Query 025357
Match_columns 254
No_of_seqs 167 out of 1020
Neff 7.7
Searched_HMMs 46136
Date Fri Mar 29 05:00:37 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025357.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025357hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK00423 tfb transcription ini 100.0 8.6E-56 1.9E-60 396.9 21.1 219 4-231 12-240 (310)
2 KOG1597 Transcription initiati 100.0 1.7E-52 3.7E-57 360.0 19.1 220 4-230 1-223 (308)
3 COG1405 SUA7 Transcription ini 100.0 7.2E-51 1.6E-55 357.9 18.2 210 4-230 2-214 (285)
4 KOG1598 Transcription initiati 99.9 5.6E-27 1.2E-31 216.7 8.5 190 4-234 1-190 (521)
5 PF00382 TFIIB: Transcription 99.8 2E-19 4.3E-24 127.5 9.8 71 113-184 1-71 (71)
6 PRK00423 tfb transcription ini 99.6 1.5E-15 3.1E-20 136.7 12.2 90 108-198 218-307 (310)
7 PF08271 TF_Zn_Ribbon: TFIIB z 99.6 3.2E-16 6.9E-21 100.1 3.3 43 4-47 1-43 (43)
8 COG1405 SUA7 Transcription ini 99.5 4.5E-14 9.7E-19 124.8 9.4 90 108-198 193-282 (285)
9 KOG1597 Transcription initiati 99.5 8.3E-14 1.8E-18 121.0 9.8 89 108-197 202-290 (308)
10 cd00043 CYCLIN Cyclin box fold 99.2 3.5E-10 7.7E-15 81.2 10.9 83 108-191 4-87 (88)
11 smart00385 CYCLIN domain prese 99.1 9E-10 2E-14 78.3 8.6 80 112-192 2-82 (83)
12 KOG0834 CDK9 kinase-activating 98.7 3.2E-08 6.9E-13 88.9 7.6 116 106-227 39-168 (323)
13 KOG1598 Transcription initiati 98.6 3.6E-08 7.8E-13 92.4 3.9 90 108-198 165-257 (521)
14 TIGR00569 ccl1 cyclin ccl1. Un 98.6 5.7E-07 1.2E-11 80.7 10.7 108 107-221 57-170 (305)
15 COG5333 CCL1 Cdk activating ki 98.1 1.2E-05 2.7E-10 71.0 7.4 114 107-226 46-166 (297)
16 KOG0835 Cyclin L [General func 98.1 3E-05 6.4E-10 69.0 9.6 118 104-227 21-158 (367)
17 PF00134 Cyclin_N: Cyclin, N-t 97.9 0.00019 4.2E-09 55.4 10.5 93 105-198 30-125 (127)
18 PF01857 RB_B: Retinoblastoma- 97.5 0.00041 8.9E-09 55.0 7.7 84 105-189 10-95 (135)
19 KOG0656 G1/S-specific cyclin D 97.2 0.0046 1E-07 56.0 11.7 115 107-227 79-199 (335)
20 KOG0794 CDK8 kinase-activating 97.2 0.00044 9.6E-09 58.9 4.4 59 108-166 43-101 (264)
21 KOG0835 Cyclin L [General func 97.0 0.0039 8.5E-08 55.8 8.7 129 107-251 139-275 (367)
22 PF11781 RRN7: RNA polymerase 96.9 0.00066 1.4E-08 41.3 2.3 27 5-34 10-36 (36)
23 PF02984 Cyclin_C: Cyclin, C-t 96.8 0.0074 1.6E-07 45.6 7.8 87 109-196 3-90 (118)
24 PF08792 A2L_zn_ribbon: A2L zi 96.8 0.0015 3.3E-08 38.9 2.9 31 1-33 1-31 (33)
25 PF01667 Ribosomal_S27e: Ribos 96.8 0.0005 1.1E-08 45.7 0.7 31 3-34 7-37 (55)
26 PRK00415 rps27e 30S ribosomal 96.7 0.00073 1.6E-08 45.5 1.4 31 3-34 11-41 (59)
27 COG5024 Cyclin [Cell division 96.6 0.014 3E-07 54.9 9.3 120 109-234 216-337 (440)
28 COG2051 RPS27A Ribosomal prote 96.6 0.0016 3.4E-08 44.7 2.1 30 4-34 20-49 (67)
29 PLN00209 ribosomal protein S27 96.3 0.0022 4.7E-08 46.3 1.6 31 3-34 36-66 (86)
30 PTZ00083 40S ribosomal protein 96.3 0.0023 5.1E-08 46.1 1.7 31 3-34 35-65 (85)
31 PHA00626 hypothetical protein 96.2 0.0044 9.6E-08 41.0 2.6 33 4-37 1-37 (59)
32 PRK00420 hypothetical protein; 96.1 0.0045 9.7E-08 47.4 2.7 31 1-34 21-51 (112)
33 PRK00398 rpoP DNA-directed RNA 96.0 0.0053 1.1E-07 39.3 2.2 31 1-33 1-31 (46)
34 KOG2496 Cdk activating kinase 95.9 0.026 5.5E-07 50.2 6.9 63 113-175 63-127 (325)
35 PF14803 Nudix_N_2: Nudix N-te 95.9 0.0027 5.8E-08 38.1 0.5 27 5-33 2-32 (34)
36 PF13248 zf-ribbon_3: zinc-rib 95.8 0.0049 1.1E-07 34.6 1.3 23 3-31 2-24 (26)
37 PF02150 RNA_POL_M_15KD: RNA p 95.7 0.01 2.2E-07 35.8 2.6 31 3-34 1-31 (35)
38 PRK11827 hypothetical protein; 95.4 0.01 2.2E-07 40.3 2.0 28 4-33 9-36 (60)
39 smart00778 Prim_Zn_Ribbon Zinc 95.4 0.013 2.8E-07 35.8 2.3 28 4-31 4-33 (37)
40 TIGR02098 MJ0042_CXXC MJ0042 f 95.4 0.0089 1.9E-07 36.5 1.6 29 4-34 3-36 (38)
41 PRK00432 30S ribosomal protein 95.4 0.011 2.4E-07 38.6 2.1 27 4-33 21-47 (50)
42 PF13240 zinc_ribbon_2: zinc-r 95.2 0.0091 2E-07 32.6 0.9 22 5-32 1-22 (23)
43 COG2835 Uncharacterized conser 95.1 0.017 3.7E-07 39.0 2.1 30 2-33 7-36 (60)
44 TIGR01206 lysW lysine biosynth 95.0 0.014 3E-07 38.8 1.7 31 3-34 2-33 (54)
45 PF14354 Lar_restr_allev: Rest 95.0 0.028 6E-07 38.0 3.1 29 2-31 2-37 (61)
46 COG1645 Uncharacterized Zn-fin 95.0 0.014 3E-07 45.8 1.8 27 3-33 28-55 (131)
47 COG1997 RPL43A Ribosomal prote 94.9 0.021 4.5E-07 41.4 2.4 29 4-34 36-64 (89)
48 KOG0653 Cyclin B and related k 94.9 0.17 3.7E-06 47.2 9.1 114 107-226 159-275 (391)
49 PF03966 Trm112p: Trm112p-like 94.8 0.034 7.3E-07 38.7 3.3 17 17-33 47-63 (68)
50 PF08274 PhnA_Zn_Ribbon: PhnA 94.8 0.03 6.5E-07 32.6 2.5 27 4-33 3-29 (30)
51 COG1998 RPS31 Ribosomal protei 94.2 0.026 5.7E-07 36.4 1.5 27 4-32 20-46 (51)
52 smart00661 RPOL9 RNA polymeras 94.2 0.034 7.4E-07 36.2 2.1 28 5-34 2-31 (52)
53 PRK10220 hypothetical protein; 94.1 0.15 3.4E-06 38.5 5.6 30 1-33 1-30 (111)
54 PF10571 UPF0547: Uncharacteri 94.0 0.027 5.9E-07 31.6 1.1 25 4-34 1-25 (26)
55 PF09297 zf-NADH-PPase: NADH p 94.0 0.074 1.6E-06 31.2 3.0 28 4-33 4-31 (32)
56 KOG1779 40s ribosomal protein 93.7 0.031 6.8E-07 39.6 1.1 30 3-33 34-63 (84)
57 TIGR03655 anti_R_Lar restricti 93.6 0.063 1.4E-06 35.4 2.5 32 3-34 1-37 (53)
58 PF06677 Auto_anti-p27: Sjogre 93.6 0.071 1.5E-06 33.3 2.5 26 2-30 16-41 (41)
59 PF08273 Prim_Zn_Ribbon: Zinc- 93.4 0.074 1.6E-06 33.1 2.4 29 4-32 4-35 (40)
60 PF09538 FYDLN_acid: Protein o 93.4 0.045 9.7E-07 41.7 1.7 31 3-36 9-39 (108)
61 KOG4164 Cyclin ik3-1/CABLES [C 93.0 0.49 1.1E-05 43.7 7.8 59 107-165 383-441 (497)
62 PRK00464 nrdR transcriptional 92.7 0.096 2.1E-06 42.5 2.7 30 4-33 1-38 (154)
63 PF13719 zinc_ribbon_5: zinc-r 92.6 0.049 1.1E-06 33.2 0.7 30 3-33 2-35 (37)
64 COG2824 PhnA Uncharacterized Z 92.5 0.34 7.5E-06 36.5 5.2 32 1-35 1-32 (112)
65 COG4888 Uncharacterized Zn rib 92.3 0.092 2E-06 39.1 1.9 29 5-34 24-57 (104)
66 KOG0655 G1/S-specific cyclin E 92.2 0.54 1.2E-05 42.5 7.0 112 109-226 148-262 (408)
67 PF05129 Elf1: Transcription e 91.9 0.072 1.6E-06 38.5 1.0 32 5-36 24-59 (81)
68 PF09862 DUF2089: Protein of u 91.8 0.15 3.2E-06 39.1 2.7 25 6-36 1-25 (113)
69 TIGR02300 FYDLN_acid conserved 91.8 0.1 2.3E-06 40.6 1.8 31 3-36 9-39 (129)
70 PRK14892 putative transcriptio 91.7 0.093 2E-06 39.3 1.4 41 4-45 22-70 (99)
71 PF01780 Ribosomal_L37ae: Ribo 91.7 0.15 3.2E-06 37.4 2.4 32 4-37 36-67 (90)
72 PF08613 Cyclin: Cyclin; Inte 91.5 4.6 9.9E-05 32.3 11.2 90 108-198 53-148 (149)
73 smart00342 HTH_ARAC helix_turn 91.3 0.92 2E-05 31.3 6.3 71 113-191 4-75 (84)
74 TIGR00686 phnA alkylphosphonat 91.2 0.6 1.3E-05 35.3 5.2 28 4-34 3-30 (109)
75 cd06571 Bac_DnaA_C C-terminal 91.1 1.1 2.4E-05 32.6 6.7 46 150-198 30-76 (90)
76 PF05460 ORC6: Origin recognit 91.0 0.066 1.4E-06 49.3 0.0 78 121-199 11-89 (353)
77 TIGR00244 transcriptional regu 91.0 0.23 5.1E-06 39.7 3.1 30 4-33 1-38 (147)
78 PF07282 OrfB_Zn_ribbon: Putat 90.8 0.16 3.4E-06 35.1 1.7 29 4-34 29-57 (69)
79 TIGR01384 TFS_arch transcripti 90.3 0.17 3.7E-06 38.0 1.7 27 5-35 2-28 (104)
80 KOG4557 Origin recognition com 90.0 7.1 0.00015 33.4 11.1 88 112-200 2-93 (262)
81 PF12760 Zn_Tnp_IS1595: Transp 89.9 0.36 7.7E-06 30.8 2.7 27 4-31 19-45 (46)
82 PTZ00255 60S ribosomal protein 89.7 0.24 5.2E-06 36.3 2.0 32 4-37 37-68 (90)
83 PF00325 Crp: Bacterial regula 89.6 0.49 1.1E-05 27.9 2.9 27 166-193 2-28 (32)
84 COG1594 RPB9 DNA-directed RNA 89.4 0.29 6.3E-06 37.6 2.4 32 3-36 2-35 (113)
85 TIGR00280 L37a ribosomal prote 88.8 0.3 6.4E-06 35.9 1.9 32 4-37 36-67 (91)
86 KOG4557 Origin recognition com 88.5 1.6 3.6E-05 37.1 6.4 80 113-195 96-181 (262)
87 PRK12495 hypothetical protein; 88.3 0.29 6.2E-06 41.7 1.8 32 1-36 40-71 (226)
88 PRK03976 rpl37ae 50S ribosomal 87.6 0.38 8.2E-06 35.3 1.9 32 4-37 37-68 (90)
89 PF03119 DNA_ligase_ZBD: NAD-d 87.4 0.56 1.2E-05 26.7 2.1 22 5-28 1-22 (28)
90 smart00834 CxxC_CXXC_SSSS Puta 87.3 0.39 8.5E-06 29.4 1.6 30 4-33 6-36 (41)
91 PF03604 DNA_RNApol_7kD: DNA d 87.3 0.37 8E-06 28.4 1.4 25 5-32 2-26 (32)
92 PRK09710 lar restriction allev 87.3 0.68 1.5E-05 31.7 2.8 30 3-33 6-37 (64)
93 smart00659 RPOLCX RNA polymera 86.9 0.51 1.1E-05 29.9 1.9 27 4-33 3-29 (44)
94 COG5349 Uncharacterized protei 86.8 0.3 6.4E-06 37.7 1.0 38 4-42 22-59 (126)
95 PF08279 HTH_11: HTH domain; 86.5 2.2 4.8E-05 27.7 5.0 33 162-195 11-43 (55)
96 PRK05978 hypothetical protein; 86.3 0.5 1.1E-05 38.0 2.1 30 4-34 34-63 (148)
97 smart00440 ZnF_C2C2 C2C2 Zinc 86.3 0.72 1.6E-05 28.6 2.3 27 5-32 2-37 (40)
98 PF13717 zinc_ribbon_4: zinc-r 86.1 0.29 6.3E-06 29.6 0.5 29 4-33 3-35 (36)
99 COG4640 Predicted membrane pro 85.8 0.4 8.7E-06 44.2 1.4 29 3-37 1-29 (465)
100 TIGR03697 NtcA_cyano global ni 85.2 4.1 8.8E-05 33.2 7.2 29 165-194 142-170 (193)
101 PF02082 Rrf2: Transcriptional 85.2 1.4 3E-05 31.5 3.8 45 149-194 8-52 (83)
102 PRK12286 rpmF 50S ribosomal pr 85.1 0.62 1.3E-05 31.3 1.7 28 4-38 28-55 (57)
103 PF14255 Cys_rich_CPXG: Cystei 85.0 0.7 1.5E-05 30.4 1.9 28 5-32 2-33 (52)
104 TIGR02443 conserved hypothetic 84.5 0.99 2.2E-05 30.4 2.5 29 4-32 10-40 (59)
105 TIGR00569 ccl1 cyclin ccl1. Un 84.1 22 0.00048 32.1 11.8 71 124-196 181-253 (305)
106 PF13545 HTH_Crp_2: Crp-like h 84.1 2.7 5.8E-05 29.0 4.8 44 151-195 3-56 (76)
107 PF12773 DZR: Double zinc ribb 83.7 0.54 1.2E-05 30.2 1.0 27 4-33 13-39 (50)
108 COG1996 RPC10 DNA-directed RNA 83.7 0.37 8.1E-06 31.3 0.2 27 4-32 7-33 (49)
109 PF01325 Fe_dep_repress: Iron 83.6 4 8.8E-05 27.4 5.3 38 155-194 12-49 (60)
110 TIGR02010 IscR iron-sulfur clu 83.3 3.3 7.2E-05 32.4 5.5 46 148-194 7-52 (135)
111 PF05191 ADK_lid: Adenylate ki 82.8 0.23 4.9E-06 30.1 -1.0 29 5-33 3-31 (36)
112 PF01096 TFIIS_C: Transcriptio 82.8 1.1 2.4E-05 27.5 2.0 28 5-32 2-37 (39)
113 COG3877 Uncharacterized protei 81.9 1.5 3.3E-05 33.0 2.9 26 4-35 7-32 (122)
114 cd00350 rubredoxin_like Rubred 81.8 1.1 2.3E-05 26.5 1.7 23 5-31 3-25 (33)
115 PF01783 Ribosomal_L32p: Ribos 81.6 0.83 1.8E-05 30.5 1.3 27 4-37 27-53 (56)
116 KOG0794 CDK8 kinase-activating 81.4 11 0.00024 32.6 8.3 99 115-223 159-258 (264)
117 PRK09678 DNA-binding transcrip 81.4 1.7 3.7E-05 30.6 2.8 31 3-34 1-40 (72)
118 PF14446 Prok-RING_1: Prokaryo 81.3 0.99 2.1E-05 29.9 1.5 27 4-34 6-32 (54)
119 TIGR01031 rpmF_bact ribosomal 81.0 1.2 2.7E-05 29.6 1.9 27 4-37 27-53 (55)
120 PHA02942 putative transposase; 81.0 0.92 2E-05 42.2 1.8 31 4-37 326-356 (383)
121 cd00092 HTH_CRP helix_turn_hel 80.7 7.3 0.00016 25.9 5.9 30 164-194 23-52 (67)
122 PRK12336 translation initiatio 80.7 1.1 2.4E-05 37.9 2.0 30 4-33 99-129 (201)
123 PF15616 TerY-C: TerY-C metal 80.2 1.1 2.3E-05 35.4 1.6 21 4-33 78-98 (131)
124 PRK10857 DNA-binding transcrip 79.7 5 0.00011 32.8 5.6 47 147-194 6-52 (164)
125 PF13613 HTH_Tnp_4: Helix-turn 79.7 4.8 0.0001 26.2 4.5 34 164-198 17-50 (53)
126 COG1327 Predicted transcriptio 79.5 1.5 3.3E-05 35.2 2.4 30 4-33 1-38 (156)
127 COG4068 Uncharacterized protei 79.4 0.39 8.5E-06 32.2 -0.9 25 4-34 9-34 (64)
128 PRK13130 H/ACA RNA-protein com 79.4 0.94 2E-05 30.3 0.9 25 2-34 4-28 (56)
129 TIGR03826 YvyF flagellar opero 79.2 0.6 1.3E-05 37.1 -0.1 29 1-34 1-29 (137)
130 PF00356 LacI: Bacterial regul 78.6 2.3 4.9E-05 27.2 2.5 44 168-224 1-44 (46)
131 PRK08402 replication factor A; 78.5 1.6 3.5E-05 40.2 2.5 27 4-32 213-239 (355)
132 PF09855 DUF2082: Nucleic-acid 78.1 1.7 3.7E-05 29.9 1.9 9 24-32 37-45 (64)
133 KOG1088 Uncharacterized conser 77.9 0.96 2.1E-05 34.7 0.7 17 17-33 92-108 (124)
134 PRK06266 transcription initiat 77.8 0.57 1.2E-05 38.9 -0.6 29 5-34 119-147 (178)
135 PF12802 MarR_2: MarR family; 77.5 6.8 0.00015 25.7 4.8 40 154-194 9-48 (62)
136 KOG1010 Rb (Retinoblastoma tum 77.2 5.1 0.00011 40.6 5.7 84 107-191 678-763 (920)
137 PF04161 Arv1: Arv1-like famil 76.9 1.1 2.5E-05 38.0 1.0 34 4-37 1-38 (208)
138 TIGR01610 phage_O_Nterm phage 76.9 27 0.00058 25.6 8.5 31 163-194 44-74 (95)
139 smart00550 Zalpha Z-DNA-bindin 76.8 8.4 0.00018 26.5 5.2 39 156-195 11-50 (68)
140 PF05876 Terminase_GpA: Phage 76.1 1.4 3E-05 43.1 1.5 43 4-46 201-255 (557)
141 KOG2906 RNA polymerase III sub 76.0 2.3 5.1E-05 31.6 2.3 29 3-33 1-31 (105)
142 PF00301 Rubredoxin: Rubredoxi 75.8 1.7 3.8E-05 27.9 1.4 14 24-37 2-15 (47)
143 PF13413 HTH_25: Helix-turn-he 75.7 5.1 0.00011 27.2 3.8 55 161-226 5-60 (62)
144 PRK11920 rirA iron-responsive 75.7 8.2 0.00018 31.0 5.7 45 148-194 7-51 (153)
145 PF13412 HTH_24: Winged helix- 75.7 9.8 0.00021 23.8 5.0 29 164-193 15-43 (48)
146 PRK11161 fumarate/nitrate redu 75.6 13 0.00028 31.4 7.2 30 165-195 183-212 (235)
147 smart00419 HTH_CRP helix_turn_ 75.5 5.2 0.00011 24.6 3.7 30 164-194 6-35 (48)
148 PF10122 Mu-like_Com: Mu-like 75.5 0.81 1.8E-05 29.9 -0.2 30 2-33 3-34 (51)
149 PF14122 YokU: YokU-like prote 75.3 2.2 4.7E-05 30.9 1.9 20 21-40 33-52 (87)
150 smart00401 ZnF_GATA zinc finge 75.1 2.4 5.2E-05 27.7 2.0 31 3-33 3-35 (52)
151 PF11672 DUF3268: Protein of u 75.0 2.8 6E-05 31.6 2.5 30 4-34 3-42 (102)
152 PF00196 GerE: Bacterial regul 74.6 4.7 0.0001 26.5 3.4 33 165-198 17-49 (58)
153 PF13730 HTH_36: Helix-turn-he 74.4 14 0.0003 23.8 5.6 25 168-193 27-51 (55)
154 PRK14559 putative protein seri 74.3 1.8 3.9E-05 43.1 1.7 9 166-174 272-280 (645)
155 PRK05508 methionine sulfoxide 74.1 2.1 4.6E-05 33.1 1.7 32 18-49 28-61 (119)
156 PF08646 Rep_fac-A_C: Replicat 74.0 3.2 7E-05 32.9 2.9 27 5-34 20-48 (146)
157 COG1326 Uncharacterized archae 73.7 1.5 3.1E-05 36.8 0.8 32 4-36 7-43 (201)
158 PRK00241 nudC NADH pyrophospha 73.6 2.5 5.3E-05 37.2 2.3 28 4-33 100-127 (256)
159 cd00730 rubredoxin Rubredoxin; 73.2 2.7 5.9E-05 27.4 1.8 14 24-37 2-15 (50)
160 COG1656 Uncharacterized conser 73.2 1.8 3.8E-05 35.4 1.1 29 3-33 97-140 (165)
161 PRK00222 methionine sulfoxide 73.1 2.4 5.2E-05 33.9 1.9 34 17-50 37-72 (142)
162 PF09526 DUF2387: Probable met 73.0 3.5 7.5E-05 29.0 2.5 30 4-33 9-40 (71)
163 TIGR00738 rrf2_super rrf2 fami 73.0 9.8 0.00021 29.2 5.4 45 149-194 8-52 (132)
164 KOG0402 60S ribosomal protein 72.8 1.2 2.7E-05 32.0 0.2 31 4-36 37-67 (92)
165 PF04545 Sigma70_r4: Sigma-70, 72.7 8.4 0.00018 24.4 4.1 31 164-195 18-48 (50)
166 TIGR02605 CxxC_CxxC_SSSS putat 72.6 2.4 5.1E-05 27.4 1.5 28 4-31 6-34 (52)
167 KOG2593 Transcription initiati 72.4 1.6 3.6E-05 40.7 0.9 31 4-34 129-164 (436)
168 PRK08351 DNA-directed RNA poly 72.3 2.1 4.6E-05 29.1 1.2 24 1-32 1-24 (61)
169 PF09723 Zn-ribbon_8: Zinc rib 71.6 2.5 5.4E-05 26.3 1.4 28 4-31 6-34 (42)
170 COG3478 Predicted nucleic-acid 71.5 2.9 6.2E-05 28.7 1.7 8 4-11 5-12 (68)
171 PRK10219 DNA-binding transcrip 71.1 29 0.00063 25.5 7.4 39 151-191 7-45 (107)
172 PRK10402 DNA-binding transcrip 70.9 14 0.0003 31.2 6.3 72 147-221 150-221 (226)
173 PF07754 DUF1610: Domain of un 70.8 3.2 6.8E-05 22.8 1.4 24 6-31 1-24 (24)
174 PF09339 HTH_IclR: IclR helix- 70.7 8.3 0.00018 24.8 3.8 38 156-194 8-45 (52)
175 PF14952 zf-tcix: Putative tre 70.5 2.3 5E-05 26.8 1.0 25 4-34 12-38 (44)
176 PF13404 HTH_AsnC-type: AsnC-t 70.5 8.3 0.00018 24.0 3.6 29 163-192 14-42 (42)
177 smart00421 HTH_LUXR helix_turn 70.4 9.5 0.00021 24.0 4.1 31 167-198 19-49 (58)
178 PF04703 FaeA: FaeA-like prote 70.2 8.6 0.00019 26.2 3.9 34 164-198 13-46 (62)
179 PF06827 zf-FPG_IleRS: Zinc fi 70.2 3 6.5E-05 23.8 1.4 28 4-31 2-29 (30)
180 TIGR02944 suf_reg_Xantho FeS a 70.1 14 0.00031 28.4 5.7 45 148-194 8-52 (130)
181 TIGR03831 YgiT_finger YgiT-typ 70.1 3.6 7.8E-05 25.5 1.9 10 24-33 33-42 (46)
182 PF14353 CpXC: CpXC protein 69.9 3.4 7.3E-05 32.0 2.1 11 23-33 38-48 (128)
183 PRK11753 DNA-binding transcrip 69.9 23 0.0005 29.1 7.4 29 165-194 167-195 (211)
184 cd00202 ZnF_GATA Zinc finger D 69.8 1.6 3.5E-05 28.8 0.2 29 5-33 1-31 (54)
185 PF10058 DUF2296: Predicted in 69.8 2.2 4.9E-05 28.2 0.9 29 4-32 23-53 (54)
186 PF00165 HTH_AraC: Bacterial r 69.7 7 0.00015 23.8 3.1 26 164-190 6-31 (42)
187 PF01726 LexA_DNA_bind: LexA D 68.9 9 0.00019 26.2 3.8 33 161-194 20-53 (65)
188 COG1959 Predicted transcriptio 68.7 15 0.00032 29.5 5.6 45 149-194 8-52 (150)
189 PRK13918 CRP/FNR family transc 68.7 20 0.00044 29.3 6.7 30 165-195 148-177 (202)
190 TIGR03830 CxxCG_CxxCG_HTH puta 68.5 4.3 9.2E-05 31.1 2.4 21 166-187 78-98 (127)
191 PF13453 zf-TFIIB: Transcripti 68.4 4.6 9.9E-05 24.9 2.0 28 5-33 1-29 (41)
192 PF01641 SelR: SelR domain; I 68.3 3.9 8.4E-05 31.9 2.1 32 18-49 32-65 (124)
193 PRK11511 DNA-binding transcrip 68.3 31 0.00068 26.5 7.3 43 147-191 7-49 (127)
194 TIGR00357 methionine-R-sulfoxi 68.2 3.3 7.1E-05 32.7 1.7 33 18-50 35-69 (134)
195 COG3809 Uncharacterized protei 68.0 5.4 0.00012 28.5 2.5 29 3-33 1-31 (88)
196 PF10668 Phage_terminase: Phag 67.8 17 0.00037 24.6 4.9 39 146-188 5-43 (60)
197 PF06397 Desulfoferrod_N: Desu 67.8 3.5 7.6E-05 24.9 1.4 22 4-26 7-28 (36)
198 cd06170 LuxR_C_like C-terminal 67.5 12 0.00027 23.5 4.2 32 166-198 15-46 (57)
199 PF01599 Ribosomal_S27: Riboso 66.9 6.6 0.00014 25.2 2.6 26 4-31 19-46 (47)
200 PRK02935 hypothetical protein; 66.8 4 8.6E-05 30.8 1.8 27 4-34 71-97 (110)
201 COG0333 RpmF Ribosomal protein 66.8 4.1 8.9E-05 27.3 1.7 28 3-37 27-54 (57)
202 PF13936 HTH_38: Helix-turn-he 66.7 12 0.00027 23.3 3.8 26 164-190 18-43 (44)
203 PF00382 TFIIB: Transcription 66.7 2.3 5E-05 29.3 0.5 16 214-229 1-16 (71)
204 PRK09391 fixK transcriptional 66.6 31 0.00068 29.2 7.6 48 146-194 153-206 (230)
205 PF13790 DUF4182: Domain of un 66.6 3.2 6.9E-05 25.4 1.0 14 21-34 1-14 (38)
206 TIGR03001 Sig-70_gmx1 RNA poly 66.2 16 0.00035 31.6 5.8 56 167-223 178-237 (244)
207 PF13542 HTH_Tnp_ISL3: Helix-t 66.2 30 0.00066 21.8 5.9 24 167-191 28-51 (52)
208 KOG3134 Predicted membrane pro 66.1 1.5 3.4E-05 37.3 -0.6 34 4-37 1-38 (225)
209 PRK12380 hydrogenase nickel in 65.6 3.8 8.2E-05 31.4 1.5 17 14-30 61-77 (113)
210 PRK14086 dnaA chromosomal repl 65.5 68 0.0015 31.9 10.4 43 153-198 558-600 (617)
211 TIGR03829 YokU_near_AblA uncha 65.1 5.7 0.00012 29.1 2.3 33 5-37 1-49 (89)
212 PF13463 HTH_27: Winged helix 65.0 15 0.00033 24.4 4.4 32 162-194 14-45 (68)
213 COG2093 DNA-directed RNA polym 64.8 3.9 8.3E-05 27.9 1.2 24 3-32 4-27 (64)
214 COG4565 CitB Response regulato 64.7 75 0.0016 27.3 9.2 87 106-195 114-201 (224)
215 PF08220 HTH_DeoR: DeoR-like h 64.6 11 0.00024 24.8 3.5 31 164-195 12-42 (57)
216 PRK14890 putative Zn-ribbon RN 64.5 5.7 0.00012 26.8 2.0 28 3-32 7-34 (59)
217 COG2888 Predicted Zn-ribbon RN 64.5 4.7 0.0001 27.2 1.6 27 4-32 10-36 (61)
218 PRK12366 replication factor A; 64.3 4.4 9.4E-05 40.4 2.1 25 4-32 533-557 (637)
219 PRK09685 DNA-binding transcrip 63.8 1E+02 0.0022 27.0 10.8 42 148-190 196-237 (302)
220 TIGR00100 hypA hydrogenase nic 63.8 4.4 9.6E-05 31.1 1.6 20 14-33 61-80 (115)
221 KOG1010 Rb (Retinoblastoma tum 63.5 28 0.00061 35.6 7.4 122 111-243 36-165 (920)
222 CHL00174 accD acetyl-CoA carbo 63.3 1.4 3E-05 39.5 -1.5 30 4-34 39-68 (296)
223 PF01978 TrmB: Sugar-specific 63.3 11 0.00024 25.5 3.4 37 156-194 13-49 (68)
224 TIGR00515 accD acetyl-CoA carb 63.3 1.4 3.1E-05 39.3 -1.4 29 4-33 27-55 (285)
225 smart00345 HTH_GNTR helix_turn 63.1 16 0.00035 23.3 4.1 26 168-194 22-47 (60)
226 COG1773 Rubredoxin [Energy pro 62.9 5.1 0.00011 26.7 1.5 11 24-34 4-14 (55)
227 PF01807 zf-CHC2: CHC2 zinc fi 62.8 6.6 0.00014 29.1 2.3 27 5-31 35-62 (97)
228 PF08281 Sigma70_r4_2: Sigma-7 62.5 16 0.00035 23.3 3.9 29 166-195 26-54 (54)
229 PRK15201 fimbriae regulatory p 62.4 28 0.0006 29.1 6.0 33 165-198 147-179 (198)
230 COG4530 Uncharacterized protei 62.2 4.2 9E-05 30.9 1.1 33 3-38 9-41 (129)
231 PRK03824 hypA hydrogenase nick 61.9 5 0.00011 31.7 1.6 21 14-34 61-81 (135)
232 PF10080 DUF2318: Predicted me 61.6 5.8 0.00013 29.9 1.8 28 4-34 36-63 (102)
233 PF04606 Ogr_Delta: Ogr/Delta- 61.4 6.3 0.00014 25.1 1.8 28 5-33 1-37 (47)
234 KOG3507 DNA-directed RNA polym 61.2 4.3 9.3E-05 27.3 0.9 26 5-33 22-47 (62)
235 TIGR00310 ZPR1_znf ZPR1 zinc f 61.2 6.5 0.00014 33.0 2.3 38 102-139 98-135 (192)
236 TIGR00155 pqiA_fam integral me 61.0 5 0.00011 37.6 1.7 30 5-34 15-44 (403)
237 PRK06030 hypothetical protein; 61.0 36 0.00079 26.5 6.3 39 154-195 59-97 (124)
238 PRK05654 acetyl-CoA carboxylas 60.9 1.7 3.6E-05 39.0 -1.4 29 4-33 28-56 (292)
239 COG3355 Predicted transcriptio 60.8 22 0.00048 27.8 5.0 37 156-193 32-68 (126)
240 PF14768 RPA_interact_C: Repli 60.7 7.3 0.00016 28.0 2.2 26 5-34 1-26 (82)
241 KOG0834 CDK9 kinase-activating 60.6 6.4 0.00014 35.8 2.2 90 108-198 150-248 (323)
242 PRK14088 dnaA chromosomal repl 60.4 16 0.00036 34.5 5.1 43 150-195 370-415 (440)
243 cd00729 rubredoxin_SM Rubredox 60.4 7.6 0.00017 23.0 1.9 8 24-31 19-26 (34)
244 PF12172 DUF35_N: Rubredoxin-l 60.4 4.5 9.7E-05 24.2 0.9 21 4-30 12-32 (37)
245 PRK00135 scpB segregation and 60.2 33 0.00071 28.7 6.3 78 147-229 4-94 (188)
246 PRK11014 transcriptional repre 60.2 22 0.00047 27.9 5.1 44 150-194 9-52 (141)
247 PRK14559 putative protein seri 60.0 4.7 0.0001 40.2 1.4 24 5-34 29-52 (645)
248 PF04216 FdhE: Protein involve 60.0 5.4 0.00012 35.5 1.7 29 4-32 173-206 (290)
249 COG4391 Uncharacterized protei 60.0 5.7 0.00012 26.9 1.4 20 14-33 38-58 (62)
250 COG1725 Predicted transcriptio 59.8 14 0.00029 29.0 3.7 27 167-194 36-62 (125)
251 cd04476 RPA1_DBD_C RPA1_DBD_C: 59.6 6.6 0.00014 31.8 2.0 27 4-33 35-61 (166)
252 PF01155 HypA: Hydrogenase exp 59.1 2.7 5.8E-05 32.1 -0.4 19 15-33 62-80 (113)
253 PF11023 DUF2614: Protein of u 59.1 3.4 7.3E-05 31.6 0.2 27 4-34 70-96 (114)
254 COG1510 Predicted transcriptio 58.8 13 0.00029 30.6 3.6 37 156-193 31-67 (177)
255 PF09986 DUF2225: Uncharacteri 58.7 7.8 0.00017 33.0 2.4 13 24-36 49-61 (214)
256 TIGR00595 priA primosomal prot 58.6 7.9 0.00017 37.4 2.7 29 4-34 223-251 (505)
257 PF03685 UPF0147: Uncharacteri 58.2 57 0.0012 23.7 6.4 54 102-159 4-57 (85)
258 PF01047 MarR: MarR family; I 57.9 34 0.00074 22.1 5.0 28 166-194 17-44 (59)
259 PF13384 HTH_23: Homeodomain-l 57.7 19 0.00042 22.5 3.6 27 166-193 17-43 (50)
260 COG4643 Uncharacterized protei 57.7 5.6 0.00012 36.2 1.4 26 5-30 34-61 (366)
261 COG1779 C4-type Zn-finger prot 57.5 5.2 0.00011 33.7 1.1 36 4-40 15-60 (201)
262 PF07191 zinc-ribbons_6: zinc- 57.2 10 0.00022 26.6 2.3 27 4-34 2-28 (70)
263 PRK05580 primosome assembly pr 57.0 8.5 0.00018 38.6 2.7 28 4-33 391-418 (679)
264 PF01485 IBR: IBR domain; Int 56.9 6.9 0.00015 25.8 1.5 28 4-33 19-50 (64)
265 PF05344 DUF746: Domain of Unk 56.9 30 0.00064 23.8 4.5 36 160-196 7-42 (65)
266 TIGR01562 FdhE formate dehydro 56.5 9.4 0.0002 34.5 2.6 9 25-33 254-262 (305)
267 PRK03564 formate dehydrogenase 56.5 10 0.00022 34.3 2.8 9 4-12 188-196 (309)
268 TIGR01384 TFS_arch transcripti 56.4 11 0.00024 28.0 2.7 28 4-32 63-99 (104)
269 PRK00085 recO DNA repair prote 56.3 7.5 0.00016 33.4 1.9 27 4-30 150-177 (247)
270 PF08299 Bac_DnaA_C: Bacterial 56.3 27 0.00059 24.1 4.4 35 154-191 35-70 (70)
271 COG0777 AccD Acetyl-CoA carbox 56.2 3 6.5E-05 36.9 -0.6 29 4-33 29-57 (294)
272 TIGR00613 reco DNA repair prot 56.2 8.1 0.00018 33.1 2.1 28 4-31 148-176 (241)
273 PRK06393 rpoE DNA-directed RNA 56.0 7.3 0.00016 26.7 1.4 29 4-46 6-34 (64)
274 PRK15103 paraquat-inducible me 55.7 6.7 0.00015 37.0 1.6 31 4-34 11-41 (419)
275 PF13824 zf-Mss51: Zinc-finger 55.6 8.1 0.00017 25.7 1.5 24 5-33 1-24 (55)
276 PF08280 HTH_Mga: M protein tr 55.5 17 0.00036 24.1 3.1 34 164-198 17-50 (59)
277 PF01022 HTH_5: Bacterial regu 55.3 34 0.00073 21.4 4.4 31 162-193 11-41 (47)
278 COG0444 DppD ABC-type dipeptid 55.3 20 0.00042 32.6 4.4 92 143-254 155-250 (316)
279 PF05225 HTH_psq: helix-turn-h 55.1 50 0.0011 20.7 5.2 26 163-190 14-39 (45)
280 cd00974 DSRD Desulforedoxin (D 54.7 9.7 0.00021 22.4 1.7 23 4-27 5-27 (34)
281 PRK06260 threonine synthase; V 54.0 5.9 0.00013 36.9 1.0 30 1-34 1-30 (397)
282 PRK05550 bifunctional methioni 53.8 16 0.00034 32.7 3.5 32 18-49 31-64 (283)
283 PRK04330 hypothetical protein; 53.8 85 0.0019 22.9 6.7 53 102-158 7-59 (88)
284 PRK09392 ftrB transcriptional 53.7 42 0.00092 28.2 6.2 29 165-194 172-200 (236)
285 PRK03681 hypA hydrogenase nick 53.7 7.9 0.00017 29.6 1.5 19 14-32 61-79 (114)
286 TIGR00319 desulf_FeS4 desulfof 53.7 11 0.00024 22.1 1.8 22 5-27 9-30 (34)
287 PHA00689 hypothetical protein 53.7 9 0.00019 24.8 1.4 27 20-47 14-40 (62)
288 PF00320 GATA: GATA zinc finge 53.6 4.7 0.0001 24.2 0.1 27 6-32 1-29 (36)
289 PF09082 DUF1922: Domain of un 53.5 11 0.00024 26.2 2.0 25 5-33 5-29 (68)
290 PF04810 zf-Sec23_Sec24: Sec23 53.0 15 0.00032 22.5 2.4 29 4-32 3-33 (40)
291 PRK14873 primosome assembly pr 53.0 9.9 0.00022 38.1 2.4 27 4-32 393-419 (665)
292 PF03833 PolC_DP2: DNA polymer 52.9 4.5 9.8E-05 41.1 0.0 11 24-34 681-691 (900)
293 PF08063 PADR1: PADR1 (NUC008) 52.8 8.6 0.00019 25.5 1.3 21 4-27 15-35 (55)
294 smart00418 HTH_ARSR helix_turn 52.7 43 0.00092 21.2 4.9 30 164-194 8-37 (66)
295 smart00354 HTH_LACI helix_turn 52.7 39 0.00084 23.1 4.8 47 168-227 2-48 (70)
296 PF01396 zf-C4_Topoisom: Topoi 52.6 17 0.00037 22.2 2.6 30 3-33 1-34 (39)
297 COG0177 Nth Predicted EndoIII- 52.2 73 0.0016 27.2 7.2 77 136-225 75-152 (211)
298 TIGR00340 zpr1_rel ZPR1-relate 51.5 11 0.00023 30.9 1.9 28 6-34 1-39 (163)
299 smart00420 HTH_DEOR helix_turn 51.4 55 0.0012 20.0 5.1 29 165-194 13-41 (53)
300 COG0229 Conserved domain frequ 51.3 10 0.00022 30.0 1.7 32 18-49 37-70 (140)
301 PRK04023 DNA polymerase II lar 51.3 10 0.00022 39.4 2.1 26 209-234 946-974 (1121)
302 PF04967 HTH_10: HTH DNA bindi 51.2 36 0.00078 22.4 4.1 27 167-194 24-50 (53)
303 PHA03074 late transcription fa 51.1 7.8 0.00017 32.7 1.1 29 3-34 4-32 (225)
304 PF13443 HTH_26: Cro/C1-type H 50.8 21 0.00045 23.5 3.0 45 167-226 11-55 (63)
305 PF14319 Zn_Tnp_IS91: Transpos 50.7 5.7 0.00012 30.3 0.2 34 4-39 43-76 (111)
306 PRK10572 DNA-binding transcrip 50.7 84 0.0018 27.4 7.8 86 113-220 202-288 (290)
307 TIGR02297 HpaA 4-hydroxyphenyl 50.6 68 0.0015 27.8 7.1 37 152-190 189-225 (287)
308 PF01710 HTH_Tnp_IS630: Transp 50.5 85 0.0018 23.8 6.8 76 112-196 20-100 (119)
309 PRK07218 replication factor A; 50.3 7 0.00015 36.9 0.8 21 4-32 298-318 (423)
310 smart00344 HTH_ASNC helix_turn 50.2 43 0.00093 24.6 5.0 66 165-232 16-95 (108)
311 smart00647 IBR In Between Ring 50.2 16 0.00034 24.1 2.4 28 4-33 19-50 (64)
312 PF01381 HTH_3: Helix-turn-hel 50.2 18 0.00038 23.0 2.6 46 165-226 8-53 (55)
313 KOG1921 Endonuclease III [Repl 50.1 59 0.0013 28.5 6.3 111 100-224 90-202 (286)
314 PF06044 DRP: Dam-replacing fa 50.1 10 0.00022 33.0 1.7 29 4-33 32-63 (254)
315 PF14471 DUF4428: Domain of un 50.0 5.5 0.00012 26.0 0.0 28 5-33 1-30 (51)
316 TIGR02392 rpoH_proteo alternat 49.9 37 0.0008 29.7 5.3 31 164-195 234-264 (270)
317 PF08006 DUF1700: Protein of u 49.8 32 0.00069 28.2 4.6 41 112-152 6-47 (181)
318 PF01412 ArfGap: Putative GTPa 49.7 6.2 0.00013 30.2 0.3 30 4-33 14-43 (116)
319 smart00709 Zpr1 Duplicated dom 49.4 14 0.00031 30.0 2.4 38 102-139 98-137 (160)
320 PF02796 HTH_7: Helix-turn-hel 49.2 22 0.00049 22.1 2.8 21 167-188 22-42 (45)
321 PF04502 DUF572: Family of unk 49.2 8 0.00017 35.1 1.0 25 4-28 78-102 (324)
322 PF00392 GntR: Bacterial regul 48.9 30 0.00064 23.1 3.6 30 164-194 21-51 (64)
323 cd07377 WHTH_GntR Winged helix 48.6 32 0.00069 22.4 3.7 26 168-194 27-52 (66)
324 KOG0856 Predicted pilin-like t 48.3 10 0.00022 30.1 1.3 33 18-50 49-83 (146)
325 PF05066 HARE-HTH: HB1, ASXL, 48.2 15 0.00032 25.3 2.1 33 129-161 19-53 (72)
326 TIGR00122 birA_repr_reg BirA b 48.2 48 0.001 22.3 4.6 30 163-193 10-39 (69)
327 PRK10840 transcriptional regul 47.9 61 0.0013 26.7 6.2 33 165-198 164-196 (216)
328 PRK13500 transcriptional activ 47.8 1.9E+02 0.0042 25.6 9.7 39 151-191 208-246 (312)
329 smart00529 HTH_DTXR Helix-turn 47.6 79 0.0017 22.5 6.0 29 113-144 2-30 (96)
330 PHA01976 helix-turn-helix prot 47.6 62 0.0013 21.4 5.1 46 165-226 14-59 (67)
331 TIGR01562 FdhE formate dehydro 47.5 11 0.00025 33.9 1.7 28 4-31 185-218 (305)
332 PRK14714 DNA polymerase II lar 47.4 10 0.00023 40.3 1.6 10 182-191 937-946 (1337)
333 PF01907 Ribosomal_L37e: Ribos 47.4 12 0.00025 24.9 1.3 23 5-32 17-39 (55)
334 PF00488 MutS_V: MutS domain V 47.4 21 0.00044 30.8 3.2 27 113-139 208-234 (235)
335 PRK04217 hypothetical protein; 47.3 34 0.00073 26.1 4.0 30 167-197 59-88 (110)
336 PRK00118 putative DNA-binding 46.7 60 0.0013 24.4 5.2 30 166-196 33-62 (104)
337 cd00090 HTH_ARSR Arsenical Res 46.5 61 0.0013 21.1 5.0 27 167-194 21-47 (78)
338 PRK01110 rpmF 50S ribosomal pr 46.5 14 0.00031 24.9 1.6 28 4-39 28-55 (60)
339 PRK11475 DNA-binding transcrip 46.1 65 0.0014 27.1 6.0 32 166-198 149-180 (207)
340 PF00126 HTH_1: Bacterial regu 46.1 71 0.0015 20.9 5.1 30 168-198 15-44 (60)
341 PF03367 zf-ZPR1: ZPR1 zinc-fi 45.7 11 0.00023 30.8 1.1 38 102-139 100-138 (161)
342 PRK09636 RNA polymerase sigma 45.5 80 0.0017 27.8 6.8 55 167-223 132-186 (293)
343 COG5333 CCL1 Cdk activating ki 45.4 46 0.001 29.9 5.1 45 126-170 169-213 (297)
344 COG4311 SoxD Sarcosine oxidase 45.1 10 0.00022 28.0 0.8 11 1-11 1-11 (97)
345 PF14206 Cys_rich_CPCC: Cystei 45.0 20 0.00044 25.6 2.3 27 4-33 2-30 (78)
346 TIGR01889 Staph_reg_Sar staphy 44.9 61 0.0013 24.1 5.2 34 160-194 37-70 (109)
347 PRK06450 threonine synthase; V 44.6 11 0.00023 34.5 1.0 29 1-34 1-29 (338)
348 cd06171 Sigma70_r4 Sigma70, re 44.6 46 0.00099 20.1 3.9 28 167-195 27-54 (55)
349 smart00400 ZnF_CHCC zinc finge 44.5 27 0.00058 22.7 2.8 34 4-39 3-37 (55)
350 COG2816 NPY1 NTP pyrophosphohy 44.1 14 0.0003 32.9 1.7 28 4-33 112-139 (279)
351 PF09889 DUF2116: Uncharacteri 43.8 6.9 0.00015 26.4 -0.2 25 4-34 4-29 (59)
352 cd07973 Spt4 Transcription elo 43.6 14 0.00031 27.5 1.4 28 3-33 3-30 (98)
353 PF03811 Zn_Tnp_IS1: InsA N-te 43.5 20 0.00043 21.6 1.8 13 4-17 6-19 (36)
354 TIGR03879 near_KaiC_dom probab 43.5 35 0.00076 24.0 3.3 24 167-191 33-56 (73)
355 COG1522 Lrp Transcriptional re 43.4 36 0.00077 26.6 3.9 32 162-194 18-49 (154)
356 PRK00564 hypA hydrogenase nick 43.4 9.7 0.00021 29.3 0.5 20 13-32 61-80 (117)
357 PF01363 FYVE: FYVE zinc finge 43.2 17 0.00036 24.7 1.6 29 4-36 10-38 (69)
358 COG1321 TroR Mn-dependent tran 43.1 54 0.0012 26.4 4.8 73 155-229 14-98 (154)
359 KOG2907 RNA polymerase I trans 43.1 8.3 0.00018 29.4 0.1 31 3-35 7-37 (116)
360 PF12840 HTH_20: Helix-turn-he 43.0 45 0.00097 21.9 3.7 31 162-193 20-50 (61)
361 PRK13719 conjugal transfer tra 43.0 45 0.00097 28.6 4.5 33 165-198 157-189 (217)
362 PRK10130 transcriptional regul 42.9 2.7E+02 0.0058 25.5 11.4 42 148-191 239-280 (350)
363 smart00105 ArfGap Putative GTP 42.6 15 0.00032 27.9 1.5 31 4-34 4-34 (112)
364 TIGR00498 lexA SOS regulatory 42.5 42 0.0009 27.8 4.3 33 161-194 20-53 (199)
365 PF09779 Ima1_N: Ima1 N-termin 42.4 16 0.00035 28.6 1.6 29 4-32 1-29 (131)
366 PRK14987 gluconate operon tran 42.4 29 0.00064 30.6 3.6 48 166-226 5-52 (331)
367 smart00346 HTH_ICLR helix_turn 42.3 99 0.0022 21.6 5.8 29 165-194 19-47 (91)
368 TIGR02642 phage_xxxx uncharact 42.3 15 0.00033 30.7 1.6 23 4-30 100-122 (186)
369 PRK06386 replication factor A; 42.2 13 0.00028 34.3 1.3 21 4-32 237-257 (358)
370 cd04762 HTH_MerR-trunc Helix-T 42.1 35 0.00075 20.5 2.9 22 168-190 2-23 (49)
371 PF04216 FdhE: Protein involve 42.0 18 0.0004 32.1 2.2 34 4-39 212-252 (290)
372 PF09862 DUF2089: Protein of u 41.6 65 0.0014 24.7 4.8 48 168-221 51-98 (113)
373 smart00351 PAX Paired Box doma 41.5 1.3E+02 0.0028 23.1 6.6 61 112-175 35-102 (125)
374 PF08221 HTH_9: RNA polymerase 41.3 87 0.0019 21.0 5.0 41 152-194 14-54 (62)
375 PRK04179 rpl37e 50S ribosomal 41.2 12 0.00027 25.4 0.7 23 4-31 18-40 (62)
376 COG1198 PriA Primosomal protei 41.2 21 0.00045 36.2 2.6 27 4-32 445-471 (730)
377 TIGR02844 spore_III_D sporulat 40.9 32 0.0007 24.6 2.9 23 165-188 18-40 (80)
378 PRK03975 tfx putative transcri 40.7 95 0.0021 24.7 5.8 31 165-196 20-50 (141)
379 PF04552 Sigma54_DBD: Sigma-54 40.7 9.1 0.0002 31.2 0.0 24 165-189 48-71 (160)
380 PRK08329 threonine synthase; V 40.7 19 0.0004 33.0 2.0 26 3-34 1-26 (347)
381 PRK08558 adenine phosphoribosy 40.6 43 0.00094 29.0 4.2 56 159-227 16-72 (238)
382 PRK15411 rcsA colanic acid cap 40.4 49 0.0011 27.7 4.4 33 165-198 151-183 (207)
383 PRK10188 DNA-binding transcrip 40.3 93 0.002 26.8 6.2 33 165-198 193-225 (240)
384 COG3677 Transposase and inacti 40.3 20 0.00044 28.1 1.9 30 3-33 30-63 (129)
385 PRK15435 bifunctional DNA-bind 40.2 1.1E+02 0.0024 28.1 7.0 74 150-227 86-179 (353)
386 PF04079 DUF387: Putative tran 40.2 81 0.0018 25.6 5.5 64 151-220 2-74 (159)
387 PRK08197 threonine synthase; V 40.2 13 0.00028 34.6 0.9 26 4-34 8-33 (394)
388 PF09334 tRNA-synt_1g: tRNA sy 40.2 14 0.00031 34.4 1.2 24 4-34 137-160 (391)
389 PF06163 DUF977: Bacterial pro 40.1 59 0.0013 25.5 4.3 45 151-198 13-57 (127)
390 smart00290 ZnF_UBP Ubiquitin C 40.0 23 0.00049 22.3 1.8 22 5-34 1-22 (50)
391 PF10005 DUF2248: Uncharacteri 40.0 16 0.00036 33.4 1.5 24 5-34 1-24 (343)
392 TIGR02395 rpoN_sigma RNA polym 39.9 61 0.0013 30.7 5.4 24 165-189 317-340 (429)
393 smart00064 FYVE Protein presen 39.8 20 0.00043 24.2 1.6 30 4-37 11-40 (68)
394 COG1571 Predicted DNA-binding 39.7 16 0.00035 34.4 1.4 33 4-39 351-383 (421)
395 PRK14714 DNA polymerase II lar 39.7 13 0.00028 39.6 0.9 8 25-32 694-701 (1337)
396 PRK10870 transcriptional repre 39.3 63 0.0014 26.4 4.8 38 156-194 61-98 (176)
397 cd04761 HTH_MerR-SF Helix-Turn 39.3 37 0.00081 20.8 2.8 21 168-189 2-22 (49)
398 COG1123 ATPase components of v 39.3 35 0.00075 33.3 3.7 60 181-254 190-251 (539)
399 TIGR02947 SigH_actino RNA poly 39.0 86 0.0019 25.5 5.7 29 167-196 148-176 (193)
400 COG2390 DeoR Transcriptional r 38.9 1.2E+02 0.0025 27.7 6.8 66 150-225 15-82 (321)
401 COG2126 RPL37A Ribosomal prote 38.7 13 0.00027 25.0 0.4 25 4-33 17-41 (61)
402 PF07295 DUF1451: Protein of u 38.7 15 0.00033 29.4 1.0 15 20-34 109-123 (146)
403 COG2771 CsgD DNA-binding HTH d 38.7 90 0.0019 20.1 4.8 31 167-198 20-50 (65)
404 PF12085 DUF3562: Protein of u 38.7 1.3E+02 0.0027 20.8 5.3 43 168-220 9-51 (66)
405 TIGR01764 excise DNA binding d 38.5 43 0.00092 20.3 2.9 22 167-189 2-23 (49)
406 COG1654 BirA Biotin operon rep 38.5 85 0.0019 22.4 4.7 35 162-198 15-49 (79)
407 PRK03573 transcriptional regul 38.4 78 0.0017 24.5 5.1 31 163-194 43-73 (144)
408 PRK09645 RNA polymerase sigma 38.4 80 0.0017 25.0 5.3 30 166-196 134-167 (173)
409 PRK09978 DNA-binding transcrip 38.2 1.5E+02 0.0033 26.2 7.4 41 148-190 141-181 (274)
410 PF12651 RHH_3: Ribbon-helix-h 38.0 75 0.0016 19.8 3.9 28 108-135 12-40 (44)
411 PRK15121 right oriC-binding tr 38.0 1.5E+02 0.0032 26.1 7.3 76 150-227 6-102 (289)
412 smart00342 HTH_ARAC helix_turn 37.8 53 0.0011 22.0 3.6 25 166-191 1-25 (84)
413 PF01371 Trp_repressor: Trp re 37.7 71 0.0015 23.3 4.3 31 162-193 45-75 (87)
414 PRK10014 DNA-binding transcrip 37.6 50 0.0011 29.2 4.3 49 166-227 6-54 (342)
415 PRK10371 DNA-binding transcrip 37.6 1.2E+02 0.0026 26.9 6.7 40 150-191 192-231 (302)
416 PRK11169 leucine-responsive tr 37.5 67 0.0015 25.8 4.7 68 162-231 24-107 (164)
417 COG3024 Uncharacterized protei 37.5 17 0.00038 24.9 0.9 28 3-32 7-36 (65)
418 PF13408 Zn_ribbon_recom: Reco 37.4 17 0.00036 23.5 0.9 14 21-34 3-16 (58)
419 PRK00149 dnaA chromosomal repl 37.3 72 0.0016 30.1 5.5 43 153-198 391-434 (450)
420 smart00347 HTH_MARR helix_turn 37.3 93 0.002 21.8 5.0 28 166-194 24-51 (101)
421 PF06676 DUF1178: Protein of u 37.2 18 0.0004 29.1 1.2 40 105-146 82-121 (148)
422 PF13913 zf-C2HC_2: zinc-finge 37.2 21 0.00046 19.5 1.1 9 3-11 2-10 (25)
423 PRK09642 RNA polymerase sigma 37.1 87 0.0019 24.5 5.2 32 161-195 119-150 (160)
424 PRK05932 RNA polymerase factor 37.0 60 0.0013 31.0 4.9 24 165-189 342-365 (455)
425 TIGR02937 sigma70-ECF RNA poly 36.8 59 0.0013 24.4 4.1 30 166-196 126-155 (158)
426 PF13878 zf-C2H2_3: zinc-finge 36.7 16 0.00034 22.6 0.6 17 21-37 11-27 (41)
427 TIGR00721 tfx DNA-binding prot 36.7 65 0.0014 25.6 4.3 32 165-197 20-51 (137)
428 PRK13501 transcriptional activ 36.7 2.6E+02 0.0056 24.3 8.7 29 161-190 187-215 (290)
429 TIGR02859 spore_sigH RNA polym 36.6 54 0.0012 26.7 4.1 31 166-197 165-195 (198)
430 TIGR01391 dnaG DNA primase, ca 36.2 33 0.00071 32.3 2.9 34 4-39 35-69 (415)
431 smart00530 HTH_XRE Helix-turn- 36.2 92 0.002 18.2 4.6 46 165-226 9-54 (56)
432 PF13560 HTH_31: Helix-turn-he 36.1 73 0.0016 21.0 4.0 50 163-227 11-60 (64)
433 PRK12542 RNA polymerase sigma 36.0 1.3E+02 0.0028 24.3 6.2 34 160-196 134-167 (185)
434 PRK07598 RNA polymerase sigma 35.9 96 0.0021 29.3 6.0 32 164-196 368-399 (415)
435 PRK14018 trifunctional thiored 35.9 21 0.00046 34.7 1.7 32 18-49 413-446 (521)
436 PRK00750 lysK lysyl-tRNA synth 35.9 29 0.00062 33.6 2.6 32 5-37 177-213 (510)
437 PRK03564 formate dehydrogenase 35.8 20 0.00044 32.4 1.4 8 23-30 226-233 (309)
438 PRK04016 DNA-directed RNA poly 35.8 15 0.00032 25.1 0.4 12 24-35 5-16 (62)
439 PF05043 Mga: Mga helix-turn-h 35.8 46 0.001 23.5 3.1 33 163-196 27-59 (87)
440 PF01418 HTH_6: Helix-turn-hel 35.7 37 0.00081 23.7 2.5 25 165-190 33-57 (77)
441 PF12728 HTH_17: Helix-turn-he 35.5 48 0.001 20.8 2.8 22 167-189 2-23 (51)
442 PRK09393 ftrA transcriptional 35.3 1.5E+02 0.0033 26.4 7.0 39 165-218 282-321 (322)
443 PRK09978 DNA-binding transcrip 35.3 1.9E+02 0.0042 25.6 7.5 49 165-228 205-254 (274)
444 PRK15340 transcriptional regul 35.2 2.1E+02 0.0045 24.5 7.4 54 123-190 95-148 (216)
445 PRK09483 response regulator; P 35.1 57 0.0012 26.4 4.0 32 166-198 163-194 (217)
446 PF06689 zf-C4_ClpX: ClpX C4-t 34.9 16 0.00035 22.5 0.5 28 4-31 2-32 (41)
447 TIGR00281 segregation and cond 34.8 1.3E+02 0.0028 25.1 6.0 42 149-195 3-46 (186)
448 COG1107 Archaea-specific RecJ- 34.7 29 0.00062 34.2 2.3 29 3-32 2-30 (715)
449 PRK03902 manganese transport t 34.6 99 0.0021 24.1 5.1 62 164-227 20-93 (142)
450 COG2260 Predicted Zn-ribbon RN 34.6 19 0.00041 24.2 0.8 23 3-33 5-27 (59)
451 cd00065 FYVE FYVE domain; Zinc 34.6 28 0.0006 22.5 1.6 31 3-37 2-32 (57)
452 PRK11179 DNA-binding transcrip 34.5 87 0.0019 24.8 4.8 32 162-194 19-50 (153)
453 PHA02591 hypothetical protein; 34.5 64 0.0014 23.1 3.4 30 159-189 52-81 (83)
454 TIGR02957 SigX4 RNA polymerase 34.2 1.8E+02 0.0038 25.5 7.2 61 166-229 124-184 (281)
455 PF13518 HTH_28: Helix-turn-he 34.1 99 0.0021 19.1 4.2 25 168-193 14-38 (52)
456 COG4608 AppF ABC-type oligopep 33.8 48 0.001 29.4 3.4 75 109-198 85-162 (268)
457 PF13551 HTH_29: Winged helix- 33.7 1.1E+02 0.0025 22.0 5.1 30 162-193 9-38 (112)
458 PRK04194 hypothetical protein; 33.7 98 0.0021 29.0 5.6 50 110-159 75-139 (392)
459 PF00376 MerR: MerR family reg 33.6 45 0.00098 20.1 2.3 19 168-187 1-19 (38)
460 PRK13501 transcriptional activ 33.6 2.1E+02 0.0046 24.9 7.6 32 158-190 232-265 (290)
461 PRK09526 lacI lac repressor; R 33.5 37 0.00081 30.0 2.8 23 166-189 5-27 (342)
462 PRK08241 RNA polymerase factor 33.4 1.1E+02 0.0024 27.4 5.9 63 166-230 169-235 (339)
463 PF00440 TetR_N: Bacterial reg 33.3 1.2E+02 0.0025 18.7 4.4 35 154-189 4-38 (47)
464 TIGR01321 TrpR trp operon repr 33.0 59 0.0013 24.1 3.3 29 162-191 51-79 (94)
465 PRK09726 antitoxin HipB; Provi 32.9 1.3E+02 0.0029 21.3 5.2 51 165-231 24-74 (88)
466 PRK12423 LexA repressor; Provi 32.8 1.4E+02 0.003 24.9 6.0 37 157-194 16-53 (202)
467 COG5525 Bacteriophage tail ass 32.8 24 0.00051 34.7 1.4 39 5-44 229-279 (611)
468 PRK12543 RNA polymerase sigma 32.8 1.1E+02 0.0023 24.6 5.2 33 160-195 129-161 (179)
469 PRK00215 LexA repressor; Valid 32.7 76 0.0016 26.3 4.4 33 161-194 18-51 (205)
470 PRK11032 hypothetical protein; 32.7 22 0.00048 29.0 1.0 14 20-33 121-134 (160)
471 PRK08173 DNA topoisomerase III 32.6 26 0.00057 36.2 1.8 27 4-34 625-651 (862)
472 PF14951 DUF4503: Domain of un 32.4 27 0.00059 32.1 1.7 33 5-38 276-309 (389)
473 PF12677 DUF3797: Domain of un 32.4 35 0.00076 22.1 1.7 8 4-11 14-21 (49)
474 TIGR01053 LSD1 zinc finger dom 32.3 60 0.0013 18.8 2.6 28 4-33 2-29 (31)
475 COG2197 CitB Response regulato 32.2 71 0.0015 26.9 4.1 33 165-198 162-194 (211)
476 COG1885 Uncharacterized protei 32.0 59 0.0013 24.5 3.1 9 4-12 50-58 (115)
477 COG5134 Uncharacterized conser 32.0 37 0.0008 29.0 2.3 25 4-28 80-104 (272)
478 PF10543 ORF6N: ORF6N domain; 31.9 64 0.0014 23.3 3.3 30 167-197 13-42 (88)
479 PF08421 Methyltransf_13: Puta 31.8 27 0.00059 23.5 1.2 17 23-39 40-56 (62)
480 TIGR02985 Sig70_bacteroi1 RNA 31.8 76 0.0016 24.4 4.0 30 166-196 129-158 (161)
481 PRK13870 transcriptional regul 31.4 67 0.0015 27.6 3.9 32 166-198 188-219 (234)
482 TIGR02384 RelB_DinJ addiction 31.2 1.5E+02 0.0032 21.2 5.1 45 119-170 6-50 (83)
483 PRK12469 RNA polymerase factor 31.2 1.2E+02 0.0026 29.3 5.8 24 165-189 368-391 (481)
484 PF08772 NOB1_Zn_bind: Nin one 31.1 26 0.00056 24.7 1.0 11 1-11 22-32 (73)
485 PF12793 SgrR_N: Sugar transpo 31.1 79 0.0017 24.1 3.8 66 163-229 16-88 (115)
486 PF07022 Phage_CI_repr: Bacter 31.0 43 0.00093 22.6 2.1 42 168-226 14-56 (66)
487 PRK06759 RNA polymerase factor 31.0 80 0.0017 24.4 4.1 30 166-196 122-151 (154)
488 COG1499 NMD3 NMD protein affec 30.9 18 0.0004 33.3 0.3 12 1-12 4-15 (355)
489 PRK10360 DNA-binding transcrip 30.6 1.5E+02 0.0032 23.4 5.7 31 167-198 153-183 (196)
490 PF14502 HTH_41: Helix-turn-he 30.6 91 0.002 20.1 3.4 28 167-195 7-34 (48)
491 TIGR02607 antidote_HigA addict 30.5 1.7E+02 0.0037 19.8 5.3 49 163-227 15-63 (78)
492 PF10886 DUF2685: Protein of u 30.5 22 0.00047 23.5 0.5 36 3-39 1-39 (54)
493 PRK15320 transcriptional activ 30.4 80 0.0017 27.0 4.0 33 165-198 178-210 (251)
494 PRK09480 slmA division inhibit 30.3 79 0.0017 25.3 4.1 42 147-189 11-52 (194)
495 PRK15418 transcriptional regul 30.2 1.1E+02 0.0024 27.6 5.2 60 165-227 28-87 (318)
496 PF07900 DUF1670: Protein of u 30.1 98 0.0021 26.6 4.5 32 165-197 104-135 (220)
497 TIGR03070 couple_hipB transcri 30.1 1.4E+02 0.0031 18.5 5.5 44 165-224 14-57 (58)
498 PRK09393 ftrA transcriptional 30.0 1.9E+02 0.004 25.8 6.7 40 150-191 219-258 (322)
499 PF00628 PHD: PHD-finger; Int 30.0 35 0.00075 21.5 1.5 24 5-33 1-24 (51)
500 PRK11923 algU RNA polymerase s 29.9 1.2E+02 0.0026 24.6 5.1 31 166-197 154-184 (193)
No 1
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=100.00 E-value=8.6e-56 Score=396.88 Aligned_cols=219 Identities=32% Similarity=0.569 Sum_probs=202.4
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeecccccccCcccccccCCCCCCCCcccCCCCCccccCCCcceEEecCCCCC
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAGG 83 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~~~~d~~r~G~~~~~~~~~~~~~t~i~~~~~~~ 83 (254)
..||+||+ +++|+|+++|++||++||+|++|++||+|||||+|++++ .+|++|+|+|.++++||.|++|.|++++.++
T Consensus 12 ~~Cp~Cg~-~~iv~d~~~Ge~vC~~CG~Vl~e~~iD~g~EWR~f~~~~-~~~~~RvG~~~~~~~~~~gl~T~I~~~~~~~ 89 (310)
T PRK00423 12 LVCPECGS-DKLIYDYERGEIVCADCGLVIEENIIDQGPEWRAFDPEQ-REKRSRVGAPMTYTIHDKGLSTDIDWRNKDS 89 (310)
T ss_pred CcCcCCCC-CCeeEECCCCeEeecccCCcccccccccCCCccCCCccc-cCCccccCCCCCccccCCCCceEeecCCccc
Confidence 57999998 789999999999999999999999999999999999754 4689999999999999999999999877666
Q ss_pred Ccccccc-------ccccccccC---CCchhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHH
Q 025357 84 STELLSG-------SLGKLQARS---SHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVA 153 (254)
Q Consensus 84 ~~~~l~~-------~l~~~~~~~---~~~~r~l~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaA 153 (254)
+|+.++. +|++||++. +++||+|..++++|+++|+.|+||+.++++|..||+++.+.++++||++++++|
T Consensus 90 ~g~~l~~~~~~~~~rl~~~~~~~~~~~~~er~l~~a~~~I~~~~~~L~Lp~~v~e~A~~iyk~~~~~~~~rgrs~~~i~A 169 (310)
T PRK00423 90 YGKSISGKNRAQLYRLRKWQRRIRVSNAAERNLAFALSELDRIASQLGLPRSVREEAAVIYRKAVEKGLIRGRSIEGVVA 169 (310)
T ss_pred ccccccHHHHHHHHHHHHHhhhcccCChHhHHHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHH
Confidence 6655542 478898865 567999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcchhhee
Q 025357 154 ACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFFLFVL 231 (254)
Q Consensus 154 AclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~v~ 231 (254)
||||+|||++++|+|++||+++ +++++++|+++|+.|.+.|+++ +++.+|++||+|||++|+|++++...|
T Consensus 170 AclYiACR~~~~prtl~eI~~~-~~v~~k~i~~~~~~l~k~L~~~------~~~~~p~~~i~r~~~~L~L~~~v~~~A 240 (310)
T PRK00423 170 AALYAACRRCKVPRTLDEIAEV-SRVSRKEIGRCYRFLLRELNLK------LPPTDPIDYVPRFASELGLSGEVQKKA 240 (310)
T ss_pred HHHHHHHHHcCCCcCHHHHHHH-hCCCHHHHHHHHHHHHHHhCCC------CCCCCHHHHHHHHHHHcCCCHHHHHHH
Confidence 9999999999999999999995 8999999999999999999987 788999999999999999999887743
No 2
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=1.7e-52 Score=359.98 Aligned_cols=220 Identities=55% Similarity=0.815 Sum_probs=200.8
Q ss_pred CCCCCCCCCCc-eEEecCCCceEcCcCceeecccccccCcccccccCCCCCCCCcccCCCCCccccCCCcceEEecCCCC
Q 025357 4 SYCADCKRLTE-VVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAG 82 (254)
Q Consensus 4 ~~Cp~Cg~~~~-lv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~~~~d~~r~G~~~~~~~~~~~~~t~i~~~~~~ 82 (254)
++|++|+..+. +|+|+.+|++||..||+|+++++||.++|||+|++++++.|++|||++.+|++.+++++|+|+++. +
T Consensus 1 ~~c~~C~~~~~~~V~d~~~gdtvC~~CGlVl~~r~Id~~sEwrtfsnd~~~~DPsrvG~~sNPlL~~g~L~T~I~~g~-g 79 (308)
T KOG1597|consen 1 MTCPDCKRHPENLVEDHSAGDTVCSECGLVLEDRIIDEGSEWRTFSNDDSDADPSRVGASSNPLLDGGDLSTFISKGT-G 79 (308)
T ss_pred CCCCCCCCCCCCeeeeccCCceecccCCeeeccccccccccccccccCCCCCCccccCCCCCCCCCCCCcceeeecCC-C
Confidence 47999998765 999999999999999999999999999999999998889999999999999999999999999987 4
Q ss_pred CCccccccccccccccC--CCchhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHH
Q 025357 83 GSTELLSGSLGKLQARS--SHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIAC 160 (254)
Q Consensus 83 ~~~~~l~~~l~~~~~~~--~~~~r~l~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~Ac 160 (254)
.++..+ ..|.++|++. ++.|+.+..++..|..+++.++||..+.++|.++|+++.+.+.++||+.++++|||||+||
T Consensus 80 ~~s~~~-s~l~~~Q~~~sm~~~d~~~~~a~~~I~~m~d~~~Lp~~I~d~A~~ifk~v~~~k~lrGks~eai~AAclyiAC 158 (308)
T KOG1597|consen 80 TSSSFA-SSLGKAQNRNSMSNSDRVLKAAFKEITAMCDRLSLPATIKDRANEIFKLVEDSKLLRGKSVEALAAACLYIAC 158 (308)
T ss_pred CCHHHH-HHHHHHhcccccCCccHHHHHHHHHHHHHHHHhCCchHHHHHHHHHHHHHHHhhhhcCccHHHHHHHHHHHHH
Confidence 444333 3488899743 6789999999999999999999999999999999999999999999999999999999999
Q ss_pred HhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcchhhe
Q 025357 161 RQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFFLFV 230 (254)
Q Consensus 161 R~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~v 230 (254)
|+++.|||++||+.+ ++|+.++|+|++|.|.+.|+...+ ...++..+||+|||+.|+|++.+++-
T Consensus 159 Rq~~~pRT~kEI~~~-anv~kKEIgr~~K~i~~~l~~s~~----~~s~~t~~~m~RFCs~L~L~~~~q~a 223 (308)
T KOG1597|consen 159 RQEDVPRTFKEISAV-ANVSKKEIGRCVKLIGEALETSVD----LISISTGDFMPRFCSNLGLPKSAQEA 223 (308)
T ss_pred HhcCCCchHHHHHHH-HcCCHHHHHHHHHHHHHHHhccch----hhhhhHHHHHHHHHHhcCCCHHHHHH
Confidence 999999999999996 789999999999999999987732 33567999999999999999999874
No 3
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=100.00 E-value=7.2e-51 Score=357.85 Aligned_cols=210 Identities=37% Similarity=0.645 Sum_probs=194.1
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeecccccccCcccccccCCCCCCCCcccCCCCCccccCCCcceEEecCCCCC
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAGG 83 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~~~~d~~r~G~~~~~~~~~~~~~t~i~~~~~~~ 83 (254)
+.||+||+ +++++|++.|++||.+||+|++|+.||.|||||.|+ + ...+ |+|.|.++.+||.|++|.|+++..+
T Consensus 2 ~~CpeCg~-~~~~~d~~~ge~VC~~CG~Vi~~~~id~gpewr~f~-e--~~~~-r~g~P~t~~~~d~~l~t~i~~~~~~- 75 (285)
T COG1405 2 MSCPECGS-TNIITDYERGEIVCADCGLVLEDSLIDPGPEWRAFD-E--RHER-RVGAPLTPSIHDKGLSTIIGWGDKD- 75 (285)
T ss_pred CCCCCCCC-ccceeeccCCeEEeccCCEEeccccccCCCCccccc-c--cccc-cccCCCccccCccchhhhcccchhH-
Confidence 68999999 799999999999999999999999999999999993 2 2334 9999999999999999999987632
Q ss_pred CccccccccccccccC---CCchhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHH
Q 025357 84 STELLSGSLGKLQARS---SHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIAC 160 (254)
Q Consensus 84 ~~~~l~~~l~~~~~~~---~~~~r~l~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~Ac 160 (254)
...+|++||.+. +.+++++..++.+|.++++.|+||.++.++|..||+++.++++++||+.++++|||+|+||
T Consensus 76 ----~~~rlr~~~~~~~v~~~~ernl~~a~~~l~~~~~~l~LP~~v~e~A~~iyr~a~~~~l~rGRsie~v~AA~iY~ac 151 (285)
T COG1405 76 ----KMYRLRKWQIRIRVSSAKERNLITALEELERIASALGLPESVRETAARIYRKAVDKGLLRGRSIESVAAACIYAAC 151 (285)
T ss_pred ----HHHHHHHHHhccccccchhhHHHHHHHHHHHHHHHhCCCchHHHHHHHHHHHHhhcCCCcCCcHHHHHHHHHHHHH
Confidence 234588998653 4689999999999999999999999999999999999999999999999999999999999
Q ss_pred HhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcchhhe
Q 025357 161 RQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFFLFV 230 (254)
Q Consensus 161 R~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~v 230 (254)
|+++.|+|+.||++ ++++++++|+++|+.+.+.|++. +++.+|.+||+|||++|+|+++|...
