Query psy12603
Match_columns 391
No_of_seqs 173 out of 355
Neff 5.8
Searched_HMMs 46136
Date Fri Aug 16 23:31:22 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12603.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12603hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2463|consensus 100.0 1E-113 3E-118 828.5 15.8 354 1-390 23-376 (376)
2 COG1439 Predicted nucleic acid 100.0 2E-41 4.3E-46 306.1 12.5 145 6-284 29-176 (177)
3 PF08772 NOB1_Zn_bind: Nin one 100.0 6.4E-40 1.4E-44 258.1 2.7 73 238-310 1-73 (73)
4 PRK12496 hypothetical protein; 100.0 9.3E-35 2E-39 263.1 12.9 135 3-274 19-156 (164)
5 PF15017 AF1Q: Drug resistance 98.8 2.2E-09 4.8E-14 87.5 3.6 25 173-197 62-86 (87)
6 PRK04358 hypothetical protein; 98.8 1.6E-08 3.4E-13 94.9 8.8 22 213-234 178-199 (217)
7 TIGR03875 RNA_lig_partner RNA 98.8 9.2E-09 2E-13 95.6 5.8 22 213-234 174-195 (206)
8 PF08745 UPF0278: UPF0278 fami 98.3 7.2E-07 1.6E-11 83.1 4.1 23 213-235 171-193 (205)
9 PF09723 Zn-ribbon_8: Zinc rib 96.0 0.0063 1.4E-07 43.2 2.8 32 244-275 3-40 (42)
10 PF13248 zf-ribbon_3: zinc-rib 95.4 0.0058 1.2E-07 39.0 0.5 25 246-271 2-26 (26)
11 smart00670 PINc Large family o 95.2 0.0035 7.7E-08 51.6 -1.0 69 4-73 25-98 (111)
12 smart00834 CxxC_CXXC_SSSS Puta 95.2 0.013 2.8E-07 40.5 2.0 31 244-275 3-39 (41)
13 TIGR02605 CxxC_CxxC_SSSS putat 94.7 0.026 5.7E-07 41.3 2.5 32 244-275 3-40 (52)
14 PF13240 zinc_ribbon_2: zinc-r 93.6 0.03 6.5E-07 34.8 0.9 22 248-270 1-22 (23)
15 PRK00564 hypA hydrogenase nick 93.6 0.052 1.1E-06 46.8 2.7 29 245-273 70-100 (117)
16 PRK13130 H/ACA RNA-protein com 93.5 0.041 9E-07 41.6 1.6 28 243-273 2-29 (56)
17 TIGR00100 hypA hydrogenase nic 93.4 0.058 1.2E-06 46.4 2.6 28 245-272 69-97 (115)
18 PRK03681 hypA hydrogenase nick 93.4 0.053 1.2E-06 46.6 2.3 29 244-272 68-98 (114)
19 PF12172 DUF35_N: Rubredoxin-l 93.3 0.051 1.1E-06 37.2 1.7 29 243-272 8-36 (37)
20 PF09151 DUF1936: Domain of un 93.0 0.16 3.4E-06 34.0 3.6 29 261-292 1-29 (36)
21 PRK12380 hydrogenase nickel in 92.9 0.071 1.5E-06 45.7 2.4 30 243-272 67-97 (113)
22 COG5257 GCD11 Translation init 92.8 0.12 2.6E-06 52.3 4.0 41 243-284 54-96 (415)
23 PF10571 UPF0547: Uncharacteri 92.7 0.06 1.3E-06 34.5 1.2 22 248-270 2-23 (26)
24 PRK00398 rpoP DNA-directed RNA 92.7 0.092 2E-06 37.7 2.4 28 246-273 3-33 (46)
25 COG1579 Zn-ribbon protein, pos 92.3 0.063 1.4E-06 51.9 1.4 33 228-270 189-230 (239)
26 PF04135 Nop10p: Nucleolar RNA 92.0 0.16 3.5E-06 38.0 2.9 28 243-273 2-29 (53)
27 PRK03824 hypA hydrogenase nick 91.6 0.13 2.9E-06 45.5 2.5 28 245-272 69-118 (135)
28 PF01155 HypA: Hydrogenase exp 91.4 0.12 2.7E-06 44.1 2.1 30 243-272 67-97 (113)
29 smart00659 RPOLCX RNA polymera 91.4 0.19 4.1E-06 36.2 2.7 30 246-275 2-33 (44)
30 PF14803 Nudix_N_2: Nudix N-te 90.0 0.15 3.3E-06 34.8 1.1 15 262-276 1-15 (34)
31 PF14205 Cys_rich_KTR: Cystein 89.7 0.16 3.4E-06 38.2 1.1 14 262-275 5-18 (55)
32 COG1545 Predicted nucleic-acid 89.5 0.34 7.5E-06 43.1 3.3 42 241-285 24-66 (140)
33 TIGR01023 rpmG_bact ribosomal 88.6 0.32 7E-06 36.5 2.1 31 244-274 9-51 (54)
34 COG1198 PriA Primosomal protei 88.2 0.31 6.6E-06 54.2 2.5 33 243-277 459-491 (730)
35 CHL00104 rpl33 ribosomal prote 88.1 0.35 7.5E-06 37.9 2.0 31 244-274 10-62 (66)
36 COG2331 Uncharacterized protei 87.8 0.25 5.3E-06 39.7 1.1 43 241-283 7-58 (82)
37 COG3364 Zn-ribbon containing p 87.8 0.27 5.9E-06 41.5 1.4 32 247-278 3-37 (112)
38 COG0267 RpmG Ribosomal protein 87.4 0.35 7.6E-06 35.8 1.6 31 244-274 5-47 (50)
39 PF09297 zf-NADH-PPase: NADH p 87.0 0.29 6.3E-06 32.5 0.9 12 261-272 3-14 (32)
40 PRK08351 DNA-directed RNA poly 87.0 0.33 7.2E-06 37.4 1.3 21 248-271 5-25 (61)
41 PRK07218 replication factor A; 86.5 0.89 1.9E-05 47.6 4.6 81 209-292 258-344 (423)
42 PRK14714 DNA polymerase II lar 86.5 0.5 1.1E-05 54.9 3.0 28 241-271 662-689 (1337)
43 PF02150 RNA_POL_M_15KD: RNA p 86.1 0.28 6.1E-06 33.5 0.5 11 262-272 2-12 (35)
44 COG2260 Predicted Zn-ribbon RN 85.8 0.35 7.6E-06 36.9 0.9 26 246-274 5-30 (59)
45 COG1645 Uncharacterized Zn-fin 85.7 0.63 1.4E-05 41.1 2.6 53 248-308 30-83 (131)
46 COG3091 SprT Zn-dependent meta 85.5 0.52 1.1E-05 42.6 2.0 30 243-273 114-152 (156)
47 COG1996 RPC10 DNA-directed RNA 85.3 0.74 1.6E-05 34.0 2.4 34 244-277 4-40 (49)
48 PRK06393 rpoE DNA-directed RNA 85.1 0.44 9.5E-06 37.1 1.2 22 247-271 6-27 (64)
49 COG0375 HybF Zn finger protein 84.8 0.58 1.3E-05 40.5 1.9 30 244-273 68-98 (115)
50 PRK04351 hypothetical protein; 84.8 1.3 2.7E-05 40.0 4.2 50 221-272 89-143 (149)
51 PRK14559 putative protein seri 84.7 0.41 8.9E-06 52.6 1.2 23 247-270 2-24 (645)
52 PF14319 Zn_Tnp_IS91: Transpos 84.5 0.59 1.3E-05 40.0 1.8 25 246-270 42-69 (111)
53 TIGR03844 cysteate_syn cysteat 84.4 0.61 1.3E-05 48.3 2.2 26 245-270 1-26 (398)
54 PRK00504 rpmG 50S ribosomal pr 84.2 0.72 1.6E-05 34.2 1.9 31 244-274 5-47 (50)
55 TIGR00595 priA primosomal prot 84.1 0.69 1.5E-05 49.3 2.5 31 245-277 239-269 (505)
56 PF09845 DUF2072: Zn-ribbon co 83.9 0.59 1.3E-05 41.3 1.6 27 247-273 2-31 (131)
57 COG1592 Rubrerythrin [Energy p 83.9 0.77 1.7E-05 42.2 2.4 25 246-270 134-158 (166)
58 PRK00432 30S ribosomal protein 83.4 0.51 1.1E-05 34.8 0.8 11 260-270 19-29 (50)
59 PF10263 SprT-like: SprT-like 83.3 1.6 3.5E-05 38.5 4.2 55 219-274 87-155 (157)
60 PF03604 DNA_RNApol_7kD: DNA d 83.2 1.1 2.4E-05 30.1 2.3 28 247-274 1-30 (32)
61 PF11023 DUF2614: Protein of u 83.1 0.73 1.6E-05 39.6 1.8 36 236-273 61-98 (114)
62 PRK00595 rpmG 50S ribosomal pr 82.8 0.84 1.8E-05 34.2 1.8 31 244-274 8-50 (53)
63 PRK00762 hypA hydrogenase nick 82.3 1.1 2.3E-05 39.1 2.6 29 244-273 68-104 (124)
64 PF00471 Ribosomal_L33: Riboso 81.9 0.66 1.4E-05 34.0 0.9 30 245-274 4-45 (48)
65 cd04476 RPA1_DBD_C RPA1_DBD_C: 81.6 2.1 4.6E-05 38.4 4.4 46 243-288 31-84 (166)
66 PRK00420 hypothetical protein; 81.6 0.82 1.8E-05 39.4 1.5 24 247-270 24-49 (112)
67 PRK07591 threonine synthase; V 80.9 1.1 2.3E-05 46.7 2.4 27 244-270 16-42 (421)
68 COG1933 Archaeal DNA polymeras 80.5 0.9 2E-05 43.9 1.6 28 246-274 167-195 (253)
69 PRK08402 replication factor A; 80.3 2.7 5.7E-05 43.1 5.0 59 231-290 196-263 (355)
70 PRK06260 threonine synthase; V 80.2 1.3 2.9E-05 45.5 2.8 26 245-270 2-28 (397)
71 COG2093 DNA-directed RNA polym 79.7 0.96 2.1E-05 35.0 1.2 25 247-272 5-29 (64)
72 PF14369 zf-RING_3: zinc-finge 79.7 1.5 3.2E-05 30.0 2.0 27 247-273 3-33 (35)
73 TIGR00354 polC DNA polymerase, 79.5 1.3 2.9E-05 50.2 2.7 29 245-273 1011-1040(1095)
74 TIGR00354 polC DNA polymerase, 79.5 1.5 3.3E-05 49.8 3.1 34 241-277 620-653 (1095)
75 TIGR02098 MJ0042_CXXC MJ0042 f 79.1 1.3 2.9E-05 30.1 1.7 26 246-271 2-35 (38)
76 COG1110 Reverse gyrase [DNA re 79.0 0.26 5.7E-06 56.0 -2.9 41 239-280 687-737 (1187)
77 cd00729 rubredoxin_SM Rubredox 78.5 1.9 4E-05 29.2 2.2 25 246-270 2-27 (34)
78 PF01780 Ribosomal_L37ae: Ribo 78.5 1 2.2E-05 37.4 1.0 20 260-279 34-53 (90)
79 cd00350 rubredoxin_like Rubred 77.6 1.8 3.8E-05 29.0 1.9 25 246-270 1-26 (33)
80 PRK12366 replication factor A; 77.4 3.2 7E-05 45.6 4.9 58 232-289 516-580 (637)
81 PRK06450 threonine synthase; V 77.3 1.7 3.6E-05 44.0 2.5 26 247-272 4-29 (338)
82 PF12773 DZR: Double zinc ribb 76.7 1.2 2.6E-05 32.0 1.0 21 247-268 30-50 (50)
83 PRK14715 DNA polymerase II lar 76.6 1.7 3.8E-05 50.8 2.6 29 245-274 1541-1570(1627)
84 PF02591 DUF164: Putative zinc 76.4 1.1 2.3E-05 33.5 0.6 22 248-269 24-54 (56)
85 PF12677 DUF3797: Domain of un 76.1 2.1 4.6E-05 31.5 2.0 10 261-270 13-22 (49)
86 PRK14559 putative protein seri 75.9 1.3 2.8E-05 48.8 1.3 26 248-274 29-54 (645)
87 PRK14873 primosome assembly pr 75.7 2.1 4.5E-05 47.4 2.8 31 245-278 409-439 (665)
88 smart00661 RPOL9 RNA polymeras 75.4 1.3 2.8E-05 32.0 0.8 10 262-271 1-10 (52)
89 PF14205 Cys_rich_KTR: Cystein 75.3 2.7 5.8E-05 31.7 2.4 29 247-275 5-42 (55)
90 PRK14890 putative Zn-ribbon RN 74.9 1.8 3.9E-05 33.2 1.5 30 247-276 8-40 (59)
91 PRK04023 DNA polymerase II lar 74.9 1.5 3.3E-05 50.0 1.6 22 246-270 626-647 (1121)
92 PRK04023 DNA polymerase II lar 74.9 2.1 4.5E-05 49.0 2.6 31 245-275 1036-1067(1121)
93 COG3478 Predicted nucleic-acid 74.4 1.5 3.4E-05 34.1 1.0 14 264-277 7-22 (68)
94 COG1458 Predicted DNA-binding 74.1 3.7 8E-05 38.8 3.6 26 210-235 175-200 (221)
95 PRK05580 primosome assembly pr 73.9 2.1 4.5E-05 47.4 2.3 32 245-278 407-438 (679)
96 COG3880 Modulator of heat shoc 73.7 0.7 1.5E-05 42.4 -1.1 52 217-270 47-101 (176)
97 COG1997 RPL43A Ribosomal prote 73.7 1.8 4E-05 35.6 1.4 20 260-279 34-53 (89)
98 PF05191 ADK_lid: Adenylate ki 73.6 2.9 6.3E-05 28.8 2.2 28 247-274 2-34 (36)
99 PRK14714 DNA polymerase II lar 73.5 2.3 5.1E-05 49.7 2.6 30 244-273 1251-1281(1337)
100 PF03119 DNA_ligase_ZBD: NAD-d 73.2 1.7 3.6E-05 28.3 0.8 10 263-272 1-10 (28)
101 smart00731 SprT SprT homologue 73.1 4.4 9.5E-05 35.9 3.8 35 238-272 104-144 (146)
102 PF04828 GFA: Glutathione-depe 72.9 2.5 5.5E-05 33.3 2.0 20 255-274 42-61 (92)
103 COG2888 Predicted Zn-ribbon RN 72.6 1.7 3.7E-05 33.3 0.9 31 246-276 9-42 (61)
104 PF12773 DZR: Double zinc ribb 72.4 2 4.3E-05 30.9 1.2 23 249-272 1-23 (50)
105 PF07295 DUF1451: Protein of u 72.0 2.5 5.4E-05 38.0 2.0 31 246-276 112-145 (146)
106 TIGR02827 RNR_anaer_Bdell anae 71.9 7.1 0.00015 42.6 5.7 44 219-271 510-556 (586)
107 TIGR02487 NrdD anaerobic ribon 71.6 2 4.3E-05 46.7 1.5 43 219-270 502-547 (579)
108 PF09538 FYDLN_acid: Protein o 71.0 2.3 5E-05 36.4 1.4 23 248-270 11-35 (108)
109 PTZ00255 60S ribosomal protein 70.4 3.6 7.9E-05 34.1 2.4 20 260-279 35-54 (90)
110 COG2405 Predicted nucleic acid 70.4 11 0.00025 33.9 5.7 62 4-73 26-87 (157)
111 TIGR00280 L37a ribosomal prote 70.3 3.8 8.1E-05 34.1 2.5 20 260-279 34-53 (91)
112 PRK11032 hypothetical protein; 69.8 3 6.5E-05 38.1 2.0 32 246-277 124-158 (160)
113 COG0846 SIR2 NAD-dependent pro 69.6 4.5 9.7E-05 39.5 3.3 37 230-272 112-157 (250)
114 PRK06386 replication factor A; 69.5 7 0.00015 40.2 4.8 48 243-293 233-284 (358)
115 PRK05767 rpl44e 50S ribosomal 69.3 4.4 9.6E-05 33.8 2.7 20 260-279 7-26 (92)
116 cd01675 RNR_III Class III ribo 68.9 3.2 6.9E-05 44.9 2.3 24 246-270 518-541 (555)
117 PRK00241 nudC NADH pyrophospha 68.5 6 0.00013 38.6 3.9 55 247-305 100-161 (256)
118 PHA00626 hypothetical protein 67.8 3.3 7.2E-05 31.5 1.5 17 262-278 1-17 (59)
119 PF14446 Prok-RING_1: Prokaryo 67.8 2.8 6.1E-05 31.6 1.1 29 246-274 5-34 (54)
120 PRK02935 hypothetical protein; 67.8 3.7 7.9E-05 35.1 1.9 57 216-274 41-100 (110)
121 KOG3084|consensus 67.5 2 4.4E-05 43.2 0.4 13 261-273 150-162 (345)
122 PRK08270 anaerobic ribonucleos 67.4 6.5 0.00014 43.5 4.3 53 208-270 591-648 (656)
123 PF13719 zinc_ribbon_5: zinc-r 67.2 4.2 9.2E-05 27.9 1.9 25 246-270 2-34 (37)
124 PTZ00157 60S ribosomal protein 66.9 4.3 9.2E-05 33.3 2.1 20 260-279 8-27 (84)
125 PRK03976 rpl37ae 50S ribosomal 66.7 5 0.00011 33.3 2.5 20 260-279 35-54 (90)
126 PF08646 Rep_fac-A_C: Replicat 66.7 5.9 0.00013 34.8 3.2 45 244-288 16-70 (146)
127 PRK07111 anaerobic ribonucleos 66.5 3.8 8.3E-05 45.8 2.4 42 219-270 658-702 (735)
128 COG0384 Predicted epimerase, P 66.4 7.1 0.00015 39.0 4.0 56 209-273 20-80 (291)
129 PRK03988 translation initiatio 66.3 3.7 8.1E-05 36.6 1.8 48 211-258 79-135 (138)
130 PF04216 FdhE: Protein involve 66.1 5.2 0.00011 39.5 3.0 46 246-292 197-243 (290)
131 PF08792 A2L_zn_ribbon: A2L zi 65.9 3.6 7.8E-05 27.8 1.3 24 247-270 4-30 (33)
132 PF13597 NRDD: Anaerobic ribon 65.6 2.6 5.5E-05 45.6 0.8 24 246-271 491-514 (546)
133 TIGR02300 FYDLN_acid conserved 65.4 3.6 7.8E-05 36.2 1.5 24 247-270 10-35 (129)
134 KOG2906|consensus 64.8 2.8 6.2E-05 35.3 0.7 11 262-272 2-12 (105)
135 COG1379 PHP family phosphoeste 64.8 2.3 4.9E-05 43.1 0.2 38 243-280 243-284 (403)
136 KOG1779|consensus 64.1 2.9 6.2E-05 33.9 0.6 26 246-271 34-63 (84)
137 PF03833 PolC_DP2: DNA polymer 63.7 2.3 5E-05 47.8 0.0 11 314-324 802-812 (900)
138 PRK00415 rps27e 30S ribosomal 62.7 3.7 8.1E-05 31.5 1.0 24 247-270 12-39 (59)
139 PF01623 Carla_C4: Carlavirus 62.6 3.5 7.6E-05 34.3 0.9 25 245-271 52-76 (91)
140 PF13717 zinc_ribbon_4: zinc-r 62.4 6 0.00013 27.1 1.9 25 246-270 2-34 (36)
141 PF07975 C1_4: TFIIH C1-like d 62.3 3.4 7.4E-05 30.7 0.7 22 249-270 2-30 (51)
142 TIGR00311 aIF-2beta translatio 62.0 5.1 0.00011 35.5 1.9 39 219-257 85-129 (133)
143 PF07754 DUF1610: Domain of un 61.9 4.9 0.00011 25.4 1.3 21 249-269 1-24 (24)
144 COG2888 Predicted Zn-ribbon RN 61.5 3 6.6E-05 32.0 0.3 21 246-269 38-58 (61)
145 PF04606 Ogr_Delta: Ogr/Delta- 61.4 5.5 0.00012 28.7 1.7 26 264-289 2-27 (47)
146 PF06906 DUF1272: Protein of u 60.6 4.6 0.0001 30.7 1.1 32 243-274 23-54 (57)
147 TIGR03831 YgiT_finger YgiT-typ 60.4 8.4 0.00018 26.7 2.4 34 238-271 9-42 (46)
148 TIGR00308 TRM1 tRNA(guanine-26 60.2 6.6 0.00014 40.5 2.6 27 244-270 231-261 (374)
149 PF07282 OrfB_Zn_ribbon: Putat 59.4 11 0.00023 28.8 3.1 45 220-270 8-55 (69)
150 PF06221 zf-C2HC5: Putative zi 59.2 5.4 0.00012 30.4 1.3 36 238-273 10-47 (57)
151 COG3791 Uncharacterized conser 59.1 4.6 0.0001 35.4 1.1 18 257-274 65-82 (133)
152 PRK12336 translation initiatio 58.8 5.9 0.00013 37.3 1.8 49 211-259 75-132 (201)
153 PF06676 DUF1178: Protein of u 58.1 10 0.00023 34.2 3.2 34 243-277 2-48 (148)
154 COG4031 Predicted metal-bindin 57.9 7.2 0.00016 36.7 2.2 32 247-281 1-32 (227)
155 smart00653 eIF2B_5 domain pres 57.4 6.3 0.00014 33.8 1.6 45 210-254 56-109 (110)
156 PRK07217 replication factor A; 57.4 16 0.00035 36.8 4.7 50 240-292 182-237 (311)
157 PF14367 DUF4411: Domain of un 57.4 18 0.00038 32.7 4.6 71 4-74 35-118 (162)
158 PF14690 zf-ISL3: zinc-finger 56.1 16 0.00034 25.7 3.3 13 261-273 2-14 (47)
159 PF14835 zf-RING_6: zf-RING of 55.2 4.5 9.8E-05 31.6 0.3 26 245-270 6-37 (65)
160 PRK08579 anaerobic ribonucleos 55.0 6.5 0.00014 43.2 1.6 44 218-270 545-591 (625)
161 PRK00432 30S ribosomal protein 54.2 6.6 0.00014 28.9 1.1 36 232-270 9-46 (50)
162 COG1096 Predicted RNA-binding 54.1 7.9 0.00017 36.3 1.8 32 247-278 150-182 (188)
163 PF01396 zf-C4_Topoisom: Topoi 54.0 7.6 0.00016 27.0 1.3 14 262-275 2-15 (39)
164 PRK08271 anaerobic ribonucleos 54.0 7.2 0.00016 42.9 1.7 36 226-270 554-589 (623)
165 PRK04860 hypothetical protein; 53.3 17 0.00036 33.2 3.7 29 242-271 115-153 (160)
166 COG0498 ThrC Threonine synthas 53.2 7.1 0.00015 40.8 1.5 33 243-275 2-35 (411)
167 TIGR03676 aRF1/eRF1 peptide ch 52.5 9.5 0.00021 39.7 2.3 27 244-270 318-351 (403)
168 PRK04338 N(2),N(2)-dimethylgua 52.3 9.8 0.00021 39.3 2.3 27 244-270 242-270 (382)
169 PF03833 PolC_DP2: DNA polymer 51.9 4.8 0.0001 45.4 0.0 10 247-256 656-665 (900)
170 PTZ00083 40S ribosomal protein 51.8 7.1 0.00015 32.0 1.0 24 247-270 36-63 (85)
171 PRK09521 exosome complex RNA-b 51.6 12 0.00026 34.6 2.6 29 248-276 151-181 (189)
172 PRK08329 threonine synthase; V 51.4 8.4 0.00018 39.0 1.6 26 246-272 1-26 (347)
173 PLN00209 ribosomal protein S27 51.1 7.1 0.00015 32.1 0.9 24 247-270 37-64 (86)
174 PF10122 Mu-like_Com: Mu-like 50.9 7.5 0.00016 29.0 0.9 24 246-269 4-32 (51)
175 PRK08197 threonine synthase; V 50.6 13 0.00028 38.3 2.9 29 245-274 6-35 (394)
176 COG4469 CoiA Competence protei 50.6 7.5 0.00016 39.5 1.1 14 261-274 25-38 (342)
177 PRK05654 acetyl-CoA carboxylas 50.3 7.6 0.00016 38.8 1.1 37 245-282 27-71 (292)
178 COG3357 Predicted transcriptio 49.7 8 0.00017 32.2 0.9 37 223-270 46-85 (97)
179 PRK00241 nudC NADH pyrophospha 49.7 7.4 0.00016 38.0 0.9 14 260-273 98-111 (256)
180 TIGR00155 pqiA_fam integral me 49.4 9 0.00019 39.9 1.5 26 246-271 215-240 (403)
181 PF10058 DUF2296: Predicted in 49.2 12 0.00025 28.1 1.7 27 243-269 19-52 (54)
182 TIGR00340 zpr1_rel ZPR1-relate 49.1 12 0.00025 34.3 2.1 14 264-277 1-14 (163)
183 COG1631 RPL42A Ribosomal prote 49.0 10 0.00022 31.7 1.4 18 261-278 8-25 (94)
184 smart00531 TFIIE Transcription 48.9 6.8 0.00015 34.9 0.5 59 214-272 67-134 (147)
185 PF13453 zf-TFIIB: Transcripti 48.7 19 0.00041 25.0 2.6 13 264-277 2-14 (41)
186 TIGR01384 TFS_arch transcripti 48.6 7.5 0.00016 32.3 0.7 12 262-273 1-12 (104)
187 PF01783 Ribosomal_L32p: Ribos 48.4 15 0.00032 27.6 2.2 21 247-269 27-47 (56)
188 PRK14715 DNA polymerase II lar 48.2 14 0.00029 43.9 2.8 27 241-270 669-695 (1627)
189 TIGR02820 formald_GSH S-(hydro 48.1 7.8 0.00017 36.2 0.7 20 256-275 84-103 (182)
190 PF09332 Mcm10: Mcm10 replicat 47.9 14 0.00031 37.7 2.7 40 238-278 278-320 (344)
191 CHL00174 accD acetyl-CoA carbo 47.8 8.7 0.00019 38.5 1.1 37 245-282 38-82 (296)
192 PF09855 DUF2082: Nucleic-acid 47.7 21 0.00045 27.8 2.9 18 263-280 2-19 (64)
193 PF01873 eIF-5_eIF-2B: Domain 47.6 8.3 0.00018 33.8 0.8 45 211-255 70-123 (125)
194 COG1656 Uncharacterized conser 47.4 11 0.00023 34.7 1.5 20 212-232 50-69 (165)
195 TIGR01562 FdhE formate dehydro 47.1 26 0.00056 35.3 4.3 24 246-270 210-233 (305)
196 TIGR00515 accD acetyl-CoA carb 46.9 9.2 0.0002 38.1 1.1 37 245-282 26-70 (285)
197 PRK14704 anaerobic ribonucleos 46.9 11 0.00024 41.4 1.8 34 227-270 548-581 (618)
198 COG2816 NPY1 NTP pyrophosphohy 46.9 8.4 0.00018 38.2 0.8 13 260-272 110-122 (279)
199 PF09538 FYDLN_acid: Protein o 46.9 8.7 0.00019 32.9 0.8 11 260-270 8-18 (108)
200 PF07191 zinc-ribbons_6: zinc- 46.8 9.9 0.00021 30.2 1.0 23 246-270 17-39 (70)
201 TIGR01079 rplX_bact ribosomal 46.4 28 0.00061 29.5 3.8 22 261-284 71-92 (104)
202 COG0675 Transposase and inacti 46.2 9.4 0.0002 36.9 1.1 26 46-71 51-76 (364)
203 KOG0402|consensus 46.1 6.6 0.00014 32.2 -0.0 20 260-279 35-54 (92)
204 KOG2768|consensus 45.5 11 0.00025 36.0 1.4 54 216-270 136-211 (231)
205 COG1594 RPB9 DNA-directed RNA 45.1 11 0.00023 32.5 1.0 13 262-274 3-15 (113)
206 PRK05417 glutathione-dependent 44.6 8.8 0.00019 36.1 0.5 21 256-276 88-108 (191)
207 COG1328 NrdD Oxygen-sensitive 44.2 19 0.00042 40.1 3.2 45 218-271 618-665 (700)
208 PF06524 NOA36: NOA36 protein; 44.0 9.3 0.0002 37.6 0.6 34 246-279 185-229 (314)
209 COG1743 Adenine-specific DNA m 44.0 15 0.00031 41.5 2.1 18 242-259 174-191 (875)
210 COG2126 RPL37A Ribosomal prote 43.4 10 0.00022 29.0 0.6 27 244-270 14-40 (61)
211 PRK05978 hypothetical protein; 43.3 7.8 0.00017 35.0 -0.0 28 243-270 30-61 (148)
212 PRK11823 DNA repair protein Ra 43.3 15 0.00032 38.7 2.0 30 244-274 5-35 (446)
213 PF01667 Ribosomal_S27e: Ribos 42.6 12 0.00027 28.3 0.9 25 246-270 7-35 (55)
214 PF10083 DUF2321: Uncharacteri 42.5 2.8 6E-05 38.1 -3.0 33 234-276 11-43 (158)
215 COG5533 UBP5 Ubiquitin C-termi 41.9 24 0.00051 35.9 3.1 47 262-311 285-333 (415)
216 PF01850 PIN: PIN domain; Int 41.8 79 0.0017 25.4 5.8 68 4-75 29-106 (121)
217 cd00730 rubredoxin Rubredoxin; 41.7 16 0.00034 27.1 1.4 24 247-270 2-43 (50)
218 PRK05638 threonine synthase; V 41.3 16 0.00035 38.2 1.9 24 246-270 1-24 (442)
219 COG2816 NPY1 NTP pyrophosphohy 41.0 29 0.00063 34.5 3.5 58 244-304 109-172 (279)
220 cd01121 Sms Sms (bacterial rad 41.0 12 0.00027 38.4 1.0 27 247-274 1-28 (372)
221 PRK09263 anaerobic ribonucleos 40.8 18 0.0004 40.4 2.4 45 219-271 620-669 (711)
222 PF10130 PIN_2: PIN domain; I 40.5 43 0.00094 29.5 4.2 68 4-75 27-107 (133)
223 PLN02569 threonine synthase 40.5 25 0.00054 37.5 3.2 53 213-271 20-74 (484)
224 PRK15103 paraquat-inducible me 40.5 14 0.00031 38.7 1.3 27 247-273 11-42 (419)
225 PF02146 SIR2: Sir2 family; I 40.2 32 0.0007 31.1 3.5 44 227-278 91-144 (178)
226 PF08271 TF_Zn_Ribbon: TFIIB z 40.0 14 0.0003 26.0 0.8 22 248-269 2-27 (43)
227 PRK11788 tetratricopeptide rep 40.0 17 0.00037 35.9 1.8 32 239-273 349-381 (389)
228 PF14569 zf-UDP: Zinc-binding 40.0 5.7 0.00012 32.1 -1.3 24 247-270 37-60 (80)
229 PF13887 MRF_C1: Myelin gene r 39.7 21 0.00046 24.7 1.6 18 39-56 10-27 (36)
230 PF09862 DUF2089: Protein of u 39.6 18 0.00038 31.3 1.6 15 264-278 1-16 (113)
231 TIGR00108 eRF peptide chain re 39.5 22 0.00047 37.2 2.5 28 244-271 322-356 (409)
232 TIGR00416 sms DNA repair prote 39.0 18 0.00039 38.2 1.9 29 245-274 6-35 (454)
233 PF02005 TRM: N2,N2-dimethylgu 38.5 19 0.0004 37.2 1.8 38 243-280 237-278 (377)
234 TIGR00028 Mtu_PIN_fam Mycobact 38.3 1.4E+02 0.003 24.9 7.0 83 4-87 34-133 (142)
235 PRK04011 peptide chain release 37.6 23 0.0005 37.0 2.4 27 244-270 326-359 (411)
236 PF01599 Ribosomal_S27: Riboso 37.6 11 0.00024 27.7 -0.0 32 238-269 13-46 (47)
237 COG1571 Predicted DNA-binding 37.3 23 0.0005 37.2 2.3 37 234-270 335-376 (421)
238 PRK00004 rplX 50S ribosomal pr 37.2 47 0.001 28.2 3.8 27 261-289 71-98 (105)
239 cd01407 SIR2-fam SIR2 family o 36.9 36 0.00078 32.0 3.4 41 224-270 92-142 (218)
240 PF04032 Rpr2: RNAse P Rpr2/Rp 36.5 11 0.00025 29.7 -0.1 18 255-272 40-57 (85)
241 COG0777 AccD Acetyl-CoA carbox 36.4 16 0.00035 36.3 0.9 65 246-330 28-100 (294)
242 cd01413 SIR2_Af2 SIR2_Af2: Arc 36.3 25 0.00054 33.3 2.2 33 231-269 104-144 (222)
243 COG5319 Uncharacterized protei 36.2 12 0.00025 33.1 -0.0 32 243-274 2-45 (142)
244 PF01907 Ribosomal_L37e: Ribos 36.1 17 0.00037 27.5 0.8 30 243-273 13-42 (55)
245 smart00709 Zpr1 Duplicated dom 35.9 28 0.00061 31.7 2.4 32 261-292 29-62 (160)
246 KOG0287|consensus 35.7 5.1 0.00011 40.8 -2.6 22 246-267 23-49 (442)
247 smart00440 ZnF_C2C2 C2C2 Zinc 35.7 17 0.00037 25.4 0.7 15 263-277 2-16 (40)
248 PF10601 zf-LITAF-like: LITAF- 35.6 34 0.00073 26.6 2.5 22 258-279 4-25 (73)
249 PRK03564 formate dehydrogenase 35.2 53 0.0011 33.2 4.4 24 246-270 212-235 (309)
250 COG1601 GCD7 Translation initi 35.0 18 0.0004 32.8 1.0 49 210-259 85-139 (151)
251 PF06044 DRP: Dam-replacing fa 34.8 18 0.00038 35.4 0.9 15 261-275 31-45 (254)
252 PRK14289 chaperone protein Dna 34.8 1.1E+02 0.0024 31.5 6.8 27 245-272 196-222 (386)
253 PF00301 Rubredoxin: Rubredoxi 34.1 37 0.00079 24.8 2.3 25 246-270 1-43 (47)
254 PF14447 Prok-RING_4: Prokaryo 34.0 26 0.00057 26.5 1.5 22 247-271 28-49 (55)
255 PF14206 Cys_rich_CPCC: Cystei 34.0 19 0.0004 29.2 0.8 56 261-325 1-56 (78)
256 PRK09678 DNA-binding transcrip 33.9 27 0.00058 27.8 1.7 21 262-282 2-22 (72)
257 PF13638 PIN_4: PIN domain; PD 33.7 41 0.0009 28.4 3.0 27 208-234 106-132 (133)
258 TIGR00375 conserved hypothetic 33.7 20 0.00044 37.1 1.2 50 220-270 213-267 (374)
259 TIGR00244 transcriptional regu 33.6 39 0.00086 30.5 2.9 8 263-270 2-9 (147)
260 PRK15103 paraquat-inducible me 33.5 24 0.00052 37.0 1.7 25 246-271 221-245 (419)
261 cd01410 SIRT7 SIRT7: Eukaryoti 33.5 30 0.00064 32.6 2.2 38 226-269 78-128 (206)
262 COG1241 MCM2 Predicted ATPase 33.4 55 0.0012 36.6 4.5 37 231-267 108-157 (682)
263 cd01411 SIR2H SIR2H: Uncharact 33.2 30 0.00065 32.9 2.2 40 224-269 101-144 (225)
264 COG4306 Uncharacterized protei 33.1 7.6 0.00017 34.3 -1.7 18 260-277 27-44 (160)
265 TIGR01031 rpmF_bact ribosomal 33.0 27 0.00059 26.2 1.5 19 248-268 28-46 (55)
266 PF13408 Zn_ribbon_recom: Reco 33.0 22 0.00047 25.8 1.0 14 260-273 4-17 (58)
267 PF14353 CpXC: CpXC protein 33.0 35 0.00075 29.3 2.4 44 262-310 2-45 (128)
268 TIGR00155 pqiA_fam integral me 32.9 28 0.0006 36.3 2.1 27 246-272 13-44 (403)
269 COG4640 Predicted membrane pro 32.9 19 0.0004 37.6 0.8 24 246-270 1-24 (465)
270 PF12760 Zn_Tnp_IS1595: Transp 32.8 24 0.00053 25.1 1.2 11 260-270 17-27 (46)
271 PF05991 NYN_YacP: YacP-like N 32.7 41 0.00089 30.5 2.9 29 208-236 94-122 (166)
272 KOG4718|consensus 32.7 22 0.00048 34.1 1.2 37 36-74 36-72 (235)
273 COG2995 PqiA Uncharacterized p 32.6 21 0.00045 37.2 1.0 27 247-273 221-247 (418)
274 PF03854 zf-P11: P-11 zinc fin 32.5 8.7 0.00019 28.3 -1.2 27 247-274 22-48 (50)
275 PRK10445 endonuclease VIII; Pr 32.5 40 0.00086 32.9 3.0 16 261-277 235-250 (263)
276 PRK06599 DNA topoisomerase I; 32.5 46 0.00099 37.0 3.8 11 263-273 639-649 (675)
277 cd01412 SIRT5_Af1_CobB SIRT5_A 32.4 30 0.00065 32.6 2.1 39 226-270 94-139 (224)
278 PRK00481 NAD-dependent deacety 32.4 36 0.00077 32.6 2.6 34 231-270 113-151 (242)
279 PF01927 Mut7-C: Mut7-C RNAse 31.0 23 0.0005 31.4 1.0 10 246-255 91-100 (147)
280 COG4423 Uncharacterized protei 30.9 70 0.0015 26.1 3.6 38 32-75 3-40 (81)
281 PRK00464 nrdR transcriptional 30.9 40 0.00086 30.6 2.5 7 264-270 3-9 (154)
282 COG5134 Uncharacterized conser 30.8 42 0.0009 32.3 2.7 52 234-285 30-107 (272)
283 smart00714 LITAF Possible memb 30.5 45 0.00098 25.5 2.4 19 261-279 3-21 (67)
284 cd02674 Peptidase_C19R A subfa 30.5 55 0.0012 30.0 3.5 37 259-296 102-139 (230)
285 PHA02942 putative transposase; 30.1 57 0.0012 33.7 3.8 9 248-256 327-335 (383)
286 PF06827 zf-FPG_IleRS: Zinc fi 30.1 19 0.00042 23.2 0.2 7 264-270 4-10 (30)
287 COG1867 TRM1 N2,N2-dimethylgua 30.0 33 0.00071 35.6 2.0 27 244-270 238-266 (380)
288 COG2401 ABC-type ATPase fused 29.7 48 0.0011 35.3 3.2 26 244-270 128-153 (593)
289 PRK03564 formate dehydrogenase 29.7 40 0.00086 34.1 2.5 38 260-297 186-224 (309)
290 PF14353 CpXC: CpXC protein 29.5 51 0.0011 28.3 2.8 32 261-292 38-70 (128)
291 PF14354 Lar_restr_allev: Rest 29.5 50 0.0011 24.5 2.5 15 262-276 4-18 (61)
292 PF08458 PH_2: Plant pleckstri 29.5 71 0.0015 27.6 3.6 32 262-293 4-35 (110)
293 COG1885 Uncharacterized protei 29.4 27 0.00059 29.9 1.0 14 258-271 46-59 (115)
294 COG4260 Membrane protease subu 29.3 24 0.00051 35.4 0.8 10 261-270 334-343 (345)
295 cd01408 SIRT1 SIRT1: Eukaryoti 29.2 49 0.0011 31.7 3.0 40 225-270 98-149 (235)
296 PTZ00357 methyltransferase; Pr 29.0 18 0.0004 40.4 -0.0 35 206-254 284-318 (1072)
297 PF01096 TFIIS_C: Transcriptio 28.9 25 0.00054 24.4 0.6 15 263-277 2-16 (39)
298 PF09862 DUF2089: Protein of u 28.8 25 0.00053 30.5 0.7 21 249-270 1-21 (113)
299 COG4311 SoxD Sarcosine oxidase 28.6 26 0.00056 29.4 0.8 12 259-270 1-12 (97)
300 COG2051 RPS27A Ribosomal prote 28.6 25 0.00053 27.7 0.6 24 247-270 20-47 (67)
301 TIGR03826 YvyF flagellar opero 28.6 18 0.00039 32.3 -0.2 23 248-270 5-27 (137)
302 PF14326 DUF4384: Domain of un 28.1 84 0.0018 24.9 3.7 31 278-308 25-58 (83)
303 PF15616 TerY-C: TerY-C metal 28.0 25 0.00054 31.2 0.6 9 262-270 78-86 (131)
304 TIGR01562 FdhE formate dehydro 28.0 30 0.00066 34.8 1.3 38 260-297 183-222 (305)
305 PHA02325 hypothetical protein 28.0 27 0.0006 27.3 0.8 14 259-272 1-14 (72)
306 PF11331 DUF3133: Protein of u 27.9 46 0.001 24.3 1.9 22 235-256 20-41 (46)
307 cd00296 SIR2 SIR2 superfamily 27.8 56 0.0012 30.3 3.0 52 211-270 83-143 (222)
308 COG2956 Predicted N-acetylgluc 27.7 20 0.00043 36.7 -0.0 32 235-269 345-376 (389)
309 PTZ00073 60S ribosomal protein 27.5 29 0.00064 28.8 0.9 28 243-271 14-41 (91)
310 PRK07418 acetolactate synthase 27.4 29 0.00062 37.8 1.1 24 247-271 593-616 (616)
311 PRK14892 putative transcriptio 27.2 28 0.00061 29.4 0.8 20 259-281 19-38 (99)
312 PRK04179 rpl37e 50S ribosomal 27.2 28 0.00061 27.0 0.7 25 247-271 18-43 (62)
313 PF06839 zf-GRF: GRF zinc fing 26.8 44 0.00096 23.7 1.7 19 263-282 2-20 (45)
314 PF10609 ParA: ParA/MinD ATPas 26.7 23 0.0005 28.8 0.2 14 257-270 61-74 (81)
315 PF11781 RRN7: RNA polymerase 26.7 23 0.00051 24.3 0.2 28 243-270 5-34 (36)
316 PRK14285 chaperone protein Dna 26.6 1.8E+02 0.0038 29.8 6.6 28 244-272 183-210 (365)
317 PF05876 Terminase_GpA: Phage 26.6 39 0.00084 36.7 1.9 31 242-272 196-240 (557)
318 PRK12286 rpmF 50S ribosomal pr 26.6 42 0.00092 25.4 1.6 19 259-277 25-43 (57)
319 smart00350 MCM minichromosome 26.4 48 0.001 35.4 2.6 41 231-271 16-71 (509)
320 COG4640 Predicted membrane pro 26.4 27 0.00058 36.4 0.6 16 262-277 2-18 (465)
321 PF13824 zf-Mss51: Zinc-finger 26.3 43 0.00093 25.4 1.5 23 249-271 2-24 (55)
322 TIGR00310 ZPR1_znf ZPR1 zinc f 26.3 46 0.001 31.3 2.1 10 261-270 30-39 (192)
323 PRK14873 primosome assembly pr 26.1 35 0.00076 37.9 1.5 13 244-256 381-393 (665)
324 COG2995 PqiA Uncharacterized p 25.9 40 0.00087 35.2 1.8 28 243-270 15-47 (418)
325 PRK06266 transcription initiat 25.9 39 0.00084 31.3 1.5 28 245-272 116-147 (178)
326 PRK13795 hypothetical protein; 25.8 52 0.0011 36.3 2.7 43 242-290 8-50 (636)
327 PRK00566 DNA-directed RNA poly 25.5 34 0.00073 40.4 1.3 52 242-298 55-108 (1156)
328 PRK10281 hypothetical protein; 25.5 58 0.0013 32.3 2.8 17 216-232 31-47 (299)
329 PTZ00408 NAD-dependent deacety 25.4 40 0.00086 32.6 1.6 39 225-269 101-145 (242)
330 COG3813 Uncharacterized protei 25.3 26 0.00057 28.1 0.3 29 246-274 26-54 (84)
331 PRK14293 chaperone protein Dna 25.3 1.4E+02 0.0031 30.6 5.7 25 247-272 187-211 (374)
332 COG3058 FdhE Uncharacterized p 25.3 40 0.00086 33.7 1.5 36 12-51 24-61 (308)
333 PTZ00410 NAD-dependent SIR2; P 25.2 82 0.0018 32.4 3.8 46 225-278 129-186 (349)
334 PRK14894 glycyl-tRNA synthetas 25.1 44 0.00096 36.1 1.9 37 235-272 78-115 (539)
335 PRK05452 anaerobic nitric oxid 24.8 48 0.001 35.2 2.2 35 32-66 75-110 (479)
336 PF12674 Zn_ribbon_2: Putative 24.2 34 0.00073 27.7 0.7 23 262-284 1-23 (81)
337 TIGR00373 conserved hypothetic 24.1 40 0.00087 30.5 1.3 26 245-270 108-137 (158)
338 COG0266 Nei Formamidopyrimidin 24.1 33 0.00071 34.1 0.7 20 248-267 247-271 (273)
339 PF15608 PELOTA_1: PELOTA RNA 24.1 1.2E+02 0.0025 25.8 3.9 35 19-53 46-80 (100)
340 TIGR03847 conserved hypothetic 24.0 36 0.00077 31.7 0.9 20 260-287 155-174 (177)
341 PHA02152 hypothetical protein 24.0 44 0.00095 27.4 1.3 15 182-196 22-36 (96)
342 PRK12495 hypothetical protein; 23.8 40 0.00086 32.5 1.2 24 247-270 43-67 (226)
343 TIGR00595 priA primosomal prot 23.8 35 0.00076 36.5 1.0 21 244-270 211-231 (505)
344 CHL00018 rpoC1 RNA polymerase 23.8 32 0.00068 38.2 0.6 53 242-299 64-121 (663)
345 PTZ00409 Sir2 (Silent Informat 23.7 40 0.00087 33.2 1.3 21 231-257 128-148 (271)
346 PF15135 UPF0515: Uncharacteri 23.5 37 0.00081 33.3 1.0 69 185-270 88-164 (278)
347 PRK00448 polC DNA polymerase I 23.3 40 0.00086 40.8 1.3 25 246-270 908-942 (1437)
348 PRK05333 NAD-dependent deacety 23.3 68 0.0015 31.6 2.8 20 231-256 119-138 (285)
349 KOG3896|consensus 23.1 33 0.00072 35.1 0.6 25 246-270 24-54 (449)
350 KOG3799|consensus 23.0 39 0.00085 30.3 0.9 20 247-273 82-102 (169)
351 PF06677 Auto_anti-p27: Sjogre 22.8 41 0.0009 23.8 0.9 15 259-273 15-29 (41)
352 COG1779 C4-type Zn-finger prot 22.8 55 0.0012 31.1 1.9 14 242-255 10-23 (201)
353 KOG1819|consensus 22.8 32 0.0007 36.9 0.4 31 247-277 902-933 (990)
354 cd03361 TOPRIM_TopoIA_RevGyr T 22.2 84 0.0018 28.6 3.0 26 244-270 75-100 (170)
355 PF03367 zf-ZPR1: ZPR1 zinc-fi 22.1 66 0.0014 29.3 2.3 14 263-276 3-16 (161)
356 COG2176 PolC DNA polymerase II 22.1 48 0.001 39.2 1.6 25 246-270 914-948 (1444)
357 PRK14138 NAD-dependent deacety 22.0 70 0.0015 30.9 2.5 34 231-270 110-152 (244)
358 PRK08223 hypothetical protein; 21.8 2.3E+02 0.005 28.3 6.2 76 185-270 104-199 (287)
359 PRK00164 moaA molybdenum cofac 21.8 1.7E+02 0.0037 28.9 5.4 72 219-298 214-286 (331)
360 KOG2907|consensus 21.8 39 0.00085 29.3 0.7 10 261-270 74-83 (116)
361 PRK03922 hypothetical protein; 21.7 45 0.00097 28.8 1.0 14 258-271 46-59 (113)
362 COG5432 RAD18 RING-finger-cont 21.5 27 0.00059 35.0 -0.4 11 260-270 58-68 (391)
363 PF14952 zf-tcix: Putative tre 21.5 39 0.00084 24.5 0.5 8 262-269 12-19 (44)
364 PRK00939 translation initiatio 21.4 51 0.0011 27.7 1.3 30 262-291 2-32 (99)
365 PLN02915 cellulose synthase A 21.4 40 0.00086 39.3 0.8 24 248-271 44-67 (1044)
366 PRK14291 chaperone protein Dna 21.1 2.2E+02 0.0047 29.3 6.1 26 245-272 194-219 (382)
367 smart00746 TRASH metallochaper 21.0 80 0.0017 19.1 1.9 23 264-286 1-24 (39)
368 PF11706 zf-CGNR: CGNR zinc fi 21.0 26 0.00055 25.3 -0.5 24 247-270 3-34 (44)
369 cd01409 SIRT4 SIRT4: Eukaryoti 20.8 73 0.0016 31.0 2.4 21 231-257 109-129 (260)
370 PF08996 zf-DNA_Pol: DNA Polym 20.6 51 0.0011 30.5 1.2 35 235-269 7-53 (188)
371 PRK04136 rpl40e 50S ribosomal 20.6 58 0.0013 24.0 1.2 27 246-273 14-40 (48)
372 PRK13794 hypothetical protein; 20.5 68 0.0015 34.2 2.3 32 243-278 7-38 (479)
373 PRK07956 ligA NAD-dependent DN 20.4 88 0.0019 34.8 3.2 50 222-272 361-415 (665)
374 PF10367 Vps39_2: Vacuolar sor 20.1 1E+02 0.0022 24.9 2.8 28 261-290 78-105 (109)
375 PF06054 CoiA: Competence prot 20.0 52 0.0011 33.9 1.2 18 259-276 28-45 (375)
No 1
>KOG2463|consensus
Probab=100.00 E-value=1.3e-113 Score=828.51 Aligned_cols=354 Identities=40% Similarity=0.618 Sum_probs=279.6
Q ss_pred CCCCceeechhHHHhhcCHHHHHHHhhCCCceEEecCChhhHHHHHHHHHHhCCCCCCChhhHHHHHHhhhhhhhccCcc
Q psy12603 1 DIGDNVITIPEVVNEVTSKRQIRRLVVLPYDLQIKEADPDSISFVTEFSKKTGDYPSLSSTDIKVIALTYELHKQHIGVD 80 (391)
Q Consensus 1 ~~a~~~yT~p~Vi~EIrD~~sR~~L~~Lp~~L~vreP~~esi~~V~~FAkkTGD~~sLS~~DI~ViALtyeLe~E~~G~~ 80 (391)
++|++|||||+|++||||+.||++|++|||+|++|+|+||+|++|++|||+||||+|||.+||+||||||+||.|.+|+|
T Consensus 23 n~a~~fYt~p~V~~EIrd~asRk~le~~pf~i~~rePspe~v~kV~~fak~TGDyssLS~tDi~vlALTYeLe~e~~g~~ 102 (376)
T KOG2463|consen 23 NKADSFYTTPEVVNEIRDAASRKRLEFLPFTIKLREPSPEYVRKVIKFAKLTGDYSSLSDTDIKVLALTYELEAEVVGGD 102 (376)
T ss_pred hhhhcccccHHHHHHhhCHHhhcchhhcccEEEEecCCHHHHHHHHHHHHhcCCccccccccceeeeeeeeeehhhcccc
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccccCCcccccccccCCCccchhccccccCCCCCCccCCCCCccccccccccccccccccchhhccccchhhhccCCccc
Q psy12603 81 SINTEPISRQISYINHSVLTDKEVLAGFYSPSRGCTFNVDGGYLEGLCRGFKNGILKQTDYLNLVQCESLEELEDHTPEV 160 (391)
Q Consensus 81 ~Lr~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 160 (391)
|||+.|++..+... ...++...+.. ++.+...+ ..++++.. .+ .+++++..++....
