DNA replication, recombination and repair]
Probab=60.01 E-value=1.7e+02 Score=28.49 Aligned_cols=150 Identities=15% Similarity=0.196 Sum_probs=83.2
Q ss_pred hHHHHHHHHHHHHhcCCCCCHHHHHHHhCc-CHHHHHHHHHHHHHHhhc---cccc--c-c--cccCChhhHHHHHHHhh
Q 009187 116 EQVQASCLYLACRQKSKPFLLIDFSNYLNI-NVYELGAVYLQLCQVLYI---ADES--N-V--LKQVDPSIFLHKFTDRL 186 (540)
Q Consensus 116 ~~vaAACLYiACR~e~~prtL~DIs~vl~V-~~~~Lgr~~~~L~~~L~i---~~~p--~-~--~~~~dP~~~I~Rf~~~L 186 (540)
..++.|.||.+ +.|.++++++.+++. +...+......+.....- .... . + .....-..|+.++...=
T Consensus 10 ~~~vEall~a~----~~pls~~~L~~il~~~~~~~~~~~l~~l~~~y~~rg~~L~~~~~~~r~~t~~~~~~~~~~l~~~~ 85 (184)
T COG1386 10 KALIEALLFAG----GEPLSLKELAEILGIVSADAIIDALAELKEEYEDRGLELVEVAEGWRLQTKQEYAEYLEKLQEQR 85 (184)
T ss_pred HHHHHHHHHhc----CCCCCHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCeeEEEEcCceeEEehHHHHHHHHHHhccc
Confidence 45666666654 789999999999997 666676666666665321 1100 0 0 00011112222221111
Q ss_pred CCCCCHHHHHHHHHHHHhhcccccccCCChhhHHHHH-HHHHHHhcCCCCCHHHHHHHHcccHHHHhhh-hcCCCCCCCC
Q 009187 187 LPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAA-LYVSALTHGLKFSKSDIIEDFMARKKELHEG-VAANLPNNGP 264 (540)
Q Consensus 187 ~~~~~~~V~~~A~~Iv~~m~~~~i~tGR~P~~IAaAA-LylAa~~~g~~~t~~eI~~~~~~~~~ti~~~-~~~~~~~~~~ 264 (540)
-+ ..+--|+ =-||...++.++|..+|.+..|+...++-.. .+...-
T Consensus 86 --------------------------~~--~~LSraalEtLAiIAY~QPiTR~eI~~iRGv~~~~~i~~L~e~glI---- 133 (184)
T COG1386 86 --------------------------PK--RELSRAALETLAIIAYKQPVTRSEIEEIRGVAVSQVISTLLERGLI---- 133 (184)
T ss_pred --------------------------cc--ccccHHHHHHHHHHHHcCCccHHHHHHHhCccHHHHHHHHHHCCCe----
Confidence 01 1222233 3467777899999999999988876543333 222220
Q ss_pred CCCCccchhhccc-cCCCCccccchhhhHHHHhhhccccCCCCCChhhHH
Q 009187 265 KVSGMNEVLCKHK-DTGKPFACGLCRSCYEEFMTISEGLEGGADPPAFQV 313 (540)
Q Consensus 265 ~~~~~~~~~~~~~-~~~~~~~~g~~~~~~~ef~~~~~~l~~~~dpPaf~~ 313 (540)
-.+-+. ..|+|..+|....=++.| |+..-.+.|-+..
T Consensus 134 -------~~~g~~~~~Grp~ly~tT~~Fl~~f-----Gl~sl~eLp~~~~ 171 (184)
T COG1386 134 -------REVGRRDTPGRPYLYGTTEKFLDYF-----GLDSLDELPDLEE 171 (184)
T ss_pred -------EecCCCCCCCCceeeeccHHHHHHh-----CccccccccCcch
Confidence 011122 256688888777666666 6776666666654
No 143
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=59.51 E-value=6.1 Score=30.50 Aligned_cols=30 Identities=20% Similarity=0.461 Sum_probs=20.8
Q ss_pred CCCCCCCCC-CeeeecCCCce----ecCcccceec
Q 009187 2 VWCSSCARH-VTGHRPYDSQL----CCDRCGKVLE 31 (540)
Q Consensus 2 ~~Cp~Cgs~-~iv~D~~~G~~----VCt~CG~Vle 31 (540)
..||+||.. .+..|...|.- =|.-|..=+.
T Consensus 1 i~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~PI~ 35 (52)
T PF14255_consen 1 IQCPYCGEPIEILIDPSAGDQEYIEDCQVCCRPIE 35 (52)
T ss_pred CCCCCCCCeeEEEEecCCCCeeEEeehhhcCCccE
Confidence 369999987 67888877731 2777765443
No 144
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=58.67 E-value=12 Score=33.12 Aligned_cols=31 Identities=19% Similarity=0.453 Sum_probs=23.2
Q ss_pred CCCCCCCCCCeeeecCCCceecCcccceecccc
Q 009187 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHN 34 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~~ 34 (540)
..||.|++. .+|+ +.+.++|..|+.--.++.
T Consensus 4 p~cp~c~sE-ytYe-d~~~~~cpec~~ew~~~~ 34 (112)
T COG2824 4 PPCPKCNSE-YTYE-DGGQLICPECAHEWNENE 34 (112)
T ss_pred CCCCccCCc-eEEe-cCceEeCchhcccccccc
Confidence 469999987 3444 357999999998766544
No 145
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=58.28 E-value=1.8e+02 Score=28.40 Aligned_cols=149 Identities=15% Similarity=0.230 Sum_probs=79.1
Q ss_pred hHHHHHHHHHHHHhcCCC-CCHHHHHHHhCcCH-HHHHHHHHHHHHHhhccccc--------cccccCCh--hhHHHHHH
Q 009187 116 EQVQASCLYLACRQKSKP-FLLIDFSNYLNINV-YELGAVYLQLCQVLYIADES--------NVLKQVDP--SIFLHKFT 183 (540)
Q Consensus 116 ~~vaAACLYiACR~e~~p-rtL~DIs~vl~V~~-~~Lgr~~~~L~~~L~i~~~p--------~~~~~~dP--~~~I~Rf~ 183 (540)
..++=|.||++ +-| .++.+|+.+++++. ..+......|.....-...+ .|.-.+.| ..||.+|.
T Consensus 3 ~~~iEAlLF~s----g~pgls~~~La~il~~~~~~~~~~~l~~l~~~~~~~~~gl~l~~~~~~y~l~tk~e~~~~i~~~~ 78 (186)
T TIGR00281 3 KAIIEALLFVS----GEPGVTLAELVRILGKEKAEKLNAIMELLEDYLSRDTAGIEIIKFGQSYSLVTKPAFADYIHRFL 78 (186)
T ss_pred HHHHHHHHHHc----CCCCCCHHHHHHHhCCCchHHHHHHHHHHHHHHhcCCCCEEEEEECCEEEEEEhHHHHHHHHHHh
Confidence 45677888887 788 99999999999884 45544444444443211111 01111122 23333332
Q ss_pred HhhCCCCCHHHHHHHHHHHHhhcccccccCCChhhHHHHHHHHHHHhcCCCCCHHHHHHHHcccHH-HHhhhhcCCCCCC
Q 009187 184 DRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLKFSKSDIIEDFMARKK-ELHEGVAANLPNN 262 (540)
Q Consensus 184 ~~L~~~~~~~V~~~A~~Iv~~m~~~~i~tGR~P~~IAaAALylAa~~~g~~~t~~eI~~~~~~~~~-ti~~~~~~~~~~~ 262 (540)
..= ... ..+.|++ -||...++.++|..+|-+.-|+... .|++..+-..--
T Consensus 79 ~~~---~~~-LS~aaLE------------------------tLAIIAY~QPITr~eIe~IRGv~s~~~l~~L~ergLI~- 129 (186)
T TIGR00281 79 PAK---LKN-LNSASLE------------------------VLAIIAYKQPITRARINEIRGVKSYQIVDDLVEKGLVV- 129 (186)
T ss_pred ccc---ccc-CCHHHHH------------------------HHHHHHHcCCcCHHHHHHHcCCCHHHHHHHHHHCCCeE-
Confidence 210 001 2222222 2455557889999999999888544 333332322210
Q ss_pred CCCCCCccchhhcccc-CCCCccccchhhhHHHHhhhccccCCCCCChhhH
Q 009187 263 GPKVSGMNEVLCKHKD-TGKPFACGLCRSCYEEFMTISEGLEGGADPPAFQ 312 (540)
Q Consensus 263 ~~~~~~~~~~~~~~~~-~~~~~~~g~~~~~~~ef~~~~~~l~~~~dpPaf~ 312 (540)
..-+++ .|+|..+|....-++.| ||..-.|=|-+.
T Consensus 130 ----------~~Gr~~~~Grp~ly~TT~~Fl~~F-----GL~sl~dLP~~~ 165 (186)
T TIGR00281 130 ----------ELGRKDTPGRSFIYETTPKFYDYF-----GIDSLDELPKLE 165 (186)
T ss_pred ----------ecCcCCCCCCCeeehhhHHHHHHh-----CCCCHhhCCCch
Confidence 011222 46688887655555555 666666655554
No 146
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=57.99 E-value=30 Score=27.20 Aligned_cols=38 Identities=13% Similarity=0.227 Sum_probs=30.6
Q ss_pred HHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 009187 122 CLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (540)
Q Consensus 122 CLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~ 160 (540)
+||.... .+.+.+..|||..++|+..++..+.++|.+.
T Consensus 12 ~Iy~l~~-~~~~v~~~~iA~~L~vs~~tvt~ml~~L~~~ 49 (60)
T PF01325_consen 12 AIYELSE-EGGPVRTKDIAERLGVSPPTVTEMLKRLAEK 49 (60)
T ss_dssp HHHHHHH-CTSSBBHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHc-CCCCccHHHHHHHHCCChHHHHHHHHHHHHC
Confidence 4555555 7889999999999999999999988888763
No 147
>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=57.95 E-value=4.5 Score=40.77 Aligned_cols=29 Identities=14% Similarity=0.552 Sum_probs=11.5
Q ss_pred CCCCCCCCCCeee---ecCCCceecCccccee
Q 009187 2 VWCSSCARHVTGH---RPYDSQLCCDRCGKVL 30 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~---D~~~G~~VCt~CG~Vl 30 (540)
+.||+||+..+.. ..-..+..|..|+--.
T Consensus 32 ~yCP~Cg~~~L~~f~NN~PVaDF~C~~C~eey 63 (254)
T PF06044_consen 32 MYCPNCGSKPLSKFENNRPVADFYCPNCNEEY 63 (254)
T ss_dssp ---TTT--SS-EE--------EEE-TTT--EE
T ss_pred CcCCCCCChhHhhccCCCccceeECCCCchHH
Confidence 4799999984422 1235789999998644
No 148
>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=56.69 E-value=7.7 Score=26.01 Aligned_cols=22 Identities=14% Similarity=0.442 Sum_probs=10.4
Q ss_pred CCCCCCCCCeeeecCCCceecCc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDR 25 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~ 25 (540)
.||.||+.. +.....-.+.|++
T Consensus 1 ~CP~C~s~l-~~~~~ev~~~C~N 22 (28)
T PF03119_consen 1 TCPVCGSKL-VREEGEVDIRCPN 22 (28)
T ss_dssp B-TTT--BE-EE-CCTTCEEE--
T ss_pred CcCCCCCEe-EcCCCCEeEECCC
Confidence 499999874 3444455777764
No 149
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=56.51 E-value=3.4 Score=42.42 Aligned_cols=30 Identities=20% Similarity=0.515 Sum_probs=22.4
Q ss_pred CCCCCCCCCCCeeeecCCCceecCccccee
Q 009187 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (540)
Q Consensus 1 m~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vl 30 (540)
+.+||.||.-...-|-.....||..||.-.
T Consensus 28 w~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ 57 (294)
T COG0777 28 WTKCPSCGEMLYRKELESNLKVCPKCGHHM 57 (294)
T ss_pred eeECCCccceeeHHHHHhhhhcccccCccc
Confidence 357999998543334457789999999864
No 150
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=56.40 E-value=7.3 Score=30.36 Aligned_cols=26 Identities=23% Similarity=0.652 Sum_probs=19.4
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceec
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vle 31 (540)
.|+.||.... +..--+||..||++.-
T Consensus 7 ~C~~Cg~~~~---~~dDiVvCp~CgapyH 32 (54)
T PF14446_consen 7 KCPVCGKKFK---DGDDIVVCPECGAPYH 32 (54)
T ss_pred cChhhCCccc---CCCCEEECCCCCCccc
Confidence 6999998632 2345789999999864
No 151
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=56.34 E-value=7.2 Score=30.73 Aligned_cols=27 Identities=19% Similarity=0.516 Sum_probs=19.3
Q ss_pred CCCCCCCCCCCeeeecCCCceecCcccceeccc
Q 009187 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVLEDH 33 (540)
Q Consensus 1 m~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~ 33 (540)
|+.|++||...+ ---||..||+--+..
T Consensus 27 ~~~c~~cG~~~l------~Hrvc~~cg~Y~g~~ 53 (57)
T COG0333 27 LSVCPNCGEYKL------PHRVCLKCGYYKGRQ 53 (57)
T ss_pred ceeccCCCCccc------CceEcCCCCCccCeE
Confidence 457999998643 456999999765433
No 152
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=56.19 E-value=3.1 Score=43.27 Aligned_cols=29 Identities=21% Similarity=0.530 Sum_probs=21.6
Q ss_pred CCCCCCCCCCeeeecCCCceecCccccee
Q 009187 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vl 30 (540)
.+||.|+.....-|-.....||..||.-.
T Consensus 28 ~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 28 TKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred eECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 47999998644444445678999999865
No 153
>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=55.96 E-value=9.1 Score=39.79 Aligned_cols=55 Identities=11% Similarity=0.051 Sum_probs=46.9
Q ss_pred hhHHHHHHHhhCCCCCHHHHHHHHHHHHhhcccccccCCChhhHHHHHHHHHHHhcC
Q 009187 176 SIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHG 232 (540)
Q Consensus 176 ~~~I~Rf~~~L~~~~~~~V~~~A~~Iv~~m~~~~i~tGR~P~~IAaAALylAa~~~g 232 (540)
..+|.++|.+|.+ +..+..+|.-+.++..-..-..+..|..||.++||||++..+
T Consensus 49 ~k~i~~l~~~L~l--p~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed 103 (297)
T COG5333 49 LKLIMDLCTRLNL--PQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVED 103 (297)
T ss_pred HHHHHHHHHhcCC--CcchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeeccc
Confidence 4678889999974 888999999888887665668899999999999999998766
No 154
>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=55.87 E-value=3.2 Score=43.01 Aligned_cols=29 Identities=14% Similarity=0.432 Sum_probs=22.0
Q ss_pred CCCCCCCCCCeeeecCCCceecCccccee
Q 009187 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vl 30 (540)
.+||.|+......|-.....||..||.-.
T Consensus 27 ~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 55 (285)
T TIGR00515 27 TKCPKCGQVLYTKELERNLEVCPKCDHHM 55 (285)
T ss_pred eECCCCcchhhHHHHHhhCCCCCCCCCcC
Confidence 47999998644444456779999999864
No 155
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=55.13 E-value=3.3 Score=43.13 Aligned_cols=29 Identities=24% Similarity=0.423 Sum_probs=22.4
Q ss_pred CCCCCCCCCCeeeecCCCceecCccccee
Q 009187 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vl 30 (540)
.+||.|+......+-.....||..||.-.
T Consensus 39 ~kc~~C~~~~~~~~l~~~~~vcp~c~~h~ 67 (296)
T CHL00174 39 VQCENCYGLNYKKFLKSKMNICEQCGYHL 67 (296)
T ss_pred eECCCccchhhHHHHHHcCCCCCCCCCCc
Confidence 47999998754445557789999999854
No 156
>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=54.29 E-value=4.7 Score=35.91 Aligned_cols=39 Identities=18% Similarity=0.289 Sum_probs=23.6
Q ss_pred CCCCCCCCCCeeeecCCCceecCcccceeccccccccccccc
Q 009187 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFVK 43 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~~Ids~~ef~~ 43 (540)
+.||+|+...-..- -..-|..||.-|.=..--++-+|.+
T Consensus 70 V~CP~C~K~TKmLG---r~D~CM~C~~pLTLd~~legkef~~ 108 (114)
T PF11023_consen 70 VECPNCGKQTKMLG---RVDACMHCKEPLTLDPSLEGKEFDE 108 (114)
T ss_pred eECCCCCChHhhhc---hhhccCcCCCcCccCchhhcchhhH
Confidence 57999998632221 1248999999875322234555654
No 157
>PF14122 YokU: YokU-like protein
Probab=54.22 E-value=7.4 Score=33.04 Aligned_cols=23 Identities=26% Similarity=0.625 Sum_probs=16.9
Q ss_pred CCceecCcccceecccccccccc
Q 009187 18 DSQLCCDRCGKVLEDHNFSTEAT 40 (540)
Q Consensus 18 ~G~~VCt~CG~Vlee~~Ids~~e 40 (540)
+-.++|++||.|.-+..+..+.+
T Consensus 33 tP~i~C~~CgmvYq~d~vi~EIE 55 (87)
T PF14122_consen 33 TPAIICSNCGMVYQDDEVIKEIE 55 (87)
T ss_pred CceeeecCCCcEEehhHHHHHHh
Confidence 34589999999987766655543
No 158
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=54.19 E-value=24 Score=26.85 Aligned_cols=34 Identities=12% Similarity=0.251 Sum_probs=29.4
Q ss_pred CCCCCHHHHHHHhCcCHHHHHHHHHHHHHHhhcc
Q 009187 131 SKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIA 164 (540)
Q Consensus 131 ~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~L~i~ 164 (540)
+.-.+..++|..+||+..++.+.+..+...|...
T Consensus 17 R~~~~~~~La~~FgIs~stvsri~~~~~~~L~~~ 50 (53)
T PF13613_consen 17 RLNLTFQDLAYRFGISQSTVSRIFHEWIPLLYQV 50 (53)
T ss_pred HcCCcHhHHhhheeecHHHHHHHHHHHHHHHHHh
Confidence 3457889999999999999999999999887653
No 159
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=54.17 E-value=7.4 Score=29.33 Aligned_cols=26 Identities=23% Similarity=0.653 Sum_probs=17.8
Q ss_pred CCCCCCCC-Ceeee-cCCCceecCcccc
Q 009187 3 WCSSCARH-VTGHR-PYDSQLCCDRCGK 28 (540)
Q Consensus 3 ~Cp~Cgs~-~iv~D-~~~G~~VCt~CG~ 28 (540)
.|+.||.. .+... .+.+.+.|..||.
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 7 RCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 59999984 32221 2246788999998
No 160
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=54.00 E-value=22 Score=35.84 Aligned_cols=57 Identities=16% Similarity=0.121 Sum_probs=43.7
Q ss_pred hhHHHHHHHhhCCCCCHHHHHHHHHHHHhhcccccccCCChhhHHHHHHHHHHHhcCCC
Q 009187 176 SIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALTHGLK 234 (540)
Q Consensus 176 ~~~I~Rf~~~L~~~~~~~V~~~A~~Iv~~m~~~~i~tGR~P~~IAaAALylAa~~~g~~ 234 (540)
..+|..++.+|.+ .+.|+.+|.-+.+|.--..-..+-.|.-+|.-||||||..-...
T Consensus 45 ~n~I~~lg~~lkl--RQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~ 101 (264)
T KOG0794|consen 45 ANVIQKLGQHLKL--RQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECP 101 (264)
T ss_pred HHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcc
Confidence 4466677777764 68888888888877543333789999999999999999976655
No 161
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=52.92 E-value=10 Score=38.72 Aligned_cols=29 Identities=14% Similarity=0.449 Sum_probs=21.1
Q ss_pred CCCCCCCCCCeeeecCCCceecCcccceec
Q 009187 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vle 31 (540)
..||.||+..... ...-..+|..||.+.=
T Consensus 100 ~fC~~CG~~~~~~-~~~~~~~C~~c~~~~y 128 (256)
T PRK00241 100 RFCGYCGHPMHPS-KTEWAMLCPHCRERYY 128 (256)
T ss_pred ccccccCCCCeec-CCceeEECCCCCCEEC
Confidence 4799999974433 3445689999998754
No 162
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=52.91 E-value=7.9 Score=34.52 Aligned_cols=36 Identities=17% Similarity=0.481 Sum_probs=21.6
Q ss_pred CCCCCCCCCCeeeecCCCceecCcccceecccccccccccc
Q 009187 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFV 42 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~~Ids~~ef~ 42 (540)
.+|+.||.. +....-...|..||.. +-.+..|.++.
T Consensus 71 ~~C~~Cg~~---~~~~~~~~~CP~Cgs~--~~~i~~G~El~ 106 (113)
T PRK12380 71 AWCWDCSQV---VEIHQHDAQCPHCHGE--RLRVDTGDSLI 106 (113)
T ss_pred EEcccCCCE---EecCCcCccCcCCCCC--CcEEccCCeEE
Confidence 369999964 2222345569999964 33455665543
No 163
>PRK05978 hypothetical protein; Provisional
Probab=52.81 E-value=10 Score=35.65 Aligned_cols=30 Identities=17% Similarity=0.336 Sum_probs=20.5
Q ss_pred CCCCCCCCCCeeeecCCCceecCcccceec
Q 009187 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vle 31 (540)
.+||+||...+-.-.-.=..-|..||.-++
T Consensus 34 grCP~CG~G~LF~g~Lkv~~~C~~CG~~~~ 63 (148)
T PRK05978 34 GRCPACGEGKLFRAFLKPVDHCAACGEDFT 63 (148)
T ss_pred CcCCCCCCCcccccccccCCCccccCCccc
Confidence 479999987552222233457999999776
No 164
>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=52.80 E-value=53 Score=25.24 Aligned_cols=31 Identities=13% Similarity=0.220 Sum_probs=26.8
Q ss_pred cCCCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 009187 130 KSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (540)
Q Consensus 130 e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~ 160 (540)
...+.+..|||+.++++...+.+.+..|.+.
T Consensus 22 ~~~~~s~~ela~~~g~s~~tv~r~l~~L~~~ 52 (67)
T cd00092 22 VQLPLTRQEIADYLGLTRETVSRTLKELEEE 52 (67)
T ss_pred ccCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 3467899999999999999999988888774
No 165
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=52.68 E-value=6.9 Score=29.86 Aligned_cols=26 Identities=27% Similarity=0.617 Sum_probs=19.7
Q ss_pred CCCCCCCCCeeeecCCCceecCcccce
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~V 29 (540)
.|-.||... ..|.....+-|..||.=
T Consensus 8 ~C~~Cg~~~-~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 8 KCARCGREV-ELDQETRGIRCPYCGSR 33 (49)
T ss_pred EhhhcCCee-ehhhccCceeCCCCCcE
Confidence 589999863 44566788999999963
No 166
>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=52.42 E-value=33 Score=27.29 Aligned_cols=38 Identities=18% Similarity=0.204 Sum_probs=30.9
Q ss_pred CChhhHHHHHHHHHHHhcCCCCCHHHHHHHHcccHHHHhhh
Q 009187 214 RKPSGLCGAALYVSALTHGLKFSKSDIIEDFMARKKELHEG 254 (540)
Q Consensus 214 R~P~~IAaAALylAa~~~g~~~t~~eI~~~~~~~~~ti~~~ 254 (540)
|.|.-=-|=-||+. ++-.++.++||+.++|+++||++.
T Consensus 5 Rsp~rdkA~e~y~~---~~g~i~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 5 RSPNRDKAFEIYKE---SNGKIKLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred CCcCHHHHHHHHHH---hCCCccHHHHHHHHCCCHHHHHHH
Confidence 55555555566755 778999999999999999999998
No 167
>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=52.32 E-value=34 Score=25.65 Aligned_cols=34 Identities=9% Similarity=0.072 Sum_probs=27.9
Q ss_pred HhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHHHh
Q 009187 128 RQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVL 161 (540)
Q Consensus 128 R~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~L 161 (540)
..++-|+|..++|+.++|+..+|.+....|...+
T Consensus 10 ~~~~~~it~~eLa~~l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 10 LESKEPITAKELAEELGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HHTTTSBEHHHHHHHCTS-HHHHHHHHHHHHHTT
T ss_pred HHcCCCcCHHHHHHHhCCCHHHHHHHHHHHHHCC
Confidence 3456679999999999999999999988886655
No 168
>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=51.97 E-value=33 Score=30.54 Aligned_cols=45 Identities=20% Similarity=0.158 Sum_probs=34.5
Q ss_pred hhHHHHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHH
Q 009187 115 TEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQ 159 (540)
Q Consensus 115 ~~~vaAACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~ 159 (540)
....+.+.+|++-...+.|.+..+||..++++...+.+....|.+
T Consensus 7 ~~~al~~l~~la~~~~~~~~s~~eia~~~~i~~~~v~~il~~L~~ 51 (132)
T TIGR00738 7 TEYALRALLDLALNPDEGPVSVKEIAERQGISRSYLEKILRTLRR 51 (132)
T ss_pred HHHHHHHHHHHHhCCCCCcCcHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 344566777777433345999999999999999999888777766
No 169
>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=51.91 E-value=5.6 Score=30.82 Aligned_cols=29 Identities=24% Similarity=0.526 Sum_probs=20.3
Q ss_pred CCCCCCCC-Ceeeec--CCCceecCcccceec
Q 009187 3 WCSSCARH-VTGHRP--YDSQLCCDRCGKVLE 31 (540)
Q Consensus 3 ~Cp~Cgs~-~iv~D~--~~G~~VCt~CG~Vle 31 (540)
.|.+||.. ...+.. ..+..+|..||.-.-
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~ 32 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWK 32 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHH
Confidence 48889876 344543 367888999988654
No 170
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=51.82 E-value=7.4 Score=38.27 Aligned_cols=29 Identities=31% Similarity=0.462 Sum_probs=20.6
Q ss_pred CCCCCCCCCC--eeeecCCCceecCccccee
Q 009187 2 VWCSSCARHV--TGHRPYDSQLCCDRCGKVL 30 (540)
Q Consensus 2 ~~Cp~Cgs~~--iv~D~~~G~~VCt~CG~Vl 30 (540)
+.|+.|++.+ ++.+...=.+.|..||..-
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 4699999974 4444333367899999863
No 171
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=51.48 E-value=61 Score=31.61 Aligned_cols=29 Identities=17% Similarity=0.222 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 009187 132 KPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (540)
Q Consensus 132 ~prtL~DIs~vl~V~~~~Lgr~~~~L~~~ 160 (540)
.|.|..+||+.+|++..++.|..++|.+.