T Consensus 152 R~~~~prtl~eIa~-a~~V~~kei~rtyr~~~~~L~l~------~~~~~p~~yi~rf~s~L~l~~~v~~~ 214 (285)
T COG1405 152 RINGVPRTLDEIAK-ALGVSKKEIGRTYRLLVRELKLK------IPPVDPSDYIPRFASKLGLSDEVRRK 214 (285)
T ss_pred HHcCCCccHHHHHH-HHCCCHHHHHHHHHHHHHhcCCC------CCCCCHHHHHHHHHHHcCCCHHHHHH
Confidence 99999999999999 48999999999999999999998 78899999999999999999999884
No 4
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=99.94 E-value=5.6e-27 Score=216.70 Aligned_cols=190 Identities=22% Similarity=0.358 Sum_probs=164.0
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeecccccccCcccccccCCCCCCCCcccCCCCCccccCCCcceEEecCCCCC
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIFANESSDHDPVRVGGPLNPLLSGGGLSTVIAKPTAGG 83 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f~~~~~~~d~~r~G~~~~~~~~~~~~~t~i~~~~~~~ 83 (254)
+.|++||+ +++-.|..+|..+|+.||.|++++.|.. | .+|.+. + -|+.|+....++
T Consensus 1 ~~C~~C~~-s~fe~d~a~g~~~C~~CG~v~E~~~ivs--e-v~F~e~-----------~---------~G~~v~~~~~g~ 56 (521)
T KOG1598|consen 1 MVCKNCGG-SNFERDEATGNLYCTACGTVLEYNNIVA--E-VTFVEG-----------A---------QGQFVRVGQSGA 56 (521)
T ss_pred CcCCCCCC-CCcccccccCCceeccccceeeccceeE--E-eeeecc-----------c---------ceeEEeccccCC
Confidence 47999999 7899999999999999999999999884 4 567632 1 134555433222
Q ss_pred CccccccccccccccCCCchhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhc
Q 025357 84 STELLSGSLGKLQARSSHPDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQE 163 (254)
Q Consensus 84 ~~~~l~~~l~~~~~~~~~~~r~l~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~ 163 (254)
.. ...++++++.++.+.|..++..|+|++ +++.|..+|+.+.+.++.+||+...++|+|+|++||++
T Consensus 57 ~~------------s~e~r~~t~~n~r~~i~~~~~~l~l~~-~~~~a~~~~k~a~~~nftkGr~~~~vvasClY~vcR~e 123 (521)
T KOG1598|consen 57 GS------------SLESREKTIYNARRLIEELTERLNLGN-KTEVAFNFFKLAPDRNFTKGRRSTEVVAACLYLVCRLE 123 (521)
T ss_pred cc------------chHHHHHHHHHHHhHHHHHHHhcCcch-HHHHHHHHHHHHhhCCCCCCcchHHHHHHHHHHHHHhh
Confidence 10 114578999999999999999999999 99999999999999999999999999999999999999
Q ss_pred CCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcchhheeeCc
Q 025357 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFFLFVLDFS 234 (254)
Q Consensus 164 ~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~v~~~~ 234 (254)
+.++.+.|++++ ++|+.+.|++.|++|.+.|.+... + .|.+||.-||+||+..|.+.+...+|+.++
T Consensus 124 ~t~hlliDfS~~-Lqv~Vy~LG~~~l~l~~~L~i~en--~-~plvDpsL~i~Rfa~~L~~g~~~~~Vv~~a 190 (521)
T KOG1598|consen 124 KTDHLLIDFSSY-LQVSVYDLGSNFLEVTDSLSIGEN--V-SPLVDPSLYIVRFSCRLLFGDKTEDVAKTA 190 (521)
T ss_pred CCceEEEEeccc-eEEehhhhhHHHHHHHHHhccccc--c-ccccCcceeeechhHhhhcCCchHHHHHHH
Confidence 999999999996 999999999999999999998743 2 688999999999999999888888888776
No 5
>PF00382 TFIIB: Transcription factor TFIIB repeat; InterPro: IPR013150 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. In eukaryotes, transcription initiation of all protein encoding genes involves the polymerase II system. This sytem is modulated by both general and specific transcription factors. The general factors (which include TFIIA, TFIIB, TFIID, TFIIE, TFIIF, TFIIG and TFIIH) operate through common promoter elements, such as the TATA box. Transcription factor IIB (TFIIB) is of central importance in transcription of class II genes. It associates with TFIID-TFIIA bound to DNA (the DA complex) to form a ternary TFIID-IIA-IBB (DAB) complex, which is recognised by RNA polymerase II [, ]. TFIIB comprises ~315-340 residues and contains an imperfect C-terminal repeat of a 75-residue domain that may contribute to the symmetry of the folded protein. The basal archaeal transcription machinery resembles that of the eukaryotic polymerase II system and includes a homologue of TFIIB []. This entry represents a cyclin-like domain which is found repeated in the C-terminal region of a variety of eukaryotic TFIIB's and their archaeal counterparts. These domains individually form the typical cyclin fold, and in the transcription complex they straddle the C-terminal region of the TATA-binding protein - an interaction essential for the formation of the transcription initiation complex [, ].; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2PHG_A 1C9B_Q 1TFB_A 1VOL_A 3K7A_M 1AIS_B 1D3U_B.
Probab=99.81 E-value=2e-19 Score=127.48 Aligned_cols=71 Identities=44% Similarity=0.836 Sum_probs=65.9
Q ss_pred HHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHH
Q 025357 113 ISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEI 184 (254)
Q Consensus 113 I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i 184 (254)
|+++|+.|+||+.+.+.|.++|+++.+.++.+||+|.+++|||||+|||+++.|+|++||+++ ++|++++|
T Consensus 1 I~r~~~~L~L~~~v~~~A~~i~~~~~~~~~~~Gr~~~~iaAA~iY~acr~~~~~~t~~eIa~~-~~Vs~~tI 71 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRERAKEIYKKAQERGLLKGRSPESIAAACIYLACRLNGVPRTLKEIAEA-AGVSEKTI 71 (71)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHHTTTSTTS-HHHHHHHHHHHHHHHTTSSSSHHHHHHH-CTSSHHHH
T ss_pred ChHHHhHcCCCHHHHHHHHHHHHHHHHcCCcccCCHHHHHHHHHHHHHHHcCCCcCHHHHHHH-hCCCCCcC
Confidence 689999999999999999999999999999999999999999999999999999999999995 99999986
No 6
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=99.64 E-value=1.5e-15 Score=136.68 Aligned_cols=90 Identities=22% Similarity=0.381 Sum_probs=86.0
Q ss_pred HHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHH
Q 025357 108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA 187 (254)
Q Consensus 108 ~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~ 187 (254)
+...+|.++|+.|+||..+.+.|.+|++++.+.+++.||+|.++||||||+||+.+|.|+|++||+++ ++|++.+|++.
T Consensus 218 ~p~~~i~r~~~~L~L~~~v~~~A~~i~~~a~~~~l~~Gr~P~sIAAAaIYlA~~~~g~~~t~keIa~v-~~Vs~~tI~~~ 296 (310)
T PRK00423 218 DPIDYVPRFASELGLSGEVQKKAIEILQKAKEKGLTSGKGPTGLAAAAIYIASLLLGERRTQREVAEV-AGVTEVTVRNR 296 (310)
T ss_pred CHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCcccCCCHHHHHHHHHHHHHHHhCCCCCHHHHHHH-cCCCHHHHHHH
Confidence 35789999999999999999999999999999999999999999999999999999999999999995 99999999999
Q ss_pred HHHHHHHhchh
Q 025357 188 KEFIVKHLEAE 198 (254)
Q Consensus 188 ~k~l~~~l~~~ 198 (254)
|++|.+.|++.
T Consensus 297 ykel~~~l~~~ 307 (310)
T PRK00423 297 YKELAEKLDIK 307 (310)
T ss_pred HHHHHHHhCcc
Confidence 99999999865
No 7
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=99.61 E-value=3.2e-16 Score=100.14 Aligned_cols=43 Identities=47% Similarity=1.025 Sum_probs=38.8
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeecccccccCcccccc
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRIF 47 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~f 47 (254)
++||+||+ +.+++|+.+|++||++||+|++|+.++.++|||+|
T Consensus 1 m~Cp~Cg~-~~~~~D~~~g~~vC~~CG~Vl~e~~i~~~~e~r~f 43 (43)
T PF08271_consen 1 MKCPNCGS-KEIVFDPERGELVCPNCGLVLEENIIDEGPEWREF 43 (43)
T ss_dssp ESBTTTSS-SEEEEETTTTEEEETTT-BBEE-TTBSCCCSCCHC
T ss_pred CCCcCCcC-CceEEcCCCCeEECCCCCCEeecccccCCcccccC
Confidence 47999999 67999999999999999999999999999999987
No 8
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=99.52 E-value=4.5e-14 Score=124.84 Aligned_cols=90 Identities=27% Similarity=0.371 Sum_probs=87.0
Q ss_pred HHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHH
Q 025357 108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA 187 (254)
Q Consensus 108 ~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~ 187 (254)
+...+|.+||+.|+||+.+...|.+|.+++.+.|++.||+|.++||||+|+|+++++.++|++||+.+ ++|++.+|++.
T Consensus 193 ~p~~yi~rf~s~L~l~~~v~~~a~ei~~~~~~~g~~~Gk~P~glAaaaiy~as~l~~~~~tq~eva~v-~~vtevTIrnr 271 (285)
T COG1405 193 DPSDYIPRFASKLGLSDEVRRKAIEIVKKAKRAGLTAGKSPAGLAAAAIYLASLLLGERRTQKEVAKV-AGVTEVTIRNR 271 (285)
T ss_pred CHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhCcccCCCchhHHHHHHHHHHHHhCCchHHHHHHHH-hCCeeeHHHHH
Confidence 66789999999999999999999999999999999999999999999999999999999999999996 99999999999
Q ss_pred HHHHHHHhchh
Q 025357 188 KEFIVKHLEAE 198 (254)
Q Consensus 188 ~k~l~~~l~~~ 198 (254)
|++|.+.+++.
T Consensus 272 ykel~~~~~i~ 282 (285)
T COG1405 272 YKELADALDIE 282 (285)
T ss_pred HHHHHHhhccc
Confidence 99999999876
No 9
>KOG1597 consensus Transcription initiation factor TFIIB [Transcription]
Probab=99.51 E-value=8.3e-14 Score=120.97 Aligned_cols=89 Identities=24% Similarity=0.342 Sum_probs=85.0
Q ss_pred HHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHH
Q 025357 108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA 187 (254)
Q Consensus 108 ~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~ 187 (254)
+...+|.+||+.|+||.++++.|.++.+++.+.....||+|.++|||+||+++++...++|++||.++ +||.+.+|+..
T Consensus 202 ~t~~~m~RFCs~L~L~~~~q~aA~e~a~ka~~~~~~~gRsPiSIAAa~IYmisqls~~kkt~keI~~v-tgVaE~TIr~s 280 (308)
T KOG1597|consen 202 STGDFMPRFCSNLGLPKSAQEAATEIAEKAEEMDIRAGRSPISIAAAAIYMISQLSDEKKTQKEIGEV-TGVAEVTIRNS 280 (308)
T ss_pred hHHHHHHHHHHhcCCCHHHHHHHHHHHHHHHHhccccCCCchhHHHHHHHHHHHhccCcccHHHHHHH-hhhhHHHHHHH
Confidence 46789999999999999999999999999999999999999999999999999999999999999995 99999999999
Q ss_pred HHHHHHHhch
Q 025357 188 KEFIVKHLEA 197 (254)
Q Consensus 188 ~k~l~~~l~~ 197 (254)
||.|..++.-
T Consensus 281 YK~Lyp~~~~ 290 (308)
T KOG1597|consen 281 YKDLYPHADK 290 (308)
T ss_pred HHHHhhchhh
Confidence 9999988753
No 10
>cd00043 CYCLIN Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB is a transcription factor that binds the TATA box. Cyclins, TFIIB and RB contain 2 copies of the domain.
Probab=99.18 E-value=3.5e-10 Score=81.21 Aligned_cols=83 Identities=24% Similarity=0.378 Sum_probs=77.6
Q ss_pred HHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCC-CHHHHHH
Q 025357 108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT-TKKEIGR 186 (254)
Q Consensus 108 ~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v-~~~~i~~ 186 (254)
.+.++|.++++.+++|..+...|..+++++...+.+.++++..+|+||+|+||+.++.|.+++|+... .+. +..+|.+
T Consensus 4 ~~~~~l~~~~~~~~~~~~~~~~A~~~~~~~~~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~-~~~~~~~~i~~ 82 (88)
T cd00043 4 TPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEIPPWLKDLVHV-TGYATEEEILR 82 (88)
T ss_pred hHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHHHHcCCCCCHHHHhHH-hCCCCHHHHHH
Confidence 46789999999999999999999999999999888889999999999999999999999999999995 889 9999998
Q ss_pred HHHHH
Q 025357 187 AKEFI 191 (254)
Q Consensus 187 ~~k~l 191 (254)
.++.+
T Consensus 83 ~e~~i 87 (88)
T cd00043 83 MEKLL 87 (88)
T ss_pred HHHHh
Confidence 88765
No 11
>smart00385 CYCLIN domain present in cyclins, TFIIB and Retinoblastoma. A helical domain present in cyclins and TFIIB (twice) and Retinoblastoma (once). A protein recognition domain functioning in cell-cycle and transcription control.
Probab=99.07 E-value=9e-10 Score=78.30 Aligned_cols=80 Identities=23% Similarity=0.303 Sum_probs=71.6
Q ss_pred HHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCC-CHHHHHHHHHH
Q 025357 112 SISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT-TKKEIGRAKEF 190 (254)
Q Consensus 112 ~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v-~~~~i~~~~k~ 190 (254)
+|.++++.+++|..+...|..+++++.....+.++++..+|+||+|+||+.++.+++..++... ++. ++.+|.+.++.
T Consensus 2 ~l~~~~~~~~~~~~~~~~a~~~~~~~l~~~~~~~~~~~~ia~a~l~lA~k~~~~~~~~~~~~~~-~~~~~~~~i~~~~~~ 80 (83)
T smart00385 2 FLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLAAKTEEIPPWTKELVHY-TGYFTEEEILRMEKL 80 (83)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHHHHHHHHhhcccCCHHHHHHHHHHHHHHHhcCCCCchhHhHh-hCCCCHHHHHHHHHH
Confidence 6889999999999999999999999987433445999999999999999999999999999995 888 99999999887
Q ss_pred HH
Q 025357 191 IV 192 (254)
Q Consensus 191 l~ 192 (254)
|.
T Consensus 81 il 82 (83)
T smart00385 81 LL 82 (83)
T ss_pred Hh
Confidence 74
No 12
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=98.72 E-value=3.2e-08 Score=88.90 Aligned_cols=116 Identities=17% Similarity=0.245 Sum_probs=95.0
Q ss_pred HHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcC-CCH--H
Q 025357 106 LIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANG-TTK--K 182 (254)
Q Consensus 106 l~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~-v~~--~ 182 (254)
-.++.++|.+++.+|++|...+.+|..+|.+..-...++.-.+..+|++|+|+|++.++.|+.++||..++.. ..+ .
T Consensus 39 r~~~~~fI~elg~~L~~~~~ti~tA~~~~hRFy~~~s~~~~~~~~vA~sclfLAgKvEetp~kl~dIi~~s~~~~~~~~~ 118 (323)
T KOG0834|consen 39 RQEGAKFIQELGVRLKMPQKTIATAIVIFHRFYMFHSFKKFDPYTVAASCLFLAGKVEETPRKLEDIIKVSYRYLNPKDL 118 (323)
T ss_pred HHHHHHHHHHHHHHcCCCccchhhhhhhhhhhhhhcccccCcHHHHHHHHHHHHhhcccCcccHHHHHHHHHHHcCcccc
Confidence 4688999999999999999999999999999988888888888999999999999999999999999886422 222 2
Q ss_pred HHHHHHHHHHH-----------HhchhcccccccCCCCHHHHHHHHHhhcCCCcch
Q 025357 183 EIGRAKEFIVK-----------HLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFF 227 (254)
Q Consensus 183 ~i~~~~k~l~~-----------~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v 227 (254)
+....|.++++ .|+++ +....|..||-+|+.+|+.....
T Consensus 119 ~~~~~~~~~~~~Iv~~E~~lL~tl~Fd------l~v~hPy~~ll~~~k~l~~~~~~ 168 (323)
T KOG0834|consen 119 ELEEVYWELKERIVQLELLLLETLGFD------LNVEHPYKYLLKYLKKLKADENL 168 (323)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHccCc------eeccCchHHHHHHHHHhhhhhhc
Confidence 45555554443 34444 66778999999999999888764
No 13
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=98.58 E-value=3.6e-08 Score=92.38 Aligned_cols=90 Identities=18% Similarity=0.221 Sum_probs=74.8
Q ss_pred HHHHHHHHHHhccCC-CH--HHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHH
Q 025357 108 QAFKSISAMSDRLGL-VT--TIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEI 184 (254)
Q Consensus 108 ~a~~~I~~i~~~L~L-p~--~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i 184 (254)
+..-+|.+++..|-. |. .++.+|..+..++..-.+..||+|..+++||||+|||.+|+++|..||+.+ ..|++.+|
T Consensus 165 DpsL~i~Rfa~~L~~g~~~~~Vv~~a~~L~~rMkrdwm~tGRRPsglcGAaLliAar~h~~~rsi~dIv~v-vhV~e~Tl 243 (521)
T KOG1598|consen 165 DPSLYIVRFSCRLLFGDKTEDVAKTATRLAQRMKRDWMQTGRRPSGLCGAALLIAARMHGFRRTIGDIAKV-VHVCESTL 243 (521)
T ss_pred CcceeeechhHhhhcCCchHHHHHHHHHHHHHHHHHHHHhCCCccchhHHHHHHHHHHcCccccHHHHHHH-HHHhHHHH
Confidence 344567777766644 33 478888888888777777789999999999999999999999999999996 89999999
Q ss_pred HHHHHHHHHHhchh
Q 025357 185 GRAKEFIVKHLEAE 198 (254)
Q Consensus 185 ~~~~k~l~~~l~~~ 198 (254)
++.|+++.+.+...
T Consensus 244 ~kRl~Ef~~T~s~~ 257 (521)
T KOG1598|consen 244 SKRLKEFSDTLSGD 257 (521)
T ss_pred HHHHHHHhcccccc
Confidence 99999998866433
No 14
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=98.55 E-value=5.7e-07 Score=80.69 Aligned_cols=108 Identities=15% Similarity=0.230 Sum_probs=92.5
Q ss_pred HHHHHHHHHHHhccC--CCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCC----
Q 025357 107 IQAFKSISAMSDRLG--LVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTT---- 180 (254)
Q Consensus 107 ~~a~~~I~~i~~~L~--Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~---- 180 (254)
......|.++|..|+ ||..++-+|..+|++.+-.+.+.--.+..++++|+|+||+.+..|+++.+++.. ..-+
T Consensus 57 ~~y~~~i~~~~~~lkp~Lpq~viaTAivyf~RFy~~~Sv~~~~p~~Ia~tclfLA~KvEE~~~si~~fv~~-~~~~~~~~ 135 (305)
T TIGR00569 57 KYYEKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLTCVFLACKVEEFNVSIDQFVGN-LKETPLKA 135 (305)
T ss_pred HHHHHHHHHHHHHhcCCCCchHHHHHHHHHhHHhccCchhhcCHHHHHHHHHHHHHhccccCcCHHHHHhh-ccCCchhh
Confidence 466789999999999 999999999999999988887777789999999999999999999999999874 3333
Q ss_pred HHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhc
Q 025357 181 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNI 221 (254)
Q Consensus 181 ~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L 221 (254)
...|...-..|.+.|++. +....|..++..|...|
T Consensus 136 ~~~Il~~E~~lL~~L~F~------L~V~hPyr~L~~~l~dl 170 (305)
T TIGR00569 136 LEQVLEYELLLIQQLNFH------LIVHNPYRPLEGFLIDI 170 (305)
T ss_pred HHHHHHHHHHHHHHCCCc------EEeeCccHHHHHHHHHH
Confidence 367777778888899887 66678888888888655
No 15
>COG5333 CCL1 Cdk activating kinase (CAK)/RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH/TFIIK, cyclin H subunit [Cell division and chromosome partitioning / Transcription / DNA replication, recombination, and repair]
Probab=98.06 E-value=1.2e-05 Score=70.97 Aligned_cols=114 Identities=21% Similarity=0.306 Sum_probs=93.7
Q ss_pred HHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHh-------cCC
Q 025357 107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVA-------NGT 179 (254)
Q Consensus 107 ~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~-------~~v 179 (254)
......|..+|.+|+||..+..+|..+|++..-+....+.++..++++|||+||+.+..|+-+.-..-.+ .--
T Consensus 46 i~~~k~i~~l~~~L~lp~~~laTAi~~f~Rf~Lk~sv~e~~~~~vv~tcv~LA~K~ed~~~~I~i~~~~~~~~~se~~~~ 125 (297)
T COG5333 46 IYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTCVYLACKVEDTPRDISIESFEARDLWSEEPKS 125 (297)
T ss_pred HHHHHHHHHHHHhcCCCcchHHHHHHHHHHHHhhcccccccHHHHHHhheeeeeecccccchhhHHHHHhhccccccccc
Confidence 4567999999999999999999999999999998889999999999999999999999765544332221 123
Q ss_pred CHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcc
Q 025357 180 TKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFF 226 (254)
Q Consensus 180 ~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~ 226 (254)
+.+.|-..-.++.+.|+.. .-...|..++..|...+.+...
T Consensus 126 sr~~Il~~E~~lLEaL~fd------~~V~hPy~~l~~f~~~~q~~~~ 166 (297)
T COG5333 126 SRERILEYEFELLEALDFD------LHVHHPYKYLEGFLKDLQEKDK 166 (297)
T ss_pred cHHHHHHHHHHHHHHcccc------eEeccccHHHHHHHHHHHhccH
Confidence 5677777778888888877 5667899999999988877655
No 16
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=98.05 E-value=3e-05 Score=69.02 Aligned_cols=118 Identities=18% Similarity=0.265 Sum_probs=97.9
Q ss_pred hhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCC----
Q 025357 104 RNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT---- 179 (254)
Q Consensus 104 r~l~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v---- 179 (254)
....-+..+|++-|=.|+||....-++.-+|++.....-+.+-..+.++.|||.+|++.+..|++++||..|+-.+
T Consensus 21 el~~LG~e~Iqea~ILL~L~q~a~atgqVLFqRf~~~ks~v~~~~e~vv~ACv~LASKiEE~Prr~rdVinVFh~L~~r~ 100 (367)
T KOG0835|consen 21 ELRILGCELIQEAGILLNLPQVAMATGQVLFQRFCYSKSFVRHDFEIVVMACVLLASKIEEEPRRIRDVINVFHYLEQRR 100 (367)
T ss_pred HHHHHhHHHHHhhhHhhcCcHHHHHHHHHHHHHHHhccccccccHHHHHHHHHHHHhhhccccccHhHHHHHHHHHHHHH
Confidence 3345678999999999999999999999999999888888889999999999999999999999999998652111
Q ss_pred -----C-----------HHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcch
Q 025357 180 -----T-----------KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFF 227 (254)
Q Consensus 180 -----~-----------~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v 227 (254)
. +..+.++..++.+.||+. +-..+|..+|--|..-|++++..
T Consensus 101 ~~~~~~~~~~~~~~~~lk~~~ir~e~~ILr~LGF~------~Hv~hPhklii~YLqtL~~~~~~ 158 (367)
T KOG0835|consen 101 ESEAAEHLILARLYINLKMQVIRAERRILRELGFD------VHVEHPHKLIIMYLQTLQLPPNL 158 (367)
T ss_pred hccCcchhhhhhHHhhhhhHHHHHHHHHHHHhCCe------eeeeccHHHHHHHHHHhcCCCch
Confidence 0 123345566778888877 55678999999999999998876
No 17
>PF00134 Cyclin_N: Cyclin, N-terminal domain; InterPro: IPR006671 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. Cyclins contain two domains of similar all-alpha fold, of which this entry is associated with the N-terminal domain.; PDB: 2W2H_B 3RGF_B 1KXU_A 1JKW_A 1URC_D 2WMB_D 1H26_D 1GY3_B 2UUE_D 1E9H_D ....
Probab=97.88 E-value=0.00019 Score=55.39 Aligned_cols=93 Identities=20% Similarity=0.331 Sum_probs=76.3
Q ss_pred hHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCC-CCCHHHHHHHhc--CCCH
Q 025357 105 NLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVAN--GTTK 181 (254)
Q Consensus 105 ~l~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~-p~tl~eIa~~~~--~v~~ 181 (254)
.-....++|..++..++++..+.-.|..++.+..........+...++++|+++||+.+.. +.++.++... . ..+.
T Consensus 30 ~r~~~~~~i~~~~~~~~l~~~~~~~A~~~~dr~~~~~~~~~~~~~li~~~cl~lA~K~~e~~~~~~~~~~~~-~~~~~~~ 108 (127)
T PF00134_consen 30 MRQIIIDWIIELCQRLKLSPETLHLAIYLFDRFLSKRPVNRSKLQLIALACLFLASKMEEDNPPSISDLIRI-SDNTFTK 108 (127)
T ss_dssp HHHHHHHHHHHHHHHTT-BHHHHHHHHHHHHHHHTTS-TTCCGHHHHHHHHHHHHHHHHTSS--HHHHHHHH-TTTSSHH
T ss_pred HHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHhhcccccchhhhhhhhHHHHhhhhhccccchHHHHHHH-HcCCCCH
Confidence 3457789999999999999999999999999998888778888999999999999999877 7888998875 4 3578
Q ss_pred HHHHHHHHHHHHHhchh
Q 025357 182 KEIGRAKEFIVKHLEAE 198 (254)
Q Consensus 182 ~~i~~~~k~l~~~l~~~ 198 (254)
++|...-+.+...|+.+
T Consensus 109 ~~i~~~E~~iL~~L~f~ 125 (127)
T PF00134_consen 109 KDILEMEREILSALNFD 125 (127)
T ss_dssp HHHHHHHHHHHHHTTT-
T ss_pred HHHHHHHHHHHHHCCCC
Confidence 88888888888887754
No 18
>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=97.54 E-value=0.00041 Score=55.04 Aligned_cols=84 Identities=11% Similarity=0.247 Sum_probs=63.0
Q ss_pred hHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhh--CCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHH
Q 025357 105 NLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVED--QKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKK 182 (254)
Q Consensus 105 ~l~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~--~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~ 182 (254)
...-|...|+.+|++|+|++.+.+..-.+++.+.. ..++++|-.+.+.-.|+|..||..+.++|.+||-.. ..--+.
T Consensus 10 vy~la~~Rl~~LC~~L~l~~~~~~~iwt~fe~~l~~~t~L~~dRHLDQiilCaiY~i~Kv~~~~~sF~~Ii~~-Yr~qpq 88 (135)
T PF01857_consen 10 VYKLAAVRLQDLCERLDLSSDLREKIWTCFEHSLTHHTELMKDRHLDQIILCAIYGICKVSKEELSFKDIIKA-YRKQPQ 88 (135)
T ss_dssp HHHHHHHHHHHHHHHHTTSTTHHHHHHHHHHHHHHHSGGGGTTS-HHHHHHHHHHHHHHHTT-S--HHHHHHH-HTTSTT
T ss_pred HHHHHHHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhhHHHHhcchHHHHHHHHHHHHHHhhcCCCCHHHHHHH-HHhccc
Confidence 44568889999999999999998998888888754 457899999999999999999999999999999883 543333
Q ss_pred HHHHHHH
Q 025357 183 EIGRAKE 189 (254)
Q Consensus 183 ~i~~~~k 189 (254)
.-...|+
T Consensus 89 ~~~~Vyr 95 (135)
T PF01857_consen 89 ASSHVYR 95 (135)
T ss_dssp --THHHH
T ss_pred ccccceE
Confidence 3333333
No 19
>KOG0656 consensus G1/S-specific cyclin D [Cell cycle control, cell division, chromosome partitioning]
Probab=97.24 E-value=0.0046 Score=56.02 Aligned_cols=115 Identities=17% Similarity=0.191 Sum_probs=92.3
Q ss_pred HHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCC-CCC--CHHHHHHHHHHHHHHhcCC--CCCHHHHHHH-hcCCC
Q 025357 107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPL-RGR--NQEAIVAACLYIACRQENK--PRTVKEFCSV-ANGTT 180 (254)
Q Consensus 107 ~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~-~Gr--~~~~iaAAclY~AcR~~~~--p~tl~eIa~~-~~~v~ 180 (254)
.+|+.+|-++|...+....+.=.|..++.+.....-+ +++ -...+|+||+.+|++.+.. |.++.-.... ..-+.
T Consensus 79 ~~A~~WIl~V~~~~~~~~~~~~LA~NYlDRFls~~~l~k~k~W~lQLlAvaCLsLAsKmeE~~vPll~dl~v~~~~~~fe 158 (335)
T KOG0656|consen 79 KQALDWILKVCEEYNFEPLVFLLAMNYLDRFLSSQKLPKDKPWMLQLLAVACLSLASKMEETDVPLLADLQVEYTDNVFE 158 (335)
T ss_pred HHHHHHHHHHHHHhCCchHHHHHHHHHHHHhhcccccCCCchHHHHHHHHHHHHHHHhhcCcCCchhhhhhhcccccccc
Confidence 4799999999999999999999999999998664433 333 2689999999999998876 6555433221 13457
Q ss_pred HHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcch
Q 025357 181 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFF 227 (254)
Q Consensus 181 ~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v 227 (254)
.++|.|.-..+...|+=. +..++|.+|+.-|+++++.....
T Consensus 159 aktI~rmELLVLstL~Wr------l~aVTP~sF~~~fl~ki~~~~~~ 199 (335)
T KOG0656|consen 159 AKTIQRMELLVLSTLKWR------LRAVTPFSFIDHFLSKISQKDHN 199 (335)
T ss_pred HHHHHHHHHHHHhhcccc------ccCCCchHHHHHHHHHcCcccch
Confidence 899999998889999876 77899999999999999886443
No 20
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=97.20 E-value=0.00044 Score=58.93 Aligned_cols=59 Identities=22% Similarity=0.406 Sum_probs=55.9
Q ss_pred HHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCC
Q 025357 108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKP 166 (254)
Q Consensus 108 ~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p 166 (254)
.....|+.+++.|+|.+.++.+|.-++++.+-+..+++-.|..+|+.|+|+||+.+..|
T Consensus 43 ~~~n~I~~lg~~lklRQ~ViATAivY~rRfy~r~S~k~~~p~lla~TClyLAcKvEE~~ 101 (264)
T KOG0794|consen 43 FMANVIQKLGQHLKLRQRVIATAIVYFRRFYLRKSLKEIEPRLLAPTCLYLACKVEECP 101 (264)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhccCHHHHHHHHHHHHhhhhhcc
Confidence 56789999999999999999999999999988888999999999999999999999988
No 21
>KOG0835 consensus Cyclin L [General function prediction only]
Probab=97.02 E-value=0.0039 Score=55.79 Aligned_cols=129 Identities=18% Similarity=0.149 Sum_probs=81.8
Q ss_pred HHHHHHHHHHHhccCCCHHH-HHHHH-HHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHH-HHHHHhcCCCHHH
Q 025357 107 IQAFKSISAMSDRLGLVTTI-KDRAN-EIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVK-EFCSVANGTTKKE 183 (254)
Q Consensus 107 ~~a~~~I~~i~~~L~Lp~~v-~e~A~-~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~-eIa~~~~~v~~~~ 183 (254)
.+..+.|-.+...|++|++. +.++. .+......-.+..--+|+++|+||+|+|+|..++|.+.. .--. +.+.++.+
T Consensus 139 ~hPhklii~YLqtL~~~~~~~l~Q~~wNfmNDslRT~v~vry~pe~iACaciyLaAR~~eIpLp~~P~Wf~-~Fd~~k~e 217 (367)
T KOG0835|consen 139 EHPHKLIIMYLQTLQLPPNLKLLQAAWNFMNDSLRTDVFVRYSPESIACACIYLAARNLEIPLPFQPHWFK-AFDTTKRE 217 (367)
T ss_pred eccHHHHHHHHHHhcCCCchhHHHHHHHhhhhccccceeeecCHHHHHHHHHHHHHhhhcCCCCCCccHHH-HcCCcHHH
Confidence 35677888889999999765 33333 333333333344445899999999999999999886554 3434 58889999
Q ss_pred HHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCC-----CcchhheeeCcceeeehhhcccccCCCC
Q 025357 184 IGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFK-----NFFFLFVLDFSSCMIFCSLWPYLSNPMH 251 (254)
Q Consensus 184 i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l-----~~~v~~v~~~~~~~~~~~~~~~~~~~~~ 251 (254)
|-.....+....... .|. ..+|.-|++++.. +++.+.+.|. +|+|.-+..-.|
T Consensus 218 id~ic~~l~~lY~~~------~p~---~~li~~~vd~~k~~~~da~~k~~~~~ds------~~~l~g~~~a~~ 275 (367)
T KOG0835|consen 218 IDEICYRLIPLYKRA------KPD---ETLIEAFVDRLKRKFSDASGKAKGANDS------ASLLGGFAPAVD 275 (367)
T ss_pred HHHHHHHHHHHHHhc------ccC---HHHHHHHHHHhhHHHHhccCCccchhhH------HHhhcccccccC
Confidence 887776666665542 121 4566666666543 4444444442 356655544333
No 22
>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=96.94 E-value=0.00066 Score=41.30 Aligned_cols=27 Identities=30% Similarity=0.562 Sum_probs=23.4
Q ss_pred CCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 5 YCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 5 ~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
.|+.|++ . .+....|..+|..||.|++
T Consensus 10 ~C~~C~~-~--~~~~~dG~~yC~~cG~~~E 36 (36)
T PF11781_consen 10 PCPVCGS-R--WFYSDDGFYYCDRCGHQSE 36 (36)
T ss_pred cCCCCCC-e--EeEccCCEEEhhhCceEcC
Confidence 4999998 3 6788899999999999974
No 23
>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=96.81 E-value=0.0074 Score=45.59 Aligned_cols=87 Identities=14% Similarity=0.129 Sum_probs=63.9
Q ss_pred HHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCC-CCCHHHHHHHhcCCCHHHHHHH
Q 025357 109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVANGTTKKEIGRA 187 (254)
Q Consensus 109 a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~-p~tl~eIa~~~~~v~~~~i~~~ 187 (254)
.+.+|+++....+....+...|..+.....-...+-+-+|..+||||+|+|.+..+. +.--..+.. ..|++..+|..+
T Consensus 3 p~~Fl~~~~~~~~~~~~~~~~a~~l~el~l~~~~fl~~~PS~iAaAai~lA~~~~~~~~~~~~~l~~-~t~~~~~~l~~c 81 (118)
T PF02984_consen 3 PYDFLRRFLKISNADQEVRNLARYLLELSLLDYEFLQYPPSVIAAAAILLARKILGKEPPWPESLEK-LTGYDKEDLKEC 81 (118)
T ss_dssp HHHHHHHHHTSSSHHHHHHHHHHHHHHHHHHSHHHTTS-HHHHHHHHHHHHHHHHHSSTCSHHHHHH-HHTS-HHHHHHH
T ss_pred HHHHHHHHHHHcCCcHHHHHHHHHHHHHHHhhccccCCCHHHHHHHHHHHHHHHhCccccCCccchh-hcCCCHHHHHHH
Confidence 466788886655566678888888888754443355678999999999999998765 333444556 378999999999
Q ss_pred HHHHHHHhc
Q 025357 188 KEFIVKHLE 196 (254)
Q Consensus 188 ~k~l~~~l~ 196 (254)
++.|.+.+.
T Consensus 82 ~~~i~~~~~ 90 (118)
T PF02984_consen 82 IELIQELLS 90 (118)
T ss_dssp HHHHHHHHH
T ss_pred HHHHHHHHH
Confidence 999988775
No 24
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=96.78 E-value=0.0015 Score=38.89 Aligned_cols=31 Identities=16% Similarity=0.446 Sum_probs=25.1
Q ss_pred CCCCCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357 1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (254)
Q Consensus 1 ~~~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl 33 (254)
|....|+.||+ +.++..+.+..+|.+||.+.
T Consensus 1 ~~~~~C~~C~~--~~i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 1 SNLKKCSKCGG--NGIVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred CCceEcCCCCC--CeEEEecCCeEEcccCCcEe
Confidence 45678999998 34555779999999999985
No 25
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=96.75 E-value=0.0005 Score=45.72 Aligned_cols=31 Identities=35% Similarity=0.740 Sum_probs=23.6
Q ss_pred CCCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
+.+||.|+. ..+|+++.+-.+.|..||.+|.
T Consensus 7 ~VkCp~C~~-~q~vFSha~t~V~C~~Cg~~L~ 37 (55)
T PF01667_consen 7 DVKCPGCYN-IQTVFSHAQTVVKCVVCGTVLA 37 (55)
T ss_dssp EEE-TTT-S-EEEEETT-SS-EE-SSSTSEEE
T ss_pred EEECCCCCC-eeEEEecCCeEEEcccCCCEec
Confidence 368999998 7899999999999999999995
No 26
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=96.73 E-value=0.00073 Score=45.46 Aligned_cols=31 Identities=35% Similarity=0.751 Sum_probs=28.5
Q ss_pred CCCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
+.+||.|+. ..+|+++.+-.+.|..||.+|.
T Consensus 11 ~VkCp~C~n-~q~vFsha~t~V~C~~Cg~~L~ 41 (59)
T PRK00415 11 KVKCPDCGN-EQVVFSHASTVVRCLVCGKTLA 41 (59)
T ss_pred EEECCCCCC-eEEEEecCCcEEECcccCCCcc
Confidence 367999998 6899999999999999999995
No 27
>COG5024 Cyclin [Cell division and chromosome partitioning]
Probab=96.59 E-value=0.014 Score=54.92 Aligned_cols=120 Identities=15% Similarity=0.183 Sum_probs=100.1
Q ss_pred HHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCC-CCCHHHHHHHh-cCCCHHHHHH
Q 025357 109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVA-NGTTKKEIGR 186 (254)
Q Consensus 109 a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~-p~tl~eIa~~~-~~v~~~~i~~ 186 (254)
...+|.++-.+++|-+.....|..|..+....+.+.=.+...+++.|+||||+-+.+ +.++++++-+. -..+.+.|.+
T Consensus 216 Lv~wlvevH~~F~llpeTL~lainiiDrfLs~~~v~l~k~QLvg~s~LfIa~K~EE~~~p~i~~l~~~t~g~~t~~~i~~ 295 (440)
T COG5024 216 LVDWLVEVHGKFGLLPETLFLAINIIDRFLSSRVVSLEKYQLVGISALFIASKYEEVNCPSIKDLVYATDGAFTRDDIIR 295 (440)
T ss_pred HHHHHHHhcccccccchHHHHHHHHHHHHhccCcccHHHHHHHHHHHHHHHHhHhHhcCHHHHHHHHHHcccccHHHHHH
Confidence 467888889999999999999999999998888776677889999999999998865 45677876642 3568999999
Q ss_pred HHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcchhheeeCc
Q 025357 187 AKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFFLFVLDFS 234 (254)
Q Consensus 187 ~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~v~~~~ 234 (254)
+.+.+...|+.. +.-..|..|+.|+.....-+.+...++.+.
T Consensus 296 aE~~ml~~l~f~------is~P~P~sFLRriSka~dyd~~srt~~k~~ 337 (440)
T COG5024 296 AERYMLEVLDFN------ISWPSPMSFLRRISKASDYDIFSRTPAKFS 337 (440)
T ss_pred HHHHHhhhcccc------cCCCChHHHHHHHHhhcccchhhhhhHhhh
Confidence 999999999987 667789999999988888887777666655
No 28
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=96.56 E-value=0.0016 Score=44.66 Aligned_cols=30 Identities=37% Similarity=0.790 Sum_probs=27.9
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
.+||.||. ..+++++.+-.+.|..||.+|-
T Consensus 20 VkCpdC~N-~q~vFshast~V~C~~CG~~l~ 49 (67)
T COG2051 20 VKCPDCGN-EQVVFSHASTVVTCLICGTTLA 49 (67)
T ss_pred EECCCCCC-EEEEeccCceEEEecccccEEE
Confidence 57999998 7899999999999999999985
No 29
>PLN00209 ribosomal protein S27; Provisional
Probab=96.27 E-value=0.0022 Score=46.32 Aligned_cols=31 Identities=35% Similarity=0.694 Sum_probs=28.5
Q ss_pred CCCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
+.+||.|+. ..+|+++.+-.+.|..||.+|.
T Consensus 36 ~VkCp~C~n-~q~VFShA~t~V~C~~Cg~~L~ 66 (86)
T PLN00209 36 DVKCQGCFN-ITTVFSHSQTVVVCGSCQTVLC 66 (86)
T ss_pred EEECCCCCC-eeEEEecCceEEEccccCCEee
Confidence 367999998 7899999999999999999995
No 30
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=96.26 E-value=0.0023 Score=46.05 Aligned_cols=31 Identities=29% Similarity=0.677 Sum_probs=28.5
Q ss_pred CCCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
+.+||.|+. ..+|+++.+-.+.|..||.+|.
T Consensus 35 ~VkCp~C~n-~q~VFShA~t~V~C~~Cg~~L~ 65 (85)
T PTZ00083 35 DVKCPGCSQ-ITTVFSHAQTVVLCGGCSSQLC 65 (85)
T ss_pred EEECCCCCC-eeEEEecCceEEEccccCCEee
Confidence 367999998 7899999999999999999995
No 31
>PHA00626 hypothetical protein
Probab=96.21 E-value=0.0044 Score=41.01 Aligned_cols=33 Identities=18% Similarity=0.489 Sum_probs=24.6
Q ss_pred CCCCCCCCCCceEEe----cCCCceEcCcCceeecccc
Q 025357 4 SYCADCKRLTEVVFD----HSAGDTICSECGLVLEAYS 37 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D----~~~G~~vC~~CG~Vl~e~~ 37 (254)
+.||.||+ .+++.- ......+|.+||+-.....
T Consensus 1 m~CP~CGS-~~Ivrcg~cr~~snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 1 MSCPKCGS-GNIAKEKTMRGWSDDYVCCDCGYNDSKDA 37 (59)
T ss_pred CCCCCCCC-ceeeeeceecccCcceEcCCCCCeechhh
Confidence 47999998 566653 2378999999999875433
No 32
>PRK00420 hypothetical protein; Validated
Probab=96.11 E-value=0.0045 Score=47.38 Aligned_cols=31 Identities=26% Similarity=0.560 Sum_probs=24.0
Q ss_pred CCCCCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 1 ~~~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
|-...||.||.+ + +-...|..+|..||.++.
T Consensus 21 ml~~~CP~Cg~p--L-f~lk~g~~~Cp~Cg~~~~ 51 (112)
T PRK00420 21 MLSKHCPVCGLP--L-FELKDGEVVCPVHGKVYI 51 (112)
T ss_pred HccCCCCCCCCc--c-eecCCCceECCCCCCeee
Confidence 334789999973 4 333799999999999874
No 33
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=95.98 E-value=0.0053 Score=39.32 Aligned_cols=31 Identities=39% Similarity=0.748 Sum_probs=25.4
Q ss_pred CCCCCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357 1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (254)
Q Consensus 1 ~~~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl 33 (254)
|....|+.||. .+.+|+..+.+.|..||.-+
T Consensus 1 ~~~y~C~~CG~--~~~~~~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 1 MAEYKCARCGR--EVELDEYGTGVRCPYCGYRI 31 (46)
T ss_pred CCEEECCCCCC--EEEECCCCCceECCCCCCeE
Confidence 56688999997 47778777799999999644
No 34
>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=95.92 E-value=0.026 Score=50.18 Aligned_cols=63 Identities=19% Similarity=0.405 Sum_probs=53.9
Q ss_pred HHHHHhcc--CCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHH
Q 025357 113 ISAMSDRL--GLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSV 175 (254)
Q Consensus 113 I~~i~~~L--~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~ 175 (254)
+-.+++++ .||..|+-+|..+|+++.=.+...--.|..+.++|+|+||+.+..-+++.+|+.-
T Consensus 63 l~~f~~k~~p~lp~~Vv~TA~~fFkRffL~nsvme~~pk~I~~tc~flA~Kieef~ISieqFvkn 127 (325)
T KOG2496|consen 63 LVNFYSKFKPNLPTSVVSTAIEFFKRFFLENSVMEYSPKIIMATCFFLACKIEEFYISIEQFVKN 127 (325)
T ss_pred HHHHHHHhcCCCchHHHHHHHHHHHHHHHhcchhhcChHHHHHHHHHHHhhhHhheecHHHHHhh
Confidence 33444444 7899999999999999987777767789999999999999999999999999884
No 35
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=95.92 E-value=0.0027 Score=38.09 Aligned_cols=27 Identities=19% Similarity=0.685 Sum_probs=16.0
Q ss_pred CCCCCCCCCceEEe----cCCCceEcCcCceee
Q 025357 5 YCADCKRLTEVVFD----HSAGDTICSECGLVL 33 (254)
Q Consensus 5 ~Cp~Cg~~~~lv~D----~~~G~~vC~~CG~Vl 33 (254)
.||.||+. +... ...-..||..||.|-
T Consensus 2 fC~~CG~~--l~~~ip~gd~r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 2 FCPQCGGP--LERRIPEGDDRERLVCPACGFIH 32 (34)
T ss_dssp B-TTT--B---EEE--TT-SS-EEEETTTTEEE
T ss_pred ccccccCh--hhhhcCCCCCccceECCCCCCEE
Confidence 69999984 3333 456678999999984
No 36
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=95.79 E-value=0.0049 Score=34.60 Aligned_cols=23 Identities=22% Similarity=0.936 Sum_probs=18.4
Q ss_pred CCCCCCCCCCCceEEecCCCceEcCcCce
Q 025357 3 DSYCADCKRLTEVVFDHSAGDTICSECGL 31 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~ 31 (254)
...||+||. . + ..+..+|..||.
T Consensus 2 ~~~Cp~Cg~-~-~----~~~~~fC~~CG~ 24 (26)
T PF13248_consen 2 EMFCPNCGA-E-I----DPDAKFCPNCGA 24 (26)
T ss_pred cCCCcccCC-c-C----CcccccChhhCC
Confidence 489999997 2 1 367899999996
No 37
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=95.74 E-value=0.01 Score=35.79 Aligned_cols=31 Identities=16% Similarity=0.452 Sum_probs=19.7
Q ss_pred CCCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
+..||+||+ --+......+...|..||++.+
T Consensus 1 m~FCp~C~n-lL~p~~~~~~~~~C~~C~Y~~~ 31 (35)
T PF02150_consen 1 MRFCPECGN-LLYPKEDKEKRVACRTCGYEEP 31 (35)
T ss_dssp --BETTTTS-BEEEEEETTTTEEESSSS-EEE
T ss_pred CeeCCCCCc-cceEcCCCccCcCCCCCCCccC
Confidence 367999997 3334444555557999999864
No 38
>PRK11827 hypothetical protein; Provisional
Probab=95.45 E-value=0.01 Score=40.31 Aligned_cols=28 Identities=18% Similarity=0.494 Sum_probs=24.6
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl 33 (254)
..||.|++ .+.+|....+++|..||++.
T Consensus 9 LaCP~ckg--~L~~~~~~~~Lic~~~~laY 36 (60)
T PRK11827 9 IACPVCNG--KLWYNQEKQELICKLDNLAF 36 (60)
T ss_pred eECCCCCC--cCeEcCCCCeEECCccCeec
Confidence 57999987 58888888899999999985
No 39
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=95.45 E-value=0.013 Score=35.82 Aligned_cols=28 Identities=32% Similarity=0.736 Sum_probs=21.5
Q ss_pred CCCCCCCCCCceEEec--CCCceEcCcCce
Q 025357 4 SYCADCKRLTEVVFDH--SAGDTICSECGL 31 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~--~~G~~vC~~CG~ 31 (254)
..||.||+....-+|. ..|..+|..||.
T Consensus 4 ~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred cCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 5799999854444554 569999999984
No 40
>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=95.44 E-value=0.0089 Score=36.53 Aligned_cols=29 Identities=28% Similarity=0.607 Sum_probs=21.0
Q ss_pred CCCCCCCCCCceEEe-----cCCCceEcCcCceeec
Q 025357 4 SYCADCKRLTEVVFD-----HSAGDTICSECGLVLE 34 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D-----~~~G~~vC~~CG~Vl~ 34 (254)
..||+|+.. ...+ ...+.+.|..||.++.
T Consensus 3 ~~CP~C~~~--~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPNCKTS--FRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCCCCCE--EEeCHHHcCCCCCEEECCCCCCEEE
Confidence 689999983 2233 2345799999999874
No 41
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=95.43 E-value=0.011 Score=38.63 Aligned_cols=27 Identities=22% Similarity=0.682 Sum_probs=21.3
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl 33 (254)
..||.||+ + +..++ .+...|..||+..
T Consensus 21 ~fCP~Cg~-~-~m~~~-~~r~~C~~Cgyt~ 47 (50)
T PRK00432 21 KFCPRCGS-G-FMAEH-LDRWHCGKCGYTE 47 (50)
T ss_pred CcCcCCCc-c-hhecc-CCcEECCCcCCEE
Confidence 57999998 5 55544 5899999999874
No 42
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=95.19 E-value=0.0091 Score=32.55 Aligned_cols=22 Identities=27% Similarity=0.916 Sum_probs=17.0
Q ss_pred CCCCCCCCCceEEecCCCceEcCcCcee
Q 025357 5 YCADCKRLTEVVFDHSAGDTICSECGLV 32 (254)
Q Consensus 5 ~Cp~Cg~~~~lv~D~~~G~~vC~~CG~V 32 (254)
.||+||.+ + ..+..+|..||.-
T Consensus 1 ~Cp~CG~~--~----~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAE--I----EDDAKFCPNCGTP 22 (23)
T ss_pred CCcccCCC--C----CCcCcchhhhCCc
Confidence 59999983 2 2578899999964
No 43
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=95.06 E-value=0.017 Score=38.96 Aligned_cols=30 Identities=30% Similarity=0.671 Sum_probs=26.6
Q ss_pred CCCCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357 2 ADSYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (254)
Q Consensus 2 ~~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl 33 (254)
+...||.|++ .+.+|.+.++++|..||...
