Query 026283
Match_columns 240
No_of_seqs 45 out of 47
Neff 2.9
Searched_HMMs 46136
Date Fri Mar 29 05:58:18 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026283.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026283hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK00420 hypothetical protein; 98.6 2.8E-08 6E-13 80.6 2.3 35 180-214 22-56 (112)
2 PF09538 FYDLN_acid: Protein o 97.0 0.0005 1.1E-08 55.4 2.9 31 181-211 9-39 (108)
3 PF11023 DUF2614: Protein of u 96.9 0.0024 5.2E-08 52.7 6.3 37 176-213 64-100 (114)
4 PRK00398 rpoP DNA-directed RNA 96.7 0.0011 2.3E-08 45.1 2.3 34 180-213 2-36 (46)
5 PRK02935 hypothetical protein; 96.6 0.0086 1.9E-07 49.3 7.1 39 175-214 64-102 (110)
6 TIGR02300 FYDLN_acid conserved 96.4 0.0017 3.7E-08 54.5 1.6 31 181-211 9-39 (129)
7 PF13248 zf-ribbon_3: zinc-rib 96.2 0.0023 4.9E-08 39.5 1.0 25 181-208 2-26 (26)
8 smart00531 TFIIE Transcription 95.9 0.0032 6.9E-08 51.7 1.3 34 181-214 99-139 (147)
9 smart00834 CxxC_CXXC_SSSS Puta 95.9 0.0038 8.3E-08 40.3 1.2 28 181-208 5-36 (41)
10 TIGR02098 MJ0042_CXXC MJ0042 f 95.9 0.007 1.5E-07 39.2 2.4 29 182-210 3-37 (38)
11 COG1645 Uncharacterized Zn-fin 95.5 0.0085 1.8E-07 50.4 2.3 33 179-212 26-59 (131)
12 PF08271 TF_Zn_Ribbon: TFIIB z 95.5 0.0078 1.7E-07 40.4 1.7 31 182-212 1-33 (43)
13 PF13240 zinc_ribbon_2: zinc-r 95.5 0.006 1.3E-07 37.2 0.9 23 183-208 1-23 (23)
14 PRK05978 hypothetical protein; 95.5 0.0081 1.7E-07 51.1 1.9 36 180-215 32-69 (148)
15 PF07754 DUF1610: Domain of un 95.4 0.012 2.5E-07 36.9 1.9 23 184-206 1-24 (24)
16 COG1592 Rubrerythrin [Energy p 95.3 0.0083 1.8E-07 51.9 1.6 24 182-207 135-158 (166)
17 PRK03824 hypA hydrogenase nick 95.1 0.013 2.8E-07 48.3 2.0 33 182-214 71-124 (135)
18 PRK03681 hypA hydrogenase nick 95.1 0.011 2.4E-07 47.4 1.5 33 182-214 71-104 (114)
19 PF13719 zinc_ribbon_5: zinc-r 94.6 0.026 5.7E-07 37.3 2.2 27 183-209 4-36 (37)
20 PF01155 HypA: Hydrogenase exp 94.5 0.011 2.4E-07 47.0 0.3 32 182-214 71-103 (113)
21 PF09986 DUF2225: Uncharacteri 94.5 0.018 3.8E-07 50.3 1.4 31 181-211 5-61 (214)
22 TIGR01206 lysW lysine biosynth 94.4 0.037 8.1E-07 40.1 2.8 32 181-212 2-36 (54)
23 PF03966 Trm112p: Trm112p-like 94.3 0.041 9E-07 40.0 2.7 32 182-213 8-68 (68)
24 smart00659 RPOLCX RNA polymera 94.2 0.047 1E-06 37.8 2.7 32 182-213 3-34 (44)
25 PF13717 zinc_ribbon_4: zinc-r 94.2 0.034 7.4E-07 36.8 1.9 25 183-207 4-34 (36)
26 PF06677 Auto_anti-p27: Sjogre 93.8 0.042 9.2E-07 37.8 1.9 28 178-205 14-41 (41)
27 PF07282 OrfB_Zn_ribbon: Putat 93.7 0.049 1.1E-06 38.9 2.2 27 181-207 28-55 (69)
28 PF14353 CpXC: CpXC protein 93.7 0.041 8.9E-07 43.6 1.9 32 181-212 1-52 (128)
29 TIGR01405 polC_Gram_pos DNA po 93.7 0.047 1E-06 58.8 2.9 54 183-238 685-746 (1213)
30 COG0675 Transposase and inacti 93.6 0.042 9E-07 46.7 2.0 22 182-207 310-331 (364)
31 PRK00564 hypA hydrogenase nick 93.5 0.04 8.7E-07 44.3 1.7 34 181-214 71-105 (117)
32 PRK12380 hydrogenase nickel in 93.5 0.039 8.5E-07 44.1 1.5 33 181-214 70-103 (113)
33 TIGR00373 conserved hypothetic 93.4 0.042 9E-07 46.1 1.7 32 182-213 110-143 (158)
34 cd00350 rubredoxin_like Rubred 93.4 0.046 1E-06 35.3 1.4 23 183-206 3-25 (33)
35 PF09862 DUF2089: Protein of u 93.3 0.052 1.1E-06 44.6 2.0 26 184-215 1-26 (113)
36 PRK14890 putative Zn-ribbon RN 93.3 0.07 1.5E-06 39.8 2.5 28 181-208 7-35 (59)
37 COG2051 RPS27A Ribosomal prote 92.9 0.078 1.7E-06 40.5 2.2 35 180-214 18-54 (67)
38 PF08274 PhnA_Zn_Ribbon: PhnA 92.8 0.055 1.2E-06 35.3 1.2 26 182-207 3-28 (30)
39 PF10571 UPF0547: Uncharacteri 92.8 0.058 1.3E-06 33.9 1.2 23 183-208 2-24 (26)
40 COG2888 Predicted Zn-ribbon RN 92.8 0.067 1.5E-06 40.2 1.8 28 183-210 11-39 (61)
41 PF01363 FYVE: FYVE zinc finge 92.7 0.083 1.8E-06 37.6 2.1 28 181-209 9-36 (69)
42 PRK06266 transcription initiat 92.6 0.049 1.1E-06 46.8 1.0 33 180-212 116-150 (178)
43 PF07191 zinc-ribbons_6: zinc- 92.5 0.077 1.7E-06 40.6 1.8 46 181-226 1-64 (70)
44 PRK12495 hypothetical protein; 92.0 0.084 1.8E-06 48.0 1.8 28 182-210 43-70 (226)
45 PRK00448 polC DNA polymerase I 91.9 0.11 2.4E-06 56.9 2.8 55 182-238 909-971 (1437)
46 cd00729 rubredoxin_SM Rubredox 91.7 0.1 2.2E-06 34.2 1.4 24 183-207 4-27 (34)
47 PLN03120 nucleic acid binding 91.3 0.23 5E-06 45.8 3.8 55 63-117 137-191 (260)
48 TIGR00100 hypA hydrogenase nic 91.3 0.12 2.5E-06 41.5 1.6 34 180-214 69-103 (115)
49 PRK00415 rps27e 30S ribosomal 91.2 0.12 2.6E-06 38.4 1.5 36 179-214 9-46 (59)
50 PRK08270 anaerobic ribonucleos 91.1 0.11 2.4E-06 52.7 1.6 29 178-210 623-651 (656)
51 COG1096 Predicted RNA-binding 91.0 0.12 2.7E-06 45.8 1.7 30 179-209 147-176 (188)
52 KOG2879 Predicted E3 ubiquitin 90.8 0.32 7E-06 45.8 4.3 28 182-209 240-287 (298)
53 TIGR02605 CxxC_CxxC_SSSS putat 90.8 0.11 2.3E-06 35.5 0.9 26 181-206 5-34 (52)
54 PF03604 DNA_RNApol_7kD: DNA d 90.7 0.19 4E-06 33.1 1.9 29 183-211 2-30 (32)
55 PRK00464 nrdR transcriptional 90.3 0.17 3.6E-06 43.2 1.9 26 182-207 1-37 (154)
56 PRK00432 30S ribosomal protein 90.3 0.23 4.9E-06 35.2 2.2 28 183-210 22-49 (50)
57 PRK12496 hypothetical protein; 90.3 0.14 3.1E-06 43.4 1.4 31 182-213 128-158 (164)
58 PF12773 DZR: Double zinc ribb 90.2 0.13 2.9E-06 34.7 0.9 26 182-207 13-38 (50)
59 PRK08579 anaerobic ribonucleos 90.1 0.15 3.2E-06 51.6 1.6 24 181-207 568-591 (625)
60 PF12773 DZR: Double zinc ribb 89.7 0.15 3.3E-06 34.4 0.9 23 184-209 1-23 (50)
61 PRK00762 hypA hydrogenase nick 89.3 0.18 4E-06 40.9 1.3 33 181-214 70-109 (124)
62 PHA02942 putative transposase; 88.6 0.33 7E-06 46.0 2.5 28 181-208 325-352 (383)
63 TIGR00686 phnA alkylphosphonat 87.8 0.31 6.7E-06 40.2 1.7 28 182-209 3-30 (109)
64 PRK00423 tfb transcription ini 87.7 0.63 1.4E-05 42.6 3.8 28 182-209 12-41 (310)
65 PF09297 zf-NADH-PPase: NADH p 87.7 0.37 8E-06 30.6 1.6 25 183-207 5-30 (32)
66 smart00064 FYVE Protein presen 87.7 0.25 5.5E-06 35.0 1.0 27 182-209 11-37 (68)
67 TIGR00155 pqiA_fam integral me 87.3 1.8 3.9E-05 41.5 6.7 28 183-212 217-244 (403)
68 COG4530 Uncharacterized protei 87.1 0.3 6.6E-06 41.0 1.2 32 182-215 10-41 (129)
69 PF04423 Rad50_zn_hook: Rad50 86.8 0.18 3.9E-06 35.2 -0.2 14 180-193 19-32 (54)
70 PF01667 Ribosomal_S27e: Ribos 86.8 0.48 1E-05 34.7 2.0 35 180-214 6-42 (55)
71 PF14257 DUF4349: Domain of un 86.3 2.9 6.3E-05 36.8 7.0 32 34-65 105-136 (262)
72 PF02591 DUF164: Putative zinc 86.0 0.45 9.9E-06 33.4 1.5 30 179-208 20-56 (56)
73 PF09723 Zn-ribbon_8: Zinc rib 86.0 0.4 8.7E-06 32.3 1.2 28 181-208 5-37 (42)
74 COG1326 Uncharacterized archae 85.9 0.4 8.7E-06 43.1 1.5 29 180-208 5-40 (201)
75 PF13453 zf-TFIIB: Transcripti 85.8 0.5 1.1E-05 31.4 1.6 32 183-215 1-35 (41)
76 PRK10220 hypothetical protein; 85.2 0.59 1.3E-05 38.7 2.0 28 182-209 4-31 (111)
77 PTZ00083 40S ribosomal protein 84.4 0.69 1.5E-05 36.8 2.0 35 180-214 34-70 (85)
78 COG3877 Uncharacterized protei 84.4 0.59 1.3E-05 39.1 1.7 28 182-215 7-34 (122)
79 PLN00209 ribosomal protein S27 84.3 0.67 1.5E-05 36.9 1.9 35 180-214 35-71 (86)
80 PRK13130 H/ACA RNA-protein com 84.1 0.5 1.1E-05 34.6 1.0 25 183-212 7-31 (56)
81 PF09334 tRNA-synt_1g: tRNA sy 84.1 0.52 1.1E-05 44.5 1.4 29 177-209 132-160 (391)
82 PRK11827 hypothetical protein; 83.8 0.82 1.8E-05 34.0 2.0 32 182-213 9-41 (60)
83 TIGR00340 zpr1_rel ZPR1-relate 83.8 0.6 1.3E-05 40.1 1.5 21 184-206 1-36 (163)
84 PF10263 SprT-like: SprT-like 83.4 0.8 1.7E-05 36.6 2.0 30 181-210 123-155 (157)
85 PF13597 NRDD: Anaerobic ribon 83.0 0.55 1.2E-05 46.5 1.1 45 163-211 465-518 (546)
86 PF14446 Prok-RING_1: Prokaryo 82.8 0.92 2E-05 33.2 2.0 30 178-208 2-31 (54)
87 TIGR03831 YgiT_finger YgiT-typ 82.8 0.77 1.7E-05 29.8 1.4 11 199-209 33-43 (46)
88 PF01927 Mut7-C: Mut7-C RNAse 82.7 0.8 1.7E-05 37.6 1.8 35 180-215 90-140 (147)
89 PRK14350 ligA NAD-dependent DN 82.6 0.48 1E-05 48.4 0.6 39 179-218 396-436 (669)
90 PRK08271 anaerobic ribonucleos 82.1 0.75 1.6E-05 46.7 1.7 24 180-206 565-588 (623)
91 KOG2593 Transcription initiati 82.0 0.63 1.4E-05 45.9 1.1 35 179-213 126-168 (436)
92 PRK14704 anaerobic ribonucleos 82.0 0.7 1.5E-05 46.8 1.4 26 178-207 556-581 (618)
93 PRK14714 DNA polymerase II lar 81.9 0.75 1.6E-05 50.5 1.7 9 182-190 668-676 (1337)
94 PRK08402 replication factor A; 81.7 0.71 1.5E-05 43.9 1.3 30 177-206 208-238 (355)
95 PRK03564 formate dehydrogenase 81.5 2 4.3E-05 40.5 4.1 10 181-190 187-196 (309)
96 PRK09263 anaerobic ribonucleos 81.2 0.83 1.8E-05 46.9 1.7 25 180-206 640-667 (711)
97 PRK07591 threonine synthase; V 81.1 1.1 2.3E-05 42.6 2.3 30 181-212 18-47 (421)
98 PRK06450 threonine synthase; V 81.0 0.92 2E-05 42.0 1.8 30 180-211 2-31 (338)
99 cd07973 Spt4 Transcription elo 80.8 0.85 1.8E-05 36.6 1.3 32 183-214 5-36 (98)
100 PF13719 zinc_ribbon_5: zinc-r 80.6 0.87 1.9E-05 30.1 1.1 18 198-215 2-19 (37)
101 PF11781 RRN7: RNA polymerase 80.6 1 2.3E-05 30.0 1.5 27 182-208 9-35 (36)
102 PRK07218 replication factor A; 80.3 0.84 1.8E-05 44.4 1.3 24 179-207 295-318 (423)
103 COG2824 PhnA Uncharacterized Z 80.2 0.96 2.1E-05 37.6 1.4 26 182-207 4-29 (112)
104 PRK04023 DNA polymerase II lar 80.0 0.9 1.9E-05 49.1 1.5 20 183-207 628-647 (1121)
105 PF14803 Nudix_N_2: Nudix N-te 79.8 1.3 2.7E-05 29.5 1.6 24 184-207 3-31 (34)
106 PF05191 ADK_lid: Adenylate ki 79.7 0.9 2E-05 30.3 0.9 30 183-212 3-35 (36)
107 TIGR02827 RNR_anaer_Bdell anae 79.4 1.1 2.3E-05 45.5 1.7 25 179-206 530-554 (586)
108 PRK06386 replication factor A; 79.1 0.99 2.1E-05 43.2 1.4 23 179-206 234-256 (358)
109 PRK06260 threonine synthase; V 79.0 1.4 3.1E-05 41.2 2.3 29 182-211 4-32 (397)
110 PRK07111 anaerobic ribonucleos 78.8 1.1 2.4E-05 46.1 1.7 22 181-206 680-701 (735)
111 cd04476 RPA1_DBD_C RPA1_DBD_C: 78.8 1.1 2.4E-05 36.7 1.4 33 178-210 31-63 (166)
112 PF14768 RPA_interact_C: Repli 78.1 2 4.4E-05 32.6 2.5 27 184-213 2-28 (82)
113 COG1656 Uncharacterized conser 77.9 0.9 1.9E-05 39.7 0.7 36 179-215 95-146 (165)
114 PF14205 Cys_rich_KTR: Cystein 77.9 1.9 4.1E-05 32.0 2.2 32 183-214 6-44 (55)
115 PRK08351 DNA-directed RNA poly 77.9 1.1 2.3E-05 33.6 0.9 22 182-208 4-25 (61)
116 cd00065 FYVE FYVE domain; Zinc 77.7 1.5 3.2E-05 29.8 1.6 28 182-210 3-30 (57)
117 smart00661 RPOL9 RNA polymeras 77.5 2.5 5.4E-05 28.4 2.6 31 183-213 2-35 (52)
118 COG0375 HybF Zn finger protein 77.5 1.5 3.2E-05 36.3 1.7 51 163-214 40-103 (115)
119 cd01407 SIR2-fam SIR2 family o 77.1 1.3 2.8E-05 38.1 1.4 32 178-209 106-144 (218)
120 PF13824 zf-Mss51: Zinc-finger 76.5 1.6 3.4E-05 32.2 1.5 26 183-210 1-26 (55)
121 COG3357 Predicted transcriptio 76.1 1.3 2.8E-05 36.0 1.1 36 179-215 56-92 (97)
122 PRK14559 putative protein seri 76.0 1.5 3.2E-05 44.9 1.6 9 200-208 29-37 (645)
123 TIGR02487 NrdD anaerobic ribon 76.0 1.5 3.3E-05 43.7 1.8 41 164-207 500-547 (579)
124 PF08646 Rep_fac-A_C: Replicat 75.5 1.4 3E-05 35.5 1.1 35 178-212 15-51 (146)
125 COG1405 SUA7 Transcription ini 75.3 2 4.4E-05 39.8 2.2 32 181-212 1-34 (285)
126 PRK15103 paraquat-inducible me 75.1 1.8 3.9E-05 41.7 1.9 27 183-212 223-249 (419)
127 TIGR01384 TFS_arch transcripti 75.0 2 4.3E-05 33.0 1.7 27 183-210 2-28 (104)
128 cd00730 rubredoxin Rubredoxin; 74.8 2.1 4.5E-05 30.5 1.7 25 183-207 3-43 (50)
129 PF15616 TerY-C: TerY-C metal 74.7 3.2 6.8E-05 35.0 3.0 32 182-213 78-120 (131)
130 COG5349 Uncharacterized protei 74.5 1.3 2.8E-05 37.5 0.7 31 180-210 20-52 (126)
131 PF06044 DRP: Dam-replacing fa 73.7 2.1 4.4E-05 39.8 1.8 34 182-215 32-72 (254)
132 PF14354 Lar_restr_allev: Rest 73.7 2.2 4.7E-05 29.8 1.6 24 183-206 5-37 (61)
133 COG0272 Lig NAD-dependent DNA 73.5 1.4 3.1E-05 45.5 0.8 38 181-218 404-445 (667)
134 TIGR01053 LSD1 zinc finger dom 73.2 2.1 4.5E-05 28.0 1.3 17 198-214 1-17 (31)
135 PRK11823 DNA repair protein Ra 73.2 1.9 4.2E-05 41.4 1.6 27 182-211 8-34 (446)
136 PF04828 GFA: Glutathione-depe 73.1 4.7 0.0001 28.7 3.2 25 188-212 38-62 (92)
137 PHA00626 hypothetical protein 73.0 2.6 5.6E-05 31.7 1.9 27 182-208 1-33 (59)
138 PRK15103 paraquat-inducible me 72.8 2.6 5.6E-05 40.7 2.4 31 183-213 12-45 (419)
139 PF08792 A2L_zn_ribbon: A2L zi 72.6 2.9 6.4E-05 27.5 1.9 25 183-207 5-30 (33)
140 TIGR03830 CxxCG_CxxCG_HTH puta 72.6 2 4.4E-05 33.0 1.3 17 196-212 29-45 (127)
141 KOG4517 Uncharacterized conser 72.3 1.6 3.4E-05 36.5 0.7 15 194-208 102-116 (117)
142 cd01675 RNR_III Class III ribo 72.2 2.1 4.5E-05 42.5 1.6 23 182-207 519-541 (555)
143 TIGR00416 sms DNA repair prote 72.1 2.1 4.5E-05 41.4 1.6 26 182-210 8-33 (454)
144 PF03119 DNA_ligase_ZBD: NAD-d 71.8 2.6 5.7E-05 26.7 1.5 15 200-214 1-15 (28)
145 PF13005 zf-IS66: zinc-finger 71.8 3.1 6.8E-05 27.7 1.9 10 200-209 4-13 (47)
146 COG1996 RPC10 DNA-directed RNA 71.7 3 6.5E-05 30.1 1.9 32 182-213 7-39 (49)
147 TIGR03826 YvyF flagellar opero 71.3 1.2 2.5E-05 37.6 -0.3 24 182-207 4-27 (137)
148 COG1675 TFA1 Transcription ini 71.2 1.2 2.6E-05 39.0 -0.2 31 182-212 114-146 (176)
149 PF15135 UPF0515: Uncharacteri 71.2 1.7 3.8E-05 40.7 0.8 31 179-209 153-185 (278)
150 PRK14351 ligA NAD-dependent DN 70.9 0.99 2.1E-05 46.3 -0.9 37 181-218 423-462 (689)
151 TIGR00398 metG methionyl-tRNA 70.9 2 4.4E-05 41.2 1.2 26 179-208 134-159 (530)
152 smart00440 ZnF_C2C2 C2C2 Zinc 70.8 2.2 4.7E-05 28.7 1.0 17 183-199 2-18 (40)
153 PRK14714 DNA polymerase II lar 70.8 2.1 4.5E-05 47.3 1.3 26 180-209 678-703 (1337)
154 PF10013 DUF2256: Uncharacteri 70.4 2 4.4E-05 30.2 0.8 17 176-192 3-19 (42)
155 PF11241 DUF3043: Protein of u 70.2 77 0.0017 27.9 11.0 55 92-146 29-89 (170)
156 PRK00133 metG methionyl-tRNA s 70.1 2 4.4E-05 43.1 1.0 25 179-208 137-162 (673)
157 PRK08115 ribonucleotide-diphos 70.0 2 4.4E-05 45.4 1.1 29 181-209 827-855 (858)
158 KOG1247 Methionyl-tRNA synthet 69.9 1.5 3.2E-05 44.2 0.0 32 173-208 144-175 (567)
159 PRK14559 putative protein seri 69.9 2.2 4.7E-05 43.7 1.2 25 182-209 28-52 (645)
160 PHA00732 hypothetical protein 69.4 4 8.6E-05 31.2 2.3 33 183-215 3-44 (79)
161 KOG2907 RNA polymerase I trans 69.1 2.1 4.5E-05 35.8 0.7 31 177-207 70-111 (116)
162 PF13451 zf-trcl: Probable zin 69.0 1.2 2.6E-05 32.0 -0.6 27 181-207 4-42 (49)
163 cd01410 SIRT7 SIRT7: Eukaryoti 69.0 3 6.5E-05 36.1 1.7 31 178-208 92-130 (206)
164 TIGR00155 pqiA_fam integral me 68.9 3.5 7.6E-05 39.6 2.3 29 183-211 15-46 (403)
165 COG0143 MetG Methionyl-tRNA sy 68.9 2.3 4.9E-05 42.9 1.1 36 173-212 134-169 (558)
166 PRK12366 replication factor A; 68.6 2.3 5.1E-05 42.9 1.1 31 176-207 527-557 (637)
167 PRK14892 putative transcriptio 68.5 3.3 7.1E-05 33.3 1.7 25 183-207 23-51 (99)
168 PF09332 Mcm10: Mcm10 replicat 68.5 2.2 4.7E-05 40.8 0.8 33 183-215 287-320 (344)
169 cd01413 SIR2_Af2 SIR2_Af2: Arc 68.3 2.7 5.8E-05 36.6 1.3 33 177-209 109-147 (222)
170 PF12677 DUF3797: Domain of un 68.2 4 8.6E-05 29.7 1.9 26 181-215 13-38 (49)
171 COG1779 C4-type Zn-finger prot 68.2 2.4 5.3E-05 38.2 1.0 27 180-206 13-51 (201)
172 TIGR01031 rpmF_bact ribosomal 67.9 3.5 7.7E-05 29.7 1.6 18 184-205 29-46 (55)
173 PF03367 zf-ZPR1: ZPR1 zinc-fi 67.7 2.1 4.6E-05 36.3 0.5 26 181-206 1-38 (161)
174 PF01783 Ribosomal_L32p: Ribos 67.6 3 6.5E-05 29.8 1.2 20 182-205 27-46 (56)
175 COG1655 Uncharacterized protei 67.6 2.3 5E-05 39.7 0.8 12 181-192 19-30 (267)
176 smart00532 LIGANc Ligase N fam 67.5 1.7 3.8E-05 42.3 -0.0 38 180-217 398-438 (441)
177 TIGR00570 cdk7 CDK-activating 67.4 3.2 6.9E-05 39.4 1.7 18 195-212 40-57 (309)
178 COG3809 Uncharacterized protei 67.3 2.9 6.2E-05 33.4 1.2 31 183-214 3-36 (88)
179 PF01096 TFIIS_C: Transcriptio 67.1 2.1 4.6E-05 28.6 0.3 12 184-195 3-14 (39)
180 KOG2906 RNA polymerase III sub 67.0 3.5 7.6E-05 34.0 1.6 16 199-214 2-17 (105)
181 COG4888 Uncharacterized Zn rib 66.9 3.1 6.8E-05 34.2 1.3 31 182-212 23-60 (104)
182 PRK14138 NAD-dependent deacety 66.8 3 6.5E-05 37.1 1.3 32 178-209 116-154 (244)
183 PRK09521 exosome complex RNA-b 66.7 3.4 7.4E-05 35.1 1.6 29 179-207 147-175 (189)
184 PF05876 Terminase_GpA: Phage 66.6 3.6 7.8E-05 40.8 2.0 30 181-210 200-241 (557)
185 PF02150 RNA_POL_M_15KD: RNA p 66.5 2.8 6.1E-05 27.6 0.8 16 199-214 2-17 (35)
186 PRK06319 DNA topoisomerase I/S 66.1 4.6 9.9E-05 42.3 2.7 16 200-215 647-662 (860)
187 PRK00241 nudC NADH pyrophospha 65.9 4.2 9.1E-05 36.6 2.1 28 181-208 99-127 (256)
188 PRK07956 ligA NAD-dependent DN 65.9 1.7 3.7E-05 44.3 -0.5 40 180-219 403-446 (665)
189 PF08996 zf-DNA_Pol: DNA Polym 65.7 2.9 6.3E-05 35.8 1.0 27 182-208 19-55 (188)
190 COG1040 ComFC Predicted amidop 65.3 2 4.3E-05 38.0 -0.1 27 182-211 25-51 (225)
191 PF14255 Cys_rich_CPXG: Cystei 64.9 3.7 8E-05 29.6 1.2 16 199-214 1-16 (52)
192 cd01412 SIRT5_Af1_CobB SIRT5_A 64.7 4.1 8.8E-05 35.1 1.7 33 177-209 105-141 (224)
193 PF06170 DUF983: Protein of un 64.4 3.4 7.3E-05 32.2 1.0 24 191-214 1-24 (86)
194 PRK12286 rpmF 50S ribosomal pr 64.0 4.9 0.00011 29.3 1.7 19 183-205 29-47 (57)
195 TIGR00375 conserved hypothetic 63.7 3.2 6.9E-05 40.0 0.9 28 181-210 240-270 (374)
196 PF01396 zf-C4_Topoisom: Topoi 63.6 4.6 0.0001 27.0 1.4 17 199-215 2-18 (39)
197 PRK04011 peptide chain release 63.5 3.6 7.9E-05 39.5 1.3 33 180-212 327-364 (411)
198 PF08209 Sgf11: Sgf11 (transcr 63.4 5.5 0.00012 26.5 1.8 14 196-209 2-15 (33)
199 PRK11088 rrmA 23S rRNA methylt 63.3 4.6 9.9E-05 35.4 1.8 24 183-207 4-27 (272)
200 PRK04023 DNA polymerase II lar 63.2 4.1 9E-05 44.3 1.7 27 179-209 636-662 (1121)
201 COG1867 TRM1 N2,N2-dimethylgua 62.8 3.8 8.2E-05 40.0 1.3 25 182-206 241-265 (380)
202 COG4311 SoxD Sarcosine oxidase 62.6 4.1 8.8E-05 33.2 1.2 33 198-234 3-35 (97)
203 PF14353 CpXC: CpXC protein 62.6 4.3 9.4E-05 32.1 1.4 14 198-211 1-14 (128)
204 PRK07217 replication factor A; 62.5 3.9 8.4E-05 38.9 1.3 21 182-207 189-211 (311)
205 PF02146 SIR2: Sir2 family; I 61.9 3 6.5E-05 34.6 0.4 29 181-209 105-140 (178)
206 TIGR00595 priA primosomal prot 61.7 5.7 0.00012 38.9 2.3 11 199-209 254-264 (505)
207 COG2093 DNA-directed RNA polym 61.5 3.9 8.5E-05 31.1 0.9 22 183-207 6-27 (64)
208 COG2835 Uncharacterized conser 61.3 6.8 0.00015 29.4 2.1 33 182-214 9-42 (60)
209 TIGR00630 uvra excinuclease AB 61.1 5.2 0.00011 42.5 2.0 31 181-211 250-290 (924)
210 PF10601 zf-LITAF-like: LITAF- 61.1 15 0.00033 26.7 3.9 19 192-210 52-70 (73)
211 PF04475 DUF555: Protein of un 61.1 4.1 8.9E-05 33.4 1.0 22 188-209 37-58 (102)
212 PRK05580 primosome assembly pr 60.5 6 0.00013 40.0 2.3 14 198-211 421-434 (679)
213 PF00628 PHD: PHD-finger; Int 60.4 9.4 0.0002 25.4 2.5 23 184-208 2-24 (51)
214 PRK00481 NAD-dependent deacety 60.3 4.8 0.0001 35.3 1.4 34 176-209 117-153 (242)
215 PF12861 zf-Apc11: Anaphase-pr 59.9 6.1 0.00013 31.3 1.7 14 197-210 70-83 (85)
216 COG2176 PolC DNA polymerase II 59.5 5.4 0.00012 44.3 1.8 33 181-214 914-954 (1444)
217 TIGR00577 fpg formamidopyrimid 59.5 5.6 0.00012 35.9 1.7 22 183-205 247-272 (272)
218 TIGR00354 polC DNA polymerase, 59.3 4.6 9.9E-05 43.9 1.2 22 182-208 626-647 (1095)
219 PF05605 zf-Di19: Drought indu 59.2 6.7 0.00014 27.2 1.7 26 182-207 3-40 (54)
220 smart00709 Zpr1 Duplicated dom 59.1 5.3 0.00011 34.1 1.4 8 183-190 2-9 (160)
221 COG1579 Zn-ribbon protein, pos 59.1 3 6.5E-05 38.1 -0.1 36 180-215 196-238 (239)
222 PRK08197 threonine synthase; V 59.0 6.5 0.00014 36.8 2.1 31 181-213 7-37 (394)
223 TIGR01206 lysW lysine biosynth 59.0 5.8 0.00012 28.8 1.4 16 198-213 2-17 (54)
224 PF06750 DiS_P_DiS: Bacterial 58.3 17 0.00037 28.3 4.0 42 168-209 12-69 (92)
225 PRK00464 nrdR transcriptional 57.8 3.8 8.2E-05 35.0 0.3 24 176-199 21-46 (154)
226 PF05180 zf-DNL: DNL zinc fing 57.8 2.8 6E-05 31.7 -0.4 33 180-212 3-43 (66)
227 COG1198 PriA Primosomal protei 57.8 6.7 0.00015 40.9 2.1 16 197-212 474-489 (730)
228 PLN02569 threonine synthase 57.6 7.5 0.00016 38.2 2.3 29 182-212 50-78 (484)
229 PF00130 C1_1: Phorbol esters/ 57.5 10 0.00022 25.5 2.3 29 180-208 10-38 (53)
230 PF14206 Cys_rich_CPCC: Cystei 57.5 6.9 0.00015 30.4 1.7 30 182-214 2-33 (78)
231 COG1110 Reverse gyrase [DNA re 56.9 4.4 9.5E-05 44.3 0.7 22 183-207 696-717 (1187)
232 PF02318 FYVE_2: FYVE-type zin 56.3 9.2 0.0002 30.5 2.3 34 180-213 53-86 (118)
233 PRK08665 ribonucleotide-diphos 56.2 11 0.00023 39.3 3.2 22 183-205 726-747 (752)
234 cd01411 SIR2H SIR2H: Uncharact 56.0 6.2 0.00014 34.5 1.4 32 178-209 115-147 (225)
235 PRK06393 rpoE DNA-directed RNA 55.9 4.9 0.00011 30.4 0.6 22 181-207 5-26 (64)
236 COG2816 NPY1 NTP pyrophosphohy 55.6 7.6 0.00017 36.4 1.9 32 173-207 106-138 (279)
237 PF04216 FdhE: Protein involve 55.4 5.6 0.00012 35.8 1.0 10 181-190 172-181 (290)
238 PRK07561 DNA topoisomerase I s 55.0 9.6 0.00021 39.9 2.7 16 200-215 647-662 (859)
239 COG1066 Sms Predicted ATP-depe 54.7 11 0.00024 37.7 2.9 22 182-206 8-29 (456)
240 TIGR00515 accD acetyl-CoA carb 54.3 4.6 9.9E-05 37.4 0.3 28 183-210 28-57 (285)
241 COG1594 RPB9 DNA-directed RNA 54.1 6.3 0.00014 31.9 1.0 26 182-207 73-109 (113)
242 COG1327 Predicted transcriptio 54.0 7.6 0.00017 33.9 1.5 25 182-206 1-36 (156)
243 COG1503 eRF1 Peptide chain rel 53.8 6.6 0.00014 38.7 1.2 32 180-211 326-361 (411)
244 PF07503 zf-HYPF: HypF finger; 53.6 2.4 5.2E-05 28.3 -1.3 28 184-211 2-34 (35)
245 smart00714 LITAF Possible memb 53.3 45 0.00098 23.9 5.2 19 192-210 46-64 (67)
246 COG4338 Uncharacterized protei 53.3 4 8.6E-05 30.1 -0.3 15 178-192 9-23 (54)
247 COG1198 PriA Primosomal protei 53.2 8.8 0.00019 40.1 2.1 25 181-213 435-459 (730)
248 PRK14973 DNA topoisomerase I; 53.1 10 0.00022 40.4 2.6 16 200-215 637-654 (936)
249 PF03563 Bunya_G2: Bunyavirus 52.8 52 0.0011 31.3 6.8 55 140-196 189-249 (285)
250 COG1439 Predicted nucleic acid 52.7 7.9 0.00017 34.3 1.5 30 182-214 140-169 (177)
251 PF08882 Acetone_carb_G: Aceto 52.6 13 0.00027 31.0 2.5 27 199-237 75-101 (112)
252 PF04216 FdhE: Protein involve 52.3 4.5 9.7E-05 36.4 -0.1 24 183-209 199-222 (290)
253 PHA02998 RNA polymerase subuni 52.3 8.2 0.00018 34.8 1.5 33 180-212 142-185 (195)
254 PRK04179 rpl37e 50S ribosomal 52.3 6.5 0.00014 29.8 0.7 25 180-206 16-40 (62)
255 PLN03121 nucleic acid binding 52.2 19 0.00041 33.3 3.9 49 66-118 153-201 (243)
256 PLN02610 probable methionyl-tR 52.1 5.5 0.00012 41.6 0.4 30 175-208 149-180 (801)
257 cd01409 SIRT4 SIRT4: Eukaryoti 52.0 7.8 0.00017 34.8 1.3 15 178-192 115-129 (260)
258 PF13913 zf-C2HC_2: zinc-finge 51.9 6.6 0.00014 24.0 0.6 9 183-191 4-12 (25)
259 TIGR00575 dnlj DNA ligase, NAD 51.9 4.5 9.7E-05 41.2 -0.2 40 180-219 391-433 (652)
260 COG3677 Transposase and inacti 51.8 22 0.00049 29.3 3.9 42 173-214 21-69 (129)
261 PF04606 Ogr_Delta: Ogr/Delta- 51.8 8.8 0.00019 26.3 1.3 25 183-207 1-36 (47)
262 PRK11463 fxsA phage T7 F exclu 51.7 71 0.0015 26.9 6.9 31 142-172 78-109 (148)
263 PF09889 DUF2116: Uncharacteri 51.7 6.3 0.00014 29.2 0.6 11 200-210 5-15 (59)
264 PF12279 DUF3619: Protein of u 51.5 76 0.0017 26.6 7.0 30 67-96 7-41 (131)
265 PF11023 DUF2614: Protein of u 51.3 7.1 0.00015 32.6 0.9 19 192-210 63-81 (114)
266 cd00029 C1 Protein kinase C co 51.2 8.3 0.00018 25.0 1.1 27 182-208 12-38 (50)
267 PRK10445 endonuclease VIII; Pr 51.0 9.6 0.00021 34.3 1.8 23 182-205 236-262 (263)
268 cd01408 SIRT1 SIRT1: Eukaryoti 50.9 8.6 0.00019 33.9 1.4 34 176-209 111-151 (235)
269 COG4469 CoiA Competence protei 50.8 8.3 0.00018 37.3 1.4 16 199-214 26-41 (342)
270 PF12760 Zn_Tnp_IS1595: Transp 50.6 12 0.00026 25.3 1.8 24 183-206 20-45 (46)
271 KOG3966 p53-mediated apoptosis 50.4 1.9E+02 0.004 28.3 10.2 52 61-113 18-69 (360)
272 COG1571 Predicted DNA-binding 50.3 8.4 0.00018 38.1 1.3 29 180-208 349-377 (421)
273 COG4481 Uncharacterized protei 50.2 6.8 0.00015 29.5 0.6 18 198-215 34-51 (60)
274 PRK08332 ribonucleotide-diphos 50.1 13 0.00027 42.5 2.8 35 172-206 1695-1734(1740)
275 PRK05333 NAD-dependent deacety 50.0 8.2 0.00018 34.9 1.2 12 198-209 179-190 (285)
276 TIGR03847 conserved hypothetic 49.9 7.5 0.00016 34.6 0.9 16 199-215 157-172 (177)
277 PRK07561 DNA topoisomerase I s 49.7 19 0.00041 37.7 3.9 18 198-215 766-783 (859)
278 COG5525 Bacteriophage tail ass 49.0 9.7 0.00021 39.3 1.6 28 183-210 229-271 (611)
279 KOG3096 Spliceosome-associated 48.6 74 0.0016 29.4 6.9 53 51-103 127-180 (225)
280 PRK14810 formamidopyrimidine-D 48.5 9.6 0.00021 34.5 1.4 23 183-205 246-271 (272)
281 PF00301 Rubredoxin: Rubredoxi 48.3 8.2 0.00018 27.2 0.7 14 183-196 3-16 (47)
282 PRK01103 formamidopyrimidine/5 48.2 10 0.00022 34.2 1.5 23 183-206 247-273 (274)
283 PF13639 zf-RING_2: Ring finge 48.2 11 0.00023 24.7 1.2 24 182-207 1-24 (44)
284 PF14311 DUF4379: Domain of un 48.1 8.5 0.00018 26.8 0.8 25 180-204 27-55 (55)
285 PF06906 DUF1272: Protein of u 47.9 8 0.00017 28.9 0.6 12 198-209 41-52 (57)
286 COG1328 NrdD Oxygen-sensitive 47.8 9.6 0.00021 39.7 1.4 24 181-207 641-664 (700)
287 PF13894 zf-C2H2_4: C2H2-type 47.7 6.8 0.00015 21.5 0.2 12 183-194 2-13 (24)
288 COG2991 Uncharacterized protei 47.3 21 0.00045 28.1 2.8 24 162-185 11-34 (77)
289 KOG3134 Predicted membrane pro 47.2 6.5 0.00014 36.1 0.1 14 195-208 21-34 (225)
290 PRK03922 hypothetical protein; 47.0 8.5 0.00018 32.1 0.7 18 191-208 42-59 (113)
291 COG3058 FdhE Uncharacterized p 46.9 39 0.00084 32.4 5.1 10 198-207 225-234 (308)
292 PF06054 CoiA: Competence prot 46.9 12 0.00027 35.4 1.9 19 196-214 28-46 (375)
293 TIGR00308 TRM1 tRNA(guanine-26 46.8 11 0.00024 35.9 1.6 30 181-210 233-264 (374)
294 smart00647 IBR In Between Ring 46.7 27 0.00059 23.6 3.1 25 183-207 20-49 (64)
295 smart00109 C1 Protein kinase C 46.4 12 0.00026 23.9 1.2 26 181-207 11-36 (49)
296 PF09862 DUF2089: Protein of u 46.3 10 0.00023 31.2 1.1 14 201-214 1-14 (113)
297 PRK02935 hypothetical protein; 45.8 8.6 0.00019 32.0 0.6 19 194-212 66-84 (110)
298 KOG1779 40s ribosomal protein 45.8 15 0.00033 29.3 1.9 34 181-214 34-69 (84)
299 PF12653 DUF3785: Protein of u 45.6 9.8 0.00021 32.7 0.9 12 197-208 119-130 (138)
300 PF12273 RCR: Chitin synthesis 45.4 27 0.0006 28.0 3.4 29 165-193 13-41 (130)
301 KOG4218 Nuclear hormone recept 45.0 9.4 0.0002 37.8 0.8 29 178-206 12-40 (475)
302 COG5257 GCD11 Translation init 44.9 12 0.00026 36.9 1.4 28 182-211 58-85 (415)
303 cd00296 SIR2 SIR2 superfamily 44.6 11 0.00024 31.7 1.1 39 177-215 109-151 (222)
304 PF03833 PolC_DP2: DNA polymer 44.6 7.3 0.00016 41.7 0.0 28 182-209 656-691 (900)
305 PRK14715 DNA polymerase II lar 44.6 11 0.00024 42.5 1.3 22 181-207 674-695 (1627)
306 PF12172 DUF35_N: Rubredoxin-l 44.5 7.8 0.00017 25.0 0.1 25 178-205 8-32 (37)
307 PF10083 DUF2321: Uncharacteri 44.3 3.7 7.9E-05 35.9 -1.9 25 178-208 25-49 (158)
308 PRK09678 DNA-binding transcrip 43.8 16 0.00034 28.0 1.7 29 182-210 2-41 (72)
309 TIGR02745 ccoG_rdxA_fixG cytoc 43.7 37 0.00081 33.3 4.6 18 173-190 177-194 (434)
310 PF10122 Mu-like_Com: Mu-like 43.7 12 0.00026 27.4 1.0 35 180-214 3-40 (51)
311 PRK05452 anaerobic nitric oxid 43.6 11 0.00024 36.7 1.0 25 183-207 427-467 (479)
312 PF04641 Rtf2: Rtf2 RING-finge 42.9 14 0.0003 33.1 1.5 13 181-193 113-125 (260)
313 PF01004 Flavi_M: Flavivirus e 42.9 31 0.00068 26.7 3.2 31 131-161 37-67 (75)
314 PF04267 SoxD: Sarcosine oxida 42.8 5.4 0.00012 31.4 -1.0 31 199-233 2-32 (84)
315 PRK04338 N(2),N(2)-dimethylgua 42.5 13 0.00029 35.3 1.4 30 181-210 244-273 (382)
316 PF14159 CAAD: CAAD domains of 42.3 62 0.0013 25.3 4.8 43 139-181 21-70 (90)
317 PRK10246 exonuclease subunit S 42.1 12 0.00027 39.7 1.2 16 175-190 496-512 (1047)
318 PRK14811 formamidopyrimidine-D 42.0 14 0.0003 33.5 1.3 23 183-206 237-263 (269)
319 PF08772 NOB1_Zn_bind: Nin one 41.7 12 0.00027 28.6 0.9 23 183-207 11-33 (73)
320 PF02005 TRM: N2,N2-dimethylgu 41.4 14 0.00029 35.4 1.2 30 181-210 240-271 (377)
321 PTZ00410 NAD-dependent SIR2; P 41.2 14 0.00029 35.5 1.2 33 177-209 143-182 (349)
322 PTZ00043 cytochrome c oxidase 41.0 20 0.00044 33.6 2.2 43 191-235 174-216 (268)
323 TIGR03676 aRF1/eRF1 peptide ch 41.0 15 0.00032 35.5 1.4 32 180-211 319-355 (403)
324 COG4260 Membrane protease subu 40.9 11 0.00024 36.3 0.6 20 22-41 127-146 (345)
325 PRK07219 DNA topoisomerase I; 40.9 23 0.00049 37.0 2.8 19 197-215 687-705 (822)
326 COG0846 SIR2 NAD-dependent pro 40.7 11 0.00024 34.4 0.5 30 177-206 118-154 (250)
327 smart00734 ZnF_Rad18 Rad18-lik 40.7 13 0.00028 23.1 0.7 9 183-191 3-11 (26)
328 COG0498 ThrC Threonine synthas 40.4 11 0.00023 36.8 0.4 33 179-212 3-35 (411)
329 smart00350 MCM minichromosome 40.4 32 0.0007 33.5 3.7 25 182-206 38-69 (509)
330 PRK01345 heat shock protein Ht 40.4 90 0.002 29.0 6.4 32 145-176 16-48 (317)
331 PF04906 Tweety: Tweety; Inte 40.0 76 0.0016 30.6 6.0 77 37-113 89-169 (406)
332 PF05478 Prominin: Prominin; 40.0 4.6E+02 0.01 27.4 15.7 47 53-101 337-383 (806)
333 PF08285 DPM3: Dolichol-phosph 39.5 67 0.0015 25.4 4.7 50 139-188 12-70 (91)
334 PRK14873 primosome assembly pr 39.5 17 0.00037 37.3 1.7 24 183-206 394-418 (665)
335 PRK13945 formamidopyrimidine-D 39.4 17 0.00037 33.0 1.5 10 130-139 176-185 (282)
336 PF03833 PolC_DP2: DNA polymer 38.9 10 0.00022 40.7 0.0 30 180-209 666-703 (900)
337 smart00355 ZnF_C2H2 zinc finge 38.7 16 0.00034 19.9 0.8 12 183-194 2-13 (26)
338 PRK08173 DNA topoisomerase III 38.7 18 0.0004 38.1 1.8 27 182-209 625-651 (862)
339 PRK02224 chromosome segregatio 38.7 17 0.00037 36.9 1.5 18 176-193 446-463 (880)
340 TIGR00595 priA primosomal prot 38.6 18 0.00039 35.5 1.7 28 184-211 225-253 (505)
341 PF10058 DUF2296: Predicted in 38.2 21 0.00046 25.7 1.5 23 184-206 25-52 (54)
342 smart00778 Prim_Zn_Ribbon Zinc 38.0 26 0.00056 23.8 1.8 24 181-205 3-32 (37)
343 PRK10996 thioredoxin 2; Provis 38.0 20 0.00043 28.7 1.6 28 182-209 3-33 (139)
344 PF14319 Zn_Tnp_IS91: Transpos 37.8 16 0.00036 29.2 1.0 28 180-207 41-69 (111)
345 smart00504 Ubox Modified RING 37.6 29 0.00063 23.5 2.1 11 181-191 35-45 (63)
346 KOG2927 Membrane component of 37.2 10 0.00023 37.0 -0.2 34 111-144 202-235 (372)
347 TIGR01374 soxD sarcosine oxida 37.1 18 0.0004 28.6 1.2 31 199-233 2-32 (84)
348 PRK14894 glycyl-tRNA synthetas 37.1 20 0.00042 36.7 1.6 25 181-206 88-112 (539)
349 PRK00349 uvrA excinuclease ABC 37.1 19 0.00042 38.5 1.7 30 183-212 254-293 (943)
350 PF13465 zf-H2C2_2: Zinc-finge 37.0 10 0.00023 22.9 -0.2 10 183-192 16-25 (26)
351 PRK00420 hypothetical protein; 36.6 19 0.00041 29.6 1.2 24 192-215 17-41 (112)
352 KOG1307 K+-dependent Ca2+/Na+ 36.5 56 0.0012 33.6 4.7 57 129-187 525-587 (588)
353 COG4965 TadB Flp pilus assembl 36.3 3.3E+02 0.0071 26.2 9.4 18 104-121 53-70 (309)
354 PTZ00409 Sir2 (Silent Informat 36.1 19 0.00042 32.8 1.3 31 178-209 134-175 (271)
355 TIGR01385 TFSII transcription 36.0 18 0.00039 33.8 1.2 26 182-207 259-295 (299)
356 PF09925 DUF2157: Predicted me 35.9 2.3E+02 0.005 22.9 7.4 45 133-177 38-84 (145)
357 PRK00418 DNA gyrase inhibitor; 35.9 19 0.00041 27.1 1.0 19 197-215 5-24 (62)
358 CHL00174 accD acetyl-CoA carbo 35.8 13 0.00028 35.0 0.2 29 183-211 40-70 (296)
359 PRK11788 tetratricopeptide rep 35.1 24 0.00052 30.9 1.7 22 183-207 356-377 (389)
360 PF08507 COPI_assoc: COPI asso 35.1 1.5E+02 0.0033 23.9 6.2 38 119-157 54-91 (136)
361 PF05280 FlhC: Flagellar trans 35.1 22 0.00047 30.9 1.4 28 179-206 132-162 (175)
362 COG0178 UvrA Excinuclease ATPa 35.0 21 0.00045 38.6 1.5 26 181-206 245-277 (935)
363 PF13994 PgaD: PgaD-like prote 34.9 1.6E+02 0.0034 24.1 6.4 28 114-143 4-31 (138)
364 PRK08382 putative monovalent c 34.8 93 0.002 27.8 5.3 57 173-239 103-162 (201)
365 PF10080 DUF2318: Predicted me 34.6 23 0.0005 28.5 1.4 34 179-212 33-66 (102)
366 PTZ00303 phosphatidylinositol 34.6 19 0.00042 39.1 1.2 40 174-213 453-496 (1374)
367 COG1379 PHP family phosphoeste 34.5 11 0.00023 37.1 -0.6 30 182-213 247-278 (403)
368 PTZ00408 NAD-dependent deacety 34.4 16 0.00034 32.7 0.5 30 177-206 113-145 (242)
369 PF01485 IBR: IBR domain; Int 34.2 25 0.00054 23.7 1.4 25 183-207 20-49 (64)
370 TIGR00319 desulf_FeS4 desulfof 34.2 38 0.00083 21.5 2.1 18 196-213 5-22 (34)
371 COG0419 SbcC ATPase involved i 33.9 20 0.00043 37.3 1.1 16 180-195 456-471 (908)
372 COG3813 Uncharacterized protei 33.9 20 0.00043 28.5 0.9 12 180-191 40-51 (84)
373 PF03884 DUF329: Domain of unk 33.8 28 0.00062 25.6 1.7 12 199-210 3-14 (57)
374 PRK09401 reverse gyrase; Revie 33.7 18 0.0004 39.4 0.9 26 180-208 677-702 (1176)
375 COG3898 Uncharacterized membra 33.7 1.1E+02 0.0024 31.2 6.1 33 150-182 34-68 (531)
376 PF09334 tRNA-synt_1g: tRNA sy 33.7 25 0.00055 33.4 1.7 10 14-23 10-19 (391)
377 KOG1729 FYVE finger containing 33.6 9.6 0.00021 35.7 -1.0 31 181-211 168-198 (288)
378 PF09845 DUF2072: Zn-ribbon co 33.5 23 0.00049 30.2 1.2 28 183-210 3-31 (131)
379 KOG1819 FYVE finger-containing 33.4 13 0.00027 38.7 -0.3 25 183-208 903-927 (990)
380 PF11833 DUF3353: Protein of u 33.3 3.3E+02 0.0071 24.0 8.4 72 66-139 8-95 (194)
381 PF00096 zf-C2H2: Zinc finger, 33.2 14 0.0003 20.9 -0.0 11 183-193 2-12 (23)
382 PF09972 DUF2207: Predicted me 32.8 2.1E+02 0.0046 26.3 7.5 12 59-70 330-341 (511)
383 PF11331 DUF3133: Protein of u 32.8 30 0.00065 24.6 1.6 19 193-211 26-44 (46)
384 PLN03121 nucleic acid binding 32.7 42 0.00092 31.1 2.9 41 65-112 135-175 (243)
385 COG1998 RPS31 Ribosomal protei 32.6 38 0.00083 24.9 2.1 29 183-211 21-50 (51)
386 PF06827 zf-FPG_IleRS: Zinc fi 32.6 23 0.00051 21.9 0.9 24 183-206 3-29 (30)
387 PF07191 zinc-ribbons_6: zinc- 32.4 26 0.00057 27.0 1.3 17 199-215 2-18 (70)
388 PF05129 Elf1: Transcription e 32.4 34 0.00075 26.3 2.0 32 181-212 22-60 (81)
389 PF11290 DUF3090: Protein of u 32.4 20 0.00042 31.7 0.7 15 200-215 156-170 (171)
390 TIGR01597 PYST-B Plasmodium yo 32.4 1.1E+02 0.0024 28.7 5.6 47 122-175 193-239 (255)
391 PHA02768 hypothetical protein; 32.2 22 0.00048 26.1 0.9 28 180-207 4-40 (55)
392 PF10367 Vps39_2: Vacuolar sor 32.1 34 0.00073 25.2 1.9 20 182-203 79-98 (109)
393 smart00837 DPBB_1 Rare lipopro 32.0 21 0.00045 27.6 0.7 9 229-237 79-87 (87)
394 PRK01741 cell division protein 31.8 34 0.00075 33.0 2.3 25 153-177 3-27 (332)
395 PF06364 DUF1068: Protein of u 31.6 41 0.00089 30.0 2.6 38 165-214 23-63 (176)
396 PF04674 Phi_1: Phosphate-indu 31.5 29 0.00063 32.6 1.7 34 176-209 114-162 (273)
397 smart00132 LIM Zinc-binding do 31.4 28 0.0006 21.0 1.1 11 183-193 1-11 (39)
398 PTZ00396 Casein kinase II subu 31.3 31 0.00067 31.9 1.8 34 179-212 118-162 (251)
399 TIGR00108 eRF peptide chain re 31.0 26 0.00056 33.8 1.3 31 180-210 323-358 (409)
400 PRK01110 rpmF 50S ribosomal pr 30.8 29 0.00062 25.5 1.3 12 198-209 27-38 (60)
401 PRK11032 hypothetical protein; 30.6 26 0.00057 30.4 1.2 26 182-207 125-151 (160)
402 PRK00635 excinuclease ABC subu 30.5 28 0.00061 40.0 1.7 31 180-210 243-283 (1809)
403 PF12273 RCR: Chitin synthesis 30.4 44 0.00095 26.9 2.4 22 151-172 2-23 (130)
404 PF06107 DUF951: Bacterial pro 30.4 21 0.00045 26.6 0.5 18 198-215 31-48 (57)
405 PRK06599 DNA topoisomerase I; 30.2 41 0.0009 34.2 2.7 16 200-215 639-654 (675)
406 cd00974 DSRD Desulforedoxin (D 30.0 49 0.0011 21.1 2.1 18 196-213 2-19 (34)
407 PRK14282 chaperone protein Dna 30.0 49 0.0011 31.1 2.9 13 193-205 190-202 (369)
408 PRK12722 transcriptional activ 29.6 54 0.0012 29.2 3.0 40 167-206 120-162 (187)
409 PF05473 Herpes_UL45: UL45 pro 29.6 1.2E+02 0.0027 26.7 5.2 15 183-197 81-95 (200)
410 PF05766 NinG: Bacteriophage L 29.6 21 0.00046 31.7 0.5 28 181-208 6-34 (189)
411 PRK03072 heat shock protein Ht 29.4 1.9E+02 0.0041 26.4 6.5 36 144-180 19-55 (288)
412 PRK12336 translation initiatio 29.4 62 0.0013 28.4 3.3 33 182-214 99-135 (201)
413 PLN00193 expansin-A; Provision 29.3 31 0.00068 31.9 1.5 10 229-238 145-154 (256)
414 PF04438 zf-HIT: HIT zinc fing 29.3 31 0.00067 22.2 1.1 21 182-208 3-23 (30)
415 PF06221 zf-C2HC5: Putative zi 29.3 32 0.00069 25.4 1.3 28 182-209 19-46 (57)
416 PLN03024 Putative EG45-like do 29.1 22 0.00048 29.4 0.5 10 229-238 115-124 (125)
417 KOG3507 DNA-directed RNA polym 28.9 31 0.00067 26.3 1.2 33 177-209 16-48 (62)
418 TIGR00143 hypF [NiFe] hydrogen 28.9 23 0.00051 36.6 0.7 31 183-213 120-155 (711)
419 TIGR00869 sec62 protein transl 28.8 76 0.0017 29.2 3.9 16 172-188 182-197 (232)
420 PF12648 TcpE: TcpE family 28.8 66 0.0014 25.1 3.1 21 165-185 64-84 (108)
421 PF11872 DUF3392: Protein of u 28.7 1.3E+02 0.0029 24.7 4.9 16 163-178 91-106 (106)
422 PF14690 zf-ISL3: zinc-finger 28.6 33 0.00072 22.5 1.2 15 199-213 3-17 (47)
423 PF06397 Desulfoferrod_N: Desu 28.3 40 0.00087 22.9 1.5 18 196-213 4-21 (36)
424 PRK05654 acetyl-CoA carboxylas 28.2 21 0.00046 33.2 0.3 29 183-211 29-59 (292)
425 KOG1088 Uncharacterized conser 28.1 36 0.00079 28.9 1.6 17 198-214 98-114 (124)
426 PLN03120 nucleic acid binding 28.1 69 0.0015 29.9 3.5 30 67-96 165-194 (260)
427 TIGR00311 aIF-2beta translatio 27.9 34 0.00073 28.7 1.4 29 182-210 98-130 (133)
428 PF12674 Zn_ribbon_2: Putative 27.8 37 0.0008 26.1 1.5 13 200-212 2-14 (81)
429 PF09567 RE_MamI: MamI restric 27.7 26 0.00056 33.4 0.7 22 182-206 83-104 (314)
430 PF05077 DUF678: Protein of un 27.6 35 0.00076 26.7 1.3 17 195-211 54-70 (74)
431 TIGR03518 ABC_perm_GldF glidin 27.6 2E+02 0.0044 25.1 6.2 28 118-145 1-28 (240)
432 PHA02893 hypothetical protein; 27.6 25 0.00053 28.4 0.5 15 196-210 67-81 (88)
433 PRK13415 flagella biosynthesis 27.5 85 0.0018 28.8 3.9 28 152-180 68-95 (219)
434 PF07295 DUF1451: Protein of u 27.4 34 0.00073 29.1 1.3 26 182-207 113-139 (146)
435 PRK03988 translation initiatio 27.1 36 0.00077 28.7 1.4 29 182-210 103-135 (138)
436 TIGR02205 septum_zipA cell div 27.0 27 0.00059 32.6 0.7 26 153-178 2-27 (284)
437 PF03733 DUF307: Domain of unk 27.0 1.9E+02 0.0042 20.6 4.9 24 134-157 2-25 (53)
438 KOG3059 N-acetylglucosaminyltr 26.8 2.6E+02 0.0057 26.8 7.1 14 117-130 209-222 (292)
439 TIGR02159 PA_CoA_Oxy4 phenylac 26.6 26 0.00056 29.6 0.5 27 182-208 106-140 (146)
440 KOG3012 Uncharacterized conser 26.6 2.1E+02 0.0047 26.9 6.4 35 121-156 68-105 (259)
441 PRK12652 putative monovalent c 26.5 1E+02 0.0023 29.4 4.5 21 173-193 232-252 (357)
442 PLN00050 expansin A; Provision 26.4 37 0.00079 31.3 1.4 10 229-238 137-146 (247)
443 TIGR01054 rgy reverse gyrase. 26.2 28 0.00062 38.0 0.8 23 182-207 679-701 (1171)
444 TIGR02230 ATPase_gene1 F0F1-AT 26.0 98 0.0021 25.1 3.6 23 134-156 48-70 (100)
445 PF07666 MpPF26: M penetrans p 26.0 1.5E+02 0.0033 25.0 4.9 54 124-189 45-98 (130)
446 PF11172 DUF2959: Protein of u 25.9 5.1E+02 0.011 23.6 8.6 25 66-90 61-85 (201)
447 PRK05580 primosome assembly pr 25.8 39 0.00084 34.4 1.6 29 183-211 392-421 (679)
448 PRK12651 putative monovalent c 25.6 1.4E+02 0.0031 24.9 4.7 12 139-150 9-20 (158)
449 TIGR00389 glyS_dimeric glycyl- 25.6 27 0.00059 35.4 0.5 48 160-207 63-133 (551)
450 PF14017 DUF4233: Protein of u 25.6 2.1E+02 0.0047 23.1 5.5 43 139-181 40-102 (107)
451 KOG1792 Reticulon [Intracellul 25.5 1.6E+02 0.0034 26.9 5.2 41 136-176 57-97 (230)
452 PF10864 DUF2663: Protein of u 25.5 1.7E+02 0.0038 24.8 5.2 63 116-178 10-80 (130)
453 PF04135 Nop10p: Nucleolar RNA 25.4 56 0.0012 23.9 2.0 28 183-215 7-35 (53)
454 COG0551 TopA Zn-finger domain 25.3 66 0.0014 26.0 2.6 23 193-215 55-78 (140)
455 COG1645 Uncharacterized Zn-fin 25.2 26 0.00057 29.8 0.3 25 192-216 22-46 (131)
456 PF01780 Ribosomal_L37ae: Ribo 25.1 40 0.00087 27.0 1.2 33 181-215 35-68 (90)
457 COG5345 Uncharacterized protei 25.0 1.2E+02 0.0027 29.5 4.7 26 150-176 29-54 (358)
458 PRK12860 transcriptional activ 24.9 67 0.0014 28.7 2.7 38 168-205 121-161 (189)
459 PF01873 eIF-5_eIF-2B: Domain 24.8 57 0.0012 26.9 2.2 26 182-207 94-123 (125)
460 PRK14288 chaperone protein Dna 24.7 36 0.00078 32.1 1.1 12 193-204 173-184 (369)
461 PRK14297 chaperone protein Dna 24.6 41 0.00088 31.7 1.4 13 193-205 186-198 (380)
462 PF06724 DUF1206: Domain of Un 24.6 1.5E+02 0.0033 21.4 4.2 32 120-151 31-63 (73)
463 PF04981 NMD3: NMD3 family ; 24.6 34 0.00073 30.2 0.8 36 178-215 10-50 (236)
464 PF03811 Zn_Tnp_IS1: InsA N-te 24.4 63 0.0014 21.6 1.9 18 197-214 4-22 (36)
465 PRK11595 DNA utilization prote 24.4 25 0.00055 30.6 0.0 9 200-208 36-44 (227)
466 PF11587 Prion_bPrPp: Major pr 24.4 61 0.0013 21.4 1.8 13 132-144 4-16 (29)
467 PRK07333 2-octaprenyl-6-methox 24.4 4.3E+02 0.0093 23.7 7.8 73 54-128 298-385 (403)
468 COG0333 RpmF Ribosomal protein 24.4 37 0.00081 25.1 0.9 11 198-208 27-37 (57)
469 PF01194 RNA_pol_N: RNA polyme 24.4 30 0.00065 25.9 0.4 14 198-211 4-17 (60)
470 PRK10633 hypothetical protein; 24.3 2.9E+02 0.0063 21.7 5.8 28 150-177 44-71 (80)
471 PF09527 ATPase_gene1: Putativ 24.3 1.2E+02 0.0025 21.0 3.3 23 157-179 6-28 (55)
472 PF05502 Dynactin_p62: Dynacti 24.1 47 0.001 32.9 1.8 36 179-214 24-68 (483)
473 TIGR02896 spore_III_AF stage I 24.1 1.9E+02 0.0042 23.4 5.0 37 134-170 3-54 (106)
474 PRK12475 thiamine/molybdopteri 23.8 59 0.0013 30.4 2.3 34 181-214 237-275 (338)
475 TIGR02163 napH_ ferredoxin-typ 23.8 5.3E+02 0.011 23.0 8.6 13 173-185 167-179 (255)
476 COG0068 HypF Hydrogenase matur 23.7 35 0.00075 36.2 0.8 30 183-212 153-187 (750)
477 PF13829 DUF4191: Domain of un 23.7 3.1E+02 0.0067 25.2 6.7 22 163-184 63-87 (224)
478 COG5005 Mu-like prophage prote 23.7 1.2E+02 0.0026 26.3 3.9 36 66-101 15-50 (140)
479 cd03509 DesA_FADS-like Fatty a 23.6 3.9E+02 0.0084 24.5 7.5 14 122-135 113-126 (288)
480 PF01214 CK_II_beta: Casein ki 23.6 50 0.0011 28.9 1.7 34 180-213 98-142 (184)
481 PRK14291 chaperone protein Dna 23.5 38 0.00083 32.0 1.0 13 193-205 190-202 (382)
482 PF04956 TrbC: TrbC/VIRB2 fami 23.5 1.2E+02 0.0027 22.6 3.6 46 117-162 36-89 (99)
483 COG1885 Uncharacterized protei 23.4 38 0.00083 28.4 0.9 12 182-193 50-61 (115)
484 PF01907 Ribosomal_L37e: Ribos 23.4 36 0.00077 25.3 0.6 26 181-208 15-40 (55)
485 cd04511 Nudix_Hydrolase_4 Memb 23.3 84 0.0018 24.2 2.7 29 184-214 1-33 (130)
486 PRK14278 chaperone protein Dna 23.3 42 0.00091 31.8 1.2 14 192-205 176-189 (378)
487 PRK07220 DNA topoisomerase I; 23.2 55 0.0012 33.9 2.1 37 178-214 632-673 (740)
488 KOG1842 FYVE finger-containing 23.2 19 0.00042 36.4 -1.0 37 173-211 173-209 (505)
489 cd01428 ADK Adenylate kinase ( 23.2 67 0.0014 25.7 2.2 37 173-214 117-153 (194)
490 PHA02446 hypothetical protein 23.1 38 0.00083 29.3 0.8 15 198-212 62-76 (166)
491 TIGR00630 uvra excinuclease AB 23.1 48 0.001 35.5 1.7 27 178-206 733-767 (924)
492 PRK14526 adenylate kinase; Pro 23.0 89 0.0019 27.2 3.1 42 173-214 114-158 (211)
493 PTZ00073 60S ribosomal protein 22.9 39 0.00085 27.3 0.8 28 179-208 14-41 (91)
494 PHA02929 N1R/p28-like protein; 22.7 50 0.0011 30.2 1.6 22 173-197 211-232 (238)
495 PRK01343 zinc-binding protein; 22.7 43 0.00093 24.9 0.9 14 179-192 7-20 (57)
496 PRK12268 methionyl-tRNA synthe 22.6 36 0.00078 33.1 0.7 27 178-208 138-164 (556)
497 PF08804 gp32: gp32 DNA bindin 22.5 11 0.00023 30.6 -2.4 15 182-196 59-75 (94)
498 TIGR00244 transcriptional regu 22.5 38 0.00082 29.3 0.7 17 183-199 30-46 (147)
499 PF12171 zf-C2H2_jaz: Zinc-fin 22.4 46 0.001 19.9 0.9 13 183-195 3-15 (27)
500 PF00452 Bcl-2: Apoptosis regu 22.3 3.1E+02 0.0067 20.4 5.6 58 92-149 2-65 (101)
No 1
>PRK00420 hypothetical protein; Validated
Probab=98.57 E-value=2.8e-08 Score=80.62 Aligned_cols=35 Identities=17% Similarity=0.428 Sum_probs=32.9
Q ss_pred hcCCCCCCCccccccccceeecCCCCceeeeeCCC
Q 026283 180 IKGACPACKREFIGSKSQIIRCAGCGNIVWQPEGD 214 (240)
Q Consensus 180 Ieg~CPvC~~eFtG~nnt~~~CpnCGe~l~v~~g~ 214 (240)
-.+.||+||++++++++.+.+||+||+++.+++++
T Consensus 22 l~~~CP~Cg~pLf~lk~g~~~Cp~Cg~~~~v~~~e 56 (112)
T PRK00420 22 LSKHCPVCGLPLFELKDGEVVCPVHGKVYIVKSDE 56 (112)
T ss_pred ccCCCCCCCCcceecCCCceECCCCCCeeeeccHH
Confidence 45999999999999999999999999999999875
No 2
>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=97.02 E-value=0.0005 Score=55.40 Aligned_cols=31 Identities=29% Similarity=0.651 Sum_probs=28.7
Q ss_pred cCCCCCCCccccccccceeecCCCCceeeee
Q 026283 181 KGACPACKREFIGSKSQIIRCAGCGNIVWQP 211 (240)
Q Consensus 181 eg~CPvC~~eFtG~nnt~~~CpnCGe~l~v~ 211 (240)
+-.||.||..|-=||...+.||.||+.....