T Consensus 183 ~~lt~~~iA~~lG~sr~tvsR~l~~l~~~ 211 (235)
T PRK11161 183 LTMTRGDIGNYLGLTVETISRLLGRFQKS 211 (235)
T ss_pred ccccHHHHHHHhCCcHHHHHHHHHHHHHC
Confidence 58899999999999999999998888775
No 172
>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=51.44 E-value=8.8 Score=28.98 Aligned_cols=13 Identities=31% Similarity=0.723 Sum_probs=7.6
Q ss_pred eecCcccceeccc
Q 009187 21 LCCDRCGKVLEDH 33 (540)
Q Consensus 21 ~VCt~CG~Vlee~ 33 (540)
.+|+.||.|.++.
T Consensus 2 y~C~~CgyvYd~~ 14 (47)
T PF00301_consen 2 YQCPVCGYVYDPE 14 (47)
T ss_dssp EEETTTSBEEETT
T ss_pred cCCCCCCEEEcCC
Confidence 3566666666554
No 173
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=51.01 E-value=3.4e+02 Score=29.04 Aligned_cols=90 Identities=9% Similarity=0.038 Sum_probs=53.4
Q ss_pred hHHHHHHHHHHHHHHHHHHhC---CCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHH--------------
Q 009187 66 SRERLMEKAFDDMRQMKNALN---IGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACR-------------- 128 (540)
Q Consensus 66 srer~L~~a~~~I~~ia~~L~---Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR-------------- 128 (540)
.+++.+..-...|..+|..+. +.-.+-+.+.-..+++.+..-...+|.+....|.-.|+-+-+
T Consensus 130 A~~~Li~~~~~lV~~iA~~~~~~~~~~eDLiQEg~igL~~a~~~fd~~~g~~FsTyA~~wIr~aI~~~i~~~~r~irip~ 209 (367)
T PRK09210 130 AKQRLAEANLRLVVSIAKRYVGRGMLFLDLIQEGNMGLMKAVEKFDYRKGFKFSTYATWWIRQAITRAIADQARTIRIPV 209 (367)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHhcCCCCCCchHHHHHHHHHHHHHHHHHHcCCceeccH
Confidence 344444455566777776662 221134455555566666555555777777766666664421
Q ss_pred ------------------hcCCCCCHHHHHHHhCcCHHHHHHHHH
Q 009187 129 ------------------QKSKPFLLIDFSNYLNINVYELGAVYL 155 (540)
Q Consensus 129 ------------------~e~~prtL~DIs~vl~V~~~~Lgr~~~ 155 (540)
..|.+-|..+||..+++++..+.....
T Consensus 210 ~~~~~~~~~~~~~~~l~~~lgr~pt~~EiA~~l~~~~~~v~~~~~ 254 (367)
T PRK09210 210 HMVETINKLIRVQRQLLQELGREPTPEEIAEEMDMPPEKVREILK 254 (367)
T ss_pred HHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCcCHHHHHHHHH
Confidence 123344677888888888888876543
No 174
>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=50.73 E-value=12 Score=24.38 Aligned_cols=24 Identities=33% Similarity=0.822 Sum_probs=14.5
Q ss_pred CCCCCCCCeeeecCCCceecCcccc
Q 009187 4 CSSCARHVTGHRPYDSQLCCDRCGK 28 (540)
Q Consensus 4 Cp~Cgs~~iv~D~~~G~~VCt~CG~ 28 (540)
|..||.... -....-...|.+||.
T Consensus 1 C~sC~~~i~-~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIA-PREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCccc-CcccCceEeCCCCCC
Confidence 777877522 111234778999884
No 175
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=50.50 E-value=72 Score=32.26 Aligned_cols=26 Identities=4% Similarity=0.111 Sum_probs=16.2
Q ss_pred CCCCHHHHHHHhCc-CHHHHHHHHHHH
Q 009187 132 KPFLLIDFSNYLNI-NVYELGAVYLQL 157 (540)
Q Consensus 132 ~prtL~DIs~vl~V-~~~~Lgr~~~~L 157 (540)
...++.+||..+|- +...+.+.|++.
T Consensus 247 t~~sI~eIA~~~GF~d~s~Fsr~FKk~ 273 (290)
T PRK10572 247 TRMPIATIGRNVGYDDQLYFSRVFKKC 273 (290)
T ss_pred CCCCHHHHHHHhCCCCHHHHHHHHHHH
Confidence 45667777777763 366666666544
No 176
>PRK08402 replication factor A; Reviewed
Probab=50.36 E-value=9.8 Score=40.70 Aligned_cols=26 Identities=27% Similarity=0.609 Sum_probs=21.4
Q ss_pred CCCCCCCCCeeeecCCCceecCcccce
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~V 29 (540)
.||.|+.. ++.|...|...|..||.|
T Consensus 214 aCp~CnKk-v~~~~~~~~~~Ce~~~~v 239 (355)
T PRK08402 214 ACPECRRK-VDYDPATDTWICPEHGEV 239 (355)
T ss_pred cCCCCCeE-EEEecCCCCEeCCCCCCc
Confidence 59999885 445777899999999975
No 177
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=50.31 E-value=24 Score=25.22 Aligned_cols=27 Identities=7% Similarity=0.114 Sum_probs=19.9
Q ss_pred CCCCCHHHHHHHhCcCHHHHHHHHHHH
Q 009187 131 SKPFLLIDFSNYLNINVYELGAVYLQL 157 (540)
Q Consensus 131 ~~prtL~DIs~vl~V~~~~Lgr~~~~L 157 (540)
..+.+|.|||..++++...+.+.|++.
T Consensus 6 ~~~~~l~~iA~~~g~S~~~f~r~Fk~~ 32 (42)
T PF00165_consen 6 QQKLTLEDIAEQAGFSPSYFSRLFKKE 32 (42)
T ss_dssp -SS--HHHHHHHHTS-HHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 457899999999999999998877754
No 178
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=50.22 E-value=11 Score=28.97 Aligned_cols=28 Identities=25% Similarity=0.539 Sum_probs=19.1
Q ss_pred CCCCCCCC-Ceeeec-CCCc-eecCccccee
Q 009187 3 WCSSCARH-VTGHRP-YDSQ-LCCDRCGKVL 30 (540)
Q Consensus 3 ~Cp~Cgs~-~iv~D~-~~G~-~VCt~CG~Vl 30 (540)
.|.+|+.. ...+.. ..|. ++|..||.-.
T Consensus 5 ~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~ 35 (52)
T smart00401 5 SCSNCGTTETPLWRRGPSGNKTLCNACGLYY 35 (52)
T ss_pred CcCCCCCCCCCccccCCCCCCcEeecccHHH
Confidence 58899876 445542 3454 8899998754
No 179
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=49.86 E-value=7.3 Score=42.28 Aligned_cols=30 Identities=20% Similarity=0.596 Sum_probs=23.5
Q ss_pred CCCCCCCC------CeeeecCCCceecCcccceecc
Q 009187 3 WCSSCARH------VTGHRPYDSQLCCDRCGKVLED 32 (540)
Q Consensus 3 ~Cp~Cgs~------~iv~D~~~G~~VCt~CG~Vlee 32 (540)
.||.|++. .-.+|..+|...|+.||.=|.+
T Consensus 130 ~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelve 165 (436)
T KOG2593|consen 130 VCPNCQKKYTSLEALQLLDNETGEFHCENCGGELVE 165 (436)
T ss_pred cCCccccchhhhHHHHhhcccCceEEEecCCCchhc
Confidence 59999986 2245677999999999986654
No 180
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.75 E-value=94 Score=27.62 Aligned_cols=67 Identities=19% Similarity=0.213 Sum_probs=47.2
Q ss_pred HHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHHHhhccccccccccCChhhH-HHHHHHhhC-CCCCHHHHHHHHH
Q 009187 123 LYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIF-LHKFTDRLL-PGGNKKVCDTARD 200 (540)
Q Consensus 123 LYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~L~i~~~p~~~~~~dP~~~-I~Rf~~~L~-~~~~~~V~~~A~~ 200 (540)
||+-||= .|+||-..+|++-.++..-+-.+.+.+|.+... -+|... =..+.++|. |+++.+ .|.+
T Consensus 52 lf~r~RG-----nlKEvEr~lg~sYptvR~kld~vlramgy~p~~-----e~~~~i~~~~i~~qle~Gei~pe---eA~~ 118 (122)
T COG3877 52 LFLRCRG-----NLKEVERELGISYPTVRTKLDEVLRAMGYNPDS-----ENSVNIGKKKIIDQLEKGEISPE---EAIK 118 (122)
T ss_pred HHHHHcc-----CHHHHHHHHCCccHHHHHHHHHHHHHcCCCCCC-----CChhhhhHHHHHHHHHcCCCCHH---HHHH
Confidence 5666663 589999999999999999999999999987543 344332 235677774 555544 4555
Q ss_pred HH
Q 009187 201 IL 202 (540)
Q Consensus 201 Iv 202 (540)
++
T Consensus 119 ~L 120 (122)
T COG3877 119 ML 120 (122)
T ss_pred Hh
Confidence 44
No 181
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.52 E-value=12 Score=33.03 Aligned_cols=27 Identities=22% Similarity=0.625 Sum_probs=22.4
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceecccc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHN 34 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~~ 34 (540)
.||.||...++. ++-|..||+-+..+.
T Consensus 8 ~cPvcg~~~iVT-----eL~c~~~etTVrg~F 34 (122)
T COG3877 8 RCPVCGRKLIVT-----ELKCSNCETTVRGNF 34 (122)
T ss_pred CCCcccccceeE-----EEecCCCCceEecce
Confidence 699999987764 578999999988553
No 182
>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=49.15 E-value=42 Score=30.01 Aligned_cols=45 Identities=18% Similarity=0.199 Sum_probs=35.6
Q ss_pred chhHHHHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHH
Q 009187 114 RTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQ 159 (540)
Q Consensus 114 ~~~~vaAACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~ 159 (540)
..+..+.+.+|+|- ..+-+.++.+|++.++++...+.+....|.+
T Consensus 7 ~~~yal~~l~~la~-~~~~~~s~~eia~~l~is~~~v~~~l~~L~~ 51 (130)
T TIGR02944 7 LTDYATLVLTTLAQ-NDSQPYSAAEIAEQTGLNAPTVSKILKQLSL 51 (130)
T ss_pred HHhHHHHHHHHHHh-CCCCCccHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 34556777888874 3456899999999999999999888777766
No 183
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=48.87 E-value=68 Score=28.75 Aligned_cols=42 Identities=10% Similarity=0.140 Sum_probs=31.5
Q ss_pred hhHHHHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHH
Q 009187 115 TEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 157 (540)
Q Consensus 115 ~~~vaAACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L 157 (540)
...+..+.-||--... .+.++.++|+.+++++..|.+.|++.
T Consensus 8 ~~~i~~~~~~I~~~~~-~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 8 AITIHSILDWIEDNLE-SPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHHHHHHHHHHhcC-CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3445556666665544 47999999999999999998777654
No 184
>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=48.75 E-value=21 Score=26.71 Aligned_cols=19 Identities=11% Similarity=0.148 Sum_probs=17.3
Q ss_pred CHHHHHHHhCcCHHHHHHH
Q 009187 135 LLIDFSNYLNINVYELGAV 153 (540)
Q Consensus 135 tL~DIs~vl~V~~~~Lgr~ 153 (540)
|++|||..+||+..++.++
T Consensus 1 Ti~dIA~~agvS~~TVSr~ 19 (46)
T PF00356_consen 1 TIKDIAREAGVSKSTVSRV 19 (46)
T ss_dssp CHHHHHHHHTSSHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 6899999999999999766
No 185
>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=48.58 E-value=14 Score=29.23 Aligned_cols=28 Identities=18% Similarity=0.418 Sum_probs=18.6
Q ss_pred CCCCCCCCCC--eeeecC-CCceecCcccce
Q 009187 2 VWCSSCARHV--TGHRPY-DSQLCCDRCGKV 29 (540)
Q Consensus 2 ~~Cp~Cgs~~--iv~D~~-~G~~VCt~CG~V 29 (540)
..||.|+.-+ ..|... .-.+-|..||.-
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~ 40 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGYQ 40 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCCc
Confidence 3699999852 233322 234789999986
No 186
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=48.21 E-value=10 Score=30.39 Aligned_cols=21 Identities=29% Similarity=0.730 Sum_probs=12.2
Q ss_pred CCCCCCCCCeeeecCCCceecCcccc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGK 28 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~ 28 (540)
.|.+|+.-. ....-+|..||.
T Consensus 6 AC~~Ck~l~-----~~d~e~CP~Cgs 26 (64)
T COG2093 6 ACKNCKRLT-----PEDTEICPVCGS 26 (64)
T ss_pred HHhhccccC-----CCCCccCCCCCC
Confidence 377777531 124457777775
No 187
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=48.20 E-value=14 Score=28.49 Aligned_cols=28 Identities=21% Similarity=0.705 Sum_probs=14.4
Q ss_pred CCCCC--CCCCCeeeecCCCc--eecCccccee
Q 009187 2 VWCSS--CARHVTGHRPYDSQ--LCCDRCGKVL 30 (540)
Q Consensus 2 ~~Cp~--Cgs~~iv~D~~~G~--~VCt~CG~Vl 30 (540)
.+||. |+.... .+..... +.|..||+..
T Consensus 19 ~~Cp~~~C~~~~~-~~~~~~~~~~~C~~C~~~f 50 (64)
T PF01485_consen 19 RWCPNPDCEYIIE-KDDGCNSPIVTCPSCGTEF 50 (64)
T ss_dssp C--TTSST---EC-S-SSTTS--CCTTSCCSEE
T ss_pred cCCCCCCCcccEE-ecCCCCCCeeECCCCCCcC
Confidence 47988 988633 3333344 8999999764
No 188
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=48.17 E-value=6.7 Score=33.10 Aligned_cols=30 Identities=27% Similarity=0.514 Sum_probs=24.4
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceeccc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDH 33 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~ 33 (540)
.|+.||...+ -....|-..|..|..|+.-.
T Consensus 38 ~CsfCGK~~v-KR~AvGiW~C~~C~kv~agg 67 (92)
T KOG0402|consen 38 TCSFCGKKTV-KRKAVGIWKCGSCKKVVAGG 67 (92)
T ss_pred hhhhcchhhh-hhhceeEEecCCccceeccc
Confidence 5999998743 45678999999999998754
No 189
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.68 E-value=9.9 Score=34.40 Aligned_cols=29 Identities=21% Similarity=0.417 Sum_probs=19.1
Q ss_pred CCCCCCCCCeeee-cCCCceecCcccceecc
Q 009187 3 WCSSCARHVTGHR-PYDSQLCCDRCGKVLED 32 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D-~~~G~~VCt~CG~Vlee 32 (540)
.||+||...+ +| .-.-.-.|..||.=+..
T Consensus 23 rCP~CGeGrL-F~gFLK~~p~C~aCG~dyg~ 52 (126)
T COG5349 23 RCPRCGEGRL-FRGFLKVVPACEACGLDYGF 52 (126)
T ss_pred CCCCCCCchh-hhhhcccCchhhhccccccC
Confidence 6999998743 32 11234579999986653
No 190
>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=47.62 E-value=9.7 Score=39.34 Aligned_cols=28 Identities=25% Similarity=0.582 Sum_probs=12.4
Q ss_pred CCCCCCCCC--eeeecCC--C--ceecCccccee
Q 009187 3 WCSSCARHV--TGHRPYD--S--QLCCDRCGKVL 30 (540)
Q Consensus 3 ~Cp~Cgs~~--iv~D~~~--G--~~VCt~CG~Vl 30 (540)
.||.||+.- -++.... | .+.|+-||+-=
T Consensus 174 ~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W 207 (290)
T PF04216_consen 174 YCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEW 207 (290)
T ss_dssp S-TTT---EEEEEEE------EEEEEETTT--EE
T ss_pred cCCCCCCcCceEEEecCCCCccEEEEcCCCCCee
Confidence 699999971 1223222 5 78999999864
No 191
>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=47.36 E-value=23 Score=25.52 Aligned_cols=30 Identities=20% Similarity=0.369 Sum_probs=20.6
Q ss_pred CCCCCCCCCCeeeecCCC-ceecCc---ccceec
Q 009187 2 VWCSSCARHVTGHRPYDS-QLCCDR---CGKVLE 31 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G-~~VCt~---CG~Vle 31 (540)
..||.||+..++-....| .+.|++ |.....
T Consensus 2 ~~CP~Cg~~lv~r~~k~g~F~~Cs~yP~C~~~~~ 35 (39)
T PF01396_consen 2 EKCPKCGGPLVLRRGKKGKFLGCSNYPECKYTEP 35 (39)
T ss_pred cCCCCCCceeEEEECCCCCEEECCCCCCcCCeEe
Confidence 479999976554444444 678987 877654
No 192
>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=47.32 E-value=14 Score=30.30 Aligned_cols=29 Identities=17% Similarity=0.272 Sum_probs=20.1
Q ss_pred CCCCCCCCC-e-ee-ecCCCceecCcccceec
Q 009187 3 WCSSCARHV-T-GH-RPYDSQLCCDRCGKVLE 31 (540)
Q Consensus 3 ~Cp~Cgs~~-i-v~-D~~~G~~VCt~CG~Vle 31 (540)
.||.|+.-+ + .| +...-.+-|..||+.-.
T Consensus 10 ~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~ 41 (71)
T PF09526_consen 10 VCPKCQAMDTIMMWRENGVEYVECVECGYTER 41 (71)
T ss_pred cCCCCcCccEEEEEEeCCceEEEecCCCCeec
Confidence 699999863 2 22 33345677999999743
No 193
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=47.16 E-value=80 Score=25.39 Aligned_cols=67 Identities=7% Similarity=0.166 Sum_probs=35.1
Q ss_pred HHHHhCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHh--cCCCCCHHHHHHHhC-cCHHHHHHHHHHH
Q 009187 81 MKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQ--KSKPFLLIDFSNYLN-INVYELGAVYLQL 157 (540)
Q Consensus 81 ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~--e~~prtL~DIs~vl~-V~~~~Lgr~~~~L 157 (540)
+|+.|+++ . ..-..+|+......+. +.+...=+-.|++. .+...++.|||..+| .+...+.+.|++.
T Consensus 1 lA~~~~~s--~---~~l~~~f~~~~g~s~~-----~~~~~~R~~~a~~~L~~~~~~~i~~ia~~~Gf~~~~~f~~~fk~~ 70 (81)
T PF12833_consen 1 LADELGMS--E---RYLSRIFKKETGMSFK-----QYLRELRLQRAKELLRQNTDLSIAEIAEECGFSSQSHFSRAFKRY 70 (81)
T ss_dssp HHHHCTS---H---HHHHHHHHHHHSS-HH-----HHHHHHHHHHHHHHHHHHTT--HHHHHHHTT-SSHHHHHHHHHHH
T ss_pred ChHHhCcC--H---HHHHHHHHHHHCcCHH-----HHHHHHHHHHHHHHHHHhhcccHHHHHHHcCCCCHHHHHHHHHHH
Confidence 46777777 2 2333445554433332 22223333344442 236789999999999 4577777776655
No 194
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=46.76 E-value=17 Score=28.00 Aligned_cols=29 Identities=21% Similarity=0.698 Sum_probs=20.1
Q ss_pred CCCC--CCCCCCeee-ecCCCceecCccccee
Q 009187 2 VWCS--SCARHVTGH-RPYDSQLCCDRCGKVL 30 (540)
Q Consensus 2 ~~Cp--~Cgs~~iv~-D~~~G~~VCt~CG~Vl 30 (540)
.+|| .|+...... +.....+.|..||...
T Consensus 19 ~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~f 50 (64)
T smart00647 19 KWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSF 50 (64)
T ss_pred cCCCCCCCcceEEecCCCCCCeeECCCCCCeE
Confidence 4799 897764433 2356788998998754
No 195
>PRK02935 hypothetical protein; Provisional
Probab=46.75 E-value=12 Score=32.97 Aligned_cols=38 Identities=21% Similarity=0.330 Sum_probs=22.6
Q ss_pred CCCCCCCCCCeeeecCCCceecCcccceecccccccccccc
Q 009187 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFV 42 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~~Ids~~ef~ 42 (540)
+.||+|+...-.. .-...|..|+.-|.=..--++.+|.
T Consensus 71 V~CP~C~K~TKmL---GrvD~CM~C~~PLTLd~~legkefd 108 (110)
T PRK02935 71 VICPSCEKPTKML---GRVDACMHCNQPLTLDRSLEGKEFD 108 (110)
T ss_pred eECCCCCchhhhc---cceeecCcCCCcCCcCccccccCcC
Confidence 4799999862111 1234899999887532223444554
No 196
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=46.62 E-value=14 Score=28.19 Aligned_cols=13 Identities=23% Similarity=0.669 Sum_probs=7.9
Q ss_pred eecCcccceeccc
Q 009187 21 LCCDRCGKVLEDH 33 (540)
Q Consensus 21 ~VCt~CG~Vlee~ 33 (540)
.+|+.||.|.++.
T Consensus 2 y~C~~CgyiYd~~ 14 (50)
T cd00730 2 YECRICGYIYDPA 14 (50)
T ss_pred cCCCCCCeEECCC
Confidence 3566666666653
No 197
>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=46.55 E-value=15 Score=26.53 Aligned_cols=10 Identities=40% Similarity=1.122 Sum_probs=7.6
Q ss_pred eecCccccee
Q 009187 21 LCCDRCGKVL 30 (540)
Q Consensus 21 ~VCt~CG~Vl 30 (540)
.+|..||-.+
T Consensus 33 ~~C~~CGE~~ 42 (46)
T TIGR03831 33 LVCPQCGEEY 42 (46)
T ss_pred cccccCCCEe
Confidence 3699999765
No 198
>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=46.29 E-value=15 Score=32.55 Aligned_cols=20 Identities=10% Similarity=0.016 Sum_probs=11.6
Q ss_pred CCCHHHHHHHhCcCHHHHHH
Q 009187 133 PFLLIDFSNYLNINVYELGA 152 (540)
Q Consensus 133 prtL~DIs~vl~V~~~~Lgr 152 (540)
-.+..++|..++++...|.+
T Consensus 78 gltq~~lA~~lg~~~~tis~ 97 (127)
T TIGR03830 78 GLSQREAAELLGGGVNAFSR 97 (127)
T ss_pred CCCHHHHHHHhCCCHHHHHH
Confidence 34556666666666655543
No 199
>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=45.14 E-value=13 Score=27.16 Aligned_cols=26 Identities=23% Similarity=0.626 Sum_probs=17.4
Q ss_pred CCCCCCCC-Ceeee-cCCCceecCcccc
Q 009187 3 WCSSCARH-VTGHR-PYDSQLCCDRCGK 28 (540)
Q Consensus 3 ~Cp~Cgs~-~iv~D-~~~G~~VCt~CG~ 28 (540)
.|+.||.. .+... .+...+.|..||.
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 59999965 22221 1256889999998
No 200
>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=45.05 E-value=13 Score=33.31 Aligned_cols=34 Identities=15% Similarity=0.389 Sum_probs=19.7
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceeccccccccccc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATF 41 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~~Ids~~ef 41 (540)
+|+.||.. +....-...|..||.. .-.|.+|.++
T Consensus 72 ~C~~Cg~~---~~~~~~~~~CP~Cgs~--~~~i~~G~El 105 (115)
T TIGR00100 72 ECEDCSEE---VSPEIDLYRCPKCHGI--MLQVRAGKEL 105 (115)
T ss_pred EcccCCCE---EecCCcCccCcCCcCC--CcEEecCCeE
Confidence 68889854 2222335679999864 2234455443
No 201
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=44.76 E-value=25 Score=25.80 Aligned_cols=28 Identities=7% Similarity=0.005 Sum_probs=18.9
Q ss_pred HHHhcCCCCCHHHHHHHHcccHHHHhhh
Q 009187 227 SALTHGLKFSKSDIIEDFMARKKELHEG 254 (540)
Q Consensus 227 Aa~~~g~~~t~~eI~~~~~~~~~ti~~~ 254 (540)
...++....|+++||+.++++.+||.++
T Consensus 13 I~~l~~~G~s~~~IA~~lg~s~sTV~re 40 (44)
T PF13936_consen 13 IEALLEQGMSIREIAKRLGRSRSTVSRE 40 (44)
T ss_dssp HHHHHCS---HHHHHHHTT--HHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHHCcCcHHHHHH
Confidence 3455677899999999999999999876
No 202
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=44.33 E-value=13 Score=34.24 Aligned_cols=11 Identities=36% Similarity=0.890 Sum_probs=6.8
Q ss_pred CceecCcccce
Q 009187 19 SQLCCDRCGKV 29 (540)
Q Consensus 19 G~~VCt~CG~V 29 (540)
....|..||..
T Consensus 106 ~~~~CP~Cgs~ 116 (135)
T PRK03824 106 AFLKCPKCGSR 116 (135)
T ss_pred cCcCCcCCCCC
Confidence 44557777754
No 203
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=44.12 E-value=1.1e+02 Score=26.28 Aligned_cols=39 Identities=8% Similarity=0.137 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHH
Q 009187 118 VQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 157 (540)
Q Consensus 118 vaAACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L 157 (540)
+..+.-|+.... ..|.++.++|+.++++...|.+.|++.
T Consensus 7 ~~~~~~~i~~~~-~~~~~~~~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 7 IQTLIAWIDEHI-DQPLNIDVVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred HHHHHHHHHHhc-CCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 444555666553 457999999999999999998877764
No 204
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=44.07 E-value=14 Score=29.56 Aligned_cols=20 Identities=25% Similarity=0.554 Sum_probs=12.7
Q ss_pred CCCCCCCCCeeeecCCCceecCcccce
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~V 29 (540)
.|.+|+.- .+.. .|..||..