T Consensus 7 eiLaCP~~kg--~L~~~~~~~~L~c~~~~~aY 36 (60)
T COG2835 7 EILACPVCKG--PLVYDEEKQELICPRCKLAY 36 (60)
T ss_pred eeeeccCcCC--cceEeccCCEEEecccCcee
Confidence 4567999997 39999999999999999985
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=95.03 E-value=0.014 Score=38.77 Aligned_cols=31 Identities=39% Similarity=0.768 Sum_probs=21.4
Q ss_pred CCCCCCCCCCCceEEecCCCc-eEcCcCceeec
Q 025357 3 DSYCADCKRLTEVVFDHSAGD-TICSECGLVLE 34 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~D~~~G~-~vC~~CG~Vl~ 34 (254)
+..||+||..-. +.|...|+ +.|..||.-++
T Consensus 2 ~~~CP~CG~~ie-v~~~~~GeiV~Cp~CGaele 33 (54)
T TIGR01206 2 QFECPDCGAEIE-LENPELGELVICDECGAELE 33 (54)
T ss_pred ccCCCCCCCEEe-cCCCccCCEEeCCCCCCEEE
Confidence 468999998322 23434455 56999999884
No 45
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=94.99 E-value=0.028 Score=38.01 Aligned_cols=29 Identities=24% Similarity=0.634 Sum_probs=21.2
Q ss_pred CCCCCCCCCCCCceEEecCCC-------ceEcCcCce
Q 025357 2 ADSYCADCKRLTEVVFDHSAG-------DTICSECGL 31 (254)
Q Consensus 2 ~~~~Cp~Cg~~~~lv~D~~~G-------~~vC~~CG~ 31 (254)
++..||.||+ ..+..+...+ .+.|.+||.
T Consensus 2 ~LkPCPFCG~-~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGS-ADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCC-cceEeecccCCCCCCEEEEEcCCCCC
Confidence 3567999987 5666665554 366999999
No 46
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=94.99 E-value=0.014 Score=45.78 Aligned_cols=27 Identities=22% Similarity=0.683 Sum_probs=21.1
Q ss_pred CCCCCCCCCCCceEEecCCCceEcCcCc-eee
Q 025357 3 DSYCADCKRLTEVVFDHSAGDTICSECG-LVL 33 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG-~Vl 33 (254)
...||.||.+ ++ - .+|+++|..|| .+.
T Consensus 28 ~~hCp~Cg~P--LF-~-KdG~v~CPvC~~~~~ 55 (131)
T COG1645 28 AKHCPKCGTP--LF-R-KDGEVFCPVCGYREV 55 (131)
T ss_pred HhhCcccCCc--ce-e-eCCeEECCCCCceEE
Confidence 3579999983 43 3 89999999999 443
No 47
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=94.93 E-value=0.021 Score=41.43 Aligned_cols=29 Identities=31% Similarity=0.573 Sum_probs=25.2
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
-.||.||+ + .|.-..+|-+.|..||.++.
T Consensus 36 ~~Cp~C~~-~-~VkR~a~GIW~C~kCg~~fA 64 (89)
T COG1997 36 HVCPFCGR-T-TVKRIATGIWKCRKCGAKFA 64 (89)
T ss_pred CcCCCCCC-c-ceeeeccCeEEcCCCCCeec
Confidence 46999998 4 67788999999999999975
No 48
>KOG0653 consensus Cyclin B and related kinase-activating proteins [Cell cycle control, cell division, chromosome partitioning]
Probab=94.87 E-value=0.17 Score=47.19 Aligned_cols=114 Identities=16% Similarity=0.238 Sum_probs=89.8
Q ss_pred HHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHH-HHHHhcCC-CCCHHHHHHHh-cCCCHHH
Q 025357 107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLY-IACRQENK-PRTVKEFCSVA-NGTTKKE 183 (254)
Q Consensus 107 ~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY-~AcR~~~~-p~tl~eIa~~~-~~v~~~~ 183 (254)
..-.+++-++-.+++|...+.-.|..|+.+......+..+....+..+|++ |||+.+.. +-.+.|+.-+. -..+..+
T Consensus 159 ~iLvdwlvevh~~F~L~~ETL~LaVnliDRfL~~~~v~~~~lqLvgvsalf~IA~K~EE~~~P~v~dlv~isd~~~s~~~ 238 (391)
T KOG0653|consen 159 AILVDWLVEVHEKFGLSPETLYLAVNLIDRFLSKVKVPLKKLQLVGVSALLSIACKYEEISLPSVEDLVLITDGAYSREE 238 (391)
T ss_pred HHHHHHHHHhhhhcCcCHHHHHHHHHHHHHHHHHhcccHHHhhHHhHHHHHHHHHhhhhccCCccceeEeeeCCccchHH
Confidence 345788999999999999999999999999988766777777777777756 99996544 33366665431 2368999
Q ss_pred HHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcc
Q 025357 184 IGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFF 226 (254)
Q Consensus 184 i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~ 226 (254)
|.+.-+.+...|+.. +....|..|+.||........+
T Consensus 239 il~mE~~il~~L~f~------l~~p~~~~FLrr~~ka~~~d~~ 275 (391)
T KOG0653|consen 239 ILRMEKYILNVLEFD------LSVPTPLSFLRRFLKAADYDIK 275 (391)
T ss_pred HHHHHHHHHhccCee------ecCCchHHHHHHHHHhhhcchh
Confidence 999999999998877 6677899999999999885444
No 49
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=94.84 E-value=0.034 Score=38.66 Aligned_cols=17 Identities=35% Similarity=0.806 Sum_probs=15.8
Q ss_pred EecCCCceEcCcCceee
Q 025357 17 FDHSAGDTICSECGLVL 33 (254)
Q Consensus 17 ~D~~~G~~vC~~CG~Vl 33 (254)
++..+|.++|.+||.+.
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 68999999999999986
No 50
>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=94.83 E-value=0.03 Score=32.57 Aligned_cols=27 Identities=26% Similarity=0.459 Sum_probs=14.8
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl 33 (254)
-+||.|++. ..-.| ...+||.+||.-.
T Consensus 3 p~Cp~C~se-~~y~D--~~~~vCp~C~~ew 29 (30)
T PF08274_consen 3 PKCPLCGSE-YTYED--GELLVCPECGHEW 29 (30)
T ss_dssp ---TTT------EE---SSSEEETTTTEEE
T ss_pred CCCCCCCCc-ceecc--CCEEeCCcccccC
Confidence 479999994 33344 7889999999753
No 51
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=94.25 E-value=0.026 Score=36.41 Aligned_cols=27 Identities=26% Similarity=0.733 Sum_probs=22.3
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCcee
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLV 32 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~V 32 (254)
..||.||. ..+..|+.. .+.|..||+.
T Consensus 20 ~~CPrCG~-gvfmA~H~d-R~~CGkCgyT 46 (51)
T COG1998 20 RFCPRCGP-GVFMADHKD-RWACGKCGYT 46 (51)
T ss_pred ccCCCCCC-cchhhhcCc-eeEeccccce
Confidence 46999996 567777766 8999999987
No 52
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=94.23 E-value=0.034 Score=36.18 Aligned_cols=28 Identities=18% Similarity=0.632 Sum_probs=19.6
Q ss_pred CCCCCCCCCceEEecCC--CceEcCcCceeec
Q 025357 5 YCADCKRLTEVVFDHSA--GDTICSECGLVLE 34 (254)
Q Consensus 5 ~Cp~Cg~~~~lv~D~~~--G~~vC~~CG~Vl~ 34 (254)
.||.||+ .+...... -..+|..||.+..
T Consensus 2 FCp~Cg~--~l~~~~~~~~~~~vC~~Cg~~~~ 31 (52)
T smart00661 2 FCPKCGN--MLIPKEGKEKRRFVCRKCGYEEP 31 (52)
T ss_pred CCCCCCC--ccccccCCCCCEEECCcCCCeEE
Confidence 6999997 33333222 3799999998854
No 53
>PRK10220 hypothetical protein; Provisional
Probab=94.11 E-value=0.15 Score=38.50 Aligned_cols=30 Identities=30% Similarity=0.548 Sum_probs=22.4
Q ss_pred CCCCCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357 1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (254)
Q Consensus 1 ~~~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl 33 (254)
|..-.||.|++ ...-.| ...+||.+||.--
T Consensus 1 m~lP~CP~C~s-eytY~d--~~~~vCpeC~hEW 30 (111)
T PRK10220 1 MSLPHCPKCNS-EYTYED--NGMYICPECAHEW 30 (111)
T ss_pred CCCCcCCCCCC-cceEcC--CCeEECCcccCcC
Confidence 67778999998 344444 5679999999753
No 54
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=94.01 E-value=0.027 Score=31.62 Aligned_cols=25 Identities=28% Similarity=0.771 Sum_probs=19.1
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
..||+|+.. | ......|..||++..
T Consensus 1 K~CP~C~~~--V----~~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 1 KTCPECGAE--V----PESAKFCPHCGYDFE 25 (26)
T ss_pred CcCCCCcCC--c----hhhcCcCCCCCCCCc
Confidence 369999983 2 356789999999863
No 55
>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=94.01 E-value=0.074 Score=31.23 Aligned_cols=28 Identities=18% Similarity=0.426 Sum_probs=16.9
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl 33 (254)
..|+.||++ .+.....-..+|.+||...
T Consensus 4 rfC~~CG~~--t~~~~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 4 RFCGRCGAP--TKPAPGGWARRCPSCGHEH 31 (32)
T ss_dssp SB-TTT--B--EEE-SSSS-EEESSSS-EE
T ss_pred cccCcCCcc--ccCCCCcCEeECCCCcCEe
Confidence 579999983 4456667889999999763
No 56
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=93.71 E-value=0.031 Score=39.57 Aligned_cols=30 Identities=30% Similarity=0.769 Sum_probs=27.2
Q ss_pred CCCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl 33 (254)
+.+||.|-. ...++.+++..++|.+|+.|+
T Consensus 34 ~VkC~gc~~-iT~vfSHaqtvVvc~~c~~il 63 (84)
T KOG1779|consen 34 DVKCPGCFK-ITTVFSHAQTVVVCEGCSTIL 63 (84)
T ss_pred EEEcCCceE-EEEEeecCceEEEcCCCceEE
Confidence 468999987 678999999999999999997
No 57
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=93.63 E-value=0.063 Score=35.39 Aligned_cols=32 Identities=22% Similarity=0.248 Sum_probs=21.1
Q ss_pred CCCCCCCCCCCceEE---e--cCCCceEcCcCceeec
Q 025357 3 DSYCADCKRLTEVVF---D--HSAGDTICSECGLVLE 34 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~---D--~~~G~~vC~~CG~Vl~ 34 (254)
+..||.||+....+. | ...|...|..||....
T Consensus 1 LkPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~ 37 (53)
T TIGR03655 1 LKPCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGP 37 (53)
T ss_pred CCCCCCCCCcceeeEeccCCCCCEEEEECCCCCCCcc
Confidence 357999999433132 3 2344557999999864
No 58
>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=93.58 E-value=0.071 Score=33.33 Aligned_cols=26 Identities=31% Similarity=0.804 Sum_probs=20.1
Q ss_pred CCCCCCCCCCCCceEEecCCCceEcCcCc
Q 025357 2 ADSYCADCKRLTEVVFDHSAGDTICSECG 30 (254)
Q Consensus 2 ~~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG 30 (254)
-...||.||. .+.. ..+|.++|..|+
T Consensus 16 L~~~Cp~C~~--PL~~-~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 16 LDEHCPDCGT--PLMR-DKDGKIYCVSCG 41 (41)
T ss_pred hcCccCCCCC--eeEE-ecCCCEECCCCC
Confidence 3468999986 3544 579999999996
No 59
>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=93.44 E-value=0.074 Score=33.07 Aligned_cols=29 Identities=31% Similarity=0.620 Sum_probs=16.0
Q ss_pred CCCCCCCCCCceE-Eec--CCCceEcCcCcee
Q 025357 4 SYCADCKRLTEVV-FDH--SAGDTICSECGLV 32 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv-~D~--~~G~~vC~~CG~V 32 (254)
..||.||+....- ++. .+|..+|..|+-+
T Consensus 4 ~pCP~CGG~DrFri~~d~~~~G~~~C~~C~~~ 35 (40)
T PF08273_consen 4 GPCPICGGKDRFRIFDDKDGRGTWICRQCGGD 35 (40)
T ss_dssp E--TTTT-TTTEEEETT----S-EEETTTTBE
T ss_pred CCCCCCcCccccccCcCcccCCCEECCCCCCc
Confidence 4699999854433 553 5699999999434
No 60
>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=93.41 E-value=0.045 Score=41.74 Aligned_cols=31 Identities=19% Similarity=0.602 Sum_probs=25.6
Q ss_pred CCCCCCCCCCCceEEecCCCceEcCcCceeeccc
Q 025357 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY 36 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~ 36 (254)
.+.||.||.. .+|-..--+||..||.++.-.
T Consensus 9 KR~Cp~CG~k---FYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 9 KRTCPSCGAK---FYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cccCCCCcch---hccCCCCCccCCCCCCccCcc
Confidence 3679999983 688778889999999998644
No 61
>KOG4164 consensus Cyclin ik3-1/CABLES [Cell cycle control, cell division, chromosome partitioning]
Probab=92.97 E-value=0.49 Score=43.68 Aligned_cols=59 Identities=14% Similarity=0.228 Sum_probs=51.0
Q ss_pred HHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCC
Q 025357 107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENK 165 (254)
Q Consensus 107 ~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~ 165 (254)
....++|++++.--+|...++.+|.-+|.++.=+|++.-.++..+|+|||.+|++.+..
T Consensus 383 rSlKREMr~l~~d~~id~~TVa~AyVYFEKliLkglisK~NRKlcAGAclLlaaKmnD~ 441 (497)
T KOG4164|consen 383 RSLKREMRELGEDCGIDVVTVAMAYVYFEKLILKGLISKQNRKLCAGACLLLAAKMNDL 441 (497)
T ss_pred HHHHHHHHHhhhccCccceeehhHHHHHHHHHHhhhhhhhhhhHHHHHHHHHHHHhhhh
Confidence 34467788888888999999999999999998888888788999999999999997764
No 62
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=92.69 E-value=0.096 Score=42.49 Aligned_cols=30 Identities=30% Similarity=0.644 Sum_probs=19.8
Q ss_pred CCCCCCCCCCceEEecC---CCceE-----cCcCceee
Q 025357 4 SYCADCKRLTEVVFDHS---AGDTI-----CSECGLVL 33 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~---~G~~v-----C~~CG~Vl 33 (254)
++||+||++..-+.|.. .|..| |.+||.-.
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence 57999998532455533 45444 99999765
No 63
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=92.55 E-value=0.049 Score=33.19 Aligned_cols=30 Identities=27% Similarity=0.527 Sum_probs=21.6
Q ss_pred CCCCCCCCCCCceEEe----cCCCceEcCcCceee
Q 025357 3 DSYCADCKRLTEVVFD----HSAGDTICSECGLVL 33 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~D----~~~G~~vC~~CG~Vl 33 (254)
...||+|+.. --+-| ...+.+-|..||.+.
T Consensus 2 ~i~CP~C~~~-f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 2 IITCPNCQTR-FRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EEECCCCCce-EEcCHHHcccCCcEEECCCCCcEe
Confidence 3689999973 22222 357789999999886
No 64
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=92.48 E-value=0.34 Score=36.45 Aligned_cols=32 Identities=28% Similarity=0.714 Sum_probs=23.6
Q ss_pred CCCCCCCCCCCCCceEEecCCCceEcCcCceeecc
Q 025357 1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (254)
Q Consensus 1 ~~~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e 35 (254)
|.+..||.|.+ .-+++ ..+.++|.+|+.--.+
T Consensus 1 ~~lp~cp~c~s--EytYe-d~~~~~cpec~~ew~~ 32 (112)
T COG2824 1 MSLPPCPKCNS--EYTYE-DGGQLICPECAHEWNE 32 (112)
T ss_pred CCCCCCCccCC--ceEEe-cCceEeCchhcccccc
Confidence 56778999998 34454 3569999999976543
No 65
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=92.25 E-value=0.092 Score=39.09 Aligned_cols=29 Identities=31% Similarity=0.834 Sum_probs=22.6
Q ss_pred CCCCCCCCCceE---Ee--cCCCceEcCcCceeec
Q 025357 5 YCADCKRLTEVV---FD--HSAGDTICSECGLVLE 34 (254)
Q Consensus 5 ~Cp~Cg~~~~lv---~D--~~~G~~vC~~CG~Vl~ 34 (254)
.||.||+ ..++ .+ ...|.++|..||+-.+
T Consensus 24 tCp~Cgh-e~vs~ctvkk~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 24 TCPRCGH-EKVSSCTVKKTVNIGTAVCGNCGLSFE 57 (104)
T ss_pred ecCccCC-eeeeEEEEEecCceeEEEcccCcceEE
Confidence 5999998 4555 44 4678999999999764
No 66
>KOG0655 consensus G1/S-specific cyclin E [Cell cycle control, cell division, chromosome partitioning]
Probab=92.22 E-value=0.54 Score=42.52 Aligned_cols=112 Identities=19% Similarity=0.217 Sum_probs=87.5
Q ss_pred HHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCC-CCCCCCHHHHHHHHHHHHHHhcCC-CCCHHHHHHHh-cCCCHHHHH
Q 025357 109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQK-PLRGRNQEAIVAACLYIACRQENK-PRTVKEFCSVA-NGTTKKEIG 185 (254)
Q Consensus 109 a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~-~~~Gr~~~~iaAAclY~AcR~~~~-p~tl~eIa~~~-~~v~~~~i~ 185 (254)
.++++-++|+...|-..+.-.|..+|.+...-. -...-....+--+|||+|++.+.+ |-.+.|+|.++ ..++..+|.
T Consensus 148 LlDWlmEVCEvykLHRETFyLAvDy~DRyl~t~~~v~kt~lQLIGitsLFIAAK~EEIYpPKl~eFAyvTDgAcs~ddIl 227 (408)
T KOG0655|consen 148 LLDWLMEVCEVYKLHRETFYLAVDYFDRYLETQVEVSKTNLQLIGITSLFIAAKLEEIYPPKLIEFAYVTDGACSEDDIL 227 (408)
T ss_pred HHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHhhccCccccceeeeccCccchHHHH
Confidence 478999999999999999999999999875532 112223456677899999998875 88889998763 356899999
Q ss_pred HHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcc
Q 025357 186 RAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFF 226 (254)
Q Consensus 186 ~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~ 226 (254)
+.-..|.+.|+-+ +.|++....+.-|..-++++..
T Consensus 228 tmE~iilkal~W~------l~PiTii~WL~vylQv~~~n~~ 262 (408)
T KOG0655|consen 228 TMELIILKALKWE------LSPITIISWLNVYLQVDALNDA 262 (408)
T ss_pred HHHHHHHHHhccc------ccceehHHHHHHHHHHHhcCCC
Confidence 9999999999887 6777777777777766665543
No 67
>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=91.90 E-value=0.072 Score=38.47 Aligned_cols=32 Identities=25% Similarity=0.500 Sum_probs=18.1
Q ss_pred CCCCCCCCCce--EEe--cCCCceEcCcCceeeccc
Q 025357 5 YCADCKRLTEV--VFD--HSAGDTICSECGLVLEAY 36 (254)
Q Consensus 5 ~Cp~Cg~~~~l--v~D--~~~G~~vC~~CG~Vl~e~ 36 (254)
.||.|+...+| ..| ...|.+.|..||...+-.
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 59999954444 444 357899999999987543
No 68
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=91.83 E-value=0.15 Score=39.14 Aligned_cols=25 Identities=32% Similarity=0.634 Sum_probs=19.8
Q ss_pred CCCCCCCCceEEecCCCceEcCcCceeeccc
Q 025357 6 CADCKRLTEVVFDHSAGDTICSECGLVLEAY 36 (254)
Q Consensus 6 Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~ 36 (254)
||.||+ .-+|+- +-|.+||+.++.+
T Consensus 1 CPvCg~-~l~vt~-----l~C~~C~t~i~G~ 25 (113)
T PF09862_consen 1 CPVCGG-ELVVTR-----LKCPSCGTEIEGE 25 (113)
T ss_pred CCCCCC-ceEEEE-----EEcCCCCCEEEee
Confidence 999998 445544 9999999999633
No 69
>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=91.75 E-value=0.1 Score=40.57 Aligned_cols=31 Identities=10% Similarity=0.203 Sum_probs=25.8
Q ss_pred CCCCCCCCCCCceEEecCCCceEcCcCceeeccc
Q 025357 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY 36 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~ 36 (254)
.+.||.||.. .+|-..--+||..||.++...
T Consensus 9 Kr~Cp~cg~k---FYDLnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 9 KRICPNTGSK---FYDLNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred cccCCCcCcc---ccccCCCCccCCCcCCccCcc
Confidence 3679999983 688888899999999998644
No 70
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=91.69 E-value=0.093 Score=39.33 Aligned_cols=41 Identities=22% Similarity=0.467 Sum_probs=28.5
Q ss_pred CCCCCCCCCCce--EEecCCCceEcCcCceeeccc------ccccCcccc
Q 025357 4 SYCADCKRLTEV--VFDHSAGDTICSECGLVLEAY------SVDETSEWR 45 (254)
Q Consensus 4 ~~Cp~Cg~~~~l--v~D~~~G~~vC~~CG~Vl~e~------~id~~~ewr 45 (254)
..||+||+ ..+ -.|...+.++|..||+.-+-. .||-..+|.
T Consensus 22 f~CP~Cge-~~v~v~~~k~~~h~~C~~CG~y~~~~V~~l~epIDVY~~wi 70 (99)
T PRK14892 22 FECPRCGK-VSISVKIKKNIAIITCGNCGLYTEFEVPSVYDEVDVYNKFI 70 (99)
T ss_pred eECCCCCC-eEeeeecCCCcceEECCCCCCccCEECCccccchhhHHHHH
Confidence 35999996 333 356678899999999986432 245556674
No 71
>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=91.68 E-value=0.15 Score=37.44 Aligned_cols=32 Identities=25% Similarity=0.446 Sum_probs=25.7
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeecccc
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYS 37 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~ 37 (254)
-.||.||. .. +.-...|-+-|..||.++....
T Consensus 36 y~Cp~Cgk-~~-vkR~a~GIW~C~~C~~~~AGGA 67 (90)
T PF01780_consen 36 YTCPFCGK-TS-VKRVATGIWKCKKCGKKFAGGA 67 (90)
T ss_dssp BEESSSSS-SE-EEEEETTEEEETTTTEEEE-BS
T ss_pred CcCCCCCC-ce-eEEeeeEEeecCCCCCEEeCCC
Confidence 46999998 45 6677999999999999986443
No 72
>PF08613 Cyclin: Cyclin; InterPro: IPR013922 Cyclins are eukaryotic proteins that play an active role in controlling nuclear cell division cycles [], and regulate cyclin dependent kinases (CDKs). Cyclins, together with the p34 (cdc2) or cdk2 kinases, form the Maturation Promoting Factor (MPF). There are two main groups of cyclins, G1/S cyclins, which are essential for the control of the cell cycle at the G1/S (start) transition, and G2/M cyclins, which are essential for the control of the cell cycle at the G2/M (mitosis) transition. G2/M cyclins accumulate steadily during G2 and are abruptly destroyed as cells exit from mitosis (at the end of the M-phase). In most species, there are multiple forms of G1 and G2 cyclins. For example, in vertebrates, there are two G2 cyclins, A and B, and at least three G1 cyclins, C, D, and E. Cyclin homologues have been found in various viruses, including Saimiriine herpesvirus 2 (Herpesvirus saimiri) and Human herpesvirus 8 (HHV-8) (Kaposi's sarcoma-associated herpesvirus). These viral homologues differ from their cellular counterparts in that the viral proteins have gained new functions and eliminated others to harness the cell and benefit the virus []. This entry includes cyclin PHO80 and other cyclins that partner with the cyclin-dependent kinase (CDK) PHO85. The PHO80/PHO85 cyclin-cdk complex is used for a regulatory process other than cell-cycle control []. This entry also includes other PHO80-like cyclins that are involved in the cell-cycle control. They belong to the P/U family and interact preferentially with CDKA1 [].; GO: 0019901 protein kinase binding, 0000079 regulation of cyclin-dependent protein kinase activity; PDB: 2PK9_D 2PMI_D.
Probab=91.53 E-value=4.6 Score=32.27 Aligned_cols=90 Identities=14% Similarity=0.129 Sum_probs=65.7
Q ss_pred HHHHHHHHHHhccCCCHHHHHHHHHHHHHHhh---CCC--CCCCCHHHHHHHHHHHHHHhc-CCCCCHHHHHHHhcCCCH
Q 025357 108 QAFKSISAMSDRLGLVTTIKDRANEIYKKVED---QKP--LRGRNQEAIVAACLYIACRQE-NKPRTVKEFCSVANGTTK 181 (254)
Q Consensus 108 ~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~---~~~--~~Gr~~~~iaAAclY~AcR~~-~~p~tl~eIa~~~~~v~~ 181 (254)
...+++.++....+++..+.-.|..+..++.. ... +...+..-+..+|+-+|.+.. ....+.+..+.+ .|++.
T Consensus 53 ~i~~fl~ri~~~~~~s~~~~i~aliYl~Rl~~~~~~~~~~~~~~~~~Rl~l~alilA~K~~~D~~~~n~~~a~v-~gis~ 131 (149)
T PF08613_consen 53 SIRDFLSRILKYTQCSPECLILALIYLDRLRQRSRKPNIPLNSSNIHRLFLTALILASKFLDDNTYSNKSWAKV-GGISL 131 (149)
T ss_dssp -HHHHHHHHHHHTT--HHHHHHHHHHHHHHHH--H-TT---STTTHHHHHHHHHHHHHHHH-SS---HHHHHHH-HTS-H
T ss_pred cHHHHHHHHHHHcCCChHHHHHHHHHHHHHHHhhcccccccccchhHHHHHHHHHHHHhhcccccccHHHHHhh-cCCCH
Confidence 35778999999999999999999999998877 222 334567778888888888854 678889999996 89999
Q ss_pred HHHHHHHHHHHHHhchh
Q 025357 182 KEIGRAKEFIVKHLEAE 198 (254)
Q Consensus 182 ~~i~~~~k~l~~~l~~~ 198 (254)
++|.+.-+.+...++.+
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 99999988888877653
No 73
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=91.29 E-value=0.92 Score=31.30 Aligned_cols=71 Identities=17% Similarity=0.218 Sum_probs=43.0
Q ss_pred HHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCC-CHHHHHHHHHHH
Q 025357 113 ISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT-TKKEIGRAKEFI 191 (254)
Q Consensus 113 I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v-~~~~i~~~~k~l 191 (254)
|..++..++++.....+ +++.........-....-+.-|.-|+.. + +.++.|||.. .|. +...+.+.|++.
T Consensus 4 ~~~la~~~~~s~~~l~~---~f~~~~~~s~~~~~~~~r~~~a~~~l~~---~-~~~~~~ia~~-~g~~s~~~f~r~Fk~~ 75 (84)
T smart00342 4 LEDLAEALGMSPRHLQR---LFKKETGTTPKQYLRDRRLERARRLLRD---T-DLSVTEIALR-VGFSSQSYFSRAFKKL 75 (84)
T ss_pred HHHHHHHhCCCHHHHHH---HHHHHhCcCHHHHHHHHHHHHHHHHHHc---C-CCCHHHHHHH-hCCCChHHHHHHHHHH
Confidence 67788888998755444 3443322211110112223344444432 2 8999999995 999 999999988764
No 74
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=91.15 E-value=0.6 Score=35.34 Aligned_cols=28 Identities=21% Similarity=0.511 Sum_probs=20.7
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
-.||.|++ .-.-.| ...+||.+||.--.
T Consensus 3 p~CP~C~s-eytY~d--g~~~iCpeC~~EW~ 30 (109)
T TIGR00686 3 PPCPKCNS-EYTYHD--GTQLICPSCLYEWN 30 (109)
T ss_pred CcCCcCCC-cceEec--CCeeECcccccccc
Confidence 47999998 344444 45799999998654
No 75
>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=91.10 E-value=1.1 Score=32.63 Aligned_cols=46 Identities=17% Similarity=0.175 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHhcC-CCHHHHHHHHHHHHHHhchh
Q 025357 150 AIVAACLYIACRQENKPRTVKEFCSVANG-TTKKEIGRAKEFIVKHLEAE 198 (254)
Q Consensus 150 ~iaAAclY~AcR~~~~p~tl~eIa~~~~~-v~~~~i~~~~k~l~~~l~~~ 198 (254)
..=..++|++-+..| .|+.+|+.. +| .+..++..+++++.+.+..+
T Consensus 30 ~aR~ia~yl~~~~~~--~s~~~Ig~~-fg~r~hStV~~a~~ri~~~~~~d 76 (90)
T cd06571 30 LARQIAMYLARELTG--LSLPEIGRA-FGGRDHSTVLHAVRKIEELLEED 76 (90)
T ss_pred hHHHHHHHHHHHHhC--CCHHHHHHH-hCCCCHhHHHHHHHHHHHHHHhC
Confidence 333466788766655 789999995 77 99999999999999988643
No 76
>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=91.00 E-value=0.066 Score=49.25 Aligned_cols=78 Identities=15% Similarity=0.204 Sum_probs=0.0
Q ss_pred CCCHHHHHHHHHHHHHHh-hCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhc
Q 025357 121 GLVTTIKDRANEIYKKVE-DQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEM 199 (254)
Q Consensus 121 ~Lp~~v~e~A~~i~k~~~-~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~ 199 (254)
++|+.++..|..+|+... ....+++..-.+-+.+|+|+||...+.+..+...... .++.++...+.|+.|.+.|+...
T Consensus 11 ~~~~~ll~~a~~L~~ls~~~~~~l~~~~EiaR~~iCa~lA~~~l~~~~dl~~~~~~-~pl~pk~y~~l~~~~~~~L~~~s 89 (353)
T PF05460_consen 11 GLPPKLLSKASELYRLSRQKKSSLKPEEEIARAHICAELACERLKEKLDLPYAIKR-SPLPPKVYKKLLNTFENLLGNSS 89 (353)
T ss_dssp --------------------------------------------------------------------------------
T ss_pred CCCHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHhCCccCchhhcCC-CCCCHHHHHHHHHHHHHHHhCCC
Confidence 456789999999999987 4566777777788999999999999999988887774 89999999999999999998774
No 77
>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=90.98 E-value=0.23 Score=39.71 Aligned_cols=30 Identities=30% Similarity=0.633 Sum_probs=22.5
Q ss_pred CCCCCCCCCCceEEec---CCCceE-----cCcCceee
Q 025357 4 SYCADCKRLTEVVFDH---SAGDTI-----CSECGLVL 33 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~---~~G~~v-----C~~CG~Vl 33 (254)
+.||.||...+-|.|. +.|..| |..||.=.
T Consensus 1 M~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RF 38 (147)
T TIGR00244 1 MHCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERF 38 (147)
T ss_pred CCCCCCCCCCCEeeeccccCCCCeeeecccCCccCCcc
Confidence 5799999865667784 567666 89998653
No 78
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=90.79 E-value=0.16 Score=35.15 Aligned_cols=29 Identities=21% Similarity=0.544 Sum_probs=21.9
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
+.||.||.. . .........+|..||...+
T Consensus 29 q~C~~CG~~-~-~~~~~~r~~~C~~Cg~~~~ 57 (69)
T PF07282_consen 29 QTCPRCGHR-N-KKRRSGRVFTCPNCGFEMD 57 (69)
T ss_pred cCccCcccc-c-ccccccceEEcCCCCCEEC
Confidence 679999973 2 2246778899999999875
No 79
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=90.29 E-value=0.17 Score=37.99 Aligned_cols=27 Identities=26% Similarity=0.733 Sum_probs=21.3
Q ss_pred CCCCCCCCCceEEecCCCceEcCcCceeecc
Q 025357 5 YCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (254)
Q Consensus 5 ~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e 35 (254)
.||.||+ .+ .+..+.++|..||.+...
T Consensus 2 fC~~Cg~--~l--~~~~~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 2 FCPKCGS--LM--TPKNGVYVCPSCGYEKEK 28 (104)
T ss_pred CCcccCc--cc--ccCCCeEECcCCCCcccc
Confidence 6999997 23 456789999999998653
No 80
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=89.97 E-value=7.1 Score=33.38 Aligned_cols=88 Identities=20% Similarity=0.247 Sum_probs=71.0
Q ss_pred HHHHHHhccCCC--HHHHHHHHHHHHHHhhC--CCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHH
Q 025357 112 SISAMSDRLGLV--TTIKDRANEIYKKVEDQ--KPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRA 187 (254)
Q Consensus 112 ~I~~i~~~L~Lp--~~v~e~A~~i~k~~~~~--~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~ 187 (254)
.|.+++.+|||. +.+.+.|.+|.+...-. +..-|-.-..-|.-|+=+|+-.-++|..-...... +|.++++-.+.
T Consensus 2 lI~~l~~klgL~~ep~~lrKa~E~~RL~~~~~~~~~~~v~E~~kaV~CldlAa~~l~i~fDr~~avKL-SGl~k~~Y~~~ 80 (262)
T KOG4557|consen 2 LISDLGRKLGLDNEPLLLRKAAEIRRLCDAQFDSSIIGVGEICKAVICLDLAATRLQIIFDRQAAVKL-SGLSKKAYSRS 80 (262)
T ss_pred cHHHHHHhcCCccChHHHHHHHHHHHHHHhhccCccccccchhHHHHhHHHHHHHhcccccHHHHHHh-ccccHHHHHHH
Confidence 478899999994 57999999998876432 33445556677888898888888998887777785 99999999999
Q ss_pred HHHHHHHhchhcc
Q 025357 188 KEFIVKHLEAEMG 200 (254)
Q Consensus 188 ~k~l~~~l~~~~~ 200 (254)
++.+...||+...
T Consensus 81 ~~sfe~llgln~~ 93 (262)
T KOG4557|consen 81 FNSFENLLGLNIK 93 (262)
T ss_pred HHHHHHHhcchhh
Confidence 9999999998743
No 81
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=89.89 E-value=0.36 Score=30.76 Aligned_cols=27 Identities=22% Similarity=0.438 Sum_probs=20.9
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCce
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGL 31 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~ 31 (254)
..||.||+ ..+..-...+..-|.+|+.
T Consensus 19 ~~CP~Cg~-~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGS-TKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCC-eeeEEeCCCCeEECCCCCC
Confidence 46999998 4555555579999999974
No 82
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=89.74 E-value=0.24 Score=36.35 Aligned_cols=32 Identities=19% Similarity=0.427 Sum_probs=25.7
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeecccc
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYS 37 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~ 37 (254)
-.||.||. .. +.-...|-+.|..||.++....
T Consensus 37 y~CpfCgk-~~-vkR~a~GIW~C~~C~~~~AGGA 68 (90)
T PTZ00255 37 YFCPFCGK-HA-VKRQAVGIWRCKGCKKTVAGGA 68 (90)
T ss_pred ccCCCCCC-Cc-eeeeeeEEEEcCCCCCEEeCCc
Confidence 57999997 55 4566889999999999986444
No 83
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=89.58 E-value=0.49 Score=27.89 Aligned_cols=27 Identities=19% Similarity=0.334 Sum_probs=21.8
Q ss_pred CCCHHHHHHHhcCCCHHHHHHHHHHHHH
Q 025357 166 PRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (254)
Q Consensus 166 p~tl~eIa~~~~~v~~~~i~~~~k~l~~ 193 (254)
|.|-.|||+. .|.+..++.|.++++.+
T Consensus 2 ~mtr~diA~~-lG~t~ETVSR~l~~l~~ 28 (32)
T PF00325_consen 2 PMTRQDIADY-LGLTRETVSRILKKLER 28 (32)
T ss_dssp E--HHHHHHH-HTS-HHHHHHHHHHHHH
T ss_pred CcCHHHHHHH-hCCcHHHHHHHHHHHHH
Confidence 6788999995 99999999999999875
No 84
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=89.37 E-value=0.29 Score=37.60 Aligned_cols=32 Identities=28% Similarity=0.659 Sum_probs=24.1
Q ss_pred CCCCCCCCCCCceEE--ecCCCceEcCcCceeeccc
Q 025357 3 DSYCADCKRLTEVVF--DHSAGDTICSECGLVLEAY 36 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~--D~~~G~~vC~~CG~Vl~e~ 36 (254)
|..||.||+ -++. |...+.++|..||...+-.
T Consensus 2 m~FCp~Cgs--ll~p~~~~~~~~l~C~kCgye~~~~ 35 (113)
T COG1594 2 MRFCPKCGS--LLYPKKDDEGGKLVCRKCGYEEEAS 35 (113)
T ss_pred ccccCCccC--eeEEeEcCCCcEEECCCCCcchhcc
Confidence 588999998 2333 3367799999999987544
No 85
>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=88.78 E-value=0.3 Score=35.93 Aligned_cols=32 Identities=25% Similarity=0.466 Sum_probs=25.9
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeecccc
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYS 37 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~ 37 (254)
-.||.||. .. +.-...|-+.|..||.++....
T Consensus 36 y~CpfCgk-~~-vkR~a~GIW~C~~C~~~~AGGA 67 (91)
T TIGR00280 36 YVCPFCGK-KT-VKRGSTGIWTCRKCGAKFAGGA 67 (91)
T ss_pred ccCCCCCC-Cc-eEEEeeEEEEcCCCCCEEeCCc
Confidence 57999997 45 5667899999999999986443
No 86
>KOG4557 consensus Origin recognition complex, subunit 6 [Replication, recombination and repair]
Probab=88.51 E-value=1.6 Score=37.13 Aligned_cols=80 Identities=14% Similarity=0.289 Sum_probs=53.6
Q ss_pred HHHHHhccCCCHHHHHHHHHHHHHHhhCCCC------CCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHH
Q 025357 113 ISAMSDRLGLVTTIKDRANEIYKKVEDQKPL------RGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGR 186 (254)
Q Consensus 113 I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~------~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~ 186 (254)
|+++|=.||+-+ ++..|.++.+...+. +- .--+....++|++|.|||..+..+.--.+.. ++|+++..+..
T Consensus 96 VrdlaVQfgc~e-vi~~a~~vl~syk~~-lpaT~~~~~D~SrP~ft~aA~~~ack~lKlKVdK~kli~-~sg~~~s~F~~ 172 (262)
T KOG4557|consen 96 VRDLAVQFGCVE-VIKSAQNVLSSYKER-LPATRRANADFSRPVFTAAAFYLACKKLKLKVDKLKLIE-VSGTSESEFSC 172 (262)
T ss_pred HHHHHHHHhHHH-HHHHHHHHHHHHHhc-CchhhhcCCcccchHHHHHHHHHHHHHHHHhhhHhhccc-ccCCCHHHHHH
Confidence 455555555543 666677766665441 11 1235567899999999999988777666667 48999988877
Q ss_pred HHHHHHHHh
Q 025357 187 AKEFIVKHL 195 (254)
Q Consensus 187 ~~k~l~~~l 195 (254)
.-+.+.+..
T Consensus 173 l~kqler~~ 181 (262)
T KOG4557|consen 173 LSKQLERNY 181 (262)
T ss_pred HHHHHHHHH
Confidence 776666544
No 87
>PRK12495 hypothetical protein; Provisional
Probab=88.33 E-value=0.29 Score=41.71 Aligned_cols=32 Identities=22% Similarity=0.668 Sum_probs=25.0
Q ss_pred CCCCCCCCCCCCCceEEecCCCceEcCcCceeeccc
Q 025357 1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLEAY 36 (254)
Q Consensus 1 ~~~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~ 36 (254)
|....|+.||.+ ++ ...|.++|..|+.++.+.
T Consensus 40 msa~hC~~CG~P---Ip-a~pG~~~Cp~CQ~~~~~~ 71 (226)
T PRK12495 40 MTNAHCDECGDP---IF-RHDGQEFCPTCQQPVTED 71 (226)
T ss_pred cchhhcccccCc---cc-CCCCeeECCCCCCccccc
Confidence 445789999983 33 458999999999998653
No 88
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=87.63 E-value=0.38 Score=35.32 Aligned_cols=32 Identities=25% Similarity=0.487 Sum_probs=25.8
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeecccc
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYS 37 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~ 37 (254)
-.||.||. .. +.-...|-+-|..||.++....
T Consensus 37 y~CpfCgk-~~-vkR~a~GIW~C~~C~~~~AGGA 68 (90)
T PRK03976 37 HVCPVCGR-PK-VKRVGTGIWECRKCGAKFAGGA 68 (90)
T ss_pred ccCCCCCC-Cc-eEEEEEEEEEcCCCCCEEeCCc
Confidence 57999987 44 4567899999999999986444
No 89
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=87.41 E-value=0.56 Score=26.73 Aligned_cols=22 Identities=23% Similarity=0.533 Sum_probs=12.3
Q ss_pred CCCCCCCCCceEEecCCCceEcCc
Q 025357 5 YCADCKRLTEVVFDHSAGDTICSE 28 (254)
Q Consensus 5 ~Cp~Cg~~~~lv~D~~~G~~vC~~ 28 (254)
.||.||+ .++.++.+-.+.|.+
T Consensus 1 ~CP~C~s--~l~~~~~ev~~~C~N 22 (28)
T PF03119_consen 1 TCPVCGS--KLVREEGEVDIRCPN 22 (28)
T ss_dssp B-TTT----BEEE-CCTTCEEE--
T ss_pred CcCCCCC--EeEcCCCCEeEECCC
Confidence 5999998 477777777778864
No 90
>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=87.31 E-value=0.39 Score=29.37 Aligned_cols=30 Identities=33% Similarity=0.544 Sum_probs=19.3
Q ss_pred CCCCCCCCCCceEEecC-CCceEcCcCceee
Q 025357 4 SYCADCKRLTEVVFDHS-AGDTICSECGLVL 33 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~-~G~~vC~~CG~Vl 33 (254)
-.|++||..-.+..... ...+.|..||.-+
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~ 36 (41)
T smart00834 6 YRCEDCGHTFEVLQKISDDPLATCPECGGDV 36 (41)
T ss_pred EEcCCCCCEEEEEEecCCCCCCCCCCCCCcc
Confidence 46999997323333322 5577899999844
No 91
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=87.29 E-value=0.37 Score=28.41 Aligned_cols=25 Identities=28% Similarity=0.589 Sum_probs=17.4
Q ss_pred CCCCCCCCCceEEecCCCceEcCcCcee
Q 025357 5 YCADCKRLTEVVFDHSAGDTICSECGLV 32 (254)
Q Consensus 5 ~Cp~Cg~~~~lv~D~~~G~~vC~~CG~V 32 (254)
.|.+||.. +.+.....+-|..||.=
T Consensus 2 ~C~~Cg~~---~~~~~~~~irC~~CG~R 26 (32)
T PF03604_consen 2 ICGECGAE---VELKPGDPIRCPECGHR 26 (32)
T ss_dssp BESSSSSS---E-BSTSSTSSBSSSS-S
T ss_pred CCCcCCCe---eEcCCCCcEECCcCCCe
Confidence 58899973 23556777899999963
No 92
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=87.28 E-value=0.68 Score=31.69 Aligned_cols=30 Identities=20% Similarity=0.353 Sum_probs=20.1
Q ss_pred CCCCCCCCCCCceEEecCCC--ceEcCcCceee
Q 025357 3 DSYCADCKRLTEVVFDHSAG--DTICSECGLVL 33 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~D~~~G--~~vC~~CG~Vl 33 (254)
...||.||.. .+..-...| ..+|..||...
T Consensus 6 lKPCPFCG~~-~~~v~~~~g~~~v~C~~CgA~~ 37 (64)
T PRK09710 6 VKPCPFCGCP-SVTVKAISGYYRAKCNGCESRT 37 (64)
T ss_pred ccCCCCCCCc-eeEEEecCceEEEEcCCCCcCc
Confidence 3679999984 443333343 36899999853
No 93
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=86.92 E-value=0.51 Score=29.94 Aligned_cols=27 Identities=30% Similarity=0.645 Sum_probs=19.9
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl 33 (254)
-.|.+||.. +..+ ..+.+-|.+||.=+
T Consensus 3 Y~C~~Cg~~--~~~~-~~~~irC~~CG~rI 29 (44)
T smart00659 3 YICGECGRE--NEIK-SKDVVRCRECGYRI 29 (44)
T ss_pred EECCCCCCE--eecC-CCCceECCCCCceE
Confidence 579999983 3333 57889999999744
No 94
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=86.78 E-value=0.3 Score=37.71 Aligned_cols=38 Identities=18% Similarity=0.373 Sum_probs=24.8
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeecccccccCc
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETS 42 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~id~~~ 42 (254)
..||+||. ..+.--.-.=.-.|..||+=+...--|++|
T Consensus 22 grCP~CGe-GrLF~gFLK~~p~C~aCG~dyg~~~a~DgP 59 (126)
T COG5349 22 GRCPRCGE-GRLFRGFLKVVPACEACGLDYGFADADDGP 59 (126)
T ss_pred CCCCCCCC-chhhhhhcccCchhhhccccccCCcccCCC
Confidence 57999998 566433444456899999877544434333
No 95
>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=86.54 E-value=2.2 Score=27.66 Aligned_cols=33 Identities=21% Similarity=0.296 Sum_probs=27.9
Q ss_pred hcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHh
Q 025357 162 QENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHL 195 (254)
Q Consensus 162 ~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l 195 (254)
.++.|+|..++|+. ++||..+|.+.++.|.+.+
T Consensus 11 ~~~~~it~~eLa~~-l~vS~rTi~~~i~~L~~~~ 43 (55)
T PF08279_consen 11 ESKEPITAKELAEE-LGVSRRTIRRDIKELREWG 43 (55)
T ss_dssp HTTTSBEHHHHHHH-CTS-HHHHHHHHHHHHHTT
T ss_pred HcCCCcCHHHHHHH-hCCCHHHHHHHHHHHHHCC
Confidence 45667999999995 9999999999999997765
No 96
>PRK05978 hypothetical protein; Provisional
Probab=86.33 E-value=0.5 Score=38.04 Aligned_cols=30 Identities=17% Similarity=0.412 Sum_probs=22.1
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
.+||+||. ..+..-+-.=..-|..||.-++
T Consensus 34 grCP~CG~-G~LF~g~Lkv~~~C~~CG~~~~ 63 (148)
T PRK05978 34 GRCPACGE-GKLFRAFLKPVDHCAACGEDFT 63 (148)
T ss_pred CcCCCCCC-CcccccccccCCCccccCCccc
Confidence 58999998 5664434444567999999875
No 97
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=86.26 E-value=0.72 Score=28.55 Aligned_cols=27 Identities=26% Similarity=0.566 Sum_probs=18.7
Q ss_pred CCCCCCCCCceEEe---------cCCCceEcCcCcee
Q 025357 5 YCADCKRLTEVVFD---------HSAGDTICSECGLV 32 (254)
Q Consensus 5 ~Cp~Cg~~~~lv~D---------~~~G~~vC~~CG~V 32 (254)
.||.||. ...++- +.+-..+|.+||..
T Consensus 2 ~Cp~C~~-~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~ 37 (40)
T smart00440 2 PCPKCGN-REATFFQLQTRSADEPMTVFYVCTKCGHR 37 (40)
T ss_pred cCCCCCC-CeEEEEEEcccCCCCCCeEEEEeCCCCCE
Confidence 6999998 454432 23447899999964
No 98
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=86.11 E-value=0.29 Score=29.61 Aligned_cols=29 Identities=28% Similarity=0.603 Sum_probs=20.2
Q ss_pred CCCCCCCCCCceEEe----cCCCceEcCcCceee
Q 025357 4 SYCADCKRLTEVVFD----HSAGDTICSECGLVL 33 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D----~~~G~~vC~~CG~Vl 33 (254)
..||+|+.. --+-| .....+-|+.||.+.
T Consensus 3 i~Cp~C~~~-y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAK-YEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCE-EeCCHHHCCCCCcEEECCCCCCEe
Confidence 689999973 22222 345678899999874
No 99
>COG4640 Predicted membrane protein [Function unknown]
Probab=85.81 E-value=0.4 Score=44.22 Aligned_cols=29 Identities=21% Similarity=0.670 Sum_probs=21.8
Q ss_pred CCCCCCCCCCCceEEecCCCceEcCcCceeecccc
Q 025357 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYS 37 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~ 37 (254)
|..||.||+. ..+++.-|+.||.-+..+.
T Consensus 1 M~fC~kcG~q------k~Ed~~qC~qCG~~~t~~~ 29 (465)
T COG4640 1 MKFCPKCGSQ------KAEDDVQCTQCGHKFTSRQ 29 (465)
T ss_pred CCcccccccc------cccccccccccCCcCCchh
Confidence 5789999983 3466777999998876443
No 100
>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=85.24 E-value=4.1 Score=33.18 Aligned_cols=29 Identities=17% Similarity=0.116 Sum_probs=26.7
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
.|.|..|||+. .|++..++.|.+++|.+.
T Consensus 142 ~~~t~~~iA~~-lG~tretvsR~l~~l~~~ 170 (193)
T TIGR03697 142 LRLSHQAIAEA-IGSTRVTITRLLGDLRKK 170 (193)
T ss_pred CCCCHHHHHHH-hCCcHHHHHHHHHHHHHC
Confidence 68999999995 999999999999999876
No 101
>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=85.23 E-value=1.4 Score=31.48 Aligned_cols=45 Identities=20% Similarity=0.279 Sum_probs=35.1
Q ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 149 EAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 149 ~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
+.-.-+.+|+|-...+.|.+.+|||+. .++++..+++..+.|.+.
T Consensus 8 ~~Al~~l~~la~~~~~~~~s~~eiA~~-~~i~~~~l~kil~~L~~~ 52 (83)
T PF02082_consen 8 DYALRILLYLARHPDGKPVSSKEIAER-LGISPSYLRKILQKLKKA 52 (83)
T ss_dssp HHHHHHHHHHHCTTTSC-BEHHHHHHH-HTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHhCCCCCCCCHHHHHHH-HCcCHHHHHHHHHHHhhC
Confidence 344556678877766778999999995 999999999999999874
No 102
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=85.08 E-value=0.62 Score=31.26 Aligned_cols=28 Identities=21% Similarity=0.533 Sum_probs=19.9
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeeccccc
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSV 38 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~i 38 (254)
..||+||+. ..--.||..||+--+..++
T Consensus 28 ~~C~~CG~~-------~~~H~vC~~CG~Y~gr~v~ 55 (57)
T PRK12286 28 VECPNCGEP-------KLPHRVCPSCGYYKGREVV 55 (57)
T ss_pred eECCCCCCc-------cCCeEECCCCCcCCCEEee
Confidence 569999972 2346899999987654443
No 103
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=84.95 E-value=0.7 Score=30.41 Aligned_cols=28 Identities=36% Similarity=0.663 Sum_probs=20.0
Q ss_pred CCCCCCCCCceEEecCCCce----EcCcCcee
Q 025357 5 YCADCKRLTEVVFDHSAGDT----ICSECGLV 32 (254)
Q Consensus 5 ~Cp~Cg~~~~lv~D~~~G~~----vC~~CG~V 32 (254)
.||+||....+..|.+.|.- =|.-|..=
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~P 33 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCCRP 33 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhcCCc
Confidence 69999987778889888852 25555543
No 104
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=84.50 E-value=0.99 Score=30.39 Aligned_cols=29 Identities=21% Similarity=0.509 Sum_probs=20.2
Q ss_pred CCCCCCCCCCceEEecCCCc--eEcCcCcee
Q 025357 4 SYCADCKRLTEVVFDHSAGD--TICSECGLV 32 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~--~vC~~CG~V 32 (254)
-.||.|+.-..|++=.+.|. +-|..||+-
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~ 40 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGYQ 40 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCCc
Confidence 47999998545544333443 779999987
No 105
>TIGR00569 ccl1 cyclin ccl1. University).
Probab=84.12 E-value=22 Score=32.10 Aligned_cols=71 Identities=6% Similarity=-0.001 Sum_probs=43.4
Q ss_pred HHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCC--CHHHHHHHHHHHHHHhc
Q 025357 124 TTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGT--TKKEIGRAKEFIVKHLE 196 (254)
Q Consensus 124 ~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v--~~~~i~~~~k~l~~~l~ 196 (254)
+.+...|-.+...+.--...---.|..+|+||||+|+|..++...-.+- ++ ..+ +...+...+..+++...
T Consensus 181 ~~l~q~a~~~lndsl~Td~~L~y~Ps~IAlAAI~lA~~~~~~~l~~~~~-e~-~~~~~~~~~~~~l~~~~~~~~~ 253 (305)
T TIGR00569 181 EYLRKHADKFLNRTLLTDAYLLYTPSQIALAAILHTASRAGLNMESYLT-EQ-LSVPGNREELPQLIDIMRELRI 253 (305)
T ss_pred HHHHHHHHHHHHHHHcCCceecCCHHHHHHHHHHHHHHHhCCCCcccch-hh-hcccccHHHHHHHHHHHHHHHH
Confidence 4455666665555433222222679999999999999999875443322 32 344 66776666655555443
No 106
>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=84.10 E-value=2.7 Score=29.03 Aligned_cols=44 Identities=18% Similarity=0.200 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHhcC----------CCCCHHHHHHHhcCCCHHHHHHHHHHHHHHh
Q 025357 151 IVAACLYIACRQEN----------KPRTVKEFCSVANGTTKKEIGRAKEFIVKHL 195 (254)
Q Consensus 151 iaAAclY~AcR~~~----------~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l 195 (254)
+|...++++-+... .|.|..+||+. +|++..++.+.+++|.+.=
T Consensus 3 la~~Ll~l~~~~~~~~~~~~~~~~~~lt~~~iA~~-~g~sr~tv~r~l~~l~~~g 56 (76)
T PF13545_consen 3 LARFLLELAERFGRRQDGDGIRIPLPLTQEEIADM-LGVSRETVSRILKRLKDEG 56 (76)
T ss_dssp HHHHHHHHHHHHEEEEETTEEEEEEESSHHHHHHH-HTSCHHHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHCCCCCCCCceEEecCCHHHHHHH-HCCCHHHHHHHHHHHHHCC
Confidence 45555666655442 57899999995 9999999999999998753
No 107
>PF12773 DZR: Double zinc ribbon
Probab=83.71 E-value=0.54 Score=30.19 Aligned_cols=27 Identities=22% Similarity=0.662 Sum_probs=12.1
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl 33 (254)
..||.||.. +. .......+|..||..+
T Consensus 13 ~fC~~CG~~--l~-~~~~~~~~C~~Cg~~~ 39 (50)
T PF12773_consen 13 KFCPHCGTP--LP-PPDQSKKICPNCGAEN 39 (50)
T ss_pred cCChhhcCC--hh-hccCCCCCCcCCcCCC
Confidence 345555542 11 2223345555555544
No 108
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=83.66 E-value=0.37 Score=31.25 Aligned_cols=27 Identities=37% Similarity=0.714 Sum_probs=21.1
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCcee
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLV 32 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~V 32 (254)
-.|-.||. .+..|.....+.|..||.=
T Consensus 7 Y~C~~Cg~--~~~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 7 YKCARCGR--EVELDQETRGIRCPYCGSR 33 (49)
T ss_pred EEhhhcCC--eeehhhccCceeCCCCCcE
Confidence 56999997 3444778889999999964
No 109
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=83.58 E-value=4 Score=27.44 Aligned_cols=38 Identities=13% Similarity=0.245 Sum_probs=30.8
Q ss_pred HHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 155 CLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 155 clY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
+||.... .+.+.+..+||+. ++|++.++..++++|.+.
T Consensus 12 ~Iy~l~~-~~~~v~~~~iA~~-L~vs~~tvt~ml~~L~~~ 49 (60)
T PF01325_consen 12 AIYELSE-EGGPVRTKDIAER-LGVSPPTVTEMLKRLAEK 49 (60)
T ss_dssp HHHHHHH-CTSSBBHHHHHHH-HTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHc-CCCCccHHHHHHH-HCCChHHHHHHHHHHHHC
Confidence 3565555 7889999999994 999999999999998753
No 110
>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=83.29 E-value=3.3 Score=32.45 Aligned_cols=46 Identities=20% Similarity=0.174 Sum_probs=38.4
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 148 QEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 148 ~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
.+.-..+++|+|-+..+.|.+..||++. .+++...+.+....|.+.
T Consensus 7 ~~YAl~~l~~La~~~~~~~~s~~~ia~~-~~ip~~~l~kil~~L~~~ 52 (135)
T TIGR02010 7 GRYAVTAMLDLALNAETGPVTLADISER-QGISLSYLEQLFAKLRKA 52 (135)
T ss_pred HHHHHHHHHHHHhCCCCCcCcHHHHHHH-HCcCHHHHHHHHHHHHHC
Confidence 4455667888887766678999999995 999999999999999874
No 111
>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=82.80 E-value=0.23 Score=30.13 Aligned_cols=29 Identities=28% Similarity=0.775 Sum_probs=19.4
Q ss_pred CCCCCCCCCceEEecCCCceEcCcCceee
Q 025357 5 YCADCKRLTEVVFDHSAGDTICSECGLVL 33 (254)
Q Consensus 5 ~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl 33 (254)
.||.||..=++.+++-.-+.+|..||.-|
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 58888874356677777778888888744
No 112
>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=82.78 E-value=1.1 Score=27.53 Aligned_cols=28 Identities=25% Similarity=0.555 Sum_probs=15.3
Q ss_pred CCCCCCCCCceEEe--------cCCCceEcCcCcee
Q 025357 5 YCADCKRLTEVVFD--------HSAGDTICSECGLV 32 (254)
Q Consensus 5 ~Cp~Cg~~~~lv~D--------~~~G~~vC~~CG~V 32 (254)
.||.||+...+.+. +.+-..+|.+||..
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 69999984333332 12334689999964
No 113
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=81.87 E-value=1.5 Score=33.02 Aligned_cols=26 Identities=27% Similarity=0.650 Sum_probs=22.0
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeecc
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e 35 (254)
..||.||. ..||+. +-|.+||+-+..
T Consensus 7 ~~cPvcg~-~~iVTe-----L~c~~~etTVrg 32 (122)
T COG3877 7 NRCPVCGR-KLIVTE-----LKCSNCETTVRG 32 (122)
T ss_pred CCCCcccc-cceeEE-----EecCCCCceEec
Confidence 67999998 577775 999999999863
No 114
>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=81.80 E-value=1.1 Score=26.46 Aligned_cols=23 Identities=26% Similarity=0.788 Sum_probs=14.9
Q ss_pred CCCCCCCCCceEEecCCCceEcCcCce
Q 025357 5 YCADCKRLTEVVFDHSAGDTICSECGL 31 (254)
Q Consensus 5 ~Cp~Cg~~~~lv~D~~~G~~vC~~CG~ 31 (254)
.|+.||- +.|.......|..||.
T Consensus 3 ~C~~CGy----~y~~~~~~~~CP~Cg~ 25 (33)
T cd00350 3 VCPVCGY----IYDGEEAPWVCPVCGA 25 (33)
T ss_pred ECCCCCC----EECCCcCCCcCcCCCC
Confidence 4777774 3555556677777775
No 115
>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=81.65 E-value=0.83 Score=30.46 Aligned_cols=27 Identities=19% Similarity=0.560 Sum_probs=18.5
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeecccc
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYS 37 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~ 37 (254)
..||.||. - ...-.||.+||+.=...+
T Consensus 27 ~~c~~cg~-~------~~~H~vc~~cG~y~~r~v 53 (56)
T PF01783_consen 27 VKCPNCGE-P------KLPHRVCPSCGYYKGRQV 53 (56)
T ss_dssp EESSSSSS-E------ESTTSBCTTTBBSSSSSS
T ss_pred eeeccCCC-E------ecccEeeCCCCeECCEEE
Confidence 46999996 1 245689999997644333
No 116
>KOG0794 consensus CDK8 kinase-activating protein cyclin C [Transcription]
Probab=81.44 E-value=11 Score=32.61 Aligned_cols=99 Identities=18% Similarity=0.159 Sum_probs=62.0
Q ss_pred HHHhccCC-CHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHH
Q 025357 115 AMSDRLGL-VTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (254)
Q Consensus 115 ~i~~~L~L-p~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~ 193 (254)
++-..+|+ +.+..+-+-.|...-+...+.-=--|..+|-||+|+||-..+.+.+-.=+++ ..++...+..+.++|.+
T Consensus 159 q~~qd~gi~d~~~l~~~W~ivNDSyr~Dl~Ll~PPh~IalAcl~Ia~~~~~k~~~~~w~~e--l~vD~ekV~~~v~~I~~ 236 (264)
T KOG0794|consen 159 QFVQDMGINDQKLLQLAWSIVNDSYRMDLCLLYPPHQIALACLYIACVIDEKDIPKAWFAE--LSVDMEKVKDIVQEILK 236 (264)
T ss_pred HHHHHhcccchhhhhhhHhhhcchhhcceeeecCHHHHHHHHHHHHHhhcCCChHHHHHHH--HhccHHHHHHHHHHHHH
Confidence 33334444 3334455544544443333322346889999999999998887765444555 46899999999988888
Q ss_pred HhchhcccccccCCCCHHHHHHHHHhhcCC
Q 025357 194 HLEAEMGQSVEMGTIHASDYLVIFLLNIFK 223 (254)
Q Consensus 194 ~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l 223 (254)
....-. ..+ +.-|....++|-+
T Consensus 237 lYe~wk-------~~~-E~~v~~ll~kl~~ 258 (264)
T KOG0794|consen 237 LYELWK-------IFD-EKKVKKLLSKLPK 258 (264)
T ss_pred HHHHHh-------hhh-HHHHHHHHHhccc
Confidence 776542 122 3337777777644
No 117
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=81.43 E-value=1.7 Score=30.61 Aligned_cols=31 Identities=13% Similarity=0.275 Sum_probs=21.5
Q ss_pred CCCCCCCCCCCceEEec-------CCCceEcC--cCceeec
Q 025357 3 DSYCADCKRLTEVVFDH-------SAGDTICS--ECGLVLE 34 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~D~-------~~G~~vC~--~CG~Vl~ 34 (254)
|+.||.||+ ...|.+. .+-.-.|+ +||....
T Consensus 1 mm~CP~Cg~-~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF~ 40 (72)
T PRK09678 1 MFHCPLCQH-AAHARTSRYITDTTKERYHQCQNVNCSATFI 40 (72)
T ss_pred CccCCCCCC-ccEEEEChhcChhhheeeeecCCCCCCCEEE
Confidence 479999998 4566653 22345688 8998764
No 118
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=81.29 E-value=0.99 Score=29.90 Aligned_cols=27 Identities=26% Similarity=0.695 Sum_probs=20.3
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
.+|+.||.. +-+..--+||..||.+.=
T Consensus 6 ~~C~~Cg~~----~~~~dDiVvCp~CgapyH 32 (54)
T PF14446_consen 6 CKCPVCGKK----FKDGDDIVVCPECGAPYH 32 (54)
T ss_pred ccChhhCCc----ccCCCCEEECCCCCCccc
Confidence 679999972 223456799999999873
No 119
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=81.05 E-value=1.2 Score=29.59 Aligned_cols=27 Identities=19% Similarity=0.596 Sum_probs=18.5
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeecccc
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYS 37 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~ 37 (254)
..||+||+. ..---||..||+--+..+
T Consensus 27 ~~C~~cG~~-------~~~H~vc~~cG~Y~gr~v 53 (55)
T TIGR01031 27 VVCPNCGEF-------KLPHRVCPSCGYYKGRQV 53 (55)
T ss_pred eECCCCCCc-------ccCeeECCccCeECCEEc
Confidence 469999972 234589999997654433
No 120
>PHA02942 putative transposase; Provisional
Probab=80.98 E-value=0.92 Score=42.25 Aligned_cols=31 Identities=16% Similarity=0.352 Sum_probs=22.3
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeecccc
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYS 37 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~ 37 (254)
+.||.||.. . .+.......|..||.+.+..+
T Consensus 326 q~Cs~CG~~-~--~~l~~r~f~C~~CG~~~drD~ 356 (383)
T PHA02942 326 VSCPKCGHK-M--VEIAHRYFHCPSCGYENDRDV 356 (383)
T ss_pred ccCCCCCCc-c--CcCCCCEEECCCCCCEeCcHH
Confidence 679999972 2 244456799999999985433
No 121
>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=80.70 E-value=7.3 Score=25.86 Aligned_cols=30 Identities=20% Similarity=0.286 Sum_probs=26.5
Q ss_pred CCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 164 ~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
..+.+..||++. .|++..++.+.++.|.+.