T Consensus 9 KR~Cp~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 9 KRTCPSCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cccCCCCcchhccCCCCCccCCCCCCccCcc
Confidence 4579999999999999999999999998887
No 3
>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=96.95 E-value=0.0024 Score=52.70 Aligned_cols=37 Identities=14% Similarity=0.272 Sum_probs=29.4
Q ss_pred hhhhhcCCCCCCCccccccccceeecCCCCceeeeeCC
Q 026283 176 NNFVIKGACPACKREFIGSKSQIIRCAGCGNIVWQPEG 213 (240)
Q Consensus 176 kRnLIeg~CPvC~~eFtG~nnt~~~CpnCGe~l~v~~g 213 (240)
--..+.-.||.|+.+.-=+..++ +|+.|+++|+....
T Consensus 64 Stkav~V~CP~C~K~TKmLGr~D-~CM~C~~pLTLd~~ 100 (114)
T PF11023_consen 64 STKAVQVECPNCGKQTKMLGRVD-ACMHCKEPLTLDPS 100 (114)
T ss_pred cccceeeECCCCCChHhhhchhh-ccCcCCCcCccCch
Confidence 44557778999999986555554 99999999998764
No 4
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=96.74 E-value=0.0011 Score=45.06 Aligned_cols=34 Identities=26% Similarity=0.441 Sum_probs=27.5
Q ss_pred hcCCCCCCCccccccccc-eeecCCCCceeeeeCC
Q 026283 180 IKGACPACKREFIGSKSQ-IIRCAGCGNIVWQPEG 213 (240)
Q Consensus 180 Ieg~CPvC~~eFtG~nnt-~~~CpnCGe~l~v~~g 213 (240)
++-.||.||.+|.--... ...||+||..+.....
T Consensus 2 ~~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~~ 36 (46)
T PRK00398 2 AEYKCARCGREVELDEYGTGVRCPYCGYRILFKER 36 (46)
T ss_pred CEEECCCCCCEEEECCCCCceECCCCCCeEEEccC
Confidence 456799999999766555 8999999999887654
No 5
>PRK02935 hypothetical protein; Provisional
Probab=96.61 E-value=0.0086 Score=49.27 Aligned_cols=39 Identities=13% Similarity=0.345 Sum_probs=31.0
Q ss_pred HhhhhhcCCCCCCCccccccccceeecCCCCceeeeeCCC
Q 026283 175 ANNFVIKGACPACKREFIGSKSQIIRCAGCGNIVWQPEGD 214 (240)
Q Consensus 175 lkRnLIeg~CPvC~~eFtG~nnt~~~CpnCGe~l~v~~g~ 214 (240)
+.-..+.-.||.|+.+ |=.-+.+-.|+.|+|||+...++
T Consensus 64 lStkavqV~CP~C~K~-TKmLGrvD~CM~C~~PLTLd~~l 102 (110)
T PRK02935 64 LSTKAVQVICPSCEKP-TKMLGRVDACMHCNQPLTLDRSL 102 (110)
T ss_pred hcccceeeECCCCCch-hhhccceeecCcCCCcCCcCccc
Confidence 4456777899999987 44556677999999999987765
No 6
>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=96.37 E-value=0.0017 Score=54.55 Aligned_cols=31 Identities=16% Similarity=0.179 Sum_probs=27.1
Q ss_pred cCCCCCCCccccccccceeecCCCCceeeee
Q 026283 181 KGACPACKREFIGSKSQIIRCAGCGNIVWQP 211 (240)
Q Consensus 181 eg~CPvC~~eFtG~nnt~~~CpnCGe~l~v~ 211 (240)
+-.||.||..|--||...+.||.||+.....
T Consensus 9 Kr~Cp~cg~kFYDLnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 9 KRICPNTGSKFYDLNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred cccCCCcCccccccCCCCccCCCcCCccCcc
Confidence 4479999999999999999999999985433
No 7
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=96.17 E-value=0.0023 Score=39.52 Aligned_cols=25 Identities=28% Similarity=0.683 Sum_probs=20.9
Q ss_pred cCCCCCCCccccccccceeecCCCCcee
Q 026283 181 KGACPACKREFIGSKSQIIRCAGCGNIV 208 (240)
Q Consensus 181 eg~CPvC~~eFtG~nnt~~~CpnCGe~l 208 (240)
+..||.|+.+ +......||+||..|
T Consensus 2 ~~~Cp~Cg~~---~~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 2 EMFCPNCGAE---IDPDAKFCPNCGAKL 26 (26)
T ss_pred cCCCcccCCc---CCcccccChhhCCCC
Confidence 4679999994 577888999999875
No 8
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=95.95 E-value=0.0032 Score=51.74 Aligned_cols=34 Identities=18% Similarity=0.549 Sum_probs=25.5
Q ss_pred cCCCCCCCccccccccc-------eeecCCCCceeeeeCCC
Q 026283 181 KGACPACKREFIGSKSQ-------IIRCAGCGNIVWQPEGD 214 (240)
Q Consensus 181 eg~CPvC~~eFtG~nnt-------~~~CpnCGe~l~v~~g~ 214 (240)
.-.||.|+..|+-..-. ...||+||++|...+..
T Consensus 99 ~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~~dn~ 139 (147)
T smart00531 99 YYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEEDDNS 139 (147)
T ss_pred EEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEEEcCch
Confidence 34599999999853221 28999999999886653
No 9
>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=95.88 E-value=0.0038 Score=40.32 Aligned_cols=28 Identities=25% Similarity=0.593 Sum_probs=22.4
Q ss_pred cCCCCCCCccccccc----cceeecCCCCcee
Q 026283 181 KGACPACKREFIGSK----SQIIRCAGCGNIV 208 (240)
Q Consensus 181 eg~CPvC~~eFtG~n----nt~~~CpnCGe~l 208 (240)
+-.||.|+.+|.-.. .....||+||..+
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~ 36 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISDDPLATCPECGGDV 36 (41)
T ss_pred EEEcCCCCCEEEEEEecCCCCCCCCCCCCCcc
Confidence 457999999887554 5678999999854
No 10
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=95.86 E-value=0.007 Score=39.21 Aligned_cols=29 Identities=31% Similarity=0.800 Sum_probs=21.4
Q ss_pred CCCCCCCcccccc------ccceeecCCCCceeee
Q 026283 182 GACPACKREFIGS------KSQIIRCAGCGNIVWQ 210 (240)
Q Consensus 182 g~CPvC~~eFtG~------nnt~~~CpnCGe~l~v 210 (240)
-.||.|+..|.== +....+||+||+.+.+
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~~ 37 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWYA 37 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEEe
Confidence 3699999876432 3446899999998865
No 11
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=95.54 E-value=0.0085 Score=50.36 Aligned_cols=33 Identities=27% Similarity=0.596 Sum_probs=26.4
Q ss_pred hhcCCCCCCCccccccccceeecCCCC-ceeeeeC
Q 026283 179 VIKGACPACKREFIGSKSQIIRCAGCG-NIVWQPE 212 (240)
Q Consensus 179 LIeg~CPvC~~eFtG~nnt~~~CpnCG-e~l~v~~ 212 (240)
.-..+||.||.+++= ++..+.||+|| ..+.|+.
T Consensus 26 ML~~hCp~Cg~PLF~-KdG~v~CPvC~~~~~~v~~ 59 (131)
T COG1645 26 MLAKHCPKCGTPLFR-KDGEVFCPVCGYREVVVEE 59 (131)
T ss_pred HHHhhCcccCCccee-eCCeEECCCCCceEEEeec
Confidence 345789999999999 88888999999 5555543
No 12
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=95.53 E-value=0.0078 Score=40.42 Aligned_cols=31 Identities=23% Similarity=0.549 Sum_probs=22.4
Q ss_pred CCCCCCCcccc--ccccceeecCCCCceeeeeC
Q 026283 182 GACPACKREFI--GSKSQIIRCAGCGNIVWQPE 212 (240)
Q Consensus 182 g~CPvC~~eFt--G~nnt~~~CpnCGe~l~v~~ 212 (240)
+.||.|+...+ =..+....|++||.+|....
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl~e~~ 33 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGLVLEENI 33 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-BBEE-TT
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCCEeeccc
Confidence 37999999764 34577889999999886543
No 13
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=95.47 E-value=0.006 Score=37.20 Aligned_cols=23 Identities=30% Similarity=0.833 Sum_probs=18.6
Q ss_pred CCCCCCccccccccceeecCCCCcee
Q 026283 183 ACPACKREFIGSKSQIIRCAGCGNIV 208 (240)
Q Consensus 183 ~CPvC~~eFtG~nnt~~~CpnCGe~l 208 (240)
.||.||.+. ......||+||.+|
T Consensus 1 ~Cp~CG~~~---~~~~~fC~~CG~~l 23 (23)
T PF13240_consen 1 YCPNCGAEI---EDDAKFCPNCGTPL 23 (23)
T ss_pred CCcccCCCC---CCcCcchhhhCCcC
Confidence 499999986 45677799999875
No 14
>PRK05978 hypothetical protein; Provisional
Probab=95.46 E-value=0.0081 Score=51.06 Aligned_cols=36 Identities=31% Similarity=0.636 Sum_probs=32.2
Q ss_pred hcCCCCCCCcc--ccccccceeecCCCCceeeeeCCCc
Q 026283 180 IKGACPACKRE--FIGSKSQIIRCAGCGNIVWQPEGDF 215 (240)
Q Consensus 180 Ieg~CPvC~~e--FtG~nnt~~~CpnCGe~l~v~~g~F 215 (240)
..+.||.|+.. |.||-...-.|++||+.+..+++++
T Consensus 32 l~grCP~CG~G~LF~g~Lkv~~~C~~CG~~~~~~~a~D 69 (148)
T PRK05978 32 FRGRCPACGEGKLFRAFLKPVDHCAACGEDFTHHRADD 69 (148)
T ss_pred HcCcCCCCCCCcccccccccCCCccccCCccccCCccc
Confidence 46899999865 8899999999999999999998765
No 15
>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=95.37 E-value=0.012 Score=36.91 Aligned_cols=23 Identities=26% Similarity=0.742 Sum_probs=20.6
Q ss_pred CCCCCccccccc-cceeecCCCCc
Q 026283 184 CPACKREFIGSK-SQIIRCAGCGN 206 (240)
Q Consensus 184 CPvC~~eFtG~n-nt~~~CpnCGe 206 (240)
|-.|+.+..+-+ .....|||||+
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCcccCceEeCCCCCC
Confidence 678999999988 88899999996
No 16
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=95.31 E-value=0.0083 Score=51.86 Aligned_cols=24 Identities=29% Similarity=0.595 Sum_probs=21.0
Q ss_pred CCCCCCCccccccccceeecCCCCce
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNI 207 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~ 207 (240)
--||||||-.-| ...-+||.||-+
T Consensus 135 ~vC~vCGy~~~g--e~P~~CPiCga~ 158 (166)
T COG1592 135 WVCPVCGYTHEG--EAPEVCPICGAP 158 (166)
T ss_pred EEcCCCCCcccC--CCCCcCCCCCCh
Confidence 359999999999 788899999964
No 17
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=95.11 E-value=0.013 Score=48.25 Aligned_cols=33 Identities=21% Similarity=0.521 Sum_probs=25.4
Q ss_pred CCCCCCCccccccc--------------------cceeecCCCCce-eeeeCCC
Q 026283 182 GACPACKREFIGSK--------------------SQIIRCAGCGNI-VWQPEGD 214 (240)
Q Consensus 182 g~CPvC~~eFtG~n--------------------nt~~~CpnCGe~-l~v~~g~ 214 (240)
..|+.||+.|.--. ....+||.||.. +.+..|+
T Consensus 71 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G~ 124 (135)
T PRK03824 71 LKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIVKGR 124 (135)
T ss_pred EECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEecCc
Confidence 36999999987652 455779999975 7887775
No 18
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=95.08 E-value=0.011 Score=47.36 Aligned_cols=33 Identities=18% Similarity=0.373 Sum_probs=26.3
Q ss_pred CCCCCCCccccccccceeecCCCCce-eeeeCCC
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNI-VWQPEGD 214 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~-l~v~~g~ 214 (240)
..|+.|++.|.--.+....||.||.. +.+..|+
T Consensus 71 ~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~~i~~G~ 104 (114)
T PRK03681 71 CWCETCQQYVTLLTQRVRRCPQCHGDMLRIVADD 104 (114)
T ss_pred EEcccCCCeeecCCccCCcCcCcCCCCcEEccCC
Confidence 46999999888777766889999964 6777664
No 19
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=94.65 E-value=0.026 Score=37.31 Aligned_cols=27 Identities=30% Similarity=0.987 Sum_probs=19.1
Q ss_pred CCCCCCccc------cccccceeecCCCCceee
Q 026283 183 ACPACKREF------IGSKSQIIRCAGCGNIVW 209 (240)
Q Consensus 183 ~CPvC~~eF------tG~nnt~~~CpnCGe~l~ 209 (240)
+||.|+..| .+-.+...+||+||++-.
T Consensus 4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred ECCCCCceEEcCHHHcccCCcEEECCCCCcEee
Confidence 588888776 345566788888887643
No 20
>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=94.51 E-value=0.011 Score=46.97 Aligned_cols=32 Identities=28% Similarity=0.588 Sum_probs=23.4
Q ss_pred CCCCCCCccccccccceeecCCCCce-eeeeCCC
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNI-VWQPEGD 214 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~-l~v~~g~ 214 (240)
..|+.|+++|.--... ..||+||.. +.+.+|+
T Consensus 71 ~~C~~Cg~~~~~~~~~-~~CP~Cgs~~~~i~~G~ 103 (113)
T PF01155_consen 71 ARCRDCGHEFEPDEFD-FSCPRCGSPDVEIISGR 103 (113)
T ss_dssp EEETTTS-EEECHHCC-HH-SSSSSS-EEEEESS
T ss_pred EECCCCCCEEecCCCC-CCCcCCcCCCcEEccCC
Confidence 4699999999765555 789999997 5777764
No 21
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=94.46 E-value=0.018 Score=50.35 Aligned_cols=31 Identities=29% Similarity=0.711 Sum_probs=22.7
Q ss_pred cCCCCCCCcccccc--------------------------ccceeecCCCCceeeee
Q 026283 181 KGACPACKREFIGS--------------------------KSQIIRCAGCGNIVWQP 211 (240)
Q Consensus 181 eg~CPvC~~eFtG~--------------------------nnt~~~CpnCGe~l~v~ 211 (240)
+-.||||+.+|+-- --.+..||+||-.-...
T Consensus 5 ~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 5 KITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred ceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 45799999999632 12467899999876544
No 22
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=94.44 E-value=0.037 Score=40.08 Aligned_cols=32 Identities=22% Similarity=0.509 Sum_probs=25.5
Q ss_pred cCCCCCCCcccc---ccccceeecCCCCceeeeeC
Q 026283 181 KGACPACKREFI---GSKSQIIRCAGCGNIVWQPE 212 (240)
Q Consensus 181 eg~CPvC~~eFt---G~nnt~~~CpnCGe~l~v~~ 212 (240)
...||+|+.++. ...+....||.||-.|.|-.
T Consensus 2 ~~~CP~CG~~iev~~~~~GeiV~Cp~CGaeleVv~ 36 (54)
T TIGR01206 2 QFECPDCGAEIELENPELGELVICDECGAELEVVS 36 (54)
T ss_pred ccCCCCCCCEEecCCCccCCEEeCCCCCCEEEEEe
Confidence 358999999874 23468899999999998854
No 23
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=94.25 E-value=0.041 Score=40.01 Aligned_cols=32 Identities=28% Similarity=0.576 Sum_probs=27.7
Q ss_pred CCCCCCCccc-----------------------------cccccceeecCCCCceeeeeCC
Q 026283 182 GACPACKREF-----------------------------IGSKSQIIRCAGCGNIVWQPEG 213 (240)
Q Consensus 182 g~CPvC~~eF-----------------------------tG~nnt~~~CpnCGe~l~v~~g 213 (240)
-.||+|+.++ +-.-.....||+||..--|.+|
T Consensus 8 L~Cp~ck~pL~~~~l~~~~~~~~~~lp~~~~~~~~~l~~~~i~eg~L~Cp~c~r~YPI~dG 68 (68)
T PF03966_consen 8 LACPVCKGPLDWEALVETAQLGLSELPKELPEDYHVLLEVEIVEGELICPECGREYPIRDG 68 (68)
T ss_dssp BB-TTTSSBEHHHHHHHHHHCCCCHCHHCHHCHCEHHCTEETTTTEEEETTTTEEEEEETT
T ss_pred hcCCCCCCcchHHHHHHHHHhCcccCCCCCccchhhhhcccccCCEEEcCCCCCEEeCCCC
Confidence 4799999999 6888899999999999988887
No 24
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=94.17 E-value=0.047 Score=37.84 Aligned_cols=32 Identities=25% Similarity=0.525 Sum_probs=27.8
Q ss_pred CCCCCCCccccccccceeecCCCCceeeeeCC
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNIVWQPEG 213 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~l~v~~g 213 (240)
-.|..||.+|.=-....++||+||--+-....
T Consensus 3 Y~C~~Cg~~~~~~~~~~irC~~CG~rIlyK~R 34 (44)
T smart00659 3 YICGECGRENEIKSKDVVRCRECGYRILYKKR 34 (44)
T ss_pred EECCCCCCEeecCCCCceECCCCCceEEEEeC
Confidence 46999999999888999999999998887654
No 25
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=94.15 E-value=0.034 Score=36.79 Aligned_cols=25 Identities=36% Similarity=1.140 Sum_probs=19.2
Q ss_pred CCCCCCccc------cccccceeecCCCCce
Q 026283 183 ACPACKREF------IGSKSQIIRCAGCGNI 207 (240)
Q Consensus 183 ~CPvC~~eF------tG~nnt~~~CpnCGe~ 207 (240)
.||.|+..| +.-+....+|++||+.
T Consensus 4 ~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKIPPKGRKVRCSKCGHV 34 (36)
T ss_pred ECCCCCCEEeCCHHHCCCCCcEEECCCCCCE
Confidence 588888877 4566678888888875
No 26
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=93.77 E-value=0.042 Score=37.82 Aligned_cols=28 Identities=29% Similarity=0.791 Sum_probs=25.0
Q ss_pred hhhcCCCCCCCccccccccceeecCCCC
Q 026283 178 FVIKGACPACKREFIGSKSQIIRCAGCG 205 (240)
Q Consensus 178 nLIeg~CPvC~~eFtG~nnt~~~CpnCG 205 (240)
.+....||.|+.+..-.++.+..||+|+
T Consensus 14 ~ML~~~Cp~C~~PL~~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 14 TMLDEHCPDCGTPLMRDKDGKIYCVSCG 41 (41)
T ss_pred hHhcCccCCCCCeeEEecCCCEECCCCC
Confidence 4567899999999999888899999996
No 27
>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=93.72 E-value=0.049 Score=38.89 Aligned_cols=27 Identities=22% Similarity=0.661 Sum_probs=24.0
Q ss_pred cCCCCCCCccccc-cccceeecCCCCce
Q 026283 181 KGACPACKREFIG-SKSQIIRCAGCGNI 207 (240)
Q Consensus 181 eg~CPvC~~eFtG-~nnt~~~CpnCGe~ 207 (240)
.-.||.||+.-.. .++....||+||..
T Consensus 28 Sq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 28 SQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred ccCccCcccccccccccceEEcCCCCCE
Confidence 4579999999888 89999999999976
No 28
>PF14353 CpXC: CpXC protein
Probab=93.69 E-value=0.041 Score=43.60 Aligned_cols=32 Identities=25% Similarity=0.547 Sum_probs=23.2
Q ss_pred cCCCCCCCccccc-----ccc--c-------------eeecCCCCceeeeeC
Q 026283 181 KGACPACKREFIG-----SKS--Q-------------IIRCAGCGNIVWQPE 212 (240)
Q Consensus 181 eg~CPvC~~eFtG-----~nn--t-------------~~~CpnCGe~l~v~~ 212 (240)
|-+||.|+.+|.- +|- + ..+||+||....++-
T Consensus 1 ~itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~ 52 (128)
T PF14353_consen 1 EITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEY 52 (128)
T ss_pred CcCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCC
Confidence 3589999999853 221 1 568999999887754
No 29
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=93.66 E-value=0.047 Score=58.81 Aligned_cols=54 Identities=28% Similarity=0.418 Sum_probs=35.4
Q ss_pred CCCCCCc-cc-------cccccceeecCCCCceeeeeCCCcccCCCCCCCCCCCCCCeeeeecc
Q 026283 183 ACPACKR-EF-------IGSKSQIIRCAGCGNIVWQPEGDFFSRNGGGKKSTKSDDDIIDVDFE 238 (240)
Q Consensus 183 ~CPvC~~-eF-------tG~nnt~~~CpnCGe~l~v~~g~F~s~~g~~~~~r~t~pgtIDVe~e 238 (240)
-||.|+| || .||.=..-.||+||+++.-..-+- .=+-+=+..|.+.|| ||++|.
T Consensus 685 ~c~~c~~~ef~~~~~~~sg~dlp~k~cp~c~~~~~~dg~~L-~FErFLn~er~~~PD-IDldF~ 746 (1213)
T TIGR01405 685 LCPNCKYSEFITDGSVGSGFDLPDKDCPKCGAPLKKDGQDI-PFETFLGFKGDKVPD-IDLNFS 746 (1213)
T ss_pred cCcccccccccccccccccccCccccCccccccccccCCCc-eeeeccCCCCCCCCC-CcccCc
Confidence 5999998 33 477777889999999876443110 001112456778887 688875
No 30
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=93.63 E-value=0.042 Score=46.66 Aligned_cols=22 Identities=27% Similarity=0.990 Sum_probs=19.7
Q ss_pred CCCCCCCccccccccceeecCCCCce
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNI 207 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~ 207 (240)
-.||.||+ +......||+||..
T Consensus 310 ~~C~~cg~----~~~r~~~C~~cg~~ 331 (364)
T COG0675 310 KTCPCCGH----LSGRLFKCPRCGFV 331 (364)
T ss_pred ccccccCC----ccceeEECCCCCCe
Confidence 56999999 77889999999985
No 31
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=93.55 E-value=0.04 Score=44.33 Aligned_cols=34 Identities=21% Similarity=0.420 Sum_probs=25.6
Q ss_pred cCCCCCCCccccccccceeecCCCCce-eeeeCCC
Q 026283 181 KGACPACKREFIGSKSQIIRCAGCGNI-VWQPEGD 214 (240)
Q Consensus 181 eg~CPvC~~eFtG~nnt~~~CpnCGe~-l~v~~g~ 214 (240)
...|+.|++.|.=-.+...+||.||.. +.+.+|+
T Consensus 71 ~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~~i~~G~ 105 (117)
T PRK00564 71 ELECKDCSHVFKPNALDYGVCEKCHSKNVIITQGN 105 (117)
T ss_pred EEEhhhCCCccccCCccCCcCcCCCCCceEEecCC
Confidence 346999998887665566679999974 6767764
No 32
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=93.49 E-value=0.039 Score=44.15 Aligned_cols=33 Identities=18% Similarity=0.363 Sum_probs=23.7
Q ss_pred cCCCCCCCccccccccceeecCCCCc-eeeeeCCC
Q 026283 181 KGACPACKREFIGSKSQIIRCAGCGN-IVWQPEGD 214 (240)
Q Consensus 181 eg~CPvC~~eFtG~nnt~~~CpnCGe-~l~v~~g~ 214 (240)
...|+.|+++|.--. ....||+||. .+.+.+|+
T Consensus 70 ~~~C~~Cg~~~~~~~-~~~~CP~Cgs~~~~i~~G~ 103 (113)
T PRK12380 70 QAWCWDCSQVVEIHQ-HDAQCPHCHGERLRVDTGD 103 (113)
T ss_pred EEEcccCCCEEecCC-cCccCcCCCCCCcEEccCC
Confidence 356999998876543 3445999996 46777774
No 33
>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=93.43 E-value=0.042 Score=46.15 Aligned_cols=32 Identities=19% Similarity=0.331 Sum_probs=23.4
Q ss_pred CCCCCCCcccccc--ccceeecCCCCceeeeeCC
Q 026283 182 GACPACKREFIGS--KSQIIRCAGCGNIVWQPEG 213 (240)
Q Consensus 182 g~CPvC~~eFtG~--nnt~~~CpnCGe~l~v~~g 213 (240)
=.||.|+.+|+=. -+-...||+||++|..-+.
T Consensus 110 Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~L~~~dn 143 (158)
T TIGR00373 110 FICPNMCVRFTFNEAMELNFTCPRCGAMLDYLDN 143 (158)
T ss_pred EECCCCCcEeeHHHHHHcCCcCCCCCCEeeeccC
Confidence 3599999887632 2246899999999976543
No 34
>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=93.36 E-value=0.046 Score=35.25 Aligned_cols=23 Identities=30% Similarity=0.785 Sum_probs=19.8
Q ss_pred CCCCCCccccccccceeecCCCCc
Q 026283 183 ACPACKREFIGSKSQIIRCAGCGN 206 (240)
Q Consensus 183 ~CPvC~~eFtG~nnt~~~CpnCGe 206 (240)
.|++|||.+.+-. ..-.||.||.
T Consensus 3 ~C~~CGy~y~~~~-~~~~CP~Cg~ 25 (33)
T cd00350 3 VCPVCGYIYDGEE-APWVCPVCGA 25 (33)
T ss_pred ECCCCCCEECCCc-CCCcCcCCCC
Confidence 5999999999865 5668999997
No 35
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=93.35 E-value=0.052 Score=44.55 Aligned_cols=26 Identities=38% Similarity=1.097 Sum_probs=21.9
Q ss_pred CCCCCccccccccceeecCCCCceeeeeCCCc
Q 026283 184 CPACKREFIGSKSQIIRCAGCGNIVWQPEGDF 215 (240)
Q Consensus 184 CPvC~~eFtG~nnt~~~CpnCGe~l~v~~g~F 215 (240)
||||+.++ .-|+..|++||..+ .|+|
T Consensus 1 CPvCg~~l---~vt~l~C~~C~t~i---~G~F 26 (113)
T PF09862_consen 1 CPVCGGEL---VVTRLKCPSCGTEI---EGEF 26 (113)
T ss_pred CCCCCCce---EEEEEEcCCCCCEE---Eeee
Confidence 99999875 47899999999876 4777
No 36
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=93.31 E-value=0.07 Score=39.76 Aligned_cols=28 Identities=21% Similarity=0.655 Sum_probs=24.4
Q ss_pred cCCCCCCCccccccc-cceeecCCCCcee
Q 026283 181 KGACPACKREFIGSK-SQIIRCAGCGNIV 208 (240)
Q Consensus 181 eg~CPvC~~eFtG~n-nt~~~CpnCGe~l 208 (240)
...|-.|+.+..+.. .+..-||||||.+
T Consensus 7 ~~~CtSCg~~i~~~~~~~~F~CPnCG~~~ 35 (59)
T PRK14890 7 PPKCTSCGIEIAPREKAVKFLCPNCGEVI 35 (59)
T ss_pred CccccCCCCcccCCCccCEeeCCCCCCee
Confidence 346999999999887 8999999999983
No 37
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=92.90 E-value=0.078 Score=40.47 Aligned_cols=35 Identities=29% Similarity=0.714 Sum_probs=29.0
Q ss_pred hcCCCCCCCcccccc--ccceeecCCCCceeeeeCCC
Q 026283 180 IKGACPACKREFIGS--KSQIIRCAGCGNIVWQPEGD 214 (240)
Q Consensus 180 Ieg~CPvC~~eFtG~--nnt~~~CpnCGe~l~v~~g~ 214 (240)
..-.||-|+++=+=| -++..+|++||..|-.|-|.
T Consensus 18 l~VkCpdC~N~q~vFshast~V~C~~CG~~l~~PTGG 54 (67)
T COG2051 18 LRVKCPDCGNEQVVFSHASTVVTCLICGTTLAEPTGG 54 (67)
T ss_pred EEEECCCCCCEEEEeccCceEEEecccccEEEecCCC
Confidence 345799999997755 46788999999999998874
No 38
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=92.81 E-value=0.055 Score=35.25 Aligned_cols=26 Identities=27% Similarity=0.823 Sum_probs=16.1
Q ss_pred CCCCCCCccccccccceeecCCCCce
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNI 207 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~ 207 (240)
.+||.|+.+++=..+.+..||.||.+
T Consensus 3 p~Cp~C~se~~y~D~~~~vCp~C~~e 28 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDGELLVCPECGHE 28 (30)
T ss_dssp ---TTT-----EE-SSSEEETTTTEE
T ss_pred CCCCCCCCcceeccCCEEeCCccccc
Confidence 58999999999999999999999975
No 39
>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=92.81 E-value=0.058 Score=33.91 Aligned_cols=23 Identities=30% Similarity=0.729 Sum_probs=17.6
Q ss_pred CCCCCCccccccccceeecCCCCcee
Q 026283 183 ACPACKREFIGSKSQIIRCAGCGNIV 208 (240)
Q Consensus 183 ~CPvC~~eFtG~nnt~~~CpnCGe~l 208 (240)
.||.|+.+- ..+...||+||-..
T Consensus 2 ~CP~C~~~V---~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEV---PESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCc---hhhcCcCCCCCCCC
Confidence 588888875 66777889998653
No 40
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=92.81 E-value=0.067 Score=40.18 Aligned_cols=28 Identities=29% Similarity=0.754 Sum_probs=24.5
Q ss_pred CCCCCCccc-cccccceeecCCCCceeee
Q 026283 183 ACPACKREF-IGSKSQIIRCAGCGNIVWQ 210 (240)
Q Consensus 183 ~CPvC~~eF-tG~nnt~~~CpnCGe~l~v 210 (240)
.|-.|+.+. .|-+.+..-||||||.+-.
T Consensus 11 ~CtSCg~~i~p~e~~v~F~CPnCGe~~I~ 39 (61)
T COG2888 11 VCTSCGREIAPGETAVKFPCPNCGEVEIY 39 (61)
T ss_pred eeccCCCEeccCCceeEeeCCCCCceeee
Confidence 688999999 8999999999999977644
No 41
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=92.70 E-value=0.083 Score=37.58 Aligned_cols=28 Identities=25% Similarity=0.676 Sum_probs=16.9
Q ss_pred cCCCCCCCccccccccceeecCCCCceee
Q 026283 181 KGACPACKREFIGSKSQIIRCAGCGNIVW 209 (240)
Q Consensus 181 eg~CPvC~~eFtG~nnt~~~CpnCGe~l~ 209 (240)
...|+.|+..| ++-+..-.|.+||+++=
T Consensus 9 ~~~C~~C~~~F-~~~~rrhhCr~CG~~vC 36 (69)
T PF01363_consen 9 ASNCMICGKKF-SLFRRRHHCRNCGRVVC 36 (69)
T ss_dssp -SB-TTT--B--BSSS-EEE-TTT--EEE
T ss_pred CCcCcCcCCcC-CCceeeEccCCCCCEEC
Confidence 46899999999 88899999999999874
No 42
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=92.63 E-value=0.049 Score=46.76 Aligned_cols=33 Identities=24% Similarity=0.549 Sum_probs=24.5
Q ss_pred hcCCCCCCCccccccc--cceeecCCCCceeeeeC
Q 026283 180 IKGACPACKREFIGSK--SQIIRCAGCGNIVWQPE 212 (240)
Q Consensus 180 Ieg~CPvC~~eFtG~n--nt~~~CpnCGe~l~v~~ 212 (240)
..=.||.|+.+|+=.. +-...||+||++|..-+
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~~~d 150 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAMEYGFRCPQCGEMLEEYD 150 (178)
T ss_pred CEEECCCCCcEEeHHHHhhcCCcCCCCCCCCeecc
Confidence 3446999999887432 23689999999997654
No 43
>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=92.49 E-value=0.077 Score=40.61 Aligned_cols=46 Identities=26% Similarity=0.600 Sum_probs=23.4
Q ss_pred cCCCCCCCccccccc------------cceeecCCCCceeeeeC--C--CcccCCCCC--CCCC
Q 026283 181 KGACPACKREFIGSK------------SQIIRCAGCGNIVWQPE--G--DFFSRNGGG--KKST 226 (240)
Q Consensus 181 eg~CPvC~~eFtG~n------------nt~~~CpnCGe~l~v~~--g--~F~s~~g~~--~~~r 226 (240)
|-.||.|+.+..=-+ ..+-.||.||++|.+=+ | +||=..|.| |++|
T Consensus 1 e~~CP~C~~~L~~~~~~~~C~~C~~~~~~~a~CPdC~~~Le~LkACGAvdYFC~~c~gLiSKkr 64 (70)
T PF07191_consen 1 ENTCPKCQQELEWQGGHYHCEACQKDYKKEAFCPDCGQPLEVLKACGAVDYFCNHCHGLISKKR 64 (70)
T ss_dssp --B-SSS-SBEEEETTEEEETTT--EEEEEEE-TTT-SB-EEEEETTEEEEE-TTTT-EE-TTT
T ss_pred CCcCCCCCCccEEeCCEEECccccccceecccCCCcccHHHHHHHhcccceeeccCCceeecce
Confidence 346888887754333 34567999999998765 3 566666666 5544
No 44
>PRK12495 hypothetical protein; Provisional
Probab=92.04 E-value=0.084 Score=48.03 Aligned_cols=28 Identities=18% Similarity=0.400 Sum_probs=24.9
Q ss_pred CCCCCCCccccccccceeecCCCCceeee
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNIVWQ 210 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~l~v 210 (240)
-.||+||.+..-+ ..+++||+|++++..
T Consensus 43 ~hC~~CG~PIpa~-pG~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 43 AHCDECGDPIFRH-DGQEFCPTCQQPVTE 70 (226)
T ss_pred hhcccccCcccCC-CCeeECCCCCCcccc
Confidence 4799999999987 778889999999885
No 45
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=91.89 E-value=0.11 Score=56.92 Aligned_cols=55 Identities=24% Similarity=0.338 Sum_probs=35.5
Q ss_pred CCCCCCCcccc--------ccccceeecCCCCceeeeeCCCcccCCCCCCCCCCCCCCeeeeecc
Q 026283 182 GACPACKREFI--------GSKSQIIRCAGCGNIVWQPEGDFFSRNGGGKKSTKSDDDIIDVDFE 238 (240)
Q Consensus 182 g~CPvC~~eFt--------G~nnt~~~CpnCGe~l~v~~g~F~s~~g~~~~~r~t~pgtIDVe~e 238 (240)
--||.|+|.=. |+.=-.--||+||+++. .+||=-.=+-+=+..|.+.|| ||++|.
T Consensus 909 y~C~~C~~~ef~~~~~~~sG~Dlpdk~Cp~Cg~~~~-kdg~~l~FErFL~~~r~~~PD-IDldF~ 971 (1437)
T PRK00448 909 YVCPNCKYSEFFTDGSVGSGFDLPDKDCPKCGTKLK-KDGHDIPFETFLGFKGDKVPD-IDLNFS 971 (1437)
T ss_pred ccCcccccccccccccccccccCccccCcccccccc-ccCCCceeeeccCCCCCCCCC-CcccCc
Confidence 35999998543 67777778999999865 444300001112446777777 688875
No 46
>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=91.72 E-value=0.1 Score=34.22 Aligned_cols=24 Identities=29% Similarity=0.696 Sum_probs=19.5
Q ss_pred CCCCCCccccccccceeecCCCCce
Q 026283 183 ACPACKREFIGSKSQIIRCAGCGNI 207 (240)
Q Consensus 183 ~CPvC~~eFtG~nnt~~~CpnCGe~ 207 (240)
.|++|||.+.|-. -.-.||.||.+
T Consensus 4 ~C~~CG~i~~g~~-~p~~CP~Cg~~ 27 (34)
T cd00729 4 VCPVCGYIHEGEE-APEKCPICGAP 27 (34)
T ss_pred ECCCCCCEeECCc-CCCcCcCCCCc
Confidence 6999999999854 44589999974
No 47
>PLN03120 nucleic acid binding protein; Provisional
Probab=91.34 E-value=0.23 Score=45.80 Aligned_cols=55 Identities=16% Similarity=0.309 Sum_probs=46.4
Q ss_pred hHHHHHHHHHhhhhhhhhhHhHHHHHHHHHHHHHHhhhhhhhhHhHHhhhhhhhh
Q 026283 63 LVFDAKKTAERIDRQYSVSRRLNSAARTAAVRARELDREFAISVRWRSFRMDFSR 117 (240)
Q Consensus 63 ~~fear~~a~r~D~~Y~vs~r~a~aa~~a~e~A~eiD~~fgi~rR~R~f~~D~~r 117 (240)
+.-.|......+|++|-+|.|++.-.-.++|++++||++|+|.-+..++..=..+
T Consensus 137 ~ss~a~a~v~~~d~k~gltek~~~g~~~v~~~~k~vDeky~vs~kt~sa~~~~~~ 191 (260)
T PLN03120 137 LTSTASAKVASLDKKIGLSEKLSAGTAVVNEKVKEVDQKYQVSEKTKSALAAAEQ 191 (260)
T ss_pred hHHHHHHHHHhhhhhcCcccccccchHHHHHHHHhhhhhhchhHHHHHHHHHHHH
Confidence 3445666778899999999999998889999999999999999999886655444
No 48
>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=91.27 E-value=0.12 Score=41.53 Aligned_cols=34 Identities=24% Similarity=0.586 Sum_probs=25.0
Q ss_pred hcCCCCCCCccccccccceeecCCCCce-eeeeCCC
Q 026283 180 IKGACPACKREFIGSKSQIIRCAGCGNI-VWQPEGD 214 (240)
Q Consensus 180 Ieg~CPvC~~eFtG~nnt~~~CpnCGe~-l~v~~g~ 214 (240)
+...|+.|+++|.--.. ...||+||.. +.+..|+
T Consensus 69 ~~~~C~~Cg~~~~~~~~-~~~CP~Cgs~~~~i~~G~ 103 (115)
T TIGR00100 69 VECECEDCSEEVSPEID-LYRCPKCHGIMLQVRAGK 103 (115)
T ss_pred cEEEcccCCCEEecCCc-CccCcCCcCCCcEEecCC
Confidence 35679999988765443 4679999974 6777775
No 49
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=91.15 E-value=0.12 Score=38.44 Aligned_cols=36 Identities=33% Similarity=0.759 Sum_probs=29.8
Q ss_pred hhcCCCCCCCcccccc--ccceeecCCCCceeeeeCCC
Q 026283 179 VIKGACPACKREFIGS--KSQIIRCAGCGNIVWQPEGD 214 (240)
Q Consensus 179 LIeg~CPvC~~eFtG~--nnt~~~CpnCGe~l~v~~g~ 214 (240)
.+.-.||.|+++=+=| -++...|+.||..|-.|-|.
T Consensus 9 F~~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~~PtGG 46 (59)
T PRK00415 9 FLKVKCPDCGNEQVVFSHASTVVRCLVCGKTLAEPTGG 46 (59)
T ss_pred EEEEECCCCCCeEEEEecCCcEEECcccCCCcccCCCc
Confidence 4556899999997655 57788999999999999874
No 50
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=91.08 E-value=0.11 Score=52.65 Aligned_cols=29 Identities=21% Similarity=0.304 Sum_probs=21.7
Q ss_pred hhhcCCCCCCCccccccccceeecCCCCceeee
Q 026283 178 FVIKGACPACKREFIGSKSQIIRCAGCGNIVWQ 210 (240)
Q Consensus 178 nLIeg~CPvC~~eFtG~nnt~~~CpnCGe~l~v 210 (240)
|---+.|++||| .+|. ...||.||+.+.+
T Consensus 623 n~~~~~C~~CG~-~~g~---~~~CP~CG~~~~v 651 (656)
T PRK08270 623 TPTFSICPKHGY-LSGE---HEFCPKCGEETEV 651 (656)
T ss_pred CCCCcccCCCCC-cCCC---CCCCcCCcCccce
Confidence 344588999998 4454 5899999988543
No 51
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=90.99 E-value=0.12 Score=45.82 Aligned_cols=30 Identities=30% Similarity=0.822 Sum_probs=26.5
Q ss_pred hhcCCCCCCCccccccccceeecCCCCceee
Q 026283 179 VIKGACPACKREFIGSKSQIIRCAGCGNIVW 209 (240)
Q Consensus 179 LIeg~CPvC~~eFtG~nnt~~~CpnCGe~l~ 209 (240)
+|...|+.|+.+..= .+.+..|||||+.-+
T Consensus 147 VI~A~CsrC~~~L~~-~~~~l~Cp~Cg~tEk 176 (188)
T COG1096 147 VIYARCSRCRAPLVK-KGNMLKCPNCGNTEK 176 (188)
T ss_pred EEEEEccCCCcceEE-cCcEEECCCCCCEEe
Confidence 567789999999998 999999999998754
No 52
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=90.84 E-value=0.32 Score=45.83 Aligned_cols=28 Identities=25% Similarity=0.566 Sum_probs=19.0
Q ss_pred CCCCCCCcc----ccc-----------cccce-----eecCCCCceee
Q 026283 182 GACPACKRE----FIG-----------SKSQI-----IRCAGCGNIVW 209 (240)
Q Consensus 182 g~CPvC~~e----FtG-----------~nnt~-----~~CpnCGe~l~ 209 (240)
-.||+||-. +++ ++.+. ..||+|||++.
T Consensus 240 ~~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 240 TECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE 287 (298)
T ss_pred ceeeccCCCCCCCeeeccccceeehhhhhhhhcchhhcccCccCCCCc
Confidence 479999853 333 33333 38999999886
No 53
>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=90.81 E-value=0.11 Score=35.51 Aligned_cols=26 Identities=27% Similarity=0.687 Sum_probs=20.7
Q ss_pred cCCCCCCCcccccccc----ceeecCCCCc
Q 026283 181 KGACPACKREFIGSKS----QIIRCAGCGN 206 (240)
Q Consensus 181 eg~CPvC~~eFtG~nn----t~~~CpnCGe 206 (240)
+-.|+.|+.+|..+.. ....||.||.
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 4579999999988753 3458999997
No 54
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=90.72 E-value=0.19 Score=33.08 Aligned_cols=29 Identities=28% Similarity=0.580 Sum_probs=22.1
Q ss_pred CCCCCCccccccccceeecCCCCceeeee
Q 026283 183 ACPACKREFIGSKSQIIRCAGCGNIVWQP 211 (240)
Q Consensus 183 ~CPvC~~eFtG~nnt~~~CpnCGe~l~v~ 211 (240)
.|.-|+.++.=-.+..++||+||--+...
T Consensus 2 ~C~~Cg~~~~~~~~~~irC~~CG~RIlyK 30 (32)
T PF03604_consen 2 ICGECGAEVELKPGDPIRCPECGHRILYK 30 (32)
T ss_dssp BESSSSSSE-BSTSSTSSBSSSS-SEEBE
T ss_pred CCCcCCCeeEcCCCCcEECCcCCCeEEEe
Confidence 48899999997777889999999766543
No 55
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=90.35 E-value=0.17 Score=43.16 Aligned_cols=26 Identities=27% Similarity=0.613 Sum_probs=17.7
Q ss_pred CCCCCCCcccc----------ccccc-eeecCCCCce
Q 026283 182 GACPACKREFI----------GSKSQ-IIRCAGCGNI 207 (240)
Q Consensus 182 g~CPvC~~eFt----------G~nnt-~~~CpnCGe~ 207 (240)
+.||-||.++| |.-.. --|||+||--
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~ 37 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKR 37 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeeeeeccccCCc
Confidence 47999998883 32221 2689999853
No 56
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=90.30 E-value=0.23 Score=35.21 Aligned_cols=28 Identities=25% Similarity=0.736 Sum_probs=23.7
Q ss_pred CCCCCCccccccccceeecCCCCceeee
Q 026283 183 ACPACKREFIGSKSQIIRCAGCGNIVWQ 210 (240)
Q Consensus 183 ~CPvC~~eFtG~nnt~~~CpnCGe~l~v 210 (240)
-||.|+.+|-........|+.||-...+
T Consensus 22 fCP~Cg~~~m~~~~~r~~C~~Cgyt~~~ 49 (50)
T PRK00432 22 FCPRCGSGFMAEHLDRWHCGKCGYTEFK 49 (50)
T ss_pred cCcCCCcchheccCCcEECCCcCCEEec
Confidence 7999998888888889999999976543
No 57
>PRK12496 hypothetical protein; Provisional
Probab=90.29 E-value=0.14 Score=43.36 Aligned_cols=31 Identities=23% Similarity=0.412 Sum_probs=22.4
Q ss_pred CCCCCCCccccccccceeecCCCCceeeeeCC
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNIVWQPEG 213 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~l~v~~g 213 (240)
-.|+.|+.+|-.-. ..-.||.||.+|.-..-
T Consensus 128 ~~C~gC~~~~~~~~-~~~~C~~CG~~~~r~~~ 158 (164)
T PRK12496 128 KVCKGCKKKYPEDY-PDDVCEICGSPVKRKMV 158 (164)
T ss_pred EECCCCCccccCCC-CCCcCCCCCChhhhcch
Confidence 45999999995422 22479999999865543
No 58
>PF12773 DZR: Double zinc ribbon
Probab=90.18 E-value=0.13 Score=34.69 Aligned_cols=26 Identities=23% Similarity=0.570 Sum_probs=15.6
Q ss_pred CCCCCCCccccccccceeecCCCCce
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNI 207 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~ 207 (240)
.-||.||..+.........||+||+.
T Consensus 13 ~fC~~CG~~l~~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 13 KFCPHCGTPLPPPDQSKKICPNCGAE 38 (50)
T ss_pred cCChhhcCChhhccCCCCCCcCCcCC
Confidence 34666666666444445566666665
No 59
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=90.06 E-value=0.15 Score=51.58 Aligned_cols=24 Identities=33% Similarity=0.758 Sum_probs=20.4
Q ss_pred cCCCCCCCccccccccceeecCCCCce
Q 026283 181 KGACPACKREFIGSKSQIIRCAGCGNI 207 (240)
Q Consensus 181 eg~CPvC~~eFtG~nnt~~~CpnCGe~ 207 (240)
-+.|+.||+++.|. .-.||.||+.
T Consensus 568 ~~~C~~CG~~~~g~---~~~CP~CGs~ 591 (625)
T PRK08579 568 ITVCNKCGRSTTGL---YTRCPRCGSE 591 (625)
T ss_pred CccCCCCCCccCCC---CCcCcCCCCc
Confidence 57899999988777 5799999963
No 60
>PF12773 DZR: Double zinc ribbon
Probab=89.70 E-value=0.15 Score=34.41 Aligned_cols=23 Identities=26% Similarity=0.678 Sum_probs=20.7
Q ss_pred CCCCCccccccccceeecCCCCceee
Q 026283 184 CPACKREFIGSKSQIIRCAGCGNIVW 209 (240)
Q Consensus 184 CPvC~~eFtG~nnt~~~CpnCGe~l~ 209 (240)
||.|+++ +......||+||..|.
T Consensus 1 Cp~Cg~~---~~~~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 1 CPHCGTP---NPDDAKFCPHCGTPLP 23 (50)
T ss_pred CCCcCCc---CCccccCChhhcCChh
Confidence 8999998 6677899999999998
No 61
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=89.32 E-value=0.18 Score=40.91 Aligned_cols=33 Identities=24% Similarity=0.526 Sum_probs=22.3
Q ss_pred cCCCCCCCccccccccc------eeecCCCC-ceeeeeCCC
Q 026283 181 KGACPACKREFIGSKSQ------IIRCAGCG-NIVWQPEGD 214 (240)
Q Consensus 181 eg~CPvC~~eFtG~nnt------~~~CpnCG-e~l~v~~g~ 214 (240)
...| .|+++|.--... ...||.|| ..+.+..|+
T Consensus 70 ~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G~ 109 (124)
T PRK00762 70 EIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHILGGR 109 (124)
T ss_pred eEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEecCC
Confidence 3469 999987643211 25799999 567777765
No 62
>PHA02942 putative transposase; Provisional
Probab=88.56 E-value=0.33 Score=46.02 Aligned_cols=28 Identities=21% Similarity=0.675 Sum_probs=22.6
Q ss_pred cCCCCCCCccccccccceeecCCCCcee
Q 026283 181 KGACPACKREFIGSKSQIIRCAGCGNIV 208 (240)
Q Consensus 181 eg~CPvC~~eFtG~nnt~~~CpnCGe~l 208 (240)
.-.||+||+.-.-+.+....||+||-..
T Consensus 325 Sq~Cs~CG~~~~~l~~r~f~C~~CG~~~ 352 (383)
T PHA02942 325 SVSCPKCGHKMVEIAHRYFHCPSCGYEN 352 (383)
T ss_pred CccCCCCCCccCcCCCCEEECCCCCCEe
Confidence 3569999987666667889999999754
No 63
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=87.84 E-value=0.31 Score=40.22 Aligned_cols=28 Identities=21% Similarity=0.498 Sum_probs=25.0
Q ss_pred CCCCCCCccccccccceeecCCCCceee
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNIVW 209 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~l~ 209 (240)
-.||.|+.|||=-.+....||-||..-.
T Consensus 3 p~CP~C~seytY~dg~~~iCpeC~~EW~ 30 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGTQLICPSCLYEWN 30 (109)
T ss_pred CcCCcCCCcceEecCCeeECcccccccc
Confidence 4799999999999999999999997643
No 64
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=87.74 E-value=0.63 Score=42.57 Aligned_cols=28 Identities=29% Similarity=0.663 Sum_probs=21.8
Q ss_pred CCCCCCCcccc--ccccceeecCCCCceee
Q 026283 182 GACPACKREFI--GSKSQIIRCAGCGNIVW 209 (240)
Q Consensus 182 g~CPvC~~eFt--G~nnt~~~CpnCGe~l~ 209 (240)
..||.||..=+ =+.+....|.+||-+|.
T Consensus 12 ~~Cp~Cg~~~iv~d~~~Ge~vC~~CG~Vl~ 41 (310)
T PRK00423 12 LVCPECGSDKLIYDYERGEIVCADCGLVIE 41 (310)
T ss_pred CcCcCCCCCCeeEECCCCeEeecccCCccc
Confidence 46999997322 45678999999999885
No 65
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=87.67 E-value=0.37 Score=30.64 Aligned_cols=25 Identities=24% Similarity=0.519 Sum_probs=11.7
Q ss_pred CCCCCCcccccccc-ceeecCCCCce
Q 026283 183 ACPACKREFIGSKS-QIIRCAGCGNI 207 (240)
Q Consensus 183 ~CPvC~~eFtG~nn-t~~~CpnCGe~ 207 (240)
-||.||.+-.=... ..-+||+||..
T Consensus 5 fC~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 5 FCGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp B-TTT--BEEE-SSSS-EEESSSS-E
T ss_pred ccCcCCccccCCCCcCEeECCCCcCE
Confidence 37777766554443 56677777754
No 66
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the 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=87.33 E-value=1.8 Score=41.47 Aligned_cols=28 Identities=21% Similarity=0.612 Sum_probs=21.9
Q ss_pred CCCCCCccccccccceeecCCCCceeeeeC
Q 026283 183 ACPACKREFIGSKSQIIRCAGCGNIVWQPE 212 (240)
Q Consensus 183 ~CPvC~~eFtG~nnt~~~CpnCGe~l~v~~ 212 (240)
.||.|+.... .+++.+||.||..|.-.+
T Consensus 217 ~C~~Cd~~~~--~~~~a~CpRC~~~L~~~~ 244 (403)
T TIGR00155 217 SCSACHTTIL--PAQEPVCPRCSTPLYVRR 244 (403)
T ss_pred cCCCCCCccC--CCCCcCCcCCCCcccCCC
Confidence 4999998553 477889999999995443
No 68
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=87.09 E-value=0.3 Score=41.04 Aligned_cols=32 Identities=19% Similarity=0.242 Sum_probs=28.0
Q ss_pred CCCCCCCccccccccceeecCCCCceeeeeCCCc
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNIVWQPEGDF 215 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~l~v~~g~F 215 (240)
-.||.||+.|--+|...+.||-||+.. |..-|
T Consensus 10 ridPetg~KFYDLNrdPiVsPytG~s~--P~s~f 41 (129)
T COG4530 10 RIDPETGKKFYDLNRDPIVSPYTGKSY--PRSYF 41 (129)
T ss_pred ccCccccchhhccCCCccccCcccccc--hHHHH
Confidence 469999999999999999999999976 65555
No 69
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=86.80 E-value=0.18 Score=35.15 Aligned_cols=14 Identities=43% Similarity=0.937 Sum_probs=7.2
Q ss_pred hcCCCCCCCccccc
Q 026283 180 IKGACPACKREFIG 193 (240)
Q Consensus 180 Ieg~CPvC~~eFtG 193 (240)
.++.||||+++|+.
T Consensus 19 ~~~~CPlC~r~l~~ 32 (54)
T PF04423_consen 19 AKGCCPLCGRPLDE 32 (54)
T ss_dssp -SEE-TTT--EE-H
T ss_pred CCCcCCCCCCCCCH
Confidence 44589999999864
No 70
>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=86.78 E-value=0.48 Score=34.70 Aligned_cols=35 Identities=26% Similarity=0.671 Sum_probs=23.9
Q ss_pred hcCCCCCCCcccccc--ccceeecCCCCceeeeeCCC
Q 026283 180 IKGACPACKREFIGS--KSQIIRCAGCGNIVWQPEGD 214 (240)
Q Consensus 180 Ieg~CPvC~~eFtG~--nnt~~~CpnCGe~l~v~~g~ 214 (240)
+.-.||.|+++=+=| -++...|.+||.+|-+|-|.
T Consensus 6 m~VkCp~C~~~q~vFSha~t~V~C~~Cg~~L~~PtGG 42 (55)
T PF01667_consen 6 MDVKCPGCYNIQTVFSHAQTVVKCVVCGTVLAQPTGG 42 (55)
T ss_dssp EEEE-TTT-SEEEEETT-SS-EE-SSSTSEEEEE-SS
T ss_pred EEEECCCCCCeeEEEecCCeEEEcccCCCEecCCCCc
Confidence 456899999987655 46778999999999999874
No 71
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=86.34 E-value=2.9 Score=36.79 Aligned_cols=32 Identities=19% Similarity=0.146 Sum_probs=19.0
Q ss_pred cchhHHHHhhhchhHHHHHHHHhhHHHHHhHH
Q 026283 34 SDFDRFARRMTSGEAWRDAWRTANNGFEQLVF 65 (240)
Q Consensus 34 ~d~d~~a~~~~~~~a~r~a~r~an~~~e~~~f 65 (240)
..||.|...+.+..-...---++.|-.+++..
