Query 033276
Match_columns 123
No_of_seqs 101 out of 282
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 11:56:45 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/033276.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/033276hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2463 Predicted RNA-binding 100.0 3.4E-34 7.3E-39 241.6 4.8 86 18-105 176-277 (376)
2 COG1439 Predicted nucleic acid 99.9 3.6E-24 7.7E-29 167.3 4.4 78 20-99 77-167 (177)
3 PRK12496 hypothetical protein; 99.8 5.1E-20 1.1E-24 140.7 4.0 67 32-99 89-158 (164)
4 PF08772 NOB1_Zn_bind: Nin one 99.7 4.6E-17 9.9E-22 111.7 2.5 41 62-104 1-43 (73)
5 TIGR03875 RNA_lig_partner RNA 97.9 7.7E-06 1.7E-10 65.9 2.6 27 32-58 169-195 (206)
6 PRK04358 hypothetical protein; 97.7 1.6E-05 3.5E-10 64.4 2.3 27 32-58 173-199 (217)
7 PF13248 zf-ribbon_3: zinc-rib 97.2 0.00019 4.1E-09 40.0 1.1 21 73-93 4-25 (26)
8 PF13240 zinc_ribbon_2: zinc-r 97.0 0.00037 8.1E-09 38.2 1.2 21 73-93 1-22 (23)
9 PF08745 UPF0278: UPF0278 fami 96.8 0.00055 1.2E-08 55.3 1.7 28 32-59 166-193 (205)
10 PF15017 AF1Q: Drug resistance 96.3 0.0019 4E-08 46.0 1.5 18 13-30 63-80 (87)
11 PF09723 Zn-ribbon_8: Zinc rib 96.2 0.0057 1.2E-07 37.3 2.8 30 68-99 3-40 (42)
12 PF10571 UPF0547: Uncharacteri 96.0 0.0033 7.1E-08 35.5 1.2 21 73-93 2-23 (26)
13 PRK12380 hydrogenase nickel in 95.8 0.008 1.7E-07 43.6 2.9 41 66-111 66-109 (113)
14 PRK03681 hypA hydrogenase nick 95.8 0.0074 1.6E-07 43.8 2.6 40 67-111 67-110 (114)
15 PRK00564 hypA hydrogenase nick 95.8 0.011 2.4E-07 43.1 3.3 39 68-111 69-111 (117)
16 PF01155 HypA: Hydrogenase exp 95.5 0.011 2.4E-07 42.7 2.6 42 65-111 65-109 (113)
17 PF12172 DUF35_N: Rubredoxin-l 95.5 0.0081 1.8E-07 35.3 1.5 25 68-93 9-34 (37)
18 PRK00398 rpoP DNA-directed RNA 95.4 0.014 3E-07 35.8 2.4 24 70-94 3-31 (46)
19 smart00834 CxxC_CXXC_SSSS Puta 95.3 0.013 2.9E-07 34.2 2.1 25 68-93 3-35 (41)
20 PRK03824 hypA hydrogenase nick 95.3 0.018 3.9E-07 42.9 3.2 38 69-111 69-130 (135)
21 TIGR00100 hypA hydrogenase nic 95.3 0.018 3.8E-07 41.8 3.1 40 67-111 67-109 (115)
22 TIGR02605 CxxC_CxxC_SSSS putat 95.2 0.029 6.2E-07 34.7 3.5 32 68-101 3-42 (52)
23 COG1545 Predicted nucleic-acid 94.7 0.031 6.8E-07 41.9 2.9 33 66-99 25-58 (140)
24 PF12773 DZR: Double zinc ribb 93.9 0.028 6.1E-07 34.4 1.1 21 74-94 1-22 (50)
25 COG0375 HybF Zn finger protein 93.6 0.072 1.6E-06 39.6 2.9 42 65-111 65-109 (115)
26 smart00659 RPOLCX RNA polymera 93.5 0.074 1.6E-06 33.1 2.4 24 70-94 2-29 (44)
27 cd00729 rubredoxin_SM Rubredox 93.3 0.063 1.4E-06 31.6 1.9 22 71-93 3-27 (34)
28 PF12773 DZR: Double zinc ribb 92.9 0.053 1.2E-06 33.1 1.2 19 73-91 31-50 (50)
29 PF10263 SprT-like: SprT-like 92.9 0.11 2.3E-06 37.9 2.9 51 43-94 87-153 (157)
30 COG1645 Uncharacterized Zn-fin 92.5 0.072 1.6E-06 40.5 1.6 21 73-93 30-53 (131)
31 COG2093 DNA-directed RNA polym 92.5 0.059 1.3E-06 36.6 1.1 21 73-93 6-27 (64)
32 PRK00762 hypA hydrogenase nick 92.5 0.13 2.8E-06 37.9 2.9 39 67-111 67-115 (124)
33 PF03604 DNA_RNApol_7kD: DNA d 91.9 0.2 4.2E-06 29.5 2.7 25 73-98 2-30 (32)
34 cd00350 rubredoxin_like Rubred 91.8 0.11 2.5E-06 30.0 1.6 22 71-93 2-26 (33)
35 PF14803 Nudix_N_2: Nudix N-te 91.2 0.1 2.2E-06 31.1 1.0 11 85-95 1-11 (34)
36 COG1996 RPC10 DNA-directed RNA 91.2 0.13 2.8E-06 33.2 1.5 26 68-94 4-34 (49)
37 COG1592 Rubrerythrin [Energy p 91.0 0.14 3.1E-06 40.0 1.9 23 70-93 134-158 (166)
38 PRK13130 H/ACA RNA-protein com 90.6 0.12 2.7E-06 34.0 1.0 20 73-93 7-26 (56)
39 PRK00420 hypothetical protein; 90.4 0.17 3.7E-06 37.4 1.7 21 73-93 25-49 (112)
40 PF11023 DUF2614: Protein of u 89.7 0.19 4.1E-06 37.5 1.5 33 65-98 64-99 (114)
41 PRK14559 putative protein seri 89.3 0.15 3.2E-06 46.9 0.8 27 73-100 29-56 (645)
42 PRK04351 hypothetical protein; 89.2 0.54 1.2E-05 35.8 3.7 50 41-94 85-142 (149)
43 COG1579 Zn-ribbon protein, pos 89.0 0.26 5.6E-06 40.6 1.9 21 73-93 199-230 (239)
44 PF07295 DUF1451: Protein of u 88.8 0.31 6.6E-06 37.3 2.1 29 70-100 112-145 (146)
45 COG5257 GCD11 Translation init 88.6 0.46 1E-05 41.8 3.3 32 68-100 55-89 (415)
46 COG1656 Uncharacterized conser 88.5 0.11 2.4E-06 40.9 -0.5 23 33-56 47-69 (165)
47 PRK14559 putative protein seri 88.1 0.18 3.9E-06 46.4 0.6 23 73-95 3-26 (645)
48 COG2260 Predicted Zn-ribbon RN 87.8 0.25 5.5E-06 33.1 0.9 23 71-94 5-27 (59)
49 PF02150 RNA_POL_M_15KD: RNA p 87.7 0.32 7E-06 28.8 1.3 10 85-94 2-11 (35)
50 PF07282 OrfB_Zn_ribbon: Putat 87.6 0.74 1.6E-05 29.7 3.1 44 43-93 7-55 (69)
51 PRK11032 hypothetical protein; 86.6 0.48 1E-05 36.9 2.0 29 70-100 124-157 (160)
52 PF09297 zf-NADH-PPase: NADH p 86.2 0.39 8.4E-06 27.4 1.0 11 84-94 3-13 (32)
53 PF14369 zf-RING_3: zinc-finge 86.0 0.8 1.7E-05 27.2 2.3 22 71-93 3-30 (35)
54 PF14205 Cys_rich_KTR: Cystein 85.9 1 2.2E-05 29.9 3.0 30 68-100 3-43 (55)
55 COG1198 PriA Primosomal protei 85.9 0.62 1.3E-05 43.7 2.7 27 69-98 461-488 (730)
56 TIGR02827 RNR_anaer_Bdell anae 85.8 0.62 1.4E-05 42.6 2.7 53 42-104 509-565 (586)
57 PF09538 FYDLN_acid: Protein o 85.4 0.47 1E-05 34.6 1.3 25 73-97 11-39 (108)
58 PF14205 Cys_rich_KTR: Cystein 85.2 0.45 9.7E-06 31.5 1.1 14 85-99 5-18 (55)
59 PF14446 Prok-RING_1: Prokaryo 85.1 0.24 5.3E-06 32.5 -0.2 35 73-108 7-44 (54)
60 PF13638 PIN_4: PIN domain; PD 85.1 1.1 2.3E-05 31.5 3.0 27 32-58 106-132 (133)
61 PF05191 ADK_lid: Adenylate ki 84.9 0.82 1.8E-05 27.3 2.1 22 73-94 3-31 (36)
62 PRK08351 DNA-directed RNA poly 84.8 0.49 1.1E-05 31.7 1.2 21 73-94 5-25 (61)
63 PF04135 Nop10p: Nucleolar RNA 84.7 1.2 2.6E-05 29.1 2.9 25 68-94 3-27 (53)
64 COG2331 Uncharacterized protei 84.6 0.74 1.6E-05 32.6 2.0 42 65-107 7-58 (82)
65 cd01675 RNR_III Class III ribo 84.6 0.89 1.9E-05 40.8 3.0 58 40-104 493-551 (555)
66 TIGR02487 NrdD anaerobic ribon 84.5 0.49 1.1E-05 42.7 1.3 43 42-93 501-547 (579)
67 PRK14714 DNA polymerase II lar 84.4 0.97 2.1E-05 45.0 3.4 32 61-94 658-689 (1337)
68 smart00731 SprT SprT homologue 84.1 1.1 2.4E-05 33.0 2.9 52 42-94 83-143 (146)
69 PRK06393 rpoE DNA-directed RNA 83.9 0.52 1.1E-05 31.9 1.0 20 73-93 7-26 (64)
70 PRK07111 anaerobic ribonucleos 83.7 0.64 1.4E-05 43.3 1.8 33 71-104 680-712 (735)
71 TIGR00595 priA primosomal prot 83.3 0.93 2E-05 40.1 2.6 26 70-98 240-266 (505)
72 PRK02935 hypothetical protein; 82.9 0.79 1.7E-05 34.1 1.7 31 67-98 67-100 (110)
73 PF13597 NRDD: Anaerobic ribon 82.2 0.49 1.1E-05 42.4 0.4 24 70-93 490-513 (546)
74 PRK08270 anaerobic ribonucleos 81.9 0.99 2.2E-05 41.6 2.3 44 42-94 602-649 (656)
75 PF04216 FdhE: Protein involve 81.8 1 2.3E-05 36.7 2.1 27 73-100 199-226 (290)
76 PF08792 A2L_zn_ribbon: A2L zi 81.7 0.87 1.9E-05 26.8 1.2 21 73-93 5-30 (33)
77 PF14319 Zn_Tnp_IS91: Transpos 81.6 0.96 2.1E-05 32.7 1.7 25 70-95 42-71 (111)
78 PRK14890 putative Zn-ribbon RN 81.1 0.97 2.1E-05 30.3 1.4 26 73-99 9-39 (59)
79 cd04476 RPA1_DBD_C RPA1_DBD_C: 81.1 2.6 5.6E-05 31.3 3.9 26 68-93 31-60 (166)
80 PRK08271 anaerobic ribonucleos 81.1 0.89 1.9E-05 41.8 1.7 43 42-93 543-589 (623)
81 TIGR02098 MJ0042_CXXC MJ0042 f 81.0 1.1 2.4E-05 26.0 1.5 22 73-94 4-35 (38)
82 PRK06260 threonine synthase; V 80.9 1 2.3E-05 38.1 1.9 25 69-94 2-29 (397)
83 PRK07591 threonine synthase; V 79.9 1.4 3.1E-05 37.8 2.5 27 68-95 16-44 (421)
84 TIGR00375 conserved hypothetic 79.4 1.2 2.6E-05 38.7 1.9 50 44-94 213-268 (374)
85 PRK08579 anaerobic ribonucleos 79.1 1.1 2.4E-05 41.2 1.6 45 40-93 543-591 (625)
86 COG2888 Predicted Zn-ribbon RN 79.1 0.85 1.8E-05 30.8 0.7 26 73-99 11-41 (61)
87 cd00730 rubredoxin Rubredoxin; 79.0 1.3 2.9E-05 28.2 1.5 22 71-93 2-43 (50)
88 PF09845 DUF2072: Zn-ribbon co 78.7 1.2 2.7E-05 33.9 1.5 21 73-93 3-28 (131)
89 PF01096 TFIIS_C: Transcriptio 78.6 2.3 5E-05 25.5 2.4 8 86-93 2-9 (39)
90 PF02591 DUF164: Putative zinc 78.5 1.2 2.6E-05 28.1 1.2 20 73-92 24-54 (56)
91 PF03119 DNA_ligase_ZBD: NAD-d 78.5 1.1 2.5E-05 25.3 1.0 9 86-94 1-9 (28)
92 TIGR03844 cysteate_syn cysteat 77.5 1.5 3.4E-05 37.7 2.0 27 69-96 1-29 (398)
93 CHL00174 accD acetyl-CoA carbo 77.4 1.2 2.7E-05 37.6 1.3 42 69-112 38-88 (296)
94 smart00661 RPOL9 RNA polymeras 77.2 1.1 2.3E-05 27.3 0.6 10 85-94 1-10 (52)
95 PRK05654 acetyl-CoA carboxylas 77.0 1.3 2.9E-05 37.1 1.4 44 68-113 26-78 (292)
96 PF06221 zf-C2HC5: Putative zi 76.9 1.5 3.1E-05 29.0 1.3 32 62-94 10-45 (57)
97 PRK00415 rps27e 30S ribosomal 76.9 2 4.4E-05 28.6 2.0 23 72-94 12-40 (59)
98 TIGR00354 polC DNA polymerase, 76.8 1.5 3.3E-05 42.8 1.9 29 68-97 1010-1041(1095)
99 TIGR00515 accD acetyl-CoA carb 76.5 1.4 3E-05 36.9 1.4 42 69-112 26-76 (285)
100 TIGR00354 polC DNA polymerase, 76.4 2.1 4.5E-05 41.9 2.7 27 65-93 620-646 (1095)
101 PRK06450 threonine synthase; V 76.0 1.7 3.7E-05 36.5 1.8 26 71-97 4-31 (338)
102 PF08271 TF_Zn_Ribbon: TFIIB z 75.9 1.7 3.7E-05 26.1 1.3 21 73-93 2-28 (43)
103 PF01396 zf-C4_Topoisom: Topoi 75.5 1.7 3.7E-05 26.1 1.2 14 85-98 2-15 (39)
104 PF01783 Ribosomal_L32p: Ribos 75.1 1.8 3.8E-05 27.9 1.3 20 73-92 28-47 (56)
105 PF09082 DUF1922: Domain of un 75.0 0.64 1.4E-05 31.9 -0.8 28 70-100 3-35 (68)
106 PF07754 DUF1610: Domain of un 75.0 1.8 3.9E-05 24.1 1.1 19 74-92 1-24 (24)
107 PF00301 Rubredoxin: Rubredoxi 74.5 2.4 5.3E-05 26.7 1.8 23 70-93 1-43 (47)
108 COG3364 Zn-ribbon containing p 73.9 1.7 3.7E-05 32.3 1.1 27 73-100 4-35 (112)
109 PRK04023 DNA polymerase II lar 73.5 2.1 4.5E-05 42.1 1.8 29 68-97 1035-1066(1121)
110 COG1933 Archaeal DNA polymeras 73.0 1.7 3.7E-05 36.4 1.0 27 67-94 164-193 (253)
111 TIGR01031 rpmF_bact ribosomal 72.8 1.9 4.2E-05 27.9 1.1 20 73-92 28-47 (55)
112 COG1096 Predicted RNA-binding 72.7 2.4 5.3E-05 34.0 1.8 30 72-102 150-182 (188)
113 PF05991 NYN_YacP: YacP-like N 72.6 4.3 9.3E-05 30.9 3.1 43 17-59 74-121 (166)
114 PRK14704 anaerobic ribonucleos 72.5 2.1 4.6E-05 39.3 1.6 23 71-93 559-581 (618)
115 PF04606 Ogr_Delta: Ogr/Delta- 72.3 2.3 4.9E-05 26.3 1.3 13 86-98 1-13 (47)
116 PRK12286 rpmF 50S ribosomal pr 72.3 2.3 4.9E-05 27.8 1.3 21 73-93 29-49 (57)
117 COG1458 Predicted DNA-binding 72.3 3.3 7E-05 34.1 2.5 29 31-59 172-200 (221)
118 PRK14714 DNA polymerase II lar 72.3 2.3 4.9E-05 42.6 1.8 29 68-97 1251-1282(1337)
119 COG3091 SprT Zn-dependent meta 71.9 1.8 3.8E-05 34.0 0.9 42 51-94 96-150 (156)
120 PF06677 Auto_anti-p27: Sjogre 71.8 2.5 5.5E-05 26.0 1.4 9 85-93 18-26 (41)
121 PRK05580 primosome assembly pr 71.3 3.2 7E-05 38.0 2.5 24 73-98 410-434 (679)
122 PF07191 zinc-ribbons_6: zinc- 70.5 2.5 5.4E-05 29.1 1.2 25 70-95 17-41 (70)
123 PRK07218 replication factor A; 70.3 2.1 4.5E-05 37.7 1.0 50 42-93 267-318 (423)
124 COG4640 Predicted membrane pro 70.0 2.3 5E-05 38.1 1.2 24 73-96 3-27 (465)
125 TIGR02300 FYDLN_acid conserved 70.0 2.7 5.9E-05 32.0 1.5 22 73-94 11-36 (129)
126 TIGR01562 FdhE formate dehydro 69.6 5.2 0.00011 33.9 3.2 21 73-93 212-233 (305)
127 PRK14873 primosome assembly pr 69.1 3.8 8.1E-05 37.9 2.5 20 73-93 412-431 (665)
128 COG0777 AccD Acetyl-CoA carbox 68.7 2.6 5.6E-05 36.0 1.2 27 67-95 26-58 (294)
129 PF13719 zinc_ribbon_5: zinc-r 68.7 2.2 4.8E-05 25.2 0.6 21 73-93 4-34 (37)
130 COG0267 RpmG Ribosomal protein 68.7 4 8.8E-05 26.4 1.9 29 68-98 5-47 (50)
131 smart00440 ZnF_C2C2 C2C2 Zinc 68.6 6.2 0.00013 23.7 2.6 8 86-93 2-9 (40)
132 PRK14715 DNA polymerase II lar 68.5 3 6.6E-05 42.2 1.8 28 68-97 1540-1570(1627)
133 PRK09263 anaerobic ribonucleos 68.3 4.5 9.7E-05 37.7 2.8 58 43-110 620-684 (711)
134 PF06906 DUF1272: Protein of u 68.1 1.7 3.7E-05 29.0 0.0 30 67-97 23-54 (57)
135 PRK03564 formate dehydrogenase 68.0 5.8 0.00013 33.8 3.2 21 73-93 214-235 (309)
136 PF09889 DUF2116: Uncharacteri 68.0 1.3 2.9E-05 29.3 -0.5 21 73-93 5-27 (59)
137 PF03833 PolC_DP2: DNA polymer 67.8 1.7 3.7E-05 41.8 0.0 20 73-93 657-676 (900)
138 TIGR01405 polC_Gram_pos DNA po 67.7 2.8 6.1E-05 41.4 1.4 22 71-93 684-717 (1213)
139 COG2176 PolC DNA polymerase II 67.5 3.3 7.1E-05 41.6 1.8 22 71-93 915-948 (1444)
140 PRK00448 polC DNA polymerase I 67.3 2.9 6.2E-05 42.1 1.4 22 71-93 909-942 (1437)
141 PF04828 GFA: Glutathione-depe 66.7 1.6 3.5E-05 28.3 -0.3 14 81-94 45-58 (92)
142 PRK05978 hypothetical protein; 66.5 2.8 6.1E-05 32.3 1.0 28 68-96 31-64 (148)
143 PRK11788 tetratricopeptide rep 66.2 3.4 7.3E-05 33.0 1.4 27 73-99 356-383 (389)
144 COG2051 RPS27A Ribosomal prote 66.1 4.2 9.1E-05 27.9 1.6 26 68-93 16-47 (67)
145 PLN02569 threonine synthase 65.8 6.1 0.00013 35.1 3.0 54 35-94 18-74 (484)
146 PTZ00083 40S ribosomal protein 65.3 6.8 0.00015 28.0 2.6 42 69-110 33-83 (85)
147 PF09332 Mcm10: Mcm10 replicat 65.1 6.3 0.00014 34.1 2.9 38 62-102 278-320 (344)
148 PF14206 Cys_rich_CPCC: Cystei 65.1 3.5 7.6E-05 28.7 1.1 20 73-92 3-28 (78)
149 PRK04860 hypothetical protein; 64.6 8.8 0.00019 29.6 3.4 55 41-97 87-156 (160)