T Consensus 23 ~~~~s~~ela~~-~g~s~~tv~r~l~~L~~~ 52 (67)
T cd00092 23 QLPLTRQEIADY-LGLTRETVSRTLKELEEE 52 (67)
T ss_pred cCCcCHHHHHHH-HCCCHHHHHHHHHHHHHC
Confidence 467999999994 999999999999998874
No 122
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=80.69 E-value=1.1 Score=37.95 Aligned_cols=30 Identities=23% Similarity=0.455 Sum_probs=22.7
Q ss_pred CCCCCCCCC-CceEEecCCCceEcCcCceee
Q 025357 4 SYCADCKRL-TEVVFDHSAGDTICSECGLVL 33 (254)
Q Consensus 4 ~~Cp~Cg~~-~~lv~D~~~G~~vC~~CG~Vl 33 (254)
..|+.|+++ +.++.+...=.+.|..||..-
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 359999996 567766555567899999873
No 123
>PF15616 TerY-C: TerY-C metal binding domain
Probab=80.16 E-value=1.1 Score=35.35 Aligned_cols=21 Identities=24% Similarity=0.725 Sum_probs=12.7
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl 33 (254)
--||+||.. .+..+| +||.|.
T Consensus 78 PgCP~CGn~--------~~fa~C-~CGkl~ 98 (131)
T PF15616_consen 78 PGCPHCGNQ--------YAFAVC-GCGKLF 98 (131)
T ss_pred CCCCCCcCh--------hcEEEe-cCCCEE
Confidence 359999973 244555 455553
No 124
>PRK10857 DNA-binding transcriptional regulator IscR; Provisional
Probab=79.74 E-value=5 Score=32.76 Aligned_cols=47 Identities=17% Similarity=0.185 Sum_probs=38.1
Q ss_pred CHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 147 NQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 147 ~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
+.+.-..+.+|+|....+.|.+..+||+ ..+++..-+.+.+..|.+.
T Consensus 6 ~~~yAl~~l~~lA~~~~~~~vs~~eIA~-~~~ip~~~l~kIl~~L~~a 52 (164)
T PRK10857 6 KGRYAVTAMLDVALNSEAGPVPLADISE-RQGISLSYLEQLFSRLRKN 52 (164)
T ss_pred HHHHHHHHHHHHHhCCCCCcCcHHHHHH-HHCcCHHHHHHHHHHHHHC
Confidence 3455566778888555567999999999 4999999999999999874
No 125
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=79.69 E-value=4.8 Score=26.19 Aligned_cols=34 Identities=12% Similarity=0.051 Sum_probs=29.1
Q ss_pred CCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchh
Q 025357 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (254)
Q Consensus 164 ~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~ 198 (254)
+...+..++|.. .||++.++.+.++.+...|...
T Consensus 17 R~~~~~~~La~~-FgIs~stvsri~~~~~~~L~~~ 50 (53)
T PF13613_consen 17 RLNLTFQDLAYR-FGISQSTVSRIFHEWIPLLYQV 50 (53)
T ss_pred HcCCcHhHHhhh-eeecHHHHHHHHHHHHHHHHHh
Confidence 355789999995 9999999999999999888654
No 126
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=79.52 E-value=1.5 Score=35.18 Aligned_cols=30 Identities=30% Similarity=0.604 Sum_probs=20.3
Q ss_pred CCCCCCCCCCceEEec---CCCce-----EcCcCceee
Q 025357 4 SYCADCKRLTEVVFDH---SAGDT-----ICSECGLVL 33 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~---~~G~~-----vC~~CG~Vl 33 (254)
+.||.|+++..-|.|. +.|.. .|.+||.=.
T Consensus 1 M~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RF 38 (156)
T COG1327 1 MKCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERF 38 (156)
T ss_pred CCCCCCCCCCCeeeecccccccchhhhhhccccccccc
Confidence 5799999865556773 34433 488888643
No 127
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=79.41 E-value=0.39 Score=32.17 Aligned_cols=25 Identities=32% Similarity=0.913 Sum_probs=19.1
Q ss_pred CCCCCCCCCCceEEecCCCceEcCc-Cceeec
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSE-CGLVLE 34 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~-CG~Vl~ 34 (254)
..|+.||.. | ..|+.+|++ ||.+++
T Consensus 9 ~HC~VCg~a--I----p~de~~CSe~C~eil~ 34 (64)
T COG4068 9 RHCVVCGKA--I----PPDEQVCSEECGEILN 34 (64)
T ss_pred ccccccCCc--C----CCccchHHHHHHHHHH
Confidence 569999973 3 357899986 998874
No 128
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=79.40 E-value=0.94 Score=30.29 Aligned_cols=25 Identities=24% Similarity=0.538 Sum_probs=18.9
Q ss_pred CCCCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 2 ADSYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 2 ~~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
-+..|+.||. -.+ ..+|..||....
T Consensus 4 ~mr~C~~Cgv-YTL-------k~~CP~CG~~t~ 28 (56)
T PRK13130 4 KIRKCPKCGV-YTL-------KEICPVCGGKTK 28 (56)
T ss_pred cceECCCCCC-EEc-------cccCcCCCCCCC
Confidence 3578999997 333 578999997753
No 129
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=79.15 E-value=0.6 Score=37.11 Aligned_cols=29 Identities=31% Similarity=0.685 Sum_probs=23.4
Q ss_pred CCCCCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 1 ~~~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
|++..||.||. ++-+ +|..+|.+|....+
T Consensus 1 m~l~nC~~Cgk----lF~~-~~~~iCp~C~~~~e 29 (137)
T TIGR03826 1 MELANCPKCGR----LFVK-TGRDVCPSCYEEEE 29 (137)
T ss_pred CCCccccccch----hhhh-cCCccCHHHhHHHH
Confidence 77889999998 2444 58899999998754
No 130
>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=78.62 E-value=2.3 Score=27.16 Aligned_cols=44 Identities=11% Similarity=0.069 Sum_probs=30.0
Q ss_pred CHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCC
Q 025357 168 TVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKN 224 (254)
Q Consensus 168 tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~ 224 (254)
|++|||+. +|++..++.+++..= -+ -.....+-|...+.+||..
T Consensus 1 Ti~dIA~~-agvS~~TVSr~ln~~---~~---------vs~~tr~rI~~~a~~lgY~ 44 (46)
T PF00356_consen 1 TIKDIARE-AGVSKSTVSRVLNGP---PR---------VSEETRERILEAAEELGYR 44 (46)
T ss_dssp CHHHHHHH-HTSSHHHHHHHHTTC---SS---------STHHHHHHHHHHHHHHTB-
T ss_pred CHHHHHHH-HCcCHHHHHHHHhCC---CC---------CCHHHHHHHHHHHHHHCCC
Confidence 78999995 999999999885431 11 1234566777777777643
No 131
>PRK08402 replication factor A; Reviewed
Probab=78.47 E-value=1.6 Score=40.21 Aligned_cols=27 Identities=37% Similarity=0.812 Sum_probs=22.2
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCcee
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLV 32 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~V 32 (254)
..||.|+. .++.|...|...|..||.|
T Consensus 213 ~aCp~CnK--kv~~~~~~~~~~Ce~~~~v 239 (355)
T PRK08402 213 DACPECRR--KVDYDPATDTWICPEHGEV 239 (355)
T ss_pred ecCCCCCe--EEEEecCCCCEeCCCCCCc
Confidence 46999987 3555888899999999975
No 132
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=78.07 E-value=1.7 Score=29.88 Aligned_cols=9 Identities=33% Similarity=1.117 Sum_probs=7.1
Q ss_pred eEcCcCcee
Q 025357 24 TICSECGLV 32 (254)
Q Consensus 24 ~vC~~CG~V 32 (254)
++|.+||+.
T Consensus 37 v~C~~CGYT 45 (64)
T PF09855_consen 37 VSCTNCGYT 45 (64)
T ss_pred EECCCCCCE
Confidence 578888876
No 133
>KOG1088 consensus Uncharacterized conserved protein [Function unknown]
Probab=77.90 E-value=0.96 Score=34.71 Aligned_cols=17 Identities=35% Similarity=0.741 Sum_probs=14.9
Q ss_pred EecCCCceEcCcCceee
Q 025357 17 FDHSAGDTICSECGLVL 33 (254)
Q Consensus 17 ~D~~~G~~vC~~CG~Vl 33 (254)
.|-.+|+++|.+||.|.
T Consensus 92 ~~v~EG~l~CpetG~vf 108 (124)
T KOG1088|consen 92 IDVIEGELVCPETGRVF 108 (124)
T ss_pred hhhccceEecCCCCcEe
Confidence 45678999999999997
No 134
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=77.85 E-value=0.57 Score=38.91 Aligned_cols=29 Identities=24% Similarity=0.557 Sum_probs=20.2
Q ss_pred CCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 5 YCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 5 ~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
.||.|+.. =-..|.-+....|..||.++.
T Consensus 119 ~Cp~C~~r-ytf~eA~~~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 119 FCPNCHIR-FTFDEAMEYGFRCPQCGEMLE 147 (178)
T ss_pred ECCCCCcE-EeHHHHhhcCCcCCCCCCCCe
Confidence 59999862 122334556789999999986
No 135
>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=77.49 E-value=6.8 Score=25.70 Aligned_cols=40 Identities=20% Similarity=0.231 Sum_probs=29.6
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 154 ACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 154 AclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
.+|++..+..+...++.||++. .++++.++.+.+++|.+.
T Consensus 9 ~vL~~l~~~~~~~~t~~~la~~-l~~~~~~vs~~v~~L~~~ 48 (62)
T PF12802_consen 9 RVLMALARHPGEELTQSELAER-LGISKSTVSRIVKRLEKK 48 (62)
T ss_dssp HHHHHHHHSTTSGEEHHHHHHH-HTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHHHCCCCCcCHHHHHHH-HCcCHHHHHHHHHHHHHC
Confidence 4455554444445899999995 999999999999998753
No 136
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=77.24 E-value=5.1 Score=40.63 Aligned_cols=84 Identities=13% Similarity=0.238 Sum_probs=67.5
Q ss_pred HHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhh--CCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHH
Q 025357 107 IQAFKSISAMSDRLGLVTTIKDRANEIYKKVED--QKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEI 184 (254)
Q Consensus 107 ~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~--~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i 184 (254)
.-|..+|+.+|++|.|.+.+.+..-.+|.-... -.+++-|-.+.+.-.|+|+.+|..+..+++++|.. +..--+...
T Consensus 678 ~LAavRL~~Lc~rL~l~~e~r~~IWtlFehsl~~et~Lm~dRHLDQillCaiy~i~KV~~~~ltF~eIm~-~YR~QPqa~ 756 (920)
T KOG1010|consen 678 HLAAVRLNDLCERLSLSDELREQIWTLFEHSLTNETELMRDRHLDQILLCAIYGIAKVKKEDLTFSEIMR-AYRRQPQAV 756 (920)
T ss_pred HHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHhccHHHHHhhhHHHHHHHHHHhheehhcccchHHHHHH-HHhcCchhh
Confidence 357889999999999999888887777776543 34677888999999999999999999999999987 465556666
Q ss_pred HHHHHHH
Q 025357 185 GRAKEFI 191 (254)
Q Consensus 185 ~~~~k~l 191 (254)
..+||.+
T Consensus 757 ~~vyRsV 763 (920)
T KOG1010|consen 757 SLVYRSV 763 (920)
T ss_pred hhhhhhe
Confidence 6666654
No 137
>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=76.90 E-value=1.1 Score=37.98 Aligned_cols=34 Identities=29% Similarity=0.662 Sum_probs=25.3
Q ss_pred CCCCCCCCC-CceEEecCCCc---eEcCcCceeecccc
Q 025357 4 SYCADCKRL-TEVVFDHSAGD---TICSECGLVLEAYS 37 (254)
Q Consensus 4 ~~Cp~Cg~~-~~lv~D~~~G~---~vC~~CG~Vl~e~~ 37 (254)
+.|-+||.+ +.+..+++.|. ..|.+||.|.|.-+
T Consensus 1 miCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~vaDkYi 38 (208)
T PF04161_consen 1 MICIECGHPVKSLYRQYSPGNIRLTKCPNCGKVADKYI 38 (208)
T ss_pred CEeccCCCcchhhhhccCCCcEEEeeccccCCccccee
Confidence 469999985 34566776663 78999999996544
No 138
>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=76.86 E-value=27 Score=25.60 Aligned_cols=31 Identities=10% Similarity=0.243 Sum_probs=27.2
Q ss_pred cCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 163 ENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 163 ~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
...+++..|||+. .|++..++.+++++|.+.
T Consensus 44 ~~~~is~~eLa~~-~g~sr~tVsr~L~~Le~~ 74 (95)
T TIGR01610 44 KQDRVTATVIAEL-TGLSRTHVSDAIKSLARR 74 (95)
T ss_pred cCCccCHHHHHHH-HCcCHHHHHHHHHHHHHC
Confidence 4678999999995 999999999999998764
No 139
>smart00550 Zalpha Z-DNA-binding domain in adenosine deaminases. Helix-turn-helix-containing domain. Also known as Zab.
Probab=76.76 E-value=8.4 Score=26.46 Aligned_cols=39 Identities=18% Similarity=0.141 Sum_probs=30.5
Q ss_pred HHHHHHhcCC-CCCHHHHHHHhcCCCHHHHHHHHHHHHHHh
Q 025357 156 LYIACRQENK-PRTVKEFCSVANGTTKKEIGRAKEFIVKHL 195 (254)
Q Consensus 156 lY~AcR~~~~-p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l 195 (254)
|+...+..+- +.++.|||+ .+|++..++++....|.+.=
T Consensus 11 IL~~L~~~g~~~~ta~eLa~-~lgl~~~~v~r~L~~L~~~G 50 (68)
T smart00550 11 ILEFLENSGDETSTALQLAK-NLGLPKKEVNRVLYSLEKKG 50 (68)
T ss_pred HHHHHHHCCCCCcCHHHHHH-HHCCCHHHHHHHHHHHHHCC
Confidence 4445556665 499999999 59999999999988887653
No 140
>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=76.12 E-value=1.4 Score=43.08 Aligned_cols=43 Identities=19% Similarity=0.516 Sum_probs=29.8
Q ss_pred CCCCCCCCCCc-----eEEe----cCCCceEcCcCceeecccc---cccCccccc
Q 025357 4 SYCADCKRLTE-----VVFD----HSAGDTICSECGLVLEAYS---VDETSEWRI 46 (254)
Q Consensus 4 ~~Cp~Cg~~~~-----lv~D----~~~G~~vC~~CG~Vl~e~~---id~~~ewr~ 46 (254)
..||+||.... +.+| +.+-..+|..||..++|.. ....-+|+.
T Consensus 201 vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e~~k~~m~~~G~Wv~ 255 (557)
T PF05876_consen 201 VPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEEHDKRRMVRRGRWVA 255 (557)
T ss_pred ccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCHHHHhhccCCeEEEe
Confidence 46999997422 3333 4567899999999998753 233457865
No 141
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=76.02 E-value=2.3 Score=31.59 Aligned_cols=29 Identities=17% Similarity=0.583 Sum_probs=20.2
Q ss_pred CCCCCCCCCCCceEEe-cCC-CceEcCcCceee
Q 025357 3 DSYCADCKRLTEVVFD-HSA-GDTICSECGLVL 33 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~D-~~~-G~~vC~~CG~Vl 33 (254)
|..||.||. .++.. .++ -...|..|++|.
T Consensus 1 m~FCP~Cgn--~Live~g~~~~rf~C~tCpY~~ 31 (105)
T KOG2906|consen 1 MLFCPTCGN--MLIVESGESCNRFSCRTCPYVF 31 (105)
T ss_pred CcccCCCCC--EEEEecCCeEeeEEcCCCCcee
Confidence 468999997 34433 222 457899999996
No 142
>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=75.75 E-value=1.7 Score=27.90 Aligned_cols=14 Identities=29% Similarity=0.669 Sum_probs=9.4
Q ss_pred eEcCcCceeecccc
Q 025357 24 TICSECGLVLEAYS 37 (254)
Q Consensus 24 ~vC~~CG~Vl~e~~ 37 (254)
..|..||.|.++..
T Consensus 2 y~C~~CgyvYd~~~ 15 (47)
T PF00301_consen 2 YQCPVCGYVYDPEK 15 (47)
T ss_dssp EEETTTSBEEETTT
T ss_pred cCCCCCCEEEcCCc
Confidence 46777777776554
No 143
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=75.75 E-value=5.1 Score=27.15 Aligned_cols=55 Identities=9% Similarity=0.058 Sum_probs=32.2
Q ss_pred HhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcccccccCC-CCHHHHHHHHHhhcCCCcc
Q 025357 161 RQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGT-IHASDYLVIFLLNIFKNFF 226 (254)
Q Consensus 161 R~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~-~~p~~~i~r~~~~L~l~~~ 226 (254)
.+.....|+.|++.. +.++...|... +.=+++ .+|. +-...||..||+.|||+.+
T Consensus 5 ~R~~~glsl~~va~~-t~I~~~~l~ai-----E~~~~~-----~lp~~~y~rg~lr~Ya~~Lgld~~ 60 (62)
T PF13413_consen 5 AREAKGLSLEDVAEE-TKISVSYLEAI-----ENGDFD-----SLPSPVYARGYLRKYARFLGLDPD 60 (62)
T ss_dssp HHHCTT--HHHHHHH-CS--HHHHHHH-----HCT-GC-----CSSSHHHHHHHHHHHHHHTT--HH
T ss_pred HHHHcCCCHHHHHHH-hCCCHHHHHHH-----HCcChh-----hCCcHHHHHHHHHHHHHHhCcCcc
Confidence 345567999999995 88888777543 111121 1332 3468899999999999865
No 144
>PRK11920 rirA iron-responsive transcriptional regulator; Reviewed
Probab=75.71 E-value=8.2 Score=31.04 Aligned_cols=45 Identities=13% Similarity=0.193 Sum_probs=36.3
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 148 QEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 148 ~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
.+.-+-+.+|+|.. .+.+.+.+|||+. .+++..-+.+.+..|++.
T Consensus 7 ~~YAlr~L~~LA~~-~~~~~s~~eIA~~-~~is~~~L~kIl~~L~~a 51 (153)
T PRK11920 7 TNYAIRMLMYCAAN-DGKLSRIPEIARA-YGVSELFLFKILQPLVEA 51 (153)
T ss_pred HhHHHHHHHHHHhC-CCCcCcHHHHHHH-HCcCHHHHHHHHHHHHHC
Confidence 34455577888844 5568899999994 899999999999999874
No 145
>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=75.66 E-value=9.8 Score=23.81 Aligned_cols=29 Identities=21% Similarity=0.229 Sum_probs=23.3
Q ss_pred CCCCCHHHHHHHhcCCCHHHHHHHHHHHHH
Q 025357 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (254)
Q Consensus 164 ~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~ 193 (254)
+-+.|.+|||+. .|++..++.+.+++|.+
T Consensus 15 ~~~~t~~ela~~-~~is~~tv~~~l~~L~~ 43 (48)
T PF13412_consen 15 NPRITQKELAEK-LGISRSTVNRYLKKLEE 43 (48)
T ss_dssp CTTS-HHHHHHH-HTS-HHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHH-hCCCHHHHHHHHHHHHH
Confidence 335999999995 99999999999998875
No 146
>PRK11161 fumarate/nitrate reduction transcriptional regulator; Provisional
Probab=75.56 E-value=13 Score=31.40 Aligned_cols=30 Identities=20% Similarity=0.017 Sum_probs=26.8
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHHHHHHHHh
Q 025357 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHL 195 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l 195 (254)
.|+|.++||+. .|++..++.|..++|.+.=
T Consensus 183 ~~lt~~~iA~~-lG~sr~tvsR~l~~l~~~g 212 (235)
T PRK11161 183 LTMTRGDIGNY-LGLTVETISRLLGRFQKSG 212 (235)
T ss_pred ccccHHHHHHH-hCCcHHHHHHHHHHHHHCC
Confidence 58999999995 9999999999999988753
No 147
>smart00419 HTH_CRP helix_turn_helix, cAMP Regulatory protein.
Probab=75.49 E-value=5.2 Score=24.63 Aligned_cols=30 Identities=23% Similarity=0.307 Sum_probs=26.0
Q ss_pred CCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 164 ~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
..|.+..|+++ ..+++..++.+.++.|.+.
T Consensus 6 ~~~~s~~~la~-~l~~s~~tv~~~l~~L~~~ 35 (48)
T smart00419 6 RLPLTRQEIAE-LLGLTRETVSRTLKRLEKE 35 (48)
T ss_pred EeccCHHHHHH-HHCCCHHHHHHHHHHHHHC
Confidence 35789999999 4999999999999988764
No 148
>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=75.48 E-value=0.81 Score=29.85 Aligned_cols=30 Identities=17% Similarity=0.476 Sum_probs=22.3
Q ss_pred CCCCCCCCCCCCceE--EecCCCceEcCcCceee
Q 025357 2 ADSYCADCKRLTEVV--FDHSAGDTICSECGLVL 33 (254)
Q Consensus 2 ~~~~Cp~Cg~~~~lv--~D~~~G~~vC~~CG~Vl 33 (254)
...+|+.|+.- +. -+....++-|..||.+-
T Consensus 3 ~eiRC~~Cnkl--La~~g~~~~leIKCpRC~tiN 34 (51)
T PF10122_consen 3 KEIRCGHCNKL--LAKAGEVIELEIKCPRCKTIN 34 (51)
T ss_pred cceeccchhHH--HhhhcCccEEEEECCCCCccc
Confidence 34789999862 22 24567899999999995
No 149
>PF14122 YokU: YokU-like protein
Probab=75.25 E-value=2.2 Score=30.93 Aligned_cols=20 Identities=35% Similarity=0.677 Sum_probs=14.8
Q ss_pred CCceEcCcCceeeccccccc
Q 025357 21 AGDTICSECGLVLEAYSVDE 40 (254)
Q Consensus 21 ~G~~vC~~CG~Vl~e~~id~ 40 (254)
+=.++|.+||.|..+..+..
T Consensus 33 tP~i~C~~CgmvYq~d~vi~ 52 (87)
T PF14122_consen 33 TPAIICSNCGMVYQDDEVIK 52 (87)
T ss_pred CceeeecCCCcEEehhHHHH
Confidence 44589999999976665543
No 150
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=75.12 E-value=2.4 Score=27.74 Aligned_cols=31 Identities=26% Similarity=0.778 Sum_probs=20.9
Q ss_pred CCCCCCCCCCCceEEe-cCCCc-eEcCcCceee
Q 025357 3 DSYCADCKRLTEVVFD-HSAGD-TICSECGLVL 33 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~D-~~~G~-~vC~~CG~Vl 33 (254)
...|.+|+.....++- ...|. ++|..||+-.
T Consensus 3 ~~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~ 35 (52)
T smart00401 3 GRSCSNCGTTETPLWRRGPSGNKTLCNACGLYY 35 (52)
T ss_pred CCCcCCCCCCCCCccccCCCCCCcEeecccHHH
Confidence 4678899875444453 34554 8899998765
No 151
>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=74.97 E-value=2.8 Score=31.59 Aligned_cols=30 Identities=20% Similarity=0.491 Sum_probs=19.5
Q ss_pred CCCCCCCCCCceEEe------c--CC-Cc-eEcCcCceeec
Q 025357 4 SYCADCKRLTEVVFD------H--SA-GD-TICSECGLVLE 34 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D------~--~~-G~-~vC~~CG~Vl~ 34 (254)
..||+||+. ....+ . .. .. .+|+.|+.-+.
T Consensus 3 ~~CpYCg~~-~~l~~~~~iYg~~~~~~~~~y~C~~C~AyVG 42 (102)
T PF11672_consen 3 IICPYCGGP-AELVDGSEIYGHRYDDGPYLYVCTPCDAYVG 42 (102)
T ss_pred cccCCCCCe-eEEcccchhcCccCCCCceeEECCCCCceee
Confidence 579999984 33344 1 12 22 78888887774
No 152
>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=74.57 E-value=4.7 Score=26.50 Aligned_cols=33 Identities=21% Similarity=0.281 Sum_probs=28.1
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchh
Q 025357 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~ 198 (254)
...+.+|||+. .++++++|....+.+.+.|++.
T Consensus 17 ~G~~~~eIA~~-l~is~~tV~~~~~~i~~Kl~~~ 49 (58)
T PF00196_consen 17 QGMSNKEIAEE-LGISEKTVKSHRRRIMKKLGVK 49 (58)
T ss_dssp TTS-HHHHHHH-HTSHHHHHHHHHHHHHHHHT-S
T ss_pred hcCCcchhHHh-cCcchhhHHHHHHHHHHHhCCC
Confidence 34789999995 9999999999999999999986
No 153
>PF13730 HTH_36: Helix-turn-helix domain
Probab=74.38 E-value=14 Score=23.76 Aligned_cols=25 Identities=12% Similarity=0.238 Sum_probs=22.9
Q ss_pred CHHHHHHHhcCCCHHHHHHHHHHHHH
Q 025357 168 TVKEFCSVANGTTKKEIGRAKEFIVK 193 (254)
Q Consensus 168 tl~eIa~~~~~v~~~~i~~~~k~l~~ 193 (254)
+..+|++. +|+++.+|.+++++|.+
T Consensus 27 S~~~la~~-~g~s~~Tv~~~i~~L~~ 51 (55)
T PF13730_consen 27 SQETLAKD-LGVSRRTVQRAIKELEE 51 (55)
T ss_pred CHHHHHHH-HCcCHHHHHHHHHHHHH
Confidence 89999995 99999999999999875
No 154
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=74.27 E-value=1.8 Score=43.07 Aligned_cols=9 Identities=11% Similarity=0.534 Sum_probs=4.8
Q ss_pred CCCHHHHHH
Q 025357 166 PRTVKEFCS 174 (254)
Q Consensus 166 p~tl~eIa~ 174 (254)
|.+|+++..
T Consensus 272 ~~~l~~Lg~ 280 (645)
T PRK14559 272 PPSLQDLGQ 280 (645)
T ss_pred CCCHHHHHH
Confidence 455555554
No 155
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=74.09 E-value=2.1 Score=33.10 Aligned_cols=32 Identities=22% Similarity=0.546 Sum_probs=27.9
Q ss_pred ecCCCceEcCcCceee--cccccccCcccccccC
Q 025357 18 DHSAGDTICSECGLVL--EAYSVDETSEWRIFAN 49 (254)
Q Consensus 18 D~~~G~~vC~~CG~Vl--~e~~id~~~ewr~f~~ 49 (254)
..+.|..+|..||.-| .+.-+|.|.-|.+|.+
T Consensus 28 ~~~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPSF~~ 61 (119)
T PRK05508 28 FFEKGTYVCKQCGAPLYRSEDKFKSGCGWPSFDD 61 (119)
T ss_pred cCCCeEEEecCCCCccccccccccCCCCCcccCc
Confidence 3679999999999987 6678899999999984
No 156
>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=73.97 E-value=3.2 Score=32.89 Aligned_cols=27 Identities=26% Similarity=0.728 Sum_probs=19.6
Q ss_pred CCC--CCCCCCceEEecCCCceEcCcCceeec
Q 025357 5 YCA--DCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 5 ~Cp--~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
.|| .|++ .+..+ ..|...|..||..++
T Consensus 20 aC~~~~C~k--Kv~~~-~~~~y~C~~C~~~~~ 48 (146)
T PF08646_consen 20 ACPNEKCNK--KVTEN-GDGSYRCEKCNKTVE 48 (146)
T ss_dssp E-TSTTTS---B-EEE-TTTEEEETTTTEEES
T ss_pred CCCCccCCC--EeecC-CCcEEECCCCCCcCC
Confidence 599 9997 35555 779999999999874
No 157
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=73.75 E-value=1.5 Score=36.77 Aligned_cols=32 Identities=34% Similarity=0.568 Sum_probs=20.2
Q ss_pred CCCCCCCCCCce--EEecCCC---ceEcCcCceeeccc
Q 025357 4 SYCADCKRLTEV--VFDHSAG---DTICSECGLVLEAY 36 (254)
Q Consensus 4 ~~Cp~Cg~~~~l--v~D~~~G---~~vC~~CG~Vl~e~ 36 (254)
..||.||+ ..+ -.--+.| .+-|.+||+|-.+.
T Consensus 7 ~~Cp~Cg~-eev~hEVik~~g~~~lvrC~eCG~V~~~~ 43 (201)
T COG1326 7 IECPSCGS-EEVSHEVIKERGREPLVRCEECGTVHPAI 43 (201)
T ss_pred EECCCCCc-chhhHHHHHhcCCceEEEccCCCcEeece
Confidence 46999995 232 0111223 47899999998553
No 158
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=73.62 E-value=2.5 Score=37.16 Aligned_cols=28 Identities=14% Similarity=0.443 Sum_probs=20.9
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl 33 (254)
..||.||+. +......-..+|..||.+.
T Consensus 100 ~fC~~CG~~--~~~~~~~~~~~C~~c~~~~ 127 (256)
T PRK00241 100 RFCGYCGHP--MHPSKTEWAMLCPHCRERY 127 (256)
T ss_pred ccccccCCC--CeecCCceeEECCCCCCEE
Confidence 679999984 3344556678999999764
No 159
>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=73.23 E-value=2.7 Score=27.38 Aligned_cols=14 Identities=21% Similarity=0.624 Sum_probs=9.5
Q ss_pred eEcCcCceeecccc
Q 025357 24 TICSECGLVLEAYS 37 (254)
Q Consensus 24 ~vC~~CG~Vl~e~~ 37 (254)
.+|..||+|.++..
T Consensus 2 y~C~~CgyiYd~~~ 15 (50)
T cd00730 2 YECRICGYIYDPAE 15 (50)
T ss_pred cCCCCCCeEECCCC
Confidence 46777888876543
No 160
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=73.21 E-value=1.8 Score=35.41 Aligned_cols=29 Identities=21% Similarity=0.398 Sum_probs=18.5
Q ss_pred CCCCCCCCCCCceEEe---------------cCCCceEcCcCceee
Q 025357 3 DSYCADCKRLTEVVFD---------------HSAGDTICSECGLVL 33 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~D---------------~~~G~~vC~~CG~Vl 33 (254)
...||+|++. ++.- ..+-..+|..||.+.
T Consensus 97 ~~RCp~CN~~--L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiY 140 (165)
T COG1656 97 FSRCPECNGE--LEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIY 140 (165)
T ss_pred cccCcccCCE--eccCcHHHHhhccchhhhhcccceeECCCCcccc
Confidence 4689999872 3221 122345699999886
No 161
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=73.08 E-value=2.4 Score=33.85 Aligned_cols=34 Identities=24% Similarity=0.473 Sum_probs=28.5
Q ss_pred EecCCCceEcCcCceee--cccccccCcccccccCC
Q 025357 17 FDHSAGDTICSECGLVL--EAYSVDETSEWRIFANE 50 (254)
Q Consensus 17 ~D~~~G~~vC~~CG~Vl--~e~~id~~~ewr~f~~~ 50 (254)
...+.|..+|..||.-| .+.-+|.|.-|.+|.+.
T Consensus 37 ~~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~~ 72 (142)
T PRK00222 37 DNKEKGIYVCIVCGEPLFSSDTKFDSGCGWPSFTKP 72 (142)
T ss_pred CCCCCeEEEecCCCchhcCCcccccCCCCCcCcCcc
Confidence 34689999999999987 56678999999999853
No 162
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=73.00 E-value=3.5 Score=28.96 Aligned_cols=30 Identities=20% Similarity=0.627 Sum_probs=21.4
Q ss_pred CCCCCCCCCCceE--EecCCCceEcCcCceee
Q 025357 4 SYCADCKRLTEVV--FDHSAGDTICSECGLVL 33 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv--~D~~~G~~vC~~CG~Vl 33 (254)
-.||.|++-..|. .+...-.+-|-+||+.-
T Consensus 9 a~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e 40 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRENGVEYVECVECGYTE 40 (71)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEecCCCCee
Confidence 5799999854444 34445566799999984
No 163
>TIGR00738 rrf2_super rrf2 family protein (putative transcriptional regulator). This model represents a superfamily of probable transcriptional regulators. One member, RRF2 of Desulfovibrio vulgaris is an apparent regulatory protein experimentally (MEDLINE:97293189). The N-terminal region appears related to the DNA-binding biotin repressor region of the BirA bifunctional according to results after three rounds of PSI-BLAST with a fairly high stringency.
Probab=72.99 E-value=9.8 Score=29.24 Aligned_cols=45 Identities=20% Similarity=0.285 Sum_probs=33.8
Q ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 149 EAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 149 ~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
+....+.+|++-...+.|.+..+|++. .+++...+++..+.|.+.
T Consensus 8 ~~al~~l~~la~~~~~~~~s~~eia~~-~~i~~~~v~~il~~L~~~ 52 (132)
T TIGR00738 8 EYALRALLDLALNPDEGPVSVKEIAER-QGISRSYLEKILRTLRRA 52 (132)
T ss_pred HHHHHHHHHHHhCCCCCcCcHHHHHHH-HCcCHHHHHHHHHHHHHC
Confidence 344455566663322458999999995 999999999999999873
No 164
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=72.77 E-value=1.2 Score=31.99 Aligned_cols=31 Identities=23% Similarity=0.413 Sum_probs=24.7
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeeccc
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAY 36 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~ 36 (254)
..|+.||. .. +-....|-+-|.+|..|+...
T Consensus 37 y~CsfCGK-~~-vKR~AvGiW~C~~C~kv~agg 67 (92)
T KOG0402|consen 37 YTCSFCGK-KT-VKRKAVGIWKCGSCKKVVAGG 67 (92)
T ss_pred hhhhhcch-hh-hhhhceeEEecCCccceeccc
Confidence 46999998 33 456788999999999998633
No 165
>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=72.65 E-value=8.4 Score=24.41 Aligned_cols=31 Identities=19% Similarity=0.228 Sum_probs=25.0
Q ss_pred CCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHh
Q 025357 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKHL 195 (254)
Q Consensus 164 ~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l 195 (254)
..+.|+.|||+. .|++..++++..++..+.|
T Consensus 18 ~~~~t~~eIa~~-lg~s~~~V~~~~~~al~kL 48 (50)
T PF04545_consen 18 FEGLTLEEIAER-LGISRSTVRRILKRALKKL 48 (50)
T ss_dssp TST-SHHHHHHH-HTSCHHHHHHHHHHHHHHH
T ss_pred cCCCCHHHHHHH-HCCcHHHHHHHHHHHHHHh
Confidence 567899999995 9999999998887766554
No 166
>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=72.59 E-value=2.4 Score=27.40 Aligned_cols=28 Identities=29% Similarity=0.536 Sum_probs=16.1
Q ss_pred CCCCCCCCCCceEEe-cCCCceEcCcCce
Q 025357 4 SYCADCKRLTEVVFD-HSAGDTICSECGL 31 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D-~~~G~~vC~~CG~ 31 (254)
-+|++||..-++..- .+...+.|..||.
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 6 YRCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 468888862122211 2245667888886
No 167
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=72.42 E-value=1.6 Score=40.74 Aligned_cols=31 Identities=29% Similarity=0.763 Sum_probs=23.6
Q ss_pred CCCCCCCCC-Cce----EEecCCCceEcCcCceeec
Q 025357 4 SYCADCKRL-TEV----VFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 4 ~~Cp~Cg~~-~~l----v~D~~~G~~vC~~CG~Vl~ 34 (254)
-.||.|++. ++| .+|..+|+..|..||.=|.
T Consensus 129 Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelv 164 (436)
T KOG2593|consen 129 YVCPNCQKKYTSLEALQLLDNETGEFHCENCGGELV 164 (436)
T ss_pred ccCCccccchhhhHHHHhhcccCceEEEecCCCchh
Confidence 469999984 222 4678899999999997653
No 168
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=72.35 E-value=2.1 Score=29.11 Aligned_cols=24 Identities=25% Similarity=0.732 Sum_probs=16.4
Q ss_pred CCCCCCCCCCCCCceEEecCCCceEcCcCcee
Q 025357 1 MADSYCADCKRLTEVVFDHSAGDTICSECGLV 32 (254)
Q Consensus 1 ~~~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~V 32 (254)
|....|.+|+. |+ +.+ .|..||-.
T Consensus 1 M~~kAC~~C~~---i~-~~~----~CP~Cgs~ 24 (61)
T PRK08351 1 MTEKACRHCHY---IT-TED----RCPVCGSR 24 (61)
T ss_pred CchhhhhhCCc---cc-CCC----cCCCCcCC
Confidence 55678999986 33 322 69999973
No 169
>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=71.60 E-value=2.5 Score=26.30 Aligned_cols=28 Identities=29% Similarity=0.586 Sum_probs=16.2
Q ss_pred CCCCCCCCCCceEEec-CCCceEcCcCce
Q 025357 4 SYCADCKRLTEVVFDH-SAGDTICSECGL 31 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~-~~G~~vC~~CG~ 31 (254)
-.|+.||..-.+..-. +.....|..||.
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 6 YRCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 3588888532222222 246778888887
No 170
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=71.47 E-value=2.9 Score=28.66 Aligned_cols=8 Identities=25% Similarity=0.754 Sum_probs=6.6
Q ss_pred CCCCCCCC
Q 025357 4 SYCADCKR 11 (254)
Q Consensus 4 ~~Cp~Cg~ 11 (254)
..||.||.
T Consensus 5 ~kCpKCgn 12 (68)
T COG3478 5 FKCPKCGN 12 (68)
T ss_pred ccCCCcCC
Confidence 45999997
No 171
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=71.06 E-value=29 Score=25.54 Aligned_cols=39 Identities=15% Similarity=0.177 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHH
Q 025357 151 IVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFI 191 (254)
Q Consensus 151 iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l 191 (254)
+..+.-|+... -..|.++.|+|+. .+++...+.+.+++.
T Consensus 7 ~~~~~~~i~~~-~~~~~~~~~lA~~-~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 7 IQTLIAWIDEH-IDQPLNIDVVAKK-SGYSKWYLQRMFRTV 45 (107)
T ss_pred HHHHHHHHHHh-cCCCCCHHHHHHH-HCCCHHHHHHHHHHH
Confidence 44445555554 3457999999995 899999999887764
No 172
>PRK10402 DNA-binding transcriptional activator YeiL; Provisional
Probab=70.94 E-value=14 Score=31.21 Aligned_cols=72 Identities=8% Similarity=-0.011 Sum_probs=43.3
Q ss_pred CHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhc
Q 025357 147 NQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNI 221 (254)
Q Consensus 147 ~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L 221 (254)
+.+.-.|..|+........|.+..|||+. .|++..++.|.+++|.+.==++.... .+...|. +.+.+++..+
T Consensus 150 ~~~~Rla~~L~~~~~~~~~~~t~~~lA~~-lG~sretvsR~L~~L~~~G~I~~~~~-~i~I~d~-~~L~~~~~~~ 221 (226)
T PRK10402 150 PLENRLAAFILLTQEGDLYHEKHTQAAEY-LGVSYRHLLYVLAQFIQDGYLKKSKR-GYLIKNR-KQLSGLALEL 221 (226)
T ss_pred hHHHHHHHHHHhcccCCcccchHHHHHHH-HCCcHHHHHHHHHHHHHCCCEEeeCC-EEEEeCH-HHHHHHHHHh
Confidence 34444555554333333456789999995 99999999999999988532221111 1223454 3444555554
No 173
>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=70.76 E-value=3.2 Score=22.81 Aligned_cols=24 Identities=29% Similarity=0.742 Sum_probs=13.5
Q ss_pred CCCCCCCCceEEecCCCceEcCcCce
Q 025357 6 CADCKRLTEVVFDHSAGDTICSECGL 31 (254)
Q Consensus 6 Cp~Cg~~~~lv~D~~~G~~vC~~CG~ 31 (254)
|..||. .|.--...-...|.+||.
T Consensus 1 C~sC~~--~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGR--PIAPREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCC--cccCcccCceEeCCCCCC
Confidence 667775 232222244677888884
No 174
>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=70.71 E-value=8.3 Score=24.77 Aligned_cols=38 Identities=21% Similarity=0.286 Sum_probs=28.7
Q ss_pred HHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 156 LYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 156 lY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
|.-+...++.+.++.||++. .|++..++.+..+.|.+.
T Consensus 8 iL~~l~~~~~~~t~~eia~~-~gl~~stv~r~L~tL~~~ 45 (52)
T PF09339_consen 8 ILEALAESGGPLTLSEIARA-LGLPKSTVHRLLQTLVEE 45 (52)
T ss_dssp HHHCHHCTBSCEEHHHHHHH-HTS-HHHHHHHHHHHHHT
T ss_pred HHHHHHcCCCCCCHHHHHHH-HCcCHHHHHHHHHHHHHC
Confidence 33344566777899999995 999999999988887653
No 175
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=70.55 E-value=2.3 Score=26.80 Aligned_cols=25 Identities=24% Similarity=0.768 Sum_probs=17.4
Q ss_pred CCCCCCCCCCceEEecCCCceEcCc--Cceeec
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSE--CGLVLE 34 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~--CG~Vl~ 34 (254)
.+||.||. ++-.+| +.|.+ |+.|..
T Consensus 12 rkCp~CGt-----~NG~R~-~~CKN~~C~~~~~ 38 (44)
T PF14952_consen 12 RKCPKCGT-----YNGTRG-LSCKNKSCPQVFN 38 (44)
T ss_pred ccCCcCcC-----ccCccc-ccccCCccchhhh
Confidence 57999997 233344 77874 988874
No 176
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=70.54 E-value=8.3 Score=23.96 Aligned_cols=29 Identities=17% Similarity=0.233 Sum_probs=22.4
Q ss_pred cCCCCCHHHHHHHhcCCCHHHHHHHHHHHH
Q 025357 163 ENKPRTVKEFCSVANGTTKKEIGRAKEFIV 192 (254)
Q Consensus 163 ~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~ 192 (254)
.+..++..+|++. .|++..++.+.+++|.
T Consensus 14 ~d~r~s~~~la~~-lglS~~~v~~Ri~rL~ 42 (42)
T PF13404_consen 14 EDGRRSYAELAEE-LGLSESTVRRRIRRLE 42 (42)
T ss_dssp H-TTS-HHHHHHH-HTS-HHHHHHHHHHHH
T ss_pred HcCCccHHHHHHH-HCcCHHHHHHHHHHhC
Confidence 4467999999995 9999999999988873
No 177
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=70.42 E-value=9.5 Score=23.99 Aligned_cols=31 Identities=23% Similarity=0.238 Sum_probs=28.0
Q ss_pred CCHHHHHHHhcCCCHHHHHHHHHHHHHHhchh
Q 025357 167 RTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (254)
Q Consensus 167 ~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~ 198 (254)
.+..||++. .+++..++.+..+.+.+.|+.+
T Consensus 19 ~s~~eia~~-l~is~~tv~~~~~~~~~kl~~~ 49 (58)
T smart00421 19 LTNKEIAER-LGISEKTVKTHLSNIMRKLGVR 49 (58)
T ss_pred CCHHHHHHH-HCCCHHHHHHHHHHHHHHHCCC
Confidence 689999995 9999999999999999988865
No 178
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=70.23 E-value=8.6 Score=26.19 Aligned_cols=34 Identities=24% Similarity=0.174 Sum_probs=27.5
Q ss_pred CCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchh
Q 025357 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (254)
Q Consensus 164 ~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~ 198 (254)
+.|.+-+|||+ ++|++..++++....|.+.=.++
T Consensus 13 ~~p~~T~eiA~-~~gls~~~aR~yL~~Le~eG~V~ 46 (62)
T PF04703_consen 13 NGPLKTREIAD-ALGLSIYQARYYLEKLEKEGKVE 46 (62)
T ss_dssp TS-EEHHHHHH-HHTS-HHHHHHHHHHHHHCTSEE
T ss_pred CCCCCHHHHHH-HhCCCHHHHHHHHHHHHHCCCEE
Confidence 77999999999 59999999999999888765554
No 179
>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=70.20 E-value=3 Score=23.77 Aligned_cols=28 Identities=18% Similarity=0.419 Sum_probs=15.6
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCce
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGL 31 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~ 31 (254)
..||.|+....-+........+|..|--
T Consensus 2 ~~C~rC~~~~~~~~~~~r~~~~C~rCq~ 29 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGRSTYLCPRCQK 29 (30)
T ss_dssp SB-TTT--BBEEEEETTEEEEE-TTTCC
T ss_pred CcCccCCCcceEeEecCCCCeECcCCcC
Confidence 5799999742223445677889988853
No 180
>TIGR02944 suf_reg_Xantho FeS assembly SUF system regulator, gammaproteobacterial. The SUF system is an oxygen-resistant iron-sulfur cluster assembly system found in both aerobes and facultative anaerobes. Its presence appears to be a marker of oxygen tolerance; strict anaerobes and microaerophiles tend to have different FeS cluster biosynthesis systems. Members of this protein family belong to the rrf2 family of transcriptional regulators and are found, typically, as the first gene of a SUF operon. It is found only in a subset of genomes that encode the SUF system, including the genus Xanthomonas. The conserved location suggests an autoregulatory role.
Probab=70.11 E-value=14 Score=28.39 Aligned_cols=45 Identities=9% Similarity=0.145 Sum_probs=35.7
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 148 QEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 148 ~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
.+....+.+|++- ..+.+.+..||++. .+++...+.+.++.|.+.
T Consensus 8 ~~yal~~l~~la~-~~~~~~s~~eia~~-l~is~~~v~~~l~~L~~~ 52 (130)
T TIGR02944 8 TDYATLVLTTLAQ-NDSQPYSAAEIAEQ-TGLNAPTVSKILKQLSLA 52 (130)
T ss_pred HhHHHHHHHHHHh-CCCCCccHHHHHHH-HCcCHHHHHHHHHHHHHC
Confidence 3445566777774 34568999999995 999999999999999874
No 181
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=70.06 E-value=3.6 Score=25.47 Aligned_cols=10 Identities=30% Similarity=0.959 Sum_probs=7.3
Q ss_pred eEcCcCceee
Q 025357 24 TICSECGLVL 33 (254)
Q Consensus 24 ~vC~~CG~Vl 33 (254)
.+|.+||..+
T Consensus 33 ~~C~~CGE~~ 42 (46)
T TIGR03831 33 LVCPQCGEEY 42 (46)
T ss_pred cccccCCCEe
Confidence 3588888765
No 182
>PF14353 CpXC: CpXC protein
Probab=69.89 E-value=3.4 Score=32.05 Aligned_cols=11 Identities=27% Similarity=0.797 Sum_probs=9.5
Q ss_pred ceEcCcCceee
Q 025357 23 DTICSECGLVL 33 (254)
Q Consensus 23 ~~vC~~CG~Vl 33 (254)
..+|..||...
T Consensus 38 ~~~CP~Cg~~~ 48 (128)
T PF14353_consen 38 SFTCPSCGHKF 48 (128)
T ss_pred EEECCCCCCce
Confidence 67999999886
No 183
>PRK11753 DNA-binding transcriptional dual regulator Crp; Provisional
Probab=69.89 E-value=23 Score=29.10 Aligned_cols=29 Identities=17% Similarity=0.318 Sum_probs=26.1
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
.|.|.+|||+. .|++..++.|.+++|.+.
T Consensus 167 ~~~t~~~lA~~-lG~tr~tvsR~l~~l~~~ 195 (211)
T PRK11753 167 IKITRQEIGRI-VGCSREMVGRVLKMLEDQ 195 (211)
T ss_pred cCCCHHHHHHH-hCCCHHHHHHHHHHHHHC
Confidence 48999999995 999999999999998875
No 184
>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=69.84 E-value=1.6 Score=28.84 Aligned_cols=29 Identities=34% Similarity=0.849 Sum_probs=17.5
Q ss_pred CCCCCCCCCceEEe--cCCCceEcCcCceee
Q 025357 5 YCADCKRLTEVVFD--HSAGDTICSECGLVL 33 (254)
Q Consensus 5 ~Cp~Cg~~~~lv~D--~~~G~~vC~~CG~Vl 33 (254)
.|.+|+....-.+- +..+..+|..||+-.
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~ 31 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYW 31 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHH
Confidence 37777764333443 236677777777765
No 185
>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=69.78 E-value=2.2 Score=28.22 Aligned_cols=29 Identities=17% Similarity=0.425 Sum_probs=21.1
Q ss_pred CCCCCCCCCCceE--EecCCCceEcCcCcee
Q 025357 4 SYCADCKRLTEVV--FDHSAGDTICSECGLV 32 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv--~D~~~G~~vC~~CG~V 32 (254)
..|+.|.+++-+. .+.+.-..+|..||..
T Consensus 23 LIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 23 LICSKCFSHNGLAPKEEFEEIQYRCPYCGAL 53 (54)
T ss_pred EECcccchhhcccccccCCceEEEcCCCCCc
Confidence 5699998753333 6677778899999863
No 186
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=69.71 E-value=7 Score=23.85 Aligned_cols=26 Identities=12% Similarity=0.126 Sum_probs=18.9
Q ss_pred CCCCCHHHHHHHhcCCCHHHHHHHHHH
Q 025357 164 NKPRTVKEFCSVANGTTKKEIGRAKEF 190 (254)
Q Consensus 164 ~~p~tl~eIa~~~~~v~~~~i~~~~k~ 190 (254)
..+.++.|||.. .|++...+.+.+++
T Consensus 6 ~~~~~l~~iA~~-~g~S~~~f~r~Fk~ 31 (42)
T PF00165_consen 6 QQKLTLEDIAEQ-AGFSPSYFSRLFKK 31 (42)
T ss_dssp -SS--HHHHHHH-HTS-HHHHHHHHHH
T ss_pred cCCCCHHHHHHH-HCCCHHHHHHHHHH
Confidence 457899999995 89999999888776
No 187
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=68.88 E-value=9 Score=26.24 Aligned_cols=33 Identities=21% Similarity=0.343 Sum_probs=25.1
Q ss_pred HhcCCCCCHHHHHHHhcCCC-HHHHHHHHHHHHHH
Q 025357 161 RQENKPRTVKEFCSVANGTT-KKEIGRAKEFIVKH 194 (254)
Q Consensus 161 R~~~~p~tl~eIa~~~~~v~-~~~i~~~~k~l~~~ 194 (254)
..+|.|-|++||++ .+|++ ..++.+.++.|.+.
T Consensus 20 ~~~G~~Pt~rEIa~-~~g~~S~~tv~~~L~~Le~k 53 (65)
T PF01726_consen 20 EENGYPPTVREIAE-ALGLKSTSTVQRHLKALERK 53 (65)
T ss_dssp HHHSS---HHHHHH-HHTSSSHHHHHHHHHHHHHT
T ss_pred HHcCCCCCHHHHHH-HhCCCChHHHHHHHHHHHHC
Confidence 46899999999999 58997 99999888888754
No 188
>COG1959 Predicted transcriptional regulator [Transcription]
Probab=68.74 E-value=15 Score=29.52 Aligned_cols=45 Identities=20% Similarity=0.225 Sum_probs=38.1
Q ss_pred HHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 149 EAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 149 ~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
+...-|.+|+|....+.|.+..+||.. .++++.-+.+.+..|++.
T Consensus 8 ~yal~~L~~LA~~~~~~~~s~~~IA~~-~~is~~~L~kil~~L~ka 52 (150)
T COG1959 8 EYALRALLYLALLPGGGPVSSAEIAER-QGISPSYLEKILSKLRKA 52 (150)
T ss_pred hHHHHHHHHHHhCCCCCcccHHHHHHH-hCcCHHHHHHHHHHHHHc
Confidence 445567788888777669999999995 999999999999999874
No 189
>PRK13918 CRP/FNR family transcriptional regulator; Provisional
Probab=68.74 E-value=20 Score=29.28 Aligned_cols=30 Identities=10% Similarity=0.121 Sum_probs=26.9
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHHHHHHHHh
Q 025357 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHL 195 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l 195 (254)
.|.|..|||+. .|++..++.|.+++|.+.=
T Consensus 148 ~~~t~~~iA~~-lG~tretvsR~l~~l~~~g 177 (202)
T PRK13918 148 IYATHDELAAA-VGSVRETVTKVIGELSREG 177 (202)
T ss_pred ecCCHHHHHHH-hCccHHHHHHHHHHHHHCC
Confidence 57999999995 9999999999999998753
No 190
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=68.48 E-value=4.3 Score=31.05 Aligned_cols=21 Identities=14% Similarity=0.115 Sum_probs=11.5
Q ss_pred CCCHHHHHHHhcCCCHHHHHHH
Q 025357 166 PRTVKEFCSVANGTTKKEIGRA 187 (254)
Q Consensus 166 p~tl~eIa~~~~~v~~~~i~~~ 187 (254)
.+|..++|+. .|++..+|.+.
T Consensus 78 gltq~~lA~~-lg~~~~tis~~ 98 (127)
T TIGR03830 78 GLSQREAAEL-LGGGVNAFSRY 98 (127)
T ss_pred CCCHHHHHHH-hCCCHHHHHHH
Confidence 3555566653 56665555444
No 191
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=68.39 E-value=4.6 Score=24.86 Aligned_cols=28 Identities=18% Similarity=0.424 Sum_probs=15.8
Q ss_pred CCCCCCCCCceEEec-CCCceEcCcCceee
Q 025357 5 YCADCKRLTEVVFDH-SAGDTICSECGLVL 33 (254)
Q Consensus 5 ~Cp~Cg~~~~lv~D~-~~G~~vC~~CG~Vl 33 (254)
.||.|+.. -..... .----+|.+||=+-
T Consensus 1 ~CP~C~~~-l~~~~~~~~~id~C~~C~G~W 29 (41)
T PF13453_consen 1 KCPRCGTE-LEPVRLGDVEIDVCPSCGGIW 29 (41)
T ss_pred CcCCCCcc-cceEEECCEEEEECCCCCeEE
Confidence 59999873 211111 12234699998763
No 192
>PF01641 SelR: SelR domain; InterPro: IPR002579 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represents MsrB, the crystal structure of which has been determined to 1.8A []. The overall structure shows no resemblance to the structures of MsrA (IPR002569 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. Unlike the MsrA domain, the MsrB domain activates the cysteine or selenocysteine nucleophile through a unique Cys-Arg-Asp/Glu catalytic triad. The collapse of the reaction intermediate most likely results in the formation of a sulphenic or selenenic acid moiety. Regeneration of the active site occurs through a series of thiol-disulphide exchange steps involving another active site Cys residue and thioredoxin. In a number of pathogenic bacteria, including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis, a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0008113 peptide-methionine-(S)-S-oxide reductase activity, 0055114 oxidation-reduction process; PDB: 1L1D_A 3E0O_D 2KZN_A 3HCG_B 3HCH_A 2L1U_A 3MAO_A 2K8D_A 3HCJ_A 3HCI_A ....
Probab=68.35 E-value=3.9 Score=31.94 Aligned_cols=32 Identities=25% Similarity=0.540 Sum_probs=26.5
Q ss_pred ecCCCceEcCcCceee--cccccccCcccccccC
Q 025357 18 DHSAGDTICSECGLVL--EAYSVDETSEWRIFAN 49 (254)
Q Consensus 18 D~~~G~~vC~~CG~Vl--~e~~id~~~ewr~f~~ 49 (254)
..+.|..+|..||.-| .+.-++.+.-|.+|.+
T Consensus 32 ~~~~G~Y~C~~Cg~pLF~S~~Kf~Sg~GWPSF~~ 65 (124)
T PF01641_consen 32 HKEEGIYVCAVCGTPLFSSDTKFDSGCGWPSFWQ 65 (124)
T ss_dssp TTSSEEEEETTTS-EEEEGGGEETSSSSSSEESS
T ss_pred CCCCEEEEcCCCCCccccCcccccCCcCCccccC
Confidence 3578999999999987 5667899999999984
No 193
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=68.25 E-value=31 Score=26.52 Aligned_cols=43 Identities=14% Similarity=0.124 Sum_probs=31.3
Q ss_pred CHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHH
Q 025357 147 NQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFI 191 (254)
Q Consensus 147 ~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l 191 (254)
....+..+.-|+--.. ..+.++.|+|+. .|+++..+.+.+++.
T Consensus 7 ~~~~i~~~~~~I~~~~-~~~~sl~~lA~~-~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 7 DAITIHSILDWIEDNL-ESPLSLEKVSER-SGYSKWHLQRMFKKE 49 (127)
T ss_pred cHHHHHHHHHHHHHhc-CCCCCHHHHHHH-HCcCHHHHHHHHHHH
Confidence 3445556666666554 347999999995 899999998887654
No 194
>TIGR00357 methionine-R-sulfoxide reductase. This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested.
Probab=68.17 E-value=3.3 Score=32.75 Aligned_cols=33 Identities=21% Similarity=0.372 Sum_probs=28.0
Q ss_pred ecCCCceEcCcCceee--cccccccCcccccccCC
Q 025357 18 DHSAGDTICSECGLVL--EAYSVDETSEWRIFANE 50 (254)
Q Consensus 18 D~~~G~~vC~~CG~Vl--~e~~id~~~ewr~f~~~ 50 (254)
..+.|..+|..||.-| .+.-+|.|.-|.+|.+.
T Consensus 35 ~~~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPSF~~~ 69 (134)
T TIGR00357 35 NKEEGIYVDITCGEPLFSSEDKFDSGCGWPSFYKP 69 (134)
T ss_pred CCCCeEEEccCCCCccccccchhcCCCCCcCcCcc
Confidence 4689999999999987 55678999999999843
No 195
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=67.99 E-value=5.4 Score=28.46 Aligned_cols=29 Identities=28% Similarity=0.519 Sum_probs=19.7
Q ss_pred CCCCCCCCCCCceEEecCCCce--EcCcCceee
Q 025357 3 DSYCADCKRLTEVVFDHSAGDT--ICSECGLVL 33 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~D~~~G~~--vC~~CG~Vl 33 (254)
++.||.|+. +++.-...|.. .|..|+=|-
T Consensus 1 ~llCP~C~v--~l~~~~rs~vEiD~CPrCrGVW 31 (88)
T COG3809 1 MLLCPICGV--ELVMSVRSGVEIDYCPRCRGVW 31 (88)
T ss_pred CcccCcCCc--eeeeeeecCceeeeCCccccEe
Confidence 367999996 35444444443 599998883
No 196
>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=67.84 E-value=17 Score=24.59 Aligned_cols=39 Identities=21% Similarity=0.216 Sum_probs=28.0
Q ss_pred CCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHH
Q 025357 146 RNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAK 188 (254)
Q Consensus 146 r~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~ 188 (254)
|+|.-=-|==+|+. ++-.++++|||+. +||+..+|++.-
T Consensus 5 Rsp~rdkA~e~y~~---~~g~i~lkdIA~~-Lgvs~~tIr~WK 43 (60)
T PF10668_consen 5 RSPNRDKAFEIYKE---SNGKIKLKDIAEK-LGVSESTIRKWK 43 (60)
T ss_pred CCcCHHHHHHHHHH---hCCCccHHHHHHH-HCCCHHHHHHHh
Confidence 44444445555643 5567899999995 999999999764
No 197
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=67.79 E-value=3.5 Score=24.95 Aligned_cols=22 Identities=23% Similarity=0.585 Sum_probs=10.8
Q ss_pred CCCCCCCCCCceEEecCCCceEc
Q 025357 4 SYCADCKRLTEVVFDHSAGDTIC 26 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC 26 (254)
-+|..||. .--+.+...|.++|
T Consensus 7 YkC~~CGn-iVev~~~g~g~lvC 28 (36)
T PF06397_consen 7 YKCEHCGN-IVEVVHDGGGPLVC 28 (36)
T ss_dssp EE-TTT---EEEEEE--SS-EEE
T ss_pred EEccCCCC-EEEEEECCCCCEEe
Confidence 46888886 33356667888888
No 198
>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=67.53 E-value=12 Score=23.52 Aligned_cols=32 Identities=22% Similarity=0.332 Sum_probs=28.4
Q ss_pred CCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchh
Q 025357 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (254)
Q Consensus 166 p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~ 198 (254)
..+.++||+. .+++..++.+..+++.+.++..
T Consensus 15 ~~s~~eia~~-l~~s~~tv~~~~~~~~~~l~~~ 46 (57)
T cd06170 15 GKTNKEIADI-LGISEKTVKTHLRNIMRKLGVK 46 (57)
T ss_pred CCCHHHHHHH-HCCCHHHHHHHHHHHHHHhCCC
Confidence 3699999995 9999999999999999988865
No 199
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=66.89 E-value=6.6 Score=25.24 Aligned_cols=26 Identities=23% Similarity=0.691 Sum_probs=18.1
Q ss_pred CCCC--CCCCCCceEEecCCCceEcCcCce
Q 025357 4 SYCA--DCKRLTEVVFDHSAGDTICSECGL 31 (254)
Q Consensus 4 ~~Cp--~Cg~~~~lv~D~~~G~~vC~~CG~ 31 (254)
..|| +||. .-...++. ....|..||+
T Consensus 19 k~CP~~~CG~-GvFMA~H~-dR~~CGKCg~ 46 (47)
T PF01599_consen 19 KECPSPRCGA-GVFMAEHK-DRHYCGKCGY 46 (47)
T ss_dssp EE-TSTTTTS-SSEEEE-S-SEEEETTTSS
T ss_pred hcCCCcccCC-ceEeeecC-CCccCCCccc
Confidence 4699 9998 54556664 5899999996
No 200
>PRK02935 hypothetical protein; Provisional
Probab=66.81 E-value=4 Score=30.78 Aligned_cols=27 Identities=22% Similarity=0.612 Sum_probs=18.4
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
..||+|+..+.+. --.-.|-.|+.-+.
T Consensus 71 V~CP~C~K~TKmL----GrvD~CM~C~~PLT 97 (110)
T PRK02935 71 VICPSCEKPTKML----GRVDACMHCNQPLT 97 (110)
T ss_pred eECCCCCchhhhc----cceeecCcCCCcCC
Confidence 4699999854332 12348999998874
No 201
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=66.78 E-value=4.1 Score=27.30 Aligned_cols=28 Identities=21% Similarity=0.514 Sum_probs=18.6
Q ss_pred CCCCCCCCCCCceEEecCCCceEcCcCceeecccc
Q 025357 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYS 37 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~ 37 (254)
+..||.||. .. .---||.+||+--+..+
T Consensus 27 ~~~c~~cG~-~~------l~Hrvc~~cg~Y~g~~v 54 (57)
T COG0333 27 LSVCPNCGE-YK------LPHRVCLKCGYYKGRQV 54 (57)
T ss_pred ceeccCCCC-cc------cCceEcCCCCCccCeEe
Confidence 367999987 22 23479999997654333
No 202
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=66.75 E-value=12 Score=23.28 Aligned_cols=26 Identities=12% Similarity=0.275 Sum_probs=17.3
Q ss_pred CCCCCHHHHHHHhcCCCHHHHHHHHHH
Q 025357 164 NKPRTVKEFCSVANGTTKKEIGRAKEF 190 (254)
Q Consensus 164 ~~p~tl~eIa~~~~~v~~~~i~~~~k~ 190 (254)
....++++||+. .|++..+|.+.+++
T Consensus 18 ~~G~s~~~IA~~-lg~s~sTV~relkR 43 (44)
T PF13936_consen 18 EQGMSIREIAKR-LGRSRSTVSRELKR 43 (44)
T ss_dssp CS---HHHHHHH-TT--HHHHHHHHHH
T ss_pred HcCCCHHHHHHH-HCcCcHHHHHHHhc
Confidence 345899999995 99999999887663
No 203
>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=66.68 E-value=2.3 Score=29.33 Aligned_cols=16 Identities=0% Similarity=-0.475 Sum_probs=11.9
Q ss_pred HHHHHhhcCCCcchhh
Q 025357 214 LVIFLLNIFKNFFFLF 229 (254)
Q Consensus 214 i~r~~~~L~l~~~v~~ 229 (254)
|+|||++|+|++.|.+
T Consensus 1 I~r~~~~L~L~~~v~~ 16 (71)
T PF00382_consen 1 IPRICSKLGLPEDVRE 16 (71)
T ss_dssp HHHHHHHTT--HHHHH
T ss_pred ChHHHhHcCCCHHHHH
Confidence 6899999999998765
No 204
>PRK09391 fixK transcriptional regulator FixK; Provisional
Probab=66.57 E-value=31 Score=29.19 Aligned_cols=48 Identities=19% Similarity=0.174 Sum_probs=34.5
Q ss_pred CCHHHHHHHHHHHHHHhcC------CCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 146 RNQEAIVAACLYIACRQEN------KPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 146 r~~~~iaAAclY~AcR~~~------~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
.+.+.-.|..|+.-++..+ .|.|.+|||+. .|++..++.|..++|.+.