T Consensus 5 AC~~C~~i---~~~~----~CP~Cgs~ 24 (61)
T PRK08351 5 ACRHCHYI---TTED----RCPVCGSR 24 (61)
T ss_pred hhhhCCcc---cCCC----cCCCCcCC
Confidence 58888863 1211 68888873
No 205
>KOG0654 consensus G2/Mitotic-specific cyclin A [Cell cycle control, cell division, chromosome partitioning]
Probab=44.05 E-value=1.7e+02 Score=31.58 Aligned_cols=164 Identities=15% Similarity=0.104 Sum_probs=85.5
Q ss_pred HHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHh-cCCCCCHHHHHHHhCcCHHHHHHH
Q 009187 75 FDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQ-KSKPFLLIDFSNYLNINVYELGAV 153 (540)
Q Consensus 75 ~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~-e~~prtL~DIs~vl~V~~~~Lgr~ 153 (540)
-+.+......|.|. ...++...........+.-. +--+|-+|+.+- +..+..+.||.-.+. +-+....+
T Consensus 148 see~r~~~e~l~ls--~~~~drfl~~~~~~~~k~ql-------~g~s~m~I~sk~ee~~~~~~~ef~~itd-~ty~~~qv 217 (359)
T KOG0654|consen 148 SEEYRLTFETLYLS--VNYRDRFLSYKEVNKQKLQL-------VGISAMLIASKYEEIKEPRVEEFCYITD-NTYTYWQV 217 (359)
T ss_pred HHHHHhhhhheeec--HHHHHHHhccCccHHHHHHH-------hCcccceeeccchhhcchHHHHHHhhhh-hhhHHHHH
Confidence 34455556666666 44444333222222121111 222566666664 444666777766554 33445555
Q ss_pred HHHHHHH---hhccccccccccCChhhHHHHHHHhhCCCCCHHHHHHHHHHHHhhcccccccCCChhhHHHHHHHHHHHh
Q 009187 154 YLQLCQV---LYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGRKPSGLCGAALYVSALT 230 (540)
Q Consensus 154 ~~~L~~~---L~i~~~p~~~~~~dP~~~I~Rf~~~L~~~~~~~V~~~A~~Iv~~m~~~~i~tGR~P~~IAaAALylAa~~ 230 (540)
++..... |.+.... .....|+.||...-.+ -.-++...+..+..-..-+...--..|+-|||||+++|=..
T Consensus 218 ~~~~~~il~~l~~~~~~-----pt~~~~l~~~~~~~~~-~~~~~e~~~~yl~elsll~~~~l~y~PSliAasAv~lA~~~ 291 (359)
T KOG0654|consen 218 LRMEIDILNALTFELVR-----PTSKTFLRRFLRVAQT-PELQVEPLANYLTELSLLDYIFLKYLPSLIAASAVFLARLT 291 (359)
T ss_pred HHHHHHHHHHhHHHHhC-----chHHHHHHHHHHhhcc-hhHHHHHHHHHHHHhhhhhHHHhccChHHHHHHHHHHHHhh
Confidence 5444443 3333211 2345677777443321 12344455555555544444566789999999999999887
Q ss_pred cCCCCCHHHHHHHHcccHHHHhhh
Q 009187 231 HGLKFSKSDIIEDFMARKKELHEG 254 (540)
Q Consensus 231 ~g~~~t~~eI~~~~~~~~~ti~~~ 254 (540)
++..-=...+.+-.+.+..++..-
T Consensus 292 ~~~~pW~~~L~~~T~y~~edl~~~ 315 (359)
T KOG0654|consen 292 LDFHPWNQTLEDYTGYKAEDLKPC 315 (359)
T ss_pred ccCCCCchhhHHhhcccHHHHHHH
Confidence 774322333445555555544433
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=43.97 E-value=11 Score=26.94 Aligned_cols=21 Identities=24% Similarity=0.442 Sum_probs=9.4
Q ss_pred CCCCCCCCCeeeecCCCceec
Q 009187 3 WCSSCARHVTGHRPYDSQLCC 23 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VC 23 (540)
+|..||.-.-+.+...|.++|
T Consensus 8 kC~~CGniVev~~~g~g~lvC 28 (36)
T PF06397_consen 8 KCEHCGNIVEVVHDGGGPLVC 28 (36)
T ss_dssp E-TTT--EEEEEE--SS-EEE
T ss_pred EccCCCCEEEEEECCCCCEEe
Confidence 477777654445555677777
No 207
>PRK08329 threonine synthase; Validated
Probab=43.77 E-value=15 Score=39.01 Aligned_cols=26 Identities=35% Similarity=0.723 Sum_probs=18.9
Q ss_pred CCCCCCCCCCCeeeecCCCceecCcccceec
Q 009187 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (540)
Q Consensus 1 m~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vle 31 (540)
|..|+.||.. ++.... ..| .||-.|+
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 7899999987 232223 789 7997765
No 208
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=43.46 E-value=54 Score=30.58 Aligned_cols=45 Identities=20% Similarity=0.183 Sum_probs=38.5
Q ss_pred hHHHHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 009187 116 EQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (540)
Q Consensus 116 ~~vaAACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~ 160 (540)
+..+=|.+|+|....+-|.++.+||...+++...|.+.+..|.+.
T Consensus 8 ~yal~~L~~LA~~~~~~~~s~~~IA~~~~is~~~L~kil~~L~ka 52 (150)
T COG1959 8 EYALRALLYLALLPGGGPVSSAEIAERQGISPSYLEKILSKLRKA 52 (150)
T ss_pred hHHHHHHHHHHhCCCCCcccHHHHHHHhCcCHHHHHHHHHHHHHc
Confidence 455668899998877779999999999999999999888888774
No 209
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=43.36 E-value=38 Score=24.15 Aligned_cols=30 Identities=10% Similarity=0.136 Sum_probs=26.0
Q ss_pred CCCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 009187 131 SKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (540)
Q Consensus 131 ~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~ 160 (540)
..|.+..|+++.++++...+.+.+..|.+.
T Consensus 6 ~~~~s~~~la~~l~~s~~tv~~~l~~L~~~ 35 (48)
T smart00419 6 RLPLTRQEIAELLGLTRETVSRTLKRLEKE 35 (48)
T ss_pred EeccCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 357899999999999999999888888764
No 210
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=43.26 E-value=16 Score=28.58 Aligned_cols=24 Identities=25% Similarity=0.751 Sum_probs=18.9
Q ss_pred CCCCCCCCCeeeecCCCceecCccccee
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vl 30 (540)
.||.|++.. ...-.+.|..||...
T Consensus 1 ~Cpv~~~~~----~~~v~~~Cp~cGipt 24 (55)
T PF13824_consen 1 LCPVCKKDL----PAHVNFECPDCGIPT 24 (55)
T ss_pred CCCCCcccc----ccccCCcCCCCCCcC
Confidence 499999863 446678999999874
No 211
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=43.13 E-value=16 Score=33.51 Aligned_cols=31 Identities=19% Similarity=0.437 Sum_probs=20.6
Q ss_pred CCCCCCCCCCCeee-ec---CCCceecCcccceec
Q 009187 1 MVWCSSCARHVTGH-RP---YDSQLCCDRCGKVLE 31 (540)
Q Consensus 1 m~~Cp~Cgs~~iv~-D~---~~G~~VCt~CG~Vle 31 (540)
|+.||.|++..+.. -. ..--..|..||.-..
T Consensus 30 ~~~cP~C~s~~~~k~g~~~~~~qRyrC~~C~~tf~ 64 (129)
T COG3677 30 KVNCPRCKSSNVVKIGGIRRGHQRYKCKSCGSTFT 64 (129)
T ss_pred cCcCCCCCccceeeECCccccccccccCCcCccee
Confidence 56899999987221 11 123678999998643
No 212
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=42.88 E-value=18 Score=33.28 Aligned_cols=28 Identities=25% Similarity=0.729 Sum_probs=19.7
Q ss_pred CCC--CCCCCCeeeecCCCceecCcccceecc
Q 009187 3 WCS--SCARHVTGHRPYDSQLCCDRCGKVLED 32 (540)
Q Consensus 3 ~Cp--~Cgs~~iv~D~~~G~~VCt~CG~Vlee 32 (540)
.|| .|+.. +..+ .+|.+.|..||..++.
T Consensus 20 aC~~~~C~kK-v~~~-~~~~y~C~~C~~~~~~ 49 (146)
T PF08646_consen 20 ACPNEKCNKK-VTEN-GDGSYRCEKCNKTVEN 49 (146)
T ss_dssp E-TSTTTS-B--EEE-TTTEEEETTTTEEESS
T ss_pred CCCCccCCCE-eecC-CCcEEECCCCCCcCCC
Confidence 499 99987 3333 5699999999998753
No 213
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=42.76 E-value=80 Score=23.26 Aligned_cols=23 Identities=9% Similarity=0.115 Sum_probs=21.1
Q ss_pred CCHHHHHHHhCcCHHHHHHHHHH
Q 009187 134 FLLIDFSNYLNINVYELGAVYLQ 156 (540)
Q Consensus 134 rtL~DIs~vl~V~~~~Lgr~~~~ 156 (540)
.++++||..++++..++.+.|..
T Consensus 28 ~s~~~vA~~~~vs~~TV~ri~~~ 50 (52)
T PF13542_consen 28 RSFKDVARELGVSWSTVRRIFDR 50 (52)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHh
Confidence 79999999999999999988765
No 214
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=42.61 E-value=5.5 Score=31.44 Aligned_cols=24 Identities=25% Similarity=0.863 Sum_probs=17.3
Q ss_pred CCCCCCCCCeeeecCCCceecC-cccceec
Q 009187 3 WCSSCARHVTGHRPYDSQLCCD-RCGKVLE 31 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt-~CG~Vle 31 (540)
.|+.||... ..|+.+|+ .||-+++
T Consensus 10 HC~VCg~aI-----p~de~~CSe~C~eil~ 34 (64)
T COG4068 10 HCVVCGKAI-----PPDEQVCSEECGEILN 34 (64)
T ss_pred cccccCCcC-----CCccchHHHHHHHHHH
Confidence 589999862 24678888 6887765
No 215
>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=42.48 E-value=16 Score=27.33 Aligned_cols=28 Identities=18% Similarity=0.526 Sum_probs=18.4
Q ss_pred CCCCCCCCCeeee-------cCCCceecCc--cccee
Q 009187 3 WCSSCARHVTGHR-------PYDSQLCCDR--CGKVL 30 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D-------~~~G~~VCt~--CG~Vl 30 (540)
.||+||+...+.- ...-...|++ ||.-.
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg~tf 37 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSPLTRELYCQCTNPECGHTF 37 (47)
T ss_pred CcCCCCCeeEEEEchhhCcceEEEEEEECCCcCCCEE
Confidence 5999999744332 1234667887 99753
No 216
>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=42.43 E-value=15 Score=32.28 Aligned_cols=31 Identities=23% Similarity=0.443 Sum_probs=23.0
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceeccccc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNF 35 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~~I 35 (540)
.|--||..- |-...+.+||..||+++.-..|
T Consensus 37 aCeiC~~~G--Y~q~g~~lvC~~C~~~~~~~~i 67 (102)
T PF10080_consen 37 ACEICGPKG--YYQEGDQLVCKNCGVRFNLPTI 67 (102)
T ss_pred eccccCCCc--eEEECCEEEEecCCCEEehhhc
Confidence 588997763 3345789999999999864433
No 217
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=42.29 E-value=15 Score=32.89 Aligned_cols=35 Identities=20% Similarity=0.460 Sum_probs=20.2
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceeccccccccccc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATF 41 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~~Ids~~ef 41 (540)
+|+.||...... ......|..||.. +-.+..|.+|
T Consensus 72 ~C~~Cg~~~~~~--~~~~~~CP~Cgs~--~~~i~~G~El 106 (114)
T PRK03681 72 WCETCQQYVTLL--TQRVRRCPQCHGD--MLRIVADDGL 106 (114)
T ss_pred EcccCCCeeecC--CccCCcCcCcCCC--CcEEccCCeE
Confidence 699999642211 1233669999965 2345555554
No 218
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=42.21 E-value=76 Score=30.99 Aligned_cols=46 Identities=20% Similarity=0.078 Sum_probs=33.6
Q ss_pred hhHHHHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 009187 115 TEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (540)
Q Consensus 115 ~~~vaAACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~ 160 (540)
...-+|.-|+........|.+..|||+.+|++..+|.|++.+|.+.
T Consensus 151 ~~~Rla~~L~~~~~~~~~~~t~~~lA~~lG~sretvsR~L~~L~~~ 196 (226)
T PRK10402 151 LENRLAAFILLTQEGDLYHEKHTQAAEYLGVSYRHLLYVLAQFIQD 196 (226)
T ss_pred HHHHHHHHHHhcccCCcccchHHHHHHHHCCcHHHHHHHHHHHHHC
Confidence 3444444444333333456788999999999999999999999885
No 219
>KOG3915 consensus Transcription regulator dachshund, contains SKI/SNO domain [Transcription]
Probab=42.16 E-value=77 Score=34.98 Aligned_cols=18 Identities=22% Similarity=0.376 Sum_probs=13.2
Q ss_pred HHHHHhhhCHHHHHHHHHHHHH
Q 009187 412 KKIIWEEMNREYLEEQAAKEAA 433 (540)
Q Consensus 412 K~~lW~~~N~eyl~eq~~Ke~~ 433 (540)
|+.||| |+|+||+-||-.
T Consensus 530 k~ELkm----d~lrerelresl 547 (641)
T KOG3915|consen 530 KTELKM----DFLRERELRESL 547 (641)
T ss_pred HHHHHH----HHHHHHHHHHHH
Confidence 678887 677777777654
No 220
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=41.83 E-value=1.1e+02 Score=29.09 Aligned_cols=29 Identities=10% Similarity=0.007 Sum_probs=26.5
Q ss_pred CCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 009187 132 KPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (540)
Q Consensus 132 ~prtL~DIs~vl~V~~~~Lgr~~~~L~~~ 160 (540)
.|.|..+||+.+|++..++.|.+++|.+.
T Consensus 167 ~~~t~~~lA~~lG~tr~tvsR~l~~l~~~ 195 (211)
T PRK11753 167 IKITRQEIGRIVGCSREMVGRVLKMLEDQ 195 (211)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 58899999999999999999999988875
No 221
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=41.45 E-value=12 Score=36.71 Aligned_cols=34 Identities=26% Similarity=0.524 Sum_probs=22.3
Q ss_pred CCCCCCCCCCe----eee-cCCC-----ceecCcccceeccccc
Q 009187 2 VWCSSCARHVT----GHR-PYDS-----QLCCDRCGKVLEDHNF 35 (540)
Q Consensus 2 ~~Cp~Cgs~~i----v~D-~~~G-----~~VCt~CG~Vlee~~I 35 (540)
+.||.||+... .+| |.-| ..+|..||+=..|-..
T Consensus 15 ~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~DV~~ 58 (201)
T COG1779 15 IDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGYRSTDVKT 58 (201)
T ss_pred ecCCcccceeeEEEeeecCCccceEEEEEEEccccCCcccceee
Confidence 46999999621 122 2344 4689999997766444
No 222
>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=41.37 E-value=13 Score=36.62 Aligned_cols=32 Identities=25% Similarity=0.480 Sum_probs=22.2
Q ss_pred CCCCCCCCCC--eeeecCCC---ceecCcccceeccc
Q 009187 2 VWCSSCARHV--TGHRPYDS---QLCCDRCGKVLEDH 33 (540)
Q Consensus 2 ~~Cp~Cgs~~--iv~D~~~G---~~VCt~CG~Vlee~ 33 (540)
+.|-+||... +-.++..| -..|.+||.|.|.-
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 4699999972 22333334 37899999998753
No 223
>PRK06030 hypothetical protein; Provisional
Probab=40.82 E-value=86 Score=28.58 Aligned_cols=39 Identities=8% Similarity=0.100 Sum_probs=32.7
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHHHh
Q 009187 121 SCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVL 161 (540)
Q Consensus 121 ACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~L 161 (540)
.|+|++-...+ .++.+|+..+|-+..++..+++++.+.+
T Consensus 59 IAMYL~r~~~~--~sl~~IG~~FGRDHSTV~haikkIe~~~ 97 (124)
T PRK06030 59 IAMYVAHVSLG--WPMNEVALAFGRDRTTVGHACHTVEDLR 97 (124)
T ss_pred HHHHHHHHHcC--CCHHHHHHHHCCChhHHHHHHHHHHHHh
Confidence 67888866655 5899999999999999999999777754
No 224
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=40.73 E-value=35 Score=31.76 Aligned_cols=36 Identities=17% Similarity=0.072 Sum_probs=24.1
Q ss_pred HHHHHHHHHHHhcC---CCCCHHHHHHHHcccHHHHhhh
Q 009187 219 LCGAALYVSALTHG---LKFSKSDIIEDFMARKKELHEG 254 (540)
Q Consensus 219 IAaAALylAa~~~g---~~~t~~eI~~~~~~~~~ti~~~ 254 (540)
+=||.|+.+-.++. -++|+.+||+++|++.+||=++
T Consensus 16 ~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tLYrW 54 (142)
T PF13022_consen 16 RKAAQLLVENELMPENGERRTQAEIAEEVGISRSTLYRW 54 (142)
T ss_dssp HHHHHHHHHHHHS------S-HHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHHHHH
Confidence 34555555555555 4699999999999999998777
No 225
>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=40.54 E-value=23 Score=25.51 Aligned_cols=28 Identities=21% Similarity=0.476 Sum_probs=17.4
Q ss_pred CCCCCCCCC---CeeeecCCCceecCcccce
Q 009187 2 VWCSSCARH---VTGHRPYDSQLCCDRCGKV 29 (540)
Q Consensus 2 ~~Cp~Cgs~---~iv~D~~~G~~VCt~CG~V 29 (540)
++|..|++- -..+|......+|.-||..
T Consensus 3 ~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp -B-TTT--BS-TTSEEETTTTEEEETTT--E
T ss_pred cccCCCCCEECCcceEcCCCCEEECcCCCCc
Confidence 579999984 4567777779999999985
No 226
>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=40.51 E-value=20 Score=40.21 Aligned_cols=29 Identities=21% Similarity=0.537 Sum_probs=22.3
Q ss_pred CCCCCCCCCCeeeecCCCceecCcccceec
Q 009187 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vle 31 (540)
..||+|+... .+....+.+.|..||....
T Consensus 223 ~~C~~C~~~l-~~h~~~~~l~Ch~Cg~~~~ 251 (505)
T TIGR00595 223 LCCPNCDVSL-TYHKKEGKLRCHYCGYQEP 251 (505)
T ss_pred cCCCCCCCce-EEecCCCeEEcCCCcCcCC
Confidence 3699999874 4445678999999998754
No 227
>KOG1088 consensus Uncharacterized conserved protein [Function unknown]
Probab=40.41 E-value=12 Score=33.56 Aligned_cols=18 Identities=22% Similarity=0.532 Sum_probs=14.7
Q ss_pred eecCCCceecCcccceec
Q 009187 14 HRPYDSQLCCDRCGKVLE 31 (540)
Q Consensus 14 ~D~~~G~~VCt~CG~Vle 31 (540)
.|-..|.++|.+||+|..
T Consensus 92 ~~v~EG~l~CpetG~vfp 109 (124)
T KOG1088|consen 92 IDVIEGELVCPETGRVFP 109 (124)
T ss_pred hhhccceEecCCCCcEee
Confidence 345689999999999953
No 228
>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=40.16 E-value=58 Score=24.04 Aligned_cols=31 Identities=13% Similarity=0.129 Sum_probs=24.9
Q ss_pred CCCCCHHHHHHHhCcCHHHHHHHHHHHHHHh
Q 009187 131 SKPFLLIDFSNYLNINVYELGAVYLQLCQVL 161 (540)
Q Consensus 131 ~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~L 161 (540)
..+.|+.|||..+|++...+.+......+.|
T Consensus 18 ~~~~t~~eIa~~lg~s~~~V~~~~~~al~kL 48 (50)
T PF04545_consen 18 FEGLTLEEIAERLGISRSTVRRILKRALKKL 48 (50)
T ss_dssp TST-SHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHHHCCcHHHHHHHHHHHHHHh
Confidence 5578999999999999999988777666554
No 229
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=39.61 E-value=22 Score=29.78 Aligned_cols=28 Identities=18% Similarity=0.205 Sum_probs=20.3
Q ss_pred CCCCCCCCCCeeeecCCCceecCcccce
Q 009187 2 VWCSSCARHVTGHRPYDSQLCCDRCGKV 29 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VCt~CG~V 29 (540)
..||-||...+..+.....-||.-|+--
T Consensus 2 ~~CPCCg~~Tl~~~~~~~ydIC~VC~WE 29 (78)
T PF14206_consen 2 YPCPCCGYYTLEERGEGTYDICPVCFWE 29 (78)
T ss_pred ccCCCCCcEEeccCCCcCceECCCCCcc
Confidence 3699999875544433238899999985
No 230
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=39.31 E-value=4.8e+02 Score=27.42 Aligned_cols=22 Identities=5% Similarity=0.066 Sum_probs=20.4
Q ss_pred CCCCHHHHHHHHcccHHHHhhh
Q 009187 233 LKFSKSDIIEDFMARKKELHEG 254 (540)
Q Consensus 233 ~~~t~~eI~~~~~~~~~ti~~~ 254 (540)
...|.++||+.++++..|++.+
T Consensus 281 e~~s~~EIA~~Lgis~~tV~~~ 302 (325)
T PRK05657 281 EAATLEDVAREIGLTRERVRQI 302 (325)
T ss_pred CCcCHHHHHHHHCcCHHHHHHH
Confidence 4699999999999999999988
No 231
>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=39.10 E-value=75 Score=24.10 Aligned_cols=41 Identities=12% Similarity=0.143 Sum_probs=30.3
Q ss_pred HHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 009187 120 ASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (540)
Q Consensus 120 AACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~ 160 (540)
..+|++..+..+-..++.||++.++++...+.+....|.+.
T Consensus 8 ~~vL~~l~~~~~~~~t~~~la~~l~~~~~~vs~~v~~L~~~ 48 (62)
T PF12802_consen 8 FRVLMALARHPGEELTQSELAERLGISKSTVSRIVKRLEKK 48 (62)
T ss_dssp HHHHHHHHHSTTSGEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHCCCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 34455555545445899999999999999999988888764
No 232
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=38.71 E-value=25 Score=25.38 Aligned_cols=27 Identities=22% Similarity=0.497 Sum_probs=16.7
Q ss_pred CCCCCCCCCeeeec-CCCceecCcccce
Q 009187 3 WCSSCARHVTGHRP-YDSQLCCDRCGKV 29 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~-~~G~~VCt~CG~V 29 (540)
.||.|+........ .---.+|..||=|
T Consensus 1 ~CP~C~~~l~~~~~~~~~id~C~~C~G~ 28 (41)
T PF13453_consen 1 KCPRCGTELEPVRLGDVEIDVCPSCGGI 28 (41)
T ss_pred CcCCCCcccceEEECCEEEEECCCCCeE
Confidence 59999986322222 1224569999876
No 233
>COG1318 Predicted transcriptional regulators [Transcription]
Probab=38.67 E-value=39 Score=32.51 Aligned_cols=25 Identities=12% Similarity=0.220 Sum_probs=22.8
Q ss_pred cCCCCCHHHHHHHHcccHHHHhhhh
Q 009187 231 HGLKFSKSDIIEDFMARKKELHEGV 255 (540)
Q Consensus 231 ~g~~~t~~eI~~~~~~~~~ti~~~~ 255 (540)
...-.|..+||++++.|+.|+|+.+
T Consensus 58 ekag~Ti~EIAeelG~TeqTir~hl 82 (182)
T COG1318 58 EKAGMTISEIAEELGRTEQTVRNHL 82 (182)
T ss_pred HHccCcHHHHHHHhCCCHHHHHHHH
Confidence 5677999999999999999999993
No 234
>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=38.56 E-value=45 Score=25.46 Aligned_cols=33 Identities=9% Similarity=0.052 Sum_probs=27.9
Q ss_pred CCCHHHHHHHhCcCHHHHHHHHHHHHHHhhccc
Q 009187 133 PFLLIDFSNYLNINVYELGAVYLQLCQVLYIAD 165 (540)
Q Consensus 133 prtL~DIs~vl~V~~~~Lgr~~~~L~~~L~i~~ 165 (540)
..+..+||..+++++.+|......|.+.|++..
T Consensus 18 G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~~ 50 (58)
T PF00196_consen 18 GMSNKEIAEELGISEKTVKSHRRRIMKKLGVKN 50 (58)
T ss_dssp TS-HHHHHHHHTSHHHHHHHHHHHHHHHHT-SS
T ss_pred cCCcchhHHhcCcchhhHHHHHHHHHHHhCCCC
Confidence 467899999999999999999999999998753
No 235
>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=38.41 E-value=7.8 Score=34.49 Aligned_cols=34 Identities=21% Similarity=0.581 Sum_probs=18.8
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceeccccccccccc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATF 41 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~~Ids~~ef 41 (540)
+|+.||.. +........|..||.-- -.|.+|.++
T Consensus 72 ~C~~Cg~~---~~~~~~~~~CP~Cgs~~--~~i~~G~el 105 (113)
T PF01155_consen 72 RCRDCGHE---FEPDEFDFSCPRCGSPD--VEIISGREL 105 (113)
T ss_dssp EETTTS-E---EECHHCCHH-SSSSSS---EEEEESS-E
T ss_pred ECCCCCCE---EecCCCCCCCcCCcCCC--cEEccCCeE
Confidence 69999985 33334447799999852 234555544
No 236
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=38.27 E-value=19 Score=39.16 Aligned_cols=29 Identities=34% Similarity=0.693 Sum_probs=17.3
Q ss_pred CCCCCCCCCeeee-cCCCceecCcccceec
Q 009187 3 WCSSCARHVTGHR-PYDSQLCCDRCGKVLE 31 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D-~~~G~~VCt~CG~Vle 31 (540)
.||+|+.-.-+-+ ...+...|..||.++-
T Consensus 15 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~ 44 (403)
T TIGR00155 15 LCSQCDMLVALPRIESGQKAACPRCGTTLT 44 (403)
T ss_pred eCCCCCCcccccCCCCCCeeECCCCCCCCc
Confidence 4888886422122 2344567888888874
No 237
>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=38.07 E-value=1.7e+02 Score=29.31 Aligned_cols=38 Identities=11% Similarity=0.184 Sum_probs=29.5
Q ss_pred HHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHH
Q 009187 119 QASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 157 (540)
Q Consensus 119 aAACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L 157 (540)
..++-||...- ..++++.++|..++++...|.+.|++.