T Consensus 103 ~Lr~~p~~~~~~~~-~~~~~~~e~~s-~~~~~~~e----------~v~E~ek~-~~---------~~E~eE~~ee~~~~- 159 (376)
T KOG2463|consen 103 RLRKKPGDALDASA-EVLSNGTEKLS-NHTEEDTE----------DVPETEKK-RE---------ANEREEHVEESGVK- 159 (376)
T ss_pred cccccCcchhhccc-cccccchhhhc-cccccCCC----------CCchhhhh-hh---------hcchhhhhhhhhcc-
Confidence 99999999877541 11111111111 11110000 00000000 00 00000000000000
Q ss_pred ccccccccccCCCCCCCCCCCCCCCccCcccHHHHHhhhhcccccCCCceEEEecCcHHHHHHHHHhCCceeccCccccc
Q psy12603 161 LQKIDHDEEEHSDDSGNEDDDDGGEWITPSNLKQAQRTMDARQYEEKPLVVSCVTTDFAMQNVLKQMGLNVVALDGRLIR 240 (391)
Q Consensus 161 ~~~~~~~~~~~~~~~~~~~ddd~~~WITp~Ni~~~~~~~~~~~~~~~~~~Vac~TtDfAMQNVllqmGL~l~s~~G~~Ik 240 (391)
+....+++ ..+-++.++|+|++|||||+||.+.+...+....+ +++.|||+|+|||||||||||||+|++++||+|+
T Consensus 160 -e~~~~~ee-~~E~~d~~ed~DdDgwitp~ni~~~~~e~~al~~p-e~~~Vac~TtDfamQNVlLqm~L~l~~~~G~~Ir 236 (376)
T KOG2463|consen 160 -EGHCNDEE-IEELEDVEEDADDDGWITPSNITEAIIELGALNRP-ENQLVACLTTDFAMQNVLLQMNLNLLAMSGMKIR 236 (376)
T ss_pred -cccCCchh-hhhhhccccccccccccccchHHHHHHhhhccccc-ccceeeeecccHHHHHHHHHhcccccCccchhhh
Confidence 00000000 01112223444444599999999998888766655 7889999999999999999999999999999999
Q ss_pred eeeeEEEEccCccccccccCcccCCCCCccceeEEEEEEcCCCcEEEeeccCCccccCCcccccCCCCCCCCCCCceeeC
Q psy12603 241 ELRTFILRCYACYKTTSIMTKVFCPKCGYKTLKRVAVSVDEQGKQKIHINLKRPLTARGKKFSLPTFKGGKHANNPIVAE 320 (391)
Q Consensus 241 ~~r~wvlRC~aCf~~t~~~~k~FCP~CGn~TL~Rvsvsvd~~G~~~~hl~~n~~~n~RG~~ySlPkPkGGk~~~~~IL~E 320 (391)
++|+|||||||||++|++|+|.|||+|||+||+||+|||+++|++++||++||+||+||++||||+|||||+.+||||||
T Consensus 237 ~~r~~iLRCh~Cfsit~~m~k~FCp~CG~~TL~K~aVsv~~dG~~~~h~k~r~~~n~RG~~YSlp~PkGgk~~kN~~LrE 316 (376)
T KOG2463|consen 237 SVRSYILRCHGCFSITSEMPKDFCPSCGHKTLTKCAVSVDEDGNGQTHFKKRFQWNNRGLQYSLPKPKGGKVAKNPILRE 316 (376)
T ss_pred hhhhheeEeeeeeEecCccchhcccccCCCeeeEEEEEecCCCceeEEeecccccccCcceeecCCCCCCccccCccccc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCccccccccccccCCCCCcccccCCCCcccccccccccccccccCCCCcccccccccCCchhhhhcc
Q psy12603 321 DQPVPDQRPTRLGRTKTNALDPDYIAGMSPFAVHDINSKSAMLGIRNNGKNNEVKYWMYKNPNAVKRKAK 390 (391)
Q Consensus 321 DQ~~~~~~~~~~~~~k~~~~d~dy~~g~spf~~~d~~sk~a~lg~r~~~~~~~~~g~~r~npn~~~~~rk 390 (391)
||++||++..+-+++..++|++ | +||..+|++||+|+||+|.. ...|. |||||++||+++
T Consensus 317 DQ~~~q~~~~q~rkk~~~~~~~-y----gpf~~~d~~s~~a~~~v~~~----~~~~k-~rnpN~skr~~~ 376 (376)
T KOG2463|consen 317 DQPEPQRRYVQTRKKVKKPLNE-Y----GPFSGHDVTSRSAILGVRQH----VRIGK-RRNPNESKRKSR 376 (376)
T ss_pred cCchHHHHHHHHHHhhhccccc-c----CCcccccccccccccchhhh----hhhhc-cCCCchhccccC
Confidence 9999999888744444899987 8 49999999999999999876 35555 889999998864
No 2
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=100.00 E-value=2e-41 Score=306.12 Aligned_cols=145 Identities=34% Similarity=0.539 Sum_probs=130.3
Q ss_pred eeechhHHHhhcCHHHHHHHhhC-C-CceEEecCChhhHHHHHHHHHHhCCCCCCChhhHHHHHHhhhhhhhccCccccc
Q psy12603 6 VITIPEVVNEVTSKRQIRRLVVL-P-YDLQIKEADPDSISFVTEFSKKTGDYPSLSSTDIKVIALTYELHKQHIGVDSIN 83 (391)
Q Consensus 6 ~yT~p~Vi~EIrD~~sR~~L~~L-p-~~L~vreP~~esi~~V~~FAkkTGD~~sLS~~DI~ViALtyeLe~E~~G~~~Lr 83 (391)
.||||+|++||||..+|-.|+.+ + +.++|++|++|+|+.|.+-|++|||+..||.+||+|||||++|-.+
T Consensus 29 ~yttp~Vv~Eikd~~s~~~~e~~~~~~~~kv~~P~~e~vk~V~e~a~~tgd~~~LS~tDi~VlalAlel~~~-------- 100 (177)
T COG1439 29 LYTTPSVVEEIKDRESRSLLELLLESGKVKVAEPSTEYVKEVREAAKKTGDLGNLSPTDIEVLALALELGEE-------- 100 (177)
T ss_pred ccccHHHHHHHhchhhhHHHHHHhhhcCeeEecCCHHHHHHHHHHHHhhCcccccChhhHHHHHHHHhhccc--------
Confidence 69999999999999999888755 3 5799999999999999999999999999999999999999998321
Q ss_pred cCCcccccccccCCCccchhccccccCCCCCCccCCCCCccccccccccccccccccchhhccccchhhhccCCcccccc
Q psy12603 84 TEPISRQISYINHSVLTDKEVLAGFYSPSRGCTFNVDGGYLEGLCRGFKNGILKQTDYLNLVQCESLEELEDHTPEVLQK 163 (391)
Q Consensus 84 ~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~ 163 (391)
T Consensus 101 -------------------------------------------------------------------------------- 100 (177)
T COG1439 101 -------------------------------------------------------------------------------- 100 (177)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred cccccccCCCCCCCCCCCCCCCccCcccHHHHHhhhhcccccCCCceEEEecCcHHHHHHHHHhCCceec-cCcccccee
Q psy12603 164 IDHDEEEHSDDSGNEDDDDGGEWITPSNLKQAQRTMDARQYEEKPLVVSCVTTDFAMQNVLKQMGLNVVA-LDGRLIREL 242 (391)
Q Consensus 164 ~~~~~~~~~~~~~~~~ddd~~~WITp~Ni~~~~~~~~~~~~~~~~~~Vac~TtDfAMQNVllqmGL~l~s-~~G~~Ik~~ 242 (391)
..|+|+|+||||||||+||||+|++ ..+..|+++
T Consensus 101 ---------------------------------------------~~v~l~TdDysvQNVa~~Lgi~~~~~~~~~~I~~v 135 (177)
T COG1439 101 ---------------------------------------------VQVALATDDYSVQNVALQLGLNVRSISYKGKIKKV 135 (177)
T ss_pred ---------------------------------------------cceeEEecchHHHHHHHHhCceEEeeeccCccceE
Confidence 2378999999999999999999997 557779999
Q ss_pred eeEEEEccCccccccccCcccCCCCCccceeEEEEEEcCCCc
Q psy12603 243 RTFILRCYACYKTTSIMTKVFCPKCGYKTLKRVAVSVDEQGK 284 (391)
Q Consensus 243 r~wvlRC~aCf~~t~~~~k~FCP~CGn~TL~Rvsvsvd~~G~ 284 (391)
+.|++||||||++++ +.+.|||.||++++++...+-+..|.
T Consensus 136 ~~w~~rC~GC~~~f~-~~~~~Cp~CG~~~~~~~~~~~~~~~~ 176 (177)
T COG1439 136 RKWRLRCHGCKRIFP-EPKDFCPICGSPLKRKRVKSRSSKGE 176 (177)
T ss_pred eeeeEEEecCceecC-CCCCcCCCCCCceEEeeechhhcccC
Confidence 999999999999999 88999999999988888776555443
No 3
>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=100.00 E-value=6.4e-40 Score=258.13 Aligned_cols=73 Identities=56% Similarity=0.966 Sum_probs=25.0
Q ss_pred ccceeeeEEEEccCccccccccCcccCCCCCccceeEEEEEEcCCCcEEEeeccCCccccCCcccccCCCCCC
Q psy12603 238 LIRELRTFILRCYACYKTTSIMTKVFCPKCGYKTLKRVAVSVDEQGKQKIHINLKRPLTARGKKFSLPTFKGG 310 (391)
Q Consensus 238 ~Ik~~r~wvlRC~aCf~~t~~~~k~FCP~CGn~TL~Rvsvsvd~~G~~~~hl~~n~~~n~RG~~ySlPkPkGG 310 (391)
+|+++|+|+|||||||++|++|+|+|||+|||+||+|||||||+||++++|+++||+||+||++||||+|+||
T Consensus 1 rIk~~k~~vlrC~aCf~~t~~~~k~FCp~CGn~TL~rvsvsv~~~G~~~~~~~~~~~~n~RG~~ySlPkPkgG 73 (73)
T PF08772_consen 1 RIKRVKTWVLRCHACFKITKDMTKQFCPKCGNATLKRVSVSVDEDGKIKLHLKKNFQWNLRGTKYSLPKPKGG 73 (73)
T ss_dssp -------EEEE-SSS--EES-SS--S-SSS--S--EEEE-B--SS---B------------------------
T ss_pred CcchhheeeEEccccccCcCCCCceeCcccCCCcceEEEEEECCCCCEEEEecCCceeccCCCCccCCCCCCC
Confidence 6999999999999999999999999999999999999999999999999999999999999999999999998
No 4
>PRK12496 hypothetical protein; Provisional
Probab=100.00 E-value=9.3e-35 Score=263.14 Aligned_cols=135 Identities=32% Similarity=0.440 Sum_probs=123.6
Q ss_pred CCceeechhHHHhhcCHHHHHHHhhCC-C-ceEEecCChhhHHHHHHHHHHhCCCCCCChhhHHHHHHhhhhhhhccCcc
Q psy12603 3 GDNVITIPEVVNEVTSKRQIRRLVVLP-Y-DLQIKEADPDSISFVTEFSKKTGDYPSLSSTDIKVIALTYELHKQHIGVD 80 (391)
Q Consensus 3 a~~~yT~p~Vi~EIrD~~sR~~L~~Lp-~-~L~vreP~~esi~~V~~FAkkTGD~~sLS~~DI~ViALtyeLe~E~~G~~ 80 (391)
..++||||+|++||+|.+++.+|+.+. + .|+|++|+++++..|.+||++||||..||.+|++|||||++|..
T Consensus 19 ~~~i~tp~~V~~Ev~d~~~~~~~~~l~~~~~i~v~~p~~~~i~~v~~~a~~tgd~~~Ls~~D~~~iaLA~el~~------ 92 (164)
T PRK12496 19 DGEHYTTPSVVEEVKDKESRLILESAISAGKLKILEPSPESIEKVEEAAIKTGDLMRLSNTDIEVLALALELNG------ 92 (164)
T ss_pred CCCEEecHHHHHHHhCHHHHHHHHHhcccCCeEEECCCHHHHHHHHHHHHhcCCccccchhhHHHHHHHHHhCC------
Confidence 467999999999999999999998663 3 39999999999999999999999999999999999999999831
Q ss_pred ccccCCcccccccccCCCccchhccccccCCCCCCccCCCCCccccccccccccccccccchhhccccchhhhccCCccc
Q psy12603 81 SINTEPISRQISYINHSVLTDKEVLAGFYSPSRGCTFNVDGGYLEGLCRGFKNGILKQTDYLNLVQCESLEELEDHTPEV 160 (391)
Q Consensus 81 ~Lr~~P~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~ 160 (391)
T Consensus 93 -------------------------------------------------------------------------------- 92 (164)
T PRK12496 93 -------------------------------------------------------------------------------- 92 (164)
T ss_pred --------------------------------------------------------------------------------
Confidence
Q ss_pred ccccccccccCCCCCCCCCCCCCCCccCcccHHHHHhhhhcccccCCCceEEEecCcHHHHHHHHHhCCceeccCccccc
Q psy12603 161 LQKIDHDEEEHSDDSGNEDDDDGGEWITPSNLKQAQRTMDARQYEEKPLVVSCVTTDFAMQNVLKQMGLNVVALDGRLIR 240 (391)
Q Consensus 161 ~~~~~~~~~~~~~~~~~~~ddd~~~WITp~Ni~~~~~~~~~~~~~~~~~~Vac~TtDfAMQNVllqmGL~l~s~~G~~Ik 240 (391)
.++|+||+||||+.+|||.++++.+.+|+
T Consensus 93 ---------------------------------------------------~lvtDD~~~~~vA~~lgi~v~~~~~~~i~ 121 (164)
T PRK12496 93 ---------------------------------------------------TLYTDDYGIQNVAKKLNIKFENIKTKGIK 121 (164)
T ss_pred ---------------------------------------------------cEECcHHHHHHHHHHcCCeEeccccccch
Confidence 18999999999999999999999999999
Q ss_pred eeeeEEEEccCcccccccc-CcccCCCCCccceeE
Q psy12603 241 ELRTFILRCYACYKTTSIM-TKVFCPKCGYKTLKR 274 (391)
Q Consensus 241 ~~r~wvlRC~aCf~~t~~~-~k~FCP~CGn~TL~R 274 (391)
+++.|.+||.||++.++.+ ...|||.||+++-+|
T Consensus 122 ~~~~w~~~C~gC~~~~~~~~~~~~C~~CG~~~~r~ 156 (164)
T PRK12496 122 KVIKWRKVCKGCKKKYPEDYPDDVCEICGSPVKRK 156 (164)
T ss_pred hheeeeEECCCCCccccCCCCCCcCCCCCChhhhc
Confidence 9999999999999999764 679999999996443
No 5
>PF15017 AF1Q: Drug resistance and apoptosis regulator
Probab=98.84 E-value=2.2e-09 Score=87.46 Aligned_cols=25 Identities=60% Similarity=1.131 Sum_probs=20.8
Q ss_pred CCCCCCCCCCCCCccCcccHHHHHh
Q psy12603 173 DDSGNEDDDDGGEWITPSNLKQAQR 197 (391)
Q Consensus 173 ~~~~~~~ddd~~~WITp~Ni~~~~~ 197 (391)
+.+++++|||+||||||+||+++++
T Consensus 62 e~eee~~ddD~gGWITPsNIkqiq~ 86 (87)
T PF15017_consen 62 EEEEEEEDDDGGGWITPSNIKQIQQ 86 (87)
T ss_pred ccccccccCCCCccccchhhhhhcc
Confidence 4455678889999999999999875
No 6
>PRK04358 hypothetical protein; Provisional
Probab=98.81 E-value=1.6e-08 Score=94.92 Aligned_cols=22 Identities=23% Similarity=0.398 Sum_probs=20.7
Q ss_pred EecCcHHHHHHHHHhCCceecc
Q psy12603 213 CVTTDFAMQNVLKQMGLNVVAL 234 (391)
Q Consensus 213 c~TtDfAMQNVllqmGL~l~s~ 234 (391)
++|+||+||||+.+|||.+++.
T Consensus 178 lvTdD~giqn~A~~LGI~~~~~ 199 (217)
T PRK04358 178 VVSADEGIRKWAERLGLRFVDA 199 (217)
T ss_pred EEeCCHHHHHHHHHcCCeeecH
Confidence 8999999999999999999874
No 7
>TIGR03875 RNA_lig_partner RNA ligase partner, MJ_0950 family. This uncharacterized protein family is found almost perfectly in the same set of genomes as the Pab1020 family described by model TIGR01209. These pairs are found mostly in Archaea, but also in a few bacteria (e.g. Alkalilimnicola ehrlichei MLHE-1, Aquifex aeolicus). While the partner protein has been described as homodimeric ligase that has RNA circularization activity, the function of this protein (also called UPF0278) is unknown.
Probab=98.77 E-value=9.2e-09 Score=95.64 Aligned_cols=22 Identities=23% Similarity=0.398 Sum_probs=20.6
Q ss_pred EecCcHHHHHHHHHhCCceecc
Q psy12603 213 CVTTDFAMQNVLKQMGLNVVAL 234 (391)
Q Consensus 213 c~TtDfAMQNVllqmGL~l~s~ 234 (391)
++|+|||||||+.+|||.+++.
T Consensus 174 lvTdD~giqn~A~~Lgi~~~~~ 195 (206)
T TIGR03875 174 VVSADEGIRKWAERLGLRFVDA 195 (206)
T ss_pred EEeCcHHHHHHHHHcCCeeecH
Confidence 8999999999999999999863
No 8
>PF08745 UPF0278: UPF0278 family; InterPro: IPR022785 This entry contains proteins of the UPF0278 family and proteins containing PIN domains. Members of the UPF0278 family are uncharacterised and about 200 amino acids in length.; PDB: 2LCQ_A.
Probab=98.26 E-value=7.2e-07 Score=83.11 Aligned_cols=23 Identities=26% Similarity=0.530 Sum_probs=14.6
Q ss_pred EecCcHHHHHHHHHhCCceeccC
Q psy12603 213 CVTTDFAMQNVLKQMGLNVVALD 235 (391)
Q Consensus 213 c~TtDfAMQNVllqmGL~l~s~~ 235 (391)
++|+||+|||++.+|||.++...
T Consensus 171 lvt~D~gi~~~A~~lGi~~i~~~ 193 (205)
T PF08745_consen 171 LVTDDYGIQNWAEKLGIRFIDAR 193 (205)
T ss_dssp EE---HHHHHHHHHTT--EE---
T ss_pred EEeCCHhHHHHHHHCCCEEEecc
Confidence 89999999999999999999664
No 9
>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=95.98 E-value=0.0063 Score=43.18 Aligned_cols=32 Identities=31% Similarity=0.784 Sum_probs=25.4
Q ss_pred eEEEEccCcccccccc------CcccCCCCCccceeEE
Q psy12603 244 TFILRCYACYKTTSIM------TKVFCPKCGYKTLKRV 275 (391)
Q Consensus 244 ~wvlRC~aCf~~t~~~------~k~FCP~CGn~TL~Rv 275 (391)
.|-++|..|...+..+ ....||.||+..++||
T Consensus 3 ~Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r~ 40 (42)
T PF09723_consen 3 IYEYRCEECGHEFEVLQSISEDDPVPCPECGSTEVRRV 40 (42)
T ss_pred CEEEEeCCCCCEEEEEEEcCCCCCCcCCCCCCCceEEe
Confidence 5899999999655422 4689999999888876
No 10
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=95.35 E-value=0.0058 Score=38.99 Aligned_cols=25 Identities=32% Similarity=0.638 Sum_probs=19.3
Q ss_pred EEEccCccccccccCcccCCCCCccc
Q psy12603 246 ILRCYACYKTTSIMTKVFCPKCGYKT 271 (391)
Q Consensus 246 vlRC~aCf~~t~~~~k~FCP~CGn~T 271 (391)
...|..|.+.. +..-.|||+||.++
T Consensus 2 ~~~Cp~Cg~~~-~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 2 EMFCPNCGAEI-DPDAKFCPNCGAKL 26 (26)
T ss_pred cCCCcccCCcC-CcccccChhhCCCC
Confidence 35799999954 45579999999863
No 11
>smart00670 PINc Large family of predicted nucleotide-binding domains. From similarities to 5'-exonucleases, these domains are predicted to be RNases. PINc domains in nematode SMG-5 and yeast NMD4p are predicted to be involved in RNAi.
Probab=95.22 E-value=0.0035 Score=51.59 Aligned_cols=69 Identities=19% Similarity=0.251 Sum_probs=52.6
Q ss_pred CceeechhHHHhhcCHH---HHHHHhhCCC--ceEEecCChhhHHHHHHHHHHhCCCCCCChhhHHHHHHhhhhh
Q psy12603 4 DNVITIPEVVNEVTSKR---QIRRLVVLPY--DLQIKEADPDSISFVTEFSKKTGDYPSLSSTDIKVIALTYELH 73 (391)
Q Consensus 4 ~~~yT~p~Vi~EIrD~~---sR~~L~~Lp~--~L~vreP~~esi~~V~~FAkkTGD~~sLS~~DI~ViALtyeLe 73 (391)
.++|+++.|+.|++... ++.+|..|.. .+.+..|.... ..+..++..+|+...++.+|..+||+|+.+.
T Consensus 25 ~~~~i~~~v~~El~~~~~~~~~~~l~~l~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~D~~il~~a~~~~ 98 (111)
T smart00670 25 GEVYIPPTVLEELEYLAKLRSLKKLEELALEGKIKLKVLKEER-KLEEEILERLSLKLELLPNDALILATAKELG 98 (111)
T ss_pred CcEEECHHHHHHHHHHHHHHHHhhHHHHHHhcccccceeecCC-CeEEEecccCChhhcCCCChHHHHHHHHHCC
Confidence 57899999999999977 6666664422 45555565553 2566777888887779999999999999984
No 12
>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=95.21 E-value=0.013 Score=40.54 Aligned_cols=31 Identities=29% Similarity=0.761 Sum_probs=23.2
Q ss_pred eEEEEccCcccccccc------CcccCCCCCccceeEE
Q psy12603 244 TFILRCYACYKTTSIM------TKVFCPKCGYKTLKRV 275 (391)
Q Consensus 244 ~wvlRC~aCf~~t~~~------~k~FCP~CGn~TL~Rv 275 (391)
.|.++|..|.+.+..+ ...-||.||. .++|+
T Consensus 3 ~Y~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~-~~~r~ 39 (41)
T smart00834 3 IYEYRCEDCGHTFEVLQKISDDPLATCPECGG-DVRRL 39 (41)
T ss_pred CEEEEcCCCCCEEEEEEecCCCCCCCCCCCCC-cceec
Confidence 5899999999866422 3567999999 45654
No 13
>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=94.68 E-value=0.026 Score=41.28 Aligned_cols=32 Identities=31% Similarity=0.782 Sum_probs=24.1
Q ss_pred eEEEEccCcccccccc------CcccCCCCCccceeEE
Q psy12603 244 TFILRCYACYKTTSIM------TKVFCPKCGYKTLKRV 275 (391)
Q Consensus 244 ~wvlRC~aCf~~t~~~------~k~FCP~CGn~TL~Rv 275 (391)
.|.++|..|...+... ...-||.||...++|+
T Consensus 3 ~Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~~r~ 40 (52)
T TIGR02605 3 IYEYRCTACGHRFEVLQKMSDDPLATCPECGGEKLRRL 40 (52)
T ss_pred CEEEEeCCCCCEeEEEEecCCCCCCCCCCCCCCceeEE
Confidence 5899999999855433 2347999999766665
No 14
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=93.64 E-value=0.03 Score=34.83 Aligned_cols=22 Identities=32% Similarity=0.705 Sum_probs=17.2
Q ss_pred EccCccccccccCcccCCCCCcc
Q psy12603 248 RCYACYKTTSIMTKVFCPKCGYK 270 (391)
Q Consensus 248 RC~aCf~~t~~~~k~FCP~CGn~ 270 (391)
+|.-|.+-..+. -.|||.||.+
T Consensus 1 ~Cp~CG~~~~~~-~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIEDD-AKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCCc-CcchhhhCCc
Confidence 488888777644 5899999976
No 15
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=93.64 E-value=0.052 Score=46.85 Aligned_cols=29 Identities=24% Similarity=0.401 Sum_probs=22.1
Q ss_pred EEEEccCccccccccC-ccc-CCCCCcccee
Q psy12603 245 FILRCYACYKTTSIMT-KVF-CPKCGYKTLK 273 (391)
Q Consensus 245 wvlRC~aCf~~t~~~~-k~F-CP~CGn~TL~ 273 (391)
-..+|..|...+.... ..+ ||+||+..+.
T Consensus 70 ~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~~ 100 (117)
T PRK00564 70 VELECKDCSHVFKPNALDYGVCEKCHSKNVI 100 (117)
T ss_pred CEEEhhhCCCccccCCccCCcCcCCCCCceE
Confidence 4789999998877653 344 9999998543
No 16
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=93.53 E-value=0.041 Score=41.65 Aligned_cols=28 Identities=39% Similarity=0.666 Sum_probs=22.8
Q ss_pred eeEEEEccCccccccccCcccCCCCCcccee
Q psy12603 243 RTFILRCYACYKTTSIMTKVFCPKCGYKTLK 273 (391)
Q Consensus 243 r~wvlRC~aCf~~t~~~~k~FCP~CGn~TL~ 273 (391)
++=|..|.+|...|- +..||.||.+|..
T Consensus 2 ks~mr~C~~CgvYTL---k~~CP~CG~~t~~ 29 (56)
T PRK13130 2 KSKIRKCPKCGVYTL---KEICPVCGGKTKN 29 (56)
T ss_pred CccceECCCCCCEEc---cccCcCCCCCCCC
Confidence 344678999999886 8899999998654
No 17
>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=93.42 E-value=0.058 Score=46.42 Aligned_cols=28 Identities=29% Similarity=0.591 Sum_probs=21.4
Q ss_pred EEEEccCccccccccCccc-CCCCCccce
Q psy12603 245 FILRCYACYKTTSIMTKVF-CPKCGYKTL 272 (391)
Q Consensus 245 wvlRC~aCf~~t~~~~k~F-CP~CGn~TL 272 (391)
-..+|+.|.+.+......| ||+||+..+
T Consensus 69 ~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~~ 97 (115)
T TIGR00100 69 VECECEDCSEEVSPEIDLYRCPKCHGIML 97 (115)
T ss_pred cEEEcccCCCEEecCCcCccCcCCcCCCc
Confidence 3689999998887654333 999999854
No 18
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=93.37 E-value=0.053 Score=46.58 Aligned_cols=29 Identities=24% Similarity=0.542 Sum_probs=21.5
Q ss_pred eEEEEccCccccccccCc--ccCCCCCccce
Q psy12603 244 TFILRCYACYKTTSIMTK--VFCPKCGYKTL 272 (391)
Q Consensus 244 ~wvlRC~aCf~~t~~~~k--~FCP~CGn~TL 272 (391)
.-..+|..|...+..... ..||+||+..+
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~ 98 (114)
T PRK03681 68 EAECWCETCQQYVTLLTQRVRRCPQCHGDML 98 (114)
T ss_pred CcEEEcccCCCeeecCCccCCcCcCcCCCCc
Confidence 347899999988876532 33999998743
No 19
>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=93.28 E-value=0.051 Score=37.20 Aligned_cols=29 Identities=31% Similarity=0.687 Sum_probs=16.7
Q ss_pred eeEEEEccCccccccccCcccCCCCCccce
Q psy12603 243 RTFILRCYACYKTTSIMTKVFCPKCGYKTL 272 (391)
Q Consensus 243 r~wvlRC~aCf~~t~~~~k~FCP~CGn~TL 272 (391)
+-.+.||.+|.++.. +.+.+||+||...|
T Consensus 8 ~l~~~rC~~Cg~~~~-pPr~~Cp~C~s~~l 36 (37)
T PF12172_consen 8 RLLGQRCRDCGRVQF-PPRPVCPHCGSDEL 36 (37)
T ss_dssp -EEEEE-TTT--EEE-S--SEETTTT----
T ss_pred EEEEEEcCCCCCEec-CCCcCCCCcCcccc
Confidence 556889999999976 56799999997644
No 20
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=93.04 E-value=0.16 Score=33.99 Aligned_cols=29 Identities=31% Similarity=0.684 Sum_probs=17.9
Q ss_pred cccCCCCCccceeEEEEEEcCCCcEEEeeccC
Q psy12603 261 KVFCPKCGYKTLKRVAVSVDEQGKQKIHINLK 292 (391)
Q Consensus 261 k~FCP~CGn~TL~Rvsvsvd~~G~~~~hl~~n 292 (391)
++.||+||-..|. .| .|+.|.++++.-.|
T Consensus 1 ~hlcpkcgvgvl~--pv-y~~kgeikvfrcsn 29 (36)
T PF09151_consen 1 QHLCPKCGVGVLE--PV-YNQKGEIKVFRCSN 29 (36)
T ss_dssp --B-TTTSSSBEE--EE-E-TTS-EEEEEES-
T ss_pred CccCCccCceEEE--Ee-ecCCCcEEEEEcCC
Confidence 3689999998874 44 38899999876554
No 21
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=92.92 E-value=0.071 Score=45.74 Aligned_cols=30 Identities=23% Similarity=0.596 Sum_probs=22.1
Q ss_pred eeEEEEccCcccccccc-CcccCCCCCccce
Q psy12603 243 RTFILRCYACYKTTSIM-TKVFCPKCGYKTL 272 (391)
Q Consensus 243 r~wvlRC~aCf~~t~~~-~k~FCP~CGn~TL 272 (391)
-.-..||..|...+... ....||+||+..+
T Consensus 67 vp~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~~ 97 (113)
T PRK12380 67 KPAQAWCWDCSQVVEIHQHDAQCPHCHGERL 97 (113)
T ss_pred eCcEEEcccCCCEEecCCcCccCcCCCCCCc
Confidence 34478999999877754 3445999998743
No 22
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=92.75 E-value=0.12 Score=52.30 Aligned_cols=41 Identities=34% Similarity=0.781 Sum_probs=31.4
Q ss_pred eeEEEEccCccccccccCcccCCCCCcc--ceeEEEEEEcCCCc
Q psy12603 243 RTFILRCYACYKTTSIMTKVFCPKCGYK--TLKRVAVSVDEQGK 284 (391)
Q Consensus 243 r~wvlRC~aCf~~t~~~~k~FCP~CGn~--TL~Rvsvsvd~~G~ 284 (391)
-.=+++|..|+.-..-.+..-||.||.. .++|||. ||.-|.
T Consensus 54 d~~i~kC~~c~~~~~y~~~~~C~~cg~~~~l~R~VSf-VDaPGH 96 (415)
T COG5257 54 DAKIYKCPECYRPECYTTEPKCPNCGAETELVRRVSF-VDAPGH 96 (415)
T ss_pred cCceEeCCCCCCCcccccCCCCCCCCCCccEEEEEEE-eeCCch
Confidence 3448899999976444567889999996 6888887 576663
No 23
>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=92.71 E-value=0.06 Score=34.54 Aligned_cols=22 Identities=36% Similarity=0.946 Sum_probs=18.4
Q ss_pred EccCccccccccCcccCCCCCcc
Q psy12603 248 RCYACYKTTSIMTKVFCPKCGYK 270 (391)
Q Consensus 248 RC~aCf~~t~~~~k~FCP~CGn~ 270 (391)
.|..|+++.+.. -.+||+||..
T Consensus 2 ~CP~C~~~V~~~-~~~Cp~CG~~ 23 (26)
T PF10571_consen 2 TCPECGAEVPES-AKFCPHCGYD 23 (26)
T ss_pred cCCCCcCCchhh-cCcCCCCCCC
Confidence 699999988755 4799999975
No 24
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=92.69 E-value=0.092 Score=37.70 Aligned_cols=28 Identities=36% Similarity=0.739 Sum_probs=21.0
Q ss_pred EEEccCcccccc---ccCcccCCCCCcccee
Q psy12603 246 ILRCYACYKTTS---IMTKVFCPKCGYKTLK 273 (391)
Q Consensus 246 vlRC~aCf~~t~---~~~k~FCP~CGn~TL~ 273 (391)
.++|..|..... .+....||.||++.+.
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYRILF 33 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCeEEE
Confidence 589999987653 3346899999998553
No 25
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=92.35 E-value=0.063 Score=51.94 Aligned_cols=33 Identities=42% Similarity=0.844 Sum_probs=23.3
Q ss_pred CCceeccCccccceeeeEEEEccCcccccccc---------CcccCCCCCcc
Q psy12603 228 GLNVVALDGRLIRELRTFILRCYACYKTTSIM---------TKVFCPKCGYK 270 (391)
Q Consensus 228 GL~l~s~~G~~Ik~~r~wvlRC~aCf~~t~~~---------~k~FCP~CGn~ 270 (391)
|+-|+.+.|. +|.||+-+-+.+ .-.|||+||-=
T Consensus 189 g~gvvpl~g~----------~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgRI 230 (239)
T COG1579 189 GVGVVPLEGR----------VCGGCHMKLPSQTLSKVRKKDEIVFCPYCGRI 230 (239)
T ss_pred CceEEeecCC----------cccCCeeeecHHHHHHHhcCCCCccCCccchH
Confidence 5555566664 799999655433 57899999963
No 26
>PF04135 Nop10p: Nucleolar RNA-binding protein, Nop10p family; InterPro: IPR007264 H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs. More than 100 mammalian H/ACA RNAs form an equal number of ribonucleoproteins (RNPs) by associating with the same four core proteins: Cbf5, Gar1, Nhp2 and Nop10. The function of these H/ACA RNPs is essential for biogenesis of the ribosome, splicing of precursor mRNAs (pre-mRNAs), maintenance of telomeres and probably for additional cellular processes []. Recent crystal structures of archaeal H/ACA protein complexes show how the same four proteins accommodate >100 distinct but related H/ACA RNAs []. The complex contains a stable core composed of Cbf5 and Nop10, to which Gar1 and Nhp2 subsequently bind, the complex interacts with snoRNAs []. In eukaryotes Nop10 is a nucleolar protein that is specifically associated with H/ACA snoRNAs. It is essential for normal 18S rRNA production and rRNA pseudouridylation by the ribonucleoprotein particles containing H/ACA snoRNAs (H/ACA snoRNPs). Nop10 is probably necessary for the stability of these RNPs [].; PDB: 2RFK_B 3LWR_B 2HVY_C 3HAX_C 3MQK_B 3LWO_B 3LWV_B 3HAY_C 3HJY_B 2EY4_E ....
Probab=91.96 E-value=0.16 Score=38.04 Aligned_cols=28 Identities=39% Similarity=0.674 Sum_probs=22.1
Q ss_pred eeEEEEccCccccccccCcccCCCCCcccee
Q psy12603 243 RTFILRCYACYKTTSIMTKVFCPKCGYKTLK 273 (391)
Q Consensus 243 r~wvlRC~aCf~~t~~~~k~FCP~CGn~TL~ 273 (391)
+.++.+|.+|...|- +.-||.||..|..
T Consensus 2 ~~~~r~c~~~~~YTL---k~~cp~cG~~T~~ 29 (53)
T PF04135_consen 2 RYYIRKCPGCRVYTL---KDKCPPCGGPTES 29 (53)
T ss_dssp EEEEEECTTTCEEES---SSBBTTTSSBSEE
T ss_pred CcccccCCCCCcEeC---CCccCCCCCCCcC
Confidence 556779999997764 3579999999863
No 27
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=91.63 E-value=0.13 Score=45.45 Aligned_cols=28 Identities=32% Similarity=0.788 Sum_probs=20.4
Q ss_pred EEEEccCcccccccc---------------------Cc-ccCCCCCccce
Q psy12603 245 FILRCYACYKTTSIM---------------------TK-VFCPKCGYKTL 272 (391)
Q Consensus 245 wvlRC~aCf~~t~~~---------------------~k-~FCP~CGn~TL 272 (391)
=.++|..|..++... .. ..||.||+..+
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~ 118 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDF 118 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCc
Confidence 468999999887654 22 33999998754
No 28
>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=91.44 E-value=0.12 Score=44.14 Aligned_cols=30 Identities=23% Similarity=0.485 Sum_probs=19.4
Q ss_pred eeEEEEccCccccccccC-cccCCCCCccce
Q psy12603 243 RTFILRCYACYKTTSIMT-KVFCPKCGYKTL 272 (391)
Q Consensus 243 r~wvlRC~aCf~~t~~~~-k~FCP~CGn~TL 272 (391)
..-..||..|...+.... ..-||.||+.-+
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~~ 97 (113)
T PF01155_consen 67 VPARARCRDCGHEFEPDEFDFSCPRCGSPDV 97 (113)
T ss_dssp E--EEEETTTS-EEECHHCCHH-SSSSSS-E
T ss_pred cCCcEECCCCCCEEecCCCCCCCcCCcCCCc
Confidence 455889999999886443 455999999854
No 29
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=91.36 E-value=0.19 Score=36.16 Aligned_cols=30 Identities=33% Similarity=0.708 Sum_probs=23.7
Q ss_pred EEEccCcccccccc--CcccCCCCCccceeEE
Q psy12603 246 ILRCYACYKTTSIM--TKVFCPKCGYKTLKRV 275 (391)
Q Consensus 246 vlRC~aCf~~t~~~--~k~FCP~CGn~TL~Rv 275 (391)
+++|-.|....... ...-||.||+..|-|.
T Consensus 2 ~Y~C~~Cg~~~~~~~~~~irC~~CG~rIlyK~ 33 (44)
T smart00659 2 IYICGECGRENEIKSKDVVRCRECGYRILYKK 33 (44)
T ss_pred EEECCCCCCEeecCCCCceECCCCCceEEEEe
Confidence 58899999765533 5789999999988764
No 30
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=89.98 E-value=0.15 Score=34.75 Aligned_cols=15 Identities=40% Similarity=1.023 Sum_probs=7.0
Q ss_pred ccCCCCCccceeEEE
Q psy12603 262 VFCPKCGYKTLKRVA 276 (391)
Q Consensus 262 ~FCP~CGn~TL~Rvs 276 (391)
.|||.||.++-.++.
T Consensus 1 kfC~~CG~~l~~~ip 15 (34)
T PF14803_consen 1 KFCPQCGGPLERRIP 15 (34)
T ss_dssp -B-TTT--B-EEE--
T ss_pred CccccccChhhhhcC
Confidence 499999999777665
No 31
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=89.74 E-value=0.16 Score=38.23 Aligned_cols=14 Identities=43% Similarity=1.094 Sum_probs=9.6
Q ss_pred ccCCCCCccceeEE
Q psy12603 262 VFCPKCGYKTLKRV 275 (391)
Q Consensus 262 ~FCP~CGn~TL~Rv 275 (391)
..||.|||+|..|+
T Consensus 5 i~CP~CgnKTR~ki 18 (55)
T PF14205_consen 5 ILCPICGNKTRLKI 18 (55)
T ss_pred EECCCCCCccceee
Confidence 35777777776665
No 32
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=89.46 E-value=0.34 Score=43.07 Aligned_cols=42 Identities=31% Similarity=0.638 Sum_probs=32.1
Q ss_pred eeeeEEEEccCccccccccCcccCCCCCccc-eeEEEEEEcCCCcE
Q psy12603 241 ELRTFILRCYACYKTTSIMTKVFCPKCGYKT-LKRVAVSVDEQGKQ 285 (391)
Q Consensus 241 ~~r~wvlRC~aCf~~t~~~~k~FCP~CGn~T-L~Rvsvsvd~~G~~ 285 (391)
+-|-..-||-.|.+++- +.+.+||.||..+ +.-|-+ ...|.+
T Consensus 24 ~~kl~g~kC~~CG~v~~-PPr~~Cp~C~~~~~~E~vel--s~~G~V 66 (140)
T COG1545 24 EGKLLGTKCKKCGRVYF-PPRAYCPKCGSETELEWVEL--SGEGKV 66 (140)
T ss_pred hCcEEEEEcCCCCeEEc-CCcccCCCCCCCCceEEEEe--CCCeEE
Confidence 34667889999999987 6799999999995 455544 456764
No 33
>TIGR01023 rpmG_bact ribosomal protein L33, bacterial type. This model describes bacterial ribosomal protein L33 and its chloroplast and mitochondrial equivalents.
Probab=88.58 E-value=0.32 Score=36.53 Aligned_cols=31 Identities=32% Similarity=0.647 Sum_probs=22.7
Q ss_pred eEEEEccCcc----cccccc--------CcccCCCCCccceeE
Q psy12603 244 TFILRCYACY----KTTSIM--------TKVFCPKCGYKTLKR 274 (391)
Q Consensus 244 ~wvlRC~aCf----~~t~~~--------~k~FCP~CGn~TL~R 274 (391)
.-.|.|.+|- .+++.. -+.|||.|+..||.+
T Consensus 9 ~i~L~ct~c~~~nY~t~Kn~~~~~~kL~lkKycp~~~khtlhk 51 (54)
T TIGR01023 9 LIRLVCTACTGINYTTTKNRRNKPEKLELRKYCPVCRKHVLHK 51 (54)
T ss_pred EEEEEecCCCCCCEEEcCCCCCCCCceEEECcCCCCCCeEeEE
Confidence 4689999993 333322 378999999999875
No 34
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=88.25 E-value=0.31 Score=54.21 Aligned_cols=33 Identities=36% Similarity=0.598 Sum_probs=25.4
Q ss_pred eeEEEEccCccccccccCcccCCCCCccceeEEEE
Q psy12603 243 RTFILRCYACYKTTSIMTKVFCPKCGYKTLKRVAV 277 (391)
Q Consensus 243 r~wvlRC~aCf~~t~~~~k~FCP~CGn~TL~Rvsv 277 (391)
.+=.|+||=|....+.+ ..||.||+..|+=+-.
T Consensus 459 ~~~~L~CH~Cg~~~~~p--~~Cp~Cgs~~L~~~G~ 491 (730)
T COG1198 459 ATGQLRCHYCGYQEPIP--QSCPECGSEHLRAVGP 491 (730)
T ss_pred CCCeeEeCCCCCCCCCC--CCCCCCCCCeeEEecc
Confidence 34589999999986544 7899999997765543
No 35
>CHL00104 rpl33 ribosomal protein L33
Probab=88.09 E-value=0.35 Score=37.88 Aligned_cols=31 Identities=42% Similarity=0.815 Sum_probs=23.5
Q ss_pred eEEEEccCc--------------ccccccc--------CcccCCCCCccceeE
Q psy12603 244 TFILRCYAC--------------YKTTSIM--------TKVFCPKCGYKTLKR 274 (391)
Q Consensus 244 ~wvlRC~aC--------------f~~t~~~--------~k~FCP~CGn~TL~R 274 (391)
.-.|.|..| |.++++. -+.|||.|...||.+
T Consensus 10 ~I~L~Ct~c~~~n~~~~~~g~~rY~T~KNkkn~p~rLelkKycp~c~kHtlhk 62 (66)
T CHL00104 10 TVILECTSCVRNGVNKESTGISRYITQKNRHNTPNRLELKKFCPYCYKHTIHK 62 (66)
T ss_pred EEEEEecCCcCCCccccCcccceEEECCCCCCCCceeEEECcCCCCCCEeeEe
Confidence 467999999 4444422 378999999999876
No 36
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=87.83 E-value=0.25 Score=39.68 Aligned_cols=43 Identities=21% Similarity=0.493 Sum_probs=32.7
Q ss_pred eeeeEEEEccCccccccc------cCcccCCCCCcc---ceeEEEEEEcCCC
Q psy12603 241 ELRTFILRCYACYKTTSI------MTKVFCPKCGYK---TLKRVAVSVDEQG 283 (391)
Q Consensus 241 ~~r~wvlRC~aCf~~t~~------~~k~FCP~CGn~---TL~Rvsvsvd~~G 283 (391)
-+=+|.++|..|...+.. ....-||.||.+ +|.+|.|....-|
T Consensus 7 lMPtY~Y~c~~cg~~~dvvq~~~ddplt~ce~c~a~~kk~l~~vgi~fKGSG 58 (82)
T COG2331 7 LMPTYSYECTECGNRFDVVQAMTDDPLTTCEECGARLKKLLNAVGIVFKGSG 58 (82)
T ss_pred cccceEEeecccchHHHHHHhcccCccccChhhChHHHHhhccceEEEecce
Confidence 345799999999877653 357789999985 7888888765544
No 37
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=87.82 E-value=0.27 Score=41.53 Aligned_cols=32 Identities=25% Similarity=0.443 Sum_probs=25.9
Q ss_pred EEccCccccccccC---cccCCCCCccceeEEEEE
Q psy12603 247 LRCYACYKTTSIMT---KVFCPKCGYKTLKRVAVS 278 (391)
Q Consensus 247 lRC~aCf~~t~~~~---k~FCP~CGn~TL~Rvsvs 278 (391)
.+|.-|.+++.+-+ ..=||+||++-.+.|+=-
T Consensus 3 H~CtrCG~vf~~g~~~il~GCp~CG~nkF~yv~~e 37 (112)
T COG3364 3 HQCTRCGEVFDDGSEEILSGCPKCGCNKFLYVPEE 37 (112)
T ss_pred ceecccccccccccHHHHccCccccchheEecccc
Confidence 58999999998743 466999999988877653
No 38
>COG0267 RpmG Ribosomal protein L33 [Translation, ribosomal structure and biogenesis]
Probab=87.42 E-value=0.35 Score=35.83 Aligned_cols=31 Identities=32% Similarity=0.690 Sum_probs=22.3
Q ss_pred eEEEEccCcc-cccc--c---------cCcccCCCCCccceeE
Q psy12603 244 TFILRCYACY-KTTS--I---------MTKVFCPKCGYKTLKR 274 (391)
Q Consensus 244 ~wvlRC~aCf-~~t~--~---------~~k~FCP~CGn~TL~R 274 (391)
.-.|.|.+|. +.+. . --+.|||+|...||.|
T Consensus 5 kI~L~ct~c~g~nY~t~kN~r~~~~rLelkKycp~~~khtlhk 47 (50)
T COG0267 5 KIKLACTACTSRNYTTTKNKRNKPERLELKKYCPVCRKHTLHK 47 (50)
T ss_pred eEEEEEeccCCeeEEEeeccCCCcceEEEEecCcccccEEEEe
Confidence 3578999998 3221 1 1378999999999876
No 39
>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=87.02 E-value=0.29 Score=32.50 Aligned_cols=12 Identities=42% Similarity=0.941 Sum_probs=7.2
Q ss_pred cccCCCCCccce
Q psy12603 261 KVFCPKCGYKTL 272 (391)
Q Consensus 261 k~FCP~CGn~TL 272 (391)
-.|||.||.+|.
T Consensus 3 ~rfC~~CG~~t~ 14 (32)
T PF09297_consen 3 HRFCGRCGAPTK 14 (32)
T ss_dssp TSB-TTT--BEE
T ss_pred CcccCcCCcccc
Confidence 379999999964
No 40
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=86.97 E-value=0.33 Score=37.43 Aligned_cols=21 Identities=33% Similarity=0.798 Sum_probs=17.2
Q ss_pred EccCccccccccCcccCCCCCccc
Q psy12603 248 RCYACYKTTSIMTKVFCPKCGYKT 271 (391)
Q Consensus 248 RC~aCf~~t~~~~k~FCP~CGn~T 271 (391)
-|.-|..++. ...||.||+.+
T Consensus 5 AC~~C~~i~~---~~~CP~Cgs~~ 25 (61)
T PRK08351 5 ACRHCHYITT---EDRCPVCGSRD 25 (61)
T ss_pred hhhhCCcccC---CCcCCCCcCCc
Confidence 6889999883 34799999976
No 41
>PRK07218 replication factor A; Provisional
Probab=86.53 E-value=0.89 Score=47.59 Aligned_cols=81 Identities=21% Similarity=0.327 Sum_probs=56.4
Q ss_pred ceEEEecCcHHHHHHHHHhCCceeccCcc--ccceeeeEEEEccCccccccccCcccCCCCCcc---ceeEEEEEEcCC-
Q psy12603 209 LVVSCVTTDFAMQNVLKQMGLNVVALDGR--LIRELRTFILRCYACYKTTSIMTKVFCPKCGYK---TLKRVAVSVDEQ- 282 (391)
Q Consensus 209 ~~Vac~TtDfAMQNVllqmGL~l~s~~G~--~Ik~~r~wvlRC~aCf~~t~~~~k~FCP~CGn~---TL~Rvsvsvd~~- 282 (391)
+.|.--++...+.+.+---|.-=+.+.|. -|++-...+.||.-|.++- .+-.||.||.. -..|+...+|..