T Consensus 153 ~~~~~Rla~~Ll~l~~~~g~~~~i~i~lt~~~IA~~-lGisretlsR~L~~L~~~ 206 (230)
T PRK09391 153 KTAMERVAAFLLEMDERLGGAGMMALPMSRRDIADY-LGLTIETVSRALSQLQDR 206 (230)
T ss_pred CCHHHHHHHHHHHHHHHhCCCCEEEecCCHHHHHHH-HCCCHHHHHHHHHHHHHC
Confidence 3444445554444344332 57899999995 999999999999999875
No 205
>PF13790 DUF4182: Domain of unknown function (DUF4182)
Probab=66.55 E-value=3.2 Score=25.42 Aligned_cols=14 Identities=21% Similarity=0.835 Sum_probs=12.3
Q ss_pred CCceEcCcCceeec
Q 025357 21 AGDTICSECGLVLE 34 (254)
Q Consensus 21 ~G~~vC~~CG~Vl~ 34 (254)
.|.+||+.|+.+++
T Consensus 1 MGtIvCq~C~~~Id 14 (38)
T PF13790_consen 1 MGTIVCQHCNETID 14 (38)
T ss_pred CCEEEeccccceee
Confidence 38899999999985
No 206
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=66.21 E-value=16 Score=31.62 Aligned_cols=56 Identities=4% Similarity=0.089 Sum_probs=36.8
Q ss_pred CCHHHHHHHhcCCCHHHHHHHHH----HHHHHhchhcccccccCCCCHHHHHHHHHhhcCC
Q 025357 167 RTVKEFCSVANGTTKKEIGRAKE----FIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFK 223 (254)
Q Consensus 167 ~tl~eIa~~~~~v~~~~i~~~~k----~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l 223 (254)
.+.+|||.. +|+++.++...+. .|++.+.-+....+++.+...+.||.-.-+.|.+
T Consensus 178 ~S~~EIA~~-Lgis~~TVk~rl~RAr~~Lr~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 237 (244)
T TIGR03001 178 LSMDRIGAM-YQVHRSTVSRWVAQARERLLERTRRRLAERLKLSSPELESLLGLVRSRLDV 237 (244)
T ss_pred CCHHHHHHH-HCcCHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhHHHH
Confidence 789999995 9999888775544 4444443333334445556677777776666644
No 207
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=66.19 E-value=30 Score=21.77 Aligned_cols=24 Identities=17% Similarity=0.194 Sum_probs=21.4
Q ss_pred CCHHHHHHHhcCCCHHHHHHHHHHH
Q 025357 167 RTVKEFCSVANGTTKKEIGRAKEFI 191 (254)
Q Consensus 167 ~tl~eIa~~~~~v~~~~i~~~~k~l 191 (254)
.|+++||.. .|++..++.+.++..
T Consensus 28 ~s~~~vA~~-~~vs~~TV~ri~~~~ 51 (52)
T PF13542_consen 28 RSFKDVARE-LGVSWSTVRRIFDRY 51 (52)
T ss_pred CCHHHHHHH-HCCCHHHHHHHHHhh
Confidence 899999995 999999999998753
No 208
>KOG3134 consensus Predicted membrane protein [Function unknown]
Probab=66.07 E-value=1.5 Score=37.28 Aligned_cols=34 Identities=26% Similarity=0.540 Sum_probs=27.4
Q ss_pred CCCCCCCCC-CceEEecCCC---ceEcCcCceeecccc
Q 025357 4 SYCADCKRL-TEVVFDHSAG---DTICSECGLVLEAYS 37 (254)
Q Consensus 4 ~~Cp~Cg~~-~~lv~D~~~G---~~vC~~CG~Vl~e~~ 37 (254)
.+|-+||++ .++-.+++.| -.-|.+|+.|+++-+
T Consensus 1 ~~CVeCg~~vksLy~~Ys~g~irlt~C~nC~e~vDkYi 38 (225)
T KOG3134|consen 1 YRCVECGSEVKSLYTQYSPGNIRLTKCPNCQEVVDKYI 38 (225)
T ss_pred CcccccCchHHHHHHhcCCCcEEEeeCCchhhHHHhHe
Confidence 369999985 5688889999 568999999987544
No 209
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=65.63 E-value=3.8 Score=31.36 Aligned_cols=17 Identities=12% Similarity=0.428 Sum_probs=8.8
Q ss_pred ceEEecCCCceEcCcCc
Q 025357 14 EVVFDHSAGDTICSECG 30 (254)
Q Consensus 14 ~lv~D~~~G~~vC~~CG 30 (254)
.+..+..-+...|.+||
T Consensus 61 ~L~I~~vp~~~~C~~Cg 77 (113)
T PRK12380 61 DLHIVYKPAQAWCWDCS 77 (113)
T ss_pred EEEEEeeCcEEEcccCC
Confidence 34444455555555555
No 210
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=65.48 E-value=68 Score=31.92 Aligned_cols=43 Identities=9% Similarity=0.123 Sum_probs=34.8
Q ss_pred HHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchh
Q 025357 153 AACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (254)
Q Consensus 153 AAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~ 198 (254)
-.|+|++-+.. ..++.+|+.. +|-+..+|..++++|.+.+...
T Consensus 558 qiAMYL~r~lt--~~Sl~~IG~~-FgRdHSTV~~A~~kI~~~~~~d 600 (617)
T PRK14086 558 QIAMYLCRELT--DLSLPKIGQQ-FGRDHTTVMHADRKIRALMAER 600 (617)
T ss_pred HHHHHHHHHHc--CCCHHHHHHH-hCCChhHHHHHHHHHHHHHHhC
Confidence 35678775544 4889999995 8899999999999999988654
No 211
>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=65.13 E-value=5.7 Score=29.14 Aligned_cols=33 Identities=27% Similarity=0.617 Sum_probs=21.9
Q ss_pred CCCCCCCC------CceEEecCCC----------ceEcCcCceeecccc
Q 025357 5 YCADCKRL------TEVVFDHSAG----------DTICSECGLVLEAYS 37 (254)
Q Consensus 5 ~Cp~Cg~~------~~lv~D~~~G----------~~vC~~CG~Vl~e~~ 37 (254)
.|+-|++. +++.+|...| .++|.+||.+.-+.-
T Consensus 1 ~C~~C~~~~~~~~~tTv~~el~~G~~~IvIknVPa~~C~~CGe~y~~de 49 (89)
T TIGR03829 1 KCRWCEEEKAIARTTTVYWELPDGTKAIEIKETPSISCSHCGMEYQDDT 49 (89)
T ss_pred CCcccCCCceecceEEEEEEecCCceEEEEecCCcccccCCCcEeecHH
Confidence 48899541 3456666555 468999999864433
No 212
>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=65.03 E-value=15 Score=24.44 Aligned_cols=32 Identities=16% Similarity=0.278 Sum_probs=24.1
Q ss_pred hcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 162 QENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 162 ~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
..+.+.++.+|++. .+++..++.+.+++|.+.
T Consensus 14 ~~~~~~t~~~l~~~-~~~~~~~vs~~i~~L~~~ 45 (68)
T PF13463_consen 14 HSDGPMTQSDLAER-LGISKSTVSRIIKKLEEK 45 (68)
T ss_dssp --TS-BEHHHHHHH-TT--HHHHHHHHHHHHHT
T ss_pred ccCCCcCHHHHHHH-HCcCHHHHHHHHHHHHHC
Confidence 56778999999995 999999999999998764
No 213
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=64.77 E-value=3.9 Score=27.87 Aligned_cols=24 Identities=33% Similarity=0.894 Sum_probs=15.8
Q ss_pred CCCCCCCCCCCceEEecCCCceEcCcCcee
Q 025357 3 DSYCADCKRLTEVVFDHSAGDTICSECGLV 32 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~V 32 (254)
...|.+|+. ++ + ...-+|..||.-
T Consensus 4 ~kAC~~Ck~---l~-~--~d~e~CP~Cgs~ 27 (64)
T COG2093 4 EKACKNCKR---LT-P--EDTEICPVCGST 27 (64)
T ss_pred hHHHhhccc---cC-C--CCCccCCCCCCc
Confidence 456888876 22 2 455788888854
No 214
>COG4565 CitB Response regulator of citrate/malate metabolism [Transcription / Signal transduction mechanisms]
Probab=64.72 E-value=75 Score=27.30 Aligned_cols=87 Identities=16% Similarity=0.149 Sum_probs=62.9
Q ss_pred HHHHHHHHHHHHhccCCCHHHHHHHHHHHHHH-hhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHH
Q 025357 106 LIQAFKSISAMSDRLGLVTTIKDRANEIYKKV-EDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEI 184 (254)
Q Consensus 106 l~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~-~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i 184 (254)
|.+-.++-..+.+.=.+++.-+++......+. ....+.+|-+...+-..+-.+. ..+.+.|..|+|. +.|+|..+.
T Consensus 114 L~~y~~~r~~l~~~~~~sQ~~lD~l~~~~~k~~~~~~LPkGi~~~Tl~~i~~~~~--~~~~~~Taeela~-~~giSRvTa 190 (224)
T COG4565 114 LTRYRQKRHALESHQQLSQKELDQLFNIQSKEQPPDDLPKGLDELTLQKVREALK--EPDQELTAEELAQ-ALGISRVTA 190 (224)
T ss_pred HHHHHHHHHHHhhhcccCHHHHHHHHhccccccCcccCCCCcCHHHHHHHHHHHh--CcCCccCHHHHHH-HhCccHHHH
Confidence 33444455556666788888888887777552 2234667877766666555555 6678999999999 599999999
Q ss_pred HHHHHHHHHHh
Q 025357 185 GRAKEFIVKHL 195 (254)
Q Consensus 185 ~~~~k~l~~~l 195 (254)
+|.+..+...=
T Consensus 191 RRYLeyl~~~~ 201 (224)
T COG4565 191 RRYLEYLVSNG 201 (224)
T ss_pred HHHHHHHHhcC
Confidence 99988887643
No 215
>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=64.65 E-value=11 Score=24.82 Aligned_cols=31 Identities=23% Similarity=0.197 Sum_probs=26.7
Q ss_pred CCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHh
Q 025357 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKHL 195 (254)
Q Consensus 164 ~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l 195 (254)
+-..++.|+++. ++||+.+|++-+..|.+.-
T Consensus 12 ~~~~s~~ela~~-~~VS~~TiRRDl~~L~~~g 42 (57)
T PF08220_consen 12 KGKVSVKELAEE-FGVSEMTIRRDLNKLEKQG 42 (57)
T ss_pred cCCEEHHHHHHH-HCcCHHHHHHHHHHHHHCC
Confidence 347899999995 9999999999999887654
No 216
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=64.50 E-value=5.7 Score=26.78 Aligned_cols=28 Identities=25% Similarity=0.557 Sum_probs=17.7
Q ss_pred CCCCCCCCCCCceEEecCCCceEcCcCcee
Q 025357 3 DSYCADCKRLTEVVFDHSAGDTICSECGLV 32 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~V 32 (254)
...|..||.. |..-...-...|.+||.+
T Consensus 7 ~~~CtSCg~~--i~~~~~~~~F~CPnCG~~ 34 (59)
T PRK14890 7 PPKCTSCGIE--IAPREKAVKFLCPNCGEV 34 (59)
T ss_pred CccccCCCCc--ccCCCccCEeeCCCCCCe
Confidence 3568889872 322222456779999987
No 217
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=64.49 E-value=4.7 Score=27.21 Aligned_cols=27 Identities=33% Similarity=0.720 Sum_probs=17.0
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCcee
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLV 32 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~V 32 (254)
..|..||. .|..+...-...|.+||.+
T Consensus 10 ~~CtSCg~--~i~p~e~~v~F~CPnCGe~ 36 (61)
T COG2888 10 PVCTSCGR--EIAPGETAVKFPCPNCGEV 36 (61)
T ss_pred ceeccCCC--EeccCCceeEeeCCCCCce
Confidence 36788876 2434555556678888844
No 218
>PRK12366 replication factor A; Reviewed
Probab=64.31 E-value=4.4 Score=40.36 Aligned_cols=25 Identities=36% Similarity=0.935 Sum_probs=20.0
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCcee
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLV 32 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~V 32 (254)
..||.|+. .++ + ..|...|..||.+
T Consensus 533 ~aCp~Cnk--Kv~-~-~~g~~~C~~c~~~ 557 (637)
T PRK12366 533 YLCPNCRK--RVE-E-VDGEYICEFCGEV 557 (637)
T ss_pred ecccccCe--EeE-c-CCCcEECCCCCCC
Confidence 46999987 243 3 5799999999988
No 219
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=63.84 E-value=1e+02 Score=26.95 Aligned_cols=42 Identities=7% Similarity=-0.031 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHH
Q 025357 148 QEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEF 190 (254)
Q Consensus 148 ~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~ 190 (254)
...+..+.-||.-.......++.+||. ..|+++..|.+.|++
T Consensus 196 ~~~l~~~~~~I~~~l~~~~ls~~~lA~-~~giS~r~L~r~Fk~ 237 (302)
T PRK09685 196 ERQFQKVVALIDQSIQEEILRPEWIAG-ELGISVRSLYRLFAE 237 (302)
T ss_pred HHHHHHHHHHHHHhcCCCCCCHHHHHH-HHCCCHHHHHHHHHH
Confidence 344556666776665554499999999 499999999988864
No 220
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=63.79 E-value=4.4 Score=31.06 Aligned_cols=20 Identities=10% Similarity=0.418 Sum_probs=12.2
Q ss_pred ceEEecCCCceEcCcCceee
Q 025357 14 EVVFDHSAGDTICSECGLVL 33 (254)
Q Consensus 14 ~lv~D~~~G~~vC~~CG~Vl 33 (254)
.+..+..-+...|.+||...
T Consensus 61 ~L~I~~~p~~~~C~~Cg~~~ 80 (115)
T TIGR00100 61 KLNIEDEPVECECEDCSEEV 80 (115)
T ss_pred EEEEEeeCcEEEcccCCCEE
Confidence 45556666666666666443
No 221
>KOG1010 consensus Rb (Retinoblastoma tumor suppressor)-related protein [Cell cycle control, cell division, chromosome partitioning]
Probab=63.50 E-value=28 Score=35.57 Aligned_cols=122 Identities=19% Similarity=0.256 Sum_probs=76.1
Q ss_pred HHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHH
Q 025357 111 KSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEF 190 (254)
Q Consensus 111 ~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~ 190 (254)
......|..|+|++....+|-+.|..+.+.-.+.|- -..+.|.++|.+||..++|.-.+-+......|+--.|-++++.
T Consensus 36 q~~~~~c~~lnld~~~~~ea~d~yta~~q~~slegs-~~hW~~cAlY~~~r~S~~~~v~~~~~~~~n~vsL~~Ilrs~k~ 114 (920)
T KOG1010|consen 36 QDSDELCRPLNLDEQTETEAWDTYTAVSQRLSLEGS-ESHWLACALYTACRRSSVPTVGGGIVEGKNEVSLTRILRSFKM 114 (920)
T ss_pred hhhhhhhhhhcccchhhhhhHHHHHHHHhHhCCCcc-HHHHHHHHHHHHHHhccCCccCcceeeecceehHHHHHHHHHH
Confidence 356678899999999999999999998776555553 5788999999999999877554444331133444444444432
Q ss_pred --------HHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcchhheeeCcceeeehhhc
Q 025357 191 --------IVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFFLFVLDFSSCMIFCSLW 243 (254)
Q Consensus 191 --------l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~v~~~~~~~~~~~~~ 243 (254)
+.+-.++. ..|..|-. .+.+|+-+..|..|.=---|.||+.|+
T Consensus 115 sv~eff~km~~w~~ma---------~s~~~f~~-~ieel~~~f~vssvl~KkY~~iF~~iF 165 (920)
T KOG1010|consen 115 SVIEFFTKMKQWVDMA---------NSPQEFRE-EIEELQRNFKVSSVLFKKYKRIFRDIF 165 (920)
T ss_pred HHHHHHHHHHHHHHHh---------cCHHHHHH-HHHHHHhccceehhHHHHHHHHHHHHH
Confidence 22222222 22333322 234555555555664445578888854
No 222
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=63.33 E-value=1.4 Score=39.55 Aligned_cols=30 Identities=23% Similarity=0.476 Sum_probs=21.8
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
.+||.|+. .-...|-+....||..||.-..
T Consensus 39 ~kc~~C~~-~~~~~~l~~~~~vcp~c~~h~r 68 (296)
T CHL00174 39 VQCENCYG-LNYKKFLKSKMNICEQCGYHLK 68 (296)
T ss_pred eECCCccc-hhhHHHHHHcCCCCCCCCCCcC
Confidence 57999997 3333345566789999999763
No 223
>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=63.29 E-value=11 Score=25.48 Aligned_cols=37 Identities=24% Similarity=0.376 Sum_probs=29.2
Q ss_pred HHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 156 LYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 156 lY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
+|.+.- ..-+.|..||++. ++++..++.+..+.|.+.
T Consensus 13 vy~~Ll-~~~~~t~~eIa~~-l~i~~~~v~~~L~~L~~~ 49 (68)
T PF01978_consen 13 VYLALL-KNGPATAEEIAEE-LGISRSTVYRALKSLEEK 49 (68)
T ss_dssp HHHHHH-HHCHEEHHHHHHH-HTSSHHHHHHHHHHHHHT
T ss_pred HHHHHH-HcCCCCHHHHHHH-HCcCHHHHHHHHHHHHHC
Confidence 444443 4457999999995 999999999999998763
No 224
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=63.28 E-value=1.4 Score=39.30 Aligned_cols=29 Identities=14% Similarity=0.458 Sum_probs=20.7
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl 33 (254)
.+||.|+. .-...|-.....||..||.-.
T Consensus 27 ~~c~~c~~-~~~~~~l~~~~~vc~~c~~h~ 55 (285)
T TIGR00515 27 TKCPKCGQ-VLYTKELERNLEVCPKCDHHM 55 (285)
T ss_pred eECCCCcc-hhhHHHHHhhCCCCCCCCCcC
Confidence 57999997 222233455678999999875
No 225
>smart00345 HTH_GNTR helix_turn_helix gluconate operon transcriptional repressor.
Probab=63.09 E-value=16 Score=23.30 Aligned_cols=26 Identities=12% Similarity=0.213 Sum_probs=23.7
Q ss_pred CHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 168 TVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 168 tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
+.+|+++. .+++..+++++++.|.+.
T Consensus 22 s~~~la~~-~~vs~~tv~~~l~~L~~~ 47 (60)
T smart00345 22 SERELAAQ-LGVSRTTVREALSRLEAE 47 (60)
T ss_pred CHHHHHHH-HCCCHHHHHHHHHHHHHC
Confidence 89999995 999999999999999863
No 226
>COG1773 Rubredoxin [Energy production and conversion]
Probab=62.87 E-value=5.1 Score=26.66 Aligned_cols=11 Identities=45% Similarity=0.912 Sum_probs=5.8
Q ss_pred eEcCcCceeec
Q 025357 24 TICSECGLVLE 34 (254)
Q Consensus 24 ~vC~~CG~Vl~ 34 (254)
..|..||+|.+
T Consensus 4 ~~C~~CG~vYd 14 (55)
T COG1773 4 WRCSVCGYVYD 14 (55)
T ss_pred eEecCCceEec
Confidence 34555555554
No 227
>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=62.80 E-value=6.6 Score=29.05 Aligned_cols=27 Identities=15% Similarity=0.315 Sum_probs=17.3
Q ss_pred CCCCCCCC-CceEEecCCCceEcCcCce
Q 025357 5 YCADCKRL-TEVVFDHSAGDTICSECGL 31 (254)
Q Consensus 5 ~Cp~Cg~~-~~lv~D~~~G~~vC~~CG~ 31 (254)
.||.|+.. +++.+++..|...|-.||.
T Consensus 35 ~CPfH~d~~pS~~i~~~k~~~~Cf~Cg~ 62 (97)
T PF01807_consen 35 LCPFHDDKTPSFSINPDKNRFKCFGCGK 62 (97)
T ss_dssp --SSS--SS--EEEETTTTEEEETTT--
T ss_pred ECcCCCCCCCceEEECCCCeEEECCCCC
Confidence 59999863 4688899999999999995
No 228
>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=62.54 E-value=16 Score=23.34 Aligned_cols=29 Identities=17% Similarity=0.197 Sum_probs=20.8
Q ss_pred CCCHHHHHHHhcCCCHHHHHHHHHHHHHHh
Q 025357 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKHL 195 (254)
Q Consensus 166 p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l 195 (254)
..+..|||+. .|+++.++...+.+-.+.|
T Consensus 26 g~s~~eIa~~-l~~s~~~v~~~l~ra~~~L 54 (54)
T PF08281_consen 26 GMSYAEIAEI-LGISESTVKRRLRRARKKL 54 (54)
T ss_dssp ---HHHHHHH-CTS-HHHHHHHHHHHHHHH
T ss_pred CcCHHHHHHH-HCcCHHHHHHHHHHHHhhC
Confidence 3789999995 9999999998887766543
No 229
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=62.40 E-value=28 Score=29.13 Aligned_cols=33 Identities=9% Similarity=0.170 Sum_probs=29.8
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchh
Q 025357 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~ 198 (254)
...+.+|||+. ++++++++....+.+.+.|++.
T Consensus 147 qGkTnKEIAe~-L~IS~rTVkth~srImkKLgV~ 179 (198)
T PRK15201 147 SGYHLSETAAL-LSLSEEQTKSLRRSIMRKLHVK 179 (198)
T ss_pred CCCCHHHHHHH-hCCCHHHHHHHHHHHHHHhCCC
Confidence 46889999995 9999999999999999999976
No 230
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=62.18 E-value=4.2 Score=30.95 Aligned_cols=33 Identities=6% Similarity=0.049 Sum_probs=26.0
Q ss_pred CCCCCCCCCCCceEEecCCCceEcCcCceeeccccc
Q 025357 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSV 38 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~i 38 (254)
.+.||+||++ .+|-.+--+||..||.-.....+
T Consensus 9 KridPetg~K---FYDLNrdPiVsPytG~s~P~s~f 41 (129)
T COG4530 9 KRIDPETGKK---FYDLNRDPIVSPYTGKSYPRSYF 41 (129)
T ss_pred cccCccccch---hhccCCCccccCcccccchHHHH
Confidence 3679999984 57888888999999987754443
No 231
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=61.90 E-value=5 Score=31.71 Aligned_cols=21 Identities=24% Similarity=0.623 Sum_probs=16.0
Q ss_pred ceEEecCCCceEcCcCceeec
Q 025357 14 EVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 14 ~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
.+..+...+...|.+||.+..
T Consensus 61 ~L~i~~~p~~~~C~~CG~~~~ 81 (135)
T PRK03824 61 EIIFEEEEAVLKCRNCGNEWS 81 (135)
T ss_pred EEEEEecceEEECCCCCCEEe
Confidence 566667778889999997754
No 232
>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=61.64 E-value=5.8 Score=29.88 Aligned_cols=28 Identities=18% Similarity=0.583 Sum_probs=21.5
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
..|--|+. .-- -.+.+.+||..||.+..
T Consensus 36 daCeiC~~-~GY--~q~g~~lvC~~C~~~~~ 63 (102)
T PF10080_consen 36 DACEICGP-KGY--YQEGDQLVCKNCGVRFN 63 (102)
T ss_pred EeccccCC-Cce--EEECCEEEEecCCCEEe
Confidence 45899986 333 25678999999999985
No 233
>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=61.43 E-value=6.3 Score=25.08 Aligned_cols=28 Identities=18% Similarity=0.458 Sum_probs=17.7
Q ss_pred CCCCCCCCCceEEe-------cCCCceEcCc--Cceee
Q 025357 5 YCADCKRLTEVVFD-------HSAGDTICSE--CGLVL 33 (254)
Q Consensus 5 ~Cp~Cg~~~~lv~D-------~~~G~~vC~~--CG~Vl 33 (254)
.||.||+. ..+.- ..+-...|++ ||.-.
T Consensus 1 ~CP~Cg~~-a~ir~S~~~s~~~~~~Y~qC~N~~Cg~tf 37 (47)
T PF04606_consen 1 RCPHCGSK-ARIRTSRQLSPLTRELYCQCTNPECGHTF 37 (47)
T ss_pred CcCCCCCe-eEEEEchhhCcceEEEEEEECCCcCCCEE
Confidence 59999983 44332 2334457777 98765
No 234
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=61.21 E-value=4.3 Score=27.27 Aligned_cols=26 Identities=27% Similarity=0.727 Sum_probs=15.9
Q ss_pred CCCCCCCCCceEEecCCCceEcCcCceee
Q 025357 5 YCADCKRLTEVVFDHSAGDTICSECGLVL 33 (254)
Q Consensus 5 ~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl 33 (254)
.|-+||.+ +.+ ...-.+-|.+||.=+
T Consensus 22 iCgdC~~e-n~l--k~~D~irCReCG~RI 47 (62)
T KOG3507|consen 22 ICGDCGQE-NTL--KRGDVIRCRECGYRI 47 (62)
T ss_pred Eecccccc-ccc--cCCCcEehhhcchHH
Confidence 58888884 322 123345689998643
No 235
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=61.20 E-value=6.5 Score=33.05 Aligned_cols=38 Identities=16% Similarity=0.163 Sum_probs=20.0
Q ss_pred chhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhh
Q 025357 102 PDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVED 139 (254)
Q Consensus 102 ~~r~l~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~ 139 (254)
.|-.|.++.+.+..........+...+.+.++.+++.+
T Consensus 98 VEGlL~~~~~~L~~~~~~d~~~~e~~~k~~~~i~kL~~ 135 (192)
T TIGR00310 98 LEGVLRRVEEELETAIRWQSEDEETKKRAEEILERLKE 135 (192)
T ss_pred eHhHHHHHHHHHHhhhhccccCHHHHHHHHHHHHHHHH
Confidence 45556666666655432212344555666666666544
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=61.03 E-value=5 Score=37.64 Aligned_cols=30 Identities=27% Similarity=0.625 Sum_probs=16.2
Q ss_pred CCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 5 YCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 5 ~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
.||+|+.-.++..-...+...|..||.++.
T Consensus 15 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~ 44 (403)
T TIGR00155 15 LCSQCDMLVALPRIESGQKAACPRCGTTLT 44 (403)
T ss_pred eCCCCCCcccccCCCCCCeeECCCCCCCCc
Confidence 477777521111112344567777777773
No 237
>PRK06030 hypothetical protein; Provisional
Probab=60.98 E-value=36 Score=26.49 Aligned_cols=39 Identities=15% Similarity=0.216 Sum_probs=32.1
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHh
Q 025357 154 ACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHL 195 (254)
Q Consensus 154 AclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l 195 (254)
.++|++-...+ .++.+|++. +|-+..++..+++++.+.+
T Consensus 59 IAMYL~r~~~~--~sl~~IG~~-FGRDHSTV~haikkIe~~~ 97 (124)
T PRK06030 59 IAMYVAHVSLG--WPMNEVALA-FGRDRTTVGHACHTVEDLR 97 (124)
T ss_pred HHHHHHHHHcC--CCHHHHHHH-HCCChhHHHHHHHHHHHHh
Confidence 46888766555 689999995 7999999999999887765
No 238
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=60.88 E-value=1.7 Score=39.01 Aligned_cols=29 Identities=21% Similarity=0.551 Sum_probs=20.7
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl 33 (254)
.+||.|+. .-...|-.....||..||.-.
T Consensus 28 ~~c~~c~~-~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 28 TKCPSCGQ-VLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred eECCCccc-hhhHHHHHhcCCCCCCCCCCe
Confidence 57999997 333334445567999999876
No 239
>COG3355 Predicted transcriptional regulator [Transcription]
Probab=60.82 E-value=22 Score=27.81 Aligned_cols=37 Identities=24% Similarity=0.398 Sum_probs=30.3
Q ss_pred HHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHH
Q 025357 156 LYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (254)
Q Consensus 156 lY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~ 193 (254)
+|.+.-..+-|.|..|||+. .+.+..++.++.+.|..
T Consensus 32 v~~~LL~~~~~~tvdelae~-lnr~rStv~rsl~~L~~ 68 (126)
T COG3355 32 VYKALLEENGPLTVDELAEI-LNRSRSTVYRSLQNLLE 68 (126)
T ss_pred HHHHHHhhcCCcCHHHHHHH-HCccHHHHHHHHHHHHH
Confidence 45555446679999999995 99999999999998875
No 240
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=60.73 E-value=7.3 Score=27.96 Aligned_cols=26 Identities=27% Similarity=0.685 Sum_probs=19.8
Q ss_pred CCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 5 YCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 5 ~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
.||.|.. .++.. ..+.+.| .||+-+.
T Consensus 1 iCPVC~~-~~L~~--~~~~i~C-~Cgl~l~ 26 (82)
T PF14768_consen 1 ICPVCQK-GNLRE--NSNVISC-SCGLRLN 26 (82)
T ss_pred CCCccCC-Ccccc--cCCeEEC-CCccEEe
Confidence 5999998 67765 5788888 6786664
No 241
>KOG0834 consensus CDK9 kinase-activating protein cyclin T [Cell cycle control, cell division, chromosome partitioning]
Probab=60.56 E-value=6.4 Score=35.83 Aligned_cols=90 Identities=10% Similarity=0.042 Sum_probs=51.4
Q ss_pred HHHHHHHHHHhccCCCHH----HHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHH---HHHhcC--
Q 025357 108 QAFKSISAMSDRLGLVTT----IKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEF---CSVANG-- 178 (254)
Q Consensus 108 ~a~~~I~~i~~~L~Lp~~----v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eI---a~~~~~-- 178 (254)
+...++-+++..|+-..+ +...|-.+.....--.+.---++..+|+||||+|+...|++.....- ... .+
T Consensus 150 hPy~~ll~~~k~l~~~~~~~~~~a~~Aw~~~nD~~~t~~cL~y~p~~IAva~i~lA~~~~~~~~~~~~~~~w~~~-~d~~ 228 (323)
T KOG0834|consen 150 HPYKYLLKYLKKLKADENLKQPLAQAAWNFVNDSLRTTLCLQYSPHSIAVACIHLAAKLLGVELPSDTDKRWWRE-FDET 228 (323)
T ss_pred CchHHHHHHHHHhhhhhhccccHHHHHHHHhchhheeeeeEeecCcEEEeehhhHHHHHcCCCCCCCcccchhhh-hccc
Confidence 444555555555544433 33333333333222221112368899999999999999875443321 121 34
Q ss_pred CCHHHHHHHHHHHHHHhchh
Q 025357 179 TTKKEIGRAKEFIVKHLEAE 198 (254)
Q Consensus 179 v~~~~i~~~~k~l~~~l~~~ 198 (254)
++...|......+...+...
T Consensus 229 vt~e~l~~i~~~~l~~y~~~ 248 (323)
T KOG0834|consen 229 VTNELLDDICHEFLDLYEQT 248 (323)
T ss_pred CCHHHHHHHHHHHHHHHhhc
Confidence 88888888888777766543
No 242
>PRK14088 dnaA chromosomal replication initiation protein; Provisional
Probab=60.41 E-value=16 Score=34.53 Aligned_cols=43 Identities=9% Similarity=0.105 Sum_probs=34.8
Q ss_pred HHHHH---HHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHh
Q 025357 150 AIVAA---CLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHL 195 (254)
Q Consensus 150 ~iaAA---clY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l 195 (254)
.++-| +.|++-+ ....++.+|+.. +|.+..++..+++++.+.+
T Consensus 370 ~i~~aR~iamyl~r~--~~~~s~~~Ig~~-fgr~hstV~~a~~~i~~~~ 415 (440)
T PRK14088 370 KALLARRIGMYVAKN--YLGSSLRTIAEK-FNRSHPVVVDSVKKVKDSL 415 (440)
T ss_pred cccHHHHHHHHHHHH--HhCCCHHHHHHH-hCCCHHHHHHHHHHHHHHH
Confidence 44445 7888844 445799999995 8999999999999999876
No 243
>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=60.39 E-value=7.6 Score=23.00 Aligned_cols=8 Identities=38% Similarity=0.995 Sum_probs=4.2
Q ss_pred eEcCcCce
Q 025357 24 TICSECGL 31 (254)
Q Consensus 24 ~vC~~CG~ 31 (254)
.+|.-||.
T Consensus 19 ~~CP~Cg~ 26 (34)
T cd00729 19 EKCPICGA 26 (34)
T ss_pred CcCcCCCC
Confidence 35555554
No 244
>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=60.35 E-value=4.5 Score=24.24 Aligned_cols=21 Identities=43% Similarity=1.103 Sum_probs=10.5
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCc
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECG 30 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG 30 (254)
++|+.||. +.+-+. .+|..||
T Consensus 12 ~rC~~Cg~---~~~pPr---~~Cp~C~ 32 (37)
T PF12172_consen 12 QRCRDCGR---VQFPPR---PVCPHCG 32 (37)
T ss_dssp EE-TTT-----EEES-----SEETTTT
T ss_pred EEcCCCCC---EecCCC---cCCCCcC
Confidence 56888876 334332 6788887
No 245
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=60.19 E-value=33 Score=28.73 Aligned_cols=78 Identities=14% Similarity=0.184 Sum_probs=53.0
Q ss_pred CHHHHHHHHHHHHHHhcCCC-CCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhc--------cccccc-CCCCHHHHHHH
Q 025357 147 NQEAIVAACLYIACRQENKP-RTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEM--------GQSVEM-GTIHASDYLVI 216 (254)
Q Consensus 147 ~~~~iaAAclY~AcR~~~~p-~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~--------~~~~~~-~~~~p~~~i~r 216 (254)
+...++=|+||. .+.| +++++|+.+ ++++..++..++..|.+.+.-.. +..+.+ ...+-..+|.+
T Consensus 4 ~~~~~iEA~LF~----sg~pgls~~~La~~-l~~~~~~v~~~l~~L~~~y~~~~~gi~i~~~~~~y~l~tk~e~~~~v~~ 78 (188)
T PRK00135 4 NYKSIIEALLFV----SGEEGLSLEQLAEI-LELEPTEVQQLLEELQEKYEGDDRGLKLIEFNDVYKLVTKEENADYLQK 78 (188)
T ss_pred cHHHHHHHHHHH----cCCCCCCHHHHHHH-HCCCHHHHHHHHHHHHHHHhhCCCCEEEEEECCEEEEEEcHHHHHHHHH
Confidence 345677788886 5776 999999995 89999999999999988875331 011111 12345678888
Q ss_pred HHhhc---CCCcchhh
Q 025357 217 FLLNI---FKNFFFLF 229 (254)
Q Consensus 217 ~~~~L---~l~~~v~~ 229 (254)
|...- .||....+
T Consensus 79 ~~~~~~~~~LS~aaLE 94 (188)
T PRK00135 79 LVKTPIKQSLSQAALE 94 (188)
T ss_pred HhcccccCCCCHHHHH
Confidence 86552 45655444
No 246
>PRK11014 transcriptional repressor NsrR; Provisional
Probab=60.15 E-value=22 Score=27.92 Aligned_cols=44 Identities=16% Similarity=0.273 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 150 AIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 150 ~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
.-.-+.+|++-...|.+.+.++||+. .+++...++++++.|.+.
T Consensus 9 YAl~~~i~la~~~~g~~~s~~~ia~~-~~is~~~vrk~l~~L~~~ 52 (141)
T PRK11014 9 YGLRALIYMASLPEGRMTSISEVTEV-YGVSRNHMVKIINQLSRA 52 (141)
T ss_pred HHHHHHHHHhcCCCCCccCHHHHHHH-HCcCHHHHHHHHHHHHhC
Confidence 33445567765556778999999995 999999999999999874
No 247
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=60.01 E-value=4.7 Score=40.16 Aligned_cols=24 Identities=21% Similarity=0.589 Sum_probs=14.2
Q ss_pred CCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 5 YCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 5 ~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
.||+||.. ...|...|.+||.-+.
T Consensus 29 ~Cp~CG~~------~~~~~~fC~~CG~~~~ 52 (645)
T PRK14559 29 PCPQCGTE------VPVDEAHCPNCGAETG 52 (645)
T ss_pred cCCCCCCC------CCcccccccccCCccc
Confidence 45555541 2356677777777653
No 248
>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=59.98 E-value=5.4 Score=35.52 Aligned_cols=29 Identities=31% Similarity=0.635 Sum_probs=12.7
Q ss_pred CCCCCCCCCCce-EEecCC--C--ceEcCcCcee
Q 025357 4 SYCADCKRLTEV-VFDHSA--G--DTICSECGLV 32 (254)
Q Consensus 4 ~~Cp~Cg~~~~l-v~D~~~--G--~~vC~~CG~V 32 (254)
..||.||+...+ +..... | .+.|+-||+-
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~ 206 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTE 206 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--E
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCe
Confidence 579999995322 233222 3 6889999875
No 249
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=59.97 E-value=5.7 Score=26.95 Aligned_cols=20 Identities=25% Similarity=0.665 Sum_probs=15.9
Q ss_pred ceEEe-cCCCceEcCcCceee
Q 025357 14 EVVFD-HSAGDTICSECGLVL 33 (254)
Q Consensus 14 ~lv~D-~~~G~~vC~~CG~Vl 33 (254)
.|..| -.+|+++|.-||++.
T Consensus 38 rV~L~mg~~gev~CPYC~t~y 58 (62)
T COG4391 38 RVFLDMGDEGEVVCPYCSTRY 58 (62)
T ss_pred EEEEEcCCCCcEecCccccEE
Confidence 45444 579999999999986
No 250
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=59.79 E-value=14 Score=28.96 Aligned_cols=27 Identities=19% Similarity=0.319 Sum_probs=24.3
Q ss_pred CCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 167 RTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 167 ~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
-|.+|+|. ..+|++.|+.|+|+.|.+.
T Consensus 36 PSvRelA~-~~~VNpnTv~raY~eLE~e 62 (125)
T COG1725 36 PSVRELAK-DLGVNPNTVQRAYQELERE 62 (125)
T ss_pred CcHHHHHH-HhCCCHHHHHHHHHHHHHC
Confidence 57899999 4999999999999999874
No 251
>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=59.58 E-value=6.6 Score=31.77 Aligned_cols=27 Identities=26% Similarity=0.726 Sum_probs=20.6
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl 33 (254)
..||.|++. ++ +...|...|..|+..+
T Consensus 35 ~aC~~C~kk--v~-~~~~~~~~C~~C~~~~ 61 (166)
T cd04476 35 PACPGCNKK--VV-EEGNGTYRCEKCNKSV 61 (166)
T ss_pred ccccccCcc--cE-eCCCCcEECCCCCCcC
Confidence 359999973 43 4344999999999887
No 252
>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=59.11 E-value=2.7 Score=32.13 Aligned_cols=19 Identities=16% Similarity=0.562 Sum_probs=6.7
Q ss_pred eEEecCCCceEcCcCceee
Q 025357 15 VVFDHSAGDTICSECGLVL 33 (254)
Q Consensus 15 lv~D~~~G~~vC~~CG~Vl 33 (254)
+..+..-+...|.+||...
T Consensus 62 L~Ie~~p~~~~C~~Cg~~~ 80 (113)
T PF01155_consen 62 LEIEEVPARARCRDCGHEF 80 (113)
T ss_dssp EEEEEE--EEEETTTS-EE
T ss_pred EEEEecCCcEECCCCCCEE
Confidence 3333334444444444443
No 253
>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=59.09 E-value=3.4 Score=31.57 Aligned_cols=27 Identities=22% Similarity=0.553 Sum_probs=17.9
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
..||+|+..+. +.- -.-.|-.|+.-+.
T Consensus 70 V~CP~C~K~TK-mLG---r~D~CM~C~~pLT 96 (114)
T PF11023_consen 70 VECPNCGKQTK-MLG---RVDACMHCKEPLT 96 (114)
T ss_pred eECCCCCChHh-hhc---hhhccCcCCCcCc
Confidence 46999998432 221 1238999998874
No 254
>COG1510 Predicted transcriptional regulators [Transcription]
Probab=58.81 E-value=13 Score=30.61 Aligned_cols=37 Identities=22% Similarity=0.277 Sum_probs=30.4
Q ss_pred HHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHH
Q 025357 156 LYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (254)
Q Consensus 156 lY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~ 193 (254)
||.+.=..+.|.|+.||++ ++|+|...+.-+.++|..
T Consensus 31 iYgilyls~~Pmtl~Ei~E-~lg~Sks~vS~~lkkL~~ 67 (177)
T COG1510 31 IYGILYLSRKPLTLDEIAE-ALGMSKSNVSMGLKKLQD 67 (177)
T ss_pred HhhhheecCCCccHHHHHH-HHCCCcchHHHHHHHHHh
Confidence 3444445688999999999 599999999999998865
No 255
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=58.67 E-value=7.8 Score=33.04 Aligned_cols=13 Identities=23% Similarity=0.572 Sum_probs=10.0
Q ss_pred eEcCcCceeeccc
Q 025357 24 TICSECGLVLEAY 36 (254)
Q Consensus 24 ~vC~~CG~Vl~e~ 36 (254)
.||.+||.-.-+.
T Consensus 49 ~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 49 WVCPHCGYAAFEE 61 (214)
T ss_pred EECCCCCCccccc
Confidence 5899999886544
No 256
>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=58.56 E-value=7.9 Score=37.41 Aligned_cols=29 Identities=21% Similarity=0.631 Sum_probs=23.6
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
..||+|+. .+++-...+.+.|..||....
T Consensus 223 ~~C~~C~~--~l~~h~~~~~l~Ch~Cg~~~~ 251 (505)
T TIGR00595 223 LCCPNCDV--SLTYHKKEGKLRCHYCGYQEP 251 (505)
T ss_pred cCCCCCCC--ceEEecCCCeEEcCCCcCcCC
Confidence 56999986 477777889999999998753
No 257
>PF03685 UPF0147: Uncharacterised protein family (UPF0147); InterPro: IPR005354 The proteins in this entry are functionally uncharacterised.; PDB: 2QZG_C 2QSB_A.
Probab=58.22 E-value=57 Score=23.70 Aligned_cols=54 Identities=13% Similarity=0.226 Sum_probs=41.0
Q ss_pred chhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHH
Q 025357 102 PDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIA 159 (254)
Q Consensus 102 ~~r~l~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~A 159 (254)
.+..+.++...++++.+--.+|.++...|.+....+.+.+ .++..-||.++++-
T Consensus 4 ~e~~i~~~~~~L~~I~~D~sVPRNIRr~a~ea~~~L~~e~----~~~~vRaataIs~L 57 (85)
T PF03685_consen 4 NEEKIKQAIQMLERIINDTSVPRNIRRAAEEAKEILNNEE----ESPGVRAATAISIL 57 (85)
T ss_dssp HHHHHHHHHHHHHHHHT-TTS-HHHHHHHHHHHHHCT-TT----S-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHhCCC----cchhHhHHHHHHHH
Confidence 3567889999999999999999999999999988876653 55667777777763
No 258
>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=57.86 E-value=34 Score=22.06 Aligned_cols=28 Identities=18% Similarity=0.185 Sum_probs=23.8
Q ss_pred CCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 166 p~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
+.++.||++. .+++..++.+.++.|.+.
T Consensus 17 ~~~~~~la~~-~~~~~~~~t~~i~~L~~~ 44 (59)
T PF01047_consen 17 GITQSELAEK-LGISRSTVTRIIKRLEKK 44 (59)
T ss_dssp SEEHHHHHHH-HTS-HHHHHHHHHHHHHT
T ss_pred CCCHHHHHHH-HCCChhHHHHHHHHHHHC
Confidence 4999999994 999999999999998764
No 259
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=57.75 E-value=19 Score=22.51 Aligned_cols=27 Identities=11% Similarity=0.122 Sum_probs=18.2
Q ss_pred CCCHHHHHHHhcCCCHHHHHHHHHHHHH
Q 025357 166 PRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (254)
Q Consensus 166 p~tl~eIa~~~~~v~~~~i~~~~k~l~~ 193 (254)
..+.++||.. +|++..++.+..+...+
T Consensus 17 G~s~~~ia~~-lgvs~~Tv~~w~kr~~~ 43 (50)
T PF13384_consen 17 GWSIREIAKR-LGVSRSTVYRWIKRYRE 43 (50)
T ss_dssp T--HHHHHHH-HTS-HHHHHHHHT----
T ss_pred CCCHHHHHHH-HCcCHHHHHHHHHHccc
Confidence 5789999995 99999999999887653
No 260
>COG4643 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=57.69 E-value=5.6 Score=36.17 Aligned_cols=26 Identities=31% Similarity=0.707 Sum_probs=21.1
Q ss_pred CCCCCCCCCceEEec-C-CCceEcCcCc
Q 025357 5 YCADCKRLTEVVFDH-S-AGDTICSECG 30 (254)
Q Consensus 5 ~Cp~Cg~~~~lv~D~-~-~G~~vC~~CG 30 (254)
.||.||+...+-+|. + .|..+|..||
T Consensus 34 ~cpvcg~k~RFr~dD~kGrGtw~c~y~~ 61 (366)
T COG4643 34 PCPVCGGKDRFRFDDRKGRGTWFCNYCG 61 (366)
T ss_pred CCCccCCccccccCCccCCccEEEEeec
Confidence 699999866665554 3 7999999999
No 261
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=57.51 E-value=5.2 Score=33.66 Aligned_cols=36 Identities=22% Similarity=0.415 Sum_probs=22.7
Q ss_pred CCCCCCCCCCce--EEe---cCCCc-----eEcCcCceeeccccccc
Q 025357 4 SYCADCKRLTEV--VFD---HSAGD-----TICSECGLVLEAYSVDE 40 (254)
Q Consensus 4 ~~Cp~Cg~~~~l--v~D---~~~G~-----~vC~~CG~Vl~e~~id~ 40 (254)
..||.||+ +-. ..+ |-.|+ .+|..||+=..|-...+
T Consensus 15 ~~CPvCg~-~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~DV~~~e 60 (201)
T COG1779 15 IDCPVCGG-TLKAHMYLYDIPYFGEVLISTGVCERCGYRSTDVKTLE 60 (201)
T ss_pred ecCCcccc-eeeEEEeeecCCccceEEEEEEEccccCCcccceeecc
Confidence 57999998 311 111 34454 58999999876554443
No 262
>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=57.18 E-value=10 Score=26.56 Aligned_cols=27 Identities=22% Similarity=0.687 Sum_probs=16.8
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
..||.|.. .+.++ .|...|..|+.-+.
T Consensus 2 ~~CP~C~~--~L~~~--~~~~~C~~C~~~~~ 28 (70)
T PF07191_consen 2 NTCPKCQQ--ELEWQ--GGHYHCEACQKDYK 28 (70)
T ss_dssp -B-SSS-S--BEEEE--TTEEEETTT--EEE
T ss_pred CcCCCCCC--ccEEe--CCEEECccccccce
Confidence 57999997 35555 59999999998653
No 263
>PRK05580 primosome assembly protein PriA; Validated
Probab=57.02 E-value=8.5 Score=38.59 Aligned_cols=28 Identities=18% Similarity=0.530 Sum_probs=23.3
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl 33 (254)
..||+|+. .+++....+.+.|..||...
T Consensus 391 ~~C~~C~~--~l~~h~~~~~l~Ch~Cg~~~ 418 (679)
T PRK05580 391 AECPHCDA--SLTLHRFQRRLRCHHCGYQE 418 (679)
T ss_pred cCCCCCCC--ceeEECCCCeEECCCCcCCC
Confidence 57999986 57777788999999999874
No 264
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=56.94 E-value=6.9 Score=25.81 Aligned_cols=28 Identities=21% Similarity=0.706 Sum_probs=15.9
Q ss_pred CCCCC--CCCCCceEEecCCCc--eEcCcCceee
Q 025357 4 SYCAD--CKRLTEVVFDHSAGD--TICSECGLVL 33 (254)
Q Consensus 4 ~~Cp~--Cg~~~~lv~D~~~G~--~vC~~CG~Vl 33 (254)
..||. |+. -+..+..... +.|..||...
T Consensus 19 ~~Cp~~~C~~--~~~~~~~~~~~~~~C~~C~~~f 50 (64)
T PF01485_consen 19 RWCPNPDCEY--IIEKDDGCNSPIVTCPSCGTEF 50 (64)
T ss_dssp C--TTSST-----ECS-SSTTS--CCTTSCCSEE
T ss_pred cCCCCCCCcc--cEEecCCCCCCeeECCCCCCcC
Confidence 57987 987 3555555555 8999999775
No 265
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=56.89 E-value=30 Score=23.84 Aligned_cols=36 Identities=17% Similarity=0.100 Sum_probs=31.3
Q ss_pred HHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhc
Q 025357 160 CRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLE 196 (254)
Q Consensus 160 cR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~ 196 (254)
.|.-+.|+++.+.++. .|+++..+.+..+.+++-+-
T Consensus 7 IrlLs~~~s~~~Aa~~-lG~~~~~v~~wv~~fR~wll 42 (65)
T PF05344_consen 7 IRLLSQQISVAQAADR-LGTDPGTVRRWVRMFRQWLL 42 (65)
T ss_pred HHHhcccccHHHHHHH-HCcCHHHHHHHHHHHHHHHH
Confidence 3577899999999995 99999999999999888663
No 266
>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=56.55 E-value=9.4 Score=34.48 Aligned_cols=9 Identities=33% Similarity=0.763 Sum_probs=5.3
Q ss_pred EcCcCceee
Q 025357 25 ICSECGLVL 33 (254)
Q Consensus 25 vC~~CG~Vl 33 (254)
+|.+||.-+
T Consensus 254 ~C~~C~~Yl 262 (305)
T TIGR01562 254 TCDSCQGYL 262 (305)
T ss_pred eccccccch
Confidence 566666554
No 267
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=56.47 E-value=10 Score=34.31 Aligned_cols=9 Identities=22% Similarity=1.006 Sum_probs=5.7
Q ss_pred CCCCCCCCC
Q 025357 4 SYCADCKRL 12 (254)
Q Consensus 4 ~~Cp~Cg~~ 12 (254)
..||.||+.
T Consensus 188 ~~CPvCGs~ 196 (309)
T PRK03564 188 QFCPVCGSM 196 (309)
T ss_pred CCCCCCCCc
Confidence 457777764
No 268
>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=56.37 E-value=11 Score=27.95 Aligned_cols=28 Identities=25% Similarity=0.547 Sum_probs=18.9
Q ss_pred CCCCCCCCCCceEEe---------cCCCceEcCcCcee
Q 025357 4 SYCADCKRLTEVVFD---------HSAGDTICSECGLV 32 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D---------~~~G~~vC~~CG~V 32 (254)
..||.||+. ..++- +.+=..+|.+||..
T Consensus 63 ~~Cp~Cg~~-~a~f~~~Q~RsadE~~T~fy~C~~C~~~ 99 (104)
T TIGR01384 63 VECPKCGHK-EAYYWLLQTRRADEPETRFYKCTKCGYV 99 (104)
T ss_pred CCCCCCCCC-eeEEEEeccCCCCCCcEEEEEeCCCCCe
Confidence 579999984 44332 23346789999964
No 269
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=56.30 E-value=7.5 Score=33.40 Aligned_cols=27 Identities=37% Similarity=0.806 Sum_probs=22.1
Q ss_pred CCCCCCCCCC-ceEEecCCCceEcCcCc
Q 025357 4 SYCADCKRLT-EVVFDHSAGDTICSECG 30 (254)
Q Consensus 4 ~~Cp~Cg~~~-~lv~D~~~G~~vC~~CG 30 (254)
..|-.||+.. ...++..+|..+|..|+
T Consensus 150 ~~C~~Cg~~~~~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 150 DHCAVCGAPGDHRYFSPKEGGAVCSECG 177 (247)
T ss_pred hhHhcCCCCCCceEEecccCCccccccc
Confidence 4699999742 35688999999999997
No 270
>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=56.26 E-value=27 Score=24.05 Aligned_cols=35 Identities=17% Similarity=0.176 Sum_probs=25.0
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHhcC-CCHHHHHHHHHHH
Q 025357 154 ACLYIACRQENKPRTVKEFCSVANG-TTKKEIGRAKEFI 191 (254)
Q Consensus 154 AclY~AcR~~~~p~tl~eIa~~~~~-v~~~~i~~~~k~l 191 (254)
.+.|++-... ..++.||+.. +| -+..++..+++++
T Consensus 35 va~yL~r~~~--~~sl~~Ig~~-fg~rdHstV~~a~~ki 70 (70)
T PF08299_consen 35 VAMYLARELT--GLSLSEIGRY-FGGRDHSTVIHAIRKI 70 (70)
T ss_dssp HHHHHHHHHS-----HHHHHHH-CTSSTHHHHHHHHHHH
T ss_pred HHHHHHHHHh--CCCHHHHHHH-hCCCCHHHHHHHHHhC
Confidence 3467665555 4889999995 77 9999999998874
No 271
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=56.25 E-value=3 Score=36.91 Aligned_cols=29 Identities=17% Similarity=0.512 Sum_probs=21.6
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl 33 (254)
.+||.||. .--.-|-.....||..||.-.
T Consensus 29 ~KCp~c~~-~~y~~eL~~n~~vcp~c~~h~ 57 (294)
T COG0777 29 TKCPSCGE-MLYRKELESNLKVCPKCGHHM 57 (294)
T ss_pred eECCCccc-eeeHHHHHhhhhcccccCccc
Confidence 57999997 333345566789999999875
No 272
>TIGR00613 reco DNA repair protein RecO. All proteins in this family for which functions are known are DNA binding proteins that are involved in the initiation of recombination or recombinational repair.
Probab=56.23 E-value=8.1 Score=33.08 Aligned_cols=28 Identities=29% Similarity=0.721 Sum_probs=21.3
Q ss_pred CCCCCCCCC-CceEEecCCCceEcCcCce
Q 025357 4 SYCADCKRL-TEVVFDHSAGDTICSECGL 31 (254)
Q Consensus 4 ~~Cp~Cg~~-~~lv~D~~~G~~vC~~CG~ 31 (254)
..|..||.. ....++...|..+|.+|+.
T Consensus 148 ~~C~~cg~~~~~~~fs~~~gg~~C~~c~~ 176 (241)
T TIGR00613 148 DKCAVCGSKEDLIYFSMTYGGALCRQCGE 176 (241)
T ss_pred CccCCCCCcCCCceEchhcCeEEChhhCc
Confidence 578899862 1256788899999999965
No 273
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=55.96 E-value=7.3 Score=26.74 Aligned_cols=29 Identities=31% Similarity=0.642 Sum_probs=18.4
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeecccccccCccccc
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVDETSEWRI 46 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~id~~~ewr~ 46 (254)
..|.+|+. |+ + ..+|..||-- +.+++|..
T Consensus 6 ~AC~~C~~---i~-~----~~~Cp~Cgs~------~~S~~w~G 34 (64)
T PRK06393 6 RACKKCKR---LT-P----EKTCPVHGDE------KTTTEWFG 34 (64)
T ss_pred hhHhhCCc---cc-C----CCcCCCCCCC------cCCcCcce
Confidence 56999986 33 2 1289999972 33456644
No 274
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=55.66 E-value=6.7 Score=36.99 Aligned_cols=31 Identities=23% Similarity=0.549 Sum_probs=19.1
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
..||+|+.-..+......+...|..||.++.
T Consensus 11 ~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~ 41 (419)
T PRK15103 11 ILCPQCDMLVALPRLEHGQKAACPRCGTTLT 41 (419)
T ss_pred ccCCCCCceeecCCCCCCCeeECCCCCCCCc
Confidence 4599998621111112334577999999984
No 275
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=55.63 E-value=8.1 Score=25.71 Aligned_cols=24 Identities=25% Similarity=0.690 Sum_probs=18.6
Q ss_pred CCCCCCCCCceEEecCCCceEcCcCceee
Q 025357 5 YCADCKRLTEVVFDHSAGDTICSECGLVL 33 (254)
Q Consensus 5 ~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl 33 (254)
.||.|++. . ...-...|.+||...
T Consensus 1 ~Cpv~~~~--~---~~~v~~~Cp~cGipt 24 (55)
T PF13824_consen 1 LCPVCKKD--L---PAHVNFECPDCGIPT 24 (55)
T ss_pred CCCCCccc--c---ccccCCcCCCCCCcC
Confidence 49999972 1 556678999999986
No 276
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=55.47 E-value=17 Score=24.15 Aligned_cols=34 Identities=18% Similarity=0.155 Sum_probs=26.2
Q ss_pred CCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchh
Q 025357 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (254)
Q Consensus 164 ~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~ 198 (254)
+-..++.|+|.. .+++..+|++.+..|...+.-.
T Consensus 17 ~~~~~~~ela~~-l~~S~rti~~~i~~L~~~f~~~ 50 (59)
T PF08280_consen 17 NKWITLKELAKK-LNISERTIKNDINELNEFFPEN 50 (59)
T ss_dssp HTSBBHHHHHHH-CTS-HHHHHHHHHHHHTT--TC
T ss_pred CCCCcHHHHHHH-HCCCHHHHHHHHHHHHHHhhhh
Confidence 345799999995 9999999999999998877543
No 277
>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=55.30 E-value=34 Score=21.36 Aligned_cols=31 Identities=16% Similarity=0.223 Sum_probs=25.6
Q ss_pred hcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHH
Q 025357 162 QENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (254)
Q Consensus 162 ~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~ 193 (254)
..+-|.+..||++. .+++..++.+-.+.|.+
T Consensus 11 L~~~~~~~~el~~~-l~~s~~~vs~hL~~L~~ 41 (47)
T PF01022_consen 11 LSEGPLTVSELAEE-LGLSQSTVSHHLKKLRE 41 (47)
T ss_dssp HTTSSEEHHHHHHH-HTS-HHHHHHHHHHHHH
T ss_pred HHhCCCchhhHHHh-ccccchHHHHHHHHHHH
Confidence 34478999999995 99999999999888865
No 278
>COG0444 DppD ABC-type dipeptide/oligopeptide/nickel transport system, ATPase component [Amino acid transport and metabolism / Inorganic ion transport and metabolism]
Probab=55.29 E-value=20 Score=32.58 Aligned_cols=92 Identities=15% Similarity=0.207 Sum_probs=49.2
Q ss_pred CCCCCHHHHHHHHHHHHHHh----cCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHH
Q 025357 143 LRGRNQEAIVAACLYIACRQ----ENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFL 218 (254)
Q Consensus 143 ~~Gr~~~~iaAAclY~AcR~----~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~ 218 (254)
--|-+.+.++|.++ +|+= ...|-|--|+.. ...|-+-+++|++..+... +-.++=-..+.++|
T Consensus 155 SGGMrQRV~IAmal--a~~P~LlIADEPTTALDvt~------QaqIl~Ll~~l~~e~~~ai-----ilITHDl~vva~~a 221 (316)
T COG0444 155 SGGMRQRVMIAMAL--ALNPKLLIADEPTTALDVTV------QAQILDLLKELQREKGTAL-----ILITHDLGVVAEIA 221 (316)
T ss_pred CCcHHHHHHHHHHH--hCCCCEEEeCCCcchhhHHH------HHHHHHHHHHHHHhcCCEE-----EEEeCCHHHHHHhc
Confidence 33555555555443 4442 345655555522 3456666777777665541 11233346677777
Q ss_pred hhcCCCcchhheeeCcceeeehhhcccccCCCCCCC
Q 025357 219 LNIFKNFFFLFVLDFSSCMIFCSLWPYLSNPMHPFT 254 (254)
Q Consensus 219 ~~L~l~~~v~~v~~~~~~~~~~~~~~~~~~~~~~~~ 254 (254)
++.-+ +.-.+|-+.+ ..-..+.||.||||
T Consensus 222 Dri~V-MYaG~iVE~g------~~~~i~~~P~HPYT 250 (316)
T COG0444 222 DRVAV-MYAGRIVEEG------PVEEIFKNPKHPYT 250 (316)
T ss_pred ceEEE-EECcEEEEeC------CHHHHhcCCCChHH
Confidence 77643 2223333332 22357889999987
No 279
>PF05225 HTH_psq: helix-turn-helix, Psq domain; InterPro: IPR007889 This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster []. In pipsqueak this domain binds to GAGA sequence []. The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex [].; GO: 0003677 DNA binding; PDB: 2COB_A.
Probab=55.07 E-value=50 Score=20.67 Aligned_cols=26 Identities=12% Similarity=0.193 Sum_probs=18.5
Q ss_pred cCCCCCHHHHHHHhcCCCHHHHHHHHHH
Q 025357 163 ENKPRTVKEFCSVANGTTKKEIGRAKEF 190 (254)
Q Consensus 163 ~~~p~tl~eIa~~~~~v~~~~i~~~~k~ 190 (254)
+|. .++++.|.. .||+..+|.+.++.