150 cd01121 Sms Sms (bacterial rad 64.5 4.4 9.6E-05 34.7 1.8 26 73-98 2-28 (372)
151 PRK09521 exosome complex RNA-b 64.2 4.3 9.3E-05 31.2 1.6 27 73-100 151-181 (189)
152 PF12677 DUF3797: Domain of un 64.0 3.5 7.7E-05 26.7 0.9 10 84-93 13-22 (49)
153 COG4031 Predicted metal-bindin 63.9 3.6 7.9E-05 33.7 1.2 19 73-93 2-21 (227)
154 PRK11823 DNA repair protein Ra 63.8 4.9 0.00011 35.0 2.1 30 68-98 5-35 (446)
155 smart00547 ZnF_RBZ Zinc finger 63.6 4.1 9E-05 21.7 1.0 21 73-93 4-25 (26)
156 PF08646 Rep_fac-A_C: Replicat 63.4 7.9 0.00017 28.2 2.8 35 68-102 15-57 (146)
157 PF10601 zf-LITAF-like: LITAF- 63.3 2.9 6.3E-05 27.5 0.4 26 82-108 5-30 (73)
158 PF08274 PhnA_Zn_Ribbon: PhnA 63.3 3.1 6.6E-05 24.2 0.5 21 73-93 4-28 (30)
159 PF10367 Vps39_2: Vacuolar sor 63.2 5.6 0.00012 26.7 1.8 11 84-94 78-88 (109)
160 PRK15103 paraquat-inducible me 62.8 4.3 9.2E-05 35.5 1.5 24 70-94 221-245 (419)
161 COG4469 CoiA Competence protei 62.6 3.5 7.6E-05 35.9 0.9 14 84-97 25-38 (342)
162 TIGR00155 pqiA_fam integral me 62.5 4.3 9.3E-05 35.2 1.4 23 73-95 217-241 (403)
163 smart00531 TFIIE Transcription 61.8 3.9 8.5E-05 30.4 1.0 26 68-94 97-133 (147)
164 PRK04023 DNA polymerase II lar 61.8 4.3 9.4E-05 40.0 1.5 20 73-93 628-647 (1121)
165 PF06676 DUF1178: Protein of u 61.4 9 0.0002 29.5 2.9 33 67-102 2-49 (148)
166 PRK06266 transcription initiat 61.3 5.3 0.00012 31.0 1.6 57 36-94 83-146 (178)
167 COG3791 Uncharacterized conser 61.0 4.9 0.00011 29.5 1.3 17 81-97 66-82 (133)
168 smart00714 LITAF Possible memb 60.7 2.7 5.8E-05 27.3 -0.1 22 84-106 3-24 (67)
169 PF13453 zf-TFIIB: Transcripti 60.6 3.9 8.5E-05 24.3 0.6 8 85-92 20-27 (41)
170 PHA02942 putative transposase; 60.1 12 0.00027 32.1 3.8 40 47-93 308-351 (383)
171 KOG3084 NADH pyrophosphatase I 59.7 4.5 9.8E-05 35.2 1.1 7 74-80 153-159 (345)
172 PF14949 ARF7EP_C: ARF7 effect 59.7 5 0.00011 29.3 1.1 15 73-93 69-83 (103)
173 COG1328 NrdD Oxygen-sensitive 59.4 6.8 0.00015 36.9 2.2 62 39-113 615-680 (700)
174 COG1885 Uncharacterized protei 58.7 7.7 0.00017 29.0 2.0 22 80-103 45-66 (115)
175 COG0846 SIR2 NAD-dependent pro 58.5 5.7 0.00012 32.7 1.4 60 35-104 94-165 (250)
176 PF08394 Arc_trans_TRASH: Arch 58.1 10 0.00022 23.1 2.1 23 87-109 1-23 (37)
177 TIGR00308 TRM1 tRNA(guanine-26 57.9 8.5 0.00019 33.1 2.5 26 68-94 231-262 (374)
178 COG2995 PqiA Uncharacterized p 57.8 4.6 0.0001 36.0 0.8 29 68-98 219-249 (418)
179 PF13408 Zn_ribbon_recom: Reco 57.7 6.4 0.00014 23.9 1.3 15 83-97 4-18 (58)
180 PF01667 Ribosomal_S27e: Ribos 57.7 6 0.00013 26.0 1.2 21 73-93 9-35 (55)
181 COG1110 Reverse gyrase [DNA re 57.6 4.6 9.9E-05 40.0 0.8 30 63-93 687-717 (1187)
182 PF01780 Ribosomal_L37ae: Ribo 57.3 7.5 0.00016 27.9 1.7 20 83-103 34-53 (90)
183 TIGR00416 sms DNA repair prote 57.2 6.6 0.00014 34.4 1.7 29 69-98 6-35 (454)
184 PRK04136 rpl40e 50S ribosomal 56.8 6.3 0.00014 25.5 1.1 24 73-97 16-40 (48)
185 PHA00626 hypothetical protein 56.7 8.1 0.00018 25.9 1.7 8 86-93 2-9 (59)
186 PRK15103 paraquat-inducible me 56.6 5.6 0.00012 34.8 1.1 24 73-96 12-42 (419)
187 PRK00241 nudC NADH pyrophospha 56.5 5.4 0.00012 32.4 1.0 21 73-93 101-126 (256)
188 COG1997 RPL43A Ribosomal prote 56.4 8.1 0.00018 27.8 1.7 17 84-101 35-51 (89)
189 PRK05452 anaerobic nitric oxid 56.3 7.2 0.00016 34.3 1.8 23 70-93 425-467 (479)
190 PRK04338 N(2),N(2)-dimethylgua 56.1 9.4 0.0002 32.8 2.4 26 68-94 242-271 (382)
191 TIGR00686 phnA alkylphosphonat 55.4 6.6 0.00014 29.2 1.2 22 73-94 4-29 (109)
192 PRK08197 threonine synthase; V 55.2 9.2 0.0002 32.4 2.2 24 70-95 7-33 (394)
193 PRK12775 putative trifunctiona 54.9 5.9 0.00013 38.0 1.1 23 70-93 821-847 (1006)
194 PF14690 zf-ISL3: zinc-finger 54.7 6.2 0.00013 23.4 0.8 10 85-94 3-12 (47)
195 COG0384 Predicted epimerase, P 54.5 9.4 0.0002 32.1 2.1 49 40-97 32-80 (291)
196 PF09862 DUF2089: Protein of u 54.3 5.2 0.00011 29.6 0.5 20 74-93 1-21 (113)
197 PRK12366 replication factor A; 54.1 16 0.00035 33.5 3.7 26 67-93 529-557 (637)
198 PF13717 zinc_ribbon_4: zinc-r 53.6 10 0.00022 22.4 1.6 21 73-93 4-34 (36)
199 COG1645 Uncharacterized Zn-fin 53.5 7.9 0.00017 29.5 1.4 26 82-121 26-51 (131)
200 PRK00504 rpmG 50S ribosomal pr 52.8 7.9 0.00017 24.8 1.1 29 68-98 5-47 (50)
201 PLN00209 ribosomal protein S27 52.8 11 0.00023 27.0 1.9 25 69-93 34-64 (86)
202 PF00641 zf-RanBP: Zn-finger i 52.3 8.2 0.00018 21.4 1.0 21 73-93 6-27 (30)
203 TIGR01384 TFS_arch transcripti 52.0 8.5 0.00018 26.6 1.3 23 73-95 2-27 (104)
204 cd01410 SIRT7 SIRT7: Eukaryoti 52.0 5 0.00011 31.4 0.1 35 69-106 94-140 (206)
205 TIGR00373 conserved hypothetic 51.4 7.6 0.00016 29.5 1.0 24 70-94 109-138 (158)
206 COG3478 Predicted nucleic-acid 50.9 8.1 0.00017 26.6 1.0 16 87-102 7-23 (68)
207 COG5270 PUA domain (predicted 50.3 12 0.00027 30.4 2.1 30 67-98 11-40 (202)
208 COG0333 RpmF Ribosomal protein 50.0 13 0.00028 24.6 1.8 21 73-93 29-49 (57)
209 PF12760 Zn_Tnp_IS1595: Transp 49.7 12 0.00026 22.7 1.6 10 84-93 18-27 (46)
210 PRK14715 DNA polymerase II lar 49.6 14 0.0003 37.8 2.7 31 65-97 669-699 (1627)
211 TIGR03831 YgiT_finger YgiT-typ 49.5 26 0.00055 20.2 2.9 13 81-93 29-41 (46)
212 PRK13764 ATPase; Provisional 49.5 15 0.00033 33.8 2.8 30 32-61 101-130 (602)
213 PF07975 C1_4: TFIIH C1-like d 49.4 7.3 0.00016 25.1 0.6 11 69-80 20-30 (51)
214 PRK00464 nrdR transcriptional 48.4 17 0.00037 28.0 2.6 27 85-113 29-56 (154)
215 PRK05638 threonine synthase; V 48.4 12 0.00026 32.3 1.8 26 70-97 1-28 (442)
216 PF11781 RRN7: RNA polymerase 48.1 9.4 0.0002 22.7 0.9 21 73-93 10-34 (36)
217 PF01907 Ribosomal_L37e: Ribos 48.1 9.8 0.00021 25.2 1.0 29 68-98 14-44 (55)
218 PF00471 Ribosomal_L33: Riboso 48.0 10 0.00022 24.0 1.0 14 84-98 32-45 (48)
219 PRK10220 hypothetical protein; 47.7 11 0.00024 28.1 1.3 22 73-94 5-30 (111)
220 TIGR02820 formald_GSH S-(hydro 47.7 8.1 0.00017 30.6 0.7 14 81-94 86-99 (182)
221 COG1594 RPB9 DNA-directed RNA 47.3 8 0.00017 28.2 0.6 11 84-94 2-12 (113)
222 KOG2906 RNA polymerase III sub 47.2 8.9 0.00019 28.3 0.8 12 85-96 2-13 (105)
223 COG1412 Uncharacterized protei 46.8 23 0.0005 26.9 3.0 30 34-63 99-128 (136)
224 PRK06386 replication factor A; 46.4 12 0.00027 32.4 1.7 23 68-93 234-257 (358)
225 COG1867 TRM1 N2,N2-dimethylgua 46.3 12 0.00025 33.1 1.5 25 68-93 238-266 (380)
226 PRK00432 30S ribosomal protein 45.9 14 0.0003 23.4 1.4 21 73-93 22-46 (50)
227 PTZ00157 60S ribosomal protein 45.8 14 0.0003 26.3 1.5 17 84-101 9-25 (84)
228 TIGR00155 pqiA_fam integral me 45.7 11 0.00025 32.6 1.4 22 73-94 15-43 (403)
229 KOG1779 40s ribosomal protein 45.7 13 0.00027 26.6 1.3 25 69-93 32-62 (84)
230 PRK00595 rpmG 50S ribosomal pr 45.6 12 0.00026 24.0 1.2 29 68-98 8-50 (53)
231 TIGR02387 rpoC1_cyan DNA-direc 45.2 7.6 0.00017 36.2 0.2 30 66-99 59-91 (619)
232 PF14354 Lar_restr_allev: Rest 44.6 19 0.0004 22.5 1.9 8 86-93 5-12 (61)
233 PRK08402 replication factor A; 44.5 33 0.00072 29.6 3.9 32 69-101 211-249 (355)
234 PF09567 RE_MamI: MamI restric 44.3 9.6 0.00021 32.6 0.7 27 72-99 83-110 (314)
235 PF09151 DUF1936: Domain of un 44.3 19 0.00041 21.7 1.7 14 85-99 2-15 (36)
236 cd00296 SIR2 SIR2 superfamily 44.2 35 0.00076 26.0 3.7 51 35-94 83-144 (222)
237 PRK08329 threonine synthase; V 44.1 15 0.00032 30.7 1.8 25 71-97 2-28 (347)
238 COG2405 Predicted nucleic acid 44.1 18 0.00038 28.5 2.0 29 32-60 85-114 (157)
239 PRK01110 rpmF 50S ribosomal pr 44.0 12 0.00026 24.6 1.0 19 73-92 29-47 (60)
240 TIGR00280 L37a ribosomal prote 43.9 26 0.00057 25.2 2.7 20 83-103 34-53 (91)
241 PF03833 PolC_DP2: DNA polymer 43.8 7.7 0.00017 37.6 0.0 27 66-93 663-689 (900)
242 PF10058 DUF2296: Predicted in 43.6 14 0.00031 23.7 1.3 26 67-93 19-53 (54)
243 TIGR01023 rpmG_bact ribosomal 43.5 14 0.0003 23.9 1.2 29 68-98 9-51 (54)
244 PF04423 Rad50_zn_hook: Rad50 43.4 7.2 0.00016 24.3 -0.2 10 85-94 21-30 (54)
245 PRK05767 rpl44e 50S ribosomal 43.3 16 0.00034 26.4 1.5 17 84-101 8-24 (92)
246 PF11672 DUF3268: Protein of u 43.2 14 0.00031 26.9 1.3 29 85-118 3-31 (102)
247 PF03854 zf-P11: P-11 zinc fin 43.2 4 8.7E-05 26.6 -1.4 22 73-94 23-45 (50)
248 PF11648 RIG-I_C-RD: C-termina 43.2 20 0.00044 26.2 2.1 27 82-119 58-85 (123)
249 PRK05417 glutathione-dependent 43.1 10 0.00023 30.1 0.7 17 82-99 91-107 (191)
250 PTZ00255 60S ribosomal protein 43.0 26 0.00057 25.1 2.6 20 83-103 35-54 (90)
251 PRK02625 rpoC1 DNA-directed RN 43.0 9.7 0.00021 35.5 0.5 30 66-99 66-98 (627)
252 cd01408 SIRT1 SIRT1: Eukaryoti 42.6 18 0.00039 28.9 1.9 43 55-106 107-160 (235)
253 PF09855 DUF2082: Nucleic-acid 42.6 11 0.00024 25.2 0.6 8 86-93 2-9 (64)
254 PF02005 TRM: N2,N2-dimethylgu 42.1 18 0.00039 31.2 2.0 27 67-94 237-269 (377)
255 PF02146 SIR2: Sir2 family; I 42.1 25 0.00054 26.3 2.5 35 68-105 103-148 (178)
256 PF15616 TerY-C: TerY-C metal 41.6 16 0.00035 27.7 1.4 22 73-95 91-116 (131)
257 PRK03976 rpl37ae 50S ribosomal 41.2 31 0.00068 24.7 2.8 20 83-103 35-54 (90)
258 PF14255 Cys_rich_CPXG: Cystei 40.9 22 0.00048 22.9 1.8 23 86-109 2-24 (52)
259 COG5134 Uncharacterized conser 40.9 20 0.00044 30.1 2.0 52 58-113 30-105 (272)
260 KOG2932 E3 ubiquitin ligase in 40.7 19 0.0004 31.7 1.9 70 36-123 42-114 (389)
261 KOG2691 RNA polymerase II subu 40.6 25 0.00054 26.3 2.3 20 83-113 72-91 (113)
262 COG2995 PqiA Uncharacterized p 40.5 16 0.00035 32.6 1.5 27 68-95 16-49 (418)
263 TIGR00201 comF comF family pro 40.2 15 0.00032 28.0 1.1 21 74-94 1-22 (190)
264 PRK04179 rpl37e 50S ribosomal 39.7 16 0.00034 24.7 1.0 21 73-93 19-42 (62)
265 PF14447 Prok-RING_4: Prokaryo 39.4 18 0.00038 23.9 1.2 20 73-94 29-49 (55)
266 COG1066 Sms Predicted ATP-depe 39.3 18 0.0004 32.6 1.7 28 69-97 6-34 (456)
267 CHL00018 rpoC1 RNA polymerase 39.0 10 0.00023 35.5 0.1 31 66-100 64-100 (663)
268 COG2956 Predicted N-acetylgluc 38.4 7.9 0.00017 34.2 -0.7 39 59-100 345-384 (389)
269 COG0675 Transposase and inacti 38.2 17 0.00036 28.2 1.1 21 73-93 311-331 (364)
270 PRK09678 DNA-binding transcrip 38.1 21 0.00046 24.4 1.5 13 85-97 2-14 (72)
271 PF02639 DUF188: Uncharacteriz 37.9 43 0.00093 24.9 3.2 29 36-64 54-82 (130)
272 PF06054 CoiA: Competence prot 37.3 18 0.00038 31.0 1.2 16 82-97 28-43 (375)
273 COG1552 RPL40A Ribosomal prote 37.2 6.6 0.00014 25.6 -1.0 24 73-97 16-40 (50)
274 COG1998 RPS31 Ribosomal protei 37.2 33 0.00072 22.4 2.2 36 54-93 6-46 (51)
275 PF01599 Ribosomal_S27: Riboso 37.1 14 0.00031 23.5 0.5 20 73-92 20-46 (47)
276 CHL00104 rpl33 ribosomal prote 37.1 19 0.00041 24.4 1.1 14 84-98 49-62 (66)
277 PRK14892 putative transcriptio 36.7 20 0.00044 25.8 1.3 21 73-93 23-51 (99)
278 TIGR02642 phage_xxxx uncharact 36.4 81 0.0017 25.1 4.7 27 70-97 99-128 (186)
279 smart00653 eIF2B_5 domain pres 36.1 21 0.00045 26.0 1.3 25 66-92 77-109 (110)
280 PRK03988 translation initiatio 36.0 21 0.00047 26.9 1.4 27 66-94 99-133 (138)
281 TIGR00311 aIF-2beta translatio 35.8 23 0.00049 26.7 1.5 27 66-94 94-128 (133)
282 PRK00566 DNA-directed RNA poly 35.7 18 0.0004 35.9 1.2 31 66-100 55-88 (1156)
283 PRK00241 nudC NADH pyrophospha 35.6 35 0.00076 27.7 2.6 12 83-94 98-109 (256)
284 COG3813 Uncharacterized protei 35.3 9.9 0.00022 26.9 -0.5 25 73-98 31-55 (84)
285 PRK07217 replication factor A; 35.3 22 0.00048 30.5 1.5 24 68-93 186-211 (311)
286 PRK00481 NAD-dependent deacety 35.2 34 0.00074 27.1 2.5 24 70-94 122-152 (242)
287 PF12387 Peptidase_C74: Pestiv 35.1 17 0.00036 29.5 0.7 23 73-95 164-186 (200)
288 KOG0823 Predicted E3 ubiquitin 35.1 14 0.00031 30.5 0.3 28 73-100 69-100 (230)
289 cd01407 SIR2-fam SIR2 family o 35.0 32 0.00069 26.8 2.2 39 48-93 92-142 (218)
290 TIGR03826 YvyF flagellar opero 34.6 12 0.00025 28.5 -0.3 20 73-92 5-26 (137)
291 cd01411 SIR2H SIR2H: Uncharact 34.5 28 0.0006 27.5 1.8 23 70-93 118-145 (225)
292 COG3058 FdhE Uncharacterized p 34.4 19 0.0004 31.0 0.9 12 82-93 183-194 (308)
293 COG2816 NPY1 NTP pyrophosphohy 34.0 22 0.00047 30.2 1.2 21 73-93 113-138 (279)
294 PF01927 Mut7-C: Mut7-C RNAse 33.5 22 0.00047 26.3 1.1 8 73-80 93-100 (147)
295 TIGR02159 PA_CoA_Oxy4 phenylac 33.1 18 0.00039 27.4 0.6 10 85-94 106-115 (146)
296 COG2126 RPL37A Ribosomal prote 33.1 21 0.00045 24.1 0.8 21 73-93 18-40 (61)
297 PF09986 DUF2225: Uncharacteri 33.1 26 0.00057 27.7 1.5 28 84-113 5-32 (214)
298 cd03361 TOPRIM_TopoIA_RevGyr T 32.9 36 0.00078 25.9 2.2 25 68-93 75-100 (170)
299 TIGR01206 lysW lysine biosynth 32.4 18 0.00039 23.5 0.4 13 86-98 4-16 (54)
300 PRK14138 NAD-dependent deacety 32.4 32 0.0007 27.6 1.9 33 70-105 119-162 (244)
301 KOG2907 RNA polymerase I trans 32.4 19 0.00042 27.0 0.6 10 84-93 74-83 (116)
302 PRK08764 ferredoxin; Provision 32.0 55 0.0012 23.9 2.9 41 39-79 48-92 (135)