T Consensus 258 i~v~~~~~~~~I~e~~~~~g~~~Vev~G~Iv~i~~gsgli~rCP~C~r~v---~~~~C~~hG~ve~~~dlrik~vLDDGt 334 (423)
T PRK07218 258 VSVSKDPPRLKIREAVERGGIFDVELVGNIISVRDGSGLIERCPECGRVI---QKGQCRSHGAVEGEDDLRIKAILDDGT 334 (423)
T ss_pred ccccCCccccchhhhhccCCcceEEEEEEEEEeccCCcceecCcCccccc---cCCcCCCCCCcCCeeeeEEEEEEECCC
Confidence 34444455556666544433333566665 5667778999999999876 45789999974 688899988875
Q ss_pred CcEEEeeccC
Q psy12603 283 GKQKIHINLK 292 (391)
Q Consensus 283 G~~~~hl~~n 292 (391)
|.+.+-|.+-
T Consensus 335 g~~~~~~~~e 344 (423)
T PRK07218 335 GSVTVILDRE 344 (423)
T ss_pred CeEEEEEChh
Confidence 8887766655
No 42
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=86.52 E-value=0.5 Score=54.90 Aligned_cols=28 Identities=36% Similarity=0.585 Sum_probs=19.7
Q ss_pred eeeeEEEEccCccccccccCcccCCCCCccc
Q psy12603 241 ELRTFILRCYACYKTTSIMTKVFCPKCGYKT 271 (391)
Q Consensus 241 ~~r~wvlRC~aCf~~t~~~~k~FCP~CGn~T 271 (391)
++.-...+|..|...+.. .|||+||.+|
T Consensus 662 eVEV~~rkCPkCG~~t~~---~fCP~CGs~t 689 (1337)
T PRK14714 662 EVEVGRRRCPSCGTETYE---NRCPDCGTHT 689 (1337)
T ss_pred EEEEEEEECCCCCCcccc---ccCcccCCcC
Confidence 345566999999986542 3777777765
No 43
>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=86.13 E-value=0.28 Score=33.50 Aligned_cols=11 Identities=45% Similarity=1.168 Sum_probs=8.6
Q ss_pred ccCCCCCccce
Q psy12603 262 VFCPKCGYKTL 272 (391)
Q Consensus 262 ~FCP~CGn~TL 272 (391)
.|||.|||=.+
T Consensus 2 ~FCp~C~nlL~ 12 (35)
T PF02150_consen 2 RFCPECGNLLY 12 (35)
T ss_dssp -BETTTTSBEE
T ss_pred eeCCCCCccce
Confidence 69999999754
No 44
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=85.77 E-value=0.35 Score=36.87 Aligned_cols=26 Identities=38% Similarity=0.628 Sum_probs=20.2
Q ss_pred EEEccCccccccccCcccCCCCCccceeE
Q psy12603 246 ILRCYACYKTTSIMTKVFCPKCGYKTLKR 274 (391)
Q Consensus 246 vlRC~aCf~~t~~~~k~FCP~CGn~TL~R 274 (391)
+.+|..|...|- +.-||.||..|.--
T Consensus 5 ~rkC~~cg~YTL---ke~Cp~CG~~t~~~ 30 (59)
T COG2260 5 IRKCPKCGRYTL---KEKCPVCGGDTKVP 30 (59)
T ss_pred hhcCcCCCceee---cccCCCCCCccccC
Confidence 567999998774 36799999987543
No 45
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=85.66 E-value=0.63 Score=41.10 Aligned_cols=53 Identities=28% Similarity=0.519 Sum_probs=30.7
Q ss_pred EccCcccc-ccccCcccCCCCCccceeEEEEEEcCCCcEEEeeccCCccccCCcccccCCCC
Q psy12603 248 RCYACYKT-TSIMTKVFCPKCGYKTLKRVAVSVDEQGKQKIHINLKRPLTARGKKFSLPTFK 308 (391)
Q Consensus 248 RC~aCf~~-t~~~~k~FCP~CGn~TL~Rvsvsvd~~G~~~~hl~~n~~~n~RG~~ySlPkPk 308 (391)
-|..|... +.-..+.|||.||. +-+-|..++.+.. . .-+...+=.++++|.+.
T Consensus 30 hCp~Cg~PLF~KdG~v~CPvC~~---~~~~v~~e~~~~~-~----~~~~~~~~~~~~~~~~~ 83 (131)
T COG1645 30 HCPKCGTPLFRKDGEVFCPVCGY---REVVVEEEEEEVE-A----EVQEQLRRSRPELPDDS 83 (131)
T ss_pred hCcccCCcceeeCCeEECCCCCc---eEEEeecccccch-h----hhhcchhhcccccccch
Confidence 49999854 44567999999998 3333443333321 1 12233355566777654
No 46
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=85.53 E-value=0.52 Score=42.64 Aligned_cols=30 Identities=30% Similarity=0.544 Sum_probs=22.7
Q ss_pred eeEEEEccCcccccc-----ccCc----ccCCCCCcccee
Q psy12603 243 RTFILRCYACYKTTS-----IMTK----VFCPKCGYKTLK 273 (391)
Q Consensus 243 r~wvlRC~aCf~~t~-----~~~k----~FCP~CGn~TL~ 273 (391)
.+|.++|+ |..-+- +..+ .+|-+||.++..
T Consensus 114 ~~~~Y~C~-C~q~~l~~RRhn~~~~g~~YrC~~C~gkL~~ 152 (156)
T COG3091 114 TTYPYRCQ-CQQHYLRIRRHNTVRRGEVYRCGKCGGKLVF 152 (156)
T ss_pred cceeEEee-cCCccchhhhcccccccceEEeccCCceEEe
Confidence 48999999 987653 2234 799999998654
No 47
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=85.27 E-value=0.74 Score=33.98 Aligned_cols=34 Identities=21% Similarity=0.534 Sum_probs=26.9
Q ss_pred eEEEEccCcccccccc---CcccCCCCCccceeEEEE
Q psy12603 244 TFILRCYACYKTTSIM---TKVFCPKCGYKTLKRVAV 277 (391)
Q Consensus 244 ~wvlRC~aCf~~t~~~---~k~FCP~CGn~TL~Rvsv 277 (391)
..+++|--|.+....+ .-.-||.||+..|-|.-.
T Consensus 4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~rIl~K~R~ 40 (49)
T COG1996 4 MMEYKCARCGREVELDQETRGIRCPYCGSRILVKERP 40 (49)
T ss_pred eEEEEhhhcCCeeehhhccCceeCCCCCcEEEEeccC
Confidence 4579999999887633 568899999998877644
No 48
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=85.09 E-value=0.44 Score=37.07 Aligned_cols=22 Identities=27% Similarity=0.582 Sum_probs=17.7
Q ss_pred EEccCccccccccCcccCCCCCccc
Q psy12603 247 LRCYACYKTTSIMTKVFCPKCGYKT 271 (391)
Q Consensus 247 lRC~aCf~~t~~~~k~FCP~CGn~T 271 (391)
+-|.-|..++. ...||.||+.+
T Consensus 6 ~AC~~C~~i~~---~~~Cp~Cgs~~ 27 (64)
T PRK06393 6 RACKKCKRLTP---EKTCPVHGDEK 27 (64)
T ss_pred hhHhhCCcccC---CCcCCCCCCCc
Confidence 46999999984 35899999974
No 49
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=84.84 E-value=0.58 Score=40.50 Aligned_cols=30 Identities=27% Similarity=0.487 Sum_probs=22.1
Q ss_pred eEEEEccCccc-cccccCcccCCCCCcccee
Q psy12603 244 TFILRCYACYK-TTSIMTKVFCPKCGYKTLK 273 (391)
Q Consensus 244 ~wvlRC~aCf~-~t~~~~k~FCP~CGn~TL~ 273 (391)
.=..+|.-|.. +..+.....||+||+..++
T Consensus 68 p~~~~C~~C~~~~~~e~~~~~CP~C~s~~~~ 98 (115)
T COG0375 68 PAECWCLDCGQEVELEELDYRCPKCGSINLR 98 (115)
T ss_pred ccEEEeccCCCeecchhheeECCCCCCCceE
Confidence 34679999954 4455567779999998665
No 50
>PRK04351 hypothetical protein; Provisional
Probab=84.82 E-value=1.3 Score=40.01 Aligned_cols=50 Identities=20% Similarity=0.305 Sum_probs=31.7
Q ss_pred HHHHHHhCCceeccCccccceeeeEEEEccCcccccc-----ccCcccCCCCCccce
Q psy12603 221 QNVLKQMGLNVVALDGRLIRELRTFILRCYACYKTTS-----IMTKVFCPKCGYKTL 272 (391)
Q Consensus 221 QNVllqmGL~l~s~~G~~Ik~~r~wvlRC~aCf~~t~-----~~~k~FCP~CGn~TL 272 (391)
|-+|.++|-.-..++-.. .-++|+++|.+|...+. +..+..|-+||....
T Consensus 89 k~~~~~v~~~r~~~~~~~--~~~~y~Y~C~~Cg~~~~r~Rr~n~~~yrCg~C~g~L~ 143 (149)
T PRK04351 89 KELLKQVGGPRYCPPLPS--QKKNYLYECQSCGQQYLRKRRINTKRYRCGKCRGKLK 143 (149)
T ss_pred HHHHHHhCCCcccCCCCC--CCceEEEECCCCCCEeeeeeecCCCcEEeCCCCcEee
Confidence 666666653112222111 23679999999997543 346899999998743
No 51
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=84.73 E-value=0.41 Score=52.60 Aligned_cols=23 Identities=35% Similarity=0.701 Sum_probs=9.9
Q ss_pred EEccCccccccccCcccCCCCCcc
Q psy12603 247 LRCYACYKTTSIMTKVFCPKCGYK 270 (391)
Q Consensus 247 lRC~aCf~~t~~~~k~FCP~CGn~ 270 (391)
++|..|....++.. .|||+||.+
T Consensus 2 ~~Cp~Cg~~n~~~a-kFC~~CG~~ 24 (645)
T PRK14559 2 LICPQCQFENPNNN-RFCQKCGTS 24 (645)
T ss_pred CcCCCCCCcCCCCC-ccccccCCC
Confidence 34555544443322 344444444
No 52
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=84.52 E-value=0.59 Score=39.99 Aligned_cols=25 Identities=28% Similarity=0.660 Sum_probs=18.7
Q ss_pred EEEccCcccccccc---CcccCCCCCcc
Q psy12603 246 ILRCYACYKTTSIM---TKVFCPKCGYK 270 (391)
Q Consensus 246 vlRC~aCf~~t~~~---~k~FCP~CGn~ 270 (391)
+++|..|....... .-.|||+||..
T Consensus 42 ~~~C~~Cg~~~~~~~SCk~R~CP~C~~~ 69 (111)
T PF14319_consen 42 RYRCEDCGHEKIVYNSCKNRHCPSCQAK 69 (111)
T ss_pred eeecCCCCceEEecCcccCcCCCCCCCh
Confidence 67899998765433 23499999986
No 53
>TIGR03844 cysteate_syn cysteate synthase. Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M.
Probab=84.36 E-value=0.61 Score=48.31 Aligned_cols=26 Identities=23% Similarity=0.356 Sum_probs=22.5
Q ss_pred EEEEccCccccccccCcccCCCCCcc
Q psy12603 245 FILRCYACYKTTSIMTKVFCPKCGYK 270 (391)
Q Consensus 245 wvlRC~aCf~~t~~~~k~FCP~CGn~ 270 (391)
|.|+|..|.+.+++.....||.||..
T Consensus 1 ~~l~C~~Cg~~~~~~~~~~C~~c~g~ 26 (398)
T TIGR03844 1 YTLRCPGCGEVLPDHYTLSCPLDCGL 26 (398)
T ss_pred CEEEeCCCCCccCCccccCCCCCCCc
Confidence 67999999999986667899999964
No 54
>PRK00504 rpmG 50S ribosomal protein L33; Validated
Probab=84.20 E-value=0.72 Score=34.18 Aligned_cols=31 Identities=35% Similarity=0.757 Sum_probs=22.1
Q ss_pred eEEEEccCcccc----cccc--------CcccCCCCCccceeE
Q psy12603 244 TFILRCYACYKT----TSIM--------TKVFCPKCGYKTLKR 274 (391)
Q Consensus 244 ~wvlRC~aCf~~----t~~~--------~k~FCP~CGn~TL~R 274 (391)
.-.|.|..|... ++.. -+.|||.|+..||.+
T Consensus 5 ~i~L~C~~c~~rnY~t~KNk~~~~~rLelkKycp~c~khtlhk 47 (50)
T PRK00504 5 KITLACTECKSRNYTTTKNKKNTPERLELKKFCPRCNKHTLHK 47 (50)
T ss_pred EEEEEEcCCCCccEeEcCCCCCCCceEEEECcCCCCCCeEeee
Confidence 457899999632 2211 378999999999875
No 55
>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=84.05 E-value=0.69 Score=49.34 Aligned_cols=31 Identities=32% Similarity=0.518 Sum_probs=24.1
Q ss_pred EEEEccCccccccccCcccCCCCCccceeEEEE
Q psy12603 245 FILRCYACYKTTSIMTKVFCPKCGYKTLKRVAV 277 (391)
Q Consensus 245 wvlRC~aCf~~t~~~~k~FCP~CGn~TL~Rvsv 277 (391)
=.|+||-|....+.+ ..||+||+..|+-+.+
T Consensus 239 ~~l~Ch~Cg~~~~~~--~~Cp~C~s~~l~~~g~ 269 (505)
T TIGR00595 239 GKLRCHYCGYQEPIP--KTCPQCGSEDLVYKGY 269 (505)
T ss_pred CeEEcCCCcCcCCCC--CCCCCCCCCeeEeecc
Confidence 378999999877755 6799999987765443
No 56
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=83.91 E-value=0.59 Score=41.26 Aligned_cols=27 Identities=22% Similarity=0.516 Sum_probs=22.1
Q ss_pred EEccCccccccccC---cccCCCCCcccee
Q psy12603 247 LRCYACYKTTSIMT---KVFCPKCGYKTLK 273 (391)
Q Consensus 247 lRC~aCf~~t~~~~---k~FCP~CGn~TL~ 273 (391)
.+|.-|.+++.+-+ ..=||.||++.-.
T Consensus 2 H~Ct~Cg~~f~dgs~eil~GCP~CGg~kF~ 31 (131)
T PF09845_consen 2 HQCTKCGRVFEDGSKEILSGCPECGGNKFQ 31 (131)
T ss_pred cccCcCCCCcCCCcHHHHccCcccCCcceE
Confidence 48999999999876 5679999998443
No 57
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=83.85 E-value=0.77 Score=42.19 Aligned_cols=25 Identities=28% Similarity=0.543 Sum_probs=22.8
Q ss_pred EEEccCccccccccCcccCCCCCcc
Q psy12603 246 ILRCYACYKTTSIMTKVFCPKCGYK 270 (391)
Q Consensus 246 vlRC~aCf~~t~~~~k~FCP~CGn~ 270 (391)
+++|.-|..++.+-+-..||.||.+
T Consensus 134 ~~vC~vCGy~~~ge~P~~CPiCga~ 158 (166)
T COG1592 134 VWVCPVCGYTHEGEAPEVCPICGAP 158 (166)
T ss_pred EEEcCCCCCcccCCCCCcCCCCCCh
Confidence 8999999999998778999999975
No 58
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=83.36 E-value=0.51 Score=34.85 Aligned_cols=11 Identities=45% Similarity=1.304 Sum_probs=7.6
Q ss_pred CcccCCCCCcc
Q psy12603 260 TKVFCPKCGYK 270 (391)
Q Consensus 260 ~k~FCP~CGn~ 270 (391)
.+.|||.||+.
T Consensus 19 ~~~fCP~Cg~~ 29 (50)
T PRK00432 19 KNKFCPRCGSG 29 (50)
T ss_pred ccCcCcCCCcc
Confidence 45678888774
No 59
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=83.25 E-value=1.6 Score=38.52 Aligned_cols=55 Identities=18% Similarity=0.428 Sum_probs=33.7
Q ss_pred HHHHHHHHhCCce------e-ccCccccc--eeeeEEEEccCccccccc-----cCcccCCCCCccceeE
Q psy12603 219 AMQNVLKQMGLNV------V-ALDGRLIR--ELRTFILRCYACYKTTSI-----MTKVFCPKCGYKTLKR 274 (391)
Q Consensus 219 AMQNVllqmGL~l------~-s~~G~~Ik--~~r~wvlRC~aCf~~t~~-----~~k~FCP~CGn~TL~R 274 (391)
+=|.++.++|+.. + ..+.+.|. +.++|.++|..|.....- ..+..|+.||.+ |..
T Consensus 87 ~fk~~~~~ig~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~~~r~~~~~~~~~~C~~C~~~-l~~ 155 (157)
T PF10263_consen 87 EFKQWARRIGASPPRGRPNPTTCHSYEIEGKEYKKYVYRCPSCGREYKRHRRSKRKRYRCGRCGGP-LVQ 155 (157)
T ss_pred HHHHHHHHHCCcccccccccccccccccccccccceEEEcCCCCCEeeeecccchhhEECCCCCCE-EEE
Confidence 5677777777733 1 12223332 337899999999954331 135579999955 443
No 60
>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=83.19 E-value=1.1 Score=30.11 Aligned_cols=28 Identities=25% Similarity=0.666 Sum_probs=19.7
Q ss_pred EEccCcccccccc--CcccCCCCCccceeE
Q psy12603 247 LRCYACYKTTSIM--TKVFCPKCGYKTLKR 274 (391)
Q Consensus 247 lRC~aCf~~t~~~--~k~FCP~CGn~TL~R 274 (391)
+.|-.|....... ...-||.||+.+|-|
T Consensus 1 Y~C~~Cg~~~~~~~~~~irC~~CG~RIlyK 30 (32)
T PF03604_consen 1 YICGECGAEVELKPGDPIRCPECGHRILYK 30 (32)
T ss_dssp EBESSSSSSE-BSTSSTSSBSSSS-SEEBE
T ss_pred CCCCcCCCeeEcCCCCcEECCcCCCeEEEe
Confidence 4688888766533 467899999998876
No 61
>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=83.11 E-value=0.73 Score=39.62 Aligned_cols=36 Identities=28% Similarity=0.501 Sum_probs=28.1
Q ss_pred ccccceeeeEEEEccCccccccccC-cccCCCCCcc-cee
Q psy12603 236 GRLIRELRTFILRCYACYKTTSIMT-KVFCPKCGYK-TLK 273 (391)
Q Consensus 236 G~~Ik~~r~wvlRC~aCf~~t~~~~-k~FCP~CGn~-TL~ 273 (391)
|+. ..|....+|..|.+.|+-.. -+-|++|+.+ ||.
T Consensus 61 Gml--Stkav~V~CP~C~K~TKmLGr~D~CM~C~~pLTLd 98 (114)
T PF11023_consen 61 GML--STKAVQVECPNCGKQTKMLGRVDACMHCKEPLTLD 98 (114)
T ss_pred hhh--cccceeeECCCCCChHhhhchhhccCcCCCcCccC
Confidence 554 55678889999999998554 4689999999 544
No 62
>PRK00595 rpmG 50S ribosomal protein L33; Validated
Probab=82.83 E-value=0.84 Score=34.15 Aligned_cols=31 Identities=13% Similarity=0.017 Sum_probs=22.1
Q ss_pred eEEEEccCccccc----ccc--------CcccCCCCCccceeE
Q psy12603 244 TFILRCYACYKTT----SIM--------TKVFCPKCGYKTLKR 274 (391)
Q Consensus 244 ~wvlRC~aCf~~t----~~~--------~k~FCP~CGn~TL~R 274 (391)
.-.|.|.+|-... +.- -+.|||.|+..||.+
T Consensus 8 ~i~L~ct~c~~~nY~t~Kn~k~~~~rL~lkKycp~~~khtlhk 50 (53)
T PRK00595 8 KIKLESTEGTGRFYTTTKNKRNTPEKLELKKYDPVLRKHVLHK 50 (53)
T ss_pred EEEEEecCCCCEEEEEccCCCCCCCceEEECcCCCCCCEEeEE
Confidence 4579999986322 111 378999999999875
No 63
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=82.31 E-value=1.1 Score=39.14 Aligned_cols=29 Identities=24% Similarity=0.568 Sum_probs=19.1
Q ss_pred eEEEEccCcccccccc--C------cccCCCCCcccee
Q psy12603 244 TFILRCYACYKTTSIM--T------KVFCPKCGYKTLK 273 (391)
Q Consensus 244 ~wvlRC~aCf~~t~~~--~------k~FCP~CGn~TL~ 273 (391)
.-..|| .|...+... . ..-||.||+..+.
T Consensus 68 p~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~ 104 (124)
T PRK00762 68 PVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAH 104 (124)
T ss_pred CeeEEe-eCcCcccccccchhccccCCcCcCCCCCCCE
Confidence 347899 999775422 1 1349999987543
No 64
>PF00471 Ribosomal_L33: Ribosomal protein L33; InterPro: IPR001705 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 L33 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L33 has been shown to be on the surface of 50S subunit. L33 belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, , ], groups: Eubacterial L33. Algal and plant chloroplast L33. Cyanelle L33. L33 is a small protein of 49 to 66 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3PIO_1 3PIP_1 3PYT_3 3MS1_3 3F1F_6 3F1H_6 3MRZ_3 3PYO_3 3D5B_6 3D5D_6 ....
Probab=81.88 E-value=0.66 Score=34.04 Aligned_cols=30 Identities=30% Similarity=0.627 Sum_probs=20.9
Q ss_pred EEEEccCcccccc----c--------cCcccCCCCCccceeE
Q psy12603 245 FILRCYACYKTTS----I--------MTKVFCPKCGYKTLKR 274 (391)
Q Consensus 245 wvlRC~aCf~~t~----~--------~~k~FCP~CGn~TL~R 274 (391)
-.|.|.+|..... + .-+.|||.|+..||.+
T Consensus 4 i~L~c~~c~~~nY~t~kn~~~~~~rL~lkKycp~~~khtlhk 45 (48)
T PF00471_consen 4 IKLVCTECGGRNYTTTKNKKNTPERLELKKYCPRCRKHTLHK 45 (48)
T ss_dssp EEEEEEESSSSEEEEEEETTTSSSSSEEEEEETSSSSEEEEE
T ss_pred EEEEEcCCCCeeEEEecCCCCCCceeeEeccCCCCCCEecEE
Confidence 3688888864321 1 1378999999998864
No 65
>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=81.59 E-value=2.1 Score=38.43 Aligned_cols=46 Identities=17% Similarity=0.317 Sum_probs=32.0
Q ss_pred eeEEEEccCcccccccc--CcccCCCCCccc-----eeEEEEEEcC-CCcEEEe
Q psy12603 243 RTFILRCYACYKTTSIM--TKVFCPKCGYKT-----LKRVAVSVDE-QGKQKIH 288 (391)
Q Consensus 243 r~wvlRC~aCf~~t~~~--~k~FCP~CGn~T-----L~Rvsvsvd~-~G~~~~h 288 (391)
.-|-.-|..|.+-.... ...+|++|+... ..++.+.+.. .|.+.+-
T Consensus 31 ~~~Y~aC~~C~kkv~~~~~~~~~C~~C~~~~~~~~~ry~l~~~i~D~Tg~~~~~ 84 (166)
T cd04476 31 NWWYPACPGCNKKVVEEGNGTYRCEKCNKSVPNPEYRYILSLNVADHTGEAWLT 84 (166)
T ss_pred CeEEccccccCcccEeCCCCcEECCCCCCcCCCccEEEEEEEEEEeCCCCEEEE
Confidence 45666799999654433 578999999864 5666676644 4776544
No 66
>PRK00420 hypothetical protein; Validated
Probab=81.57 E-value=0.82 Score=39.40 Aligned_cols=24 Identities=25% Similarity=0.360 Sum_probs=18.9
Q ss_pred EEccCcccccc--ccCcccCCCCCcc
Q psy12603 247 LRCYACYKTTS--IMTKVFCPKCGYK 270 (391)
Q Consensus 247 lRC~aCf~~t~--~~~k~FCP~CGn~ 270 (391)
-.|..|..... ..++.|||.||..
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGKV 49 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCCe
Confidence 46999986544 4579999999984
No 67
>PRK07591 threonine synthase; Validated
Probab=80.86 E-value=1.1 Score=46.73 Aligned_cols=27 Identities=19% Similarity=0.385 Sum_probs=22.1
Q ss_pred eEEEEccCccccccccCcccCCCCCcc
Q psy12603 244 TFILRCYACYKTTSIMTKVFCPKCGYK 270 (391)
Q Consensus 244 ~wvlRC~aCf~~t~~~~k~FCP~CGn~ 270 (391)
.+.|+|..|.+.++.....-||.||..
T Consensus 16 ~~~l~C~~Cg~~~~~~~~~~C~~cg~~ 42 (421)
T PRK07591 16 AVALKCRECGAEYPLGPIHVCEECFGP 42 (421)
T ss_pred eeEEEeCCCCCcCCCCCCccCCCCCCe
Confidence 456999999999986555789999964
No 68
>COG1933 Archaeal DNA polymerase II, large subunit [DNA replication, recombination, and repair]
Probab=80.47 E-value=0.9 Score=43.94 Aligned_cols=28 Identities=25% Similarity=0.491 Sum_probs=21.9
Q ss_pred EEEccCccccccccC-cccCCCCCccceeE
Q psy12603 246 ILRCYACYKTTSIMT-KVFCPKCGYKTLKR 274 (391)
Q Consensus 246 vlRC~aCf~~t~~~~-k~FCP~CGn~TL~R 274 (391)
-.||.+|.+-+.-++ ..-||+||| ++.+
T Consensus 167 ~~rc~~c~~k~rr~pl~g~c~kcg~-~~~l 195 (253)
T COG1933 167 EFRCVKCNTKFRRPPLDGKCPICGG-KIVL 195 (253)
T ss_pred eeehHhhhhhhcCCCccccccccCC-eEEE
Confidence 689999998777554 678999999 4443
No 69
>PRK08402 replication factor A; Reviewed
Probab=80.33 E-value=2.7 Score=43.12 Aligned_cols=59 Identities=15% Similarity=0.334 Sum_probs=39.4
Q ss_pred eeccCcc--ccceeeeEEEEccCcccccc-c--cCcccCCCCC--cc-ceeEEEEEEcCC-CcEEEeec
Q psy12603 231 VVALDGR--LIRELRTFILRCYACYKTTS-I--MTKVFCPKCG--YK-TLKRVAVSVDEQ-GKQKIHIN 290 (391)
Q Consensus 231 l~s~~G~--~Ik~~r~wvlRC~aCf~~t~-~--~~k~FCP~CG--n~-TL~Rvsvsvd~~-G~~~~hl~ 290 (391)
.+++.|. -|+. ..|..+|..|.+..- + ...-.|+.|| .+ -..+++++|+.. |.+.+-+-
T Consensus 196 ~v~v~g~Iv~i~~-~~~y~aCp~CnKkv~~~~~~~~~~Ce~~~~v~p~~ryil~~~l~D~TG~~~vt~f 263 (355)
T PRK08402 196 FVEVRGTIAKVYR-VLVYDACPECRRKVDYDPATDTWICPEHGEVEPIKITILDFGLDDGTGYIRVTLF 263 (355)
T ss_pred EEEEEEEEEEEec-CeeEecCCCCCeEEEEecCCCCEeCCCCCCcCcceeEEEEEEEEcCCCcEEEEEe
Confidence 3455553 1333 348999999997653 2 2467899999 55 566778888665 88766553
No 70
>PRK06260 threonine synthase; Validated
Probab=80.24 E-value=1.3 Score=45.53 Aligned_cols=26 Identities=31% Similarity=0.657 Sum_probs=20.8
Q ss_pred EEEEccCccccccccC-cccCCCCCcc
Q psy12603 245 FILRCYACYKTTSIMT-KVFCPKCGYK 270 (391)
Q Consensus 245 wvlRC~aCf~~t~~~~-k~FCP~CGn~ 270 (391)
|.|+|..|.+.++... ..-||.||..
T Consensus 2 ~~~~C~~cg~~~~~~~~~~~Cp~cg~~ 28 (397)
T PRK06260 2 YWLKCIECGKEYDPDEIIYTCPECGGL 28 (397)
T ss_pred CEEEECCCCCCCCCCCccccCCCCCCe
Confidence 5699999999997543 4569999965
No 71
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=79.71 E-value=0.96 Score=35.00 Aligned_cols=25 Identities=32% Similarity=0.684 Sum_probs=19.4
Q ss_pred EEccCccccccccCcccCCCCCccce
Q psy12603 247 LRCYACYKTTSIMTKVFCPKCGYKTL 272 (391)
Q Consensus 247 lRC~aCf~~t~~~~k~FCP~CGn~TL 272 (391)
+-|+-|.+++.+- ...||.||..-+
T Consensus 5 kAC~~Ck~l~~~d-~e~CP~Cgs~~~ 29 (64)
T COG2093 5 KACKNCKRLTPED-TEICPVCGSTDL 29 (64)
T ss_pred HHHhhccccCCCC-CccCCCCCCccc
Confidence 4599999998755 456999999833
No 72
>PF14369 zf-RING_3: zinc-finger
Probab=79.69 E-value=1.5 Score=30.01 Aligned_cols=27 Identities=26% Similarity=0.613 Sum_probs=19.1
Q ss_pred EEccCccccccc----cCcccCCCCCcccee
Q psy12603 247 LRCYACYKTTSI----MTKVFCPKCGYKTLK 273 (391)
Q Consensus 247 lRC~aCf~~t~~----~~k~FCP~CGn~TL~ 273 (391)
+.||.|-+.... ..-.+||.|++.-|-
T Consensus 3 ywCh~C~~~V~~~~~~~~~~~CP~C~~gFvE 33 (35)
T PF14369_consen 3 YWCHQCNRFVRIAPSPDSDVACPRCHGGFVE 33 (35)
T ss_pred EeCccCCCEeEeCcCCCCCcCCcCCCCcEeE
Confidence 679999966552 234579999987553
No 73
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=79.49 E-value=1.3 Score=50.20 Aligned_cols=29 Identities=24% Similarity=0.411 Sum_probs=24.2
Q ss_pred EEEEccCccccccccC-cccCCCCCcccee
Q psy12603 245 FILRCYACYKTTSIMT-KVFCPKCGYKTLK 273 (391)
Q Consensus 245 wvlRC~aCf~~t~~~~-k~FCP~CGn~TL~ 273 (391)
=..||..|..-++-|+ ..-||+||++.+.
T Consensus 1011 Q~fRC~kC~~kYRR~PL~G~C~kCGg~lil 1040 (1095)
T TIGR00354 1011 QEVRCTKCNTKYRRIPLVGKCLKCGNNLTL 1040 (1095)
T ss_pred cceeecccCCccccCCCCCcccccCCeEEE
Confidence 3689999999998886 7889999997544
No 74
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=79.48 E-value=1.5 Score=49.80 Aligned_cols=34 Identities=29% Similarity=0.423 Sum_probs=27.2
Q ss_pred eeeeEEEEccCccccccccCcccCCCCCccceeEEEE
Q psy12603 241 ELRTFILRCYACYKTTSIMTKVFCPKCGYKTLKRVAV 277 (391)
Q Consensus 241 ~~r~wvlRC~aCf~~t~~~~k~FCP~CGn~TL~Rvsv 277 (391)
.+--.+.+|..|.+.|. +..||.||..|...-.|
T Consensus 620 ~vev~~RKCPkCG~yTl---k~rCP~CG~~Te~~~pc 653 (1095)
T TIGR00354 620 EVEIAIRKCPQCGKESF---WLKCPVCGELTEQLYYG 653 (1095)
T ss_pred EEEEEEEECCCCCcccc---cccCCCCCCccccccce
Confidence 57778899999999875 67899999998554444
No 75
>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=79.13 E-value=1.3 Score=30.13 Aligned_cols=26 Identities=31% Similarity=0.634 Sum_probs=18.9
Q ss_pred EEEccCcccccccc--------CcccCCCCCccc
Q psy12603 246 ILRCYACYKTTSIM--------TKVFCPKCGYKT 271 (391)
Q Consensus 246 vlRC~aCf~~t~~~--------~k~FCP~CGn~T 271 (391)
.+.|..|.+.+... .+..||+||+..
T Consensus 2 ~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 2 RIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EEECCCCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 36899999855432 257999999863
No 76
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=79.03 E-value=0.26 Score=56.04 Aligned_cols=41 Identities=29% Similarity=0.558 Sum_probs=29.8
Q ss_pred cceeeeEEEEccCccccccccCcccCCCCCcc----------ceeEEEEEEc
Q psy12603 239 IRELRTFILRCYACYKTTSIMTKVFCPKCGYK----------TLKRVAVSVD 280 (391)
Q Consensus 239 Ik~~r~wvlRC~aCf~~t~~~~k~FCP~CGn~----------TL~Rvsvsvd 280 (391)
..=+..=+.||..|...+.+. ..+||.||+. .|+++|..||
T Consensus 687 ~vPvY~tIKrC~dcg~q~~~~-~~~cP~Cgs~~v~d~~~~ve~lRelA~EvD 737 (1187)
T COG1110 687 YVPVYDTIKRCRDCGEQFVDS-EDKCPRCGSRNVEDKTETVEALRELALEVD 737 (1187)
T ss_pred eEehHHHHHHHhhcCceeccc-cccCCCCCCccccccHHHHHHHHHHHhhcC
Confidence 444445568999999998887 5599999993 3566665553
No 77
>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=78.53 E-value=1.9 Score=29.24 Aligned_cols=25 Identities=24% Similarity=0.457 Sum_probs=19.3
Q ss_pred EEEccCcccccccc-CcccCCCCCcc
Q psy12603 246 ILRCYACYKTTSIM-TKVFCPKCGYK 270 (391)
Q Consensus 246 vlRC~aCf~~t~~~-~k~FCP~CGn~ 270 (391)
+++|.-|..+.... .-..||.||.+
T Consensus 2 ~~~C~~CG~i~~g~~~p~~CP~Cg~~ 27 (34)
T cd00729 2 VWVCPVCGYIHEGEEAPEKCPICGAP 27 (34)
T ss_pred eEECCCCCCEeECCcCCCcCcCCCCc
Confidence 47899999986533 23689999986
No 78
>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=78.46 E-value=1 Score=37.41 Aligned_cols=20 Identities=45% Similarity=0.881 Sum_probs=16.9
Q ss_pred CcccCCCCCccceeEEEEEE
Q psy12603 260 TKVFCPKCGYKTLKRVAVSV 279 (391)
Q Consensus 260 ~k~FCP~CGn~TL~Rvsvsv 279 (391)
.+.+||.||...++|+++-+
T Consensus 34 ~ky~Cp~Cgk~~vkR~a~GI 53 (90)
T PF01780_consen 34 AKYTCPFCGKTSVKRVATGI 53 (90)
T ss_dssp S-BEESSSSSSEEEEEETTE
T ss_pred CCCcCCCCCCceeEEeeeEE
Confidence 58999999999999999844
No 79
>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=77.59 E-value=1.8 Score=29.00 Aligned_cols=25 Identities=24% Similarity=0.421 Sum_probs=19.4
Q ss_pred EEEccCcccccccc-CcccCCCCCcc
Q psy12603 246 ILRCYACYKTTSIM-TKVFCPKCGYK 270 (391)
Q Consensus 246 vlRC~aCf~~t~~~-~k~FCP~CGn~ 270 (391)
+++|..|..++... .-..||.||.+
T Consensus 1 ~~~C~~CGy~y~~~~~~~~CP~Cg~~ 26 (33)
T cd00350 1 KYVCPVCGYIYDGEEAPWVCPVCGAP 26 (33)
T ss_pred CEECCCCCCEECCCcCCCcCcCCCCc
Confidence 36899999986543 45689999985
No 80
>PRK12366 replication factor A; Reviewed
Probab=77.39 E-value=3.2 Score=45.64 Aligned_cols=58 Identities=22% Similarity=0.429 Sum_probs=37.9
Q ss_pred eccCcc--ccceeeeEEEEccCccccccc-cCcccCCCCCcc---ceeEEEEEEcCC-CcEEEee
Q psy12603 232 VALDGR--LIRELRTFILRCYACYKTTSI-MTKVFCPKCGYK---TLKRVAVSVDEQ-GKQKIHI 289 (391)
Q Consensus 232 ~s~~G~--~Ik~~r~wvlRC~aCf~~t~~-~~k~FCP~CGn~---TL~Rvsvsvd~~-G~~~~hl 289 (391)
+++.|. .|+.-.-|..+|..|.+.-.. ...-.||+||.. -+.++++.++.. |.+.+-+
T Consensus 516 ~~v~g~i~~i~~~~~~y~aCp~CnkKv~~~~g~~~C~~c~~~~p~~~~~l~~~i~D~TG~~~~t~ 580 (637)
T PRK12366 516 VEIRGTVVDIRKQKIILYLCPNCRKRVEEVDGEYICEFCGEVEPNELLMLNFTLDDGTGTINCRF 580 (637)
T ss_pred EEEEEEEEEEeCCCEEEecccccCeEeEcCCCcEECCCCCCCCCcEEEEEEEEEEcCCCCEEEEE
Confidence 444453 344455788999999865432 234589999983 445677777654 8775544
No 81
>PRK06450 threonine synthase; Validated
Probab=77.33 E-value=1.7 Score=44.02 Aligned_cols=26 Identities=27% Similarity=0.503 Sum_probs=21.3
Q ss_pred EEccCccccccccCcccCCCCCccce
Q psy12603 247 LRCYACYKTTSIMTKVFCPKCGYKTL 272 (391)
Q Consensus 247 lRC~aCf~~t~~~~k~FCP~CGn~TL 272 (391)
|+|..|.+.+.......||.||.+..
T Consensus 4 ~~C~~Cg~~~~~~~~~~C~~cg~~l~ 29 (338)
T PRK06450 4 EVCMKCGKERESIYEIRCKKCGGPFE 29 (338)
T ss_pred eEECCcCCcCCCcccccCCcCCCEeE
Confidence 89999999987655678999997633
No 82
>PF12773 DZR: Double zinc ribbon
Probab=76.68 E-value=1.2 Score=32.03 Aligned_cols=21 Identities=33% Similarity=0.833 Sum_probs=10.9
Q ss_pred EEccCccccccccCcccCCCCC
Q psy12603 247 LRCYACYKTTSIMTKVFCPKCG 268 (391)
Q Consensus 247 lRC~aCf~~t~~~~k~FCP~CG 268 (391)
..|..|.+... ..-.||++||
T Consensus 30 ~~C~~Cg~~~~-~~~~fC~~CG 50 (50)
T PF12773_consen 30 KICPNCGAENP-PNAKFCPNCG 50 (50)
T ss_pred CCCcCCcCCCc-CCcCccCccc
Confidence 44556655432 3345666665
No 83
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=76.64 E-value=1.7 Score=50.84 Aligned_cols=29 Identities=34% Similarity=0.626 Sum_probs=23.7
Q ss_pred EEEEccCccccccccC-cccCCCCCccceeE
Q psy12603 245 FILRCYACYKTTSIMT-KVFCPKCGYKTLKR 274 (391)
Q Consensus 245 wvlRC~aCf~~t~~~~-k~FCP~CGn~TL~R 274 (391)
=..|| -|..-++-|+ ..-||+||++.+.-
T Consensus 1541 Q~~RC-kC~~kyRR~PL~G~C~kCGg~~ilT 1570 (1627)
T PRK14715 1541 QEFRC-KCGAKYRRVPLKGKCPKCGSKLILT 1570 (1627)
T ss_pred cceee-cCCCccccCCCCCcCcccCCeEEEE
Confidence 36899 9999988886 78899999975543
No 84
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=76.42 E-value=1.1 Score=33.48 Aligned_cols=22 Identities=36% Similarity=0.872 Sum_probs=16.4
Q ss_pred EccCcccccccc---------CcccCCCCCc
Q psy12603 248 RCYACYKTTSIM---------TKVFCPKCGY 269 (391)
Q Consensus 248 RC~aCf~~t~~~---------~k~FCP~CGn 269 (391)
+|.||+-.-+.. .-.|||.||-
T Consensus 24 ~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgR 54 (56)
T PF02591_consen 24 TCSGCHMELPPQELNEIRKGDEIVFCPNCGR 54 (56)
T ss_pred ccCCCCEEcCHHHHHHHHcCCCeEECcCCCc
Confidence 899999654422 4689999993
No 85
>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=76.05 E-value=2.1 Score=31.52 Aligned_cols=10 Identities=50% Similarity=1.135 Sum_probs=8.7
Q ss_pred cccCCCCCcc
Q psy12603 261 KVFCPKCGYK 270 (391)
Q Consensus 261 k~FCP~CGn~ 270 (391)
-.+||+|||.
T Consensus 13 Y~~Cp~CGN~ 22 (49)
T PF12677_consen 13 YCKCPKCGND 22 (49)
T ss_pred hccCcccCCc
Confidence 4689999998
No 86
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=75.94 E-value=1.3 Score=48.79 Aligned_cols=26 Identities=27% Similarity=0.632 Sum_probs=20.5
Q ss_pred EccCccccccccCcccCCCCCccceeE
Q psy12603 248 RCYACYKTTSIMTKVFCPKCGYKTLKR 274 (391)
Q Consensus 248 RC~aCf~~t~~~~k~FCP~CGn~TL~R 274 (391)
.|..|....+.. -.|||.||.++-+.
T Consensus 29 ~Cp~CG~~~~~~-~~fC~~CG~~~~~~ 54 (645)
T PRK14559 29 PCPQCGTEVPVD-EAHCPNCGAETGTI 54 (645)
T ss_pred cCCCCCCCCCcc-cccccccCCcccch
Confidence 599999987644 46999999985444
No 87
>PRK14873 primosome assembly protein PriA; Provisional
Probab=75.67 E-value=2.1 Score=47.40 Aligned_cols=31 Identities=32% Similarity=0.625 Sum_probs=23.2
Q ss_pred EEEEccCccccccccCcccCCCCCccceeEEEEE
Q psy12603 245 FILRCYACYKTTSIMTKVFCPKCGYKTLKRVAVS 278 (391)
Q Consensus 245 wvlRC~aCf~~t~~~~k~FCP~CGn~TL~Rvsvs 278 (391)
=.|+||-|.... . -..||+||+..|+-+-+-
T Consensus 409 ~~l~Ch~CG~~~--~-p~~Cp~Cgs~~l~~~g~G 439 (665)
T PRK14873 409 GTPRCRWCGRAA--P-DWRCPRCGSDRLRAVVVG 439 (665)
T ss_pred CeeECCCCcCCC--c-CccCCCCcCCcceeeecc
Confidence 379999998753 2 368999999987765543
No 88
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=75.38 E-value=1.3 Score=32.00 Aligned_cols=10 Identities=60% Similarity=1.384 Sum_probs=8.1
Q ss_pred ccCCCCCccc
Q psy12603 262 VFCPKCGYKT 271 (391)
Q Consensus 262 ~FCP~CGn~T 271 (391)
.|||.||+-+
T Consensus 1 ~FCp~Cg~~l 10 (52)
T smart00661 1 KFCPKCGNML 10 (52)
T ss_pred CCCCCCCCcc
Confidence 4999999943
No 89
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=75.27 E-value=2.7 Score=31.72 Aligned_cols=29 Identities=34% Similarity=0.670 Sum_probs=21.2
Q ss_pred EEccCcccccc-----cc----CcccCCCCCccceeEE
Q psy12603 247 LRCYACYKTTS-----IM----TKVFCPKCGYKTLKRV 275 (391)
Q Consensus 247 lRC~aCf~~t~-----~~----~k~FCP~CGn~TL~Rv 275 (391)
+.|.-|..-|+ |. --.|||+|-+.||-.|
T Consensus 5 i~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~EtlI~v 42 (55)
T PF14205_consen 5 ILCPICGNKTRLKIREDTVLKNFPLYCPKCKQETLIDV 42 (55)
T ss_pred EECCCCCCccceeeecCceeccccccCCCCCceEEEEe
Confidence 47999995553 22 2479999999988654
No 90
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=74.92 E-value=1.8 Score=33.18 Aligned_cols=30 Identities=27% Similarity=0.626 Sum_probs=21.5
Q ss_pred EEccCcccccccc---CcccCCCCCccceeEEE
Q psy12603 247 LRCYACYKTTSIM---TKVFCPKCGYKTLKRVA 276 (391)
Q Consensus 247 lRC~aCf~~t~~~---~k~FCP~CGn~TL~Rvs 276 (391)
..|.+|...-... .+-.||.||..++.|++
T Consensus 8 ~~CtSCg~~i~~~~~~~~F~CPnCG~~~I~RC~ 40 (59)
T PRK14890 8 PKCTSCGIEIAPREKAVKFLCPNCGEVIIYRCE 40 (59)
T ss_pred ccccCCCCcccCCCccCEeeCCCCCCeeEeech
Confidence 4688888665422 46789999988777754
No 91
>PRK04023 DNA polymerase II large subunit; Validated
Probab=74.90 E-value=1.5 Score=49.99 Aligned_cols=22 Identities=36% Similarity=0.664 Sum_probs=13.4
Q ss_pred EEEccCccccccccCcccCCCCCcc
Q psy12603 246 ILRCYACYKTTSIMTKVFCPKCGYK 270 (391)
Q Consensus 246 vlRC~aCf~~t~~~~k~FCP~CGn~ 270 (391)
..+|..|.+.+ ...+||+||..
T Consensus 626 ~RfCpsCG~~t---~~frCP~CG~~ 647 (1121)
T PRK04023 626 RRKCPSCGKET---FYRRCPFCGTH 647 (1121)
T ss_pred CccCCCCCCcC---CcccCCCCCCC
Confidence 44777777764 34566666654
No 92
>PRK04023 DNA polymerase II large subunit; Validated
Probab=74.86 E-value=2.1 Score=48.97 Aligned_cols=31 Identities=29% Similarity=0.477 Sum_probs=25.3
Q ss_pred EEEEccCccccccccC-cccCCCCCccceeEE
Q psy12603 245 FILRCYACYKTTSIMT-KVFCPKCGYKTLKRV 275 (391)
Q Consensus 245 wvlRC~aCf~~t~~~~-k~FCP~CGn~TL~Rv 275 (391)
=..||..|..-++-|+ ..-||+||++.+.-|
T Consensus 1036 Q~fRC~kC~~kYRR~PL~G~C~kCGg~lilTV 1067 (1121)
T PRK04023 1036 QEFRCTKCGAKYRRPPLSGKCPKCGGNLILTV 1067 (1121)
T ss_pred cceeecccCcccccCCCCCcCccCCCeEEEEE
Confidence 3689999999998886 678999999865433
No 93
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=74.43 E-value=1.5 Score=34.11 Aligned_cols=14 Identities=50% Similarity=1.080 Sum_probs=9.5
Q ss_pred CCCCCcc--ceeEEEE
Q psy12603 264 CPKCGYK--TLKRVAV 277 (391)
Q Consensus 264 CP~CGn~--TL~Rvsv 277 (391)
||+|||. -.+-++.
T Consensus 7 CpKCgn~~~~ekei~~ 22 (68)
T COG3478 7 CPKCGNTNYEEKEIAA 22 (68)
T ss_pred CCCcCCcchhhceeec
Confidence 9999997 3444443
No 94
>COG1458 Predicted DNA-binding protein containing PIN domain [General function prediction only]
Probab=74.12 E-value=3.7 Score=38.80 Aligned_cols=26 Identities=19% Similarity=0.266 Sum_probs=20.6
Q ss_pred eEEEecCcHHHHHHHHHhCCceeccC
Q psy12603 210 VVSCVTTDFAMQNVLKQMGLNVVALD 235 (391)
Q Consensus 210 ~Vac~TtDfAMQNVllqmGL~l~s~~ 235 (391)
..|++++|..+---+-+|||.+|...
T Consensus 175 daavVssD~Gir~WAe~LGlrfv~a~ 200 (221)
T COG1458 175 DAAVVSSDEGIRTWAEKLGLRFVDAF 200 (221)
T ss_pred CceEEecchhHHHHHHHhCCeeeCHh
Confidence 34688888888888889999888543
No 95
>PRK05580 primosome assembly protein PriA; Validated
Probab=73.88 E-value=2.1 Score=47.39 Aligned_cols=32 Identities=34% Similarity=0.578 Sum_probs=22.8
Q ss_pred EEEEccCccccccccCcccCCCCCccceeEEEEE
Q psy12603 245 FILRCYACYKTTSIMTKVFCPKCGYKTLKRVAVS 278 (391)
Q Consensus 245 wvlRC~aCf~~t~~~~k~FCP~CGn~TL~Rvsvs 278 (391)
=.|+||-|....... ..||+||+..+.-...-
T Consensus 407 ~~l~Ch~Cg~~~~~~--~~Cp~Cg~~~l~~~g~G 438 (679)
T PRK05580 407 RRLRCHHCGYQEPIP--KACPECGSTDLVPVGPG 438 (679)
T ss_pred CeEECCCCcCCCCCC--CCCCCCcCCeeEEeecc
Confidence 357888898776544 56999999866654443
No 96
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=73.75 E-value=0.7 Score=42.43 Aligned_cols=52 Identities=23% Similarity=0.300 Sum_probs=33.1
Q ss_pred cHHHHHHHHHhCCceeccCccccceeeeEEEEccCcccccccc--Cccc-CCCCCcc
Q psy12603 217 DFAMQNVLKQMGLNVVALDGRLIRELRTFILRCYACYKTTSIM--TKVF-CPKCGYK 270 (391)
Q Consensus 217 DfAMQNVllqmGL~l~s~~G~~Ik~~r~wvlRC~aCf~~t~~~--~k~F-CP~CGn~ 270 (391)
=|+|+|||.++==++-+.-+-...... .|+||-|+.++++. +..| |..|=..