T Consensus 14 ~g~-~S~r~AA~~-ygVp~sTL~~r~~g 39 (45)
T PF05225_consen 14 NGK-MSIRKAAKK-YGVPRSTLRRRLRG 39 (45)
T ss_dssp TTS-S-HHHHHHH-HT--HHHHHHHHHH
T ss_pred hCC-CCHHHHHHH-HCcCHHHHHHHHcC
Confidence 554 999999995 99999999976653
No 280
>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=54.70 E-value=9.7 Score=22.37 Aligned_cols=23 Identities=22% Similarity=0.530 Sum_probs=13.0
Q ss_pred CCCCCCCCCCceEEecCCCceEcC
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICS 27 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~ 27 (254)
-+|..||. .-.+.+...|.++|-
T Consensus 5 ykC~~CGn-iv~v~~~~~~~l~Cc 27 (34)
T cd00974 5 YKCEICGN-IVEVLNVGGGTLVCC 27 (34)
T ss_pred EEcCCCCc-EEEEEECCCcceeec
Confidence 45777775 333445556666664
No 281
>PRK06260 threonine synthase; Validated
Probab=53.97 E-value=5.9 Score=36.88 Aligned_cols=30 Identities=33% Similarity=0.594 Sum_probs=22.6
Q ss_pred CCCCCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 1 ~~~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
|....|+.||.. ++...-...|..||-.++
T Consensus 1 ~~~~~C~~cg~~----~~~~~~~~~Cp~cg~~l~ 30 (397)
T PRK06260 1 MYWLKCIECGKE----YDPDEIIYTCPECGGLLE 30 (397)
T ss_pred CCEEEECCCCCC----CCCCCccccCCCCCCeEE
Confidence 667899999983 455555678999998764
No 282
>PRK05550 bifunctional methionine sulfoxide reductase B/A protein; Provisional
Probab=53.77 E-value=16 Score=32.68 Aligned_cols=32 Identities=22% Similarity=0.569 Sum_probs=27.8
Q ss_pred ecCCCceEcCcCceee--cccccccCcccccccC
Q 025357 18 DHSAGDTICSECGLVL--EAYSVDETSEWRIFAN 49 (254)
Q Consensus 18 D~~~G~~vC~~CG~Vl--~e~~id~~~ewr~f~~ 49 (254)
..+.|..+|..||.-| .+.-+|+|.-|.+|.+
T Consensus 31 ~~~~G~y~c~~c~~~LF~s~~Kf~sg~GWPsF~~ 64 (283)
T PRK05550 31 HDEKGVYLCRRCGAPLFRSEDKFNSGCGWPSFDD 64 (283)
T ss_pred CCCCcEEEcCCCCchhcCChhhccCCCCCcCcCc
Confidence 3689999999999987 5667899999999984
No 283
>PRK04330 hypothetical protein; Provisional
Probab=53.77 E-value=85 Score=22.94 Aligned_cols=53 Identities=13% Similarity=0.216 Sum_probs=44.3
Q ss_pred chhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHH
Q 025357 102 PDRNLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYI 158 (254)
Q Consensus 102 ~~r~l~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~ 158 (254)
.+..+.++...++++.+--.+|.++...|.+....+.+.+ .++-.-||.++++
T Consensus 7 ~e~~ik~~~~~L~~I~~D~sVPRNIRraa~ea~~~L~~e~----~~~~vRaA~AIs~ 59 (88)
T PRK04330 7 NEEKIKQAIQMLEEIINDTSVPRNIRRAATEAKEILLNEE----ESPGVRAATAISI 59 (88)
T ss_pred hHHHHHHHHHHHHHHhcCCCCChHHHHHHHHHHHHHhCcC----cchhHHHHHHHHH
Confidence 4678889999999999999999999999999999887764 4455667777775
No 284
>PRK09392 ftrB transcriptional activator FtrB; Provisional
Probab=53.73 E-value=42 Score=28.23 Aligned_cols=29 Identities=24% Similarity=0.312 Sum_probs=25.1
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
.|.+..|||+. .|++..++.|..++|.+.
T Consensus 172 i~~t~~~iA~~-lG~tretvsR~l~~L~~~ 200 (236)
T PRK09392 172 LPYEKRVLASY-LGMTPENLSRAFAALASH 200 (236)
T ss_pred eeCCHHHHHHH-hCCChhHHHHHHHHHHhC
Confidence 46778999995 999999999999998754
No 285
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=53.70 E-value=7.9 Score=29.63 Aligned_cols=19 Identities=11% Similarity=0.468 Sum_probs=10.8
Q ss_pred ceEEecCCCceEcCcCcee
Q 025357 14 EVVFDHSAGDTICSECGLV 32 (254)
Q Consensus 14 ~lv~D~~~G~~vC~~CG~V 32 (254)
.+..+..-+...|.+||..
T Consensus 61 ~L~i~~~p~~~~C~~Cg~~ 79 (114)
T PRK03681 61 KLHLEEQEAECWCETCQQY 79 (114)
T ss_pred EEEEEeeCcEEEcccCCCe
Confidence 4555555566666666643
No 286
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=53.67 E-value=11 Score=22.11 Aligned_cols=22 Identities=23% Similarity=0.600 Sum_probs=11.6
Q ss_pred CCCCCCCCCceEEecCCCceEcC
Q 025357 5 YCADCKRLTEVVFDHSAGDTICS 27 (254)
Q Consensus 5 ~Cp~Cg~~~~lv~D~~~G~~vC~ 27 (254)
+|..||. .-.+.+...|.++|-
T Consensus 9 kC~~Cgn-iv~v~~~~~~~l~Cc 30 (34)
T TIGR00319 9 KCEVCGN-IVEVLHAGGGQLVCC 30 (34)
T ss_pred EcCCCCc-EEEEEECCCcceecc
Confidence 4666665 233444455556664
No 287
>PHA00689 hypothetical protein
Probab=53.66 E-value=9 Score=24.83 Aligned_cols=27 Identities=22% Similarity=0.506 Sum_probs=16.2
Q ss_pred CCCceEcCcCceeecccccccCcccccc
Q 025357 20 SAGDTICSECGLVLEAYSVDETSEWRIF 47 (254)
Q Consensus 20 ~~G~~vC~~CG~Vl~e~~id~~~ewr~f 47 (254)
+--.+.|..||..- -+.-|+|.||.-.
T Consensus 14 epravtckrcgktg-lrweddggewvlm 40 (62)
T PHA00689 14 EPRAVTCKRCGKTG-LRWEDDGGEWVLM 40 (62)
T ss_pred CcceeehhhccccC-ceeecCCCcEEEE
Confidence 34456677777652 3555667777543
No 288
>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=53.55 E-value=4.7 Score=24.18 Aligned_cols=27 Identities=26% Similarity=0.827 Sum_probs=14.0
Q ss_pred CCCCCCCCceEEe-cCCCce-EcCcCcee
Q 025357 6 CADCKRLTEVVFD-HSAGDT-ICSECGLV 32 (254)
Q Consensus 6 Cp~Cg~~~~lv~D-~~~G~~-vC~~CG~V 32 (254)
|-+|+......+- ...|.. +|..||+-
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~ 29 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLY 29 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHH
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHH
Confidence 6778764333333 345666 88888864
No 289
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=53.48 E-value=11 Score=26.17 Aligned_cols=25 Identities=36% Similarity=0.739 Sum_probs=19.4
Q ss_pred CCCCCCCCCceEEecCCCceEcCcCceee
Q 025357 5 YCADCKRLTEVVFDHSAGDTICSECGLVL 33 (254)
Q Consensus 5 ~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl 33 (254)
.| .||. .+..|...-.--| .||..+
T Consensus 5 rC-~Cgr--~lya~e~~kTkkC-~CG~~l 29 (68)
T PF09082_consen 5 RC-DCGR--YLYAKEGAKTKKC-VCGKTL 29 (68)
T ss_dssp EE-TTS----EEEETT-SEEEE-TTTEEE
T ss_pred Ee-cCCC--EEEecCCcceeEe-cCCCee
Confidence 58 7997 5788888999999 999997
No 290
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=53.03 E-value=15 Score=22.48 Aligned_cols=29 Identities=28% Similarity=0.599 Sum_probs=18.2
Q ss_pred CCCCCCCCC--CceEEecCCCceEcCcCcee
Q 025357 4 SYCADCKRL--TEVVFDHSAGDTICSECGLV 32 (254)
Q Consensus 4 ~~Cp~Cg~~--~~lv~D~~~G~~vC~~CG~V 32 (254)
.+|..|++- .-..+|......+|.-||..
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 579999873 34578888889999999986
No 291
>PRK14873 primosome assembly protein PriA; Provisional
Probab=52.95 E-value=9.9 Score=38.06 Aligned_cols=27 Identities=22% Similarity=0.608 Sum_probs=21.2
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCcee
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLV 32 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~V 32 (254)
..||+|+. .+++-...+.+.|..||..
T Consensus 393 ~~C~~C~~--~L~~h~~~~~l~Ch~CG~~ 419 (665)
T PRK14873 393 ARCRHCTG--PLGLPSAGGTPRCRWCGRA 419 (665)
T ss_pred eECCCCCC--ceeEecCCCeeECCCCcCC
Confidence 56999986 4666666788999999984
No 292
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=52.92 E-value=4.5 Score=41.10 Aligned_cols=11 Identities=36% Similarity=1.217 Sum_probs=0.0
Q ss_pred eEcCcCceeec
Q 025357 24 TICSECGLVLE 34 (254)
Q Consensus 24 ~vC~~CG~Vl~ 34 (254)
.+|..||..+.
T Consensus 681 ~~Cp~C~~~~~ 691 (900)
T PF03833_consen 681 YVCPDCGIEVE 691 (900)
T ss_dssp -----------
T ss_pred eeccccccccC
Confidence 45666666554
No 293
>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=52.78 E-value=8.6 Score=25.51 Aligned_cols=21 Identities=33% Similarity=0.730 Sum_probs=13.8
Q ss_pred CCCCCCCCCCceEEecCCCceEcC
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICS 27 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~ 27 (254)
..||.|++ ..+++|.. ..+|+
T Consensus 15 ~~Cp~C~~-~~l~~~~~--~Y~C~ 35 (55)
T PF08063_consen 15 EPCPKCKG-GQLYFDGS--GYKCT 35 (55)
T ss_dssp ---SSSSE--EEEEETT--EEEEE
T ss_pred CCCCCCCC-CeEEecCC--ccEeC
Confidence 57999998 68888854 67786
No 294
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=52.70 E-value=43 Score=21.22 Aligned_cols=30 Identities=10% Similarity=0.138 Sum_probs=26.0
Q ss_pred CCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 164 ~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
+.+.++.||++. .+++..++.+.++.|.+.
T Consensus 8 ~~~~~~~~i~~~-l~is~~~v~~~l~~L~~~ 37 (66)
T smart00418 8 EGELCVCELAEI-LGLSQSTVSHHLKKLREA 37 (66)
T ss_pred cCCccHHHHHHH-HCCCHHHHHHHHHHHHHC
Confidence 567899999995 999999999999988763
No 295
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=52.69 E-value=39 Score=23.06 Aligned_cols=47 Identities=11% Similarity=0.125 Sum_probs=31.8
Q ss_pred CHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcch
Q 025357 168 TVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFF 227 (254)
Q Consensus 168 tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v 227 (254)
+++|||+. +|++..++.++++ -. .. + .....+-|.+++.+||..+..
T Consensus 2 t~~~iA~~-~gvS~~TVSr~ln-------~~--~~--v-~~~t~~~i~~~~~~~gy~~~~ 48 (70)
T smart00354 2 TIKDVARL-AGVSKATVSRVLN-------GN--GR--V-SEETREKVLAAMEELGYIPNR 48 (70)
T ss_pred CHHHHHHH-HCCCHHHHHHHHC-------CC--CC--C-CHHHHHHHHHHHHHhCCCCCH
Confidence 78899994 9999999988652 11 00 1 122345688888888876553
No 296
>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=52.64 E-value=17 Score=22.15 Aligned_cols=30 Identities=23% Similarity=0.365 Sum_probs=18.4
Q ss_pred CCCCCCCCCCCceEEecCCC-ceEcCc---Cceee
Q 025357 3 DSYCADCKRLTEVVFDHSAG-DTICSE---CGLVL 33 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~D~~~G-~~vC~~---CG~Vl 33 (254)
+..||.||+ ..++.....| .+.|++ |....
T Consensus 1 ~~~CP~Cg~-~lv~r~~k~g~F~~Cs~yP~C~~~~ 34 (39)
T PF01396_consen 1 VEKCPKCGG-PLVLRRGKKGKFLGCSNYPECKYTE 34 (39)
T ss_pred CcCCCCCCc-eeEEEECCCCCEEECCCCCCcCCeE
Confidence 368999997 4444444443 346775 66654
No 297
>COG0177 Nth Predicted EndoIII-related endonuclease [DNA replication, recombination, and repair]
Probab=52.18 E-value=73 Score=27.21 Aligned_cols=77 Identities=12% Similarity=0.049 Sum_probs=48.5
Q ss_pred HHhhCCCCCCCCHHHHHHHHHHHHHHhc-CCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHH
Q 025357 136 KVEDQKPLRGRNQEAIVAACLYIACRQE-NKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYL 214 (254)
Q Consensus 136 ~~~~~~~~~Gr~~~~iaAAclY~AcR~~-~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i 214 (254)
.+...|+.+.|....+..|=+ +.-+-. .+|.+..|+.+. -||..|+-.=. |...+| .|.+--..+|
T Consensus 75 ~I~~iGlyr~KAk~I~~~~~~-l~e~~~g~vP~~~~eL~~L-PGVGrKTAnvV---L~~a~g--------~p~i~VDTHV 141 (211)
T COG0177 75 LIKSIGLYRNKAKNIKELARI-LLEKFGGEVPDTREELLSL-PGVGRKTANVV---LSFAFG--------IPAIAVDTHV 141 (211)
T ss_pred HHHhcCCcHHHHHHHHHHHHH-HHHHcCCCCCchHHHHHhC-CCcchHHHHHH---HHhhcC--------CCcccccchH
Confidence 334567766554433333333 333322 469999999995 89999886433 223333 3344557899
Q ss_pred HHHHhhcCCCc
Q 025357 215 VIFLLNIFKNF 225 (254)
Q Consensus 215 ~r~~~~L~l~~ 225 (254)
.|.++++||.+
T Consensus 142 ~Rvs~R~gl~~ 152 (211)
T COG0177 142 HRVSNRLGLVP 152 (211)
T ss_pred HHHHHHhCCCC
Confidence 99999999986
No 298
>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=51.49 E-value=11 Score=30.95 Aligned_cols=28 Identities=29% Similarity=0.590 Sum_probs=17.4
Q ss_pred CCCCCCCCceEE-----e-cCCC-----ceEcCcCceeec
Q 025357 6 CADCKRLTEVVF-----D-HSAG-----DTICSECGLVLE 34 (254)
Q Consensus 6 Cp~Cg~~~~lv~-----D-~~~G-----~~vC~~CG~Vl~ 34 (254)
||.||+. .+.. + |--| ...|..||+=-.
T Consensus 1 CP~Cg~~-~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~ 39 (163)
T TIGR00340 1 CPVCGSR-TLKAVTYDYDIPYFGKIMLSTYICEKCGYRST 39 (163)
T ss_pred CCCCCCc-ceEeeeEeccCCCcceEEEEEEECCCCCCchh
Confidence 9999973 2211 1 2334 357999998754
No 299
>smart00420 HTH_DEOR helix_turn_helix, Deoxyribose operon repressor.
Probab=51.45 E-value=55 Score=20.03 Aligned_cols=29 Identities=17% Similarity=0.249 Sum_probs=25.4
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
.+.+..+++.. .+++..++.+.++.|.+.
T Consensus 13 ~~~s~~~l~~~-l~~s~~tv~~~l~~L~~~ 41 (53)
T smart00420 13 GKVSVEELAEL-LGVSEMTIRRDLNKLEEQ 41 (53)
T ss_pred CCcCHHHHHHH-HCCCHHHHHHHHHHHHHC
Confidence 46899999995 899999999999888765
No 300
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=51.32 E-value=10 Score=30.02 Aligned_cols=32 Identities=25% Similarity=0.548 Sum_probs=27.5
Q ss_pred ecCCCceEcCcCceee--cccccccCcccccccC
Q 025357 18 DHSAGDTICSECGLVL--EAYSVDETSEWRIFAN 49 (254)
Q Consensus 18 D~~~G~~vC~~CG~Vl--~e~~id~~~ewr~f~~ 49 (254)
..+.|..+|.-||.-| .+.-+|+|--|.+|.+
T Consensus 37 ~~~~GiY~c~~cg~pLF~S~~KfdSgcGWPSF~~ 70 (140)
T COG0229 37 NKEKGIYVCIVCGEPLFSSEDKFDSGCGWPSFTK 70 (140)
T ss_pred ccCCceEEeecCCCccccccccccCCCCCccccc
Confidence 3578999999999886 6667899999999984
No 301
>PRK04023 DNA polymerase II large subunit; Validated
Probab=51.28 E-value=10 Score=39.44 Aligned_cols=26 Identities=12% Similarity=-0.153 Sum_probs=14.9
Q ss_pred CHHHHHHHHHhhcCCCcchhh---eeeCc
Q 025357 209 HASDYLVIFLLNIFKNFFFLF---VLDFS 234 (254)
Q Consensus 209 ~p~~~i~r~~~~L~l~~~v~~---v~~~~ 234 (254)
+.+++|.+.-.+|+-+.+... -+||+
T Consensus 946 ev~~~i~~ve~rlgt~~qy~g~~fTHdTs 974 (1121)
T PRK04023 946 EVEDIMDTVEDRLGTPEQYEGFMFTHDTS 974 (1121)
T ss_pred HHHHHHHHHHHhcCCchhccCcccccCCc
Confidence 344557777777776664333 25555
No 302
>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=51.24 E-value=36 Score=22.35 Aligned_cols=27 Identities=15% Similarity=0.175 Sum_probs=21.8
Q ss_pred CCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 167 RTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 167 ~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
.++.|+|+. .||+..++...+++-.+.
T Consensus 24 ~tl~elA~~-lgis~st~~~~LRrae~k 50 (53)
T PF04967_consen 24 ITLEELAEE-LGISKSTVSEHLRRAERK 50 (53)
T ss_pred CCHHHHHHH-hCCCHHHHHHHHHHHHHH
Confidence 789999995 999999988777665443
No 303
>PHA03074 late transcription factor VLTF-3; Provisional
Probab=51.11 E-value=7.8 Score=32.71 Aligned_cols=29 Identities=21% Similarity=0.564 Sum_probs=24.3
Q ss_pred CCCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
...|..|++ ..+|.+ .|-..|-.|+.|..
T Consensus 4 l~~C~~C~~-ngiv~~--k~~efC~fC~~~f~ 32 (225)
T PHA03074 4 LKLCSGCRH-NGIVSE--KDYEFCIFCESVFQ 32 (225)
T ss_pred hhhcCCCCC-CCeeee--cCEEEeecHHHHHh
Confidence 467999998 577765 79999999999875
No 304
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=50.79 E-value=21 Score=23.51 Aligned_cols=45 Identities=13% Similarity=-0.001 Sum_probs=27.4
Q ss_pred CCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcc
Q 025357 167 RTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFF 226 (254)
Q Consensus 167 ~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~ 226 (254)
++..++|+. .|++..+|.+.++.=. ..-..+.|.++|..|+++.+
T Consensus 11 it~~~La~~-~gis~~tl~~~~~~~~--------------~~~~~~~l~~ia~~l~~~~~ 55 (63)
T PF13443_consen 11 ITQKDLARK-TGISRSTLSRILNGKP--------------SNPSLDTLEKIAKALNCSPE 55 (63)
T ss_dssp --HHHHHHH-HT--HHHHHHHHTTT-------------------HHHHHHHHHHHT--HH
T ss_pred CCHHHHHHH-HCcCHHHHHHHHhccc--------------ccccHHHHHHHHHHcCCCHH
Confidence 489999995 8999999988765210 11235889999999988754
No 305
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=50.70 E-value=5.7 Score=30.29 Aligned_cols=34 Identities=18% Similarity=0.540 Sum_probs=24.7
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeecccccc
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVD 39 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~id 39 (254)
..|++||. ..++...-... .|..||..-.+..++
T Consensus 43 ~~C~~Cg~-~~~~~~SCk~R-~CP~C~~~~~~~W~~ 76 (111)
T PF14319_consen 43 YRCEDCGH-EKIVYNSCKNR-HCPSCQAKATEQWIE 76 (111)
T ss_pred eecCCCCc-eEEecCcccCc-CCCCCCChHHHHHHH
Confidence 46999998 56666654444 999999997655443
No 306
>PRK10572 DNA-binding transcriptional regulator AraC; Provisional
Probab=50.65 E-value=84 Score=27.36 Aligned_cols=86 Identities=13% Similarity=0.115 Sum_probs=0.0
Q ss_pred HHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCC-HHHHHHHHHHH
Q 025357 113 ISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTT-KKEIGRAKEFI 191 (254)
Q Consensus 113 I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~-~~~i~~~~k~l 191 (254)
|..+|+.++++.....+ +||+........=....-+-.|+..+.- ...++.|||. ..|.+ ...+.|.||+
T Consensus 202 l~~lA~~~~lS~~~l~r---~Fk~~~G~tp~~~l~~~Rl~~A~~lL~~----t~~sI~eIA~-~~GF~d~s~Fsr~FKk- 272 (290)
T PRK10572 202 IESVAQHVCLSPSRLAH---LFRQQLGISVLRWREDQRISRAKLLLQT----TRMPIATIGR-NVGYDDQLYFSRVFKK- 272 (290)
T ss_pred HHHHHHHHCCCHHHHHH---HHHHHHCcCHHHHHHHHHHHHHHHHHHc----CCCCHHHHHH-HhCCCCHHHHHHHHHH-
Q ss_pred HHHhchhcccccccCCCCHHHHHHHHHhh
Q 025357 192 VKHLEAEMGQSVEMGTIHASDYLVIFLLN 220 (254)
Q Consensus 192 ~~~l~~~~~~~~~~~~~~p~~~i~r~~~~ 220 (254)
.-..+|.+|-.+....
T Consensus 273 -------------~~G~SP~~yR~~~~~~ 288 (290)
T PRK10572 273 -------------CTGASPSEFRARCEEK 288 (290)
T ss_pred -------------HHCcCHHHHHHHhhhc
No 307
>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=50.59 E-value=68 Score=27.78 Aligned_cols=37 Identities=8% Similarity=0.048 Sum_probs=28.5
Q ss_pred HHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHH
Q 025357 152 VAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEF 190 (254)
Q Consensus 152 aAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~ 190 (254)
..+.-|+...- ..++|+.++|+. +++++..+.+.+++
T Consensus 189 ~~~~~~I~~~~-~~~~sl~~lA~~-~~~S~~~l~r~Fk~ 225 (287)
T TIGR02297 189 NRFNFLIEENY-KQHLRLPEYADR-LGISESRLNDICRR 225 (287)
T ss_pred HHHHHHHHHhh-ccCCCHHHHHHH-HCCCHHHHHHHHHH
Confidence 34445665443 458999999995 99999999998876
No 308
>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=50.47 E-value=85 Score=23.85 Aligned_cols=76 Identities=25% Similarity=0.274 Sum_probs=45.7
Q ss_pred HHHHHHhccCCCHHHHHHHHHHHHHHhhCCCC----CCC-CHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHH
Q 025357 112 SISAMSDRLGLVTTIKDRANEIYKKVEDQKPL----RGR-NQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGR 186 (254)
Q Consensus 112 ~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~----~Gr-~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~ 186 (254)
-+..+|..++++...+.. ++++ .+.|.+ +|+ +.+ . - -+.+.-.++--.|+.|++.. ++|+..+|.+
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 SIREAAKRFGVSRNTVYR---WLKR-KETGDLEPKPRGRKKID-R-D--ELKALVEENPDATLRELAER-LGVSPSTIWR 90 (119)
T ss_pred hHHHHHHHhCcHHHHHHH---HHHh-ccccccccccccccccc-H-H--HHHHHHHHCCCcCHHHHHHH-cCCCHHHHHH
Confidence 577788888888765554 4442 222222 232 221 1 1 12222234455999999995 9999999999
Q ss_pred HHHHHHHHhc
Q 025357 187 AKEFIVKHLE 196 (254)
Q Consensus 187 ~~k~l~~~l~ 196 (254)
..+++--..+
T Consensus 91 ~Lkrlg~t~K 100 (119)
T PF01710_consen 91 ALKRLGITRK 100 (119)
T ss_pred HHHHcCchhc
Confidence 9887654443
No 309
>PRK07218 replication factor A; Provisional
Probab=50.32 E-value=7 Score=36.94 Aligned_cols=21 Identities=29% Similarity=0.798 Sum_probs=16.0
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCcee
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLV 32 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~V 32 (254)
.+||+|+.. + + ..+|..||.|
T Consensus 298 ~rCP~C~r~--v--~----~~~C~~hG~v 318 (423)
T PRK07218 298 ERCPECGRV--I--Q----KGQCRSHGAV 318 (423)
T ss_pred ecCcCcccc--c--c----CCcCCCCCCc
Confidence 579999972 2 2 2699999988
No 310
>smart00344 HTH_ASNC helix_turn_helix ASNC type. AsnC: an autogenously regulated activator of asparagine synthetase A transcription in Escherichia coli
Probab=50.20 E-value=43 Score=24.56 Aligned_cols=66 Identities=14% Similarity=-0.017 Sum_probs=42.2
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhc-----c---------cccccCCCCHHHHHHHHHhhcCCCcchhhe
Q 025357 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEM-----G---------QSVEMGTIHASDYLVIFLLNIFKNFFFLFV 230 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~-----~---------~~~~~~~~~p~~~i~r~~~~L~l~~~v~~v 230 (254)
-+.+..+|++. .|+++.++.+.++.|.+.=-+.. + ..+.+...+| ..+.++.+.|.=-++|.++
T Consensus 16 ~~~~~~~la~~-l~~s~~tv~~~l~~L~~~g~i~~~~~~~~~~~~g~~~~~~v~i~~~~~-~~~~~v~~~l~~~p~v~~~ 93 (108)
T smart00344 16 ARISLAELAKK-VGLSPSTVHNRVKRLEEEGVIKGYTAVINPKKLGLSVTAFVGVDLESP-DKLEEFLEKLEKLPEVVEV 93 (108)
T ss_pred CCCCHHHHHHH-HCcCHHHHHHHHHHHHHCCCeeceEEEeCHHHcCCCEEEEEEEEECCh-hHHHHHHHHHhCCcceEEe
Confidence 47899999995 99999999999999987421110 0 0000111113 3567777777666777665
Q ss_pred ee
Q 025357 231 LD 232 (254)
Q Consensus 231 ~~ 232 (254)
..
T Consensus 94 ~~ 95 (108)
T smart00344 94 YL 95 (108)
T ss_pred eE
Confidence 43
No 311
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=50.20 E-value=16 Score=24.06 Aligned_cols=28 Identities=21% Similarity=0.869 Sum_probs=20.2
Q ss_pred CCCC--CCCCCCceEEe--cCCCceEcCcCceee
Q 025357 4 SYCA--DCKRLTEVVFD--HSAGDTICSECGLVL 33 (254)
Q Consensus 4 ~~Cp--~Cg~~~~lv~D--~~~G~~vC~~CG~Vl 33 (254)
..|| .|+. .+..+ .....+.|..||...
T Consensus 19 ~~CP~~~C~~--~~~~~~~~~~~~v~C~~C~~~f 50 (64)
T smart00647 19 KWCPAPDCSA--AIIVTEEEGCNRVTCPKCGFSF 50 (64)
T ss_pred cCCCCCCCcc--eEEecCCCCCCeeECCCCCCeE
Confidence 5699 9986 23343 367789999999765
No 312
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=50.17 E-value=18 Score=23.05 Aligned_cols=46 Identities=17% Similarity=0.040 Sum_probs=31.8
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcc
Q 025357 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFF 226 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~ 226 (254)
...|++|+|+. .|++..+|.+..+- + ...+.+.+.++++.|+++.+
T Consensus 8 ~gls~~~la~~-~gis~~~i~~~~~g-------~--------~~~~~~~~~~ia~~l~~~~~ 53 (55)
T PF01381_consen 8 KGLSQKELAEK-LGISRSTISRIENG-------K--------RNPSLDTLKKIAKALGVSPE 53 (55)
T ss_dssp TTS-HHHHHHH-HTS-HHHHHHHHTT-------S--------STSBHHHHHHHHHHHTSEHH
T ss_pred cCCCHHHHHHH-hCCCcchhHHHhcC-------C--------CCCCHHHHHHHHHHHCCCHH
Confidence 35789999994 89999999877433 1 11236888899999988754
No 313
>KOG1921 consensus Endonuclease III [Replication, recombination and repair]
Probab=50.15 E-value=59 Score=28.53 Aligned_cols=111 Identities=12% Similarity=0.004 Sum_probs=61.1
Q ss_pred CCchhhHHHHHHHHHHHHhccCCCHHHHHHH--HHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhc
Q 025357 100 SHPDRNLIQAFKSISAMSDRLGLVTTIKDRA--NEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVAN 177 (254)
Q Consensus 100 ~~~~r~l~~a~~~I~~i~~~L~Lp~~v~e~A--~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~ 177 (254)
+-+|.....|...|.+.+ +|.-.-+..+ ..|-+.+..-|+...+-....--|-|..-==..++|.++.|+... -
T Consensus 90 QTKDevt~~Am~rL~~~~---gLT~e~v~~~de~~l~~LI~~VgFy~rKA~ylkkta~IL~d~f~gDIP~~v~dLlsL-P 165 (286)
T KOG1921|consen 90 QTKDEVTAAAMLRLKEYG---GLTLEAVLKIDEPTLNELIYPVGFYTRKAKYLKKTAKILQDKFDGDIPDTVEDLLSL-P 165 (286)
T ss_pred chHHHHHHHHHHHHHHhc---CCCHHHHhccChHhHHhhhhhccchHHHHHHHHHHHHHHHHHhCCCCchhHHHHhcC-C
Confidence 345666667777777666 5543222111 222233333454443322222222222222233799999999885 8
Q ss_pred CCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCC
Q 025357 178 GTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKN 224 (254)
Q Consensus 178 ~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~ 224 (254)
||.++- +|.-|....|. +.-+....+|+|+|+.|+.=
T Consensus 166 GVGPKM---a~L~m~~AWn~-------i~GI~VDtHVHRi~nrlgWv 202 (286)
T KOG1921|consen 166 GVGPKM---AHLTMQVAWNK-------IVGICVDTHVHRICNRLGWV 202 (286)
T ss_pred CCchHH---HHHHHHHHhcc-------ceeEEeehHHHHHHHHhccc
Confidence 988763 34445555543 23345578999999999873
No 314
>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=50.14 E-value=10 Score=32.98 Aligned_cols=29 Identities=21% Similarity=0.613 Sum_probs=10.6
Q ss_pred CCCCCCCCCCceEE---ecCCCceEcCcCceee
Q 025357 4 SYCADCKRLTEVVF---DHSAGDTICSECGLVL 33 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~---D~~~G~~vC~~CG~Vl 33 (254)
..||.||+ ..+.. +.--.+..|.+|+.-.
T Consensus 32 ~yCP~Cg~-~~L~~f~NN~PVaDF~C~~C~eey 63 (254)
T PF06044_consen 32 MYCPNCGS-KPLSKFENNRPVADFYCPNCNEEY 63 (254)
T ss_dssp ---TTT---SS-EE--------EEE-TTT--EE
T ss_pred CcCCCCCC-hhHhhccCCCccceeECCCCchHH
Confidence 47999998 33321 1233568999998765
No 315
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=49.97 E-value=5.5 Score=26.01 Aligned_cols=28 Identities=32% Similarity=0.654 Sum_probs=18.4
Q ss_pred CCCCCCCCCceE--EecCCCceEcCcCceee
Q 025357 5 YCADCKRLTEVV--FDHSAGDTICSECGLVL 33 (254)
Q Consensus 5 ~Cp~Cg~~~~lv--~D~~~G~~vC~~CG~Vl 33 (254)
.|+-||.+..+. +-.+.| .||.+|--=+
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 499999752221 235678 7999997444
No 316
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=49.85 E-value=37 Score=29.72 Aligned_cols=31 Identities=19% Similarity=0.329 Sum_probs=23.3
Q ss_pred CCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHh
Q 025357 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKHL 195 (254)
Q Consensus 164 ~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l 195 (254)
..+.|++|||.. +||+..+|++..++..+.|
T Consensus 234 ~~~~t~~eIA~~-lgvS~~~V~q~~~~Al~kL 264 (270)
T TIGR02392 234 DDKLTLQELAAE-YGVSAERIRQIEKNAMKKL 264 (270)
T ss_pred CCCcCHHHHHHH-HCCCHHHHHHHHHHHHHHH
Confidence 347999999995 9999999995554444433
No 317
>PF08006 DUF1700: Protein of unknown function (DUF1700); InterPro: IPR012963 This family contains many hypothetical bacterial proteins and two putative membrane proteins (Q6GFD0 from SWISSPROT and Q6G806 from SWISSPROT).
Probab=49.76 E-value=32 Score=28.21 Aligned_cols=41 Identities=20% Similarity=0.316 Sum_probs=30.8
Q ss_pred HHHHHHhcc-CCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHH
Q 025357 112 SISAMSDRL-GLVTTIKDRANEIYKKVEDQKPLRGRNQEAIV 152 (254)
Q Consensus 112 ~I~~i~~~L-~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~ia 152 (254)
+++.+-..| +||++-.+++.+.|+...+.+.-.|++-+.++
T Consensus 6 fL~~L~~~L~~lp~~e~~e~l~~Y~e~f~d~~~~G~sEeeii 47 (181)
T PF08006_consen 6 FLNELEKYLKKLPEEEREEILEYYEEYFDDAGEEGKSEEEII 47 (181)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHhhhCCCCHHHHH
Confidence 455555555 48999999999999999887777788766543
No 318
>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=49.67 E-value=6.2 Score=30.19 Aligned_cols=30 Identities=27% Similarity=0.475 Sum_probs=18.8
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl 33 (254)
..|-+||+...--.+..-|..+|..|.-|-
T Consensus 14 ~~CaDCg~~~p~w~s~~~GiflC~~Cag~H 43 (116)
T PF01412_consen 14 KVCADCGAPNPTWASLNYGIFLCLECAGIH 43 (116)
T ss_dssp TB-TTT-SBS--EEETTTTEEE-HHHHHHH
T ss_pred CcCCCCCCCCCCEEEeecChhhhHHHHHHH
Confidence 579999984333445567999999999775
No 319
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=49.42 E-value=14 Score=30.05 Aligned_cols=38 Identities=13% Similarity=0.170 Sum_probs=21.3
Q ss_pred chhhHHHHHHHHHHHHhcc-C-CCHHHHHHHHHHHHHHhh
Q 025357 102 PDRNLIQAFKSISAMSDRL-G-LVTTIKDRANEIYKKVED 139 (254)
Q Consensus 102 ~~r~l~~a~~~I~~i~~~L-~-Lp~~v~e~A~~i~k~~~~ 139 (254)
.|-.|.++...+...+... + .++...+.+.++.+++.+
T Consensus 98 VEGlL~~i~~~L~~~~~~~~~~~~~e~~~k~~~~~~~L~~ 137 (160)
T smart00709 98 VEGLLSRVREVLSQAIQETRDDSDPETKEKIDEFLEKLKE 137 (160)
T ss_pred hHHHHHHHHHHHHhhhhhhcccCCHHHHHHHHHHHHHHHH
Confidence 4556666666666554322 1 244556667777776644
No 320
>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=49.20 E-value=22 Score=22.09 Aligned_cols=21 Identities=14% Similarity=0.215 Sum_probs=15.8
Q ss_pred CCHHHHHHHhcCCCHHHHHHHH
Q 025357 167 RTVKEFCSVANGTTKKEIGRAK 188 (254)
Q Consensus 167 ~tl~eIa~~~~~v~~~~i~~~~ 188 (254)
.+..+||+. +||+..+|.+..
T Consensus 22 ~si~~IA~~-~gvsr~TvyR~l 42 (45)
T PF02796_consen 22 MSIAEIAKQ-FGVSRSTVYRYL 42 (45)
T ss_dssp --HHHHHHH-TTS-HHHHHHHH
T ss_pred CCHHHHHHH-HCcCHHHHHHHH
Confidence 889999995 999999997765
No 321
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=49.19 E-value=8 Score=35.14 Aligned_cols=25 Identities=20% Similarity=0.328 Sum_probs=19.3
Q ss_pred CCCCCCCCCCceEEecCCCceEcCc
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSE 28 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~ 28 (254)
++|+.|++.-.+.+||.+++.||..
T Consensus 78 ~kC~~C~~~i~~kTDPkn~dY~~~~ 102 (324)
T PF04502_consen 78 IKCPRCSNEIEFKTDPKNTDYVVES 102 (324)
T ss_pred EEcCCCCCEEeeecCCCCCCeeeec
Confidence 4699998765678888888777765
No 322
>PF00392 GntR: Bacterial regulatory proteins, gntR family; InterPro: IPR000524 Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon []. Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined []. In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies []. This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1HW1_B 1H9T_A 1HW2_A 1H9G_A 1E2X_A 3IHU_A 3C7J_A 2RA5_A 3BY6_C 3IC7_A ....
Probab=48.89 E-value=30 Score=23.06 Aligned_cols=30 Identities=10% Similarity=0.165 Sum_probs=23.6
Q ss_pred CCCC-CHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 164 NKPR-TVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 164 ~~p~-tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
|..+ +..++++. .+|+..+++++++.|...
T Consensus 21 g~~lps~~~la~~-~~vsr~tvr~al~~L~~~ 51 (64)
T PF00392_consen 21 GDRLPSERELAER-YGVSRTTVREALRRLEAE 51 (64)
T ss_dssp TSBE--HHHHHHH-HTS-HHHHHHHHHHHHHT
T ss_pred CCEeCCHHHHHHH-hccCCcHHHHHHHHHHHC
Confidence 3456 89999995 999999999999998754
No 323
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=48.56 E-value=32 Score=22.36 Aligned_cols=26 Identities=12% Similarity=0.190 Sum_probs=23.0
Q ss_pred CHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 168 TVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 168 tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
+..+|++. .+++..++++.+++|.+.
T Consensus 27 ~~~~la~~-~~is~~~v~~~l~~L~~~ 52 (66)
T cd07377 27 SERELAEE-LGVSRTTVREALRELEAE 52 (66)
T ss_pred CHHHHHHH-HCCCHHHHHHHHHHHHHC
Confidence 69999995 899999999999998763
No 324
>KOG0856 consensus Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones]
Probab=48.32 E-value=10 Score=30.08 Aligned_cols=33 Identities=24% Similarity=0.571 Sum_probs=27.9
Q ss_pred ecCCCceEcCcCceee--cccccccCcccccccCC
Q 025357 18 DHSAGDTICSECGLVL--EAYSVDETSEWRIFANE 50 (254)
Q Consensus 18 D~~~G~~vC~~CG~Vl--~e~~id~~~ewr~f~~~ 50 (254)
-.+.|..+|..||.-| .+.-+|.|-.|.+|.+.
T Consensus 49 ~~e~GvY~C~~C~~pLykS~tKfdsgcGWPAF~e~ 83 (146)
T KOG0856|consen 49 HFEEGVYVCAGCGTPLYKSTTKFDSGCGWPAFFEA 83 (146)
T ss_pred ccCCceEEEeecCCccccccccccCCCCCchhhhc
Confidence 3589999999999987 55678999999999854
No 325
>PF05066 HARE-HTH: HB1, ASXL, restriction endonuclease HTH domain; InterPro: IPR007759 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. The delta protein is a dispensable subunit of Bacillus subtilis RNA polymerase (RNAP) that has major effects on the biochemical properties of the purified enzyme. In the presence of delta, RNAP displays an increased specificity of transcription, a decreased affinity for nucleic acids, and an increased efficiency of RNA synthesis because of enhanced recycling []. The delta protein, contains two distinct regions, an N-terminal domain and a glutamate and aspartate residue-rich C-terminal region [].; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent; PDB: 2KRC_A.
Probab=48.17 E-value=15 Score=25.29 Aligned_cols=33 Identities=27% Similarity=0.543 Sum_probs=25.0
Q ss_pred HHHHHHHHHhhCCCCC--CCCHHHHHHHHHHHHHH
Q 025357 129 RANEIYKKVEDQKPLR--GRNQEAIVAACLYIACR 161 (254)
Q Consensus 129 ~A~~i~k~~~~~~~~~--Gr~~~~iaAAclY~AcR 161 (254)
...+|++++.+.++.. |+.|...++|.+|--.+
T Consensus 19 ~~~eI~~~i~~~~~~~~~~k~p~~~i~a~ly~~~~ 53 (72)
T PF05066_consen 19 TFKEIWEEIQERGLYKKSGKTPEATIAAQLYTDIK 53 (72)
T ss_dssp EHHHHHHHHHHHHTS---GGGGGHHHH-HHHHHHH
T ss_pred CHHHHHHHHHHhCCCCcccCCHHHHHHHHHHHHcc
Confidence 3456777777777776 89999999999998887
No 326
>TIGR00122 birA_repr_reg BirA biotin operon repressor domain. This model may recognize some other putative repressor proteins, such as DnrO of Streptomyces peucetius with scores below the noise cutoff but with significance shown by low E-value.
Probab=48.16 E-value=48 Score=22.34 Aligned_cols=30 Identities=7% Similarity=0.228 Sum_probs=25.7
Q ss_pred cCCCCCHHHHHHHhcCCCHHHHHHHHHHHHH
Q 025357 163 ENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (254)
Q Consensus 163 ~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~ 193 (254)
.+.+.+..+++.. .+++..+|++..+.|.+
T Consensus 10 ~~~~~~~~eLa~~-l~vS~~tv~~~l~~L~~ 39 (69)
T TIGR00122 10 ADNPFSGEKLGEA-LGMSRTAVNKHIQTLRE 39 (69)
T ss_pred HcCCcCHHHHHHH-HCCCHHHHHHHHHHHHH
Confidence 3446889999994 99999999999999965
No 327
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=47.94 E-value=61 Score=26.69 Aligned_cols=33 Identities=21% Similarity=0.146 Sum_probs=29.7
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchh
Q 025357 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~ 198 (254)
...|-+|||+. .+++.+|++...+.|.+.|+++
T Consensus 164 ~G~s~~eIA~~-l~iS~~TV~~h~~~i~~Kl~v~ 196 (216)
T PRK10840 164 EGFLVTEIAKK-LNRSIKTISSQKKSAMMKLGVE 196 (216)
T ss_pred CCCCHHHHHHH-HCCCHHHHHHHHHHHHHHcCCC
Confidence 45899999995 9999999999999999999976
No 328
>PRK13500 transcriptional activator RhaR; Provisional
Probab=47.80 E-value=1.9e+02 Score=25.63 Aligned_cols=39 Identities=10% Similarity=0.194 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHH
Q 025357 151 IVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFI 191 (254)
Q Consensus 151 iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l 191 (254)
+...+-|+-- ....++++.++|+. .++++..+.+.+|+.
T Consensus 208 l~~i~~yI~~-~~~e~isl~~lA~~-~~iS~~~L~r~FK~~ 246 (312)
T PRK13500 208 LDKLITRLAA-SLKSPFALDKFCDE-ASCSERVLRQQFRQQ 246 (312)
T ss_pred HHHHHHHHHH-cccCCCCHHHHHHH-HCcCHHHHHHHHHHH
Confidence 4444444443 34567999999995 999999999998763
No 329
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=47.65 E-value=79 Score=22.47 Aligned_cols=29 Identities=21% Similarity=0.366 Sum_probs=20.6
Q ss_pred HHHHHhccCCCHHHHHHHHHHHHHHhhCCCCC
Q 025357 113 ISAMSDRLGLVTTIKDRANEIYKKVEDQKPLR 144 (254)
Q Consensus 113 I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~ 144 (254)
+.++++.|+++...+.. +++.+.+.|++.
T Consensus 2 ~~ela~~l~is~stvs~---~l~~L~~~glI~ 30 (96)
T smart00529 2 TSEIAERLNVSPPTVTQ---MLKKLEKDGLVE 30 (96)
T ss_pred HHHHHHHhCCChHHHHH---HHHHHHHCCCEE
Confidence 56789999999876665 555555667663
No 330
>PHA01976 helix-turn-helix protein
Probab=47.57 E-value=62 Score=21.40 Aligned_cols=46 Identities=9% Similarity=0.020 Sum_probs=33.2
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcc
Q 025357 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFF 226 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~ 226 (254)
...|+.++|+. .|++..+|.+..+ +.. .| +.+.+.+++..|+++.+
T Consensus 14 ~glt~~~lA~~-~gvs~~~v~~~e~------g~~------~p---~~~~l~~ia~~l~v~~~ 59 (67)
T PHA01976 14 RAWSAPELSRR-AGVRHSLIYDFEA------DKR------LP---NLKTLLRLADALGVTLD 59 (67)
T ss_pred cCCCHHHHHHH-hCCCHHHHHHHHc------CCC------CC---CHHHHHHHHHHHCcCHH
Confidence 34799999995 8999988887521 111 12 35778899999998765
No 331
>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=47.51 E-value=11 Score=33.91 Aligned_cols=28 Identities=25% Similarity=0.544 Sum_probs=17.7
Q ss_pred CCCCCCCCCC--ceEEec--CCC--ceEcCcCce
Q 025357 4 SYCADCKRLT--EVVFDH--SAG--DTICSECGL 31 (254)
Q Consensus 4 ~~Cp~Cg~~~--~lv~D~--~~G--~~vC~~CG~ 31 (254)
..||.||+.. .++... .+| .+.|.-|++
T Consensus 185 ~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~t 218 (305)
T TIGR01562 185 TLCPACGSPPVASMVRQGGKETGLRYLSCSLCAT 218 (305)
T ss_pred CcCCCCCChhhhhhhcccCCCCCceEEEcCCCCC
Confidence 4799999953 223331 344 678888875
No 332
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=47.43 E-value=10 Score=40.27 Aligned_cols=10 Identities=20% Similarity=-0.200 Sum_probs=4.4
Q ss_pred HHHHHHHHHH
Q 025357 182 KEIGRAKEFI 191 (254)
Q Consensus 182 ~~i~~~~k~l 191 (254)
..|+..+.++
T Consensus 937 vpIrelVEEl 946 (1337)
T PRK14714 937 DPIRIFVEER 946 (1337)
T ss_pred eeHHHHHHHH
Confidence 3444444444
No 333
>PF01907 Ribosomal_L37e: Ribosomal protein L37e; InterPro: IPR001569 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A19_A 4A1D_A 4A18_A 4A1B_A 1S1I_Y 3O5H_d 3IZS_l 3O58_d 2ZKR_2 3IZR_l ....
Probab=47.36 E-value=12 Score=24.92 Aligned_cols=23 Identities=26% Similarity=0.847 Sum_probs=13.8
Q ss_pred CCCCCCCCCceEEecCCCceEcCcCcee
Q 025357 5 YCADCKRLTEVVFDHSAGDTICSECGLV 32 (254)
Q Consensus 5 ~Cp~Cg~~~~lv~D~~~G~~vC~~CG~V 32 (254)
.|..||+ .+ +- --.-+|..||+=
T Consensus 17 ~CrRCG~-~s--yH--~qK~~CasCGyp 39 (55)
T PF01907_consen 17 LCRRCGR-RS--YH--IQKKTCASCGYP 39 (55)
T ss_dssp E-TTTSS-EE--EE--TTTTEETTTBTT
T ss_pred eecccCC-ee--ee--cCCCcccccCCC
Confidence 4888887 22 22 345678888864
No 334
>PF00488 MutS_V: MutS domain V C-terminus.; InterPro: IPR000432 Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication []. MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base []. MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch []. MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level []. Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA. MutS is a modular protein with a complex structure [], and is composed of: N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts. The MutS family of proteins is named after the Salmonella typhimurium MutS protein involved in mismatch repair. Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein [].This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions []. Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts []. This entry represents the C-terminal domain found in proteins in the MutS family of DNA mismatch repair proteins. The C-terminal region of MutS is comprised of the ATPase domain and the HTH (helix-turn-helix) domain, the latter being involved in dimer contacts. Yeast MSH3 [], bacterial proteins involved in DNA mismatch repair, and the predicted protein product of the Rep-3 gene of mouse share extensive sequence similarity. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. ; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 1FW6_A 1EWQ_A 1EWR_B 1NNE_B 2WTU_A 1OH7_A 1OH5_B 1W7A_B 1NG9_A 1OH8_B ....
Probab=47.35 E-value=21 Score=30.83 Aligned_cols=27 Identities=33% Similarity=0.490 Sum_probs=21.2
Q ss_pred HHHHHhccCCCHHHHHHHHHHHHHHhh
Q 025357 113 ISAMSDRLGLVTTIKDRANEIYKKVED 139 (254)
Q Consensus 113 I~~i~~~L~Lp~~v~e~A~~i~k~~~~ 139 (254)
=-++|..+|+|+.++++|.++++++.+
T Consensus 208 ai~iA~~~g~p~~II~rA~~i~~~l~~ 234 (235)
T PF00488_consen 208 AIEIAKLAGLPEEIIERAKEILKQLEE 234 (235)
T ss_dssp HHHHHHHTT--HHHHHHHHHHHHHHHT
T ss_pred HHHHHHHhCcCHHHHHHHHHHHHHHhc
Confidence 345778899999999999999998864
No 335
>PRK04217 hypothetical protein; Provisional
Probab=47.34 E-value=34 Score=26.10 Aligned_cols=30 Identities=20% Similarity=0.098 Sum_probs=24.5
Q ss_pred CCHHHHHHHhcCCCHHHHHHHHHHHHHHhch
Q 025357 167 RTVKEFCSVANGTTKKEIGRAKEFIVKHLEA 197 (254)
Q Consensus 167 ~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~ 197 (254)
.+++|||+. +|++..+|.+.++...+.|..
T Consensus 59 lS~~EIAk~-LGIS~sTV~r~L~RArkkLre 88 (110)
T PRK04217 59 LTQEEAGKR-MGVSRGTVWRALTSARKKVAQ 88 (110)
T ss_pred CCHHHHHHH-HCcCHHHHHHHHHHHHHHHHH
Confidence 389999995 999999999888777666643
No 336
>PRK00118 putative DNA-binding protein; Validated
Probab=46.66 E-value=60 Score=24.45 Aligned_cols=30 Identities=13% Similarity=0.079 Sum_probs=24.2
Q ss_pred CCCHHHHHHHhcCCCHHHHHHHHHHHHHHhc
Q 025357 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKHLE 196 (254)
Q Consensus 166 p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~ 196 (254)
-.|..|||+. .|++..++.+.+.+..+.+.
T Consensus 33 g~S~~EIAe~-lGIS~~TV~r~L~RArkkLr 62 (104)
T PRK00118 33 DYSLGEIAEE-FNVSRQAVYDNIKRTEKLLE 62 (104)
T ss_pred CCCHHHHHHH-HCcCHHHHHHHHHHHHHHHH
Confidence 4789999995 99999999988776666553
No 337
>cd00090 HTH_ARSR Arsenical Resistance Operon Repressor and similar prokaryotic, metal regulated homodimeric repressors. ARSR subfamily of helix-turn-helix bacterial transcription regulatory proteins (winged helix topology). Includes several proteins that appear to dissociate from DNA in the presence of metal ions.
Probab=46.47 E-value=61 Score=21.11 Aligned_cols=27 Identities=19% Similarity=0.223 Sum_probs=23.8
Q ss_pred CCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 167 RTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 167 ~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
.+..||++. .+++..++.+.++.|.+.
T Consensus 21 ~~~~ei~~~-~~i~~~~i~~~l~~L~~~ 47 (78)
T cd00090 21 LTVSELAER-LGLSQSTVSRHLKKLEEA 47 (78)
T ss_pred cCHHHHHHH-HCcCHhHHHHHHHHHHHC
Confidence 899999995 899999999999988653
No 338
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=46.46 E-value=14 Score=24.93 Aligned_cols=28 Identities=7% Similarity=-0.045 Sum_probs=18.1
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeecccccc
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVD 39 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~id 39 (254)
..||+||.. . .---||. ||+--+..+++
T Consensus 28 ~~c~~cg~~-~------~pH~vc~-cG~Y~gr~v~~ 55 (60)
T PRK01110 28 SVDKTTGEY-H------LPHHVSP-KGYYKGRKVLK 55 (60)
T ss_pred eEcCCCCce-e------ccceecC-CcccCCeEeec
Confidence 458888862 1 2346799 99876655544
No 339
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=46.12 E-value=65 Score=27.10 Aligned_cols=32 Identities=13% Similarity=0.057 Sum_probs=25.6
Q ss_pred CCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchh
Q 025357 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (254)
Q Consensus 166 p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~ 198 (254)
..|-+|||+. ++++++|+......|.+.|+++
T Consensus 149 G~snkeIA~~-L~iS~~TV~~h~~~I~~KLgv~ 180 (207)
T PRK11475 149 GYSMPQIAEQ-LERNIKTIRAHKFNVMSKLGVS 180 (207)
T ss_pred CCCHHHHHHH-HCCCHHHHHHHHHHHHHHcCCC
Confidence 4778888884 8888888888888888888765
No 340
>PF00126 HTH_1: Bacterial regulatory helix-turn-helix protein, lysR family; InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI [, , , , ]. The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3T1B_D 3SZP_A 1O7L_C 1B9N_A 1B9M_A 3FZJ_J 3FXR_B 3FXQ_A 3FXU_A 2IJL_B ....
Probab=46.08 E-value=71 Score=20.91 Aligned_cols=30 Identities=10% Similarity=0.213 Sum_probs=26.6
Q ss_pred CHHHHHHHhcCCCHHHHHHHHHHHHHHhchh
Q 025357 168 TVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (254)
Q Consensus 168 tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~ 198 (254)
++...|+ ..+++..+|.+.++.|.+.++.+
T Consensus 15 s~~~AA~-~l~is~~~vs~~i~~LE~~lg~~ 44 (60)
T PF00126_consen 15 SISAAAE-ELGISQSAVSRQIKQLEEELGVP 44 (60)
T ss_dssp SHHHHHH-HCTSSHHHHHHHHHHHHHHHTS-
T ss_pred CHHHHHH-HhhccchHHHHHHHHHHHHhCCe
Confidence 5888888 49999999999999999999986
No 341
>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=45.69 E-value=11 Score=30.82 Aligned_cols=38 Identities=11% Similarity=0.200 Sum_probs=20.2
Q ss_pred chhhHHHHHHHHHHHHhc-cCCCHHHHHHHHHHHHHHhh
Q 025357 102 PDRNLIQAFKSISAMSDR-LGLVTTIKDRANEIYKKVED 139 (254)
Q Consensus 102 ~~r~l~~a~~~I~~i~~~-L~Lp~~v~e~A~~i~k~~~~ 139 (254)
.|-.|.++...+...+.. -...+...+...++.+++.+
T Consensus 100 VEGlL~~i~~~L~~~~~~~~~~~~e~~~~~~~~i~~L~~ 138 (161)
T PF03367_consen 100 VEGLLMRIIDNLERLQPERDSDDPEEKEKIEEFIEKLDE 138 (161)
T ss_dssp HHHHHHHHHHHHHTTHHCCCHH-HHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHhhhhccccCCHHHHHHHHHHHHHHHH
Confidence 455666666666666651 11234455555566655544
No 342
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=45.45 E-value=80 Score=27.84 Aligned_cols=55 Identities=13% Similarity=0.141 Sum_probs=39.3
Q ss_pred CCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCC
Q 025357 167 RTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFK 223 (254)
Q Consensus 167 ~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l 223 (254)
.+.+|||+. .|+++.+++..+.+-++.|.-... ....++....+.+.+|...++=
T Consensus 132 ~s~~EIA~~-lg~s~~tVk~~l~RAr~~Lr~~~~-~~~~~~~~~~~~v~~f~~A~~~ 186 (293)
T PRK09636 132 VPFDEIAST-LGRSPAACRQLASRARKHVRAARP-RFPVSDEEGAELVEAFFAALAS 186 (293)
T ss_pred CCHHHHHHH-HCCCHHHHHHHHHHHHHHHHhhCC-CCCCCchHHHHHHHHHHHHHHh
Confidence 789999995 999999988777766666654321 1113445567789999988854
No 343
>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=45.38 E-value=46 Score=29.91 Aligned_cols=45 Identities=20% Similarity=0.085 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHH
Q 025357 126 IKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVK 170 (254)
Q Consensus 126 v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~ 170 (254)
..+.|-.+...+....+.---.|..+|.||+++||+..+.|.-..
T Consensus 169 ~~~~aw~~inDa~~t~~~llypphiIA~a~l~ia~~~~~~~~~~~ 213 (297)
T COG5333 169 LLQIAWKIINDALRTDLCLLYPPHIIALAALLIACEVLGMPIIKL 213 (297)
T ss_pred HHHHHHHHHHhhhhceeeeecChHHHHHHHHHHHHHhcCCccchh
Confidence 455555555555443333334688999999999999998874433
No 344
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=45.14 E-value=10 Score=28.00 Aligned_cols=11 Identities=27% Similarity=0.425 Sum_probs=9.6
Q ss_pred CCCCCCCCCCC
Q 025357 1 MADSYCADCKR 11 (254)
Q Consensus 1 ~~~~~Cp~Cg~ 11 (254)
|....||+||.
T Consensus 1 mlLI~CP~Cg~ 11 (97)
T COG4311 1 MLLIPCPYCGE 11 (97)
T ss_pred CceecCCCCCC
Confidence 77889999997
No 345
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=44.96 E-value=20 Score=25.57 Aligned_cols=27 Identities=19% Similarity=0.320 Sum_probs=19.5
Q ss_pred CCCCCCCCCCceEEecCCC--ceEcCcCceee
Q 025357 4 SYCADCKRLTEVVFDHSAG--DTICSECGLVL 33 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G--~~vC~~CG~Vl 33 (254)
..||-||. - +++...+ .-||.-|+.--
T Consensus 2 ~~CPCCg~-~--Tl~~~~~~~ydIC~VC~WEd 30 (78)
T PF14206_consen 2 YPCPCCGY-Y--TLEERGEGTYDICPVCFWED 30 (78)
T ss_pred ccCCCCCc-E--EeccCCCcCceECCCCCccc
Confidence 47999997 2 3444444 88999999863
No 346
>TIGR01889 Staph_reg_Sar staphylococcal accessory regulator family. This model represents a family of transcriptional regulatory proteins in Staphylococcus aureus and Staphylococcus epidermidis. Some members contain two tandem copies of this region. This family is related to the MarR transcriptional regulator family described by pfam model pfam01047.
Probab=44.90 E-value=61 Score=24.09 Aligned_cols=34 Identities=12% Similarity=0.036 Sum_probs=29.2
Q ss_pred HHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 160 CRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 160 cR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
+...+-+.++.||+.. .+++..++.+.++.|.+.
T Consensus 37 ~~~~~~~~t~~eL~~~-l~~~~stvs~~i~~Le~k 70 (109)
T TIGR01889 37 LENNEGKLTLKEIIKE-ILIKQSALVKIIKKLSKK 70 (109)
T ss_pred hhccCCcCcHHHHHHH-HCCCHHHHHHHHHHHHHC
Confidence 4556678999999995 999999999999999764
No 347
>PRK06450 threonine synthase; Validated
Probab=44.65 E-value=11 Score=34.53 Aligned_cols=29 Identities=24% Similarity=0.607 Sum_probs=20.7
Q ss_pred CCCCCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 1 MADSYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 1 ~~~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
|....|+.||. . ++. .-...|..||-.++
T Consensus 1 ~~~~~C~~Cg~-~---~~~-~~~~~C~~cg~~l~ 29 (338)
T PRK06450 1 MVKEVCMKCGK-E---RES-IYEIRCKKCGGPFE 29 (338)
T ss_pred CceeEECCcCC-c---CCC-cccccCCcCCCEeE
Confidence 56679999998 3 233 33578999997764
No 348
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=44.64 E-value=46 Score=20.12 Aligned_cols=28 Identities=14% Similarity=0.262 Sum_probs=23.4
Q ss_pred CCHHHHHHHhcCCCHHHHHHHHHHHHHHh
Q 025357 167 RTVKEFCSVANGTTKKEIGRAKEFIVKHL 195 (254)
Q Consensus 167 ~tl~eIa~~~~~v~~~~i~~~~k~l~~~l 195 (254)
.+..+|++. .|++..+|.+......+.+
T Consensus 27 ~~~~~ia~~-~~~s~~~i~~~~~~~~~~l 54 (55)
T cd06171 27 LSYEEIAEI-LGISRSTVRQRLHRALKKL 54 (55)
T ss_pred CCHHHHHHH-HCcCHHHHHHHHHHHHHHc
Confidence 689999995 9999999998888776654
No 349
>smart00400 ZnF_CHCC zinc finger.
Probab=44.49 E-value=27 Score=22.71 Aligned_cols=34 Identities=12% Similarity=0.182 Sum_probs=24.7
Q ss_pred CCCCCCCCC-CceEEecCCCceEcCcCceeecccccc
Q 025357 4 SYCADCKRL-TEVVFDHSAGDTICSECGLVLEAYSVD 39 (254)
Q Consensus 4 ~~Cp~Cg~~-~~lv~D~~~G~~vC~~CG~Vl~e~~id 39 (254)
..||.+... .++.++...+..-|-.||. ..++|+
T Consensus 3 ~~cPfh~d~~pSf~v~~~kn~~~Cf~cg~--gGd~i~ 37 (55)
T smart00400 3 GLCPFHGEKTPSFSVSPDKQFFHCFGCGA--GGNVIS 37 (55)
T ss_pred ccCcCCCCCCCCEEEECCCCEEEEeCCCC--CCCHHH
Confidence 359999764 4677888889999999983 334444
No 350
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=44.15 E-value=14 Score=32.87 Aligned_cols=28 Identities=18% Similarity=0.523 Sum_probs=18.9
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl 33 (254)
..|+.||++ +... ...=..+|.+||...
T Consensus 112 RFCg~CG~~-~~~~-~~g~~~~C~~cg~~~ 139 (279)
T COG2816 112 RFCGRCGTK-TYPR-EGGWARVCPKCGHEH 139 (279)
T ss_pred cCCCCCCCc-Cccc-cCceeeeCCCCCCcc
Confidence 569999984 2211 223346899999875
No 351
>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=43.77 E-value=6.9 Score=26.42 Aligned_cols=25 Identities=20% Similarity=0.608 Sum_probs=17.8
Q ss_pred CCCCCCCCCCceEEecCCCceEcC-cCceeec
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICS-ECGLVLE 34 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~-~CG~Vl~ 34 (254)
..||.||.+ |- ..+..|+ +|+....
T Consensus 4 kHC~~CG~~--Ip----~~~~fCS~~C~~~~~ 29 (59)
T PF09889_consen 4 KHCPVCGKP--IP----PDESFCSPKCREEYR 29 (59)
T ss_pred CcCCcCCCc--CC----cchhhhCHHHHHHHH
Confidence 579999973 32 2488995 7987754
No 352
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=43.56 E-value=14 Score=27.53 Aligned_cols=28 Identities=18% Similarity=0.310 Sum_probs=18.0
Q ss_pred CCCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl 33 (254)
...|..|+- |+.+..--...|.+||.++
T Consensus 3 lrAC~~C~~---I~~~~qf~~~gCpnC~~~l 30 (98)
T cd07973 3 LRACLLCSL---IKTEDQFERDGCPNCEGYL 30 (98)
T ss_pred CchhccCCc---ccccccccCCCCCCCcchh
Confidence 457888875 3333333456799998665
No 353
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=43.47 E-value=20 Score=21.59 Aligned_cols=13 Identities=38% Similarity=0.657 Sum_probs=9.4
Q ss_pred CCCCCCCCCCc-eEE
Q 025357 4 SYCADCKRLTE-VVF 17 (254)
Q Consensus 4 ~~Cp~Cg~~~~-lv~ 17 (254)
..||.|++ +. |+-
T Consensus 6 v~CP~C~s-~~~v~k 19 (36)
T PF03811_consen 6 VHCPRCQS-TEGVKK 19 (36)
T ss_pred eeCCCCCC-CCccee
Confidence 67999998 55 443
No 354
>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=43.46 E-value=35 Score=24.04 Aligned_cols=24 Identities=17% Similarity=0.142 Sum_probs=20.7
Q ss_pred CCHHHHHHHhcCCCHHHHHHHHHHH
Q 025357 167 RTVKEFCSVANGTTKKEIGRAKEFI 191 (254)
Q Consensus 167 ~tl~eIa~~~~~v~~~~i~~~~k~l 191 (254)
.|.+|||+. .|+++.+|+..++.+
T Consensus 33 lS~kEIAe~-LGIS~~TVk~~l~~~ 56 (73)
T TIGR03879 33 KTASEIAEE-LGRTEQTVRNHLKGE 56 (73)
T ss_pred CCHHHHHHH-HCcCHHHHHHHHhcC
Confidence 689999995 999999999887653
No 355
>COG1522 Lrp Transcriptional regulators [Transcription]
Probab=43.40 E-value=36 Score=26.65 Aligned_cols=32 Identities=16% Similarity=0.140 Sum_probs=27.4
Q ss_pred hcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 162 QENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 162 ~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
+.+.++++.+||+. .|++..++.+.+++|.+.