T Consensus 105 ~~~~~~l~~l~~~g~v~~~~~~~~DvT~~y~D 136 (262)
T PF14257_consen 105 DKFDSFLDELSELGKVTSRNISSEDVTEQYVD 136 (262)
T ss_pred HHHHHHHHHHhccCceeeeeccccchHHHHHH
Confidence 56777877776443444444556666666543
No 72
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=86.00 E-value=0.45 Score=33.35 Aligned_cols=30 Identities=33% Similarity=0.805 Sum_probs=22.4
Q ss_pred hhcCCCCCCCccccc-------cccceeecCCCCcee
Q 026283 179 VIKGACPACKREFIG-------SKSQIIRCAGCGNIV 208 (240)
Q Consensus 179 LIeg~CPvC~~eFtG-------~nnt~~~CpnCGe~l 208 (240)
+..+.|-.|..+..- -.+....|||||-+|
T Consensus 20 v~~~~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 20 VEGGTCSGCHMELPPQELNEIRKGDEIVFCPNCGRIL 56 (56)
T ss_pred eeCCccCCCCEEcCHHHHHHHHcCCCeEECcCCCccC
Confidence 567889999876542 225789999999775
No 73
>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=86.00 E-value=0.4 Score=32.33 Aligned_cols=28 Identities=29% Similarity=0.647 Sum_probs=20.8
Q ss_pred cCCCCCCCccccccc----cceeecCCCCc-ee
Q 026283 181 KGACPACKREFIGSK----SQIIRCAGCGN-IV 208 (240)
Q Consensus 181 eg~CPvC~~eFtG~n----nt~~~CpnCGe-~l 208 (240)
+=.|+.||.+|.=+- .....||.||. .+
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~ 37 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISEDDPVPCPECGSTEV 37 (42)
T ss_pred EEEeCCCCCEEEEEEEcCCCCCCcCCCCCCCce
Confidence 457999998875432 36789999998 44
No 74
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=85.92 E-value=0.4 Score=43.08 Aligned_cols=29 Identities=31% Similarity=0.847 Sum_probs=22.2
Q ss_pred hcCCCCCCCcccc-------ccccceeecCCCCcee
Q 026283 180 IKGACPACKREFI-------GSKSQIIRCAGCGNIV 208 (240)
Q Consensus 180 Ieg~CPvC~~eFt-------G~nnt~~~CpnCGe~l 208 (240)
|...||.|+.|=+ +-++--.+|++||..-
T Consensus 5 iy~~Cp~Cg~eev~hEVik~~g~~~lvrC~eCG~V~ 40 (201)
T COG1326 5 IYIECPSCGSEEVSHEVIKERGREPLVRCEECGTVH 40 (201)
T ss_pred EEEECCCCCcchhhHHHHHhcCCceEEEccCCCcEe
Confidence 5678999996665 3444688999999764
No 75
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=85.82 E-value=0.5 Score=31.42 Aligned_cols=32 Identities=34% Similarity=0.895 Sum_probs=22.0
Q ss_pred CCCCCCcccccccc---ceeecCCCCceeeeeCCCc
Q 026283 183 ACPACKREFIGSKS---QIIRCAGCGNIVWQPEGDF 215 (240)
Q Consensus 183 ~CPvC~~eFtG~nn---t~~~CpnCGe~l~v~~g~F 215 (240)
+||.|+.+..-.+- ..-+||+||-+ |...|.|
T Consensus 1 ~CP~C~~~l~~~~~~~~~id~C~~C~G~-W~d~~el 35 (41)
T PF13453_consen 1 KCPRCGTELEPVRLGDVEIDVCPSCGGI-WFDAGEL 35 (41)
T ss_pred CcCCCCcccceEEECCEEEEECCCCCeE-EccHHHH
Confidence 69999987665443 44579999864 5555544
No 76
>PRK10220 hypothetical protein; Provisional
Probab=85.24 E-value=0.59 Score=38.73 Aligned_cols=28 Identities=21% Similarity=0.570 Sum_probs=24.9
Q ss_pred CCCCCCCccccccccceeecCCCCceee
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNIVW 209 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~l~ 209 (240)
-.||.|+.+||=-.+....||-||..-.
T Consensus 4 P~CP~C~seytY~d~~~~vCpeC~hEW~ 31 (111)
T PRK10220 4 PHCPKCNSEYTYEDNGMYICPECAHEWN 31 (111)
T ss_pred CcCCCCCCcceEcCCCeEECCcccCcCC
Confidence 4799999999999999999999997643
No 77
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=84.43 E-value=0.69 Score=36.76 Aligned_cols=35 Identities=26% Similarity=0.680 Sum_probs=28.9
Q ss_pred hcCCCCCCCcccccc--ccceeecCCCCceeeeeCCC
Q 026283 180 IKGACPACKREFIGS--KSQIIRCAGCGNIVWQPEGD 214 (240)
Q Consensus 180 Ieg~CPvC~~eFtG~--nnt~~~CpnCGe~l~v~~g~ 214 (240)
+.-.||.|+++=+=| -+++..|.+||.+|-+|-|.
T Consensus 34 m~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~PTGG 70 (85)
T PTZ00083 34 MDVKCPGCSQITTVFSHAQTVVLCGGCSSQLCQPTGG 70 (85)
T ss_pred EEEECCCCCCeeEEEecCceEEEccccCCEeeccCCC
Confidence 455799999997755 46788999999999999874
No 78
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=84.41 E-value=0.59 Score=39.12 Aligned_cols=28 Identities=36% Similarity=1.026 Sum_probs=22.8
Q ss_pred CCCCCCCccccccccceeecCCCCceeeeeCCCc
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNIVWQPEGDF 215 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~l~v~~g~F 215 (240)
..||||+.+.+ -|...|+||+.-| .|.|
T Consensus 7 ~~cPvcg~~~i---VTeL~c~~~etTV---rg~F 34 (122)
T COG3877 7 NRCPVCGRKLI---VTELKCSNCETTV---RGNF 34 (122)
T ss_pred CCCCcccccce---eEEEecCCCCceE---ecce
Confidence 47999999865 6889999999765 4667
No 79
>PLN00209 ribosomal protein S27; Provisional
Probab=84.35 E-value=0.67 Score=36.87 Aligned_cols=35 Identities=20% Similarity=0.541 Sum_probs=29.0
Q ss_pred hcCCCCCCCcccccc--ccceeecCCCCceeeeeCCC
Q 026283 180 IKGACPACKREFIGS--KSQIIRCAGCGNIVWQPEGD 214 (240)
Q Consensus 180 Ieg~CPvC~~eFtG~--nnt~~~CpnCGe~l~v~~g~ 214 (240)
+.-.||.|+++=+=| -+++..|.+||.+|-+|-|.
T Consensus 35 m~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~PTGG 71 (86)
T PLN00209 35 MDVKCQGCFNITTVFSHSQTVVVCGSCQTVLCQPTGG 71 (86)
T ss_pred EEEECCCCCCeeEEEecCceEEEccccCCEeeccCCC
Confidence 456899999997655 46788999999999999874
No 80
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=84.11 E-value=0.5 Score=34.65 Aligned_cols=25 Identities=28% Similarity=0.634 Sum_probs=19.6
Q ss_pred CCCCCCccccccccceeecCCCCceeeeeC
Q 026283 183 ACPACKREFIGSKSQIIRCAGCGNIVWQPE 212 (240)
Q Consensus 183 ~CPvC~~eFtG~nnt~~~CpnCGe~l~v~~ 212 (240)
.||.|+--.. ..+||.||++.....
T Consensus 7 ~C~~CgvYTL-----k~~CP~CG~~t~~~~ 31 (56)
T PRK13130 7 KCPKCGVYTL-----KEICPVCGGKTKNPH 31 (56)
T ss_pred ECCCCCCEEc-----cccCcCCCCCCCCCC
Confidence 5999986444 678999999977665
No 81
>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....
Probab=84.09 E-value=0.52 Score=44.48 Aligned_cols=29 Identities=24% Similarity=0.607 Sum_probs=19.1
Q ss_pred hhhhcCCCCCCCccccccccceeecCCCCceee
Q 026283 177 NFVIKGACPACKREFIGSKSQIIRCAGCGNIVW 209 (240)
Q Consensus 177 RnLIeg~CPvC~~eFtG~nnt~~~CpnCGe~l~ 209 (240)
..-|+|.||.|+++-.. .-+|.+||.++.
T Consensus 132 e~~v~g~CP~C~~~~a~----g~~Ce~cG~~~~ 160 (391)
T PF09334_consen 132 ESFVEGTCPYCGSDKAR----GDQCENCGRPLE 160 (391)
T ss_dssp GGGETCEETTT--SSCT----TTEETTTSSBEE
T ss_pred cceeeccccCcCccccC----CCcccCCCCCcc
Confidence 34488999999965332 247888888776
No 82
>PRK11827 hypothetical protein; Provisional
Probab=83.81 E-value=0.82 Score=33.97 Aligned_cols=32 Identities=22% Similarity=0.318 Sum_probs=25.8
Q ss_pred CCCCCCCcccccc-ccceeecCCCCceeeeeCC
Q 026283 182 GACPACKREFIGS-KSQIIRCAGCGNIVWQPEG 213 (240)
Q Consensus 182 g~CPvC~~eFtG~-nnt~~~CpnCGe~l~v~~g 213 (240)
-.||+|+-++.=- ..+...|..||-.--|.+|
T Consensus 9 LaCP~ckg~L~~~~~~~~Lic~~~~laYPI~dg 41 (60)
T PRK11827 9 IACPVCNGKLWYNQEKQELICKLDNLAFPLRDG 41 (60)
T ss_pred eECCCCCCcCeEcCCCCeEECCccCeeccccCC
Confidence 4799999988732 3567999999988888776
No 83
>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=83.79 E-value=0.6 Score=40.10 Aligned_cols=21 Identities=33% Similarity=0.838 Sum_probs=14.4
Q ss_pred CCCCCccccccccc---------------eeecCCCCc
Q 026283 184 CPACKREFIGSKSQ---------------IIRCAGCGN 206 (240)
Q Consensus 184 CPvC~~eFtG~nnt---------------~~~CpnCGe 206 (240)
||||+.+ +++.. -..|++||-
T Consensus 1 CP~Cg~~--~~~~~~~~~~IP~F~evii~sf~C~~CGy 36 (163)
T TIGR00340 1 CPVCGSR--TLKAVTYDYDIPYFGKIMLSTYICEKCGY 36 (163)
T ss_pred CCCCCCc--ceEeeeEeccCCCcceEEEEEEECCCCCC
Confidence 8999876 33331 457999984
No 84
>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=83.42 E-value=0.8 Score=36.63 Aligned_cols=30 Identities=33% Similarity=0.750 Sum_probs=23.9
Q ss_pred cCCCCCCCccccccccc---eeecCCCCceeee
Q 026283 181 KGACPACKREFIGSKSQ---IIRCAGCGNIVWQ 210 (240)
Q Consensus 181 eg~CPvC~~eFtG~nnt---~~~CpnCGe~l~v 210 (240)
.-.|+.|+.++..-+.. ...|+.||.+|.+
T Consensus 123 ~~~C~~C~~~~~r~~~~~~~~~~C~~C~~~l~~ 155 (157)
T PF10263_consen 123 VYRCPSCGREYKRHRRSKRKRYRCGRCGGPLVQ 155 (157)
T ss_pred EEEcCCCCCEeeeecccchhhEECCCCCCEEEE
Confidence 44699999998877774 5579999998875
No 85
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=82.96 E-value=0.55 Score=46.46 Aligned_cols=45 Identities=24% Similarity=0.256 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHHhhhhh--------cCCCCCCCccccccccceeecCCCCce-eeee
Q 026283 163 LPIAAPLLIGTVANNFVI--------KGACPACKREFIGSKSQIIRCAGCGNI-VWQP 211 (240)
Q Consensus 163 lPvaap~li~wWlkRnLI--------eg~CPvC~~eFtG~nnt~~~CpnCGe~-l~v~ 211 (240)
-|=++--++....++.-| -+.|+.|||.-.+ .-.||.||+. +.+=
T Consensus 465 n~~al~~lv~~~~~~~~i~Y~~in~~~~~C~~CG~~~~~----~~~CP~CGs~~~~~~ 518 (546)
T PF13597_consen 465 NPEALEKLVRYAMENTGIPYFTINPPIDICPDCGYIGGE----GDKCPKCGSENIEVY 518 (546)
T ss_dssp -HHHHHHHHHHHHH--H-SEEEEE--EEEETTT---S------EEE-CCC----EEEE
T ss_pred CHHHHHHHHHHHHHhCCCCeEEEecCcccccCCCcCCCC----CCCCCCCCCcccceE
Confidence 344444445555553322 3789999986544 7789999998 5543
No 86
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=82.81 E-value=0.92 Score=33.25 Aligned_cols=30 Identities=27% Similarity=0.656 Sum_probs=23.8
Q ss_pred hhhcCCCCCCCccccccccceeecCCCCcee
Q 026283 178 FVIKGACPACKREFIGSKSQIIRCAGCGNIV 208 (240)
Q Consensus 178 nLIeg~CPvC~~eFtG~nnt~~~CpnCGe~l 208 (240)
|-....||+|+..|+ -.....+||-||.+.
T Consensus 2 ~~~~~~C~~Cg~~~~-~~dDiVvCp~Cgapy 31 (54)
T PF14446_consen 2 NYEGCKCPVCGKKFK-DGDDIVVCPECGAPY 31 (54)
T ss_pred CccCccChhhCCccc-CCCCEEECCCCCCcc
Confidence 345678999999996 235788999999875
No 87
>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=82.78 E-value=0.77 Score=29.80 Aligned_cols=11 Identities=27% Similarity=0.791 Sum_probs=8.6
Q ss_pred eecCCCCceee
Q 026283 199 IRCAGCGNIVW 209 (240)
Q Consensus 199 ~~CpnCGe~l~ 209 (240)
..|++|||.+.
T Consensus 33 ~~C~~CGE~~~ 43 (46)
T TIGR03831 33 LVCPQCGEEYL 43 (46)
T ss_pred cccccCCCEee
Confidence 36999999865
No 88
>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=82.74 E-value=0.8 Score=37.62 Aligned_cols=35 Identities=31% Similarity=0.881 Sum_probs=26.3
Q ss_pred hcCCCCCCCccccccccc----------------eeecCCCCceeeeeCCCc
Q 026283 180 IKGACPACKREFIGSKSQ----------------IIRCAGCGNIVWQPEGDF 215 (240)
Q Consensus 180 Ieg~CPvC~~eFtG~nnt----------------~~~CpnCGe~l~v~~g~F 215 (240)
+...||.|+.++.-.... -.+||+||.+-|. +.|+
T Consensus 90 ~~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~-GsH~ 140 (147)
T PF01927_consen 90 IFSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWE-GSHW 140 (147)
T ss_pred CCCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecc-cccH
Confidence 346899999988766444 5699999999984 4443
No 89
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=82.57 E-value=0.48 Score=48.40 Aligned_cols=39 Identities=26% Similarity=0.612 Sum_probs=30.5
Q ss_pred hhcCCCCCCCccccccccceeecCC--CCceeeeeCCCcccC
Q 026283 179 VIKGACPACKREFIGSKSQIIRCAG--CGNIVWQPEGDFFSR 218 (240)
Q Consensus 179 LIeg~CPvC~~eFtG~nnt~~~Cpn--CGe~l~v~~g~F~s~ 218 (240)
.+-..||+|+.+.+- ++...+|+| |-..+...=-||.|+
T Consensus 396 ~~P~~CP~C~s~l~~-~~~~~~C~n~~C~aq~~~~i~hf~sr 436 (669)
T PRK14350 396 KIPDNCPSCKTALIK-EGAHLFCVNNHCPSVIVERIKYFCSK 436 (669)
T ss_pred CCCCCCCCCCCEeee-CCEEEEECCCCCHHHHHhhhheeccC
Confidence 356799999999875 567899986 988887766788554
No 90
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=82.09 E-value=0.75 Score=46.74 Aligned_cols=24 Identities=25% Similarity=0.431 Sum_probs=19.1
Q ss_pred hcCCCCCCCccccccccceeecCCCCc
Q 026283 180 IKGACPACKREFIGSKSQIIRCAGCGN 206 (240)
Q Consensus 180 Ieg~CPvC~~eFtG~nnt~~~CpnCGe 206 (240)
--+.||+|||..+| ..-.||.||+
T Consensus 565 ~~~iC~~CG~~~~g---~~~~CP~CGs 588 (623)
T PRK08271 565 KITICNDCHHIDKR---TGKRCPICGS 588 (623)
T ss_pred CCccCCCCCCcCCC---CCcCCcCCCC
Confidence 34789999997555 3589999995
No 91
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=82.01 E-value=0.63 Score=45.92 Aligned_cols=35 Identities=23% Similarity=0.648 Sum_probs=27.7
Q ss_pred hhcCCCCCCCccccccc------c--ceeecCCCCceeeeeCC
Q 026283 179 VIKGACPACKREFIGSK------S--QIIRCAGCGNIVWQPEG 213 (240)
Q Consensus 179 LIeg~CPvC~~eFtG~n------n--t~~~CpnCGe~l~v~~g 213 (240)
.-.--||+|+..|+.|. + ....|-+||..|.....
T Consensus 126 ~~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelveDe~ 168 (436)
T KOG2593|consen 126 VAGYVCPNCQKKYTSLEALQLLDNETGEFHCENCGGELVEDEN 168 (436)
T ss_pred cccccCCccccchhhhHHHHhhcccCceEEEecCCCchhcccc
Confidence 33447999999999873 3 67899999999976654
No 92
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=82.00 E-value=0.7 Score=46.80 Aligned_cols=26 Identities=27% Similarity=0.477 Sum_probs=19.0
Q ss_pred hhhcCCCCCCCccccccccceeecCCCCce
Q 026283 178 FVIKGACPACKREFIGSKSQIIRCAGCGNI 207 (240)
Q Consensus 178 nLIeg~CPvC~~eFtG~nnt~~~CpnCGe~ 207 (240)
|---+.|+.||| .|-- ...||.||+.
T Consensus 556 n~~~~~C~~CGy--~g~~--~~~CP~CG~~ 581 (618)
T PRK14704 556 NHPVDRCKCCSY--HGVI--GNECPSCGNE 581 (618)
T ss_pred CCCCeecCCCCC--CCCc--CccCcCCCCC
Confidence 445578999998 4432 3789999964
No 93
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=81.92 E-value=0.75 Score=50.54 Aligned_cols=9 Identities=44% Similarity=1.198 Sum_probs=6.3
Q ss_pred CCCCCCCcc
Q 026283 182 GACPACKRE 190 (240)
Q Consensus 182 g~CPvC~~e 190 (240)
-.||.||.+
T Consensus 668 rkCPkCG~~ 676 (1337)
T PRK14714 668 RRCPSCGTE 676 (1337)
T ss_pred EECCCCCCc
Confidence 468887775
No 94
>PRK08402 replication factor A; Reviewed
Probab=81.67 E-value=0.71 Score=43.87 Aligned_cols=30 Identities=23% Similarity=0.624 Sum_probs=23.8
Q ss_pred hhhhcCCCCCCCcccc-ccccceeecCCCCc
Q 026283 177 NFVIKGACPACKREFI-GSKSQIIRCAGCGN 206 (240)
Q Consensus 177 RnLIeg~CPvC~~eFt-G~nnt~~~CpnCGe 206 (240)
.+.+.-+||.|++.++ --.+..-+|++||+
T Consensus 208 ~~~~y~aCp~CnKkv~~~~~~~~~~Ce~~~~ 238 (355)
T PRK08402 208 RVLVYDACPECRRKVDYDPATDTWICPEHGE 238 (355)
T ss_pred cCeeEecCCCCCeEEEEecCCCCEeCCCCCC
Confidence 3667889999999987 44445679999995
No 95
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=81.53 E-value=2 Score=40.50 Aligned_cols=10 Identities=30% Similarity=0.893 Sum_probs=8.6
Q ss_pred cCCCCCCCcc
Q 026283 181 KGACPACKRE 190 (240)
Q Consensus 181 eg~CPvC~~e 190 (240)
.+.|||||..
T Consensus 187 ~~~CPvCGs~ 196 (309)
T PRK03564 187 RQFCPVCGSM 196 (309)
T ss_pred CCCCCCCCCc
Confidence 4899999987
No 96
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=81.21 E-value=0.83 Score=46.88 Aligned_cols=25 Identities=28% Similarity=0.594 Sum_probs=17.4
Q ss_pred hcCCCCCCCcccccccc---ceeecCCCCc
Q 026283 180 IKGACPACKREFIGSKS---QIIRCAGCGN 206 (240)
Q Consensus 180 Ieg~CPvC~~eFtG~nn---t~~~CpnCGe 206 (240)
--+.|++||| .|--+ ..-.||+||+
T Consensus 640 ~~~~C~~CG~--~Ge~~~~~~~~~CP~CG~ 667 (711)
T PRK09263 640 PIDECYECGF--TGEFECTEKGFTCPKCGN 667 (711)
T ss_pred CCcccCCCCC--CccccCCCCCCcCcCCCC
Confidence 3488999998 34331 1268999996
No 97
>PRK07591 threonine synthase; Validated
Probab=81.13 E-value=1.1 Score=42.59 Aligned_cols=30 Identities=17% Similarity=0.208 Sum_probs=24.3
Q ss_pred cCCCCCCCccccccccceeecCCCCceeeeeC
Q 026283 181 KGACPACKREFIGSKSQIIRCAGCGNIVWQPE 212 (240)
Q Consensus 181 eg~CPvC~~eFtG~nnt~~~CpnCGe~l~v~~ 212 (240)
.-.|+.|+.+|-- ... .+||.||.+|.+.-
T Consensus 18 ~l~C~~Cg~~~~~-~~~-~~C~~cg~~l~~~y 47 (421)
T PRK07591 18 ALKCRECGAEYPL-GPI-HVCEECFGPLEVAY 47 (421)
T ss_pred EEEeCCCCCcCCC-CCC-ccCCCCCCeEEEEe
Confidence 4689999999863 333 88999999999884
No 98
>PRK06450 threonine synthase; Validated
Probab=81.03 E-value=0.92 Score=41.98 Aligned_cols=30 Identities=30% Similarity=0.506 Sum_probs=23.6
Q ss_pred hcCCCCCCCccccccccceeecCCCCceeeee
Q 026283 180 IKGACPACKREFIGSKSQIIRCAGCGNIVWQP 211 (240)
Q Consensus 180 Ieg~CPvC~~eFtG~nnt~~~CpnCGe~l~v~ 211 (240)
|+-.|+.|++++.- ....+||.||.+|.+.
T Consensus 2 ~~~~C~~Cg~~~~~--~~~~~C~~cg~~l~~~ 31 (338)
T PRK06450 2 VKEVCMKCGKERES--IYEIRCKKCGGPFEIL 31 (338)
T ss_pred ceeEECCcCCcCCC--cccccCCcCCCEeEEe
Confidence 44589999999843 3357899999988876
No 99
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=80.80 E-value=0.85 Score=36.56 Aligned_cols=32 Identities=16% Similarity=0.249 Sum_probs=22.5
Q ss_pred CCCCCCccccccccceeecCCCCceeeeeCCC
Q 026283 183 ACPACKREFIGSKSQIIRCAGCGNIVWQPEGD 214 (240)
Q Consensus 183 ~CPvC~~eFtG~nnt~~~CpnCGe~l~v~~g~ 214 (240)
+|-.|++=-+.=.-....|||||..|..++++
T Consensus 5 AC~~C~~I~~~~qf~~~gCpnC~~~l~~~g~~ 36 (98)
T cd07973 5 ACLLCSLIKTEDQFERDGCPNCEGYLDMKGNH 36 (98)
T ss_pred hhccCCcccccccccCCCCCCCcchhccCCCc
Confidence 79999876543222236899999888777765
No 100
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=80.62 E-value=0.87 Score=30.08 Aligned_cols=18 Identities=28% Similarity=0.713 Sum_probs=16.2
Q ss_pred eeecCCCCceeeeeCCCc
Q 026283 198 IIRCAGCGNIVWQPEGDF 215 (240)
Q Consensus 198 ~~~CpnCGe~l~v~~g~F 215 (240)
.++||||+....+++.+.
T Consensus 2 ~i~CP~C~~~f~v~~~~l 19 (37)
T PF13719_consen 2 IITCPNCQTRFRVPDDKL 19 (37)
T ss_pred EEECCCCCceEEcCHHHc
Confidence 479999999999999876
No 101
>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=80.61 E-value=1 Score=30.01 Aligned_cols=27 Identities=26% Similarity=0.706 Sum_probs=21.5
Q ss_pred CCCCCCCccccccccceeecCCCCcee
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNIV 208 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~l 208 (240)
..||+|+..+.=.+.-...|-.||.+.
T Consensus 9 ~~C~~C~~~~~~~~dG~~yC~~cG~~~ 35 (36)
T PF11781_consen 9 EPCPVCGSRWFYSDDGFYYCDRCGHQS 35 (36)
T ss_pred CcCCCCCCeEeEccCCEEEhhhCceEc
Confidence 348899888877788888888888754
No 102
>PRK07218 replication factor A; Provisional
Probab=80.34 E-value=0.84 Score=44.42 Aligned_cols=24 Identities=29% Similarity=0.643 Sum_probs=19.2
Q ss_pred hhcCCCCCCCccccccccceeecCCCCce
Q 026283 179 VIKGACPACKREFIGSKSQIIRCAGCGNI 207 (240)
Q Consensus 179 LIeg~CPvC~~eFtG~nnt~~~CpnCGe~ 207 (240)
.+-..||.|++-. +.-+||.||++
T Consensus 295 gli~rCP~C~r~v-----~~~~C~~hG~v 318 (423)
T PRK07218 295 GLIERCPECGRVI-----QKGQCRSHGAV 318 (423)
T ss_pred cceecCcCccccc-----cCCcCCCCCCc
Confidence 3445899999988 44799999986
No 103
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=80.20 E-value=0.96 Score=37.56 Aligned_cols=26 Identities=23% Similarity=0.689 Sum_probs=23.9
Q ss_pred CCCCCCCccccccccceeecCCCCce
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNI 207 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~ 207 (240)
-.||-|+.|+|==.+.+..||.|+.+
T Consensus 4 p~cp~c~sEytYed~~~~~cpec~~e 29 (112)
T COG2824 4 PPCPKCNSEYTYEDGGQLICPECAHE 29 (112)
T ss_pred CCCCccCCceEEecCceEeCchhccc
Confidence 36999999999999999999999976
No 104
>PRK04023 DNA polymerase II large subunit; Validated
Probab=80.01 E-value=0.9 Score=49.10 Aligned_cols=20 Identities=40% Similarity=0.938 Sum_probs=16.8
Q ss_pred CCCCCCccccccccceeecCCCCce
Q 026283 183 ACPACKREFIGSKSQIIRCAGCGNI 207 (240)
Q Consensus 183 ~CPvC~~eFtG~nnt~~~CpnCGe~ 207 (240)
.||.||.+. ...+||+||+.
T Consensus 628 fCpsCG~~t-----~~frCP~CG~~ 647 (1121)
T PRK04023 628 KCPSCGKET-----FYRRCPFCGTH 647 (1121)
T ss_pred cCCCCCCcC-----CcccCCCCCCC
Confidence 799999984 56789999986
No 105
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=79.78 E-value=1.3 Score=29.49 Aligned_cols=24 Identities=33% Similarity=0.915 Sum_probs=9.0
Q ss_pred CCCCCccc-----cccccceeecCCCCce
Q 026283 184 CPACKREF-----IGSKSQIIRCAGCGNI 207 (240)
Q Consensus 184 CPvC~~eF-----tG~nnt~~~CpnCGe~ 207 (240)
||.||.+. .|=+..-..||+||.+
T Consensus 3 C~~CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 3 CPQCGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp -TTT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred cccccChhhhhcCCCCCccceECCCCCCE
Confidence 55555543 2334444555666544
No 106
>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=79.66 E-value=0.9 Score=30.31 Aligned_cols=30 Identities=27% Similarity=0.520 Sum_probs=21.7
Q ss_pred CCCCCCccccccccc---eeecCCCCceeeeeC
Q 026283 183 ACPACKREFIGSKSQ---IIRCAGCGNIVWQPE 212 (240)
Q Consensus 183 ~CPvC~~eFtG~nnt---~~~CpnCGe~l~v~~ 212 (240)
.||.||.-|-=..+. .-.|.+||+.|.|..
T Consensus 3 ~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L~qR~ 35 (36)
T PF05191_consen 3 ICPKCGRIYHIEFNPPKVEGVCDNCGGELVQRK 35 (36)
T ss_dssp EETTTTEEEETTTB--SSTTBCTTTTEBEBEEG
T ss_pred CcCCCCCccccccCCCCCCCccCCCCCeeEeCC
Confidence 489999877654443 567999999887753
No 107
>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=79.37 E-value=1.1 Score=45.45 Aligned_cols=25 Identities=24% Similarity=0.650 Sum_probs=17.8
Q ss_pred hhcCCCCCCCccccccccceeecCCCCc
Q 026283 179 VIKGACPACKREFIGSKSQIIRCAGCGN 206 (240)
Q Consensus 179 LIeg~CPvC~~eFtG~nnt~~~CpnCGe 206 (240)
.--+.||+||| .+|- ..-.||.||+
T Consensus 530 ~~~siC~~CGy-~~g~--~~~~CP~CGs 554 (586)
T TIGR02827 530 IKITICNDCHH-IDKR--TLHRCPVCGS 554 (586)
T ss_pred CCCeecCCCCC-cCCC--cCCcCcCCCC
Confidence 34478999998 3331 2379999994
No 108
>PRK06386 replication factor A; Reviewed
Probab=79.09 E-value=0.99 Score=43.18 Aligned_cols=23 Identities=17% Similarity=0.354 Sum_probs=18.6
Q ss_pred hhcCCCCCCCccccccccceeecCCCCc
Q 026283 179 VIKGACPACKREFIGSKSQIIRCAGCGN 206 (240)
Q Consensus 179 LIeg~CPvC~~eFtG~nnt~~~CpnCGe 206 (240)
.+-..||.|++-.. + -+||.||+
T Consensus 234 gli~rCP~C~R~l~--~---g~C~~HG~ 256 (358)
T PRK06386 234 RIFTKCSVCNKIIE--D---GVCKDHPD 256 (358)
T ss_pred EeEecCcCCCeEcc--C---CcCCCCCC
Confidence 44568999999988 2 39999998
No 109
>PRK06260 threonine synthase; Validated
Probab=78.95 E-value=1.4 Score=41.17 Aligned_cols=29 Identities=24% Similarity=0.577 Sum_probs=23.1
Q ss_pred CCCCCCCccccccccceeecCCCCceeeee
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNIVWQP 211 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~l~v~ 211 (240)
-.|+.|+.++- .+.....||.||.+|.+.
T Consensus 4 ~~C~~cg~~~~-~~~~~~~Cp~cg~~l~~~ 32 (397)
T PRK06260 4 LKCIECGKEYD-PDEIIYTCPECGGLLEVI 32 (397)
T ss_pred EEECCCCCCCC-CCCccccCCCCCCeEEEE
Confidence 47999999985 344457899999998876
No 110
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=78.85 E-value=1.1 Score=46.14 Aligned_cols=22 Identities=27% Similarity=0.582 Sum_probs=16.5
Q ss_pred cCCCCCCCccccccccceeecCCCCc
Q 026283 181 KGACPACKREFIGSKSQIIRCAGCGN 206 (240)
Q Consensus 181 eg~CPvC~~eFtG~nnt~~~CpnCGe 206 (240)
-+.||+|||.. |+ .-.||.||+
T Consensus 680 ~~~C~~CG~~~-~~---~~~CP~CG~ 701 (735)
T PRK07111 680 VDRCPVCGYLG-VI---EDKCPKCGS 701 (735)
T ss_pred CeecCCCCCCC-Cc---CccCcCCCC
Confidence 37899999632 33 379999995
No 111
>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=78.80 E-value=1.1 Score=36.71 Aligned_cols=33 Identities=24% Similarity=0.528 Sum_probs=26.9
Q ss_pred hhhcCCCCCCCccccccccceeecCCCCceeee
Q 026283 178 FVIKGACPACKREFIGSKSQIIRCAGCGNIVWQ 210 (240)
Q Consensus 178 nLIeg~CPvC~~eFtG~nnt~~~CpnCGe~l~v 210 (240)
++...+||.|+...+-.......|++|++.+..
T Consensus 31 ~~~Y~aC~~C~kkv~~~~~~~~~C~~C~~~~~~ 63 (166)
T cd04476 31 NWWYPACPGCNKKVVEEGNGTYRCEKCNKSVPN 63 (166)
T ss_pred CeEEccccccCcccEeCCCCcEECCCCCCcCCC
Confidence 567789999999988665588999999998533
No 112
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=78.07 E-value=2 Score=32.60 Aligned_cols=27 Identities=30% Similarity=0.866 Sum_probs=22.1
Q ss_pred CCCCCccccccccceeecCCCCceeeeeCC
Q 026283 184 CPACKREFIGSKSQIIRCAGCGNIVWQPEG 213 (240)
Q Consensus 184 CPvC~~eFtG~nnt~~~CpnCGe~l~v~~g 213 (240)
||||+..--..++..+.| .|| |.++-+
T Consensus 2 CPVC~~~~L~~~~~~i~C-~Cg--l~l~~~ 28 (82)
T PF14768_consen 2 CPVCQKGNLRENSNVISC-SCG--LRLNTQ 28 (82)
T ss_pred CCccCCCcccccCCeEEC-CCc--cEEecC
Confidence 999999999999999999 566 555443
No 113
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=77.93 E-value=0.9 Score=39.73 Aligned_cols=36 Identities=28% Similarity=0.721 Sum_probs=26.6
Q ss_pred hhcCCCCCCCccccccccce----------------eecCCCCceeeeeCCCc
Q 026283 179 VIKGACPACKREFIGSKSQI----------------IRCAGCGNIVWQPEGDF 215 (240)
Q Consensus 179 LIeg~CPvC~~eFtG~nnt~----------------~~CpnCGe~l~v~~g~F 215 (240)
.....||.|+-+..=..-.. .+||+||.+-|. ++|+
T Consensus 95 ~e~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~-GsHw 146 (165)
T COG1656 95 PEFSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYWK-GSHW 146 (165)
T ss_pred cccccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccccC-chHH
Confidence 44689999999887655444 349999999884 4454
No 114
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=77.92 E-value=1.9 Score=31.97 Aligned_cols=32 Identities=22% Similarity=0.361 Sum_probs=24.9
Q ss_pred CCCCCCc-------cccccccceeecCCCCceeeeeCCC
Q 026283 183 ACPACKR-------EFIGSKSQIIRCAGCGNIVWQPEGD 214 (240)
Q Consensus 183 ~CPvC~~-------eFtG~nnt~~~CpnCGe~l~v~~g~ 214 (240)
-||+||+ +=|-++|=...||.|-..--+.-.+
T Consensus 6 ~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~EtlI~v~~ 44 (55)
T PF14205_consen 6 LCPICGNKTRLKIREDTVLKNFPLYCPKCKQETLIDVKQ 44 (55)
T ss_pred ECCCCCCccceeeecCceeccccccCCCCCceEEEEeec
Confidence 4999994 5688999999999998765554333
No 115
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=77.92 E-value=1.1 Score=33.56 Aligned_cols=22 Identities=32% Similarity=0.551 Sum_probs=16.8
Q ss_pred CCCCCCCccccccccceeecCCCCcee
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNIV 208 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~l 208 (240)
.+|..|++=-. ..+|||||..-
T Consensus 4 kAC~~C~~i~~-----~~~CP~Cgs~~ 25 (61)
T PRK08351 4 KACRHCHYITT-----EDRCPVCGSRD 25 (61)
T ss_pred hhhhhCCcccC-----CCcCCCCcCCc
Confidence 48999998663 33799999854
No 116
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=77.74 E-value=1.5 Score=29.84 Aligned_cols=28 Identities=25% Similarity=0.668 Sum_probs=23.0
Q ss_pred CCCCCCCccccccccceeecCCCCceeee
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNIVWQ 210 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~l~v 210 (240)
..|+.|+.+|.- ....-.|.+||+++=-
T Consensus 3 ~~C~~C~~~F~~-~~rk~~Cr~Cg~~~C~ 30 (57)
T cd00065 3 SSCMGCGKPFTL-TRRRHHCRNCGRIFCS 30 (57)
T ss_pred CcCcccCccccC-CccccccCcCcCCcCh
Confidence 579999999876 5577899999998643
No 117
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=77.53 E-value=2.5 Score=28.39 Aligned_cols=31 Identities=26% Similarity=0.497 Sum_probs=20.9
Q ss_pred CCCCCCcccccc--c-cceeecCCCCceeeeeCC
Q 026283 183 ACPACKREFIGS--K-SQIIRCAGCGNIVWQPEG 213 (240)
Q Consensus 183 ~CPvC~~eFtG~--n-nt~~~CpnCGe~l~v~~g 213 (240)
-||.||.-..-- + +....||.||-...+...
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEEPIEQK 35 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCeEECCCc
Confidence 499999866432 2 247889999977655443
No 118
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=77.45 E-value=1.5 Score=36.33 Aligned_cols=51 Identities=25% Similarity=0.385 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHHhhhhhcC------------CCCCCCccccccccceeecCCCC-ceeeeeCCC
Q 026283 163 LPIAAPLLIGTVANNFVIKG------------ACPACKREFIGSKSQIIRCAGCG-NIVWQPEGD 214 (240)
Q Consensus 163 lPvaap~li~wWlkRnLIeg------------~CPvC~~eFtG~nnt~~~CpnCG-e~l~v~~g~ 214 (240)
=|-+.=|.|-...+..+.+| .|.-|+.++.--..... ||.|| -.+.+-+|+
T Consensus 40 ~~~~l~FaFev~~egT~aega~l~Ie~~p~~~~C~~C~~~~~~e~~~~~-CP~C~s~~~~i~~G~ 103 (115)
T COG0375 40 EPEALRFAFEVVAEGTIAEGAELHIEEEPAECWCLDCGQEVELEELDYR-CPKCGSINLRIIGGD 103 (115)
T ss_pred CHHHHHHHHHHHhccCcccCCEEEEEEeccEEEeccCCCeecchhheeE-CCCCCCCceEEecCC
Confidence 34444555656666666555 59999888887766666 99999 777777775
No 119
>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=77.11 E-value=1.3 Score=38.09 Aligned_cols=32 Identities=22% Similarity=0.737 Sum_probs=22.9
Q ss_pred hhhcCCCCCCCccccc-------cccceeecCCCCceee
Q 026283 178 FVIKGACPACKREFIG-------SKSQIIRCAGCGNIVW 209 (240)
Q Consensus 178 nLIeg~CPvC~~eFtG-------~nnt~~~CpnCGe~l~ 209 (240)
++-+..|..|++++.- .....-.||+||.+|.
T Consensus 106 ~~~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~lr 144 (218)
T cd01407 106 SLFRVRCTKCGKEYPRDELQADIDREEVPRCPKCGGLLR 144 (218)
T ss_pred CcCcceeCCCcCCCcHHHHhHhhccCCCCcCCCCCCccC
Confidence 4445689999988752 2345678999998764
No 120
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=76.52 E-value=1.6 Score=32.19 Aligned_cols=26 Identities=27% Similarity=0.749 Sum_probs=20.1
Q ss_pred CCCCCCccccccccceeecCCCCceeee
Q 026283 183 ACPACKREFIGSKSQIIRCAGCGNIVWQ 210 (240)
Q Consensus 183 ~CPvC~~eFtG~nnt~~~CpnCGe~l~v 210 (240)
-||+|+... =......||.||=+.--
T Consensus 1 ~Cpv~~~~~--~~~v~~~Cp~cGipthc 26 (55)
T PF13824_consen 1 LCPVCKKDL--PAHVNFECPDCGIPTHC 26 (55)
T ss_pred CCCCCcccc--ccccCCcCCCCCCcCcc
Confidence 399999875 45677899999977543
No 121
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=76.11 E-value=1.3 Score=35.99 Aligned_cols=36 Identities=33% Similarity=0.664 Sum_probs=27.6
Q ss_pred hhcCCCCCCCccccccc-cceeecCCCCceeeeeCCCc
Q 026283 179 VIKGACPACKREFIGSK-SQIIRCAGCGNIVWQPEGDF 215 (240)
Q Consensus 179 LIeg~CPvC~~eFtG~n-nt~~~CpnCGe~l~v~~g~F 215 (240)
++-..|-.|||+|--.+ |-..+||-|--. |++.-.|
T Consensus 56 v~Pa~CkkCGfef~~~~ik~pSRCP~CKSE-~Ie~prF 92 (97)
T COG3357 56 VRPARCKKCGFEFRDDKIKKPSRCPKCKSE-WIEEPRF 92 (97)
T ss_pred ecChhhcccCccccccccCCcccCCcchhh-cccCCce
Confidence 45568999999999843 347899999654 7777666
No 122
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=76.03 E-value=1.5 Score=44.86 Aligned_cols=9 Identities=44% Similarity=1.080 Sum_probs=4.6
Q ss_pred ecCCCCcee
Q 026283 200 RCAGCGNIV 208 (240)
Q Consensus 200 ~CpnCGe~l 208 (240)
.||+||..+
T Consensus 29 ~Cp~CG~~~ 37 (645)
T PRK14559 29 PCPQCGTEV 37 (645)
T ss_pred cCCCCCCCC
Confidence 455555553
No 123
>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=76.03 E-value=1.5 Score=43.68 Aligned_cols=41 Identities=22% Similarity=0.356 Sum_probs=25.5
Q ss_pred HHHHHHHHHHHHhh-------hhhcCCCCCCCccccccccceeecCCCCce
Q 026283 164 PIAAPLLIGTVANN-------FVIKGACPACKREFIGSKSQIIRCAGCGNI 207 (240)
Q Consensus 164 Pvaap~li~wWlkR-------nLIeg~CPvC~~eFtG~nnt~~~CpnCGe~ 207 (240)
|=+..=++....+. |---+.|+.||| +|-.. .-.||.||+.
T Consensus 500 ~eal~~lv~~a~~~~i~Y~~~n~~~~~C~~CG~--~g~~~-~~~CP~Cgs~ 547 (579)
T TIGR02487 500 PEALKDITKKAMKNGIGYFGINPPVDVCEDCGY--TGEGL-NDKCPKCGSH 547 (579)
T ss_pred HHHHHHHHHHHHhcCCceEEeccCCccCCCCCC--CCCCC-CCcCcCCCCc
Confidence 33434445555555 334578999997 55442 2679999963
No 124
>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=75.52 E-value=1.4 Score=35.49 Aligned_cols=35 Identities=26% Similarity=0.558 Sum_probs=25.1
Q ss_pred hhhcCCCC--CCCccccccccceeecCCCCceeeeeC
Q 026283 178 FVIKGACP--ACKREFIGSKSQIIRCAGCGNIVWQPE 212 (240)
Q Consensus 178 nLIeg~CP--vC~~eFtG~nnt~~~CpnCGe~l~v~~ 212 (240)
++...+|| .|+.-.+--.+..-+|++|++.+..+.
T Consensus 15 ~~~Y~aC~~~~C~kKv~~~~~~~y~C~~C~~~~~~~~ 51 (146)
T PF08646_consen 15 NWYYPACPNEKCNKKVTENGDGSYRCEKCNKTVENPK 51 (146)
T ss_dssp TTEEEE-TSTTTS-B-EEETTTEEEETTTTEEESS-E
T ss_pred CcEECCCCCccCCCEeecCCCcEEECCCCCCcCCCee
Confidence 66778999 999988777667889999999874443
No 125
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=75.29 E-value=2 Score=39.75 Aligned_cols=32 Identities=25% Similarity=0.534 Sum_probs=24.3
Q ss_pred cCCCCCCCcc--ccccccceeecCCCCceeeeeC
Q 026283 181 KGACPACKRE--FIGSKSQIIRCAGCGNIVWQPE 212 (240)
Q Consensus 181 eg~CPvC~~e--FtG~nnt~~~CpnCGe~l~v~~ 212 (240)
++.||.|+-. -.=+.+....|-+||.++...-
T Consensus 1 ~~~CpeCg~~~~~~d~~~ge~VC~~CG~Vi~~~~ 34 (285)
T COG1405 1 VMSCPECGSTNIITDYERGEIVCADCGLVLEDSL 34 (285)
T ss_pred CCCCCCCCCccceeeccCCeEEeccCCEEecccc
Confidence 4689999987 1224468999999999987643
No 126
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=75.12 E-value=1.8 Score=41.73 Aligned_cols=27 Identities=15% Similarity=0.431 Sum_probs=20.7
Q ss_pred CCCCCCccccccccceeecCCCCceeeeeC
Q 026283 183 ACPACKREFIGSKSQIIRCAGCGNIVWQPE 212 (240)
Q Consensus 183 ~CPvC~~eFtG~nnt~~~CpnCGe~l~v~~ 212 (240)
.||.|+.-.. +++..||.||..|.-..
T Consensus 223 ~C~~Cd~l~~---~~~a~CpRC~~~L~~~~ 249 (419)
T PRK15103 223 SCSCCTAILP---ADQPVCPRCHTKGYVRR 249 (419)
T ss_pred cCCCCCCCCC---CCCCCCCCCCCcCcCCC
Confidence 4999999653 45668999999995433
No 127
>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=74.98 E-value=2 Score=33.01 Aligned_cols=27 Identities=26% Similarity=0.623 Sum_probs=21.2
Q ss_pred CCCCCCccccccccceeecCCCCceeee
Q 026283 183 ACPACKREFIGSKSQIIRCAGCGNIVWQ 210 (240)
Q Consensus 183 ~CPvC~~eFtG~nnt~~~CpnCGe~l~v 210 (240)
-||.||.-+. ..+....|++||.....
T Consensus 2 fC~~Cg~~l~-~~~~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 2 FCPKCGSLMT-PKNGVYVCPSCGYEKEK 28 (104)
T ss_pred CCcccCcccc-cCCCeEECcCCCCcccc
Confidence 5999999996 34567999999976544
No 128
>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=74.80 E-value=2.1 Score=30.54 Aligned_cols=25 Identities=20% Similarity=0.444 Sum_probs=17.7
Q ss_pred CCCCCCccccccccc----------------eeecCCCCce
Q 026283 183 ACPACKREFIGSKSQ----------------IIRCAGCGNI 207 (240)
Q Consensus 183 ~CPvC~~eFtG~nnt----------------~~~CpnCGe~ 207 (240)
.|++|+|.+..-.+. .-.||-||..
T Consensus 3 ~C~~CgyiYd~~~Gd~~~~i~pGt~f~~Lp~~w~CP~C~a~ 43 (50)
T cd00730 3 ECRICGYIYDPAEGDPDEGIPPGTPFEDLPDDWVCPVCGAG 43 (50)
T ss_pred CCCCCCeEECCCCCCcccCcCCCCCHhHCCCCCCCCCCCCc
Confidence 699999998854321 2389999853
No 129
>PF15616 TerY-C: TerY-C metal binding domain
Probab=74.72 E-value=3.2 Score=35.01 Aligned_cols=32 Identities=25% Similarity=0.571 Sum_probs=23.6
Q ss_pred CCCCCCCccc----------ccccc-ceeecCCCCceeeeeCC
Q 026283 182 GACPACKREF----------IGSKS-QIIRCAGCGNIVWQPEG 213 (240)
Q Consensus 182 g~CPvC~~eF----------tG~nn-t~~~CpnCGe~l~v~~g 213 (240)
..||-|+.++ ..++. ....||.||+.+....+
T Consensus 78 PgCP~CGn~~~fa~C~CGkl~Ci~g~~~~~CPwCg~~g~~~~~ 120 (131)
T PF15616_consen 78 PGCPHCGNQYAFAVCGCGKLFCIDGEGEVTCPWCGNEGSFGAG 120 (131)
T ss_pred CCCCCCcChhcEEEecCCCEEEeCCCCCEECCCCCCeeeeccc
Confidence 6799999982 33333 35789999998887765
No 130
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=74.52 E-value=1.3 Score=37.50 Aligned_cols=31 Identities=32% Similarity=0.674 Sum_probs=26.7
Q ss_pred hcCCCCCCC--ccccccccceeecCCCCceeee
Q 026283 180 IKGACPACK--REFIGSKSQIIRCAGCGNIVWQ 210 (240)
Q Consensus 180 Ieg~CPvC~--~eFtG~nnt~~~CpnCGe~l~v 210 (240)
..+.||.|+ +=|-||=...-.|..||+..--
T Consensus 20 l~grCP~CGeGrLF~gFLK~~p~C~aCG~dyg~ 52 (126)
T COG5349 20 LRGRCPRCGEGRLFRGFLKVVPACEACGLDYGF 52 (126)
T ss_pred hcCCCCCCCCchhhhhhcccCchhhhccccccC
Confidence 468999997 5699999999999999998743
No 131
>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=73.71 E-value=2.1 Score=39.85 Aligned_cols=34 Identities=15% Similarity=0.357 Sum_probs=14.5
Q ss_pred CCCCCCCcc-ccccccc----eeecCCCCceeeee--CCCc
Q 026283 182 GACPACKRE-FIGSKSQ----IIRCAGCGNIVWQP--EGDF 215 (240)
Q Consensus 182 g~CPvC~~e-FtG~nnt----~~~CpnCGe~l~v~--~g~F 215 (240)
..||.||.+ ..-+.|- ...||+|+|.-... +|.+
T Consensus 32 ~yCP~Cg~~~L~~f~NN~PVaDF~C~~C~eeyELKSk~~~l 72 (254)
T PF06044_consen 32 MYCPNCGSKPLSKFENNRPVADFYCPNCNEEYELKSKKKKL 72 (254)
T ss_dssp ---TTT--SS-EE--------EEE-TTT--EEEEEEEESS-
T ss_pred CcCCCCCChhHhhccCCCccceeECCCCchHHhhhhhcccc
Confidence 689999998 6666553 46899999975544 4554
No 132
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=73.65 E-value=2.2 Score=29.77 Aligned_cols=24 Identities=25% Similarity=0.746 Sum_probs=19.0
Q ss_pred CCCCCCcccccccc---------ceeecCCCCc
Q 026283 183 ACPACKREFIGSKS---------QIIRCAGCGN 206 (240)
Q Consensus 183 ~CPvC~~eFtG~nn---------t~~~CpnCGe 206 (240)
-||-||..-+.... ..+.|.+||-
T Consensus 5 PCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 5 PCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 49999988777665 4567999998
No 133
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=73.46 E-value=1.4 Score=45.46 Aligned_cols=38 Identities=29% Similarity=0.620 Sum_probs=30.5
Q ss_pred cCCCCCCCccccc-cccceeecCC---CCceeeeeCCCcccC
Q 026283 181 KGACPACKREFIG-SKSQIIRCAG---CGNIVWQPEGDFFSR 218 (240)
Q Consensus 181 eg~CPvC~~eFtG-~nnt~~~Cpn---CGe~l~v~~g~F~s~ 218 (240)
-..||+|+.++.= -....++|+| |.......=-||.|+
T Consensus 404 P~~CP~C~s~l~r~~~e~~~rC~n~~~C~aq~~e~l~hfvSr 445 (667)
T COG0272 404 PTHCPVCGSELVREEGEVVIRCTNGLNCPAQLKERLIHFVSR 445 (667)
T ss_pred CCCCCCCCCeeEeccCceeEecCCCCCChHHHhhheeeEecC
Confidence 4579999999985 4467789998 999888888888554
No 134
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=73.18 E-value=2.1 Score=27.97 Aligned_cols=17 Identities=29% Similarity=0.882 Sum_probs=14.9
Q ss_pred eeecCCCCceeeeeCCC
Q 026283 198 IIRCAGCGNIVWQPEGD 214 (240)
Q Consensus 198 ~~~CpnCGe~l~v~~g~ 214 (240)
|..|.+|+..|+.|.|-
T Consensus 1 q~~C~~C~t~L~yP~gA 17 (31)
T TIGR01053 1 QVVCGGCRTLLMYPRGA 17 (31)
T ss_pred CcCcCCCCcEeecCCCC
Confidence 56899999999999884
No 135
>PRK11823 DNA repair protein RadA; Provisional
Probab=73.15 E-value=1.9 Score=41.39 Aligned_cols=27 Identities=26% Similarity=0.395 Sum_probs=20.0
Q ss_pred CCCCCCCccccccccceeecCCCCceeeee
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNIVWQP 211 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~l~v~ 211 (240)
-.|..|||+..-. .-+||+||+-=+++
T Consensus 8 y~C~~Cg~~~~~~---~g~Cp~C~~w~t~~ 34 (446)
T PRK11823 8 YVCQECGAESPKW---LGRCPECGAWNTLV 34 (446)
T ss_pred EECCcCCCCCccc---CeeCcCCCCcccee
Confidence 4699999987644 56899999754443
No 136
>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=73.05 E-value=4.7 Score=28.74 Aligned_cols=25 Identities=20% Similarity=0.550 Sum_probs=17.0
Q ss_pred CccccccccceeecCCCCceeeeeC
Q 026283 188 KREFIGSKSQIIRCAGCGNIVWQPE 212 (240)
Q Consensus 188 ~~eFtG~nnt~~~CpnCGe~l~v~~ 212 (240)
.|++.|-..+...|++||.+|....
T Consensus 38 ~y~~s~~~~~r~FC~~CGs~l~~~~ 62 (92)
T PF04828_consen 38 EYQFSGKGVERYFCPTCGSPLFSED 62 (92)
T ss_dssp EC--TTSSCEEEEETTT--EEEEEE
T ss_pred EEEeCCCcCcCcccCCCCCeeeccc
Confidence 3455677888899999999999753
No 137
>PHA00626 hypothetical protein
Probab=72.95 E-value=2.6 Score=31.65 Aligned_cols=27 Identities=30% Similarity=0.566 Sum_probs=18.2
Q ss_pred CCCCCCCcccccc-----c-cceeecCCCCcee
Q 026283 182 GACPACKREFIGS-----K-SQIIRCAGCGNIV 208 (240)
Q Consensus 182 g~CPvC~~eFtG~-----n-nt~~~CpnCGe~l 208 (240)
+.||.||..=+-. + .+.-.||.||---
T Consensus 1 m~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~f 33 (59)
T PHA00626 1 MSCPKCGSGNIAKEKTMRGWSDDYVCCDCGYND 33 (59)
T ss_pred CCCCCCCCceeeeeceecccCcceEcCCCCCee
Confidence 4699999952222 2 4667899998643
No 138
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=72.77 E-value=2.6 Score=40.69 Aligned_cols=31 Identities=23% Similarity=0.435 Sum_probs=22.2
Q ss_pred CCCCCCccc--ccc-ccceeecCCCCceeeeeCC
Q 026283 183 ACPACKREF--IGS-KSQIIRCAGCGNIVWQPEG 213 (240)
Q Consensus 183 ~CPvC~~eF--tG~-nnt~~~CpnCGe~l~v~~g 213 (240)
.||.|+.-. .-+ .+++-+||.||..|.-.+.
T Consensus 12 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~~~~~ 45 (419)
T PRK15103 12 LCPQCDMLVALPRLEHGQKAACPRCGTTLTVRWD 45 (419)
T ss_pred cCCCCCceeecCCCCCCCeeECCCCCCCCcCCCC
Confidence 499999754 222 3567889999999965443
No 139
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=72.63 E-value=2.9 Score=27.48 Aligned_cols=25 Identities=24% Similarity=0.493 Sum_probs=20.5
Q ss_pred CCCCCCccccc-cccceeecCCCCce
Q 026283 183 ACPACKREFIG-SKSQIIRCAGCGNI 207 (240)
Q Consensus 183 ~CPvC~~eFtG-~nnt~~~CpnCGe~ 207 (240)
.|++|+.+-.= -++....|++||.+
T Consensus 5 ~C~~C~~~~i~~~~~~~~~C~~Cg~~ 30 (33)
T PF08792_consen 5 KCSKCGGNGIVNKEDDYEVCIFCGSS 30 (33)
T ss_pred EcCCCCCCeEEEecCCeEEcccCCcE
Confidence 58999988766 67778899999975
No 140
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=72.58 E-value=2 Score=33.01 Aligned_cols=17 Identities=29% Similarity=0.638 Sum_probs=12.0
Q ss_pred cceeecCCCCceeeeeC
Q 026283 196 SQIIRCAGCGNIVWQPE 212 (240)
Q Consensus 196 nt~~~CpnCGe~l~v~~ 212 (240)
-....|+.|||.+.-++
T Consensus 29 ~~~~~C~~CGe~~~~~e 45 (127)
T TIGR03830 29 VPGWYCPACGEELLDPE 45 (127)
T ss_pred eeeeECCCCCCEEEcHH
Confidence 34568999999876543
No 141
>KOG4517 consensus Uncharacterized conserved protein [Function unknown]
Probab=72.27 E-value=1.6 Score=36.54 Aligned_cols=15 Identities=27% Similarity=0.563 Sum_probs=10.5
Q ss_pred cccceeecCCCCcee
Q 026283 194 SKSQIIRCAGCGNIV 208 (240)
Q Consensus 194 ~nnt~~~CpnCGe~l 208 (240)
+--++-+|||||+.+
T Consensus 102 ~alr~rrc~ncg~~f 116 (117)
T KOG4517|consen 102 FALRKRRCPNCGPTF 116 (117)
T ss_pred HhhhhccCCCccccc
Confidence 345677888888764
No 142
>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=72.24 E-value=2.1 Score=42.52 Aligned_cols=23 Identities=26% Similarity=0.589 Sum_probs=18.2
Q ss_pred CCCCCCCccccccccceeecCCCCce
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNI 207 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~ 207 (240)
+.|+.|||...|. .-.||.||+.
T Consensus 519 ~~C~~CG~~~~~~---~~~CP~CGs~ 541 (555)
T cd01675 519 DICNDCGYIGEGE---GFKCPKCGSE 541 (555)
T ss_pred ccCCCCCCCCcCC---CCCCcCCCCc
Confidence 4999999866544 4899999964
No 143
>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=72.07 E-value=2.1 Score=41.42 Aligned_cols=26 Identities=15% Similarity=0.221 Sum_probs=19.6
Q ss_pred CCCCCCCccccccccceeecCCCCceeee
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNIVWQ 210 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~l~v 210 (240)
-.|..|||++.-. .-+||+||+==++
T Consensus 8 y~C~~Cg~~~~~~---~g~Cp~C~~w~t~ 33 (454)
T TIGR00416 8 FVCQHCGADSPKW---QGKCPACHAWNTI 33 (454)
T ss_pred EECCcCCCCCccc---cEECcCCCCcccc
Confidence 4699999997654 5689999974333
No 144
>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=71.84 E-value=2.6 Score=26.67 Aligned_cols=15 Identities=33% Similarity=0.851 Sum_probs=8.4
Q ss_pred ecCCCCceeeeeCCC
Q 026283 200 RCAGCGNIVWQPEGD 214 (240)
Q Consensus 200 ~CpnCGe~l~v~~g~ 214 (240)
.||.||..|....|.
T Consensus 1 ~CP~C~s~l~~~~~e 15 (28)
T PF03119_consen 1 TCPVCGSKLVREEGE 15 (28)
T ss_dssp B-TTT--BEEE-CCT
T ss_pred CcCCCCCEeEcCCCC
Confidence 589999988877664
No 145
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=71.79 E-value=3.1 Score=27.68 Aligned_cols=10 Identities=30% Similarity=0.847 Sum_probs=5.3
Q ss_pred ecCCCCceee
Q 026283 200 RCAGCGNIVW 209 (240)
Q Consensus 200 ~CpnCGe~l~ 209 (240)
.||+||..|.
T Consensus 4 ~C~~Cg~~l~ 13 (47)
T PF13005_consen 4 ACPDCGGELK 13 (47)
T ss_pred cCCCCCceee
Confidence 4555555554
No 146
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=71.71 E-value=3 Score=30.09 Aligned_cols=32 Identities=31% Similarity=0.570 Sum_probs=25.1
Q ss_pred CCCCCCCcccccc-ccceeecCCCCceeeeeCC
Q 026283 182 GACPACKREFIGS-KSQIIRCAGCGNIVWQPEG 213 (240)
Q Consensus 182 g~CPvC~~eFtG~-nnt~~~CpnCGe~l~v~~g 213 (240)
-.|--||.+|.=. ....++||.||--+-+..-
T Consensus 7 Y~C~~Cg~~~~~~~~~~~irCp~Cg~rIl~K~R 39 (49)
T COG1996 7 YKCARCGREVELDQETRGIRCPYCGSRILVKER 39 (49)
T ss_pred EEhhhcCCeeehhhccCceeCCCCCcEEEEecc
Confidence 3588999999633 6778999999988877643
No 147
>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=71.28 E-value=1.2 Score=37.62 Aligned_cols=24 Identities=29% Similarity=0.681 Sum_probs=19.4
Q ss_pred CCCCCCCccccccccceeecCCCCce
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNI 207 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~ 207 (240)
-+||.||.-|+- + .+..||.|.+.