T Consensus 47 ~fs~~~~ls~~l~~~~t~~~~~~~~~e--~l~C~~C~~Tfk~f~~~g~fGCaeCY~t 101 (176)
T COG3880 47 VFSIHNVLSGELDNLKTKWQIEQEDEE--LLGCHNCGMTFKEFIQSGLFGCAECYKT 101 (176)
T ss_pred chhHHHHHHHHHhccccccchhhhHHH--HhcCccccccHHHHHHhcccchHHHHHH
Confidence 489999998762222233232122222 79999999998865 4555 9998553
No 97
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=73.69 E-value=1.8 Score=35.63 Aligned_cols=20 Identities=45% Similarity=0.921 Sum_probs=17.3
Q ss_pred CcccCCCCCccceeEEEEEE
Q psy12603 260 TKVFCPKCGYKTLKRVAVSV 279 (391)
Q Consensus 260 ~k~FCP~CGn~TL~Rvsvsv 279 (391)
.++-||.||.++++|++.-+
T Consensus 34 ~~~~Cp~C~~~~VkR~a~GI 53 (89)
T COG1997 34 AKHVCPFCGRTTVKRIATGI 53 (89)
T ss_pred cCCcCCCCCCcceeeeccCe
Confidence 57889999999999998754
No 98
>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=73.65 E-value=2.9 Score=28.76 Aligned_cols=28 Identities=25% Similarity=0.530 Sum_probs=21.0
Q ss_pred EEccCcccccccc-----CcccCCCCCccceeE
Q psy12603 247 LRCYACYKTTSIM-----TKVFCPKCGYKTLKR 274 (391)
Q Consensus 247 lRC~aCf~~t~~~-----~k~FCP~CGn~TL~R 274 (391)
..|..|.+++... .-..|..||..+..|
T Consensus 2 r~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L~qR 34 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNPPKVEGVCDNCGGELVQR 34 (36)
T ss_dssp EEETTTTEEEETTTB--SSTTBCTTTTEBEBEE
T ss_pred cCcCCCCCccccccCCCCCCCccCCCCCeeEeC
Confidence 4688898887654 247899999976665
No 99
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=73.54 E-value=2.3 Score=49.66 Aligned_cols=30 Identities=27% Similarity=0.485 Sum_probs=24.6
Q ss_pred eEEEEccCccccccccC-cccCCCCCcccee
Q psy12603 244 TFILRCYACYKTTSIMT-KVFCPKCGYKTLK 273 (391)
Q Consensus 244 ~wvlRC~aCf~~t~~~~-k~FCP~CGn~TL~ 273 (391)
+=..||..|..-++-|+ ..-||+||++.+.
T Consensus 1251 rQ~~RC~kC~~kyRR~PL~G~C~kCGg~iil 1281 (1337)
T PRK14714 1251 RQEFRCLKCGTKYRRMPLAGKCRKCGGRIIL 1281 (1337)
T ss_pred ccceeecccCcccccCCCCCcccccCCeEEE
Confidence 33689999999999886 7889999997443
No 100
>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=73.23 E-value=1.7 Score=28.30 Aligned_cols=10 Identities=50% Similarity=1.168 Sum_probs=5.8
Q ss_pred cCCCCCccce
Q psy12603 263 FCPKCGYKTL 272 (391)
Q Consensus 263 FCP~CGn~TL 272 (391)
+||.||.++.
T Consensus 1 ~CP~C~s~l~ 10 (28)
T PF03119_consen 1 TCPVCGSKLV 10 (28)
T ss_dssp B-TTT--BEE
T ss_pred CcCCCCCEeE
Confidence 6999999965
No 101
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=73.09 E-value=4.4 Score=35.89 Aligned_cols=35 Identities=29% Similarity=0.628 Sum_probs=25.5
Q ss_pred ccceeeeEEEEccCcccccc------ccCcccCCCCCccce
Q psy12603 238 LIRELRTFILRCYACYKTTS------IMTKVFCPKCGYKTL 272 (391)
Q Consensus 238 ~Ik~~r~wvlRC~aCf~~t~------~~~k~FCP~CGn~TL 272 (391)
.+..+++|.++|..|..... +..+..|-+||....
T Consensus 104 ~~~~~~~~~y~C~~C~~~~~~~rr~~~~~~y~C~~C~g~l~ 144 (146)
T smart00731 104 LIESVKKYPYRCTGCGQRYLRVRRSNNVSRYRCGKCGGKLI 144 (146)
T ss_pred cccccceEEEECCCCCCCCceEccccCcceEEcCCCCCEEE
Confidence 34444789999999987543 225689999998743
No 102
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=72.87 E-value=2.5 Score=33.30 Aligned_cols=20 Identities=25% Similarity=0.702 Sum_probs=14.4
Q ss_pred cccccCcccCCCCCccceeE
Q psy12603 255 TTSIMTKVFCPKCGYKTLKR 274 (391)
Q Consensus 255 ~t~~~~k~FCP~CGn~TL~R 274 (391)
-.+.+.+.||+.||.++...
T Consensus 42 s~~~~~r~FC~~CGs~l~~~ 61 (92)
T PF04828_consen 42 SGKGVERYFCPTCGSPLFSE 61 (92)
T ss_dssp TTSSCEEEEETTT--EEEEE
T ss_pred CCCcCcCcccCCCCCeeecc
Confidence 56667899999999997754
No 103
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=72.60 E-value=1.7 Score=33.34 Aligned_cols=31 Identities=29% Similarity=0.517 Sum_probs=22.9
Q ss_pred EEEccCccccc-ccc--CcccCCCCCccceeEEE
Q psy12603 246 ILRCYACYKTT-SIM--TKVFCPKCGYKTLKRVA 276 (391)
Q Consensus 246 vlRC~aCf~~t-~~~--~k~FCP~CGn~TL~Rvs 276 (391)
.-+|.+|...- +.- .+--||.||+.++.|++
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~~I~Rc~ 42 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGEVEIYRCA 42 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCceeeehhh
Confidence 56899999776 322 46679999998887765
No 104
>PF12773 DZR: Double zinc ribbon
Probab=72.43 E-value=2 Score=30.93 Aligned_cols=23 Identities=30% Similarity=0.710 Sum_probs=11.9
Q ss_pred ccCccccccccCcccCCCCCccce
Q psy12603 249 CYACYKTTSIMTKVFCPKCGYKTL 272 (391)
Q Consensus 249 C~aCf~~t~~~~k~FCP~CGn~TL 272 (391)
|..|.+...+ .-.|||+||.++.
T Consensus 1 Cp~Cg~~~~~-~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 1 CPHCGTPNPD-DAKFCPHCGTPLP 23 (50)
T ss_pred CCCcCCcCCc-cccCChhhcCChh
Confidence 4455554432 2456666666544
No 105
>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=72.03 E-value=2.5 Score=38.03 Aligned_cols=31 Identities=29% Similarity=0.605 Sum_probs=23.3
Q ss_pred EEEccCcccccccc---CcccCCCCCccceeEEE
Q psy12603 246 ILRCYACYKTTSIM---TKVFCPKCGYKTLKRVA 276 (391)
Q Consensus 246 vlRC~aCf~~t~~~---~k~FCP~CGn~TL~Rvs 276 (391)
.|+|..|....... .-.-||+||+..-.|.+
T Consensus 112 ~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~~F~R~~ 145 (146)
T PF07295_consen 112 TLVCENCGHEVELTHPERLPPCPKCGHTEFTRQP 145 (146)
T ss_pred eEecccCCCEEEecCCCcCCCCCCCCCCeeeeCC
Confidence 68999998654322 35679999999888765
No 106
>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.
Probab=71.93 E-value=7.1 Score=42.64 Aligned_cols=44 Identities=23% Similarity=0.476 Sum_probs=28.8
Q ss_pred HHHHHHHH---hCCceeccCccccceeeeEEEEccCccccccccCcccCCCCCccc
Q psy12603 219 AMQNVLKQ---MGLNVVALDGRLIRELRTFILRCYACYKTTSIMTKVFCPKCGYKT 271 (391)
Q Consensus 219 AMQNVllq---mGL~l~s~~G~~Ik~~r~wvlRC~aCf~~t~~~~k~FCP~CGn~T 271 (391)
|+.+++.. .||...+++-- +-+|..|..+.... ...||+||+..
T Consensus 510 a~~~lv~~~~~~~i~Y~tin~~--------~siC~~CGy~~g~~-~~~CP~CGs~~ 556 (586)
T TIGR02827 510 GYRKLLRVAADTGCNYFCFNIK--------ITICNDCHHIDKRT-LHRCPVCGSAN 556 (586)
T ss_pred HHHHHHHHHHhcCCceEEeCCC--------CeecCCCCCcCCCc-CCcCcCCCCcc
Confidence 45554443 36777766543 56899999854322 36899999864
No 107
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=71.60 E-value=2 Score=46.70 Aligned_cols=43 Identities=26% Similarity=0.516 Sum_probs=26.9
Q ss_pred HHHHHHH---HhCCceeccCccccceeeeEEEEccCccccccccCcccCCCCCcc
Q psy12603 219 AMQNVLK---QMGLNVVALDGRLIRELRTFILRCYACYKTTSIMTKVFCPKCGYK 270 (391)
Q Consensus 219 AMQNVll---qmGL~l~s~~G~~Ik~~r~wvlRC~aCf~~t~~~~k~FCP~CGn~ 270 (391)
|+..|+. ..|++.++++-- +-+|..|..+.. .....||+||+.
T Consensus 502 al~~lv~~a~~~~i~Y~~~n~~--------~~~C~~CG~~g~-~~~~~CP~Cgs~ 547 (579)
T TIGR02487 502 ALKDITKKAMKNGIGYFGINPP--------VDVCEDCGYTGE-GLNDKCPKCGSH 547 (579)
T ss_pred HHHHHHHHHHhcCCceEEeccC--------CccCCCCCCCCC-CCCCcCcCCCCc
Confidence 4444443 345666666432 568999997332 323689999986
No 108
>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=71.05 E-value=2.3 Score=36.38 Aligned_cols=23 Identities=35% Similarity=0.840 Sum_probs=16.2
Q ss_pred EccCccccccccCc--ccCCCCCcc
Q psy12603 248 RCYACYKTTSIMTK--VFCPKCGYK 270 (391)
Q Consensus 248 RC~aCf~~t~~~~k--~FCP~CGn~ 270 (391)
.|..|.+-+.++.| ..||+||.-
T Consensus 11 ~Cp~CG~kFYDLnk~PivCP~CG~~ 35 (108)
T PF09538_consen 11 TCPSCGAKFYDLNKDPIVCPKCGTE 35 (108)
T ss_pred cCCCCcchhccCCCCCccCCCCCCc
Confidence 58888877777653 458888875
No 109
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=70.44 E-value=3.6 Score=34.14 Aligned_cols=20 Identities=50% Similarity=1.002 Sum_probs=17.9
Q ss_pred CcccCCCCCccceeEEEEEE
Q psy12603 260 TKVFCPKCGYKTLKRVAVSV 279 (391)
Q Consensus 260 ~k~FCP~CGn~TL~Rvsvsv 279 (391)
.+.+||.||...++|+++-+
T Consensus 35 a~y~CpfCgk~~vkR~a~GI 54 (90)
T PTZ00255 35 AKYFCPFCGKHAVKRQAVGI 54 (90)
T ss_pred CCccCCCCCCCceeeeeeEE
Confidence 58999999999999999854
No 110
>COG2405 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=70.39 E-value=11 Score=33.87 Aligned_cols=62 Identities=23% Similarity=0.217 Sum_probs=40.1
Q ss_pred CceeechhHHHhhcCHHHHHHHhhCCCceEEecCChhhHHHHHHHHHHhCCCCCCChhhHHHHHHhhhhh
Q psy12603 4 DNVITIPEVVNEVTSKRQIRRLVVLPYDLQIKEADPDSISFVTEFSKKTGDYPSLSSTDIKVIALTYELH 73 (391)
Q Consensus 4 ~~~yT~p~Vi~EIrD~~sR~~L~~Lp~~L~vreP~~esi~~V~~FAkkTGD~~sLS~~DI~ViALtyeLe 73 (391)
++++++..|..|+-+-..+..+-.+|--++|..+++..+ |.-+=- .|-+-.-+-||||.++.
T Consensus 26 e~viip~~v~~E~~~~~~s~~~~~~l~~iei~~~~n~~l--v~~lre------~Ld~GEa~aIALA~e~~ 87 (157)
T COG2405 26 EKVIIPEQVAEEFEFGVNSGVLPALLGWIEILRLKNRDL--VNLLRE------KLDKGEAEAIALALELK 87 (157)
T ss_pred hcccCCchHHHHHHHhhcccccccccCceEEeccCcHHH--HHHHHH------hcccchHHHHHHHHHcC
Confidence 457788889999988766664445555588888887632 222221 14444567788888873
No 111
>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=70.25 E-value=3.8 Score=34.12 Aligned_cols=20 Identities=45% Similarity=0.855 Sum_probs=18.1
Q ss_pred CcccCCCCCccceeEEEEEE
Q psy12603 260 TKVFCPKCGYKTLKRVAVSV 279 (391)
Q Consensus 260 ~k~FCP~CGn~TL~Rvsvsv 279 (391)
.+.+||.||...++|+++-+
T Consensus 34 a~y~CpfCgk~~vkR~a~GI 53 (91)
T TIGR00280 34 AKYVCPFCGKKTVKRGSTGI 53 (91)
T ss_pred cCccCCCCCCCceEEEeeEE
Confidence 58999999999999999875
No 112
>PRK11032 hypothetical protein; Provisional
Probab=69.75 E-value=3 Score=38.13 Aligned_cols=32 Identities=28% Similarity=0.638 Sum_probs=24.3
Q ss_pred EEEccCcccccccc---CcccCCCCCccceeEEEE
Q psy12603 246 ILRCYACYKTTSIM---TKVFCPKCGYKTLKRVAV 277 (391)
Q Consensus 246 vlRC~aCf~~t~~~---~k~FCP~CGn~TL~Rvsv 277 (391)
+|+|-.|...+... .-.-||+||+..-.|++.
T Consensus 124 ~LvC~~Cg~~~~~~~p~~i~pCp~C~~~~F~R~~~ 158 (160)
T PRK11032 124 NLVCEKCHHHLAFYTPEVLPLCPKCGHDQFQRRPF 158 (160)
T ss_pred eEEecCCCCEEEecCCCcCCCCCCCCCCeeeeCCC
Confidence 68999998654422 356799999998888753
No 113
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=69.62 E-value=4.5 Score=39.53 Aligned_cols=37 Identities=35% Similarity=0.567 Sum_probs=25.5
Q ss_pred ceeccCccccceeeeEEEEccCcccccc-cc----Ccc----cCCCCCccce
Q psy12603 230 NVVALDGRLIRELRTFILRCYACYKTTS-IM----TKV----FCPKCGYKTL 272 (391)
Q Consensus 230 ~l~s~~G~~Ik~~r~wvlRC~aCf~~t~-~~----~k~----FCP~CGn~TL 272 (391)
+|+-++|- -+..||..|...+. +. ... -||+||.+.|
T Consensus 112 ~Vi~lHGs------l~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~~l 157 (250)
T COG0846 112 NVIELHGS------LKRVRCSKCGNQYYDEDVIKFIEDGLIPRCPKCGGPVL 157 (250)
T ss_pred cEEEeccc------eeeeEeCCCcCccchhhhhhhcccCCCCcCccCCCccc
Confidence 66788886 46788999976654 11 223 3999999833
No 114
>PRK06386 replication factor A; Reviewed
Probab=69.53 E-value=7 Score=40.17 Aligned_cols=48 Identities=13% Similarity=0.128 Sum_probs=36.1
Q ss_pred eeEEEEccCccccccccCcccCCCCCcc---ceeEEEEEEcCC-CcEEEeeccCC
Q psy12603 243 RTFILRCYACYKTTSIMTKVFCPKCGYK---TLKRVAVSVDEQ-GKQKIHINLKR 293 (391)
Q Consensus 243 r~wvlRC~aCf~~t~~~~k~FCP~CGn~---TL~Rvsvsvd~~-G~~~~hl~~n~ 293 (391)
..-+.||+-|.++-. +-+||.||-. -..|+-..+|.. |.+.+-|.+.-
T Consensus 233 sgli~rCP~C~R~l~---~g~C~~HG~v~~~~dlr~k~vLDDGtg~~~~~l~~e~ 284 (358)
T PRK06386 233 SRIFTKCSVCNKIIE---DGVCKDHPDAPVYLDIFGYFTISDGTGFVTCYANKDS 284 (358)
T ss_pred cEeEecCcCCCeEcc---CCcCCCCCCCCCeeEEEEEEEEECCCCeEEEEEChHH
Confidence 456889999999865 4699999974 567776667654 88888777653
No 115
>PRK05767 rpl44e 50S ribosomal protein L44e; Validated
Probab=69.27 E-value=4.4 Score=33.76 Aligned_cols=20 Identities=25% Similarity=0.551 Sum_probs=17.6
Q ss_pred CcccCCCCCccceeEEEEEE
Q psy12603 260 TKVFCPKCGYKTLKRVAVSV 279 (391)
Q Consensus 260 ~k~FCP~CGn~TL~Rvsvsv 279 (391)
-+-|||.|+..|+.+|+-+=
T Consensus 7 ~~tyCp~CkkHt~HkV~qyK 26 (92)
T PRK05767 7 IRTYCPYCKTHTEHEVEKVK 26 (92)
T ss_pred ccccCcCCCCcccEEEEEEe
Confidence 36799999999999999874
No 116
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=68.93 E-value=3.2 Score=44.91 Aligned_cols=24 Identities=33% Similarity=0.599 Sum_probs=18.4
Q ss_pred EEEccCccccccccCcccCCCCCcc
Q psy12603 246 ILRCYACYKTTSIMTKVFCPKCGYK 270 (391)
Q Consensus 246 vlRC~aCf~~t~~~~k~FCP~CGn~ 270 (391)
+.+|..|..+.. .....||+||+.
T Consensus 518 ~~~C~~CG~~~~-~~~~~CP~CGs~ 541 (555)
T cd01675 518 IDICNDCGYIGE-GEGFKCPKCGSE 541 (555)
T ss_pred CccCCCCCCCCc-CCCCCCcCCCCc
Confidence 449999998663 234789999987
No 117
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=68.49 E-value=6 Score=38.57 Aligned_cols=55 Identities=15% Similarity=0.257 Sum_probs=32.7
Q ss_pred EEccCcccccc---ccCcccCCCCCcccee----EEEEEEcCCCcEEEeeccCCccccCCcccccC
Q psy12603 247 LRCYACYKTTS---IMTKVFCPKCGYKTLK----RVAVSVDEQGKQKIHINLKRPLTARGKKFSLP 305 (391)
Q Consensus 247 lRC~aCf~~t~---~~~k~FCP~CGn~TL~----Rvsvsvd~~G~~~~hl~~n~~~n~RG~~ySlP 305 (391)
..|..|...+. .-.+..||+||.---- -|.|.|..+|++-+ -++..+ ....|++|
T Consensus 100 ~fC~~CG~~~~~~~~~~~~~C~~c~~~~yp~~~paViv~V~~~~~iLL--~rr~~~--~~g~wslP 161 (256)
T PRK00241 100 RFCGYCGHPMHPSKTEWAMLCPHCRERYYPRIAPCIIVAVRRGDEILL--ARHPRH--RNGVYTVL 161 (256)
T ss_pred ccccccCCCCeecCCceeEECCCCCCEECCCCCCEEEEEEEeCCEEEE--EEccCC--CCCcEeCc
Confidence 36888887653 2347789999975322 25555665555443 333323 25588976
No 118
>PHA00626 hypothetical protein
Probab=67.82 E-value=3.3 Score=31.46 Aligned_cols=17 Identities=29% Similarity=0.747 Sum_probs=13.0
Q ss_pred ccCCCCCccceeEEEEE
Q psy12603 262 VFCPKCGYKTLKRVAVS 278 (391)
Q Consensus 262 ~FCP~CGn~TL~Rvsvs 278 (391)
.+||.||+..+.|..+.
T Consensus 1 m~CP~CGS~~Ivrcg~c 17 (59)
T PHA00626 1 MSCPKCGSGNIAKEKTM 17 (59)
T ss_pred CCCCCCCCceeeeecee
Confidence 37999999877776653
No 119
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=67.80 E-value=2.8 Score=31.59 Aligned_cols=29 Identities=28% Similarity=0.483 Sum_probs=22.8
Q ss_pred EEEccCcccccc-ccCcccCCCCCccceeE
Q psy12603 246 ILRCYACYKTTS-IMTKVFCPKCGYKTLKR 274 (391)
Q Consensus 246 vlRC~aCf~~t~-~~~k~FCP~CGn~TL~R 274 (391)
.-+|..|....+ ....++||.||-+-=+.
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~ 34 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAPYHRD 34 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCcccHH
Confidence 458999998775 66789999999874443
No 120
>PRK02935 hypothetical protein; Provisional
Probab=67.75 E-value=3.7 Score=35.06 Aligned_cols=57 Identities=28% Similarity=0.407 Sum_probs=34.6
Q ss_pred CcHHHHHHHHHhCCcee-ccCccccceeeeEEEEccCccccccccC-cccCCCCCcc-ceeE
Q psy12603 216 TDFAMQNVLKQMGLNVV-ALDGRLIRELRTFILRCYACYKTTSIMT-KVFCPKCGYK-TLKR 274 (391)
Q Consensus 216 tDfAMQNVllqmGL~l~-s~~G~~Ik~~r~wvlRC~aCf~~t~~~~-k~FCP~CGn~-TL~R 274 (391)
+.|-+=-+|.-|+=-++ ---||.= .|.-...|..|.|.|+-.. -.-|..|+.+ ||.+
T Consensus 41 ~ifm~~G~l~~l~S~vvYFwiGmlS--tkavqV~CP~C~K~TKmLGrvD~CM~C~~PLTLd~ 100 (110)
T PRK02935 41 TIFMLLGFLAVIASTVVYFWIGMLS--TKAVQVICPSCEKPTKMLGRVDACMHCNQPLTLDR 100 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhc--ccceeeECCCCCchhhhccceeecCcCCCcCCcCc
Confidence 34444444444432222 2235432 3455569999999999665 4689999999 5543
No 121
>KOG3084|consensus
Probab=67.50 E-value=2 Score=43.25 Aligned_cols=13 Identities=46% Similarity=0.938 Sum_probs=9.3
Q ss_pred cccCCCCCcccee
Q psy12603 261 KVFCPKCGYKTLK 273 (391)
Q Consensus 261 k~FCP~CGn~TL~ 273 (391)
-+|||.||++|.-
T Consensus 150 ykFCp~CG~~tkp 162 (345)
T KOG3084|consen 150 YKFCPGCGSPTKP 162 (345)
T ss_pred hccCcccCCCccc
Confidence 3688888887653
No 122
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=67.44 E-value=6.5 Score=43.50 Aligned_cols=53 Identities=23% Similarity=0.375 Sum_probs=35.9
Q ss_pred CceEEEecCc-HHHHHHHHHh----CCceeccCccccceeeeEEEEccCccccccccCcccCCCCCcc
Q psy12603 208 PLVVSCVTTD-FAMQNVLKQM----GLNVVALDGRLIRELRTFILRCYACYKTTSIMTKVFCPKCGYK 270 (391)
Q Consensus 208 ~~~Vac~TtD-fAMQNVllqm----GL~l~s~~G~~Ik~~r~wvlRC~aCf~~t~~~~k~FCP~CGn~ 270 (391)
++-+.-+..| =|+.+++..| ++...+++-- +-+|+.|..+... ..-||+||++
T Consensus 591 hv~l~e~~~n~~a~~~lv~~~~~~~~i~Y~~in~~--------~~~C~~CG~~~g~--~~~CP~CG~~ 648 (656)
T PRK08270 591 HLYLGEAISDAEACKKLVKKALENYRLPYITITPT--------FSICPKHGYLSGE--HEFCPKCGEE 648 (656)
T ss_pred EEECCCCCCCHHHHHHHHHHHHHhCCCceEEeCCC--------CcccCCCCCcCCC--CCCCcCCcCc
Confidence 3344555555 5777777655 5777776543 5689999986533 4779999987
No 123
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=67.22 E-value=4.2 Score=27.91 Aligned_cols=25 Identities=40% Similarity=0.831 Sum_probs=18.5
Q ss_pred EEEccCcccccccc--------CcccCCCCCcc
Q psy12603 246 ILRCYACYKTTSIM--------TKVFCPKCGYK 270 (391)
Q Consensus 246 vlRC~aCf~~t~~~--------~k~FCP~CGn~ 270 (391)
+.+|..|.+.+... .+.-||+||+-
T Consensus 2 ~i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~ 34 (37)
T PF13719_consen 2 IITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHV 34 (37)
T ss_pred EEECCCCCceEEcCHHHcccCCcEEECCCCCcE
Confidence 35788898777644 36789999974
No 124
>PTZ00157 60S ribosomal protein L36a; Provisional
Probab=66.93 E-value=4.3 Score=33.29 Aligned_cols=20 Identities=35% Similarity=0.698 Sum_probs=17.5
Q ss_pred CcccCCCCCccceeEEEEEE
Q psy12603 260 TKVFCPKCGYKTLKRVAVSV 279 (391)
Q Consensus 260 ~k~FCP~CGn~TL~Rvsvsv 279 (391)
-+-|||.|+..|+.+|+-+=
T Consensus 8 ~~tyC~~C~kHt~HkV~qyK 27 (84)
T PTZ00157 8 RKTYCKKCGKHTSHKVSQYK 27 (84)
T ss_pred ccccCcCCCCCccEEEEEec
Confidence 36799999999999999863
No 125
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=66.74 E-value=5 Score=33.30 Aligned_cols=20 Identities=40% Similarity=0.869 Sum_probs=18.1
Q ss_pred CcccCCCCCccceeEEEEEE
Q psy12603 260 TKVFCPKCGYKTLKRVAVSV 279 (391)
Q Consensus 260 ~k~FCP~CGn~TL~Rvsvsv 279 (391)
.+..||.||...++|+++-+
T Consensus 35 a~y~CpfCgk~~vkR~a~GI 54 (90)
T PRK03976 35 AKHVCPVCGRPKVKRVGTGI 54 (90)
T ss_pred cCccCCCCCCCceEEEEEEE
Confidence 58899999999999999865
No 126
>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=66.71 E-value=5.9 Score=34.83 Aligned_cols=45 Identities=22% Similarity=0.378 Sum_probs=27.5
Q ss_pred eEEEEcc--Cccc-ccccc-CcccCCCCCccc-----eeEEEEEE-cCCCcEEEe
Q psy12603 244 TFILRCY--ACYK-TTSIM-TKVFCPKCGYKT-----LKRVAVSV-DEQGKQKIH 288 (391)
Q Consensus 244 ~wvlRC~--aCf~-~t~~~-~k~FCP~CGn~T-----L~Rvsvsv-d~~G~~~~h 288 (391)
-|=.-|. .|.+ +.... +..+|++||... ..++++.| |..|.+.+-
T Consensus 16 ~~Y~aC~~~~C~kKv~~~~~~~y~C~~C~~~~~~~~~ry~l~~~i~D~tg~~~~~ 70 (146)
T PF08646_consen 16 WYYPACPNEKCNKKVTENGDGSYRCEKCNKTVENPKYRYRLSLKISDGTGSIWVT 70 (146)
T ss_dssp TEEEE-TSTTTS-B-EEETTTEEEETTTTEEESS-EEEEEEEEEEEETTEEEEEE
T ss_pred cEECCCCCccCCCEeecCCCcEEECCCCCCcCCCeeEEEEEEEEEEeCCCeEEEE
Confidence 4777899 9997 55552 467999999762 33455544 445776543
No 127
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=66.54 E-value=3.8 Score=45.85 Aligned_cols=42 Identities=24% Similarity=0.488 Sum_probs=26.6
Q ss_pred HHHHHHH---HhCCceeccCccccceeeeEEEEccCccccccccCcccCCCCCcc
Q psy12603 219 AMQNVLK---QMGLNVVALDGRLIRELRTFILRCYACYKTTSIMTKVFCPKCGYK 270 (391)
Q Consensus 219 AMQNVll---qmGL~l~s~~G~~Ik~~r~wvlRC~aCf~~t~~~~k~FCP~CGn~ 270 (391)
||-.+.. ..|+..++++-- +-+|..|..+.. -...||+|||.
T Consensus 658 al~~lvk~~~~~~i~Y~sin~~--------~~~C~~CG~~~~--~~~~CP~CG~~ 702 (735)
T PRK07111 658 AFEIIVKAMKNTNIGYGSINHP--------VDRCPVCGYLGV--IEDKCPKCGST 702 (735)
T ss_pred HHHHHHHHHHhCCCceEEeCCC--------CeecCCCCCCCC--cCccCcCCCCc
Confidence 4444443 335555555432 668999995443 24789999985
No 128
>COG0384 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]
Probab=66.40 E-value=7.1 Score=39.00 Aligned_cols=56 Identities=23% Similarity=0.167 Sum_probs=33.2
Q ss_pred ceEEEec-----CcHHHHHHHHHhCCceeccCccccceeeeEEEEccCccccccccCcccCCCCCcccee
Q psy12603 209 LVVSCVT-----TDFAMQNVLKQMGLNVVALDGRLIRELRTFILRCYACYKTTSIMTKVFCPKCGYKTLK 273 (391)
Q Consensus 209 ~~Vac~T-----tDfAMQNVllqmGL~l~s~~G~~Ik~~r~wvlRC~aCf~~t~~~~k~FCP~CGn~TL~ 273 (391)
.++|++. +|-.||+++.+||+.--+.=- +...-..|.+|= +|+....-| ||++||=
T Consensus 20 Np~aVv~~a~~Lsd~~MQ~IA~e~n~SET~Fv~-~~~~~~~~rlR~-----FTP~~Evpf---~GHaTlg 80 (291)
T COG0384 20 NPLAVVLDADGLSDEQMQAIAREFNLSETAFVL-PPDDPADARLRI-----FTPTTEVPF---AGHATLG 80 (291)
T ss_pred CceEEEeCCCCCCHHHHHHHHHHhCCceeEEEc-CCCCcCceEEEE-----eCCCccccc---CCCHHHH
Confidence 4566665 899999999999997442100 000002344441 355455555 8999876
No 129
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=66.26 E-value=3.7 Score=36.58 Aligned_cols=48 Identities=25% Similarity=0.479 Sum_probs=33.7
Q ss_pred EEEecCcH---HHHHHHHHhCCc-ee-----ccCccccceeeeEEEEccCccccccc
Q psy12603 211 VSCVTTDF---AMQNVLKQMGLN-VV-----ALDGRLIRELRTFILRCYACYKTTSI 258 (391)
Q Consensus 211 Vac~TtDf---AMQNVllqmGL~-l~-----s~~G~~Ik~~r~wvlRC~aCf~~t~~ 258 (391)
-+.+++.| -+|++|.+.=-. |+ +++...|+.-|.|.|+|.||....+.
T Consensus 79 ~lii~G~~~~~~i~~~L~~yI~~yVlC~~C~spdT~l~k~~r~~~l~C~ACGa~~~V 135 (138)
T PRK03988 79 RLILQGKFSPRVINEKIDRYVKEYVICPECGSPDTKLIKEGRIWVLKCEACGAETPV 135 (138)
T ss_pred EEEEEEeeCHHHHHHHHHHHHHhcEECCCCCCCCcEEEEcCCeEEEEcccCCCCCcC
Confidence 44555555 467777654333 22 67888899989999999999987653
No 130
>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=66.11 E-value=5.2 Score=39.45 Aligned_cols=46 Identities=17% Similarity=0.481 Sum_probs=22.0
Q ss_pred EEEccCccccccccCcccCCCCCccceeEEEE-EEcCCCcEEEeeccC
Q psy12603 246 ILRCYACYKTTSIMTKVFCPKCGYKTLKRVAV-SVDEQGKQKIHINLK 292 (391)
Q Consensus 246 vlRC~aCf~~t~~~~k~FCP~CGn~TL~Rvsv-svd~~G~~~~hl~~n 292 (391)
.|.|.-|.+-.. ..|.-||.|||.--.+..+ +++.++.++++.=..
T Consensus 197 ~L~Cs~C~t~W~-~~R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~ 243 (290)
T PF04216_consen 197 YLHCSLCGTEWR-FVRIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCES 243 (290)
T ss_dssp EEEETTT--EEE---TTS-TTT---SS-EEE--------SEEEEEETT
T ss_pred EEEcCCCCCeee-ecCCCCcCCCCCCCcceeeEecCCCCcEEEEECCc
Confidence 589999998876 5589999999974444444 356666677765444
No 131
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=65.95 E-value=3.6 Score=27.81 Aligned_cols=24 Identities=21% Similarity=0.390 Sum_probs=17.7
Q ss_pred EEccCccc--cc-cccCcccCCCCCcc
Q psy12603 247 LRCYACYK--TT-SIMTKVFCPKCGYK 270 (391)
Q Consensus 247 lRC~aCf~--~t-~~~~k~FCP~CGn~ 270 (391)
.+|..|.. +. ++-...||+.||.-
T Consensus 4 ~~C~~C~~~~i~~~~~~~~~C~~Cg~~ 30 (33)
T PF08792_consen 4 KKCSKCGGNGIVNKEDDYEVCIFCGSS 30 (33)
T ss_pred eEcCCCCCCeEEEecCCeEEcccCCcE
Confidence 47888874 33 55678999999974
No 132
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=65.64 E-value=2.6 Score=45.56 Aligned_cols=24 Identities=33% Similarity=0.556 Sum_probs=12.2
Q ss_pred EEEccCccccccccCcccCCCCCccc
Q psy12603 246 ILRCYACYKTTSIMTKVFCPKCGYKT 271 (391)
Q Consensus 246 vlRC~aCf~~t~~~~k~FCP~CGn~T 271 (391)
+-+|..|..+... ...||+||+.-
T Consensus 491 ~~~C~~CG~~~~~--~~~CP~CGs~~ 514 (546)
T PF13597_consen 491 IDICPDCGYIGGE--GDKCPKCGSEN 514 (546)
T ss_dssp EEEETTT---S----EEE-CCC----
T ss_pred cccccCCCcCCCC--CCCCCCCCCcc
Confidence 6789999988765 67899999985
No 133
>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=65.43 E-value=3.6 Score=36.24 Aligned_cols=24 Identities=13% Similarity=0.113 Sum_probs=18.8
Q ss_pred EEccCccccccccCc--ccCCCCCcc
Q psy12603 247 LRCYACYKTTSIMTK--VFCPKCGYK 270 (391)
Q Consensus 247 lRC~aCf~~t~~~~k--~FCP~CGn~ 270 (391)
..|+.|.+-+.++.| ..||+||..
T Consensus 10 r~Cp~cg~kFYDLnk~p~vcP~cg~~ 35 (129)
T TIGR02300 10 RICPNTGSKFYDLNRRPAVSPYTGEQ 35 (129)
T ss_pred ccCCCcCccccccCCCCccCCCcCCc
Confidence 359999988887753 689999975
No 134
>KOG2906|consensus
Probab=64.84 E-value=2.8 Score=35.29 Aligned_cols=11 Identities=45% Similarity=1.355 Sum_probs=9.4
Q ss_pred ccCCCCCccce
Q psy12603 262 VFCPKCGYKTL 272 (391)
Q Consensus 262 ~FCP~CGn~TL 272 (391)
.|||.|||-++
T Consensus 2 ~FCP~Cgn~Li 12 (105)
T KOG2906|consen 2 LFCPTCGNMLI 12 (105)
T ss_pred cccCCCCCEEE
Confidence 69999999754
No 135
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=64.77 E-value=2.3 Score=43.15 Aligned_cols=38 Identities=34% Similarity=0.583 Sum_probs=27.0
Q ss_pred eeEEEEccCcccccccc----CcccCCCCCccceeEEEEEEc
Q psy12603 243 RTFILRCYACYKTTSIM----TKVFCPKCGYKTLKRVAVSVD 280 (391)
Q Consensus 243 r~wvlRC~aCf~~t~~~----~k~FCP~CGn~TL~Rvsvsvd 280 (391)
|-+.--|..||+.++-. .+--||+||....+-|+--|.
T Consensus 243 KY~~TAC~rC~t~y~le~A~~~~wrCpkCGg~ikKGV~dRv~ 284 (403)
T COG1379 243 KYHLTACSRCYTRYSLEEAKSLRWRCPKCGGKIKKGVSDRVL 284 (403)
T ss_pred chhHHHHHHhhhccCcchhhhhcccCcccccchhhhHHHHHH
Confidence 56667899999877633 256799999966665655443
No 136
>KOG1779|consensus
Probab=64.15 E-value=2.9 Score=33.86 Aligned_cols=26 Identities=31% Similarity=0.747 Sum_probs=20.3
Q ss_pred EEEccCcccccccc----CcccCCCCCccc
Q psy12603 246 ILRCYACYKTTSIM----TKVFCPKCGYKT 271 (391)
Q Consensus 246 vlRC~aCf~~t~~~----~k~FCP~CGn~T 271 (391)
.-+|.+||++|... +-..|+.|+--.
T Consensus 34 ~VkC~gc~~iT~vfSHaqtvVvc~~c~~il 63 (84)
T KOG1779|consen 34 DVKCPGCFKITTVFSHAQTVVVCEGCSTIL 63 (84)
T ss_pred EEEcCCceEEEEEeecCceEEEcCCCceEE
Confidence 45899999998744 567899998653
No 137
>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=63.70 E-value=2.3 Score=47.83 Aligned_cols=11 Identities=36% Similarity=0.658 Sum_probs=0.0
Q ss_pred CCceeeCCCCC
Q psy12603 314 NNPIVAEDQPV 324 (391)
Q Consensus 314 ~~~IL~EDQ~~ 324 (391)
.+|+-.+||..
T Consensus 802 G~pL~~~dQiv 812 (900)
T PF03833_consen 802 GKPLESDDQIV 812 (900)
T ss_dssp -----------
T ss_pred CCccCCcccee
Confidence 46788899853
No 138
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=62.75 E-value=3.7 Score=31.47 Aligned_cols=24 Identities=29% Similarity=0.641 Sum_probs=17.3
Q ss_pred EEccCccccccc----cCcccCCCCCcc
Q psy12603 247 LRCYACYKTTSI----MTKVFCPKCGYK 270 (391)
Q Consensus 247 lRC~aCf~~t~~----~~k~FCP~CGn~ 270 (391)
.+|..|+.+.-. .+...|+.||..
T Consensus 12 VkCp~C~n~q~vFsha~t~V~C~~Cg~~ 39 (59)
T PRK00415 12 VKCPDCGNEQVVFSHASTVVRCLVCGKT 39 (59)
T ss_pred EECCCCCCeEEEEecCCcEEECcccCCC
Confidence 478899887632 256888888875
No 139
>PF01623 Carla_C4: Carlavirus putative nucleic acid binding protein; InterPro: IPR002568 This family of carlavirus nucleic acid binding proteins includes a motif for a potential C-4 type zinc finger this has four highly conserved cysteine residues and is a conserved feature of the carlaviruses 3' terminal ORF []. These proteins may function as viral transcriptional regulators. The carlavirus family includes Garlic latent virus and Potato virus S and Potato virus M, these viruses are positive strand, ssRNA with no DNA stage.; GO: 0003676 nucleic acid binding, 0006355 regulation of transcription, DNA-dependent
Probab=62.56 E-value=3.5 Score=34.28 Aligned_cols=25 Identities=36% Similarity=0.708 Sum_probs=19.6
Q ss_pred EEEEccCccccccccCcccCCCCCccc
Q psy12603 245 FILRCYACYKTTSIMTKVFCPKCGYKT 271 (391)
Q Consensus 245 wvlRC~aCf~~t~~~~k~FCP~CGn~T 271 (391)
-+-|||-||++++.. .|=.+|-|.|
T Consensus 52 sigRC~RCyRv~Ppf--~~t~rCDnkT 76 (91)
T PF01623_consen 52 SIGRCHRCYRVYPPF--YFTKRCDNKT 76 (91)
T ss_pred HhCCCCCCeeecCCc--eeCccCCCCc
Confidence 367999999999743 5667888876
No 140
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=62.43 E-value=6 Score=27.10 Aligned_cols=25 Identities=40% Similarity=0.746 Sum_probs=18.3
Q ss_pred EEEccCcccccccc--------CcccCCCCCcc
Q psy12603 246 ILRCYACYKTTSIM--------TKVFCPKCGYK 270 (391)
Q Consensus 246 vlRC~aCf~~t~~~--------~k~FCP~CGn~ 270 (391)
..+|..|.+.+... .+.-||+||+.
T Consensus 2 ~i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 2 IITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHV 34 (36)
T ss_pred EEECCCCCCEEeCCHHHCCCCCcEEECCCCCCE
Confidence 35788998877644 35789999973
No 141
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=62.32 E-value=3.4 Score=30.75 Aligned_cols=22 Identities=32% Similarity=0.801 Sum_probs=12.8
Q ss_pred ccCcccccccc-------CcccCCCCCcc
Q psy12603 249 CYACYKTTSIM-------TKVFCPKCGYK 270 (391)
Q Consensus 249 C~aCf~~t~~~-------~k~FCP~CGn~ 270 (391)
|+||.+..+.. .+.-||+|++.
T Consensus 2 CfgC~~~~~~~~~~~~~~~~y~C~~C~~~ 30 (51)
T PF07975_consen 2 CFGCQKPFPDGPEKKADSSRYRCPKCKNH 30 (51)
T ss_dssp ETTTTEE-TTS-------EEE--TTTT--
T ss_pred CccCCCCCCCcccccccCCeEECCCCCCc
Confidence 78888777765 46778888764
No 142
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=62.02 E-value=5.1 Score=35.51 Aligned_cols=39 Identities=26% Similarity=0.451 Sum_probs=28.3
Q ss_pred HHHHHHHHhCCc-ee-----ccCccccceeeeEEEEccCcccccc
Q psy12603 219 AMQNVLKQMGLN-VV-----ALDGRLIRELRTFILRCYACYKTTS 257 (391)
Q Consensus 219 AMQNVllqmGL~-l~-----s~~G~~Ik~~r~wvlRC~aCf~~t~ 257 (391)
-+|++|...=-. |+ +++...|+.-|.|.|+|.||....+
T Consensus 85 ~i~~~L~~yI~~yVlC~~C~sPdT~l~k~~r~~~l~C~ACGa~~~ 129 (133)
T TIGR00311 85 LLNERIEDYVRKYVICRECNRPDTRIIKEGRVSLLKCEACGAKAP 129 (133)
T ss_pred HHHHHHHHHHhheEECCCCCCCCcEEEEeCCeEEEecccCCCCCc
Confidence 467777654322 22 6788888888999999999987654
No 143
>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=61.93 E-value=4.9 Score=25.39 Aligned_cols=21 Identities=29% Similarity=0.888 Sum_probs=12.6
Q ss_pred ccCcccccccc---CcccCCCCCc
Q psy12603 249 CYACYKTTSIM---TKVFCPKCGY 269 (391)
Q Consensus 249 C~aCf~~t~~~---~k~FCP~CGn 269 (391)
|..|...-... ..--||+||.
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCcccCceEeCCCCCC
Confidence 66775443322 3556999993
No 144
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=61.50 E-value=3 Score=32.00 Aligned_cols=21 Identities=48% Similarity=1.097 Sum_probs=14.8
Q ss_pred EEEccCccccccccCcccCCCCCc
Q psy12603 246 ILRCYACYKTTSIMTKVFCPKCGY 269 (391)
Q Consensus 246 vlRC~aCf~~t~~~~k~FCP~CGn 269 (391)
|.||+-|-+.. ...-||+||-
T Consensus 38 I~Rc~~CRk~g---~~Y~Cp~CGF 58 (61)
T COG2888 38 IYRCAKCRKLG---NPYRCPKCGF 58 (61)
T ss_pred eehhhhHHHcC---CceECCCcCc
Confidence 56777777654 3467999994
No 145
>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=61.42 E-value=5.5 Score=28.72 Aligned_cols=26 Identities=23% Similarity=0.474 Sum_probs=19.4
Q ss_pred CCCCCccceeEEEEEEcCCCcEEEee
Q psy12603 264 CPKCGYKTLKRVAVSVDEQGKQKIHI 289 (391)
Q Consensus 264 CP~CGn~TL~Rvsvsvd~~G~~~~hl 289 (391)
||.||.+...|.|--+.......++-
T Consensus 2 CP~Cg~~a~ir~S~~~s~~~~~~Y~q 27 (47)
T PF04606_consen 2 CPHCGSKARIRTSRQLSPLTRELYCQ 27 (47)
T ss_pred cCCCCCeeEEEEchhhCcceEEEEEE
Confidence 99999998888887776665544443
No 146
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=60.65 E-value=4.6 Score=30.67 Aligned_cols=32 Identities=25% Similarity=0.604 Sum_probs=25.3
Q ss_pred eeEEEEccCccccccccCcccCCCCCccceeE
Q psy12603 243 RTFILRCYACYKTTSIMTKVFCPKCGYKTLKR 274 (391)
Q Consensus 243 r~wvlRC~aCf~~t~~~~k~FCP~CGn~TL~R 274 (391)
+.-.+-|+-|-.-...+-...||+||+..++|
T Consensus 23 ~ICSfECTFC~~C~e~~l~~~CPNCgGelv~R 54 (57)
T PF06906_consen 23 YICSFECTFCADCAETMLNGVCPNCGGELVRR 54 (57)
T ss_pred eEEeEeCcccHHHHHHHhcCcCcCCCCccccC
Confidence 44557888888877777678999999987765
No 147
>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=60.39 E-value=8.4 Score=26.70 Aligned_cols=34 Identities=18% Similarity=0.243 Sum_probs=20.2
Q ss_pred ccceeeeEEEEccCccccccccCcccCCCCCccc
Q psy12603 238 LIRELRTFILRCYACYKTTSIMTKVFCPKCGYKT 271 (391)
Q Consensus 238 ~Ik~~r~wvlRC~aCf~~t~~~~k~FCP~CGn~T 271 (391)
..+.++++.+.--+...+..+++-.+|+.||-..
T Consensus 9 ~~~~~~~~~~~~~~~~~~i~~vp~~~C~~CGE~~ 42 (46)
T TIGR03831 9 LEGKTTTETYEYGGELIVIENVPALVCPQCGEEY 42 (46)
T ss_pred ecceEEEEEEEeCCEEEEEeCCCccccccCCCEe
Confidence 3444444444446666666666767777777653
No 148
>TIGR00308 TRM1 tRNA(guanine-26,N2-N2) methyltransferase. This enzyme is responsible for two methylations of a characteristic guanine of most tRNA molecules. The activity has been demonstrated for eukaryotic and archaeal proteins, which are active when expressed in E. coli, a species that lacks this enzyme. At least one Eubacterium, Aquifex aeolicus, has an ortholog, as do all completed archaeal genomes.
Probab=60.22 E-value=6.6 Score=40.48 Aligned_cols=27 Identities=22% Similarity=0.643 Sum_probs=20.2
Q ss_pred eEEEEccCccccccc----cCcccCCCCCcc
Q psy12603 244 TFILRCYACYKTTSI----MTKVFCPKCGYK 270 (391)
Q Consensus 244 ~wvlRC~aCf~~t~~----~~k~FCP~CGn~ 270 (391)
.|++.|+.|+..... .....||.||..
T Consensus 231 g~v~~C~~c~~~~~~~~~~~~~~~C~~c~~~ 261 (374)
T TIGR00308 231 GYTYHCSRCLHNKPVNGISQRKGRCKECGGE 261 (374)
T ss_pred eeEEECCCcccccccccccCCCCCCCCCCCc
Confidence 789999999876432 235689999984
No 149
>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=59.36 E-value=11 Score=28.84 Aligned_cols=45 Identities=22% Similarity=0.559 Sum_probs=30.0
Q ss_pred HHHHHHHhCCceeccCccccceeeeEEEEccCccccccc--c-CcccCCCCCcc
Q psy12603 220 MQNVLKQMGLNVVALDGRLIRELRTFILRCYACYKTTSI--M-TKVFCPKCGYK 270 (391)
Q Consensus 220 MQNVllqmGL~l~s~~G~~Ik~~r~wvlRC~aCf~~t~~--~-~k~FCP~CGn~ 270 (391)
|+-.+..-|+.|+-++=.--. ..|+.|...... . ....||.||..
T Consensus 8 L~yka~~~G~~v~~v~~~~TS------q~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 8 LEYKAEEYGIQVVEVDEAYTS------QTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred HHHHHHHhCCEEEEECCCCCc------cCccCcccccccccccceEEcCCCCCE
Confidence 444566678888777644332 359999887766 2 35679999864
No 150
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 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 zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. 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, 0005634 nucleus
Probab=59.16 E-value=5.4 Score=30.39 Aligned_cols=36 Identities=25% Similarity=0.369 Sum_probs=27.7
Q ss_pred ccceeeeEEEEccCcccccccc-C-cccCCCCCcccee
Q psy12603 238 LIRELRTFILRCYACYKTTSIM-T-KVFCPKCGYKTLK 273 (391)
Q Consensus 238 ~Ik~~r~wvlRC~aCf~~t~~~-~-k~FCP~CGn~TL~ 273 (391)
++..+-.|+--|..|.+|.=.. . ..-||.||++.+.
T Consensus 10 ~~H~L~~~~~NCl~CGkIiC~~Eg~~~pC~fCg~~l~~ 47 (57)
T PF06221_consen 10 RRHPLFPYAPNCLNCGKIICEQEGPLGPCPFCGTPLLS 47 (57)
T ss_pred ccCCCccccccccccChhhcccccCcCcCCCCCCcccC
Confidence 4566677889999999985444 3 5899999988654
No 151
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=59.07 E-value=4.6 Score=35.42 Aligned_cols=18 Identities=33% Similarity=0.739 Sum_probs=13.2
Q ss_pred cccCcccCCCCCccceeE
Q psy12603 257 SIMTKVFCPKCGYKTLKR 274 (391)
Q Consensus 257 ~~~~k~FCP~CGn~TL~R 274 (391)
....+.|||.||.++--+
T Consensus 65 ~~~~r~FC~~CGs~l~~~ 82 (133)
T COG3791 65 GSAGRGFCPTCGSPLFWR 82 (133)
T ss_pred CCCCCeecccCCCceEEe
Confidence 334577999999986544
No 152
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=58.75 E-value=5.9 Score=37.34 Aligned_cols=49 Identities=27% Similarity=0.470 Sum_probs=34.2
Q ss_pred EEEecCcHH---HHHHHHHh-CCcee-----ccCccccceeeeEEEEccCcccccccc
Q psy12603 211 VSCVTTDFA---MQNVLKQM-GLNVV-----ALDGRLIRELRTFILRCYACYKTTSIM 259 (391)
Q Consensus 211 Vac~TtDfA---MQNVllqm-GL~l~-----s~~G~~Ik~~r~wvlRC~aCf~~t~~~ 259 (391)
-+.+++.|. +|++|.+. --.|+ +++...|+.-|.|.|+|.||....+.-
T Consensus 75 ~~ii~G~~~~~~i~~~l~~yi~~yV~C~~C~~pdT~l~k~~~~~~l~C~aCGa~~~v~ 132 (201)
T PRK12336 75 RAVFNGKFTEEDIQAAIDAYVDEYVICSECGLPDTRLVKEDRVLMLRCDACGAHRPVK 132 (201)
T ss_pred EEEEEeeeCHHHHHHHHHHHHHheEECCCCCCCCcEEEEcCCeEEEEcccCCCCcccc
Confidence 456666663 66666552 22333 678888888899999999999887644
No 153
>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=58.07 E-value=10 Score=34.23 Aligned_cols=34 Identities=24% Similarity=0.384 Sum_probs=25.0
Q ss_pred eeEEEEccCccccccc-------------cCcccCCCCCccceeEEEE
Q psy12603 243 RTFILRCYACYKTTSI-------------MTKVFCPKCGYKTLKRVAV 277 (391)
Q Consensus 243 r~wvlRC~aCf~~t~~-------------~~k~FCP~CGn~TL~Rvsv 277 (391)
+.|-|+|. |...+-- ....-||.||+..+.|.-.