T Consensus 18 ~~d~r~~~~eia~~-lglS~~~v~~Ri~~L~~~ 49 (154)
T COG1522 18 QEDARISNAELAER-VGLSPSTVLRRIKRLEEE 49 (154)
T ss_pred HHhCCCCHHHHHHH-HCCCHHHHHHHHHHHHHC
Confidence 34456999999995 999999999999999873
No 356
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=43.37 E-value=9.7 Score=29.27 Aligned_cols=20 Identities=15% Similarity=0.305 Sum_probs=12.9
Q ss_pred CceEEecCCCceEcCcCcee
Q 025357 13 TEVVFDHSAGDTICSECGLV 32 (254)
Q Consensus 13 ~~lv~D~~~G~~vC~~CG~V 32 (254)
..+..+..-+...|.+||..
T Consensus 61 a~L~Ie~vp~~~~C~~Cg~~ 80 (117)
T PRK00564 61 AILDIVDEKVELECKDCSHV 80 (117)
T ss_pred CEEEEEecCCEEEhhhCCCc
Confidence 35666666677777777744
No 357
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=43.19 E-value=17 Score=24.72 Aligned_cols=29 Identities=28% Similarity=0.537 Sum_probs=15.5
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeeccc
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAY 36 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~ 36 (254)
..|..|+.. +..-...--|..||.|+=..
T Consensus 10 ~~C~~C~~~----F~~~~rrhhCr~CG~~vC~~ 38 (69)
T PF01363_consen 10 SNCMICGKK----FSLFRRRHHCRNCGRVVCSS 38 (69)
T ss_dssp SB-TTT--B-----BSSS-EEE-TTT--EEECC
T ss_pred CcCcCcCCc----CCCceeeEccCCCCCEECCc
Confidence 679999973 45567888899999988543
No 358
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=43.10 E-value=54 Score=26.44 Aligned_cols=73 Identities=11% Similarity=0.029 Sum_probs=48.3
Q ss_pred HHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhc--cccccc---------CCCCHHHHHHHHHh-hcC
Q 025357 155 CLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEM--GQSVEM---------GTIHASDYLVIFLL-NIF 222 (254)
Q Consensus 155 clY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~--~~~~~~---------~~~~p~~~i~r~~~-~L~ 222 (254)
+||...+ .+.+...+|||+. ++|+..++..+.++|.+.==++- -..+.+ ....-...+.+|.. .||
T Consensus 14 ~Iy~l~~-~~~~~~~~diA~~-L~Vsp~sVt~ml~rL~~~GlV~~~~y~gi~LT~~G~~~a~~~~r~hrlle~fL~~~lg 91 (154)
T COG1321 14 TIYELLE-EKGFARTKDIAER-LKVSPPSVTEMLKRLERLGLVEYEPYGGVTLTEKGREKAKELLRKHRLLERFLVDVLG 91 (154)
T ss_pred HHHHHHh-ccCcccHHHHHHH-hCCCcHHHHHHHHHHHHCCCeEEecCCCeEEChhhHHHHHHHHHHHHHHHHHHHHHhC
Confidence 4676666 6778899999995 99999999999999976311110 000111 11234567777877 488
Q ss_pred CCcchhh
Q 025357 223 KNFFFLF 229 (254)
Q Consensus 223 l~~~v~~ 229 (254)
++.+...
T Consensus 92 ~~~~~~~ 98 (154)
T COG1321 92 LDWEEAH 98 (154)
T ss_pred CCHHHHH
Confidence 8887754
No 359
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=43.05 E-value=8.3 Score=29.44 Aligned_cols=31 Identities=16% Similarity=0.501 Sum_probs=20.7
Q ss_pred CCCCCCCCCCCceEEecCCCceEcCcCceeecc
Q 025357 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEA 35 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e 35 (254)
...|+.||+ -|-.-...+.++|..|+.+..-
T Consensus 7 ~~FC~~CG~--ll~~~~~~~~~~C~~Ck~~~~v 37 (116)
T KOG2907|consen 7 LDFCSDCGS--LLEEPSAQSTVLCIRCKIEYPV 37 (116)
T ss_pred cchhhhhhh--hcccccccCceEeccccccCCH
Confidence 356999987 1323345666779999988643
No 360
>PF12840 HTH_20: Helix-turn-helix domain; PDB: 1ULY_A 2CWE_A 1Y0U_B 2QUF_B 2QLZ_C 2OQG_B 2ZKZ_C 3PQK_A 3PQJ_D 3F6O_B ....
Probab=43.02 E-value=45 Score=21.95 Aligned_cols=31 Identities=19% Similarity=0.258 Sum_probs=26.4
Q ss_pred hcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHH
Q 025357 162 QENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (254)
Q Consensus 162 ~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~ 193 (254)
..+-|.+..||++. ++++..++.+.++.|.+
T Consensus 20 ~~~~~~t~~ela~~-l~~~~~t~s~hL~~L~~ 50 (61)
T PF12840_consen 20 ASNGPMTVSELAEE-LGISQSTVSYHLKKLEE 50 (61)
T ss_dssp HHCSTBEHHHHHHH-HTS-HHHHHHHHHHHHH
T ss_pred hcCCCCCHHHHHHH-HCCCHHHHHHHHHHHHH
Confidence 46779999999995 99999999999998876
No 361
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=42.99 E-value=45 Score=28.62 Aligned_cols=33 Identities=9% Similarity=-0.090 Sum_probs=30.0
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchh
Q 025357 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~ 198 (254)
...|-+|||+. ++++++++.+....|.+.|++.
T Consensus 157 ~G~SnkEIA~~-L~IS~~TVk~hvs~I~~KLgv~ 189 (217)
T PRK13719 157 FGFSHEYIAQL-LNITVGSSKNKISEILKFFGIS 189 (217)
T ss_pred CCCCHHHHHHH-hCCCHHHHHHHHHHHHHHhCCC
Confidence 35889999995 9999999999999999999986
No 362
>PRK10130 transcriptional regulator EutR; Provisional
Probab=42.88 E-value=2.7e+02 Score=25.52 Aligned_cols=42 Identities=19% Similarity=0.304 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHH
Q 025357 148 QEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFI 191 (254)
Q Consensus 148 ~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l 191 (254)
...+..+.=|+--.. ..|+++.|||+. .+++..++.+.|++.
T Consensus 239 ~~~v~~~~~~i~~~~-~~~ltv~~lA~~-~gvS~r~L~r~Fk~~ 280 (350)
T PRK10130 239 RRLLSRAREYVLENM-SEPVTVLDLCNQ-LHVSRRTLQNAFHAI 280 (350)
T ss_pred HHHHHHHHHHHHhhh-cCCCCHHHHHHH-HCCCHHHHHHHHHHH
Confidence 445566666766443 558999999995 999999999988763
No 363
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=42.62 E-value=15 Score=27.86 Aligned_cols=31 Identities=23% Similarity=0.425 Sum_probs=21.7
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
..|-+||+...--....-|..||.+|.-|-.
T Consensus 4 ~~CaDC~~~~p~w~s~~~GifvC~~CsgiHR 34 (112)
T smart00105 4 KKCFDCGAPNPTWASVNLGVFLCIECSGIHR 34 (112)
T ss_pred CcccCCCCCCCCcEEeccceeEhHHhHHHHH
Confidence 5699999842222334579999999988864
No 364
>TIGR00498 lexA SOS regulatory protein LexA. LexA acts as a homodimer to repress a number of genes involved in the response to DNA damage (SOS response), including itself and RecA. RecA, in the presence of single-stranded DNA, acts as a co-protease to activate a latent autolytic protease activity (EC 3.4.21.88) of LexA, where the active site Ser is part of LexA. The autolytic cleavage site is an Ala-Gly bond in LexA (at position 84-85 in E. coli LexA; this sequence is replaced by Gly-Gly in Synechocystis). The cleavage leads to derepression of the SOS regulon and eventually to DNA repair. LexA in Bacillus subtilis is called DinR. LexA is much less broadly distributed than RecA.
Probab=42.48 E-value=42 Score=27.79 Aligned_cols=33 Identities=12% Similarity=0.219 Sum_probs=29.3
Q ss_pred HhcCCCCCHHHHHHHhcCCC-HHHHHHHHHHHHHH
Q 025357 161 RQENKPRTVKEFCSVANGTT-KKEIGRAKEFIVKH 194 (254)
Q Consensus 161 R~~~~p~tl~eIa~~~~~v~-~~~i~~~~k~l~~~ 194 (254)
+.++.|.+++|||+ ..+++ ..++.+.++.|.+.
T Consensus 20 ~~~~~~~~~~ela~-~~~~~s~~tv~~~l~~L~~~ 53 (199)
T TIGR00498 20 ESTGYPPSIREIAR-AVGLRSPSAAEEHLKALERK 53 (199)
T ss_pred HhcCCCCcHHHHHH-HhCCCChHHHHHHHHHHHHC
Confidence 66789999999999 59998 99999999998774
No 365
>PF09779 Ima1_N: Ima1 N-terminal domain; InterPro: IPR018617 Members of this family of uncharacterised novel proteins have no known function.
Probab=42.40 E-value=16 Score=28.64 Aligned_cols=29 Identities=21% Similarity=0.501 Sum_probs=22.3
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCcee
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLV 32 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~V 32 (254)
..|-.||..+.+-.+...-...|..|+.+
T Consensus 1 v~C~fC~~~s~~~~~~~~~~w~C~~C~q~ 29 (131)
T PF09779_consen 1 VNCWFCGQNSKVPYDNRNSNWTCPHCEQY 29 (131)
T ss_pred CeeccCCCCCCCCCCCCCCeeECCCCCCc
Confidence 36999998655656655556999999988
No 366
>PRK14987 gluconate operon transcriptional regulator; Provisional
Probab=42.36 E-value=29 Score=30.64 Aligned_cols=48 Identities=10% Similarity=0.008 Sum_probs=33.5
Q ss_pred CCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcc
Q 025357 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFF 226 (254)
Q Consensus 166 p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~ 226 (254)
..|++|||+. +|||..|++|+++.- .. + ......-|.+.+.+||-.+.
T Consensus 5 ~~ti~dIA~~-agVS~~TVSrvLn~~---------~~--v-s~~tr~rV~~~a~elgY~pn 52 (331)
T PRK14987 5 RPVLQDVADR-VGVTKMTVSRFLRNP---------EQ--V-SVALRGKIAAALDELGYIPN 52 (331)
T ss_pred CCcHHHHHHH-hCCCHHHhhhhhCCC---------CC--C-CHHHHHHHHHHHHHhCCCcc
Confidence 3699999995 899999999987421 01 1 12456667778888876544
No 367
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=42.35 E-value=99 Score=21.61 Aligned_cols=29 Identities=17% Similarity=0.103 Sum_probs=25.8
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
.|.++.||++. .+++..++.+..+.|.+.
T Consensus 19 ~~~t~~~ia~~-l~i~~~tv~r~l~~L~~~ 47 (91)
T smart00346 19 GGLTLAELAER-LGLSKSTAHRLLNTLQEL 47 (91)
T ss_pred CCcCHHHHHHH-hCCCHHHHHHHHHHHHHC
Confidence 48999999995 899999999999998764
No 368
>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=42.33 E-value=15 Score=30.68 Aligned_cols=23 Identities=17% Similarity=0.583 Sum_probs=13.9
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCc
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECG 30 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG 30 (254)
..||.|++...+ ... .-.|..|+
T Consensus 100 ~~C~~C~G~G~~-i~~---~~~C~~C~ 122 (186)
T TIGR02642 100 CKCPRCRGTGLI-QRR---QRECDTCA 122 (186)
T ss_pred CcCCCCCCeeEE-ecC---CCCCCCCC
Confidence 689999983333 321 14577774
No 369
>PRK06386 replication factor A; Reviewed
Probab=42.17 E-value=13 Score=34.31 Aligned_cols=21 Identities=19% Similarity=0.754 Sum_probs=14.8
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCcee
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLV 32 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~V 32 (254)
.+||+|+.. .+ .| .|..||.|
T Consensus 237 ~rCP~C~R~----l~--~g--~C~~HG~v 257 (358)
T PRK06386 237 TKCSVCNKI----IE--DG--VCKDHPDA 257 (358)
T ss_pred ecCcCCCeE----cc--CC--cCCCCCCC
Confidence 469999872 22 23 89999975
No 370
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=42.13 E-value=35 Score=20.53 Aligned_cols=22 Identities=23% Similarity=0.191 Sum_probs=18.6
Q ss_pred CHHHHHHHhcCCCHHHHHHHHHH
Q 025357 168 TVKEFCSVANGTTKKEIGRAKEF 190 (254)
Q Consensus 168 tl~eIa~~~~~v~~~~i~~~~k~ 190 (254)
++.|+|+. +||+..+|.+..+.
T Consensus 2 s~~e~a~~-lgvs~~tl~~~~~~ 23 (49)
T cd04762 2 TTKEAAEL-LGVSPSTLRRWVKE 23 (49)
T ss_pred CHHHHHHH-HCcCHHHHHHHHHc
Confidence 67899995 99999999888664
No 371
>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=42.04 E-value=18 Score=32.11 Aligned_cols=34 Identities=24% Similarity=0.503 Sum_probs=17.7
Q ss_pred CCCCCCCCCCceEEe-------cCCCceEcCcCceeecccccc
Q 025357 4 SYCADCKRLTEVVFD-------HSAGDTICSECGLVLEAYSVD 39 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D-------~~~G~~vC~~CG~Vl~e~~id 39 (254)
..||+||........ +...-.+|.+||.-+ .++|
T Consensus 212 ~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~Yl--K~vd 252 (290)
T PF04216_consen 212 IKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYL--KTVD 252 (290)
T ss_dssp TS-TTT---SS-EEE--------SEEEEEETTTTEEE--EEEE
T ss_pred CCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchH--HHHh
Confidence 579999974222111 223346899999987 4444
No 372
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=41.58 E-value=65 Score=24.71 Aligned_cols=48 Identities=17% Similarity=0.087 Sum_probs=35.3
Q ss_pred CHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhc
Q 025357 168 TVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNI 221 (254)
Q Consensus 168 tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L 221 (254)
+++|+++. +|||=-|++..+.+|.+.|+... .+..........+.++|
T Consensus 51 nlKe~e~~-lgiSYPTvR~rLd~ii~~lg~~~-----~~~~~~~~~~~~IL~~L 98 (113)
T PF09862_consen 51 NLKEMEKE-LGISYPTVRNRLDKIIEKLGYEE-----DEEEEEEDERKEILDKL 98 (113)
T ss_pred CHHHHHHH-HCCCcHHHHHHHHHHHHHhCCCC-----CcccccchhHHHHHHHH
Confidence 49999995 99999999999999999999831 12233344555555555
No 373
>smart00351 PAX Paired Box domain.
Probab=41.48 E-value=1.3e+02 Score=23.11 Aligned_cols=61 Identities=16% Similarity=0.122 Sum_probs=34.7
Q ss_pred HHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCC-----CCCHHHHH-HHHHHH-HHHhcCCCCCHHHHHHH
Q 025357 112 SISAMSDRLGLVTTIKDRANEIYKKVEDQKPLR-----GRNQEAIV-AACLYI-ACRQENKPRTVKEFCSV 175 (254)
Q Consensus 112 ~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~-----Gr~~~~ia-AAclY~-AcR~~~~p~tl~eIa~~ 175 (254)
-...+|..|+++...+..-..-| .+.|.+. |+++..+. ....++ ....++-..|+.|+++.
T Consensus 35 s~~~iA~~~gvs~~tV~kwi~r~---~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~p~~t~~el~~~ 102 (125)
T smart00351 35 RPCDISRQLCVSHGCVSKILGRY---YETGSIRPGAIGGSKPKVATPKVVKKIADYKQENPGIFAWEIRDR 102 (125)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHH---HHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHCCCCCHHHHHHH
Confidence 36788999999987666644444 4444332 32332221 222232 24556666899998764
No 374
>PF08221 HTH_9: RNA polymerase III subunit RPC82 helix-turn-helix domain; InterPro: IPR013197 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae (Baker's yeast) RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In S. cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa []. This region is probably a DNA-binding helix-turn-helix.; PDB: 2XV4_S 2XUB_A.
Probab=41.31 E-value=87 Score=20.99 Aligned_cols=41 Identities=17% Similarity=0.255 Sum_probs=27.4
Q ss_pred HHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 152 VAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 152 aAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
.++.++-..-.+| +.|+.+|.. .++++.+.++++.-.|.++
T Consensus 14 ~~~~V~~~Ll~~G-~ltl~~i~~-~t~l~~~~Vk~~L~~LiQh 54 (62)
T PF08221_consen 14 IVAKVGEVLLSRG-RLTLREIVR-RTGLSPKQVKKALVVLIQH 54 (62)
T ss_dssp HHHHHHHHHHHC--SEEHHHHHH-HHT--HHHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHcC-CcCHHHHHH-HhCCCHHHHHHHHHHHHHc
Confidence 3444444444455 789999999 4899999999998777653
No 375
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=41.25 E-value=12 Score=25.39 Aligned_cols=23 Identities=26% Similarity=0.736 Sum_probs=15.2
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCce
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGL 31 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~ 31 (254)
..|..||.. + +---...|..||+
T Consensus 18 t~CrRCG~~-s----yh~qK~~CasCGy 40 (62)
T PRK04179 18 IRCRRCGRH-S----YNVRKKYCAACGF 40 (62)
T ss_pred chhcccCcc-c----ccccccchhhcCC
Confidence 458888873 2 2234568888887
No 376
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=41.20 E-value=21 Score=36.16 Aligned_cols=27 Identities=22% Similarity=0.731 Sum_probs=22.5
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCcee
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLV 32 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~V 32 (254)
..||+|.. .+++-..+|.+.|-.||..
T Consensus 445 ~~Cp~Cd~--~lt~H~~~~~L~CH~Cg~~ 471 (730)
T COG1198 445 AECPNCDS--PLTLHKATGQLRCHYCGYQ 471 (730)
T ss_pred ccCCCCCc--ceEEecCCCeeEeCCCCCC
Confidence 46899986 4777778899999999988
No 377
>TIGR02844 spore_III_D sporulation transcriptional regulator SpoIIID. Members of this protein are the transcriptional regulator SpoIIID, or stage III sporulation protein D. It is present in genomes if and only if the species is capable of endospore formation as occurs in the model species Bacillus subtilis. SpoIIID is a DNA binding protein that, in B. subtilis, downregulates many genes but also turns on ten genes.
Probab=40.88 E-value=32 Score=24.62 Aligned_cols=23 Identities=26% Similarity=0.342 Sum_probs=20.0
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHH
Q 025357 165 KPRTVKEFCSVANGTTKKEIGRAK 188 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v~~~~i~~~~ 188 (254)
-..|++|||+. +||+..++++.+
T Consensus 18 ~~~ti~dvA~~-~gvS~~TVsr~L 40 (80)
T TIGR02844 18 TKATVRETAKV-FGVSKSTVHKDV 40 (80)
T ss_pred CCCCHHHHHHH-hCCCHHHHHHHh
Confidence 45799999995 999999999965
No 378
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=40.72 E-value=95 Score=24.73 Aligned_cols=31 Identities=16% Similarity=0.309 Sum_probs=24.5
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhc
Q 025357 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHLE 196 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~ 196 (254)
...|.+|||+. +|++..+|++..+...+.|.
T Consensus 20 ~GlTq~EIAe~-LGiS~~tVs~ie~ra~kkLr 50 (141)
T PRK03975 20 RGLTQQEIADI-LGTSRANVSSIEKRARENIE 50 (141)
T ss_pred cCCCHHHHHHH-HCCCHHHHHHHHHHHHHHHH
Confidence 44899999995 99999998887766665543
No 379
>PF04552 Sigma54_DBD: Sigma-54, DNA binding domain; InterPro: IPR007634 This DNA-binding domain is based on peptide fragmentation data. This domain is proximal to DNA in the promoter/holoenzyme complex. Furthermore, this region contains a putative helix-turn-helix motif. At the C terminus, there is a highly conserved region known as the RpoN box and is the signature of the sigma-54 proteins [].; PDB: 2AHQ_A 2O9L_A 2O8K_A.
Probab=40.70 E-value=9.1 Score=31.18 Aligned_cols=24 Identities=29% Similarity=0.446 Sum_probs=0.0
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHHH
Q 025357 165 KPRTVKEFCSVANGTTKKEIGRAKE 189 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v~~~~i~~~~k 189 (254)
.|.|++|||+. .|+++.||.|+++
T Consensus 48 ~PLt~~~iA~~-lgl~~STVSRav~ 71 (160)
T PF04552_consen 48 KPLTMKDIADE-LGLHESTVSRAVK 71 (160)
T ss_dssp -------------------------
T ss_pred cCCCHHHHHHH-hCCCHhHHHHHHc
Confidence 58999999994 9999999999976
No 380
>PRK08329 threonine synthase; Validated
Probab=40.68 E-value=19 Score=32.96 Aligned_cols=26 Identities=27% Similarity=0.639 Sum_probs=17.8
Q ss_pred CCCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
|.+|+.||.. ++.... ..| .||-.++
T Consensus 1 ~l~C~~Cg~~----~~~~~~-~~C-~c~~~l~ 26 (347)
T PRK08329 1 MLRCTKCGRT----YEEKFK-LRC-DCGGTLL 26 (347)
T ss_pred CcCcCCCCCC----cCCCCc-eec-CCCCcEE
Confidence 3789999983 333333 789 7987663
No 381
>PRK08558 adenine phosphoribosyltransferase; Provisional
Probab=40.63 E-value=43 Score=28.98 Aligned_cols=56 Identities=14% Similarity=0.045 Sum_probs=41.3
Q ss_pred HHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcccccccCC-CCHHHHHHHHHhhcCCCcch
Q 025357 159 ACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGT-IHASDYLVIFLLNIFKNFFF 227 (254)
Q Consensus 159 AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~-~~p~~~i~r~~~~L~l~~~v 227 (254)
+.|.-+.-.|.+|+++. +|+++..|+|..+ +-. +|. ....+++.+++.++.+...+
T Consensus 16 ~lr~lk~~~ty~el~~~-~g~p~~~l~RYv~------g~~------~P~~~~a~~~~~~l~~~~~~~~~l 72 (238)
T PRK08558 16 VLRSLKKTYTYEELSSI-TGLPESVLNRYVN------GHV------LPSVERAREIVEKLGPYYNLEEEV 72 (238)
T ss_pred HHHHHhcccCHHHHHHH-HCCCHHHHHHHHc------CCc------CCCHHHHHHHHHHHHHhhhhHHHH
Confidence 44666667899999995 9999999988753 111 444 34889999999999884444
No 382
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=40.38 E-value=49 Score=27.70 Aligned_cols=33 Identities=9% Similarity=0.112 Sum_probs=28.5
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchh
Q 025357 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~ 198 (254)
...|-+|||+. ++++++++....+.|.+.|+.+
T Consensus 151 ~G~snkeIA~~-L~iS~~TVk~h~~~I~~KL~v~ 183 (207)
T PRK15411 151 AGQGTIQISDQ-MNIKAKTVSSHKGNIKRKIKTH 183 (207)
T ss_pred cCCCHHHHHHH-cCCCHHHHHHHHHHHHHHhCCC
Confidence 35788999995 8999999999999999999876
No 383
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=40.31 E-value=93 Score=26.78 Aligned_cols=33 Identities=12% Similarity=0.195 Sum_probs=29.1
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchh
Q 025357 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~ 198 (254)
...|-+|||.+ .++++.++....+.+.+.|+..
T Consensus 193 ~G~t~~eIa~~-l~is~~TV~~h~~~~~~KL~~~ 225 (240)
T PRK10188 193 EGKTSAEIAMI-LSISENTVNFHQKNMQKKFNAP 225 (240)
T ss_pred cCCCHHHHHHH-hCCCHHHHHHHHHHHHHHhCCC
Confidence 34889999996 9999999999999999999875
No 384
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=40.26 E-value=20 Score=28.07 Aligned_cols=30 Identities=27% Similarity=0.566 Sum_probs=19.4
Q ss_pred CCCCCCCCCCCceEEe----cCCCceEcCcCceee
Q 025357 3 DSYCADCKRLTEVVFD----HSAGDTICSECGLVL 33 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~D----~~~G~~vC~~CG~Vl 33 (254)
+..||.|++ .+++.- ...-...|.+||.-.
T Consensus 30 ~~~cP~C~s-~~~~k~g~~~~~~qRyrC~~C~~tf 63 (129)
T COG3677 30 KVNCPRCKS-SNVVKIGGIRRGHQRYKCKSCGSTF 63 (129)
T ss_pred cCcCCCCCc-cceeeECCccccccccccCCcCcce
Confidence 367999998 453222 113356899998765
No 385
>PRK15435 bifunctional DNA-binding transcriptional dual regulator/O6-methylguanine-DNA methyltransferase; Provisional
Probab=40.25 E-value=1.1e+02 Score=28.11 Aligned_cols=74 Identities=16% Similarity=0.115 Sum_probs=44.0
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHH--------Hhch-------hcccc-----cccCCCC
Q 025357 150 AIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVK--------HLEA-------EMGQS-----VEMGTIH 209 (254)
Q Consensus 150 ~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~--------~l~~-------~~~~~-----~~~~~~~ 209 (254)
.+..++-|+-- +.+.++.++|.. .|+++..+.+.|++... .+.+ ....+ +...-.+
T Consensus 86 ~i~~a~~~I~~---~~~lsl~eLA~~-lG~S~~~L~R~Fkk~~G~TP~~yl~~~Rl~~A~~lL~~~~sI~eIA~~~Gf~s 161 (353)
T PRK15435 86 KITHACRLLEQ---ETPVTLEALADQ-VAMSPFHLHRLFKATTGMTPKAWQQAWRARRLREALAKGESVTTSILNAGFPD 161 (353)
T ss_pred HHHHHHHHHHh---CCCCCHHHHHHH-HCCCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCCC
Confidence 44555555532 467899999984 89999999888776411 0000 00000 1133356
Q ss_pred HHHHHHHHHhhcCCCcch
Q 025357 210 ASDYLVIFLLNIFKNFFF 227 (254)
Q Consensus 210 p~~~i~r~~~~L~l~~~v 227 (254)
+..|-..|-..+|+++.-
T Consensus 162 ~s~F~~~Fkk~~G~TPs~ 179 (353)
T PRK15435 162 SSSYYRKADETLGMTAKQ 179 (353)
T ss_pred hHHHHHHHHHHHCcCchh
Confidence 777777777777776654
No 386
>PF04079 DUF387: Putative transcriptional regulators (Ypuh-like); InterPro: IPR005234 This family represents ScpB, which along with ScpA (IPR003768 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation [, ]. The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli [], where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions. In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes []. ; GO: 0051304 chromosome separation; PDB: 1T6S_B 2Z99_A.
Probab=40.23 E-value=81 Score=25.57 Aligned_cols=64 Identities=17% Similarity=0.313 Sum_probs=41.9
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcc--------cccc-cCCCCHHHHHHHHHhh
Q 025357 151 IVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMG--------QSVE-MGTIHASDYLVIFLLN 220 (254)
Q Consensus 151 iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~--------~~~~-~~~~~p~~~i~r~~~~ 220 (254)
++=|.||. .+.|+++.+++++ ++ +...+.....+|.+.++-... ..+. ....+-.+||.++...
T Consensus 2 ~iEAlLF~----s~~pvs~~~La~~-l~-~~~~v~~~l~~L~~~y~~~~~gl~l~~~~~~y~l~tk~~~~~~v~~~~~~ 74 (159)
T PF04079_consen 2 IIEALLFA----SGEPVSIEELAEI-LG-SEDEVEEALEELQEEYNEEDRGLELVEVGGGYRLQTKPEYAEYVEKLFKK 74 (159)
T ss_dssp HHHHHHHH-----SS-B-HHHHHHH-CT--HHHHHHHHHHHHHHHHHCT-SEEEEEETTEEEEEE-GGGHHHHHHHHCT
T ss_pred hhHhhHHH----cCCCCCHHHHHHH-hC-CHHHHHHHHHHHHHHhccCCCCEEEEEECCEEEEEEhHHHHHHHHHHhcc
Confidence 44567775 4679999999995 89 999999999999998843211 1111 1234667888888776
No 387
>PRK08197 threonine synthase; Validated
Probab=40.22 E-value=13 Score=34.62 Aligned_cols=26 Identities=27% Similarity=0.713 Sum_probs=19.1
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
.+|+.||.. ++.......| +||-.++
T Consensus 8 ~~C~~Cg~~----~~~~~~~~~C-~cg~~l~ 33 (394)
T PRK08197 8 LECSKCGET----YDADQVHNLC-KCGKPLL 33 (394)
T ss_pred EEECCCCCC----CCCCCcceec-CCCCeeE
Confidence 679999983 4445556889 8987763
No 388
>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....
Probab=40.16 E-value=14 Score=34.44 Aligned_cols=24 Identities=33% Similarity=0.747 Sum_probs=14.5
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
..||.||.. ...| -.|..||..++
T Consensus 137 g~CP~C~~~------~a~g-~~Ce~cG~~~~ 160 (391)
T PF09334_consen 137 GTCPYCGSD------KARG-DQCENCGRPLE 160 (391)
T ss_dssp CEETTT--S------SCTT-TEETTTSSBEE
T ss_pred ccccCcCcc------ccCC-CcccCCCCCcc
Confidence 568888851 2233 56788888876
No 389
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=40.09 E-value=59 Score=25.45 Aligned_cols=45 Identities=16% Similarity=0.208 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchh
Q 025357 151 IVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (254)
Q Consensus 151 iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~ 198 (254)
+.+-.|= -.|++| ..|++|+... +|++..++++.+++|+..=.+-
T Consensus 13 Lk~rIvE-lVRe~G-RiTi~ql~~~-TGasR~Tvk~~lreLVa~G~l~ 57 (127)
T PF06163_consen 13 LKARIVE-LVREHG-RITIKQLVAK-TGASRNTVKRYLRELVARGDLY 57 (127)
T ss_pred HHHHHHH-HHHHcC-CccHHHHHHH-HCCCHHHHHHHHHHHHHcCCeE
Confidence 3444333 446555 6999999995 9999999999999998864443
No 390
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=40.03 E-value=23 Score=22.31 Aligned_cols=22 Identities=32% Similarity=0.637 Sum_probs=16.7
Q ss_pred CCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 5 YCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 5 ~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
+|..|+.. + ...+|-.||.|.-
T Consensus 1 ~C~~C~~~-~-------~l~~CL~C~~~~c 22 (50)
T smart00290 1 RCSVCGTI-E-------NLWLCLTCGQVGC 22 (50)
T ss_pred CcccCCCc-C-------CeEEecCCCCccc
Confidence 58899873 2 2679999999975
No 391
>PF10005 DUF2248: Uncharacterized protein conserved in bacteria (DUF2248); InterPro: IPR011201 This is a family of uncharacterised bacterial proteins.
Probab=39.95 E-value=16 Score=33.36 Aligned_cols=24 Identities=38% Similarity=0.928 Sum_probs=18.7
Q ss_pred CCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 5 YCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 5 ~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
.|+.||. .|.++. ..|..||.-|.
T Consensus 1 ~C~~Cg~--~v~FeN----t~C~~Cg~~LG 24 (343)
T PF10005_consen 1 SCPNCGQ--PVFFEN----TRCLSCGSALG 24 (343)
T ss_pred CCCCCCC--cceeCC----CccccCCcccc
Confidence 5999997 465553 78999999885
No 392
>TIGR02395 rpoN_sigma RNA polymerase sigma-54 factor. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called sigma-54, or RpoN (unrelated to sigma 70-type factors such as RpoD/SigA). RpoN is responsible for enhancer-dependent transcription, and its presence characteristically is associated with varied panels of activators, most of which are enhancer-binding proteins (but see Brahmachary, et al., PubMed:15231786). RpoN may be responsible for transcription of nitrogen fixation genes, flagellins, pilins, etc., and synonyms for the gene symbol rpoN, such as ntrA, reflect these observations
Probab=39.87 E-value=61 Score=30.71 Aligned_cols=24 Identities=33% Similarity=0.440 Sum_probs=21.7
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHHH
Q 025357 165 KPRTVKEFCSVANGTTKKEIGRAKE 189 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v~~~~i~~~~k 189 (254)
.|.|++|||+. .|+.+.||+|+.+
T Consensus 317 kPLtlkdiA~~-lglheSTVSRav~ 340 (429)
T TIGR02395 317 KPLTLREVAEE-LGLHESTISRAIN 340 (429)
T ss_pred cCCcHHHHHHH-hCCCccchhhhhc
Confidence 59999999995 9999999999964
No 393
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=39.75 E-value=16 Score=34.40 Aligned_cols=33 Identities=15% Similarity=0.370 Sum_probs=23.0
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeecccccc
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLEAYSVD 39 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~id 39 (254)
-.||.||. +. .--..+..-|..||+-..+..+-
T Consensus 351 p~Cp~Cg~-~m--~S~G~~g~rC~kCg~~~~~~~~~ 383 (421)
T COG1571 351 PVCPRCGG-RM--KSAGRNGFRCKKCGTRARETLIK 383 (421)
T ss_pred CCCCccCC-ch--hhcCCCCcccccccccCCccccc
Confidence 37999998 32 22334469999999998766544
No 395
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=39.69 E-value=13 Score=39.61 Aligned_cols=8 Identities=38% Similarity=1.360 Sum_probs=3.8
Q ss_pred EcCcCcee
Q 025357 25 ICSECGLV 32 (254)
Q Consensus 25 vC~~CG~V 32 (254)
.|.+||.-
T Consensus 694 ~CPsCGae 701 (1337)
T PRK14714 694 VCPDCGAE 701 (1337)
T ss_pred eCccCCCc
Confidence 44455543
No 396
>PRK10870 transcriptional repressor MprA; Provisional
Probab=39.33 E-value=63 Score=26.43 Aligned_cols=38 Identities=21% Similarity=0.235 Sum_probs=30.0
Q ss_pred HHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 156 LYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 156 lY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
++...+..+.+.++.||++. .+++..++.+.+++|.+.
T Consensus 61 L~~L~~~~~~~it~~eLa~~-l~l~~~tvsr~v~rLe~k 98 (176)
T PRK10870 61 LITLESQENHSIQPSELSCA-LGSSRTNATRIADELEKR 98 (176)
T ss_pred HHHHhcCCCCCcCHHHHHHH-HCCCHHHHHHHHHHHHHC
Confidence 33333445678999999995 999999999999998763
No 397
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=39.31 E-value=37 Score=20.82 Aligned_cols=21 Identities=14% Similarity=0.317 Sum_probs=17.5
Q ss_pred CHHHHHHHhcCCCHHHHHHHHH
Q 025357 168 TVKEFCSVANGTTKKEIGRAKE 189 (254)
Q Consensus 168 tl~eIa~~~~~v~~~~i~~~~k 189 (254)
++.|+|+. +||++.+|++..+
T Consensus 2 ~~~e~a~~-~gv~~~tlr~~~~ 22 (49)
T cd04761 2 TIGELAKL-TGVSPSTLRYYER 22 (49)
T ss_pred cHHHHHHH-HCcCHHHHHHHHH
Confidence 67899995 9999999987743
No 398
>COG1123 ATPase components of various ABC-type transport systems, contain duplicated ATPase [General function prediction only]
Probab=39.26 E-value=35 Score=33.34 Aligned_cols=60 Identities=17% Similarity=0.118 Sum_probs=40.4
Q ss_pred HHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCC--CcchhheeeCcceeeehhhcccccCCCCCCC
Q 025357 181 KKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFK--NFFFLFVLDFSSCMIFCSLWPYLSNPMHPFT 254 (254)
Q Consensus 181 ~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l--~~~v~~v~~~~~~~~~~~~~~~~~~~~~~~~ 254 (254)
...|-..++.+.+..++.. +-..+=-..+.++|++.-+ ..++.+...+. --++||+||+|
T Consensus 190 q~qIL~llk~l~~e~g~a~-----l~ITHDl~Vva~~aDrv~Vm~~G~iVE~G~~~---------~i~~~p~hpYT 251 (539)
T COG1123 190 QAQILDLLKDLQRELGMAV-----LFITHDLGVVAELADRVVVMYKGEIVETGPTE---------EILSNPQHPYT 251 (539)
T ss_pred HHHHHHHHHHHHHHcCcEE-----EEEcCCHHHHHHhcCeEEEEECCEEEEecCHH---------HHHhccCCccc
Confidence 4677788888888888762 2223344788888888855 44554444444 34789999987
No 399
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=39.01 E-value=86 Score=25.49 Aligned_cols=29 Identities=21% Similarity=0.092 Sum_probs=23.1
Q ss_pred CCHHHHHHHhcCCCHHHHHHHHHHHHHHhc
Q 025357 167 RTVKEFCSVANGTTKKEIGRAKEFIVKHLE 196 (254)
Q Consensus 167 ~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~ 196 (254)
.+.+|||.. +|+++.+++..+.+-++.|.
T Consensus 148 ~s~~EIA~~-lgis~~tVk~~l~Rar~~Lr 176 (193)
T TIGR02947 148 FAYKEIAEI-MGTPIGTVMSRLHRGRKQLR 176 (193)
T ss_pred CCHHHHHHH-HCCCHHHHHHHHHHHHHHHH
Confidence 789999995 99999998877666555553
No 400
>COG2390 DeoR Transcriptional regulator, contains sigma factor-related N-terminal domain [Transcription]
Probab=38.90 E-value=1.2e+02 Score=27.67 Aligned_cols=66 Identities=12% Similarity=-0.018 Sum_probs=42.3
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHh--chhcccccccCCCCHHHHHHHHHhhcCCCc
Q 025357 150 AIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHL--EAEMGQSVEMGTIHASDYLVIFLLNIFKNF 225 (254)
Q Consensus 150 ~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l--~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~ 225 (254)
..-+|-+|+. .+.|+.|||+. +|++..+++|...+.++.= ++. +..+...-.++=.++-++++|..
T Consensus 15 ~~~~A~lYY~-----~gltQ~eIA~~-LgiSR~~v~rlL~~Ar~~GiV~I~----i~~~~~~~~~Le~~L~~~fgL~~ 82 (321)
T COG2390 15 LARAAWLYYV-----EGLTQSEIAER-LGISRATVSRLLAKAREEGIVKIS----INSPVEGCLELEQQLKERFGLKE 82 (321)
T ss_pred HHHHHHHHHh-----cCCCHHHHHHH-hCCCHHHHHHHHHHHHHCCeEEEE----eCCCCcchHHHHHHHHHhcCCCe
Confidence 3445666654 67999999995 9999999999887766531 221 11222333334466667777764
No 401
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=38.71 E-value=13 Score=25.04 Aligned_cols=25 Identities=24% Similarity=0.683 Sum_probs=15.5
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl 33 (254)
..|..||.. + + ---.-.|+.||+=-
T Consensus 17 ~~CRRCGr~-s--y--hv~k~~CaaCGfgr 41 (61)
T COG2126 17 IRCRRCGRR-S--Y--HVRKKYCAACGFGR 41 (61)
T ss_pred ehhhhccch-h--e--eeccceecccCCCC
Confidence 458888873 2 1 12346788888763
No 402
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=38.70 E-value=15 Score=29.42 Aligned_cols=15 Identities=33% Similarity=0.919 Sum_probs=13.2
Q ss_pred CCCceEcCcCceeec
Q 025357 20 SAGDTICSECGLVLE 34 (254)
Q Consensus 20 ~~G~~vC~~CG~Vl~ 34 (254)
..|.+||.+||..+.
T Consensus 109 g~G~l~C~~Cg~~~~ 123 (146)
T PF07295_consen 109 GPGTLVCENCGHEVE 123 (146)
T ss_pred cCceEecccCCCEEE
Confidence 579999999999874
No 403
>COG2771 CsgD DNA-binding HTH domain-containing proteins [Transcription]
Probab=38.69 E-value=90 Score=20.09 Aligned_cols=31 Identities=16% Similarity=0.291 Sum_probs=28.1
Q ss_pred CCHHHHHHHhcCCCHHHHHHHHHHHHHHhchh
Q 025357 167 RTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (254)
Q Consensus 167 ~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~ 198 (254)
.+..||+.. .+++..++..-.+.+.+.++..
T Consensus 20 ~s~~eia~~-l~is~~tV~~h~~~i~~Kl~~~ 50 (65)
T COG2771 20 KSNKEIARI-LGISEETVKTHLRNIYRKLGVK 50 (65)
T ss_pred CCHHHHHHH-HCCCHHHHHHHHHHHHHHHCCC
Confidence 889999995 9999999999999999998875
No 404
>PF12085 DUF3562: Protein of unknown function (DUF3562); InterPro: IPR021945 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 62 to 84 amino acids in length. This protein has two completely conserved residues (A and Y) that may be functionally important.
Probab=38.68 E-value=1.3e+02 Score=20.84 Aligned_cols=43 Identities=19% Similarity=0.382 Sum_probs=33.9
Q ss_pred CHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhh
Q 025357 168 TVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLN 220 (254)
Q Consensus 168 tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~ 220 (254)
.+++||.. .+++..++++.|..-...|.-. ....+||+=|+.+
T Consensus 9 ~i~~iA~~-t~~P~e~V~~my~dt~~~l~~~---------ARV~DYl~lfaaR 51 (66)
T PF12085_consen 9 VIRSIAEE-TGTPAETVRRMYDDTMRELSSG---------ARVHDYLPLFAAR 51 (66)
T ss_pred HHHHHHHH-HCCCHHHHHHHHHHHHHHHHcC---------CchhhhHHHHHHH
Confidence 47789885 8999999999998877777533 4568999888754
No 405
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=38.46 E-value=43 Score=20.26 Aligned_cols=22 Identities=27% Similarity=0.235 Sum_probs=18.2
Q ss_pred CCHHHHHHHhcCCCHHHHHHHHH
Q 025357 167 RTVKEFCSVANGTTKKEIGRAKE 189 (254)
Q Consensus 167 ~tl~eIa~~~~~v~~~~i~~~~k 189 (254)
.|+.|+++. +|++..+|.+..+
T Consensus 2 lt~~e~a~~-lgis~~ti~~~~~ 23 (49)
T TIGR01764 2 LTVEEAAEY-LGVSKDTVYRLIH 23 (49)
T ss_pred CCHHHHHHH-HCCCHHHHHHHHH
Confidence 478899995 9999999987754
No 406
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=38.45 E-value=85 Score=22.39 Aligned_cols=35 Identities=3% Similarity=0.018 Sum_probs=29.2
Q ss_pred hcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchh
Q 025357 162 QENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (254)
Q Consensus 162 ~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~ 198 (254)
..+.+++-.+|++. +|++...|++.++.|++ -|++
T Consensus 15 ~~~~~~SGe~La~~-LgiSRtaVwK~Iq~Lr~-~G~~ 49 (79)
T COG1654 15 LTGNFVSGEKLAEE-LGISRTAVWKHIQQLRE-EGVD 49 (79)
T ss_pred cCCCcccHHHHHHH-HCccHHHHHHHHHHHHH-hCCc
Confidence 35678999999994 99999999999999984 4443
No 407
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=38.43 E-value=78 Score=24.53 Aligned_cols=31 Identities=6% Similarity=0.096 Sum_probs=26.4
Q ss_pred cCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 163 ENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 163 ~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
.+-+.++.||++. .+++..++.+.+++|.+.
T Consensus 43 ~~~~~t~~eLa~~-l~~~~~tvt~~v~~Le~~ 73 (144)
T PRK03573 43 LPPEQSQIQLAKA-IGIEQPSLVRTLDQLEEK 73 (144)
T ss_pred cCCCCCHHHHHHH-hCCChhhHHHHHHHHHHC
Confidence 3445789999995 999999999999999774
No 408
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=38.36 E-value=80 Score=25.05 Aligned_cols=30 Identities=10% Similarity=0.071 Sum_probs=22.0
Q ss_pred CCCHHHHHHHhcCCCHHHHHH----HHHHHHHHhc
Q 025357 166 PRTVKEFCSVANGTTKKEIGR----AKEFIVKHLE 196 (254)
Q Consensus 166 p~tl~eIa~~~~~v~~~~i~~----~~k~l~~~l~ 196 (254)
..+.+|||+. +|+++.+++. +.+.|++.|+
T Consensus 134 g~s~~EIA~~-lgis~~tV~~~l~ra~~~Lr~~l~ 167 (173)
T PRK09645 134 GWSTAQIAAD-LGIPEGTVKSRLHYALRALRLALQ 167 (173)
T ss_pred CCCHHHHHHH-HCcCHHHHHHHHHHHHHHHHHHhh
Confidence 3789999995 9999988854 4555555554
No 409
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=38.16 E-value=1.5e+02 Score=26.24 Aligned_cols=41 Identities=10% Similarity=0.000 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHH
Q 025357 148 QEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEF 190 (254)
Q Consensus 148 ~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~ 190 (254)
+..+.-++-|+-.... .+.++.++|.. .++++..+.|.+++
T Consensus 141 ~~~~~~v~~yI~~~~~-~~lsl~~lA~~-~g~S~~~L~R~Fk~ 181 (274)
T PRK09978 141 PNMRTRVCTVINNNIA-HEWTLARIASE-LLMSPSLLKKKLRE 181 (274)
T ss_pred HHHHHHHHHHHHhccc-CCCCHHHHHHH-HCcCHHHHHHHHHh
Confidence 3445556667666544 48999999995 99999999998864
No 410
>PF12651 RHH_3: Ribbon-helix-helix domain
Probab=38.01 E-value=75 Score=19.82 Aligned_cols=28 Identities=18% Similarity=0.360 Sum_probs=22.7
Q ss_pred HHHHHHHHHHhccCCCH-HHHHHHHHHHH
Q 025357 108 QAFKSISAMSDRLGLVT-TIKDRANEIYK 135 (254)
Q Consensus 108 ~a~~~I~~i~~~L~Lp~-~v~e~A~~i~k 135 (254)
+....+..++...++|. .+++.|.+.|=
T Consensus 12 el~~~L~~ls~~t~i~~S~Ll~eAle~~l 40 (44)
T PF12651_consen 12 ELYEKLKELSEETGIPKSKLLREALEDYL 40 (44)
T ss_pred HHHHHHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 44678999999999996 78899887764
No 411
>PRK15121 right oriC-binding transcriptional activator; Provisional
Probab=37.98 E-value=1.5e+02 Score=26.05 Aligned_cols=76 Identities=8% Similarity=0.108 Sum_probs=48.9
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHH--------HHhchhc--------ccc-----cccCCC
Q 025357 150 AIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFIV--------KHLEAEM--------GQS-----VEMGTI 208 (254)
Q Consensus 150 ~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~--------~~l~~~~--------~~~-----~~~~~~ 208 (254)
.+..++-|+-... ..+.++.++|+. ++++...+.|.|+... +.+.++. +.+ ....-.
T Consensus 6 ~i~~~~~~i~~~~-~~~~~l~~lA~~-~~~S~~~l~r~F~~~~g~s~~~yi~~~Rl~~A~~~L~~~~~~i~~iA~~~Gf~ 83 (289)
T PRK15121 6 IIRDLLIWLEGHL-DQPLSLDNVAAK-AGYSKWHLQRMFKDVTGHAIGAYIRARRLSKAAVALRLTSRPILDIALQYRFD 83 (289)
T ss_pred HHHHHHHHHHhcc-cCCCCHHHHHHH-HCcCHHHHHHHHHHHHCcCHHHHHHHHHHHHHHHHHHcCCCCHHHHHHHHCCC
Confidence 4555666766554 457999999995 8999999999887651 1111110 001 113445
Q ss_pred CHHHHHHHHHhhcCCCcch
Q 025357 209 HASDYLVIFLLNIFKNFFF 227 (254)
Q Consensus 209 ~p~~~i~r~~~~L~l~~~v 227 (254)
++..|-.-|=...|+++.-
T Consensus 84 s~~~f~r~Fk~~~g~sP~~ 102 (289)
T PRK15121 84 SQQTFTRAFKKQFAQTPAL 102 (289)
T ss_pred CHHHHHHHHHHHHCcCHHH
Confidence 7888888888888887654
No 412
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=37.85 E-value=53 Score=22.03 Aligned_cols=25 Identities=16% Similarity=0.276 Sum_probs=20.6
Q ss_pred CCCHHHHHHHhcCCCHHHHHHHHHHH
Q 025357 166 PRTVKEFCSVANGTTKKEIGRAKEFI 191 (254)
Q Consensus 166 p~tl~eIa~~~~~v~~~~i~~~~k~l 191 (254)
|.++.+||.. .|++...+.+.++..
T Consensus 1 ~~~~~~la~~-~~~s~~~l~~~f~~~ 25 (84)
T smart00342 1 PLTLEDLAEA-LGMSPRHLQRLFKKE 25 (84)
T ss_pred CCCHHHHHHH-hCCCHHHHHHHHHHH
Confidence 5689999995 899999998887754
No 413
>PF01371 Trp_repressor: Trp repressor protein; InterPro: IPR000831 The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan []. The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3FRW_H 3KOR_A 3SSW_N 1P6Z_N 1CO0_B 1JHG_A 1WRT_S 1WRS_R 1WRP_R 1RCS_B ....
Probab=37.71 E-value=71 Score=23.27 Aligned_cols=31 Identities=13% Similarity=0.206 Sum_probs=25.5
Q ss_pred hcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHH
Q 025357 162 QENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (254)
Q Consensus 162 ~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~ 193 (254)
.-....|.+||++. +|++.-+|.|.-+.|..
T Consensus 45 lL~~g~syreIa~~-tgvS~aTItRvsr~Lk~ 75 (87)
T PF01371_consen 45 LLDEGKSYREIAEE-TGVSIATITRVSRCLKY 75 (87)
T ss_dssp HHHTTSSHHHHHHH-HTSTHHHHHHHHHHHHH
T ss_pred HHHCCCCHHHHHHH-hCCCHHHHHHHHHHHHc
Confidence 44456899999995 99999999999877764
No 414
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=37.59 E-value=50 Score=29.22 Aligned_cols=49 Identities=4% Similarity=-0.124 Sum_probs=34.4
Q ss_pred CCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcch
Q 025357 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFF 227 (254)
Q Consensus 166 p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v 227 (254)
..|++|||+. +|||..|+.++++. + .. -...+.+-|.+.+.+||-.+..
T Consensus 6 ~~Ti~dIA~~-agVS~~TVSr~Ln~-------~--~~---vs~~tr~~V~~~a~elgY~p~~ 54 (342)
T PRK10014 6 KITIHDVALA-AGVSVSTVSLVLSG-------K--GR---ISTATGERVNQAIEELGFVRNR 54 (342)
T ss_pred CCcHHHHHHH-hCCCHHHHHHHHCC-------C--CC---CCHHHHHHHHHHHHHhCCCcCH
Confidence 4799999995 89999999999642 1 01 1234566777778888775543
No 415
>PRK10371 DNA-binding transcriptional regulator MelR; Provisional
Probab=37.57 E-value=1.2e+02 Score=26.91 Aligned_cols=40 Identities=8% Similarity=-0.029 Sum_probs=31.0
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHH
Q 025357 150 AIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFI 191 (254)
Q Consensus 150 ~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l 191 (254)
.+..++-|+..... .+.++.++|+. .|+++..+.+.+++.
T Consensus 192 ~i~~~~~~i~~~~~-~~~tl~~lA~~-~~~S~~~l~r~Fk~~ 231 (302)
T PRK10371 192 YVSQMLGFIAENYD-QALTINDVAEH-VKLNANYAMGIFQRV 231 (302)
T ss_pred HHHHHHHHHHHhhc-CCCCHHHHHHH-HCcCHHHHHHHHHHH
Confidence 35566667666544 68999999995 899999999888773
No 416
>PRK11169 leucine-responsive transcriptional regulator; Provisional
Probab=37.54 E-value=67 Score=25.83 Aligned_cols=68 Identities=10% Similarity=-0.074 Sum_probs=44.9
Q ss_pred hcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhc----------c----cc--cccCCCCHHHHHHHHHhhcCCCc
Q 025357 162 QENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEM----------G----QS--VEMGTIHASDYLVIFLLNIFKNF 225 (254)
Q Consensus 162 ~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~----------~----~~--~~~~~~~p~~~i~r~~~~L~l~~ 225 (254)
+.+-..+..|||+. .|++..++.+.+++|.+.=-+.. + .. +++.+ +..+.+.+|...|.--+
T Consensus 24 q~d~R~s~~eiA~~-lglS~~tv~~Ri~rL~~~GvI~~~~~~v~p~~lg~~~~a~v~i~~~~-~~~~~~~~~~~~l~~~p 101 (164)
T PRK11169 24 QKDGRISNVELSKR-VGLSPTPCLERVRRLERQGFIQGYTALLNPHYLDASLLVFVEITLNR-GAPDVFEQFNAAVQKLE 101 (164)
T ss_pred ccCCCCCHHHHHHH-HCcCHHHHHHHHHHHHHCCCeEEEEEEECHHHhCCCEEEEEEEEEcC-CChHHHHHHHHHHhcCc
Confidence 35557899999995 99999999999999987422210 0 00 11111 23456777877776666
Q ss_pred chhhee
Q 025357 226 FFLFVL 231 (254)
Q Consensus 226 ~v~~v~ 231 (254)
+|.++.
T Consensus 102 ~V~~~~ 107 (164)
T PRK11169 102 EIQECH 107 (164)
T ss_pred ceeeee
Confidence 777653
No 417
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.49 E-value=17 Score=24.85 Aligned_cols=28 Identities=32% Similarity=0.734 Sum_probs=17.1
Q ss_pred CCCCCCCCCCCceEE-ecCCCceEcC-cCcee
Q 025357 3 DSYCADCKRLTEVVF-DHSAGDTICS-ECGLV 32 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~-D~~~G~~vC~-~CG~V 32 (254)
...||.||.. +++ +.+.=.-+|+ .|-+|
T Consensus 7 ~v~CP~Cgkp--v~w~~~s~frPFCSkRCklI 36 (65)
T COG3024 7 TVPCPTCGKP--VVWGEESPFRPFCSKRCKLI 36 (65)
T ss_pred cccCCCCCCc--ccccccCCcCcchhHhhhhc
Confidence 4679999983 455 3334445665 47554
No 418
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=37.38 E-value=17 Score=23.50 Aligned_cols=14 Identities=29% Similarity=0.698 Sum_probs=12.1
Q ss_pred CCceEcCcCceeec
Q 025357 21 AGDTICSECGLVLE 34 (254)
Q Consensus 21 ~G~~vC~~CG~Vl~ 34 (254)
+|.++|..||.-+-
T Consensus 3 ~g~l~C~~CG~~m~ 16 (58)
T PF13408_consen 3 SGLLRCGHCGSKMT 16 (58)
T ss_pred CCcEEcccCCcEeE
Confidence 68899999998864
No 419
>PRK00149 dnaA chromosomal replication initiation protein; Reviewed
Probab=37.32 E-value=72 Score=30.11 Aligned_cols=43 Identities=21% Similarity=0.243 Sum_probs=34.8
Q ss_pred HHHHHHHHHhcCCCCCHHHHHHHhc-CCCHHHHHHHHHHHHHHhchh
Q 025357 153 AACLYIACRQENKPRTVKEFCSVAN-GTTKKEIGRAKEFIVKHLEAE 198 (254)
Q Consensus 153 AAclY~AcR~~~~p~tl~eIa~~~~-~v~~~~i~~~~k~l~~~l~~~ 198 (254)
-.+.|++-+..+ .|+.+|+.. + |-+..++..+++++.+.+..+
T Consensus 391 ~iamyl~~~~~~--~s~~~Ig~~-fg~rdhstV~~a~~~i~~~~~~d 434 (450)
T PRK00149 391 QIAMYLAKELTD--LSLPEIGRA-FGGRDHTTVLHAVRKIEKLLEED 434 (450)
T ss_pred HHHHHHHHHhcC--CCHHHHHHH-cCCCCHhHHHHHHHHHHHHHHhC
Confidence 456787766555 689999995 7 699999999999999988643
No 420
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=37.27 E-value=93 Score=21.79 Aligned_cols=28 Identities=21% Similarity=0.335 Sum_probs=25.4
Q ss_pred CCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 166 p~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
+.+..+|+.. .+++..+|.+.+++|.+.
T Consensus 24 ~~~~~~la~~-~~~s~~~i~~~l~~L~~~ 51 (101)
T smart00347 24 PLSVSELAKR-LGVSPSTVTRVLDRLEKK 51 (101)
T ss_pred CcCHHHHHHH-HCCCchhHHHHHHHHHHC
Confidence 6899999995 899999999999999875
No 421
>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=37.21 E-value=18 Score=29.07 Aligned_cols=40 Identities=13% Similarity=0.191 Sum_probs=22.7
Q ss_pred hHHHHHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCC
Q 025357 105 NLIQAFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGR 146 (254)
Q Consensus 105 ~l~~a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr 146 (254)
.+.++.++|..=++ .+-+...++|..|..--.+...++|.
T Consensus 82 ~l~~~~~~v~~n~e--~VG~~FAeEAR~iHyGea~~R~I~G~ 121 (148)
T PF06676_consen 82 ALRKLRRHVEKNSE--DVGDRFAEEARKIHYGEAEERGIYGE 121 (148)
T ss_pred HHHHHHHHHHHhCc--chhHHHHHHHHHHHcCCCccccCcCc
Confidence 34444444544444 44567778887776544455556665
No 422
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=37.19 E-value=21 Score=19.46 Aligned_cols=9 Identities=33% Similarity=0.556 Sum_probs=6.7
Q ss_pred CCCCCCCCC
Q 025357 3 DSYCADCKR 11 (254)
Q Consensus 3 ~~~Cp~Cg~ 11 (254)
+..||.||.
T Consensus 2 l~~C~~CgR 10 (25)
T PF13913_consen 2 LVPCPICGR 10 (25)
T ss_pred CCcCCCCCC
Confidence 567888886
No 423
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=37.08 E-value=87 Score=24.47 Aligned_cols=32 Identities=13% Similarity=0.026 Sum_probs=23.1
Q ss_pred HhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHh
Q 025357 161 RQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHL 195 (254)
Q Consensus 161 R~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l 195 (254)
..+| .+.+|||+. +|+++.++...+.+.++.|
T Consensus 119 ~~~g--~s~~EIA~~-lgis~~tV~~~l~Rar~~L 150 (160)
T PRK09642 119 YLEE--KSYQEIALQ-EKIEVKTVEMKLYRARKWI 150 (160)
T ss_pred HHhC--CCHHHHHHH-HCCCHHHHHHHHHHHHHHH
Confidence 3455 789999995 9999999976555444444
No 424
>PRK05932 RNA polymerase factor sigma-54; Reviewed
Probab=37.02 E-value=60 Score=31.02 Aligned_cols=24 Identities=29% Similarity=0.439 Sum_probs=21.6
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHHH
Q 025357 165 KPRTVKEFCSVANGTTKKEIGRAKE 189 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v~~~~i~~~~k 189 (254)
.|.|++|||+. .|+.+.||.|+.+
T Consensus 342 kPLtlkdvAe~-lglheSTVSRav~ 365 (455)
T PRK05932 342 KPLVLKDIAEE-LGMHESTISRATT 365 (455)
T ss_pred cCccHHHHHHH-hCCCccchhhhhc
Confidence 58999999995 9999999999964
No 425
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=36.78 E-value=59 Score=24.41 Aligned_cols=30 Identities=20% Similarity=0.193 Sum_probs=25.8
Q ss_pred CCCHHHHHHHhcCCCHHHHHHHHHHHHHHhc
Q 025357 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKHLE 196 (254)
Q Consensus 166 p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~ 196 (254)
..+..|||.. .|+++.+|.+..++..+.+.
T Consensus 126 g~s~~eIA~~-l~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 126 GLSYKEIAEI-LGISVGTVKRRLKRARKKLR 155 (158)
T ss_pred CCCHHHHHHH-HCCCHHHHHHHHHHHHHHHH
Confidence 4789999995 99999999999888877664
No 426
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=36.73 E-value=16 Score=22.61 Aligned_cols=17 Identities=35% Similarity=0.767 Sum_probs=13.1
Q ss_pred CCceEcCcCceeecccc
Q 025357 21 AGDTICSECGLVLEAYS 37 (254)
Q Consensus 21 ~G~~vC~~CG~Vl~e~~ 37 (254)
-|.+.|..||.+.....
T Consensus 11 ~~~~~C~~CgM~Y~~~~ 27 (41)
T PF13878_consen 11 FGATTCPTCGMLYSPGS 27 (41)
T ss_pred cCCcCCCCCCCEECCCC
Confidence 36789999999986443
No 427
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=36.72 E-value=65 Score=25.56 Aligned_cols=32 Identities=19% Similarity=0.215 Sum_probs=26.5
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhch
Q 025357 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEA 197 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~ 197 (254)
...|.+|||+. .|++..++.+..++..+.|+.
T Consensus 20 ~GlTq~EIAe~-LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 20 KGLSQKEIAKE-LKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCHHHHHHH-HCcCHHHHHHHHHhHHHHHHH
Confidence 45799999995 999999999888777777763
No 428
>PRK13501 transcriptional activator RhaR; Provisional
Probab=36.67 E-value=2.6e+02 Score=24.29 Aligned_cols=29 Identities=10% Similarity=0.177 Sum_probs=24.3
Q ss_pred HhcCCCCCHHHHHHHhcCCCHHHHHHHHHH
Q 025357 161 RQENKPRTVKEFCSVANGTTKKEIGRAKEF 190 (254)
Q Consensus 161 R~~~~p~tl~eIa~~~~~v~~~~i~~~~k~ 190 (254)
.....++++.++|+. +++++..+.+.+++
T Consensus 187 ~~~~e~~sl~~lA~~-~~lS~~~l~r~Fk~ 215 (290)
T PRK13501 187 QSLGAYFDMADFCHK-NQLVERSLKQLFRQ 215 (290)
T ss_pred HhhccCCCHHHHHHH-HCcCHHHHHHHHHH
Confidence 344668999999995 89999999998875
No 429
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=36.64 E-value=54 Score=26.66 Aligned_cols=31 Identities=19% Similarity=0.206 Sum_probs=26.9
Q ss_pred CCCHHHHHHHhcCCCHHHHHHHHHHHHHHhch
Q 025357 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKHLEA 197 (254)
Q Consensus 166 p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~ 197 (254)
..+.+|||+. .|++..+|..++.+.++.|..