T Consensus 189 ~~~~~~I~~~~-~~~~sl~~lA~~~~~S~~~l~r~Fk~~ 226 (287)
T TIGR02297 189 NRFNFLIEENY-KQHLRLPEYADRLGISESRLNDICRRF 226 (287)
T ss_pred HHHHHHHHHhh-ccCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 34555666443 348999999999999999999888765
No 238
>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=37.67 E-value=56 Score=25.30 Aligned_cols=30 Identities=17% Similarity=0.282 Sum_probs=23.0
Q ss_pred HHHHHhcCC-----CCCHHHHHHHHcccHHHHhhh
Q 009187 225 YVSALTHGL-----KFSKSDIIEDFMARKKELHEG 254 (540)
Q Consensus 225 ylAa~~~g~-----~~t~~eI~~~~~~~~~ti~~~ 254 (540)
+.+|.-.|| +.|..|||++++++.+|+-.+
T Consensus 9 L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~ 43 (53)
T PF04967_consen 9 LKAAYELGYFDVPRRITLEELAEELGISKSTVSEH 43 (53)
T ss_pred HHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHH
Confidence 344444555 578999999999999988766
No 239
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=37.32 E-value=23 Score=37.26 Aligned_cols=27 Identities=19% Similarity=0.465 Sum_probs=17.0
Q ss_pred CCCCCCCCC---ee-eecCCC--ceecCcccce
Q 009187 3 WCSSCARHV---TG-HRPYDS--QLCCDRCGKV 29 (540)
Q Consensus 3 ~Cp~Cgs~~---iv-~D~~~G--~~VCt~CG~V 29 (540)
.||.||+.- ++ .....| .+.|+-||+-
T Consensus 189 ~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~te 221 (309)
T PRK03564 189 FCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESE 221 (309)
T ss_pred CCCCCCCcchhheeeccCCCCceEEEcCCCCCc
Confidence 699999962 22 212345 6778777764
No 240
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=36.90 E-value=80 Score=25.62 Aligned_cols=45 Identities=18% Similarity=0.078 Sum_probs=35.2
Q ss_pred HHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHHHhhccccccccccCChhhHHH
Q 009187 127 CRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLH 180 (540)
Q Consensus 127 CR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~L~i~~~p~~~~~~dP~~~I~ 180 (540)
.|.-+.|+++.+.++.+|+++..+.+....+.+-|-. .||+-...
T Consensus 7 IrlLs~~~s~~~Aa~~lG~~~~~v~~wv~~fR~wll~---------LDPSG~~E 51 (65)
T PF05344_consen 7 IRLLSQQISVAQAADRLGTDPGTVRRWVRMFRQWLLQ---------LDPSGHWE 51 (65)
T ss_pred HHHhcccccHHHHHHHHCcCHHHHHHHHHHHHHHHHH---------cCCCCChH
Confidence 3677899999999999999999999887777765431 56665544
No 241
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=36.63 E-value=1.6e+02 Score=28.88 Aligned_cols=29 Identities=21% Similarity=0.323 Sum_probs=26.6
Q ss_pred CCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 009187 132 KPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (540)
Q Consensus 132 ~prtL~DIs~vl~V~~~~Lgr~~~~L~~~ 160 (540)
.|.|..+||+.+|++..+|.|+.++|.+.
T Consensus 178 i~lt~~~IA~~lGisretlsR~L~~L~~~ 206 (230)
T PRK09391 178 LPMSRRDIADYLGLTIETVSRALSQLQDR 206 (230)
T ss_pred ecCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 57899999999999999999999998875
No 242
>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=36.50 E-value=1.1e+02 Score=22.31 Aligned_cols=28 Identities=11% Similarity=0.086 Sum_probs=22.5
Q ss_pred CCCCHHHHHHHhCcCHHHHHHHHHHHHH
Q 009187 132 KPFLLIDFSNYLNINVYELGAVYLQLCQ 159 (540)
Q Consensus 132 ~prtL~DIs~vl~V~~~~Lgr~~~~L~~ 159 (540)
-+.|..|+|..++++...+.+.+++|.+
T Consensus 16 ~~~t~~ela~~~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 16 PRITQKELAEKLGISRSTVNRYLKKLEE 43 (48)
T ss_dssp TTS-HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 3489999999999999999988888765
No 243
>PRK05580 primosome assembly protein PriA; Validated
Probab=36.08 E-value=25 Score=40.92 Aligned_cols=29 Identities=21% Similarity=0.531 Sum_probs=22.4
Q ss_pred CCCCCCCCCCeeeecCCCceecCcccceec
Q 009187 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vle 31 (540)
..||+|+.. +.+....+.+.|..||....
T Consensus 391 ~~C~~C~~~-l~~h~~~~~l~Ch~Cg~~~~ 419 (679)
T PRK05580 391 AECPHCDAS-LTLHRFQRRLRCHHCGYQEP 419 (679)
T ss_pred cCCCCCCCc-eeEECCCCeEECCCCcCCCC
Confidence 369999986 45555688999999998754
No 244
>PRK05901 RNA polymerase sigma factor; Provisional
Probab=36.01 E-value=6.9e+02 Score=28.27 Aligned_cols=89 Identities=9% Similarity=0.082 Sum_probs=52.9
Q ss_pred chHHHHHHHHHHHHHHHHHHh---CCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHH--------------
Q 009187 65 ASRERLMEKAFDDMRQMKNAL---NIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLAC-------------- 127 (540)
Q Consensus 65 ~srer~L~~a~~~I~~ia~~L---~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiAC-------------- 127 (540)
..+++.+..-++.+..+|.++ |++-.+-|.+--.-+.+-+..-...+|-+....|.=+|--+.
T Consensus 271 ~Ar~~LI~sNLrLVvsIAkrY~~~Gl~~eDLIQEGnIGLikAvekFDp~rG~rFSTYA~wWIRqaI~raI~d~~r~IRvP 350 (509)
T PRK05901 271 RAKNHLLEANLRLVVSLAKRYTNRGLSFLDLIQEGNLGLIKAVEKFDYTKGYKFSTYATWWIRQAITRAMADQARTIRIP 350 (509)
T ss_pred HHHHHHHHHhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHhCcccCCCchhhhHHHHHHHHHHHHHHcCCceecC
Confidence 344455555667777777776 333214445555557776666666777666655554442221
Q ss_pred ------------------HhcCCCCCHHHHHHHhCcCHHHHHHH
Q 009187 128 ------------------RQKSKPFLLIDFSNYLNINVYELGAV 153 (540)
Q Consensus 128 ------------------R~e~~prtL~DIs~vl~V~~~~Lgr~ 153 (540)
...|.+-|..+||..+++++..|...
T Consensus 351 ~~~~e~i~kl~~~~~~L~~~lgr~PT~eELAe~Lgis~e~V~~~ 394 (509)
T PRK05901 351 VHMVETINKLGRIERELLQELGREPTPEELAKEMGFTPEKVREI 394 (509)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCHHHHHHHhCCCHHHHHHH
Confidence 11244446778888888888887665
No 245
>PRK14873 primosome assembly protein PriA; Provisional
Probab=35.89 E-value=23 Score=41.10 Aligned_cols=27 Identities=19% Similarity=0.522 Sum_probs=20.5
Q ss_pred CCCCCCCCCCeeeecCCCceecCcccce
Q 009187 2 VWCSSCARHVTGHRPYDSQLCCDRCGKV 29 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VCt~CG~V 29 (540)
..||+|+.... +....+.+.|..||..
T Consensus 393 ~~C~~C~~~L~-~h~~~~~l~Ch~CG~~ 419 (665)
T PRK14873 393 ARCRHCTGPLG-LPSAGGTPRCRWCGRA 419 (665)
T ss_pred eECCCCCCcee-EecCCCeeECCCCcCC
Confidence 36999998743 4345689999999984
No 246
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=35.61 E-value=1.5e+02 Score=27.87 Aligned_cols=29 Identities=7% Similarity=-0.156 Sum_probs=26.9
Q ss_pred CCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 009187 132 KPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (540)
Q Consensus 132 ~prtL~DIs~vl~V~~~~Lgr~~~~L~~~ 160 (540)
.|.|..+||+.+|++..++.|.+++|.+.
T Consensus 148 ~~~t~~~iA~~lG~tretvsR~l~~l~~~ 176 (202)
T PRK13918 148 IYATHDELAAAVGSVRETVTKVIGELSRE 176 (202)
T ss_pred ecCCHHHHHHHhCccHHHHHHHHHHHHHC
Confidence 68899999999999999999999999875
No 247
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=35.40 E-value=19 Score=28.63 Aligned_cols=27 Identities=4% Similarity=-0.162 Sum_probs=18.4
Q ss_pred CCCCCCCCCCeeeecCCCceecCcccceeccccc
Q 009187 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNF 35 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~~I 35 (540)
+.|++||...+ -.-||. ||+--+..++
T Consensus 28 ~~c~~cg~~~~------pH~vc~-cG~Y~gr~v~ 54 (60)
T PRK01110 28 SVDKTTGEYHL------PHHVSP-KGYYKGRKVL 54 (60)
T ss_pred eEcCCCCceec------cceecC-CcccCCeEee
Confidence 46999997532 446799 9987665444
No 248
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=35.25 E-value=83 Score=37.25 Aligned_cols=58 Identities=26% Similarity=0.333 Sum_probs=47.0
Q ss_pred HHHHHHHHHHhCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCC
Q 009187 75 FDDMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFL 135 (540)
Q Consensus 75 ~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~prt 135 (540)
.+.....|..|+++ ......|...|..+..+-..-| +..++.|.+||.+||...+|.-
T Consensus 35 ~q~~~~~c~~lnld--~~~~~ea~d~yta~~q~~sleg-s~~hW~~cAlY~~~r~S~~~~v 92 (920)
T KOG1010|consen 35 EQDSDELCRPLNLD--EQTETEAWDTYTAVSQRLSLEG-SESHWLACALYTACRRSSVPTV 92 (920)
T ss_pred hhhhhhhhhhhccc--chhhhhhHHHHHHHHhHhCCCc-cHHHHHHHHHHHHHHhccCCcc
Confidence 34567789999999 8999999999988877655555 4678999999999999976643
No 249
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=35.05 E-value=72 Score=23.08 Aligned_cols=31 Identities=10% Similarity=0.075 Sum_probs=27.5
Q ss_pred CCHHHHHHHhCcCHHHHHHHHHHHHHHhhcc
Q 009187 134 FLLIDFSNYLNINVYELGAVYLQLCQVLYIA 164 (540)
Q Consensus 134 rtL~DIs~vl~V~~~~Lgr~~~~L~~~L~i~ 164 (540)
.+..+||..++++..++.+....+.+.|+.+
T Consensus 19 ~s~~eia~~l~is~~tv~~~~~~~~~kl~~~ 49 (58)
T smart00421 19 LTNKEIAERLGISEKTVKTHLSNIMRKLGVR 49 (58)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence 5889999999999999999888888888764
No 250
>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=34.99 E-value=11 Score=26.62 Aligned_cols=25 Identities=28% Similarity=0.717 Sum_probs=14.7
Q ss_pred CCCCCCC-Ceeeec-CCCce-ecCcccc
Q 009187 4 CSSCARH-VTGHRP-YDSQL-CCDRCGK 28 (540)
Q Consensus 4 Cp~Cgs~-~iv~D~-~~G~~-VCt~CG~ 28 (540)
|.+|+.+ ...+.. ..|.. +|..||.
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~ 28 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGL 28 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHH
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHH
Confidence 7889876 344442 35777 9999986
No 251
>PRK10130 transcriptional regulator EutR; Provisional
Probab=34.94 E-value=3.3e+02 Score=28.99 Aligned_cols=53 Identities=19% Similarity=0.385 Sum_probs=38.8
Q ss_pred hHHHHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHHHhhccccccccccCChhhHHHHH
Q 009187 116 EQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKF 182 (540)
Q Consensus 116 ~~vaAACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~L~i~~~p~~~~~~dP~~~I~Rf 182 (540)
..|..+.-||--.. .-|+++.|||..++++...|.+.|++. +| ..|..||.++
T Consensus 240 ~~v~~~~~~i~~~~-~~~ltv~~lA~~~gvS~r~L~r~Fk~~---~G----------~sp~~ylr~~ 292 (350)
T PRK10130 240 RLLSRAREYVLENM-SEPVTVLDLCNQLHVSRRTLQNAFHAI---LG----------IGPNAWLKRI 292 (350)
T ss_pred HHHHHHHHHHHhhh-cCCCCHHHHHHHHCCCHHHHHHHHHHH---HC----------cCHHHHHHHH
Confidence 44556666776444 458999999999999999999888755 44 3466777643
No 252
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=34.79 E-value=21 Score=41.25 Aligned_cols=25 Identities=24% Similarity=0.550 Sum_probs=17.0
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceecc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee 32 (540)
.||+||... ..|.-+|..||+-+..
T Consensus 29 ~Cp~CG~~~-----~~~~~fC~~CG~~~~~ 53 (645)
T PRK14559 29 PCPQCGTEV-----PVDEAHCPNCGAETGT 53 (645)
T ss_pred cCCCCCCCC-----CcccccccccCCcccc
Confidence 466666542 3577889999987764
No 253
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=34.76 E-value=57 Score=35.82 Aligned_cols=68 Identities=13% Similarity=0.151 Sum_probs=46.4
Q ss_pred hHHHHHHHHHHHHHHhCcccCCCchhHHHHH---HHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHHHh
Q 009187 91 DEIVHVAKRFYGIAVARNFTKGRRTEQVQAS---CLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVL 161 (540)
Q Consensus 91 ~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAA---CLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~L 161 (540)
+.|++..+.+|..-.+.=..++|. ..++-| +.|++-+ -+..++.+|+..+|.+..++.++++++.+.+
T Consensus 345 ~~I~~~V~~~~~i~~~~l~s~~R~-~~i~~aR~iamyl~r~--~~~~s~~~Ig~~fgr~hstV~~a~~~i~~~~ 415 (440)
T PRK14088 345 DELIEIVAKVTGVSREEILSNSRN-VKALLARRIGMYVAKN--YLGSSLRTIAEKFNRSHPVVVDSVKKVKDSL 415 (440)
T ss_pred HHHHHHHHHHcCCcHHHHhCCCCC-ccccHHHHHHHHHHHH--HhCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 455566666664432221222333 345555 8888844 5567999999999999999999999998865
No 254
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=34.73 E-value=96 Score=35.77 Aligned_cols=71 Identities=13% Similarity=0.163 Sum_probs=46.1
Q ss_pred hHHHHHHHHHHHHHHhCcccCCCchhHHHH--HHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHHHhhc
Q 009187 91 DEIVHVAKRFYGIAVARNFTKGRRTEQVQA--SCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYI 163 (540)
Q Consensus 91 ~~i~e~A~~iyk~a~~~~~~rGR~~~~vaA--ACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~L~i 163 (540)
+.|++....+|..-.+.=..++|+...+.| .|+|++-+. +..+|.+|...+|-+..+|..++++|.+.+.-
T Consensus 527 d~I~~~Va~~f~v~~~dl~s~~R~~~i~~aRqiAMYL~r~l--t~~Sl~~IG~~FgRdHSTV~~A~~kI~~~~~~ 599 (617)
T PRK14086 527 AAIMAATADYFGLTVEDLCGTSRSRVLVTARQIAMYLCREL--TDLSLPKIGQQFGRDHTTVMHADRKIRALMAE 599 (617)
T ss_pred HHHHHHHHHHhCCCHHHHhCCCCCcccchHHHHHHHHHHHH--cCCCHHHHHHHhCCChhHHHHHHHHHHHHHHh
Confidence 345555555554433322223343333333 678887664 45678999999999999999999999997754
No 255
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=34.67 E-value=1e+02 Score=24.63 Aligned_cols=38 Identities=11% Similarity=0.102 Sum_probs=28.8
Q ss_pred HHHHHHhcCC-CCCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 009187 123 LYLACRQKSK-PFLLIDFSNYLNINVYELGAVYLQLCQV 160 (540)
Q Consensus 123 LYiACR~e~~-prtL~DIs~vl~V~~~~Lgr~~~~L~~~ 160 (540)
|+...+..+- +.++.|||..++++...+.+....|.+.
T Consensus 11 IL~~L~~~g~~~~ta~eLa~~lgl~~~~v~r~L~~L~~~ 49 (68)
T smart00550 11 ILEFLENSGDETSTALQLAKNLGLPKKEVNRVLYSLEKK 49 (68)
T ss_pred HHHHHHHCCCCCcCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 3444555665 4999999999999999988776666554
No 256
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=34.67 E-value=26 Score=32.89 Aligned_cols=27 Identities=22% Similarity=0.682 Sum_probs=20.7
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceec
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vle 31 (540)
.||.|++... +...|...|..|+..++
T Consensus 36 aC~~C~kkv~--~~~~~~~~C~~C~~~~~ 62 (166)
T cd04476 36 ACPGCNKKVV--EEGNGTYRCEKCNKSVP 62 (166)
T ss_pred cccccCcccE--eCCCCcEECCCCCCcCC
Confidence 5999999732 22339999999999874
No 257
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=33.62 E-value=32 Score=24.02 Aligned_cols=24 Identities=25% Similarity=0.566 Sum_probs=13.8
Q ss_pred CCCCCCCCCeeeecCCCceecCcccce
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~V 29 (540)
.|+.||-. ++...-..+|..||.-
T Consensus 4 ~C~~CG~i---~~g~~~p~~CP~Cg~~ 27 (34)
T cd00729 4 VCPVCGYI---HEGEEAPEKCPICGAP 27 (34)
T ss_pred ECCCCCCE---eECCcCCCcCcCCCCc
Confidence 47788753 2222234578888763
No 258
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=33.61 E-value=71 Score=25.52 Aligned_cols=34 Identities=12% Similarity=0.193 Sum_probs=26.0
Q ss_pred CCCCCHHHHHHHhCcCHHHHHHHHHHHHHHhhcc
Q 009187 131 SKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIA 164 (540)
Q Consensus 131 ~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~L~i~ 164 (540)
+.|.+-.|||+.++++.+.+.+....|.+.=.+.
T Consensus 13 ~~p~~T~eiA~~~gls~~~aR~yL~~Le~eG~V~ 46 (62)
T PF04703_consen 13 NGPLKTREIADALGLSIYQARYYLEKLEKEGKVE 46 (62)
T ss_dssp TS-EEHHHHHHHHTS-HHHHHHHHHHHHHCTSEE
T ss_pred CCCCCHHHHHHHhCCCHHHHHHHHHHHHHCCCEE
Confidence 7899999999999999999987777776654343
No 259
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=33.45 E-value=26 Score=24.21 Aligned_cols=20 Identities=30% Similarity=0.576 Sum_probs=9.5
Q ss_pred CCCCCCCCeeeecCCCceec
Q 009187 4 CSSCARHVTGHRPYDSQLCC 23 (540)
Q Consensus 4 Cp~Cgs~~iv~D~~~G~~VC 23 (540)
|..||.-..+.+...|.++|
T Consensus 10 C~~Cgniv~v~~~~~~~l~C 29 (34)
T TIGR00319 10 CEVCGNIVEVLHAGGGQLVC 29 (34)
T ss_pred cCCCCcEEEEEECCCcceec
Confidence 55555543333434445555
No 260
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=33.44 E-value=27 Score=34.16 Aligned_cols=30 Identities=30% Similarity=0.656 Sum_probs=18.3
Q ss_pred CCCCCCCCC----eeee--cCCC-----ceecCcccceecc
Q 009187 3 WCSSCARHV----TGHR--PYDS-----QLCCDRCGKVLED 32 (540)
Q Consensus 3 ~Cp~Cgs~~----iv~D--~~~G-----~~VCt~CG~Vlee 32 (540)
.||+||... ..++ |.=| ...|..||.=-.|
T Consensus 2 ~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~e 42 (192)
T TIGR00310 2 DCPSCGGECETVMKTVNDIPYFGEVLETSTICEHCGYRSND 42 (192)
T ss_pred cCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCCCccce
Confidence 599999651 1222 1122 4679999986443
No 261
>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=33.42 E-value=28 Score=36.55 Aligned_cols=9 Identities=22% Similarity=0.925 Sum_probs=5.9
Q ss_pred ceecCcccc
Q 009187 20 QLCCDRCGK 28 (540)
Q Consensus 20 ~~VCt~CG~ 28 (540)
-+-|+.||.
T Consensus 224 R~~C~~Cg~ 232 (305)
T TIGR01562 224 RVKCSHCEE 232 (305)
T ss_pred CccCCCCCC
Confidence 356777774
No 262
>PF12116 SpoIIID: Stage III sporulation protein D; InterPro: IPR014208 Members of this entry represent the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if, and only if, the species is capable of endospore formation. In Bacillus subtilis SpoIIID is a DNA binding protein that is involved in gene repression as well as activation [].; PDB: 2L0K_A.
Probab=33.15 E-value=33 Score=28.90 Aligned_cols=30 Identities=13% Similarity=0.114 Sum_probs=20.1
Q ss_pred HHHHHhcCCCCCHHHHHHHHcccHHHHhhh
Q 009187 225 YVSALTHGLKFSKSDIIEDFMARKKELHEG 254 (540)
Q Consensus 225 ylAa~~~g~~~t~~eI~~~~~~~~~ti~~~ 254 (540)
-+|-.+.+.+.|++..|.+||++.+|+-+-
T Consensus 10 ~i~~yIi~~~aTVR~~Ak~FGvSKSTVHkD 39 (82)
T PF12116_consen 10 EIANYIIETKATVRQAAKVFGVSKSTVHKD 39 (82)
T ss_dssp HHHHHHHHH---HHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHcccHHHHHHHHHCCcHHHHHHH
Confidence 344444566889999999999999998776
No 263
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=33.14 E-value=24 Score=28.44 Aligned_cols=19 Identities=26% Similarity=0.592 Sum_probs=12.2
Q ss_pred CCCCCCCCCeeeecCCCceecCcccc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGK 28 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~ 28 (540)
.|.+|+.- + + .-+|..||.
T Consensus 7 AC~~C~~i--~-~----~~~Cp~Cgs 25 (64)
T PRK06393 7 ACKKCKRL--T-P----EKTCPVHGD 25 (64)
T ss_pred hHhhCCcc--c-C----CCcCCCCCC
Confidence 48888763 2 1 128888887
No 264
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=33.05 E-value=21 Score=32.00 Aligned_cols=35 Identities=11% Similarity=0.309 Sum_probs=19.4
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceeccccccccccc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATF 41 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~~Ids~~ef 41 (540)
+|+.||.... .+ ..+...|..||.- +-.|.+|.++
T Consensus 73 ~C~~Cg~~~~-~~-~~~~~~CP~Cgs~--~~~i~~G~El 107 (117)
T PRK00564 73 ECKDCSHVFK-PN-ALDYGVCEKCHSK--NVIITQGNEM 107 (117)
T ss_pred EhhhCCCccc-cC-CccCCcCcCCCCC--ceEEecCCEE
Confidence 6888885421 11 1244558899864 2234555554
No 265
>PRK13501 transcriptional activator RhaR; Provisional
Probab=32.91 E-value=1.6e+02 Score=29.85 Aligned_cols=34 Identities=12% Similarity=0.073 Sum_probs=21.4
Q ss_pred HHHHHh-cCCCCCHHHHHHHhCc-CHHHHHHHHHHH
Q 009187 124 YLACRQ-KSKPFLLIDFSNYLNI-NVYELGAVYLQL 157 (540)
Q Consensus 124 YiACR~-e~~prtL~DIs~vl~V-~~~~Lgr~~~~L 157 (540)
-.|+++ .....++.|||..+|- +...+.|.|++.
T Consensus 231 ~~A~~LL~~t~~sI~eIA~~~GF~~~s~F~r~FKk~ 266 (290)
T PRK13501 231 CHAKCLLRGSEHRISDIAARCGFEDSNYFSAVFTRE 266 (290)
T ss_pred HHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHH
Confidence 344444 3455678888888874 566677666654
No 266
>PRK13503 transcriptional activator RhaS; Provisional
Probab=32.87 E-value=2.2e+02 Score=28.34 Aligned_cols=36 Identities=8% Similarity=-0.022 Sum_probs=20.1
Q ss_pred HHHHHHHhc-CCCCCHHHHHHHhC-cCHHHHHHHHHHH
Q 009187 122 CLYLACRQK-SKPFLLIDFSNYLN-INVYELGAVYLQL 157 (540)
Q Consensus 122 CLYiACR~e-~~prtL~DIs~vl~-V~~~~Lgr~~~~L 157 (540)
=|..|+++- ....++.|||..+| -+...+.+.|++.