T Consensus 2 I~y~L~C~-~gH~FEgWF~ss~~fd~Q~~~glv~CP~Cgs~~V~K~lm 48 (148)
T PF06676_consen 2 IVYDLRCE-NGHEFEGWFRSSAAFDRQQARGLVSCPVCGSTEVSKALM 48 (148)
T ss_pred eeEEEecC-CCCccceecCCHHHHHHHHHcCCccCCCCCCCeEeeecC
Confidence 57899998 6665531 2567899999998877654
No 154
>COG4031 Predicted metal-binding protein [General function prediction only]
Probab=57.89 E-value=7.2 Score=36.66 Aligned_cols=32 Identities=34% Similarity=0.600 Sum_probs=21.3
Q ss_pred EEccCccccccccCcccCCCCCccceeEEEEEEcC
Q psy12603 247 LRCYACYKTTSIMTKVFCPKCGYKTLKRVAVSVDE 281 (391)
Q Consensus 247 lRC~aCf~~t~~~~k~FCP~CGn~TL~Rvsvsvd~ 281 (391)
++| -|..--..+ .||+.||-.-.--+-|++++
T Consensus 1 ~~C-rCG~~l~~p--~~Cl~Cg~~~av~~~vy~~~ 32 (227)
T COG4031 1 LIC-RCGAELSSP--AFCLNCGRRHAVGCGVYVSE 32 (227)
T ss_pred Ccc-ccCCccccc--chhcccCCcceeEeeeeccc
Confidence 478 787655444 99999999844444455443
No 155
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=57.45 E-value=6.3 Score=33.78 Aligned_cols=45 Identities=33% Similarity=0.483 Sum_probs=30.5
Q ss_pred eEEEecCcH---HHHHHHHHhC-Ccee-----ccCccccceeeeEEEEccCccc
Q psy12603 210 VVSCVTTDF---AMQNVLKQMG-LNVV-----ALDGRLIRELRTFILRCYACYK 254 (391)
Q Consensus 210 ~Vac~TtDf---AMQNVllqmG-L~l~-----s~~G~~Ik~~r~wvlRC~aCf~ 254 (391)
.-+.+++.| .+|++|...= --|+ ++|...|+.-|.|.|+|.||..
T Consensus 56 ~rlii~G~~~~~~i~~~l~~yI~~yVlC~~C~spdT~l~k~~r~~~l~C~aCGa 109 (110)
T smart00653 56 GRLIVNGRFTPKKLQDLLRRYIKEYVLCPECGSPDTELIKENRLFFLKCEACGA 109 (110)
T ss_pred CeEEEEEeeCHHHHHHHHHHHHHhcEECCCCCCCCcEEEEeCCeEEEEccccCC
Confidence 345666666 4666665432 2233 6788888888899999999974
No 156
>PRK07217 replication factor A; Reviewed
Probab=57.44 E-value=16 Score=36.85 Aligned_cols=50 Identities=20% Similarity=0.282 Sum_probs=37.1
Q ss_pred ceeeeEEEEccC--ccccccccCcccCCCCCcc---ceeEEEEEEcCC-CcEEEeeccC
Q psy12603 240 RELRTFILRCYA--CYKTTSIMTKVFCPKCGYK---TLKRVAVSVDEQ-GKQKIHINLK 292 (391)
Q Consensus 240 k~~r~wvlRC~a--Cf~~t~~~~k~FCP~CGn~---TL~Rvsvsvd~~-G~~~~hl~~n 292 (391)
+.=-..+.||.- |.++- .+-.||.||.. -..|+-..+|.. |.+.+-|++-
T Consensus 182 ~~GsglI~rCP~~~C~Rvl---~~g~C~~HG~ve~~~DLrik~vlDDGt~~~~~~~~~e 237 (311)
T PRK07217 182 QSGSGLIKRCPEEDCTRVL---QNGRCSEHGKVEGEFDLRIKGVLDDGEEVQEVIFNRE 237 (311)
T ss_pred eCCCCCeecCCccccCccc---cCCCCCCCCCcCCceeeEEEEEEECCCCeEEEEEChH
Confidence 333456889999 99976 56789999974 577888888764 6677666654
No 157
>PF14367 DUF4411: Domain of unknown function (DUF4411)
Probab=57.40 E-value=18 Score=32.71 Aligned_cols=71 Identities=17% Similarity=0.102 Sum_probs=44.1
Q ss_pred CceeechhHHHhhc--CHHHHHHHhhCCC-ceEEecCChhh---HHHHHHHH-HHhCCC------CCCChhhHHHHHHhh
Q psy12603 4 DNVITIPEVVNEVT--SKRQIRRLVVLPY-DLQIKEADPDS---ISFVTEFS-KKTGDY------PSLSSTDIKVIALTY 70 (391)
Q Consensus 4 ~~~yT~p~Vi~EIr--D~~sR~~L~~Lp~-~L~vreP~~es---i~~V~~FA-kkTGD~------~sLS~~DI~ViALty 70 (391)
..++++.+|.+||. +..-...+..++. ...+-.++... +..|..++ ..++-| .-|+..|--|||.|+
T Consensus 35 g~i~~~~~V~~El~~~~d~l~~W~k~~~~~~~~~~~~d~~~~~~~~~v~~~~~~~~~~~~~~a~~~f~~~ADp~LIA~A~ 114 (162)
T PF14367_consen 35 GRIISPDEVYDELERGDDELAKWAKNNEPKFFFFSTDDEAIQAEYAEVLNWVIINSQQYKKGAKDEFLSVADPWLIAYAK 114 (162)
T ss_pred CeEeehHHHHHHHhhCChhHHHHHHhCCccccccCCChHHHHHHHHHHHHHHhhcchhhchhHHhhhcccCCHHHHHHHH
Confidence 57899999999999 3333355554432 23444455334 44455553 222323 336999999999999
Q ss_pred hhhh
Q psy12603 71 ELHK 74 (391)
Q Consensus 71 eLe~ 74 (391)
....
T Consensus 115 ~~~~ 118 (162)
T PF14367_consen 115 AYGA 118 (162)
T ss_pred hcCC
Confidence 8544
No 158
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=56.14 E-value=16 Score=25.67 Aligned_cols=13 Identities=31% Similarity=0.861 Sum_probs=10.2
Q ss_pred cccCCCCCcccee
Q psy12603 261 KVFCPKCGYKTLK 273 (391)
Q Consensus 261 k~FCP~CGn~TL~ 273 (391)
...||.||+.++.
T Consensus 2 ~~~Cp~Cg~~~~~ 14 (47)
T PF14690_consen 2 PPRCPHCGSPSVH 14 (47)
T ss_pred CccCCCcCCCceE
Confidence 3579999998744
No 159
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=55.25 E-value=4.5 Score=31.59 Aligned_cols=26 Identities=27% Similarity=0.704 Sum_probs=13.7
Q ss_pred EEEEccCcccccccc------CcccCCCCCcc
Q psy12603 245 FILRCYACYKTTSIM------TKVFCPKCGYK 270 (391)
Q Consensus 245 wvlRC~aCf~~t~~~------~k~FCP~CGn~ 270 (391)
+.|||..|+.+.+++ +..||..|=..
T Consensus 6 ~lLrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~ 37 (65)
T PF14835_consen 6 ELLRCSICFDILKEPVCLGGCEHIFCSSCIRD 37 (65)
T ss_dssp HTTS-SSS-S--SS-B---SSS--B-TTTGGG
T ss_pred HhcCCcHHHHHhcCCceeccCccHHHHHHhHH
Confidence 358999999988766 57888888655
No 160
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=54.99 E-value=6.5 Score=43.24 Aligned_cols=44 Identities=25% Similarity=0.440 Sum_probs=28.4
Q ss_pred HHHHHHHHHh---CCceeccCccccceeeeEEEEccCccccccccCcccCCCCCcc
Q psy12603 218 FAMQNVLKQM---GLNVVALDGRLIRELRTFILRCYACYKTTSIMTKVFCPKCGYK 270 (391)
Q Consensus 218 fAMQNVllqm---GL~l~s~~G~~Ik~~r~wvlRC~aCf~~t~~~~k~FCP~CGn~ 270 (391)
=|+-.|...| ++...+++- =+-+|..|...... ....||+||+.
T Consensus 545 ~al~~lv~~~~~~~i~Y~~inp--------~~~~C~~CG~~~~g-~~~~CP~CGs~ 591 (625)
T PRK08579 545 EALAKLTKRIMNTKLVYWSYTP--------AITVCNKCGRSTTG-LYTRCPRCGSE 591 (625)
T ss_pred HHHHHHHHHHHhcCCceEEeCC--------CCccCCCCCCccCC-CCCcCcCCCCc
Confidence 4666766664 344444432 15689999985432 35789999986
No 161
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=54.17 E-value=6.6 Score=28.95 Aligned_cols=36 Identities=28% Similarity=0.701 Sum_probs=23.6
Q ss_pred eccCccccceeeeEEEEccCccc--cccccCcccCCCCCcc
Q psy12603 232 VALDGRLIRELRTFILRCYACYK--TTSIMTKVFCPKCGYK 270 (391)
Q Consensus 232 ~s~~G~~Ik~~r~wvlRC~aCf~--~t~~~~k~FCP~CGn~ 270 (391)
-.|++-.|++++.+ |.-|.. +.....+.-|++||..
T Consensus 9 y~v~~~~v~~~~~f---CP~Cg~~~m~~~~~r~~C~~Cgyt 46 (50)
T PRK00432 9 YEVDGGKVKRKNKF---CPRCGSGFMAEHLDRWHCGKCGYT 46 (50)
T ss_pred EEECCCEEEEccCc---CcCCCcchheccCCcEECCCcCCE
Confidence 35666678777764 555554 3333468899999964
No 162
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=54.09 E-value=7.9 Score=36.28 Aligned_cols=32 Identities=25% Similarity=0.607 Sum_probs=22.8
Q ss_pred EEccCcccc-ccccCcccCCCCCccceeEEEEE
Q psy12603 247 LRCYACYKT-TSIMTKVFCPKCGYKTLKRVAVS 278 (391)
Q Consensus 247 lRC~aCf~~-t~~~~k~FCP~CGn~TL~Rvsvs 278 (391)
-+|.-|... .+.-..+-||+|||--.+|+|.-
T Consensus 150 A~CsrC~~~L~~~~~~l~Cp~Cg~tEkRKia~~ 182 (188)
T COG1096 150 ARCSRCRAPLVKKGNMLKCPNCGNTEKRKIAKD 182 (188)
T ss_pred EEccCCCcceEEcCcEEECCCCCCEEeeeeccc
Confidence 367777643 22334588999999999999874
No 163
>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=54.03 E-value=7.6 Score=27.03 Aligned_cols=14 Identities=43% Similarity=0.755 Sum_probs=10.4
Q ss_pred ccCCCCCccceeEE
Q psy12603 262 VFCPKCGYKTLKRV 275 (391)
Q Consensus 262 ~FCP~CGn~TL~Rv 275 (391)
..||.||+....|-
T Consensus 2 ~~CP~Cg~~lv~r~ 15 (39)
T PF01396_consen 2 EKCPKCGGPLVLRR 15 (39)
T ss_pred cCCCCCCceeEEEE
Confidence 46999997766554
No 164
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=54.00 E-value=7.2 Score=42.91 Aligned_cols=36 Identities=31% Similarity=0.588 Sum_probs=25.5
Q ss_pred HhCCceeccCccccceeeeEEEEccCccccccccCcccCCCCCcc
Q psy12603 226 QMGLNVVALDGRLIRELRTFILRCYACYKTTSIMTKVFCPKCGYK 270 (391)
Q Consensus 226 qmGL~l~s~~G~~Ik~~r~wvlRC~aCf~~t~~~~k~FCP~CGn~ 270 (391)
..|++..+++-. +-+|..|..+.. .....||+||+.
T Consensus 554 ~~~i~Yf~in~~--------~~iC~~CG~~~~-g~~~~CP~CGs~ 589 (623)
T PRK08271 554 KTGCNYFAFNVK--------ITICNDCHHIDK-RTGKRCPICGSE 589 (623)
T ss_pred HcCCceEEeCCC--------CccCCCCCCcCC-CCCcCCcCCCCc
Confidence 346777766543 568999998732 345789999986
No 165
>PRK04860 hypothetical protein; Provisional
Probab=53.28 E-value=17 Score=33.24 Aligned_cols=29 Identities=28% Similarity=0.501 Sum_probs=20.1
Q ss_pred eeeEEEEccCcccccc----------ccCcccCCCCCccc
Q psy12603 242 LRTFILRCYACYKTTS----------IMTKVFCPKCGYKT 271 (391)
Q Consensus 242 ~r~wvlRC~aCf~~t~----------~~~k~FCP~CGn~T 271 (391)
.++|.++|. |.+... ...+.-|..||...
T Consensus 115 ~~~~~Y~C~-C~~~~~~~rrH~ri~~g~~~YrC~~C~~~l 153 (160)
T PRK04860 115 GKTFPYRCK-CQEHQLTVRRHNRVVRGEAVYRCRRCGETL 153 (160)
T ss_pred cCEEEEEcC-CCCeeCHHHHHHHHhcCCccEECCCCCcee
Confidence 367999997 954221 12458899999984
No 166
>COG0498 ThrC Threonine synthase [Amino acid transport and metabolism]
Probab=53.24 E-value=7.1 Score=40.84 Aligned_cols=33 Identities=27% Similarity=0.556 Sum_probs=25.4
Q ss_pred eeEEEEccCcccccccc-CcccCCCCCccceeEE
Q psy12603 243 RTFILRCYACYKTTSIM-TKVFCPKCGYKTLKRV 275 (391)
Q Consensus 243 r~wvlRC~aCf~~t~~~-~k~FCP~CGn~TL~Rv 275 (391)
+-+.+||+.|...+.+- -..+||.||..+....
T Consensus 2 ~~~~~rc~~cg~~f~~a~~~~~c~~cGl~lp~~~ 35 (411)
T COG0498 2 KYVSLRCLKCGREFSQALLQGLCPDCGLFLPAEY 35 (411)
T ss_pred ceeEeecCCCCcchhhHHhhCcCCcCCccccccc
Confidence 45789999999888743 4699999999755433
No 167
>TIGR03676 aRF1/eRF1 peptide chain release factor 1, archaeal and eukaryotic forms. Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. This model identifies both archaeal (aRF1) and eukaryotic (eRF1) of the protein. Also known as translation termination factor 1.
Probab=52.47 E-value=9.5 Score=39.72 Aligned_cols=27 Identities=26% Similarity=0.594 Sum_probs=20.2
Q ss_pred eEEEEccCccccccc-------cCcccCCCCCcc
Q psy12603 244 TFILRCYACYKTTSI-------MTKVFCPKCGYK 270 (391)
Q Consensus 244 ~wvlRC~aCf~~t~~-------~~k~FCP~CGn~ 270 (391)
++.+||..|...... ....|||.||..
T Consensus 318 r~~~rc~~c~~~~~~~~~~~~~~~~~~~~~~~~~ 351 (403)
T TIGR03676 318 RVTFKCPNCGYEEEKTVKPEEGDKSEACPKCGSE 351 (403)
T ss_pred eEEEEcCCCCcceeeecccccccccccCcccCcc
Confidence 579999999875431 123789999997
No 168
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=52.33 E-value=9.8 Score=39.28 Aligned_cols=27 Identities=26% Similarity=0.643 Sum_probs=20.0
Q ss_pred eEEEEccCcccccccc--CcccCCCCCcc
Q psy12603 244 TFILRCYACYKTTSIM--TKVFCPKCGYK 270 (391)
Q Consensus 244 ~wvlRC~aCf~~t~~~--~k~FCP~CGn~ 270 (391)
.|++.|+.|....-.. ....||.||.+
T Consensus 242 g~~~~C~~c~~~~~~~~~~~~~C~~c~~~ 270 (382)
T PRK04338 242 GYVYYCPKCLYREEVEGLPPEECPVCGGK 270 (382)
T ss_pred eeEEECCCCCcEEEecCCCCCCCCCCCCc
Confidence 6899999999765322 24579999984
No 169
>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=51.87 E-value=4.8 Score=45.39 Aligned_cols=10 Identities=50% Similarity=0.786 Sum_probs=0.0
Q ss_pred EEccCccccc
Q psy12603 247 LRCYACYKTT 256 (391)
Q Consensus 247 lRC~aCf~~t 256 (391)
.+|..|.+.|
T Consensus 656 r~Cp~Cg~~t 665 (900)
T PF03833_consen 656 RRCPKCGKET 665 (900)
T ss_dssp ----------
T ss_pred ccCcccCCcc
Confidence 3455554443
No 170
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=51.81 E-value=7.1 Score=32.04 Aligned_cols=24 Identities=29% Similarity=0.820 Sum_probs=18.7
Q ss_pred EEccCcccccccc----CcccCCCCCcc
Q psy12603 247 LRCYACYKTTSIM----TKVFCPKCGYK 270 (391)
Q Consensus 247 lRC~aCf~~t~~~----~k~FCP~CGn~ 270 (391)
.+|.+|+.++..- +-+.|..||..
T Consensus 36 VkCp~C~n~q~VFShA~t~V~C~~Cg~~ 63 (85)
T PTZ00083 36 VKCPGCSQITTVFSHAQTVVLCGGCSSQ 63 (85)
T ss_pred EECCCCCCeeEEEecCceEEEccccCCE
Confidence 4799999887644 57889999975
No 171
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=51.57 E-value=12 Score=34.63 Aligned_cols=29 Identities=21% Similarity=0.613 Sum_probs=23.3
Q ss_pred EccCcccc-cccc-CcccCCCCCccceeEEE
Q psy12603 248 RCYACYKT-TSIM-TKVFCPKCGYKTLKRVA 276 (391)
Q Consensus 248 RC~aCf~~-t~~~-~k~FCP~CGn~TL~Rvs 276 (391)
+|..|... .+.. ....||.||+-=.+|||
T Consensus 151 ~~~~~g~~~~~~~~~~~~c~~~~~~e~rkva 181 (189)
T PRK09521 151 MCSRCRTPLVKKGENELKCPNCGNIETRKLS 181 (189)
T ss_pred EccccCCceEECCCCEEECCCCCCEEeeccc
Confidence 88889874 4433 57899999998889998
No 172
>PRK08329 threonine synthase; Validated
Probab=51.43 E-value=8.4 Score=38.96 Aligned_cols=26 Identities=38% Similarity=0.715 Sum_probs=20.5
Q ss_pred EEEccCccccccccCcccCCCCCccce
Q psy12603 246 ILRCYACYKTTSIMTKVFCPKCGYKTL 272 (391)
Q Consensus 246 vlRC~aCf~~t~~~~k~FCP~CGn~TL 272 (391)
+|+|..|.+.++......| .||.+..
T Consensus 1 ~l~C~~Cg~~~~~~~~~~C-~c~~~l~ 26 (347)
T PRK08329 1 MLRCTKCGRTYEEKFKLRC-DCGGTLL 26 (347)
T ss_pred CcCcCCCCCCcCCCCceec-CCCCcEE
Confidence 4899999999986555779 6997643
No 173
>PLN00209 ribosomal protein S27; Provisional
Probab=51.11 E-value=7.1 Score=32.12 Aligned_cols=24 Identities=29% Similarity=0.854 Sum_probs=18.3
Q ss_pred EEccCcccccccc----CcccCCCCCcc
Q psy12603 247 LRCYACYKTTSIM----TKVFCPKCGYK 270 (391)
Q Consensus 247 lRC~aCf~~t~~~----~k~FCP~CGn~ 270 (391)
.+|.+|++++-.- +-+.|..||..
T Consensus 37 VkCp~C~n~q~VFShA~t~V~C~~Cg~~ 64 (86)
T PLN00209 37 VKCQGCFNITTVFSHSQTVVVCGSCQTV 64 (86)
T ss_pred EECCCCCCeeEEEecCceEEEccccCCE
Confidence 4799999876543 57889999875
No 174
>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=50.87 E-value=7.5 Score=28.98 Aligned_cols=24 Identities=29% Similarity=0.701 Sum_probs=17.3
Q ss_pred EEEccCcccccccc-----CcccCCCCCc
Q psy12603 246 ILRCYACYKTTSIM-----TKVFCPKCGY 269 (391)
Q Consensus 246 vlRC~aCf~~t~~~-----~k~FCP~CGn 269 (391)
-+||..|.++-... -..-||+||.
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~t 32 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKT 32 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCc
Confidence 36999999875542 2456999996
No 175
>PRK08197 threonine synthase; Validated
Probab=50.63 E-value=13 Score=38.27 Aligned_cols=29 Identities=34% Similarity=0.584 Sum_probs=21.6
Q ss_pred EEEEccCccccccccC-cccCCCCCccceeE
Q psy12603 245 FILRCYACYKTTSIMT-KVFCPKCGYKTLKR 274 (391)
Q Consensus 245 wvlRC~aCf~~t~~~~-k~FCP~CGn~TL~R 274 (391)
+.|+|..|.+.++... ...| .||.+....
T Consensus 6 ~~~~C~~Cg~~~~~~~~~~~C-~cg~~l~~~ 35 (394)
T PRK08197 6 SHLECSKCGETYDADQVHNLC-KCGKPLLVR 35 (394)
T ss_pred eEEEECCCCCCCCCCCcceec-CCCCeeEEE
Confidence 3599999999997554 4568 899875433
No 176
>COG4469 CoiA Competence protein CoiA-like family, contains a predicted nuclease domain [General function prediction only]
Probab=50.62 E-value=7.5 Score=39.47 Aligned_cols=14 Identities=36% Similarity=1.148 Sum_probs=11.3
Q ss_pred cccCCCCCccceeE
Q psy12603 261 KVFCPKCGYKTLKR 274 (391)
Q Consensus 261 k~FCP~CGn~TL~R 274 (391)
+-|||.||.+...|
T Consensus 25 ~ffCPaC~~~l~lK 38 (342)
T COG4469 25 RFFCPACGSQLILK 38 (342)
T ss_pred ccccCCCCCeeeee
Confidence 47999999996555
No 177
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=50.29 E-value=7.6 Score=38.76 Aligned_cols=37 Identities=27% Similarity=0.624 Sum_probs=25.3
Q ss_pred EEEEccCccccccc--c--CcccCCCCCccc----eeEEEEEEcCC
Q psy12603 245 FILRCYACYKTTSI--M--TKVFCPKCGYKT----LKRVAVSVDEQ 282 (391)
Q Consensus 245 wvlRC~aCf~~t~~--~--~k~FCP~CGn~T----L~Rvsvsvd~~ 282 (391)
| .+|..|..+... . ....||+||++- -.|+..-+|++
T Consensus 27 ~-~~c~~c~~~~~~~~l~~~~~vc~~c~~h~rl~areRi~~L~D~g 71 (292)
T PRK05654 27 W-TKCPSCGQVLYRKELEANLNVCPKCGHHMRISARERLDLLLDEG 71 (292)
T ss_pred e-eECCCccchhhHHHHHhcCCCCCCCCCCeeCCHHHHHHHHccCC
Confidence 5 489999987542 2 357899999973 24566656654
No 178
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=49.73 E-value=8 Score=32.24 Aligned_cols=37 Identities=27% Similarity=0.404 Sum_probs=24.6
Q ss_pred HHHHhCCceeccCccccceeeeEEEEccCcccccccc--C-cccCCCCCcc
Q psy12603 223 VLKQMGLNVVALDGRLIRELRTFILRCYACYKTTSIM--T-KVFCPKCGYK 270 (391)
Q Consensus 223 VllqmGL~l~s~~G~~Ik~~r~wvlRC~aCf~~t~~~--~-k~FCP~CGn~ 270 (391)
.|..+|-.|+-. --+|.-|...+.+. . ---||+|-+.
T Consensus 46 ~lkr~g~~Llv~-----------Pa~CkkCGfef~~~~ik~pSRCP~CKSE 85 (97)
T COG3357 46 SLKRKGKRLLVR-----------PARCKKCGFEFRDDKIKKPSRCPKCKSE 85 (97)
T ss_pred HHHhCCceEEec-----------ChhhcccCccccccccCCcccCCcchhh
Confidence 366777665522 24799999988872 1 2349999875
No 179
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=49.68 E-value=7.4 Score=37.96 Aligned_cols=14 Identities=29% Similarity=0.645 Sum_probs=11.5
Q ss_pred CcccCCCCCcccee
Q psy12603 260 TKVFCPKCGYKTLK 273 (391)
Q Consensus 260 ~k~FCP~CGn~TL~ 273 (391)
...|||.||.+|..
T Consensus 98 ~~~fC~~CG~~~~~ 111 (256)
T PRK00241 98 SHRFCGYCGHPMHP 111 (256)
T ss_pred cCccccccCCCCee
Confidence 46899999999754
No 180
>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=49.35 E-value=9 Score=39.89 Aligned_cols=26 Identities=27% Similarity=0.612 Sum_probs=21.1
Q ss_pred EEEccCccccccccCcccCCCCCccc
Q psy12603 246 ILRCYACYKTTSIMTKVFCPKCGYKT 271 (391)
Q Consensus 246 vlRC~aCf~~t~~~~k~FCP~CGn~T 271 (391)
+..||.|..+.....+-.||+||...
T Consensus 215 ~~~C~~Cd~~~~~~~~a~CpRC~~~L 240 (403)
T TIGR00155 215 LRSCSACHTTILPAQEPVCPRCSTPL 240 (403)
T ss_pred CCcCCCCCCccCCCCCcCCcCCCCcc
Confidence 44699999876666678899999985
No 181
>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=49.18 E-value=12 Score=28.14 Aligned_cols=27 Identities=26% Similarity=0.707 Sum_probs=18.9
Q ss_pred eeEEEEccCcccccc-------ccCcccCCCCCc
Q psy12603 243 RTFILRCYACYKTTS-------IMTKVFCPKCGY 269 (391)
Q Consensus 243 r~wvlRC~aCf~~t~-------~~~k~FCP~CGn 269 (391)
.+|.|.|.-|+...- ...+--||.||.
T Consensus 19 ~r~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 19 NRYALICSKCFSHNGLAPKEEFEEIQYRCPYCGA 52 (54)
T ss_pred CceeEECcccchhhcccccccCCceEEEcCCCCC
Confidence 478899999986532 223566999985
No 182
>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=49.14 E-value=12 Score=34.34 Aligned_cols=14 Identities=57% Similarity=1.148 Sum_probs=9.7
Q ss_pred CCCCCccceeEEEE
Q psy12603 264 CPKCGYKTLKRVAV 277 (391)
Q Consensus 264 CP~CGn~TL~Rvsv 277 (391)
||.||+++++...+
T Consensus 1 CP~Cg~~~~~~~~~ 14 (163)
T TIGR00340 1 CPVCGSRTLKAVTY 14 (163)
T ss_pred CCCCCCcceEeeeE
Confidence 78888777766433
No 183
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=48.96 E-value=10 Score=31.65 Aligned_cols=18 Identities=28% Similarity=0.791 Sum_probs=16.2
Q ss_pred cccCCCCCccceeEEEEE
Q psy12603 261 KVFCPKCGYKTLKRVAVS 278 (391)
Q Consensus 261 k~FCP~CGn~TL~Rvsvs 278 (391)
+-|||.|...|+..|+-+
T Consensus 8 ~tyCp~CkkhT~H~V~~~ 25 (94)
T COG1631 8 RTYCPYCKKHTIHKVERV 25 (94)
T ss_pred eecCcccccceeeeeeeh
Confidence 679999999999999875
No 184
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=48.90 E-value=6.8 Score=34.87 Aligned_cols=59 Identities=19% Similarity=0.377 Sum_probs=31.8
Q ss_pred ecCcHHHHHHHHHhCCceeccCccccceeeeEEEEccCcccccccc--------C-cccCCCCCccce
Q psy12603 214 VTTDFAMQNVLKQMGLNVVALDGRLIRELRTFILRCYACYKTTSIM--------T-KVFCPKCGYKTL 272 (391)
Q Consensus 214 ~TtDfAMQNVllqmGL~l~s~~G~~Ik~~r~wvlRC~aCf~~t~~~--------~-k~FCP~CGn~TL 272 (391)
+--+.+.+.|..+|-.-+-.+....-...-+-.+.|..|...+.-+ + +-.||.||....
T Consensus 67 i~y~~~~~vik~r~~~~~~~L~~~l~~e~~~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 67 INYDTLLDVVKYKLDKMRKRLEDKLEDETNNAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELE 134 (147)
T ss_pred ecHHHHHHHHHHHHHHHHHHHHHHHhcccCCcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEE
Confidence 3334444444444322221223333333345589999999766522 2 266999999743
No 185
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=48.72 E-value=19 Score=25.01 Aligned_cols=13 Identities=46% Similarity=1.198 Sum_probs=8.8
Q ss_pred CCCCCccceeEEEE
Q psy12603 264 CPKCGYKTLKRVAV 277 (391)
Q Consensus 264 CP~CGn~TL~Rvsv 277 (391)
||+|++ .|..+.+
T Consensus 2 CP~C~~-~l~~~~~ 14 (41)
T PF13453_consen 2 CPRCGT-ELEPVRL 14 (41)
T ss_pred cCCCCc-ccceEEE
Confidence 888877 4665555
No 186
>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=48.63 E-value=7.5 Score=32.28 Aligned_cols=12 Identities=50% Similarity=1.087 Sum_probs=9.2
Q ss_pred ccCCCCCcccee
Q psy12603 262 VFCPKCGYKTLK 273 (391)
Q Consensus 262 ~FCP~CGn~TL~ 273 (391)
.|||.||+-+..
T Consensus 1 ~fC~~Cg~~l~~ 12 (104)
T TIGR01384 1 KFCPKCGSLMTP 12 (104)
T ss_pred CCCcccCccccc
Confidence 489999988643
No 187
>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=48.35 E-value=15 Score=27.56 Aligned_cols=21 Identities=33% Similarity=1.081 Sum_probs=15.2
Q ss_pred EEccCccccccccCcccCCCCCc
Q psy12603 247 LRCYACYKTTSIMTKVFCPKCGY 269 (391)
Q Consensus 247 lRC~aCf~~t~~~~k~FCP~CGn 269 (391)
-.|..|..+. +....||.||.
T Consensus 27 ~~c~~cg~~~--~~H~vc~~cG~ 47 (56)
T PF01783_consen 27 VKCPNCGEPK--LPHRVCPSCGY 47 (56)
T ss_dssp EESSSSSSEE--STTSBCTTTBB
T ss_pred eeeccCCCEe--cccEeeCCCCe
Confidence 5788888654 46788888873
No 188
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=48.17 E-value=14 Score=43.93 Aligned_cols=27 Identities=26% Similarity=0.678 Sum_probs=23.3
Q ss_pred eeeeEEEEccCccccccccCcccCCCCCcc
Q psy12603 241 ELRTFILRCYACYKTTSIMTKVFCPKCGYK 270 (391)
Q Consensus 241 ~~r~wvlRC~aCf~~t~~~~k~FCP~CGn~ 270 (391)
.+--...||..|.+++. ...||.||..
T Consensus 669 ~vei~~~~Cp~Cg~~~~---~~~Cp~CG~~ 695 (1627)
T PRK14715 669 DIEIAFFKCPKCGKVGL---YHVCPFCGTR 695 (1627)
T ss_pred eEEEEeeeCCCCCCccc---cccCcccCCc
Confidence 67778899999999875 5779999987
No 189
>TIGR02820 formald_GSH S-(hydroxymethyl)glutathione synthase. The formation of S-(hydroxymethyl)glutathione synthase from glutathione and formaldehyde occurs naturally, but this enzyme speeds its formation in some species as part of a pathway of formaldehyde detoxification.
Probab=48.05 E-value=7.8 Score=36.17 Aligned_cols=20 Identities=20% Similarity=0.594 Sum_probs=15.1
Q ss_pred ccccCcccCCCCCccceeEE
Q psy12603 256 TSIMTKVFCPKCGYKTLKRV 275 (391)
Q Consensus 256 t~~~~k~FCP~CGn~TL~Rv 275 (391)
.....+.|||.||..+..+.
T Consensus 84 s~~~~R~FC~~CGS~L~~~~ 103 (182)
T TIGR02820 84 SATIQRHACKGCGTHMYGRI 103 (182)
T ss_pred CCCEEeecCCCCCCcccccc
Confidence 34446889999999976554
No 190
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=47.87 E-value=14 Score=37.72 Aligned_cols=40 Identities=23% Similarity=0.558 Sum_probs=17.8
Q ss_pred ccceeeeEEEEccCcccccc---ccCcccCCCCCccceeEEEEE
Q psy12603 238 LIRELRTFILRCYACYKTTS---IMTKVFCPKCGYKTLKRVAVS 278 (391)
Q Consensus 238 ~Ik~~r~wvlRC~aCf~~t~---~~~k~FCP~CGn~TL~Rvsvs 278 (391)
.+.-+|+| .+|..|..-|. .++..-|++||+.--.|+++-
T Consensus 278 ~~~a~KRF-FkC~~C~~Rt~sl~r~P~~~C~~Cg~~~wer~~M~ 320 (344)
T PF09332_consen 278 WHDAVKRF-FKCKDCGNRTISLERLPKKHCSNCGSSKWERTGML 320 (344)
T ss_dssp EEEEE-EE-EE-T-TS-EEEESSSS--S--TTT-S---EEE---
T ss_pred Eeeeeeee-EECCCCCCeeeecccCCCCCCCcCCcCceeehhhh
Confidence 45556777 58999986322 346789999999999999985
No 191
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=47.80 E-value=8.7 Score=38.47 Aligned_cols=37 Identities=24% Similarity=0.751 Sum_probs=26.2
Q ss_pred EEEEccCcccccc--cc--CcccCCCCCccc----eeEEEEEEcCC
Q psy12603 245 FILRCYACYKTTS--IM--TKVFCPKCGYKT----LKRVAVSVDEQ 282 (391)
Q Consensus 245 wvlRC~aCf~~t~--~~--~k~FCP~CGn~T----L~Rvsvsvd~~ 282 (391)
|. +|..|.++.. +. ....||+||++. ..|+..-+|++
T Consensus 38 w~-kc~~C~~~~~~~~l~~~~~vcp~c~~h~rltAreRI~~L~D~g 82 (296)
T CHL00174 38 WV-QCENCYGLNYKKFLKSKMNICEQCGYHLKMSSSDRIELLIDPG 82 (296)
T ss_pred ee-ECCCccchhhHHHHHHcCCCCCCCCCCcCCCHHHHHHHHccCC
Confidence 65 7999998754 22 357899999973 25777766754
No 192
>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=47.74 E-value=21 Score=27.79 Aligned_cols=18 Identities=33% Similarity=0.700 Sum_probs=12.5
Q ss_pred cCCCCCccceeEEEEEEc
Q psy12603 263 FCPKCGYKTLKRVAVSVD 280 (391)
Q Consensus 263 FCP~CGn~TL~Rvsvsvd 280 (391)
-||+|||....-=.|.+.
T Consensus 2 ~C~KCg~~~~e~~~v~~t 19 (64)
T PF09855_consen 2 KCPKCGNEEYESGEVRAT 19 (64)
T ss_pred CCCCCCCcceecceEEcc
Confidence 399999986655555543
No 193
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=47.55 E-value=8.3 Score=33.78 Aligned_cols=45 Identities=29% Similarity=0.485 Sum_probs=31.2
Q ss_pred EEEecCcH---HHHHHHHHhCCc-ee-----ccCccccceeeeEEEEccCcccc
Q psy12603 211 VSCVTTDF---AMQNVLKQMGLN-VV-----ALDGRLIRELRTFILRCYACYKT 255 (391)
Q Consensus 211 Vac~TtDf---AMQNVllqmGL~-l~-----s~~G~~Ik~~r~wvlRC~aCf~~ 255 (391)
.+.+.+-| .||++|...=-. |+ +++...++.-|.|.|+|.||...
T Consensus 70 ~lii~G~~~~~~i~~~L~~fI~~yVlC~~C~spdT~l~k~~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 70 RLIINGRFSSKQIQDLLDKFIKEYVLCPECGSPDTELIKEGRLIFLKCKACGAS 123 (125)
T ss_dssp EEEEESSSSCCHHHHHHHHHHCHHSSCTSTSSSSEEEEEETTCCEEEETTTSCE
T ss_pred EEEEEEecCHHHHHHHHHHHHHHEEEcCCCCCCccEEEEcCCEEEEEecccCCc
Confidence 44555555 577777654211 22 67888888899999999999864
No 194
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=47.36 E-value=11 Score=34.71 Aligned_cols=20 Identities=15% Similarity=0.313 Sum_probs=14.2
Q ss_pred EEecCcHHHHHHHHHhCCcee
Q psy12603 212 SCVTTDFAMQNVLKQMGLNVV 232 (391)
Q Consensus 212 ac~TtDfAMQNVllqmGL~l~ 232 (391)
.++|.|+-+=-=+ .+|++-+
T Consensus 50 IllTRDr~L~~r~-k~g~~~i 69 (165)
T COG1656 50 ILLTRDRELYKRA-KLGIKAI 69 (165)
T ss_pred EEEeccHHHHHHh-hccCceE
Confidence 3789998886555 5777655
No 195
>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=47.08 E-value=26 Score=35.28 Aligned_cols=24 Identities=25% Similarity=0.560 Sum_probs=20.3
Q ss_pred EEEccCccccccccCcccCCCCCcc
Q psy12603 246 ILRCYACYKTTSIMTKVFCPKCGYK 270 (391)
Q Consensus 246 vlRC~aCf~~t~~~~k~FCP~CGn~ 270 (391)
.|.|.-|..-.. +.|.-||.|||.
T Consensus 210 yL~CslC~teW~-~~R~~C~~Cg~~ 233 (305)
T TIGR01562 210 YLSCSLCATEWH-YVRVKCSHCEES 233 (305)
T ss_pred EEEcCCCCCccc-ccCccCCCCCCC
Confidence 588999998776 568999999985
No 196
>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=46.94 E-value=9.2 Score=38.06 Aligned_cols=37 Identities=24% Similarity=0.566 Sum_probs=25.6
Q ss_pred EEEEccCccccccc--c--CcccCCCCCccc----eeEEEEEEcCC
Q psy12603 245 FILRCYACYKTTSI--M--TKVFCPKCGYKT----LKRVAVSVDEQ 282 (391)
Q Consensus 245 wvlRC~aCf~~t~~--~--~k~FCP~CGn~T----L~Rvsvsvd~~ 282 (391)
|. +|..|..+... . .-..||+||++. ..|+..-+|++
T Consensus 26 ~~-~c~~c~~~~~~~~l~~~~~vc~~c~~h~rl~areRi~~L~D~g 70 (285)
T TIGR00515 26 WT-KCPKCGQVLYTKELERNLEVCPKCDHHMRMDARERIESLLDEG 70 (285)
T ss_pred ee-ECCCCcchhhHHHHHhhCCCCCCCCCcCcCCHHHHHHHceeCC
Confidence 65 79999987542 2 457899999972 34666666643
No 197
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=46.92 E-value=11 Score=41.42 Aligned_cols=34 Identities=24% Similarity=0.595 Sum_probs=22.3
Q ss_pred hCCceeccCccccceeeeEEEEccCccccccccCcccCCCCCcc
Q psy12603 227 MGLNVVALDGRLIRELRTFILRCYACYKTTSIMTKVFCPKCGYK 270 (391)
Q Consensus 227 mGL~l~s~~G~~Ik~~r~wvlRC~aCf~~t~~~~k~FCP~CGn~ 270 (391)
.|+..++++-- +-+|..|.. ... -..-||+||+.
T Consensus 548 ~~i~Y~sin~~--------~~~C~~CGy-~g~-~~~~CP~CG~~ 581 (618)
T PRK14704 548 HGVGYGSINHP--------VDRCKCCSY-HGV-IGNECPSCGNE 581 (618)
T ss_pred cCCceEEeCCC--------CeecCCCCC-CCC-cCccCcCCCCC
Confidence 35555555432 568999996 222 23569999986
No 198
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=46.90 E-value=8.4 Score=38.25 Aligned_cols=13 Identities=46% Similarity=1.065 Sum_probs=10.3
Q ss_pred CcccCCCCCccce
Q psy12603 260 TKVFCPKCGYKTL 272 (391)
Q Consensus 260 ~k~FCP~CGn~TL 272 (391)
+-.|||+||.+|-
T Consensus 110 ~~RFCg~CG~~~~ 122 (279)
T COG2816 110 SHRFCGRCGTKTY 122 (279)
T ss_pred hCcCCCCCCCcCc
Confidence 4589999999853
No 199
>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=46.89 E-value=8.7 Score=32.86 Aligned_cols=11 Identities=64% Similarity=1.204 Sum_probs=10.1
Q ss_pred CcccCCCCCcc
Q psy12603 260 TKVFCPKCGYK 270 (391)
Q Consensus 260 ~k~FCP~CGn~ 270 (391)
+|+.||+||.+
T Consensus 8 tKR~Cp~CG~k 18 (108)
T PF09538_consen 8 TKRTCPSCGAK 18 (108)
T ss_pred CcccCCCCcch
Confidence 69999999987
No 200
>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=46.77 E-value=9.9 Score=30.16 Aligned_cols=23 Identities=39% Similarity=0.904 Sum_probs=15.7
Q ss_pred EEEccCccccccccCcccCCCCCcc
Q psy12603 246 ILRCYACYKTTSIMTKVFCPKCGYK 270 (391)
Q Consensus 246 vlRC~aCf~~t~~~~k~FCP~CGn~ 270 (391)
.++|-+|.+-+.. .-|||.||.+
T Consensus 17 ~~~C~~C~~~~~~--~a~CPdC~~~ 39 (70)
T PF07191_consen 17 HYHCEACQKDYKK--EAFCPDCGQP 39 (70)
T ss_dssp EEEETTT--EEEE--EEE-TTT-SB
T ss_pred EEECcccccccee--cccCCCcccH
Confidence 6799999987653 4899999998
No 201
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=46.37 E-value=28 Score=29.50 Aligned_cols=22 Identities=45% Similarity=0.753 Sum_probs=19.0
Q ss_pred cccCCCCCccceeEEEEEEcCCCc
Q psy12603 261 KVFCPKCGYKTLKRVAVSVDEQGK 284 (391)
Q Consensus 261 k~FCP~CGn~TL~Rvsvsvd~~G~ 284 (391)
..+||.|+.+| ||..-++++|+
T Consensus 71 ~lv~p~~~k~~--rv~~~~~~~g~ 92 (104)
T TIGR01079 71 MLFDPKTGKAT--RVGIRFEEDGK 92 (104)
T ss_pred EEEcCcCCCCe--EEEEEEccCCc
Confidence 47999999998 88888888885
No 202
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=46.20 E-value=9.4 Score=36.91 Aligned_cols=26 Identities=15% Similarity=0.121 Sum_probs=16.8
Q ss_pred HHHHHHhCCCCCCChhhHHHHHHhhh
Q psy12603 46 TEFSKKTGDYPSLSSTDIKVIALTYE 71 (391)
Q Consensus 46 ~~FAkkTGD~~sLS~~DI~ViALtye 71 (391)
....++.+.+..|+.......++...
T Consensus 51 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 76 (364)
T COG0675 51 LTLLKKLEVYSELKELYSQALQQSSH 76 (364)
T ss_pred hhhhhhhccchhhhhhhhHHHHHHHH
Confidence 44556777777777777666655543
No 203
>KOG0402|consensus
Probab=46.08 E-value=6.6 Score=32.19 Aligned_cols=20 Identities=50% Similarity=0.801 Sum_probs=17.8
Q ss_pred CcccCCCCCccceeEEEEEE
Q psy12603 260 TKVFCPKCGYKTLKRVAVSV 279 (391)
Q Consensus 260 ~k~FCP~CGn~TL~Rvsvsv 279 (391)
.+.+|+-||..|++|-+|-+
T Consensus 35 aky~CsfCGK~~vKR~AvGi 54 (92)
T KOG0402|consen 35 AKYTCSFCGKKTVKRKAVGI 54 (92)
T ss_pred hhhhhhhcchhhhhhhceeE
Confidence 68899999999999998865
No 204
>KOG2768|consensus
Probab=45.49 E-value=11 Score=36.00 Aligned_cols=54 Identities=35% Similarity=0.803 Sum_probs=28.1
Q ss_pred CcHHHHHHHHHhCCceeccCccc---c---------ce-eeeEEE---EccCcccccccc---Cccc---CCCCCcc
Q psy12603 216 TDFAMQNVLKQMGLNVVALDGRL---I---------RE-LRTFIL---RCYACYKTTSIM---TKVF---CPKCGYK 270 (391)
Q Consensus 216 tDfAMQNVllqmGL~l~s~~G~~---I---------k~-~r~wvl---RC~aCf~~t~~~---~k~F---CP~CGn~ 270 (391)
.|--||=.|-+||-. -|+||.. | .. +|+||. .||.|.-.-... ++.| |.+||..
T Consensus 136 pdHv~~FLlAELgTs-GSidg~~rLviKGrfq~kq~e~VLRrYI~eyV~C~~CkSpdt~L~kenRLfFL~C~~cgs~ 211 (231)
T KOG2768|consen 136 PDHVMQFLLAELGTS-GSIDGQQRLVIKGRFQQKQFENVLRRYIKEYVTCKTCKSPDTILQKENRLFFLRCEKCGSR 211 (231)
T ss_pred hHHHHHHHHHHhccc-cccCCCceEEEeccccHHHHHHHHHHHHHHheEeeecCChhHHhhhhcceEEEEecCCCCe
Confidence 444566666676643 2444432 1 11 234442 588887543222 3444 8888876
No 205
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=45.11 E-value=11 Score=32.52 Aligned_cols=13 Identities=46% Similarity=1.081 Sum_probs=10.6
Q ss_pred ccCCCCCccceeE
Q psy12603 262 VFCPKCGYKTLKR 274 (391)
Q Consensus 262 ~FCP~CGn~TL~R 274 (391)
.|||+|||-.+-|
T Consensus 3 ~FCp~Cgsll~p~ 15 (113)
T COG1594 3 RFCPKCGSLLYPK 15 (113)
T ss_pred cccCCccCeeEEe
Confidence 7999999976554
No 206
>PRK05417 glutathione-dependent formaldehyde-activating enzyme; Provisional
Probab=44.64 E-value=8.8 Score=36.08 Aligned_cols=21 Identities=19% Similarity=0.615 Sum_probs=15.1
Q ss_pred ccccCcccCCCCCccceeEEE
Q psy12603 256 TSIMTKVFCPKCGYKTLKRVA 276 (391)
Q Consensus 256 t~~~~k~FCP~CGn~TL~Rvs 276 (391)
.....+.|||.||.++..++.
T Consensus 88 s~~i~R~FC~~CGS~L~~~~e 108 (191)
T PRK05417 88 SATIQRHACKECGVHMYGRIE 108 (191)
T ss_pred CCCeEeeeCCCCCCccccccc
Confidence 334468899999998765543
No 207
>COG1328 NrdD Oxygen-sensitive ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]
Probab=44.19 E-value=19 Score=40.13 Aligned_cols=45 Identities=22% Similarity=0.401 Sum_probs=26.4
Q ss_pred HHHHHHHH---HhCCceeccCccccceeeeEEEEccCccccccccCcccCCCCCccc
Q psy12603 218 FAMQNVLK---QMGLNVVALDGRLIRELRTFILRCYACYKTTSIMTKVFCPKCGYKT 271 (391)
Q Consensus 218 fAMQNVll---qmGL~l~s~~G~~Ik~~r~wvlRC~aCf~~t~~~~k~FCP~CGn~T 271 (391)
=|+.||.. .+++..++.+- . +-.|+-|.....-.... ||+||+.=
T Consensus 618 eal~~l~k~~~~~ri~Y~~~n~-~-------i~~C~~cg~~~~~~~~~-Cp~CG~~d 665 (700)
T COG1328 618 EALMDLTKYIYKTRIGYWGYTT-P-------ISVCNRCGYSGEGLRTR-CPKCGSED 665 (700)
T ss_pred HHHHHHHHHHHhcCcceEecCC-C-------ceeeccCCccccccccc-CCCCCCcc
Confidence 45666544 24666666532 3 44688898753311112 99999874
No 208
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=44.05 E-value=9.3 Score=37.64 Aligned_cols=34 Identities=35% Similarity=0.861 Sum_probs=20.9
Q ss_pred EEEccCcccccccc---------CcccCCCCCcccee--EEEEEE
Q psy12603 246 ILRCYACYKTTSIM---------TKVFCPKCGYKTLK--RVAVSV 279 (391)
Q Consensus 246 vlRC~aCf~~t~~~---------~k~FCP~CGn~TL~--Rvsvsv 279 (391)
-|||..||=-.-.- .-.-||+||..|-. -.|+|+
T Consensus 185 CLRCK~cfCddHvrrKg~ky~k~k~~PCPKCg~et~eTkdLSmSt 229 (314)
T PF06524_consen 185 CLRCKICFCDDHVRRKGFKYEKGKPIPCPKCGYETQETKDLSMST 229 (314)
T ss_pred hhheeeeehhhhhhhcccccccCCCCCCCCCCCcccccccceeee
Confidence 58999998321111 23459999998643 344443
No 209
>COG1743 Adenine-specific DNA methylase containing a Zn-ribbon [DNA replication, recombination, and repair]
Probab=43.97 E-value=15 Score=41.46 Aligned_cols=18 Identities=22% Similarity=0.613 Sum_probs=14.1
Q ss_pred eeeEEEEccCcccccccc
Q psy12603 242 LRTFILRCYACYKTTSIM 259 (391)
Q Consensus 242 ~r~wvlRC~aCf~~t~~~ 259 (391)
+=+|.-+|..|...|+-+
T Consensus 174 iw~w~VkCP~CG~~tP~v 191 (875)
T COG1743 174 IWTWEVKCPRCGRLTPLV 191 (875)
T ss_pred EEEEEEecCCcCccccCc
Confidence 457889999999888644
No 210
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=43.39 E-value=10 Score=29.04 Aligned_cols=27 Identities=26% Similarity=0.755 Sum_probs=23.7
Q ss_pred eEEEEccCccccccccCcccCCCCCcc
Q psy12603 244 TFILRCYACYKTTSIMTKVFCPKCGYK 270 (391)
Q Consensus 244 ~wvlRC~aCf~~t~~~~k~FCP~CGn~ 270 (391)
.--.+|.-|.+-....-|..|..||-+
T Consensus 14 ~tH~~CRRCGr~syhv~k~~CaaCGfg 40 (61)
T COG2126 14 KTHIRCRRCGRRSYHVRKKYCAACGFG 40 (61)
T ss_pred cceehhhhccchheeeccceecccCCC
Confidence 445689999999998999999999987
No 211
>PRK05978 hypothetical protein; Provisional
Probab=43.29 E-value=7.8 Score=35.02 Aligned_cols=28 Identities=32% Similarity=0.570 Sum_probs=19.3
Q ss_pred eeEEEEccCccc--ccccc--CcccCCCCCcc
Q psy12603 243 RTFILRCYACYK--TTSIM--TKVFCPKCGYK 270 (391)
Q Consensus 243 r~wvlRC~aCf~--~t~~~--~k~FCP~CGn~ 270 (391)
|-+..||..|.+ +++-. ...-||.||-.