303 PRK14289 chaperone protein Dna 31.8 69 0.0015 27.3 3.9 26 70-96 197-223 (386)
304 PF14353 CpXC: CpXC protein 31.6 21 0.00046 25.5 0.7 11 84-94 38-48 (128)
305 PTZ00073 60S ribosomal protein 31.5 22 0.00048 25.7 0.8 26 67-94 14-41 (91)
306 PTZ00408 NAD-dependent deacety 31.1 26 0.00056 28.3 1.2 36 69-105 116-158 (242)
307 TIGR00595 priA primosomal prot 31.0 27 0.00058 31.0 1.3 21 73-97 215-235 (505)
308 PF08996 zf-DNA_Pol: DNA Polym 30.9 27 0.00058 27.0 1.2 34 59-93 7-54 (188)
309 PRK07418 acetolactate synthase 30.8 25 0.00054 31.4 1.1 21 73-93 594-615 (616)
310 cd03472 Rieske_RO_Alpha_BPDO_l 30.7 74 0.0016 23.0 3.4 93 23-116 22-126 (128)
311 COG1631 RPL42A Ribosomal prote 30.7 32 0.00069 25.0 1.5 16 84-100 8-23 (94)
312 PRK14873 primosome assembly pr 30.7 27 0.00059 32.4 1.4 26 68-98 381-406 (665)
313 COG1040 ComFC Predicted amidop 30.6 12 0.00026 29.9 -0.8 22 73-94 26-48 (225)
314 PRK12495 hypothetical protein; 30.3 27 0.00059 28.9 1.2 21 73-93 44-67 (226)
315 cd01413 SIR2_Af2 SIR2_Af2: Arc 30.1 21 0.00046 28.0 0.5 24 69-93 112-145 (222)
316 smart00290 ZnF_UBP Ubiquitin C 29.9 31 0.00066 20.6 1.1 19 73-92 1-19 (50)
317 PF13005 zf-IS66: zinc-finger 29.8 49 0.0011 19.6 2.0 18 60-78 30-47 (47)
318 PHA02325 hypothetical protein 29.7 25 0.00053 24.4 0.7 11 83-93 2-12 (72)
319 TIGR00627 tfb4 transcription f 29.3 37 0.0008 28.4 1.8 25 67-93 252-278 (279)
320 PRK14906 DNA-directed RNA poly 29.2 20 0.00043 36.6 0.3 30 66-99 57-89 (1460)
321 COG2401 ABC-type ATPase fused 29.0 39 0.00085 31.2 2.0 71 36-116 104-194 (593)
322 TIGR00575 dnlj DNA ligase, NAD 28.6 96 0.0021 28.8 4.5 47 46-94 349-402 (652)
323 KOG3799 Rab3 effector RIM1 and 28.4 30 0.00066 27.2 1.1 14 84-97 89-102 (169)
324 PRK14810 formamidopyrimidine-D 28.3 31 0.00067 28.2 1.2 11 84-94 244-254 (272)
325 PTZ00410 NAD-dependent SIR2; P 27.9 63 0.0014 28.0 3.1 35 69-106 146-191 (349)
326 PF13824 zf-Mss51: Zinc-finger 27.7 42 0.00091 22.1 1.5 20 74-93 2-23 (55)
327 COG3529 Predicted nucleic-acid 27.6 17 0.00038 24.8 -0.3 21 73-93 12-41 (66)
328 PF07131 DUF1382: Protein of u 27.5 49 0.0011 22.3 1.8 17 43-59 14-30 (61)
329 PF14569 zf-UDP: Zinc-binding 27.4 11 0.00025 26.6 -1.3 21 73-93 38-60 (80)
330 PRK12267 methionyl-tRNA synthe 27.3 94 0.002 28.2 4.1 57 43-111 104-165 (648)
331 PRK03922 hypothetical protein; 27.2 47 0.001 24.9 1.9 14 80-93 45-58 (113)
332 KOG3022 Predicted ATPase, nucl 27.2 80 0.0017 27.2 3.5 45 35-94 185-232 (300)
333 COG1327 Predicted transcriptio 27.1 56 0.0012 25.7 2.4 39 73-113 2-56 (156)
334 TIGR00622 ssl1 transcription f 27.1 38 0.00083 25.1 1.4 20 73-93 3-24 (112)
335 PRK12336 translation initiatio 26.9 37 0.0008 26.8 1.4 21 58-79 107-127 (201)
336 smart00778 Prim_Zn_Ribbon Zinc 26.9 29 0.00063 20.9 0.6 10 85-94 4-13 (37)
337 COG1379 PHP family phosphoeste 26.6 14 0.0003 32.7 -1.2 34 65-99 240-279 (403)
338 PF11682 DUF3279: Protein of u 26.6 44 0.00094 25.3 1.6 31 61-94 90-120 (128)
339 PF06827 zf-FPG_IleRS: Zinc fi 26.2 47 0.001 18.2 1.4 10 85-94 2-11 (30)
340 cd01409 SIRT4 SIRT4: Eukaryoti 26.2 35 0.00075 27.7 1.1 20 86-107 171-190 (260)
341 PF00609 DAGK_acc: Diacylglyce 26.2 56 0.0012 24.3 2.2 9 106-114 152-160 (161)
342 PF04475 DUF555: Protein of un 26.1 50 0.0011 24.3 1.8 14 80-93 43-56 (102)
343 TIGR03655 anti_R_Lar restricti 25.9 45 0.00097 20.7 1.4 11 85-95 2-12 (53)
344 PF06044 DRP: Dam-replacing fa 25.6 32 0.00069 29.0 0.8 15 84-99 31-45 (254)
345 PRK10445 endonuclease VIII; Pr 25.6 41 0.00089 27.3 1.5 11 84-94 235-245 (263)
346 PF10122 Mu-like_Com: Mu-like 25.6 30 0.00065 22.6 0.5 25 73-97 6-37 (51)
347 cd07973 Spt4 Transcription elo 25.5 36 0.00079 24.5 1.0 19 73-91 5-27 (98)
348 PF10083 DUF2321: Uncharacteri 25.5 7 0.00015 30.7 -2.9 34 59-94 12-49 (158)
349 TIGR03676 aRF1/eRF1 peptide ch 25.5 48 0.0011 28.9 1.9 27 67-94 317-352 (403)
350 PF10013 DUF2256: Uncharacteri 25.4 23 0.0005 22.2 -0.0 15 81-95 5-19 (42)
351 COG4888 Uncharacterized Zn rib 25.1 69 0.0015 23.7 2.4 13 84-97 22-34 (104)
352 TIGR00244 transcriptional regu 25.1 73 0.0016 24.7 2.7 39 73-113 2-56 (147)
353 PRK14289 chaperone protein Dna 25.1 1.2E+02 0.0026 25.9 4.2 31 64-94 147-181 (386)
354 KOG0856 Predicted pilin-like t 24.9 53 0.0011 25.6 1.8 45 47-93 32-78 (146)
355 cd01412 SIRT5_Af1_CobB SIRT5_A 24.8 62 0.0014 25.1 2.3 24 69-93 108-139 (224)
356 PRK13795 hypothetical protein; 24.7 79 0.0017 29.0 3.2 32 66-101 8-39 (636)
357 KOG3475 60S ribosomal protein 24.3 25 0.00054 25.4 -0.0 32 64-97 11-44 (92)
358 PRK04011 peptide chain release 24.3 53 0.0012 28.6 2.0 26 68-94 326-360 (411)
359 PF08273 Prim_Zn_Ribbon: Zinc- 24.2 40 0.00086 20.6 0.9 10 85-94 4-13 (40)
360 cd00817 ValRS_core catalytic c 24.2 1.9E+02 0.0042 24.5 5.3 45 62-112 132-176 (382)
361 TIGR00577 fpg formamidopyrimid 24.2 46 0.001 27.1 1.5 12 84-95 245-256 (272)
362 PF05876 Terminase_GpA: Phage 24.1 54 0.0012 29.6 2.1 29 66-95 196-240 (557)
363 COG1571 Predicted DNA-binding 24.1 41 0.00088 30.1 1.2 32 62-93 339-376 (421)
364 PF01485 IBR: IBR domain; Int 24.0 43 0.00093 20.2 1.0 21 73-93 20-49 (64)
365 PTZ00409 Sir2 (Silent Informat 24.0 36 0.00079 28.0 0.9 33 69-105 136-183 (271)
366 PRK14811 formamidopyrimidine-D 23.9 42 0.00091 27.4 1.2 12 84-95 235-246 (269)
367 PF13913 zf-C2HC_2: zinc-finge 23.8 39 0.00085 18.3 0.7 10 84-93 2-11 (25)
368 PF03850 Tfb4: Transcription f 23.6 40 0.00088 28.0 1.1 25 66-91 249-276 (276)
369 PF09334 tRNA-synt_1g: tRNA sy 23.4 45 0.00098 28.6 1.4 31 43-80 99-129 (391)
370 PRK01103 formamidopyrimidine/5 23.3 44 0.00095 27.2 1.2 11 84-94 245-255 (274)
371 PRK05333 NAD-dependent deacety 23.2 76 0.0017 25.9 2.6 8 86-93 181-188 (285)
372 PF04161 Arv1: Arv1-like famil 23.0 33 0.00072 26.9 0.4 21 73-93 2-33 (208)
373 PRK00124 hypothetical protein; 23.0 1.2E+02 0.0026 23.4 3.5 40 23-63 58-97 (151)
374 PF01020 Ribosomal_L40e: Ribos 23.0 79 0.0017 20.7 2.1 25 73-97 19-46 (52)
375 PF14471 DUF4428: Domain of un 23.0 35 0.00076 21.6 0.5 11 86-96 1-11 (51)
376 COG3357 Predicted transcriptio 22.9 40 0.00087 24.6 0.8 21 73-93 60-85 (97)
377 smart00532 LIGANc Ligase N fam 22.7 47 0.001 29.4 1.3 47 45-94 355-409 (441)
378 COG1138 CcmF Cytochrome c biog 22.7 40 0.00086 31.8 0.9 18 35-52 59-76 (648)
379 PF05495 zf-CHY: CHY zinc fing 22.6 40 0.00088 22.3 0.7 22 70-92 41-69 (71)
380 TIGR00269 conserved hypothetic 22.6 39 0.00084 23.7 0.7 17 73-90 82-98 (104)
381 PRK14276 chaperone protein Dna 22.5 1.2E+02 0.0027 25.8 3.8 35 73-108 148-186 (380)
382 PF02132 RecR: RecR protein; 22.5 5.6 0.00012 23.9 -3.1 28 64-93 11-38 (41)
383 PRK07225 DNA-directed RNA poly 22.4 56 0.0012 30.2 1.8 28 73-100 546-578 (605)
384 PF00628 PHD: PHD-finger; Int 22.4 63 0.0014 19.1 1.5 20 73-92 1-22 (51)
385 PRK13945 formamidopyrimidine-D 22.3 48 0.001 27.2 1.3 11 84-94 254-264 (282)
386 PF00645 zf-PARP: Poly(ADP-rib 22.2 45 0.00098 21.9 0.9 39 83-123 6-45 (82)
387 PF02348 CTP_transf_3: Cytidyl 22.0 1.3E+02 0.0027 22.3 3.4 28 33-60 41-68 (217)
388 PF12674 Zn_ribbon_2: Putative 21.8 42 0.00091 23.1 0.7 11 85-95 1-11 (81)
389 PF11062 DUF2863: Protein of u 21.8 40 0.00087 30.0 0.8 20 82-114 362-381 (398)
390 PF13920 zf-C3HC4_3: Zinc fing 21.4 18 0.0004 21.8 -1.0 22 73-94 25-47 (50)
391 PF14599 zinc_ribbon_6: Zinc-r 21.1 1.1E+02 0.0023 20.3 2.5 31 64-96 25-60 (61)
392 KOG3507 DNA-directed RNA polym 20.9 32 0.00069 23.3 -0.0 29 65-94 15-47 (62)
393 KOG4718 Non-SMC (structural ma 20.7 48 0.001 27.6 1.0 28 64-92 188-224 (235)
394 PF04502 DUF572: Family of unk 20.7 54 0.0012 27.6 1.3 17 63-80 33-49 (324)
395 PF09526 DUF2387: Probable met 20.7 53 0.0012 22.3 1.0 21 73-93 10-39 (71)
396 PRK00076 recR recombination pr 20.7 41 0.00089 26.9 0.5 38 63-102 46-83 (196)
397 TIGR02386 rpoC_TIGR DNA-direct 20.6 50 0.0011 33.0 1.2 31 65-99 46-79 (1140)
398 COG1671 Uncharacterized protei 20.4 1.4E+02 0.0029 23.3 3.3 42 20-62 54-95 (150)
399 PRK00423 tfb transcription ini 20.2 53 0.0012 27.2 1.1 21 73-93 13-39 (310)
400 PRK14290 chaperone protein Dna 20.1 1.5E+02 0.0033 25.0 3.9 24 73-96 193-217 (365)
No 1
>KOG2463 consensus Predicted RNA-binding protein Nob1p involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3.4e-34 Score=241.61 Aligned_cols=86 Identities=36% Similarity=0.665 Sum_probs=77.7
Q ss_pred CCCCCCceeccCC--------------CCceeEEecccHHHHHHHHHhCceeeCCCCCcceeeeEEeeccccCCccc--c
Q 033276 18 DECSEQSWMLRSL--------------SESTVACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSS--P 81 (123)
Q Consensus 18 ~~~~~~~WIt~~~--------------~~~~va~vTdDyAmQNVllqlGL~l~sv~g~~I~~v~~wvl~rC~gC~k~--~ 81 (123)
||.++++||||+| ....|||+|+||||||||+||||+++++.|++|+++|+|++ ||+|||++ +
T Consensus 176 ed~DdDgwitp~ni~~~~~e~~al~~pe~~~Vac~TtDfamQNVlLqm~L~l~~~~G~~Ir~~r~~iL-RCh~Cfsit~~ 254 (376)
T KOG2463|consen 176 EDADDDGWITPSNITEAIIELGALNRPENQLVACLTTDFAMQNVLLQMNLNLLAMSGMKIRSVRSYIL-RCHGCFSITSE 254 (376)
T ss_pred cccccccccccchHHHHHHhhhcccccccceeeeecccHHHHHHHHHhcccccCccchhhhhhhhhee-EeeeeeEecCc
Confidence 4444444999995 36679999999999999999999999999999999999999 99999998 7
Q ss_pred cCccccccCCCCCeeeEEEEEeeE
Q 033276 82 FPLVICIKSNHEIRISPVFMLILI 105 (123)
Q Consensus 82 ~~~~fCp~CG~~~tl~rV~~~~~~ 105 (123)
+++.|||+||++ ||+||+|+++.
T Consensus 255 m~k~FCp~CG~~-TL~K~aVsv~~ 277 (376)
T KOG2463|consen 255 MPKDFCPSCGHK-TLTKCAVSVDE 277 (376)
T ss_pred cchhcccccCCC-eeeEEEEEecC
Confidence 899999999999 99999998864
No 2
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=99.89 E-value=3.6e-24 Score=167.33 Aligned_cols=78 Identities=23% Similarity=0.310 Sum_probs=65.0
Q ss_pred CCCCceeccCC-----------CCceeEEecccHHHHHHHHHhCceeeCCC-CCcceeeeEEeeccccCCccc-ccCccc
Q 033276 20 CSEQSWMLRSL-----------SESTVACITGDYAMQNVILQMGLRLLAPG-GMQIRQLHRYIVDKCLKLFSS-PFPLVI 86 (123)
Q Consensus 20 ~~~~~WIt~~~-----------~~~~va~vTdDyAmQNVllqlGL~l~sv~-g~~I~~v~~wvl~rC~gC~k~-~~~~~f 86 (123)
.++-.|++++. .+.+|+++||||||||||+||||+|+++. +.+|+++++|++ ||+||+++ +++.+|
T Consensus 77 tgd~~~LS~tDi~VlalAlel~~~~~v~l~TdDysvQNVa~~Lgi~~~~~~~~~~I~~v~~w~~-rC~GC~~~f~~~~~~ 155 (177)
T COG1439 77 TGDLGNLSPTDIEVLALALELGEEVQVALATDDYSVQNVALQLGLNVRSISYKGKIKKVRKWRL-RCHGCKRIFPEPKDF 155 (177)
T ss_pred hCcccccChhhHHHHHHHHhhccccceeEEecchHHHHHHHHhCceEEeeeccCccceEeeeeE-EEecCceecCCCCCc
Confidence 34445787762 23458999999999999999999999854 566999999999 99999999 888999
Q ss_pred cccCCCCCeeeEE
Q 033276 87 CIKSNHEIRISPV 99 (123)
Q Consensus 87 Cp~CG~~~tl~rV 99 (123)
||.||++ ++++.
T Consensus 156 Cp~CG~~-~~~~~ 167 (177)
T COG1439 156 CPICGSP-LKRKR 167 (177)
T ss_pred CCCCCCc-eEEee
Confidence 9999999 44443
No 3
>PRK12496 hypothetical protein; Provisional
Probab=99.79 E-value=5.1e-20 Score=140.68 Aligned_cols=67 Identities=19% Similarity=0.320 Sum_probs=60.0
Q ss_pred CceeEEecccHHHHHHHHHhCceeeCCCCCcceeeeEEeeccccCCccc-c--cCccccccCCCCCeeeEE
Q 033276 32 ESTVACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSS-P--FPLVICIKSNHEIRISPV 99 (123)
Q Consensus 32 ~~~va~vTdDyAmQNVllqlGL~l~sv~g~~I~~v~~wvl~rC~gC~k~-~--~~~~fCp~CG~~~tl~rV 99 (123)
++.+.++||||++||||++|||++.++++++|+++++|++ +|+||++. + .+.+|||+||+++.++++
T Consensus 89 el~~~lvtDD~~~~~vA~~lgi~v~~~~~~~i~~~~~w~~-~C~gC~~~~~~~~~~~~C~~CG~~~~r~~~ 158 (164)
T PRK12496 89 ELNGTLYTDDYGIQNVAKKLNIKFENIKTKGIKKVIKWRK-VCKGCKKKYPEDYPDDVCEICGSPVKRKMV 158 (164)
T ss_pred HhCCcEECcHHHHHHHHHHcCCeEeccccccchhheeeeE-ECCCCCccccCCCCCCcCCCCCChhhhcch
Confidence 3457999999999999999999999999999999999999 99999998 4 467999999999655544
No 4
>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=99.65 E-value=4.6e-17 Score=111.73 Aligned_cols=41 Identities=15% Similarity=0.406 Sum_probs=19.5
Q ss_pred cceeeeEEeeccccCCccc--ccCccccccCCCCCeeeEEEEEee
Q 033276 62 QIRQLHRYIVDKCLKLFSS--PFPLVICIKSNHEIRISPVFMLIL 104 (123)
Q Consensus 62 ~I~~v~~wvl~rC~gC~k~--~~~~~fCp~CG~~~tl~rV~~~~~ 104 (123)
+|+++|+|++ ||+|||++ ++++.|||+|||+ ||+||+|++.
T Consensus 1 rIk~~k~~vl-rC~aCf~~t~~~~k~FCp~CGn~-TL~rvsvsv~ 43 (73)
T PF08772_consen 1 RIKRVKTWVL-RCHACFKITKDMTKQFCPKCGNA-TLKRVSVSVD 43 (73)
T ss_dssp -------EEE-E-SSS--EES-SS--S-SSS--S---EEEE-B--
T ss_pred CcchhheeeE-EccccccCcCCCCceeCcccCCC-cceEEEEEEC
Confidence 6899999999 99999998 7999999999999 9999999876
No 5
>TIGR03875 RNA_lig_partner RNA ligase partner, MJ_0950 family. This uncharacterized protein family is found almost perfectly in the same set of genomes as the Pab1020 family described by model TIGR01209. These pairs are found mostly in Archaea, but also in a few bacteria (e.g. Alkalilimnicola ehrlichei MLHE-1, Aquifex aeolicus). While the partner protein has been described as homodimeric ligase that has RNA circularization activity, the function of this protein (also called UPF0278) is unknown.