T Consensus 4 ~nC~~CgklF~~-~-~~~iCp~C~~~ 27 (137)
T TIGR03826 4 ANCPKCGRLFVK-T-GRDVCPSCYEE 27 (137)
T ss_pred ccccccchhhhh-c-CCccCHHHhHH
Confidence 379999999998 4 55669999864
No 148
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=71.23 E-value=1.2 Score=39.01 Aligned_cols=31 Identities=19% Similarity=0.517 Sum_probs=23.1
Q ss_pred CCCCCCCcccc--ccccceeecCCCCceeeeeC
Q 026283 182 GACPACKREFI--GSKSQIIRCAGCGNIVWQPE 212 (240)
Q Consensus 182 g~CPvC~~eFt--G~nnt~~~CpnCGe~l~v~~ 212 (240)
-.||.|...++ --...+..||-||+.|..-+
T Consensus 114 y~C~~~~~r~sfdeA~~~~F~Cp~Cg~~L~~~d 146 (176)
T COG1675 114 YVCPNCHVKYSFDEAMELGFTCPKCGEDLEEYD 146 (176)
T ss_pred eeCCCCCCcccHHHHHHhCCCCCCCCchhhhcc
Confidence 47999976554 44556689999999997544
No 149
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=71.23 E-value=1.7 Score=40.68 Aligned_cols=31 Identities=35% Similarity=0.817 Sum_probs=25.2
Q ss_pred hhcCCCCCCCcccccccc--ceeecCCCCceee
Q 026283 179 VIKGACPACKREFIGSKS--QIIRCAGCGNIVW 209 (240)
Q Consensus 179 LIeg~CPvC~~eFtG~nn--t~~~CpnCGe~l~ 209 (240)
+-|-.||.|++.|+|+-+ ...-|-+||.+|.
T Consensus 153 ~aef~C~~C~h~F~G~~qm~v~sPCy~C~~~v~ 185 (278)
T PF15135_consen 153 IAEFHCPKCRHNFRGFAQMGVPSPCYGCGNPVY 185 (278)
T ss_pred eeeeecccccccchhhhhcCCCCCccCCCCccC
Confidence 557799999999999954 3456999999983
No 150
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=70.88 E-value=0.99 Score=46.28 Aligned_cols=37 Identities=22% Similarity=0.536 Sum_probs=28.7
Q ss_pred cCCCCCCCccccccccceeecCC---CCceeeeeCCCcccC
Q 026283 181 KGACPACKREFIGSKSQIIRCAG---CGNIVWQPEGDFFSR 218 (240)
Q Consensus 181 eg~CPvC~~eFtG~nnt~~~Cpn---CGe~l~v~~g~F~s~ 218 (240)
-..||+|+.+.+- ++....|+| |-..+...=-||.|+
T Consensus 423 P~~CP~C~~~l~~-~~~~~~C~n~~~Cpaq~~~~l~hf~sr 462 (689)
T PRK14351 423 PDTCPVCDSAVER-DGPLAFCTGGLACPAQLERSIEHYASR 462 (689)
T ss_pred CCCCCCCCCEeee-CCceEEcCCCCCCHHHHHHHHHHHhcc
Confidence 4699999999875 567888985 988777666788554
No 151
>TIGR00398 metG methionyl-tRNA synthetase. The methionyl-tRNA synthetase (metG) is a class I amino acyl-tRNA ligase. This model appears to recognize the methionyl-tRNA synthetase of every species, including eukaryotic cytosolic and mitochondrial forms. The UPGMA difference tree calculated after search and alignment according to this model shows an unusual deep split between two families of MetG. One family contains forms from the Archaea, yeast cytosol, spirochetes, and E. coli, among others. The other family includes forms from yeast mitochondrion, Synechocystis sp., Bacillus subtilis, the Mycoplasmas, Aquifex aeolicus, and Helicobacter pylori. The E. coli enzyme is homodimeric, although monomeric forms can be prepared that are fully active. Activity of this enzyme in bacteria includes aminoacylation of fMet-tRNA with Met; subsequent formylation of the Met to fMet is catalyzed by a separate enzyme. Note that the protein from Aquifex aeolicus is split into an alpha (large) and beta (sma
Probab=70.86 E-value=2 Score=41.24 Aligned_cols=26 Identities=31% Similarity=0.827 Sum_probs=18.0
Q ss_pred hhcCCCCCCCccccccccceeecCCCCcee
Q 026283 179 VIKGACPACKREFIGSKSQIIRCAGCGNIV 208 (240)
Q Consensus 179 LIeg~CPvC~~eFtG~nnt~~~CpnCGe~l 208 (240)
-|+|.||.|+++ ..--.+|.+||..+
T Consensus 134 ~v~g~cp~c~~~----~~~g~~ce~cg~~~ 159 (530)
T TIGR00398 134 YVEGTCPKCGSE----DARGDHCEVCGRHL 159 (530)
T ss_pred hhcCCCCCCCCc----ccccchhhhccccC
Confidence 457999999885 12245688888754
No 152
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=70.83 E-value=2.2 Score=28.75 Aligned_cols=17 Identities=18% Similarity=0.282 Sum_probs=9.8
Q ss_pred CCCCCCcccccccccee
Q 026283 183 ACPACKREFIGSKSQII 199 (240)
Q Consensus 183 ~CPvC~~eFtG~nnt~~ 199 (240)
.||.|++.=.-+.+.|+
T Consensus 2 ~Cp~C~~~~a~~~q~Q~ 18 (40)
T smart00440 2 PCPKCGNREATFFQLQT 18 (40)
T ss_pred cCCCCCCCeEEEEEEcc
Confidence 47777766555554443
No 153
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=70.82 E-value=2.1 Score=47.31 Aligned_cols=26 Identities=27% Similarity=0.646 Sum_probs=18.1
Q ss_pred hcCCCCCCCccccccccceeecCCCCceee
Q 026283 180 IKGACPACKREFIGSKSQIIRCAGCGNIVW 209 (240)
Q Consensus 180 Ieg~CPvC~~eFtG~nnt~~~CpnCGe~l~ 209 (240)
.+..||.||.+.. ....||+||..+.
T Consensus 678 ~~~fCP~CGs~te----~vy~CPsCGaev~ 703 (1337)
T PRK14714 678 YENRCPDCGTHTE----PVYVCPDCGAEVP 703 (1337)
T ss_pred ccccCcccCCcCC----CceeCccCCCccC
Confidence 4568999998852 3457777777654
No 154
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=70.35 E-value=2 Score=30.24 Aligned_cols=17 Identities=29% Similarity=0.710 Sum_probs=14.5
Q ss_pred hhhhhcCCCCCCCcccc
Q 026283 176 NNFVIKGACPACKREFI 192 (240)
Q Consensus 176 kRnLIeg~CPvC~~eFt 192 (240)
|.+|-+-.||+|+.+|+
T Consensus 3 K~~lp~K~C~~C~rpf~ 19 (42)
T PF10013_consen 3 KSNLPSKICPVCGRPFT 19 (42)
T ss_pred cccCCCCcCcccCCcch
Confidence 45778889999999997
No 155
>PF11241 DUF3043: Protein of unknown function (DUF3043); InterPro: IPR021403 Some members in this family of proteins with unknown function are annotated as membrane proteins. This cannot be confirmed.
Probab=70.20 E-value=77 Score=27.92 Aligned_cols=55 Identities=25% Similarity=0.326 Sum_probs=26.5
Q ss_pred HHHHHHhhhhhhhhHhHHhhhhhhhhhchh----HHHHHHHhhCCC--CchHHHHHHHHHH
Q 026283 92 AVRARELDREFAISVRWRSFRMDFSRNWPR----YRKQLNDFLNTP--LGRSFATIFFLWF 146 (240)
Q Consensus 92 ~e~A~eiD~~fgi~rR~R~f~~D~~r~wP~----yrrql~~F~~T~--lG~wL~tl~~~wl 146 (240)
+.+++|--++-.-++|-++.+-|=+-.-|+ -|+-+-|+-|+. +|.++.-++++-+
T Consensus 29 k~~~R~~~r~~r~~~r~aM~~GDeryLp~RDrGP~Rr~vRD~VDsR~~i~e~fmP~alv~l 89 (170)
T PF11241_consen 29 KKRAREARRERRARQREAMMTGDERYLPPRDRGPVRRYVRDYVDSRRNIGEFFMPVALVLL 89 (170)
T ss_pred HHHHHHHHHHHHHHHHHHHHcChhhcCCcccccchhhhhhhhhhcccchHHHHHHHHHHHH
Confidence 333333333333445666666664333333 345555665553 6776644444333
No 156
>PRK00133 metG methionyl-tRNA synthetase; Reviewed
Probab=70.05 E-value=2 Score=43.11 Aligned_cols=25 Identities=40% Similarity=0.930 Sum_probs=17.5
Q ss_pred hhcCCCCCCCcc-ccccccceeecCCCCcee
Q 026283 179 VIKGACPACKRE-FIGSKSQIIRCAGCGNIV 208 (240)
Q Consensus 179 LIeg~CPvC~~e-FtG~nnt~~~CpnCGe~l 208 (240)
-|+|.||.|+++ .-| .+|-+||..+
T Consensus 137 ~v~g~cp~C~~~d~~g-----~~ce~cg~~~ 162 (673)
T PRK00133 137 FVKGTCPKCGAEDQYG-----DNCEVCGATY 162 (673)
T ss_pred heecccCCCCCcccCC-----chhhhccccC
Confidence 467999999987 222 3577777654
No 157
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=70.00 E-value=2 Score=45.43 Aligned_cols=29 Identities=21% Similarity=0.611 Sum_probs=21.5
Q ss_pred cCCCCCCCccccccccceeecCCCCceee
Q 026283 181 KGACPACKREFIGSKSQIIRCAGCGNIVW 209 (240)
Q Consensus 181 eg~CPvC~~eFtG~nnt~~~CpnCGe~l~ 209 (240)
.+.||+|+..=+---+.--.|+|||-.|+
T Consensus 827 ~~~cp~c~~~~~~~~~~c~~c~~c~~~~~ 855 (858)
T PRK08115 827 GNTCPVCREGTVEEIGGCNTCTNCGAQLK 855 (858)
T ss_pred CCCCCccCCCceeecCCCccccchhhhhc
Confidence 46899999866544445557999998775
No 158
>KOG1247 consensus Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=69.95 E-value=1.5 Score=44.16 Aligned_cols=32 Identities=28% Similarity=0.661 Sum_probs=25.0
Q ss_pred HHHhhhhhcCCCCCCCccccccccceeecCCCCcee
Q 026283 173 TVANNFVIKGACPACKREFIGSKSQIIRCAGCGNIV 208 (240)
Q Consensus 173 wWlkRnLIeg~CPvC~~eFtG~nnt~~~CpnCGe~l 208 (240)
..|-.+.|||.||-|+|.=. .--||-+||+.|
T Consensus 144 ~fladr~veg~cp~C~yd~A----RGDqcd~cG~l~ 175 (567)
T KOG1247|consen 144 TFLADRFVEGKCPFCGYDDA----RGDQCDKCGKLV 175 (567)
T ss_pred ccccchhhhccCCCCCCccc----cchhhhhhhhhc
Confidence 44567899999999999743 446899999865
No 159
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=69.87 E-value=2.2 Score=43.66 Aligned_cols=25 Identities=28% Similarity=0.675 Sum_probs=16.9
Q ss_pred CCCCCCCccccccccceeecCCCCceee
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNIVW 209 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~l~ 209 (240)
..||.||++ ..-..-.||+||..+-
T Consensus 28 ~~Cp~CG~~---~~~~~~fC~~CG~~~~ 52 (645)
T PRK14559 28 KPCPQCGTE---VPVDEAHCPNCGAETG 52 (645)
T ss_pred CcCCCCCCC---CCcccccccccCCccc
Confidence 467777777 3345567888887653
No 160
>PHA00732 hypothetical protein
Probab=69.44 E-value=4 Score=31.18 Aligned_cols=33 Identities=18% Similarity=0.479 Sum_probs=25.0
Q ss_pred CCCCCCccccccc---------cceeecCCCCceeeeeCCCc
Q 026283 183 ACPACKREFIGSK---------SQIIRCAGCGNIVWQPEGDF 215 (240)
Q Consensus 183 ~CPvC~~eFtG~n---------nt~~~CpnCGe~l~v~~g~F 215 (240)
.|+.|++.|.-.. .+.-.|+.||+.....+-|+
T Consensus 3 ~C~~Cgk~F~s~s~Lk~H~r~~H~~~~C~~CgKsF~~l~~H~ 44 (79)
T PHA00732 3 KCPICGFTTVTLFALKQHARRNHTLTKCPVCNKSYRRLNQHF 44 (79)
T ss_pred cCCCCCCccCCHHHHHHHhhcccCCCccCCCCCEeCChhhhh
Confidence 5999999986411 12237999999999888887
No 161
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=69.06 E-value=2.1 Score=35.79 Aligned_cols=31 Identities=29% Similarity=0.604 Sum_probs=24.8
Q ss_pred hhhhcCCCCCCCcccccccccee-----------ecCCCCce
Q 026283 177 NFVIKGACPACKREFIGSKSQII-----------RCAGCGNI 207 (240)
Q Consensus 177 RnLIeg~CPvC~~eFtG~nnt~~-----------~CpnCGe~ 207 (240)
...|+-.||.||++=--|.--|. .||+|+--
T Consensus 70 ga~I~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k 111 (116)
T KOG2907|consen 70 GAVIKHKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYK 111 (116)
T ss_pred ccchhccCcccCCchhhhhhhhcccccCCceEEEEcCcccee
Confidence 36789999999999888876665 49999853
No 162
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=68.97 E-value=1.2 Score=32.03 Aligned_cols=27 Identities=30% Similarity=0.739 Sum_probs=21.6
Q ss_pred cCCCCCCCcccc------------ccccceeecCCCCce
Q 026283 181 KGACPACKREFI------------GSKSQIIRCAGCGNI 207 (240)
Q Consensus 181 eg~CPvC~~eFt------------G~nnt~~~CpnCGe~ 207 (240)
+-.|--||.+|+ |+.|...+||.|...
T Consensus 4 ~l~C~dCg~~FvfTa~EQ~fy~eKgf~n~p~RC~~CR~~ 42 (49)
T PF13451_consen 4 TLTCKDCGAEFVFTAGEQKFYAEKGFDNEPKRCPSCRQA 42 (49)
T ss_pred eEEcccCCCeEEEehhHHHHHHhcCCcCCCccCHHHHHH
Confidence 346888998886 888899999999754
No 163
>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=68.96 E-value=3 Score=36.14 Aligned_cols=31 Identities=29% Similarity=0.712 Sum_probs=21.0
Q ss_pred hhhcCCCCCCCccccc--------cccceeecCCCCcee
Q 026283 178 FVIKGACPACKREFIG--------SKSQIIRCAGCGNIV 208 (240)
Q Consensus 178 nLIeg~CPvC~~eFtG--------~nnt~~~CpnCGe~l 208 (240)
++-+..|+.|+..+.- ...+.-.||+||.+|
T Consensus 92 ~~~~~~C~~C~~~~~~~~~~~~~~~~~~~p~C~~Cgg~l 130 (206)
T cd01410 92 NMFIEVCKSCGPEYVRDDVVETRGDKETGRRCHACGGIL 130 (206)
T ss_pred CcCcccCCCCCCccchHHHHHHhhcCCCCCcCCCCcCcc
Confidence 3445789999987641 123457799998764
No 164
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=68.92 E-value=3.5 Score=39.57 Aligned_cols=29 Identities=21% Similarity=0.423 Sum_probs=21.7
Q ss_pred CCCCCCcccc---ccccceeecCCCCceeeee
Q 026283 183 ACPACKREFI---GSKSQIIRCAGCGNIVWQP 211 (240)
Q Consensus 183 ~CPvC~~eFt---G~nnt~~~CpnCGe~l~v~ 211 (240)
.||.|+.-.. --.+++-+||.||..|.-.
T Consensus 15 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~~~ 46 (403)
T TIGR00155 15 LCSQCDMLVALPRIESGQKAACPRCGTTLTVG 46 (403)
T ss_pred eCCCCCCcccccCCCCCCeeECCCCCCCCcCC
Confidence 5999996552 2256778999999999543
No 165
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=68.85 E-value=2.3 Score=42.92 Aligned_cols=36 Identities=25% Similarity=0.561 Sum_probs=25.9
Q ss_pred HHHhhhhhcCCCCCCCccccccccceeecCCCCceeeeeC
Q 026283 173 TVANNFVIKGACPACKREFIGSKSQIIRCAGCGNIVWQPE 212 (240)
Q Consensus 173 wWlkRnLIeg~CPvC~~eFtG~nnt~~~CpnCGe~l~v~~ 212 (240)
-++-..-|+|.||-|+++=.+- -||-|||..+.-.+
T Consensus 134 ~fl~dr~v~g~cp~cg~~~arG----D~Ce~Cg~~~~P~~ 169 (558)
T COG0143 134 RFLPDRYVEGTCPKCGGEDARG----DQCENCGRTLDPTE 169 (558)
T ss_pred ccccchheeccCCCcCccccCc----chhhhccCcCCchh
Confidence 3455667899999999886654 46888887665443
No 166
>PRK12366 replication factor A; Reviewed
Probab=68.58 E-value=2.3 Score=42.91 Aligned_cols=31 Identities=23% Similarity=0.550 Sum_probs=25.4
Q ss_pred hhhhhcCCCCCCCccccccccceeecCCCCce
Q 026283 176 NNFVIKGACPACKREFIGSKSQIIRCAGCGNI 207 (240)
Q Consensus 176 kRnLIeg~CPvC~~eFtG~nnt~~~CpnCGe~ 207 (240)
..+....+||.|++-.+- ....-+||.||+.
T Consensus 527 ~~~~~y~aCp~CnkKv~~-~~g~~~C~~c~~~ 557 (637)
T PRK12366 527 KQKIILYLCPNCRKRVEE-VDGEYICEFCGEV 557 (637)
T ss_pred CCCEEEecccccCeEeEc-CCCcEECCCCCCC
Confidence 567788999999998874 4556789999986
No 167
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=68.51 E-value=3.3 Score=33.31 Aligned_cols=25 Identities=36% Similarity=0.864 Sum_probs=15.6
Q ss_pred CCCCCCccccc----cccceeecCCCCce
Q 026283 183 ACPACKREFIG----SKSQIIRCAGCGNI 207 (240)
Q Consensus 183 ~CPvC~~eFtG----~nnt~~~CpnCGe~ 207 (240)
.||.|+..-+- =+-....||+||.-
T Consensus 23 ~CP~Cge~~v~v~~~k~~~h~~C~~CG~y 51 (99)
T PRK14892 23 ECPRCGKVSISVKIKKNIAIITCGNCGLY 51 (99)
T ss_pred ECCCCCCeEeeeecCCCcceEECCCCCCc
Confidence 59999842221 12347789999864
No 168
>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=68.49 E-value=2.2 Score=40.83 Aligned_cols=33 Identities=24% Similarity=0.664 Sum_probs=16.3
Q ss_pred CCCCCCccccccccce-eecCCCCceeeeeCCCc
Q 026283 183 ACPACKREFIGSKSQI-IRCAGCGNIVWQPEGDF 215 (240)
Q Consensus 183 ~CPvC~~eFtG~nnt~-~~CpnCGe~l~v~~g~F 215 (240)
.|+.|++..|.|.--. ..|++||+.-|-..|-+
T Consensus 287 kC~~C~~Rt~sl~r~P~~~C~~Cg~~~wer~~M~ 320 (344)
T PF09332_consen 287 KCKDCGNRTISLERLPKKHCSNCGSSKWERTGML 320 (344)
T ss_dssp E-T-TS-EEEESSSS--S--TTT-S---EEE---
T ss_pred ECCCCCCeeeecccCCCCCCCcCCcCceeehhhh
Confidence 6999999988875433 68999999999888876
No 169
>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=68.31 E-value=2.7 Score=36.62 Aligned_cols=33 Identities=24% Similarity=0.597 Sum_probs=23.4
Q ss_pred hhhhcCCCCCCCcccccc------ccceeecCCCCceee
Q 026283 177 NFVIKGACPACKREFIGS------KSQIIRCAGCGNIVW 209 (240)
Q Consensus 177 RnLIeg~CPvC~~eFtG~------nnt~~~CpnCGe~l~ 209 (240)
-++-+..|..|+..+.-- ....-.||+||.++.
T Consensus 109 G~l~~~~C~~C~~~~~~~~~~~~~~~~~p~C~~Cgg~lr 147 (222)
T cd01413 109 GTLQTAYCVNCGSKYDLEEVKYAKKHEVPRCPKCGGIIR 147 (222)
T ss_pred CCcCcceECCCCCCcchhHHHHhccCCCCcCCCCCCccC
Confidence 345567899999877522 345678999998764
No 170
>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=68.20 E-value=4 Score=29.70 Aligned_cols=26 Identities=23% Similarity=0.528 Sum_probs=19.5
Q ss_pred cCCCCCCCccccccccceeecCCCCceeeeeCCCc
Q 026283 181 KGACPACKREFIGSKSQIIRCAGCGNIVWQPEGDF 215 (240)
Q Consensus 181 eg~CPvC~~eFtG~nnt~~~CpnCGe~l~v~~g~F 215 (240)
..+||+||++.+|=..- .|-|+++.|
T Consensus 13 Y~~Cp~CGN~~vGngEG---------~liV~edtf 38 (49)
T PF12677_consen 13 YCKCPKCGNDKVGNGEG---------TLIVEEDTF 38 (49)
T ss_pred hccCcccCCcEeecCcc---------eEEEeccce
Confidence 57899999998884433 357888888
No 171
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=68.19 E-value=2.4 Score=38.16 Aligned_cols=27 Identities=22% Similarity=0.524 Sum_probs=18.6
Q ss_pred hcCCCCCCCcccccc------------ccceeecCCCCc
Q 026283 180 IKGACPACKREFIGS------------KSQIIRCAGCGN 206 (240)
Q Consensus 180 Ieg~CPvC~~eFtG~------------nnt~~~CpnCGe 206 (240)
-...||||+..+.-. --+...|-+||-
T Consensus 13 ~~~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgY 51 (201)
T COG1779 13 TRIDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGY 51 (201)
T ss_pred eeecCCcccceeeEEEeeecCCccceEEEEEEEccccCC
Confidence 356899999866432 124568999984
No 172
>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=67.91 E-value=3.5 Score=29.70 Aligned_cols=18 Identities=39% Similarity=0.951 Sum_probs=12.9
Q ss_pred CCCCCccccccccceeecCCCC
Q 026283 184 CPACKREFIGSKSQIIRCAGCG 205 (240)
Q Consensus 184 CPvC~~eFtG~nnt~~~CpnCG 205 (240)
||.||. +.-.-..||+||
T Consensus 29 C~~cG~----~~~~H~vc~~cG 46 (55)
T TIGR01031 29 CPNCGE----FKLPHRVCPSCG 46 (55)
T ss_pred CCCCCC----cccCeeECCccC
Confidence 777775 556667777777
No 173
>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=67.74 E-value=2.1 Score=36.35 Aligned_cols=26 Identities=27% Similarity=0.643 Sum_probs=11.9
Q ss_pred cCCCCCCCcccc-c--------ccc---ceeecCCCCc
Q 026283 181 KGACPACKREFI-G--------SKS---QIIRCAGCGN 206 (240)
Q Consensus 181 eg~CPvC~~eFt-G--------~nn---t~~~CpnCGe 206 (240)
|-.||+|+.+-+ = |+. ....|++||-
T Consensus 1 ~s~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGy 38 (161)
T PF03367_consen 1 ESLCPNCGENGTTRILLTDIPYFKEVIIMSFECEHCGY 38 (161)
T ss_dssp -EE-TTTSSCCEEEEEEEEETTTEEEEEEEEE-TTT--
T ss_pred CCcCCCCCCCcEEEEEEEcCCCCceEEEEEeECCCCCC
Confidence 346999998631 1 111 2247999984
No 174
>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=67.61 E-value=3 Score=29.82 Aligned_cols=20 Identities=35% Similarity=0.848 Sum_probs=14.5
Q ss_pred CCCCCCCccccccccceeecCCCC
Q 026283 182 GACPACKREFIGSKSQIIRCAGCG 205 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCG 205 (240)
..||.||. +.-.-..||+||
T Consensus 27 ~~c~~cg~----~~~~H~vc~~cG 46 (56)
T PF01783_consen 27 VKCPNCGE----PKLPHRVCPSCG 46 (56)
T ss_dssp EESSSSSS----EESTTSBCTTTB
T ss_pred eeeccCCC----EecccEeeCCCC
Confidence 56888884 456667788887
No 175
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=67.56 E-value=2.3 Score=39.65 Aligned_cols=12 Identities=33% Similarity=0.916 Sum_probs=9.3
Q ss_pred cCCCCCCCcccc
Q 026283 181 KGACPACKREFI 192 (240)
Q Consensus 181 eg~CPvC~~eFt 192 (240)
+-.||||+.-|.
T Consensus 19 ~ieCPvC~tkFk 30 (267)
T COG1655 19 TIECPVCNTKFK 30 (267)
T ss_pred eeccCcccchhh
Confidence 457999998763
No 176
>smart00532 LIGANc Ligase N family.
Probab=67.54 E-value=1.7 Score=42.29 Aligned_cols=38 Identities=26% Similarity=0.541 Sum_probs=26.5
Q ss_pred hcCCCCCCCcccccc-ccceeecCC--CCceeeeeCCCccc
Q 026283 180 IKGACPACKREFIGS-KSQIIRCAG--CGNIVWQPEGDFFS 217 (240)
Q Consensus 180 Ieg~CPvC~~eFtG~-nnt~~~Cpn--CGe~l~v~~g~F~s 217 (240)
.-..||+|+.+++=. +....+|+| |-..+...=-||.|
T Consensus 398 ~P~~CP~C~s~l~~~~~~~~~~C~n~~C~aq~~~~l~hf~s 438 (441)
T smart00532 398 MPTHCPSCGSELVREEGEVDIRCPNPLCPAQLIERIIHFAS 438 (441)
T ss_pred CCCCCCCCCCEeEecCCceEEEeCCCCCHHHHHHHHHhhhc
Confidence 457999999998633 335677986 87776655567644
No 177
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=67.42 E-value=3.2 Score=39.36 Aligned_cols=18 Identities=11% Similarity=0.239 Sum_probs=13.0
Q ss_pred ccceeecCCCCceeeeeC
Q 026283 195 KSQIIRCAGCGNIVWQPE 212 (240)
Q Consensus 195 nnt~~~CpnCGe~l~v~~ 212 (240)
......||.|+++|.-.+
T Consensus 40 ~~~~~~CP~C~~~lrk~~ 57 (309)
T TIGR00570 40 VRGSGSCPECDTPLRKNN 57 (309)
T ss_pred cCCCCCCCCCCCccchhh
Confidence 344568999999887653
No 178
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=67.33 E-value=2.9 Score=33.45 Aligned_cols=31 Identities=35% Similarity=0.834 Sum_probs=22.6
Q ss_pred CCCCCCcccccc---ccceeecCCCCceeeeeCCC
Q 026283 183 ACPACKREFIGS---KSQIIRCAGCGNIVWQPEGD 214 (240)
Q Consensus 183 ~CPvC~~eFtG~---nnt~~~CpnCGe~l~v~~g~ 214 (240)
-||+|+-+.+-. +--.-+||.|+. ||...|.
T Consensus 3 lCP~C~v~l~~~~rs~vEiD~CPrCrG-VWLDrGE 36 (88)
T COG3809 3 LCPICGVELVMSVRSGVEIDYCPRCRG-VWLDRGE 36 (88)
T ss_pred ccCcCCceeeeeeecCceeeeCCcccc-Eeecchh
Confidence 599999888654 334568999986 4766664
No 179
>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=67.08 E-value=2.1 Score=28.58 Aligned_cols=12 Identities=25% Similarity=0.459 Sum_probs=4.5
Q ss_pred CCCCCccccccc
Q 026283 184 CPACKREFIGSK 195 (240)
Q Consensus 184 CPvC~~eFtG~n 195 (240)
||.|+.+=.-+.
T Consensus 3 Cp~Cg~~~a~~~ 14 (39)
T PF01096_consen 3 CPKCGHNEAVFF 14 (39)
T ss_dssp -SSS-SSEEEEE
T ss_pred CcCCCCCeEEEE
Confidence 555554444333
No 180
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=66.96 E-value=3.5 Score=33.96 Aligned_cols=16 Identities=31% Similarity=0.879 Sum_probs=14.4
Q ss_pred eecCCCCceeeeeCCC
Q 026283 199 IRCAGCGNIVWQPEGD 214 (240)
Q Consensus 199 ~~CpnCGe~l~v~~g~ 214 (240)
..||.||+.|.|+.|.
T Consensus 2 ~FCP~Cgn~Live~g~ 17 (105)
T KOG2906|consen 2 LFCPTCGNMLIVESGE 17 (105)
T ss_pred cccCCCCCEEEEecCC
Confidence 4699999999999986
No 181
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=66.90 E-value=3.1 Score=34.21 Aligned_cols=31 Identities=23% Similarity=0.421 Sum_probs=23.6
Q ss_pred CCCCCCCccccc-------cccceeecCCCCceeeeeC
Q 026283 182 GACPACKREFIG-------SKSQIIRCAGCGNIVWQPE 212 (240)
Q Consensus 182 g~CPvC~~eFtG-------~nnt~~~CpnCGe~l~v~~ 212 (240)
-+||.|+.+-+- .+--...|-|||-.-..+-
T Consensus 23 FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~ev 60 (104)
T COG4888 23 FTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFECEV 60 (104)
T ss_pred EecCccCCeeeeEEEEEecCceeEEEcccCcceEEEec
Confidence 479999999876 4555678999997655443
No 182
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=66.76 E-value=3 Score=37.06 Aligned_cols=32 Identities=25% Similarity=0.584 Sum_probs=22.2
Q ss_pred hhhcCCCCCCCcccccc-------ccceeecCCCCceee
Q 026283 178 FVIKGACPACKREFIGS-------KSQIIRCAGCGNIVW 209 (240)
Q Consensus 178 nLIeg~CPvC~~eFtG~-------nnt~~~CpnCGe~l~ 209 (240)
++-+.+|..|++.+.-- ..+.-.||.||.++.
T Consensus 116 ~~~~~~C~~C~~~~~~~~~~~~~~~~~~p~Cp~Cgg~lr 154 (244)
T PRK14138 116 NVEEYYCVRCGKRYTVEDVIEKLEKSDVPRCDDCSGLIR 154 (244)
T ss_pred CcCeeEECCCCCcccHHHHHHHHhcCCCCCCCCCCCeEC
Confidence 44456799999887631 224568999997654
No 183
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=66.69 E-value=3.4 Score=35.14 Aligned_cols=29 Identities=31% Similarity=0.858 Sum_probs=23.5
Q ss_pred hhcCCCCCCCccccccccceeecCCCCce
Q 026283 179 VIKGACPACKREFIGSKSQIIRCAGCGNI 207 (240)
Q Consensus 179 LIeg~CPvC~~eFtG~nnt~~~CpnCGe~ 207 (240)
+|...||.|+...+=..-+...||+||..
T Consensus 147 vv~a~~~~~g~~~~~~~~~~~~c~~~~~~ 175 (189)
T PRK09521 147 VIYAMCSRCRTPLVKKGENELKCPNCGNI 175 (189)
T ss_pred EEEEEccccCCceEECCCCEEECCCCCCE
Confidence 45668999999988777577999999954
No 184
>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=66.58 E-value=3.6 Score=40.82 Aligned_cols=30 Identities=23% Similarity=0.537 Sum_probs=21.9
Q ss_pred cCCCCCCCcccc----cc--------ccceeecCCCCceeee
Q 026283 181 KGACPACKREFI----GS--------KSQIIRCAGCGNIVWQ 210 (240)
Q Consensus 181 eg~CPvC~~eFt----G~--------nnt~~~CpnCGe~l~v 210 (240)
.-.||.|+.++. ++ .....+||.||..+.-
T Consensus 200 ~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e 241 (557)
T PF05876_consen 200 YVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEE 241 (557)
T ss_pred EccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCH
Confidence 347999998775 22 2356799999998764
No 185
>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=66.55 E-value=2.8 Score=27.61 Aligned_cols=16 Identities=31% Similarity=0.821 Sum_probs=13.5
Q ss_pred eecCCCCceeeeeCCC
Q 026283 199 IRCAGCGNIVWQPEGD 214 (240)
Q Consensus 199 ~~CpnCGe~l~v~~g~ 214 (240)
..||.||+.|..+++.
T Consensus 2 ~FCp~C~nlL~p~~~~ 17 (35)
T PF02150_consen 2 RFCPECGNLLYPKEDK 17 (35)
T ss_dssp -BETTTTSBEEEEEET
T ss_pred eeCCCCCccceEcCCC
Confidence 4699999999998875
No 186
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=66.12 E-value=4.6 Score=42.29 Aligned_cols=16 Identities=31% Similarity=0.661 Sum_probs=14.1
Q ss_pred ecCCCCceeeeeCCCc
Q 026283 200 RCAGCGNIVWQPEGDF 215 (240)
Q Consensus 200 ~CpnCGe~l~v~~g~F 215 (240)
.||.||..+....|+|
T Consensus 647 ~CP~Cg~~m~lK~gr~ 662 (860)
T PRK06319 647 PCPLCGGEMKVRHGRF 662 (860)
T ss_pred cCccCCCeeEEecCCC
Confidence 7999999999888876
No 187
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=65.88 E-value=4.2 Score=36.59 Aligned_cols=28 Identities=14% Similarity=0.344 Sum_probs=21.4
Q ss_pred cCCCCCCCccccc-cccceeecCCCCcee
Q 026283 181 KGACPACKREFIG-SKSQIIRCAGCGNIV 208 (240)
Q Consensus 181 eg~CPvC~~eFtG-~nnt~~~CpnCGe~l 208 (240)
..-||.||.+..- -....-+|++||...
T Consensus 99 ~~fC~~CG~~~~~~~~~~~~~C~~c~~~~ 127 (256)
T PRK00241 99 HRFCGYCGHPMHPSKTEWAMLCPHCRERY 127 (256)
T ss_pred CccccccCCCCeecCCceeEECCCCCCEE
Confidence 6789999998753 345667899999654
No 188
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=65.86 E-value=1.7 Score=44.30 Aligned_cols=40 Identities=28% Similarity=0.642 Sum_probs=28.8
Q ss_pred hcCCCCCCCccccc-cccceeecCC---CCceeeeeCCCcccCC
Q 026283 180 IKGACPACKREFIG-SKSQIIRCAG---CGNIVWQPEGDFFSRN 219 (240)
Q Consensus 180 Ieg~CPvC~~eFtG-~nnt~~~Cpn---CGe~l~v~~g~F~s~~ 219 (240)
.-..||+|+.+.+= -++...+|+| |-..+...=-||.|+.
T Consensus 403 ~P~~CP~Cgs~l~~~~~~~~~~C~n~~~C~aq~~~~l~hf~sr~ 446 (665)
T PRK07956 403 MPTHCPVCGSELVRVEGEAVLRCTNGLSCPAQLKERLIHFVSRN 446 (665)
T ss_pred CCCCCCCCCCEeEecCCCeEEECCCCCCCHHHHHHHHHHhhccc
Confidence 44789999998863 2346788985 9887776667885543
No 189
>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=65.68 E-value=2.9 Score=35.83 Aligned_cols=27 Identities=30% Similarity=0.754 Sum_probs=14.2
Q ss_pred CCCCCCCccc--cccc--------cceeecCCCCcee
Q 026283 182 GACPACKREF--IGSK--------SQIIRCAGCGNIV 208 (240)
Q Consensus 182 g~CPvC~~eF--tG~n--------nt~~~CpnCGe~l 208 (240)
-.||.|+.+| .|+. ..-..||+|+..+
T Consensus 19 ~~C~~C~~~~~f~g~~~~~~~~~~~~~~~C~~C~~~~ 55 (188)
T PF08996_consen 19 LTCPSCGTEFEFPGVFEEDGDDVSPSGLQCPNCSTPL 55 (188)
T ss_dssp EE-TTT--EEEE-SSS--SSEEEETTEEEETTT--B-
T ss_pred eECCCCCCCccccccccCCccccccCcCcCCCCCCcC
Confidence 4699999876 5553 3468899999854
No 190
>COG1040 ComFC Predicted amidophosphoribosyltransferases [General function prediction only]
Probab=65.29 E-value=2 Score=37.96 Aligned_cols=27 Identities=22% Similarity=0.509 Sum_probs=24.5
Q ss_pred CCCCCCCccccccccceeecCCCCceeeee
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNIVWQP 211 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~l~v~ 211 (240)
+.|+.|+..+.=+.+ .|+.||.++...
T Consensus 25 ~~C~~C~~~~~~~~~---~C~~C~~~l~~~ 51 (225)
T COG1040 25 GLCSGCQADLPLIGN---LCPLCGLPLSSH 51 (225)
T ss_pred CcChhhhhchhHHHh---hhHhhhChhccc
Confidence 599999999988877 999999999887
No 191
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=64.88 E-value=3.7 Score=29.60 Aligned_cols=16 Identities=25% Similarity=0.439 Sum_probs=12.9
Q ss_pred eecCCCCceeeeeCCC
Q 026283 199 IRCAGCGNIVWQPEGD 214 (240)
Q Consensus 199 ~~CpnCGe~l~v~~g~ 214 (240)
++||.|||.+.+.=..
T Consensus 1 i~CPyCge~~~~~iD~ 16 (52)
T PF14255_consen 1 IQCPYCGEPIEILIDP 16 (52)
T ss_pred CCCCCCCCeeEEEEec
Confidence 4799999999886554
No 192
>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=64.72 E-value=4.1 Score=35.07 Aligned_cols=33 Identities=18% Similarity=0.531 Sum_probs=23.1
Q ss_pred hhhhcCCCCCCCcccccc----ccceeecCCCCceee
Q 026283 177 NFVIKGACPACKREFIGS----KSQIIRCAGCGNIVW 209 (240)
Q Consensus 177 RnLIeg~CPvC~~eFtG~----nnt~~~CpnCGe~l~ 209 (240)
-++-+.+|..|++++.-- ....-.||.||..+.
T Consensus 105 G~~~~~~C~~C~~~~~~~~~~~~~~~p~C~~Cgg~lr 141 (224)
T cd01412 105 GSLFRVRCSSCGYVGENNEEIPEEELPRCPKCGGLLR 141 (224)
T ss_pred CCcCccccCCCCCCCCcchhhhccCCCCCCCCCCccC
Confidence 345567899999987642 233468999998654
No 193
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=64.44 E-value=3.4 Score=32.22 Aligned_cols=24 Identities=29% Similarity=0.438 Sum_probs=18.8
Q ss_pred ccccccceeecCCCCceeeeeCCC
Q 026283 191 FIGSKSQIIRCAGCGNIVWQPEGD 214 (240)
Q Consensus 191 FtG~nnt~~~CpnCGe~l~v~~g~ 214 (240)
|.||=...-+|++||+.+...+.+
T Consensus 1 F~g~Lk~~~~C~~CG~d~~~~~ad 24 (86)
T PF06170_consen 1 FRGYLKVAPRCPHCGLDYSHARAD 24 (86)
T ss_pred CCccccCCCcccccCCccccCCcC
Confidence 567777788899999988777654
No 194
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=63.98 E-value=4.9 Score=29.28 Aligned_cols=19 Identities=37% Similarity=0.957 Sum_probs=13.3
Q ss_pred CCCCCCccccccccceeecCCCC
Q 026283 183 ACPACKREFIGSKSQIIRCAGCG 205 (240)
Q Consensus 183 ~CPvC~~eFtG~nnt~~~CpnCG 205 (240)
.||.||. +...-..||+||
T Consensus 29 ~C~~CG~----~~~~H~vC~~CG 47 (57)
T PRK12286 29 ECPNCGE----PKLPHRVCPSCG 47 (57)
T ss_pred ECCCCCC----ccCCeEECCCCC
Confidence 4777775 455677788887
No 195
>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=63.66 E-value=3.2 Score=39.95 Aligned_cols=28 Identities=29% Similarity=0.676 Sum_probs=20.4
Q ss_pred cCCCCCCCccccccccce---eecCCCCceeee
Q 026283 181 KGACPACKREFIGSKSQI---IRCAGCGNIVWQ 210 (240)
Q Consensus 181 eg~CPvC~~eFtG~nnt~---~~CpnCGe~l~v 210 (240)
.+.|-.|+..+. ...+. ..|| ||..+++
T Consensus 240 ~~~c~~C~~~~~-~~~~~~~~~~Cp-CG~~i~~ 270 (374)
T TIGR00375 240 QTACEACGEPAV-SEDAETACANCP-CGGRIKK 270 (374)
T ss_pred hhhhcccCCcCC-chhhhhcCCCCC-CCCccee
Confidence 468999988877 33333 7899 9999553
No 196
>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=63.55 E-value=4.6 Score=27.02 Aligned_cols=17 Identities=24% Similarity=0.540 Sum_probs=13.3
Q ss_pred eecCCCCceeeeeCCCc
Q 026283 199 IRCAGCGNIVWQPEGDF 215 (240)
Q Consensus 199 ~~CpnCGe~l~v~~g~F 215 (240)
..||.||..|.+..|.+
T Consensus 2 ~~CP~Cg~~lv~r~~k~ 18 (39)
T PF01396_consen 2 EKCPKCGGPLVLRRGKK 18 (39)
T ss_pred cCCCCCCceeEEEECCC
Confidence 46889998888887764
No 197
>PRK04011 peptide chain release factor 1; Provisional
Probab=63.48 E-value=3.6 Score=39.50 Aligned_cols=33 Identities=24% Similarity=0.417 Sum_probs=23.6
Q ss_pred hcCCCCCCCcccccccc-----ceeecCCCCceeeeeC
Q 026283 180 IKGACPACKREFIGSKS-----QIIRCAGCGNIVWQPE 212 (240)
Q Consensus 180 Ieg~CPvC~~eFtG~nn-----t~~~CpnCGe~l~v~~ 212 (240)
++-.||.|+++.+-+-. ....||+||..+.+..
T Consensus 327 ~~~~c~~c~~~~~~~~~~~~~~~~~~c~~~~~~~~~~~ 364 (411)
T PRK04011 327 VTYKCPNCGYEEEKTVKRREELPEKTCPKCGSELEIVE 364 (411)
T ss_pred EEEEcCCCCcceeeecccccccccccCcccCcccccch
Confidence 34569999998765333 3358999999876643
No 198
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=63.44 E-value=5.5 Score=26.47 Aligned_cols=14 Identities=36% Similarity=0.776 Sum_probs=9.6
Q ss_pred cceeecCCCCceee
Q 026283 196 SQIIRCAGCGNIVW 209 (240)
Q Consensus 196 nt~~~CpnCGe~l~ 209 (240)
+..+.||||+.+|.
T Consensus 2 ~~~~~C~nC~R~v~ 15 (33)
T PF08209_consen 2 SPYVECPNCGRPVA 15 (33)
T ss_dssp S-EEE-TTTSSEEE
T ss_pred CCeEECCCCcCCcc
Confidence 46688999999765
No 199
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=63.33 E-value=4.6 Score=35.42 Aligned_cols=24 Identities=17% Similarity=0.462 Sum_probs=18.4
Q ss_pred CCCCCCccccccccceeecCCCCce
Q 026283 183 ACPACKREFIGSKSQIIRCAGCGNI 207 (240)
Q Consensus 183 ~CPvC~~eFtG~nnt~~~CpnCGe~ 207 (240)
.||+|+.+++= .+...+|+|+-.-
T Consensus 4 ~CP~C~~~l~~-~~~~~~C~~~h~f 27 (272)
T PRK11088 4 QCPLCHQPLTL-EENSWICPQNHQF 27 (272)
T ss_pred cCCCCCcchhc-CCCEEEcCCCCCC
Confidence 69999999853 5566899997544
No 200
>PRK04023 DNA polymerase II large subunit; Validated
Probab=63.17 E-value=4.1 Score=44.30 Aligned_cols=27 Identities=30% Similarity=0.672 Sum_probs=20.3
Q ss_pred hhcCCCCCCCccccccccceeecCCCCceee
Q 026283 179 VIKGACPACKREFIGSKSQIIRCAGCGNIVW 209 (240)
Q Consensus 179 LIeg~CPvC~~eFtG~nnt~~~CpnCGe~l~ 209 (240)
...-.||.||.+ ..+..+||.||..+.
T Consensus 636 t~~frCP~CG~~----Te~i~fCP~CG~~~~ 662 (1121)
T PRK04023 636 TFYRRCPFCGTH----TEPVYRCPRCGIEVE 662 (1121)
T ss_pred CCcccCCCCCCC----CCcceeCccccCcCC
Confidence 367899999988 456678888876543
No 201
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=62.84 E-value=3.8 Score=39.99 Aligned_cols=25 Identities=20% Similarity=0.458 Sum_probs=23.0
Q ss_pred CCCCCCCccccccccceeecCCCCc
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGN 206 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe 206 (240)
-.|+.|+....++......||.||.
T Consensus 241 ~~c~~cg~~~~~~~~~~~~c~~Cg~ 265 (380)
T COG1867 241 YHCSRCGEIVGSFREVDEKCPHCGG 265 (380)
T ss_pred EEcccccceecccccccccCCcccc
Confidence 5799999999999999999999994
No 202
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=62.59 E-value=4.1 Score=33.21 Aligned_cols=33 Identities=27% Similarity=0.611 Sum_probs=23.3
Q ss_pred eeecCCCCceeeeeCCCcccCCCCCCCCCCCCCCeee
Q 026283 198 IIRCAGCGNIVWQPEGDFFSRNGGGKKSTKSDDDIID 234 (240)
Q Consensus 198 ~~~CpnCGe~l~v~~g~F~s~~g~~~~~r~t~pgtID 234 (240)
-+.||.||+ -+...| .-.|-+.-.|+.+|..++
T Consensus 3 LI~CP~Cg~---R~e~EF-t~~G~A~i~RP~d~a~~s 35 (97)
T COG4311 3 LIPCPYCGE---RPEEEF-TYAGDAHIARPADPADAS 35 (97)
T ss_pred eecCCCCCC---Cchhhe-eecccccccCCCCcccCC
Confidence 478999999 677777 656656666776665544
No 203
>PF14353 CpXC: CpXC protein
Probab=62.56 E-value=4.3 Score=32.13 Aligned_cols=14 Identities=29% Similarity=0.496 Sum_probs=11.1
Q ss_pred eeecCCCCceeeee
Q 026283 198 IIRCAGCGNIVWQP 211 (240)
Q Consensus 198 ~~~CpnCGe~l~v~ 211 (240)
+++||+||+...++
T Consensus 1 ~itCP~C~~~~~~~ 14 (128)
T PF14353_consen 1 EITCPHCGHEFEFE 14 (128)
T ss_pred CcCCCCCCCeeEEE
Confidence 47899999986654
No 204
>PRK07217 replication factor A; Reviewed
Probab=62.50 E-value=3.9 Score=38.85 Aligned_cols=21 Identities=38% Similarity=0.871 Sum_probs=16.9
Q ss_pred CCCCC--CCccccccccceeecCCCCce
Q 026283 182 GACPA--CKREFIGSKSQIIRCAGCGNI 207 (240)
Q Consensus 182 g~CPv--C~~eFtG~nnt~~~CpnCGe~ 207 (240)
-.||. |++-. |.-+||.||++
T Consensus 189 ~rCP~~~C~Rvl-----~~g~C~~HG~v 211 (311)
T PRK07217 189 KRCPEEDCTRVL-----QNGRCSEHGKV 211 (311)
T ss_pred ecCCccccCccc-----cCCCCCCCCCc
Confidence 46999 99988 44689999964
No 205
>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=61.94 E-value=3 Score=34.58 Aligned_cols=29 Identities=24% Similarity=0.704 Sum_probs=21.5
Q ss_pred cCCCCCCCcccccc-------ccceeecCCCCceee
Q 026283 181 KGACPACKREFIGS-------KSQIIRCAGCGNIVW 209 (240)
Q Consensus 181 eg~CPvC~~eFtG~-------nnt~~~CpnCGe~l~ 209 (240)
+..|..|++++..- +...-.||.||..|.
T Consensus 105 ~~~C~~C~~~~~~~~~~~~~~~~~~~~C~~C~~~lr 140 (178)
T PF02146_consen 105 RLRCSKCGKEYDREDIVDSIDEEEPPRCPKCGGLLR 140 (178)
T ss_dssp EEEETTTSBEEEGHHHHHHHHTTSSCBCTTTSCBEE
T ss_pred eeeecCCCccccchhhcccccccccccccccCccCC
Confidence 36799999987532 344568999999765
No 206
>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=61.73 E-value=5.7 Score=38.88 Aligned_cols=11 Identities=27% Similarity=0.643 Sum_probs=6.7
Q ss_pred eecCCCCceee
Q 026283 199 IRCAGCGNIVW 209 (240)
Q Consensus 199 ~~CpnCGe~l~ 209 (240)
.+||+||..-.
T Consensus 254 ~~Cp~C~s~~l 264 (505)
T TIGR00595 254 KTCPQCGSEDL 264 (505)
T ss_pred CCCCCCCCCee
Confidence 46777776533
No 207
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=61.50 E-value=3.9 Score=31.13 Aligned_cols=22 Identities=36% Similarity=0.744 Sum_probs=10.6
Q ss_pred CCCCCCccccccccceeecCCCCce
Q 026283 183 ACPACKREFIGSKSQIIRCAGCGNI 207 (240)
Q Consensus 183 ~CPvC~~eFtG~nnt~~~CpnCGe~ 207 (240)
+|-.|+|=- +...-+||+||-.
T Consensus 6 AC~~Ck~l~---~~d~e~CP~Cgs~ 27 (64)
T COG2093 6 ACKNCKRLT---PEDTEICPVCGST 27 (64)
T ss_pred HHhhccccC---CCCCccCCCCCCc
Confidence 455555432 2233346666654
No 208
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=61.34 E-value=6.8 Score=29.44 Aligned_cols=33 Identities=27% Similarity=0.483 Sum_probs=26.4
Q ss_pred CCCCCCCccccccc-cceeecCCCCceeeeeCCC
Q 026283 182 GACPACKREFIGSK-SQIIRCAGCGNIVWQPEGD 214 (240)
Q Consensus 182 g~CPvC~~eFtG~n-nt~~~CpnCGe~l~v~~g~ 214 (240)
-.||+|+....=.. ++...|+.|+..--+.+|-
T Consensus 9 LaCP~~kg~L~~~~~~~~L~c~~~~~aYpI~dGI 42 (60)
T COG2835 9 LACPVCKGPLVYDEEKQELICPRCKLAYPIRDGI 42 (60)
T ss_pred eeccCcCCcceEeccCCEEEecccCceeecccCc
Confidence 47999998855433 4578999999999998885
No 209
>TIGR00630 uvra excinuclease ABC, A subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=61.14 E-value=5.2 Score=42.47 Aligned_cols=31 Identities=26% Similarity=0.422 Sum_probs=25.3
Q ss_pred cCCCCCCCcccc-------ccccceeecCCC---Cceeeee
Q 026283 181 KGACPACKREFI-------GSKSQIIRCAGC---GNIVWQP 211 (240)
Q Consensus 181 eg~CPvC~~eFt-------G~nnt~~~CpnC---Ge~l~v~ 211 (240)
...||.|+++|. .||+..--||.| |+.+.+.
T Consensus 250 ~~~c~~~g~~~~~~~~~~FSfNsp~G~Cp~C~G~G~~~~~d 290 (924)
T TIGR00630 250 HAACPECGFSLPELEPRLFSFNSPYGACPECSGLGIKQEFD 290 (924)
T ss_pred cccCcccCcccCcCChhhcCCCCCcCCCCCCccceeeeecC
Confidence 467999999988 688889999999 7665443
No 210
>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=61.08 E-value=15 Score=26.74 Aligned_cols=19 Identities=21% Similarity=0.405 Sum_probs=14.5
Q ss_pred cccccceeecCCCCceeee
Q 026283 192 IGSKSQIIRCAGCGNIVWQ 210 (240)
Q Consensus 192 tG~nnt~~~CpnCGe~l~v 210 (240)
.+.++..-.|||||..|-.
T Consensus 52 ~~~kd~~H~Cp~C~~~lg~ 70 (73)
T PF10601_consen 52 DSCKDVYHYCPNCGAFLGT 70 (73)
T ss_pred ccccCceEECCCCCCEeEE
Confidence 4567888889999887754
No 211
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=61.08 E-value=4.1 Score=33.45 Aligned_cols=22 Identities=14% Similarity=0.344 Sum_probs=16.6
Q ss_pred CccccccccceeecCCCCceee
Q 026283 188 KREFIGSKSQIIRCAGCGNIVW 209 (240)
Q Consensus 188 ~~eFtG~nnt~~~CpnCGe~l~ 209 (240)
+-.|+-+.-..+.||.|||++.
T Consensus 37 ~~~~VeIevG~~~cP~Cge~~~ 58 (102)
T PF04475_consen 37 DLDYVEIEVGDTICPKCGEELD 58 (102)
T ss_pred CCCeEEEecCcccCCCCCCccC
Confidence 4567777778888999998763
No 212
>PRK05580 primosome assembly protein PriA; Validated
Probab=60.46 E-value=6 Score=40.04 Aligned_cols=14 Identities=29% Similarity=0.634 Sum_probs=8.5
Q ss_pred eeecCCCCceeeee
Q 026283 198 IIRCAGCGNIVWQP 211 (240)
Q Consensus 198 ~~~CpnCGe~l~v~ 211 (240)
..+||+||......
T Consensus 421 ~~~Cp~Cg~~~l~~ 434 (679)
T PRK05580 421 PKACPECGSTDLVP 434 (679)
T ss_pred CCCCCCCcCCeeEE
Confidence 34688887764443
No 213
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=60.41 E-value=9.4 Score=25.38 Aligned_cols=23 Identities=26% Similarity=0.878 Sum_probs=20.3
Q ss_pred CCCCCccccccccceeecCCCCcee
Q 026283 184 CPACKREFIGSKSQIIRCAGCGNIV 208 (240)
Q Consensus 184 CPvC~~eFtG~nnt~~~CpnCGe~l 208 (240)
|++|+. .+-.+..++|-+|++-.
T Consensus 2 C~vC~~--~~~~~~~i~C~~C~~~~ 24 (51)
T PF00628_consen 2 CPVCGQ--SDDDGDMIQCDSCNRWY 24 (51)
T ss_dssp BTTTTS--SCTTSSEEEBSTTSCEE
T ss_pred CcCCCC--cCCCCCeEEcCCCChhh
Confidence 899999 88899999999999654
No 214
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=60.29 E-value=4.8 Score=35.26 Aligned_cols=34 Identities=24% Similarity=0.610 Sum_probs=22.4
Q ss_pred hhhhhcCCCCCCCccccc--c-ccceeecCCCCceee
Q 026283 176 NNFVIKGACPACKREFIG--S-KSQIIRCAGCGNIVW 209 (240)
Q Consensus 176 kRnLIeg~CPvC~~eFtG--~-nnt~~~CpnCGe~l~ 209 (240)
.-++-+-.|..|++.+.. + .+..-.||.||.++.
T Consensus 117 HG~~~~~~C~~C~~~~~~~~~~~~~~p~C~~Cgg~lr 153 (242)
T PRK00481 117 HGSLLRARCTKCGQTYDLDEYLKPEPPRCPKCGGILR 153 (242)
T ss_pred cCCcCceeeCCCCCCcChhhhccCCCCCCCCCCCccC
Confidence 345566789999987642 1 233445999997654
No 215
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=59.92 E-value=6.1 Score=31.27 Aligned_cols=14 Identities=14% Similarity=0.081 Sum_probs=8.2
Q ss_pred ceeecCCCCceeee
Q 026283 197 QIIRCAGCGNIVWQ 210 (240)
Q Consensus 197 t~~~CpnCGe~l~v 210 (240)
++.+||-|..+-+.
T Consensus 70 ~~~~CPmCR~~w~~ 83 (85)
T PF12861_consen 70 SKGQCPMCRQPWKF 83 (85)
T ss_pred CCCCCCCcCCeeee
Confidence 34567777665443
No 216
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=59.52 E-value=5.4 Score=44.32 Aligned_cols=33 Identities=30% Similarity=0.684 Sum_probs=24.8
Q ss_pred cCCCCCCCcc-c-------cccccceeecCCCCceeeeeCCC
Q 026283 181 KGACPACKRE-F-------IGSKSQIIRCAGCGNIVWQPEGD 214 (240)
Q Consensus 181 eg~CPvC~~e-F-------tG~nnt~~~CpnCGe~l~v~~g~ 214 (240)
.--||.|+|. | .||.--.--||.||+++ ..+||
T Consensus 914 HY~Cp~Cky~Ef~~d~svgsGfDLpdK~CPkCg~pl-~kDG~ 954 (1444)
T COG2176 914 HYLCPECKYSEFIDDGSVGSGFDLPDKDCPKCGTPL-KKDGH 954 (1444)
T ss_pred cccCCCCceeeeecCCCcCCCCCCCCCCCCcCCCcc-ccCCC
Confidence 3469999983 3 36777788999999995 45665
No 217
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=59.52 E-value=5.6 Score=35.87 Aligned_cols=22 Identities=23% Similarity=0.575 Sum_probs=10.9
Q ss_pred CCCCCCcccc----ccccceeecCCCC
Q 026283 183 ACPACKREFI----GSKSQIIRCAGCG 205 (240)
Q Consensus 183 ~CPvC~~eFt----G~nnt~~~CpnCG 205 (240)
.||+||.+.. | ..+-..||+|+
T Consensus 247 pC~~Cg~~I~~~~~~-gR~t~~CP~CQ 272 (272)
T TIGR00577 247 PCRRCGTPIEKIKVG-GRGTHFCPQCQ 272 (272)
T ss_pred CCCCCCCeeEEEEEC-CCCCEECCCCC
Confidence 4666665433 3 13334566663
No 218
>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=59.29 E-value=4.6 Score=43.85 Aligned_cols=22 Identities=36% Similarity=1.026 Sum_probs=17.9
Q ss_pred CCCCCCCccccccccceeecCCCCcee
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNIV 208 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~l 208 (240)
-.||.|+.+ .-..+||.||+..
T Consensus 626 RKCPkCG~y-----Tlk~rCP~CG~~T 647 (1095)
T TIGR00354 626 RKCPQCGKE-----SFWLKCPVCGELT 647 (1095)
T ss_pred EECCCCCcc-----cccccCCCCCCcc
Confidence 379999987 3467899999885
No 219
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=59.17 E-value=6.7 Score=27.19 Aligned_cols=26 Identities=31% Similarity=0.666 Sum_probs=17.7
Q ss_pred CCCCCCCcccc------------ccccceeecCCCCce
Q 026283 182 GACPACKREFI------------GSKSQIIRCAGCGNI 207 (240)
Q Consensus 182 g~CPvC~~eFt------------G~nnt~~~CpnCGe~ 207 (240)
=.||.|+.+|. -.......||=|.+.
T Consensus 3 f~CP~C~~~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~ 40 (54)
T PF05605_consen 3 FTCPYCGKGFSESSLVEHCEDEHRSESKNVVCPICSSR 40 (54)
T ss_pred cCCCCCCCccCHHHHHHHHHhHCcCCCCCccCCCchhh
Confidence 36899988765 223446788888763
No 220
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=59.14 E-value=5.3 Score=34.14 Aligned_cols=8 Identities=38% Similarity=1.257 Sum_probs=6.1
Q ss_pred CCCCCCcc
Q 026283 183 ACPACKRE 190 (240)
Q Consensus 183 ~CPvC~~e 190 (240)
.||+|+.+
T Consensus 2 ~Cp~C~~~ 9 (160)
T smart00709 2 DCPSCGGN 9 (160)
T ss_pred cCCCCCCC
Confidence 48888866
No 221
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=59.06 E-value=3 Score=38.14 Aligned_cols=36 Identities=25% Similarity=0.571 Sum_probs=27.0
Q ss_pred hcCCCCCCCcccc-------ccccceeecCCCCceeeeeCCCc
Q 026283 180 IKGACPACKREFI-------GSKSQIIRCAGCGNIVWQPEGDF 215 (240)
Q Consensus 180 Ieg~CPvC~~eFt-------G~nnt~~~CpnCGe~l~v~~g~F 215 (240)
.-..|-.|..... --++...+||+||-+|--..+++
T Consensus 196 ~g~~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgRILy~~e~~~ 238 (239)
T COG1579 196 EGRVCGGCHMKLPSQTLSKVRKKDEIVFCPYCGRILYYDESEE 238 (239)
T ss_pred cCCcccCCeeeecHHHHHHHhcCCCCccCCccchHHHhhhccc
Confidence 4567888876543 22788999999999998777654
No 222
>PRK08197 threonine synthase; Validated
Probab=58.96 E-value=6.5 Score=36.79 Aligned_cols=31 Identities=16% Similarity=0.384 Sum_probs=23.4
Q ss_pred cCCCCCCCccccccccceeecCCCCceeeeeCC
Q 026283 181 KGACPACKREFIGSKSQIIRCAGCGNIVWQPEG 213 (240)
Q Consensus 181 eg~CPvC~~eFtG~nnt~~~CpnCGe~l~v~~g 213 (240)
.-.|+.|+.++. .......| .||.+|.+.-+
T Consensus 7 ~~~C~~Cg~~~~-~~~~~~~C-~cg~~l~~~~d 37 (394)
T PRK08197 7 HLECSKCGETYD-ADQVHNLC-KCGKPLLVRYD 37 (394)
T ss_pred EEEECCCCCCCC-CCCcceec-CCCCeeEEEec
Confidence 468999999985 34445679 79999888743
No 223
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=58.95 E-value=5.8 Score=28.82 Aligned_cols=16 Identities=19% Similarity=0.470 Sum_probs=13.6
Q ss_pred eeecCCCCceeeeeCC
Q 026283 198 IIRCAGCGNIVWQPEG 213 (240)
Q Consensus 198 ~~~CpnCGe~l~v~~g 213 (240)
+..||.||+.+.+++.