T Consensus 224 Rl~~A~~LL~~~~~sI~eIA~~~GF~~~s~F~r~FKk~ 261 (278)
T PRK13503 224 RLLKARHLLRHSDASVTDIAYRCGFGDSNHFSTLFRRE 261 (278)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHHHHH
Confidence 344455543 33466777777776 3555666665544
No 267
>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=32.84 E-value=62 Score=23.59 Aligned_cols=26 Identities=12% Similarity=0.155 Sum_probs=19.7
Q ss_pred HhcCCCCCHHHHHHHHcccHHHHhhh
Q 009187 229 LTHGLKFSKSDIIEDFMARKKELHEG 254 (540)
Q Consensus 229 ~~~g~~~t~~eI~~~~~~~~~ti~~~ 254 (540)
...+-+.|..+|++.+|+++.++.+|
T Consensus 12 Lq~d~r~s~~~la~~lglS~~~v~~R 37 (42)
T PF13404_consen 12 LQEDGRRSYAELAEELGLSESTVRRR 37 (42)
T ss_dssp HHH-TTS-HHHHHHHHTS-HHHHHHH
T ss_pred HHHcCCccHHHHHHHHCcCHHHHHHH
Confidence 34567888999999999999999887
No 268
>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=32.78 E-value=18 Score=34.12 Aligned_cols=15 Identities=13% Similarity=0.503 Sum_probs=7.7
Q ss_pred ecCcccceecccccc
Q 009187 22 CCDRCGKVLEDHNFS 36 (540)
Q Consensus 22 VCt~CG~Vlee~~Id 36 (540)
.|.+|++=|.-...+
T Consensus 41 ~Cp~C~~~IrG~y~v 55 (158)
T PF10083_consen 41 SCPNCSTPIRGDYHV 55 (158)
T ss_pred HCcCCCCCCCCceec
Confidence 366666655544333
No 269
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=32.68 E-value=31 Score=36.30 Aligned_cols=11 Identities=36% Similarity=0.936 Sum_probs=6.8
Q ss_pred eecCcccceec
Q 009187 21 LCCDRCGKVLE 31 (540)
Q Consensus 21 ~VCt~CG~Vle 31 (540)
.+|..||.-+-
T Consensus 253 e~C~~C~~YlK 263 (309)
T PRK03564 253 ESCGDCGTYLK 263 (309)
T ss_pred eecccccccce
Confidence 56666666553
No 270
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=32.63 E-value=25 Score=38.49 Aligned_cols=30 Identities=30% Similarity=0.615 Sum_probs=19.1
Q ss_pred CCCCCCCCCeeee-cCCCceecCcccceecc
Q 009187 3 WCSSCARHVTGHR-PYDSQLCCDRCGKVLED 32 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D-~~~G~~VCt~CG~Vlee 32 (540)
.||+|+.-.-..+ ...+...|..||.+|..
T Consensus 12 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~~ 42 (419)
T PRK15103 12 LCPQCDMLVALPRLEHGQKAACPRCGTTLTV 42 (419)
T ss_pred cCCCCCceeecCCCCCCCeeECCCCCCCCcC
Confidence 4999987422222 22446779999998853
No 271
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=32.63 E-value=35 Score=28.62 Aligned_cols=26 Identities=23% Similarity=0.631 Sum_probs=20.0
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceec
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vle 31 (540)
+||.|....+.. ..+.+.| .||.-|.
T Consensus 1 iCPVC~~~~L~~--~~~~i~C-~Cgl~l~ 26 (82)
T PF14768_consen 1 ICPVCQKGNLRE--NSNVISC-SCGLRLN 26 (82)
T ss_pred CCCccCCCcccc--cCCeEEC-CCccEEe
Confidence 599999987655 4688888 7786665
No 272
>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=32.45 E-value=28 Score=24.08 Aligned_cols=22 Identities=23% Similarity=0.333 Sum_probs=12.3
Q ss_pred CCCCCCCCCeeeecCCCceecC
Q 009187 3 WCSSCARHVTGHRPYDSQLCCD 24 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt 24 (540)
+|..||.-..+.+...|.++|-
T Consensus 6 kC~~CGniv~v~~~~~~~l~Cc 27 (34)
T cd00974 6 KCEICGNIVEVLNVGGGTLVCC 27 (34)
T ss_pred EcCCCCcEEEEEECCCcceeec
Confidence 4666666544444455566664
No 273
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=32.27 E-value=89 Score=22.74 Aligned_cols=32 Identities=9% Similarity=0.027 Sum_probs=28.2
Q ss_pred CCCHHHHHHHhCcCHHHHHHHHHHHHHHhhcc
Q 009187 133 PFLLIDFSNYLNINVYELGAVYLQLCQVLYIA 164 (540)
Q Consensus 133 prtL~DIs~vl~V~~~~Lgr~~~~L~~~L~i~ 164 (540)
..+..+||..+++++.++......+.+.++..
T Consensus 15 ~~s~~eia~~l~~s~~tv~~~~~~~~~~l~~~ 46 (57)
T cd06170 15 GKTNKEIADILGISEKTVKTHLRNIMRKLGVK 46 (57)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHhCCC
Confidence 36899999999999999999988888888764
No 274
>PF13790 DUF4182: Domain of unknown function (DUF4182)
Probab=32.01 E-value=23 Score=25.62 Aligned_cols=14 Identities=14% Similarity=0.838 Sum_probs=12.6
Q ss_pred CceecCcccceecc
Q 009187 19 SQLCCDRCGKVLED 32 (540)
Q Consensus 19 G~~VCt~CG~Vlee 32 (540)
|.+||..|+.+|+.
T Consensus 2 GtIvCq~C~~~Id~ 15 (38)
T PF13790_consen 2 GTIVCQHCNETIDH 15 (38)
T ss_pred CEEEeccccceeee
Confidence 88999999999973
No 275
>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=31.97 E-value=42 Score=25.44 Aligned_cols=25 Identities=24% Similarity=0.587 Sum_probs=18.0
Q ss_pred CCC--CCCCCCeeeecCCCceecCcccc
Q 009187 3 WCS--SCARHVTGHRPYDSQLCCDRCGK 28 (540)
Q Consensus 3 ~Cp--~Cgs~~iv~D~~~G~~VCt~CG~ 28 (540)
.|| .||...+--++ ..-..|..||.
T Consensus 20 ~CP~~~CG~GvFMA~H-~dR~~CGKCg~ 46 (47)
T PF01599_consen 20 ECPSPRCGAGVFMAEH-KDRHYCGKCGY 46 (47)
T ss_dssp E-TSTTTTSSSEEEE--SSEEEETTTSS
T ss_pred cCCCcccCCceEeeec-CCCccCCCccc
Confidence 499 99998655555 46889999996
No 276
>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=31.82 E-value=1.3e+02 Score=24.05 Aligned_cols=24 Identities=13% Similarity=0.127 Sum_probs=19.7
Q ss_pred cCCCCCHHHHHHHhCcCHHHHHHH
Q 009187 130 KSKPFLLIDFSNYLNINVYELGAV 153 (540)
Q Consensus 130 e~~prtL~DIs~vl~V~~~~Lgr~ 153 (540)
++--++++|||+.++|+..+|.+-
T Consensus 19 ~~g~i~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 19 SNGKIKLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred hCCCccHHHHHHHHCCCHHHHHHH
Confidence 444578999999999999998653
No 277
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=31.71 E-value=96 Score=28.27 Aligned_cols=46 Identities=11% Similarity=0.162 Sum_probs=37.1
Q ss_pred hhHHHHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 009187 115 TEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (540)
Q Consensus 115 ~~~vaAACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~ 160 (540)
.+.-+-+.+|++-...+.+.+..+||..++|+...|.+++..|.+.
T Consensus 7 ~~YAl~~~i~la~~~~g~~~s~~~ia~~~~is~~~vrk~l~~L~~~ 52 (141)
T PRK11014 7 TDYGLRALIYMASLPEGRMTSISEVTEVYGVSRNHMVKIINQLSRA 52 (141)
T ss_pred HhHHHHHHHHHhcCCCCCccCHHHHHHHHCcCHHHHHHHHHHHHhC
Confidence 3444556777776566778899999999999999999998888775
No 278
>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=31.67 E-value=2.1e+02 Score=22.13 Aligned_cols=44 Identities=11% Similarity=0.094 Sum_probs=30.1
Q ss_pred HHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHH
Q 009187 98 KRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQ 159 (540)
Q Consensus 98 ~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~ 159 (540)
..+++.|++.|++.--+ -.++.|+|+.++|+..++....+.-.+
T Consensus 6 ~e~L~~A~~~GYfd~PR------------------~~tl~elA~~lgis~st~~~~LRrae~ 49 (53)
T PF04967_consen 6 REILKAAYELGYFDVPR------------------RITLEELAEELGISKSTVSEHLRRAER 49 (53)
T ss_pred HHHHHHHHHcCCCCCCC------------------cCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 45566677777664322 148899999999999888766555433
No 279
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=31.66 E-value=1.2e+02 Score=31.02 Aligned_cols=41 Identities=10% Similarity=0.233 Sum_probs=32.4
Q ss_pred hHHHHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHH
Q 009187 116 EQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 157 (540)
Q Consensus 116 ~~vaAACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L 157 (540)
..+..++-||-.... .+.++.++|..++++.+.|.|.|+..
T Consensus 5 ~~i~~~~~~i~~~~~-~~~~l~~lA~~~~~S~~~l~r~F~~~ 45 (289)
T PRK15121 5 GIIRDLLIWLEGHLD-QPLSLDNVAAKAGYSKWHLQRMFKDV 45 (289)
T ss_pred HHHHHHHHHHHhccc-CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 345567777776544 57999999999999999999887755
No 280
>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=31.36 E-value=25 Score=27.33 Aligned_cols=27 Identities=30% Similarity=0.593 Sum_probs=18.9
Q ss_pred CCCCCCCCC---eeeecCCCceecCcccce
Q 009187 3 WCSSCARHV---TGHRPYDSQLCCDRCGKV 29 (540)
Q Consensus 3 ~Cp~Cgs~~---iv~D~~~G~~VCt~CG~V 29 (540)
.|++|.+.+ ...+...-..+|..||..
T Consensus 24 IC~~C~~hNGla~~~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 24 ICSKCFSHNGLAPKEEFEEIQYRCPYCGAL 53 (54)
T ss_pred ECcccchhhcccccccCCceEEEcCCCCCc
Confidence 589998752 235555668899999863
No 281
>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=31.36 E-value=88 Score=23.36 Aligned_cols=36 Identities=14% Similarity=0.190 Sum_probs=26.2
Q ss_pred HHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHH
Q 009187 124 YLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQ 159 (540)
Q Consensus 124 YiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~ 159 (540)
.-+...++-|.++.||+..++++..++.+....|..
T Consensus 9 L~~l~~~~~~~t~~eia~~~gl~~stv~r~L~tL~~ 44 (52)
T PF09339_consen 9 LEALAESGGPLTLSEIARALGLPKSTVHRLLQTLVE 44 (52)
T ss_dssp HHCHHCTBSCEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHcCCCCCCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 334455667789999999999999888776655554
No 282
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=30.89 E-value=1.7e+02 Score=30.16 Aligned_cols=86 Identities=10% Similarity=0.060 Sum_probs=54.8
Q ss_pred HHHHHHHhCCCCchHHHHHHHHHHHHHHhCcccCCCchhH-HHHHHHHHHHHhc-CCCCCHHHHHHHhC-cCHHHHHHHH
Q 009187 78 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQ-VQASCLYLACRQK-SKPFLLIDFSNYLN-INVYELGAVY 154 (540)
Q Consensus 78 I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~-vaAACLYiACR~e-~~prtL~DIs~vl~-V~~~~Lgr~~ 154 (540)
|..+|..++++ ... =.++|+. . |.++.. +--.-+-.||++- ....++.+||..+| -+...+.++|
T Consensus 161 l~~lA~~~g~S--~~~---L~R~Fk~------~-G~S~~~yl~~~Rl~~A~~LL~~t~~sI~eIA~~~GF~s~S~Fsr~F 228 (274)
T PRK09978 161 LARIASELLMS--PSL---LKKKLRE------E-ETSYSQLLTECRMQRALQLIVIHGFSIKRVAVSCGYHSVSYFIYVF 228 (274)
T ss_pred HHHHHHHHCcC--HHH---HHHHHHh------c-CCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHH
Confidence 45577777777 322 1222321 1 445433 3334444455543 35689999999999 4788888888
Q ss_pred HHHHHHhhccccccccccCChhhHHHHHHHhhCC
Q 009187 155 LQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLP 188 (540)
Q Consensus 155 ~~L~~~L~i~~~p~~~~~~dP~~~I~Rf~~~L~~ 188 (540)
++. .| +.|..|-.++...+.+
T Consensus 229 Kk~---~G----------~TPs~yRk~~~~~~~~ 249 (274)
T PRK09978 229 RNY---YG----------MTPTEYQERSAQGLPN 249 (274)
T ss_pred HHH---HC----------cCHHHHHHHhhccCCc
Confidence 876 33 5689999999988863
No 283
>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=30.79 E-value=28 Score=36.53 Aligned_cols=28 Identities=18% Similarity=0.456 Sum_probs=19.5
Q ss_pred CCCCCCCCC---eeee--cCCC--ceecCccccee
Q 009187 3 WCSSCARHV---TGHR--PYDS--QLCCDRCGKVL 30 (540)
Q Consensus 3 ~Cp~Cgs~~---iv~D--~~~G--~~VCt~CG~Vl 30 (540)
.||.||+.- ++.. ...| .+.|+-||+-=
T Consensus 186 ~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW 220 (305)
T TIGR01562 186 LCPACGSPPVASMVRQGGKETGLRYLSCSLCATEW 220 (305)
T ss_pred cCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcc
Confidence 699999963 2222 1345 89999999853
No 284
>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=30.42 E-value=34 Score=26.42 Aligned_cols=20 Identities=20% Similarity=0.365 Sum_probs=0.0
Q ss_pred CCCHHHHHHHHcccHHHHhh
Q 009187 234 KFSKSDIIEDFMARKKELHE 253 (540)
Q Consensus 234 ~~t~~eI~~~~~~~~~ti~~ 253 (540)
.++..++++.|++++.|||.
T Consensus 14 ~~s~~ela~~~~VS~~TiRR 33 (57)
T PF08220_consen 14 KVSVKELAEEFGVSEMTIRR 33 (57)
T ss_pred CEEHHHHHHHHCcCHHHHHH
No 285
>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=30.37 E-value=24 Score=23.56 Aligned_cols=26 Identities=27% Similarity=0.432 Sum_probs=14.2
Q ss_pred CCCCCCCCCe-eeecCCCceecCcccc
Q 009187 3 WCSSCARHVT-GHRPYDSQLCCDRCGK 28 (540)
Q Consensus 3 ~Cp~Cgs~~i-v~D~~~G~~VCt~CG~ 28 (540)
.|+.|+.... +.....+..+|..|-.
T Consensus 3 ~C~rC~~~~~~~~~~~r~~~~C~rCq~ 29 (30)
T PF06827_consen 3 KCPRCWNYIEDIGINGRSTYLCPRCQK 29 (30)
T ss_dssp B-TTT--BBEEEEETTEEEEE-TTTCC
T ss_pred cCccCCCcceEeEecCCCCeECcCCcC
Confidence 6999998732 2223567899998854
No 286
>PHA03074 late transcription factor VLTF-3; Provisional
Probab=30.31 E-value=27 Score=34.40 Aligned_cols=27 Identities=22% Similarity=0.460 Sum_probs=23.4
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceec
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vle 31 (540)
.|..|++..++.. .|...|..|+.|..
T Consensus 6 ~C~~C~~ngiv~~--k~~efC~fC~~~f~ 32 (225)
T PHA03074 6 LCSGCRHNGIVSE--KDYEFCIFCESVFQ 32 (225)
T ss_pred hcCCCCCCCeeee--cCEEEeecHHHHHh
Confidence 5999999988764 69999999999865
No 287
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=30.14 E-value=1.7e+02 Score=30.34 Aligned_cols=83 Identities=10% Similarity=0.093 Sum_probs=47.2
Q ss_pred HHHHHHHhCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCCHHHHHHHhCc-CHHHHHHHHHH
Q 009187 78 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNI-NVYELGAVYLQ 156 (540)
Q Consensus 78 I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~prtL~DIs~vl~V-~~~~Lgr~~~~ 156 (540)
|.++|..++++ .. +-.++|+......+.+-.....+.-|+-.+ .....++.+||..+|. +...+.+.|++
T Consensus 237 l~~lA~~~~~S--~~---~l~r~fk~~~g~s~~~~~~~~Rl~~A~~lL----~~~~~~i~~IA~~~Gf~~~s~F~r~Fk~ 307 (322)
T PRK09393 237 VASLAARAAMS--PR---TFLRRFEAATGMTPAEWLLRERLARARDLL----ESSALSIDQIAERAGFGSEESLRHHFRR 307 (322)
T ss_pred HHHHHHHHCcC--HH---HHHHHHHHHHCcCHHHHHHHHHHHHHHHHH----HcCCCCHHHHHHHhCCCCHHHHHHHHHH
Confidence 56677777777 22 233445554443332222222233333332 2346899999999995 67888888876
Q ss_pred HHHHhhccccccccccCChhhHHHHH
Q 009187 157 LCQVLYIADESNVLKQVDPSIFLHKF 182 (540)
Q Consensus 157 L~~~L~i~~~p~~~~~~dP~~~I~Rf 182 (540)
. .| ..|..|-.++
T Consensus 308 ~---~G----------~tP~~yr~~~ 320 (322)
T PRK09393 308 R---AA----------TSPAAYRKRF 320 (322)
T ss_pred H---HC----------cCHHHHHHHh
Confidence 5 33 4477776665
No 288
>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=30.10 E-value=3.5e+02 Score=23.91 Aligned_cols=72 Identities=11% Similarity=0.165 Sum_probs=43.6
Q ss_pred HHHHHHHHhCCCCchHHHHHHHHHHHHHHhCccc----CCCchhHHHHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHH
Q 009187 77 DMRQMKNALNIGESDEIVHVAKRFYGIAVARNFT----KGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGA 152 (540)
Q Consensus 77 ~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~----rGR~~~~vaAACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr 152 (540)
.+.++|..++++ . .+..+|++. .+.|-+ +|++ .+- .=.+.+.=.++--.|+.|++..++|+...|++
T Consensus 20 s~~eaa~~F~VS--~---~Tv~~W~k~-~~~G~~~~k~r~~~--Kid-~~~L~~~v~~~pd~tl~Ela~~l~Vs~~ti~~ 90 (119)
T PF01710_consen 20 SIREAAKRFGVS--R---NTVYRWLKR-KETGDLEPKPRGRK--KID-RDELKALVEENPDATLRELAERLGVSPSTIWR 90 (119)
T ss_pred hHHHHHHHhCcH--H---HHHHHHHHh-cccccccccccccc--ccc-HHHHHHHHHHCCCcCHHHHHHHcCCCHHHHHH
Confidence 588899999998 3 455566663 233322 2332 111 11122222345567899999999999999987
Q ss_pred HHHHH
Q 009187 153 VYLQL 157 (540)
Q Consensus 153 ~~~~L 157 (540)
..++|
T Consensus 91 ~Lkrl 95 (119)
T PF01710_consen 91 ALKRL 95 (119)
T ss_pred HHHHc
Confidence 65544
No 289
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=29.86 E-value=31 Score=35.70 Aligned_cols=29 Identities=17% Similarity=0.454 Sum_probs=20.2
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceecc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee 32 (540)
.|+.||+.....+ ..=-.+|.+||...=.
T Consensus 113 FCg~CG~~~~~~~-~g~~~~C~~cg~~~fP 141 (279)
T COG2816 113 FCGRCGTKTYPRE-GGWARVCPKCGHEHFP 141 (279)
T ss_pred CCCCCCCcCcccc-CceeeeCCCCCCccCC
Confidence 6999999743322 2236799999997643
No 290
>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=29.50 E-value=27 Score=32.85 Aligned_cols=26 Identities=15% Similarity=0.189 Sum_probs=15.0
Q ss_pred CCCCchHHHHHHHHHHHHHHhCcccCCC
Q 009187 86 NIGESDEIVHVAKRFYGIAVARNFTKGR 113 (540)
Q Consensus 86 ~Lp~~~~i~e~A~~iyk~a~~~~~~rGR 113 (540)
.++ +...+.|..|..--......+|.
T Consensus 96 ~VG--~~FAeEAR~iHyGea~~R~I~G~ 121 (148)
T PF06676_consen 96 DVG--DRFAEEARKIHYGEAEERGIYGE 121 (148)
T ss_pred chh--HHHHHHHHHHHcCCCccccCcCc
Confidence 355 77888888875333333344554
No 291
>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=29.31 E-value=1.4e+02 Score=24.13 Aligned_cols=35 Identities=14% Similarity=0.212 Sum_probs=25.1
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHhC-cCHHHHHHHHHHH
Q 009187 121 SCLYLACRQKSKPFLLIDFSNYLN-INVYELGAVYLQL 157 (540)
Q Consensus 121 ACLYiACR~e~~prtL~DIs~vl~-V~~~~Lgr~~~~L 157 (540)
.+.|++-... ..++.+|+..++ -+..++..+++++
T Consensus 35 va~yL~r~~~--~~sl~~Ig~~fg~rdHstV~~a~~ki 70 (70)
T PF08299_consen 35 VAMYLARELT--GLSLSEIGRYFGGRDHSTVIHAIRKI 70 (70)
T ss_dssp HHHHHHHHHS-----HHHHHHHCTSSTHHHHHHHHHHH
T ss_pred HHHHHHHHHh--CCCHHHHHHHhCCCCHHHHHHHHHhC
Confidence 4567765555 478999999999 9999998887764
No 292
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=29.21 E-value=25 Score=37.08 Aligned_cols=9 Identities=33% Similarity=0.973 Sum_probs=4.7
Q ss_pred ecCccccee
Q 009187 22 CCDRCGKVL 30 (540)
Q Consensus 22 VCt~CG~Vl 30 (540)
-|+.|+-.|
T Consensus 79 kC~~C~~~i 87 (324)
T PF04502_consen 79 KCPRCSNEI 87 (324)
T ss_pred EcCCCCCEE
Confidence 355555544
No 293
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=29.21 E-value=32 Score=27.27 Aligned_cols=24 Identities=25% Similarity=0.646 Sum_probs=12.9
Q ss_pred CCCCCCCCCeeeecCCCceecCcccc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGK 28 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~ 28 (540)
.|.+||..+.+- ..-.+-|.+||.
T Consensus 22 iCgdC~~en~lk--~~D~irCReCG~ 45 (62)
T KOG3507|consen 22 ICGDCGQENTLK--RGDVIRCRECGY 45 (62)
T ss_pred Eecccccccccc--CCCcEehhhcch
Confidence 377777664332 122344777775
No 294
>PHA00689 hypothetical protein
Probab=28.89 E-value=32 Score=26.28 Aligned_cols=9 Identities=56% Similarity=1.446 Sum_probs=5.1
Q ss_pred ceecCcccc
Q 009187 20 QLCCDRCGK 28 (540)
Q Consensus 20 ~~VCt~CG~ 28 (540)
-+.|..||.
T Consensus 17 avtckrcgk 25 (62)
T PHA00689 17 AVTCKRCGK 25 (62)
T ss_pred eeehhhccc
Confidence 455666664
No 295
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.63 E-value=31 Score=27.56 Aligned_cols=14 Identities=14% Similarity=0.544 Sum_probs=12.6
Q ss_pred CCCceecCccccee
Q 009187 17 YDSQLCCDRCGKVL 30 (540)
Q Consensus 17 ~~G~~VCt~CG~Vl 30 (540)
.+|+++|.-||++.
T Consensus 45 ~~gev~CPYC~t~y 58 (62)
T COG4391 45 DEGEVVCPYCSTRY 58 (62)
T ss_pred CCCcEecCccccEE
Confidence 58999999999985
No 296
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=28.39 E-value=4.8e+02 Score=28.99 Aligned_cols=78 Identities=14% Similarity=0.138 Sum_probs=50.4
Q ss_pred HHHHHHHHhCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcC-C------------------CCCHH
Q 009187 77 DMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKS-K------------------PFLLI 137 (540)
Q Consensus 77 ~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~-~------------------prtL~ 137 (540)
-+..++..|+++ ...++.|..+++.+.-.|+.. |+ ..=||.+=.+..+ . -.-+.
T Consensus 140 ~~~eia~~l~~~--~~~v~~~l~~lQ~leP~GigA-r~----L~ECLllQl~~~~~~~~~~~~~~il~~~le~la~~~~~ 212 (455)
T PRK05932 140 DLEEIAESLGVE--LDEVEAVLKRIQSFDPAGVGA-RD----LQECLLLQLEQLDDTPRLDEAMEIISDHLDLLARRDFR 212 (455)
T ss_pred CHHHHHHHcCCC--HHHHHHHHHHHhcCCCCccCc-CC----HHHHHHHHHhccCCCchHHHHHHHHHHHHHHHHcCCHH
Confidence 478899999999 899999999888865555432 11 1123333333211 0 12356
Q ss_pred HHHHHhCcCHHHHHHHHHHHHHHhh
Q 009187 138 DFSNYLNINVYELGAVYLQLCQVLY 162 (540)
Q Consensus 138 DIs~vl~V~~~~Lgr~~~~L~~~L~ 162 (540)
.|+..++++..+|..+...| +.|+
T Consensus 213 ~ia~~l~is~~~v~~~~~~I-r~L~ 236 (455)
T PRK05932 213 TLAKKLGVKEEDLQEALDLI-RSLD 236 (455)
T ss_pred HHHHHHCcCHHHHHHHHHHH-hCCC
Confidence 78889999999998887655 4454
No 297
>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=28.37 E-value=46 Score=24.34 Aligned_cols=26 Identities=12% Similarity=0.043 Sum_probs=18.3
Q ss_pred HhcCCCCCHHHHHHHHcccHHHHhhh
Q 009187 229 LTHGLKFSKSDIIEDFMARKKELHEG 254 (540)
Q Consensus 229 ~~~g~~~t~~eI~~~~~~~~~ti~~~ 254 (540)
.|+....|+.+||+.|+++..||..-
T Consensus 16 ~l~~~G~si~~IA~~~gvsr~TvyR~ 41 (45)
T PF02796_consen 16 ELYAEGMSIAEIAKQFGVSRSTVYRY 41 (45)
T ss_dssp HHHHTT--HHHHHHHTTS-HHHHHHH
T ss_pred HHHHCCCCHHHHHHHHCcCHHHHHHH
Confidence 34444589999999999999998765
No 298
>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=28.31 E-value=2.1e+02 Score=28.71 Aligned_cols=69 Identities=7% Similarity=0.010 Sum_probs=37.0
Q ss_pred HHHHHHHhCCCCchHHHHHHHHHHHHHHhCcccCCCch-hHHHHHHHHHHHHh-cCCCCCHHHHHHHhCc-CHHHHHHHH
Q 009187 78 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRT-EQVQASCLYLACRQ-KSKPFLLIDFSNYLNI-NVYELGAVY 154 (540)
Q Consensus 78 I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~-~~vaAACLYiACR~-e~~prtL~DIs~vl~V-~~~~Lgr~~ 154 (540)
+..+|..++++ . ..-.++|+... |.++ +.+..--|-.|+++ .....++.|||..+|- +...+.+.|
T Consensus 205 l~~lA~~~~~S--~---~~l~r~Fk~~~------G~t~~~yi~~~Rl~~A~~lL~~t~~sI~eIA~~~GF~s~s~Fsr~F 273 (287)
T TIGR02297 205 LPEYADRLGIS--E---SRLNDICRRFS------ALSPKRLIIERVMQEARRLLLFTQHSINQIAYDLGYKDPAYFARFF 273 (287)
T ss_pred HHHHHHHHCCC--H---HHHHHHHHHHh------CCCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHhCCCCHHHHHHHH
Confidence 44466666665 2 22233444433 3332 23333444455553 3566788888888874 566677776
Q ss_pred HHH
Q 009187 155 LQL 157 (540)
Q Consensus 155 ~~L 157 (540)
++.