Probab=97.89 E-value=7.7e-06 Score=65.89 Aligned_cols=27 Identities=22% Similarity=0.416 Sum_probs=25.1
Q ss_pred CceeEEecccHHHHHHHHHhCceeeCC
Q 033276 32 ESTVACITGDYAMQNVILQMGLRLLAP 58 (123)
Q Consensus 32 ~~~va~vTdDyAmQNVllqlGL~l~sv 58 (123)
+++++++||||+|||+|.+|||++++.
T Consensus 169 ELda~lvTdD~giqn~A~~Lgi~~~~~ 195 (206)
T TIGR03875 169 ELDAAVVSADEGIRKWAERLGLRFVDA 195 (206)
T ss_pred HcCcEEEeCcHHHHHHHHHcCCeeecH
Confidence 678999999999999999999999974
No 6
>PRK04358 hypothetical protein; Provisional
Probab=97.74 E-value=1.6e-05 Score=64.43 Aligned_cols=27 Identities=22% Similarity=0.416 Sum_probs=25.0
Q ss_pred CceeEEecccHHHHHHHHHhCceeeCC
Q 033276 32 ESTVACITGDYAMQNVILQMGLRLLAP 58 (123)
Q Consensus 32 ~~~va~vTdDyAmQNVllqlGL~l~sv 58 (123)
+++++++|+||+|||+|.+|||++++.
T Consensus 173 ELda~lvTdD~giqn~A~~LGI~~~~~ 199 (217)
T PRK04358 173 ELDAAVVSADEGIRKWAERLGLRFVDA 199 (217)
T ss_pred HhCCEEEeCCHHHHHHHHHcCCeeecH
Confidence 568899999999999999999999985
No 7
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=97.15 E-value=0.00019 Score=40.01 Aligned_cols=21 Identities=10% Similarity=0.078 Sum_probs=19.1
Q ss_pred cccCCccc-ccCccccccCCCC
Q 033276 73 KCLKLFSS-PFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~-~~~~~fCp~CG~~ 93 (123)
.|+.|++. +....|||.||.+
T Consensus 4 ~Cp~Cg~~~~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 4 FCPNCGAEIDPDAKFCPNCGAK 25 (26)
T ss_pred CCcccCCcCCcccccChhhCCC
Confidence 79999998 7778999999987
No 8
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=96.96 E-value=0.00037 Score=38.22 Aligned_cols=21 Identities=10% Similarity=0.070 Sum_probs=18.3
Q ss_pred cccCCccc-ccCccccccCCCC
Q 033276 73 KCLKLFSS-PFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~-~~~~~fCp~CG~~ 93 (123)
+|+-|++. +..-.|||.||.+
T Consensus 1 ~Cp~CG~~~~~~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIEDDAKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCCcCcchhhhCCc
Confidence 59999998 6667999999987
No 9
>PF08745 UPF0278: UPF0278 family; InterPro: IPR022785 This entry contains proteins of the UPF0278 family and proteins containing PIN domains. Members of the UPF0278 family are uncharacterised and about 200 amino acids in length.; PDB: 2LCQ_A.
Probab=96.84 E-value=0.00055 Score=55.27 Aligned_cols=28 Identities=29% Similarity=0.523 Sum_probs=16.9
Q ss_pred CceeEEecccHHHHHHHHHhCceeeCCC
Q 033276 32 ESTVACITGDYAMQNVILQMGLRLLAPG 59 (123)
Q Consensus 32 ~~~va~vTdDyAmQNVllqlGL~l~sv~ 59 (123)
+++++++|+||+|||++.+|||+++...
T Consensus 166 El~a~lvt~D~gi~~~A~~lGi~~i~~~ 193 (205)
T PF08745_consen 166 ELDAVLVTDDYGIQNWAEKLGIRFIDAR 193 (205)
T ss_dssp HHT--EE---HHHHHHHHHTT--EE---
T ss_pred HcCCEEEeCCHhHHHHHHHCCCEEEecc
Confidence 5678999999999999999999999874
No 10
>PF15017 AF1Q: Drug resistance and apoptosis regulator
Probab=96.34 E-value=0.0019 Score=46.03 Aligned_cols=18 Identities=11% Similarity=0.213 Sum_probs=13.3
Q ss_pred ccccCCCCCCCceeccCC
Q 033276 13 VSYVDDECSEQSWMLRSL 30 (123)
Q Consensus 13 ~~~~~~~~~~~~WIt~~~ 30 (123)
.+++++++++|+||||+|
T Consensus 63 ~eee~~ddD~gGWITPsN 80 (87)
T PF15017_consen 63 EEEEEEDDDGGGWITPSN 80 (87)
T ss_pred cccccccCCCCccccchh
Confidence 344456677899999996
No 11
>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=96.16 E-value=0.0057 Score=37.30 Aligned_cols=30 Identities=17% Similarity=0.184 Sum_probs=23.0
Q ss_pred EEeeccccCCccc--------ccCccccccCCCCCeeeEE
Q 033276 68 RYIVDKCLKLFSS--------PFPLVICIKSNHEIRISPV 99 (123)
Q Consensus 68 ~wvl~rC~gC~k~--------~~~~~fCp~CG~~~tl~rV 99 (123)
.|.| +|..|+.. +.....||.||+. .++|+
T Consensus 3 ~Yey-~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~-~~~r~ 40 (42)
T PF09723_consen 3 IYEY-RCEECGHEFEVLQSISEDDPVPCPECGST-EVRRV 40 (42)
T ss_pred CEEE-EeCCCCCEEEEEEEcCCCCCCcCCCCCCC-ceEEe
Confidence 4788 99999954 2346889999996 66665
No 12
>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=96.05 E-value=0.0033 Score=35.50 Aligned_cols=21 Identities=14% Similarity=0.284 Sum_probs=19.0
Q ss_pred cccCCccc-ccCccccccCCCC
Q 033276 73 KCLKLFSS-PFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~-~~~~~fCp~CG~~ 93 (123)
.|+.|++. +..-.+||.||+.
T Consensus 2 ~CP~C~~~V~~~~~~Cp~CG~~ 23 (26)
T PF10571_consen 2 TCPECGAEVPESAKFCPHCGYD 23 (26)
T ss_pred cCCCCcCCchhhcCcCCCCCCC
Confidence 79999998 7778999999987
No 13
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=95.85 E-value=0.008 Score=43.59 Aligned_cols=41 Identities=10% Similarity=-0.039 Sum_probs=29.6
Q ss_pred eeEEeeccccCCccc-c--cCccccccCCCCCeeeEEEEEeeEEEEEee
Q 033276 66 LHRYIVDKCLKLFSS-P--FPLVICIKSNHEIRISPVFMLILICLYIQV 111 (123)
Q Consensus 66 v~~wvl~rC~gC~k~-~--~~~~fCp~CG~~~tl~rV~~~~~~~~~~~~ 111 (123)
...=+. +|..|+.. . .....||.||+. .+.++-|.-+||++
T Consensus 66 ~vp~~~-~C~~Cg~~~~~~~~~~~CP~Cgs~----~~~i~~G~El~i~~ 109 (113)
T PRK12380 66 YKPAQA-WCWDCSQVVEIHQHDAQCPHCHGE----RLRVDTGDSLIVKS 109 (113)
T ss_pred eeCcEE-EcccCCCEEecCCcCccCcCCCCC----CcEEccCCeEEEEE
Confidence 334466 99999987 3 234559999988 35667788888874
No 14
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=95.83 E-value=0.0074 Score=43.82 Aligned_cols=40 Identities=10% Similarity=-0.007 Sum_probs=28.8
Q ss_pred eEEeeccccCCccc-ccC--c-cccccCCCCCeeeEEEEEeeEEEEEee
Q 033276 67 HRYIVDKCLKLFSS-PFP--L-VICIKSNHEIRISPVFMLILICLYIQV 111 (123)
Q Consensus 67 ~~wvl~rC~gC~k~-~~~--~-~fCp~CG~~~tl~rV~~~~~~~~~~~~ 111 (123)
..=.. +|..|+.. +.. . ..||.||+. . +.++-|.-++|++
T Consensus 67 ~p~~~-~C~~Cg~~~~~~~~~~~~CP~Cgs~-~---~~i~~G~El~i~~ 110 (114)
T PRK03681 67 QEAEC-WCETCQQYVTLLTQRVRRCPQCHGD-M---LRIVADDGLQIRR 110 (114)
T ss_pred eCcEE-EcccCCCeeecCCccCCcCcCcCCC-C---cEEccCCeEEEEE
Confidence 34456 89999987 432 2 449999988 2 5566788888874
No 15
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=95.75 E-value=0.011 Score=43.07 Aligned_cols=39 Identities=10% Similarity=-0.004 Sum_probs=28.1
Q ss_pred EEeeccccCCccc-cc--Cccc-cccCCCCCeeeEEEEEeeEEEEEee
Q 033276 68 RYIVDKCLKLFSS-PF--PLVI-CIKSNHEIRISPVFMLILICLYIQV 111 (123)
Q Consensus 68 ~wvl~rC~gC~k~-~~--~~~f-Cp~CG~~~tl~rV~~~~~~~~~~~~ 111 (123)
.-.. +|..|++. +. ...+ ||.||++ . +.++-|.-+||++
T Consensus 69 p~~~-~C~~Cg~~~~~~~~~~~~CP~Cgs~-~---~~i~~G~El~I~~ 111 (117)
T PRK00564 69 KVEL-ECKDCSHVFKPNALDYGVCEKCHSK-N---VIITQGNEMRLLS 111 (117)
T ss_pred CCEE-EhhhCCCccccCCccCCcCcCCCCC-c---eEEecCCEEEEEE
Confidence 4456 89999987 33 2234 9999998 3 5556688888874
No 16
>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=95.54 E-value=0.011 Score=42.68 Aligned_cols=42 Identities=12% Similarity=-0.043 Sum_probs=26.6
Q ss_pred eeeEEeeccccCCccc---ccCccccccCCCCCeeeEEEEEeeEEEEEee
Q 033276 65 QLHRYIVDKCLKLFSS---PFPLVICIKSNHEIRISPVFMLILICLYIQV 111 (123)
Q Consensus 65 ~v~~wvl~rC~gC~k~---~~~~~fCp~CG~~~tl~rV~~~~~~~~~~~~ 111 (123)
....-+. +|..|++. +.....||.||+. . +.++-|.-+||++
T Consensus 65 e~~p~~~-~C~~Cg~~~~~~~~~~~CP~Cgs~-~---~~i~~G~el~i~~ 109 (113)
T PF01155_consen 65 EEVPARA-RCRDCGHEFEPDEFDFSCPRCGSP-D---VEIISGRELRIKS 109 (113)
T ss_dssp EEE--EE-EETTTS-EEECHHCCHH-SSSSSS-----EEEEESS-EEEEE
T ss_pred EecCCcE-ECCCCCCEEecCCCCCCCcCCcCC-C---cEEccCCeEEEEE
Confidence 3445567 99999987 2344669999999 3 4556788888875
No 17
>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=95.51 E-value=0.0081 Score=35.30 Aligned_cols=25 Identities=12% Similarity=0.109 Sum_probs=15.0
Q ss_pred EEeeccccCCccc-ccCccccccCCCC
Q 033276 68 RYIVDKCLKLFSS-PFPLVICIKSNHE 93 (123)
Q Consensus 68 ~wvl~rC~gC~k~-~~~~~fCp~CG~~ 93 (123)
-... ||..|++. -+++.+||.||+.
T Consensus 9 l~~~-rC~~Cg~~~~pPr~~Cp~C~s~ 34 (37)
T PF12172_consen 9 LLGQ-RCRDCGRVQFPPRPVCPHCGSD 34 (37)
T ss_dssp EEEE-E-TTT--EEES--SEETTTT--
T ss_pred EEEE-EcCCCCCEecCCCcCCCCcCcc
Confidence 3445 99999999 6778999999976
No 18
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=95.41 E-value=0.014 Score=35.84 Aligned_cols=24 Identities=21% Similarity=0.085 Sum_probs=18.7
Q ss_pred eeccccCCccc---c--cCccccccCCCCC
Q 033276 70 IVDKCLKLFSS---P--FPLVICIKSNHEI 94 (123)
Q Consensus 70 vl~rC~gC~k~---~--~~~~fCp~CG~~~ 94 (123)
.+ +|..|+.. + .....||.||+++
T Consensus 3 ~y-~C~~CG~~~~~~~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 3 EY-KCARCGREVELDEYGTGVRCPYCGYRI 31 (46)
T ss_pred EE-ECCCCCCEEEECCCCCceECCCCCCeE
Confidence 46 99999986 2 2258899999994
No 19
>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=95.34 E-value=0.013 Score=34.22 Aligned_cols=25 Identities=20% Similarity=0.349 Sum_probs=19.5
Q ss_pred EEeeccccCCccc-c-------cCccccccCCCC
Q 033276 68 RYIVDKCLKLFSS-P-------FPLVICIKSNHE 93 (123)
Q Consensus 68 ~wvl~rC~gC~k~-~-------~~~~fCp~CG~~ 93 (123)
.|.+ +|..|++. . .....||.||.+
T Consensus 3 ~Y~y-~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~ 35 (41)
T smart00834 3 IYEY-RCEDCGHTFEVLQKISDDPLATCPECGGD 35 (41)
T ss_pred CEEE-EcCCCCCEEEEEEecCCCCCCCCCCCCCc
Confidence 4788 99999985 1 235679999996
No 20
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=95.33 E-value=0.018 Score=42.93 Aligned_cols=38 Identities=16% Similarity=0.267 Sum_probs=28.1
Q ss_pred EeeccccCCccc-cc-----------------------CccccccCCCCCeeeEEEEEeeEEEEEee
Q 033276 69 YIVDKCLKLFSS-PF-----------------------PLVICIKSNHEIRISPVFMLILICLYIQV 111 (123)
Q Consensus 69 wvl~rC~gC~k~-~~-----------------------~~~fCp~CG~~~tl~rV~~~~~~~~~~~~ 111 (123)
=.+ +|..|+.. .. ....||.||+. . +.++-|.-+||++
T Consensus 69 ~~~-~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~-~---~~i~~G~el~i~~ 130 (135)
T PRK03824 69 AVL-KCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR-D---FEIVKGRGVYIEE 130 (135)
T ss_pred eEE-ECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCC-C---cEEecCceEEEEE
Confidence 456 89999987 32 23449999988 2 5667799999984
No 21
>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=95.31 E-value=0.018 Score=41.83 Aligned_cols=40 Identities=13% Similarity=0.006 Sum_probs=28.9
Q ss_pred eEEeeccccCCccc-cc--CccccccCCCCCeeeEEEEEeeEEEEEee
Q 033276 67 HRYIVDKCLKLFSS-PF--PLVICIKSNHEIRISPVFMLILICLYIQV 111 (123)
Q Consensus 67 ~~wvl~rC~gC~k~-~~--~~~fCp~CG~~~tl~rV~~~~~~~~~~~~ 111 (123)
..=.. +|..|++. +. ....||.||++ . +.++-|.-++|++
T Consensus 67 ~p~~~-~C~~Cg~~~~~~~~~~~CP~Cgs~-~---~~i~~G~El~I~~ 109 (115)
T TIGR00100 67 EPVEC-ECEDCSEEVSPEIDLYRCPKCHGI-M---LQVRAGKELNLKS 109 (115)
T ss_pred eCcEE-EcccCCCEEecCCcCccCcCCcCC-C---cEEecCCeEEEEE
Confidence 34456 89999987 33 24559999998 3 5566788888874
No 22
>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=95.24 E-value=0.029 Score=34.72 Aligned_cols=32 Identities=19% Similarity=0.342 Sum_probs=22.7
Q ss_pred EEeeccccCCccc-c-------cCccccccCCCCCeeeEEEE
Q 033276 68 RYIVDKCLKLFSS-P-------FPLVICIKSNHEIRISPVFM 101 (123)
Q Consensus 68 ~wvl~rC~gC~k~-~-------~~~~fCp~CG~~~tl~rV~~ 101 (123)
.|.| +|..|+.. . .....||.||+. .++|+--
T Consensus 3 ~Yey-~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~-~~~r~~s 42 (52)
T TIGR02605 3 IYEY-RCTACGHRFEVLQKMSDDPLATCPECGGE-KLRRLLS 42 (52)
T ss_pred CEEE-EeCCCCCEeEEEEecCCCCCCCCCCCCCC-ceeEEec
Confidence 4789 99999984 1 123479999996 5666543
No 23
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=94.66 E-value=0.031 Score=41.88 Aligned_cols=33 Identities=24% Similarity=0.121 Sum_probs=25.5
Q ss_pred eeEEeeccccCCccc-ccCccccccCCCCCeeeEE
Q 033276 66 LHRYIVDKCLKLFSS-PFPLVICIKSNHEIRISPV 99 (123)
Q Consensus 66 v~~wvl~rC~gC~k~-~~~~~fCp~CG~~~tl~rV 99 (123)
-+-..- ||..|+++ -+++.+||.||+++.+.-|
T Consensus 25 ~kl~g~-kC~~CG~v~~PPr~~Cp~C~~~~~~E~v 58 (140)
T COG1545 25 GKLLGT-KCKKCGRVYFPPRAYCPKCGSETELEWV 58 (140)
T ss_pred CcEEEE-EcCCCCeEEcCCcccCCCCCCCCceEEE
Confidence 344555 99999999 7889999999999543444
No 24
>PF12773 DZR: Double zinc ribbon
Probab=93.94 E-value=0.028 Score=34.41 Aligned_cols=21 Identities=14% Similarity=0.279 Sum_probs=13.8
Q ss_pred ccCCccc-ccCccccccCCCCC
Q 033276 74 CLKLFSS-PFPLVICIKSNHEI 94 (123)
Q Consensus 74 C~gC~k~-~~~~~fCp~CG~~~ 94 (123)
|+.|++. +....|||.||.++
T Consensus 1 Cp~Cg~~~~~~~~fC~~CG~~l 22 (50)
T PF12773_consen 1 CPHCGTPNPDDAKFCPHCGTPL 22 (50)
T ss_pred CCCcCCcCCccccCChhhcCCh
Confidence 5667766 55567777777764
No 25
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=93.57 E-value=0.072 Score=39.62 Aligned_cols=42 Identities=14% Similarity=-0.074 Sum_probs=30.4
Q ss_pred eeeEEeeccccCCccc---ccCccccccCCCCCeeeEEEEEeeEEEEEee
Q 033276 65 QLHRYIVDKCLKLFSS---PFPLVICIKSNHEIRISPVFMLILICLYIQV 111 (123)
Q Consensus 65 ~v~~wvl~rC~gC~k~---~~~~~fCp~CG~~~tl~rV~~~~~~~~~~~~ 111 (123)
+...=.. +|.-|... ......||+||++ ++.+.-|..++|++
T Consensus 65 e~~p~~~-~C~~C~~~~~~e~~~~~CP~C~s~----~~~i~~G~el~i~~ 109 (115)
T COG0375 65 EEEPAEC-WCLDCGQEVELEELDYRCPKCGSI----NLRIIGGDELIIKS 109 (115)
T ss_pred EEeccEE-EeccCCCeecchhheeECCCCCCC----ceEEecCCeeEEEE
Confidence 3344556 89999776 3345569999999 35567789998875
No 26
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=93.46 E-value=0.074 Score=33.14 Aligned_cols=24 Identities=21% Similarity=0.204 Sum_probs=19.3
Q ss_pred eeccccCCccc----ccCccccccCCCCC
Q 033276 70 IVDKCLKLFSS----PFPLVICIKSNHEI 94 (123)
Q Consensus 70 vl~rC~gC~k~----~~~~~fCp~CG~~~ 94 (123)
.| +|..|++. ......||.||+++
T Consensus 2 ~Y-~C~~Cg~~~~~~~~~~irC~~CG~rI 29 (44)
T smart00659 2 IY-ICGECGRENEIKSKDVVRCRECGYRI 29 (44)
T ss_pred EE-ECCCCCCEeecCCCCceECCCCCceE
Confidence 47 89999986 24468899999994
No 27
>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=93.35 E-value=0.063 Score=31.63 Aligned_cols=22 Identities=9% Similarity=-0.173 Sum_probs=17.5
Q ss_pred eccccCCccc---ccCccccccCCCC
Q 033276 71 VDKCLKLFSS---PFPLVICIKSNHE 93 (123)
Q Consensus 71 l~rC~gC~k~---~~~~~fCp~CG~~ 93 (123)
+ +|.-|+.+ +..-..||.||.+
T Consensus 3 ~-~C~~CG~i~~g~~~p~~CP~Cg~~ 27 (34)
T cd00729 3 W-VCPVCGYIHEGEEAPEKCPICGAP 27 (34)
T ss_pred E-ECCCCCCEeECCcCCCcCcCCCCc
Confidence 5 89999988 2234789999987
No 28
>PF12773 DZR: Double zinc ribbon
Probab=92.91 E-value=0.053 Score=33.14 Aligned_cols=19 Identities=16% Similarity=0.242 Sum_probs=10.4
Q ss_pred cccCCccc-ccCccccccCC
Q 033276 73 KCLKLFSS-PFPLVICIKSN 91 (123)
Q Consensus 73 rC~gC~k~-~~~~~fCp~CG 91 (123)
+|+.|++. +....||+.||
T Consensus 31 ~C~~Cg~~~~~~~~fC~~CG 50 (50)
T PF12773_consen 31 ICPNCGAENPPNAKFCPNCG 50 (50)
T ss_pred CCcCCcCCCcCCcCccCccc
Confidence 45555555 44445555555
No 29
>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=92.86 E-value=0.11 Score=37.92 Aligned_cols=51 Identities=12% Similarity=0.234 Sum_probs=34.2
Q ss_pred HHHHHHHHhCceee----CC---CCCcce--eeeEEeeccccCCccc---c----cCccccccCCCCC
Q 033276 43 AMQNVILQMGLRLL----AP---GGMQIR--QLHRYIVDKCLKLFSS---P----FPLVICIKSNHEI 94 (123)
Q Consensus 43 AmQNVllqlGL~l~----sv---~g~~I~--~v~~wvl~rC~gC~k~---~----~~~~fCp~CG~~~ 94 (123)
+=|.++.++|..+. .+ +...|. +.++|.+ +|..|+.. . ..+..|+.||.++
T Consensus 87 ~fk~~~~~ig~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~C~~C~~~~~r~~~~~~~~~~C~~C~~~l 153 (157)
T PF10263_consen 87 EFKQWARRIGASPPRGRPNPTTCHSYEIEGKEYKKYVY-RCPSCGREYKRHRRSKRKRYRCGRCGGPL 153 (157)
T ss_pred HHHHHHHHHCCcccccccccccccccccccccccceEE-EcCCCCCEeeeecccchhhEECCCCCCEE
Confidence 67889999998542 11 222232 2368999 99999965 1 2245799999773
No 30
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=92.51 E-value=0.072 Score=40.50 Aligned_cols=21 Identities=19% Similarity=0.145 Sum_probs=18.1
Q ss_pred cccCCccc---ccCccccccCCCC
Q 033276 73 KCLKLFSS---PFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~---~~~~~fCp~CG~~ 93 (123)
-|+.|+.+ .....|||+||..