T Consensus 2 ~~~CP~CG~~iev~~~ 17 (54)
T TIGR01206 2 QFECPDCGAEIELENP 17 (54)
T ss_pred ccCCCCCCCEEecCCC
Confidence 3579999999999875
No 224
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=58.29 E-value=17 Score=28.30 Aligned_cols=42 Identities=21% Similarity=0.271 Sum_probs=28.4
Q ss_pred HHHHHHHHhh------hhhc--CCCCCCCcccccccc--------ceeecCCCCceee
Q 026283 168 PLLIGTVANN------FVIK--GACPACKREFIGSKS--------QIIRCAGCGNIVW 209 (240)
Q Consensus 168 p~li~wWlkR------nLIe--g~CPvC~~eFtG~nn--------t~~~CpnCGe~l~ 209 (240)
.++.|+-.+. +++. -.||.|+++..-+.+ +.-+|..|++++.
T Consensus 12 ~~~~R~p~~~~~~~~~~i~~~rS~C~~C~~~L~~~~lIPi~S~l~lrGrCr~C~~~I~ 69 (92)
T PF06750_consen 12 VLAYRLPRGEELEPSLSIIFPRSHCPHCGHPLSWWDLIPILSYLLLRGRCRYCGAPIP 69 (92)
T ss_pred HHHHHhHhHhhhccCCCccCCCCcCcCCCCcCcccccchHHHHHHhCCCCcccCCCCC
Confidence 3444554454 5553 689999998766655 5668999998764
No 225
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=57.85 E-value=3.8 Score=35.01 Aligned_cols=24 Identities=21% Similarity=0.452 Sum_probs=18.9
Q ss_pred hhhhhc--CCCCCCCcccccccccee
Q 026283 176 NNFVIK--GACPACKREFIGSKSQII 199 (240)
Q Consensus 176 kRnLIe--g~CPvC~~eFtG~nnt~~ 199 (240)
..|+|+ -+||.||+.|++|..-..
T Consensus 21 ~~~~~~~~~~c~~c~~~f~~~e~~~~ 46 (154)
T PRK00464 21 DGNAIRRRRECLACGKRFTTFERVEL 46 (154)
T ss_pred CCCceeeeeeccccCCcceEeEeccC
Confidence 356777 899999999999865443
No 226
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 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 DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=57.82 E-value=2.8 Score=31.74 Aligned_cols=33 Identities=24% Similarity=0.482 Sum_probs=19.4
Q ss_pred hcCCCCCCCcccccccc--------ceeecCCCCceeeeeC
Q 026283 180 IKGACPACKREFIGSKS--------QIIRCAGCGNIVWQPE 212 (240)
Q Consensus 180 Ieg~CPvC~~eFtG~nn--------t~~~CpnCGe~l~v~~ 212 (240)
++=+|.+|+.+-+=.-+ -.+|||+|.+.-.+.+
T Consensus 3 l~FTC~~C~~Rs~~~~sk~aY~~GvViv~C~gC~~~HlIaD 43 (66)
T PF05180_consen 3 LTFTCNKCGTRSAKMFSKQAYHKGVVIVQCPGCKNRHLIAD 43 (66)
T ss_dssp EEEEETTTTEEEEEEEEHHHHHTSEEEEE-TTS--EEES--
T ss_pred EEEEcCCCCCccceeeCHHHHhCCeEEEECCCCcceeeehh
Confidence 45579999877653222 3579999999877776
No 227
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=57.82 E-value=6.7 Score=40.92 Aligned_cols=16 Identities=19% Similarity=0.374 Sum_probs=10.2
Q ss_pred ceeecCCCCceeeeeC
Q 026283 197 QIIRCAGCGNIVWQPE 212 (240)
Q Consensus 197 t~~~CpnCGe~l~v~~ 212 (240)
...+||+||....+.-
T Consensus 474 ~p~~Cp~Cgs~~L~~~ 489 (730)
T COG1198 474 IPQSCPECGSEHLRAV 489 (730)
T ss_pred CCCCCCCCCCCeeEEe
Confidence 3457888887755444
No 228
>PLN02569 threonine synthase
Probab=57.56 E-value=7.5 Score=38.24 Aligned_cols=29 Identities=14% Similarity=0.309 Sum_probs=23.3
Q ss_pred CCCCCCCccccccccceeecCCCCceeeeeC
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNIVWQPE 212 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~l~v~~ 212 (240)
-.|+.|+.+| ........| .||.+|.+.-
T Consensus 50 l~C~~Cg~~y-~~~~~~~~C-~cgg~l~~~~ 78 (484)
T PLN02569 50 LECPLTGEKY-SLDEVVYRS-KSGGLLDVRH 78 (484)
T ss_pred cEeCCCCCcC-CCccccccC-CCCCeEEEec
Confidence 4899999997 445556789 6999999884
No 229
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=57.54 E-value=10 Score=25.52 Aligned_cols=29 Identities=28% Similarity=0.527 Sum_probs=23.7
Q ss_pred hcCCCCCCCccccccccceeecCCCCcee
Q 026283 180 IKGACPACKREFIGSKSQIIRCAGCGNIV 208 (240)
Q Consensus 180 Ieg~CPvC~~eFtG~nnt~~~CpnCGe~l 208 (240)
.-..|-+|+....|+..+..+|..|+..+
T Consensus 10 ~~~~C~~C~~~i~g~~~~g~~C~~C~~~~ 38 (53)
T PF00130_consen 10 KPTYCDVCGKFIWGLGKQGYRCSWCGLVC 38 (53)
T ss_dssp STEB-TTSSSBECSSSSCEEEETTTT-EE
T ss_pred CCCCCcccCcccCCCCCCeEEECCCCChH
Confidence 34579999999999999999999999765
No 230
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=57.54 E-value=6.9 Score=30.37 Aligned_cols=30 Identities=23% Similarity=0.624 Sum_probs=22.4
Q ss_pred CCCCCCCccccccccc--eeecCCCCceeeeeCCC
Q 026283 182 GACPACKREFIGSKSQ--IIRCAGCGNIVWQPEGD 214 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt--~~~CpnCGe~l~v~~g~ 214 (240)
-.||.|+|.-..-+.. ---||-|+ |+-+|.
T Consensus 2 ~~CPCCg~~Tl~~~~~~~ydIC~VC~---WEdD~~ 33 (78)
T PF14206_consen 2 YPCPCCGYYTLEERGEGTYDICPVCF---WEDDGV 33 (78)
T ss_pred ccCCCCCcEEeccCCCcCceECCCCC---cccCCc
Confidence 3699999987765554 77899998 666653
No 231
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=56.87 E-value=4.4 Score=44.30 Aligned_cols=22 Identities=32% Similarity=0.948 Sum_probs=18.8
Q ss_pred CCCCCCccccccccceeecCCCCce
Q 026283 183 ACPACKREFIGSKSQIIRCAGCGNI 207 (240)
Q Consensus 183 ~CPvC~~eFtG~nnt~~~CpnCGe~ 207 (240)
.|--|+++|+.. +. .||+||-.
T Consensus 696 rC~dcg~q~~~~--~~-~cP~Cgs~ 717 (1187)
T COG1110 696 RCRDCGEQFVDS--ED-KCPRCGSR 717 (1187)
T ss_pred HHhhcCceeccc--cc-cCCCCCCc
Confidence 599999999999 22 89999973
No 232
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=56.29 E-value=9.2 Score=30.46 Aligned_cols=34 Identities=21% Similarity=0.314 Sum_probs=25.8
Q ss_pred hcCCCCCCCccccccccceeecCCCCceeeeeCC
Q 026283 180 IKGACPACKREFIGSKSQIIRCAGCGNIVWQPEG 213 (240)
Q Consensus 180 Ieg~CPvC~~eFtG~nnt~~~CpnCGe~l~v~~g 213 (240)
-+-.|.-|+.+|.=+.|+-..|+.|+..|=..=|
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~ 86 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCG 86 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSE
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccC
Confidence 3558999999999888999999999987754433
No 233
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=56.20 E-value=11 Score=39.29 Aligned_cols=22 Identities=32% Similarity=0.874 Sum_probs=10.1
Q ss_pred CCCCCCccccccccceeecCCCC
Q 026283 183 ACPACKREFIGSKSQIIRCAGCG 205 (240)
Q Consensus 183 ~CPvC~~eFtG~nnt~~~CpnCG 205 (240)
.||.|+.... +..-=..|++||
T Consensus 726 ~Cp~Cg~~l~-~~~GC~~C~~CG 747 (752)
T PRK08665 726 ACPECGSILE-HEEGCVVCHSCG 747 (752)
T ss_pred CCCCCCcccE-ECCCCCcCCCCC
Confidence 4666664322 112223566666
No 234
>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=56.03 E-value=6.2 Score=34.49 Aligned_cols=32 Identities=16% Similarity=0.304 Sum_probs=21.0
Q ss_pred hhhcCCCCCCCccccccc-cceeecCCCCceee
Q 026283 178 FVIKGACPACKREFIGSK-SQIIRCAGCGNIVW 209 (240)
Q Consensus 178 nLIeg~CPvC~~eFtG~n-nt~~~CpnCGe~l~ 209 (240)
++-+..|..|+.++.--. ...-.||+||.+|.
T Consensus 115 ~~~~~~C~~C~~~~~~~~~~~~p~C~~Cgg~lr 147 (225)
T cd01411 115 SLYRIYCTVCGKTVDWEEYLKSPYHAKCGGVIR 147 (225)
T ss_pred CcCeeEeCCCCCccchhhcCCCCCCCCCCCEeC
Confidence 344578999987764211 23467999998764
No 235
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=55.88 E-value=4.9 Score=30.42 Aligned_cols=22 Identities=32% Similarity=0.490 Sum_probs=15.6
Q ss_pred cCCCCCCCccccccccceeecCCCCce
Q 026283 181 KGACPACKREFIGSKSQIIRCAGCGNI 207 (240)
Q Consensus 181 eg~CPvC~~eFtG~nnt~~~CpnCGe~ 207 (240)
+-+|..|++=- ...+||+||-.
T Consensus 5 ~~AC~~C~~i~-----~~~~Cp~Cgs~ 26 (64)
T PRK06393 5 YRACKKCKRLT-----PEKTCPVHGDE 26 (64)
T ss_pred hhhHhhCCccc-----CCCcCCCCCCC
Confidence 45788888755 23389999874
No 236
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=55.61 E-value=7.6 Score=36.42 Aligned_cols=32 Identities=16% Similarity=0.313 Sum_probs=23.5
Q ss_pred HHHhhhhhcCCCCCCCccccccc-cceeecCCCCce
Q 026283 173 TVANNFVIKGACPACKREFIGSK-SQIIRCAGCGNI 207 (240)
Q Consensus 173 wWlkRnLIeg~CPvC~~eFtG~n-nt~~~CpnCGe~ 207 (240)
-|.+.+ --||.||.+-.... ....+||+||+.
T Consensus 106 ~w~~~~---RFCg~CG~~~~~~~~g~~~~C~~cg~~ 138 (279)
T COG2816 106 EWYRSH---RFCGRCGTKTYPREGGWARVCPKCGHE 138 (279)
T ss_pred HHHhhC---cCCCCCCCcCccccCceeeeCCCCCCc
Confidence 455444 46999998876554 467899999985
No 237
>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=55.37 E-value=5.6 Score=35.82 Aligned_cols=10 Identities=40% Similarity=1.198 Sum_probs=4.8
Q ss_pred cCCCCCCCcc
Q 026283 181 KGACPACKRE 190 (240)
Q Consensus 181 eg~CPvC~~e 190 (240)
.+.|||||..
T Consensus 172 ~g~CPvCGs~ 181 (290)
T PF04216_consen 172 RGYCPVCGSP 181 (290)
T ss_dssp -SS-TTT---
T ss_pred CCcCCCCCCc
Confidence 4899999975
No 238
>PRK07561 DNA topoisomerase I subunit omega; Validated
Probab=54.96 E-value=9.6 Score=39.88 Aligned_cols=16 Identities=25% Similarity=0.490 Sum_probs=13.9
Q ss_pred ecCCCCceeeeeCCCc
Q 026283 200 RCAGCGNIVWQPEGDF 215 (240)
Q Consensus 200 ~CpnCGe~l~v~~g~F 215 (240)
.||.||.++.+..|.|
T Consensus 647 ~~P~cg~~i~~r~Gr~ 662 (859)
T PRK07561 647 ADPECGTAMVLRSGRF 662 (859)
T ss_pred CCCCCCCeeEEecCCC
Confidence 5799999999998876
No 239
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=54.67 E-value=11 Score=37.67 Aligned_cols=22 Identities=23% Similarity=0.546 Sum_probs=17.5
Q ss_pred CCCCCCCccccccccceeecCCCCc
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGN 206 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe 206 (240)
-.|-.|||++. .-.-+||+||+
T Consensus 8 f~C~~CG~~s~---KW~GkCp~Cg~ 29 (456)
T COG1066 8 FVCQECGYVSP---KWLGKCPACGA 29 (456)
T ss_pred EEcccCCCCCc---cccccCCCCCC
Confidence 46999999975 44568999994
No 240
>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=54.34 E-value=4.6 Score=37.42 Aligned_cols=28 Identities=18% Similarity=0.554 Sum_probs=21.3
Q ss_pred CCCCCCccccc--cccceeecCCCCceeee
Q 026283 183 ACPACKREFIG--SKSQIIRCAGCGNIVWQ 210 (240)
Q Consensus 183 ~CPvC~~eFtG--~nnt~~~CpnCGe~l~v 210 (240)
.||.|+.-..- +....-.||+||--...
T Consensus 28 ~c~~c~~~~~~~~l~~~~~vc~~c~~h~rl 57 (285)
T TIGR00515 28 KCPKCGQVLYTKELERNLEVCPKCDHHMRM 57 (285)
T ss_pred ECCCCcchhhHHHHHhhCCCCCCCCCcCcC
Confidence 69999987765 44455789999987654
No 241
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=54.10 E-value=6.3 Score=31.91 Aligned_cols=26 Identities=27% Similarity=0.533 Sum_probs=21.8
Q ss_pred CCCCCCCccccccccceee-----------cCCCCce
Q 026283 182 GACPACKREFIGSKSQIIR-----------CAGCGNI 207 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~-----------CpnCGe~ 207 (240)
-.||.|+++=..|.+.|++ |..||..
T Consensus 73 ~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~ 109 (113)
T COG1594 73 EKCPKCGNKEAYYWQLQTRSADEPETRFYKCTRCGYR 109 (113)
T ss_pred ccCCCCCCceeEEEeeehhccCCCceEEEEecccCCE
Confidence 4699999999999998876 8888864
No 242
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=53.98 E-value=7.6 Score=33.94 Aligned_cols=25 Identities=28% Similarity=0.595 Sum_probs=14.9
Q ss_pred CCCCCCCccccccccc-------e----eecCCCCc
Q 026283 182 GACPACKREFIGSKSQ-------I----IRCAGCGN 206 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt-------~----~~CpnCGe 206 (240)
+.||-|+++=|-.-.+ . -.|++||+
T Consensus 1 M~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~ 36 (156)
T COG1327 1 MKCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGE 36 (156)
T ss_pred CCCCCCCCCCCeeeecccccccchhhhhhccccccc
Confidence 4688888765543222 1 24888875
No 243
>COG1503 eRF1 Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]
Probab=53.80 E-value=6.6 Score=38.66 Aligned_cols=32 Identities=28% Similarity=0.619 Sum_probs=21.6
Q ss_pred hcCCCCCCCcccccc--ccc--eeecCCCCceeeee
Q 026283 180 IKGACPACKREFIGS--KSQ--IIRCAGCGNIVWQP 211 (240)
Q Consensus 180 Ieg~CPvC~~eFtG~--nnt--~~~CpnCGe~l~v~ 211 (240)
++-.||.|++++.=- .+. ..+||.||.+....
T Consensus 326 ~~~~c~~~~~e~~~t~~~~~~~~~~~~~~~~e~~~v 361 (411)
T COG1503 326 VTYKCPTCGYENLKSKREFEQKRFRCPECGSEMEEV 361 (411)
T ss_pred eeecCCCcchhhhhcccccccccccCccccccccch
Confidence 466899999998321 111 23999999876543
No 244
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 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. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=53.55 E-value=2.4 Score=28.35 Aligned_cols=28 Identities=29% Similarity=0.683 Sum_probs=16.6
Q ss_pred CCCCCcccccc-----ccceeecCCCCceeeee
Q 026283 184 CPACKREFIGS-----KSQIIRCAGCGNIVWQP 211 (240)
Q Consensus 184 CPvC~~eFtG~-----nnt~~~CpnCGe~l~v~ 211 (240)
|+.|..|+.-- .-+-+-|++||=.+++-
T Consensus 2 C~~C~~Ey~~p~~RR~~~~~isC~~CGPr~~i~ 34 (35)
T PF07503_consen 2 CDDCLKEYFDPSNRRFHYQFISCTNCGPRYSII 34 (35)
T ss_dssp -HHHHHHHCSTTSTTTT-TT--BTTCC-SCCCE
T ss_pred CHHHHHHHcCCCCCcccCcCccCCCCCCCEEEe
Confidence 77787777653 34668899999877653
No 245
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=53.33 E-value=45 Score=23.93 Aligned_cols=19 Identities=21% Similarity=0.317 Sum_probs=15.1
Q ss_pred cccccceeecCCCCceeee
Q 026283 192 IGSKSQIIRCAGCGNIVWQ 210 (240)
Q Consensus 192 tG~nnt~~~CpnCGe~l~v 210 (240)
.++++..-.||+||..|-+
T Consensus 46 ~~~kd~~H~Cp~C~~~lg~ 64 (67)
T smart00714 46 DSFKDVNHYCPNCGAFLGT 64 (67)
T ss_pred ccccCccEECCCCCCEeEE
Confidence 4678888899999988754
No 246
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=53.28 E-value=4 Score=30.10 Aligned_cols=15 Identities=33% Similarity=0.826 Sum_probs=11.9
Q ss_pred hhhcCCCCCCCcccc
Q 026283 178 FVIKGACPACKREFI 192 (240)
Q Consensus 178 nLIeg~CPvC~~eFt 192 (240)
.|-+--||||+++|+
T Consensus 9 ~lp~KICpvCqRPFs 23 (54)
T COG4338 9 TLPDKICPVCQRPFS 23 (54)
T ss_pred ccchhhhhhhcCchH
Confidence 355667999999996
No 247
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=53.22 E-value=8.8 Score=40.06 Aligned_cols=25 Identities=16% Similarity=0.348 Sum_probs=18.5
Q ss_pred cCCCCCCCccccccccceeecCCCCceeeeeCC
Q 026283 181 KGACPACKREFIGSKSQIIRCAGCGNIVWQPEG 213 (240)
Q Consensus 181 eg~CPvC~~eFtG~nnt~~~CpnCGe~l~v~~g 213 (240)
.-.|+.|||-+ +||||.-.++..+.
T Consensus 435 ~l~C~~Cg~v~--------~Cp~Cd~~lt~H~~ 459 (730)
T COG1198 435 LLLCRDCGYIA--------ECPNCDSPLTLHKA 459 (730)
T ss_pred eeecccCCCcc--------cCCCCCcceEEecC
Confidence 34699998854 68888888777664
No 248
>PRK14973 DNA topoisomerase I; Provisional
Probab=53.07 E-value=10 Score=40.44 Aligned_cols=16 Identities=13% Similarity=0.034 Sum_probs=12.2
Q ss_pred ecCCCCc--eeeeeCCCc
Q 026283 200 RCAGCGN--IVWQPEGDF 215 (240)
Q Consensus 200 ~CpnCGe--~l~v~~g~F 215 (240)
.||.||. ++.+..|+|
T Consensus 637 ~Cp~CG~p~~~~~r~Gr~ 654 (936)
T PRK14973 637 VCPIHHLNHVRLIRKGAR 654 (936)
T ss_pred CCCCCCCCceEEeecCCC
Confidence 5999997 555678875
No 249
>PF03563 Bunya_G2: Bunyavirus glycoprotein G2; InterPro: IPR005168 Bunyavirus has three genomic segments: small (S), middle-sized (M), and large (L). The S segment encodes the nucleocapsid and a non-structural protein. The M segment codes for two glycoproteins, G1 and G2, and another non-structural protein (NSm). The L segment codes for an RNA polymerase. This entry represents the polyprotein region forming the G2 glycoprotein, which interacts with the IPR005167 from INTERPRO G1 glycoprotein [].
Probab=52.84 E-value=52 Score=31.31 Aligned_cols=55 Identities=20% Similarity=0.405 Sum_probs=35.9
Q ss_pred HHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHH--HHHHHhhhhhcCCCCCCCcccccccc
Q 026283 140 TIFFLWFALSGWLFRILI----LATWVLPIAAPLL--IGTVANNFVIKGACPACKREFIGSKS 196 (240)
Q Consensus 140 tl~~~wll~SGWLvn~~l----~l~~vlPvaap~l--i~wWlkRnLIeg~CPvC~~eFtG~nn 196 (240)
+|+++.|.+.+-++-.+| +.-+++|+..|+. -||..||-- -.||.|+-..-=|-|
T Consensus 189 lIil~~~~~~~~i~~~IltktYi~YlliPiF~P~~~~Yg~~ynk~c--k~C~nC~La~HPFtn 249 (285)
T PF03563_consen 189 LIILTCLTLIIFIFLIILTKTYICYLLIPIFYPIAYLYGWLYNKSC--KKCKNCGLAYHPFTN 249 (285)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh--hhCcccCeeccCCCC
Confidence 444455555555555554 7778899999988 678888754 468888755444433
No 250
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=52.72 E-value=7.9 Score=34.25 Aligned_cols=30 Identities=27% Similarity=0.428 Sum_probs=23.9
Q ss_pred CCCCCCCccccccccceeecCCCCceeeeeCCC
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNIVWQPEGD 214 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~l~v~~g~ 214 (240)
-.|-.|+..|. --.-.||.||-++....-.
T Consensus 140 ~rC~GC~~~f~---~~~~~Cp~CG~~~~~~~~~ 169 (177)
T COG1439 140 LRCHGCKRIFP---EPKDFCPICGSPLKRKRVK 169 (177)
T ss_pred EEEecCceecC---CCCCcCCCCCCceEEeeec
Confidence 36999999999 4456799999998776543
No 251
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=52.61 E-value=13 Score=31.05 Aligned_cols=27 Identities=22% Similarity=0.334 Sum_probs=19.9
Q ss_pred eecCCCCceeeeeCCCcccCCCCCCCCCCCCCCeeeeec
Q 026283 199 IRCAGCGNIVWQPEGDFFSRNGGGKKSTKSDDDIIDVDF 237 (240)
Q Consensus 199 ~~CpnCGe~l~v~~g~F~s~~g~~~~~r~t~pgtIDVe~ 237 (240)
-.||+||..|-|+-=. +--|-|.|+|.
T Consensus 75 yyCP~Cgt~levE~~~------------Pg~P~~hD~ep 101 (112)
T PF08882_consen 75 YYCPGCGTQLEVEAPP------------PGYPPIHDFEP 101 (112)
T ss_pred EECCCCcceeEEccCC------------CCCCceEeccc
Confidence 4699999999998642 44566777664
No 252
>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=52.35 E-value=4.5 Score=36.44 Aligned_cols=24 Identities=33% Similarity=0.666 Sum_probs=11.0
Q ss_pred CCCCCCccccccccceeecCCCCceee
Q 026283 183 ACPACKREFIGSKSQIIRCAGCGNIVW 209 (240)
Q Consensus 183 ~CPvC~~eFtG~nnt~~~CpnCGe~l~ 209 (240)
.|..|+.+--= ....||+|||.=.
T Consensus 199 ~Cs~C~t~W~~---~R~~Cp~Cg~~~~ 222 (290)
T PF04216_consen 199 HCSLCGTEWRF---VRIKCPYCGNTDH 222 (290)
T ss_dssp EETTT--EEE-----TTS-TTT---SS
T ss_pred EcCCCCCeeee---cCCCCcCCCCCCC
Confidence 58888877633 3456888888633
No 253
>PHA02998 RNA polymerase subunit; Provisional
Probab=52.33 E-value=8.2 Score=34.77 Aligned_cols=33 Identities=24% Similarity=0.527 Sum_probs=25.1
Q ss_pred hcCCCCCCCccccccccceee-----------cCCCCceeeeeC
Q 026283 180 IKGACPACKREFIGSKSQIIR-----------CAGCGNIVWQPE 212 (240)
Q Consensus 180 Ieg~CPvC~~eFtG~nnt~~~-----------CpnCGe~l~v~~ 212 (240)
++-.||.|++.=+-+-+-|+| |.+||..-.-|.
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkppk 185 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKPPK 185 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCCcc
Confidence 556899999988887777764 999998655443
No 254
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=52.28 E-value=6.5 Score=29.78 Aligned_cols=25 Identities=28% Similarity=0.582 Sum_probs=21.1
Q ss_pred hcCCCCCCCccccccccceeecCCCCc
Q 026283 180 IKGACPACKREFIGSKSQIIRCAGCGN 206 (240)
Q Consensus 180 Ieg~CPvC~~eFtG~nnt~~~CpnCGe 206 (240)
..--|.-||.. .|+.|.-+|.+||-
T Consensus 16 tHt~CrRCG~~--syh~qK~~CasCGy 40 (62)
T PRK04179 16 THIRCRRCGRH--SYNVRKKYCAACGF 40 (62)
T ss_pred ccchhcccCcc--cccccccchhhcCC
Confidence 44579999987 78999999999996
No 255
>PLN03121 nucleic acid binding protein; Provisional
Probab=52.20 E-value=19 Score=33.30 Aligned_cols=49 Identities=12% Similarity=0.218 Sum_probs=36.3
Q ss_pred HHHHHHHhhhhhhhhhHhHHHHHHHHHHHHHHhhhhhhhhHhHHhhhhhhhhh
Q 026283 66 DAKKTAERIDRQYSVSRRLNSAARTAAVRARELDREFAISVRWRSFRMDFSRN 118 (240)
Q Consensus 66 ear~~a~r~D~~Y~vs~r~a~aa~~a~e~A~eiD~~fgi~rR~R~f~~D~~r~ 118 (240)
-|.....+||++.-+|.|++.-. +..+++|++|.+.-+-+++..-.-++
T Consensus 153 ~a~a~v~~~d~~iglt~k~~~g~----~~vk~vDeky~vs~~tksA~~aa~~~ 201 (243)
T PLN03121 153 TAAAKVAELSKRIGLTDKIFAGM----EAVRSVDEKYHVSEFTKSAATATGRT 201 (243)
T ss_pred hhhhhhhhhhhhccchhhhhhhH----HHHHhhhhhhhhHHHHHHHHHHHHHH
Confidence 34445557777777777777655 66799999999999999877766553
No 256
>PLN02610 probable methionyl-tRNA synthetase
Probab=52.09 E-value=5.5 Score=41.56 Aligned_cols=30 Identities=23% Similarity=0.784 Sum_probs=18.8
Q ss_pred HhhhhhcCCCCC--CCccccccccceeecCCCCcee
Q 026283 175 ANNFVIKGACPA--CKREFIGSKSQIIRCAGCGNIV 208 (240)
Q Consensus 175 lkRnLIeg~CPv--C~~eFtG~nnt~~~CpnCGe~l 208 (240)
|-...|+|.||. |+++= ..--||-+||..+
T Consensus 149 l~d~~v~G~CP~~~C~~~~----a~Gd~Ce~Cg~~~ 180 (801)
T PLN02610 149 LADRLVEGTCPTEGCNYDS----ARGDQCEKCGKLL 180 (801)
T ss_pred cchHHhcCcCCccccCccc----cccchhhhccccC
Confidence 334467899999 87762 2234677777533
No 257
>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=52.03 E-value=7.8 Score=34.84 Aligned_cols=15 Identities=13% Similarity=0.211 Sum_probs=11.1
Q ss_pred hhhcCCCCCCCcccc
Q 026283 178 FVIKGACPACKREFI 192 (240)
Q Consensus 178 nLIeg~CPvC~~eFt 192 (240)
|+-+..|+.|++++.
T Consensus 115 ~~~~~~C~~C~~~~~ 129 (260)
T cd01409 115 SLHRVVCLSCGFRTP 129 (260)
T ss_pred ecCEEEeCCCcCccC
Confidence 344567999999874
No 258
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=51.93 E-value=6.6 Score=24.02 Aligned_cols=9 Identities=56% Similarity=1.549 Sum_probs=7.6
Q ss_pred CCCCCCccc
Q 026283 183 ACPACKREF 191 (240)
Q Consensus 183 ~CPvC~~eF 191 (240)
.||.|++.|
T Consensus 4 ~C~~CgR~F 12 (25)
T PF13913_consen 4 PCPICGRKF 12 (25)
T ss_pred cCCCCCCEE
Confidence 688888888
No 259
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=51.87 E-value=4.5 Score=41.21 Aligned_cols=40 Identities=28% Similarity=0.598 Sum_probs=27.1
Q ss_pred hcCCCCCCCcccccc-ccceeecC--CCCceeeeeCCCcccCC
Q 026283 180 IKGACPACKREFIGS-KSQIIRCA--GCGNIVWQPEGDFFSRN 219 (240)
Q Consensus 180 Ieg~CPvC~~eFtG~-nnt~~~Cp--nCGe~l~v~~g~F~s~~ 219 (240)
.-..||+|+.+++=- +....+|+ +|-..+...=-||.|+.
T Consensus 391 ~P~~CP~C~s~l~~~~~~~~~~C~n~~C~aq~~~~l~hf~sr~ 433 (652)
T TIGR00575 391 FPTHCPSCGSPLVKIEEEAVIRCPNLNCPAQRVERIKHFASRN 433 (652)
T ss_pred CCCCCCCCCCEeEecCCcEEEEECCCCCHHHHHHHhHHhhcCC
Confidence 447999999988642 33567886 57776665556885543
No 260
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=51.84 E-value=22 Score=29.30 Aligned_cols=42 Identities=31% Similarity=0.615 Sum_probs=31.2
Q ss_pred HHHhhhhhc-CCCCCCCccc---ccc--c-cceeecCCCCceeeeeCCC
Q 026283 173 TVANNFVIK-GACPACKREF---IGS--K-SQIIRCAGCGNIVWQPEGD 214 (240)
Q Consensus 173 wWlkRnLIe-g~CPvC~~eF---tG~--n-nt~~~CpnCGe~l~v~~g~ 214 (240)
....+..+. -.||-|+.+- .|. + -|--+|++|+-..+.+.|.
T Consensus 21 ~~~~~~~~~~~~cP~C~s~~~~k~g~~~~~~qRyrC~~C~~tf~~~~~~ 69 (129)
T COG3677 21 AYAIRMQITKVNCPRCKSSNVVKIGGIRRGHQRYKCKSCGSTFTVETGS 69 (129)
T ss_pred HHHHhhhcccCcCCCCCccceeeECCccccccccccCCcCcceeeeccC
Confidence 344556666 7999999877 122 2 4677899999999999985
No 261
>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=51.81 E-value=8.8 Score=26.33 Aligned_cols=25 Identities=24% Similarity=0.716 Sum_probs=15.3
Q ss_pred CCCCCCcccc---------ccccceeecCC--CCce
Q 026283 183 ACPACKREFI---------GSKSQIIRCAG--CGNI 207 (240)
Q Consensus 183 ~CPvC~~eFt---------G~nnt~~~Cpn--CGe~ 207 (240)
.||.||..-. .++..-.||.| ||--
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg~t 36 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSPLTRELYCQCTNPECGHT 36 (47)
T ss_pred CcCCCCCeeEEEEchhhCcceEEEEEEECCCcCCCE
Confidence 4777776432 44556677777 7753
No 262
>PRK11463 fxsA phage T7 F exclusion suppressor FxsA; Reviewed
Probab=51.73 E-value=71 Score=26.95 Aligned_cols=31 Identities=16% Similarity=-0.008 Sum_probs=18.6
Q ss_pred HHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHH
Q 026283 142 FFLWFALS-GWLFRILILATWVLPIAAPLLIG 172 (240)
Q Consensus 142 ~~~wll~S-GWLvn~~l~l~~vlPvaap~li~ 172 (240)
++..+|+. =-++-.++++++++|..--++-+
T Consensus 78 ~~gg~LLi~PGf~tD~~Gllll~P~~R~~~~~ 109 (148)
T PRK11463 78 AVAGVLLLLPGFVTDILGLLLLLPPTRALLRP 109 (148)
T ss_pred HHHHHHHHccHHHHHHHHHHHHcchhHHHHHH
Confidence 34344333 34566777888888887555533
No 263
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=51.68 E-value=6.3 Score=29.19 Aligned_cols=11 Identities=27% Similarity=0.706 Sum_probs=9.0
Q ss_pred ecCCCCceeee
Q 026283 200 RCAGCGNIVWQ 210 (240)
Q Consensus 200 ~CpnCGe~l~v 210 (240)
-||+||+++-.
T Consensus 5 HC~~CG~~Ip~ 15 (59)
T PF09889_consen 5 HCPVCGKPIPP 15 (59)
T ss_pred cCCcCCCcCCc
Confidence 59999998864
No 264
>PF12279 DUF3619: Protein of unknown function (DUF3619); InterPro: IPR022064 This protein is found in bacteria. Proteins in this family are about 140 amino acids in length. This protein has two conserved sequence motifs: AAR and DDLP.
Probab=51.45 E-value=76 Score=26.56 Aligned_cols=30 Identities=33% Similarity=0.500 Sum_probs=21.6
Q ss_pred HHHHHHhhhhh-----hhhhHhHHHHHHHHHHHHH
Q 026283 67 AKKTAERIDRQ-----YSVSRRLNSAARTAAVRAR 96 (240)
Q Consensus 67 ar~~a~r~D~~-----Y~vs~r~a~aa~~a~e~A~ 96 (240)
|++++..||+. ++++.|++.|=+.|-++.+
T Consensus 7 a~~i~~~Ld~~a~~Lp~~i~~RL~aAR~~ALa~~k 41 (131)
T PF12279_consen 7 ARRIARALDESADDLPPDISERLAAARRQALARKK 41 (131)
T ss_pred HHHHHHHhhcccccCCHHHHHHHHHHHHHHHHhcc
Confidence 67778888774 7888998877666655543
No 265
>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=51.30 E-value=7.1 Score=32.60 Aligned_cols=19 Identities=21% Similarity=0.594 Sum_probs=14.1
Q ss_pred cccccceeecCCCCceeee
Q 026283 192 IGSKSQIIRCAGCGNIVWQ 210 (240)
Q Consensus 192 tG~nnt~~~CpnCGe~l~v 210 (240)
...+-.|.+|||||.+-++
T Consensus 63 lStkav~V~CP~C~K~TKm 81 (114)
T PF11023_consen 63 LSTKAVQVECPNCGKQTKM 81 (114)
T ss_pred hcccceeeECCCCCChHhh
Confidence 3445578999999987654
No 266
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=51.18 E-value=8.3 Score=25.04 Aligned_cols=27 Identities=26% Similarity=0.562 Sum_probs=22.8
Q ss_pred CCCCCCCccccccccceeecCCCCcee
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNIV 208 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~l 208 (240)
..|-+|+..+.|+-.+-.+|..|+-.+
T Consensus 12 ~~C~~C~~~i~~~~~~~~~C~~C~~~~ 38 (50)
T cd00029 12 TFCDVCRKSIWGLFKQGLRCSWCKVKC 38 (50)
T ss_pred CChhhcchhhhccccceeEcCCCCCch
Confidence 459999999999878889999997554
No 267
>PRK10445 endonuclease VIII; Provisional
Probab=51.01 E-value=9.6 Score=34.31 Aligned_cols=23 Identities=30% Similarity=0.679 Sum_probs=12.1
Q ss_pred CCCCCCCcccc----ccccceeecCCCC
Q 026283 182 GACPACKREFI----GSKSQIIRCAGCG 205 (240)
Q Consensus 182 g~CPvC~~eFt----G~nnt~~~CpnCG 205 (240)
..||+||.... |- .+-..||+|+
T Consensus 236 ~~Cp~Cg~~I~~~~~~g-R~t~~CP~CQ 262 (263)
T PRK10445 236 EACERCGGIIEKTTLSS-RPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCEeEEEEECC-CCcEECCCCc
Confidence 35777765432 22 3344577775
No 268
>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=50.92 E-value=8.6 Score=33.94 Aligned_cols=34 Identities=24% Similarity=0.668 Sum_probs=23.0
Q ss_pred hhhhhcCCCCCCCccccc------c-ccceeecCCCCceee
Q 026283 176 NNFVIKGACPACKREFIG------S-KSQIIRCAGCGNIVW 209 (240)
Q Consensus 176 kRnLIeg~CPvC~~eFtG------~-nnt~~~CpnCGe~l~ 209 (240)
.-|+-+-.|..|+..+.- + +...-.||.||..|.
T Consensus 111 HG~l~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cgg~lr 151 (235)
T cd01408 111 HGSFATAHCIKCKHKYPGDWMREDIFNQEVPKCPRCGGLVK 151 (235)
T ss_pred CcCCCccccccCCCcCCHHHHHHHHhCCCCccCCCCCCCcc
Confidence 445666789999987642 1 123568999997654
No 269
>COG4469 CoiA Competence protein CoiA-like family, contains a predicted nuclease domain [General function prediction only]
Probab=50.79 E-value=8.3 Score=37.27 Aligned_cols=16 Identities=25% Similarity=0.611 Sum_probs=14.4
Q ss_pred eecCCCCceeeeeCCC
Q 026283 199 IRCAGCGNIVWQPEGD 214 (240)
Q Consensus 199 ~~CpnCGe~l~v~~g~ 214 (240)
..||.||++|-+.+|.
T Consensus 26 ffCPaC~~~l~lK~G~ 41 (342)
T COG4469 26 FFCPACGSQLILKQGL 41 (342)
T ss_pred cccCCCCCeeeeecCc
Confidence 5899999999999984
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=50.64 E-value=12 Score=25.34 Aligned_cols=24 Identities=29% Similarity=0.751 Sum_probs=16.7
Q ss_pred CCCCCCc-ccccccc-ceeecCCCCc
Q 026283 183 ACPACKR-EFIGSKS-QIIRCAGCGN 206 (240)
Q Consensus 183 ~CPvC~~-eFtG~nn-t~~~CpnCGe 206 (240)
.||-|+. +..-+++ ..-+|-+|+.
T Consensus 20 ~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 20 VCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 4999987 3444444 7788888874
No 271
>KOG3966 consensus p53-mediated apoptosis protein EI24/PIG8 [Signal transduction mechanisms; Defense mechanisms]
Probab=50.42 E-value=1.9e+02 Score=28.27 Aligned_cols=52 Identities=15% Similarity=0.094 Sum_probs=36.2
Q ss_pred HHhHHHHHHHHHhhhhhhhhhHhHHHHHHHHHHHHHHhhhhhhhhHhHHhhhh
Q 026283 61 EQLVFDAKKTAERIDRQYSVSRRLNSAARTAAVRARELDREFAISVRWRSFRM 113 (240)
Q Consensus 61 e~~~fear~~a~r~D~~Y~vs~r~a~aa~~a~e~A~eiD~~fgi~rR~R~f~~ 113 (240)
|+...+.|.+++..-|.+-=|-+...+++--.|.|.++..| .=+|+.|+..+
T Consensus 18 qe~~~~~~~~~~D~arg~~ds~~gi~~v~iree~akq~~ee-~~~r~~~~vL~ 69 (360)
T KOG3966|consen 18 QEHMVKFQIIARDFARGFIDSFKGITFVRIREEEAKQVKEE-PPKRVERTVLM 69 (360)
T ss_pred HHHHHHHHHHHHHHhhcCCccccchhhhhhhHHHHHHhhhc-CCchHHHHHHh
Confidence 67777777777777777776777777777777777776554 33566666655
No 272
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=50.31 E-value=8.4 Score=38.07 Aligned_cols=29 Identities=24% Similarity=0.674 Sum_probs=21.1
Q ss_pred hcCCCCCCCccccccccceeecCCCCcee
Q 026283 180 IKGACPACKREFIGSKSQIIRCAGCGNIV 208 (240)
Q Consensus 180 Ieg~CPvC~~eFtG~nnt~~~CpnCGe~l 208 (240)
+.-.||.||...-..-..-.+|+.||...
T Consensus 349 ~~p~Cp~Cg~~m~S~G~~g~rC~kCg~~~ 377 (421)
T COG1571 349 VNPVCPRCGGRMKSAGRNGFRCKKCGTRA 377 (421)
T ss_pred cCCCCCccCCchhhcCCCCcccccccccC
Confidence 34579999987654433389999999754
No 273
>COG4481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.25 E-value=6.8 Score=29.47 Aligned_cols=18 Identities=44% Similarity=0.946 Sum_probs=16.6
Q ss_pred eeecCCCCceeeeeCCCc
Q 026283 198 IIRCAGCGNIVWQPEGDF 215 (240)
Q Consensus 198 ~~~CpnCGe~l~v~~g~F 215 (240)
.+.|.|||-++..+.-+|
T Consensus 34 kikC~nC~h~vm~pR~~F 51 (60)
T COG4481 34 KIKCENCGHSVMMPRYDF 51 (60)
T ss_pred EEEecCCCcEEEecHHHH
Confidence 578999999999999888
No 274
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=50.09 E-value=13 Score=42.55 Aligned_cols=35 Identities=20% Similarity=0.440 Sum_probs=23.3
Q ss_pred HHHHhhhhhcCCCCCCCcc---cc--ccccceeecCCCCc
Q 026283 172 GTVANNFVIKGACPACKRE---FI--GSKSQIIRCAGCGN 206 (240)
Q Consensus 172 ~wWlkRnLIeg~CPvC~~e---Ft--G~nnt~~~CpnCGe 206 (240)
.+-+++-+....||+|+.. ++ =....-..||+||=
T Consensus 1695 ~~~~~~~~~~~~cp~c~~~~~~~~~~~~~~gc~~c~~cg~ 1734 (1740)
T PRK08332 1695 EEKIRELLGVVYCPVCYEKEGKLVELRMESGCATCPVCGW 1734 (1740)
T ss_pred HHHHHHHhccCCCCCCCCCCCcceeeEecCCceeCCCCCC
Confidence 4556666677779999987 11 22333458999993
No 275
>PRK05333 NAD-dependent deacetylase; Provisional
Probab=50.00 E-value=8.2 Score=34.94 Aligned_cols=12 Identities=33% Similarity=0.916 Sum_probs=9.4
Q ss_pred eeecCCCCceee
Q 026283 198 IIRCAGCGNIVW 209 (240)
Q Consensus 198 ~~~CpnCGe~l~ 209 (240)
.-.||+||.+|.
T Consensus 179 iP~C~~Cgg~lr 190 (285)
T PRK05333 179 VPACPACGGILK 190 (285)
T ss_pred CCCCCCCCCccc
Confidence 357999998764
No 276
>TIGR03847 conserved hypothetical protein. The conserved hypothetical protein described here occurs as part of the trio of uncharacterized proteins common in the Actinobacteria.
Probab=49.94 E-value=7.5 Score=34.56 Aligned_cols=16 Identities=31% Similarity=0.875 Sum_probs=12.9
Q ss_pred eecCCCCceeeeeCCCc
Q 026283 199 IRCAGCGNIVWQPEGDF 215 (240)
Q Consensus 199 ~~CpnCGe~l~v~~g~F 215 (240)
-.||.||++| =++||+
T Consensus 157 P~CPlCg~Pl-dP~GH~ 172 (177)
T TIGR03847 157 PPCPLCGRPI-DPDGHI 172 (177)
T ss_pred CCCCCCCCCC-CCCCcc
Confidence 4689999998 567887
No 277
>PRK07561 DNA topoisomerase I subunit omega; Validated
Probab=49.69 E-value=19 Score=37.75 Aligned_cols=18 Identities=17% Similarity=0.422 Sum_probs=13.7
Q ss_pred eeecCCCCceeeeeCCCc
Q 026283 198 IIRCAGCGNIVWQPEGDF 215 (240)
Q Consensus 198 ~~~CpnCGe~l~v~~g~F 215 (240)
.+-||.||+.+.+.+|.|
T Consensus 766 ~~g~p~~g~~i~~~~Gr~ 783 (859)
T PRK07561 766 ELGCPKSGAPFVLRDGRY 783 (859)
T ss_pred ccCCCCCCCeEEEecCCC
Confidence 455788888888888864
No 278
>COG5525 Bacteriophage tail assembly protein [General function prediction only]
Probab=48.97 E-value=9.7 Score=39.30 Aligned_cols=28 Identities=36% Similarity=0.838 Sum_probs=21.3
Q ss_pred CCCCCCcccc----------ccccce-----eecCCCCceeee
Q 026283 183 ACPACKREFI----------GSKSQI-----IRCAGCGNIVWQ 210 (240)
Q Consensus 183 ~CPvC~~eFt----------G~nnt~-----~~CpnCGe~l~v 210 (240)
.||.||+++. |+.-.. ++|+.|+.++.+
T Consensus 229 pCPHCGe~q~l~~~e~~~~~g~~~~~~~~~~~~c~h~~~~i~~ 271 (611)
T COG5525 229 PCPHCGEEQQLKFGEKSGPRGLKDTPAEAAFIQCEHCGCVIRP 271 (611)
T ss_pred eCCCCCchhhccccccCCCcCcccchhhhhhhhccccCceeee
Confidence 6999999763 333333 499999999988
No 279
>KOG3096 consensus Spliceosome-associated coiled-coil protein [Function unknown]
Probab=48.64 E-value=74 Score=29.40 Aligned_cols=53 Identities=28% Similarity=0.481 Sum_probs=40.4
Q ss_pred HHHHHhhHHHHHhHHHHHHHHHhhhhhh-hhhHhHHHHHHHHHHHHHHhhhhhh
Q 026283 51 DAWRTANNGFEQLVFDAKKTAERIDRQY-SVSRRLNSAARTAAVRARELDREFA 103 (240)
Q Consensus 51 ~a~r~an~~~e~~~fear~~a~r~D~~Y-~vs~r~a~aa~~a~e~A~eiD~~fg 103 (240)
.||++-|+.+|-|...|.|.+++....- +|.+.=--+--+|.++.++++++++
T Consensus 127 eaw~~~ne~le~~l~~aqkelq~~kk~iq~vn~~RK~~Q~~ag~rL~~le~~wv 180 (225)
T KOG3096|consen 127 EAWKQYNEVLEVMLTHAQKELQKTKKLIQDVNRQRKHAQLTAGERLRELEQKWV 180 (225)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence 7999999999999999999988775432 3444444455678888888888764
No 280
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=48.54 E-value=9.6 Score=34.46 Aligned_cols=23 Identities=22% Similarity=0.491 Sum_probs=13.1
Q ss_pred CCCCCCcccccc---ccceeecCCCC
Q 026283 183 ACPACKREFIGS---KSQIIRCAGCG 205 (240)
Q Consensus 183 ~CPvC~~eFtG~---nnt~~~CpnCG 205 (240)
.||+||.+..-. ..+-..||+|+
T Consensus 246 pCprCG~~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 246 PCLNCKTPIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred cCCCCCCeeEEEEECCCccEECcCCc
Confidence 677777654311 13345677775
No 281
>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=48.34 E-value=8.2 Score=27.22 Aligned_cols=14 Identities=29% Similarity=0.695 Sum_probs=9.0
Q ss_pred CCCCCCcccccccc
Q 026283 183 ACPACKREFIGSKS 196 (240)
Q Consensus 183 ~CPvC~~eFtG~nn 196 (240)
.|++|+|.+---.+
T Consensus 3 ~C~~CgyvYd~~~G 16 (47)
T PF00301_consen 3 QCPVCGYVYDPEKG 16 (47)
T ss_dssp EETTTSBEEETTTB
T ss_pred CCCCCCEEEcCCcC
Confidence 57777776655443
No 282
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=48.24 E-value=10 Score=34.15 Aligned_cols=23 Identities=22% Similarity=0.625 Sum_probs=14.1
Q ss_pred CCCCCCcccc----ccccceeecCCCCc
Q 026283 183 ACPACKREFI----GSKSQIIRCAGCGN 206 (240)
Q Consensus 183 ~CPvC~~eFt----G~nnt~~~CpnCGe 206 (240)
.||+||.... | ..+-..||+|+.
T Consensus 247 pC~~Cg~~I~~~~~~-gR~t~~CP~CQ~ 273 (274)
T PRK01103 247 PCRRCGTPIEKIKQG-GRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCeeEEEEEC-CCCcEECcCCCC
Confidence 4888886532 2 234566888864
No 283
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=48.16 E-value=11 Score=24.69 Aligned_cols=24 Identities=29% Similarity=0.928 Sum_probs=15.8
Q ss_pred CCCCCCCccccccccceeecCCCCce
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNI 207 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~ 207 (240)
|.||+|..+|.. .......+ ||-.
T Consensus 1 d~C~IC~~~~~~-~~~~~~l~-C~H~ 24 (44)
T PF13639_consen 1 DECPICLEEFED-GEKVVKLP-CGHV 24 (44)
T ss_dssp -CETTTTCBHHT-TSCEEEET-TSEE
T ss_pred CCCcCCChhhcC-CCeEEEcc-CCCe
Confidence 689999999976 44444555 7643
No 284
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=48.05 E-value=8.5 Score=26.75 Aligned_cols=25 Identities=28% Similarity=0.602 Sum_probs=15.9
Q ss_pred hcCCCCCCCcccccccc----ceeecCCC
Q 026283 180 IKGACPACKREFIGSKS----QIIRCAGC 204 (240)
Q Consensus 180 Ieg~CPvC~~eFtG~nn----t~~~CpnC 204 (240)
|-=.||.|++++..-=+ ....||-|
T Consensus 27 v~W~C~~Cgh~w~~~v~~R~~~~~~CP~C 55 (55)
T PF14311_consen 27 VWWKCPKCGHEWKASVNDRTRRGKGCPYC 55 (55)
T ss_pred EEEECCCCCCeeEccHhhhccCCCCCCCC
Confidence 33468999888876322 24567776
No 285
>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=47.85 E-value=8 Score=28.91 Aligned_cols=12 Identities=25% Similarity=0.498 Sum_probs=8.8
Q ss_pred eeecCCCCceee
Q 026283 198 IIRCAGCGNIVW 209 (240)
Q Consensus 198 ~~~CpnCGe~l~ 209 (240)
.-.|||||..|.
T Consensus 41 ~~~CPNCgGelv 52 (57)
T PF06906_consen 41 NGVCPNCGGELV 52 (57)
T ss_pred cCcCcCCCCccc
Confidence 457999987764
No 286
>COG1328 NrdD Oxygen-sensitive ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]
Probab=47.79 E-value=9.6 Score=39.73 Aligned_cols=24 Identities=25% Similarity=0.646 Sum_probs=17.5
Q ss_pred cCCCCCCCccccccccceeecCCCCce
Q 026283 181 KGACPACKREFIGSKSQIIRCAGCGNI 207 (240)
Q Consensus 181 eg~CPvC~~eFtG~nnt~~~CpnCGe~ 207 (240)
-+-|+-|++.--|+--. ||+||+.
T Consensus 641 i~~C~~cg~~~~~~~~~---Cp~CG~~ 664 (700)
T COG1328 641 ISVCNRCGYSGEGLRTR---CPKCGSE 664 (700)
T ss_pred ceeeccCCccccccccc---CCCCCCc
Confidence 46899999975444333 9999955
No 287
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=47.75 E-value=6.8 Score=21.46 Aligned_cols=12 Identities=33% Similarity=1.013 Sum_probs=7.0
Q ss_pred CCCCCCcccccc
Q 026283 183 ACPACKREFIGS 194 (240)
Q Consensus 183 ~CPvC~~eFtG~ 194 (240)
.||.|++.|...
T Consensus 2 ~C~~C~~~~~~~ 13 (24)
T PF13894_consen 2 QCPICGKSFRSK 13 (24)
T ss_dssp E-SSTS-EESSH
T ss_pred CCcCCCCcCCcH
Confidence 488888887643
No 288
>COG2991 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.35 E-value=21 Score=28.15 Aligned_cols=24 Identities=33% Similarity=0.510 Sum_probs=19.1
Q ss_pred HHHHHHHHHHHHHHhhhhhcCCCC
Q 026283 162 VLPIAAPLLIGTVANNFVIKGACP 185 (240)
Q Consensus 162 vlPvaap~li~wWlkRnLIeg~CP 185 (240)
++-+++...+|.+.+|.-|.|.|-
T Consensus 11 Fllvi~gMsiG~I~krk~I~GSCG 34 (77)
T COG2991 11 FLLVIAGMSIGYIFKRKSIKGSCG 34 (77)
T ss_pred HHHHHHHHhHhhheeccccccccc
Confidence 344455667999999999999996
No 289
>KOG3134 consensus Predicted membrane protein [Function unknown]
Probab=47.24 E-value=6.5 Score=36.09 Aligned_cols=14 Identities=21% Similarity=0.845 Sum_probs=12.0
Q ss_pred ccceeecCCCCcee
Q 026283 195 KSQIIRCAGCGNIV 208 (240)
Q Consensus 195 nnt~~~CpnCGe~l 208 (240)
|.+..+||||+|++
T Consensus 21 ~irlt~C~nC~e~v 34 (225)
T KOG3134|consen 21 NIRLTKCPNCQEVV 34 (225)
T ss_pred cEEEeeCCchhhHH
Confidence 67788999999975
No 290
>PRK03922 hypothetical protein; Provisional
Probab=46.99 E-value=8.5 Score=32.14 Aligned_cols=18 Identities=17% Similarity=0.604 Sum_probs=11.3
Q ss_pred ccccccceeecCCCCcee
Q 026283 191 FIGSKSQIIRCAGCGNIV 208 (240)
Q Consensus 191 FtG~nnt~~~CpnCGe~l 208 (240)
|+-..-....||.|||++
T Consensus 42 yVeievG~~~cP~cge~~ 59 (113)
T PRK03922 42 YVEVEVGLTICPKCGEPF 59 (113)
T ss_pred eEEEecCcccCCCCCCcC
Confidence 444455566777777765
No 291
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=46.91 E-value=39 Score=32.43 Aligned_cols=10 Identities=20% Similarity=0.866 Sum_probs=7.7
Q ss_pred eeecCCCCce
Q 026283 198 IIRCAGCGNI 207 (240)
Q Consensus 198 ~~~CpnCGe~ 207 (240)
.+.|-|||+.
T Consensus 225 R~KC~nC~~t 234 (308)
T COG3058 225 RVKCSNCEQS 234 (308)
T ss_pred HHHhcccccc
Confidence 3579999975
No 292
>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=46.90 E-value=12 Score=35.39 Aligned_cols=19 Identities=32% Similarity=0.625 Sum_probs=17.0
Q ss_pred cceeecCCCCceeeeeCCC
Q 026283 196 SQIIRCAGCGNIVWQPEGD 214 (240)
Q Consensus 196 nt~~~CpnCGe~l~v~~g~ 214 (240)
+....||.||++|....|.
T Consensus 28 ~~~~~CP~C~~~v~lk~G~ 46 (375)
T PF06054_consen 28 KGKYFCPGCGEPVILKKGK 46 (375)
T ss_pred CCcEECCCCCCeeEEEEcC
Confidence 6788999999999999885
No 293
>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=46.79 E-value=11 Score=35.87 Aligned_cols=30 Identities=23% Similarity=0.431 Sum_probs=20.7
Q ss_pred cCCCCCCCccc--cccccceeecCCCCceeee
Q 026283 181 KGACPACKREF--IGSKSQIIRCAGCGNIVWQ 210 (240)
Q Consensus 181 eg~CPvC~~eF--tG~nnt~~~CpnCGe~l~v 210 (240)
-..||.|++.- .|+....-.||.||..+.+
T Consensus 233 v~~C~~c~~~~~~~~~~~~~~~C~~c~~~~~~ 264 (374)
T TIGR00308 233 TYHCSRCLHNKPVNGISQRKGRCKECGGEYHL 264 (374)
T ss_pred EEECCCcccccccccccCCCCCCCCCCCccee
Confidence 45799998742 2344555689999987654
No 294
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=46.70 E-value=27 Score=23.56 Aligned_cols=25 Identities=28% Similarity=0.713 Sum_probs=17.8
Q ss_pred CCC--CCCcccccc---ccceeecCCCCce
Q 026283 183 ACP--ACKREFIGS---KSQIIRCAGCGNI 207 (240)
Q Consensus 183 ~CP--vC~~eFtG~---nnt~~~CpnCGe~ 207 (240)
-|| -|++-..-- ......||.||-.
T Consensus 20 ~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~ 49 (64)
T smart00647 20 WCPAPDCSAAIIVTEEEGCNRVTCPKCGFS 49 (64)
T ss_pred CCCCCCCcceEEecCCCCCCeeECCCCCCe
Confidence 488 887766554 5678888888754
No 295
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=46.37 E-value=12 Score=23.90 Aligned_cols=26 Identities=31% Similarity=0.623 Sum_probs=20.8
Q ss_pred cCCCCCCCccccccccceeecCCCCce
Q 026283 181 KGACPACKREFIGSKSQIIRCAGCGNI 207 (240)
Q Consensus 181 eg~CPvC~~eFtG~nnt~~~CpnCGe~ 207 (240)
...|-+|+..+.|+. +-.+|+.|+-.
T Consensus 11 ~~~C~~C~~~i~~~~-~~~~C~~C~~~ 36 (49)
T smart00109 11 PTKCCVCRKSIWGSF-QGLRCSWCKVK 36 (49)
T ss_pred CCCccccccccCcCC-CCcCCCCCCch
Confidence 345999999999876 67899999743
No 296
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=46.29 E-value=10 Score=31.24 Aligned_cols=14 Identities=21% Similarity=0.444 Sum_probs=12.0
Q ss_pred cCCCCceeeeeCCC
Q 026283 201 CAGCGNIVWQPEGD 214 (240)
Q Consensus 201 CpnCGe~l~v~~g~ 214 (240)
||.||..|.|..=+
T Consensus 1 CPvCg~~l~vt~l~ 14 (113)
T PF09862_consen 1 CPVCGGELVVTRLK 14 (113)
T ss_pred CCCCCCceEEEEEE
Confidence 99999999998633
No 297
>PRK02935 hypothetical protein; Provisional
Probab=45.84 E-value=8.6 Score=31.99 Aligned_cols=19 Identities=16% Similarity=0.293 Sum_probs=14.6
Q ss_pred cccceeecCCCCceeeeeC
Q 026283 194 SKSQIIRCAGCGNIVWQPE 212 (240)
Q Consensus 194 ~nnt~~~CpnCGe~l~v~~ 212 (240)
-+-.|.+||||+.+-++=.
T Consensus 66 tkavqV~CP~C~K~TKmLG 84 (110)
T PRK02935 66 TKAVQVICPSCEKPTKMLG 84 (110)
T ss_pred ccceeeECCCCCchhhhcc
Confidence 4556889999999877643
No 298
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=45.79 E-value=15 Score=29.31 Aligned_cols=34 Identities=29% Similarity=0.705 Sum_probs=26.6
Q ss_pred cCCCCCCCcccccc--ccceeecCCCCceeeeeCCC
Q 026283 181 KGACPACKREFIGS--KSQIIRCAGCGNIVWQPEGD 214 (240)
Q Consensus 181 eg~CPvC~~eFtG~--nnt~~~CpnCGe~l~v~~g~ 214 (240)
.-.||-|-+--+-| -+++..|+||+.++-|+-|.
T Consensus 34 ~VkC~gc~~iT~vfSHaqtvVvc~~c~~il~~~tgg 69 (84)
T KOG1779|consen 34 DVKCPGCFKITTVFSHAQTVVVCEGCSTILCQPTGG 69 (84)
T ss_pred EEEcCCceEEEEEeecCceEEEcCCCceEEEEecCC
Confidence 34699987765555 46788999999999998774
No 299
>PF12653 DUF3785: Protein of unknown function (DUF3785); InterPro: IPR024210 This family of proteins is functionally uncharacterised. Proteins in this family are approximately 140 amino acids in length and share two CXXC motifs suggesting these are zinc binding proteins. In clostridia proteins are found in an operon with three signalling proteins, suggesting that they are involved in DNA-binding transcription regulator downstream of an as yet unknown signalling pathway.
Probab=45.59 E-value=9.8 Score=32.67 Aligned_cols=12 Identities=50% Similarity=1.071 Sum_probs=9.9
Q ss_pred ceeecCCCCcee
Q 026283 197 QIIRCAGCGNIV 208 (240)
Q Consensus 197 t~~~CpnCGe~l 208 (240)
+++.|||||+-.
T Consensus 119 si~VC~nCG~y~ 130 (138)
T PF12653_consen 119 SIIVCPNCGNYS 130 (138)
T ss_pred EEEECCCCCceE
Confidence 678999999843
No 300
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=45.37 E-value=27 Score=28.01 Aligned_cols=29 Identities=10% Similarity=0.093 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHhhhhhcCCCCCCCccccc
Q 026283 165 IAAPLLIGTVANNFVIKGACPACKREFIG 193 (240)
Q Consensus 165 vaap~li~wWlkRnLIeg~CPvC~~eFtG 193 (240)
++.++++-+..+|..-.|.=|.=+.....
T Consensus 13 ~l~~~~~~~~~rRR~r~G~~P~~gt~w~~ 41 (130)
T PF12273_consen 13 LLFLFLFYCHNRRRRRRGLQPIYGTRWMA 41 (130)
T ss_pred HHHHHHHHHHHHHHhhcCCCCcCCceecC
Confidence 33345566778888888888876666555
No 301
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=44.98 E-value=9.4 Score=37.77 Aligned_cols=29 Identities=21% Similarity=0.600 Sum_probs=24.4
Q ss_pred hhhcCCCCCCCccccccccceeecCCCCc
Q 026283 178 FVIKGACPACKREFIGSKSQIIRCAGCGN 206 (240)
Q Consensus 178 nLIeg~CPvC~~eFtG~nnt~~~CpnCGe 206 (240)
+=.+.-|||||-.-.||.-.-..|.+|-.