T Consensus 274 Kk~ 276 (287)
T TIGR02297 274 QKE 276 (287)
T ss_pred HHH
Confidence 654
No 299
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=28.18 E-value=33 Score=34.11 Aligned_cols=25 Identities=24% Similarity=0.687 Sum_probs=20.5
Q ss_pred CCCCCCCC--CeeeecCCCceecCccc
Q 009187 3 WCSSCARH--VTGHRPYDSQLCCDRCG 27 (540)
Q Consensus 3 ~Cp~Cgs~--~iv~D~~~G~~VCt~CG 27 (540)
.|-.||.. ...++...|-.+|..|+
T Consensus 151 ~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 151 HCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred hHhcCCCCCCceEEecccCCccccccc
Confidence 59999976 24567789999999998
No 300
>PF13463 HTH_27: Winged helix DNA-binding domain; PDB: 3GFL_A 2YR2_B 3GFM_A 3GFJ_A 3GF2_A 3GEZ_A 2GXG_A 3GFI_A 2EB7_A.
Probab=28.11 E-value=1.2e+02 Score=23.42 Aligned_cols=32 Identities=16% Similarity=0.232 Sum_probs=24.2
Q ss_pred hcCCCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 009187 129 QKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (540)
Q Consensus 129 ~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~ 160 (540)
..+-+.++.+|++.++++...+.+..++|.+.
T Consensus 14 ~~~~~~t~~~l~~~~~~~~~~vs~~i~~L~~~ 45 (68)
T PF13463_consen 14 HSDGPMTQSDLAERLGISKSTVSRIIKKLEEK 45 (68)
T ss_dssp --TS-BEHHHHHHHTT--HHHHHHHHHHHHHT
T ss_pred ccCCCcCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 56778899999999999999999988888774
No 301
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=28.10 E-value=2.7e+02 Score=23.70 Aligned_cols=71 Identities=8% Similarity=0.155 Sum_probs=38.9
Q ss_pred HHHHHHHhCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCCHHHHHHHhC-cCHHHHHHHHHH
Q 009187 78 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLN-INVYELGAVYLQ 156 (540)
Q Consensus 78 I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~prtL~DIs~vl~-V~~~~Lgr~~~~ 156 (540)
+.++|..++++ . .+-.++|+......+..--....+..|+-.+ .....++.+||..+| -+...+.+.|++
T Consensus 24 ~~~lA~~~~~S--~---~~l~r~f~~~~g~s~~~~i~~~Rl~~a~~~L----~~~~~~i~~iA~~~Gf~~~s~f~~~Fk~ 94 (107)
T PRK10219 24 IDVVAKKSGYS--K---WYLQRMFRTVTHQTLGDYIRQRRLLLAAVEL----RTTERPIFDIAMDLGYVSQQTFSRVFRR 94 (107)
T ss_pred HHHHHHHHCCC--H---HHHHHHHHHHHCcCHHHHHHHHHHHHHHHHH----HccCCCHHHHHHHHCCCCHHHHHHHHHH
Confidence 66778888887 2 2334455554333322211111222222222 334578999999998 467777777765
Q ss_pred H
Q 009187 157 L 157 (540)
Q Consensus 157 L 157 (540)
.
T Consensus 95 ~ 95 (107)
T PRK10219 95 Q 95 (107)
T ss_pred H
Confidence 5
No 302
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=28.04 E-value=5.9e+02 Score=25.06 Aligned_cols=22 Identities=5% Similarity=0.176 Sum_probs=20.3
Q ss_pred CCCCHHHHHHHHcccHHHHhhh
Q 009187 233 LKFSKSDIIEDFMARKKELHEG 254 (540)
Q Consensus 233 ~~~t~~eI~~~~~~~~~ti~~~ 254 (540)
...|+++|++.++++..++++.
T Consensus 195 ~~~t~~EIA~~lgis~~~V~q~ 216 (238)
T TIGR02393 195 RPHTLEEVGKEFNVTRERIRQI 216 (238)
T ss_pred CCccHHHHHHHHCCCHHHHHHH
Confidence 5799999999999999998888
No 303
>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=27.96 E-value=80 Score=23.24 Aligned_cols=24 Identities=8% Similarity=-0.025 Sum_probs=20.6
Q ss_pred cCCCCCHHHHHHHHcccHHHHhhh
Q 009187 231 HGLKFSKSDIIEDFMARKKELHEG 254 (540)
Q Consensus 231 ~g~~~t~~eI~~~~~~~~~ti~~~ 254 (540)
+....|..+|++.++++..++++.
T Consensus 17 y~~~~t~~eIa~~lg~s~~~V~~~ 40 (50)
T PF04545_consen 17 YFEGLTLEEIAERLGISRSTVRRI 40 (50)
T ss_dssp HTST-SHHHHHHHHTSCHHHHHHH
T ss_pred hcCCCCHHHHHHHHCCcHHHHHHH
Confidence 367899999999999999999877
No 304
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=27.93 E-value=3.1e+02 Score=27.67 Aligned_cols=41 Identities=15% Similarity=0.060 Sum_probs=32.5
Q ss_pred hhHHHHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHH
Q 009187 115 TEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYL 155 (540)
Q Consensus 115 ~~~vaAACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~ 155 (540)
...+..++-||.-....-..++.+||..+++++..|.+.|+
T Consensus 196 ~~~l~~~~~~I~~~l~~~~ls~~~lA~~~giS~r~L~r~Fk 236 (302)
T PRK09685 196 ERQFQKVVALIDQSIQEEILRPEWIAGELGISVRSLYRLFA 236 (302)
T ss_pred HHHHHHHHHHHHHhcCCCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34455677777776665558999999999999999988875
No 305
>PRK12366 replication factor A; Reviewed
Probab=27.84 E-value=28 Score=40.17 Aligned_cols=24 Identities=33% Similarity=0.948 Sum_probs=19.6
Q ss_pred CCCCCCCCCeeeecCCCceecCcccce
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~V 29 (540)
.||.|+...+ + ..|.+.|..||.+
T Consensus 534 aCp~CnkKv~--~-~~g~~~C~~c~~~ 557 (637)
T PRK12366 534 LCPNCRKRVE--E-VDGEYICEFCGEV 557 (637)
T ss_pred cccccCeEeE--c-CCCcEECCCCCCC
Confidence 5999988632 2 4799999999998
No 306
>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=27.59 E-value=33 Score=29.56 Aligned_cols=27 Identities=22% Similarity=0.453 Sum_probs=16.9
Q ss_pred CCCCCCCCC--CeeeecCCCceecCcccc
Q 009187 2 VWCSSCARH--VTGHRPYDSQLCCDRCGK 28 (540)
Q Consensus 2 ~~Cp~Cgs~--~iv~D~~~G~~VCt~CG~ 28 (540)
..||.|+.. .+.+++..|...|-.||.
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 359999864 567778889999999995
No 307
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=27.52 E-value=22 Score=27.26 Aligned_cols=27 Identities=26% Similarity=0.573 Sum_probs=18.4
Q ss_pred CCCCCCCCCee---eecCCCceecCccccee
Q 009187 3 WCSSCARHVTG---HRPYDSQLCCDRCGKVL 30 (540)
Q Consensus 3 ~Cp~Cgs~~iv---~D~~~G~~VCt~CG~Vl 30 (540)
.|+-||...-. +.-.+| +||.+|--=+
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 49999986322 224578 7999998544
No 308
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=27.39 E-value=34 Score=30.44 Aligned_cols=32 Identities=13% Similarity=0.338 Sum_probs=23.1
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceeccccc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNF 35 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~~I 35 (540)
.|++||...+++-.= +.-.|..||..-.+..+
T Consensus 44 ~C~~Cg~~~~~~~SC-k~R~CP~C~~~~~~~W~ 75 (111)
T PF14319_consen 44 RCEDCGHEKIVYNSC-KNRHCPSCQAKATEQWI 75 (111)
T ss_pred ecCCCCceEEecCcc-cCcCCCCCCChHHHHHH
Confidence 599999887766543 44499999998665443
No 309
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=27.36 E-value=2.5e+02 Score=25.04 Aligned_cols=71 Identities=7% Similarity=0.097 Sum_probs=40.1
Q ss_pred HHHHHHHhCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCCHHHHHHHhC-cCHHHHHHHHHH
Q 009187 78 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLN-INVYELGAVYLQ 156 (540)
Q Consensus 78 I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~prtL~DIs~vl~-V~~~~Lgr~~~~ 156 (540)
|.++|..+|++ . .+-.++|+......+..-.....+-.|+-++ .....++.+||..+| -+...+.+.|++
T Consensus 28 l~~lA~~~g~S--~---~~l~r~Fk~~~G~s~~~~l~~~Rl~~A~~~L----~~t~~~i~eIA~~~Gf~s~s~F~r~Fkk 98 (127)
T PRK11511 28 LEKVSERSGYS--K---WHLQRMFKKETGHSLGQYIRSRKMTEIAQKL----KESNEPILYLAERYGFESQQTLTRTFKN 98 (127)
T ss_pred HHHHHHHHCcC--H---HHHHHHHHHHHCcCHHHHHHHHHHHHHHHHH----HcCCCCHHHHHHHhCCCCHHHHHHHHHH
Confidence 56677777887 2 2334456665443332221112222223222 234578999999998 567778777765
Q ss_pred H
Q 009187 157 L 157 (540)
Q Consensus 157 L 157 (540)
.
T Consensus 99 ~ 99 (127)
T PRK11511 99 Y 99 (127)
T ss_pred H
Confidence 5
No 310
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=27.27 E-value=25 Score=42.33 Aligned_cols=43 Identities=26% Similarity=0.348 Sum_probs=34.7
Q ss_pred hccCCCCCCHHHHHHHHHHhcccccccCHHHHhhhhCCCCccc
Q 009187 481 AKNSGPAQTALEATRRMLTKKRLSSKINYDVLEKLFDDSVCLY 523 (540)
Q Consensus 481 ~~~~~~a~ta~EA~~~ml~~K~~S~KINYdvl~~L~~~~~~~~ 523 (540)
-++++|+=|..+..+..-.+=+||..--+.+..+||..--++|
T Consensus 891 ~~~PlPPyTTDt~L~dAs~~L~lsa~~~M~iaQdLFE~GlITY 933 (1187)
T COG1110 891 EKNPLPPYTTDTMLRDASRRLRLSADETMQIAQDLFEGGLITY 933 (1187)
T ss_pred ccCCCCCcCcchHHHHHHHHhCCChhHHHHHHHHHHhccceEE
Confidence 3578899999888887777779999888999999998754443
No 311
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=27.16 E-value=1.9e+02 Score=28.21 Aligned_cols=29 Identities=17% Similarity=0.304 Sum_probs=25.6
Q ss_pred CCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 009187 132 KPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (540)
Q Consensus 132 ~prtL~DIs~vl~V~~~~Lgr~~~~L~~~ 160 (540)
+|.+..|||+.+|++..++.|+.++|.+.
T Consensus 172 i~~t~~~iA~~lG~tretvsR~l~~L~~~ 200 (236)
T PRK09392 172 LPYEKRVLASYLGMTPENLSRAFAALASH 200 (236)
T ss_pred eeCCHHHHHHHhCCChhHHHHHHHHHHhC
Confidence 47788999999999999999998887764
No 312
>PRK07218 replication factor A; Provisional
Probab=27.01 E-value=31 Score=37.82 Aligned_cols=31 Identities=19% Similarity=0.430 Sum_probs=20.4
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceecccccccccccc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFV 42 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~~Ids~~ef~ 42 (540)
.||.|+... ...+|..||.| +...+.-.-|.
T Consensus 299 rCP~C~r~v-------~~~~C~~hG~v--e~~~dlrik~v 329 (423)
T PRK07218 299 RCPECGRVI-------QKGQCRSHGAV--EGEDDLRIKAI 329 (423)
T ss_pred cCcCccccc-------cCCcCCCCCCc--CCeeeeEEEEE
Confidence 699999863 22699999998 33344433343
No 313
>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=27.00 E-value=1e+02 Score=22.92 Aligned_cols=27 Identities=7% Similarity=0.038 Sum_probs=19.4
Q ss_pred CCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 009187 134 FLLIDFSNYLNINVYELGAVYLQLCQV 160 (540)
Q Consensus 134 rtL~DIs~vl~V~~~~Lgr~~~~L~~~ 160 (540)
.+..|||..+++++..+...+..-.+.
T Consensus 27 ~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 27 MSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp --HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 467899999999999998776665543
No 314
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=26.97 E-value=1.2e+02 Score=33.17 Aligned_cols=71 Identities=17% Similarity=0.217 Sum_probs=47.5
Q ss_pred hHHHHHHHHHHHHHHhCcccCCCchhHHHH--HHHHHHHHhcCCCCCHHHHHHHh-CcCHHHHHHHHHHHHHHhhc
Q 009187 91 DEIVHVAKRFYGIAVARNFTKGRRTEQVQA--SCLYLACRQKSKPFLLIDFSNYL-NINVYELGAVYLQLCQVLYI 163 (540)
Q Consensus 91 ~~i~e~A~~iyk~a~~~~~~rGR~~~~vaA--ACLYiACR~e~~prtL~DIs~vl-~V~~~~Lgr~~~~L~~~L~i 163 (540)
+.|++..+.+|..-...=..++|+...+.| .+.|++-+.-+ .++.+|+..+ +-+..++..+++++.+.+.-
T Consensus 360 ~~i~~~v~~~~~i~~~~l~~~~R~~~~~~aR~iamyl~~~~~~--~s~~~Ig~~fg~rdhstV~~a~~~i~~~~~~ 433 (450)
T PRK00149 360 ENIQKVVAEYYNIKVSDLKSKSRTRNIARPRQIAMYLAKELTD--LSLPEIGRAFGGRDHTTVLHAVRKIEKLLEE 433 (450)
T ss_pred HHHHHHHHHHcCCCHHHHhCCCCCcccChHHHHHHHHHHHhcC--CCHHHHHHHcCCCCHhHHHHHHHHHHHHHHh
Confidence 455555555555433332333444333333 67788766555 5899999999 59999999999999997753
No 315
>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=26.66 E-value=45 Score=28.69 Aligned_cols=14 Identities=29% Similarity=0.887 Sum_probs=10.4
Q ss_pred ceecCcccceeccc
Q 009187 20 QLCCDRCGKVLEDH 33 (540)
Q Consensus 20 ~~VCt~CG~Vlee~ 33 (540)
-.+|..||.+.-+.
T Consensus 35 a~~C~~CGe~y~~d 48 (89)
T TIGR03829 35 SISCSHCGMEYQDD 48 (89)
T ss_pred cccccCCCcEeecH
Confidence 46899999876443
No 316
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=26.58 E-value=1.2e+02 Score=22.40 Aligned_cols=26 Identities=8% Similarity=0.004 Sum_probs=24.0
Q ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHH
Q 009187 135 LLIDFSNYLNINVYELGAVYLQLCQV 160 (540)
Q Consensus 135 tL~DIs~vl~V~~~~Lgr~~~~L~~~ 160 (540)
+..++++.++++...+.+.+..|.+.
T Consensus 22 s~~~la~~~~vs~~tv~~~l~~L~~~ 47 (60)
T smart00345 22 SERELAAQLGVSRTTVREALSRLEAE 47 (60)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 89999999999999999999988874
No 317
>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=26.41 E-value=35 Score=28.05 Aligned_cols=26 Identities=19% Similarity=0.510 Sum_probs=15.5
Q ss_pred CCCCCCCCCCeeeecCCCceecCccccee
Q 009187 2 VWCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vl 30 (540)
..||.|... +.+ ..|.+.|..|+.-.
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 369999986 444 35899999888754
No 318
>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=26.34 E-value=80 Score=24.81 Aligned_cols=37 Identities=22% Similarity=0.183 Sum_probs=28.7
Q ss_pred HHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 009187 123 LYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (540)
Q Consensus 123 LYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~ 160 (540)
+|.+.- ..-+.|..||+..++++...+.++...|.+.
T Consensus 13 vy~~Ll-~~~~~t~~eIa~~l~i~~~~v~~~L~~L~~~ 49 (68)
T PF01978_consen 13 VYLALL-KNGPATAEEIAEELGISRSTVYRALKSLEEK 49 (68)
T ss_dssp HHHHHH-HHCHEEHHHHHHHHTSSHHHHHHHHHHHHHT
T ss_pred HHHHHH-HcCCCCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 344433 4457899999999999999999888887763
No 319
>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=26.32 E-value=41 Score=33.27 Aligned_cols=26 Identities=19% Similarity=0.501 Sum_probs=19.6
Q ss_pred CCCCCCCC--CeeeecCCCceecCcccc
Q 009187 3 WCSSCARH--VTGHRPYDSQLCCDRCGK 28 (540)
Q Consensus 3 ~Cp~Cgs~--~iv~D~~~G~~VCt~CG~ 28 (540)
.|..||.. ...++...|-.+|..|+.
T Consensus 149 ~C~~cg~~~~~~~fs~~~gg~~C~~c~~ 176 (241)
T TIGR00613 149 KCAVCGSKEDLIYFSMTYGGALCRQCGE 176 (241)
T ss_pred ccCCCCCcCCCceEchhcCeEEChhhCc
Confidence 58888863 245677789999999876
No 320
>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=26.12 E-value=1.8e+02 Score=21.83 Aligned_cols=37 Identities=11% Similarity=0.088 Sum_probs=27.6
Q ss_pred HHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 009187 122 CLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (540)
Q Consensus 122 CLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~ 160 (540)
+|++..... +.++.+|+..++++...+.+...+|.+.
T Consensus 8 iL~~l~~~~--~~~~~~la~~~~~~~~~~t~~i~~L~~~ 44 (59)
T PF01047_consen 8 ILRILYENG--GITQSELAEKLGISRSTVTRIIKRLEKK 44 (59)
T ss_dssp HHHHHHHHS--SEEHHHHHHHHTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHcC--CCCHHHHHHHHCCChhHHHHHHHHHHHC
Confidence 344444433 3899999999999999999998888774
No 321
>PRK08197 threonine synthase; Validated
Probab=25.98 E-value=36 Score=36.72 Aligned_cols=25 Identities=32% Similarity=0.642 Sum_probs=18.7
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceec
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vle 31 (540)
.|..||.. ++.......| .||-.++
T Consensus 9 ~C~~Cg~~---~~~~~~~~~C-~cg~~l~ 33 (394)
T PRK08197 9 ECSKCGET---YDADQVHNLC-KCGKPLL 33 (394)
T ss_pred EECCCCCC---CCCCCcceec-CCCCeeE
Confidence 69999986 3444456889 8997765
No 322
>COG1773 Rubredoxin [Energy production and conversion]
Probab=25.77 E-value=42 Score=26.27 Aligned_cols=21 Identities=24% Similarity=0.436 Sum_probs=11.5
Q ss_pred CCCCCCCCeeeecCCCceecCccc
Q 009187 4 CSSCARHVTGHRPYDSQLCCDRCG 27 (540)
Q Consensus 4 Cp~Cgs~~iv~D~~~G~~VCt~CG 27 (540)
|..||- +||++.|+-.|..|+
T Consensus 6 C~~CG~---vYd~e~Gdp~~gi~p 26 (55)
T COG1773 6 CSVCGY---VYDPEKGDPRCGIAP 26 (55)
T ss_pred ecCCce---EeccccCCccCCCCC
Confidence 666663 455555555555544
No 323
>PRK15340 transcriptional regulator InvF; Provisional
Probab=25.69 E-value=3e+02 Score=27.48 Aligned_cols=71 Identities=11% Similarity=0.059 Sum_probs=39.1
Q ss_pred HHHHHHHhCCCCchHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCCHHHHHHHhCc-CHHHHHHHHHH
Q 009187 78 MRQMKNALNIGESDEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNI-NVYELGAVYLQ 156 (540)
Q Consensus 78 I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~prtL~DIs~vl~V-~~~~Lgr~~~~ 156 (540)
+.++|..+|++ . .+-.++|+..+......--....+..|++- ......++.|||..+|. +...+.+.|++
T Consensus 128 leeLA~~~gvS--~---r~f~RlFk~~~G~tpk~yl~~~Rl~~all~----L~~s~~sItdIA~~~GY~d~ShFsr~FKk 198 (216)
T PRK15340 128 MRMLGEDYGVS--Y---THFRRLCSRALGGKAKSELRNWRMAQSLLN----SVEGHENITQLAVNHGYSSPSHFSSEIKE 198 (216)
T ss_pred HHHHHHHHCcC--H---HHHHHHHHHHHCcCHHHHHHHHHHHHHHHh----hhcCCCCHHHHHHHhCCCCHHHHHHHHHH
Confidence 56677777777 2 333455666554443211111122223221 12346788999988884 67777777665
Q ss_pred H
Q 009187 157 L 157 (540)
Q Consensus 157 L 157 (540)
.
T Consensus 199 ~ 199 (216)
T PRK15340 199 L 199 (216)
T ss_pred H
Confidence 4
No 324
>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=25.66 E-value=21 Score=31.72 Aligned_cols=29 Identities=14% Similarity=0.336 Sum_probs=16.0
Q ss_pred CCCCCCCCCeeee-cCCCceecCcccceec
Q 009187 3 WCSSCARHVTGHR-PYDSQLCCDRCGKVLE 31 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D-~~~G~~VCt~CG~Vle 31 (540)
.|-.||+....|= -.-|..||..|.-|.-
T Consensus 15 ~CaDCg~~~p~w~s~~~GiflC~~Cag~HR 44 (116)
T PF01412_consen 15 VCADCGAPNPTWASLNYGIFLCLECAGIHR 44 (116)
T ss_dssp B-TTT-SBS--EEETTTTEEE-HHHHHHHH
T ss_pred cCCCCCCCCCCEEEeecChhhhHHHHHHHH
Confidence 5888887655443 2358888888887654
No 325
>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=25.34 E-value=34 Score=35.31 Aligned_cols=29 Identities=24% Similarity=0.494 Sum_probs=13.1
Q ss_pred CCCCCCCCCe-----e-ee--cCCCceecCcccceec
Q 009187 3 WCSSCARHVT-----G-HR--PYDSQLCCDRCGKVLE 31 (540)
Q Consensus 3 ~Cp~Cgs~~i-----v-~D--~~~G~~VCt~CG~Vle 31 (540)
.||+||.... . .+ +.-.-.+|..||.-+-
T Consensus 213 ~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK 249 (290)
T PF04216_consen 213 KCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLK 249 (290)
T ss_dssp S-TTT---SS-EEE--------SEEEEEETTTTEEEE
T ss_pred CCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHH
Confidence 5888887521 1 11 1223567888887764
No 326
>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=25.32 E-value=1.1e+02 Score=24.39 Aligned_cols=32 Identities=9% Similarity=0.117 Sum_probs=22.3
Q ss_pred HhcCCCCCHHHHHHHhCcC-HHHHHHHHHHHHH
Q 009187 128 RQKSKPFLLIDFSNYLNIN-VYELGAVYLQLCQ 159 (540)
Q Consensus 128 R~e~~prtL~DIs~vl~V~-~~~Lgr~~~~L~~ 159 (540)
..+|.|-|++||++.++++ ...+......|.+
T Consensus 20 ~~~G~~Pt~rEIa~~~g~~S~~tv~~~L~~Le~ 52 (65)
T PF01726_consen 20 EENGYPPTVREIAEALGLKSTSTVQRHLKALER 52 (65)
T ss_dssp HHHSS---HHHHHHHHTSSSHHHHHHHHHHHHH
T ss_pred HHcCCCCCHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 4689999999999999987 7777666555544
No 327
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=25.26 E-value=40 Score=36.84 Aligned_cols=32 Identities=16% Similarity=0.506 Sum_probs=23.8
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceecccccc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFS 36 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~~Id 36 (540)
.||.||.+.- ....|.+-|..||+-..+..+.
T Consensus 352 ~Cp~Cg~~m~--S~G~~g~rC~kCg~~~~~~~~~ 383 (421)
T COG1571 352 VCPRCGGRMK--SAGRNGFRCKKCGTRARETLIK 383 (421)
T ss_pred CCCccCCchh--hcCCCCcccccccccCCccccc
Confidence 6999999732 1234478999999998876654
No 328
>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=25.20 E-value=25 Score=27.92 Aligned_cols=24 Identities=17% Similarity=0.700 Sum_probs=17.0
Q ss_pred CCCCCCCCCeeeecCCCceecC-cccceec
Q 009187 3 WCSSCARHVTGHRPYDSQLCCD-RCGKVLE 31 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt-~CG~Vle 31 (540)
.||+||.... ....+|+ .|+.+..
T Consensus 5 HC~~CG~~Ip-----~~~~fCS~~C~~~~~ 29 (59)
T PF09889_consen 5 HCPVCGKPIP-----PDESFCSPKCREEYR 29 (59)
T ss_pred cCCcCCCcCC-----cchhhhCHHHHHHHH
Confidence 5999997621 2588996 8887654
No 329
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=25.12 E-value=1.1e+02 Score=23.60 Aligned_cols=31 Identities=19% Similarity=0.228 Sum_probs=22.7
Q ss_pred CCCHHHHHHHhCcCHHHHHHHHHHHHHHhhccccc
Q 009187 133 PFLLIDFSNYLNINVYELGAVYLQLCQVLYIADES 167 (540)
Q Consensus 133 prtL~DIs~vl~V~~~~Lgr~~~~L~~~L~i~~~p 167 (540)
..++.|.|..+||+...| +++|+.+||.-.|
T Consensus 15 hlp~~eAA~~Lgv~~T~L----Kr~CR~~GI~RWP 45 (52)
T PF02042_consen 15 HLPIKEAAKELGVSVTTL----KRRCRRLGIPRWP 45 (52)
T ss_pred CCCHHHHHHHhCCCHHHH----HHHHHHcCCCCCC
Confidence 456778888888887666 5667888886555
No 330
>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=25.05 E-value=34 Score=32.05 Aligned_cols=15 Identities=33% Similarity=0.809 Sum_probs=13.2
Q ss_pred CCCceecCcccceec
Q 009187 17 YDSQLCCDRCGKVLE 31 (540)
Q Consensus 17 ~~G~~VCt~CG~Vle 31 (540)
.-|.+||.+||..+.