T Consensus 30 hCp~Cg~PLF~KdG~v~CPvC~~~ 53 (131)
T COG1645 30 HCPKCGTPLFRKDGEVFCPVCGYR 53 (131)
T ss_pred hCcccCCcceeeCCeEECCCCCce
Confidence 79999987 4668999999975
No 31
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=92.51 E-value=0.059 Score=36.62 Aligned_cols=21 Identities=19% Similarity=0.222 Sum_probs=18.7
Q ss_pred cccCCccc-ccCccccccCCCC
Q 033276 73 KCLKLFSS-PFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~-~~~~~fCp~CG~~ 93 (123)
.|.-|++. +...+.||+||++
T Consensus 6 AC~~Ck~l~~~d~e~CP~Cgs~ 27 (64)
T COG2093 6 ACKNCKRLTPEDTEICPVCGST 27 (64)
T ss_pred HHhhccccCCCCCccCCCCCCc
Confidence 69999998 7777889999998
No 32
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=92.48 E-value=0.13 Score=37.86 Aligned_cols=39 Identities=10% Similarity=0.072 Sum_probs=27.0
Q ss_pred eEEeeccccCCccc-cc---C------ccccccCCCCCeeeEEEEEeeEEEEEee
Q 033276 67 HRYIVDKCLKLFSS-PF---P------LVICIKSNHEIRISPVFMLILICLYIQV 111 (123)
Q Consensus 67 ~~wvl~rC~gC~k~-~~---~------~~fCp~CG~~~tl~rV~~~~~~~~~~~~ 111 (123)
..=.. +| .|++. .. . ...||.||+. . +.++-|.-+||++
T Consensus 67 vp~~~-~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~-~---~~i~~G~El~i~~ 115 (124)
T PRK00762 67 IPVEI-EC-ECGYEGVVDEDEIDHYAAVIECPVCGNK-R---AHILGGRECNVKN 115 (124)
T ss_pred cCeeE-Ee-eCcCcccccccchhccccCCcCcCCCCC-C---CEEecCCeEEEEE
Confidence 34456 89 99977 22 1 1459999988 3 5566788888874
No 33
>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=91.94 E-value=0.2 Score=29.53 Aligned_cols=25 Identities=16% Similarity=0.212 Sum_probs=17.8
Q ss_pred cccCCccc----ccCccccccCCCCCeeeE
Q 033276 73 KCLKLFSS----PFPLVICIKSNHEIRISP 98 (123)
Q Consensus 73 rC~gC~k~----~~~~~fCp~CG~~~tl~r 98 (123)
.|..|++. .....-||.||+. .|.|
T Consensus 2 ~C~~Cg~~~~~~~~~~irC~~CG~R-IlyK 30 (32)
T PF03604_consen 2 ICGECGAEVELKPGDPIRCPECGHR-ILYK 30 (32)
T ss_dssp BESSSSSSE-BSTSSTSSBSSSS-S-EEBE
T ss_pred CCCcCCCeeEcCCCCcEECCcCCCe-EEEe
Confidence 78999986 3345789999999 4443
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=91.81 E-value=0.11 Score=30.04 Aligned_cols=22 Identities=9% Similarity=-0.099 Sum_probs=17.6
Q ss_pred eccccCCccc-cc--CccccccCCCC
Q 033276 71 VDKCLKLFSS-PF--PLVICIKSNHE 93 (123)
Q Consensus 71 l~rC~gC~k~-~~--~~~fCp~CG~~ 93 (123)
+ +|..|+.+ +. .-..||.||.+
T Consensus 2 ~-~C~~CGy~y~~~~~~~~CP~Cg~~ 26 (33)
T cd00350 2 Y-VCPVCGYIYDGEEAPWVCPVCGAP 26 (33)
T ss_pred E-ECCCCCCEECCCcCCCcCcCCCCc
Confidence 5 89999988 32 35789999987
No 35
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=91.21 E-value=0.1 Score=31.08 Aligned_cols=11 Identities=9% Similarity=0.350 Sum_probs=5.2
Q ss_pred cccccCCCCCe
Q 033276 85 VICIKSNHEIR 95 (123)
Q Consensus 85 ~fCp~CG~~~t 95 (123)
.|||.||+++.
T Consensus 1 kfC~~CG~~l~ 11 (34)
T PF14803_consen 1 KFCPQCGGPLE 11 (34)
T ss_dssp -B-TTT--B-E
T ss_pred CccccccChhh
Confidence 59999999943
No 36
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=91.20 E-value=0.13 Score=33.22 Aligned_cols=26 Identities=15% Similarity=0.105 Sum_probs=20.5
Q ss_pred EEeeccccCCccc-c----cCccccccCCCCC
Q 033276 68 RYIVDKCLKLFSS-P----FPLVICIKSNHEI 94 (123)
Q Consensus 68 ~wvl~rC~gC~k~-~----~~~~fCp~CG~~~ 94 (123)
.-.| +|.-|++. . .....||.||+++
T Consensus 4 ~~~Y-~C~~Cg~~~~~~~~~~~irCp~Cg~rI 34 (49)
T COG1996 4 MMEY-KCARCGREVELDQETRGIRCPYCGSRI 34 (49)
T ss_pred eEEE-EhhhcCCeeehhhccCceeCCCCCcEE
Confidence 3568 99999987 2 3467899999994
No 37
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=91.05 E-value=0.14 Score=40.05 Aligned_cols=23 Identities=9% Similarity=-0.014 Sum_probs=19.5
Q ss_pred eeccccCCccc--ccCccccccCCCC
Q 033276 70 IVDKCLKLFSS--PFPLVICIKSNHE 93 (123)
Q Consensus 70 vl~rC~gC~k~--~~~~~fCp~CG~~ 93 (123)
++ +|+-|+.+ ..+-..||+||.+
T Consensus 134 ~~-vC~vCGy~~~ge~P~~CPiCga~ 158 (166)
T COG1592 134 VW-VCPVCGYTHEGEAPEVCPICGAP 158 (166)
T ss_pred EE-EcCCCCCcccCCCCCcCCCCCCh
Confidence 78 99999998 5445889999987
No 38
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=90.59 E-value=0.12 Score=33.99 Aligned_cols=20 Identities=25% Similarity=0.261 Sum_probs=17.6
Q ss_pred cccCCcccccCccccccCCCC
Q 033276 73 KCLKLFSSPFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~~~~~~fCp~CG~~ 93 (123)
+|..|+.... +..||.||.+
T Consensus 7 ~C~~CgvYTL-k~~CP~CG~~ 26 (56)
T PRK13130 7 KCPKCGVYTL-KEICPVCGGK 26 (56)
T ss_pred ECCCCCCEEc-cccCcCCCCC
Confidence 8999998844 7899999998
No 39
>PRK00420 hypothetical protein; Validated
Probab=90.44 E-value=0.17 Score=37.39 Aligned_cols=21 Identities=14% Similarity=0.047 Sum_probs=18.1
Q ss_pred cccCCccc----ccCccccccCCCC
Q 033276 73 KCLKLFSS----PFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~----~~~~~fCp~CG~~ 93 (123)
.|+.|+.+ .....|||.||..
T Consensus 25 ~CP~Cg~pLf~lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 25 HCPVCGLPLFELKDGEVVCPVHGKV 49 (112)
T ss_pred CCCCCCCcceecCCCceECCCCCCe
Confidence 89999987 3567999999998
No 40
>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=89.74 E-value=0.19 Score=37.54 Aligned_cols=33 Identities=12% Similarity=0.316 Sum_probs=25.3
Q ss_pred eeeEEeeccccCCccc-cc--CccccccCCCCCeeeE
Q 033276 65 QLHRYIVDKCLKLFSS-PF--PLVICIKSNHEIRISP 98 (123)
Q Consensus 65 ~v~~wvl~rC~gC~k~-~~--~~~fCp~CG~~~tl~r 98 (123)
..+.... +|+.|.|. .+ ..+-|+.|+.|+|+.|
T Consensus 64 Stkav~V-~CP~C~K~TKmLGr~D~CM~C~~pLTLd~ 99 (114)
T PF11023_consen 64 STKAVQV-ECPNCGKQTKMLGRVDACMHCKEPLTLDP 99 (114)
T ss_pred cccceee-ECCCCCChHhhhchhhccCcCCCcCccCc
Confidence 3445667 99999998 32 2478999999998876
No 41
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=89.29 E-value=0.15 Score=46.95 Aligned_cols=27 Identities=15% Similarity=0.192 Sum_probs=20.3
Q ss_pred cccCCccc-ccCccccccCCCCCeeeEEE
Q 033276 73 KCLKLFSS-PFPLVICIKSNHEIRISPVF 100 (123)
Q Consensus 73 rC~gC~k~-~~~~~fCp~CG~~~tl~rV~ 100 (123)
.|+.|++. +..-.|||.||.+ +-++-.
T Consensus 29 ~Cp~CG~~~~~~~~fC~~CG~~-~~~~~~ 56 (645)
T PRK14559 29 PCPQCGTEVPVDEAHCPNCGAE-TGTIWW 56 (645)
T ss_pred cCCCCCCCCCcccccccccCCc-ccchhh
Confidence 68899987 7777899999988 444433
No 42
>PRK04351 hypothetical protein; Provisional
Probab=89.19 E-value=0.54 Score=35.80 Aligned_cols=50 Identities=18% Similarity=0.206 Sum_probs=34.4
Q ss_pred cHHHHHHHHHhCc-eeeCCCCCcceeeeEEeeccccCCccc-------ccCccccccCCCCC
Q 033276 41 DYAMQNVILQMGL-RLLAPGGMQIRQLHRYIVDKCLKLFSS-------PFPLVICIKSNHEI 94 (123)
Q Consensus 41 DyAmQNVllqlGL-~l~sv~g~~I~~v~~wvl~rC~gC~k~-------~~~~~fCp~CG~~~ 94 (123)
|-.=|-+|.++|- +..+ +-.. .-++|.| +|.+|+.. +..+..|-.||+.+
T Consensus 85 g~~fk~~~~~v~~~r~~~-~~~~--~~~~y~Y-~C~~Cg~~~~r~Rr~n~~~yrCg~C~g~L 142 (149)
T PRK04351 85 DRDFKELLKQVGGPRYCP-PLPS--QKKNYLY-ECQSCGQQYLRKRRINTKRYRCGKCRGKL 142 (149)
T ss_pred CHHHHHHHHHhCCCcccC-CCCC--CCceEEE-ECCCCCCEeeeeeecCCCcEEeCCCCcEe
Confidence 4445888888863 3222 2222 2357999 99999974 45678999999985
No 43
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=88.96 E-value=0.26 Score=40.57 Aligned_cols=21 Identities=19% Similarity=0.262 Sum_probs=16.4
Q ss_pred cccCCccc-c----------cCccccccCCCC
Q 033276 73 KCLKLFSS-P----------FPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~-~----------~~~~fCp~CG~~ 93 (123)
+|.||+=. + .+..|||.||.=
T Consensus 199 ~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgRI 230 (239)
T COG1579 199 VCGGCHMKLPSQTLSKVRKKDEIVFCPYCGRI 230 (239)
T ss_pred cccCCeeeecHHHHHHHhcCCCCccCCccchH
Confidence 99999954 2 346899999964
No 44
>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=88.75 E-value=0.31 Score=37.26 Aligned_cols=29 Identities=21% Similarity=0.230 Sum_probs=22.7
Q ss_pred eeccccCCccc-----ccCccccccCCCCCeeeEEE
Q 033276 70 IVDKCLKLFSS-----PFPLVICIKSNHEIRISPVF 100 (123)
Q Consensus 70 vl~rC~gC~k~-----~~~~~fCp~CG~~~tl~rV~ 100 (123)
.| +|..|+.. +....-||+||+. .-+|.+
T Consensus 112 ~l-~C~~Cg~~~~~~~~~~l~~Cp~C~~~-~F~R~~ 145 (146)
T PF07295_consen 112 TL-VCENCGHEVELTHPERLPPCPKCGHT-EFTRQP 145 (146)
T ss_pred eE-ecccCCCEEEecCCCcCCCCCCCCCC-eeeeCC
Confidence 57 99999985 3446789999999 676654
No 45
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=88.60 E-value=0.46 Score=41.85 Aligned_cols=32 Identities=19% Similarity=0.194 Sum_probs=24.5
Q ss_pred EEeeccccCCccc--ccCccccccCCCCC-eeeEEE
Q 033276 68 RYIVDKCLKLFSS--PFPLVICIKSNHEI-RISPVF 100 (123)
Q Consensus 68 ~wvl~rC~gC~k~--~~~~~fCp~CG~~~-tl~rV~ 100 (123)
.=.+ +|+.|++. ......||.||.++ -+||||
T Consensus 55 ~~i~-kC~~c~~~~~y~~~~~C~~cg~~~~l~R~VS 89 (415)
T COG5257 55 AKIY-KCPECYRPECYTTEPKCPNCGAETELVRRVS 89 (415)
T ss_pred CceE-eCCCCCCCcccccCCCCCCCCCCccEEEEEE
Confidence 3467 99999986 45678899999874 357787
No 46
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=88.50 E-value=0.11 Score=40.87 Aligned_cols=23 Identities=13% Similarity=0.278 Sum_probs=12.9
Q ss_pred ceeEEecccHHHHHHHHHhCceee
Q 033276 33 STVACITGDYAMQNVILQMGLRLL 56 (123)
Q Consensus 33 ~~va~vTdDyAmQNVllqlGL~l~ 56 (123)
.+.+++|.|+.+=-=+ .+|++-+
T Consensus 47 e~rIllTRDr~L~~r~-k~g~~~i 69 (165)
T COG1656 47 EGRILLTRDRELYKRA-KLGIKAI 69 (165)
T ss_pred CCeEEEeccHHHHHHh-hccCceE
Confidence 3456777777665444 4555433
No 47
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=88.15 E-value=0.18 Score=46.39 Aligned_cols=23 Identities=17% Similarity=0.252 Sum_probs=19.4
Q ss_pred cccCCccc-ccCccccccCCCCCe
Q 033276 73 KCLKLFSS-PFPLVICIKSNHEIR 95 (123)
Q Consensus 73 rC~gC~k~-~~~~~fCp~CG~~~t 95 (123)
+|+.|+.. +..-.|||.||.+++
T Consensus 3 ~Cp~Cg~~n~~~akFC~~CG~~l~ 26 (645)
T PRK14559 3 ICPQCQFENPNNNRFCQKCGTSLT 26 (645)
T ss_pred cCCCCCCcCCCCCccccccCCCCC
Confidence 79999988 666789999999864
No 48
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=87.76 E-value=0.25 Score=33.11 Aligned_cols=23 Identities=17% Similarity=0.226 Sum_probs=17.9
Q ss_pred eccccCCcccccCccccccCCCCC
Q 033276 71 VDKCLKLFSSPFPLVICIKSNHEI 94 (123)
Q Consensus 71 l~rC~gC~k~~~~~~fCp~CG~~~ 94 (123)
+-+|..|+..... +.||+||..+
T Consensus 5 ~rkC~~cg~YTLk-e~Cp~CG~~t 27 (59)
T COG2260 5 IRKCPKCGRYTLK-EKCPVCGGDT 27 (59)
T ss_pred hhcCcCCCceeec-ccCCCCCCcc
Confidence 3389999987433 7899999993
No 49
>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=87.71 E-value=0.32 Score=28.79 Aligned_cols=10 Identities=10% Similarity=0.361 Sum_probs=7.6
Q ss_pred cccccCCCCC
Q 033276 85 VICIKSNHEI 94 (123)
Q Consensus 85 ~fCp~CG~~~ 94 (123)
.|||.|||=+
T Consensus 2 ~FCp~C~nlL 11 (35)
T PF02150_consen 2 RFCPECGNLL 11 (35)
T ss_dssp -BETTTTSBE
T ss_pred eeCCCCCccc
Confidence 6899999874
No 50
>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=87.63 E-value=0.74 Score=29.66 Aligned_cols=44 Identities=11% Similarity=0.179 Sum_probs=32.0
Q ss_pred HHHHHHHHhCceeeCCCCCcceeeeEEeeccccCCccc--c---cCccccccCCCC
Q 033276 43 AMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSS--P---FPLVICIKSNHE 93 (123)
Q Consensus 43 AmQNVllqlGL~l~sv~g~~I~~v~~wvl~rC~gC~k~--~---~~~~fCp~CG~~ 93 (123)
.|+-.+..-|+.++.++-..-.+ .|+.|+.. . ...-.||.||..