T Consensus 165 ~~s~~eIA~~-l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 165 GKSYQEIACD-LNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred CCCHHHHHHH-HCCCHHHHHHHHHHHHHHHHH
Confidence 4889999995 999999999998888887753
No 430
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=36.20 E-value=33 Score=32.28 Aligned_cols=34 Identities=12% Similarity=0.206 Sum_probs=26.2
Q ss_pred CCCCCCCCC-CceEEecCCCceEcCcCceeecccccc
Q 025357 4 SYCADCKRL-TEVVFDHSAGDTICSECGLVLEAYSVD 39 (254)
Q Consensus 4 ~~Cp~Cg~~-~~lv~D~~~G~~vC~~CG~Vl~e~~id 39 (254)
..||.|+.. ++..+++..|..-|..||. ..++|+
T Consensus 35 ~~CPfh~ek~pSf~v~~~k~~~~Cf~Cg~--~Gd~i~ 69 (415)
T TIGR01391 35 GLCPFHHEKTPSFSVSPEKQFYHCFGCGA--GGDAIK 69 (415)
T ss_pred eeCCCCCCCCCeEEEEcCCCcEEECCCCC--CCCHHH
Confidence 359999864 4688889999999999996 335554
No 431
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=36.16 E-value=92 Score=18.25 Aligned_cols=46 Identities=13% Similarity=0.096 Sum_probs=32.4
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcc
Q 025357 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFF 226 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~ 226 (254)
..++..++++. .+++..+|.+... + . ...+.+.+.+++..|+++.+
T Consensus 9 ~~~s~~~la~~-~~i~~~~i~~~~~------~-~--------~~~~~~~~~~i~~~~~~~~~ 54 (56)
T smart00530 9 KGLTQEELAEK-LGVSRSTLSRIEN------G-K--------RKPSLETLKKLAKALGVSLD 54 (56)
T ss_pred cCCCHHHHHHH-hCCCHHHHHHHHC------C-C--------CCCCHHHHHHHHHHhCCChh
Confidence 35789999994 8999888865311 1 1 11257888999999988764
No 432
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=36.07 E-value=73 Score=21.02 Aligned_cols=50 Identities=10% Similarity=-0.031 Sum_probs=32.1
Q ss_pred cCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcch
Q 025357 163 ENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFF 227 (254)
Q Consensus 163 ~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v 227 (254)
.....|..++|+. .|++..+|.+.-+ |- .+ ..+.+.+.+++.-|+++.+.
T Consensus 11 ~~~gls~~~lA~~-~g~s~s~v~~iE~------G~-------~~-~p~~~~l~~l~~~l~~~~~~ 60 (64)
T PF13560_consen 11 ERAGLSQAQLADR-LGVSQSTVSRIER------GR-------RP-RPSPDTLQRLARALGVPPDE 60 (64)
T ss_dssp HCHTS-HHHHHHH-HTS-HHHHHHHHT------TS-------SS-S-BHHHHHHHHHHTT--HHH
T ss_pred HHcCCCHHHHHHH-HCcCHHHHHHHHC------CC-------CC-CCCHHHHHHHHHHHCcCHHH
Confidence 3445899999995 9999999877622 11 11 23468999999999997653
No 433
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=36.05 E-value=1.3e+02 Score=24.26 Aligned_cols=34 Identities=26% Similarity=0.187 Sum_probs=24.9
Q ss_pred HHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhc
Q 025357 160 CRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLE 196 (254)
Q Consensus 160 cR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~ 196 (254)
....| .+.+|||.. +|++..++...+.+-++.|.
T Consensus 134 ~~~~g--~s~~EIA~~-lgis~~tVk~~l~Rar~~Lr 167 (185)
T PRK12542 134 KVFYN--LTYQEISSV-MGITEANVRKQFERARKRVQ 167 (185)
T ss_pred HHHcC--CCHHHHHHH-HCCCHHHHHHHHHHHHHHHH
Confidence 33455 789999995 99999888876655555553
No 434
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=35.90 E-value=96 Score=29.30 Aligned_cols=32 Identities=6% Similarity=0.155 Sum_probs=27.2
Q ss_pred CCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhc
Q 025357 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLE 196 (254)
Q Consensus 164 ~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~ 196 (254)
+.+.|++||+.. +|++..+|+....+-.+.|.
T Consensus 368 ~~~~Tl~EIA~~-LGvS~erVRqie~rAl~KLR 399 (415)
T PRK07598 368 GHTYSLAEIGRA-LDLSRERVRQIESKALQKLR 399 (415)
T ss_pred CCCCCHHHHHHH-HCcCHHHHHHHHHHHHHHHh
Confidence 478999999995 99999999988777666665
No 435
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=35.89 E-value=21 Score=34.66 Aligned_cols=32 Identities=22% Similarity=0.227 Sum_probs=27.7
Q ss_pred ecCCCceEcCcCceee--cccccccCcccccccC
Q 025357 18 DHSAGDTICSECGLVL--EAYSVDETSEWRIFAN 49 (254)
Q Consensus 18 D~~~G~~vC~~CG~Vl--~e~~id~~~ewr~f~~ 49 (254)
..+.|..+|..||.-| .+.-+|.|..|.+|.+
T Consensus 413 ~~~~G~y~c~~c~~pLf~s~~Kf~sg~GWPsF~~ 446 (521)
T PRK14018 413 LFKPGIYVDVVSGEPLFSSADKYDSGCGWPSFTR 446 (521)
T ss_pred CCCCEEEEecCCCCccccCcccccCCCCCcccCc
Confidence 3579999999999987 5567899999999984
No 436
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=35.88 E-value=29 Score=33.64 Aligned_cols=32 Identities=31% Similarity=0.638 Sum_probs=20.6
Q ss_pred CCCCCCCCCce---EEecCCCc--eEcCcCceeecccc
Q 025357 5 YCADCKRLTEV---VFDHSAGD--TICSECGLVLEAYS 37 (254)
Q Consensus 5 ~Cp~Cg~~~~l---v~D~~~G~--~vC~~CG~Vl~e~~ 37 (254)
.||+||..... -+|.+.|. ..| .||.-.+-.+
T Consensus 177 ic~~cg~~~~~~~~~~d~~~~~v~y~~-~cG~~~~~~~ 213 (510)
T PRK00750 177 ICPKCGKVLTTPVISYDAEAGTVTYDC-ECGHEGEVPV 213 (510)
T ss_pred eCCCCCccceEEEEEEeCCCCEEEEEc-CCCCEEEEec
Confidence 59999985332 25777773 455 4998865444
No 437
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=35.84 E-value=20 Score=32.39 Aligned_cols=8 Identities=38% Similarity=0.953 Sum_probs=4.4
Q ss_pred ceEcCcCc
Q 025357 23 DTICSECG 30 (254)
Q Consensus 23 ~~vC~~CG 30 (254)
.+-|..||
T Consensus 226 R~~C~~Cg 233 (309)
T PRK03564 226 RVKCSNCE 233 (309)
T ss_pred CccCCCCC
Confidence 35556665
No 438
>PRK04016 DNA-directed RNA polymerase subunit N; Provisional
Probab=35.82 E-value=15 Score=25.10 Aligned_cols=12 Identities=33% Similarity=0.789 Sum_probs=10.4
Q ss_pred eEcCcCceeecc
Q 025357 24 TICSECGLVLEA 35 (254)
Q Consensus 24 ~vC~~CG~Vl~e 35 (254)
+.|..||.|+.+
T Consensus 5 vRCFTCGkvi~~ 16 (62)
T PRK04016 5 VRCFTCGKVIAE 16 (62)
T ss_pred eEecCCCCChHH
Confidence 689999999973
No 439
>PF05043 Mga: Mga helix-turn-helix domain; InterPro: IPR007737 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions []. The family also contains VirR like proteins which match only at the C terminus of the alignment.; PDB: 3SQN_A.
Probab=35.79 E-value=46 Score=23.49 Aligned_cols=33 Identities=15% Similarity=0.128 Sum_probs=26.5
Q ss_pred cCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhc
Q 025357 163 ENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLE 196 (254)
Q Consensus 163 ~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~ 196 (254)
.+.+.++.++|+. ..+|..++.+..+.+.+.|.
T Consensus 27 ~~~~~s~~~la~~-~~iS~sti~~~i~~l~~~l~ 59 (87)
T PF05043_consen 27 NNEYVSIEDLAEE-LFISRSTIYRDIKKLNKYLK 59 (87)
T ss_dssp H-SEEEHHHHHHH-HT--HHHHHHHHHHHHHHHH
T ss_pred cCCCcCHHHHHHH-HCCCHHHHHHHHHHHHHHHH
Confidence 5667999999995 89999999999999988774
No 440
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=35.72 E-value=37 Score=23.67 Aligned_cols=25 Identities=16% Similarity=0.120 Sum_probs=16.8
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHHHH
Q 025357 165 KPRTVKEFCSVANGTTKKEIGRAKEF 190 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v~~~~i~~~~k~ 190 (254)
...|+.|||+. ++|++.+|.|-.++
T Consensus 33 ~~~si~elA~~-~~vS~sti~Rf~kk 57 (77)
T PF01418_consen 33 AFMSISELAEK-AGVSPSTIVRFCKK 57 (77)
T ss_dssp CT--HHHHHHH-CTS-HHHHHHHHHH
T ss_pred HHccHHHHHHH-cCCCHHHHHHHHHH
Confidence 34889999994 89999988776544
No 441
>PF12728 HTH_17: Helix-turn-helix domain
Probab=35.48 E-value=48 Score=20.79 Aligned_cols=22 Identities=27% Similarity=0.250 Sum_probs=18.0
Q ss_pred CCHHHHHHHhcCCCHHHHHHHHH
Q 025357 167 RTVKEFCSVANGTTKKEIGRAKE 189 (254)
Q Consensus 167 ~tl~eIa~~~~~v~~~~i~~~~k 189 (254)
.|..|+|+. +|++..+|.+..+
T Consensus 2 lt~~e~a~~-l~is~~tv~~~~~ 23 (51)
T PF12728_consen 2 LTVKEAAEL-LGISRSTVYRWIR 23 (51)
T ss_pred CCHHHHHHH-HCcCHHHHHHHHH
Confidence 478899995 9999999877653
No 442
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=35.30 E-value=1.5e+02 Score=26.36 Aligned_cols=39 Identities=8% Similarity=0.091 Sum_probs=26.9
Q ss_pred CCCCHHHHHHHhcCC-CHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHH
Q 025357 165 KPRTVKEFCSVANGT-TKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFL 218 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v-~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~ 218 (254)
...++.|||.. .|. +...+.+.||+. .|+ +|.+|-.++.
T Consensus 282 ~~~~i~~IA~~-~Gf~~~s~F~r~Fk~~---~G~-----------tP~~yr~~~~ 321 (322)
T PRK09393 282 SALSIDQIAER-AGFGSEESLRHHFRRR---AAT-----------SPAAYRKRFG 321 (322)
T ss_pred CCCCHHHHHHH-hCCCCHHHHHHHHHHH---HCc-----------CHHHHHHHhh
Confidence 36889999984 777 468887777653 443 4777776653
No 443
>PRK09978 DNA-binding transcriptional regulator GadX; Provisional
Probab=35.27 E-value=1.9e+02 Score=25.63 Aligned_cols=49 Identities=6% Similarity=-0.115 Sum_probs=36.5
Q ss_pred CCCCHHHHHHHhcCC-CHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcchh
Q 025357 165 KPRTVKEFCSVANGT-TKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFFL 228 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v-~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~ 228 (254)
...++.|||.. .|. +...+.++||+. .| .+|.+|-.++...+.+..-..
T Consensus 205 t~~sI~eIA~~-~GF~s~S~Fsr~FKk~---~G-----------~TPs~yRk~~~~~~~~~~~~~ 254 (274)
T PRK09978 205 HGFSIKRVAVS-CGYHSVSYFIYVFRNY---YG-----------MTPTEYQERSAQGLPNRDSAA 254 (274)
T ss_pred CCCCHHHHHHH-hCCCCHHHHHHHHHHH---HC-----------cCHHHHHHHhhccCCchhhcc
Confidence 45889999985 776 477888887763 44 358999999999987765443
No 444
>PRK15340 transcriptional regulator InvF; Provisional
Probab=35.22 E-value=2.1e+02 Score=24.54 Aligned_cols=54 Identities=13% Similarity=0.086 Sum_probs=36.5
Q ss_pred CHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHH
Q 025357 123 VTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEF 190 (254)
Q Consensus 123 p~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~ 190 (254)
|+...+.+..+.++.+..++ ..|+- .....+.++.++|+. .|+++..+.|.|++
T Consensus 95 ~d~~~~~~~~~~r~~e~y~l------------~~~Ll-~~~~~~~sleeLA~~-~gvS~r~f~RlFk~ 148 (216)
T PRK15340 95 PSPAFNKVLALLRKSESYWL------------VGYLL-AQSTSGNTMRMLGED-YGVSYTHFRRLCSR 148 (216)
T ss_pred CChhHHHHHHHHHHHHHHHH------------HHHHH-hCccCCCCHHHHHHH-HCcCHHHHHHHHHH
Confidence 56788888888888754332 12322 233456788888884 88888888887765
No 445
>PRK09483 response regulator; Provisional
Probab=35.08 E-value=57 Score=26.36 Aligned_cols=32 Identities=13% Similarity=0.140 Sum_probs=28.4
Q ss_pred CCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchh
Q 025357 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (254)
Q Consensus 166 p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~ 198 (254)
..+.++||.. .++++.++....+.|.+.|++.
T Consensus 163 G~~~~~Ia~~-l~is~~TV~~~~~~i~~Kl~v~ 194 (217)
T PRK09483 163 GQKVNEISEQ-LNLSPKTVNSYRYRMFSKLNIS 194 (217)
T ss_pred CCCHHHHHHH-hCCCHHHHHHHHHHHHHHcCCC
Confidence 4788899995 8999999999999999999875
No 446
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=34.85 E-value=16 Score=22.54 Aligned_cols=28 Identities=29% Similarity=0.568 Sum_probs=14.1
Q ss_pred CCCCCCCCCC---ceEEecCCCceEcCcCce
Q 025357 4 SYCADCKRLT---EVVFDHSAGDTICSECGL 31 (254)
Q Consensus 4 ~~Cp~Cg~~~---~lv~D~~~G~~vC~~CG~ 31 (254)
.+|..||.+. .....-..|-.||.+|=.
T Consensus 2 ~~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~ 32 (41)
T PF06689_consen 2 KRCSFCGRPESEVGRLISGPNGAYICDECVE 32 (41)
T ss_dssp -B-TTT--BTTTSSSEEEES-SEEEEHHHHH
T ss_pred CCccCCCCCHHHHhceecCCCCcEECHHHHH
Confidence 5799999741 123333447889988743
No 447
>TIGR00281 segregation and condensation protein B. Shown to be required for chromosome segregation and condensation in B. subtilis.
Probab=34.82 E-value=1.3e+02 Score=25.07 Aligned_cols=42 Identities=24% Similarity=0.472 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHHHhcCCC-CCHHHHHHHhcCCC-HHHHHHHHHHHHHHh
Q 025357 149 EAIVAACLYIACRQENKP-RTVKEFCSVANGTT-KKEIGRAKEFIVKHL 195 (254)
Q Consensus 149 ~~iaAAclY~AcR~~~~p-~tl~eIa~~~~~v~-~~~i~~~~k~l~~~l 195 (254)
.+++=|+||.+ +.| +++++|+++ ++++ ...+......|.+..
T Consensus 3 ~~~iEAlLF~s----g~pgls~~~La~i-l~~~~~~~~~~~l~~l~~~~ 46 (186)
T TIGR00281 3 KAIIEALLFVS----GEPGVTLAELVRI-LGKEKAEKLNAIMELLEDYL 46 (186)
T ss_pred HHHHHHHHHHc----CCCCCCHHHHHHH-hCCCchHHHHHHHHHHHHHH
Confidence 45677888866 788 999999995 8888 446666666666654
No 448
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=34.74 E-value=29 Score=34.17 Aligned_cols=29 Identities=17% Similarity=0.459 Sum_probs=16.4
Q ss_pred CCCCCCCCCCCceEEecCCCceEcCcCcee
Q 025357 3 DSYCADCKRLTEVVFDHSAGDTICSECGLV 32 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~V 32 (254)
+..||.|++...++.- .+-..+|..-|.+
T Consensus 2 ~~~C~~C~g~G~i~v~-~e~c~vc~gtG~~ 30 (715)
T COG1107 2 IKKCPECGGKGKIVVG-EEECPVCHGTGFS 30 (715)
T ss_pred CccccccCCCceEeee-eeecccccccccc
Confidence 4789999885444432 2233445555555
No 449
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=34.62 E-value=99 Score=24.09 Aligned_cols=62 Identities=13% Similarity=0.035 Sum_probs=40.3
Q ss_pred CCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhc---ccccccCC---------CCHHHHHHHHHhhcCCCcch
Q 025357 164 NKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEM---GQSVEMGT---------IHASDYLVIFLLNIFKNFFF 227 (254)
Q Consensus 164 ~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~---~~~~~~~~---------~~p~~~i~r~~~~L~l~~~v 227 (254)
+-+.++.+|++ ..+++..++.+.+++|.+. |+-. ...+.+.+ ..-..++..|...|+.+.+.
T Consensus 20 ~~~~~~~ela~-~l~vs~~svs~~l~~L~~~-Gli~~~~~~~i~LT~~G~~~a~~~~~~h~~~e~~l~~l~~~~~~ 93 (142)
T PRK03902 20 KGYARVSDIAE-ALSVHPSSVTKMVQKLDKD-EYLIYEKYRGLVLTPKGKKIGKRLVYRHELLEQFLRIIGVDESK 93 (142)
T ss_pred CCCcCHHHHHH-HhCCChhHHHHHHHHHHHC-CCEEEecCceEEECHHHHHHHHHHHHHHHHHHHHHHHhCcCHHH
Confidence 34568899999 5999999999999999876 3221 11111111 12234567888888777665
No 450
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=34.59 E-value=19 Score=24.19 Aligned_cols=23 Identities=26% Similarity=0.564 Sum_probs=16.8
Q ss_pred CCCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl 33 (254)
+..|+.||. =.+ ...|..||-+.
T Consensus 5 ~rkC~~cg~-YTL-------ke~Cp~CG~~t 27 (59)
T COG2260 5 IRKCPKCGR-YTL-------KEKCPVCGGDT 27 (59)
T ss_pred hhcCcCCCc-eee-------cccCCCCCCcc
Confidence 478999997 222 15899999875
No 451
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=34.58 E-value=28 Score=22.48 Aligned_cols=31 Identities=23% Similarity=0.573 Sum_probs=22.9
Q ss_pred CCCCCCCCCCCceEEecCCCceEcCcCceeecccc
Q 025357 3 DSYCADCKRLTEVVFDHSAGDTICSECGLVLEAYS 37 (254)
Q Consensus 3 ~~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~e~~ 37 (254)
...|..|+.. +.......-|..||.|+=..-
T Consensus 2 ~~~C~~C~~~----F~~~~rk~~Cr~Cg~~~C~~C 32 (57)
T cd00065 2 ASSCMGCGKP----FTLTRRRHHCRNCGRIFCSKC 32 (57)
T ss_pred cCcCcccCcc----ccCCccccccCcCcCCcChHH
Confidence 3679999873 455677889999999985443
No 452
>PRK11179 DNA-binding transcriptional regulator AsnC; Provisional
Probab=34.52 E-value=87 Score=24.81 Aligned_cols=32 Identities=19% Similarity=0.122 Sum_probs=27.6
Q ss_pred hcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHH
Q 025357 162 QENKPRTVKEFCSVANGTTKKEIGRAKEFIVKH 194 (254)
Q Consensus 162 ~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~ 194 (254)
+.+-..+..+||+. .|+++.++.+.+++|.+.
T Consensus 19 q~d~R~s~~eiA~~-lglS~~tV~~Ri~rL~~~ 50 (153)
T PRK11179 19 MENARTPYAELAKQ-FGVSPGTIHVRVEKMKQA 50 (153)
T ss_pred HHcCCCCHHHHHHH-HCcCHHHHHHHHHHHHHC
Confidence 34467899999995 999999999999999874
No 453
>PHA02591 hypothetical protein; Provisional
Probab=34.51 E-value=64 Score=23.10 Aligned_cols=30 Identities=23% Similarity=0.268 Sum_probs=23.3
Q ss_pred HHHhcCCCCCHHHHHHHhcCCCHHHHHHHHH
Q 025357 159 ACRQENKPRTVKEFCSVANGTTKKEIGRAKE 189 (254)
Q Consensus 159 AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k 189 (254)
|-++.....|+.+||.. +|++..++++..+
T Consensus 52 A~eL~eqGlSqeqIA~~-LGVsqetVrKYL~ 81 (83)
T PHA02591 52 THELARKGFTVEKIASL-LGVSVRKVRRYLE 81 (83)
T ss_pred HHHHHHcCCCHHHHHHH-hCCCHHHHHHHHh
Confidence 44455566899999995 9999999987654
No 454
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=34.18 E-value=1.8e+02 Score=25.52 Aligned_cols=61 Identities=15% Similarity=0.067 Sum_probs=40.7
Q ss_pred CCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcchhh
Q 025357 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFFLF 229 (254)
Q Consensus 166 p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~ 229 (254)
-.+.+|||+. +|+++.+++..+.+-++.|.-... .+..++..-..++.+|...+. +.++..
T Consensus 124 g~s~~EIA~~-lg~s~~tVr~~l~RAr~~Lr~~~~-~~~~~~~~~~~~~~~f~~a~~-~gD~~~ 184 (281)
T TIGR02957 124 DYPYEEIASI-VGKSEANCRQLVSRARRHLDARRP-RFEVSREESRQLLERFVEAAQ-TGDLDG 184 (281)
T ss_pred CCCHHHHHHH-HCCCHHHHHHHHHHHHHHHHhhCC-CCCCChHHHHHHHHHHHHHHH-hCCHHH
Confidence 3679999995 999999999888877777764311 111222334567999988874 344443
No 455
>PF13518 HTH_28: Helix-turn-helix domain
Probab=34.12 E-value=99 Score=19.08 Aligned_cols=25 Identities=16% Similarity=0.166 Sum_probs=22.2
Q ss_pred CHHHHHHHhcCCCHHHHHHHHHHHHH
Q 025357 168 TVKEFCSVANGTTKKEIGRAKEFIVK 193 (254)
Q Consensus 168 tl~eIa~~~~~v~~~~i~~~~k~l~~ 193 (254)
++.++|.. +||+..+|.+.++....
T Consensus 14 s~~~~a~~-~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 14 SVREIARE-FGISRSTVYRWIKRYRE 38 (52)
T ss_pred CHHHHHHH-HCCCHhHHHHHHHHHHh
Confidence 99999995 99999999988887765
No 456
>COG4608 AppF ABC-type oligopeptide transport system, ATPase component [Amino acid transport and metabolism]
Probab=33.76 E-value=48 Score=29.36 Aligned_cols=75 Identities=17% Similarity=0.135 Sum_probs=39.3
Q ss_pred HHHHHHHHHhccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCC--CCHHHHHHHhcCCC-HHHHH
Q 025357 109 AFKSISAMSDRLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKP--RTVKEFCSVANGTT-KKEIG 185 (254)
Q Consensus 109 a~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p--~tl~eIa~~~~~v~-~~~i~ 185 (254)
..+.|.++-+..||++....+ +.+.+--|.+.....|=++- -.| +-..|..+ +..++ ...|-
T Consensus 85 ~~~~v~elL~~Vgl~~~~~~r--------yPhelSGGQrQRi~IARALa------l~P~liV~DEpvS-aLDvSiqaqIl 149 (268)
T COG4608 85 RRERVLELLEKVGLPEEFLYR--------YPHELSGGQRQRIGIARALA------LNPKLIVADEPVS-ALDVSVQAQIL 149 (268)
T ss_pred HHHHHHHHHHHhCCCHHHhhc--------CCcccCchhhhhHHHHHHHh------hCCcEEEecCchh-hcchhHHHHHH
Confidence 344566666677777644332 33444445555533333322 122 22233333 23333 35677
Q ss_pred HHHHHHHHHhchh
Q 025357 186 RAKEFIVKHLEAE 198 (254)
Q Consensus 186 ~~~k~l~~~l~~~ 198 (254)
+.++.|.+.+++.
T Consensus 150 nLL~dlq~~~~lt 162 (268)
T COG4608 150 NLLKDLQEELGLT 162 (268)
T ss_pred HHHHHHHHHhCCe
Confidence 7888888888876
No 457
>PF13551 HTH_29: Winged helix-turn helix
Probab=33.70 E-value=1.1e+02 Score=22.05 Aligned_cols=30 Identities=17% Similarity=0.169 Sum_probs=24.8
Q ss_pred hcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHH
Q 025357 162 QENKPRTVKEFCSVANGTTKKEIGRAKEFIVK 193 (254)
Q Consensus 162 ~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~ 193 (254)
.+|.+ +..+||.. +|++..++.+..+.+.+
T Consensus 9 ~~g~~-~~~~ia~~-lg~s~~Tv~r~~~~~~~ 38 (112)
T PF13551_consen 9 AEGVS-TIAEIARR-LGISRRTVYRWLKRYRE 38 (112)
T ss_pred HcCCC-cHHHHHHH-HCcCHHHHHHHHHHHHc
Confidence 35555 79999995 99999999999988764
No 458
>PRK04194 hypothetical protein; Provisional
Probab=33.69 E-value=98 Score=29.02 Aligned_cols=50 Identities=24% Similarity=0.466 Sum_probs=35.3
Q ss_pred HHHHHHHHhccCCCHHHHHHHHHHHHHHhhC-CCCCCC--------------CHHHHHHHHHHHH
Q 025357 110 FKSISAMSDRLGLVTTIKDRANEIYKKVEDQ-KPLRGR--------------NQEAIVAACLYIA 159 (254)
Q Consensus 110 ~~~I~~i~~~L~Lp~~v~e~A~~i~k~~~~~-~~~~Gr--------------~~~~iaAAclY~A 159 (254)
+..|..+.+..+||+.+.+.|..+|+.+.+. .-+.|. +..-++++|+-+-
T Consensus 75 ~~~I~~ii~~s~l~~~vk~~a~~iF~~lA~AEa~VHG~~~e~VHFHEVGa~DsIvDIvG~~~~l~ 139 (392)
T PRK04194 75 LSEIKALIENSDLPEKVKERALAVFERLAEAEAKVHGIDLEKVHFHEVGAIDAIVDIVGACLALD 139 (392)
T ss_pred HHHHHHHHHhCCCCHHHHHHHHHHHHHHHHHHHHhcCCCHHHeeEeeccchhhHHHHHHHHHHHH
Confidence 3456666678899999999999999998653 235565 4456666666543
No 459
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=33.62 E-value=45 Score=20.10 Aligned_cols=19 Identities=16% Similarity=0.274 Sum_probs=15.1
Q ss_pred CHHHHHHHhcCCCHHHHHHH
Q 025357 168 TVKEFCSVANGTTKKEIGRA 187 (254)
Q Consensus 168 tl~eIa~~~~~v~~~~i~~~ 187 (254)
|+.|+|+. +||+..+|+..
T Consensus 1 ti~e~A~~-~gvs~~tlR~y 19 (38)
T PF00376_consen 1 TIGEVAKL-LGVSPRTLRYY 19 (38)
T ss_dssp EHHHHHHH-HTS-HHHHHHH
T ss_pred CHHHHHHH-HCCCHHHHHHH
Confidence 46799995 99999999876
No 460
>PRK13501 transcriptional activator RhaR; Provisional
Probab=33.55 E-value=2.1e+02 Score=24.86 Aligned_cols=32 Identities=6% Similarity=-0.072 Sum_probs=19.4
Q ss_pred HHHHhc-CCCCCHHHHHHHhcCC-CHHHHHHHHHH
Q 025357 158 IACRQE-NKPRTVKEFCSVANGT-TKKEIGRAKEF 190 (254)
Q Consensus 158 ~AcR~~-~~p~tl~eIa~~~~~v-~~~~i~~~~k~ 190 (254)
.|+++- ....++.|||.. .|- +...+.|.||+
T Consensus 232 ~A~~LL~~t~~sI~eIA~~-~GF~~~s~F~r~FKk 265 (290)
T PRK13501 232 HAKCLLRGSEHRISDIAAR-CGFEDSNYFSAVFTR 265 (290)
T ss_pred HHHHHHHcCCCCHHHHHHH-hCCCCHHHHHHHHHH
Confidence 444443 344678888874 666 46666666654
No 461
>PRK09526 lacI lac repressor; Reviewed
Probab=33.49 E-value=37 Score=30.01 Aligned_cols=23 Identities=17% Similarity=0.349 Sum_probs=19.9
Q ss_pred CCCHHHHHHHhcCCCHHHHHHHHH
Q 025357 166 PRTVKEFCSVANGTTKKEIGRAKE 189 (254)
Q Consensus 166 p~tl~eIa~~~~~v~~~~i~~~~k 189 (254)
+.|++|||+. +|||..|+.|+++
T Consensus 5 ~~ti~dIA~~-aGVS~~TVSrvLn 27 (342)
T PRK09526 5 PVTLYDVARY-AGVSYQTVSRVLN 27 (342)
T ss_pred CCcHHHHHHH-hCCCHHHHHHHhc
Confidence 4699999995 8999999998864
No 462
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=33.40 E-value=1.1e+02 Score=27.43 Aligned_cols=63 Identities=10% Similarity=-0.019 Sum_probs=43.6
Q ss_pred CCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhccc----ccccCCCCHHHHHHHHHhhcCCCcchhhe
Q 025357 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQ----SVEMGTIHASDYLVIFLLNIFKNFFFLFV 230 (254)
Q Consensus 166 p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~----~~~~~~~~p~~~i~r~~~~L~l~~~v~~v 230 (254)
..+.+|||+. +|+++.+++..+.+-++.|.-.... ............+.+|...++ ..++..+
T Consensus 169 g~s~~EIA~~-lgis~~tVk~~l~RAr~~Lr~~~~~~~~~~~~~~~~~~~~~v~~~~~A~~-~gD~~~l 235 (339)
T PRK08241 169 GWSAAEVAEL-LDTSVAAVNSALQRARATLAERGPSAADTLREPDDPEERALLARYVAAFE-AYDVDAL 235 (339)
T ss_pred CCCHHHHHHH-hCCCHHHHHHHHHHHHHHHhhcCCCcccccCCCCChHHHHHHHHHHHHHh-cCCHHHH
Confidence 3789999995 9999999998877777777652110 011334567888999999985 4455554
No 463
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=33.33 E-value=1.2e+02 Score=18.72 Aligned_cols=35 Identities=14% Similarity=0.188 Sum_probs=24.6
Q ss_pred HHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHH
Q 025357 154 ACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKE 189 (254)
Q Consensus 154 AclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k 189 (254)
|++-+..+.-=...|+++|++. .|+++..|-+.|.
T Consensus 4 aa~~l~~~~G~~~~s~~~Ia~~-~gvs~~~~y~~f~ 38 (47)
T PF00440_consen 4 AALELFAEKGYEAVSIRDIARR-AGVSKGSFYRYFP 38 (47)
T ss_dssp HHHHHHHHHHTTTSSHHHHHHH-HTSCHHHHHHHCS
T ss_pred HHHHHHHHhCHHhCCHHHHHHH-HccchhhHHHHcC
Confidence 3344444433346999999995 8999999977654
No 464
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=33.04 E-value=59 Score=24.08 Aligned_cols=29 Identities=21% Similarity=0.178 Sum_probs=23.5
Q ss_pred hcCCCCCHHHHHHHhcCCCHHHHHHHHHHH
Q 025357 162 QENKPRTVKEFCSVANGTTKKEIGRAKEFI 191 (254)
Q Consensus 162 ~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l 191 (254)
+.+.+.|.+||+.. +||+..+|.|.-+.+
T Consensus 51 Ll~~~~tQrEIa~~-lGiS~atIsR~sn~l 79 (94)
T TIGR01321 51 LLNGNMSQREIASK-LGVSIATITRGSNNL 79 (94)
T ss_pred HHhCCCCHHHHHHH-hCCChhhhhHHHhhc
Confidence 33467999999995 999999999986554
No 465
>PRK09726 antitoxin HipB; Provisional
Probab=32.94 E-value=1.3e+02 Score=21.33 Aligned_cols=51 Identities=10% Similarity=0.038 Sum_probs=36.7
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcchhhee
Q 025357 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFFLFVL 231 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v~~v~ 231 (254)
...|..++|.. .|++..+|.+..+ +.. . .+.+-+.++++.||++.++...+
T Consensus 24 ~gltq~elA~~-~gvs~~tis~~e~------g~~------~---ps~~~l~~ia~~lgv~~~~~~~~ 74 (88)
T PRK09726 24 NGWTQSELAKK-IGIKQATISNFEN------NPD------N---TTLTTFFKILQSLELSMTLCDAK 74 (88)
T ss_pred cCCCHHHHHHH-HCcCHHHHHHHHC------CCC------C---CCHHHHHHHHHHcCCCcchhccc
Confidence 35899999995 8999998876633 211 1 13567899999999998874433
No 466
>PRK12423 LexA repressor; Provisional
Probab=32.82 E-value=1.4e+02 Score=24.95 Aligned_cols=37 Identities=14% Similarity=0.206 Sum_probs=31.0
Q ss_pred HHHHHhcCCCCCHHHHHHHhcC-CCHHHHHHHHHHHHHH
Q 025357 157 YIACRQENKPRTVKEFCSVANG-TTKKEIGRAKEFIVKH 194 (254)
Q Consensus 157 Y~AcR~~~~p~tl~eIa~~~~~-v~~~~i~~~~k~l~~~ 194 (254)
--..+..+.|.|.+||++ .+| ++..++++.++.|.+.
T Consensus 16 ~~~i~~~g~~Ps~~eia~-~~g~~s~~~v~~~l~~L~~~ 53 (202)
T PRK12423 16 RERIAQAGQPPSLAEIAQ-AFGFASRSVARKHVQALAEA 53 (202)
T ss_pred HHHHHHcCCCCCHHHHHH-HhCCCChHHHHHHHHHHHHC
Confidence 345567788999999999 599 5899999999999884
No 467
>COG5525 Bacteriophage tail assembly protein [General function prediction only]
Probab=32.78 E-value=24 Score=34.68 Aligned_cols=39 Identities=21% Similarity=0.483 Sum_probs=25.5
Q ss_pred CCCCCCCCCceEEecC------------CCceEcCcCceeecccccccCccc
Q 025357 5 YCADCKRLTEVVFDHS------------AGDTICSECGLVLEAYSVDETSEW 44 (254)
Q Consensus 5 ~Cp~Cg~~~~lv~D~~------------~G~~vC~~CG~Vl~e~~id~~~ew 44 (254)
.||+||....+.++.. .-.+.|..|+.++.+. .+..-.|
T Consensus 229 pCPHCGe~q~l~~~e~~~~~g~~~~~~~~~~~~c~h~~~~i~~~-~~~~gv~ 279 (611)
T COG5525 229 PCPHCGEEQQLKFGEKSGPRGLKDTPAEAAFIQCEHCGCVIRPK-LNGRGVC 279 (611)
T ss_pred eCCCCCchhhccccccCCCcCcccchhhhhhhhccccCceeeee-ccCccch
Confidence 5999997545555322 2346899999999873 3333344
No 468
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=32.77 E-value=1.1e+02 Score=24.61 Aligned_cols=33 Identities=9% Similarity=0.020 Sum_probs=23.1
Q ss_pred HHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHh
Q 025357 160 CRQENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHL 195 (254)
Q Consensus 160 cR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l 195 (254)
...+| .+.+|||+. +|+++.++...+.+..+.|
T Consensus 129 ~~~e~--~s~~EIA~~-lgis~~tV~~~l~ra~~~L 161 (179)
T PRK12543 129 RYLHD--YSQEEIAQL-LQIPIGTVKSRIHAALKKL 161 (179)
T ss_pred HHHcc--CCHHHHHHH-HCCCHHHHHHHHHHHHHHH
Confidence 34555 589999995 9999988775554444433
No 469
>PRK00215 LexA repressor; Validated
Probab=32.73 E-value=76 Score=26.33 Aligned_cols=33 Identities=12% Similarity=0.232 Sum_probs=29.0
Q ss_pred HhcCCCCCHHHHHHHhcCC-CHHHHHHHHHHHHHH
Q 025357 161 RQENKPRTVKEFCSVANGT-TKKEIGRAKEFIVKH 194 (254)
Q Consensus 161 R~~~~p~tl~eIa~~~~~v-~~~~i~~~~k~l~~~ 194 (254)
.+++.|.+++||++ ..|+ +..++.+.++.|.+.
T Consensus 18 ~~~~~~~s~~ela~-~~~~~~~~tv~~~l~~L~~~ 51 (205)
T PRK00215 18 EETGYPPSRREIAD-ALGLRSPSAVHEHLKALERK 51 (205)
T ss_pred HHhCCCCCHHHHHH-HhCCCChHHHHHHHHHHHHC
Confidence 45688999999999 4999 999999999999875
No 470
>PRK11032 hypothetical protein; Provisional
Probab=32.66 E-value=22 Score=28.98 Aligned_cols=14 Identities=29% Similarity=0.783 Sum_probs=12.5
Q ss_pred CCCceEcCcCceee
Q 025357 20 SAGDTICSECGLVL 33 (254)
Q Consensus 20 ~~G~~vC~~CG~Vl 33 (254)
.-|.+||.+||.-+
T Consensus 121 g~G~LvC~~Cg~~~ 134 (160)
T PRK11032 121 GLGNLVCEKCHHHL 134 (160)
T ss_pred ecceEEecCCCCEE
Confidence 57999999999987
No 471
>PRK08173 DNA topoisomerase III; Validated
Probab=32.58 E-value=26 Score=36.23 Aligned_cols=27 Identities=19% Similarity=0.541 Sum_probs=19.1
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceeec
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVLE 34 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl~ 34 (254)
..||.||+ . ++. ..+...|++|+..+.
T Consensus 625 ~~CP~Cg~-~-~~~--~~~~~~Cs~C~f~~~ 651 (862)
T PRK08173 625 TPCPNCGG-V-VKE--NYRRFACTKCDFSIS 651 (862)
T ss_pred ccCCcccc-c-ccc--cCceeEcCCCCcccc
Confidence 46999997 2 322 234499999998873
No 472
>PF14951 DUF4503: Domain of unknown function (DUF4503)
Probab=32.45 E-value=27 Score=32.14 Aligned_cols=33 Identities=18% Similarity=0.475 Sum_probs=25.8
Q ss_pred CCCCCCCCCceEEec-CCCceEcCcCceeeccccc
Q 025357 5 YCADCKRLTEVVFDH-SAGDTICSECGLVLEAYSV 38 (254)
Q Consensus 5 ~Cp~Cg~~~~lv~D~-~~G~~vC~~CG~Vl~e~~i 38 (254)
.|..||+ +++...+ .+|..-|.+|-.|+.+..+
T Consensus 276 vCd~CGn-~rLe~~pe~rg~~~C~~Cs~~V~sP~~ 309 (389)
T PF14951_consen 276 VCDRCGN-GRLEQSPEDRGAFSCGDCSRVVTSPVL 309 (389)
T ss_pred cccccCC-ccceeCccCCCceeccchhhhccCcce
Confidence 4999998 6776554 4777999999999875554
No 473
>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=32.43 E-value=35 Score=22.06 Aligned_cols=8 Identities=25% Similarity=0.874 Sum_probs=6.7
Q ss_pred CCCCCCCC
Q 025357 4 SYCADCKR 11 (254)
Q Consensus 4 ~~Cp~Cg~ 11 (254)
..||.||.
T Consensus 14 ~~Cp~CGN 21 (49)
T PF12677_consen 14 CKCPKCGN 21 (49)
T ss_pred ccCcccCC
Confidence 46999997
No 474
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=32.31 E-value=60 Score=18.82 Aligned_cols=28 Identities=21% Similarity=0.599 Sum_probs=20.0
Q ss_pred CCCCCCCCCCceEEecCCCceEcCcCceee
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSECGLVL 33 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl 33 (254)
..|..|+. -+.+=+....+-|+-|..|-
T Consensus 2 ~~C~~C~t--~L~yP~gA~~vrCs~C~~vt 29 (31)
T TIGR01053 2 VVCGGCRT--LLMYPRGASSVRCALCQTVN 29 (31)
T ss_pred cCcCCCCc--EeecCCCCCeEECCCCCeEe
Confidence 46888875 46666677778888887763
No 475
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=32.24 E-value=71 Score=26.88 Aligned_cols=33 Identities=15% Similarity=0.148 Sum_probs=27.4
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchh
Q 025357 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~ 198 (254)
...+-+|||+. ++++++|++.....|.+.|++.
T Consensus 162 ~G~snkeIA~~-L~iS~~TVk~h~~~i~~KL~v~ 194 (211)
T COG2197 162 EGLSNKEIAEE-LNLSEKTVKTHVSNILRKLGVR 194 (211)
T ss_pred CCCCHHHHHHH-HCCCHhHHHHHHHHHHHHcCCC
Confidence 45778889884 8899999988888888888876
No 476
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=32.05 E-value=59 Score=24.54 Aligned_cols=9 Identities=22% Similarity=0.755 Sum_probs=5.6
Q ss_pred CCCCCCCCC
Q 025357 4 SYCADCKRL 12 (254)
Q Consensus 4 ~~Cp~Cg~~ 12 (254)
..||.||.+
T Consensus 50 t~CP~Cg~~ 58 (115)
T COG1885 50 TSCPKCGEP 58 (115)
T ss_pred ccCCCCCCc
Confidence 457777763
No 477
>COG5134 Uncharacterized conserved protein [Function unknown]
Probab=32.03 E-value=37 Score=29.03 Aligned_cols=25 Identities=16% Similarity=0.272 Sum_probs=19.3
Q ss_pred CCCCCCCCCCceEEecCCCceEcCc
Q 025357 4 SYCADCKRLTEVVFDHSAGDTICSE 28 (254)
Q Consensus 4 ~~Cp~Cg~~~~lv~D~~~G~~vC~~ 28 (254)
..||.|+..-.+-+|+.+|+.|=..
T Consensus 80 I~C~~C~n~i~~RTDPkN~~YV~Es 104 (272)
T COG5134 80 IKCHLCSNPIDVRTDPKNTEYVVES 104 (272)
T ss_pred EEccCCCCceeeecCCCCceEEEec
Confidence 4688998766678888888887665
No 478
>PF10543 ORF6N: ORF6N domain; InterPro: IPR018873 This entry represents an N-terminal DNA-binding domain found in a wide range of proteins from bacterial and eukaryotic DNA viruses and there bacterial homologues, they include the poxvirus D6R/N1R and baculoviral Bro protein families. The KilA-N domain is considered to be homologous to the fungal DNA-binding APSES domain. Both the KilA-N and APSES domains share a common fold with the nucleic acid-binding modules of the LAGLIDADG nucleases and the amino-terminal domains of the tRNA endonuclease []. This entry represents the amino-terminal domain of the Enterobacteria phage P22 antirepressor ((P03037 from SWISSPROT) []. It is found associated with IPR018876 from INTERPRO.
Probab=31.92 E-value=64 Score=23.26 Aligned_cols=30 Identities=17% Similarity=0.158 Sum_probs=27.0
Q ss_pred CCHHHHHHHhcCCCHHHHHHHHHHHHHHhch
Q 025357 167 RTVKEFCSVANGTTKKEIGRAKEFIVKHLEA 197 (254)
Q Consensus 167 ~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~ 197 (254)
+|.++||++ .|++.++|.+.++.-.+.+..
T Consensus 13 ~t~~~lA~~-yg~~~~~i~~~~~rN~~rF~e 42 (88)
T PF10543_consen 13 MTDEDLAEL-YGVETKTINRNFKRNKDRFIE 42 (88)
T ss_pred EEHHHHHHH-hCcCHHHHHHHHHHHHHhCCC
Confidence 788999995 999999999999999888863
No 479
>PF08421 Methyltransf_13: Putative zinc binding domain; InterPro: IPR013630 This domain is found at the N terminus of bacterial methyltransferases. ; PDB: 4E2X_A 3NDJ_A 3NDI_A 4E32_A 4E33_A 4E31_A 4E2Y_A 4E2W_A 4E2Z_A 4E30_A.
Probab=31.82 E-value=27 Score=23.51 Aligned_cols=17 Identities=35% Similarity=0.622 Sum_probs=9.5
Q ss_pred ceEcCcCceeecccccc
Q 025357 23 DTICSECGLVLEAYSVD 39 (254)
Q Consensus 23 ~~vC~~CG~Vl~e~~id 39 (254)
-.+|.+||+|.-+..++
T Consensus 40 l~~C~~CglvQl~~~v~ 56 (62)
T PF08421_consen 40 LYVCEDCGLVQLEEVVP 56 (62)
T ss_dssp EEEETTT--EEESS---
T ss_pred EEECCCCCchhcCCcCC
Confidence 46899999997666654
No 480
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=31.75 E-value=76 Score=24.43 Aligned_cols=30 Identities=20% Similarity=0.196 Sum_probs=24.9
Q ss_pred CCCHHHHHHHhcCCCHHHHHHHHHHHHHHhc
Q 025357 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKHLE 196 (254)
Q Consensus 166 p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~ 196 (254)
..+..|||.. +|+++.+++.......+.|.
T Consensus 129 ~~~~~eIA~~-lgis~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 129 GKSYKEIAEE-LGISVKTVEYHISKALKELR 158 (161)
T ss_pred CCCHHHHHHH-HCCCHHHHHHHHHHHHHHHH
Confidence 4689999995 99999999988877776664
No 481
>PRK13870 transcriptional regulator TraR; Provisional
Probab=31.37 E-value=67 Score=27.56 Aligned_cols=32 Identities=16% Similarity=0.270 Sum_probs=25.4
Q ss_pred CCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchh
Q 025357 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (254)
Q Consensus 166 p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~ 198 (254)
.+|-.||+.+ +||++.++...++..++.|+..
T Consensus 188 GKT~~EIa~I-LgISe~TV~~Hl~na~~KLga~ 219 (234)
T PRK13870 188 GKTMEEIADV-EGVKYNSVRVKLREAMKRFDVR 219 (234)
T ss_pred CCCHHHHHHH-HCCCHHHHHHHHHHHHHHcCCC
Confidence 4778888885 8888888888888888887754
No 482
>TIGR02384 RelB_DinJ addiction module antitoxin, RelB/DinJ family. Plasmids may be maintained stably in bacterial populations through the action of addiction modules, in which a toxin and antidote are encoded in a cassette on the plasmid. In any daughter cell that lacks the plasmid, the toxin persists and is lethal after the antidote protein is depleted. Toxin/antitoxin pairs are also found on main chromosomes, and likely represent selfish DNA. Sequences in the seed for this alignment all were found adjacent to toxin genes. The resulting model appears to describe a narrower set of proteins than Pfam model pfam04221, although many in the scope of this model are not obviously paired with toxin proteins. Several toxin/antitoxin pairs may occur in a single species.
Probab=31.19 E-value=1.5e+02 Score=21.19 Aligned_cols=45 Identities=13% Similarity=0.310 Sum_probs=32.5
Q ss_pred ccCCCHHHHHHHHHHHHHHhhCCCCCCCCHHHHHHHHHHHHHHhcCCCCCHH
Q 025357 119 RLGLVTTIKDRANEIYKKVEDQKPLRGRNQEAIVAACLYIACRQENKPRTVK 170 (254)
Q Consensus 119 ~L~Lp~~v~e~A~~i~k~~~~~~~~~Gr~~~~iaAAclY~AcR~~~~p~tl~ 170 (254)
..++++.+.+.|..+++.+ |-++...+=..+.-+.+..++|..+.
T Consensus 6 ~~Rvd~~lK~~a~~i~~~l-------Gl~~s~ai~~fl~qvv~~~~lPF~~~ 50 (83)
T TIGR02384 6 SIRIDEELKKEAYAVFEEL-------GLTPSTAIRMFLKQVIREQGLPFDLR 50 (83)
T ss_pred EEeeCHHHHHHHHHHHHHh-------CCCHHHHHHHHHHHHHHhCCCCCCcC
Confidence 3567778888888888764 56666666666777777888887664
No 483
>PRK12469 RNA polymerase factor sigma-54; Provisional
Probab=31.18 E-value=1.2e+02 Score=29.31 Aligned_cols=24 Identities=25% Similarity=0.400 Sum_probs=21.5
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHHH
Q 025357 165 KPRTVKEFCSVANGTTKKEIGRAKE 189 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v~~~~i~~~~k 189 (254)
.|.+++|||+. .|+.+.||.|+..
T Consensus 368 kPLtlkdVAe~-lglHeSTVSRa~~ 391 (481)
T PRK12469 368 KPLVLRDVAEE-LGLHESTISRATG 391 (481)
T ss_pred cCCcHHHHHHH-hCCCcchhhHHhc
Confidence 59999999995 9999999999964
No 484
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=31.14 E-value=26 Score=24.71 Aligned_cols=11 Identities=27% Similarity=1.020 Sum_probs=3.6
Q ss_pred CCCCCCCCCCC
Q 025357 1 MADSYCADCKR 11 (254)
Q Consensus 1 ~~~~~Cp~Cg~ 11 (254)
|....||.||.
T Consensus 22 ~~k~FCp~CGn 32 (73)
T PF08772_consen 22 MTKQFCPKCGN 32 (73)
T ss_dssp SS--S-SSS--
T ss_pred CCceeCcccCC
Confidence 34456777776
No 485
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=31.11 E-value=79 Score=24.14 Aligned_cols=66 Identities=8% Similarity=-0.078 Sum_probs=42.7
Q ss_pred cCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchh--cc-----cccccCCCCHHHHHHHHHhhcCCCcchhh
Q 025357 163 ENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE--MG-----QSVEMGTIHASDYLVIFLLNIFKNFFFLF 229 (254)
Q Consensus 163 ~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~--~~-----~~~~~~~~~p~~~i~r~~~~L~l~~~v~~ 229 (254)
...++|+.|+|++ ..+|+...+...+++.+.==+. .. .+.-.=..+|++.+...+.++=-..++..
T Consensus 16 ~~~~vtl~elA~~-l~cS~Rn~r~lLkkm~~~gWi~W~pg~GRG~~S~L~~l~~~~~~~~~~~~~~l~~g~~~~ 88 (115)
T PF12793_consen 16 QPVEVTLDELAEL-LFCSRRNARTLLKKMQEEGWITWQPGRGRGNRSQLTFLKSPEELLEQQAEELLEQGKYEQ 88 (115)
T ss_pred CCcceeHHHHHHH-hCCCHHHHHHHHHHHHHCCCeeeeCCCCCCCCCeeEEeeCHHHHHHHHHHHHHHcCCHHH
Confidence 3457899999995 8999999999999998742111 00 00001125778888777777644444443
No 486
>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=31.02 E-value=43 Score=22.65 Aligned_cols=42 Identities=17% Similarity=0.150 Sum_probs=25.8
Q ss_pred CHHHHHHHhcCCCHHHHH-HHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcc
Q 025357 168 TVKEFCSVANGTTKKEIG-RAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFF 226 (254)
Q Consensus 168 tl~eIa~~~~~v~~~~i~-~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~ 226 (254)
+.+|+|+. .||+..+|. ...++ ..-|.+++.+++..+|++-+
T Consensus 14 ~~~~lA~~-lgis~st~s~~~~~r----------------~~~P~~~l~~ia~~~gvsl~ 56 (66)
T PF07022_consen 14 SDKELAER-LGISKSTLSNNWKKR----------------GSIPAEWLIKIALETGVSLD 56 (66)
T ss_dssp SCHHHHCC-TT--HHHHH-HHHHS----------------SS--HHHHHHHHHHH---HH
T ss_pred CHHHHHHH-hCcCHHHhhHHHHhC----------------CCCCHHHHHHHHHHHCcCHH
Confidence 56799994 999999998 44321 12358999999999988743
No 487
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=30.96 E-value=80 Score=24.41 Aligned_cols=30 Identities=10% Similarity=0.066 Sum_probs=24.6
Q ss_pred CCCHHHHHHHhcCCCHHHHHHHHHHHHHHhc
Q 025357 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKHLE 196 (254)
Q Consensus 166 p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~ 196 (254)
..+..|||+. +|++..++.....+..+.|.
T Consensus 122 ~~s~~EIA~~-l~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 122 GKTMGEIALE-TEMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred CCCHHHHHHH-HCCCHHHHHHHHHHHHHHHh
Confidence 3789999995 99999999988777666654
No 488
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=30.85 E-value=18 Score=33.34 Aligned_cols=12 Identities=25% Similarity=0.636 Sum_probs=9.1
Q ss_pred CCCCCCCCCCCC
Q 025357 1 MADSYCADCKRL 12 (254)
Q Consensus 1 ~~~~~Cp~Cg~~ 12 (254)
|.++.|+.||.+
T Consensus 4 ~~~~~C~~CGr~ 15 (355)
T COG1499 4 ASTILCVRCGRS 15 (355)
T ss_pred CcccEeccCCCc
Confidence 345789999974
No 489
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=30.64 E-value=1.5e+02 Score=23.36 Aligned_cols=31 Identities=19% Similarity=0.263 Sum_probs=26.4
Q ss_pred CCHHHHHHHhcCCCHHHHHHHHHHHHHHhchh
Q 025357 167 RTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (254)
Q Consensus 167 ~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~ 198 (254)
.+.++|+.. .++++.+|....+.+.+.|+.+
T Consensus 153 ~~~~~Ia~~-l~~s~~tv~~~~~~l~~Kl~~~ 183 (196)
T PRK10360 153 MAVKEIAAE-LGLSPKTVHVHRANLMEKLGVS 183 (196)
T ss_pred CCHHHHHHH-hCCCHHHHHHHHHHHHHHhCCC
Confidence 688899884 8899999999889999888865
No 490
>PF14502 HTH_41: Helix-turn-helix domain
Probab=30.59 E-value=91 Score=20.11 Aligned_cols=28 Identities=21% Similarity=0.350 Sum_probs=24.1
Q ss_pred CCHHHHHHHhcCCCHHHHHHHHHHHHHHh
Q 025357 167 RTVKEFCSVANGTTKKEIGRAKEFIVKHL 195 (254)
Q Consensus 167 ~tl~eIa~~~~~v~~~~i~~~~k~l~~~l 195 (254)
.|+.|.++. ++++.-+|.++++.|.+.=
T Consensus 7 ~tI~e~~~~-~~vs~GtiQ~Alk~Le~~g 34 (48)
T PF14502_consen 7 PTISEYSEK-FGVSRGTIQNALKFLEENG 34 (48)
T ss_pred CCHHHHHHH-hCcchhHHHHHHHHHHHCC
Confidence 578899995 9999999999999987653
No 491
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=30.53 E-value=1.7e+02 Score=19.78 Aligned_cols=49 Identities=12% Similarity=0.159 Sum_probs=33.9
Q ss_pred cCCCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcch
Q 025357 163 ENKPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFF 227 (254)
Q Consensus 163 ~~~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v 227 (254)
.....|+.|+|.. .|++..+|.+..+ + . ..+ +.+.+.+++..|+++.+.
T Consensus 15 ~~~~~t~~~lA~~-~gis~~tis~~~~------g-~-------~~~-~~~~~~~l~~~l~v~~~~ 63 (78)
T TIGR02607 15 EPLGLSIRALAKA-LGVSRSTLSRIVN------G-R-------RGI-TADMALRLAKALGTSPEF 63 (78)
T ss_pred HHcCCCHHHHHHH-hCCCHHHHHHHHc------C-C-------CCC-CHHHHHHHHHHcCCCHHH
Confidence 3445789999995 8999998887532 1 1 112 346778899999887654
No 492
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=30.52 E-value=22 Score=23.54 Aligned_cols=36 Identities=25% Similarity=0.532 Sum_probs=24.4
Q ss_pred CCCCCCCCCC--CceEEecCCCceEcCc-Cceeecccccc
Q 025357 3 DSYCADCKRL--TEVVFDHSAGDTICSE-CGLVLEAYSVD 39 (254)
Q Consensus 3 ~~~Cp~Cg~~--~~lv~D~~~G~~vC~~-CG~Vl~e~~id 39 (254)
|.+|..|+.+ ..++++...| .||.. |-.-++|..+.
T Consensus 1 m~~CvVCKqpi~~a~~v~T~~G-~VH~g~C~~y~~e~~~S 39 (54)
T PF10886_consen 1 MEICVVCKQPIDDALVVETESG-PVHPGVCAQYLEELPVS 39 (54)
T ss_pred CCeeeeeCCccCcceEEEcCCC-ccCcHHHHHHHHhcccc
Confidence 4689999975 3467777777 66664 76666666543
No 493
>PRK15320 transcriptional activator SprB; Provisional
Probab=30.41 E-value=80 Score=26.99 Aligned_cols=33 Identities=12% Similarity=0.142 Sum_probs=29.9
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchh
Q 025357 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAE 198 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~ 198 (254)
...+.+|||+. ++++.++|.+...+|.+.|+..
T Consensus 178 kG~SNKEIAek-L~LS~KTVSTYKnRLLeKLgAk 210 (251)
T PRK15320 178 SGHPAIELAKK-FGLGTKTVSIYRKKVMYRLGMD 210 (251)
T ss_pred cCCCHHHHHHH-hccchhhHHHHHHHHHHHcCCC
Confidence 45789999995 8999999999999999999987
No 494
>PRK09480 slmA division inhibitor protein; Provisional
Probab=30.31 E-value=79 Score=25.34 Aligned_cols=42 Identities=14% Similarity=0.121 Sum_probs=28.9
Q ss_pred CHHHHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHH
Q 025357 147 NQEAIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKE 189 (254)
Q Consensus 147 ~~~~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k 189 (254)
+...++.|++-+.....|...|+.+|++. +||++.+|-+.|+
T Consensus 11 ~r~~Il~aa~~l~~~~~G~~~ti~~Ia~~-agvs~gt~Y~~F~ 52 (194)
T PRK09480 11 RREQILQALAQMLESPPGERITTAKLAAR-VGVSEAALYRHFP 52 (194)
T ss_pred HHHHHHHHHHHHHHhcCCCccCHHHHHHH-hCCCHhHHHHHCC
Confidence 34455555554443344577999999995 8999988887653
No 495
>PRK15418 transcriptional regulator LsrR; Provisional
Probab=30.19 E-value=1.1e+02 Score=27.65 Aligned_cols=60 Identities=10% Similarity=-0.115 Sum_probs=39.7
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCCcch
Q 025357 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKNFFF 227 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~~~v 227 (254)
...|+.|||+. +|++..++.|..++=++ .|+=.. .+..|.....++=.++.++++|..-+
T Consensus 28 ~g~tQ~eIA~~-lgiSR~~VsRlL~~Ar~-~GiV~I-~I~~~~~~~~~Le~~L~~~fgLk~~i 87 (318)
T PRK15418 28 DGLTQSEIGER-LGLTRLKVSRLLEKGRQ-SGIIRV-QINSRFEGCLELENALRQHFSLQHIR 87 (318)
T ss_pred cCCCHHHHHHH-hCCCHHHHHHHHHHHHH-cCcEEE-EEeCCCccHHHHHHHHHHHhCCCEEE
Confidence 45899999995 99999999998777554 222110 01124445566777788888876543
No 496
>PF07900 DUF1670: Protein of unknown function (DUF1670); InterPro: IPR012872 The hypothetical eukaryotic proteins found in this family are of unknown function.
Probab=30.15 E-value=98 Score=26.59 Aligned_cols=32 Identities=13% Similarity=0.101 Sum_probs=26.7
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhch
Q 025357 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEA 197 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~ 197 (254)
.-.|..|++.+ +++|..+|++-++.+.+.-|+
T Consensus 104 glLT~~Dla~L-L~~S~~TI~~~i~~yq~e~g~ 135 (220)
T PF07900_consen 104 GLLTQEDLAML-LGISPRTISKDIKEYQKEHGV 135 (220)
T ss_pred CcccHHHHHHH-HCCCHHHHHHHHHHHHHHcCc
Confidence 34788999985 999999999999999888544
No 497
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=30.08 E-value=1.4e+02 Score=18.51 Aligned_cols=44 Identities=11% Similarity=0.015 Sum_probs=31.1
Q ss_pred CCCCHHHHHHHhcCCCHHHHHHHHHHHHHHhchhcccccccCCCCHHHHHHHHHhhcCCC
Q 025357 165 KPRTVKEFCSVANGTTKKEIGRAKEFIVKHLEAEMGQSVEMGTIHASDYLVIFLLNIFKN 224 (254)
Q Consensus 165 ~p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~~~~~~~~~~~~~p~~~i~r~~~~L~l~ 224 (254)
...|+.|+|+. .|++..+|.+..+ + . . ....+.+.+++..|+++
T Consensus 14 ~gltq~~lA~~-~gvs~~~vs~~e~------g-~------~--~~~~~~~~~i~~~lgv~ 57 (58)
T TIGR03070 14 LGLTQADLADL-AGVGLRFIRDVEN------G-K------P--TVRLDKVLRVLDALGLE 57 (58)
T ss_pred cCCCHHHHHHH-hCCCHHHHHHHHC------C-C------C--CCCHHHHHHHHHHcCCC
Confidence 45789999995 8999988877631 1 1 1 11356788999988875
No 498
>PRK09393 ftrA transcriptional activator FtrA; Provisional
Probab=29.97 E-value=1.9e+02 Score=25.76 Aligned_cols=40 Identities=13% Similarity=0.129 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHhcCCCHHHHHHHHHHH
Q 025357 150 AIVAACLYIACRQENKPRTVKEFCSVANGTTKKEIGRAKEFI 191 (254)
Q Consensus 150 ~iaAAclY~AcR~~~~p~tl~eIa~~~~~v~~~~i~~~~k~l 191 (254)
.+.-+.-|+-- .-..++++.++|+. .++++.++.+.+++.
T Consensus 219 ~~~~~~~~i~~-~~~~~~sl~~lA~~-~~~S~~~l~r~fk~~ 258 (322)
T PRK09393 219 RLGPLIDWMRA-HLAEPHTVASLAAR-AAMSPRTFLRRFEAA 258 (322)
T ss_pred HHHHHHHHHHh-ccCCCCCHHHHHHH-HCcCHHHHHHHHHHH
Confidence 34444445443 33568999999995 999999999887763
No 499
>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=29.95 E-value=35 Score=21.46 Aligned_cols=24 Identities=25% Similarity=0.636 Sum_probs=19.3
Q ss_pred CCCCCCCCCceEEecCCCceEcCcCceee
Q 025357 5 YCADCKRLTEVVFDHSAGDTICSECGLVL 33 (254)
Q Consensus 5 ~Cp~Cg~~~~lv~D~~~G~~vC~~CG~Vl 33 (254)
.|+.||. .+.....+.|..|+..+
T Consensus 1 ~C~vC~~-----~~~~~~~i~C~~C~~~~ 24 (51)
T PF00628_consen 1 YCPVCGQ-----SDDDGDMIQCDSCNRWY 24 (51)
T ss_dssp EBTTTTS-----SCTTSSEEEBSTTSCEE
T ss_pred eCcCCCC-----cCCCCCeEEcCCCChhh
Confidence 4888987 35678889999999876
No 500
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=29.93 E-value=1.2e+02 Score=24.57 Aligned_cols=31 Identities=6% Similarity=-0.041 Sum_probs=25.3
Q ss_pred CCCHHHHHHHhcCCCHHHHHHHHHHHHHHhch
Q 025357 166 PRTVKEFCSVANGTTKKEIGRAKEFIVKHLEA 197 (254)
Q Consensus 166 p~tl~eIa~~~~~v~~~~i~~~~k~l~~~l~~ 197 (254)
..+.+|||+. +|++..+++..+.+.++.|..
T Consensus 154 g~s~~eIA~~-lgis~~tv~~~l~Rar~~Lr~ 184 (193)
T PRK11923 154 GLSYEDIASV-MQCPVGTVRSRIFRAREAIDK 184 (193)
T ss_pred CCCHHHHHHH-HCCCHHHHHHHHHHHHHHHHH
Confidence 3789999995 999999999887777776653
Done!