T Consensus 109 g~G~l~C~~Cg~~~~ 123 (146)
T PF07295_consen 109 GPGTLVCENCGHEVE 123 (146)
T ss_pred cCceEecccCCCEEE
Confidence 579999999999875
No 331
>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=24.65 E-value=78 Score=23.65 Aligned_cols=24 Identities=4% Similarity=0.225 Sum_probs=20.1
Q ss_pred cCCCCCHHHHHHHHcccHHHHhhh
Q 009187 231 HGLKFSKSDIIEDFMARKKELHEG 254 (540)
Q Consensus 231 ~g~~~t~~eI~~~~~~~~~ti~~~ 254 (540)
++-.+|..++|+.++++..||++.
T Consensus 12 ~~~~it~~eLa~~l~vS~rTi~~~ 35 (55)
T PF08279_consen 12 SKEPITAKELAEELGVSRRTIRRD 35 (55)
T ss_dssp TTTSBEHHHHHHHCTS-HHHHHHH
T ss_pred cCCCcCHHHHHHHhCCCHHHHHHH
Confidence 344599999999999999999987
No 332
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=24.64 E-value=50 Score=38.77 Aligned_cols=26 Identities=27% Similarity=0.571 Sum_probs=21.0
Q ss_pred CCCCCCCCCeeeecCCCceecCcccce
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~V 29 (540)
.||+|.... ++-..+|.+.|-.||..
T Consensus 446 ~Cp~Cd~~l-t~H~~~~~L~CH~Cg~~ 471 (730)
T COG1198 446 ECPNCDSPL-TLHKATGQLRCHYCGYQ 471 (730)
T ss_pred cCCCCCcce-EEecCCCeeEeCCCCCC
Confidence 699998874 44456799999999997
No 333
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=24.61 E-value=50 Score=24.38 Aligned_cols=23 Identities=30% Similarity=0.564 Sum_probs=17.5
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceecc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee 32 (540)
+|..|+... ...+|-.||.|.--
T Consensus 1 ~C~~C~~~~-------~l~~CL~C~~~~c~ 23 (50)
T smart00290 1 RCSVCGTIE-------NLWLCLTCGQVGCG 23 (50)
T ss_pred CcccCCCcC-------CeEEecCCCCcccC
Confidence 588999642 37799999998753
No 334
>PRK15435 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional
Probab=24.58 E-value=1.9e+02 Score=30.85 Aligned_cols=50 Identities=12% Similarity=0.333 Sum_probs=37.0
Q ss_pred hHHHHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHHHhhccccccccccCChhhHHHH
Q 009187 116 EQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHK 181 (540)
Q Consensus 116 ~~vaAACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~L~i~~~p~~~~~~dP~~~I~R 181 (540)
..+..++-||-- +.+.++.++|..++++...|.+.|++. +| +.|..|+.+
T Consensus 85 ~~i~~a~~~I~~---~~~lsl~eLA~~lG~S~~~L~R~Fkk~---~G----------~TP~~yl~~ 134 (353)
T PRK15435 85 DKITHACRLLEQ---ETPVTLEALADQVAMSPFHLHRLFKAT---TG----------MTPKAWQQA 134 (353)
T ss_pred HHHHHHHHHHHh---CCCCCHHHHHHHHCCCHHHHHHHHHHH---HC----------cCHHHHHHH
Confidence 346666667633 568999999999999999999887765 33 446777654
No 335
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=24.57 E-value=2.3e+02 Score=28.63 Aligned_cols=25 Identities=4% Similarity=-0.013 Sum_probs=13.5
Q ss_pred CCCHHHHHHHhC-cCHHHHHHHHHHH
Q 009187 133 PFLLIDFSNYLN-INVYELGAVYLQL 157 (540)
Q Consensus 133 prtL~DIs~vl~-V~~~~Lgr~~~~L 157 (540)
..++.|||...| -+...+.++|++.
T Consensus 264 ~~sI~eIA~~~GF~d~s~Fsr~Fkk~ 289 (302)
T PRK09685 264 DEKITSIAYKWGFSDSSHFSTAFKQR 289 (302)
T ss_pred CCCHHHHHHHhCCCCHHHHHHHHHHH
Confidence 345666666665 3455555555543
No 336
>PRK13500 transcriptional activator RhaR; Provisional
Probab=24.48 E-value=5.8e+02 Score=26.24 Aligned_cols=39 Identities=21% Similarity=0.179 Sum_probs=28.8
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHH
Q 009187 118 VQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 157 (540)
Q Consensus 118 vaAACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L 157 (540)
+...+-||--. -..++++.++|+.+++++..|.+.|++.
T Consensus 208 l~~i~~yI~~~-~~e~isl~~lA~~~~iS~~~L~r~FK~~ 246 (312)
T PRK13500 208 LDKLITRLAAS-LKSPFALDKFCDEASCSERVLRQQFRQQ 246 (312)
T ss_pred HHHHHHHHHHc-ccCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 44444454432 3557999999999999999999887754
No 337
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=24.23 E-value=1.1e+02 Score=22.35 Aligned_cols=21 Identities=10% Similarity=0.102 Sum_probs=16.9
Q ss_pred CCCHHHHHHHHcccHHHHhhh
Q 009187 234 KFSKSDIIEDFMARKKELHEG 254 (540)
Q Consensus 234 ~~t~~eI~~~~~~~~~ti~~~ 254 (540)
..|.++|++.++++..|+.+.
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w 37 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRW 37 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHH
Confidence 789999999999999999887
No 338
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=24.19 E-value=39 Score=21.90 Aligned_cols=10 Identities=40% Similarity=0.953 Sum_probs=7.7
Q ss_pred CCCCCCCCCC
Q 009187 1 MVWCSSCARH 10 (540)
Q Consensus 1 m~~Cp~Cgs~ 10 (540)
|+.||.||..
T Consensus 2 l~~C~~CgR~ 11 (25)
T PF13913_consen 2 LVPCPICGRK 11 (25)
T ss_pred CCcCCCCCCE
Confidence 5678888875
No 339
>smart00351 PAX Paired Box domain.
Probab=24.08 E-value=4e+02 Score=23.89 Aligned_cols=62 Identities=8% Similarity=0.125 Sum_probs=36.8
Q ss_pred HHHHHHHHhCCCCchHHHHHHHHHHHHHHhCcccC-----CCchhHHH-HHHHH-HHHHhcCCCCCHHHHHHHh
Q 009187 77 DMRQMKNALNIGESDEIVHVAKRFYGIAVARNFTK-----GRRTEQVQ-ASCLY-LACRQKSKPFLLIDFSNYL 143 (540)
Q Consensus 77 ~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~~~~~~r-----GR~~~~va-AACLY-iACR~e~~prtL~DIs~vl 143 (540)
-+.++|..|+++ .. ++..+.+++.+.|.+. |+++..+. ....| +..+.++-..++.++++.+
T Consensus 35 s~~~iA~~~gvs--~~---tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~p~~t~~el~~~L 103 (125)
T smart00351 35 RPCDISRQLCVS--HG---CVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQENPGIFAWEIRDRL 103 (125)
T ss_pred CHHHHHHHHCcC--HH---HHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHCCCCCHHHHHHHH
Confidence 478899999999 44 4455566655555442 32333222 22223 3356666677888888765
No 340
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=23.91 E-value=5.9e+02 Score=27.95 Aligned_cols=46 Identities=22% Similarity=0.202 Sum_probs=35.3
Q ss_pred ccccccCCChhhHHHH---HHHHHHHhcCCCCCHHHHHHHHcccHHHHhhh
Q 009187 207 RDWITTGRKPSGLCGA---ALYVSALTHGLKFSKSDIIEDFMARKKELHEG 254 (540)
Q Consensus 207 ~~~i~tGR~P~~IAaA---ALylAa~~~g~~~t~~eI~~~~~~~~~ti~~~ 254 (540)
...|..+++-..|+-| |.|++-.+.+. |..+|+..||.+.+|+-..
T Consensus 359 ~~~l~s~~R~~~i~~aR~iamyl~r~~~~~--s~~~Ig~~fgr~hstV~~a 407 (440)
T PRK14088 359 REEILSNSRNVKALLARRIGMYVAKNYLGS--SLRTIAEKFNRSHPVVVDS 407 (440)
T ss_pred HHHHhCCCCCccccHHHHHHHHHHHHHhCC--CHHHHHHHhCCCHHHHHHH
Confidence 4456667777788888 99999776555 9999999999777766554
No 341
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=23.79 E-value=1.7e+02 Score=24.30 Aligned_cols=23 Identities=13% Similarity=0.203 Sum_probs=20.7
Q ss_pred CCCCHHHHHHHHcccHHHHhhhh
Q 009187 233 LKFSKSDIIEDFMARKKELHEGV 255 (540)
Q Consensus 233 ~~~t~~eI~~~~~~~~~ti~~~~ 255 (540)
...|++|||+.+++++.|+++..
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l 53 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHL 53 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHH
Confidence 45799999999999999999993
No 342
>PRK13502 transcriptional activator RhaR; Provisional
Probab=23.75 E-value=3.5e+02 Score=27.06 Aligned_cols=37 Identities=11% Similarity=0.081 Sum_probs=22.0
Q ss_pred HHHHHHHHhc-CCCCCHHHHHHHhC-cCHHHHHHHHHHH
Q 009187 121 SCLYLACRQK-SKPFLLIDFSNYLN-INVYELGAVYLQL 157 (540)
Q Consensus 121 ACLYiACR~e-~~prtL~DIs~vl~-V~~~~Lgr~~~~L 157 (540)
.-|=.|+++- ....++.|||..+| -+...+.+.|++.
T Consensus 228 ~Rl~~A~~lL~~t~~sI~eIA~~~GF~d~s~F~r~FKk~ 266 (282)
T PRK13502 228 VRICHAQYLLQHSPLMISEISMQCGFEDSNYFSVVFTRE 266 (282)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHcCCCCHHHHHHHHHHH
Confidence 3334444443 34567778877777 3566677666654
No 343
>PRK06260 threonine synthase; Validated
Probab=23.74 E-value=41 Score=36.28 Aligned_cols=26 Identities=31% Similarity=0.768 Sum_probs=20.0
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceec
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vle 31 (540)
.|..||.. ++.......|..||-.|+
T Consensus 5 ~C~~cg~~---~~~~~~~~~Cp~cg~~l~ 30 (397)
T PRK06260 5 KCIECGKE---YDPDEIIYTCPECGGLLE 30 (397)
T ss_pred EECCCCCC---CCCCCccccCCCCCCeEE
Confidence 69999986 444445678999998776
No 344
>PF14369 zf-RING_3: zinc-finger
Probab=23.65 E-value=50 Score=23.29 Aligned_cols=26 Identities=38% Similarity=0.902 Sum_probs=16.5
Q ss_pred CCCCCCCCCeeeecCCCceecCcccc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGK 28 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~ 28 (540)
+|=.|....-+.......+.|..|+-
T Consensus 4 wCh~C~~~V~~~~~~~~~~~CP~C~~ 29 (35)
T PF14369_consen 4 WCHQCNRFVRIAPSPDSDVACPRCHG 29 (35)
T ss_pred eCccCCCEeEeCcCCCCCcCCcCCCC
Confidence 68889887433323344556999973
No 345
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=23.59 E-value=5.6e+02 Score=25.79 Aligned_cols=89 Identities=8% Similarity=0.048 Sum_probs=66.3
Q ss_pred HHHHHHHHHHHHHHHHHhCCCCchHHHHHHHHHHHHHH-hCcccCCCchhHHHHHHHHHHHHhcCCCCCHHHHHHHhCcC
Q 009187 68 ERLMEKAFDDMRQMKNALNIGESDEIVHVAKRFYGIAV-ARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNIN 146 (540)
Q Consensus 68 er~L~~a~~~I~~ia~~L~Lp~~~~i~e~A~~iyk~a~-~~~~~rGR~~~~vaAACLYiACR~e~~prtL~DIs~vl~V~ 146 (540)
+.+|.+..++-..+...=+++ +.-+|....+..+.. ...+.+|-+...+-.-+-.+. ..+.++|..|++..++++
T Consensus 111 ~~aL~~y~~~r~~l~~~~~~s--Q~~lD~l~~~~~k~~~~~~LPkGi~~~Tl~~i~~~~~--~~~~~~Taeela~~~giS 186 (224)
T COG4565 111 QQALTRYRQKRHALESHQQLS--QKELDQLFNIQSKEQPPDDLPKGLDELTLQKVREALK--EPDQELTAEELAQALGIS 186 (224)
T ss_pred HHHHHHHHHHHHHHhhhcccC--HHHHHHHHhccccccCcccCCCCcCHHHHHHHHHHHh--CcCCccCHHHHHHHhCcc
Confidence 345555566666677777888 999999888875522 345678877766666666665 678999999999999999
Q ss_pred HHHHHHHHHHHHHH
Q 009187 147 VYELGAVYLQLCQV 160 (540)
Q Consensus 147 ~~~Lgr~~~~L~~~ 160 (540)
..+..|....|...
T Consensus 187 RvTaRRYLeyl~~~ 200 (224)
T COG4565 187 RVTARRYLEYLVSN 200 (224)
T ss_pred HHHHHHHHHHHHhc
Confidence 99998876666654
No 346
>PF13730 HTH_36: Helix-turn-helix domain
Probab=23.46 E-value=2e+02 Score=21.40 Aligned_cols=25 Identities=8% Similarity=0.017 Sum_probs=22.6
Q ss_pred CHHHHHHHhCcCHHHHHHHHHHHHH
Q 009187 135 LLIDFSNYLNINVYELGAVYLQLCQ 159 (540)
Q Consensus 135 tL~DIs~vl~V~~~~Lgr~~~~L~~ 159 (540)
+...|++.++++..+|.++...|.+
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKELEE 51 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 8999999999999999998887765
No 347
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=23.38 E-value=1.7e+02 Score=26.89 Aligned_cols=38 Identities=16% Similarity=0.204 Sum_probs=31.2
Q ss_pred HHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 009187 123 LYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (540)
Q Consensus 123 LYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~ 160 (540)
+|.+.=..+-|.|.-|||+.++.+..++.+..+.|...
T Consensus 32 v~~~LL~~~~~~tvdelae~lnr~rStv~rsl~~L~~~ 69 (126)
T COG3355 32 VYKALLEENGPLTVDELAEILNRSRSTVYRSLQNLLEA 69 (126)
T ss_pred HHHHHHhhcCCcCHHHHHHHHCccHHHHHHHHHHHHHc
Confidence 35555556789999999999999999998888887763
No 348
>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=23.26 E-value=49 Score=35.45 Aligned_cols=29 Identities=17% Similarity=0.557 Sum_probs=17.5
Q ss_pred CCCCCCCCC-C--eeeecCCC--ceecCcccceec
Q 009187 2 VWCSSCARH-V--TGHRPYDS--QLCCDRCGKVLE 31 (540)
Q Consensus 2 ~~Cp~Cgs~-~--iv~D~~~G--~~VCt~CG~Vle 31 (540)
..|+.||.- . +.+|.+.| .+.| .||...+
T Consensus 170 p~c~~cg~~~~~v~~~d~~~~~v~y~c-~cG~~g~ 203 (353)
T cd00674 170 PYCEKCGKDTTTVEAYDAKAGTVTYKC-ECGHEET 203 (353)
T ss_pred eecCCcCcceeEEEEEeCCCCeEEEEc-CCCCEEE
Confidence 468888853 2 23554444 6678 5887654
No 349
>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=23.10 E-value=80 Score=25.04 Aligned_cols=51 Identities=20% Similarity=0.237 Sum_probs=29.8
Q ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHhhccccccccccCChhhHHHHHHHhhCCCCCHHHHHHHHHHHHhhcccccccCC
Q 009187 135 LLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASMKRDWITTGR 214 (540)
Q Consensus 135 tL~DIs~vl~V~~~~Lgr~~~~L~~~L~i~~~p~~~~~~dP~~~I~Rf~~~L~~~~~~~V~~~A~~Iv~~m~~~~i~tGR 214 (540)
+-.|||+.++|+...|...+++ .. .-|..++.+++..++. .-+|+.+|.
T Consensus 14 ~~~~lA~~lgis~st~s~~~~~-------r~-------~~P~~~l~~ia~~~gv-----------------sl~WLltG~ 62 (66)
T PF07022_consen 14 SDKELAERLGISKSTLSNNWKK-------RG-------SIPAEWLIKIALETGV-----------------SLDWLLTGK 62 (66)
T ss_dssp SCHHHHCCTT--HHHHH-HHHH-------SS-------S--HHHHHHHHHHH--------------------HHHHHC-S
T ss_pred CHHHHHHHhCcCHHHhhHHHHh-------CC-------CCCHHHHHHHHHHHCc-----------------CHHHHHhCC
Confidence 5579999999999888732221 11 2368889999888874 135888887
Q ss_pred Ch
Q 009187 215 KP 216 (540)
Q Consensus 215 ~P 216 (540)
.|
T Consensus 63 g~ 64 (66)
T PF07022_consen 63 GE 64 (66)
T ss_dssp S-
T ss_pred CC
Confidence 65
No 350
>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=23.02 E-value=37 Score=26.44 Aligned_cols=20 Identities=15% Similarity=0.213 Sum_probs=13.8
Q ss_pred CCCCCCCCCeeeecCCCceecC
Q 009187 3 WCSSCARHVTGHRPYDSQLCCD 24 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt 24 (540)
.||.|++..+.++.. .++|+
T Consensus 16 ~Cp~C~~~~l~~~~~--~Y~C~ 35 (55)
T PF08063_consen 16 PCPKCKGGQLYFDGS--GYKCT 35 (55)
T ss_dssp --SSSSE-EEEEETT--EEEEE
T ss_pred CCCCCCCCeEEecCC--ccEeC
Confidence 699999988888753 78886
No 351
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=23.00 E-value=1.5e+02 Score=23.44 Aligned_cols=54 Identities=20% Similarity=0.091 Sum_probs=29.4
Q ss_pred HHhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHHHhhccccccccccCChhhHHHHHHHhhCC
Q 009187 127 CRQKSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLP 188 (540)
Q Consensus 127 CR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~L~i~~~p~~~~~~dP~~~I~Rf~~~L~~ 188 (540)
-.++....|+.|+|..+++++..|.. .+.=+++..| ..+=-..||..||..|++
T Consensus 4 ~~R~~~glsl~~va~~t~I~~~~l~a-----iE~~~~~~lp---~~~y~rg~lr~Ya~~Lgl 57 (62)
T PF13413_consen 4 EAREAKGLSLEDVAEETKISVSYLEA-----IENGDFDSLP---SPVYARGYLRKYARFLGL 57 (62)
T ss_dssp HHHHCTT--HHHHHHHCS--HHHHHH-----HHCT-GCCSS---SHHHHHHHHHHHHHHTT-
T ss_pred HHHHHcCCCHHHHHHHhCCCHHHHHH-----HHCcChhhCC---cHHHHHHHHHHHHHHhCc
Confidence 34567788999999999999877742 1222222222 001124678888888885
No 352
>PRK13502 transcriptional activator RhaR; Provisional
Probab=22.84 E-value=2.8e+02 Score=27.71 Aligned_cols=41 Identities=17% Similarity=0.067 Sum_probs=31.7
Q ss_pred hHHHHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHH
Q 009187 116 EQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 157 (540)
Q Consensus 116 ~~vaAACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L 157 (540)
..+..++-||.-.. ..+.++.++|..+++++..|.+.|++.
T Consensus 176 ~~~~~~~~~I~~~~-~~~~~~~~lA~~~~iS~~~L~r~fk~~ 216 (282)
T PRK13502 176 TLLDKLITALANSL-ECPFALDAFCQQEQCSERVLRQQFRAQ 216 (282)
T ss_pred HHHHHHHHHHHhcc-cCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 34566777777544 447999999999999999998877753
No 353
>PRK08173 DNA topoisomerase III; Validated
Probab=22.81 E-value=47 Score=39.79 Aligned_cols=25 Identities=20% Similarity=0.579 Sum_probs=18.3
Q ss_pred CCCCCCCCCeeeecCCCceecCccccee
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVL 30 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vl 30 (540)
.||.||+.. +. ..+.+.|++|+..+
T Consensus 626 ~CP~Cg~~~-~~--~~~~~~Cs~C~f~~ 650 (862)
T PRK08173 626 PCPNCGGVV-KE--NYRRFACTKCDFSI 650 (862)
T ss_pred cCCcccccc-cc--cCceeEcCCCCccc
Confidence 599999863 21 23459999999886
No 354
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=22.77 E-value=2.2e+02 Score=20.82 Aligned_cols=20 Identities=10% Similarity=-0.012 Sum_probs=18.6
Q ss_pred CCHHHHHHHHcccHHHHhhh
Q 009187 235 FSKSDIIEDFMARKKELHEG 254 (540)
Q Consensus 235 ~t~~eI~~~~~~~~~ti~~~ 254 (540)
.|+++||+.++++..|+..-
T Consensus 28 ~s~~~vA~~~~vs~~TV~ri 47 (52)
T PF13542_consen 28 RSFKDVARELGVSWSTVRRI 47 (52)
T ss_pred CCHHHHHHHHCCCHHHHHHH
Confidence 89999999999999998876
No 355
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=22.63 E-value=97 Score=28.30 Aligned_cols=26 Identities=15% Similarity=0.231 Sum_probs=24.5
Q ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHH
Q 009187 135 LLIDFSNYLNINVYELGAVYLQLCQV 160 (540)
Q Consensus 135 tL~DIs~vl~V~~~~Lgr~~~~L~~~ 160 (540)
|++++|..++|++-++.|+|..|.+.
T Consensus 37 SvRelA~~~~VNpnTv~raY~eLE~e 62 (125)
T COG1725 37 SVRELAKDLGVNPNTVQRAYQELERE 62 (125)
T ss_pred cHHHHHHHhCCCHHHHHHHHHHHHHC
Confidence 88999999999999999999999885
No 356
>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=22.61 E-value=1.8e+02 Score=21.15 Aligned_cols=29 Identities=10% Similarity=0.063 Sum_probs=21.8
Q ss_pred hcCCCCCHHHHHHHhCcCHHHHHHHHHHH
Q 009187 129 QKSKPFLLIDFSNYLNINVYELGAVYLQL 157 (540)
Q Consensus 129 ~e~~prtL~DIs~vl~V~~~~Lgr~~~~L 157 (540)
+.+..+++.+|+..+|++..++.+.+.+|
T Consensus 13 q~d~r~s~~~la~~lglS~~~v~~Ri~rL 41 (42)
T PF13404_consen 13 QEDGRRSYAELAEELGLSESTVRRRIRRL 41 (42)
T ss_dssp HH-TTS-HHHHHHHHTS-HHHHHHHHHHH
T ss_pred HHcCCccHHHHHHHHCcCHHHHHHHHHHh
Confidence 44567899999999999999998877765
No 357
>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=22.41 E-value=49 Score=36.04 Aligned_cols=25 Identities=28% Similarity=0.610 Sum_probs=14.7
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceec
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vle 31 (540)
.|++|+-.. ...+...|..||.++.
T Consensus 217 ~C~~Cd~~~----~~~~~a~CpRC~~~L~ 241 (403)
T TIGR00155 217 SCSACHTTI----LPAQEPVCPRCSTPLY 241 (403)
T ss_pred cCCCCCCcc----CCCCCcCCcCCCCccc
Confidence 377777631 1234566777777763
No 358
>PRK00118 putative DNA-binding protein; Validated
Probab=22.31 E-value=3.1e+02 Score=24.22 Aligned_cols=59 Identities=12% Similarity=0.108 Sum_probs=37.9
Q ss_pred CCCHHHHHHHhCcCHHHHHHHHHHHHHHhhccccccccccCChhhHHHHHHHhhCCCCCHHHHHHHHHHHHhh
Q 009187 133 PFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLLPGGNKKVCDTARDILASM 205 (540)
Q Consensus 133 prtL~DIs~vl~V~~~~Lgr~~~~L~~~L~i~~~p~~~~~~dP~~~I~Rf~~~L~~~~~~~V~~~A~~Iv~~m 205 (540)
-.+..+||..+|++..+|.+...+..+.|.-- ++--.|+.|+.+. +++...+.++.+..
T Consensus 33 g~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~--------~~~~~~~~~~~~~------~~~~~~~~~~~~~~ 91 (104)
T PRK00118 33 DYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDY--------EEKLHLYEKFIER------NELFDKIAYLKEKY 91 (104)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH--------HHHHChHHHHHHH------HHHHHHHHHHHHcc
Confidence 35789999999999999987776666655421 2233466666554 34555555555544
No 359
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=22.30 E-value=52 Score=36.94 Aligned_cols=29 Identities=21% Similarity=0.498 Sum_probs=16.9
Q ss_pred CCCCCCCCCC--e--eeecCCC--ceecCcccceec
Q 009187 2 VWCSSCARHV--T--GHRPYDS--QLCCDRCGKVLE 31 (540)
Q Consensus 2 ~~Cp~Cgs~~--i--v~D~~~G--~~VCt~CG~Vle 31 (540)
..|++||.-. + .+|...| .++| .||.-.+
T Consensus 176 pic~~cg~~~~~~~~~~d~~~~~v~y~~-~cG~~~~ 210 (510)
T PRK00750 176 PICPKCGKVLTTPVISYDAEAGTVTYDC-ECGHEGE 210 (510)
T ss_pred eeCCCCCccceEEEEEEeCCCCEEEEEc-CCCCEEE
Confidence 3588888741 2 3566655 4445 4777654
No 360
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=22.26 E-value=47 Score=24.81 Aligned_cols=24 Identities=25% Similarity=0.641 Sum_probs=16.1
Q ss_pred CCCCCCCCCeeeecCCCceecC--cccceec
Q 009187 3 WCSSCARHVTGHRPYDSQLCCD--RCGKVLE 31 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt--~CG~Vle 31 (540)
.||.||..+ -.+| +.|. .|+.|..