T Consensus 30 rGl~grCP~CG~G~LF~g~Lkv~~~C~~CG~~ 61 (148)
T PRK05978 30 RGFRGRCPACGEGKLFRAFLKPVDHCAACGED 61 (148)
T ss_pred HHHcCcCCCCCCCcccccccccCCCccccCCc
Confidence 456789999973 33222 36779999986
No 212
>PRK11823 DNA repair protein RadA; Provisional
Probab=43.26 E-value=15 Score=38.71 Aligned_cols=30 Identities=27% Similarity=0.493 Sum_probs=23.8
Q ss_pred eEEEEccCccccccccCcccCCCCCc-cceeE
Q psy12603 244 TFILRCYACYKTTSIMTKVFCPKCGY-KTLKR 274 (391)
Q Consensus 244 ~wvlRC~aCf~~t~~~~k~FCP~CGn-~TL~R 274 (391)
.-.|+|..|...+..- --.||.||. .|+..
T Consensus 5 ~~~y~C~~Cg~~~~~~-~g~Cp~C~~w~t~~e 35 (446)
T PRK11823 5 KTAYVCQECGAESPKW-LGRCPECGAWNTLVE 35 (446)
T ss_pred CCeEECCcCCCCCccc-CeeCcCCCCccceee
Confidence 3478999999888744 467999998 48876
No 213
>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=42.63 E-value=12 Score=28.27 Aligned_cols=25 Identities=32% Similarity=0.782 Sum_probs=14.5
Q ss_pred EEEccCcccccccc----CcccCCCCCcc
Q psy12603 246 ILRCYACYKTTSIM----TKVFCPKCGYK 270 (391)
Q Consensus 246 vlRC~aCf~~t~~~----~k~FCP~CGn~ 270 (391)
-.+|.+|++++-.- +-..|..||..
T Consensus 7 ~VkCp~C~~~q~vFSha~t~V~C~~Cg~~ 35 (55)
T PF01667_consen 7 DVKCPGCYNIQTVFSHAQTVVKCVVCGTV 35 (55)
T ss_dssp EEE-TTT-SEEEEETT-SS-EE-SSSTSE
T ss_pred EEECCCCCCeeEEEecCCeEEEcccCCCE
Confidence 35788888876533 56788888874
No 214
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=42.49 E-value=2.8 Score=38.13 Aligned_cols=33 Identities=33% Similarity=0.780 Sum_probs=23.9
Q ss_pred cCccccceeeeEEEEccCccccccccCcccCCCCCccceeEEE
Q psy12603 234 LDGRLIRELRTFILRCYACYKTTSIMTKVFCPKCGYKTLKRVA 276 (391)
Q Consensus 234 ~~G~~Ik~~r~wvlRC~aCf~~t~~~~k~FCP~CGn~TL~Rvs 276 (391)
++|..|.. +|...+...-.||.+||..|+..+.
T Consensus 11 ~NGH~~t~----------~~~~~p~~~~~fC~kCG~~tI~~Cp 43 (158)
T PF10083_consen 11 LNGHVITD----------SYDKNPELREKFCSKCGAKTITSCP 43 (158)
T ss_pred cCcccccc----------ccccCchHHHHHHHHhhHHHHHHCc
Confidence 45777663 5555666667899999999888774
No 215
>COG5533 UBP5 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=41.92 E-value=24 Score=35.91 Aligned_cols=47 Identities=34% Similarity=0.477 Sum_probs=34.8
Q ss_pred ccCCCCCcc--ceeEEEEEEcCCCcEEEeeccCCccccCCcccccCCCCCCC
Q psy12603 262 VFCPKCGYK--TLKRVAVSVDEQGKQKIHINLKRPLTARGKKFSLPTFKGGK 311 (391)
Q Consensus 262 ~FCP~CGn~--TL~Rvsvsvd~~G~~~~hl~~n~~~n~RG~~ySlPkPkGGk 311 (391)
--||+||-+ .-+++.+++-.+ .+.+||++-. +..-| +|+|-.|.|=+
T Consensus 285 W~CpkC~~k~ss~K~~~I~~lP~-~LII~i~RF~-i~V~~-~~kiD~p~gw~ 333 (415)
T COG5533 285 WRCPKCGRKESSRKRMEILVLPD-VLIIHISRFH-ISVMG-RKKIDTPQGWK 333 (415)
T ss_pred ccCchhcccccchheEEEEecCc-eEEEEeeeee-EEeec-ccccCCCcchh
Confidence 469999975 778888887766 5778887654 44444 57888888755
No 216
>PF01850 PIN: PIN domain; InterPro: IPR002716 The PilT protein, N-terminal domain (PIN) is a compact domain of about 100 amino acids. The domain has two nearly invariant aspartates and forms a coiled-coil with other monomer units to polymerise a pilus fibre []. The function of the PIN domain is unknown but a role in signalling appears likely given the presence of this domain in some bacterial plasmid stability proteins and Dis3 from yeast that is implicated in mitotic control [].; PDB: 3TND_G 2H1O_B 2BSQ_B 2H1C_A 2FE1_A 3ZVK_C 1V8P_F 1V8O_C 3H87_A 1O4W_A ....
Probab=41.78 E-value=79 Score=25.41 Aligned_cols=68 Identities=18% Similarity=0.161 Sum_probs=52.3
Q ss_pred CceeechhHHHhhcCHHHH--------HHH--hhCCCceEEecCChhhHHHHHHHHHHhCCCCCCChhhHHHHHHhhhhh
Q psy12603 4 DNVITIPEVVNEVTSKRQI--------RRL--VVLPYDLQIKEADPDSISFVTEFSKKTGDYPSLSSTDIKVIALTYELH 73 (391)
Q Consensus 4 ~~~yT~p~Vi~EIrD~~sR--------~~L--~~Lp~~L~vreP~~esi~~V~~FAkkTGD~~sLS~~DI~ViALtyeLe 73 (391)
..+|+++-|+.|+----.| ..+ ..+...+.+...+.+.+....+.+.+.| |+..|.-++|+|....
T Consensus 29 ~~~~is~~~~~E~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~----~~~~Da~~~a~A~~~~ 104 (121)
T PF01850_consen 29 IEIVISSLVLAELLYVLRRRSKQQKAIALLELLILLSNFNILPITSEVFERAAELMRKYG----LDFADALIAATAKENG 104 (121)
T ss_dssp SEEEEEHHHHHHHHHHHHHSHCHHHHHHHHHHHHHHCTSEEEEBCHHHHHHHHHHHHHHH----SSHHHHHHHHHHHHHT
T ss_pred CCEEEcHHHHHHHHHHhhhccccchhhhHHHHHHHHhhhccccchhHHHHHHHHHHHhcc----CChhHHHHHHHHHHcC
Confidence 5688999999998765544 111 1222347888899999999999999988 9999999999998876
Q ss_pred hh
Q psy12603 74 KQ 75 (391)
Q Consensus 74 ~E 75 (391)
+.
T Consensus 105 ~~ 106 (121)
T PF01850_consen 105 AP 106 (121)
T ss_dssp -E
T ss_pred CE
Confidence 64
No 217
>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=41.71 E-value=16 Score=27.05 Aligned_cols=24 Identities=25% Similarity=0.527 Sum_probs=17.8
Q ss_pred EEccCccccccc------------------cCcccCCCCCcc
Q psy12603 247 LRCYACYKTTSI------------------MTKVFCPKCGYK 270 (391)
Q Consensus 247 lRC~aCf~~t~~------------------~~k~FCP~CGn~ 270 (391)
++|..|.-++.. +.---||.||.+
T Consensus 2 y~C~~CgyiYd~~~Gd~~~~i~pGt~f~~Lp~~w~CP~C~a~ 43 (50)
T cd00730 2 YECRICGYIYDPAEGDPDEGIPPGTPFEDLPDDWVCPVCGAG 43 (50)
T ss_pred cCCCCCCeEECCCCCCcccCcCCCCCHhHCCCCCCCCCCCCc
Confidence 689999988873 122369999975
No 218
>PRK05638 threonine synthase; Validated
Probab=41.30 E-value=16 Score=38.20 Aligned_cols=24 Identities=25% Similarity=0.628 Sum_probs=19.4
Q ss_pred EEEccCccccccccCcccCCCCCcc
Q psy12603 246 ILRCYACYKTTSIMTKVFCPKCGYK 270 (391)
Q Consensus 246 vlRC~aCf~~t~~~~k~FCP~CGn~ 270 (391)
.|+|..|.+.++......| .||..
T Consensus 1 ~l~C~~Cg~~~~~~~~~~C-~c~~~ 24 (442)
T PRK05638 1 KMKCPKCGREYNSYIPPFC-ICGEL 24 (442)
T ss_pred CeEeCCCCCCCCCCCceec-CCCCc
Confidence 3799999999875555779 89976
No 219
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=40.97 E-value=29 Score=34.52 Aligned_cols=58 Identities=22% Similarity=0.337 Sum_probs=33.9
Q ss_pred eEEEEccCcccccccc---CcccCCCCCccceeEE---EEEEcCCCcEEEeeccCCccccCCccccc
Q psy12603 244 TFILRCYACYKTTSIM---TKVFCPKCGYKTLKRV---AVSVDEQGKQKIHINLKRPLTARGKKFSL 304 (391)
Q Consensus 244 ~wvlRC~aCf~~t~~~---~k~FCP~CGn~TL~Rv---svsvd~~G~~~~hl~~n~~~n~RG~~ySl 304 (391)
...--|..|..-+... .+.-||+||+..-=|+ .+.+=.+|...+-+...+++ +-.||+
T Consensus 109 ~~~RFCg~CG~~~~~~~~g~~~~C~~cg~~~fPR~dP~vIv~v~~~~~ilLa~~~~h~---~g~yS~ 172 (279)
T COG2816 109 RSHRFCGRCGTKTYPREGGWARVCPKCGHEHFPRIDPCVIVAVIRGDEILLARHPRHF---PGMYSL 172 (279)
T ss_pred hhCcCCCCCCCcCccccCceeeeCCCCCCccCCCCCCeEEEEEecCCceeecCCCCCC---Ccceee
Confidence 3445699998665432 5889999999755443 23223344334545555443 455664
No 220
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=40.96 E-value=12 Score=38.40 Aligned_cols=27 Identities=30% Similarity=0.554 Sum_probs=21.8
Q ss_pred EEccCccccccccCcccCCCCCc-cceeE
Q psy12603 247 LRCYACYKTTSIMTKVFCPKCGY-KTLKR 274 (391)
Q Consensus 247 lRC~aCf~~t~~~~k~FCP~CGn-~TL~R 274 (391)
++|..|...++.- --.||.||. +|+..
T Consensus 1 ~~c~~cg~~~~~~-~g~cp~c~~w~~~~e 28 (372)
T cd01121 1 YVCSECGYVSPKW-LGKCPECGEWNTLVE 28 (372)
T ss_pred CCCCCCCCCCCCc-cEECcCCCCceeeee
Confidence 5899999887744 467999998 58876
No 221
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=40.81 E-value=18 Score=40.39 Aligned_cols=45 Identities=27% Similarity=0.500 Sum_probs=25.5
Q ss_pred HHHHHHHHh--CCceeccCccccceeeeEEEEccCcccccc---ccCcccCCCCCccc
Q psy12603 219 AMQNVLKQM--GLNVVALDGRLIRELRTFILRCYACYKTTS---IMTKVFCPKCGYKT 271 (391)
Q Consensus 219 AMQNVllqm--GL~l~s~~G~~Ik~~r~wvlRC~aCf~~t~---~~~k~FCP~CGn~T 271 (391)
|+.+|+..| |+...+++-- +-+|+.|...-- .+...-||+|||.-
T Consensus 620 a~~~lv~~~~~~i~Y~~in~~--------~~~C~~CG~~Ge~~~~~~~~~CP~CG~~~ 669 (711)
T PRK09263 620 ALEAVWDYSYDRVGYLGTNTP--------IDECYECGFTGEFECTEKGFTCPKCGNHD 669 (711)
T ss_pred HHHHHHHHHHHCCCeEEeCCC--------CcccCCCCCCccccCCCCCCcCcCCCCCC
Confidence 555554432 4555554322 568999997211 11135799999853
No 222
>PF10130 PIN_2: PIN domain; InterPro: IPR019298 This entry represents a set of bacterial and archaeal proteins that are predicted to be RNases (from similarities to 5'-exonucleases).
Probab=40.49 E-value=43 Score=29.49 Aligned_cols=68 Identities=15% Similarity=0.113 Sum_probs=48.3
Q ss_pred CceeechhHHHhhcCHHHH-------------HHHhhCCCceEEecCChhhHHHHHHHHHHhCCCCCCChhhHHHHHHhh
Q psy12603 4 DNVITIPEVVNEVTSKRQI-------------RRLVVLPYDLQIKEADPDSISFVTEFSKKTGDYPSLSSTDIKVIALTY 70 (391)
Q Consensus 4 ~~~yT~p~Vi~EIrD~~sR-------------~~L~~Lp~~L~vreP~~esi~~V~~FAkkTGD~~sLS~~DI~ViALty 70 (391)
-.|||+..++.||+....+ ..|..|.-.+++- |...+-....+..+..+|. -.-|+-.+|||.
T Consensus 27 ~~f~~p~~~~~Ei~kh~~~I~~k~~l~~~~~~~~l~~l~~~I~iv-~~~~~~~~~~~A~~~~~~~---D~~D~p~vALaL 102 (133)
T PF10130_consen 27 IEFFAPDYALEEIEKHLPKIAKKSKLSEEELEEVLNILFSRIKIV-PEEIYSENIEEAREIIRDR---DPDDWPFVALAL 102 (133)
T ss_pred hheeccHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHHhheEEe-cHHHhHHHHHHHHHHhcCC---CcchHHHHHHHH
Confidence 3689999999999864432 1122333235555 4555558888888888875 678999999999
Q ss_pred hhhhh
Q psy12603 71 ELHKQ 75 (391)
Q Consensus 71 eLe~E 75 (391)
+|.+-
T Consensus 103 ~l~~~ 107 (133)
T PF10130_consen 103 QLNAP 107 (133)
T ss_pred HcCCC
Confidence 99773
No 223
>PLN02569 threonine synthase
Probab=40.47 E-value=25 Score=37.54 Aligned_cols=53 Identities=15% Similarity=0.007 Sum_probs=34.5
Q ss_pred EecCcHHHHHHHHH-hCCceeccCccccceeeeEEEEccCccccccccC-cccCCCCCccc
Q psy12603 213 CVTTDFAMQNVLKQ-MGLNVVALDGRLIRELRTFILRCYACYKTTSIMT-KVFCPKCGYKT 271 (391)
Q Consensus 213 c~TtDfAMQNVllq-mGL~l~s~~G~~Ik~~r~wvlRC~aCf~~t~~~~-k~FCP~CGn~T 271 (391)
-.|.|-++|-+..+ .+.. .+.+--+ ..+-|+|..|.+.++... ...| .||..+
T Consensus 20 ~~~~~~~~~~~~~~~~~~~---~~~~~~~--~~~~l~C~~Cg~~y~~~~~~~~C-~cgg~l 74 (484)
T PLN02569 20 KFTADENIRDEARRGPPAP---PDEFSAK--YVPFLECPLTGEKYSLDEVVYRS-KSGGLL 74 (484)
T ss_pred ccCcchhhhhhhhhcCCCC---Ccccccc--cccccEeCCCCCcCCCccccccC-CCCCeE
Confidence 46889999999988 2222 2222212 223599999999987554 4568 799654
No 224
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=40.46 E-value=14 Score=38.67 Aligned_cols=27 Identities=26% Similarity=0.631 Sum_probs=20.9
Q ss_pred EEccCcccccccc-----CcccCCCCCcccee
Q psy12603 247 LRCYACYKTTSIM-----TKVFCPKCGYKTLK 273 (391)
Q Consensus 247 lRC~aCf~~t~~~-----~k~FCP~CGn~TL~ 273 (391)
..||.|..+.... .+-.||.||...-+
T Consensus 11 ~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~~ 42 (419)
T PRK15103 11 ILCPQCDMLVALPRLEHGQKAACPRCGTTLTV 42 (419)
T ss_pred ccCCCCCceeecCCCCCCCeeECCCCCCCCcC
Confidence 5599999988644 36789999998543
No 225
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=40.19 E-value=32 Score=31.12 Aligned_cols=44 Identities=39% Similarity=0.602 Sum_probs=28.6
Q ss_pred hCC-ceeccCccccceeeeEEEEccCcccccccc---------CcccCCCCCccceeEEEEE
Q psy12603 227 MGL-NVVALDGRLIRELRTFILRCYACYKTTSIM---------TKVFCPKCGYKTLKRVAVS 278 (391)
Q Consensus 227 mGL-~l~s~~G~~Ik~~r~wvlRC~aCf~~t~~~---------~k~FCP~CGn~TL~Rvsvs 278 (391)
-|+ +|+-+.|. .+.++|..|.+.+... ...-||.||.. .|-.|.
T Consensus 91 AG~~~vielHG~------l~~~~C~~C~~~~~~~~~~~~~~~~~~~~C~~C~~~--lrp~vv 144 (178)
T PF02146_consen 91 AGSPKVIELHGS------LFRLRCSKCGKEYDREDIVDSIDEEEPPRCPKCGGL--LRPDVV 144 (178)
T ss_dssp TTESCEEETTEE------EEEEEETTTSBEEEGHHHHHHHHTTSSCBCTTTSCB--EEEEE-
T ss_pred ccchhhHHHHhh------hceeeecCCCccccchhhcccccccccccccccCcc--CCCCee
Confidence 443 55567774 5678999999976422 23479999993 444443
No 226
>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=40.01 E-value=14 Score=25.97 Aligned_cols=22 Identities=27% Similarity=0.759 Sum_probs=10.0
Q ss_pred EccCccccc--cc--cCcccCCCCCc
Q psy12603 248 RCYACYKTT--SI--MTKVFCPKCGY 269 (391)
Q Consensus 248 RC~aCf~~t--~~--~~k~FCP~CGn 269 (391)
+|..|.... .| ....+|+.||.
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCGL 27 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-B
T ss_pred CCcCCcCCceEEcCCCCeEECCCCCC
Confidence 456665432 11 13446666664
No 227
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=39.99 E-value=17 Score=35.92 Aligned_cols=32 Identities=25% Similarity=0.541 Sum_probs=24.1
Q ss_pred cceeeeEEEEccCccccccccCcccCCCCCcc-cee
Q psy12603 239 IRELRTFILRCYACYKTTSIMTKVFCPKCGYK-TLK 273 (391)
Q Consensus 239 Ik~~r~wvlRC~aCf~~t~~~~k~FCP~CGn~-TL~ 273 (391)
|+.-..|+ |.-|..++.... -.||+||.- ||+
T Consensus 349 ~~~~p~~~--c~~cg~~~~~~~-~~c~~c~~~~~~~ 381 (389)
T PRK11788 349 LKRKPRYR--CRNCGFTARTLY-WHCPSCKAWETIK 381 (389)
T ss_pred HhCCCCEE--CCCCCCCCccce-eECcCCCCccCcC
Confidence 55555566 999999887664 789999984 654
No 228
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=39.95 E-value=5.7 Score=32.13 Aligned_cols=24 Identities=25% Similarity=0.695 Sum_probs=15.9
Q ss_pred EEccCccccccccCcccCCCCCcc
Q psy12603 247 LRCYACYKTTSIMTKVFCPKCGYK 270 (391)
Q Consensus 247 lRC~aCf~~t~~~~k~FCP~CGn~ 270 (391)
..|+.||..-..+..+-||.|+..
T Consensus 37 PvCr~CyEYErkeg~q~CpqCkt~ 60 (80)
T PF14569_consen 37 PVCRPCYEYERKEGNQVCPQCKTR 60 (80)
T ss_dssp ---HHHHHHHHHTS-SB-TTT--B
T ss_pred ccchhHHHHHhhcCcccccccCCC
Confidence 459999999999999999999965
No 229
>PF13887 MRF_C1: Myelin gene regulatory factor -C-terminal domain 1
Probab=39.69 E-value=21 Score=24.70 Aligned_cols=18 Identities=22% Similarity=0.314 Sum_probs=15.7
Q ss_pred hhhHHHHHHHHHHhCCCC
Q psy12603 39 PDSISFVTEFSKKTGDYP 56 (391)
Q Consensus 39 ~esi~~V~~FAkkTGD~~ 56 (391)
-|.|.+|.+.+|.||++.
T Consensus 10 mEnV~AvqeLck~t~~Le 27 (36)
T PF13887_consen 10 MENVGAVQELCKLTDNLE 27 (36)
T ss_pred HHHHHHHHHHHHHhccHH
Confidence 478999999999999864
No 230
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=39.61 E-value=18 Score=31.35 Aligned_cols=15 Identities=33% Similarity=0.913 Sum_probs=9.3
Q ss_pred CCCCCcc-ceeEEEEE
Q psy12603 264 CPKCGYK-TLKRVAVS 278 (391)
Q Consensus 264 CP~CGn~-TL~Rvsvs 278 (391)
||.||++ ...|+.|.
T Consensus 1 CPvCg~~l~vt~l~C~ 16 (113)
T PF09862_consen 1 CPVCGGELVVTRLKCP 16 (113)
T ss_pred CCCCCCceEEEEEEcC
Confidence 7777766 55555553
No 231
>TIGR00108 eRF peptide chain release factor eRF/aRF, subunit 1. Alternative names include eRF1, SUP45, omnipotent suppressor protein 1.
Probab=39.46 E-value=22 Score=37.16 Aligned_cols=28 Identities=21% Similarity=0.572 Sum_probs=19.3
Q ss_pred eEEEEccCcccccc-------ccCcccCCCCCccc
Q psy12603 244 TFILRCYACYKTTS-------IMTKVFCPKCGYKT 271 (391)
Q Consensus 244 ~wvlRC~aCf~~t~-------~~~k~FCP~CGn~T 271 (391)
++.+||..|..+-. +.....||.||...
T Consensus 322 r~~~r~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~ 356 (409)
T TIGR00108 322 RVTYKCAECGEVIEKTVRELKDKKFAICPACGQEM 356 (409)
T ss_pred eEEEEcCCCCceeecccccccccccccCcccCccc
Confidence 47899999985311 11235799999873
No 232
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=39.02 E-value=18 Score=38.17 Aligned_cols=29 Identities=21% Similarity=0.439 Sum_probs=23.2
Q ss_pred EEEEccCccccccccCcccCCCCCc-cceeE
Q psy12603 245 FILRCYACYKTTSIMTKVFCPKCGY-KTLKR 274 (391)
Q Consensus 245 wvlRC~aCf~~t~~~~k~FCP~CGn-~TL~R 274 (391)
-.|+|..|...++.. --.||.||. +|+.-
T Consensus 6 ~~y~C~~Cg~~~~~~-~g~Cp~C~~w~t~~~ 35 (454)
T TIGR00416 6 SKFVCQHCGADSPKW-QGKCPACHAWNTITE 35 (454)
T ss_pred CeEECCcCCCCCccc-cEECcCCCCccccch
Confidence 479999999888744 456999998 58876
No 233
>PF02005 TRM: N2,N2-dimethylguanosine tRNA methyltransferase; InterPro: IPR002905 This enzyme 2.1.1.32 from EC uses S-adenosyl-L-methionine to methylate tRNA: S-AdoMet + tRNA = S-adenosyl-L-homocysteine + tRNA containing N2-methylguanine The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs []. The enzyme is found in both eukaryotes and archaea [].; GO: 0003723 RNA binding, 0004809 tRNA (guanine-N2-)-methyltransferase activity, 0008033 tRNA processing; PDB: 2YTZ_B 2DUL_A 2EJU_A 2EJT_A 3AXT_A 3AXS_A.
Probab=38.51 E-value=19 Score=37.25 Aligned_cols=38 Identities=21% Similarity=0.411 Sum_probs=20.8
Q ss_pred eeEEEEccCcccc--ccccC--cccCCCCCccceeEEEEEEc
Q psy12603 243 RTFILRCYACYKT--TSIMT--KVFCPKCGYKTLKRVAVSVD 280 (391)
Q Consensus 243 r~wvlRC~aCf~~--t~~~~--k~FCP~CGn~TL~Rvsvsvd 280 (391)
-.|++.|+.|... ..... +..||.||...-.-=++.++
T Consensus 237 ~G~v~~C~~C~~~~~~~~~~~~~~~c~~cg~~~~~~GPlWlG 278 (377)
T PF02005_consen 237 LGYVYYCPSCGYREEVKGLQKLKSKCPECGSKLHISGPLWLG 278 (377)
T ss_dssp EEEEEEETTT--EECCT-GCC--CEETTT-SCCCEEEEEE-S
T ss_pred eeEEEECCCccccccccCccccCCcCCCCCCccceecCcccc
Confidence 4799999999742 12121 37799999885444444443
No 234
>TIGR00028 Mtu_PIN_fam Mycobacterium tuberculosis PIN domain family. Members of this protein consist almost entirely of a PIN (PilT N terminus) domain (see Pfam pfam01850). This family was originally defined a set of twelve closely related paralogs found in Mycobacterium tuberculosis. Two more are now found in Synechococcus sp. WH8102. The specific function is unknown but may be in signal transduction.
Probab=38.34 E-value=1.4e+02 Score=24.94 Aligned_cols=83 Identities=11% Similarity=0.051 Sum_probs=47.8
Q ss_pred CceeechhHHHhhcC--------------HHHHHHHhhC--CCceEEecCChhhHHHHHHHHHHhCCCCCCChhhHHHHH
Q psy12603 4 DNVITIPEVVNEVTS--------------KRQIRRLVVL--PYDLQIKEADPDSISFVTEFSKKTGDYPSLSSTDIKVIA 67 (391)
Q Consensus 4 ~~~yT~p~Vi~EIrD--------------~~sR~~L~~L--p~~L~vreP~~esi~~V~~FAkkTGD~~sLS~~DI~ViA 67 (391)
..+++++.|+.|+.- ...++.|..+ ...+.+-.|.+........+++.-|+ ..++-.|..++|
T Consensus 34 ~~~~~~~~vl~E~~~~l~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~D~~i~a 112 (142)
T TIGR00028 34 GDWATCPLTLAGFVRLLTNPRVLPAPLSPAEAIAVVAAFLATPRHRLLWPGPRHLAVLRGLADPVIA-GGRLVTDAHLAA 112 (142)
T ss_pred CCceechhhhhhheeeeccCCcCCCCCCHHHHHHHHHHHHhCCCeeecCCCcchHHHHHHHHHHhcc-CCCCchHHHHHH
Confidence 346788899999722 2223434432 12355556666544444555555443 346789999999
Q ss_pred HhhhhhhhccC-ccccccCCc
Q psy12603 68 LTYELHKQHIG-VDSINTEPI 87 (391)
Q Consensus 68 LtyeLe~E~~G-~~~Lr~~P~ 87 (391)
+|.+..+.-.. ..+++..++
T Consensus 113 ~A~~~~~~lvT~D~~f~~~~~ 133 (142)
T TIGR00028 113 LAREHGAELVTFDRGFARFAG 133 (142)
T ss_pred HHHHcCCEEEecCCCccccCC
Confidence 99988754222 225554443
No 235
>PRK04011 peptide chain release factor 1; Provisional
Probab=37.62 E-value=23 Score=36.98 Aligned_cols=27 Identities=26% Similarity=0.651 Sum_probs=20.5
Q ss_pred eEEEEccCcccccc-------ccCcccCCCCCcc
Q psy12603 244 TFILRCYACYKTTS-------IMTKVFCPKCGYK 270 (391)
Q Consensus 244 ~wvlRC~aCf~~t~-------~~~k~FCP~CGn~ 270 (391)
++.+||..|..... ......||.||..
T Consensus 326 r~~~~c~~c~~~~~~~~~~~~~~~~~~c~~~~~~ 359 (411)
T PRK04011 326 RVTYKCPNCGYEEEKTVKRREELPEKTCPKCGSE 359 (411)
T ss_pred eEEEEcCCCCcceeeecccccccccccCcccCcc
Confidence 47999999987532 1245799999987
No 236
>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=37.57 E-value=11 Score=27.67 Aligned_cols=32 Identities=31% Similarity=0.575 Sum_probs=17.7
Q ss_pred ccceeeeEEE--EccCccccccccCcccCCCCCc
Q psy12603 238 LIRELRTFIL--RCYACYKTTSIMTKVFCPKCGY 269 (391)
Q Consensus 238 ~Ik~~r~wvl--RC~aCf~~t~~~~k~FCP~CGn 269 (391)
.|.++|..=- +|-+--.+-.--.|..|.+||.
T Consensus 13 kv~r~rk~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 13 KVKRLRKECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp EEEESSEE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred cEEEhhhcCCCcccCCceEeeecCCCccCCCccc
Confidence 4777666544 4444222333346888888884
No 237
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=37.34 E-value=23 Score=37.20 Aligned_cols=37 Identities=22% Similarity=0.423 Sum_probs=27.7
Q ss_pred cCccccceeeeEEE---EccCccccccccCc--ccCCCCCcc
Q psy12603 234 LDGRLIRELRTFIL---RCYACYKTTSIMTK--VFCPKCGYK 270 (391)
Q Consensus 234 ~~G~~Ik~~r~wvl---RC~aCf~~t~~~~k--~FCP~CGn~ 270 (391)
+.-++|.+|-.|.. +|.-|...++.-.+ --||+||..
T Consensus 335 ~ek~~v~~l~~~~~~~p~Cp~Cg~~m~S~G~~g~rC~kCg~~ 376 (421)
T COG1571 335 LEKFQVLKLARYERVNPVCPRCGGRMKSAGRNGFRCKKCGTR 376 (421)
T ss_pred EEEEEEEEeeeeEEcCCCCCccCCchhhcCCCCccccccccc
Confidence 44567777777776 79999988876554 459999975
No 238
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=37.22 E-value=47 Score=28.16 Aligned_cols=27 Identities=33% Similarity=0.443 Sum_probs=20.8
Q ss_pred cccCCCCCccceeEEEEEEcCCCc-EEEee
Q psy12603 261 KVFCPKCGYKTLKRVAVSVDEQGK-QKIHI 289 (391)
Q Consensus 261 k~FCP~CGn~TL~Rvsvsvd~~G~-~~~hl 289 (391)
..+||.|+.+| ||.+-++++|+ +.+..
T Consensus 71 ~lv~p~~~~~~--rv~~~~~~~g~kvRv~k 98 (105)
T PRK00004 71 ALVDPKTGKAT--RVGFKFLEDGKKVRVAK 98 (105)
T ss_pred EEEeCcCCCCe--EEEEEEccCCcEEEEEe
Confidence 57999999886 99999888885 34433
No 239
>cd01407 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.
Probab=36.87 E-value=36 Score=31.98 Aligned_cols=41 Identities=34% Similarity=0.596 Sum_probs=27.6
Q ss_pred HHHhCC-ceeccCccccceeeeEEEEccCcccccccc---------CcccCCCCCcc
Q psy12603 224 LKQMGL-NVVALDGRLIRELRTFILRCYACYKTTSIM---------TKVFCPKCGYK 270 (391)
Q Consensus 224 llqmGL-~l~s~~G~~Ik~~r~wvlRC~aCf~~t~~~---------~k~FCP~CGn~ 270 (391)
..+.|. +|+-+.|. -+.++|..|.+.+... .---||.||..
T Consensus 92 ~~~aG~~~v~elHG~------~~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~ 142 (218)
T cd01407 92 HQRAGSPKVIELHGS------LFRVRCTKCGKEYPRDELQADIDREEVPRCPKCGGL 142 (218)
T ss_pred HHHcCCCCEEECcCC------cCcceeCCCcCCCcHHHHhHhhccCCCCcCCCCCCc
Confidence 445566 47788885 3457899998766421 22469999965
No 240
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=36.48 E-value=11 Score=29.73 Aligned_cols=18 Identities=22% Similarity=0.602 Sum_probs=9.0
Q ss_pred cccccCcccCCCCCccce
Q psy12603 255 TTSIMTKVFCPKCGYKTL 272 (391)
Q Consensus 255 ~t~~~~k~FCP~CGn~TL 272 (391)
+.++..+.||.+||...+
T Consensus 40 l~~~~kr~~Ck~C~~~li 57 (85)
T PF04032_consen 40 LPPEIKRTICKKCGSLLI 57 (85)
T ss_dssp -STTCCCTB-TTT--B--
T ss_pred CChHHhcccccCCCCEEe
Confidence 344567889999998643
No 241
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=36.35 E-value=16 Score=36.34 Aligned_cols=65 Identities=22% Similarity=0.324 Sum_probs=39.4
Q ss_pred EEEccCcccccccc----CcccCCCCCccc----eeEEEEEEcCCCcEEEeeccCCccccCCcccccCCCCCCCCCCCce
Q psy12603 246 ILRCYACYKTTSIM----TKVFCPKCGYKT----LKRVAVSVDEQGKQKIHINLKRPLTARGKKFSLPTFKGGKHANNPI 317 (391)
Q Consensus 246 vlRC~aCf~~t~~~----~k~FCP~CGn~T----L~Rvsvsvd~~G~~~~hl~~n~~~n~RG~~ySlPkPkGGk~~~~~I 317 (391)
...|.+|..+..-. ....||+||+.. ..|+...+|++. -..+..|. ...||+
T Consensus 28 w~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ri~A~~Ri~~llD~gs-----------------f~el~~~l---~~~dPL 87 (294)
T COG0777 28 WTKCPSCGEMLYRKELESNLKVCPKCGHHMRISARERLEALLDEGS-----------------FEELDSPL---EPKDPL 87 (294)
T ss_pred eeECCCccceeeHHHHHhhhhcccccCcccccCHHHHHHHhhCCCc-----------------ceecccCC---CcCCcc
Confidence 45899999875422 467899999973 344444445432 22333332 335677
Q ss_pred eeCCCCCcccccc
Q psy12603 318 VAEDQPVPDQRPT 330 (391)
Q Consensus 318 L~EDQ~~~~~~~~ 330 (391)
-.-|.+-|..|+.
T Consensus 88 ~F~d~k~Y~~rL~ 100 (294)
T COG0777 88 KFPDSKKYKDRLE 100 (294)
T ss_pred cCCcchhhHHHHH
Confidence 7777766666654
No 242
>cd01413 SIR2_Af2 SIR2_Af2: Archaeal and prokaryotic group which includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus solfataricus ssSir2, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The Sir2 homolog from the archaea Sulfolobus solftaricus deacetylates the non-specific DNA protein Alba to mediate transcription repression.
Probab=36.25 E-value=25 Score=33.34 Aligned_cols=33 Identities=30% Similarity=0.572 Sum_probs=22.0
Q ss_pred eeccCccccceeeeEEEEccCcccccccc--------CcccCCCCCc
Q psy12603 231 VVALDGRLIRELRTFILRCYACYKTTSIM--------TKVFCPKCGY 269 (391)
Q Consensus 231 l~s~~G~~Ik~~r~wvlRC~aCf~~t~~~--------~k~FCP~CGn 269 (391)
|+-+.|. -+.++|..|.+.+... ..-.||.||.
T Consensus 104 v~elHG~------l~~~~C~~C~~~~~~~~~~~~~~~~~p~C~~Cgg 144 (222)
T cd01413 104 VIELHGT------LQTAYCVNCGSKYDLEEVKYAKKHEVPRCPKCGG 144 (222)
T ss_pred EEEccCC------cCcceECCCCCCcchhHHHHhccCCCCcCCCCCC
Confidence 6677775 3457799998776422 1246999984
No 243
>COG5319 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.25 E-value=12 Score=33.15 Aligned_cols=32 Identities=25% Similarity=0.525 Sum_probs=20.3
Q ss_pred eeEEEEccCccc------cc------cccCcccCCCCCccceeE
Q psy12603 243 RTFILRCYACYK------TT------SIMTKVFCPKCGYKTLKR 274 (391)
Q Consensus 243 r~wvlRC~aCf~------~t------~~~~k~FCP~CGn~TL~R 274 (391)
+.|-|||--=.. -. ..+...-||.||+.+..|
T Consensus 2 i~y~L~Cd~~HeFEGWF~ssaDfd~Q~~rgLv~CPvCgs~~VsK 45 (142)
T COG5319 2 IRYALRCDKGHEFEGWFGSSADFDRQRERGLVTCPVCGSTEVSK 45 (142)
T ss_pred ceeeeeccCCCcccccccCchhHHHHHHcCceeCCCCCcHHHHH
Confidence 468888853322 22 234677899999976554
No 244
>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=36.12 E-value=17 Score=27.52 Aligned_cols=30 Identities=30% Similarity=0.671 Sum_probs=22.7
Q ss_pred eeEEEEccCccccccccCcccCCCCCcccee
Q psy12603 243 RTFILRCYACYKTTSIMTKVFCPKCGYKTLK 273 (391)
Q Consensus 243 r~wvlRC~aCf~~t~~~~k~FCP~CGn~TL~ 273 (391)
++.+ +|.-|.+...-.-|.-|.+||.+.-+
T Consensus 13 ktH~-~CrRCG~~syH~qK~~CasCGyp~~k 42 (55)
T PF01907_consen 13 KTHT-LCRRCGRRSYHIQKKTCASCGYPAAK 42 (55)
T ss_dssp -SEE-E-TTTSSEEEETTTTEETTTBTTTSS
T ss_pred ccEe-eecccCCeeeecCCCcccccCCCccc
Confidence 3444 69999999888899999999998433
No 245
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=35.91 E-value=28 Score=31.74 Aligned_cols=32 Identities=16% Similarity=0.510 Sum_probs=18.2
Q ss_pred cccCCCCCcc-ceeEEEEEEcCCCc-EEEeeccC
Q psy12603 261 KVFCPKCGYK-TLKRVAVSVDEQGK-QKIHINLK 292 (391)
Q Consensus 261 k~FCP~CGn~-TL~Rvsvsvd~~G~-~~~hl~~n 292 (391)
--.||+||.+ +=-+.+=.+.+.|. +++++...
T Consensus 29 sf~C~~CGyk~~ev~~~~~~~p~G~r~~l~V~~~ 62 (160)
T smart00709 29 SFECEHCGYRNNEVKSGGAIEPKGTRITLKVESP 62 (160)
T ss_pred EEECCCCCCccceEEECcccCCCceEEEEEECCh
Confidence 4579999987 33333334444553 45555444
No 246
>KOG0287|consensus
Probab=35.66 E-value=5.1 Score=40.79 Aligned_cols=22 Identities=36% Similarity=0.981 Sum_probs=15.6
Q ss_pred EEEccCcccccccc-----CcccCCCC
Q psy12603 246 ILRCYACYKTTSIM-----TKVFCPKC 267 (391)
Q Consensus 246 vlRC~aCf~~t~~~-----~k~FCP~C 267 (391)
.||||-||..++.+ +.-||.-|
T Consensus 23 lLRC~IC~eyf~ip~itpCsHtfCSlC 49 (442)
T KOG0287|consen 23 LLRCGICFEYFNIPMITPCSHTFCSLC 49 (442)
T ss_pred HHHHhHHHHHhcCceeccccchHHHHH
Confidence 58999999887755 35566555
No 247
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=35.65 E-value=17 Score=25.40 Aligned_cols=15 Identities=33% Similarity=0.782 Sum_probs=9.8
Q ss_pred cCCCCCccceeEEEE
Q psy12603 263 FCPKCGYKTLKRVAV 277 (391)
Q Consensus 263 FCP~CGn~TL~Rvsv 277 (391)
-||+||+.-..=..+
T Consensus 2 ~Cp~C~~~~a~~~q~ 16 (40)
T smart00440 2 PCPKCGNREATFFQL 16 (40)
T ss_pred cCCCCCCCeEEEEEE
Confidence 399999874443333
No 248
>PF10601 zf-LITAF-like: LITAF-like zinc ribbon domain; InterPro: IPR006629 Members of this family display a conserved zinc ribbon structure [] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [].
Probab=35.59 E-value=34 Score=26.61 Aligned_cols=22 Identities=23% Similarity=0.572 Sum_probs=17.6
Q ss_pred ccCcccCCCCCccceeEEEEEE
Q psy12603 258 IMTKVFCPKCGYKTLKRVAVSV 279 (391)
Q Consensus 258 ~~~k~FCP~CGn~TL~Rvsvsv 279 (391)
.+...+||.||+....+|....
T Consensus 4 ~p~~~~CP~C~~~~~T~v~~~~ 25 (73)
T PF10601_consen 4 EPVRIYCPYCQQQVQTRVEYKS 25 (73)
T ss_pred CceeeECCCCCCEEEEEEEEEe
Confidence 4557899999999988887653
No 249
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=35.22 E-value=53 Score=33.19 Aligned_cols=24 Identities=25% Similarity=0.613 Sum_probs=19.4
Q ss_pred EEEccCccccccccCcccCCCCCcc
Q psy12603 246 ILRCYACYKTTSIMTKVFCPKCGYK 270 (391)
Q Consensus 246 vlRC~aCf~~t~~~~k~FCP~CGn~ 270 (391)
.|.|.-|.+... +.|.-||.||+.
T Consensus 212 yL~CslC~teW~-~~R~~C~~Cg~~ 235 (309)
T PRK03564 212 YLHCNLCESEWH-VVRVKCSNCEQS 235 (309)
T ss_pred EEEcCCCCCccc-ccCccCCCCCCC
Confidence 578999988776 568889999984
No 250
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=35.00 E-value=18 Score=32.77 Aligned_cols=49 Identities=24% Similarity=0.373 Sum_probs=34.8
Q ss_pred eEEEecCcHHHHHHHHHh-CCcee-----ccCccccceeeeEEEEccCcccccccc
Q psy12603 210 VVSCVTTDFAMQNVLKQM-GLNVV-----ALDGRLIRELRTFILRCYACYKTTSIM 259 (391)
Q Consensus 210 ~Vac~TtDfAMQNVllqm-GL~l~-----s~~G~~Ik~~r~wvlRC~aCf~~t~~~ 259 (391)
-.+|+ +|.=+||++..- +.-|+ +++...|+.-|.|.|.|-||..+.+.-
T Consensus 85 l~g~f-~~~~i~~~i~~yi~~yv~C~~c~s~dt~l~~~~R~~~l~c~acGa~~pv~ 139 (151)
T COG1601 85 LQGKF-SDSEIVNEIERYIAEYVKCKECGSPDTELIKEERLLFLKCEACGAIRPVK 139 (151)
T ss_pred EEecc-cHHHHHHHHHHHHHheeEeccCCCCchhhhhhhhhHhhHHHHhCCcccch
Confidence 34444 456677776654 44444 677778888999999999999887643
No 251
>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=34.84 E-value=18 Score=35.39 Aligned_cols=15 Identities=40% Similarity=1.194 Sum_probs=6.6
Q ss_pred cccCCCCCccceeEE
Q psy12603 261 KVFCPKCGYKTLKRV 275 (391)
Q Consensus 261 k~FCP~CGn~TL~Rv 275 (391)
..+||.||+.-|.+.
T Consensus 31 n~yCP~Cg~~~L~~f 45 (254)
T PF06044_consen 31 NMYCPNCGSKPLSKF 45 (254)
T ss_dssp H---TTT--SS-EE-
T ss_pred CCcCCCCCChhHhhc
Confidence 478999999977765
No 252
>PRK14289 chaperone protein DnaJ; Provisional
Probab=34.76 E-value=1.1e+02 Score=31.45 Aligned_cols=27 Identities=30% Similarity=0.534 Sum_probs=20.0
Q ss_pred EEEEccCccccccccCcccCCCCCccce
Q psy12603 245 FILRCYACYKTTSIMTKVFCPKCGYKTL 272 (391)
Q Consensus 245 wvlRC~aCf~~t~~~~k~FCP~CGn~TL 272 (391)
+.-.|..|.-.-.. .+.+|+.|++.-.
T Consensus 196 ~~~~C~~C~G~G~~-~~~~C~~C~G~g~ 222 (386)
T PRK14289 196 TQSTCPTCNGEGKI-IKKKCKKCGGEGI 222 (386)
T ss_pred EEEecCCCCccccc-cCcCCCCCCCCcE
Confidence 36789999876543 3678999999843
No 253
>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=34.12 E-value=37 Score=24.79 Aligned_cols=25 Identities=24% Similarity=0.509 Sum_probs=16.4
Q ss_pred EEEccCccccccccC------------------cccCCCCCcc
Q psy12603 246 ILRCYACYKTTSIMT------------------KVFCPKCGYK 270 (391)
Q Consensus 246 vlRC~aCf~~t~~~~------------------k~FCP~CGn~ 270 (391)
.++|..|..++.... ---||.||.+
T Consensus 1 ky~C~~CgyvYd~~~Gd~~~~i~pGt~F~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 1 KYQCPVCGYVYDPEKGDPENGIPPGTPFEDLPDDWVCPVCGAP 43 (47)
T ss_dssp EEEETTTSBEEETTTBBGGGTB-TT--GGGS-TT-B-TTTSSB
T ss_pred CcCCCCCCEEEcCCcCCcccCcCCCCCHHHCCCCCcCcCCCCc
Confidence 368999998875332 1269999965
No 254
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=34.03 E-value=26 Score=26.52 Aligned_cols=22 Identities=32% Similarity=0.692 Sum_probs=15.9
Q ss_pred EEccCccccccccCcccCCCCCccc
Q psy12603 247 LRCYACYKTTSIMTKVFCPKCGYKT 271 (391)
Q Consensus 247 lRC~aCf~~t~~~~k~FCP~CGn~T 271 (391)
+.|.+||-..+- -=||-||-+.
T Consensus 28 ~I~~~~f~~~rY---ngCPfC~~~~ 49 (55)
T PF14447_consen 28 LICDNCFPGERY---NGCPFCGTPF 49 (55)
T ss_pred eeeccccChhhc---cCCCCCCCcc
Confidence 568899976543 3499999763
No 255
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=34.00 E-value=19 Score=29.19 Aligned_cols=56 Identities=29% Similarity=0.447 Sum_probs=30.3
Q ss_pred cccCCCCCccceeEEEEEEcCCCcEEEeeccCCccccCCcccccCCCCCCCCCCCceeeCCCCCc
Q psy12603 261 KVFCPKCGYKTLKRVAVSVDEQGKQKIHINLKRPLTARGKKFSLPTFKGGKHANNPIVAEDQPVP 325 (391)
Q Consensus 261 k~FCP~CGn~TL~Rvsvsvd~~G~~~~hl~~n~~~n~RG~~ySlPkPkGGk~~~~~IL~EDQ~~~ 325 (391)
|..||-||..||. +.|.-.+.|=.-=-|-.=|..+.-|--.||-. ..=|.|=|..|
T Consensus 1 K~~CPCCg~~Tl~-------~~~~~~ydIC~VC~WEdD~~q~~~pd~~~G~N--~~SL~eAr~ny 56 (78)
T PF14206_consen 1 KYPCPCCGYYTLE-------ERGEGTYDICPVCFWEDDGVQLRDPDYYGGAN--HMSLNEARENY 56 (78)
T ss_pred CccCCCCCcEEec-------cCCCcCceECCCCCcccCCccccCCcccCCCC--HHHHHHHHHHH
Confidence 5679999999763 33332234444423555555555555455543 34455555443
No 256
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=33.89 E-value=27 Score=27.83 Aligned_cols=21 Identities=19% Similarity=0.491 Sum_probs=14.3
Q ss_pred ccCCCCCccceeEEEEEEcCC
Q psy12603 262 VFCPKCGYKTLKRVAVSVDEQ 282 (391)
Q Consensus 262 ~FCP~CGn~TL~Rvsvsvd~~ 282 (391)
..||.||++...|-|-.+++.
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~ 22 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDT 22 (72)
T ss_pred ccCCCCCCccEEEEChhcChh
Confidence 468888888766666665543
No 257
>PF13638 PIN_4: PIN domain; PDB: 2HWW_C 2HWX_A 2DOK_B 2HWY_B 2WP8_J.
Probab=33.74 E-value=41 Score=28.40 Aligned_cols=27 Identities=22% Similarity=0.186 Sum_probs=19.3
Q ss_pred CceEEEecCcHHHHHHHHHhCCceecc
Q psy12603 208 PLVVSCVTTDFAMQNVLKQMGLNVVAL 234 (391)
Q Consensus 208 ~~~Vac~TtDfAMQNVllqmGL~l~s~ 234 (391)
...|.++|.|-.|.+.+...||..++.
T Consensus 106 ~~~vvLvT~D~~l~~~A~~~gi~~~~~ 132 (133)
T PF13638_consen 106 GRKVVLVTNDKNLRLKARAEGIPAVSY 132 (133)
T ss_dssp CEEEEEEE--HHHHHHHHHTT--EE--
T ss_pred CCeEEEEeCCHHHHHHHhhcccccccC
Confidence 467999999999999999999998875
No 258
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=33.69 E-value=20 Score=37.07 Aligned_cols=50 Identities=22% Similarity=0.244 Sum_probs=25.8
Q ss_pred HHHHHHHhCCcee-ccCccccceeeeEEEEccCcccccc-ccCc---ccCCCCCcc
Q psy12603 220 MQNVLKQMGLNVV-ALDGRLIRELRTFILRCYACYKTTS-IMTK---VFCPKCGYK 270 (391)
Q Consensus 220 MQNVllqmGL~l~-s~~G~~Ik~~r~wvlRC~aCf~~t~-~~~k---~FCP~CGn~ 270 (391)
+..+|..+.-+-+ ..-|+--+.=|-+.--|..|+.... ..++ .-|| ||.+
T Consensus 213 ~~~~l~ai~~~~i~~~~g~~P~~GKYh~~~c~~C~~~~~~~~~~~~~~~Cp-CG~~ 267 (374)
T TIGR00375 213 FALALKAIDDRKIIANYGLDPLLGKYHQTACEACGEPAVSEDAETACANCP-CGGR 267 (374)
T ss_pred HHHHHHHhhCCceEeeeeECcCCCccchhhhcccCCcCCchhhhhcCCCCC-CCCc
Confidence 5566665433222 1113333333444446777776443 2223 6799 9998
No 259
>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=33.63 E-value=39 Score=30.53 Aligned_cols=8 Identities=38% Similarity=1.024 Sum_probs=5.2
Q ss_pred cCCCCCcc
Q psy12603 263 FCPKCGYK 270 (391)
Q Consensus 263 FCP~CGn~ 270 (391)
-||.||+.