T Consensus 7 ~L~yka~~~G~~v~~v~~~~TSq-------~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 7 RLEYKAEEYGIQVVEVDEAYTSQ-------TCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred HHHHHHHHhCCEEEEECCCCCcc-------CccCcccccccccccceEEcCCCCCE
Confidence 35666778899998887554444 89999987 2 225789999975
No 51
>PRK11032 hypothetical protein; Provisional
Probab=86.57 E-value=0.48 Score=36.87 Aligned_cols=29 Identities=24% Similarity=0.362 Sum_probs=23.2
Q ss_pred eeccccCCccc-----ccCccccccCCCCCeeeEEE
Q 033276 70 IVDKCLKLFSS-----PFPLVICIKSNHEIRISPVF 100 (123)
Q Consensus 70 vl~rC~gC~k~-----~~~~~fCp~CG~~~tl~rV~ 100 (123)
.+ +|..|+.. +....-||+||+. .-+|.+
T Consensus 124 ~L-vC~~Cg~~~~~~~p~~i~pCp~C~~~-~F~R~~ 157 (160)
T PRK11032 124 NL-VCEKCHHHLAFYTPEVLPLCPKCGHD-QFQRRP 157 (160)
T ss_pred eE-EecCCCCEEEecCCCcCCCCCCCCCC-eeeeCC
Confidence 47 99999985 4557889999999 777765
No 52
>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=86.24 E-value=0.39 Score=27.43 Aligned_cols=11 Identities=9% Similarity=0.166 Sum_probs=6.5
Q ss_pred ccccccCCCCC
Q 033276 84 LVICIKSNHEI 94 (123)
Q Consensus 84 ~~fCp~CG~~~ 94 (123)
..|||.||+++
T Consensus 3 ~rfC~~CG~~t 13 (32)
T PF09297_consen 3 HRFCGRCGAPT 13 (32)
T ss_dssp TSB-TTT--BE
T ss_pred CcccCcCCccc
Confidence 47999999994
No 53
>PF14369 zf-RING_3: zinc-finger
Probab=85.97 E-value=0.8 Score=27.16 Aligned_cols=22 Identities=14% Similarity=0.051 Sum_probs=16.1
Q ss_pred eccccCCccc-c-----cCccccccCCCC
Q 033276 71 VDKCLKLFSS-P-----FPLVICIKSNHE 93 (123)
Q Consensus 71 l~rC~gC~k~-~-----~~~~fCp~CG~~ 93 (123)
| .|+.|.+. . ....+||.|++.
T Consensus 3 y-wCh~C~~~V~~~~~~~~~~~CP~C~~g 30 (35)
T PF14369_consen 3 Y-WCHQCNRFVRIAPSPDSDVACPRCHGG 30 (35)
T ss_pred E-eCccCCCEeEeCcCCCCCcCCcCCCCc
Confidence 5 79999975 1 233469999998
No 54
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=85.94 E-value=1 Score=29.86 Aligned_cols=30 Identities=20% Similarity=0.244 Sum_probs=21.1
Q ss_pred EEeeccccCCccc-------cc----CccccccCCCCCeeeEEE
Q 033276 68 RYIVDKCLKLFSS-------PF----PLVICIKSNHEIRISPVF 100 (123)
Q Consensus 68 ~wvl~rC~gC~k~-------~~----~~~fCp~CG~~~tl~rV~ 100 (123)
.|++ |+-|+.. |. --.|||+|-++ +|-.|.
T Consensus 3 ~Wi~--CP~CgnKTR~kir~DT~LkNfPlyCpKCK~E-tlI~v~ 43 (55)
T PF14205_consen 3 EWIL--CPICGNKTRLKIREDTVLKNFPLYCPKCKQE-TLIDVK 43 (55)
T ss_pred eEEE--CCCCCCccceeeecCceeccccccCCCCCce-EEEEee
Confidence 6887 9999932 21 13799999999 665554
No 55
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=85.90 E-value=0.62 Score=43.68 Aligned_cols=27 Identities=19% Similarity=0.348 Sum_probs=20.1
Q ss_pred EeeccccCCccc-ccCccccccCCCCCeeeE
Q 033276 69 YIVDKCLKLFSS-PFPLVICIKSNHEIRISP 98 (123)
Q Consensus 69 wvl~rC~gC~k~-~~~~~fCp~CG~~~tl~r 98 (123)
=.+ +||=|++. +.+ ..||.||+. .|+-
T Consensus 461 ~~L-~CH~Cg~~~~~p-~~Cp~Cgs~-~L~~ 488 (730)
T COG1198 461 GQL-RCHYCGYQEPIP-QSCPECGSE-HLRA 488 (730)
T ss_pred Cee-EeCCCCCCCCCC-CCCCCCCCC-eeEE
Confidence 356 78888877 555 789999999 6654
No 56
>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=85.84 E-value=0.62 Score=42.57 Aligned_cols=53 Identities=11% Similarity=0.025 Sum_probs=33.2
Q ss_pred HHHHHHHHHh---CceeeCCCCCcceeeeEEeeccccCCccc-ccCccccccCCCCCeeeEEEEEee
Q 033276 42 YAMQNVILQM---GLRLLAPGGMQIRQLHRYIVDKCLKLFSS-PFPLVICIKSNHEIRISPVFMLIL 104 (123)
Q Consensus 42 yAmQNVllql---GL~l~sv~g~~I~~v~~wvl~rC~gC~k~-~~~~~fCp~CG~~~tl~rV~~~~~ 104 (123)
-|+.++.+.+ |+...++.- ..++|..|+.+ ......||+||++ .+...+=++|
T Consensus 509 ea~~~lv~~~~~~~i~Y~tin~---------~~siC~~CGy~~g~~~~~CP~CGs~-~~ev~sRv~G 565 (586)
T TIGR02827 509 DGYRKLLRVAADTGCNYFCFNI---------KITICNDCHHIDKRTLHRCPVCGSA-NIDYGTRVIG 565 (586)
T ss_pred HHHHHHHHHHHhcCCceEEeCC---------CCeecCCCCCcCCCcCCcCcCCCCc-cceEEEeecc
Confidence 4666666554 566665532 33589999986 3334789999987 4444444444
No 57
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=85.36 E-value=0.47 Score=34.63 Aligned_cols=25 Identities=16% Similarity=0.295 Sum_probs=18.4
Q ss_pred cccCCccc--ccCc--cccccCCCCCeee
Q 033276 73 KCLKLFSS--PFPL--VICIKSNHEIRIS 97 (123)
Q Consensus 73 rC~gC~k~--~~~~--~fCp~CG~~~tl~ 97 (123)
.|+.|++. ++.| ..||+||....+.
T Consensus 11 ~Cp~CG~kFYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 11 TCPSCGAKFYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cCCCCcchhccCCCCCccCCCCCCccCcc
Confidence 89999986 4332 5699999875444
No 58
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=85.22 E-value=0.45 Score=31.53 Aligned_cols=14 Identities=7% Similarity=0.320 Sum_probs=10.6
Q ss_pred cccccCCCCCeeeEE
Q 033276 85 VICIKSNHEIRISPV 99 (123)
Q Consensus 85 ~fCp~CG~~~tl~rV 99 (123)
..||+||++ |..|+
T Consensus 5 i~CP~CgnK-TR~ki 18 (55)
T PF14205_consen 5 ILCPICGNK-TRLKI 18 (55)
T ss_pred EECCCCCCc-cceee
Confidence 469999999 55544
No 59
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=85.15 E-value=0.24 Score=32.51 Aligned_cols=35 Identities=14% Similarity=0.133 Sum_probs=25.6
Q ss_pred cccCCccc---ccCccccccCCCCCeeeEEEEEeeEEEE
Q 033276 73 KCLKLFSS---PFPLVICIKSNHEIRISPVFMLILICLY 108 (123)
Q Consensus 73 rC~gC~k~---~~~~~fCp~CG~~~tl~rV~~~~~~~~~ 108 (123)
+|..|++. .....+||.||.+ -=|..-...|.|++
T Consensus 7 ~C~~Cg~~~~~~dDiVvCp~Cgap-yHR~C~~~~g~C~~ 44 (54)
T PF14446_consen 7 KCPVCGKKFKDGDDIVVCPECGAP-YHRDCWEKAGGCIN 44 (54)
T ss_pred cChhhCCcccCCCCEEECCCCCCc-ccHHHHhhCCceEe
Confidence 89999987 4568999999998 55555545555544
No 60
>PF13638 PIN_4: PIN domain; PDB: 2HWW_C 2HWX_A 2DOK_B 2HWY_B 2WP8_J.
Probab=85.10 E-value=1.1 Score=31.49 Aligned_cols=27 Identities=15% Similarity=0.137 Sum_probs=19.5
Q ss_pred CceeEEecccHHHHHHHHHhCceeeCC
Q 033276 32 ESTVACITGDYAMQNVILQMGLRLLAP 58 (123)
Q Consensus 32 ~~~va~vTdDyAmQNVllqlGL~l~sv 58 (123)
..+|+++|.|..|++.|...||+..+.
T Consensus 106 ~~~vvLvT~D~~l~~~A~~~gi~~~~~ 132 (133)
T PF13638_consen 106 GRKVVLVTNDKNLRLKARAEGIPAVSY 132 (133)
T ss_dssp CEEEEEEE--HHHHHHHHHTT--EE--
T ss_pred CCeEEEEeCCHHHHHHHhhcccccccC
Confidence 568999999999999999999998865
No 61
>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=84.94 E-value=0.82 Score=27.33 Aligned_cols=22 Identities=23% Similarity=0.230 Sum_probs=17.1
Q ss_pred cccCCccc-------ccCccccccCCCCC
Q 033276 73 KCLKLFSS-------PFPLVICIKSNHEI 94 (123)
Q Consensus 73 rC~gC~k~-------~~~~~fCp~CG~~~ 94 (123)
.|+.|+++ +.....|.+||+++
T Consensus 3 ~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L 31 (36)
T PF05191_consen 3 ICPKCGRIYHIEFNPPKVEGVCDNCGGEL 31 (36)
T ss_dssp EETTTTEEEETTTB--SSTTBCTTTTEBE
T ss_pred CcCCCCCccccccCCCCCCCccCCCCCee
Confidence 69999987 12358999999983
No 62
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=84.81 E-value=0.49 Score=31.68 Aligned_cols=21 Identities=10% Similarity=0.009 Sum_probs=16.2
Q ss_pred cccCCcccccCccccccCCCCC
Q 033276 73 KCLKLFSSPFPLVICIKSNHEI 94 (123)
Q Consensus 73 rC~gC~k~~~~~~fCp~CG~~~ 94 (123)
.|.-|.++. +.+.||+||+..
T Consensus 5 AC~~C~~i~-~~~~CP~Cgs~~ 25 (61)
T PRK08351 5 ACRHCHYIT-TEDRCPVCGSRD 25 (61)
T ss_pred hhhhCCccc-CCCcCCCCcCCc
Confidence 699999882 234799999983
No 63
>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=84.73 E-value=1.2 Score=29.09 Aligned_cols=25 Identities=20% Similarity=0.195 Sum_probs=18.9
Q ss_pred EEeeccccCCcccccCccccccCCCCC
Q 033276 68 RYIVDKCLKLFSSPFPLVICIKSNHEI 94 (123)
Q Consensus 68 ~wvl~rC~gC~k~~~~~~fCp~CG~~~ 94 (123)
.++. .|.+|...... +-||.||.++
T Consensus 3 ~~~r-~c~~~~~YTLk-~~cp~cG~~T 27 (53)
T PF04135_consen 3 YYIR-KCPGCRVYTLK-DKCPPCGGPT 27 (53)
T ss_dssp EEEE-ECTTTCEEESS-SBBTTTSSBS
T ss_pred cccc-cCCCCCcEeCC-CccCCCCCCC
Confidence 4455 89999976333 6899999993
No 64
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=84.61 E-value=0.74 Score=32.62 Aligned_cols=42 Identities=14% Similarity=0.196 Sum_probs=30.0
Q ss_pred eeeEEeeccccCCccc--------ccCccccccCCCCC--eeeEEEEEeeEEE
Q 033276 65 QLHRYIVDKCLKLFSS--------PFPLVICIKSNHEI--RISPVFMLILICL 107 (123)
Q Consensus 65 ~v~~wvl~rC~gC~k~--------~~~~~fCp~CG~~~--tl~rV~~~~~~~~ 107 (123)
-+-.|.| +|..|+.. +.+...||.||.++ ++.||.++.+-+=
T Consensus 7 lMPtY~Y-~c~~cg~~~dvvq~~~ddplt~ce~c~a~~kk~l~~vgi~fKGSG 58 (82)
T COG2331 7 LMPTYSY-ECTECGNRFDVVQAMTDDPLTTCEECGARLKKLLNAVGIVFKGSG 58 (82)
T ss_pred cccceEE-eecccchHHHHHHhcccCccccChhhChHHHHhhccceEEEecce
Confidence 3457899 99999975 45688999999752 4556666665443
No 65
>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=84.60 E-value=0.89 Score=40.82 Aligned_cols=58 Identities=12% Similarity=0.032 Sum_probs=33.3
Q ss_pred ccHHHHHHHHHhCceeeCCCCCcceeeeEEeeccccCCccc-ccCccccccCCCCCeeeEEEEEee
Q 033276 40 GDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSS-PFPLVICIKSNHEIRISPVFMLIL 104 (123)
Q Consensus 40 dDyAmQNVllqlGL~l~sv~g~~I~~v~~wvl~rC~gC~k~-~~~~~fCp~CG~~~tl~rV~~~~~ 104 (123)
+=-|+.++.+.+ . -.|..--....=.. +|..|+.. ......||+||+. -+.+++=++|
T Consensus 493 n~~al~~lv~~a-~----~~~~~y~~~~~p~~-~C~~CG~~~~~~~~~CP~CGs~-~~~~~~Rv~G 551 (555)
T cd01675 493 NPEALEALVKKA-A----KRGVIYFGINTPID-ICNDCGYIGEGEGFKCPKCGSE-DVEVISRITG 551 (555)
T ss_pred CHHHHHHHHHHH-H----HcCCceEEEecCCc-cCCCCCCCCcCCCCCCcCCCCc-CceEEEeeee
Confidence 445677766653 0 01222223334455 89999987 3556899999987 3444433333
No 66
>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=84.50 E-value=0.49 Score=42.72 Aligned_cols=43 Identities=16% Similarity=0.124 Sum_probs=27.7
Q ss_pred HHHHHHHHHh---CceeeCCCCCcceeeeEEeeccccCCccc-ccCccccccCCCC
Q 033276 42 YAMQNVILQM---GLRLLAPGGMQIRQLHRYIVDKCLKLFSS-PFPLVICIKSNHE 93 (123)
Q Consensus 42 yAmQNVllql---GL~l~sv~g~~I~~v~~wvl~rC~gC~k~-~~~~~fCp~CG~~ 93 (123)
=|+.++.+.+ |++..++. ..+++|..|+.. ......||+||++
T Consensus 501 eal~~lv~~a~~~~i~Y~~~n---------~~~~~C~~CG~~g~~~~~~CP~Cgs~ 547 (579)
T TIGR02487 501 EALKDITKKAMKNGIGYFGIN---------PPVDVCEDCGYTGEGLNDKCPKCGSH 547 (579)
T ss_pred HHHHHHHHHHHhcCCceEEec---------cCCccCCCCCCCCCCCCCcCcCCCCc
Confidence 4666665543 44555442 234599999987 3333689999986
No 67
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=84.45 E-value=0.97 Score=45.04 Aligned_cols=32 Identities=6% Similarity=0.043 Sum_probs=23.9
Q ss_pred CcceeeeEEeeccccCCcccccCccccccCCCCC
Q 033276 61 MQIRQLHRYIVDKCLKLFSSPFPLVICIKSNHEI 94 (123)
Q Consensus 61 ~~I~~v~~wvl~rC~gC~k~~~~~~fCp~CG~~~ 94 (123)
.++-++.-... +|+.|++... ..|||.||+++
T Consensus 658 ~G~ieVEV~~r-kCPkCG~~t~-~~fCP~CGs~t 689 (1337)
T PRK14714 658 GGVIEVEVGRR-RCPSCGTETY-ENRCPDCGTHT 689 (1337)
T ss_pred CCeEEEEEEEE-ECCCCCCccc-cccCcccCCcC
Confidence 44456777888 9999998722 24999999884
No 68
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=84.06 E-value=1.1 Score=33.03 Aligned_cols=52 Identities=12% Similarity=0.092 Sum_probs=33.0
Q ss_pred HHHHHHHHHhCceeeC-CCCCcceeeeEEeeccccCCccc--------ccCccccccCCCCC
Q 033276 42 YAMQNVILQMGLRLLA-PGGMQIRQLHRYIVDKCLKLFSS--------PFPLVICIKSNHEI 94 (123)
Q Consensus 42 yAmQNVllqlGL~l~s-v~g~~I~~v~~wvl~rC~gC~k~--------~~~~~fCp~CG~~~ 94 (123)
-.=|..+.++|-..-. -+...+..+++|.+ +|.+|+.. +..+..|-+||+++
T Consensus 83 ~~f~~~~~~~~~~~~~~~h~~~~~~~~~~~y-~C~~C~~~~~~~rr~~~~~~y~C~~C~g~l 143 (146)
T smart00731 83 DEWKRWMRQVNGLFPERCHTFLIESVKKYPY-RCTGCGQRYLRVRRSNNVSRYRCGKCGGKL 143 (146)
T ss_pred HHHHHHHHHHcCCCcceEcCCcccccceEEE-ECCCCCCCCceEccccCcceEEcCCCCCEE
Confidence 3446666666543111 12333444478999 99999975 12458899999984
No 69
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=83.85 E-value=0.52 Score=31.92 Aligned_cols=20 Identities=25% Similarity=0.320 Sum_probs=16.2
Q ss_pred cccCCcccccCccccccCCCC
Q 033276 73 KCLKLFSSPFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~~~~~~fCp~CG~~ 93 (123)
.|..|.++. +...||.||+.
T Consensus 7 AC~~C~~i~-~~~~Cp~Cgs~ 26 (64)
T PRK06393 7 ACKKCKRLT-PEKTCPVHGDE 26 (64)
T ss_pred hHhhCCccc-CCCcCCCCCCC
Confidence 699999982 23589999998
No 70
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=83.66 E-value=0.64 Score=43.33 Aligned_cols=33 Identities=18% Similarity=0.079 Sum_probs=21.5
Q ss_pred eccccCCcccccCccccccCCCCCeeeEEEEEee
Q 033276 71 VDKCLKLFSSPFPLVICIKSNHEIRISPVFMLIL 104 (123)
Q Consensus 71 l~rC~gC~k~~~~~~fCp~CG~~~tl~rV~~~~~ 104 (123)
+++|..|+........||+||+. .+.+.+=++|
T Consensus 680 ~~~C~~CG~~~~~~~~CP~CG~~-~~~~~~Ri~G 712 (735)
T PRK07111 680 VDRCPVCGYLGVIEDKCPKCGST-NIQRIRRITG 712 (735)
T ss_pred CeecCCCCCCCCcCccCcCCCCc-cceeeehhhh
Confidence 45899999763234789999986 3444433333
No 71
>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=83.33 E-value=0.93 Score=40.07 Aligned_cols=26 Identities=19% Similarity=0.361 Sum_probs=18.2
Q ss_pred eeccccCCccc-ccCccccccCCCCCeeeE
Q 033276 70 IVDKCLKLFSS-PFPLVICIKSNHEIRISP 98 (123)
Q Consensus 70 vl~rC~gC~k~-~~~~~fCp~CG~~~tl~r 98 (123)
.+ +||-|+.. +.+ ..||.||++ .++.
T Consensus 240 ~l-~Ch~Cg~~~~~~-~~Cp~C~s~-~l~~ 266 (505)
T TIGR00595 240 KL-RCHYCGYQEPIP-KTCPQCGSE-DLVY 266 (505)
T ss_pred eE-EcCCCcCcCCCC-CCCCCCCCC-eeEe
Confidence 45 67777776 444 679999998 5553
No 72
>PRK02935 hypothetical protein; Provisional
Probab=82.93 E-value=0.79 Score=34.07 Aligned_cols=31 Identities=13% Similarity=0.271 Sum_probs=24.0
Q ss_pred eEEeeccccCCccc-cc--CccccccCCCCCeeeE
Q 033276 67 HRYIVDKCLKLFSS-PF--PLVICIKSNHEIRISP 98 (123)
Q Consensus 67 ~~wvl~rC~gC~k~-~~--~~~fCp~CG~~~tl~r 98 (123)
|.-.. .|+.|.|. .+ ..+-|..|+.|+||.+
T Consensus 67 kavqV-~CP~C~K~TKmLGrvD~CM~C~~PLTLd~ 100 (110)
T PRK02935 67 KAVQV-ICPSCEKPTKMLGRVDACMHCNQPLTLDR 100 (110)
T ss_pred cceee-ECCCCCchhhhccceeecCcCCCcCCcCc
Confidence 34455 89999998 32 3478999999998865
No 73
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=82.23 E-value=0.49 Score=42.43 Aligned_cols=24 Identities=21% Similarity=0.026 Sum_probs=11.6
Q ss_pred eeccccCCcccccCccccccCCCC
Q 033276 70 IVDKCLKLFSSPFPLVICIKSNHE 93 (123)
Q Consensus 70 vl~rC~gC~k~~~~~~fCp~CG~~ 93 (123)
..++|..|+........||+||++
T Consensus 490 ~~~~C~~CG~~~~~~~~CP~CGs~ 513 (546)
T PF13597_consen 490 PIDICPDCGYIGGEGDKCPKCGSE 513 (546)
T ss_dssp -EEEETTT---S--EEE-CCC---
T ss_pred CcccccCCCcCCCCCCCCCCCCCc
Confidence 345899999983237899999999
No 74
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=81.89 E-value=0.99 Score=41.59 Aligned_cols=44 Identities=16% Similarity=0.093 Sum_probs=31.0
Q ss_pred HHHHHHHHHh----CceeeCCCCCcceeeeEEeeccccCCcccccCccccccCCCCC
Q 033276 42 YAMQNVILQM----GLRLLAPGGMQIRQLHRYIVDKCLKLFSSPFPLVICIKSNHEI 94 (123)
Q Consensus 42 yAmQNVllql----GL~l~sv~g~~I~~v~~wvl~rC~gC~k~~~~~~fCp~CG~~~ 94 (123)
=|+.++.+.+ ++...++.. .+++|..|+........||+||+++
T Consensus 602 ~a~~~lv~~~~~~~~i~Y~~in~---------~~~~C~~CG~~~g~~~~CP~CG~~~ 649 (656)
T PRK08270 602 EACKKLVKKALENYRLPYITITP---------TFSICPKHGYLSGEHEFCPKCGEET 649 (656)
T ss_pred HHHHHHHHHHHHhCCCceEEeCC---------CCcccCCCCCcCCCCCCCcCCcCcc
Confidence 5777777754 566666632 2358999998633357899999873
No 75
>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=81.75 E-value=1 Score=36.69 Aligned_cols=27 Identities=11% Similarity=0.118 Sum_probs=14.3
Q ss_pred cccCCccc-ccCccccccCCCCCeeeEEE
Q 033276 73 KCLKLFSS-PFPLVICIKSNHEIRISPVF 100 (123)
Q Consensus 73 rC~gC~k~-~~~~~fCp~CG~~~tl~rV~ 100 (123)
.|.-|++. ...+.-||.||+. --.+..