T Consensus 13 kCp~CGt~N----G~R~-~~CKN~~C~~~~~ 38 (44)
T PF14952_consen 13 KCPKCGTYN----GTRG-LSCKNKSCPQVFN 38 (44)
T ss_pred cCCcCcCcc----Cccc-ccccCCccchhhh
Confidence 699999743 2334 6676 6888765
No 361
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=22.25 E-value=25 Score=33.99 Aligned_cols=30 Identities=23% Similarity=0.600 Sum_probs=21.3
Q ss_pred CCCCCCCCCeeeecC-CCceecCcccceeccc
Q 009187 3 WCSSCARHVTGHRPY-DSQLCCDRCGKVLEDH 33 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~-~G~~VCt~CG~Vlee~ 33 (540)
.||.|... ..+|.+ .-...|..||.+|++.
T Consensus 115 ~C~~~~~r-~sfdeA~~~~F~Cp~Cg~~L~~~ 145 (176)
T COG1675 115 VCPNCHVK-YSFDEAMELGFTCPKCGEDLEEY 145 (176)
T ss_pred eCCCCCCc-ccHHHHHHhCCCCCCCCchhhhc
Confidence 59888875 334533 3458999999999853
No 362
>PF01846 FF: FF domain; InterPro: IPR002713 The FF domain may be involved in protein-protein interaction []. It often occurs as multiple copies and often accompanies WW domains IPR001202 from INTERPRO. PRP40 from yeast encodes a novel, essential splicing component that associates with the yeast U1 small nuclear ribonucleoprotein particle [].; PDB: 3HFH_B 2KIS_A 2DOD_A 2JUC_A 2LKS_A 1UZC_A 2KZG_A 2L9V_A 2DOF_A 2KFD_A ....
Probab=22.22 E-value=1.1e+02 Score=22.62 Aligned_cols=36 Identities=14% Similarity=0.260 Sum_probs=29.5
Q ss_pred HHHHHHHHHHhcccccccCHHHHhhhhCCCCccccc
Q 009187 490 ALEATRRMLTKKRLSSKINYDVLEKLFDDSVCLYSI 525 (540)
Q Consensus 490 a~EA~~~ml~~K~~S~KINYdvl~~L~~~~~~~~~~ 525 (540)
|.++.++||+...++....++-+..++...+-+..+
T Consensus 2 a~~~F~~lL~e~~i~~~s~W~~~~~~l~~dpry~~i 37 (51)
T PF01846_consen 2 AREAFKELLKEHKITPYSSWEEVKPKLSKDPRYKAI 37 (51)
T ss_dssp HHHHHHHHHHHTTS-TTSSHHHHHHHHTTSCHHHHS
T ss_pred HHHHHHHHHHhCCCCCCCcHHHHHHHHccCHHHHHh
Confidence 568999999998899999999999998777766544
No 363
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=22.18 E-value=7.3e+02 Score=24.11 Aligned_cols=23 Identities=0% Similarity=-0.086 Sum_probs=20.1
Q ss_pred CCCCCHHHHHHHHcccHHHHhhh
Q 009187 232 GLKFSKSDIIEDFMARKKELHEG 254 (540)
Q Consensus 232 g~~~t~~eI~~~~~~~~~ti~~~ 254 (540)
....|+++|++.++++..++++.
T Consensus 197 ~~~~t~~eIA~~lgis~~~V~~~ 219 (231)
T TIGR02885 197 FKDKTQTEVANMLGISQVQVSRL 219 (231)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHH
Confidence 35689999999999999988776
No 364
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=22.11 E-value=56 Score=31.19 Aligned_cols=29 Identities=28% Similarity=0.713 Sum_probs=17.8
Q ss_pred CCCCCCCCee-----ee-cCCC-----ceecCcccceecc
Q 009187 4 CSSCARHVTG-----HR-PYDS-----QLCCDRCGKVLED 32 (540)
Q Consensus 4 Cp~Cgs~~iv-----~D-~~~G-----~~VCt~CG~Vlee 32 (540)
||.||..... ++ |.=| ...|..||.=-.|
T Consensus 1 CP~Cg~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~e 40 (163)
T TIGR00340 1 CPVCGSRTLKAVTYDYDIPYFGKIMLSTYICEKCGYRSTD 40 (163)
T ss_pred CCCCCCcceEeeeEeccCCCcceEEEEEEECCCCCCchhh
Confidence 9999975211 11 2223 4579999986544
No 365
>PRK04023 DNA polymerase II large subunit; Validated
Probab=22.03 E-value=51 Score=39.76 Aligned_cols=6 Identities=50% Similarity=1.597 Sum_probs=2.8
Q ss_pred CCCCCC
Q 009187 4 CSSCAR 9 (540)
Q Consensus 4 Cp~Cgs 9 (540)
||.||.
T Consensus 629 CpsCG~ 634 (1121)
T PRK04023 629 CPSCGK 634 (1121)
T ss_pred CCCCCC
Confidence 444444
No 366
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=21.85 E-value=1.3e+02 Score=23.44 Aligned_cols=25 Identities=20% Similarity=0.356 Sum_probs=20.7
Q ss_pred CCCHHHHHHHhCcCHHHHHHHHHHH
Q 009187 133 PFLLIDFSNYLNINVYELGAVYLQL 157 (540)
Q Consensus 133 prtL~DIs~vl~V~~~~Lgr~~~~L 157 (540)
|.++.+||..++++...|.+.|...
T Consensus 1 ~~~~~~la~~~~~s~~~l~~~f~~~ 25 (84)
T smart00342 1 PLTLEDLAEALGMSPRHLQRLFKKE 25 (84)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHH
Confidence 5689999999999999887776643
No 367
>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=21.64 E-value=50 Score=23.10 Aligned_cols=20 Identities=35% Similarity=0.986 Sum_probs=9.6
Q ss_pred CCCCCCCCCeeeecCCCceecCccc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCG 27 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG 27 (540)
.|+.||.. .+-+ ..+|..||
T Consensus 13 rC~~Cg~~--~~pP---r~~Cp~C~ 32 (37)
T PF12172_consen 13 RCRDCGRV--QFPP---RPVCPHCG 32 (37)
T ss_dssp E-TTT--E--EES-----SEETTTT
T ss_pred EcCCCCCE--ecCC---CcCCCCcC
Confidence 57888864 2322 26788887
No 368
>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=21.51 E-value=5.1e+02 Score=21.98 Aligned_cols=31 Identities=6% Similarity=0.033 Sum_probs=27.0
Q ss_pred cCCCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 009187 130 KSKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (540)
Q Consensus 130 e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~ 160 (540)
...+.+..||++.++++..++.++...|.+.
T Consensus 44 ~~~~is~~eLa~~~g~sr~tVsr~L~~Le~~ 74 (95)
T TIGR01610 44 KQDRVTATVIAELTGLSRTHVSDAIKSLARR 74 (95)
T ss_pred cCCccCHHHHHHHHCcCHHHHHHHHHHHHHC
Confidence 5678999999999999999999988887764
No 369
>smart00760 Bac_DnaA_C Bacterial dnaA protein helix-turn-helix domain. Could be involved in DNA-binding.
Probab=21.48 E-value=1.7e+02 Score=22.64 Aligned_cols=22 Identities=18% Similarity=0.255 Sum_probs=15.4
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHhC
Q 009187 121 SCLYLACRQKSKPFLLIDFSNYLN 144 (540)
Q Consensus 121 ACLYiACR~e~~prtL~DIs~vl~ 144 (540)
.+.|++-+..+. ++.+|+..++
T Consensus 35 iamyla~~~~~~--sl~~Ig~~fg 56 (60)
T smart00760 35 IAMYLARELTDL--SLPEIGKIFG 56 (60)
T ss_pred HHHHHHHHHHCC--CHHHHHHHhC
Confidence 566887666654 6788887775
No 370
>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=21.43 E-value=2.4e+02 Score=20.50 Aligned_cols=31 Identities=10% Similarity=0.183 Sum_probs=24.8
Q ss_pred hcCCCCCHHHHHHHhCcCHHHHHHHHHHHHH
Q 009187 129 QKSKPFLLIDFSNYLNINVYELGAVYLQLCQ 159 (540)
Q Consensus 129 ~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~ 159 (540)
..+-|.++.||++.++++...+.+-.+.|.+
T Consensus 11 L~~~~~~~~el~~~l~~s~~~vs~hL~~L~~ 41 (47)
T PF01022_consen 11 LSEGPLTVSELAEELGLSQSTVSHHLKKLRE 41 (47)
T ss_dssp HTTSSEEHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHhCCCchhhHHHhccccchHHHHHHHHHHH
Confidence 4457899999999999999999887766654
No 371
>COG4753 Response regulator containing CheY-like receiver domain and AraC-type DNA-binding domain [Signal transduction mechanisms]
Probab=21.37 E-value=4.1e+02 Score=29.78 Aligned_cols=32 Identities=22% Similarity=0.324 Sum_probs=27.5
Q ss_pred HhcCCCCCHHHHHHHhCcCHHHHHHHHHHHHH
Q 009187 128 RQKSKPFLLIDFSNYLNINVYELGAVYLQLCQ 159 (540)
Q Consensus 128 R~e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~ 159 (540)
+-..-|.||+++|+++++++..||..|++...
T Consensus 383 ~h~se~LtL~~la~~f~in~~Ylgqlfk~~~~ 414 (475)
T COG4753 383 KHFSENLTLKDLAKVFHINPVYLGQLFKKETG 414 (475)
T ss_pred HHhcCCCCHHHHHHHhCcCHHHHHHHHHHHhh
Confidence 45567999999999999999999998887644
No 372
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=21.31 E-value=30 Score=30.94 Aligned_cols=32 Identities=25% Similarity=0.517 Sum_probs=21.7
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceeccccc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNF 35 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~~I 35 (540)
.|+.||+- +..-...+.++|..|+.+..-..+
T Consensus 9 FC~~CG~l-l~~~~~~~~~~C~~Ck~~~~v~~~ 40 (116)
T KOG2907|consen 9 FCSDCGSL-LEEPSAQSTVLCIRCKIEYPVSQF 40 (116)
T ss_pred hhhhhhhh-cccccccCceEeccccccCCHHHh
Confidence 69999974 222235677779999988754444
No 373
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=21.28 E-value=1.6e+02 Score=21.41 Aligned_cols=25 Identities=4% Similarity=0.006 Sum_probs=16.3
Q ss_pred CCCCCHHHHHHHhCcCHHHHHHHHH
Q 009187 131 SKPFLLIDFSNYLNINVYELGAVYL 155 (540)
Q Consensus 131 ~~prtL~DIs~vl~V~~~~Lgr~~~ 155 (540)
....++.+||..++++..+|.+..+
T Consensus 18 ~~G~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 18 EQGMSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp CS---HHHHHHHTT--HHHHHHHHH
T ss_pred HcCCCHHHHHHHHCcCcHHHHHHHh
Confidence 3458899999999999999976544
No 374
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=21.28 E-value=49 Score=25.18 Aligned_cols=26 Identities=15% Similarity=0.507 Sum_probs=17.5
Q ss_pred CCCCCCCCCCeeee-----------cCCCceecCcccc
Q 009187 2 VWCSSCARHVTGHR-----------PYDSQLCCDRCGK 28 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D-----------~~~G~~VCt~CG~ 28 (540)
-.||+||.. +.+. .+...++|.-|..
T Consensus 3 f~CP~C~~~-~~~~~L~~H~~~~H~~~~~~v~CPiC~~ 39 (54)
T PF05605_consen 3 FTCPYCGKG-FSESSLVEHCEDEHRSESKNVVCPICSS 39 (54)
T ss_pred cCCCCCCCc-cCHHHHHHHHHhHCcCCCCCccCCCchh
Confidence 469999983 3221 1245799999975
No 375
>PRK15320 transcriptional activator SprB; Provisional
Probab=21.23 E-value=2e+02 Score=28.71 Aligned_cols=36 Identities=6% Similarity=0.050 Sum_probs=32.3
Q ss_pred CCCCHHHHHHHhCcCHHHHHHHHHHHHHHhhccccc
Q 009187 132 KPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADES 167 (540)
Q Consensus 132 ~prtL~DIs~vl~V~~~~Lgr~~~~L~~~L~i~~~p 167 (540)
...+.++||+.++++.+++...-..|...|+++..|
T Consensus 178 kG~SNKEIAekL~LS~KTVSTYKnRLLeKLgAkN~~ 213 (251)
T PRK15320 178 SGHPAIELAKKFGLGTKTVSIYRKKVMYRLGMDSSP 213 (251)
T ss_pred cCCCHHHHHHHhccchhhHHHHHHHHHHHcCCCCCc
Confidence 457889999999999999999999999999988665
No 376
>PLN02569 threonine synthase
Probab=21.09 E-value=52 Score=36.74 Aligned_cols=25 Identities=12% Similarity=0.187 Sum_probs=19.9
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceec
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vle 31 (540)
.|+.||.. ++...-...| .||-.|+
T Consensus 51 ~C~~Cg~~---y~~~~~~~~C-~cgg~l~ 75 (484)
T PLN02569 51 ECPLTGEK---YSLDEVVYRS-KSGGLLD 75 (484)
T ss_pred EeCCCCCc---CCCccccccC-CCCCeEE
Confidence 69999986 5555667889 7998886
No 377
>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=21.01 E-value=51 Score=31.30 Aligned_cols=30 Identities=27% Similarity=0.640 Sum_probs=15.2
Q ss_pred CCCCCCCCCCe----eee-cCCCc-----eecCcccceec
Q 009187 2 VWCSSCARHVT----GHR-PYDSQ-----LCCDRCGKVLE 31 (540)
Q Consensus 2 ~~Cp~Cgs~~i----v~D-~~~G~-----~VCt~CG~Vle 31 (540)
+.||+||.... .++ |.=|+ ..|..||.=-.
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 46999998621 222 33333 47999998644
No 378
>PRK13503 transcriptional activator RhaS; Provisional
Probab=20.97 E-value=1.4e+02 Score=29.84 Aligned_cols=40 Identities=8% Similarity=0.052 Sum_probs=29.4
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHH
Q 009187 117 QVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 157 (540)
Q Consensus 117 ~vaAACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L 157 (540)
.+-.+.=||--. -..++|+.|+|+.++++...|.+.|++.
T Consensus 172 ~i~~~~~~I~~~-~~~~~tl~~lA~~~~lS~~~l~r~Fk~~ 211 (278)
T PRK13503 172 RLNQLLAWLEDH-FAEEVNWEALADQFSLSLRTLHRQLKQQ 211 (278)
T ss_pred HHHHHHHHHHHh-hcCCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 344444555443 3458999999999999999998887744
No 379
>PRK06386 replication factor A; Reviewed
Probab=20.85 E-value=46 Score=35.73 Aligned_cols=20 Identities=25% Similarity=0.649 Sum_probs=15.0
Q ss_pred CCCCCCCCCeeeecCCCceecCcccce
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKV 29 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~V 29 (540)
.||.|+... + .| .|..||.|
T Consensus 238 rCP~C~R~l---~--~g--~C~~HG~v 257 (358)
T PRK06386 238 KCSVCNKII---E--DG--VCKDHPDA 257 (358)
T ss_pred cCcCCCeEc---c--CC--cCCCCCCC
Confidence 699999852 1 24 89999985
No 380
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=20.79 E-value=1.2e+02 Score=18.87 Aligned_cols=21 Identities=14% Similarity=0.033 Sum_probs=17.5
Q ss_pred CCCHHHHHHHHcccHHHHhhh
Q 009187 234 KFSKSDIIEDFMARKKELHEG 254 (540)
Q Consensus 234 ~~t~~eI~~~~~~~~~ti~~~ 254 (540)
..+..+|++.++++..|+.+.
T Consensus 21 ~~s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 21 GESVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CCCHHHHHHHHCCCHHHHHHh
Confidence 459999999999998887654
No 381
>PRK15340 transcriptional regulator InvF; Provisional
Probab=20.78 E-value=7e+02 Score=24.87 Aligned_cols=54 Identities=6% Similarity=-0.026 Sum_probs=38.5
Q ss_pred hHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhcCCCCCHHHHHHHhCcCHHHHHHHHHHH
Q 009187 91 DEIVHVAKRFYGIAVARNFTKGRRTEQVQASCLYLACRQKSKPFLLIDFSNYLNINVYELGAVYLQL 157 (540)
Q Consensus 91 ~~i~e~A~~iyk~a~~~~~~rGR~~~~vaAACLYiACR~e~~prtL~DIs~vl~V~~~~Lgr~~~~L 157 (540)
+...+.+..+.++...-++. .|+ ......++++.++|+.+++++..+.|.|++.
T Consensus 96 d~~~~~~~~~~r~~e~y~l~------------~~L-l~~~~~~~sleeLA~~~gvS~r~f~RlFk~~ 149 (216)
T PRK15340 96 SPAFNKVLALLRKSESYWLV------------GYL-LAQSTSGNTMRMLGEDYGVSYTHFRRLCSRA 149 (216)
T ss_pred ChhHHHHHHHHHHHHHHHHH------------HHH-HhCccCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 77888888888776544331 122 2333456799999999999999998877654
No 382
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=20.77 E-value=2.4e+02 Score=20.59 Aligned_cols=30 Identities=7% Similarity=0.144 Sum_probs=25.6
Q ss_pred CCCCCHHHHHHHhCcCHHHHHHHHHHHHHH
Q 009187 131 SKPFLLIDFSNYLNINVYELGAVYLQLCQV 160 (540)
Q Consensus 131 ~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~ 160 (540)
+-|.++.+|+..++++...+.+....|.+.
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L~~~ 37 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKLREA 37 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 557899999999999999998888877763
No 383
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=20.76 E-value=47 Score=26.32 Aligned_cols=33 Identities=21% Similarity=0.440 Sum_probs=22.0
Q ss_pred CCCCCCCCCCCeeeecCCCceecCcccceeccccccccccccc
Q 009187 1 MVWCSSCARHVTGHRPYDSQLCCDRCGKVLEDHNFSTEATFVK 43 (540)
Q Consensus 1 m~~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~~Ids~~ef~~ 43 (540)
|-.|+.||.-.+- -.|..||-+.- +..-+-|+-
T Consensus 5 ~rkC~~cg~YTLk-------e~Cp~CG~~t~---~~~PprFSP 37 (59)
T COG2260 5 IRKCPKCGRYTLK-------EKCPVCGGDTK---VPHPPRFSP 37 (59)
T ss_pred hhcCcCCCceeec-------ccCCCCCCccc---cCCCCCCCc
Confidence 3479999986432 47999998743 444555654
No 384
>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=20.67 E-value=68 Score=24.50 Aligned_cols=10 Identities=20% Similarity=0.651 Sum_probs=8.1
Q ss_pred CCCCCCCCCe
Q 009187 3 WCSSCARHVT 12 (540)
Q Consensus 3 ~Cp~Cgs~~i 12 (540)
.||.||...+
T Consensus 15 ~Cp~CGN~~v 24 (49)
T PF12677_consen 15 KCPKCGNDKV 24 (49)
T ss_pred cCcccCCcEe
Confidence 6999998754
No 385
>PRK09401 reverse gyrase; Reviewed
Probab=20.66 E-value=37 Score=42.02 Aligned_cols=25 Identities=24% Similarity=0.679 Sum_probs=17.5
Q ss_pred CCCCCCCCCeeeecCCCceecCcccc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGK 28 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~ 28 (540)
.||+||+......-..| +.|..|=-
T Consensus 9 ~cpnc~g~i~~~rl~~g-~~c~~cl~ 33 (1176)
T PRK09401 9 SCPNCGGDISDERLEKG-LPCEKCLP 33 (1176)
T ss_pred cCCCCCCcCcHhHHhcC-CcChhhCC
Confidence 69999997433333345 89999954
No 386
>PF14951 DUF4503: Domain of unknown function (DUF4503)
Probab=20.66 E-value=58 Score=34.85 Aligned_cols=33 Identities=18% Similarity=0.546 Sum_probs=27.2
Q ss_pred CCCCCCCCCeeeec-CCCceecCcccceeccccc
Q 009187 3 WCSSCARHVTGHRP-YDSQLCCDRCGKVLEDHNF 35 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~-~~G~~VCt~CG~Vlee~~I 35 (540)
.|..||+..+.-.+ ++|.+.|.+|-.|+...++
T Consensus 276 vCd~CGn~rLe~~pe~rg~~~C~~Cs~~V~sP~~ 309 (389)
T PF14951_consen 276 VCDRCGNGRLEQSPEDRGAFSCGDCSRVVTSPVL 309 (389)
T ss_pred cccccCCccceeCccCCCceeccchhhhccCcce
Confidence 59999999777655 4788999999999987654
No 387
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=20.53 E-value=7.6e+02 Score=25.43 Aligned_cols=61 Identities=11% Similarity=0.022 Sum_probs=40.0
Q ss_pred cCCCCCHHHHHHHhCcCHHHHHHHHHHHHHHhhccccccccccCChhhHHHHHHHhhC-CC---CCHHHHHHHH
Q 009187 130 KSKPFLLIDFSNYLNINVYELGAVYLQLCQVLYIADESNVLKQVDPSIFLHKFTDRLL-PG---GNKKVCDTAR 199 (540)
Q Consensus 130 e~~prtL~DIs~vl~V~~~~Lgr~~~~L~~~L~i~~~p~~~~~~dP~~~I~Rf~~~L~-~~---~~~~V~~~A~ 199 (540)
-++|.++.|+...-||-.+- +|+-|....+.... +--..+++|+|++|+ .+ ++.+-.+.|+
T Consensus 152 gDIP~~v~dLlsLPGVGPKM---a~L~m~~AWn~i~G------I~VDtHVHRi~nrlgWv~~ktkspE~TR~aL 216 (286)
T KOG1921|consen 152 GDIPDTVEDLLSLPGVGPKM---AHLTMQVAWNKIVG------ICVDTHVHRICNRLGWVDTKTKSPEQTRVAL 216 (286)
T ss_pred CCCchhHHHHhcCCCCchHH---HHHHHHHHhcccee------EEeehHHHHHHHHhcccccccCCHHHHHHHH
Confidence 38999999999999998753 35555555553322 333468999999997 21 2344455554
No 388
>PF00628 PHD: PHD-finger; InterPro: IPR019787 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 PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=20.36 E-value=75 Score=23.43 Aligned_cols=26 Identities=19% Similarity=0.690 Sum_probs=20.1
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceecc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLED 32 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee 32 (540)
+|+.||. .+.....+.|..|+...-.
T Consensus 1 ~C~vC~~----~~~~~~~i~C~~C~~~~H~ 26 (51)
T PF00628_consen 1 YCPVCGQ----SDDDGDMIQCDSCNRWYHQ 26 (51)
T ss_dssp EBTTTTS----SCTTSSEEEBSTTSCEEET
T ss_pred eCcCCCC----cCCCCCeEEcCCCChhhCc
Confidence 4889998 3456788999999987653
No 389
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=20.29 E-value=74 Score=30.22 Aligned_cols=31 Identities=29% Similarity=0.578 Sum_probs=18.5
Q ss_pred CCCCCCCCCCe----eee-cCCC-----ceecCcccceecc
Q 009187 2 VWCSSCARHVT----GHR-PYDS-----QLCCDRCGKVLED 32 (540)
Q Consensus 2 ~~Cp~Cgs~~i----v~D-~~~G-----~~VCt~CG~Vlee 32 (540)
+.||+||.... .++ |.=| ...|..||.=-.|
T Consensus 1 s~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~e 41 (160)
T smart00709 1 SDCPSCGGNGTTRMLLTSIPYFREVIIMSFECEHCGYRNNE 41 (160)
T ss_pred CcCCCCCCCCEEEEEEecCCCcceEEEEEEECCCCCCccce
Confidence 36999986521 112 2223 4579999986443
No 390
>PRK07591 threonine synthase; Validated
Probab=20.20 E-value=53 Score=35.81 Aligned_cols=25 Identities=24% Similarity=0.422 Sum_probs=18.9
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceec
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLE 31 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vle 31 (540)
.|..||.. ++...- ..|..||-.|+
T Consensus 20 ~C~~Cg~~---~~~~~~-~~C~~cg~~l~ 44 (421)
T PRK07591 20 KCRECGAE---YPLGPI-HVCEECFGPLE 44 (421)
T ss_pred EeCCCCCc---CCCCCC-ccCCCCCCeEE
Confidence 69999986 333333 88999998886
No 391
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=20.14 E-value=60 Score=40.09 Aligned_cols=25 Identities=24% Similarity=0.741 Sum_probs=0.0
Q ss_pred CCCCCCCCCeeeecCCCceecCcccceeccc
Q 009187 3 WCSSCARHVTGHRPYDSQLCCDRCGKVLEDH 33 (540)
Q Consensus 3 ~Cp~Cgs~~iv~D~~~G~~VCt~CG~Vlee~ 33 (540)
.||.||+. ..-...|.+||..+...
T Consensus 681 fCP~CGs~------te~vy~CPsCGaev~~d 705 (1337)
T PRK14714 681 RCPDCGTH------TEPVYVCPDCGAEVPPD 705 (1337)
T ss_pred cCcccCCc------CCCceeCccCCCccCCC
No 392
>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=20.02 E-value=62 Score=31.58 Aligned_cols=23 Identities=30% Similarity=0.579 Sum_probs=14.7
Q ss_pred CCCCCCCCCCeeeecCCCceecCccc
Q 009187 2 VWCSSCARHVTGHRPYDSQLCCDRCG 27 (540)
Q Consensus 2 ~~Cp~Cgs~~iv~D~~~G~~VCt~CG 27 (540)
..||.|+++-.++. +.-.|..|+
T Consensus 100 ~~C~~C~G~G~~i~---~~~~C~~C~ 122 (186)
T TIGR02642 100 CKCPRCRGTGLIQR---RQRECDTCA 122 (186)
T ss_pred CcCCCCCCeeEEec---CCCCCCCCC
Confidence 46999998733332 124588884
Done!