T Consensus 12 edl~ElCPVCGDkVSGYHYGLLTCESCKG 40 (475)
T KOG4218|consen 12 EDLGELCPVCGDKVSGYHYGLLTCESCKG 40 (475)
T ss_pred cccccccccccCccccceeeeeehhhhhh
Confidence 33456799999999999999999999964
No 302
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=44.92 E-value=12 Score=36.93 Aligned_cols=28 Identities=25% Similarity=0.477 Sum_probs=20.4
Q ss_pred CCCCCCCccccccccceeecCCCCceeeee
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNIVWQP 211 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~l~v~ 211 (240)
..||.|.+. -+ ..+.-.||+||......
T Consensus 58 ~kC~~c~~~-~~-y~~~~~C~~cg~~~~l~ 85 (415)
T COG5257 58 YKCPECYRP-EC-YTTEPKCPNCGAETELV 85 (415)
T ss_pred EeCCCCCCC-cc-cccCCCCCCCCCCccEE
Confidence 579999987 33 34566799999876443
No 303
>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=44.60 E-value=11 Score=31.71 Aligned_cols=39 Identities=23% Similarity=0.565 Sum_probs=25.2
Q ss_pred hhhhcCCCCCCCccccccc----cceeecCCCCceeeeeCCCc
Q 026283 177 NFVIKGACPACKREFIGSK----SQIIRCAGCGNIVWQPEGDF 215 (240)
Q Consensus 177 RnLIeg~CPvC~~eFtG~n----nt~~~CpnCGe~l~v~~g~F 215 (240)
-++-+..|..|+..+.--. +....||.||.+|.-.--.|
T Consensus 109 G~~~~~~C~~C~~~~~~~~~~~~~~~p~C~~C~~~l~p~v~~f 151 (222)
T cd00296 109 GSLDRVRCTSCGKEYPRDEVLEREKPPRCPKCGGLLRPDVVDF 151 (222)
T ss_pred CCCCccEECCCCCCcchhhhhhccCCCCCCCCCCcccCceEEC
Confidence 3455678999986653322 34578999998875444444
No 304
>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=44.58 E-value=7.3 Score=41.70 Aligned_cols=28 Identities=29% Similarity=0.668 Sum_probs=0.0
Q ss_pred CCCCCCCcccccccc--------ceeecCCCCceee
Q 026283 182 GACPACKREFIGSKS--------QIIRCAGCGNIVW 209 (240)
Q Consensus 182 g~CPvC~~eFtG~nn--------t~~~CpnCGe~l~ 209 (240)
-.||.|+.+-....- ..-.||.||..+.
T Consensus 656 r~Cp~Cg~~t~~~~Cp~CG~~T~~~~~Cp~C~~~~~ 691 (900)
T PF03833_consen 656 RRCPKCGKETFYNRCPECGSHTEPVYVCPDCGIEVE 691 (900)
T ss_dssp ------------------------------------
T ss_pred ccCcccCCcchhhcCcccCCccccceeccccccccC
Confidence 468888876433221 2335666666553
No 305
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=44.56 E-value=11 Score=42.46 Aligned_cols=22 Identities=27% Similarity=0.572 Sum_probs=17.7
Q ss_pred cCCCCCCCccccccccceeecCCCCce
Q 026283 181 KGACPACKREFIGSKSQIIRCAGCGNI 207 (240)
Q Consensus 181 eg~CPvC~~eFtG~nnt~~~CpnCGe~ 207 (240)
.-.||.|+.+ .-..+||.||..
T Consensus 674 ~~~Cp~Cg~~-----~~~~~Cp~CG~~ 695 (1627)
T PRK14715 674 FFKCPKCGKV-----GLYHVCPFCGTR 695 (1627)
T ss_pred eeeCCCCCCc-----cccccCcccCCc
Confidence 3579999987 345689999987
No 306
>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=44.55 E-value=7.8 Score=25.02 Aligned_cols=25 Identities=24% Similarity=0.565 Sum_probs=10.5
Q ss_pred hhhcCCCCCCCccccccccceeecCCCC
Q 026283 178 FVIKGACPACKREFIGSKSQIIRCAGCG 205 (240)
Q Consensus 178 nLIeg~CPvC~~eFtG~nnt~~~CpnCG 205 (240)
.|+-..|+.|+.-+. --...||+||
T Consensus 8 ~l~~~rC~~Cg~~~~---pPr~~Cp~C~ 32 (37)
T PF12172_consen 8 RLLGQRCRDCGRVQF---PPRPVCPHCG 32 (37)
T ss_dssp -EEEEE-TTT--EEE---S--SEETTTT
T ss_pred EEEEEEcCCCCCEec---CCCcCCCCcC
Confidence 345556666665532 2235666665
No 307
>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=44.30 E-value=3.7 Score=35.90 Aligned_cols=25 Identities=20% Similarity=0.588 Sum_probs=19.4
Q ss_pred hhhcCCCCCCCccccccccceeecCCCCcee
Q 026283 178 FVIKGACPACKREFIGSKSQIIRCAGCGNIV 208 (240)
Q Consensus 178 nLIeg~CPvC~~eFtG~nnt~~~CpnCGe~l 208 (240)
.+.++-|.-||.+ +...||||+.++
T Consensus 25 ~~~~~fC~kCG~~------tI~~Cp~C~~~I 49 (158)
T PF10083_consen 25 ELREKFCSKCGAK------TITSCPNCSTPI 49 (158)
T ss_pred hHHHHHHHHhhHH------HHHHCcCCCCCC
Confidence 4567778888865 678899998876
No 308
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=43.85 E-value=16 Score=27.99 Aligned_cols=29 Identities=21% Similarity=0.510 Sum_probs=22.8
Q ss_pred CCCCCCCccc---------cccccceeecC--CCCceeee
Q 026283 182 GACPACKREF---------IGSKSQIIRCA--GCGNIVWQ 210 (240)
Q Consensus 182 g~CPvC~~eF---------tG~nnt~~~Cp--nCGe~l~v 210 (240)
+.||.||..- -+++..-.||. +||.--+-
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF~t 41 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDTTKERYHQCQNVNCSATFIT 41 (72)
T ss_pred ccCCCCCCccEEEEChhcChhhheeeeecCCCCCCCEEEE
Confidence 5799999765 36888899998 99986443
No 309
>TIGR02745 ccoG_rdxA_fixG cytochrome c oxidase accessory protein FixG. Member of this ferredoxin-like protein family are found exclusively in species with an operon encoding the cbb3 type of cytochrome c oxidase (cco-cbb3), and near the cco-cbb3 operon in about half the cases. The cco-cbb3 is found in a variety of proteobacteria and almost nowhere else, and is associated with oxygen use under microaerobic conditions. Some (but not all) of these proteobacteria are also nitrogen-fixing, hence the gene symbol fixG. FixG was shown essential for functional cco-cbb3 expression in Bradyrhizobium japonicum.
Probab=43.71 E-value=37 Score=33.29 Aligned_cols=18 Identities=11% Similarity=0.110 Sum_probs=13.1
Q ss_pred HHHhhhhhcCCCCCCCcc
Q 026283 173 TVANNFVIKGACPACKRE 190 (240)
Q Consensus 173 wWlkRnLIeg~CPvC~~e 190 (240)
-|+++..=...||.-..+
T Consensus 177 ~~~re~~C~~~CP~g~~q 194 (434)
T TIGR02745 177 GWMREQFCIYMCPYARIQ 194 (434)
T ss_pred HeeccchhhhhCCHHHHH
Confidence 388888888888855444
No 310
>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=43.66 E-value=12 Score=27.36 Aligned_cols=35 Identities=17% Similarity=0.334 Sum_probs=26.6
Q ss_pred hcCCCCCCCcccc---ccccceeecCCCCceeeeeCCC
Q 026283 180 IKGACPACKREFI---GSKSQIIRCAGCGNIVWQPEGD 214 (240)
Q Consensus 180 Ieg~CPvC~~eFt---G~nnt~~~CpnCGe~l~v~~g~ 214 (240)
-|-.|+.|++-+. ++..-++.||.||.+-.+..-.
T Consensus 3 ~eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a~~ 40 (51)
T PF10122_consen 3 KEIRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRATS 40 (51)
T ss_pred cceeccchhHHHhhhcCccEEEEECCCCCccceEeccC
Confidence 4567999987653 3556799999999988776654
No 311
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=43.55 E-value=11 Score=36.66 Aligned_cols=25 Identities=20% Similarity=0.485 Sum_probs=16.8
Q ss_pred CCCCCCcccccccc---------c-------eeecCCCCce
Q 026283 183 ACPACKREFIGSKS---------Q-------IIRCAGCGNI 207 (240)
Q Consensus 183 ~CPvC~~eFtG~nn---------t-------~~~CpnCGe~ 207 (240)
.|++|+|.+-.-.+ | .-.||-||..
T Consensus 427 ~c~~c~~~yd~~~g~~~~~~~~gt~~~~lp~~~~cp~c~~~ 467 (479)
T PRK05452 427 QCSVCQWIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSLG 467 (479)
T ss_pred EECCCCeEECCCCCCcccCCCCCCChhhCCCCCcCcCCCCc
Confidence 38888888766433 2 2378888864
No 312
>PF04641 Rtf2: Rtf2 RING-finger
Probab=42.92 E-value=14 Score=33.13 Aligned_cols=13 Identities=38% Similarity=0.805 Sum_probs=10.2
Q ss_pred cCCCCCCCccccc
Q 026283 181 KGACPACKREFIG 193 (240)
Q Consensus 181 eg~CPvC~~eFtG 193 (240)
.-.|||++.+|+|
T Consensus 113 ~~~CPvt~~~~~~ 125 (260)
T PF04641_consen 113 RFICPVTGKEFNG 125 (260)
T ss_pred eeECCCCCcccCC
Confidence 3469999998866
No 313
>PF01004 Flavi_M: Flavivirus envelope glycoprotein M; InterPro: IPR000069 Flaviviruses are small enveloped viruses with virions comprised of three proteins called C, M and E [, , ]. The envelope glycoprotein M is made as a precursor, called prM. The precursor portion of the protein is the signal peptide for the proteins entry into the membrane. prM is cleaved to form M in a late-stage cleavage event. Associated with this cleavage is a change in the infectivity and fusion activity of the virus.; GO: 0019058 viral infectious cycle, 0019028 viral capsid
Probab=42.89 E-value=31 Score=26.68 Aligned_cols=31 Identities=16% Similarity=0.250 Sum_probs=22.9
Q ss_pred CCCCchHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026283 131 NTPLGRSFATIFFLWFALSGWLFRILILATW 161 (240)
Q Consensus 131 ~T~lG~wL~tl~~~wll~SGWLvn~~l~l~~ 161 (240)
...=|..++..++.|++++...=+.+|++++
T Consensus 37 lrNp~~al~a~~l~w~lg~s~~Qrvi~iill 67 (75)
T PF01004_consen 37 LRNPGYALAAVALAWMLGSSTTQRVIFIILL 67 (75)
T ss_pred hcCchHHHHHHHHHHHHcCCchHHHHHHHHH
Confidence 3445677788899999999888787764433
No 314
>PF04267 SoxD: Sarcosine oxidase, delta subunit family ; InterPro: IPR006279 These sequences represent the delta subunit of a family of known and putative heterotetrameric sarcosine oxidases. Five operons of such oxidases are found in Rhizobium loti (Mesorhizobium loti) and three in Agrobacterium tumefaciens, a high enough copy number to suggest that not all members share the same function. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate []. Bacterial sarcosine oxidases have been isolated from over a dozen different organisms and fall into two major classes (1) monomeric form that contains only covalent flavin and (2) heterotetrameric (alpha, beta, gamma, delta) form that contain a covalent and noncovalent flavin, this entry represents the heterotetrameric form.; GO: 0008115 sarcosine oxidase activity, 0046653 tetrahydrofolate metabolic process; PDB: 3AD7_D 1X31_D 1VRQ_D 3AD8_D 3ADA_D 3AD9_D 2GAG_D 2GAH_D.
Probab=42.77 E-value=5.4 Score=31.43 Aligned_cols=31 Identities=26% Similarity=0.608 Sum_probs=18.2
Q ss_pred eecCCCCceeeeeCCCcccCCCCCCCCCCCCCCee
Q 026283 199 IRCAGCGNIVWQPEGDFFSRNGGGKKSTKSDDDII 233 (240)
Q Consensus 199 ~~CpnCGe~l~v~~g~F~s~~g~~~~~r~t~pgtI 233 (240)
+.||-||+ =+...| .-.|-+.-.|+.+|..+
T Consensus 2 I~CP~CG~---R~~~EF-~y~G~a~i~rP~~~~~~ 32 (84)
T PF04267_consen 2 IPCPHCGP---RDESEF-TYGGEAHIARPADPASV 32 (84)
T ss_dssp EEETTTEE---EEGGGS-EEEEESS----S-GGGS
T ss_pred ccCCCCCc---cchhhe-ecCcEeccccCCCCCcC
Confidence 67999998 566667 54555566777777664
No 315
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=42.50 E-value=13 Score=35.30 Aligned_cols=30 Identities=20% Similarity=0.244 Sum_probs=20.3
Q ss_pred cCCCCCCCccccccccceeecCCCCceeee
Q 026283 181 KGACPACKREFIGSKSQIIRCAGCGNIVWQ 210 (240)
Q Consensus 181 eg~CPvC~~eFtG~nnt~~~CpnCGe~l~v 210 (240)
-..|+.|++.-+-.......||.||..+.+
T Consensus 244 ~~~C~~c~~~~~~~~~~~~~C~~c~~~~~~ 273 (382)
T PRK04338 244 VYYCPKCLYREEVEGLPPEECPVCGGKFGT 273 (382)
T ss_pred EEECCCCCcEEEecCCCCCCCCCCCCccee
Confidence 467999998654221445679999976544
No 316
>PF14159 CAAD: CAAD domains of cyanobacterial aminoacyl-tRNA synthetase
Probab=42.33 E-value=62 Score=25.32 Aligned_cols=43 Identities=14% Similarity=0.215 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHhhhhhc
Q 026283 139 ATIFFLWFALSGWLFRILILATWVLPIAAPLL-------IGTVANNFVIK 181 (240)
Q Consensus 139 ~tl~~~wll~SGWLvn~~l~l~~vlPvaap~l-------i~wWlkRnLIe 181 (240)
+...++-.+.+.|+...++-.+=-+|++.+++ ..|+.-|||..
T Consensus 21 ~~~~ii~~iv~l~v~~~vl~aIn~iPll~~llElvGlgyt~wF~~ryLL~ 70 (90)
T PF14159_consen 21 TIGAIIAVIVALWVSAAVLDAINSIPLLPGLLELVGLGYTGWFVYRYLLF 70 (90)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHcCcchHHHHHHHHHHHHhHHHHHHHcC
Confidence 34444455556787777776666677766554 33888888864
No 317
>PRK10246 exonuclease subunit SbcC; Provisional
Probab=42.09 E-value=12 Score=39.69 Aligned_cols=16 Identities=25% Similarity=0.648 Sum_probs=13.3
Q ss_pred HhhhhhcCC-CCCCCcc
Q 026283 175 ANNFVIKGA-CPACKRE 190 (240)
Q Consensus 175 lkRnLIeg~-CPvC~~e 190 (240)
|...|.+|. |||||..
T Consensus 496 Lr~~L~~GePCPVCGS~ 512 (1047)
T PRK10246 496 QRAQLQAGQPCPLCGST 512 (1047)
T ss_pred HHHhCCCCCCcCCCCcc
Confidence 788888885 9999974
No 318
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=41.99 E-value=14 Score=33.50 Aligned_cols=23 Identities=26% Similarity=0.681 Sum_probs=14.5
Q ss_pred CCCCCCcccc----ccccceeecCCCCc
Q 026283 183 ACPACKREFI----GSKSQIIRCAGCGN 206 (240)
Q Consensus 183 ~CPvC~~eFt----G~nnt~~~CpnCGe 206 (240)
.||+||.... |- .+-..||+|+.
T Consensus 237 pC~~Cg~~I~~~~~~g-R~ty~Cp~CQ~ 263 (269)
T PRK14811 237 PCPRCGTPIEKIVVGG-RGTHFCPQCQP 263 (269)
T ss_pred CCCcCCCeeEEEEECC-CCcEECCCCcC
Confidence 5888886543 32 34456888864
No 319
>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=41.75 E-value=12 Score=28.60 Aligned_cols=23 Identities=30% Similarity=0.577 Sum_probs=9.3
Q ss_pred CCCCCCccccccccceeecCCCCce
Q 026283 183 ACPACKREFIGSKSQIIRCAGCGNI 207 (240)
Q Consensus 183 ~CPvC~~eFtG~nnt~~~CpnCGe~ 207 (240)
.|-+|-.--. ..+...||+||+.
T Consensus 11 rC~aCf~~t~--~~~k~FCp~CGn~ 33 (73)
T PF08772_consen 11 RCHACFKITK--DMTKQFCPKCGNA 33 (73)
T ss_dssp E-SSS--EES---SS--S-SSS--S
T ss_pred EccccccCcC--CCCceeCcccCCC
Confidence 3666644332 5678899999985
No 320
>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=41.40 E-value=14 Score=35.35 Aligned_cols=30 Identities=27% Similarity=0.587 Sum_probs=17.8
Q ss_pred cCCCCCCCc--cccccccceeecCCCCceeee
Q 026283 181 KGACPACKR--EFIGSKSQIIRCAGCGNIVWQ 210 (240)
Q Consensus 181 eg~CPvC~~--eFtG~nnt~~~CpnCGe~l~v 210 (240)
-..|+.|++ ...|+..-...||.||..+.+
T Consensus 240 v~~C~~C~~~~~~~~~~~~~~~c~~cg~~~~~ 271 (377)
T PF02005_consen 240 VYYCPSCGYREEVKGLQKLKSKCPECGSKLHI 271 (377)
T ss_dssp EEEETTT--EECCT-GCC--CEETTT-SCCCE
T ss_pred EEECCCccccccccCccccCCcCCCCCCccce
Confidence 357999986 344544445899999998766
No 321
>PTZ00410 NAD-dependent SIR2; Provisional
Probab=41.20 E-value=14 Score=35.53 Aligned_cols=33 Identities=21% Similarity=0.516 Sum_probs=22.1
Q ss_pred hhhhcCCCCCCCccccc-------cccceeecCCCCceee
Q 026283 177 NFVIKGACPACKREFIG-------SKSQIIRCAGCGNIVW 209 (240)
Q Consensus 177 RnLIeg~CPvC~~eFtG-------~nnt~~~CpnCGe~l~ 209 (240)
-++-+..|..|+..+.- ..+.+-.||.||.+|.
T Consensus 143 Gsl~~~~C~~C~~~~~~~~~~~~~~~~~vP~C~~CgG~lR 182 (349)
T PTZ00410 143 GSFSAASCIECHTPYDIEQAYLEARSGKVPHCSTCGGIVK 182 (349)
T ss_pred cCCCeeEeCCCCCCcchhHHHHHhhcCCCCCCCCCCCccC
Confidence 34555789999977641 1234568999997654
No 322
>PTZ00043 cytochrome c oxidase subunit; Provisional
Probab=40.97 E-value=20 Score=33.58 Aligned_cols=43 Identities=26% Similarity=0.390 Sum_probs=27.3
Q ss_pred ccccccceeecCCCCceeeeeCCCcccCCCCCCCCCCCCCCeeee
Q 026283 191 FIGSKSQIIRCAGCGNIVWQPEGDFFSRNGGGKKSTKSDDDIIDV 235 (240)
Q Consensus 191 FtG~nnt~~~CpnCGe~l~v~~g~F~s~~g~~~~~r~t~pgtIDV 235 (240)
|.--.+...+||.||...+...=.. | -|-|...-..+|++-||
T Consensus 174 FwLrEGkpqRCpECGqVFKLVr~~~-s-~~dg~dp~~~dpdv~dv 216 (268)
T PTZ00043 174 FRCREGFLYRCGECDQIFMLVRVLY-S-LPDGEDPFPNDPDVDDV 216 (268)
T ss_pred EEecCCCCccCCCCCcEEEEEEEEe-e-cCCCCCCCCCCCchhhh
Confidence 4445667889999999988755322 2 22233345667777766
No 323
>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=40.97 E-value=15 Score=35.48 Aligned_cols=32 Identities=22% Similarity=0.370 Sum_probs=22.0
Q ss_pred hcCCCCCCCccccccccce-----eecCCCCceeeee
Q 026283 180 IKGACPACKREFIGSKSQI-----IRCAGCGNIVWQP 211 (240)
Q Consensus 180 Ieg~CPvC~~eFtG~nnt~-----~~CpnCGe~l~v~ 211 (240)
++-.||.|+++-+-+-... -.||.||..+.+.
T Consensus 319 ~~~rc~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 355 (403)
T TIGR03676 319 VTFKCPNCGYEEEKTVKPEEGDKSEACPKCGSELEIV 355 (403)
T ss_pred EEEEcCCCCcceeeecccccccccccCcccCcccccc
Confidence 3468999999866433211 3599999987754
No 324
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=40.91 E-value=11 Score=36.30 Aligned_cols=20 Identities=20% Similarity=0.084 Sum_probs=10.4
Q ss_pred cchhhhhhhhcccchhHHHH
Q 026283 22 RRRAATVRAFRRSDFDRFAR 41 (240)
Q Consensus 22 ~~~~~~~~af~~~d~d~~a~ 41 (240)
+-|+--+.+|+=-|--.|..
T Consensus 127 ~lRa~Gtys~kvtDpi~fi~ 146 (345)
T COG4260 127 FLRAHGTYSIKVTDPILFIQ 146 (345)
T ss_pred EEeecceEEEEecCHHHHHH
Confidence 34555555665455444544
No 325
>PRK07219 DNA topoisomerase I; Validated
Probab=40.91 E-value=23 Score=36.97 Aligned_cols=19 Identities=21% Similarity=0.391 Sum_probs=14.9
Q ss_pred ceeecCCCCceeeeeCCCc
Q 026283 197 QIIRCAGCGNIVWQPEGDF 215 (240)
Q Consensus 197 t~~~CpnCGe~l~v~~g~F 215 (240)
....||.||..+.+..|.|
T Consensus 687 ~~~~CP~Cg~~l~~k~gr~ 705 (822)
T PRK07219 687 VIGPCPKCGGELAIKQLKY 705 (822)
T ss_pred ccccCCCCCCeeEEEcCCC
Confidence 3568999998888877665
No 326
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=40.67 E-value=11 Score=34.37 Aligned_cols=30 Identities=23% Similarity=0.620 Sum_probs=21.4
Q ss_pred hhhhcCCCCCCCccccccc---cc----eeecCCCCc
Q 026283 177 NFVIKGACPACKREFIGSK---SQ----IIRCAGCGN 206 (240)
Q Consensus 177 RnLIeg~CPvC~~eFtG~n---nt----~~~CpnCGe 206 (240)
-++-.-.|.-|++.+.+-. .+ .-+||.||.
T Consensus 118 Gsl~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~ 154 (250)
T COG0846 118 GSLKRVRCSKCGNQYYDEDVIKFIEDGLIPRCPKCGG 154 (250)
T ss_pred cceeeeEeCCCcCccchhhhhhhcccCCCCcCccCCC
Confidence 3455678999999888332 33 346999999
No 327
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=40.66 E-value=13 Score=23.06 Aligned_cols=9 Identities=56% Similarity=1.316 Sum_probs=6.4
Q ss_pred CCCCCCccc
Q 026283 183 ACPACKREF 191 (240)
Q Consensus 183 ~CPvC~~eF 191 (240)
+||+|+..+
T Consensus 3 ~CPiC~~~v 11 (26)
T smart00734 3 QCPVCFREV 11 (26)
T ss_pred cCCCCcCcc
Confidence 578887665
No 328
>COG0498 ThrC Threonine synthase [Amino acid transport and metabolism]
Probab=40.38 E-value=11 Score=36.83 Aligned_cols=33 Identities=24% Similarity=0.390 Sum_probs=25.4
Q ss_pred hhcCCCCCCCccccccccceeecCCCCceeeeeC
Q 026283 179 VIKGACPACKREFIGSKSQIIRCAGCGNIVWQPE 212 (240)
Q Consensus 179 LIeg~CPvC~~eFtG~nnt~~~CpnCGe~l~v~~ 212 (240)
++.-.|..|+.+|.--.- +..||.||-.|-+.=
T Consensus 3 ~~~~rc~~cg~~f~~a~~-~~~c~~cGl~lp~~~ 35 (411)
T COG0498 3 YVSLRCLKCGREFSQALL-QGLCPDCGLFLPAEY 35 (411)
T ss_pred eeEeecCCCCcchhhHHh-hCcCCcCCccccccc
Confidence 456689999999974333 788999999887743
No 329
>smart00350 MCM minichromosome maintenance proteins.
Probab=40.37 E-value=32 Score=33.54 Aligned_cols=25 Identities=20% Similarity=0.539 Sum_probs=17.5
Q ss_pred CCCCCCCcccc-----ccccceeecCC--CCc
Q 026283 182 GACPACKREFI-----GSKSQIIRCAG--CGN 206 (240)
Q Consensus 182 g~CPvC~~eFt-----G~nnt~~~Cpn--CGe 206 (240)
-.|..|+.++. |.......||+ |++
T Consensus 38 f~C~~C~~~~~~~~~~~~~~~p~~C~~~~C~~ 69 (509)
T smart00350 38 FTCEKCGATLGPEIQSGRETEPTVCPPRECQS 69 (509)
T ss_pred EEecCCCCEEeEEecCCcccCCCcCCCCcCCC
Confidence 35999998652 33345668999 986
No 330
>PRK01345 heat shock protein HtpX; Provisional
Probab=40.37 E-value=90 Score=29.03 Aligned_cols=32 Identities=25% Similarity=0.048 Sum_probs=15.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHh
Q 026283 145 WFALSGWLFRILILATWVLPIAA-PLLIGTVAN 176 (240)
Q Consensus 145 wll~SGWLvn~~l~l~~vlPvaa-p~li~wWlk 176 (240)
-+++.||++.+...+++.+++++ +.++.+|.-
T Consensus 16 ~~~~~g~l~~~~~~~~~~~~~~~~~~~~~~~~~ 48 (317)
T PRK01345 16 LFMGVGYLIGGAGGMMIALVIAAGMNLFSYWNS 48 (317)
T ss_pred HHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHh
Confidence 33444888877654333333332 233444433
No 331
>PF04906 Tweety: Tweety; InterPro: IPR006990 None of the members of the tweety (tty) family have been functionally characterised. However, they are considered to be transmembrane proteins with five potential membrane-spanning regions. A number of potential functions have been suggested on the basis of homology to the yeast FTR1 and FTH1 iron transporter proteins and the mammalian neurotensin receptors 1 and 2 in that they have a similar hydrophobicity profiles although there is no detectable sequence homology to the tweety-related proteins. It has been proposed that the tweety-related proteins could be involved in transport of iron or other divalent cations or alternatively that they may be membrane-bound receptors [].
Probab=40.05 E-value=76 Score=30.58 Aligned_cols=77 Identities=13% Similarity=0.135 Sum_probs=44.1
Q ss_pred hHHHHhhhchhHHHHHHHHh----hHHHHHhHHHHHHHHHhhhhhhhhhHhHHHHHHHHHHHHHHhhhhhhhhHhHHhhh
Q 026283 37 DRFARRMTSGEAWRDAWRTA----NNGFEQLVFDAKKTAERIDRQYSVSRRLNSAARTAAVRARELDREFAISVRWRSFR 112 (240)
Q Consensus 37 d~~a~~~~~~~a~r~a~r~a----n~~~e~~~fear~~a~r~D~~Y~vs~r~a~aa~~a~e~A~eiD~~fgi~rR~R~f~ 112 (240)
|+.-.-..|.+.-++-.-+. ++--+.+...++....+|+.-++-.....++.+...+++.+|-++..-=..|+...
T Consensus 89 ~gv~~~~~s~~~~n~t~~~i~~~v~~~~~~l~~~v~~~l~~Le~~~~~~~~~~~~~~~~~~~~~~v~~~l~~l~~~~~~~ 168 (406)
T PF04906_consen 89 DGVYQLIYSLRNANHTLSGIDNLVSDTTEALNSTVEQHLTRLEEIFAKRTDLLQALQFLQQQAENVVQQLDELPFWRNVS 168 (406)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCcccccCC
Confidence 44433333444444433333 22334455566777778888887666677777777777776666555444565544
Q ss_pred h
Q 026283 113 M 113 (240)
Q Consensus 113 ~ 113 (240)
+
T Consensus 169 ~ 169 (406)
T PF04906_consen 169 L 169 (406)
T ss_pred C
Confidence 4
No 332
>PF05478 Prominin: Prominin; InterPro: IPR008795 The prominins are an emerging family of proteins that, among the multispan membrane proteins, display a novel topology. Mouse and Homo sapiens prominin and (Mus musculus) prominin-like 1 (PROML1) are predicted to contain five membrane spanning domains, with an N-terminal domain exposed to the extracellular space followed by four, alternating small cytoplasmic and large extracellular, loops and a cytoplasmic C-terminal domain []. The exact function of prominin is unknown although in humans defects in PROM1, the gene coding for prominin, cause retinal degeneration [].; GO: 0016021 integral to membrane
Probab=39.97 E-value=4.6e+02 Score=27.44 Aligned_cols=47 Identities=13% Similarity=0.273 Sum_probs=19.4
Q ss_pred HHHhhHHHHHhHHHHHHHHHhhhhhhhhhHhHHHHHHHHHHHHHHhhhh
Q 026283 53 WRTANNGFEQLVFDAKKTAERIDRQYSVSRRLNSAARTAAVRARELDRE 101 (240)
Q Consensus 53 ~r~an~~~e~~~fear~~a~r~D~~Y~vs~r~a~aa~~a~e~A~eiD~~ 101 (240)
.+.+|+.|+....++++.-..+- .++-+.+++......+.|.+|-..
T Consensus 337 v~~~~~~~~~ip~~v~~qt~~~v--~~ik~~l~~~~~~i~~~a~~i~~~ 383 (806)
T PF05478_consen 337 VQEGNSRFNDIPEKVQNQTSDVV--PPIKRDLDSIGKQIRSQAKQIPNQ 383 (806)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhh--HHHHHHHHHHHHHHHHHHHHhHHH
Confidence 33444444444444443222211 134444444444444444444433
No 333
>PF08285 DPM3: Dolichol-phosphate mannosyltransferase subunit 3 (DPM3); InterPro: IPR013174 This family corresponds to subunit 3 of dolichol-phosphate mannosyltransferase, an enzyme which generates mannosyl donors for glycosylphosphatidylinositols, N-glycan and protein O- and C-mannosylation. DPM3 is an integral membrane protein and plays a role in stabilising the dolichol-phosphate mannosyl transferase complex [].
Probab=39.52 E-value=67 Score=25.37 Aligned_cols=50 Identities=26% Similarity=0.315 Sum_probs=30.1
Q ss_pred HHHHHHHHHHH-HHHH---HHHHHHHHHHHHHHHHHHH-----HHHhhhhhcCCCCCCC
Q 026283 139 ATIFFLWFALS-GWLF---RILILATWVLPIAAPLLIG-----TVANNFVIKGACPACK 188 (240)
Q Consensus 139 ~tl~~~wll~S-GWLv---n~~l~l~~vlPvaap~li~-----wWlkRnLIeg~CPvC~ 188 (240)
+++..+|+++. +++- ...--+++.+|+.+.+.|| ...-+-..-..||--.
T Consensus 12 ~~l~~~w~~l~~~~~~~~~~~~~~ii~~lP~~~Lv~fG~Ysl~~lgy~v~tFnDcpeA~ 70 (91)
T PF08285_consen 12 LLLSALWLALLLGLLPLPPEPQQEIIPYLPFYALVSFGCYSLFTLGYGVATFNDCPEAA 70 (91)
T ss_pred HHHHHHHHHHHHccCCCCchhHHHHHHHhhHHHHHHHHHHHHHHHHHhhhccCCCHHHH
Confidence 44555666665 4432 1123577889998888877 4455555566777443
No 334
>PRK14873 primosome assembly protein PriA; Provisional
Probab=39.46 E-value=17 Score=37.31 Aligned_cols=24 Identities=25% Similarity=0.544 Sum_probs=10.6
Q ss_pred CCCCCCccccccc-cceeecCCCCc
Q 026283 183 ACPACKREFIGSK-SQIIRCAGCGN 206 (240)
Q Consensus 183 ~CPvC~~eFtG~n-nt~~~CpnCGe 206 (240)
.||.|+-.++=-+ ....+|..||-
T Consensus 394 ~C~~C~~~L~~h~~~~~l~Ch~CG~ 418 (665)
T PRK14873 394 RCRHCTGPLGLPSAGGTPRCRWCGR 418 (665)
T ss_pred ECCCCCCceeEecCCCeeECCCCcC
Confidence 4555554444211 22444555554
No 335
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=39.39 E-value=17 Score=33.02 Aligned_cols=10 Identities=20% Similarity=0.501 Sum_probs=6.0
Q ss_pred hCCCCchHHH
Q 026283 130 LNTPLGRSFA 139 (240)
Q Consensus 130 ~~T~lG~wL~ 139 (240)
.-.|+|++.+
T Consensus 176 ~vaGIGNiya 185 (282)
T PRK13945 176 IVAGIGNIYA 185 (282)
T ss_pred eEeccchhHH
Confidence 3466777654
No 336
>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=38.92 E-value=10 Score=40.69 Aligned_cols=30 Identities=23% Similarity=0.523 Sum_probs=0.0
Q ss_pred hcCCCCCCCcccc--------ccccceeecCCCCceee
Q 026283 180 IKGACPACKREFI--------GSKSQIIRCAGCGNIVW 209 (240)
Q Consensus 180 Ieg~CPvC~~eFt--------G~nnt~~~CpnCGe~l~ 209 (240)
+.-.||.||.+=. |.......||+||....
T Consensus 666 ~~~~Cp~CG~~T~~~~~Cp~C~~~~~~~~C~~C~~~~~ 703 (900)
T PF03833_consen 666 FYNRCPECGSHTEPVYVCPDCGIEVEEDECPKCGRETT 703 (900)
T ss_dssp --------------------------------------
T ss_pred hhhcCcccCCccccceeccccccccCccccccccccCc
Confidence 4456777776622 33334448888887654
No 337
>smart00355 ZnF_C2H2 zinc finger.
Probab=38.72 E-value=16 Score=19.90 Aligned_cols=12 Identities=33% Similarity=0.974 Sum_probs=8.9
Q ss_pred CCCCCCcccccc
Q 026283 183 ACPACKREFIGS 194 (240)
Q Consensus 183 ~CPvC~~eFtG~ 194 (240)
.|+.|++.|..-
T Consensus 2 ~C~~C~~~f~~~ 13 (26)
T smart00355 2 RCPECGKVFKSK 13 (26)
T ss_pred CCCCCcchhCCH
Confidence 588888888654
No 338
>PRK08173 DNA topoisomerase III; Validated
Probab=38.69 E-value=18 Score=38.11 Aligned_cols=27 Identities=19% Similarity=0.490 Sum_probs=19.5
Q ss_pred CCCCCCCccccccccceeecCCCCceee
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNIVW 209 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~l~ 209 (240)
+.||.|+.+.. .+.....|.||+-.+|
T Consensus 625 ~~CP~Cg~~~~-~~~~~~~Cs~C~f~~~ 651 (862)
T PRK08173 625 TPCPNCGGVVK-ENYRRFACTKCDFSIS 651 (862)
T ss_pred ccCCccccccc-ccCceeEcCCCCcccc
Confidence 67999998652 1234489999986665
No 339
>PRK02224 chromosome segregation protein; Provisional
Probab=38.67 E-value=17 Score=36.89 Aligned_cols=18 Identities=28% Similarity=0.778 Sum_probs=13.8
Q ss_pred hhhhhcCCCCCCCccccc
Q 026283 176 NNFVIKGACPACKREFIG 193 (240)
Q Consensus 176 kRnLIeg~CPvC~~eFtG 193 (240)
+..|.++.||+|+.+|.+
T Consensus 446 ~~~l~~~~Cp~C~r~~~~ 463 (880)
T PRK02224 446 EALLEAGKCPECGQPVEG 463 (880)
T ss_pred HHHHhcccCCCCCCcCCC
Confidence 334578999999998854
No 340
>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=38.61 E-value=18 Score=35.47 Aligned_cols=28 Identities=32% Similarity=0.650 Sum_probs=15.4
Q ss_pred CCCCCccccc-cccceeecCCCCceeeee
Q 026283 184 CPACKREFIG-SKSQIIRCAGCGNIVWQP 211 (240)
Q Consensus 184 CPvC~~eFtG-~nnt~~~CpnCGe~l~v~ 211 (240)
||.|+-..|= -+....+|..||....++
T Consensus 225 C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~ 253 (505)
T TIGR00595 225 CPNCDVSLTYHKKEGKLRCHYCGYQEPIP 253 (505)
T ss_pred CCCCCCceEEecCCCeEEcCCCcCcCCCC
Confidence 5555544442 133456677777666555
No 341
>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=38.16 E-value=21 Score=25.69 Aligned_cols=23 Identities=26% Similarity=0.547 Sum_probs=15.8
Q ss_pred CCCCCccc-----cccccceeecCCCCc
Q 026283 184 CPACKREF-----IGSKSQIIRCAGCGN 206 (240)
Q Consensus 184 CPvC~~eF-----tG~nnt~~~CpnCGe 206 (240)
|+.|..+- ..+...+-+||+||.
T Consensus 25 C~~C~~hNGla~~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 25 CSKCFSHNGLAPKEEFEEIQYRCPYCGA 52 (54)
T ss_pred CcccchhhcccccccCCceEEEcCCCCC
Confidence 77776543 233566889999986
No 342
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=38.01 E-value=26 Score=23.77 Aligned_cols=24 Identities=33% Similarity=0.829 Sum_probs=16.0
Q ss_pred cCCCCCCCc--ccccccc----ceeecCCCC
Q 026283 181 KGACPACKR--EFIGSKS----QIIRCAGCG 205 (240)
Q Consensus 181 eg~CPvC~~--eFtG~nn----t~~~CpnCG 205 (240)
.+.||+|+- .|- +++ ---.|-.||
T Consensus 3 ~~pCP~CGG~DrFr-~~d~~g~G~~~C~~Cg 32 (37)
T smart00778 3 HGPCPNCGGSDRFR-FDDKDGRGTWFCSVCG 32 (37)
T ss_pred ccCCCCCCCccccc-cccCCCCcCEEeCCCC
Confidence 467899986 566 666 445677775
No 343
>PRK10996 thioredoxin 2; Provisional
Probab=38.01 E-value=20 Score=28.68 Aligned_cols=28 Identities=18% Similarity=0.516 Sum_probs=18.9
Q ss_pred CCCCCCCccccc---cccceeecCCCCceee
Q 026283 182 GACPACKREFIG---SKSQIIRCAGCGNIVW 209 (240)
Q Consensus 182 g~CPvC~~eFtG---~nnt~~~CpnCGe~l~ 209 (240)
..||.|+-+.-- .---+.+||.||+.+-
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 33 (139)
T PRK10996 3 TVCTSCQAINRLPDERIEDAAKCGRCGHDLF 33 (139)
T ss_pred EECCCCCCcCCCCCccccCCCcCCCCCCccC
Confidence 469998865422 2234678999998775
No 344
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=37.79 E-value=16 Score=29.19 Aligned_cols=28 Identities=25% Similarity=0.398 Sum_probs=14.8
Q ss_pred hcCCCCCCCcccccccccee-ecCCCCce
Q 026283 180 IKGACPACKREFIGSKSQII-RCAGCGNI 207 (240)
Q Consensus 180 Ieg~CPvC~~eFtG~nnt~~-~CpnCGe~ 207 (240)
....|+.|+.+..=++.=.- -||+||..
T Consensus 41 ~~~~C~~Cg~~~~~~~SCk~R~CP~C~~~ 69 (111)
T PF14319_consen 41 HRYRCEDCGHEKIVYNSCKNRHCPSCQAK 69 (111)
T ss_pred ceeecCCCCceEEecCcccCcCCCCCCCh
Confidence 34567777766544332111 46777654
No 345
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=37.65 E-value=29 Score=23.52 Aligned_cols=11 Identities=18% Similarity=0.416 Sum_probs=6.7
Q ss_pred cCCCCCCCccc
Q 026283 181 KGACPACKREF 191 (240)
Q Consensus 181 eg~CPvC~~eF 191 (240)
.+.||+|+.++
T Consensus 35 ~~~cP~~~~~~ 45 (63)
T smart00504 35 HGTDPVTGQPL 45 (63)
T ss_pred CCCCCCCcCCC
Confidence 45666666655
No 346
>KOG2927 consensus Membrane component of ER protein translocation complex [Intracellular trafficking, secretion, and vesicular transport]
Probab=37.19 E-value=10 Score=36.99 Aligned_cols=34 Identities=26% Similarity=0.364 Sum_probs=20.7
Q ss_pred hhhhhhhhchhHHHHHHHhhCCCCchHHHHHHHH
Q 026283 111 FRMDFSRNWPRYRKQLNDFLNTPLGRSFATIFFL 144 (240)
Q Consensus 111 f~~D~~r~wP~yrrql~~F~~T~lG~wL~tl~~~ 144 (240)
++.=.=..||++-||-.-++.-|.|+.|+.|+++
T Consensus 202 laivLFPLWP~~mR~gvyY~sig~~gfl~~IlvL 235 (372)
T KOG2927|consen 202 LAIVLFPLWPRRMRQGVYYLSIGAGGFLAFILVL 235 (372)
T ss_pred HHHHhcccCcHHHhcceeeeecchhHHHHHHHHH
Confidence 3333446777777777666666677766555543
No 347
>TIGR01374 soxD sarcosine oxidase, delta subunit family, heterotetrameric form. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate. The enzyme is known in monomeric and heterotetrameric (alpha,beta,gamma,delta) form
Probab=37.13 E-value=18 Score=28.56 Aligned_cols=31 Identities=29% Similarity=0.612 Sum_probs=19.4
Q ss_pred eecCCCCceeeeeCCCcccCCCCCCCCCCCCCCee
Q 026283 199 IRCAGCGNIVWQPEGDFFSRNGGGKKSTKSDDDII 233 (240)
Q Consensus 199 ~~CpnCGe~l~v~~g~F~s~~g~~~~~r~t~pgtI 233 (240)
+.||.||+ =+...| +-.|-+.-.|+.+|+..
T Consensus 2 I~CP~CG~---R~~~EF-~y~G~A~~~rP~~~~~~ 32 (84)
T TIGR01374 2 IPCPYCGP---RPEEEF-TYGGDAHIVRPADPAAA 32 (84)
T ss_pred ccCCCCCC---ccHhhE-eccceecccCCCCCCcC
Confidence 67999993 566677 54555554566555543
No 348
>PRK14894 glycyl-tRNA synthetase; Provisional
Probab=37.07 E-value=20 Score=36.66 Aligned_cols=25 Identities=24% Similarity=0.557 Sum_probs=17.1
Q ss_pred cCCCCCCCccccccccceeecCCCCc
Q 026283 181 KGACPACKREFIGSKSQIIRCAGCGN 206 (240)
Q Consensus 181 eg~CPvC~~eFtG~nnt~~~CpnCGe 206 (240)
--.|+.|+..|-.=. -.++||+||+
T Consensus 88 mV~CkkCk~ryRaD~-LiikCP~CGs 112 (539)
T PRK14894 88 LVDCRDCKMRWRADH-IQGVCPNCGS 112 (539)
T ss_pred eeECCCCCccccCcc-ceeeCCCCCC
Confidence 346889998774322 2367999995
No 349
>PRK00349 uvrA excinuclease ABC subunit A; Reviewed
Probab=37.06 E-value=19 Score=38.49 Aligned_cols=30 Identities=27% Similarity=0.448 Sum_probs=23.8
Q ss_pred CCCCCCcccc-------ccccceeecCCC---CceeeeeC
Q 026283 183 ACPACKREFI-------GSKSQIIRCAGC---GNIVWQPE 212 (240)
Q Consensus 183 ~CPvC~~eFt-------G~nnt~~~CpnC---Ge~l~v~~ 212 (240)
.||.|+..|. .||+..--||.| |..+.+..
T Consensus 254 ~c~~~g~~~~~~~p~~FSfN~p~G~Cp~C~G~G~~~~~d~ 293 (943)
T PRK00349 254 ACPVCGFSIPELEPRLFSFNSPYGACPTCDGLGVKLEFDP 293 (943)
T ss_pred cCcccCCCcCcCChhhcCCCCccCCCCcCCCceeEeecCH
Confidence 6999999877 789999999999 65544433
No 350
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=36.99 E-value=10 Score=22.94 Aligned_cols=10 Identities=40% Similarity=1.165 Sum_probs=7.8
Q ss_pred CCCCCCcccc
Q 026283 183 ACPACKREFI 192 (240)
Q Consensus 183 ~CPvC~~eFt 192 (240)
.||.|++.|.
T Consensus 16 ~C~~C~k~F~ 25 (26)
T PF13465_consen 16 KCPYCGKSFS 25 (26)
T ss_dssp EESSSSEEES
T ss_pred CCCCCcCeeC
Confidence 5888888774
No 351
>PRK00420 hypothetical protein; Validated
Probab=36.61 E-value=19 Score=29.65 Aligned_cols=24 Identities=25% Similarity=0.585 Sum_probs=18.9
Q ss_pred cccccceeecCCCCceeee-eCCCc
Q 026283 192 IGSKSQIIRCAGCGNIVWQ-PEGDF 215 (240)
Q Consensus 192 tG~nnt~~~CpnCGe~l~v-~~g~F 215 (240)
-|..-....||.||-+|.- .+|+.
T Consensus 17 ~Ga~ml~~~CP~Cg~pLf~lk~g~~ 41 (112)
T PRK00420 17 KGAKMLSKHCPVCGLPLFELKDGEV 41 (112)
T ss_pred hHHHHccCCCCCCCCcceecCCCce
Confidence 3555566899999999998 77776
No 352
>KOG1307 consensus K+-dependent Ca2+/Na+ exchanger NCKX1 and related proteins [Inorganic ion transport and metabolism; Signal transduction mechanisms]
Probab=36.49 E-value=56 Score=33.63 Aligned_cols=57 Identities=23% Similarity=0.333 Sum_probs=41.7
Q ss_pred hhCCCCchHHHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCC
Q 026283 129 FLNTPLGRSFATIFFLWF------ALSGWLFRILILATWVLPIAAPLLIGTVANNFVIKGACPAC 187 (240)
Q Consensus 129 F~~T~lG~wL~tl~~~wl------l~SGWLvn~~l~l~~vlPvaap~li~wWlkRnLIeg~CPvC 187 (240)
-++.+|=|.+++||+..+ +++.|-.|=++++++++--.+|+.+---+.-+++ .||+|
T Consensus 525 vsS~GL~csi~lLf~ml~v~v~~ia~~rWrMnK~lG~~m~llY~~Fl~~svmlE~~v~--tcp~~ 587 (588)
T KOG1307|consen 525 VSSNGLVCSIGLLFAMLIVLVLGIALSRWRMNKILGFLMILLYFVFLIISVMLETDVL--TCPLS 587 (588)
T ss_pred ecCCceehHHHHHHHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHHhhhheeccee--cccCC
Confidence 356688888877665333 3349999999988888888888888776666655 47776
No 353
>COG4965 TadB Flp pilus assembly protein TadB [Intracellular trafficking and secretion]
Probab=36.25 E-value=3.3e+02 Score=26.16 Aligned_cols=18 Identities=22% Similarity=0.080 Sum_probs=13.6
Q ss_pred hhHhHHhhhhhhhhhchh
Q 026283 104 ISVRWRSFRMDFSRNWPR 121 (240)
Q Consensus 104 i~rR~R~f~~D~~r~wP~ 121 (240)
...|.+.+.+++.+-|-+
T Consensus 53 ~~~r~~~~~~~l~~~~~~ 70 (309)
T COG4965 53 LSSRRLSAQDSLKRLDRK 70 (309)
T ss_pred chhhcccccchhhhHhhh
Confidence 677888889888776543
No 354
>PTZ00409 Sir2 (Silent Information Regulator) protein; Provisional
Probab=36.12 E-value=19 Score=32.82 Aligned_cols=31 Identities=23% Similarity=0.532 Sum_probs=18.9
Q ss_pred hhhcCCCCCCCcccccc-----------ccceeecCCCCceee
Q 026283 178 FVIKGACPACKREFIGS-----------KSQIIRCAGCGNIVW 209 (240)
Q Consensus 178 nLIeg~CPvC~~eFtG~-----------nnt~~~CpnCGe~l~ 209 (240)
|+-+..|..|++++--- ....-.|| ||.+|.
T Consensus 134 ~l~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~P~C~-Cgg~lr 175 (271)
T PTZ00409 134 SVFEARCCTCRKTIQLNKIMLQKTSHFMHQLPPECP-CGGIFK 175 (271)
T ss_pred CcCcceeCCCCCCcccCHHHHhhhhhhccCCCCCCC-CCCccc
Confidence 44567899998776410 11234799 986543
No 355
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=35.97 E-value=18 Score=33.83 Aligned_cols=26 Identities=27% Similarity=0.499 Sum_probs=18.8
Q ss_pred CCCCCCCcccccccccee-----------ecCCCCce
Q 026283 182 GACPACKREFIGSKSQII-----------RCAGCGNI 207 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~-----------~CpnCGe~ 207 (240)
-.||.|+..=.-|.+.|+ +|.+||..
T Consensus 259 ~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~ 295 (299)
T TIGR01385 259 FTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNR 295 (299)
T ss_pred ccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCe
Confidence 479999987776665543 58888863
No 356
>PF09925 DUF2157: Predicted membrane protein (DUF2157); InterPro: IPR018677 This family of various hypothetical prokaryotic proteins has no known function.
Probab=35.91 E-value=2.3e+02 Score=22.93 Aligned_cols=45 Identities=16% Similarity=0.196 Sum_probs=31.8
Q ss_pred CCchHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHhh
Q 026283 133 PLGRSFATIFFLWFALSGW--LFRILILATWVLPIAAPLLIGTVANN 177 (240)
Q Consensus 133 ~lG~wL~tl~~~wll~SGW--Lvn~~l~l~~vlPvaap~li~wWlkR 177 (240)
-+|-.+..+.+++|...-| +=...-+.+.+.++++..+.++++.+
T Consensus 38 ~lGall~~~gii~fvA~nW~~i~~~~k~~~~~~~~~~~~~~~~~~~~ 84 (145)
T PF09925_consen 38 YLGALLLGLGIILFVAANWDDIPRLAKLGLLLALLLLSYVGGFWLWR 84 (145)
T ss_pred HHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3788888889999999988 33444455566667767777777643
No 357
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=35.86 E-value=19 Score=27.11 Aligned_cols=19 Identities=32% Similarity=0.842 Sum_probs=11.2
Q ss_pred ceeecCCCCcee-eeeCCCc
Q 026283 197 QIIRCAGCGNIV-WQPEGDF 215 (240)
Q Consensus 197 t~~~CpnCGe~l-~v~~g~F 215 (240)
+...||.||.++ |.++..|
T Consensus 5 ~~v~CP~C~k~~~w~~~~~~ 24 (62)
T PRK00418 5 ITVNCPTCGKPVEWGEISPF 24 (62)
T ss_pred ccccCCCCCCcccccCCCCc
Confidence 346788888765 3444443
No 358
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=35.83 E-value=13 Score=35.03 Aligned_cols=29 Identities=24% Similarity=0.415 Sum_probs=20.5
Q ss_pred CCCCCCccccc--cccceeecCCCCceeeee
Q 026283 183 ACPACKREFIG--SKSQIIRCAGCGNIVWQP 211 (240)
Q Consensus 183 ~CPvC~~eFtG--~nnt~~~CpnCGe~l~v~ 211 (240)
.||.|+....- +....-.||+||--....
T Consensus 40 kc~~C~~~~~~~~l~~~~~vcp~c~~h~rlt 70 (296)
T CHL00174 40 QCENCYGLNYKKFLKSKMNICEQCGYHLKMS 70 (296)
T ss_pred ECCCccchhhHHHHHHcCCCCCCCCCCcCCC
Confidence 69999987654 334446899999866543
No 359
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=35.13 E-value=24 Score=30.94 Aligned_cols=22 Identities=18% Similarity=0.465 Sum_probs=15.6
Q ss_pred CCCCCCccccccccceeecCCCCce
Q 026283 183 ACPACKREFIGSKSQIIRCAGCGNI 207 (240)
Q Consensus 183 ~CPvC~~eFtG~nnt~~~CpnCGe~ 207 (240)
.|..||+--. .=.-.||+||..
T Consensus 356 ~c~~cg~~~~---~~~~~c~~c~~~ 377 (389)
T PRK11788 356 RCRNCGFTAR---TLYWHCPSCKAW 377 (389)
T ss_pred ECCCCCCCCc---cceeECcCCCCc
Confidence 4888876543 346789999964
No 360
>PF08507 COPI_assoc: COPI associated protein; InterPro: IPR013714 Proteins in this family co-localise with COPI vesicle coat proteins []. In yeast it is a Golgi membrane protein involved in vesicular trafficking, interacting with TVP18 [].
Probab=35.09 E-value=1.5e+02 Score=23.91 Aligned_cols=38 Identities=34% Similarity=0.611 Sum_probs=26.1
Q ss_pred chhHHHHHHHhhCCCCchHHHHHHHHHHHHHHHHHHHHH
Q 026283 119 WPRYRKQLNDFLNTPLGRSFATIFFLWFALSGWLFRILI 157 (240)
Q Consensus 119 wP~yrrql~~F~~T~lG~wL~tl~~~wll~SGWLvn~~l 157 (240)
+|..++.. .|+.+.+|+-+.-+|+.-+..+.-++..++
T Consensus 54 ~~~i~~~~-~FL~~~~GRGlfyif~G~l~~~~~~~~~i~ 91 (136)
T PF08507_consen 54 WPFIRKYF-GFLYSYIGRGLFYIFLGTLCLGQSILSIII 91 (136)
T ss_pred cHHHHHhH-hHHHhHHHHHHHHHHHHHHHHhhHHHHHHH
Confidence 33355555 999999999998888876666643333333
No 361
>PF05280 FlhC: Flagellar transcriptional activator (FlhC); InterPro: IPR007944 This family consists of several bacterial flagellar transcriptional activator (FlhC) proteins. FlhC combines with FlhD to form a regulatory complex in Escherichia coli, this complex has been shown to be a global regulator involved in many cellular processes as well as a flagellar transcriptional activator [].; GO: 0003677 DNA binding, 0030092 regulation of flagellum assembly, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2AVU_E.
Probab=35.08 E-value=22 Score=30.94 Aligned_cols=28 Identities=18% Similarity=0.488 Sum_probs=13.6
Q ss_pred hhcCCCCCCCccccccccc---eeecCCCCc
Q 026283 179 VIKGACPACKREFIGSKSQ---IIRCAGCGN 206 (240)
Q Consensus 179 LIeg~CPvC~~eFtG~nnt---~~~CpnCGe 206 (240)
|---.|+.|+-+|+-.+++ ...||-|..
T Consensus 132 l~l~~C~~C~~~fv~~~~~~~~~~~Cp~C~~ 162 (175)
T PF05280_consen 132 LQLAPCRRCGGHFVTHAHDPRHSFVCPFCQP 162 (175)
T ss_dssp EEEEE-TTT--EEEEESS--SS----TT---
T ss_pred ccccCCCCCCCCeECcCCCCCcCcCCCCCCC
Confidence 3444799999999998776 488999984
No 362
>COG0178 UvrA Excinuclease ATPase subunit [DNA replication, recombination, and repair]
Probab=34.97 E-value=21 Score=38.60 Aligned_cols=26 Identities=27% Similarity=0.585 Sum_probs=21.7
Q ss_pred cCCCCCCCccc-------cccccceeecCCCCc
Q 026283 181 KGACPACKREF-------IGSKSQIIRCAGCGN 206 (240)
Q Consensus 181 eg~CPvC~~eF-------tG~nnt~~~CpnCGe 206 (240)
..+||+|++.+ ..||+..--||.|.-
T Consensus 245 ~~acp~~g~~~~eleprlFSFNsP~GaCp~C~G 277 (935)
T COG0178 245 NFACPVCGFSIPELEPRLFSFNSPFGACPTCDG 277 (935)
T ss_pred ccCCCccCcccCCCCcccccCCCCCCCCCcCCC
Confidence 35899999876 678999999999953
No 363
>PF13994 PgaD: PgaD-like protein
Probab=34.86 E-value=1.6e+02 Score=24.11 Aligned_cols=28 Identities=25% Similarity=0.249 Sum_probs=16.9
Q ss_pred hhhhhchhHHHHHHHhhCCCCchHHHHHHH
Q 026283 114 DFSRNWPRYRKQLNDFLNTPLGRSFATIFF 143 (240)
Q Consensus 114 D~~r~wP~yrrql~~F~~T~lG~wL~tl~~ 143 (240)
|-.|..|+++|-++.+. ++-.|+..+.+
T Consensus 4 ~~~r~~~~~~r~~~~~l--T~~~W~~~~yL 31 (138)
T PF13994_consen 4 TEPRLLPRHQRLIDYFL--TLLFWGGFIYL 31 (138)
T ss_pred ccccccchHHHHHHHHH--HHHHHHHHHHH
Confidence 55788888888885554 23445444433
No 364
>PRK08382 putative monovalent cation/H+ antiporter subunit E; Reviewed
Probab=34.83 E-value=93 Score=27.76 Aligned_cols=57 Identities=12% Similarity=0.057 Sum_probs=29.9
Q ss_pred HHHhhhhhcCCCCCCCccccccccceeecCCCCceeeeeCCCcccCCCC---CCCCCCCCCCeeeeeccc
Q 026283 173 TVANNFVIKGACPACKREFIGSKSQIIRCAGCGNIVWQPEGDFFSRNGG---GKKSTKSDDDIIDVDFEE 239 (240)
Q Consensus 173 wWlkRnLIeg~CPvC~~eFtG~nnt~~~CpnCGe~l~v~~g~F~s~~g~---~~~~r~t~pgtIDVe~e~ 239 (240)
+|+=..++..+.-|+..-++ .+- + -..+.++-.-= +.-|. +++-.+ -|||+-||+++
T Consensus 103 ~~l~~eivkANi~Va~~VL~-~~i------~-Pgiv~v~~~l~-~~~~~~~LAnsITL-TPGTltvdvs~ 162 (201)
T PRK08382 103 IIMAFRLLESNLKVAKHVIF-MDI------N-PGIVKIKTDLH-SDTGITILANSITL-TPGTLTLDVVK 162 (201)
T ss_pred HHHHHHHHHHHHHHHHHHhC-CCC------C-CcEEEEeccCC-ChHHHHHHHHHHhc-CCCeEEEEeec
Confidence 55555666777777776665 221 1 23456655431 21122 244444 47888777763
No 365
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=34.61 E-value=23 Score=28.52 Aligned_cols=34 Identities=24% Similarity=0.411 Sum_probs=25.9
Q ss_pred hhcCCCCCCCccccccccceeecCCCCceeeeeC
Q 026283 179 VIKGACPACKREFIGSKSQIIRCAGCGNIVWQPE 212 (240)
Q Consensus 179 LIeg~CPvC~~eFtG~nnt~~~CpnCGe~l~v~~ 212 (240)
++-|+|-+|+-.=--..+.+..|-+||.....+.
T Consensus 33 va~daCeiC~~~GY~q~g~~lvC~~C~~~~~~~~ 66 (102)
T PF10080_consen 33 VAFDACEICGPKGYYQEGDQLVCKNCGVRFNLPT 66 (102)
T ss_pred EEEEeccccCCCceEEECCEEEEecCCCEEehhh
Confidence 3458999995543335677899999999887776
No 366
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=34.59 E-value=19 Score=39.15 Aligned_cols=40 Identities=23% Similarity=0.424 Sum_probs=27.6
Q ss_pred HHhhhhhcCCCCCCCccccccc----cceeecCCCCceeeeeCC
Q 026283 174 VANNFVIKGACPACKREFIGSK----SQIIRCAGCGNIVWQPEG 213 (240)
Q Consensus 174 WlkRnLIeg~CPvC~~eFtG~n----nt~~~CpnCGe~l~v~~g 213 (240)
|..-.-..+.|..|+..|+-+. +.+--|-+||.++=..=.
T Consensus 453 WqpDDEaSdtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~CS 496 (1374)
T PTZ00303 453 WQKDDESSDSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFCI 496 (1374)
T ss_pred CCCCcccCCcccCcCCcccccccccccccccccCCccccCcccc
Confidence 3333334567999999998652 456669999998765443
No 367
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=34.52 E-value=11 Score=37.10 Aligned_cols=30 Identities=33% Similarity=0.635 Sum_probs=20.7
Q ss_pred CCCCCCCcc--ccccccceeecCCCCceeeeeCC
Q 026283 182 GACPACKRE--FIGSKSQIIRCAGCGNIVWQPEG 213 (240)
Q Consensus 182 g~CPvC~~e--FtG~nnt~~~CpnCGe~l~v~~g 213 (240)
-+|-.|... ..-...-..+||+||. ++..|
T Consensus 247 TAC~rC~t~y~le~A~~~~wrCpkCGg--~ikKG 278 (403)
T COG1379 247 TACSRCYTRYSLEEAKSLRWRCPKCGG--KIKKG 278 (403)
T ss_pred HHHHHhhhccCcchhhhhcccCccccc--chhhh
Confidence 468888733 3455556689999999 55554
No 368
>PTZ00408 NAD-dependent deacetylase; Provisional
Probab=34.41 E-value=16 Score=32.73 Aligned_cols=30 Identities=27% Similarity=0.371 Sum_probs=19.8
Q ss_pred hhhhcCCCCCCCccccc---cccceeecCCCCc
Q 026283 177 NFVIKGACPACKREFIG---SKSQIIRCAGCGN 206 (240)
Q Consensus 177 RnLIeg~CPvC~~eFtG---~nnt~~~CpnCGe 206 (240)
-++-+..|..|++.|.- +..+.-.||.||.