T Consensus 199 ~Cs~C~t~W~~~R~~Cp~Cg~~-~~~~l~ 226 (290)
T PF04216_consen 199 HCSLCGTEWRFVRIKCPYCGNT-DHEKLE 226 (290)
T ss_dssp EETTT--EEE--TTS-TTT----SS-EEE
T ss_pred EcCCCCCeeeecCCCCcCCCCC-CCccee
Confidence 59999988 8888999999988 455554
No 76
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=81.71 E-value=0.87 Score=26.81 Aligned_cols=21 Identities=24% Similarity=0.297 Sum_probs=15.4
Q ss_pred cccCCccc-----ccCccccccCCCC
Q 033276 73 KCLKLFSS-----PFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~-----~~~~~fCp~CG~~ 93 (123)
+|.+|+.. .....||+.||.-
T Consensus 5 ~C~~C~~~~i~~~~~~~~~C~~Cg~~ 30 (33)
T PF08792_consen 5 KCSKCGGNGIVNKEDDYEVCIFCGSS 30 (33)
T ss_pred EcCCCCCCeEEEecCCeEEcccCCcE
Confidence 68888875 3457888888864
No 77
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=81.61 E-value=0.96 Score=32.69 Aligned_cols=25 Identities=8% Similarity=-0.025 Sum_probs=18.4
Q ss_pred eeccccCCccc---ccC--ccccccCCCCCe
Q 033276 70 IVDKCLKLFSS---PFP--LVICIKSNHEIR 95 (123)
Q Consensus 70 vl~rC~gC~k~---~~~--~~fCp~CG~~~t 95 (123)
.+ +|..|+.. ..+ ..+||.||+..+
T Consensus 42 ~~-~C~~Cg~~~~~~~SCk~R~CP~C~~~~~ 71 (111)
T PF14319_consen 42 RY-RCEDCGHEKIVYNSCKNRHCPSCQAKAT 71 (111)
T ss_pred ee-ecCCCCceEEecCcccCcCCCCCCChHH
Confidence 46 99999986 221 459999998743
No 78
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=81.13 E-value=0.97 Score=30.26 Aligned_cols=26 Identities=19% Similarity=0.220 Sum_probs=18.3
Q ss_pred cccCCccc--c---cCccccccCCCCCeeeEE
Q 033276 73 KCLKLFSS--P---FPLVICIKSNHEIRISPV 99 (123)
Q Consensus 73 rC~gC~k~--~---~~~~fCp~CG~~~tl~rV 99 (123)
.|.+|+.. + ..+-.||.||.. ++.|.
T Consensus 9 ~CtSCg~~i~~~~~~~~F~CPnCG~~-~I~RC 39 (59)
T PRK14890 9 KCTSCGIEIAPREKAVKFLCPNCGEV-IIYRC 39 (59)
T ss_pred cccCCCCcccCCCccCEeeCCCCCCe-eEeec
Confidence 68888876 2 235679999887 56664
No 79
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=81.10 E-value=2.6 Score=31.31 Aligned_cols=26 Identities=15% Similarity=0.130 Sum_probs=21.1
Q ss_pred EEeeccccCCccc--cc--CccccccCCCC
Q 033276 68 RYIVDKCLKLFSS--PF--PLVICIKSNHE 93 (123)
Q Consensus 68 ~wvl~rC~gC~k~--~~--~~~fCp~CG~~ 93 (123)
.|-|..|+.|.+. +. ..-+|++|+..
T Consensus 31 ~~~Y~aC~~C~kkv~~~~~~~~~C~~C~~~ 60 (166)
T cd04476 31 NWWYPACPGCNKKVVEEGNGTYRCEKCNKS 60 (166)
T ss_pred CeEEccccccCcccEeCCCCcEECCCCCCc
Confidence 5777799999987 22 56899999987
No 80
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=81.10 E-value=0.89 Score=41.83 Aligned_cols=43 Identities=12% Similarity=0.040 Sum_probs=29.0
Q ss_pred HHHHHHHHH---hCceeeCCCCCcceeeeEEeeccccCCccc-ccCccccccCCCC
Q 033276 42 YAMQNVILQ---MGLRLLAPGGMQIRQLHRYIVDKCLKLFSS-PFPLVICIKSNHE 93 (123)
Q Consensus 42 yAmQNVllq---lGL~l~sv~g~~I~~v~~wvl~rC~gC~k~-~~~~~fCp~CG~~ 93 (123)
-|+.++++. .|+...++.. ..++|..|+.. ......||+||++
T Consensus 543 eal~~lv~~~~~~~i~Yf~in~---------~~~iC~~CG~~~~g~~~~CP~CGs~ 589 (623)
T PRK08271 543 EGYRKLLNIAAKTGCNYFAFNV---------KITICNDCHHIDKRTGKRCPICGSE 589 (623)
T ss_pred HHHHHHHHHHHHcCCceEEeCC---------CCccCCCCCCcCCCCCcCCcCCCCc
Confidence 455555444 3566665532 33589999987 5567899999976
No 81
>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=81.01 E-value=1.1 Score=25.98 Aligned_cols=22 Identities=27% Similarity=0.209 Sum_probs=16.5
Q ss_pred cccCCccc---c-------cCccccccCCCCC
Q 033276 73 KCLKLFSS---P-------FPLVICIKSNHEI 94 (123)
Q Consensus 73 rC~gC~k~---~-------~~~~fCp~CG~~~ 94 (123)
.|+.|++. + ..+..||+||+.+
T Consensus 4 ~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 4 QCPNCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred ECCCCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 79999984 2 1247999999983
No 82
>PRK06260 threonine synthase; Validated
Probab=80.92 E-value=1 Score=38.12 Aligned_cols=25 Identities=16% Similarity=0.312 Sum_probs=18.7
Q ss_pred EeeccccCCccc-cc--CccccccCCCCC
Q 033276 69 YIVDKCLKLFSS-PF--PLVICIKSNHEI 94 (123)
Q Consensus 69 wvl~rC~gC~k~-~~--~~~fCp~CG~~~ 94 (123)
+.+ +|..|++. +. ....||.||..+
T Consensus 2 ~~~-~C~~cg~~~~~~~~~~~Cp~cg~~l 29 (397)
T PRK06260 2 YWL-KCIECGKEYDPDEIIYTCPECGGLL 29 (397)
T ss_pred CEE-EECCCCCCCCCCCccccCCCCCCeE
Confidence 357 99999998 32 335699999864
No 83
>PRK07591 threonine synthase; Validated
Probab=79.88 E-value=1.4 Score=37.85 Aligned_cols=27 Identities=19% Similarity=0.369 Sum_probs=20.3
Q ss_pred EEeeccccCCccc-c-cCccccccCCCCCe
Q 033276 68 RYIVDKCLKLFSS-P-FPLVICIKSNHEIR 95 (123)
Q Consensus 68 ~wvl~rC~gC~k~-~-~~~~fCp~CG~~~t 95 (123)
.+.+ +|..|++. + .....||.||+.+.
T Consensus 16 ~~~l-~C~~Cg~~~~~~~~~~C~~cg~~l~ 44 (421)
T PRK07591 16 AVAL-KCRECGAEYPLGPIHVCEECFGPLE 44 (421)
T ss_pred eeEE-EeCCCCCcCCCCCCccCCCCCCeEE
Confidence 4468 99999998 3 23467999998753
No 84
>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=79.44 E-value=1.2 Score=38.66 Aligned_cols=50 Identities=12% Similarity=0.011 Sum_probs=28.4
Q ss_pred HHHHHHHhCceeeCCCCCcceeeeEEeeccccCCccc-cc--Cc---cccccCCCCC
Q 033276 44 MQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSS-PF--PL---VICIKSNHEI 94 (123)
Q Consensus 44 mQNVllqlGL~l~sv~g~~I~~v~~wvl~rC~gC~k~-~~--~~---~fCp~CG~~~ 94 (123)
++.+++.+.-+-+......--+.-+|-++.|..|+.. ++ +. ..|| ||+++
T Consensus 213 ~~~~l~ai~~~~i~~~~g~~P~~GKYh~~~c~~C~~~~~~~~~~~~~~~Cp-CG~~i 268 (374)
T TIGR00375 213 FALALKAIDDRKIIANYGLDPLLGKYHQTACEACGEPAVSEDAETACANCP-CGGRI 268 (374)
T ss_pred HHHHHHHhhCCceEeeeeECcCCCccchhhhcccCCcCCchhhhhcCCCCC-CCCcc
Confidence 6666665432211111111223445666799999987 32 22 6799 99995
No 85
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=79.11 E-value=1.1 Score=41.18 Aligned_cols=45 Identities=16% Similarity=0.098 Sum_probs=29.6
Q ss_pred ccHHHHHHHHHh---CceeeCCCCCcceeeeEEeeccccCCccc-ccCccccccCCCC
Q 033276 40 GDYAMQNVILQM---GLRLLAPGGMQIRQLHRYIVDKCLKLFSS-PFPLVICIKSNHE 93 (123)
Q Consensus 40 dDyAmQNVllql---GL~l~sv~g~~I~~v~~wvl~rC~gC~k~-~~~~~fCp~CG~~ 93 (123)
+=-|+..+.+.+ ++...++. -..++|..|+.. ......||+||++
T Consensus 543 n~~al~~lv~~~~~~~i~Y~~in---------p~~~~C~~CG~~~~g~~~~CP~CGs~ 591 (625)
T PRK08579 543 DPEALAKLTKRIMNTKLVYWSYT---------PAITVCNKCGRSTTGLYTRCPRCGSE 591 (625)
T ss_pred CHHHHHHHHHHHHhcCCceEEeC---------CCCccCCCCCCccCCCCCcCcCCCCc
Confidence 446777777774 33333332 133589999985 4446889999986
No 86
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=79.06 E-value=0.85 Score=30.78 Aligned_cols=26 Identities=15% Similarity=0.144 Sum_probs=17.2
Q ss_pred cccCCccc--c---cCccccccCCCCCeeeEE
Q 033276 73 KCLKLFSS--P---FPLVICIKSNHEIRISPV 99 (123)
Q Consensus 73 rC~gC~k~--~---~~~~fCp~CG~~~tl~rV 99 (123)
+|++|+.. + ..+--||.||.. .+.|.
T Consensus 11 ~CtSCg~~i~p~e~~v~F~CPnCGe~-~I~Rc 41 (61)
T COG2888 11 VCTSCGREIAPGETAVKFPCPNCGEV-EIYRC 41 (61)
T ss_pred eeccCCCEeccCCceeEeeCCCCCce-eeehh
Confidence 78888876 2 224558888877 56554
No 87
>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=78.99 E-value=1.3 Score=28.22 Aligned_cols=22 Identities=9% Similarity=-0.069 Sum_probs=16.2
Q ss_pred eccccCCccc-ccC-------------------ccccccCCCC
Q 033276 71 VDKCLKLFSS-PFP-------------------LVICIKSNHE 93 (123)
Q Consensus 71 l~rC~gC~k~-~~~-------------------~~fCp~CG~~ 93 (123)
+ +|..|+.+ ++. --.||.||.+
T Consensus 2 y-~C~~CgyiYd~~~Gd~~~~i~pGt~f~~Lp~~w~CP~C~a~ 43 (50)
T cd00730 2 Y-ECRICGYIYDPAEGDPDEGIPPGTPFEDLPDDWVCPVCGAG 43 (50)
T ss_pred c-CCCCCCeEECCCCCCcccCcCCCCCHhHCCCCCCCCCCCCc
Confidence 5 89999987 432 1279999976
No 88
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=78.69 E-value=1.2 Score=33.86 Aligned_cols=21 Identities=19% Similarity=0.162 Sum_probs=17.0
Q ss_pred cccCCccc--ccC---ccccccCCCC
Q 033276 73 KCLKLFSS--PFP---LVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~--~~~---~~fCp~CG~~ 93 (123)
+|+.|+++ +.. +.=||.||++
T Consensus 3 ~Ct~Cg~~f~dgs~eil~GCP~CGg~ 28 (131)
T PF09845_consen 3 QCTKCGRVFEDGSKEILSGCPECGGN 28 (131)
T ss_pred ccCcCCCCcCCCcHHHHccCcccCCc
Confidence 89999998 322 4679999998
No 89
>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=78.64 E-value=2.3 Score=25.46 Aligned_cols=8 Identities=38% Similarity=0.725 Sum_probs=4.5
Q ss_pred ccccCCCC
Q 033276 86 ICIKSNHE 93 (123)
Q Consensus 86 fCp~CG~~ 93 (123)
.||+||++
T Consensus 2 ~Cp~Cg~~ 9 (39)
T PF01096_consen 2 KCPKCGHN 9 (39)
T ss_dssp --SSS-SS
T ss_pred CCcCCCCC
Confidence 48999988
No 90
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=78.47 E-value=1.2 Score=28.11 Aligned_cols=20 Identities=20% Similarity=0.438 Sum_probs=15.7
Q ss_pred cccCCccc-c----------cCccccccCCC
Q 033276 73 KCLKLFSS-P----------FPLVICIKSNH 92 (123)
Q Consensus 73 rC~gC~k~-~----------~~~~fCp~CG~ 92 (123)
+|.||+-. + ....+||.||-
T Consensus 24 ~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgR 54 (56)
T PF02591_consen 24 TCSGCHMELPPQELNEIRKGDEIVFCPNCGR 54 (56)
T ss_pred ccCCCCEEcCHHHHHHHHcCCCeEECcCCCc
Confidence 89999965 2 24689999994
No 91
>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=78.46 E-value=1.1 Score=25.33 Aligned_cols=9 Identities=11% Similarity=0.405 Sum_probs=4.9
Q ss_pred ccccCCCCC
Q 033276 86 ICIKSNHEI 94 (123)
Q Consensus 86 fCp~CG~~~ 94 (123)
+||.||+++
T Consensus 1 ~CP~C~s~l 9 (28)
T PF03119_consen 1 TCPVCGSKL 9 (28)
T ss_dssp B-TTT--BE
T ss_pred CcCCCCCEe
Confidence 699999993
No 92
>TIGR03844 cysteate_syn cysteate synthase. Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M.
Probab=77.47 E-value=1.5 Score=37.67 Aligned_cols=27 Identities=19% Similarity=0.290 Sum_probs=20.3
Q ss_pred EeeccccCCccc-c-cCccccccCCCCCee
Q 033276 69 YIVDKCLKLFSS-P-FPLVICIKSNHEIRI 96 (123)
Q Consensus 69 wvl~rC~gC~k~-~-~~~~fCp~CG~~~tl 96 (123)
|.+ +|..|++. + .....||.||+.+.+
T Consensus 1 ~~l-~C~~Cg~~~~~~~~~~C~~c~g~l~~ 29 (398)
T TIGR03844 1 YTL-RCPGCGEVLPDHYTLSCPLDCGLLRA 29 (398)
T ss_pred CEE-EeCCCCCccCCccccCCCCCCCceEE
Confidence 467 99999998 4 345789999976443
No 93
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=77.40 E-value=1.2 Score=37.63 Aligned_cols=42 Identities=14% Similarity=0.308 Sum_probs=27.4
Q ss_pred EeeccccCCccc----c--cCccccccCCCCCee---eEEEEEeeEEEEEeeC
Q 033276 69 YIVDKCLKLFSS----P--FPLVICIKSNHEIRI---SPVFMLILICLYIQVD 112 (123)
Q Consensus 69 wvl~rC~gC~k~----~--~~~~fCp~CG~~~tl---~rV~~~~~~~~~~~~~ 112 (123)
|.. |+.|++. + .....||+||++..+ .|+..++-..-|...|
T Consensus 38 w~k--c~~C~~~~~~~~l~~~~~vcp~c~~h~rltAreRI~~L~D~gSF~E~~ 88 (296)
T CHL00174 38 WVQ--CENCYGLNYKKFLKSKMNICEQCGYHLKMSSSDRIELLIDPGTWNPMD 88 (296)
T ss_pred eeE--CCCccchhhHHHHHHcCCCCCCCCCCcCCCHHHHHHHHccCCccEEcC
Confidence 776 9999987 2 346799999998544 3555444444444443
No 94
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=77.23 E-value=1.1 Score=27.30 Aligned_cols=10 Identities=20% Similarity=0.464 Sum_probs=8.0
Q ss_pred cccccCCCCC
Q 033276 85 VICIKSNHEI 94 (123)
Q Consensus 85 ~fCp~CG~~~ 94 (123)
.|||.||+-+
T Consensus 1 ~FCp~Cg~~l 10 (52)
T smart00661 1 KFCPKCGNML 10 (52)
T ss_pred CCCCCCCCcc
Confidence 4899999874
No 95
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=77.04 E-value=1.3 Score=37.05 Aligned_cols=44 Identities=20% Similarity=0.344 Sum_probs=27.7
Q ss_pred EEeeccccCCccc----c--cCccccccCCCCCee---eEEEEEeeEEEEEeeCC
Q 033276 68 RYIVDKCLKLFSS----P--FPLVICIKSNHEIRI---SPVFMLILICLYIQVDT 113 (123)
Q Consensus 68 ~wvl~rC~gC~k~----~--~~~~fCp~CG~~~tl---~rV~~~~~~~~~~~~~~ 113 (123)
-|.. |+.|++. + .....||+||++..+ .|+..++-..-|...+.