T Consensus 2 ~CP~C~~~ 9 (147)
T TIGR00244 2 HCPFCQHH 9 (147)
T ss_pred CCCCCCCC
Confidence 37777765
No 260
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=33.51 E-value=24 Score=36.99 Aligned_cols=25 Identities=24% Similarity=0.658 Sum_probs=19.4
Q ss_pred EEEccCccccccccCcccCCCCCccc
Q psy12603 246 ILRCYACYKTTSIMTKVFCPKCGYKT 271 (391)
Q Consensus 246 vlRC~aCf~~t~~~~k~FCP~CGn~T 271 (391)
...||.|..+.+. .+..||.||...
T Consensus 221 l~~C~~Cd~l~~~-~~a~CpRC~~~L 245 (419)
T PRK15103 221 LRSCSCCTAILPA-DQPVCPRCHTKG 245 (419)
T ss_pred CCcCCCCCCCCCC-CCCCCCCCCCcC
Confidence 3459999998753 466899999984
No 261
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=33.48 E-value=30 Score=32.55 Aligned_cols=38 Identities=32% Similarity=0.514 Sum_probs=24.3
Q ss_pred HhCC---ceeccCccccceeeeEEEEccCcccccccc----------CcccCCCCCc
Q psy12603 226 QMGL---NVVALDGRLIRELRTFILRCYACYKTTSIM----------TKVFCPKCGY 269 (391)
Q Consensus 226 qmGL---~l~s~~G~~Ik~~r~wvlRC~aCf~~t~~~----------~k~FCP~CGn 269 (391)
+-|+ +|+-++|. -+.++|..|...+... .---||.||.
T Consensus 78 ~AG~~~~~vielHG~------~~~~~C~~C~~~~~~~~~~~~~~~~~~~p~C~~Cgg 128 (206)
T cd01410 78 RSGLPREKLSELHGN------MFIEVCKSCGPEYVRDDVVETRGDKETGRRCHACGG 128 (206)
T ss_pred HcCcCcccEEEecCC------cCcccCCCCCCccchHHHHHHhhcCCCCCcCCCCcC
Confidence 3455 47777775 4456899999765421 1234999985
No 262
>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]
Probab=33.42 E-value=55 Score=36.58 Aligned_cols=37 Identities=22% Similarity=0.609 Sum_probs=26.0
Q ss_pred eeccCccccc------eeeeEEEEccCcccccccc-------CcccCCCC
Q psy12603 231 VVALDGRLIR------ELRTFILRCYACYKTTSIM-------TKVFCPKC 267 (391)
Q Consensus 231 l~s~~G~~Ik------~~r~wvlRC~aCf~~t~~~-------~k~FCP~C 267 (391)
||+++|+.++ +++.-.+.|..|..++... ...+||+|
T Consensus 108 LV~v~GiV~r~s~v~p~~~~~~~~C~~Cg~~~~~~~~~~~~~~~~~C~~~ 157 (682)
T COG1241 108 LVSVEGIVTRASEVRPRLKKAVFECPKCGREVEVEQSEFRVEPPRECENC 157 (682)
T ss_pred EEEEEEEEEecccccceeEEEEEEcCCCCCEEEEEeccccccCCccCCCc
Confidence 5577776443 5667788899998766533 34789999
No 263
>cd01411 SIR2H SIR2H: Uncharacterized prokaryotic Sir2 homologs from several gram positive bacterial species and Fusobacteria; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=33.20 E-value=30 Score=32.91 Aligned_cols=40 Identities=30% Similarity=0.551 Sum_probs=25.2
Q ss_pred HHHhCC-ceeccCccccceeeeEEEEccCcccccccc---CcccCCCCCc
Q psy12603 224 LKQMGL-NVVALDGRLIRELRTFILRCYACYKTTSIM---TKVFCPKCGY 269 (391)
Q Consensus 224 llqmGL-~l~s~~G~~Ik~~r~wvlRC~aCf~~t~~~---~k~FCP~CGn 269 (391)
..+-|. +|+-++|. -+.++|..|...+... ..-.||.||.
T Consensus 101 h~~aG~~~v~elHG~------~~~~~C~~C~~~~~~~~~~~~p~C~~Cgg 144 (225)
T cd01411 101 HQKAGSKNVVEFHGS------LYRIYCTVCGKTVDWEEYLKSPYHAKCGG 144 (225)
T ss_pred hhhcCCCcEEEeCCC------cCeeEeCCCCCccchhhcCCCCCCCCCCC
Confidence 334454 46677774 3346899998766421 1246999985
No 264
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.13 E-value=7.6 Score=34.27 Aligned_cols=18 Identities=33% Similarity=0.890 Sum_probs=14.0
Q ss_pred CcccCCCCCccceeEEEE
Q psy12603 260 TKVFCPKCGYKTLKRVAV 277 (391)
Q Consensus 260 ~k~FCP~CGn~TL~Rvsv 277 (391)
..-||.+||-.|+..+..
T Consensus 27 ~eafcskcgeati~qcp~ 44 (160)
T COG4306 27 MEAFCSKCGEATITQCPI 44 (160)
T ss_pred HHHHHhhhchHHHhcCCc
Confidence 457999999998876653
No 265
>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=33.01 E-value=27 Score=26.23 Aligned_cols=19 Identities=32% Similarity=0.905 Sum_probs=8.5
Q ss_pred EccCccccccccCcccCCCCC
Q psy12603 248 RCYACYKTTSIMTKVFCPKCG 268 (391)
Q Consensus 248 RC~aCf~~t~~~~k~FCP~CG 268 (391)
.|..|..+. ++-..||.||
T Consensus 28 ~C~~cG~~~--~~H~vc~~cG 46 (55)
T TIGR01031 28 VCPNCGEFK--LPHRVCPSCG 46 (55)
T ss_pred ECCCCCCcc--cCeeECCccC
Confidence 355554432 2344455555
No 266
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=33.01 E-value=22 Score=25.75 Aligned_cols=14 Identities=29% Similarity=0.622 Sum_probs=10.9
Q ss_pred CcccCCCCCcccee
Q psy12603 260 TKVFCPKCGYKTLK 273 (391)
Q Consensus 260 ~k~FCP~CGn~TL~ 273 (391)
.+.||+.||++...
T Consensus 4 g~l~C~~CG~~m~~ 17 (58)
T PF13408_consen 4 GLLRCGHCGSKMTR 17 (58)
T ss_pred CcEEcccCCcEeEE
Confidence 46899999988443
No 267
>PF14353 CpXC: CpXC protein
Probab=32.95 E-value=35 Score=29.30 Aligned_cols=44 Identities=25% Similarity=0.426 Sum_probs=27.6
Q ss_pred ccCCCCCccceeEEEEEEcCCCcEEEeeccCCccccCCcccccCCCCCC
Q psy12603 262 VFCPKCGYKTLKRVAVSVDEQGKQKIHINLKRPLTARGKKFSLPTFKGG 310 (391)
Q Consensus 262 ~FCP~CGn~TL~Rvsvsvd~~G~~~~hl~~n~~~n~RG~~ySlPkPkGG 310 (391)
.-||+||...-..+--+|+.+-.- -++.. =+.|+.|+.-=|.=|
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p--~l~e~---il~g~l~~~~CP~Cg 45 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDP--ELKEK---ILDGSLFSFTCPSCG 45 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCH--HHHHH---HHcCCcCEEECCCCC
Confidence 459999999888888887754321 01111 136777777777644
No 268
>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=32.89 E-value=28 Score=36.29 Aligned_cols=27 Identities=26% Similarity=0.640 Sum_probs=20.6
Q ss_pred EEEccCcccccccc-----CcccCCCCCccce
Q psy12603 246 ILRCYACYKTTSIM-----TKVFCPKCGYKTL 272 (391)
Q Consensus 246 vlRC~aCf~~t~~~-----~k~FCP~CGn~TL 272 (391)
..+||.|-.+.... .+-.||.||...-
T Consensus 13 ~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~ 44 (403)
T TIGR00155 13 HILCSQCDMLVALPRIESGQKAACPRCGTTLT 44 (403)
T ss_pred eeeCCCCCCcccccCCCCCCeeECCCCCCCCc
Confidence 45799999887543 4668999999853
No 269
>COG4640 Predicted membrane protein [Function unknown]
Probab=32.88 E-value=19 Score=37.56 Aligned_cols=24 Identities=29% Similarity=0.574 Sum_probs=16.1
Q ss_pred EEEccCccccccccCcccCCCCCcc
Q psy12603 246 ILRCYACYKTTSIMTKVFCPKCGYK 270 (391)
Q Consensus 246 vlRC~aCf~~t~~~~k~FCP~CGn~ 270 (391)
|+-|.-|..--.+-. .|||.||.+
T Consensus 1 M~fC~kcG~qk~Ed~-~qC~qCG~~ 24 (465)
T COG4640 1 MKFCPKCGSQKAEDD-VQCTQCGHK 24 (465)
T ss_pred CCccccccccccccc-ccccccCCc
Confidence 456888885443333 459999987
No 270
>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=32.77 E-value=24 Score=25.11 Aligned_cols=11 Identities=36% Similarity=1.062 Sum_probs=8.7
Q ss_pred CcccCCCCCcc
Q psy12603 260 TKVFCPKCGYK 270 (391)
Q Consensus 260 ~k~FCP~CGn~ 270 (391)
....||+||+.
T Consensus 17 ~g~~CP~Cg~~ 27 (46)
T PF12760_consen 17 DGFVCPHCGST 27 (46)
T ss_pred CCCCCCCCCCe
Confidence 34569999997
No 271
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=32.74 E-value=41 Score=30.52 Aligned_cols=29 Identities=24% Similarity=0.350 Sum_probs=25.4
Q ss_pred CceEEEecCcHHHHHHHHHhCCceeccCc
Q psy12603 208 PLVVSCVTTDFAMQNVLKQMGLNVVALDG 236 (391)
Q Consensus 208 ~~~Vac~TtDfAMQNVllqmGL~l~s~~G 236 (391)
...|-++|+|.++|..+...|-..+|...
T Consensus 94 ~~~v~VVTSD~~iq~~~~~~GA~~iss~e 122 (166)
T PF05991_consen 94 PRQVTVVTSDREIQRAARGRGAKRISSEE 122 (166)
T ss_pred CCeEEEEeCCHHHHHHHhhCCCEEEcHHH
Confidence 35788999999999999999999998754
No 272
>KOG4718|consensus
Probab=32.72 E-value=22 Score=34.08 Aligned_cols=37 Identities=19% Similarity=0.374 Sum_probs=28.2
Q ss_pred cCChhhHHHHHHHHHHhCCCCCCChhhHHHHHHhhhhhh
Q psy12603 36 EADPDSISFVTEFSKKTGDYPSLSSTDIKVIALTYELHK 74 (391)
Q Consensus 36 eP~~esi~~V~~FAkkTGD~~sLS~~DI~ViALtyeLe~ 74 (391)
.-.+.+...|.+|--.+-| +|+.-|+.|.-.-|.++.
T Consensus 36 ~~~~g~k~~~edfinein~--~lhnld~~ikr~~~~~dg 72 (235)
T KOG4718|consen 36 TTKPGSKEAIEDFINEIND--TLHNLDQLIKRIKYPVDG 72 (235)
T ss_pred ccccchHhHHHHHHHHHHH--HHhhhhhhheeeeecCCC
Confidence 3456777888888888886 899999888776666654
No 273
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=32.61 E-value=21 Score=37.22 Aligned_cols=27 Identities=26% Similarity=0.557 Sum_probs=20.8
Q ss_pred EEccCccccccccCcccCCCCCcccee
Q psy12603 247 LRCYACYKTTSIMTKVFCPKCGYKTLK 273 (391)
Q Consensus 247 lRC~aCf~~t~~~~k~FCP~CGn~TL~ 273 (391)
--|++|..+...-.+--||.||.+.-.
T Consensus 221 ~~C~~C~~~~~~~~~~~CpRC~~~Ly~ 247 (418)
T COG2995 221 RSCLCCHYILPHDAEPRCPRCGSKLYV 247 (418)
T ss_pred eecccccccCCHhhCCCCCCCCChhhc
Confidence 359999887765468899999998433
No 274
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 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 RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=32.54 E-value=8.7 Score=28.33 Aligned_cols=27 Identities=22% Similarity=0.497 Sum_probs=15.8
Q ss_pred EEccCccccccccCcccCCCCCccceeE
Q psy12603 247 LRCYACYKTTSIMTKVFCPKCGYKTLKR 274 (391)
Q Consensus 247 lRC~aCf~~t~~~~k~FCP~CGn~TL~R 274 (391)
+-|..|..+.-. .-.|||.||.+.-+|
T Consensus 22 YLCl~CLt~ml~-~s~~C~iC~~~LPtk 48 (50)
T PF03854_consen 22 YLCLNCLTLMLS-RSDRCPICGKPLPTK 48 (50)
T ss_dssp EEEHHHHHHT-S-SSSEETTTTEE----
T ss_pred hHHHHHHHHHhc-cccCCCcccCcCccc
Confidence 457777765442 248999999875443
No 275
>PRK10445 endonuclease VIII; Provisional
Probab=32.52 E-value=40 Score=32.94 Aligned_cols=16 Identities=19% Similarity=0.615 Sum_probs=9.7
Q ss_pred cccCCCCCccceeEEEE
Q psy12603 261 KVFCPKCGYKTLKRVAV 277 (391)
Q Consensus 261 k~FCP~CGn~TL~Rvsv 277 (391)
..-||.||.+ +.++.|
T Consensus 235 g~~Cp~Cg~~-I~~~~~ 250 (263)
T PRK10445 235 GEACERCGGI-IEKTTL 250 (263)
T ss_pred CCCCCCCCCE-eEEEEE
Confidence 4668888866 344443
No 276
>PRK06599 DNA topoisomerase I; Validated
Probab=32.50 E-value=46 Score=36.96 Aligned_cols=11 Identities=45% Similarity=0.936 Sum_probs=8.2
Q ss_pred cCCCCCcccee
Q psy12603 263 FCPKCGYKTLK 273 (391)
Q Consensus 263 FCP~CGn~TL~ 273 (391)
-||.||...+.
T Consensus 639 ~Cp~C~~~~~~ 649 (675)
T PRK06599 639 KCPKCGGPLVL 649 (675)
T ss_pred CCCCCCCeeEE
Confidence 69999987443
No 277
>cd01412 SIRT5_Af1_CobB SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. CobB is a bacterial sirtuin that deacetylates acetyl-CoA synthetase at an active site lysine to stimulate its enzymatic activity.
Probab=32.44 E-value=30 Score=32.58 Aligned_cols=39 Identities=36% Similarity=0.629 Sum_probs=25.2
Q ss_pred HhCC-ceeccCccccceeeeEEEEccCcccccccc------CcccCCCCCcc
Q psy12603 226 QMGL-NVVALDGRLIRELRTFILRCYACYKTTSIM------TKVFCPKCGYK 270 (391)
Q Consensus 226 qmGL-~l~s~~G~~Ik~~r~wvlRC~aCf~~t~~~------~k~FCP~CGn~ 270 (391)
+-|. +|+-+.|. -+.++|..|...+... .---||.||..
T Consensus 94 ~aG~~~v~e~HG~------~~~~~C~~C~~~~~~~~~~~~~~~p~C~~Cgg~ 139 (224)
T cd01412 94 RAGSRNVIELHGS------LFRVRCSSCGYVGENNEEIPEEELPRCPKCGGL 139 (224)
T ss_pred HhCCCceEeeCCC------cCccccCCCCCCCCcchhhhccCCCCCCCCCCc
Confidence 3343 35567775 3457899999876542 12469999964
No 278
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=32.40 E-value=36 Score=32.61 Aligned_cols=34 Identities=35% Similarity=0.655 Sum_probs=22.3
Q ss_pred eeccCccccceeeeEEEEccCcccccccc-----CcccCCCCCcc
Q psy12603 231 VVALDGRLIRELRTFILRCYACYKTTSIM-----TKVFCPKCGYK 270 (391)
Q Consensus 231 l~s~~G~~Ik~~r~wvlRC~aCf~~t~~~-----~k~FCP~CGn~ 270 (391)
|+-+.|. -+-++|..|.+.+... ...-||.||..
T Consensus 113 v~elHG~------~~~~~C~~C~~~~~~~~~~~~~~p~C~~Cgg~ 151 (242)
T PRK00481 113 VIELHGS------LLRARCTKCGQTYDLDEYLKPEPPRCPKCGGI 151 (242)
T ss_pred eeeccCC------cCceeeCCCCCCcChhhhccCCCCCCCCCCCc
Confidence 5577775 3457899998776421 12239999865
No 279
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=30.95 E-value=23 Score=31.40 Aligned_cols=10 Identities=30% Similarity=0.690 Sum_probs=5.3
Q ss_pred EEEccCcccc
Q psy12603 246 ILRCYACYKT 255 (391)
Q Consensus 246 vlRC~aCf~~ 255 (391)
.-||..|...
T Consensus 91 ~sRC~~CN~~ 100 (147)
T PF01927_consen 91 FSRCPKCNGP 100 (147)
T ss_pred CCccCCCCcE
Confidence 3456666543
No 280
>COG4423 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.92 E-value=70 Score=26.13 Aligned_cols=38 Identities=32% Similarity=0.389 Sum_probs=31.2
Q ss_pred eEEecCChhhHHHHHHHHHHhCCCCCCChhhHHHHHHhhhhhhh
Q psy12603 32 LQIKEADPDSISFVTEFSKKTGDYPSLSSTDIKVIALTYELHKQ 75 (391)
Q Consensus 32 L~vreP~~esi~~V~~FAkkTGD~~sLS~~DI~ViALtyeLe~E 75 (391)
|-|+.|+. -+.|.+||+.||- |.||-=+.||..+|...
T Consensus 3 LnIKDp~~--d~lar~LA~rtg~----S~t~AV~~Al~~~lar~ 40 (81)
T COG4423 3 LNIKDPEV--DRLARELAARTGE----SKTDAVRDALKERLARL 40 (81)
T ss_pred CccCChHH--HHHHHHHHHHhCC----cHHHHHHHHHHHHHHHH
Confidence 45565544 5678999999994 99999999999999875
No 281
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=30.86 E-value=40 Score=30.63 Aligned_cols=7 Identities=57% Similarity=1.478 Sum_probs=3.9
Q ss_pred CCCCCcc
Q psy12603 264 CPKCGYK 270 (391)
Q Consensus 264 CP~CGn~ 270 (391)
||.||++
T Consensus 3 cp~c~~~ 9 (154)
T PRK00464 3 CPFCGHP 9 (154)
T ss_pred CCCCCCC
Confidence 5555554
No 282
>COG5134 Uncharacterized conserved protein [Function unknown]
Probab=30.84 E-value=42 Score=32.31 Aligned_cols=52 Identities=27% Similarity=0.345 Sum_probs=34.5
Q ss_pred cCccccceeeeEEEEccCccccccccC----------------------cccCCCCCccceeEE----EEEEcCCCcE
Q psy12603 234 LDGRLIRELRTFILRCYACYKTTSIMT----------------------KVFCPKCGYKTLKRV----AVSVDEQGKQ 285 (391)
Q Consensus 234 ~~G~~Ik~~r~wvlRC~aCf~~t~~~~----------------------k~FCP~CGn~TL~Rv----svsvd~~G~~ 285 (391)
+.|.-||=.--|-.||-.|........ -.-||.|||++--|. +++|-+-|.+
T Consensus 30 prglSiRL~TPF~~RCL~C~~YI~K~~rfNavkE~~~dK~y~~~kiYRf~I~C~~C~n~i~~RTDPkN~~YV~EsGg~ 107 (272)
T COG5134 30 PRGLSIRLETPFPVRCLNCENYIQKGTRFNAVKEEIGDKSYYTTKIYRFSIKCHLCSNPIDVRTDPKNTEYVVESGGR 107 (272)
T ss_pred cccceEEeccCcceeecchhhhhhcccchhHHHHHhcccccceeEEEEEEEEccCCCCceeeecCCCCceEEEecCce
Confidence 457777777788999999976543221 235999999955443 4555555544
No 283
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=30.52 E-value=45 Score=25.47 Aligned_cols=19 Identities=32% Similarity=0.861 Sum_probs=15.9
Q ss_pred cccCCCCCccceeEEEEEE
Q psy12603 261 KVFCPKCGYKTLKRVAVSV 279 (391)
Q Consensus 261 k~FCP~CGn~TL~Rvsvsv 279 (391)
..+||.||+....+|....
T Consensus 3 ~i~Cp~C~~~~~T~v~~~~ 21 (67)
T smart00714 3 QLFCPRCQNNVTTRVETET 21 (67)
T ss_pred ceECCCCCCEEEEEEEEEe
Confidence 4789999999888888763
No 284
>cd02674 Peptidase_C19R A subfamily of peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=30.49 E-value=55 Score=30.00 Aligned_cols=37 Identities=19% Similarity=0.327 Sum_probs=24.8
Q ss_pred cCcccCCCCCccceeEEEEEEcCC-CcEEEeeccCCccc
Q psy12603 259 MTKVFCPKCGYKTLKRVAVSVDEQ-GKQKIHINLKRPLT 296 (391)
Q Consensus 259 ~~k~FCP~CGn~TL~Rvsvsvd~~-G~~~~hl~~n~~~n 296 (391)
..+.+|++||..+......++..= --+.+||+ ||.++
T Consensus 102 ~~~~~C~~C~~~~~~~~~~~i~~lP~iLii~l~-R~~~~ 139 (230)
T cd02674 102 DNAWKCPKCKKKRKATKKLTISRLPKVLIIHLK-RFSFS 139 (230)
T ss_pred CCceeCCCCCCccceEEEEEEecCChhhEeEhh-heecC
Confidence 357899999998655555555543 45788888 44444
No 285
>PHA02942 putative transposase; Provisional
Probab=30.14 E-value=57 Score=33.72 Aligned_cols=9 Identities=22% Similarity=0.571 Sum_probs=4.2
Q ss_pred EccCccccc
Q psy12603 248 RCYACYKTT 256 (391)
Q Consensus 248 RC~aCf~~t 256 (391)
.|+.|..+.
T Consensus 327 ~Cs~CG~~~ 335 (383)
T PHA02942 327 SCPKCGHKM 335 (383)
T ss_pred cCCCCCCcc
Confidence 455555443
No 286
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=30.13 E-value=19 Score=23.20 Aligned_cols=7 Identities=43% Similarity=1.227 Sum_probs=2.3
Q ss_pred CCCCCcc
Q psy12603 264 CPKCGYK 270 (391)
Q Consensus 264 CP~CGn~ 270 (391)
||.||+.
T Consensus 4 C~rC~~~ 10 (30)
T PF06827_consen 4 CPRCWNY 10 (30)
T ss_dssp -TTT--B
T ss_pred CccCCCc
Confidence 5555555
No 287
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=29.96 E-value=33 Score=35.56 Aligned_cols=27 Identities=30% Similarity=0.719 Sum_probs=18.3
Q ss_pred eEEEEccCcccccccc--CcccCCCCCcc
Q psy12603 244 TFILRCYACYKTTSIM--TKVFCPKCGYK 270 (391)
Q Consensus 244 ~wvlRC~aCf~~t~~~--~k~FCP~CGn~ 270 (391)
.|++-|..|.++.... .+.-||.||..
T Consensus 238 g~~~~c~~cg~~~~~~~~~~~~c~~Cg~~ 266 (380)
T COG1867 238 GYIYHCSRCGEIVGSFREVDEKCPHCGGK 266 (380)
T ss_pred CcEEEcccccceecccccccccCCccccc
Confidence 3688899996443322 36779999973
No 288
>COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]
Probab=29.73 E-value=48 Score=35.32 Aligned_cols=26 Identities=35% Similarity=0.616 Sum_probs=22.5
Q ss_pred eEEEEccCccccccccCcccCCCCCcc
Q psy12603 244 TFILRCYACYKTTSIMTKVFCPKCGYK 270 (391)
Q Consensus 244 ~wvlRC~aCf~~t~~~~k~FCP~CGn~ 270 (391)
-=+.||.-|..+..-.+|--| .||.+
T Consensus 128 va~w~c~~cg~~iean~kp~c-~cg~~ 153 (593)
T COG2401 128 VALWRCEKCGTIIEANTKPEC-KCGSH 153 (593)
T ss_pred EEEEecchhchhhhhcCCccc-CCCCc
Confidence 346799999999988889999 99985
No 289
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=29.70 E-value=40 Score=34.07 Aligned_cols=38 Identities=29% Similarity=0.498 Sum_probs=21.9
Q ss_pred CcccCCCCCccceeEEEEEEcCCCcEEEeeccC-Ccccc
Q psy12603 260 TKVFCPKCGYKTLKRVAVSVDEQGKQKIHINLK-RPLTA 297 (391)
Q Consensus 260 ~k~FCP~CGn~TL~Rvsvsvd~~G~~~~hl~~n-~~~n~ 297 (391)
.+.+||.||..-.--|-..-..+|.-.+|-+-= ..|+.
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~ 224 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHV 224 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccc
Confidence 579999999974322211123457777776543 44443
No 290
>PF14353 CpXC: CpXC protein
Probab=29.53 E-value=51 Score=28.27 Aligned_cols=32 Identities=25% Similarity=0.242 Sum_probs=17.2
Q ss_pred cccCCCCCcccee-EEEEEEcCCCcEEEeeccC
Q psy12603 261 KVFCPKCGYKTLK-RVAVSVDEQGKQKIHINLK 292 (391)
Q Consensus 261 k~FCP~CGn~TL~-Rvsvsvd~~G~~~~hl~~n 292 (391)
..-||+||..... =--++.|...++.+++...
T Consensus 38 ~~~CP~Cg~~~~~~~p~lY~D~~~~~~i~~~P~ 70 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEYPLLYHDPEKKFMIYYFPD 70 (128)
T ss_pred EEECCCCCCceecCCCEEEEcCCCCEEEEEcCC
Confidence 4569999997432 2223345555554444433
No 291
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=29.50 E-value=50 Score=24.47 Aligned_cols=15 Identities=27% Similarity=0.472 Sum_probs=8.9
Q ss_pred ccCCCCCccceeEEE
Q psy12603 262 VFCPKCGYKTLKRVA 276 (391)
Q Consensus 262 ~FCP~CGn~TL~Rvs 276 (391)
.=||-||.+.+.--.
T Consensus 4 kPCPFCG~~~~~~~~ 18 (61)
T PF14354_consen 4 KPCPFCGSADVLIRQ 18 (61)
T ss_pred cCCCCCCCcceEeec
Confidence 348888877544333
No 292
>PF08458 PH_2: Plant pleckstrin homology-like region; InterPro: IPR013666 This domain describes a pleckstrin homology (PH)-like region found in several plant proteins of unknown function.
Probab=29.45 E-value=71 Score=27.56 Aligned_cols=32 Identities=19% Similarity=0.282 Sum_probs=28.0
Q ss_pred ccCCCCCccceeEEEEEEcCCCcEEEeeccCC
Q psy12603 262 VFCPKCGYKTLKRVAVSVDEQGKQKIHINLKR 293 (391)
Q Consensus 262 ~FCP~CGn~TL~Rvsvsvd~~G~~~~hl~~n~ 293 (391)
.-|-.||.=-++.|||.++..|++.+-+++..
T Consensus 4 lk~tr~G~l~~k~Vsvyink~~qVilKmKskh 35 (110)
T PF08458_consen 4 LKRTRKGDLHWKTVSVYINKKGQVILKMKSKH 35 (110)
T ss_pred eEecCCCceEEEEEEEEECCCcEEEEEeecch
Confidence 34778999899999999999999999988875
No 293
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=29.38 E-value=27 Score=29.86 Aligned_cols=14 Identities=36% Similarity=0.714 Sum_probs=10.3
Q ss_pred ccCcccCCCCCccc
Q psy12603 258 IMTKVFCPKCGYKT 271 (391)
Q Consensus 258 ~~~k~FCP~CGn~T 271 (391)
++.-.-||+||.++
T Consensus 46 e~G~t~CP~Cg~~~ 59 (115)
T COG1885 46 EVGSTSCPKCGEPF 59 (115)
T ss_pred ecccccCCCCCCcc
Confidence 34446699999985
No 294
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=29.34 E-value=24 Score=35.41 Aligned_cols=10 Identities=50% Similarity=1.348 Sum_probs=5.6
Q ss_pred cccCCCCCcc
Q psy12603 261 KVFCPKCGYK 270 (391)
Q Consensus 261 k~FCP~CGn~ 270 (391)
-.|||.||.+
T Consensus 334 a~fcp~cgq~ 343 (345)
T COG4260 334 AKFCPECGQG 343 (345)
T ss_pred hhhChhhcCC
Confidence 3566666654
No 295
>cd01408 SIRT1 SIRT1: Eukaryotic group (class1) which includes human sirtuins SIRT1-3 and yeast Hst1-4; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The nuclear SIRT1 has been shown to target the p53 tumor suppressor protein for deacetylation to suppress DNA damage, and the cytoplasmic SIRT2 homolog has been shown to target alpha-tubulin for deacetylation for the maintenance of cell integrity.
Probab=29.18 E-value=49 Score=31.67 Aligned_cols=40 Identities=20% Similarity=0.448 Sum_probs=26.0
Q ss_pred HHhCC---ceeccCccccceeeeEEEEccCcccccccc---------CcccCCCCCcc
Q psy12603 225 KQMGL---NVVALDGRLIRELRTFILRCYACYKTTSIM---------TKVFCPKCGYK 270 (391)
Q Consensus 225 lqmGL---~l~s~~G~~Ik~~r~wvlRC~aCf~~t~~~---------~k~FCP~CGn~ 270 (391)
.+-|. +|+-+.|. -+.++|..|.+.+... ..--||.||+.
T Consensus 98 ~raG~~~~~V~elHG~------l~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cgg~ 149 (235)
T cd01408 98 RVAGVPDDRIIEAHGS------FATAHCIKCKHKYPGDWMREDIFNQEVPKCPRCGGL 149 (235)
T ss_pred HHcCCCccCEEEeCcC------CCccccccCCCcCCHHHHHHHHhCCCCccCCCCCCC
Confidence 34465 47778885 3456899999876411 12359999954
No 296
>PTZ00357 methyltransferase; Provisional
Probab=28.96 E-value=18 Score=40.44 Aligned_cols=35 Identities=20% Similarity=0.563 Sum_probs=25.4
Q ss_pred CCCceEEEecCcHHHHHHHHHhCCceeccCccccceeeeEEEEccCccc
Q psy12603 206 EKPLVVSCVTTDFAMQNVLKQMGLNVVALDGRLIRELRTFILRCYACYK 254 (391)
Q Consensus 206 ~~~~~Vac~TtDfAMQNVllqmGL~l~s~~G~~Ik~~r~wvlRC~aCf~ 254 (391)
+..+.|||+..|.-+-= -.+-.++|-|| ||-||.-
T Consensus 284 ~~~~~~~~~~~~~~~~~-------------~~~~~~~~~~~-~~~~~~~ 318 (1072)
T PTZ00357 284 QRNIRVACLAADVVLSF-------------IQQCTRVKVWV-RCDACNP 318 (1072)
T ss_pred hhhHHHHHHHHHHHHHH-------------HHhCCeeEEEE-EccCCCH
Confidence 36788999998864321 12467889998 9999963
No 297
>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=28.86 E-value=25 Score=24.39 Aligned_cols=15 Identities=33% Similarity=0.722 Sum_probs=8.2
Q ss_pred cCCCCCccceeEEEE
Q psy12603 263 FCPKCGYKTLKRVAV 277 (391)
Q Consensus 263 FCP~CGn~TL~Rvsv 277 (391)
-||+||+.-..-+.+
T Consensus 2 ~Cp~Cg~~~a~~~~~ 16 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQI 16 (39)
T ss_dssp --SSS-SSEEEEEEE
T ss_pred CCcCCCCCeEEEEEe
Confidence 499999975544444
No 298
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=28.77 E-value=25 Score=30.46 Aligned_cols=21 Identities=33% Similarity=0.863 Sum_probs=16.1
Q ss_pred ccCccccccccCcccCCCCCcc
Q psy12603 249 CYACYKTTSIMTKVFCPKCGYK 270 (391)
Q Consensus 249 C~aCf~~t~~~~k~FCP~CGn~ 270 (391)
|..|..-.. .++..||+||-.
T Consensus 1 CPvCg~~l~-vt~l~C~~C~t~ 21 (113)
T PF09862_consen 1 CPVCGGELV-VTRLKCPSCGTE 21 (113)
T ss_pred CCCCCCceE-EEEEEcCCCCCE
Confidence 888886543 468999999965
No 299
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=28.61 E-value=26 Score=29.43 Aligned_cols=12 Identities=42% Similarity=0.980 Sum_probs=9.7
Q ss_pred cCcccCCCCCcc
Q psy12603 259 MTKVFCPKCGYK 270 (391)
Q Consensus 259 ~~k~FCP~CGn~ 270 (391)
|...+||.||-.
T Consensus 1 mlLI~CP~Cg~R 12 (97)
T COG4311 1 MLLIPCPYCGER 12 (97)
T ss_pred CceecCCCCCCC
Confidence 456899999984
No 300
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=28.61 E-value=25 Score=27.68 Aligned_cols=24 Identities=29% Similarity=0.652 Sum_probs=14.6
Q ss_pred EEccCccccccc----cCcccCCCCCcc
Q psy12603 247 LRCYACYKTTSI----MTKVFCPKCGYK 270 (391)
Q Consensus 247 lRC~aCf~~t~~----~~k~FCP~CGn~ 270 (391)
-+|..|+..+-. .+..-|+.||--
T Consensus 20 VkCpdC~N~q~vFshast~V~C~~CG~~ 47 (67)
T COG2051 20 VKCPDCGNEQVVFSHASTVVTCLICGTT 47 (67)
T ss_pred EECCCCCCEEEEeccCceEEEecccccE
Confidence 357777765432 246677777753
No 301
>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=28.56 E-value=18 Score=32.28 Aligned_cols=23 Identities=22% Similarity=0.512 Sum_probs=20.2
Q ss_pred EccCccccccccCcccCCCCCcc
Q psy12603 248 RCYACYKTTSIMTKVFCPKCGYK 270 (391)
Q Consensus 248 RC~aCf~~t~~~~k~FCP~CGn~ 270 (391)
.|.-|.+++.-+....||+|...
T Consensus 5 nC~~CgklF~~~~~~iCp~C~~~ 27 (137)
T TIGR03826 5 NCPKCGRLFVKTGRDVCPSCYEE 27 (137)
T ss_pred cccccchhhhhcCCccCHHHhHH
Confidence 69999999887788999999974
No 302
>PF14326 DUF4384: Domain of unknown function (DUF4384)
Probab=28.11 E-value=84 Score=24.92 Aligned_cols=31 Identities=16% Similarity=0.335 Sum_probs=22.3
Q ss_pred EEcCCCcEEEeeccCCcccc---CCcccccCCCC
Q psy12603 278 SVDEQGKQKIHINLKRPLTA---RGKKFSLPTFK 308 (391)
Q Consensus 278 svd~~G~~~~hl~~n~~~n~---RG~~ySlPkPk 308 (391)
.+|++|++.+-+...++-++ -|..|.||.+.
T Consensus 25 ~~~~~G~v~~L~Pn~~~~~~~v~ag~~~~iP~~~ 58 (83)
T PF14326_consen 25 YIDADGKVTLLFPNRYQPDNFVKAGQTYTIPDPG 58 (83)
T ss_pred EECCCCCEEEEecCccccCceEcCCceEEcCCCC
Confidence 45889998777766555444 48899999663
No 303
>PF15616 TerY-C: TerY-C metal binding domain
Probab=28.04 E-value=25 Score=31.22 Aligned_cols=9 Identities=44% Similarity=1.143 Sum_probs=7.8
Q ss_pred ccCCCCCcc
Q psy12603 262 VFCPKCGYK 270 (391)
Q Consensus 262 ~FCP~CGn~ 270 (391)
-=||+|||.
T Consensus 78 PgCP~CGn~ 86 (131)
T PF15616_consen 78 PGCPHCGNQ 86 (131)
T ss_pred CCCCCCcCh
Confidence 459999998
No 304
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=28.04 E-value=30 Score=34.80 Aligned_cols=38 Identities=21% Similarity=0.386 Sum_probs=21.5
Q ss_pred CcccCCCCCccc-eeEEEEEEcCCCcEEEeeccC-Ccccc
Q psy12603 260 TKVFCPKCGYKT-LKRVAVSVDEQGKQKIHINLK-RPLTA 297 (391)
Q Consensus 260 ~k~FCP~CGn~T-L~Rvsvsvd~~G~~~~hl~~n-~~~n~ 297 (391)
.+.+||.||+.- +-.|-..-..+|.-.+|-+.= ..|+.
T Consensus 183 ~~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~ 222 (305)
T TIGR01562 183 SRTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHY 222 (305)
T ss_pred CCCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccc
Confidence 467999999864 222222112467777776543 44543
No 305
>PHA02325 hypothetical protein
Probab=27.96 E-value=27 Score=27.30 Aligned_cols=14 Identities=50% Similarity=1.073 Sum_probs=10.3
Q ss_pred cCcccCCCCCccce
Q psy12603 259 MTKVFCPKCGYKTL 272 (391)
Q Consensus 259 ~~k~FCP~CGn~TL 272 (391)
|....||+||.-=|
T Consensus 1 m~~k~CPkC~A~Wl 14 (72)
T PHA02325 1 MDTKICPKCGARWL 14 (72)
T ss_pred CCccccCccCCEeE
Confidence 45678999997633
No 306
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=27.87 E-value=46 Score=24.30 Aligned_cols=22 Identities=23% Similarity=0.285 Sum_probs=15.2
Q ss_pred CccccceeeeEEEEccCccccc
Q psy12603 235 DGRLIRELRTFILRCYACYKTT 256 (391)
Q Consensus 235 ~G~~Ik~~r~wvlRC~aCf~~t 256 (391)
.+..+.+-+...|||-+|..+-
T Consensus 20 ~~~~~~~k~~~klrCGaCs~vl 41 (46)
T PF11331_consen 20 AKFSLSKKNQQKLRCGACSEVL 41 (46)
T ss_pred CccCCCccceeEEeCCCCceeE
Confidence 4445555567888899998764
No 307
>cd00296 SIR2 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer. Also included in this superfamily is a group of uncharacterized Sir2-like proteins which lack certain key catalytic
Probab=27.76 E-value=56 Score=30.33 Aligned_cols=52 Identities=27% Similarity=0.461 Sum_probs=32.5
Q ss_pred EEEecCcHHHHHHHHHhCCc---eeccCccccceeeeEEEEccCcccccccc------CcccCCCCCcc
Q psy12603 211 VSCVTTDFAMQNVLKQMGLN---VVALDGRLIRELRTFILRCYACYKTTSIM------TKVFCPKCGYK 270 (391)
Q Consensus 211 Vac~TtDfAMQNVllqmGL~---l~s~~G~~Ik~~r~wvlRC~aCf~~t~~~------~k~FCP~CGn~ 270 (391)
+.++|+=| -|...+.|.. |+-++|. -...+|..|.+.+... ..--||.||..
T Consensus 83 ~~iiTqNi--D~L~~~ag~~~~~v~~lHG~------~~~~~C~~C~~~~~~~~~~~~~~~p~C~~C~~~ 143 (222)
T cd00296 83 KRIITQNV--DGLHERAGSRRNRVIELHGS------LDRVRCTSCGKEYPRDEVLEREKPPRCPKCGGL 143 (222)
T ss_pred ceEEecCh--HHHHHHhCCCcCcEEEecCC------CCccEECCCCCCcchhhhhhccCCCCCCCCCCc
Confidence 45667543 4556667764 7788885 2346688887654311 23569999875
No 308
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=27.65 E-value=20 Score=36.72 Aligned_cols=32 Identities=28% Similarity=0.527 Sum_probs=24.4
Q ss_pred CccccceeeeEEEEccCccccccccCcccCCCCCc
Q psy12603 235 DGRLIRELRTFILRCYACYKTTSIMTKVFCPKCGY 269 (391)
Q Consensus 235 ~G~~Ik~~r~wvlRC~aCf~~t~~~~k~FCP~CGn 269 (391)
-|.+|++ +-.+||+-|...+... ---||+|-+
T Consensus 345 vge~l~~--~~~YRC~~CGF~a~~l-~W~CPsC~~ 376 (389)
T COG2956 345 VGEQLRR--KPRYRCQNCGFTAHTL-YWHCPSCRA 376 (389)
T ss_pred HHHHHhh--cCCceecccCCcceee-eeeCCCccc
Confidence 4778875 7789999999876533 345999976
No 309
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=27.48 E-value=29 Score=28.82 Aligned_cols=28 Identities=32% Similarity=0.679 Sum_probs=22.8
Q ss_pred eeEEEEccCccccccccCcccCCCCCccc
Q psy12603 243 RTFILRCYACYKTTSIMTKVFCPKCGYKT 271 (391)
Q Consensus 243 r~wvlRC~aCf~~t~~~~k~FCP~CGn~T 271 (391)
++.+ .|.-|.+...-..|.-|.+||.+.
T Consensus 14 ktHt-lCrRCG~~syH~qK~~CasCGyps 41 (91)
T PTZ00073 14 KTHT-LCRRCGKRSFHVQKKRCASCGYPS 41 (91)
T ss_pred cCcc-hhcccCccccccccccchhcCCch
Confidence 4443 699999988888899999999973
No 310
>PRK07418 acetolactate synthase 3 catalytic subunit; Reviewed
Probab=27.36 E-value=29 Score=37.83 Aligned_cols=24 Identities=38% Similarity=0.840 Sum_probs=16.5
Q ss_pred EEccCccccccccCcccCCCCCccc
Q psy12603 247 LRCYACYKTTSIMTKVFCPKCGYKT 271 (391)
Q Consensus 247 lRC~aCf~~t~~~~k~FCP~CGn~T 271 (391)
..|+.|..-. .+.+.||+.||..+
T Consensus 593 ~~~~~~~~~~-~~~~~f~~~~g~~~ 616 (616)
T PRK07418 593 IYCSNCGAKN-PSTHRFCPECGTKL 616 (616)
T ss_pred ccCCCCCCcC-ccccccchhhCCCC
Confidence 4688888742 24468999998763
No 311
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=27.17 E-value=28 Score=29.36 Aligned_cols=20 Identities=25% Similarity=0.670 Sum_probs=14.0
Q ss_pred cCcccCCCCCccceeEEEEEEcC
Q psy12603 259 MTKVFCPKCGYKTLKRVAVSVDE 281 (391)
Q Consensus 259 ~~k~FCP~CGn~TL~Rvsvsvd~ 281 (391)
.+..-||.||+ .+|+|.++.
T Consensus 19 pt~f~CP~Cge---~~v~v~~~k 38 (99)
T PRK14892 19 PKIFECPRCGK---VSISVKIKK 38 (99)
T ss_pred CcEeECCCCCC---eEeeeecCC
Confidence 34566999995 467777665
No 312
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=27.15 E-value=28 Score=26.96 Aligned_cols=25 Identities=28% Similarity=0.934 Sum_probs=21.4
Q ss_pred EEccCccccccccCcccCCCCCc-cc
Q psy12603 247 LRCYACYKTTSIMTKVFCPKCGY-KT 271 (391)
Q Consensus 247 lRC~aCf~~t~~~~k~FCP~CGn-~T 271 (391)
-+|.-|.+......|.-|.+||. +.
T Consensus 18 t~CrRCG~~syh~qK~~CasCGygps 43 (62)
T PRK04179 18 IRCRRCGRHSYNVRKKYCAACGFGRS 43 (62)
T ss_pred chhcccCcccccccccchhhcCCCcc
Confidence 46999999888888999999998 53
No 313
>PF06839 zf-GRF: GRF zinc finger; InterPro: IPR010666 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 presumed zinc-binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to IPR000380 from INTERPRO. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=26.80 E-value=44 Score=23.65 Aligned_cols=19 Identities=26% Similarity=0.705 Sum_probs=14.1
Q ss_pred cCCCCCccceeEEEEEEcCC
Q psy12603 263 FCPKCGYKTLKRVAVSVDEQ 282 (391)
Q Consensus 263 FCP~CGn~TL~Rvsvsvd~~ 282 (391)
.|+ ||...+.+++...+.|
T Consensus 2 ~C~-Cg~~~~~~~s~k~~~N 20 (45)
T PF06839_consen 2 KCP-CGEPAVRRTSKKTGPN 20 (45)
T ss_pred CCC-CCCEeEEEEEeCCCCC
Confidence 699 9988888888833443
No 314
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=26.74 E-value=23 Score=28.78 Aligned_cols=14 Identities=36% Similarity=0.930 Sum_probs=7.8
Q ss_pred cccCcccCCCCCcc
Q psy12603 257 SIMTKVFCPKCGYK 270 (391)
Q Consensus 257 ~~~~k~FCP~CGn~ 270 (391)
.+|+-..||+||+.
T Consensus 61 ENMs~~~Cp~Cg~~ 74 (81)
T PF10609_consen 61 ENMSYFVCPHCGER 74 (81)
T ss_dssp ECT-EEE-TTT--E
T ss_pred ECCCccCCCCCCCe
Confidence 36788889999976
No 315
>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=26.74 E-value=23 Score=24.29 Aligned_cols=28 Identities=21% Similarity=0.318 Sum_probs=18.4
Q ss_pred eeEEEEccCcccccc--ccCcccCCCCCcc
Q psy12603 243 RTFILRCYACYKTTS--IMTKVFCPKCGYK 270 (391)
Q Consensus 243 r~wvlRC~aCf~~t~--~~~k~FCP~CGn~ 270 (391)
+.+..+|..|....- +-.+.||-.||+.
T Consensus 5 ~~~~~~C~~C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 5 RGPNEPCPVCGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred ccCCCcCCCCCCeEeEccCCEEEhhhCceE
Confidence 334456888876532 3368888888874
No 316
>PRK14285 chaperone protein DnaJ; Provisional
Probab=26.64 E-value=1.8e+02 Score=29.83 Aligned_cols=28 Identities=25% Similarity=0.458 Sum_probs=20.2
Q ss_pred eEEEEccCccccccccCcccCCCCCccce
Q psy12603 244 TFILRCYACYKTTSIMTKVFCPKCGYKTL 272 (391)
Q Consensus 244 ~wvlRC~aCf~~t~~~~k~FCP~CGn~TL 272 (391)
++...|..|.-.-.. .+..|+.|.+...
T Consensus 183 ~~~~~C~~C~G~G~~-~~~~C~~C~G~g~ 210 (365)
T PRK14285 183 RVTTTCPKCYGNGKI-ISNPCKSCKGKGS 210 (365)
T ss_pred EEeeecCCCCCcccc-cCCCCCCCCCCCE
Confidence 357789999866553 3567999999754
No 317
>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=26.62 E-value=39 Score=36.69 Aligned_cols=31 Identities=23% Similarity=0.619 Sum_probs=23.1
Q ss_pred eeeEEEEccCcccccc--------------ccCcccCCCCCccce
Q psy12603 242 LRTFILRCYACYKTTS--------------IMTKVFCPKCGYKTL 272 (391)
Q Consensus 242 ~r~wvlRC~aCf~~t~--------------~~~k~FCP~CGn~TL 272 (391)
-+.|-..|..|..... ...+.-||+||...-
T Consensus 196 qr~~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~ 240 (557)
T PF05876_consen 196 QRRYYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIE 240 (557)
T ss_pred ceEEEccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCC
Confidence 3699999999986543 224678999998743
No 318
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=26.59 E-value=42 Score=25.42 Aligned_cols=19 Identities=32% Similarity=0.541 Sum_probs=11.8
Q ss_pred cCcccCCCCCccceeEEEE
Q psy12603 259 MTKVFCPKCGYKTLKRVAV 277 (391)
Q Consensus 259 ~~k~FCP~CGn~TL~Rvsv 277 (391)
..-..||.||+..|....|
T Consensus 25 ~~l~~C~~CG~~~~~H~vC 43 (57)
T PRK12286 25 PGLVECPNCGEPKLPHRVC 43 (57)
T ss_pred CcceECCCCCCccCCeEEC
Confidence 3456677777776655544
No 319
>smart00350 MCM minichromosome maintenance proteins.
Probab=26.44 E-value=48 Score=35.39 Aligned_cols=41 Identities=27% Similarity=0.527 Sum_probs=27.5
Q ss_pred eeccCccccc------eeeeEEEEccCccccccc-------cCcccCCC--CCccc
Q psy12603 231 VVALDGRLIR------ELRTFILRCYACYKTTSI-------MTKVFCPK--CGYKT 271 (391)
Q Consensus 231 l~s~~G~~Ik------~~r~wvlRC~aCf~~t~~-------~~k~FCP~--CGn~T 271 (391)
||++.|..|| .++.-.++|..|...+.. ..-..||. |++..
T Consensus 16 lV~v~GiV~r~s~v~p~~~~~~f~C~~C~~~~~~~~~~~~~~~p~~C~~~~C~~~~ 71 (509)
T smart00350 16 LVRVSGIVTRTSGVRPKLKRASFTCEKCGATLGPEIQSGRETEPTVCPPRECQSPT 71 (509)
T ss_pred EEEEEEEEEEccCceEEEEEEEEEecCCCCEEeEEecCCcccCCCcCCCCcCCCCC
Confidence 4566666443 456678999999975432 13457999 99864
No 320
>COG4640 Predicted membrane protein [Function unknown]
Probab=26.41 E-value=27 Score=36.42 Aligned_cols=16 Identities=50% Similarity=1.007 Sum_probs=10.4
Q ss_pred ccCCCCC-ccceeEEEE
Q psy12603 262 VFCPKCG-YKTLKRVAV 277 (391)
Q Consensus 262 ~FCP~CG-n~TL~Rvsv 277 (391)
.|||+|| ++.-.-+-|
T Consensus 2 ~fC~kcG~qk~Ed~~qC 18 (465)
T COG4640 2 KFCPKCGSQKAEDDVQC 18 (465)
T ss_pred Ccccccccccccccccc
Confidence 6999999 444444443
No 321
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=26.27 E-value=43 Score=25.40 Aligned_cols=23 Identities=35% Similarity=0.782 Sum_probs=14.1
Q ss_pred ccCccccccccCcccCCCCCccc
Q psy12603 249 CYACYKTTSIMTKVFCPKCGYKT 271 (391)
Q Consensus 249 C~aCf~~t~~~~k~FCP~CGn~T 271 (391)
|.-|..--+.....-||.||=+|
T Consensus 2 Cpv~~~~~~~~v~~~Cp~cGipt 24 (55)
T PF13824_consen 2 CPVCKKDLPAHVNFECPDCGIPT 24 (55)
T ss_pred CCCCccccccccCCcCCCCCCcC
Confidence 55555433334456799999775
No 322
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=26.26 E-value=46 Score=31.25 Aligned_cols=10 Identities=40% Similarity=1.374 Sum_probs=7.9
Q ss_pred cccCCCCCcc
Q psy12603 261 KVFCPKCGYK 270 (391)
Q Consensus 261 k~FCP~CGn~ 270 (391)
--.||+||..