T Consensus 113 G~~~~~~C~~C~~~~~~~~~~~~~~p~C~~Cg~ 145 (242)
T PTZ00408 113 GELLKVRCTATGHVFDWTEDVVHGSSRCKCCGC 145 (242)
T ss_pred CccceEEECCCCcccCchhhhhcCCCccccCCC
Confidence 44555789999987642 1223467999983
No 369
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=34.24 E-value=25 Score=23.67 Aligned_cols=25 Identities=24% Similarity=0.638 Sum_probs=10.8
Q ss_pred CCCC--CCccccccccce---eecCCCCce
Q 026283 183 ACPA--CKREFIGSKSQI---IRCAGCGNI 207 (240)
Q Consensus 183 ~CPv--C~~eFtG~nnt~---~~CpnCGe~ 207 (240)
.||. |++-+..-.... .+|+.||..
T Consensus 20 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 49 (64)
T PF01485_consen 20 WCPNPDCEYIIEKDDGCNSPIVTCPSCGTE 49 (64)
T ss_dssp --TTSST---ECS-SSTTS--CCTTSCCSE
T ss_pred CCCCCCCcccEEecCCCCCCeeECCCCCCc
Confidence 6766 776665443332 567777653
No 370
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=34.21 E-value=38 Score=21.54 Aligned_cols=18 Identities=39% Similarity=0.713 Sum_probs=14.9
Q ss_pred cceeecCCCCceeeeeCC
Q 026283 196 SQIIRCAGCGNIVWQPEG 213 (240)
Q Consensus 196 nt~~~CpnCGe~l~v~~g 213 (240)
....+|..||++|.+-++
T Consensus 5 ~~~ykC~~Cgniv~v~~~ 22 (34)
T TIGR00319 5 GQVYKCEVCGNIVEVLHA 22 (34)
T ss_pred CcEEEcCCCCcEEEEEEC
Confidence 567899999999987754
No 371
>COG0419 SbcC ATPase involved in DNA repair [DNA replication, recombination, and repair]
Probab=33.93 E-value=20 Score=37.29 Aligned_cols=16 Identities=25% Similarity=0.646 Sum_probs=12.1
Q ss_pred hcCCCCCCCccccccc
Q 026283 180 IKGACPACKREFIGSK 195 (240)
Q Consensus 180 Ieg~CPvC~~eFtG~n 195 (240)
..+.|||||.+..+..
T Consensus 456 ~~~~CPvCg~~l~~~~ 471 (908)
T COG0419 456 AGEKCPVCGQELPEEH 471 (908)
T ss_pred CCCCCCCCCCCCCcHH
Confidence 4689999998776543
No 372
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.86 E-value=20 Score=28.48 Aligned_cols=12 Identities=42% Similarity=1.182 Sum_probs=5.5
Q ss_pred hcCCCCCCCccc
Q 026283 180 IKGACPACKREF 191 (240)
Q Consensus 180 Ieg~CPvC~~eF 191 (240)
..|.||.||-|+
T Consensus 40 l~g~CPnCGGel 51 (84)
T COG3813 40 LHGLCPNCGGEL 51 (84)
T ss_pred hcCcCCCCCchh
Confidence 344444444444
No 373
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=33.78 E-value=28 Score=25.63 Aligned_cols=12 Identities=33% Similarity=0.717 Sum_probs=5.9
Q ss_pred eecCCCCceeee
Q 026283 199 IRCAGCGNIVWQ 210 (240)
Q Consensus 199 ~~CpnCGe~l~v 210 (240)
..||.||.++..
T Consensus 3 v~CP~C~k~~~~ 14 (57)
T PF03884_consen 3 VKCPICGKPVEW 14 (57)
T ss_dssp EE-TTT--EEE-
T ss_pred ccCCCCCCeecc
Confidence 468888887777
No 374
>PRK09401 reverse gyrase; Reviewed
Probab=33.71 E-value=18 Score=39.42 Aligned_cols=26 Identities=23% Similarity=0.627 Sum_probs=20.4
Q ss_pred hcCCCCCCCccccccccceeecCCCCcee
Q 026283 180 IKGACPACKREFIGSKSQIIRCAGCGNIV 208 (240)
Q Consensus 180 Ieg~CPvC~~eFtG~nnt~~~CpnCGe~l 208 (240)
+...|+.||++|+.-- -.||.||..+
T Consensus 677 ~~k~c~~~g~~f~~~~---~~~~~c~~~~ 702 (1176)
T PRK09401 677 TIKRCRDCGYQFTDES---DKCPRCGSTN 702 (1176)
T ss_pred eecccccccccccccc---cccccccccc
Confidence 4467999999999853 3999999543
No 375
>COG3898 Uncharacterized membrane-bound protein [Function unknown]
Probab=33.67 E-value=1.1e+02 Score=31.21 Aligned_cols=33 Identities=12% Similarity=0.182 Sum_probs=21.6
Q ss_pred HHHHHHHH--HHHHHHHHHHHHHHHHHHhhhhhcC
Q 026283 150 GWLFRILI--LATWVLPIAAPLLIGTVANNFVIKG 182 (240)
Q Consensus 150 GWLvn~~l--~l~~vlPvaap~li~wWlkRnLIeg 182 (240)
||.++.-+ ...+++-+++-++|-||+-+.+++-
T Consensus 34 G~~~emslm~Aa~~iva~vaav~llwwlv~~iw~s 68 (531)
T COG3898 34 GQQYEMSLMVAASIIVALVAAVLLLWWLVRSIWES 68 (531)
T ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 88887664 3333344444666779998888864
No 376
>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....
Probab=33.66 E-value=25 Score=33.35 Aligned_cols=10 Identities=40% Similarity=0.836 Sum_probs=5.5
Q ss_pred CCcccccccc
Q 026283 14 PKTTLHIGRR 23 (240)
Q Consensus 14 ~~~~~~~~~~ 23 (240)
|+..+|++--
T Consensus 10 ~Ng~lHlGH~ 19 (391)
T PF09334_consen 10 PNGDLHLGHL 19 (391)
T ss_dssp TSSS-BHHHH
T ss_pred CCCCCCCChh
Confidence 5667777543
No 377
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=33.63 E-value=9.6 Score=35.68 Aligned_cols=31 Identities=26% Similarity=0.569 Sum_probs=25.3
Q ss_pred cCCCCCCCccccccccceeecCCCCceeeee
Q 026283 181 KGACPACKREFIGSKSQIIRCAGCGNIVWQP 211 (240)
Q Consensus 181 eg~CPvC~~eFtG~nnt~~~CpnCGe~l~v~ 211 (240)
...|++|+....++.+..--|-+||-++-.+
T Consensus 168 a~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~~ 198 (288)
T KOG1729|consen 168 ATECMVCGCTEFTLSERRHHCRNCGDIVCAP 198 (288)
T ss_pred ceecccCCCccccHHHHHHHHHhcchHhhhh
Confidence 3479999995666778888899999998773
No 378
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=33.48 E-value=23 Score=30.21 Aligned_cols=28 Identities=29% Similarity=0.699 Sum_probs=20.6
Q ss_pred CCCCCCccccccc-cceeecCCCCceeee
Q 026283 183 ACPACKREFIGSK-SQIIRCAGCGNIVWQ 210 (240)
Q Consensus 183 ~CPvC~~eFtG~n-nt~~~CpnCGe~l~v 210 (240)
+|-.||..|---. .--.=||+||.-..+
T Consensus 3 ~Ct~Cg~~f~dgs~eil~GCP~CGg~kF~ 31 (131)
T PF09845_consen 3 QCTKCGRVFEDGSKEILSGCPECGGNKFQ 31 (131)
T ss_pred ccCcCCCCcCCCcHHHHccCcccCCcceE
Confidence 6999999996333 445569999976554
No 379
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=33.44 E-value=13 Score=38.73 Aligned_cols=25 Identities=32% Similarity=0.804 Sum_probs=20.1
Q ss_pred CCCCCCccccccccceeecCCCCcee
Q 026283 183 ACPACKREFIGSKSQIIRCAGCGNIV 208 (240)
Q Consensus 183 ~CPvC~~eFtG~nnt~~~CpnCGe~l 208 (240)
+|-+|+.+|+.++... -|.|||.+.
T Consensus 903 ~cmacq~pf~afrrrh-hcrncggif 927 (990)
T KOG1819|consen 903 QCMACQMPFNAFRRRH-HCRNCGGIF 927 (990)
T ss_pred hhhhccCcHHHHHHhh-hhcccCcee
Confidence 5679999999988654 599999765
No 380
>PF11833 DUF3353: Protein of unknown function (DUF3353); InterPro: IPR021788 This family of proteins are functionally uncharacterised. This protein is found in bacteria and eukaryotes. Proteins in this family are typically between 205 to 258 amino acids in length.
Probab=33.27 E-value=3.3e+02 Score=24.04 Aligned_cols=72 Identities=18% Similarity=0.193 Sum_probs=40.9
Q ss_pred HHHHHHHhhhhhhhhhHhHHHHHHHHHHHHHHhhhhhh--------hhHhHHhhhh--------hhhhhchhHHHHHHHh
Q 026283 66 DAKKTAERIDRQYSVSRRLNSAARTAAVRARELDREFA--------ISVRWRSFRM--------DFSRNWPRYRKQLNDF 129 (240)
Q Consensus 66 ear~~a~r~D~~Y~vs~r~a~aa~~a~e~A~eiD~~fg--------i~rR~R~f~~--------D~~r~wP~yrrql~~F 129 (240)
|.+++-+++-.+|.=-.+.-+..+.|-|.- +=+.+. +..++|..-. .-...-|.|-+++...
T Consensus 8 EIq~Arn~ll~~y~gd~~~~~~IEaAYD~I--LM~rL~~Rq~Gki~v~~~ir~ad~~~~~~~~~~~~~~~p~wl~~~~~~ 85 (194)
T PF11833_consen 8 EIQAARNRLLAQYAGDEKSREAIEAAYDAI--LMERLRQRQKGKIKVPERIRYADREEPKPPNPKPSNPSPPWLQRLLPS 85 (194)
T ss_pred HHHHHHHHHHHHhcCCHHHHHHHHHHHHHH--HHHHHHHHHcCCCCccHHHHHhhhccccccCCCCCCccchHHHhcccc
Confidence 445556677778876666666666666532 112222 3344443222 2335677888877555
Q ss_pred hCCCCchHHH
Q 026283 130 LNTPLGRSFA 139 (240)
Q Consensus 130 ~~T~lG~wL~ 139 (240)
.++|=+.-+.
T Consensus 86 ~~~P~~~~l~ 95 (194)
T PF11833_consen 86 FDTPSSQDLL 95 (194)
T ss_pred eeCCCcchHH
Confidence 6677776553
No 381
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 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 C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=33.20 E-value=14 Score=20.86 Aligned_cols=11 Identities=36% Similarity=1.114 Sum_probs=7.6
Q ss_pred CCCCCCccccc
Q 026283 183 ACPACKREFIG 193 (240)
Q Consensus 183 ~CPvC~~eFtG 193 (240)
.||.|+..|.-
T Consensus 2 ~C~~C~~~f~~ 12 (23)
T PF00096_consen 2 KCPICGKSFSS 12 (23)
T ss_dssp EETTTTEEESS
T ss_pred CCCCCCCccCC
Confidence 47888877753
No 382
>PF09972 DUF2207: Predicted membrane protein (DUF2207); InterPro: IPR018702 This domain has no known function.
Probab=32.82 E-value=2.1e+02 Score=26.28 Aligned_cols=12 Identities=17% Similarity=0.207 Sum_probs=5.7
Q ss_pred HHHHhHHHHHHH
Q 026283 59 GFEQLVFDAKKT 70 (240)
Q Consensus 59 ~~e~~~fear~~ 70 (240)
..|+..+++=..
T Consensus 330 ~~E~~ll~~l~~ 341 (511)
T PF09972_consen 330 PYERALLDWLFN 341 (511)
T ss_pred HHHHHHHHHHhc
Confidence 455555544333
No 383
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=32.81 E-value=30 Score=24.64 Aligned_cols=19 Identities=21% Similarity=0.576 Sum_probs=15.3
Q ss_pred ccccceeecCCCCceeeee
Q 026283 193 GSKSQIIRCAGCGNIVWQP 211 (240)
Q Consensus 193 G~nnt~~~CpnCGe~l~v~ 211 (240)
.-|.+..||-.|.|++...
T Consensus 26 ~k~~~klrCGaCs~vl~~s 44 (46)
T PF11331_consen 26 KKNQQKLRCGACSEVLSFS 44 (46)
T ss_pred ccceeEEeCCCCceeEEEe
Confidence 4457899999999998753
No 384
>PLN03121 nucleic acid binding protein; Provisional
Probab=32.70 E-value=42 Score=31.09 Aligned_cols=41 Identities=27% Similarity=0.244 Sum_probs=33.1
Q ss_pred HHHHHHHHhhhhhhhhhHhHHHHHHHHHHHHHHhhhhhhhhHhHHhhh
Q 026283 65 FDAKKTAERIDRQYSVSRRLNSAARTAAVRARELDREFAISVRWRSFR 112 (240)
Q Consensus 65 fear~~a~r~D~~Y~vs~r~a~aa~~a~e~A~eiD~~fgi~rR~R~f~ 112 (240)
.+|=.-|..+|+++.||. +|....-+||+++||..++-+-.
T Consensus 135 kda~~KAkafDE~h~lss-------~a~a~v~~~d~~iglt~k~~~g~ 175 (243)
T PLN03121 135 KDALSKAKAFDESHQVSA-------TAAAKVAELSKRIGLTDKIFAGM 175 (243)
T ss_pred HHHHHHHHHHHHhcCccH-------hhhhhhhhhhhhccchhhhhhhH
Confidence 346566889999999995 66778889999999999986533
No 385
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=32.61 E-value=38 Score=24.89 Aligned_cols=29 Identities=24% Similarity=0.698 Sum_probs=19.1
Q ss_pred CCCCCCc-cccccccceeecCCCCceeeee
Q 026283 183 ACPACKR-EFIGSKSQIIRCAGCGNIVWQP 211 (240)
Q Consensus 183 ~CPvC~~-eFtG~nnt~~~CpnCGe~l~v~ 211 (240)
.||-||- .|-.--.....|--||-..|+.
T Consensus 21 ~CPrCG~gvfmA~H~dR~~CGkCgyTe~~~ 50 (51)
T COG1998 21 FCPRCGPGVFMADHKDRWACGKCGYTEFKK 50 (51)
T ss_pred cCCCCCCcchhhhcCceeEeccccceEeec
Confidence 5777775 5666666677777777665543
No 386
>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=32.60 E-value=23 Score=21.87 Aligned_cols=24 Identities=21% Similarity=0.504 Sum_probs=11.0
Q ss_pred CCCCCCcccccccc---ceeecCCCCc
Q 026283 183 ACPACKREFIGSKS---QIIRCAGCGN 206 (240)
Q Consensus 183 ~CPvC~~eFtG~nn---t~~~CpnCGe 206 (240)
.||.|+....-... .-..||.|.+
T Consensus 3 ~C~rC~~~~~~~~~~~r~~~~C~rCq~ 29 (30)
T PF06827_consen 3 KCPRCWNYIEDIGINGRSTYLCPRCQK 29 (30)
T ss_dssp B-TTT--BBEEEEETTEEEEE-TTTCC
T ss_pred cCccCCCcceEeEecCCCCeECcCCcC
Confidence 57788777633222 3355777765
No 387
>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=32.45 E-value=26 Score=26.96 Aligned_cols=17 Identities=18% Similarity=0.435 Sum_probs=12.8
Q ss_pred eecCCCCceeeeeCCCc
Q 026283 199 IRCAGCGNIVWQPEGDF 215 (240)
Q Consensus 199 ~~CpnCGe~l~v~~g~F 215 (240)
..||.|+.+|...+|+|
T Consensus 2 ~~CP~C~~~L~~~~~~~ 18 (70)
T PF07191_consen 2 NTCPKCQQELEWQGGHY 18 (70)
T ss_dssp -B-SSS-SBEEEETTEE
T ss_pred CcCCCCCCccEEeCCEE
Confidence 57999999999999887
No 388
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=32.43 E-value=34 Score=26.26 Aligned_cols=32 Identities=25% Similarity=0.507 Sum_probs=15.5
Q ss_pred cCCCCCCCcc-ccc------cccceeecCCCCceeeeeC
Q 026283 181 KGACPACKRE-FIG------SKSQIIRCAGCGNIVWQPE 212 (240)
Q Consensus 181 eg~CPvC~~e-FtG------~nnt~~~CpnCGe~l~v~~ 212 (240)
.-+||.|+++ -+. .+.-.+.|-+||+.-..+=
T Consensus 22 ~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~i 60 (81)
T PF05129_consen 22 VFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTKI 60 (81)
T ss_dssp ----TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE-
T ss_pred eEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEcc
Confidence 4579999944 222 2345789999998876663
No 389
>PF11290 DUF3090: Protein of unknown function (DUF3090); InterPro: IPR021441 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=32.40 E-value=20 Score=31.75 Aligned_cols=15 Identities=40% Similarity=0.860 Sum_probs=10.5
Q ss_pred ecCCCCceeeeeCCCc
Q 026283 200 RCAGCGNIVWQPEGDF 215 (240)
Q Consensus 200 ~CpnCGe~l~v~~g~F 215 (240)
.||.||++|- +.|||
T Consensus 156 ~CPlCg~PlD-P~GH~ 170 (171)
T PF11290_consen 156 PCPLCGEPLD-PEGHI 170 (171)
T ss_pred CCCCCCCCCC-CCCCc
Confidence 5888888864 45765
No 390
>TIGR01597 PYST-B Plasmodium yoelii subtelomeric family PYST-B. This model represents a paralogous family of Plasmodium yoelii genes preferentially located in the subtelomeric regions of the chromosomes. There are no obvious homologs to these genes in any other organism.
Probab=32.36 E-value=1.1e+02 Score=28.73 Aligned_cols=47 Identities=11% Similarity=0.184 Sum_probs=23.6
Q ss_pred HHHHHHHhhCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 026283 122 YRKQLNDFLNTPLGRSFATIFFLWFALSGWLFRILILATWVLPIAAPLLIGTVA 175 (240)
Q Consensus 122 yrrql~~F~~T~lG~wL~tl~~~wll~SGWLvn~~l~l~~vlPvaap~li~wWl 175 (240)
+++....+. +.+.+.+..++.++.|||+- ++++++|.+..+-..||-
T Consensus 193 lkK~~~kli---~~~l~~i~~~~~i~isG~~~----l~~l~i~~~~si~~~~~~ 239 (255)
T TIGR01597 193 LKKLVKKLI---VRCLTFIVIVCSILVSGPVY----LLALIIPSLISIYWSIWR 239 (255)
T ss_pred HHHHHHHHH---HHHHHHHHHHHHHhhcchHH----HHHHHHHHHHHHHHHHHH
Confidence 444444444 33333333344556679972 334556666455555654
No 391
>PHA02768 hypothetical protein; Provisional
Probab=32.18 E-value=22 Score=26.11 Aligned_cols=28 Identities=29% Similarity=0.651 Sum_probs=20.3
Q ss_pred hcCCCCCCCcccccccc---------ceeecCCCCce
Q 026283 180 IKGACPACKREFIGSKS---------QIIRCAGCGNI 207 (240)
Q Consensus 180 Ieg~CPvC~~eFtG~nn---------t~~~CpnCGe~ 207 (240)
.--.||.|+..|+-..+ ..-.|.+||..
T Consensus 4 ~~y~C~~CGK~Fs~~~~L~~H~r~H~k~~kc~~C~k~ 40 (55)
T PHA02768 4 LGYECPICGEIYIKRKSMITHLRKHNTNLKLSNCKRI 40 (55)
T ss_pred cccCcchhCCeeccHHHHHHHHHhcCCcccCCcccce
Confidence 34589999999975432 35689999875
No 392
>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=32.08 E-value=34 Score=25.23 Aligned_cols=20 Identities=15% Similarity=0.356 Sum_probs=13.0
Q ss_pred CCCCCCCccccccccceeecCC
Q 026283 182 GACPACKREFIGSKSQIIRCAG 203 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~Cpn 203 (240)
..|++|+.++.. +.-...|+
T Consensus 79 ~~C~vC~k~l~~--~~f~~~p~ 98 (109)
T PF10367_consen 79 TKCSVCGKPLGN--SVFVVFPC 98 (109)
T ss_pred CCccCcCCcCCC--ceEEEeCC
Confidence 569999988844 44444444
No 393
>smart00837 DPBB_1 Rare lipoprotein A (RlpA)-like double-psi beta-barrel. Rare lipoprotein A (RlpA) contains a conserved region that has the double-psi beta-barrel (DPBB) fold. The function of RlpA is not well understood, but it has been shown to act as a prc mutant suppressor in Escherichia coli. The DPBB fold is often an enzymatic domain. The members of this family are quite diverse, and if catalytic this family may contain several different functions. Another example of this domain is found in the N terminus of pollen allergen.
Probab=32.02 E-value=21 Score=27.64 Aligned_cols=9 Identities=22% Similarity=0.582 Sum_probs=6.8
Q ss_pred CCCeeeeec
Q 026283 229 DDDIIDVDF 237 (240)
Q Consensus 229 ~pgtIDVe~ 237 (240)
..|+|+|++
T Consensus 79 ~~Gvi~v~y 87 (87)
T smart00837 79 KAGIVPVKY 87 (87)
T ss_pred cCCEEeeEC
Confidence 349999885
No 394
>PRK01741 cell division protein ZipA; Provisional
Probab=31.85 E-value=34 Score=33.01 Aligned_cols=25 Identities=16% Similarity=0.287 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhh
Q 026283 153 FRILILATWVLPIAAPLLIGTVANN 177 (240)
Q Consensus 153 vn~~l~l~~vlPvaap~li~wWlkR 177 (240)
+|.|||++-++-++++++.|-|.+|
T Consensus 3 Ln~iliILg~lal~~Lv~hgiWsnR 27 (332)
T PRK01741 3 LNTILIILGILALVALVAHGIWSNR 27 (332)
T ss_pred ceehHHHHHHHHHHHHHHhhhhhhh
Confidence 4677888888888889999999887
No 395
>PF06364 DUF1068: Protein of unknown function (DUF1068); InterPro: IPR010471 This family consists of several hypothetical plant proteins from Arabidopsis thaliana and Oryza sativa. The function of this family is unknown.
Probab=31.58 E-value=41 Score=30.03 Aligned_cols=38 Identities=24% Similarity=0.460 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHhhhhh---cCCCCCCCccccccccceeecCCCCceeeeeCCC
Q 026283 165 IAAPLLIGTVANNFVI---KGACPACKREFIGSKSQIIRCAGCGNIVWQPEGD 214 (240)
Q Consensus 165 vaap~li~wWlkRnLI---eg~CPvC~~eFtG~nnt~~~CpnCGe~l~v~~g~ 214 (240)
|++|.+ -|=++.++. ...||.|- |-|| .-..|.++.|-
T Consensus 23 ivGP~L-YWh~~~~~~~~s~~sCppC~----------CDCs-~~~ll~ip~gl 63 (176)
T PF06364_consen 23 IVGPPL-YWHLSEGLAAVSSSSCPPCD----------CDCS-SQPLLSIPPGL 63 (176)
T ss_pred eeCchH-HHHHHHhhhcccCCCCCCCC----------CCCC-CHHHHHhcccc
Confidence 334433 355555544 58999996 8888 78888999774
No 396
>PF04674 Phi_1: Phosphate-induced protein 1 conserved region; InterPro: IPR006766 This entry represents a family of conserved plant proteins. A conserved region in these proteins was identified in a phosphate-induced protein of unknown function [].
Probab=31.49 E-value=29 Score=32.56 Aligned_cols=34 Identities=18% Similarity=0.375 Sum_probs=24.3
Q ss_pred hhhhhcCCCC-CCCccccccc-------------cceeecCC-CCceee
Q 026283 176 NNFVIKGACP-ACKREFIGSK-------------SQIIRCAG-CGNIVW 209 (240)
Q Consensus 176 kRnLIeg~CP-vC~~eFtG~n-------------nt~~~Cpn-CGe~l~ 209 (240)
....|||-|- .|+++-.... |...|||+ |.=|.-
T Consensus 114 ~DV~v~gFC~~~CG~H~~~~~~~~~~~~~YawVGns~~qCPg~CAwPf~ 162 (273)
T PF04674_consen 114 ADVAVEGFCMSRCGFHGSTFPSSVGKRLPYAWVGNSETQCPGQCAWPFH 162 (273)
T ss_pred ccceecccccccccCCcCCcccccccceeEEEecCccCCCCCCCCCCCc
Confidence 4556899997 6999855543 46689997 964433
No 397
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=31.43 E-value=28 Score=20.96 Aligned_cols=11 Identities=27% Similarity=0.899 Sum_probs=7.3
Q ss_pred CCCCCCccccc
Q 026283 183 ACPACKREFIG 193 (240)
Q Consensus 183 ~CPvC~~eFtG 193 (240)
.|+.|+..+.+
T Consensus 1 ~C~~C~~~i~~ 11 (39)
T smart00132 1 KCAGCGKPIRG 11 (39)
T ss_pred CccccCCcccC
Confidence 36777776665
No 398
>PTZ00396 Casein kinase II subunit beta; Provisional
Probab=31.28 E-value=31 Score=31.92 Aligned_cols=34 Identities=18% Similarity=0.521 Sum_probs=24.9
Q ss_pred hhcCCCC--CCCcc---------ccccccceeecCCCCceeeeeC
Q 026283 179 VIKGACP--ACKRE---------FIGSKSQIIRCAGCGNIVWQPE 212 (240)
Q Consensus 179 LIeg~CP--vC~~e---------FtG~nnt~~~CpnCGe~l~v~~ 212 (240)
-+-|.|| -|+.+ -.|.....+.||+|.++-.-+.
T Consensus 118 g~FG~CPRv~C~~q~~LPvGlSd~~g~~~VKlyCP~C~DvY~p~s 162 (251)
T PTZ00396 118 GKFGHCPRVLCEGQNVLPIGLSDVLKTSRVKVYCPRCQEVYHPKK 162 (251)
T ss_pred CCCCCCCCccCCCCcccccccCCCcCcCceeEeCCCchhhcCCCC
Confidence 4568999 57744 4566777889999999875443
No 399
>TIGR00108 eRF peptide chain release factor eRF/aRF, subunit 1. Alternative names include eRF1, SUP45, omnipotent suppressor protein 1.
Probab=30.97 E-value=26 Score=33.80 Aligned_cols=31 Identities=16% Similarity=0.446 Sum_probs=20.0
Q ss_pred hcCCCCCCCcccccc-----ccceeecCCCCceeee
Q 026283 180 IKGACPACKREFIGS-----KSQIIRCAGCGNIVWQ 210 (240)
Q Consensus 180 Ieg~CPvC~~eFtG~-----nnt~~~CpnCGe~l~v 210 (240)
++-.||.|+++-... +.....||+||..+.+
T Consensus 323 ~~~r~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~~~ 358 (409)
T TIGR00108 323 VTYKCAECGEVIEKTVRELKDKKFAICPACGQEMDV 358 (409)
T ss_pred EEEEcCCCCceeecccccccccccccCcccCccccc
Confidence 456899999841111 1234589999988743
No 400
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=30.80 E-value=29 Score=25.50 Aligned_cols=12 Identities=8% Similarity=-0.056 Sum_probs=9.6
Q ss_pred eeecCCCCceee
Q 026283 198 IIRCAGCGNIVW 209 (240)
Q Consensus 198 ~~~CpnCGe~l~ 209 (240)
...||+|||...
T Consensus 27 ~~~c~~cg~~~~ 38 (60)
T PRK01110 27 LSVDKTTGEYHL 38 (60)
T ss_pred eeEcCCCCceec
Confidence 578999999764
No 401
>PRK11032 hypothetical protein; Provisional
Probab=30.56 E-value=26 Score=30.35 Aligned_cols=26 Identities=19% Similarity=0.469 Sum_probs=19.0
Q ss_pred CCCCCCCccccccc-cceeecCCCCce
Q 026283 182 GACPACKREFIGSK-SQIIRCAGCGNI 207 (240)
Q Consensus 182 g~CPvC~~eFtG~n-nt~~~CpnCGe~ 207 (240)
..|-.|+++..=.. ....-||.||..
T Consensus 125 LvC~~Cg~~~~~~~p~~i~pCp~C~~~ 151 (160)
T PRK11032 125 LVCEKCHHHLAFYTPEVLPLCPKCGHD 151 (160)
T ss_pred EEecCCCCEEEecCCCcCCCCCCCCCC
Confidence 35889998876555 456689999864
No 402
>PRK00635 excinuclease ABC subunit A; Provisional
Probab=30.53 E-value=28 Score=39.98 Aligned_cols=31 Identities=19% Similarity=0.438 Sum_probs=24.1
Q ss_pred hcCCCCCCCcccc-------ccccceeecCCC---Cceeee
Q 026283 180 IKGACPACKREFI-------GSKSQIIRCAGC---GNIVWQ 210 (240)
Q Consensus 180 Ieg~CPvC~~eFt-------G~nnt~~~CpnC---Ge~l~v 210 (240)
..-.||.|++.|. .||+..--||.| |....+
T Consensus 243 ~~~~cp~~~~~~~~~~p~~FSfNsp~GaCp~C~GlG~~~~~ 283 (1809)
T PRK00635 243 TQATIPETQQTYTPLTPQLFSPHSLEDRCPQCQGSGIFISI 283 (1809)
T ss_pred ccccCCccCcccCcCChhhcCCCCccccCCCCCCccccccc
Confidence 4567999998765 788889999999 655444
No 403
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=30.42 E-value=44 Score=26.85 Aligned_cols=22 Identities=14% Similarity=0.255 Sum_probs=11.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 026283 151 WLFRILILATWVLPIAAPLLIG 172 (240)
Q Consensus 151 WLvn~~l~l~~vlPvaap~li~ 172 (240)
|+|-++|++++++-|+++..++
T Consensus 2 W~l~~iii~~i~l~~~~~~~~~ 23 (130)
T PF12273_consen 2 WVLFAIIIVAILLFLFLFYCHN 23 (130)
T ss_pred eeeHHHHHHHHHHHHHHHHHHH
Confidence 6555555444444455555544
No 404
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=30.40 E-value=21 Score=26.60 Aligned_cols=18 Identities=39% Similarity=1.006 Sum_probs=15.9
Q ss_pred eeecCCCCceeeeeCCCc
Q 026283 198 IIRCAGCGNIVWQPEGDF 215 (240)
Q Consensus 198 ~~~CpnCGe~l~v~~g~F 215 (240)
.+.|.+||-.++.+.-.|
T Consensus 31 kikC~gCg~~imlpR~~f 48 (57)
T PF06107_consen 31 KIKCLGCGRQIMLPRSKF 48 (57)
T ss_pred EEEECCCCCEEEEeHHHH
Confidence 367999999999998887
No 405
>PRK06599 DNA topoisomerase I; Validated
Probab=30.19 E-value=41 Score=34.24 Aligned_cols=16 Identities=25% Similarity=0.810 Sum_probs=12.3
Q ss_pred ecCCCCceeeeeCCCc
Q 026283 200 RCAGCGNIVWQPEGDF 215 (240)
Q Consensus 200 ~CpnCGe~l~v~~g~F 215 (240)
.||.||..+.+.+|.+
T Consensus 639 ~Cp~C~~~~~~kkgk~ 654 (675)
T PRK06599 639 KCPKCGGPLVLKKGRY 654 (675)
T ss_pred CCCCCCCeeEEEeCCC
Confidence 7888888877777664
No 406
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=30.04 E-value=49 Score=21.12 Aligned_cols=18 Identities=33% Similarity=0.566 Sum_probs=14.3
Q ss_pred cceeecCCCCceeeeeCC
Q 026283 196 SQIIRCAGCGNIVWQPEG 213 (240)
Q Consensus 196 nt~~~CpnCGe~l~v~~g 213 (240)
+...+|..||+++.+-++
T Consensus 2 ~~~ykC~~CGniv~v~~~ 19 (34)
T cd00974 2 LEVYKCEICGNIVEVLNV 19 (34)
T ss_pred CcEEEcCCCCcEEEEEEC
Confidence 346789999999987764
No 407
>PRK14282 chaperone protein DnaJ; Provisional
Probab=29.98 E-value=49 Score=31.11 Aligned_cols=13 Identities=31% Similarity=0.636 Sum_probs=8.9
Q ss_pred ccccceeecCCCC
Q 026283 193 GSKSQIIRCAGCG 205 (240)
Q Consensus 193 G~nnt~~~CpnCG 205 (240)
|+-.++..|+.|+
T Consensus 190 G~~~~~~~C~~C~ 202 (369)
T PRK14282 190 GVFVSERTCERCG 202 (369)
T ss_pred cceEEEEECCCCC
Confidence 5666677777774
No 408
>PRK12722 transcriptional activator FlhC; Provisional
Probab=29.61 E-value=54 Score=29.22 Aligned_cols=40 Identities=20% Similarity=0.409 Sum_probs=28.8
Q ss_pred HHHHHHHHHhhhhhcCCCCCCCccccccccce---eecCCCCc
Q 026283 167 APLLIGTVANNFVIKGACPACKREFIGSKSQI---IRCAGCGN 206 (240)
Q Consensus 167 ap~li~wWlkRnLIeg~CPvC~~eFtG~nnt~---~~CpnCGe 206 (240)
|+-|.+..-...|---.|.-|+-+|+.-++.. ..||-|.-
T Consensus 120 Aw~LvRf~~s~~L~l~~C~~Cgg~fv~~~~e~~~~f~CplC~~ 162 (187)
T PRK12722 120 AWTLVRFVDSGMLQLSSCNCCGGHFVTHAHDPVGSFVCGLCQP 162 (187)
T ss_pred HHHHHHHHhcCcEeeccCCCCCCCeeccccccCCCCcCCCCCC
Confidence 34445555555566667999999999777654 67999986
No 409
>PF05473 Herpes_UL45: UL45 protein; InterPro: IPR008646 This family consists several UL45 proteins and homologues found in the herpes simplex virus family. The herpes simplex virus UL45 gene encodes an 18 kDa virion envelope protein whose function remains unknown. It has been suggested that the 18 kDa UL45 gene product is required for efficient growth in the central nervous system at low doses and may play an important role under the conditions of a naturally acquired infection []. The Equine herpesvirus 1 UL45 protein represents a type II membrane glycoprotein which has found to be non-essential for EHV-1 growth in vitro but deletion reduces the viruses' replication efficiency [].
Probab=29.60 E-value=1.2e+02 Score=26.67 Aligned_cols=15 Identities=27% Similarity=0.837 Sum_probs=10.6
Q ss_pred CCCCCCccccccccc
Q 026283 183 ACPACKREFIGSKSQ 197 (240)
Q Consensus 183 ~CPvC~~eFtG~nnt 197 (240)
.|+.|-.+-+||+|.
T Consensus 81 ~~~~CP~~Wi~~~~~ 95 (200)
T PF05473_consen 81 GCGPCPKGWIGYNNS 95 (200)
T ss_pred cCCCCCccceeeCCE
Confidence 567777777777753
No 410
>PF05766 NinG: Bacteriophage Lambda NinG protein; InterPro: IPR008713 The ninR region of phage lambda contains two recombination genes, ninB (also known as orf) and ninG (also known as rap). These genes are involved in the RecF and RecBCD recombination pathways of Escherichia coli that operate on phage lambda [, ]. NinB and NinG participate in Red recombination, the primary pathway operating when wild-type lambda grows lytically in rec+ cells [].
Probab=29.59 E-value=21 Score=31.73 Aligned_cols=28 Identities=18% Similarity=0.449 Sum_probs=19.9
Q ss_pred cCCCCCCCcccccccccee-ecCCCCcee
Q 026283 181 KGACPACKREFIGSKSQII-RCAGCGNIV 208 (240)
Q Consensus 181 eg~CPvC~~eFtG~nnt~~-~CpnCGe~l 208 (240)
.-.|.+|+..|+=.+..|. =||.||..+
T Consensus 6 ~rKCKvCg~~F~P~~s~q~vCSpeCa~a~ 34 (189)
T PF05766_consen 6 RRKCKVCGEWFVPARSNQKVCSPECAIAL 34 (189)
T ss_pred CCcCcccCCccccCCCceeeeCHHHHhHH
Confidence 4579999999995544444 468898544
No 411
>PRK03072 heat shock protein HtpX; Provisional
Probab=29.42 E-value=1.9e+02 Score=26.43 Aligned_cols=36 Identities=14% Similarity=-0.094 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHhhhhh
Q 026283 144 LWFALSGWLFRILILATWVLPIA-APLLIGTVANNFVI 180 (240)
Q Consensus 144 ~wll~SGWLvn~~l~l~~vlPva-ap~li~wWlkRnLI 180 (240)
+-+++.||++ +..++++.+.++ +..++.+|.-..++
T Consensus 19 ~~~~~~g~~~-~~~~~~~~~~~~~~~~~~~~~~s~~~~ 55 (288)
T PRK03072 19 ALIVFIGALF-GRTGLGIAVLIAVGMNAYVYWNSDKLA 55 (288)
T ss_pred HHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHhHHHH
Confidence 3344448888 444333333332 23335555444443
No 412
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=29.41 E-value=62 Score=28.42 Aligned_cols=33 Identities=18% Similarity=0.335 Sum_probs=25.0
Q ss_pred CCCCCCCcccccccc----ceeecCCCCceeeeeCCC
Q 026283 182 GACPACKREFIGSKS----QIIRCAGCGNIVWQPEGD 214 (240)
Q Consensus 182 g~CPvC~~eFtG~nn----t~~~CpnCGe~l~v~~g~ 214 (240)
-.||.|+++=|=+.. -...|-.||..=.|..-.
T Consensus 99 V~C~~C~~pdT~l~k~~~~~~l~C~aCGa~~~v~~~~ 135 (201)
T PRK12336 99 VICSECGLPDTRLVKEDRVLMLRCDACGAHRPVKKRK 135 (201)
T ss_pred EECCCCCCCCcEEEEcCCeEEEEcccCCCCccccccc
Confidence 369999998887753 356999999877666544
No 413
>PLN00193 expansin-A; Provisional
Probab=29.35 E-value=31 Score=31.87 Aligned_cols=10 Identities=30% Similarity=0.481 Sum_probs=7.9
Q ss_pred CCCeeeeecc
Q 026283 229 DDDIIDVDFE 238 (240)
Q Consensus 229 ~pgtIDVe~e 238 (240)
..|+|||++.
T Consensus 145 ~~Giv~V~yr 154 (256)
T PLN00193 145 RGGIVPVLFQ 154 (256)
T ss_pred cCCeEeEEEE
Confidence 4599999875
No 414
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 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 HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=29.32 E-value=31 Score=22.18 Aligned_cols=21 Identities=29% Similarity=0.755 Sum_probs=12.2
Q ss_pred CCCCCCCccccccccceeecCCCCcee
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNIV 208 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~l 208 (240)
..|-||++ ...-.||.||..+
T Consensus 3 ~~C~vC~~------~~kY~Cp~C~~~~ 23 (30)
T PF04438_consen 3 KLCSVCGN------PAKYRCPRCGARY 23 (30)
T ss_dssp EEETSSSS------EESEE-TTT--EE
T ss_pred CCCccCcC------CCEEECCCcCCce
Confidence 35778876 3466899998763
No 415
>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=29.29 E-value=32 Score=25.36 Aligned_cols=28 Identities=18% Similarity=0.468 Sum_probs=13.2
Q ss_pred CCCCCCCccccccccceeecCCCCceee
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNIVW 209 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~l~ 209 (240)
.+|..||+=.--.+...--|+.||++|.
T Consensus 19 ~NCl~CGkIiC~~Eg~~~pC~fCg~~l~ 46 (57)
T PF06221_consen 19 PNCLNCGKIICEQEGPLGPCPFCGTPLL 46 (57)
T ss_pred ccccccChhhcccccCcCcCCCCCCccc
Confidence 4455555443333332444556655553
No 416
>PLN03024 Putative EG45-like domain containing protein 1; Provisional
Probab=29.09 E-value=22 Score=29.44 Aligned_cols=10 Identities=30% Similarity=0.577 Sum_probs=7.8
Q ss_pred CCCeeeeecc
Q 026283 229 DDDIIDVDFE 238 (240)
Q Consensus 229 ~pgtIDVe~e 238 (240)
..|+|+|+++
T Consensus 115 ~aG~v~V~y~ 124 (125)
T PLN03024 115 VAGIINIDYI 124 (125)
T ss_pred cCCEEEEEEe
Confidence 4589999885
No 417
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=28.88 E-value=31 Score=26.25 Aligned_cols=33 Identities=24% Similarity=0.541 Sum_probs=25.9
Q ss_pred hhhhcCCCCCCCccccccccceeecCCCCceee
Q 026283 177 NFVIKGACPACKREFIGSKSQIIRCAGCGNIVW 209 (240)
Q Consensus 177 RnLIeg~CPvC~~eFtG~nnt~~~CpnCGe~l~ 209 (240)
-+.+.--|--|+.|-+=-...++||-.||--+.
T Consensus 16 ~~~miYiCgdC~~en~lk~~D~irCReCG~RIl 48 (62)
T KOG3507|consen 16 TATMIYICGDCGQENTLKRGDVIRCRECGYRIL 48 (62)
T ss_pred cccEEEEeccccccccccCCCcEehhhcchHHH
Confidence 344555688999999988889999999996543
No 418
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=28.86 E-value=23 Score=36.60 Aligned_cols=31 Identities=29% Similarity=0.647 Sum_probs=24.3
Q ss_pred CCCCCCccccccc-----cceeecCCCCceeeeeCC
Q 026283 183 ACPACKREFIGSK-----SQIIRCAGCGNIVWQPEG 213 (240)
Q Consensus 183 ~CPvC~~eFtG~n-----nt~~~CpnCGe~l~v~~g 213 (240)
-||.|..|+.--+ -+-+-||+||=.|+..+.
T Consensus 120 ~C~~C~~ey~~p~~rr~h~~~~~C~~Cgp~l~l~~~ 155 (711)
T TIGR00143 120 LCPDCAKEYKDPLDRRFHAQPIACPRCGPQLNFVSR 155 (711)
T ss_pred CCHHHHHHhcCCccccCCCCCccCCCCCcEEEEEeC
Confidence 5999999975432 367889999999988654
No 419
>TIGR00869 sec62 protein translocation protein, Sec62 family. protein secretary systems of yeast microsomes. They are also the non-selective cation (NS) channels of the mammalian cytoplasmic membrane. The yeast Sec62 protein has been shown to be essential for cell growth. The mammalian NS channel proteins has been implicated in platelet derived growth factor(PGDF) dependent single channel current in fibroblasts. These channels are essentially closed in serum deprived tissue-culture cells and are specifically opened by exposure to PDGF. These channels are reported to exhibit equal selectivity for Na+, K+ and Cs+ with low permeability to Ca2+, and no permeability to anions.
Probab=28.83 E-value=76 Score=29.19 Aligned_cols=16 Identities=6% Similarity=-0.141 Sum_probs=11.5
Q ss_pred HHHHhhhhhcCCCCCCC
Q 026283 172 GTVANNFVIKGACPACK 188 (240)
Q Consensus 172 ~wWlkRnLIeg~CPvC~ 188 (240)
+.|+==||-|| |++..
T Consensus 182 ~fWlfPNLfeD-~Gf~e 197 (232)
T TIGR00869 182 GIWIFPNLFAD-VGFLD 197 (232)
T ss_pred Ceeeecchhcc-cCcce
Confidence 46777788888 87654
No 420
>PF12648 TcpE: TcpE family
Probab=28.81 E-value=66 Score=25.08 Aligned_cols=21 Identities=14% Similarity=0.126 Sum_probs=15.5
Q ss_pred HHHHHHHHHHHhhhhhcCCCC
Q 026283 165 IAAPLLIGTVANNFVIKGACP 185 (240)
Q Consensus 165 vaap~li~wWlkRnLIeg~CP 185 (240)
++.|.++.|++.+.=.+|+=|
T Consensus 64 ~~iP~~l~~~~~~~k~DGK~~ 84 (108)
T PF12648_consen 64 FVIPYGLAWFLSKKKPDGKKP 84 (108)
T ss_pred HhHHHHHHHHHhhcCcCCCCH
Confidence 346888999998887777543
No 421
>PF11872 DUF3392: Protein of unknown function (DUF3392); InterPro: IPR021813 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 110 amino acids in length.
Probab=28.70 E-value=1.3e+02 Score=24.70 Aligned_cols=16 Identities=25% Similarity=0.385 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHhhh
Q 026283 163 LPIAAPLLIGTVANNF 178 (240)
Q Consensus 163 lPvaap~li~wWlkRn 178 (240)
.-++.++++|.|++||
T Consensus 91 ~vl~~F~~iG~lAqR~ 106 (106)
T PF11872_consen 91 VVLLSFILIGVLAQRN 106 (106)
T ss_pred HHHHHHHHHHHHhccC
Confidence 3344577799999987
No 422
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=28.60 E-value=33 Score=22.48 Aligned_cols=15 Identities=33% Similarity=0.725 Sum_probs=9.3
Q ss_pred eecCCCCceeeeeCC
Q 026283 199 IRCAGCGNIVWQPEG 213 (240)
Q Consensus 199 ~~CpnCGe~l~v~~g 213 (240)
..||.||..-.+.+|
T Consensus 3 ~~Cp~Cg~~~~~~~g 17 (47)
T PF14690_consen 3 PRCPHCGSPSVHRHG 17 (47)
T ss_pred ccCCCcCCCceECCc
Confidence 568888866544444
No 423
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=28.27 E-value=40 Score=22.87 Aligned_cols=18 Identities=33% Similarity=0.693 Sum_probs=11.1
Q ss_pred cceeecCCCCceeeeeCC
Q 026283 196 SQIIRCAGCGNIVWQPEG 213 (240)
Q Consensus 196 nt~~~CpnCGe~l~v~~g 213 (240)
.+.-.|.-||++|.+-++
T Consensus 4 ~~~YkC~~CGniVev~~~ 21 (36)
T PF06397_consen 4 GEFYKCEHCGNIVEVVHD 21 (36)
T ss_dssp TEEEE-TTT--EEEEEE-
T ss_pred ccEEEccCCCCEEEEEEC
Confidence 456789999999988765
No 424
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=28.20 E-value=21 Score=33.18 Aligned_cols=29 Identities=21% Similarity=0.636 Sum_probs=20.4
Q ss_pred CCCCCCccccc--cccceeecCCCCceeeee
Q 026283 183 ACPACKREFIG--SKSQIIRCAGCGNIVWQP 211 (240)
Q Consensus 183 ~CPvC~~eFtG--~nnt~~~CpnCGe~l~v~ 211 (240)
.||.|+....- +....-.||.||.-....
T Consensus 29 ~c~~c~~~~~~~~l~~~~~vc~~c~~h~rl~ 59 (292)
T PRK05654 29 KCPSCGQVLYRKELEANLNVCPKCGHHMRIS 59 (292)
T ss_pred ECCCccchhhHHHHHhcCCCCCCCCCCeeCC
Confidence 69999976543 222245899999887764
No 425
>KOG1088 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.14 E-value=36 Score=28.88 Aligned_cols=17 Identities=18% Similarity=0.349 Sum_probs=13.3
Q ss_pred eeecCCCCceeeeeCCC
Q 026283 198 IIRCAGCGNIVWQPEGD 214 (240)
Q Consensus 198 ~~~CpnCGe~l~v~~g~ 214 (240)
+.+||+||.+--+.+|-
T Consensus 98 ~l~CpetG~vfpI~~GI 114 (124)
T KOG1088|consen 98 ELVCPETGRVFPISDGI 114 (124)
T ss_pred eEecCCCCcEeecccCC
Confidence 57888888888887773
No 426
>PLN03120 nucleic acid binding protein; Provisional
Probab=28.14 E-value=69 Score=29.91 Aligned_cols=30 Identities=23% Similarity=0.421 Sum_probs=24.0
Q ss_pred HHHHHHhhhhhhhhhHhHHHHHHHHHHHHH
Q 026283 67 AKKTAERIDRQYSVSRRLNSAARTAAVRAR 96 (240)
Q Consensus 67 ar~~a~r~D~~Y~vs~r~a~aa~~a~e~A~ 96 (240)
++..+..+|.+|.||.|...|.-.+...+-
T Consensus 165 v~~~~k~vDeky~vs~kt~sa~~~~~~~~~ 194 (260)
T PLN03120 165 VNEKVKEVDQKYQVSEKTKSALAAAEQKVS 194 (260)
T ss_pred HHHHHHhhhhhhchhHHHHHHHHHHHHHHH
Confidence 446788999999999999888877766543
No 427
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=27.93 E-value=34 Score=28.67 Aligned_cols=29 Identities=21% Similarity=0.493 Sum_probs=21.4
Q ss_pred CCCCCCCcccccccc----ceeecCCCCceeee
Q 026283 182 GACPACKREFIGSKS----QIIRCAGCGNIVWQ 210 (240)
Q Consensus 182 g~CPvC~~eFtG~nn----t~~~CpnCGe~l~v 210 (240)
-.||.|+.+=|=+.. ....|-.||..=.|
T Consensus 98 VlC~~C~sPdT~l~k~~r~~~l~C~ACGa~~~v 130 (133)
T TIGR00311 98 VICRECNRPDTRIIKEGRVSLLKCEACGAKAPL 130 (133)
T ss_pred EECCCCCCCCcEEEEeCCeEEEecccCCCCCcc
Confidence 359999998887753 34699999975433
No 428
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=27.76 E-value=37 Score=26.15 Aligned_cols=13 Identities=31% Similarity=0.634 Sum_probs=11.9
Q ss_pred ecCCCCceeeeeC
Q 026283 200 RCAGCGNIVWQPE 212 (240)
Q Consensus 200 ~CpnCGe~l~v~~ 212 (240)
.|.+||-|+..+.
T Consensus 2 ~CQSCGMPl~~~~ 14 (81)
T PF12674_consen 2 FCQSCGMPLSKDE 14 (81)
T ss_pred cCCcCcCccCCcc
Confidence 5999999999888
No 429
>PF09567 RE_MamI: MamI restriction endonuclease; InterPro: IPR019067 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the MamI restriction endonuclease which recognises and cleaves GATNN^NNATC. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=27.70 E-value=26 Score=33.42 Aligned_cols=22 Identities=27% Similarity=0.735 Sum_probs=16.0
Q ss_pred CCCCCCCccccccccceeecCCCCc
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGN 206 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe 206 (240)
|.|-.||.+-.. -+.-|||||-
T Consensus 83 ~~C~~CGa~V~~---~e~~Cp~C~S 104 (314)
T PF09567_consen 83 GKCNNCGANVSR---LEESCPNCGS 104 (314)
T ss_pred hhhccccceeee---hhhcCCCCCc
Confidence 678888866544 4678999984
No 430
>PF05077 DUF678: Protein of unknown function (DUF678); InterPro: IPR007769 This family contains poxvirus proteins belonging to the A19 family. The proteins are of unknown function.
Probab=27.65 E-value=35 Score=26.73 Aligned_cols=17 Identities=24% Similarity=0.655 Sum_probs=13.0
Q ss_pred ccceeecCCCCceeeee
Q 026283 195 KSQIIRCAGCGNIVWQP 211 (240)
Q Consensus 195 nnt~~~CpnCGe~l~v~ 211 (240)
++....|..||-.|.-=
T Consensus 54 ~~~tLsCsACGS~L~~L 70 (74)
T PF05077_consen 54 KGNTLSCSACGSELRPL 70 (74)
T ss_pred CCCeEeehhccccceec
Confidence 36778999999887643
No 431
>TIGR03518 ABC_perm_GldF gliding motility-associated ABC transporter permease protein GldF. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldF is believed to be a ABC transporter permease protein (along with ATP-binding subunit, GldA and a sunstrate-binding subunit, GldG) and is linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockouts of GldF abolish the gliding phenotype. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. Bacteroidetes with members of this protein family appear to have all of the genes associated with gliding motility.
Probab=27.64 E-value=2e+02 Score=25.15 Aligned_cols=28 Identities=25% Similarity=0.573 Sum_probs=22.9
Q ss_pred hchhHHHHHHHhhCCCCchHHHHHHHHH
Q 026283 118 NWPRYRKQLNDFLNTPLGRSFATIFFLW 145 (240)
Q Consensus 118 ~wP~yrrql~~F~~T~lG~wL~tl~~~w 145 (240)
+++-+||++.++..||++-.+.+++.+.
T Consensus 1 ~~~i~~kEl~~~f~sp~~yv~~~~~~~~ 28 (240)
T TIGR03518 1 MKAIFKKEFNSFFSSPIGYLVIAVFLLA 28 (240)
T ss_pred CHHHHHHHHHHHhcCHHHHHHHHHHHHH
Confidence 3577999999999999999877766543
No 432
>PHA02893 hypothetical protein; Provisional
Probab=27.63 E-value=25 Score=28.35 Aligned_cols=15 Identities=27% Similarity=0.786 Sum_probs=12.0
Q ss_pred cceeecCCCCceeee
Q 026283 196 SQIIRCAGCGNIVWQ 210 (240)
Q Consensus 196 nt~~~CpnCGe~l~v 210 (240)
+..+.|..||-.|.-
T Consensus 67 ~~tL~CaACGS~L~~ 81 (88)
T PHA02893 67 NSNIKCIACGSSLCH 81 (88)
T ss_pred CCceeehhhchhhhh
Confidence 677889999988753
No 433
>PRK13415 flagella biosynthesis protein FliZ; Provisional
Probab=27.46 E-value=85 Score=28.77 Aligned_cols=28 Identities=7% Similarity=0.127 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 026283 152 LFRILILATWVLPIAAPLLIGTVANNFVI 180 (240)
Q Consensus 152 Lvn~~l~l~~vlPvaap~li~wWlkRnLI 180 (240)
++..+..+++|+-++ +++.+|+.+|+-.
T Consensus 68 l~qmi~aL~~VI~Li-y~l~rwL~rR~~~ 95 (219)
T PRK13415 68 FVKLIGATLFVIFLI-YALVKWLNKRNRL 95 (219)
T ss_pred HHHHHHHHHHHHHHH-HHHHHHHHHhccc
Confidence 555555555553333 5556788887643
No 434
>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=27.43 E-value=34 Score=29.09 Aligned_cols=26 Identities=23% Similarity=0.597 Sum_probs=16.4
Q ss_pred CCCCCCCccccccc-cceeecCCCCce
Q 026283 182 GACPACKREFIGSK-SQIIRCAGCGNI 207 (240)
Q Consensus 182 g~CPvC~~eFtG~n-nt~~~CpnCGe~ 207 (240)
-.|-.||++..=.. ....-||.||..
T Consensus 113 l~C~~Cg~~~~~~~~~~l~~Cp~C~~~ 139 (146)
T PF07295_consen 113 LVCENCGHEVELTHPERLPPCPKCGHT 139 (146)
T ss_pred EecccCCCEEEecCCCcCCCCCCCCCC
Confidence 35888887643322 345578888864
No 435
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=27.07 E-value=36 Score=28.68 Aligned_cols=29 Identities=21% Similarity=0.471 Sum_probs=22.0
Q ss_pred CCCCCCCcccccccc----ceeecCCCCceeee
Q 026283 182 GACPACKREFIGSKS----QIIRCAGCGNIVWQ 210 (240)
Q Consensus 182 g~CPvC~~eFtG~nn----t~~~CpnCGe~l~v 210 (240)
-.||.|+.+=|=+.. -...|-.||..=.|
T Consensus 103 VlC~~C~spdT~l~k~~r~~~l~C~ACGa~~~V 135 (138)
T PRK03988 103 VICPECGSPDTKLIKEGRIWVLKCEACGAETPV 135 (138)
T ss_pred EECCCCCCCCcEEEEcCCeEEEEcccCCCCCcC
Confidence 469999998887753 46789999975433
No 436
>TIGR02205 septum_zipA cell division protein ZipA. This model represents the full length of bacterial cell division protein ZipA. The N-terminal hydrophobic stretch is an uncleaved signal-anchor sequence. This is followed by an unconserved, variable length, low complexity region, and then a conserved C-terminal region of about 140 amino acids (see pfam04354) that interacts with the tubulin-like cell division protein FtsZ.
Probab=27.01 E-value=27 Score=32.63 Aligned_cols=26 Identities=31% Similarity=0.427 Sum_probs=21.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhh
Q 026283 153 FRILILATWVLPIAAPLLIGTVANNF 178 (240)
Q Consensus 153 vn~~l~l~~vlPvaap~li~wWlkRn 178 (240)
+|.+||++.++-|+|+++-|||-+|.
T Consensus 2 Lr~iLIIvGaiaI~aLl~hGlwt~Rk 27 (284)
T TIGR02205 2 LRIILIIVGILAIAALLFHGLWTSRK 27 (284)
T ss_pred ceehHHHHHHHHHHHHHHcccccccc
Confidence 35677888888888899999998765
No 437
>PF03733 DUF307: Domain of unknown function (DUF307); InterPro: IPR005185 This proteins contain a domain which occurs as one or more copies in a small family of putative membrane proteins.
Probab=27.00 E-value=1.9e+02 Score=20.62 Aligned_cols=24 Identities=33% Similarity=0.672 Sum_probs=16.3
Q ss_pred CchHHHHHHHHHHHHHHHHHHHHH
Q 026283 134 LGRSFATIFFLWFALSGWLFRILI 157 (240)
Q Consensus 134 lG~wL~tl~~~wll~SGWLvn~~l 157 (240)
+|+.+=++++.|.+..+|++-+++
T Consensus 2 l~NilW~i~~G~~lal~~~~~~~~ 25 (53)
T PF03733_consen 2 LGNILWFIFFGWWLALIWLLAGIL 25 (53)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHH
Confidence 466666677777777777666654
No 438
>KOG3059 consensus N-acetylglucosaminyltransferase complex, subunit PIG-C/GPI2, required for phosphatidylinositol biosynthesis [Lipid transport and metabolism]
Probab=26.78 E-value=2.6e+02 Score=26.83 Aligned_cols=14 Identities=21% Similarity=0.598 Sum_probs=11.7
Q ss_pred hhchhHHHHHHHhh
Q 026283 117 RNWPRYRKQLNDFL 130 (240)
Q Consensus 117 r~wP~yrrql~~F~ 130 (240)
--||.|++.+.++.
T Consensus 209 al~p~~~~~i~~~~ 222 (292)
T KOG3059|consen 209 ALLPNFRKRIKKVI 222 (292)
T ss_pred HHHHHHHHHhhccc
Confidence 45899999998776
No 439
>TIGR02159 PA_CoA_Oxy4 phenylacetate-CoA oxygenase, PaaJ subunit. Phenylacetate-CoA oxygenase is comprised of a five gene complex responsible for the hydroxylation of phenylacetate-CoA (PA-CoA) as the second catabolic step in phenylacetic acid (PA) degradation. Although the exact function of this enzyme has not been determined, it has been shown to be required for phenylacetic acid degradation and has been proposed to function in a multicomponent oxygenase acting on phenylacetate-CoA.
Probab=26.64 E-value=26 Score=29.58 Aligned_cols=27 Identities=26% Similarity=0.572 Sum_probs=17.5
Q ss_pred CCCCCCCcccccccc--------ceeecCCCCcee
Q 026283 182 GACPACKREFIGSKS--------QIIRCAGCGNIV 208 (240)
Q Consensus 182 g~CPvC~~eFtG~nn--------t~~~CpnCGe~l 208 (240)
-.||-||..-|-.-+ ..-+|-.|.|+.
T Consensus 106 ~~cp~c~s~~t~~~s~fg~t~cka~~~c~~c~epf 140 (146)
T TIGR02159 106 VQCPRCGSADTTITSIFGPTACKALYRCRACKEPF 140 (146)
T ss_pred CcCCCCCCCCcEeecCCCChhhHHHhhhhhhCCcH
Confidence 578888877665433 234678887764
No 440
>KOG3012 consensus Uncharacterized conserved protein [Function unknown]
Probab=26.59 E-value=2.1e+02 Score=26.95 Aligned_cols=35 Identities=29% Similarity=0.401 Sum_probs=21.1
Q ss_pred hHHHHHHHhhCCCCchHHHHHHHHHHHHH--HH-HHHHH
Q 026283 121 RYRKQLNDFLNTPLGRSFATIFFLWFALS--GW-LFRIL 156 (240)
Q Consensus 121 ~yrrql~~F~~T~lG~wL~tl~~~wll~S--GW-Lvn~~ 156 (240)
.||||. +=..-.=-+.+..|..+|+..| || ++.++
T Consensus 68 ~YrKQT-KnQwARDDPaFlVl~s~~l~vssi~~a~~~~l 105 (259)
T KOG3012|consen 68 HYRKQT-KNQWARDDPAFLVLLSLLLVVSSIGWAYVLDL 105 (259)
T ss_pred hhhhhh-hhhhhccCchHHHHHHHHHHHHHHHHHHHhcc
Confidence 588887 2233333345667777777777 88 55443
No 441
>PRK12652 putative monovalent cation/H+ antiporter subunit E; Reviewed
Probab=26.53 E-value=1e+02 Score=29.39 Aligned_cols=21 Identities=5% Similarity=-0.183 Sum_probs=14.4
Q ss_pred HHHhhhhhcCCCCCCCccccc
Q 026283 173 TVANNFVIKGACPACKREFIG 193 (240)
Q Consensus 173 wWlkRnLIeg~CPvC~~eFtG 193 (240)
+|+=..++..+--|+..-+..