T Consensus 30 sf~C~~CGyr 39 (192)
T TIGR00310 30 STICEHCGYR 39 (192)
T ss_pred EEECCCCCCc
Confidence 3569999986
No 323
>PRK14873 primosome assembly protein PriA; Provisional
Probab=26.05 E-value=35 Score=37.94 Aligned_cols=13 Identities=23% Similarity=0.437 Sum_probs=7.7
Q ss_pred eEEEEccCccccc
Q psy12603 244 TFILRCYACYKTT 256 (391)
Q Consensus 244 ~wvlRC~aCf~~t 256 (391)
.-.+.|+.|..+.
T Consensus 381 ap~l~C~~Cg~~~ 393 (665)
T PRK14873 381 VPSLACARCRTPA 393 (665)
T ss_pred CCeeEhhhCcCee
Confidence 3466677776553
No 324
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=25.91 E-value=40 Score=35.16 Aligned_cols=28 Identities=25% Similarity=0.731 Sum_probs=21.7
Q ss_pred eeEEEEccCcccccccc-----CcccCCCCCcc
Q psy12603 243 RTFILRCYACYKTTSIM-----TKVFCPKCGYK 270 (391)
Q Consensus 243 r~wvlRC~aCf~~t~~~-----~k~FCP~CGn~ 270 (391)
+.-..+|..|--...-+ .+-+||.||..
T Consensus 15 ~~~~~~C~eCd~~~~~P~l~~~q~A~CPRC~~~ 47 (418)
T COG2995 15 PGHLILCPECDMLVSLPRLDSGQSAYCPRCGHT 47 (418)
T ss_pred ccceecCCCCCceeccccCCCCCcccCCCCCCc
Confidence 45578999998776644 47799999986
No 325
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=25.89 E-value=39 Score=31.27 Aligned_cols=28 Identities=21% Similarity=0.477 Sum_probs=19.1
Q ss_pred EEEEccCcccccccc---C-cccCCCCCccce
Q psy12603 245 FILRCYACYKTTSIM---T-KVFCPKCGYKTL 272 (391)
Q Consensus 245 wvlRC~aCf~~t~~~---~-k~FCP~CGn~TL 272 (391)
=-+.|..|...++-. . ---||.||+...
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~ 147 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAMEYGFRCPQCGEMLE 147 (178)
T ss_pred CEEECCCCCcEEeHHHHhhcCCcCCCCCCCCe
Confidence 468899998655422 2 344999999854
No 326
>PRK13795 hypothetical protein; Provisional
Probab=25.83 E-value=52 Score=36.33 Aligned_cols=43 Identities=21% Similarity=0.400 Sum_probs=29.2
Q ss_pred eeeEEEEccCccccccccCcccCCCCCccceeEEEEEEcCCCcEEEeec
Q psy12603 242 LRTFILRCYACYKTTSIMTKVFCPKCGYKTLKRVAVSVDEQGKQKIHIN 290 (391)
Q Consensus 242 ~r~wvlRC~aCf~~t~~~~k~FCP~CGn~TL~Rvsvsvd~~G~~~~hl~ 290 (391)
-+.|++.|..|.--. ..+ -|..||+.+ .+|.+| .-|-.++-++
T Consensus 8 ~~~~~~wc~~cn~p~--~~~-~c~~c~~~~-~~~~~t--~p~d~r~a~~ 50 (636)
T PRK13795 8 GKDHIYWCEKCNVPL--LGK-KCGICGKEG-FKVRLT--PPGDVRPAFP 50 (636)
T ss_pred cceeEEEcccCCCee--ccc-cccccCCCc-eEeecC--CCCCCCcCCH
Confidence 367999999998432 333 399999998 666664 5555555443
No 327
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=25.54 E-value=34 Score=40.39 Aligned_cols=52 Identities=17% Similarity=0.462 Sum_probs=31.6
Q ss_pred eeeEEEEccCcccccccc-CcccCCCCCcc-ceeEEEEEEcCCCcEEEeeccCCccccC
Q psy12603 242 LRTFILRCYACYKTTSIM-TKVFCPKCGYK-TLKRVAVSVDEQGKQKIHINLKRPLTAR 298 (391)
Q Consensus 242 ~r~wvlRC~aCf~~t~~~-~k~FCP~CGn~-TL~Rvsvsvd~~G~~~~hl~~n~~~n~R 298 (391)
+|.| .| +|.+....- .-.||++||-. |..||-- ..-|.+.+...=-..|-.+
T Consensus 55 ~kd~--eC-~Cgkyk~~~~~~~~C~~cgve~~~~~vrr--~rmGhI~La~Pv~Hiwy~k 108 (1156)
T PRK00566 55 TKDY--EC-LCGKYKRVRYKGIICERCGVEVTRSKVRR--ERMGHIELAAPVAHIWFFK 108 (1156)
T ss_pred ccCc--EE-eCccccccCcCCcCCCCCCceeeechhhh--hhcceeeecCceeeeeecC
Confidence 3455 46 777643321 24899999987 5555443 2458777665555566666
No 328
>PRK10281 hypothetical protein; Provisional
Probab=25.54 E-value=58 Score=32.34 Aligned_cols=17 Identities=12% Similarity=0.243 Sum_probs=13.9
Q ss_pred CcHHHHHHHHHhCCcee
Q psy12603 216 TDFAMQNVLKQMGLNVV 232 (391)
Q Consensus 216 tDfAMQNVllqmGL~l~ 232 (391)
+|=-||+++.+|||.--
T Consensus 31 ~~~~Mq~IAre~n~SET 47 (299)
T PRK10281 31 SEAQMQLIARELNHSET 47 (299)
T ss_pred CHHHHHHHHHHhCCceE
Confidence 55689999999999643
No 329
>PTZ00408 NAD-dependent deacetylase; Provisional
Probab=25.42 E-value=40 Score=32.62 Aligned_cols=39 Identities=23% Similarity=0.448 Sum_probs=22.6
Q ss_pred HHhCCc-eeccCccccceeeeEEEEccCcccccccc---C--cccCCCCCc
Q psy12603 225 KQMGLN-VVALDGRLIRELRTFILRCYACYKTTSIM---T--KVFCPKCGY 269 (391)
Q Consensus 225 lqmGL~-l~s~~G~~Ik~~r~wvlRC~aCf~~t~~~---~--k~FCP~CGn 269 (391)
.+.|.. |+-++|- -+-++|..|.+.+.-. . --.||.||.
T Consensus 101 ~~AG~~~v~elHG~------~~~~~C~~C~~~~~~~~~~~~~~p~C~~Cg~ 145 (242)
T PTZ00408 101 ERAGSTHVLHMHGE------LLKVRCTATGHVFDWTEDVVHGSSRCKCCGC 145 (242)
T ss_pred hHcCCCcEEEecCc------cceEEECCCCcccCchhhhhcCCCccccCCC
Confidence 344543 5566664 3346788888765321 1 135999984
No 330
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.35 E-value=26 Score=28.07 Aligned_cols=29 Identities=24% Similarity=0.606 Sum_probs=17.8
Q ss_pred EEEccCccccccccCcccCCCCCccceeE
Q psy12603 246 ILRCYACYKTTSIMTKVFCPKCGYKTLKR 274 (391)
Q Consensus 246 vlRC~aCf~~t~~~~k~FCP~CGn~TL~R 274 (391)
-+-|+-|----.+.-...||.||+..+.|
T Consensus 26 tfEcTFCadCae~~l~g~CPnCGGelv~R 54 (84)
T COG3813 26 TFECTFCADCAENRLHGLCPNCGGELVAR 54 (84)
T ss_pred EEeeehhHhHHHHhhcCcCCCCCchhhcC
Confidence 34455554333333357799999987665
No 331
>PRK14293 chaperone protein DnaJ; Provisional
Probab=25.32 E-value=1.4e+02 Score=30.57 Aligned_cols=25 Identities=24% Similarity=0.596 Sum_probs=19.0
Q ss_pred EEccCccccccccCcccCCCCCccce
Q psy12603 247 LRCYACYKTTSIMTKVFCPKCGYKTL 272 (391)
Q Consensus 247 lRC~aCf~~t~~~~k~FCP~CGn~TL 272 (391)
..|..|.-.-... +..|++|.+...
T Consensus 187 ~~C~~C~G~G~~~-~~~C~~C~G~g~ 211 (374)
T PRK14293 187 SECPTCNGTGQVI-EDPCDACGGQGV 211 (374)
T ss_pred eeCCCCCcceeEe-ccCCCCCCCCcc
Confidence 5999998766543 567999998643
No 332
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=25.27 E-value=40 Score=33.68 Aligned_cols=36 Identities=17% Similarity=0.195 Sum_probs=20.6
Q ss_pred HHHhhcCHHHHH--HHhhCCCceEEecCChhhHHHHHHHHHH
Q psy12603 12 VVNEVTSKRQIR--RLVVLPYDLQIKEADPDSISFVTEFSKK 51 (391)
Q Consensus 12 Vi~EIrD~~sR~--~L~~Lp~~L~vreP~~esi~~V~~FAkk 51 (391)
...-.|+--+|+ ||..| .-..|-..++.|+...++.
T Consensus 24 Lf~n~k~Lf~rR~~Rl~~L----ae~~Pl~dYL~F~a~I~e~ 61 (308)
T COG3058 24 LFPNLKNLFNRRAERLRQL----AENHPLGDYLNFAAGIAEA 61 (308)
T ss_pred hcCCHHHHHHHHHHHHHHH----HhcCChHHHHHHHHHHHHH
Confidence 334445555555 55543 3455777777777766654
No 333
>PTZ00410 NAD-dependent SIR2; Provisional
Probab=25.20 E-value=82 Score=32.38 Aligned_cols=46 Identities=22% Similarity=0.404 Sum_probs=29.0
Q ss_pred HHhCCc---eeccCccccceeeeEEEEccCcccccccc---------CcccCCCCCccceeEEEEE
Q psy12603 225 KQMGLN---VVALDGRLIRELRTFILRCYACYKTTSIM---------TKVFCPKCGYKTLKRVAVS 278 (391)
Q Consensus 225 lqmGL~---l~s~~G~~Ik~~r~wvlRC~aCf~~t~~~---------~k~FCP~CGn~TL~Rvsvs 278 (391)
.+-|+. |+-++|. -+.++|..|.+.+... .--.||.||.. .|-.|.
T Consensus 129 ~rAG~~~~~ViElHGs------l~~~~C~~C~~~~~~~~~~~~~~~~~vP~C~~CgG~--lRPdVV 186 (349)
T PTZ00410 129 RAAGVPPSLLVEAHGS------FSAASCIECHTPYDIEQAYLEARSGKVPHCSTCGGI--VKPDVV 186 (349)
T ss_pred hhcCCCcccEEEeccC------CCeeEeCCCCCCcchhHHHHHhhcCCCCCCCCCCCc--cCCcEE
Confidence 345764 7788885 3457899998766421 12359999974 444444
No 334
>PRK14894 glycyl-tRNA synthetase; Provisional
Probab=25.07 E-value=44 Score=36.14 Aligned_cols=37 Identities=22% Similarity=0.526 Sum_probs=24.8
Q ss_pred CccccceeeeEEEEccCcccccccc-CcccCCCCCccce
Q psy12603 235 DGRLIRELRTFILRCYACYKTTSIM-TKVFCPKCGYKTL 272 (391)
Q Consensus 235 ~G~~Ik~~r~wvlRC~aCf~~t~~~-~k~FCP~CGn~TL 272 (391)
+|. +..---|+..|.-|.+.++-- -...||.||+..|
T Consensus 78 SGH-~~~F~DpmV~CkkCk~ryRaD~LiikCP~CGs~dL 115 (539)
T PRK14894 78 SGH-EETFNDPLVDCRDCKMRWRADHIQGVCPNCGSRDL 115 (539)
T ss_pred ccC-CCCCCCceeECCCCCccccCccceeeCCCCCCcCC
Confidence 453 455567788999998877632 1245999996433
No 335
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=24.79 E-value=48 Score=35.22 Aligned_cols=35 Identities=26% Similarity=0.360 Sum_probs=19.8
Q ss_pred eEEecCChhhHHHHHHHHHHhCCCCC-CChhhHHHH
Q psy12603 32 LQIKEADPDSISFVTEFSKKTGDYPS-LSSTDIKVI 66 (391)
Q Consensus 32 L~vreP~~esi~~V~~FAkkTGD~~s-LS~~DI~Vi 66 (391)
|.+-+..++.+-.+..+.++..+..+ .|......|
T Consensus 75 IilTH~H~DH~Ggl~~Ll~~~p~a~V~~s~~~~~~l 110 (479)
T PRK05452 75 IVINHAEEDHAGALTELMAQIPDTPIYCTANAIDSI 110 (479)
T ss_pred EEeCCCCcchhchHHHHHHHCCCCEEEECHHHHHHH
Confidence 66667777777666666666444333 344444433
No 336
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=24.21 E-value=34 Score=27.73 Aligned_cols=23 Identities=26% Similarity=0.611 Sum_probs=15.7
Q ss_pred ccCCCCCccceeEEEEEEcCCCc
Q psy12603 262 VFCPKCGYKTLKRVAVSVDEQGK 284 (391)
Q Consensus 262 ~FCP~CGn~TL~Rvsvsvd~~G~ 284 (391)
+||-+||-|.-...-...++||.
T Consensus 1 k~CQSCGMPl~~~~~~Gte~dGs 23 (81)
T PF12674_consen 1 KFCQSCGMPLSKDEDFGTEADGS 23 (81)
T ss_pred CcCCcCcCccCCccccccccCCC
Confidence 58999999955544455555664
No 337
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=24.13 E-value=40 Score=30.45 Aligned_cols=26 Identities=19% Similarity=0.513 Sum_probs=17.9
Q ss_pred EEEEccCcccccccc---C-cccCCCCCcc
Q psy12603 245 FILRCYACYKTTSIM---T-KVFCPKCGYK 270 (391)
Q Consensus 245 wvlRC~aCf~~t~~~---~-k~FCP~CGn~ 270 (391)
=-+.|..|..-++-. . ---||.||+.
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAMELNFTCPRCGAM 137 (158)
T ss_pred CeEECCCCCcEeeHHHHHHcCCcCCCCCCE
Confidence 367899998655422 2 2349999997
No 338
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=24.09 E-value=33 Score=34.09 Aligned_cols=20 Identities=25% Similarity=0.859 Sum_probs=10.0
Q ss_pred EccCcccccccc-----CcccCCCC
Q psy12603 248 RCYACYKTTSIM-----TKVFCPKC 267 (391)
Q Consensus 248 RC~aCf~~t~~~-----~k~FCP~C 267 (391)
-|..|..+-... +-.|||.|
T Consensus 247 pC~~CGt~I~k~~~~gR~t~~CP~C 271 (273)
T COG0266 247 PCRRCGTPIEKIKLGGRSTFYCPVC 271 (273)
T ss_pred CCCccCCEeEEEEEcCCcCEeCCCC
Confidence 366665443211 34566666
No 339
>PF15608 PELOTA_1: PELOTA RNA binding domain
Probab=24.07 E-value=1.2e+02 Score=25.83 Aligned_cols=35 Identities=11% Similarity=0.330 Sum_probs=32.3
Q ss_pred HHHHHHHhhCCCceEEecCChhhHHHHHHHHHHhC
Q psy12603 19 KRQIRRLVVLPYDLQIKEADPDSISFVTEFSKKTG 53 (391)
Q Consensus 19 ~~sR~~L~~Lp~~L~vreP~~esi~~V~~FAkkTG 53 (391)
+.||-.|-..|..|-|++|....++.+...|+.-|
T Consensus 46 EaTRvLLRRvP~~vLVr~~~~pd~~Hl~~LA~ekg 80 (100)
T PF15608_consen 46 EATRVLLRRVPWKVLVRDPDDPDLAHLLLLAEEKG 80 (100)
T ss_pred HHHHHHHhcCCCEEEECCCCCccHHHHHHHHHHcC
Confidence 57899999999999999999999999999998877
No 340
>TIGR03847 conserved hypothetical protein. The conserved hypothetical protein described here occurs as part of the trio of uncharacterized proteins common in the Actinobacteria.
Probab=24.02 E-value=36 Score=31.65 Aligned_cols=20 Identities=30% Similarity=0.614 Sum_probs=14.9
Q ss_pred CcccCCCCCccceeEEEEEEcCCCcEEE
Q psy12603 260 TKVFCPKCGYKTLKRVAVSVDEQGKQKI 287 (391)
Q Consensus 260 ~k~FCP~CGn~TL~Rvsvsvd~~G~~~~ 287 (391)
.|-.||-||.+ +|.+|.+-.
T Consensus 155 GRP~CPlCg~P--------ldP~GH~Cp 174 (177)
T TIGR03847 155 GRPPCPLCGRP--------IDPDGHICP 174 (177)
T ss_pred CCCCCCCCCCC--------CCCCCccCC
Confidence 57889999998 577776543
No 341
>PHA02152 hypothetical protein
Probab=23.99 E-value=44 Score=27.38 Aligned_cols=15 Identities=33% Similarity=0.857 Sum_probs=12.4
Q ss_pred CCCCccCcccHHHHH
Q psy12603 182 DGGEWITPSNLKQAQ 196 (391)
Q Consensus 182 d~~~WITp~Ni~~~~ 196 (391)
+.-|||.|+||+..+
T Consensus 22 gnhgwisp~~i~~a~ 36 (96)
T PHA02152 22 GNHGWVSPSNIRYAE 36 (96)
T ss_pred cccCccChhHHHHHH
Confidence 456899999999774
No 342
>PRK12495 hypothetical protein; Provisional
Probab=23.84 E-value=40 Score=32.48 Aligned_cols=24 Identities=25% Similarity=0.599 Sum_probs=16.3
Q ss_pred EEccCccccc-cccCcccCCCCCcc
Q psy12603 247 LRCYACYKTT-SIMTKVFCPKCGYK 270 (391)
Q Consensus 247 lRC~aCf~~t-~~~~k~FCP~CGn~ 270 (391)
+.|.-|..-. ..+...|||.|+.-
T Consensus 43 ~hC~~CG~PIpa~pG~~~Cp~CQ~~ 67 (226)
T PRK12495 43 AHCDECGDPIFRHDGQEFCPTCQQP 67 (226)
T ss_pred hhcccccCcccCCCCeeECCCCCCc
Confidence 4577787543 34468899999854
No 343
>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=23.83 E-value=35 Score=36.49 Aligned_cols=21 Identities=29% Similarity=0.668 Sum_probs=14.0
Q ss_pred eEEEEccCccccccccCcccCCCCCcc
Q psy12603 244 TFILRCYACYKTTSIMTKVFCPKCGYK 270 (391)
Q Consensus 244 ~wvlRC~aCf~~t~~~~k~FCP~CGn~ 270 (391)
.-.+.|+.|..+.. ||+|+.+
T Consensus 211 a~~~~C~~Cg~~~~------C~~C~~~ 231 (505)
T TIGR00595 211 SKNLLCRSCGYILC------CPNCDVS 231 (505)
T ss_pred CCeeEhhhCcCccC------CCCCCCc
Confidence 34678888887643 7777543
No 344
>CHL00018 rpoC1 RNA polymerase beta' subunit
Probab=23.75 E-value=32 Score=38.21 Aligned_cols=53 Identities=26% Similarity=0.425 Sum_probs=30.8
Q ss_pred eeeEEEEccCccccccc----cCcccCCCCCcc-ceeEEEEEEcCCCcEEEeeccCCccccCC
Q psy12603 242 LRTFILRCYACYKTTSI----MTKVFCPKCGYK-TLKRVAVSVDEQGKQKIHINLKRPLTARG 299 (391)
Q Consensus 242 ~r~wvlRC~aCf~~t~~----~~k~FCP~CGn~-TL~Rvsvsvd~~G~~~~hl~~n~~~n~RG 299 (391)
++.|. | +|.+.-.. -...||++||-. |..||-- -.-|.+.+...=-..|-+||
T Consensus 64 ~k~~~--C-~CGkyk~~~~~~~~~~~C~~CgVE~t~s~vRR--~RMG~I~La~PV~HiWylk~ 121 (663)
T CHL00018 64 IKSGI--C-ACGNYRVIGDEKEDPKFCEQCGVEFTDSRVRR--YRMGYIKLACPVTHVWYLKR 121 (663)
T ss_pred CcCCE--E-eCCCccccCccccCCCccCCcCCEechhhhhH--hhcCceeecCcceeehhhcC
Confidence 45665 4 55543221 234699999986 6666432 23477766555555566663
No 345
>PTZ00409 Sir2 (Silent Information Regulator) protein; Provisional
Probab=23.69 E-value=40 Score=33.19 Aligned_cols=21 Identities=43% Similarity=0.825 Sum_probs=14.4
Q ss_pred eeccCccccceeeeEEEEccCcccccc
Q psy12603 231 VVALDGRLIRELRTFILRCYACYKTTS 257 (391)
Q Consensus 231 l~s~~G~~Ik~~r~wvlRC~aCf~~t~ 257 (391)
|+-++|. -+.++|..|.+.+.
T Consensus 128 V~ElHG~------l~~~~C~~C~~~~~ 148 (271)
T PTZ00409 128 VIPLHGS------VFEARCCTCRKTIQ 148 (271)
T ss_pred EEEeccC------cCcceeCCCCCCcc
Confidence 5666774 45677999976654
No 346
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=23.47 E-value=37 Score=33.31 Aligned_cols=69 Identities=22% Similarity=0.368 Sum_probs=40.7
Q ss_pred CccCcccHHHHHhhhhcccccCCCceEEEecCcHHHHHHHHHhCCceeccCccccceeeeEEEEccCcccccccc-----
Q psy12603 185 EWITPSNLKQAQRTMDARQYEEKPLVVSCVTTDFAMQNVLKQMGLNVVALDGRLIRELRTFILRCYACYKTTSIM----- 259 (391)
Q Consensus 185 ~WITp~Ni~~~~~~~~~~~~~~~~~~Vac~TtDfAMQNVllqmGL~l~s~~G~~Ik~~r~wvlRC~aCf~~t~~~----- 259 (391)
-|+|..|+.-+....... .+...-+.||-.-||- -. +++.+ |.=|-||+.|.+-+.-.
T Consensus 88 lPLTe~Nlrm~d~a~~~~-ip~~drqFaC~~Cd~~----Ww-----------Rrvp~-rKeVSRCr~C~~rYDPVP~dkm 150 (278)
T PF15135_consen 88 LPLTEENLRMFDDAQENL-IPSVDRQFACSSCDHM----WW-----------RRVPQ-RKEVSRCRKCRKRYDPVPCDKM 150 (278)
T ss_pred CCchHHHHHHhhhhhhcc-ccccceeeeccccchH----HH-----------hccCc-ccccccccccccccCCCccccc
Confidence 488899988775432211 1223445667665542 11 12332 33488999999876422
Q ss_pred ---CcccCCCCCcc
Q psy12603 260 ---TKVFCPKCGYK 270 (391)
Q Consensus 260 ---~k~FCP~CGn~ 270 (391)
..--||+||+.
T Consensus 151 wG~aef~C~~C~h~ 164 (278)
T PF15135_consen 151 WGIAEFHCPKCRHN 164 (278)
T ss_pred cceeeeeccccccc
Confidence 34459999986
No 347
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=23.32 E-value=40 Score=40.82 Aligned_cols=25 Identities=32% Similarity=0.599 Sum_probs=18.8
Q ss_pred EEEccCcccccc----------ccCcccCCCCCcc
Q psy12603 246 ILRCYACYKTTS----------IMTKVFCPKCGYK 270 (391)
Q Consensus 246 vlRC~aCf~~t~----------~~~k~FCP~CGn~ 270 (391)
-+||.-|...-- |++-.-||+||.+
T Consensus 908 hy~C~~C~~~ef~~~~~~~sG~Dlpdk~Cp~Cg~~ 942 (1437)
T PRK00448 908 HYVCPNCKYSEFFTDGSVGSGFDLPDKDCPKCGTK 942 (1437)
T ss_pred cccCcccccccccccccccccccCccccCcccccc
Confidence 379999986533 4566779999987
No 348
>PRK05333 NAD-dependent deacetylase; Provisional
Probab=23.27 E-value=68 Score=31.59 Aligned_cols=20 Identities=35% Similarity=0.614 Sum_probs=13.5
Q ss_pred eeccCccccceeeeEEEEccCccccc
Q psy12603 231 VVALDGRLIRELRTFILRCYACYKTT 256 (391)
Q Consensus 231 l~s~~G~~Ik~~r~wvlRC~aCf~~t 256 (391)
|+-+.|. -+.++|..|.+.+
T Consensus 119 ViElHG~------~~~~~C~~C~~~~ 138 (285)
T PRK05333 119 VIELHGR------LDGVRCMGCGARH 138 (285)
T ss_pred EEeecCC------cCEEEECCCCCcC
Confidence 4566674 3457899999654
No 349
>KOG3896|consensus
Probab=23.09 E-value=33 Score=35.10 Aligned_cols=25 Identities=28% Similarity=0.773 Sum_probs=15.8
Q ss_pred EEEccCccccc------cccCcccCCCCCcc
Q psy12603 246 ILRCYACYKTT------SIMTKVFCPKCGYK 270 (391)
Q Consensus 246 vlRC~aCf~~t------~~~~k~FCP~CGn~ 270 (391)
.+-|.-||++- -+..-+|||+|=-+
T Consensus 24 L~FCRyC~klrc~~Cv~hEvdshfCp~CLEn 54 (449)
T KOG3896|consen 24 LVFCRYCFKLRCDDCVLHEVDSHFCPRCLEN 54 (449)
T ss_pred eeeeecccccccccccccccccccchhhccC
Confidence 45566666653 34467999998543
No 350
>KOG3799|consensus
Probab=23.03 E-value=39 Score=30.26 Aligned_cols=20 Identities=35% Similarity=1.002 Sum_probs=14.1
Q ss_pred EEccCccccccccCcccCCCCCcc-cee
Q psy12603 247 LRCYACYKTTSIMTKVFCPKCGYK-TLK 273 (391)
Q Consensus 247 lRC~aCf~~t~~~~k~FCP~CGn~-TL~ 273 (391)
..||-|. -.||..||+. +|+
T Consensus 82 H~C~YCq-------~r~CARCGGrv~lr 102 (169)
T KOG3799|consen 82 HNCSYCQ-------TRFCARCGGRVSLR 102 (169)
T ss_pred cccchhh-------hhHHHhcCCeeeec
Confidence 3466665 3799999997 554
No 351
>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=22.85 E-value=41 Score=23.84 Aligned_cols=15 Identities=33% Similarity=0.908 Sum_probs=9.6
Q ss_pred cCcccCCCCCcccee
Q psy12603 259 MTKVFCPKCGYKTLK 273 (391)
Q Consensus 259 ~~k~FCP~CGn~TL~ 273 (391)
|.-..||.||.+.++
T Consensus 15 ML~~~Cp~C~~PL~~ 29 (41)
T PF06677_consen 15 MLDEHCPDCGTPLMR 29 (41)
T ss_pred HhcCccCCCCCeeEE
Confidence 344668888777554
No 352
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=22.77 E-value=55 Score=31.08 Aligned_cols=14 Identities=21% Similarity=0.221 Sum_probs=7.7
Q ss_pred eeeEEEEccCcccc
Q psy12603 242 LRTFILRCYACYKT 255 (391)
Q Consensus 242 ~r~wvlRC~aCf~~ 255 (391)
.....+-|..|...
T Consensus 10 ~~~~~~~CPvCg~~ 23 (201)
T COG1779 10 EFETRIDCPVCGGT 23 (201)
T ss_pred eeeeeecCCcccce
Confidence 34445566666653
No 353
>KOG1819|consensus
Probab=22.75 E-value=32 Score=36.89 Aligned_cols=31 Identities=19% Similarity=0.465 Sum_probs=20.4
Q ss_pred EEccCcccccccc-CcccCCCCCccceeEEEE
Q psy12603 247 LRCYACYKTTSIM-TKVFCPKCGYKTLKRVAV 277 (391)
Q Consensus 247 lRC~aCf~~t~~~-~k~FCP~CGn~TL~Rvsv 277 (391)
-+|.||..-+.-. -++.|-.||.-.--+|+|
T Consensus 902 ~~cmacq~pf~afrrrhhcrncggifcg~cs~ 933 (990)
T KOG1819|consen 902 EQCMACQMPFNAFRRRHHCRNCGGIFCGKCSC 933 (990)
T ss_pred hhhhhccCcHHHHHHhhhhcccCceeeccccc
Confidence 4899997544322 367788888766556655
No 354
>cd03361 TOPRIM_TopoIA_RevGyr TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to the ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=22.23 E-value=84 Score=28.63 Aligned_cols=26 Identities=31% Similarity=0.628 Sum_probs=18.5
Q ss_pred eEEEEccCccccccccCcccCCCCCcc
Q psy12603 244 TFILRCYACYKTTSIMTKVFCPKCGYK 270 (391)
Q Consensus 244 ~wvlRC~aCf~~t~~~~k~FCP~CGn~ 270 (391)
.+..+|-+|.+.+. ....+||.||..
T Consensus 75 ~~~~~c~pc~~lF~-~~~~~cp~c~~~ 100 (170)
T cd03361 75 DSIKRCRDCGYQFT-EDSDKCPRCGSE 100 (170)
T ss_pred eEeeccCCcccccc-cccccCCcCCCc
Confidence 34568999987774 234579999954
No 355
>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=22.09 E-value=66 Score=29.27 Aligned_cols=14 Identities=36% Similarity=1.009 Sum_probs=9.6
Q ss_pred cCCCCCccceeEEE
Q psy12603 263 FCPKCGYKTLKRVA 276 (391)
Q Consensus 263 FCP~CGn~TL~Rvs 276 (391)
-||.||.+...|+-
T Consensus 3 ~Cp~C~~~~~~~~~ 16 (161)
T PF03367_consen 3 LCPNCGENGTTRIL 16 (161)
T ss_dssp E-TTTSSCCEEEEE
T ss_pred cCCCCCCCcEEEEE
Confidence 49999988766663
No 356
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=22.06 E-value=48 Score=39.25 Aligned_cols=25 Identities=28% Similarity=0.587 Sum_probs=18.6
Q ss_pred EEEccCcccc--cc--------ccCcccCCCCCcc
Q psy12603 246 ILRCYACYKT--TS--------IMTKVFCPKCGYK 270 (391)
Q Consensus 246 vlRC~aCf~~--t~--------~~~k~FCP~CGn~ 270 (391)
-|+|.-|... .. |++-.-||+||.+
T Consensus 914 HY~Cp~Cky~Ef~~d~svgsGfDLpdK~CPkCg~p 948 (1444)
T COG2176 914 HYLCPECKYSEFIDDGSVGSGFDLPDKDCPKCGTP 948 (1444)
T ss_pred cccCCCCceeeeecCCCcCCCCCCCCCCCCcCCCc
Confidence 4899999743 22 4566789999999
No 357
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=22.00 E-value=70 Score=30.86 Aligned_cols=34 Identities=24% Similarity=0.401 Sum_probs=20.9
Q ss_pred eeccCccccceeeeEEEEccCcccccccc---------CcccCCCCCcc
Q psy12603 231 VVALDGRLIRELRTFILRCYACYKTTSIM---------TKVFCPKCGYK 270 (391)
Q Consensus 231 l~s~~G~~Ik~~r~wvlRC~aCf~~t~~~---------~k~FCP~CGn~ 270 (391)
|+-+.|. -+.++|..|.+.+... .---||.||..
T Consensus 110 VielHG~------~~~~~C~~C~~~~~~~~~~~~~~~~~~p~Cp~Cgg~ 152 (244)
T PRK14138 110 VIELHGN------VEEYYCVRCGKRYTVEDVIEKLEKSDVPRCDDCSGL 152 (244)
T ss_pred EEEccCC------cCeeEECCCCCcccHHHHHHHHhcCCCCCCCCCCCe
Confidence 5566664 3446798898766421 11349999864
No 358
>PRK08223 hypothetical protein; Validated
Probab=21.81 E-value=2.3e+02 Score=28.29 Aligned_cols=76 Identities=16% Similarity=-0.016 Sum_probs=43.2
Q ss_pred CccCcccHHHHHhhhhcccccCCCceEEEecCc------HHHHHHHHHhCCceec--cCccccceeeeEE--EEccCccc
Q psy12603 185 EWITPSNLKQAQRTMDARQYEEKPLVVSCVTTD------FAMQNVLKQMGLNVVA--LDGRLIRELRTFI--LRCYACYK 254 (391)
Q Consensus 185 ~WITp~Ni~~~~~~~~~~~~~~~~~~Vac~TtD------fAMQNVllqmGL~l~s--~~G~~Ik~~r~wv--lRC~aCf~ 254 (391)
..||++|+.++... ..+.| ..|+. |.+-+.....|+.+++ +.|+. -++-.|. --|+.|+.
T Consensus 104 ~~l~~~n~~~ll~~--------~DlVv-D~~D~~~~~~r~~ln~~c~~~~iP~V~~~~~g~~-gqv~v~~p~~p~~~~~f 173 (287)
T PRK08223 104 EGIGKENADAFLDG--------VDVYV-DGLDFFEFDARRLVFAACQQRGIPALTAAPLGMG-TALLVFDPGGMSFDDYF 173 (287)
T ss_pred cccCccCHHHHHhC--------CCEEE-ECCCCCcHHHHHHHHHHHHHcCCCEEEEeccCCe-EEEEEEcCCCCchhhhc
Confidence 46788888776432 12222 33333 4566778899999994 33432 2233333 36777775
Q ss_pred cc-cccC---------cccCCCCCcc
Q psy12603 255 TT-SIMT---------KVFCPKCGYK 270 (391)
Q Consensus 255 ~t-~~~~---------k~FCP~CGn~ 270 (391)
-+ ..++ ..-+|+|...
T Consensus 174 ~~~~~~~~~~~~~~~~~~~~p~c~~~ 199 (287)
T PRK08223 174 DLSDGMNEVEKAVRFLAGLAPSMLHR 199 (287)
T ss_pred CCCCCCCchhhhcccCCcCCCccccC
Confidence 44 2122 2578999876
No 359
>PRK00164 moaA molybdenum cofactor biosynthesis protein A; Reviewed
Probab=21.77 E-value=1.7e+02 Score=28.91 Aligned_cols=72 Identities=17% Similarity=0.229 Sum_probs=40.6
Q ss_pred HHHHHHHHhCCceeccCccccceeeeEEEE-ccCccccccccCcccCCCCCccceeEEEEEEcCCCcEEEeeccCCcccc
Q psy12603 219 AMQNVLKQMGLNVVALDGRLIRELRTFILR-CYACYKTTSIMTKVFCPKCGYKTLKRVAVSVDEQGKQKIHINLKRPLTA 297 (391)
Q Consensus 219 AMQNVllqmGL~l~s~~G~~Ik~~r~wvlR-C~aCf~~t~~~~k~FCP~CGn~TL~Rvsvsvd~~G~~~~hl~~n~~~n~ 297 (391)
.+...|.+.|+.+.... ..-...+.|.+. -.+-+-+-..++..||..|. |+. |.++|.+..=|-.+.-+++
T Consensus 214 ~~~~~l~~~~~~~~~~~-~~~~~~~~~~~~~~~~~ig~i~~~s~~fC~~c~-----r~r--~t~dG~l~~Cl~~~~~~~l 285 (331)
T PRK00164 214 EIRARLAERGWTLQPRA-RSGGPAQYFRHPDYGGEIGLIAPVTHDFCASCN-----RLR--LTADGKLHLCLFAEDGVDL 285 (331)
T ss_pred HHHHHHHhccCcccccC-CCCCCCEEEEECCCCeEEEEEeCCCCcccccCC-----eEE--EcCCCcEEEcCCCCCCcCH
Confidence 34555666565544331 000122333332 34445555567788999997 444 4689999887777655555
Q ss_pred C
Q psy12603 298 R 298 (391)
Q Consensus 298 R 298 (391)
|
T Consensus 286 ~ 286 (331)
T PRK00164 286 R 286 (331)
T ss_pred H
Confidence 4
No 360
>KOG2907|consensus
Probab=21.76 E-value=39 Score=29.25 Aligned_cols=10 Identities=60% Similarity=1.241 Sum_probs=8.1
Q ss_pred cccCCCCCcc
Q psy12603 261 KVFCPKCGYK 270 (391)
Q Consensus 261 k~FCP~CGn~ 270 (391)
++-||+||+.
T Consensus 74 ~~kCpkCghe 83 (116)
T KOG2907|consen 74 KHKCPKCGHE 83 (116)
T ss_pred hccCcccCCc
Confidence 3569999996
No 361
>PRK03922 hypothetical protein; Provisional
Probab=21.73 E-value=45 Score=28.75 Aligned_cols=14 Identities=36% Similarity=0.752 Sum_probs=11.4
Q ss_pred ccCcccCCCCCccc
Q psy12603 258 IMTKVFCPKCGYKT 271 (391)
Q Consensus 258 ~~~k~FCP~CGn~T 271 (391)
++.-..||+||.+.
T Consensus 46 evG~~~cP~cge~~ 59 (113)
T PRK03922 46 EVGLTICPKCGEPF 59 (113)
T ss_pred ecCcccCCCCCCcC
Confidence 56678999999984
No 362
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=21.54 E-value=27 Score=35.02 Aligned_cols=11 Identities=45% Similarity=1.056 Sum_probs=8.5
Q ss_pred CcccCCCCCcc
Q psy12603 260 TKVFCPKCGYK 270 (391)
Q Consensus 260 ~k~FCP~CGn~ 270 (391)
+..|||.|--.
T Consensus 58 ~qp~CP~Cr~~ 68 (391)
T COG5432 58 TQPFCPVCRED 68 (391)
T ss_pred CCCCCcccccc
Confidence 56799999764
No 363
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=21.45 E-value=39 Score=24.47 Aligned_cols=8 Identities=63% Similarity=1.381 Sum_probs=6.4
Q ss_pred ccCCCCCc
Q psy12603 262 VFCPKCGY 269 (391)
Q Consensus 262 ~FCP~CGn 269 (391)
.-||+||-
T Consensus 12 rkCp~CGt 19 (44)
T PF14952_consen 12 RKCPKCGT 19 (44)
T ss_pred ccCCcCcC
Confidence 45999995
No 364
>PRK00939 translation initiation factor Sui1; Reviewed
Probab=21.41 E-value=51 Score=27.73 Aligned_cols=30 Identities=30% Similarity=0.533 Sum_probs=16.4
Q ss_pred ccCCCCCcc-ceeEEEEEEcCCCcEEEeecc
Q psy12603 262 VFCPKCGYK-TLKRVAVSVDEQGKQKIHINL 291 (391)
Q Consensus 262 ~FCP~CGn~-TL~Rvsvsvd~~G~~~~hl~~ 291 (391)
..||.||.. .+-.+.....+++.+++++.+
T Consensus 2 ~~c~~c~~~~~~c~c~~~~~~~~~i~I~~ek 32 (99)
T PRK00939 2 EICPVCGLPKELCVCEEVAKEQQRIKIKVDK 32 (99)
T ss_pred CcCccCCCCHHHccCcccCccCceEEEEEEe
Confidence 359999997 453333333334455555443
No 365
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=21.36 E-value=40 Score=39.25 Aligned_cols=24 Identities=25% Similarity=0.708 Sum_probs=21.4
Q ss_pred EccCccccccccCcccCCCCCccc
Q psy12603 248 RCYACYKTTSIMTKVFCPKCGYKT 271 (391)
Q Consensus 248 RC~aCf~~t~~~~k~FCP~CGn~T 271 (391)
.|+.||........+-||.|+..-
T Consensus 44 vCr~cyeye~~~g~~~cp~c~t~y 67 (1044)
T PLN02915 44 VCKPCYEYERSEGNQCCPQCNTRY 67 (1044)
T ss_pred cccchhhhhhhcCCccCCccCCch
Confidence 499999999988999999999873
No 366
>PRK14291 chaperone protein DnaJ; Provisional
Probab=21.10 E-value=2.2e+02 Score=29.32 Aligned_cols=26 Identities=23% Similarity=0.448 Sum_probs=19.4
Q ss_pred EEEEccCccccccccCcccCCCCCccce
Q psy12603 245 FILRCYACYKTTSIMTKVFCPKCGYKTL 272 (391)
Q Consensus 245 wvlRC~aCf~~t~~~~k~FCP~CGn~TL 272 (391)
+.-.|..|.-.-. .+..|+.|.+.-.
T Consensus 194 ~~~~C~~C~G~G~--~~~~C~~C~G~g~ 219 (382)
T PRK14291 194 ISQTCPTCGGEGV--LREPCSKCNGRGL 219 (382)
T ss_pred EEecCCCCCCceE--EccCCCCCCCCce
Confidence 4668999987663 3678999998743
No 367
>smart00746 TRASH metallochaperone-like domain.
Probab=21.05 E-value=80 Score=19.12 Aligned_cols=23 Identities=26% Similarity=0.471 Sum_probs=12.5
Q ss_pred CCCCCccce-eEEEEEEcCCCcEE
Q psy12603 264 CPKCGYKTL-KRVAVSVDEQGKQK 286 (391)
Q Consensus 264 CP~CGn~TL-~Rvsvsvd~~G~~~ 286 (391)
||.||.... ..-...+..+|.+.
T Consensus 1 c~~C~~~~~~~~~~~~~~~~g~~~ 24 (39)
T smart00746 1 CSFCGKDIYNPGTGIMVVNDGKVF 24 (39)
T ss_pred CCCCCCCccCCCCceEEEECCEEE
Confidence 788888754 22233333556554
No 368
>PF11706 zf-CGNR: CGNR zinc finger; InterPro: IPR021005 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 C-terminal zinc finger domain. It seems likely to be DNA-binding given the conservation of many positively charged residues. The domain is named after a highly conserved motif found in many members of the family. ; PDB: 3H0N_A.
Probab=21.03 E-value=26 Score=25.26 Aligned_cols=24 Identities=25% Similarity=0.642 Sum_probs=11.0
Q ss_pred EEc--cCcccccccc----CcccCC--CCCcc
Q psy12603 247 LRC--YACYKTTSIM----TKVFCP--KCGYK 270 (391)
Q Consensus 247 lRC--~aCf~~t~~~----~k~FCP--~CGn~ 270 (391)
-+| +.|..++-|. .+.||. .|||.
T Consensus 3 r~C~~~~C~~~F~D~sr~~~RrwCsm~~Cgnr 34 (44)
T PF11706_consen 3 RRCANPDCRWVFLDTSRNGRRRWCSMERCGNR 34 (44)
T ss_dssp EE--STT---EEE--SSS-----SS-HHHHHH
T ss_pred cccCCCCCceEEEeCCCCCCceecCcccccCH
Confidence 467 7888776654 699999 99985
No 369
>cd01409 SIRT4 SIRT4: Eukaryotic and prokaryotic group (class2) which includes human sirtuin SIRT4 and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=20.76 E-value=73 Score=31.05 Aligned_cols=21 Identities=33% Similarity=0.526 Sum_probs=14.2
Q ss_pred eeccCccccceeeeEEEEccCcccccc
Q psy12603 231 VVALDGRLIRELRTFILRCYACYKTTS 257 (391)
Q Consensus 231 l~s~~G~~Ik~~r~wvlRC~aCf~~t~ 257 (391)
|+-++|. -+.++|..|.+.+.
T Consensus 109 vielHG~------~~~~~C~~C~~~~~ 129 (260)
T cd01409 109 VVELHGS------LHRVVCLSCGFRTP 129 (260)
T ss_pred EEEEeee------cCEEEeCCCcCccC
Confidence 6666674 44577999987653
No 370
>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 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 DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.
Probab=20.60 E-value=51 Score=30.52 Aligned_cols=35 Identities=20% Similarity=0.518 Sum_probs=19.5
Q ss_pred CccccceeeeEEEEccCccccccc------------cCcccCCCCCc
Q psy12603 235 DGRLIRELRTFILRCYACYKTTSI------------MTKVFCPKCGY 269 (391)
Q Consensus 235 ~G~~Ik~~r~wvlRC~aCf~~t~~------------~~k~FCP~CGn 269 (391)
|-.+-+....+.++|++|.+.+.- .....||+|+.
T Consensus 7 d~erf~~c~~l~~~C~~C~~~~~f~g~~~~~~~~~~~~~~~C~~C~~ 53 (188)
T PF08996_consen 7 DEERFKDCEPLKLTCPSCGTEFEFPGVFEEDGDDVSPSGLQCPNCST 53 (188)
T ss_dssp -TTTTTT---EEEE-TTT--EEEE-SSS--SSEEEETTEEEETTT--
T ss_pred HHHHhcCCCceEeECCCCCCCccccccccCCccccccCcCcCCCCCC
Confidence 445677888999999999876632 23678999998
No 371
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=20.58 E-value=58 Score=24.03 Aligned_cols=27 Identities=33% Similarity=0.709 Sum_probs=19.3
Q ss_pred EEEccCccccccccCcccCCCCCcccee
Q psy12603 246 ILRCYACYKTTSIMTKVFCPKCGYKTLK 273 (391)
Q Consensus 246 vlRC~aCf~~t~~~~k~FCP~CGn~TL~ 273 (391)
.+.|.-|+.--+.- -.-|-+||+.-|+
T Consensus 14 k~ICrkC~ARnp~~-A~~CRKCg~~~LR 40 (48)
T PRK04136 14 KKICMRCNARNPWR-ATKCRKCGYKNLR 40 (48)
T ss_pred ccchhcccCCCCcc-ccccccCCCCCcC
Confidence 56788999766533 4569999987553
No 372
>PRK13794 hypothetical protein; Provisional
Probab=20.53 E-value=68 Score=34.20 Aligned_cols=32 Identities=25% Similarity=0.605 Sum_probs=22.9
Q ss_pred eeEEEEccCccccccccCcccCCCCCccceeEEEEE
Q psy12603 243 RTFILRCYACYKTTSIMTKVFCPKCGYKTLKRVAVS 278 (391)
Q Consensus 243 r~wvlRC~aCf~~t~~~~k~FCP~CGn~TL~Rvsvs 278 (391)
+.|++.|..|.--. ..+. |..||+. -.+|.+|
T Consensus 7 ~~~~~wc~~cn~p~--~~~~-c~~cg~~-~~~~~~~ 38 (479)
T PRK13794 7 KIHLKWCDNCNVPV--LGKK-CAICGSE-TREVKVT 38 (479)
T ss_pred ceEEEEcCCCCCee--cCCc-hhHhCCC-eeEEecC
Confidence 46899999998433 3333 9999997 5566664
No 373
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=20.39 E-value=88 Score=34.84 Aligned_cols=50 Identities=20% Similarity=0.433 Sum_probs=30.6
Q ss_pred HHHHHhCCce-----eccCccccceeeeEEEEccCccccccccCcccCCCCCccce
Q psy12603 222 NVLKQMGLNV-----VALDGRLIRELRTFILRCYACYKTTSIMTKVFCPKCGYKTL 272 (391)
Q Consensus 222 NVllqmGL~l-----~s~~G~~Ik~~r~wvlRC~aCf~~t~~~~k~FCP~CGn~TL 272 (391)
+-+.++||++ |.-.|..|-+|-.-+.....=-...-.++ .+||.||.++.
T Consensus 361 ~~i~~~~i~iGD~V~V~raGdVIP~i~~vv~~~r~~~~~~~~~P-~~CP~Cgs~l~ 415 (665)
T PRK07956 361 DEIERKDIRIGDTVVVRRAGDVIPEVVGVVLEKRPGDEREIVMP-THCPVCGSELV 415 (665)
T ss_pred HHHHHcCCCCCCEEEEEECCCccceeeeeecccCCCCCccCcCC-CCCCCCCCEeE
Confidence 3456677653 35569999998886665542111111122 48999999874
No 374
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=20.12 E-value=1e+02 Score=24.88 Aligned_cols=28 Identities=21% Similarity=0.333 Sum_probs=19.3
Q ss_pred cccCCCCCccceeEEEEEEcCCCcEEEeec
Q psy12603 261 KVFCPKCGYKTLKRVAVSVDEQGKQKIHIN 290 (391)
Q Consensus 261 k~FCP~CGn~TL~Rvsvsvd~~G~~~~hl~ 290 (391)
...|+.||.+.... .+.|-.+| -.+|..
T Consensus 78 ~~~C~vC~k~l~~~-~f~~~p~~-~v~H~~ 105 (109)
T PF10367_consen 78 STKCSVCGKPLGNS-VFVVFPCG-HVVHYS 105 (109)
T ss_pred CCCccCcCCcCCCc-eEEEeCCC-eEEecc
Confidence 35599999997764 34556788 446754
No 375
>PF06054 CoiA: Competence protein CoiA-like family; InterPro: IPR010330 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. Many of the members of this family are described as transcription factors. CoiA falls within a competence-specific operon in Streptococcus. CoiA is an uncharacterised protein.
Probab=20.01 E-value=52 Score=33.92 Aligned_cols=18 Identities=33% Similarity=0.770 Sum_probs=13.5
Q ss_pred cCcccCCCCCccceeEEE
Q psy12603 259 MTKVFCPKCGYKTLKRVA 276 (391)
Q Consensus 259 ~~k~FCP~CGn~TL~Rvs 276 (391)
-..-|||.||.+...|..
T Consensus 28 ~~~~~CP~C~~~v~lk~G 45 (375)
T PF06054_consen 28 KGKYFCPGCGEPVILKKG 45 (375)
T ss_pred CCcEECCCCCCeeEEEEc
Confidence 346899999999666543
Done!