T Consensus 232 ~~~l~eiv~Ani~VA~~vL~p 252 (357)
T PRK12652 232 PYLLWEIVKANVAIAYVILHP 252 (357)
T ss_pred HHHHHHHHHHHHHHHHHHcCC
Confidence 555666777777777776664
No 442
>PLN00050 expansin A; Provisional
Probab=26.45 E-value=37 Score=31.26 Aligned_cols=10 Identities=20% Similarity=0.551 Sum_probs=7.6
Q ss_pred CCCeeeeecc
Q 026283 229 DDDIIDVDFE 238 (240)
Q Consensus 229 ~pgtIDVe~e 238 (240)
..|+|||++.
T Consensus 137 ~aGii~V~yR 146 (247)
T PLN00050 137 KAGIVPVQYR 146 (247)
T ss_pred cCCeeeeEEE
Confidence 3499999874
No 443
>TIGR01054 rgy reverse gyrase. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.
Probab=26.16 E-value=28 Score=37.96 Aligned_cols=23 Identities=26% Similarity=0.751 Sum_probs=18.4
Q ss_pred CCCCCCCccccccccceeecCCCCce
Q 026283 182 GACPACKREFIGSKSQIIRCAGCGNI 207 (240)
Q Consensus 182 g~CPvC~~eFtG~nnt~~~CpnCGe~ 207 (240)
-.|+.|+++|+.-. -.||.||..
T Consensus 679 k~~~~~~~~f~~~~---~~~p~~~~~ 701 (1171)
T TIGR01054 679 KRCRDCGYQFTEDR---ESCPKCGSE 701 (1171)
T ss_pred ccCCchhhhccccc---ccccccccc
Confidence 46999999999843 489999843
No 444
>TIGR02230 ATPase_gene1 F0F1-ATPase subunit, putative. This model represents a protein found encoded in F1F0-ATPase operons in several genomes, including Methanosarcina barkeri (archaeal) and Chlorobium tepidum (bacterial). It is a small protein (about 100 amino acids) with long hydrophic stretches and is presumed to be a subunit of the enzyme.
Probab=26.01 E-value=98 Score=25.06 Aligned_cols=23 Identities=35% Similarity=0.371 Sum_probs=11.9
Q ss_pred CchHHHHHHHHHHHHHHHHHHHH
Q 026283 134 LGRSFATIFFLWFALSGWLFRIL 156 (240)
Q Consensus 134 lG~wL~tl~~~wll~SGWLvn~~ 156 (240)
+|-.+++-.++.+.+=-||=+-+
T Consensus 48 IG~~~v~pil~G~~lG~WLD~~~ 70 (100)
T TIGR02230 48 IGWSVAIPTLLGVAVGIWLDRHY 70 (100)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhc
Confidence 44444444444444445665555
No 445
>PF07666 MpPF26: M penetrans paralogue family 26; InterPro: IPR011655 These proteins include those ascribed to M penetrans paralogue family 26 in [].
Probab=25.97 E-value=1.5e+02 Score=24.99 Aligned_cols=54 Identities=11% Similarity=0.207 Sum_probs=28.9
Q ss_pred HHHHHhhCCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCCCCc
Q 026283 124 KQLNDFLNTPLGRSFATIFFLWFALSGWLFRILILATWVLPIAAPLLIGTVANNFVIKGACPACKR 189 (240)
Q Consensus 124 rql~~F~~T~lG~wL~tl~~~wll~SGWLvn~~l~l~~vlPvaap~li~wWlkRnLIeg~CPvC~~ 189 (240)
.+.++++.-..|.|+.+++.+++.+.-++++.++.+++. .|=...++.||.++.
T Consensus 45 ~~~~~~~~~~~~~l~igil~i~~~~i~~i~~~Il~Ivl~------------iKis~~k~~~~~~~k 98 (130)
T PF07666_consen 45 NNYEEESSMSIGNLVIGILLIIFSGIFYIVNFILGIVLI------------IKISSLKNKHPEFKK 98 (130)
T ss_pred cccccccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH------------HHHHHHhccCccccc
Confidence 344556666667766666655555554555554433322 233345666776654
No 446
>PF11172 DUF2959: Protein of unknown function (DUF2959); InterPro: IPR021342 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=25.89 E-value=5.1e+02 Score=23.63 Aligned_cols=25 Identities=12% Similarity=0.238 Sum_probs=19.2
Q ss_pred HHHHHHHhhhhhhhhhHhHHHHHHH
Q 026283 66 DAKKTAERIDRQYSVSRRLNSAART 90 (240)
Q Consensus 66 ear~~a~r~D~~Y~vs~r~a~aa~~ 90 (240)
+-.+.+++++.+|+-|++.|+.++.
T Consensus 61 dLe~~Y~~ln~~ye~s~~~A~~V~~ 85 (201)
T PF11172_consen 61 DLEDKYNALNDEYESSEDAAEEVSD 85 (201)
T ss_pred cHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567889999999988877666543
No 447
>PRK05580 primosome assembly protein PriA; Validated
Probab=25.82 E-value=39 Score=34.42 Aligned_cols=29 Identities=28% Similarity=0.611 Sum_probs=16.0
Q ss_pred CCCCCCccccc-cccceeecCCCCceeeee
Q 026283 183 ACPACKREFIG-SKSQIIRCAGCGNIVWQP 211 (240)
Q Consensus 183 ~CPvC~~eFtG-~nnt~~~CpnCGe~l~v~ 211 (240)
.||.|+-.++= .+.....|..||-.-..+
T Consensus 392 ~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~ 421 (679)
T PRK05580 392 ECPHCDASLTLHRFQRRLRCHHCGYQEPIP 421 (679)
T ss_pred CCCCCCCceeEECCCCeEECCCCcCCCCCC
Confidence 45566554442 134456777777665544
No 448
>PRK12651 putative monovalent cation/H+ antiporter subunit E; Reviewed
Probab=25.64 E-value=1.4e+02 Score=24.91 Aligned_cols=12 Identities=33% Similarity=0.811 Sum_probs=9.6
Q ss_pred HHHHHHHHHHHH
Q 026283 139 ATIFFLWFALSG 150 (240)
Q Consensus 139 ~tl~~~wll~SG 150 (240)
..++++|++++|
T Consensus 9 l~L~~~W~lL~g 20 (158)
T PRK12651 9 IILAVLWLFLTG 20 (158)
T ss_pred HHHHHHHHHHhC
Confidence 567889999884
No 449
>TIGR00389 glyS_dimeric glycyl-tRNA synthetase, dimeric type. This model describes a glycyl-tRNA synthetase distinct from the two alpha and two beta chains of the tetrameric E. coli glycyl-tRNA synthetase. This enzyme is a homodimeric class II tRNA synthetase and is recognized by pfam model tRNA-synt_2b, which recognizes His, Ser, Pro, and this set of glycyl-tRNA synthetases.
Probab=25.63 E-value=27 Score=35.40 Aligned_cols=48 Identities=27% Similarity=0.422 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHHHHHhhhhhcCCCCCCCcccc--------------ccccc---------eeecCCCCce
Q 026283 160 TWVLPIAAPLLIGTVANNFVIKGACPACKREFI--------------GSKSQ---------IIRCAGCGNI 207 (240)
Q Consensus 160 ~~vlPvaap~li~wWlkRnLIeg~CPvC~~eFt--------------G~nnt---------~~~CpnCGe~ 207 (240)
..++|-.++-.-|+|-+=+=.--.|+.|+..|- |++.. .+.||+||+.
T Consensus 63 ~~i~~~~v~~aSGh~~~F~D~mv~~~~~~~~~RaD~l~e~~~~~~~~~~~~~~~~~~i~~~~i~~p~~g~~ 133 (551)
T TIGR00389 63 PIITPEEVLKASGHVDNFTDWMVDCKSCKERFRADHLIEEKLGKRLWGFSGPELNEVMEKYDINCPNCGGE 133 (551)
T ss_pred cccCCHHHHHhcCCccccCCceeecCCCCCEecchHHHHHHhhhhcccCCHHHHHHHHHHcCCCCCCCCCC
Confidence 344555555556677666655667889986542 33333 3789999986
No 450
>PF14017 DUF4233: Protein of unknown function (DUF4233)
Probab=25.62 E-value=2.1e+02 Score=23.13 Aligned_cols=43 Identities=16% Similarity=0.338 Sum_probs=23.7
Q ss_pred HHHHHHHHHHH-----------HHHHHHHH-HHHHHHHHHHHHH--------HHHHHhhhhhc
Q 026283 139 ATIFFLWFALS-----------GWLFRILI-LATWVLPIAAPLL--------IGTVANNFVIK 181 (240)
Q Consensus 139 ~tl~~~wll~S-----------GWLvn~~l-~l~~vlPvaap~l--------i~wWlkRnLIe 181 (240)
..+++++++++ ||++..++ ...++.|..+.++ ...++++++.+
T Consensus 40 ~~lav~~i~~~gl~~rpwa~~~g~~lQv~~i~~g~v~p~m~vvG~iF~~~W~~~l~lg~~i~~ 102 (107)
T PF14017_consen 40 GVLAVLCILLAGLQRRPWAYWLGWVLQVLLIAGGFVHPAMFVVGVIFAAVWWYALYLGRRIDR 102 (107)
T ss_pred HHHHHHHHHHHHhcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45555666655 78777774 3444455544433 23556666554
No 451
>KOG1792 consensus Reticulon [Intracellular trafficking, secretion, and vesicular transport]
Probab=25.53 E-value=1.6e+02 Score=26.90 Aligned_cols=41 Identities=15% Similarity=0.222 Sum_probs=31.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026283 136 RSFATIFFLWFALSGWLFRILILATWVLPIAAPLLIGTVAN 176 (240)
Q Consensus 136 ~wL~tl~~~wll~SGWLvn~~l~l~~vlPvaap~li~wWlk 176 (240)
-.|+...++|++...-=++++.+...++++++.++|+|--.
T Consensus 57 ~vl~~~~~~w~lf~~~~~~~vt~~~~i~ll~~~i~F~w~~~ 97 (230)
T KOG1792|consen 57 TVLGVATALWLLFEFFSYNSVTLLCHILLLALAILFLWSKA 97 (230)
T ss_pred eehHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566677888888777888888888888888888887643
No 452
>PF10864 DUF2663: Protein of unknown function (DUF2663); InterPro: IPR020210 This entry represents a group of uncharacterised transmembrane proteins.
Probab=25.47 E-value=1.7e+02 Score=24.83 Aligned_cols=63 Identities=16% Similarity=0.280 Sum_probs=33.8
Q ss_pred hhhchhHHHHHHHhhCCCCchHHHHHHHHHHHHHH--H--HHHHH----HHHHHHHHHHHHHHHHHHHhhh
Q 026283 116 SRNWPRYRKQLNDFLNTPLGRSFATIFFLWFALSG--W--LFRIL----ILATWVLPIAAPLLIGTVANNF 178 (240)
Q Consensus 116 ~r~wP~yrrql~~F~~T~lG~wL~tl~~~wll~SG--W--Lvn~~----l~l~~vlPvaap~li~wWlkRn 178 (240)
-++|-+|.+|..-.+...+.+..+.+..+-..+.+ | ++..| +.++|++-+++.+..-.+++..
T Consensus 10 K~K~e~l~k~~~~~~~~~l~~~~~~~~y~~~~~~~~s~~~~~s~~~~~~~~l~~ll~~~~~~~~~~~~~kK 80 (130)
T PF10864_consen 10 KEKWERLKKQHLFWQWLFLFSLFLFFIYFYIKVIGYSFSSFLSAILGSPVHLFWLLALAFSYWAMYYLKKK 80 (130)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCHHHHHHHHHcChHHHHHHHHHHHHHHHHHHHHhh
Confidence 36888999998777765555544333333333323 3 22223 3555555555455555555543
No 453
>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=25.39 E-value=56 Score=23.85 Aligned_cols=28 Identities=29% Similarity=0.783 Sum_probs=18.8
Q ss_pred CCCCCCccccccccceeecCCCCceeeeeC-CCc
Q 026283 183 ACPACKREFIGSKSQIIRCAGCGNIVWQPE-GDF 215 (240)
Q Consensus 183 ~CPvC~~eFtG~nnt~~~CpnCGe~l~v~~-g~F 215 (240)
.|+.|+. +| ++ -.||-||++...+. -.|
T Consensus 7 ~c~~~~~-YT-Lk---~~cp~cG~~T~~ahPaRF 35 (53)
T PF04135_consen 7 KCPGCRV-YT-LK---DKCPPCGGPTESAHPARF 35 (53)
T ss_dssp ECTTTCE-EE-SS---SBBTTTSSBSEESSSSSS
T ss_pred cCCCCCc-Ee-CC---CccCCCCCCCcCCcCCCC
Confidence 4777771 11 11 48999999988877 455
No 454
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=25.26 E-value=66 Score=25.96 Aligned_cols=23 Identities=22% Similarity=0.619 Sum_probs=15.6
Q ss_pred ccccceeecCCCC-ceeeeeCCCc
Q 026283 193 GSKSQIIRCAGCG-NIVWQPEGDF 215 (240)
Q Consensus 193 G~nnt~~~CpnCG-e~l~v~~g~F 215 (240)
++..+...||+|| -.+....|+|
T Consensus 55 ~~~~~~~~Cp~C~~~~~~~k~~~~ 78 (140)
T COG0551 55 IAEKTGVKCPKCGKGLLVLKKGRF 78 (140)
T ss_pred ccccCceeCCCCCCCceEEEeccC
Confidence 3445568999999 4666666654
No 455
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=25.17 E-value=26 Score=29.75 Aligned_cols=25 Identities=28% Similarity=0.744 Sum_probs=20.3
Q ss_pred cccccceeecCCCCceeeeeCCCcc
Q 026283 192 IGSKSQIIRCAGCGNIVWQPEGDFF 216 (240)
Q Consensus 192 tG~nnt~~~CpnCGe~l~v~~g~F~ 216 (240)
.|..-....||-||-||...+|+-|
T Consensus 22 ~GAkML~~hCp~Cg~PLF~KdG~v~ 46 (131)
T COG1645 22 QGAKMLAKHCPKCGTPLFRKDGEVF 46 (131)
T ss_pred hhhHHHHhhCcccCCcceeeCCeEE
Confidence 3555566789999999999999874
No 456
>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=25.05 E-value=40 Score=27.03 Aligned_cols=33 Identities=27% Similarity=0.677 Sum_probs=20.3
Q ss_pred cCCCCCCCcccccccc-ceeecCCCCceeeeeCCCc
Q 026283 181 KGACPACKREFIGSKS-QIIRCAGCGNIVWQPEGDF 215 (240)
Q Consensus 181 eg~CPvC~~eFtG~nn-t~~~CpnCGe~l~v~~g~F 215 (240)
+-.||.|+..-+-=.. -+-+|..||+. +..|-+
T Consensus 35 ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~--~AGGAy 68 (90)
T PF01780_consen 35 KYTCPFCGKTSVKRVATGIWKCKKCGKK--FAGGAY 68 (90)
T ss_dssp -BEESSSSSSEEEEEETTEEEETTTTEE--EE-BSS
T ss_pred CCcCCCCCCceeEEeeeEEeecCCCCCE--EeCCCc
Confidence 4579999987532222 23689999964 455554
No 457
>COG5345 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.05 E-value=1.2e+02 Score=29.54 Aligned_cols=26 Identities=12% Similarity=0.020 Sum_probs=18.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 026283 150 GWLFRILILATWVLPIAAPLLIGTVAN 176 (240)
Q Consensus 150 GWLvn~~l~l~~vlPvaap~li~wWlk 176 (240)
+||++++++|+.+--.+ .+..+||-+
T Consensus 29 ~Wlvkv~~~L~g~Y~~f-~~~tq~w~n 54 (358)
T COG5345 29 PWLVKVVGGLLGIYLYF-AWQTQWWTN 54 (358)
T ss_pred ccHHHHHHHHHHHHHHH-HHHHHhhhc
Confidence 89999877766665544 455677754
No 458
>PRK12860 transcriptional activator FlhC; Provisional
Probab=24.85 E-value=67 Score=28.72 Aligned_cols=38 Identities=16% Similarity=0.340 Sum_probs=27.7
Q ss_pred HHHHHHHHhhhhhcCCCCCCCccccccccc---eeecCCCC
Q 026283 168 PLLIGTVANNFVIKGACPACKREFIGSKSQ---IIRCAGCG 205 (240)
Q Consensus 168 p~li~wWlkRnLIeg~CPvC~~eFtG~nnt---~~~CpnCG 205 (240)
+-|.+..-...|---.|.-|+-+|+.-++. ...||-|.
T Consensus 121 w~LvRf~~s~~L~l~~C~~Cgg~fv~~~~e~~~~f~CplC~ 161 (189)
T PRK12860 121 WTLVRFFDAGMLQLARCCRCGGKFVTHAHDLRHNFVCGLCQ 161 (189)
T ss_pred HHHHHHhcCCCeeeccCCCCCCCeeccccccCCCCcCCCCC
Confidence 334444444456666899999999988775 47899998
No 459
>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=24.79 E-value=57 Score=26.95 Aligned_cols=26 Identities=23% Similarity=0.568 Sum_probs=20.4
Q ss_pred CCCCCCCccccccc----cceeecCCCCce
Q 026283 182 GACPACKREFIGSK----SQIIRCAGCGNI 207 (240)
Q Consensus 182 g~CPvC~~eFtG~n----nt~~~CpnCGe~ 207 (240)
-.||.|+.+=|-+. --...|-.||..
T Consensus 94 VlC~~C~spdT~l~k~~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 94 VLCPECGSPDTELIKEGRLIFLKCKACGAS 123 (125)
T ss_dssp SSCTSTSSSSEEEEEETTCCEEEETTTSCE
T ss_pred EEcCCCCCCccEEEEcCCEEEEEecccCCc
Confidence 47999999988773 356789999964
No 460
>PRK14288 chaperone protein DnaJ; Provisional
Probab=24.71 E-value=36 Score=32.09 Aligned_cols=12 Identities=33% Similarity=0.642 Sum_probs=5.8
Q ss_pred ccccceeecCCC
Q 026283 193 GSKSQIIRCAGC 204 (240)
Q Consensus 193 G~nnt~~~CpnC 204 (240)
|+.+++..||.|
T Consensus 173 g~~~~~~~C~~C 184 (369)
T PRK14288 173 GFMSFAQTCGAC 184 (369)
T ss_pred ceEEEEEecCCC
Confidence 344444455555
No 461
>PRK14297 chaperone protein DnaJ; Provisional
Probab=24.63 E-value=41 Score=31.75 Aligned_cols=13 Identities=38% Similarity=0.807 Sum_probs=9.0
Q ss_pred ccccceeecCCCC
Q 026283 193 GSKSQIIRCAGCG 205 (240)
Q Consensus 193 G~nnt~~~CpnCG 205 (240)
|+-+++..|+.|+
T Consensus 186 G~~~~~~~C~~C~ 198 (380)
T PRK14297 186 GSFVSTTTCDKCG 198 (380)
T ss_pred ceeEEEEeCCCCC
Confidence 5556677787774
No 462
>PF06724 DUF1206: Domain of Unknown Function (DUF1206); InterPro: IPR009597 This region consists of two a pair of transmembrane helices and occurs three times in each of the family member proteins.
Probab=24.60 E-value=1.5e+02 Score=21.39 Aligned_cols=32 Identities=22% Similarity=0.194 Sum_probs=21.3
Q ss_pred hhHHHHHHHhhCCCCchHHHHHHHHHHHHH-HH
Q 026283 120 PRYRKQLNDFLNTPLGRSFATIFFLWFALS-GW 151 (240)
Q Consensus 120 P~yrrql~~F~~T~lG~wL~tl~~~wll~S-GW 151 (240)
+.-+--+...+.+|.|+|+..+.-+-+++. .|
T Consensus 31 ~~~~~~~~~l~~~p~G~~ll~~vg~gli~~gi~ 63 (73)
T PF06724_consen 31 QGSQGALAWLLEQPFGRWLLGAVGLGLIGYGIW 63 (73)
T ss_pred CCHHHHHHHHHhCCCcHHHHHHHHHHHHHHHHH
Confidence 334455677889999998866665555554 44
No 463
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=24.59 E-value=34 Score=30.20 Aligned_cols=36 Identities=25% Similarity=0.599 Sum_probs=24.1
Q ss_pred hhhcCCCCCCCcccccccc-----ceeecCCCCceeeeeCCCc
Q 026283 178 FVIKGACPACKREFIGSKS-----QIIRCAGCGNIVWQPEGDF 215 (240)
Q Consensus 178 nLIeg~CPvC~~eFtG~nn-----t~~~CpnCGe~l~v~~g~F 215 (240)
.++++-||.|=.+=.++-. +..+||.||-...- |+.
T Consensus 10 ~~~~~lC~~C~~~~~~i~ei~~~i~v~~C~~Cg~~~~~--~~W 50 (236)
T PF04981_consen 10 PLIDGLCPDCYLKRFDIIEIPDRIEVTICPKCGRYRIG--GRW 50 (236)
T ss_pred CcccccChHHhcccCCeeecCCccCceECCCCCCEECC--CEe
Confidence 3566788888665555522 67899999986543 444
No 464
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=24.45 E-value=63 Score=21.65 Aligned_cols=18 Identities=17% Similarity=0.446 Sum_probs=13.6
Q ss_pred ceeecCCCCcee-eeeCCC
Q 026283 197 QIIRCAGCGNIV-WQPEGD 214 (240)
Q Consensus 197 t~~~CpnCGe~l-~v~~g~ 214 (240)
-.+.||.|+..- .+.+|+
T Consensus 4 i~v~CP~C~s~~~v~k~G~ 22 (36)
T PF03811_consen 4 IDVHCPRCQSTEGVKKNGK 22 (36)
T ss_pred EeeeCCCCCCCCcceeCCC
Confidence 456799998887 667775
No 465
>PRK11595 DNA utilization protein GntX; Provisional
Probab=24.43 E-value=25 Score=30.59 Aligned_cols=9 Identities=33% Similarity=0.785 Sum_probs=5.0
Q ss_pred ecCCCCcee
Q 026283 200 RCAGCGNIV 208 (240)
Q Consensus 200 ~CpnCGe~l 208 (240)
.|+.||.++
T Consensus 36 ~C~~Cg~~~ 44 (227)
T PRK11595 36 CCPQCGLPA 44 (227)
T ss_pred cCccCCCcC
Confidence 466666543
No 466
>PF11587 Prion_bPrPp: Major prion protein bPrPp - N terminal; PDB: 1SKH_A.
Probab=24.42 E-value=61 Score=21.44 Aligned_cols=13 Identities=23% Similarity=0.360 Sum_probs=10.0
Q ss_pred CCCchHHHHHHHH
Q 026283 132 TPLGRSFATIFFL 144 (240)
Q Consensus 132 T~lG~wL~tl~~~ 144 (240)
+.+|||+..||++
T Consensus 4 ~~lgcWilvLfva 16 (29)
T PF11587_consen 4 SHLGCWILVLFVA 16 (29)
T ss_dssp TTTTTHHHHHHHH
T ss_pred ccccHHHHHHHHH
Confidence 4689999877763
No 467
>PRK07333 2-octaprenyl-6-methoxyphenyl hydroxylase; Provisional
Probab=24.42 E-value=4.3e+02 Score=23.69 Aligned_cols=73 Identities=18% Similarity=0.234 Sum_probs=42.0
Q ss_pred HHhhHHHHHhHHHHHHHHHhhh-----------hhhhhhHhHHHHHHHHHHHHHHhhhhhh----hhHhHHhhhhhhhhh
Q 026283 54 RTANNGFEQLVFDAKKTAERID-----------RQYSVSRRLNSAARTAAVRARELDREFA----ISVRWRSFRMDFSRN 118 (240)
Q Consensus 54 r~an~~~e~~~fear~~a~r~D-----------~~Y~vs~r~a~aa~~a~e~A~eiD~~fg----i~rR~R~f~~D~~r~ 118 (240)
+++|.++|...--|...+..++ ++|+-.|| ..++.....++.+.+.|. ..+..|.+......+
T Consensus 298 qG~n~ai~Da~~La~~L~~~~~~~~~~~~~~~L~~Ye~~R~--~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~ 375 (403)
T PRK07333 298 QGLNLGLKDVAALAEVVVEAARLGLDIGSLDVLERYQRWRR--FDTVRMGVTTDVLNRLFSNDSTLLRSVRDIGLGLVDR 375 (403)
T ss_pred cchhhhHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHh--HHHHHHHHHHHHHHHHHcCCchHHHHHHHHHHHHHhc
Confidence 4566677766665555544331 45664333 223333344444554443 556778888888888
Q ss_pred chhHHHHHHH
Q 026283 119 WPRYRKQLND 128 (240)
Q Consensus 119 wP~yrrql~~ 128 (240)
.|..++.+.+
T Consensus 376 ~~~~~~~~~~ 385 (403)
T PRK07333 376 LPKLKSFFIR 385 (403)
T ss_pred CHHHHHHHHH
Confidence 8887776643
No 468
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=24.40 E-value=37 Score=25.14 Aligned_cols=11 Identities=27% Similarity=0.842 Sum_probs=8.6
Q ss_pred eeecCCCCcee
Q 026283 198 IIRCAGCGNIV 208 (240)
Q Consensus 198 ~~~CpnCGe~l 208 (240)
...||||||..
T Consensus 27 ~~~c~~cG~~~ 37 (57)
T COG0333 27 LSVCPNCGEYK 37 (57)
T ss_pred ceeccCCCCcc
Confidence 56799999864
No 469
>PF01194 RNA_pol_N: RNA polymerases N / 8 kDa subunit; InterPro: IPR000268 In eukaryotes, there are three different forms of DNA-dependent RNA polymerases (2.7.7.6 from EC) transcribing different sets of genes. Each class of RNA polymerase is an assemblage of ten to twelve different polypeptides. In archaebacteria, there is generally a single form of RNA polymerase which also consists of an oligomeric assemblage of 10 to 13 polypeptides. Archaebacterial subunit N (gene rpoN) [] is a small protein of about 8 kDa, it is evolutionary related [] to a 8.3 kDa component shared by all three forms of eukaryotic RNA polymerases (gene RPB10 in yeast and POLR2J in mammals) as well as to African swine fever virus (ASFV) protein CP80R []. There is a conserved region which is located at the N-terminal extremity of these polymerase subunits; this region contains two cysteines that binds a zinc ion [].; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_N 3HKZ_N 1EF4_A 3H0G_V 2Y0S_N 2R92_J 3M4O_J 3S2D_J 1R9S_J 1Y1W_J ....
Probab=24.37 E-value=30 Score=25.92 Aligned_cols=14 Identities=29% Similarity=0.821 Sum_probs=9.9
Q ss_pred eeecCCCCceeeee
Q 026283 198 IIRCAGCGNIVWQP 211 (240)
Q Consensus 198 ~~~CpnCGe~l~v~ 211 (240)
.++|..||.++.-.
T Consensus 4 PVRCFTCGkvi~~~ 17 (60)
T PF01194_consen 4 PVRCFTCGKVIGNK 17 (60)
T ss_dssp SSS-STTTSBTCGH
T ss_pred ceecCCCCCChhHh
Confidence 36899999998543
No 470
>PRK10633 hypothetical protein; Provisional
Probab=24.33 E-value=2.9e+02 Score=21.69 Aligned_cols=28 Identities=11% Similarity=0.241 Sum_probs=14.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 026283 150 GWLFRILILATWVLPIAAPLLIGTVANN 177 (240)
Q Consensus 150 GWLvn~~l~l~~vlPvaap~li~wWlkR 177 (240)
-|.+-|-|++.++.-++..+.++...|.
T Consensus 44 ~WF~~sCi~~p~lfi~l~~~~Vk~vFkD 71 (80)
T PRK10633 44 HWFEMACLLLPLLFILLCWLMVKFIFRD 71 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 4655555554444444444445554443
No 471
>PF09527 ATPase_gene1: Putative F0F1-ATPase subunit (ATPase_gene1)
Probab=24.27 E-value=1.2e+02 Score=20.95 Aligned_cols=23 Identities=17% Similarity=0.288 Sum_probs=17.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhh
Q 026283 157 ILATWVLPIAAPLLIGTVANNFV 179 (240)
Q Consensus 157 l~l~~vlPvaap~li~wWlkRnL 179 (240)
+++.++.|+++...++||+-+.+
T Consensus 6 lg~~~~~~i~~g~~~G~~lD~~~ 28 (55)
T PF09527_consen 6 LGFTMAAPILVGFFLGYWLDKWF 28 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHc
Confidence 46677778887888888887765
No 472
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=24.13 E-value=47 Score=32.90 Aligned_cols=36 Identities=22% Similarity=0.328 Sum_probs=26.3
Q ss_pred hhcCCCCCCCccccccc----cce-----eecCCCCceeeeeCCC
Q 026283 179 VIKGACPACKREFIGSK----SQI-----IRCAGCGNIVWQPEGD 214 (240)
Q Consensus 179 LIeg~CPvC~~eFtG~n----nt~-----~~CpnCGe~l~v~~g~ 214 (240)
++.--||.|-.++..-+ +.. .+||.|+.+|.+..-+
T Consensus 24 i~~~yCp~CL~~~p~~e~~~~~nrC~r~Cf~CP~C~~~L~~~~~~ 68 (483)
T PF05502_consen 24 IDSYYCPNCLFEVPSSEARSEKNRCSRNCFDCPICFSPLSVRASD 68 (483)
T ss_pred cceeECccccccCChhhheeccceeccccccCCCCCCcceeEecc
Confidence 44456999988887643 222 4699999999998655
No 473
>TIGR02896 spore_III_AF stage III sporulation protein AF. This family represents the stage III sporulation protein AF of the bacterial endospore formation program, which exists in some but not all members of the Firmicutes (formerly called low-GC Gram-positives). The C-terminal region of this protein is poorly conserved, so only the N-terminal region, which includes two predicted transmembrane domains, is included in the seed alignment.
Probab=24.10 E-value=1.9e+02 Score=23.36 Aligned_cols=37 Identities=19% Similarity=0.145 Sum_probs=19.4
Q ss_pred CchHHHHHHHHHHHHH--------------HHHHHHH-HHHHHHHHHHHHHH
Q 026283 134 LGRSFATIFFLWFALS--------------GWLFRIL-ILATWVLPIAAPLL 170 (240)
Q Consensus 134 lG~wL~tl~~~wll~S--------------GWLvn~~-l~l~~vlPvaap~l 170 (240)
+..|+..|.++-++.+ .=+|-|+ ++++++.|++.++.
T Consensus 3 l~~Wv~~i~~~~il~t~~~~llP~~~~kkYvr~v~Gl~Li~~il~Pi~~l~~ 54 (106)
T TIGR02896 3 LKEWVTNIIVLILLATILEMLLPNSSLKKYVKFVVGLILMVVILNPIIKLLT 54 (106)
T ss_pred HHHHHHHHHHHHHHHHHHHHHCCCccHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 3457766666555554 1122222 45666677775554
No 474
>PRK12475 thiamine/molybdopterin biosynthesis MoeB-like protein; Provisional
Probab=23.85 E-value=59 Score=30.36 Aligned_cols=34 Identities=29% Similarity=0.445 Sum_probs=18.5
Q ss_pred cCCCCCCCcc----ccccccceeecCCCC-ceeeeeCCC
Q 026283 181 KGACPACKRE----FIGSKSQIIRCAGCG-NIVWQPEGD 214 (240)
Q Consensus 181 eg~CPvC~~e----FtG~nnt~~~CpnCG-e~l~v~~g~ 214 (240)
..+||+|+.. +....++...-.-|| +.+++..+.
T Consensus 237 ~p~Cp~Cg~~~~~~~l~~~~~~~~~~LCgr~~vq~~~~~ 275 (338)
T PRK12475 237 KDTCPSCGLTRTYPSLTFENQTKTEVLCGRNTVQIRPGV 275 (338)
T ss_pred CCCCCcCCCCCcccccccccCCCeeeccCCceeeeecCc
Confidence 4668888742 223344444456677 455555553
No 475
>TIGR02163 napH_ ferredoxin-type protein, NapH/MauN family. Most members of this family are the NapH protein, found next to NapG,in operons that encode the periplasmic nitrate reductase. Some species with this reductase lack NapC but accomplish electron transfer to NapAB in some other manner, likely to involve NapH, NapG, and/or some other protein. A few members of this protein are designated MauN and are found in methylamine utilization operons in species that appear to lack a periplasmic nitrate reductase.
Probab=23.82 E-value=5.3e+02 Score=23.04 Aligned_cols=13 Identities=15% Similarity=0.197 Sum_probs=7.4
Q ss_pred HHHhhhhhcCCCC
Q 026283 173 TVANNFVIKGACP 185 (240)
Q Consensus 173 wWlkRnLIeg~CP 185 (240)
.+.+|..=.--||
T Consensus 167 ~~~~r~~C~~~CP 179 (255)
T TIGR02163 167 LFSERGWCGHLCP 179 (255)
T ss_pred HhcCCchhhCcCC
Confidence 4455555555666
No 476
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=23.71 E-value=35 Score=36.22 Aligned_cols=30 Identities=30% Similarity=0.759 Sum_probs=24.5
Q ss_pred CCCCCCcccccccc-----ceeecCCCCceeeeeC
Q 026283 183 ACPACKREFIGSKS-----QIIRCAGCGNIVWQPE 212 (240)
Q Consensus 183 ~CPvC~~eFtG~nn-----t~~~CpnCGe~l~v~~ 212 (240)
-||.|..|+.--.| |.+-||.||=.++..+
T Consensus 153 lC~~C~~EY~dP~nRRfHAQp~aCp~CGP~~~l~~ 187 (750)
T COG0068 153 LCPFCDKEYKDPLNRRFHAQPIACPKCGPHLFLVN 187 (750)
T ss_pred CCHHHHHHhcCccccccccccccCcccCCCeEEEc
Confidence 48999998877655 6678999999888874
No 477
>PF13829 DUF4191: Domain of unknown function (DUF4191)
Probab=23.71 E-value=3.1e+02 Score=25.25 Aligned_cols=22 Identities=23% Similarity=0.211 Sum_probs=11.4
Q ss_pred HHHHHHHHHHHHHhhhh---hcCCC
Q 026283 163 LPIAAPLLIGTVANNFV---IKGAC 184 (240)
Q Consensus 163 lPvaap~li~wWlkRnL---Ieg~C 184 (240)
.-+++.++|+.-+++.. +||+=
T Consensus 63 g~l~am~vl~rra~ra~Y~qieGqp 87 (224)
T PF13829_consen 63 GLLAAMIVLSRRAQRAAYAQIEGQP 87 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcCCC
Confidence 33444555666666543 45543
No 478
>COG5005 Mu-like prophage protein gpG [General function prediction only]
Probab=23.69 E-value=1.2e+02 Score=26.27 Aligned_cols=36 Identities=19% Similarity=0.245 Sum_probs=30.1
Q ss_pred HHHHHHHhhhhhhhhhHhHHHHHHHHHHHHHHhhhh
Q 026283 66 DAKKTAERIDRQYSVSRRLNSAARTAAVRARELDRE 101 (240)
Q Consensus 66 ear~~a~r~D~~Y~vs~r~a~aa~~a~e~A~eiD~~ 101 (240)
...+.|+-.|.+|.+.|++|+.-++|.+++=|+..+
T Consensus 15 ~~~~laq~~~~rk~Lmr~vA~~m~sav~~nF~~~gr 50 (140)
T COG5005 15 KLEALAQVTDGRKDLMRSVAGTMRSAVEKNFELEGR 50 (140)
T ss_pred HHHHHHHhhccccHHHHHHHHHHHHHHHHHHHhcCC
Confidence 445678889999999999999999999988776543
No 479
>cd03509 DesA_FADS-like Fatty acid desaturase protein family subgroup, a delta-12 acyl-lipid desaturase-like, DesA-like, yet uncharacterized subgroup of membrane fatty acid desaturase proteins found in alpha-, beta-, and gamma-proteobacteria. Sequences of this domain family appear to be structurally related to membrane fatty acid desaturases and alkane hydroxylases. They all share in common extensive hydrophobic regions that would be capable of spanning the membrane bilayer at least twice. Comparison of these sequences also reveals three regions of conserved histidine cluster motifs that contain eight histidine residues: HXXXH, HXXHH, and HXXHH. These histidine residues are reported to be catalytically essential and proposed to be the ligands for the iron atoms contained within homologs, stearoyl CoA desaturase and alkane hydroxylase.
Probab=23.64 E-value=3.9e+02 Score=24.53 Aligned_cols=14 Identities=36% Similarity=0.432 Sum_probs=5.7
Q ss_pred HHHHHHHhhCCCCc
Q 026283 122 YRKQLNDFLNTPLG 135 (240)
Q Consensus 122 yrrql~~F~~T~lG 135 (240)
++|.++..+.+++|
T Consensus 113 ~~r~~~~~~~~~~~ 126 (288)
T cd03509 113 WQRALLRANNTLLG 126 (288)
T ss_pred HHHHHHHHhhcchh
Confidence 34444444444333
No 480
>PF01214 CK_II_beta: Casein kinase II regulatory subunit; InterPro: IPR000704 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. Casein kinase, a ubiquitous, well-conserved protein kinase involved in cell metabolism and differentiation, is characterised by its preference for Ser or Thr in acidic stretches of amino acids. The enzyme is a tetramer of 2 alpha- and 2 beta-subunits [, ]. However, some species (e.g., mammals) possess 2 related forms of the alpha-subunit (alpha and alpha'), while others (e.g., fungi) possess 2 related beta-subunits (beta and beta') []. The alpha-subunit is the catalytic unit and contains regions characteristic of serine/threonine protein kinases. The beta-subunit is believed to be regulatory, possessing an N-terminal auto-phosphorylation site, an internal acidic domain, and a potential metal-binding motif []. The beta subunit is a highly conserved protein of about 25kDa that contains, in its central section, a cysteine-rich motif, CX(n)C, that could be involved in binding a metal such as zinc []. The mammalian beta-subunit gene promoter shares common features with those of other mammalian protein kinases and is closely related to the promoter of the regulatory subunit of cAMP-dependent protein kinase [].; GO: 0019887 protein kinase regulator activity, 0005956 protein kinase CK2 complex; PDB: 2R6M_B 1RQF_K 1DS5_G 1QF8_B 3EED_A 4DGL_A 1JWH_D.
Probab=23.60 E-value=50 Score=28.89 Aligned_cols=34 Identities=24% Similarity=0.612 Sum_probs=20.6
Q ss_pred hcCCCC--CCCcc---------ccccccceeecCCCCceeeeeCC
Q 026283 180 IKGACP--ACKRE---------FIGSKSQIIRCAGCGNIVWQPEG 213 (240)
Q Consensus 180 Ieg~CP--vC~~e---------FtG~nnt~~~CpnCGe~l~v~~g 213 (240)
+-|.|| -|+.+ =.|-......||+|.++-..++.
T Consensus 98 ~FG~CPRv~C~~~~lLPiGlsd~~g~~~vKlyCP~C~dvY~p~~~ 142 (184)
T PF01214_consen 98 DFGRCPRVYCNGQPLLPIGLSDTPGESTVKLYCPRCKDVYHPPSS 142 (184)
T ss_dssp TT-B-SBGGGTT-B-EEEBS-SSTTS-BBEEEETTTTEEE--SSG
T ss_pred cCCcCCcccCCCCceeCccCCCCCCccceeEECCCCccccCCCCc
Confidence 458999 67754 23666778999999998776443
No 481
>PRK14291 chaperone protein DnaJ; Provisional
Probab=23.50 E-value=38 Score=32.02 Aligned_cols=13 Identities=31% Similarity=0.598 Sum_probs=7.1
Q ss_pred ccccceeecCCCC
Q 026283 193 GSKSQIIRCAGCG 205 (240)
Q Consensus 193 G~nnt~~~CpnCG 205 (240)
|+-+++..|+.|+
T Consensus 190 g~~~~~~~C~~C~ 202 (382)
T PRK14291 190 GFFRISQTCPTCG 202 (382)
T ss_pred ceEEEEecCCCCC
Confidence 4444555666663
No 482
>PF04956 TrbC: TrbC/VIRB2 family; InterPro: IPR007039 Conjugal transfer protein, TrbC has been identified as a subunit of the pilus precursor in bacteria. The protein undergoes three processing steps before gaining its mature cyclic structure[]. This family also contains several VirB2 type IV secretion proteins. The virB2 gene encodes a putative type IV secretion system and is known to be a pathogenicity factor in Bartonella species [].
Probab=23.45 E-value=1.2e+02 Score=22.59 Aligned_cols=46 Identities=22% Similarity=0.524 Sum_probs=30.9
Q ss_pred hhchhHHHHHHHhhCCCCchHHHHHHHHHHHHH--------HHHHHHHHHHHHH
Q 026283 117 RNWPRYRKQLNDFLNTPLGRSFATIFFLWFALS--------GWLFRILILATWV 162 (240)
Q Consensus 117 r~wP~yrrql~~F~~T~lG~wL~tl~~~wll~S--------GWLvn~~l~l~~v 162 (240)
-+|=..=..+.++...|+|..+.++.+++.... +|+++.++++.++
T Consensus 36 ~~~~~~l~~i~~~l~gp~~~~i~~i~ii~~g~~~~~g~~~~~~~~~~v~G~~iv 89 (99)
T PF04956_consen 36 DPWTSFLCKIIDWLTGPIGKAIAIIAIIVAGIMMMFGRQSWRWFIGVVIGIIIV 89 (99)
T ss_pred ccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCcCHHHHHHHHHHHHHH
Confidence 344455566777888889999988887766555 6677766644433
No 483
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=23.39 E-value=38 Score=28.38 Aligned_cols=12 Identities=33% Similarity=0.935 Sum_probs=9.0
Q ss_pred CCCCCCCccccc
Q 026283 182 GACPACKREFIG 193 (240)
Q Consensus 182 g~CPvC~~eFtG 193 (240)
-.||.||.+|-+
T Consensus 50 t~CP~Cg~~~e~ 61 (115)
T COG1885 50 TSCPKCGEPFES 61 (115)
T ss_pred ccCCCCCCccce
Confidence 468888888754
No 484
>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=23.38 E-value=36 Score=25.28 Aligned_cols=26 Identities=31% Similarity=0.615 Sum_probs=18.8
Q ss_pred cCCCCCCCccccccccceeecCCCCcee
Q 026283 181 KGACPACKREFIGSKSQIIRCAGCGNIV 208 (240)
Q Consensus 181 eg~CPvC~~eFtG~nnt~~~CpnCGe~l 208 (240)
--.|.-||.. .|+-|.-+|.+||-+-
T Consensus 15 H~~CrRCG~~--syH~qK~~CasCGyp~ 40 (55)
T PF01907_consen 15 HTLCRRCGRR--SYHIQKKTCASCGYPA 40 (55)
T ss_dssp EEE-TTTSSE--EEETTTTEETTTBTTT
T ss_pred EeeecccCCe--eeecCCCcccccCCCc
Confidence 3458888875 5788888899998653
No 485
>cd04511 Nudix_Hydrolase_4 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, U=I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specifici
Probab=23.33 E-value=84 Score=24.17 Aligned_cols=29 Identities=17% Similarity=0.233 Sum_probs=18.8
Q ss_pred CCCCCcccccccccee----ecCCCCceeeeeCCC
Q 026283 184 CPACKREFIGSKSQII----RCAGCGNIVWQPEGD 214 (240)
Q Consensus 184 CPvC~~eFtG~nnt~~----~CpnCGe~l~v~~g~ 214 (240)
||+|++.. +.+... -+-+.|++|-+++.+
T Consensus 1 c~~~~~~~--~~~~~~~v~~ii~~~~~vLL~kr~~ 33 (130)
T cd04511 1 CPDCGYIH--YQNPKIIVGCVPEWEGKVLLCRRAI 33 (130)
T ss_pred CCCCcccc--CCCCcEEEEEEEecCCEEEEEEecC
Confidence 99999844 344422 235668888887643
No 486
>PRK14278 chaperone protein DnaJ; Provisional
Probab=23.29 E-value=42 Score=31.76 Aligned_cols=14 Identities=21% Similarity=0.539 Sum_probs=8.1
Q ss_pred cccccceeecCCCC
Q 026283 192 IGSKSQIIRCAGCG 205 (240)
Q Consensus 192 tG~nnt~~~CpnCG 205 (240)
.|.-+++..|+.|+
T Consensus 176 ~g~~~~~~~C~~C~ 189 (378)
T PRK14278 176 LGQVMTSRPCPTCR 189 (378)
T ss_pred ceeEEEEEECCCCC
Confidence 35555566677773
No 487
>PRK07220 DNA topoisomerase I; Validated
Probab=23.23 E-value=55 Score=33.92 Aligned_cols=37 Identities=22% Similarity=0.377 Sum_probs=0.0
Q ss_pred hhhcCCCCCCCc-cccccccc----eeecCCCCceeeeeCCC
Q 026283 178 FVIKGACPACKR-EFIGSKSQ----IIRCAGCGNIVWQPEGD 214 (240)
Q Consensus 178 nLIeg~CPvC~~-eFtG~nnt----~~~CpnCGe~l~v~~g~ 214 (240)
..+...||.|+. .+.-.+.. ...||+|.-.-++....
T Consensus 632 ~~~~~~Cp~Cg~~~~k~~~~g~~~~~~~Cp~C~~~~~~~~~~ 673 (740)
T PRK07220 632 IVTDKVCEAHGLNHIRIINGGKRPWDLGCPQCNFIEWQKKQK 673 (740)
T ss_pred ccCCCCCCCCCCceEEEEecCCccceeeCCCCCCccccCCcc
No 488
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=23.19 E-value=19 Score=36.37 Aligned_cols=37 Identities=22% Similarity=0.592 Sum_probs=26.3
Q ss_pred HHHhhhhhcCCCCCCCccccccccceeecCCCCceeeee
Q 026283 173 TVANNFVIKGACPACKREFIGSKSQIIRCAGCGNIVWQP 211 (240)
Q Consensus 173 wWlkRnLIeg~CPvC~~eFtG~nnt~~~CpnCGe~l~v~ 211 (240)
-|+...-| --||-|+..| |+.+.+--|-=||-++=-.
T Consensus 173 pW~DDs~V-~~CP~Ca~~F-~l~rRrHHCRLCG~VmC~~ 209 (505)
T KOG1842|consen 173 PWLDDSSV-QFCPECANSF-GLTRRRHHCRLCGRVMCRD 209 (505)
T ss_pred cccCCCcc-cccccccchh-hhHHHhhhhhhcchHHHHH
Confidence 34444333 3599999998 6888888899999876433
No 489
>cd01428 ADK Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP). This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.
Probab=23.19 E-value=67 Score=25.73 Aligned_cols=37 Identities=16% Similarity=0.200 Sum_probs=28.7
Q ss_pred HHHhhhhhcCCCCCCCccccccccceeecCCCCceeeeeCCC
Q 026283 173 TVANNFVIKGACPACKREFIGSKSQIIRCAGCGNIVWQPEGD 214 (240)
Q Consensus 173 wWlkRnLIeg~CPvC~~eFtG~nnt~~~CpnCGe~l~v~~g~ 214 (240)
..++|..--..||.|+..|-= ..|++|+.+|....++
T Consensus 117 ~~~~Rl~~R~~~~~~~~~~~~-----~~~~~~~~~l~~r~dd 153 (194)
T cd01428 117 VLIERILGRRICPVSGRVYHL-----GKDDVTGEPLSQRSDD 153 (194)
T ss_pred HHHHHHHcCCcCCCcCCcCCc-----CCCcccCCccccCCCC
Confidence 556676667889999988765 8999999998865543
No 490
>PHA02446 hypothetical protein
Probab=23.13 E-value=38 Score=29.32 Aligned_cols=15 Identities=27% Similarity=0.683 Sum_probs=12.8
Q ss_pred eeecCCCCceeeeeC
Q 026283 198 IIRCAGCGNIVWQPE 212 (240)
Q Consensus 198 ~~~CpnCGe~l~v~~ 212 (240)
+.+||-||+--||..
T Consensus 62 ~q~cp~cg~dawv~~ 76 (166)
T PHA02446 62 QQQCPLCGQDAWVIH 76 (166)
T ss_pred hhcCCCcccceeEee
Confidence 568999999999865
No 491
>TIGR00630 uvra excinuclease ABC, A subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.11 E-value=48 Score=35.54 Aligned_cols=27 Identities=30% Similarity=0.642 Sum_probs=18.4
Q ss_pred hhhcCCCCCCC--------ccccccccceeecCCCCc
Q 026283 178 FVIKGACPACK--------REFIGSKSQIIRCAGCGN 206 (240)
Q Consensus 178 nLIeg~CPvC~--------~eFtG~nnt~~~CpnCGe 206 (240)
|.-+|.||.|+ ..| +......||.|+-
T Consensus 733 N~~~G~C~~C~G~G~~~~~~~f--~~~~~~~C~~C~G 767 (924)
T TIGR00630 733 NVKGGRCEACQGDGVIKIEMHF--LPDVYVPCEVCKG 767 (924)
T ss_pred CCCCCCCCCCccceEEEEEccC--CCCcccCCCCcCC
Confidence 55579999996 223 3445678999974
No 492
>PRK14526 adenylate kinase; Provisional
Probab=22.98 E-value=89 Score=27.18 Aligned_cols=42 Identities=17% Similarity=0.282 Sum_probs=28.7
Q ss_pred HHHhhhhhcCCCCCCCccccccccc---eeecCCCCceeeeeCCC
Q 026283 173 TVANNFVIKGACPACKREFIGSKSQ---IIRCAGCGNIVWQPEGD 214 (240)
Q Consensus 173 wWlkRnLIeg~CPvC~~eFtG~nnt---~~~CpnCGe~l~v~~g~ 214 (240)
...+|-.--..||+||..|-=..+. .-.|..||+.|.+..++
T Consensus 114 ~~~~Rl~~R~~~~~~g~~y~~~~~pp~~~~~~~~~~~~l~~R~DD 158 (211)
T PRK14526 114 LLIKRLSGRRICKSCNNIFNIYTLPTKEKGICDVCKGDLYQRKDD 158 (211)
T ss_pred HHHHHHHCCCcccccCCccccccCCCCccCcCCCCCCeeeccCCC
Confidence 3446666667899999887544332 34699999988766554
No 493
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=22.87 E-value=39 Score=27.34 Aligned_cols=28 Identities=29% Similarity=0.564 Sum_probs=21.9
Q ss_pred hhcCCCCCCCccccccccceeecCCCCcee
Q 026283 179 VIKGACPACKREFIGSKSQIIRCAGCGNIV 208 (240)
Q Consensus 179 LIeg~CPvC~~eFtG~nnt~~~CpnCGe~l 208 (240)
-..--|.-||.. .|+-|.-+|.+||-+-
T Consensus 14 ktHtlCrRCG~~--syH~qK~~CasCGyps 41 (91)
T PTZ00073 14 KTHTLCRRCGKR--SFHVQKKRCASCGYPS 41 (91)
T ss_pred cCcchhcccCcc--ccccccccchhcCCch
Confidence 344569999986 5788899999999753
No 494
>PHA02929 N1R/p28-like protein; Provisional
Probab=22.68 E-value=50 Score=30.18 Aligned_cols=22 Identities=27% Similarity=0.661 Sum_probs=14.9
Q ss_pred HHHhhhhhcCCCCCCCccccccccc
Q 026283 173 TVANNFVIKGACPACKREFIGSKSQ 197 (240)
Q Consensus 173 wWlkRnLIeg~CPvC~~eFtG~nnt 197 (240)
-|+++ ...||+|..+|+++..+
T Consensus 211 ~Wl~~---~~tCPlCR~~~~~v~~~ 232 (238)
T PHA02929 211 IWKKE---KNTCPVCRTPFISVIKS 232 (238)
T ss_pred HHHhc---CCCCCCCCCEeeEEeee
Confidence 35554 46899999888865443
No 495
>PRK01343 zinc-binding protein; Provisional
Probab=22.68 E-value=43 Score=24.88 Aligned_cols=14 Identities=21% Similarity=0.551 Sum_probs=9.7
Q ss_pred hhcCCCCCCCcccc
Q 026283 179 VIKGACPACKREFI 192 (240)
Q Consensus 179 LIeg~CPvC~~eFt 192 (240)
+-.-.||+|+.+++
T Consensus 7 ~p~~~CP~C~k~~~ 20 (57)
T PRK01343 7 RPTRPCPECGKPST 20 (57)
T ss_pred CCCCcCCCCCCcCc
Confidence 34567888888775
No 496
>PRK12268 methionyl-tRNA synthetase; Reviewed
Probab=22.57 E-value=36 Score=33.07 Aligned_cols=27 Identities=33% Similarity=1.030 Sum_probs=16.7
Q ss_pred hhhcCCCCCCCccccccccceeecCCCCcee
Q 026283 178 FVIKGACPACKREFIGSKSQIIRCAGCGNIV 208 (240)
Q Consensus 178 nLIeg~CPvC~~eFtG~nnt~~~CpnCGe~l 208 (240)
..|.|.||.|+.+ +..+. .|-+||..+
T Consensus 138 ~~v~g~cp~c~~~--~~~G~--~ce~cg~~~ 164 (556)
T PRK12268 138 RYVEGTCPYCGYE--GARGD--QCDNCGALL 164 (556)
T ss_pred cceeccCCCCCCc--ccCCc--hhhhccccC
Confidence 4566899999852 22332 367777654
No 497
>PF08804 gp32: gp32 DNA binding protein like; InterPro: IPR012339 This entry is represented by the Bacteriophage T4, Gp32, single-stranded DNA-binding protein. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Gp32 is essential for T4 DNA replication, recombination and repair, acting to stimulate replisome processing and accuracy through its binding to ssDNA as the replication fork advances. The crystal structure of Gp32 shows an ssDNA binding cleft comprised of regions from three structural subdomains, through which ssDNA can slide freely []. The structure of Gp32 is similar to other phage ssDNA-binding proteins such as Gp2.5 from bacteriophage T4, and gene V protein, both of which have a nucleic acid-binding OB-type fold. However, Gp32 contains a zinc-finger subdomain at residues 63-111 that is not found in the other two phage proteins.; GO: 0003697 single-stranded DNA binding; PDB: 1GPC_A 2A1K_B 2ATQ_B.
Probab=22.52 E-value=11 Score=30.64 Aligned_cols=15 Identities=27% Similarity=0.510 Sum_probs=10.6
Q ss_pred CCCCCCCc--ccccccc
Q 026283 182 GACPACKR--EFIGSKS 196 (240)
Q Consensus 182 g~CPvC~~--eFtG~nn 196 (240)
|.||||++ +.-.+|+
T Consensus 59 d~cPVc~~~~~~~lwn~ 75 (94)
T PF08804_consen 59 DSCPVCEHISNRDLWNS 75 (94)
T ss_dssp TTSHHHHHHHHTTHHHH
T ss_pred CCCCccccccccccccc
Confidence 58999998 6555543
No 498
>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=22.52 E-value=38 Score=29.31 Aligned_cols=17 Identities=18% Similarity=0.501 Sum_probs=14.7
Q ss_pred CCCCCCcccccccccee
Q 026283 183 ACPACKREFIGSKSQII 199 (240)
Q Consensus 183 ~CPvC~~eFtG~nnt~~ 199 (240)
.|+.|++.||=|.--+.
T Consensus 30 eC~~C~~RFTTyErve~ 46 (147)
T TIGR00244 30 ECLECHERFTTFERAEL 46 (147)
T ss_pred cCCccCCccceeeeccc
Confidence 69999999999987665
No 499
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=22.37 E-value=46 Score=19.87 Aligned_cols=13 Identities=31% Similarity=0.759 Sum_probs=10.1
Q ss_pred CCCCCCccccccc
Q 026283 183 ACPACKREFIGSK 195 (240)
Q Consensus 183 ~CPvC~~eFtG~n 195 (240)
-|++|+..|..-+
T Consensus 3 ~C~~C~k~f~~~~ 15 (27)
T PF12171_consen 3 YCDACDKYFSSEN 15 (27)
T ss_dssp BBTTTTBBBSSHH
T ss_pred CcccCCCCcCCHH
Confidence 4999999887643
No 500
>PF00452 Bcl-2: Apoptosis regulator proteins, Bcl-2 family; InterPro: IPR000712 Apoptosis, or programmed cell death (PCD), is a common and evolutionarily conserved property of all metazoans []. In many biological processes, apoptosis is required to eliminate supernumerary or dangerous (such as pre-cancerous) cells and to promote normal development. Dysregulation of apoptosis can, therefore, contribute to the development of many major diseases including cancer, autoimmunity and neurodegenerative disorders. In most cases, proteins of the caspase family execute the genetic programme that leads to cell death. Bcl-2 proteins are central regulators of caspase activation, and play a key role in cell death by regulating the integrity of the mitochondrial and endoplasmic reticulum (ER) membranes []. At least 20 Bcl-2 proteins have been reported in mammals, and several others have been identified in viruses. Bcl-2 family proteins fall roughly into three subtypes, which either promote cell survival (anti-apoptotic) or trigger cell death (pro-apoptotic). All members contain at least one of four conserved motifs, termed Bcl-2 Homology (BH) domains. Bcl-2 subfamily proteins, which contain at least BH1 and BH2, promote cell survival by inhibiting the adapters needed for the activation of caspases. Pro-apoptotic members potentially exert their effects by displacing the adapters from the pro-survival proteins; these proteins belong either to the Bax subfamily, which contain BH1-BH3, or to the BH3 subfamily, which mostly only feature BH3 []. Thus, the balance between antagonistic family members is believed to play a role in determining cell fate. Members of the wider Bcl-2 family, which also includes Bcl-x, Bcl-w and Mcl-1, are described by their similarity to Bcl-2 protein, a member of the pro-survival Bcl-2 subfamily []. Full-length Bcl-2 proteins feature all four BH domains, seven alpha-helices, and a C-terminal hydrophobic motif that targets the protein to the outer mitochondrial membrane, ER and nuclear envelope. Active cell suicide (apoptosis) is induced by events such as growth factor withdrawal and toxins. It is controlled by regulators, which have either an inhibitory effect on programmed cell death (anti-apoptotic) or block the protective effect of inhibitors (pro-apoptotic) [, ]. Many viruses have found a way of countering defensive apoptosis by encoding their own anti-apoptosis genes preventing their target-cells from dying too soon. All proteins belonging to the Bcl-2 family [] contain either a BH1, BH2, BH3, or BH4 domain. All anti-apoptotic proteins contain BH1 and BH2 domains, some of them contain an additional N-terminal BH4 domain (Bcl-2, Bcl-x(L), Bcl-w), which is never seen in pro-apoptotic proteins, except for Bcl-x(S). On the other hand, all pro-apoptotic proteins contain a BH3 domain (except for Bad) necessary for dimerisation with other proteins of Bcl-2 family and crucial for their killing activity, some of them also contain BH1 and BH2 domains (Bax, Bak). The BH3 domain is also present in some anti-apoptotic protein, such as Bcl-2 or Bcl-x(L). Proteins that are known to contain these domains include vertebrate Bcl-2 (alpha and beta isoforms) and Bcl-x (isoforms (Bcl-x(L) and Bcl-x(S)); mammalian proteins Bax and Bak; mouse protein Bid; Xenopus laevis proteins Xr1 and Xr11; human induced myeloid leukemia cell differentiation protein MCL1 and Caenorhabditis elegans protein ced-9.; GO: 0042981 regulation of apoptosis; PDB: 2WH6_A 1K3K_A 1AF3_A 3PK1_B 2K7W_A 1F16_A 3PL7_C 2VM6_A 3I1H_A 3MQP_A ....
Probab=22.34 E-value=3.1e+02 Score=20.39 Aligned_cols=58 Identities=14% Similarity=0.213 Sum_probs=0.0
Q ss_pred HHHHHHhhhhhh--hhHhHHhhhh-hhhhhchhHHHHHHHhhCC---CCchHHHHHHHHHHHHH
Q 026283 92 AVRARELDREFA--ISVRWRSFRM-DFSRNWPRYRKQLNDFLNT---PLGRSFATIFFLWFALS 149 (240)
Q Consensus 92 ~e~A~eiD~~fg--i~rR~R~f~~-D~~r~wP~yrrql~~F~~T---~lG~wL~tl~~~wll~S 149 (240)
.+.+.+++++|. +++-.+.+.. +-......|..-..+.... .+|+.+++|.|...+..
T Consensus 2 ~~i~~~~e~~~~~~f~~~~~~l~~~~~~~~~~~f~~v~~~lf~d~~inWGRIval~~f~~~l~~ 65 (101)
T PF00452_consen 2 RRIADELERKYEDFFENMLNQLNINTPDNAYETFNEVAEELFEDGGINWGRIVALFAFAGALAV 65 (101)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHCSSSTTTHHHHHHHHHHHHTTTSSTCHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCCCcchHHHHHHHHHHHHhccCCCCHHHHHHHHHHHHHHHH
Done!