T Consensus 26 ~~~~--c~~c~~~~~~~~l~~~~~vc~~c~~h~rl~areRi~~L~D~gsF~E~~~ 78 (292)
T PRK05654 26 LWTK--CPSCGQVLYRKELEANLNVCPKCGHHMRISARERLDLLLDEGSFVELDA 78 (292)
T ss_pred CeeE--CCCccchhhHHHHHhcCCCCCCCCCCeeCCHHHHHHHHccCCccEEecC
Confidence 3876 9999987 2 345799999998544 34444444433444433
No 96
>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=76.87 E-value=1.5 Score=29.00 Aligned_cols=32 Identities=19% Similarity=0.178 Sum_probs=24.4
Q ss_pred cceeeeEEeeccccCCccc---ccC-ccccccCCCCC
Q 033276 62 QIRQLHRYIVDKCLKLFSS---PFP-LVICIKSNHEI 94 (123)
Q Consensus 62 ~I~~v~~wvl~rC~gC~k~---~~~-~~fCp~CG~~~ 94 (123)
+...+..|.- -|..|+++ ... ..-|+.||+++
T Consensus 10 ~~H~L~~~~~-NCl~CGkIiC~~Eg~~~pC~fCg~~l 45 (57)
T PF06221_consen 10 RRHPLFPYAP-NCLNCGKIICEQEGPLGPCPFCGTPL 45 (57)
T ss_pred ccCCCccccc-cccccChhhcccccCcCcCCCCCCcc
Confidence 3445566777 99999998 344 68999999883
No 97
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=76.85 E-value=2 Score=28.65 Aligned_cols=23 Identities=17% Similarity=0.309 Sum_probs=18.4
Q ss_pred ccccCCccc------ccCccccccCCCCC
Q 033276 72 DKCLKLFSS------PFPLVICIKSNHEI 94 (123)
Q Consensus 72 ~rC~gC~k~------~~~~~fCp~CG~~~ 94 (123)
-+|++|+++ ......|+.||..+
T Consensus 12 VkCp~C~n~q~vFsha~t~V~C~~Cg~~L 40 (59)
T PRK00415 12 VKCPDCGNEQVVFSHASTVVRCLVCGKTL 40 (59)
T ss_pred EECCCCCCeEEEEecCCcEEECcccCCCc
Confidence 389999986 24568999999873
No 98
>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=76.84 E-value=1.5 Score=42.85 Aligned_cols=29 Identities=21% Similarity=0.363 Sum_probs=21.3
Q ss_pred EEeeccccCCccc---ccCccccccCCCCCeee
Q 033276 68 RYIVDKCLKLFSS---PFPLVICIKSNHEIRIS 97 (123)
Q Consensus 68 ~wvl~rC~gC~k~---~~~~~fCp~CG~~~tl~ 97 (123)
+=.+ ||..|++. .+-..-||+||+++.|+
T Consensus 1010 rQ~f-RC~kC~~kYRR~PL~G~C~kCGg~lilT 1041 (1095)
T TIGR00354 1010 RQEV-RCTKCNTKYRRIPLVGKCLKCGNNLTLT 1041 (1095)
T ss_pred ccce-eecccCCccccCCCCCcccccCCeEEEE
Confidence 3467 99999975 23357899999996543
No 99
>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=76.53 E-value=1.4 Score=36.87 Aligned_cols=42 Identities=19% Similarity=0.297 Sum_probs=27.4
Q ss_pred EeeccccCCccc----c--cCccccccCCCCCee---eEEEEEeeEEEEEeeC
Q 033276 69 YIVDKCLKLFSS----P--FPLVICIKSNHEIRI---SPVFMLILICLYIQVD 112 (123)
Q Consensus 69 wvl~rC~gC~k~----~--~~~~fCp~CG~~~tl---~rV~~~~~~~~~~~~~ 112 (123)
|.. |+.|++. + .....||+||++..+ .|+..++-..-|...+
T Consensus 26 ~~~--c~~c~~~~~~~~l~~~~~vc~~c~~h~rl~areRi~~L~D~gsF~E~~ 76 (285)
T TIGR00515 26 WTK--CPKCGQVLYTKELERNLEVCPKCDHHMRMDARERIESLLDEGSFEEFN 76 (285)
T ss_pred eeE--CCCCcchhhHHHHHhhCCCCCCCCCcCcCCHHHHHHHceeCCeeEEeC
Confidence 876 9999987 1 346899999998443 3455455444444443
No 100
>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=76.37 E-value=2.1 Score=41.91 Aligned_cols=27 Identities=15% Similarity=0.082 Sum_probs=22.1
Q ss_pred eeeEEeeccccCCcccccCccccccCCCC
Q 033276 65 QLHRYIVDKCLKLFSSPFPLVICIKSNHE 93 (123)
Q Consensus 65 ~v~~wvl~rC~gC~k~~~~~~fCp~CG~~ 93 (123)
++---.. +|+.|++. ..+..||.||.+
T Consensus 620 ~vev~~R-KCPkCG~y-Tlk~rCP~CG~~ 646 (1095)
T TIGR00354 620 EVEIAIR-KCPQCGKE-SFWLKCPVCGEL 646 (1095)
T ss_pred EEEEEEE-ECCCCCcc-cccccCCCCCCc
Confidence 5666778 99999998 334779999999
No 101
>PRK06450 threonine synthase; Validated
Probab=76.02 E-value=1.7 Score=36.47 Aligned_cols=26 Identities=19% Similarity=0.175 Sum_probs=19.3
Q ss_pred eccccCCccc-cc-CccccccCCCCCeee
Q 033276 71 VDKCLKLFSS-PF-PLVICIKSNHEIRIS 97 (123)
Q Consensus 71 l~rC~gC~k~-~~-~~~fCp~CG~~~tl~ 97 (123)
+ +|..|++. +. ....||.||.++.+.
T Consensus 4 ~-~C~~Cg~~~~~~~~~~C~~cg~~l~~~ 31 (338)
T PRK06450 4 E-VCMKCGKERESIYEIRCKKCGGPFEIL 31 (338)
T ss_pred e-EECCcCCcCCCcccccCCcCCCEeEEe
Confidence 6 99999998 33 346799999875443
No 102
>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=75.92 E-value=1.7 Score=26.12 Aligned_cols=21 Identities=19% Similarity=0.189 Sum_probs=13.7
Q ss_pred cccCCccc----c--cCccccccCCCC
Q 033276 73 KCLKLFSS----P--FPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~----~--~~~~fCp~CG~~ 93 (123)
+|+.|+.. + ....+|+.||.-
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCGLV 28 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-BB
T ss_pred CCcCCcCCceEEcCCCCeEECCCCCCE
Confidence 78888874 3 234589999864
No 103
>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=75.49 E-value=1.7 Score=26.08 Aligned_cols=14 Identities=14% Similarity=0.221 Sum_probs=10.4
Q ss_pred cccccCCCCCeeeE
Q 033276 85 VICIKSNHEIRISP 98 (123)
Q Consensus 85 ~fCp~CG~~~tl~r 98 (123)
..||.||+++.+++
T Consensus 2 ~~CP~Cg~~lv~r~ 15 (39)
T PF01396_consen 2 EKCPKCGGPLVLRR 15 (39)
T ss_pred cCCCCCCceeEEEE
Confidence 46999998855444
No 104
>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=75.14 E-value=1.8 Score=27.86 Aligned_cols=20 Identities=20% Similarity=0.378 Sum_probs=16.9
Q ss_pred cccCCcccccCccccccCCC
Q 033276 73 KCLKLFSSPFPLVICIKSNH 92 (123)
Q Consensus 73 rC~gC~k~~~~~~fCp~CG~ 92 (123)
.|+.|+....+...||.||.
T Consensus 28 ~c~~cg~~~~~H~vc~~cG~ 47 (56)
T PF01783_consen 28 KCPNCGEPKLPHRVCPSCGY 47 (56)
T ss_dssp ESSSSSSEESTTSBCTTTBB
T ss_pred eeccCCCEecccEeeCCCCe
Confidence 79999988666789999984
No 105
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=75.02 E-value=0.64 Score=31.88 Aligned_cols=28 Identities=11% Similarity=0.183 Sum_probs=17.6
Q ss_pred eeccccCCccc---c--cCccccccCCCCCeeeEEE
Q 033276 70 IVDKCLKLFSS---P--FPLVICIKSNHEIRISPVF 100 (123)
Q Consensus 70 vl~rC~gC~k~---~--~~~~fCp~CG~~~tl~rV~ 100 (123)
++ || .|++. + ....-| .||..+-++++.
T Consensus 3 if-rC-~Cgr~lya~e~~kTkkC-~CG~~l~vk~~r 35 (68)
T PF09082_consen 3 IF-RC-DCGRYLYAKEGAKTKKC-VCGKTLKVKERR 35 (68)
T ss_dssp EE-EE-TTS--EEEETT-SEEEE-TTTEEEE--SSS
T ss_pred EE-Ee-cCCCEEEecCCcceeEe-cCCCeeeeeeEE
Confidence 56 99 89996 2 335779 999987776655
No 106
>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=74.96 E-value=1.8 Score=24.14 Aligned_cols=19 Identities=16% Similarity=0.223 Sum_probs=12.1
Q ss_pred ccCCccc--c---cCccccccCCC
Q 033276 74 CLKLFSS--P---FPLVICIKSNH 92 (123)
Q Consensus 74 C~gC~k~--~---~~~~fCp~CG~ 92 (123)
|..|+.. + ...--||+||.
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCcccCceEeCCCCCC
Confidence 6778665 2 22456999983
No 107
>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=74.51 E-value=2.4 Score=26.75 Aligned_cols=23 Identities=9% Similarity=-0.055 Sum_probs=14.9
Q ss_pred eeccccCCccc-ccCc-------------------cccccCCCC
Q 033276 70 IVDKCLKLFSS-PFPL-------------------VICIKSNHE 93 (123)
Q Consensus 70 vl~rC~gC~k~-~~~~-------------------~fCp~CG~~ 93 (123)
++ +|..|+.+ ++.. -.||.||.+
T Consensus 1 ky-~C~~CgyvYd~~~Gd~~~~i~pGt~F~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 1 KY-QCPVCGYVYDPEKGDPENGIPPGTPFEDLPDDWVCPVCGAP 43 (47)
T ss_dssp EE-EETTTSBEEETTTBBGGGTB-TT--GGGS-TT-B-TTTSSB
T ss_pred Cc-CCCCCCEEEcCCcCCcccCcCCCCCHHHCCCCCcCcCCCCc
Confidence 36 89999877 3222 179999976
No 108
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=73.94 E-value=1.7 Score=32.35 Aligned_cols=27 Identities=19% Similarity=0.137 Sum_probs=19.6
Q ss_pred cccCCccc-cc-C---ccccccCCCCCeeeEEE
Q 033276 73 KCLKLFSS-PF-P---LVICIKSNHEIRISPVF 100 (123)
Q Consensus 73 rC~gC~k~-~~-~---~~fCp~CG~~~tl~rV~ 100 (123)
+|+.|+++ +. . ..=||+||++ -...|+
T Consensus 4 ~CtrCG~vf~~g~~~il~GCp~CG~n-kF~yv~ 35 (112)
T COG3364 4 QCTRCGEVFDDGSEEILSGCPKCGCN-KFLYVP 35 (112)
T ss_pred eecccccccccccHHHHccCccccch-heEecc
Confidence 89999998 32 1 4669999998 454444
No 109
>PRK04023 DNA polymerase II large subunit; Validated
Probab=73.50 E-value=2.1 Score=42.10 Aligned_cols=29 Identities=21% Similarity=0.252 Sum_probs=21.3
Q ss_pred EEeeccccCCccc---ccCccccccCCCCCeee
Q 033276 68 RYIVDKCLKLFSS---PFPLVICIKSNHEIRIS 97 (123)
Q Consensus 68 ~wvl~rC~gC~k~---~~~~~fCp~CG~~~tl~ 97 (123)
+=.+ ||..|++. .+-..-||+||+++.|+
T Consensus 1035 rQ~f-RC~kC~~kYRR~PL~G~C~kCGg~lilT 1066 (1121)
T PRK04023 1035 RQEF-RCTKCGAKYRRPPLSGKCPKCGGNLILT 1066 (1121)
T ss_pred ccce-eecccCcccccCCCCCcCccCCCeEEEE
Confidence 3467 99999976 23347899999996543
No 110
>COG1933 Archaeal DNA polymerase II, large subunit [DNA replication, recombination, and repair]
Probab=72.95 E-value=1.7 Score=36.37 Aligned_cols=27 Identities=22% Similarity=0.242 Sum_probs=19.9
Q ss_pred eEEeeccccCCccc---ccCccccccCCCCC
Q 033276 67 HRYIVDKCLKLFSS---PFPLVICIKSNHEI 94 (123)
Q Consensus 67 ~~wvl~rC~gC~k~---~~~~~fCp~CG~~~ 94 (123)
.+-.. ||.+|.+. .+-..-||+||+.+
T Consensus 164 ~rq~~-rc~~c~~k~rr~pl~g~c~kcg~~~ 193 (253)
T COG1933 164 TRQEF-RCVKCNTKFRRPPLDGKCPICGGKI 193 (253)
T ss_pred hhhee-ehHhhhhhhcCCCccccccccCCeE
Confidence 34467 99999976 33347899999963
No 111
>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=72.82 E-value=1.9 Score=27.87 Aligned_cols=20 Identities=15% Similarity=0.243 Sum_probs=14.9
Q ss_pred cccCCcccccCccccccCCC
Q 033276 73 KCLKLFSSPFPLVICIKSNH 92 (123)
Q Consensus 73 rC~gC~k~~~~~~fCp~CG~ 92 (123)
.|+.|++...+...||.||.
T Consensus 28 ~C~~cG~~~~~H~vc~~cG~ 47 (55)
T TIGR01031 28 VCPNCGEFKLPHRVCPSCGY 47 (55)
T ss_pred ECCCCCCcccCeeECCccCe
Confidence 68888877556677888884
No 112
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=72.69 E-value=2.4 Score=34.03 Aligned_cols=30 Identities=7% Similarity=0.127 Sum_probs=24.1
Q ss_pred ccccCCccc---ccCccccccCCCCCeeeEEEEE
Q 033276 72 DKCLKLFSS---PFPLVICIKSNHEIRISPVFML 102 (123)
Q Consensus 72 ~rC~gC~k~---~~~~~fCp~CG~~~tl~rV~~~ 102 (123)
.+|.-|+.. .....-||+||+. -.||+|.-
T Consensus 150 A~CsrC~~~L~~~~~~l~Cp~Cg~t-EkRKia~~ 182 (188)
T COG1096 150 ARCSRCRAPLVKKGNMLKCPNCGNT-EKRKIAKD 182 (188)
T ss_pred EEccCCCcceEEcCcEEECCCCCCE-Eeeeeccc
Confidence 389999987 3345789999998 89998854
No 113
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=72.62 E-value=4.3 Score=30.85 Aligned_cols=43 Identities=14% Similarity=0.257 Sum_probs=32.6
Q ss_pred CCCCCCCceeccCC----C-CceeEEecccHHHHHHHHHhCceeeCCC
Q 033276 17 DDECSEQSWMLRSL----S-ESTVACITGDYAMQNVILQMGLRLLAPG 59 (123)
Q Consensus 17 ~~~~~~~~WIt~~~----~-~~~va~vTdDyAmQNVllqlGL~l~sv~ 59 (123)
.+.++.++||-+-. . ...+.++|+|.++|+.++..|-..++..
T Consensus 74 ~~~~tAD~~Ie~~v~~~~~~~~~v~VVTSD~~iq~~~~~~GA~~iss~ 121 (166)
T PF05991_consen 74 KEGETADDYIERLVRELKNRPRQVTVVTSDREIQRAARGRGAKRISSE 121 (166)
T ss_pred CCCCCHHHHHHHHHHHhccCCCeEEEEeCCHHHHHHHhhCCCEEEcHH
Confidence 34455567886431 2 4688999999999999999999888763
No 114
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=72.49 E-value=2.1 Score=39.27 Aligned_cols=23 Identities=22% Similarity=0.174 Sum_probs=17.0
Q ss_pred eccccCCcccccCccccccCCCC
Q 033276 71 VDKCLKLFSSPFPLVICIKSNHE 93 (123)
Q Consensus 71 l~rC~gC~k~~~~~~fCp~CG~~ 93 (123)
+++|..|+..-.-...||+||++
T Consensus 559 ~~~C~~CGy~g~~~~~CP~CG~~ 581 (618)
T PRK14704 559 VDRCKCCSYHGVIGNECPSCGNE 581 (618)
T ss_pred CeecCCCCCCCCcCccCcCCCCC
Confidence 46899999752223679999976
No 115
>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=72.33 E-value=2.3 Score=26.27 Aligned_cols=13 Identities=23% Similarity=0.422 Sum_probs=9.8
Q ss_pred ccccCCCCCeeeE
Q 033276 86 ICIKSNHEIRISP 98 (123)
Q Consensus 86 fCp~CG~~~tl~r 98 (123)
.||.||++..+++
T Consensus 1 ~CP~Cg~~a~ir~ 13 (47)
T PF04606_consen 1 RCPHCGSKARIRT 13 (47)
T ss_pred CcCCCCCeeEEEE
Confidence 3999999965554
No 116
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=72.32 E-value=2.3 Score=27.83 Aligned_cols=21 Identities=14% Similarity=0.286 Sum_probs=15.5
Q ss_pred cccCCcccccCccccccCCCC
Q 033276 73 KCLKLFSSPFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~~~~~~fCp~CG~~ 93 (123)
.|+.|+....+...||.||.=
T Consensus 29 ~C~~CG~~~~~H~vC~~CG~Y 49 (57)
T PRK12286 29 ECPNCGEPKLPHRVCPSCGYY 49 (57)
T ss_pred ECCCCCCccCCeEECCCCCcC
Confidence 688888775556778888854
No 117
>COG1458 Predicted DNA-binding protein containing PIN domain [General function prediction only]
Probab=72.29 E-value=3.3 Score=34.05 Aligned_cols=29 Identities=21% Similarity=0.324 Sum_probs=26.2
Q ss_pred CCceeEEecccHHHHHHHHHhCceeeCCC
Q 033276 31 SESTVACITGDYAMQNVILQMGLRLLAPG 59 (123)
Q Consensus 31 ~~~~va~vTdDyAmQNVllqlGL~l~sv~ 59 (123)
.++++++++.|..+.--+.+|||+|+...
T Consensus 172 kELdaavVssD~Gir~WAe~LGlrfv~a~ 200 (221)
T COG1458 172 KELDAAVVSSDEGIRTWAEKLGLRFVDAF 200 (221)
T ss_pred HHhCceEEecchhHHHHHHHhCCeeeCHh
Confidence 36789999999999999999999999864
No 118
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=72.27 E-value=2.3 Score=42.57 Aligned_cols=29 Identities=24% Similarity=0.223 Sum_probs=21.2
Q ss_pred EEeeccccCCccc---ccCccccccCCCCCeee
Q 033276 68 RYIVDKCLKLFSS---PFPLVICIKSNHEIRIS 97 (123)
Q Consensus 68 ~wvl~rC~gC~k~---~~~~~fCp~CG~~~tl~ 97 (123)
+=.+ ||..|++. .+-..-||+||+++.|+
T Consensus 1251 rQ~~-RC~kC~~kyRR~PL~G~C~kCGg~iilT 1282 (1337)
T PRK14714 1251 RQEF-RCLKCGTKYRRMPLAGKCRKCGGRIILT 1282 (1337)
T ss_pred ccce-eecccCcccccCCCCCcccccCCeEEEE
Confidence 3467 99999975 23347899999996443
No 119
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=71.91 E-value=1.8 Score=33.96 Aligned_cols=42 Identities=17% Similarity=0.322 Sum_probs=29.9
Q ss_pred hCceeeCCCCCcceee--eEEeeccccCCccc-------ccCc----cccccCCCCC
Q 033276 51 MGLRLLAPGGMQIRQL--HRYIVDKCLKLFSS-------PFPL----VICIKSNHEI 94 (123)
Q Consensus 51 lGL~l~sv~g~~I~~v--~~wvl~rC~gC~k~-------~~~~----~fCp~CG~~~ 94 (123)
.|+++....+.-++++ .+|-| +|. |+.. +..+ -.|-+||.++
T Consensus 96 ~~l~~~~~h~~~~~~v~~~~~~Y-~C~-C~q~~l~~RRhn~~~~g~~YrC~~C~gkL 150 (156)
T COG3091 96 LGLRFCRTHQFEVQSVRRTTYPY-RCQ-CQQHYLRIRRHNTVRRGEVYRCGKCGGKL 150 (156)
T ss_pred CCCCCCccchHHHhhccccceeE-Eee-cCCccchhhhcccccccceEEeccCCceE
Confidence 3666666555555554 48999 999 9974 3334 7899999994
No 120
>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=71.84 E-value=2.5 Score=26.03 Aligned_cols=9 Identities=11% Similarity=0.187 Sum_probs=4.3
Q ss_pred cccccCCCC
Q 033276 85 VICIKSNHE 93 (123)
Q Consensus 85 ~fCp~CG~~ 93 (123)
..||.||.|
T Consensus 18 ~~Cp~C~~P 26 (41)
T PF06677_consen 18 EHCPDCGTP 26 (41)
T ss_pred CccCCCCCe
Confidence 345555544
No 121
>PRK05580 primosome assembly protein PriA; Validated
Probab=71.32 E-value=3.2 Score=38.00 Aligned_cols=24 Identities=21% Similarity=0.523 Sum_probs=16.2
Q ss_pred cccCCccc-ccCccccccCCCCCeeeE
Q 033276 73 KCLKLFSS-PFPLVICIKSNHEIRISP 98 (123)
Q Consensus 73 rC~gC~k~-~~~~~fCp~CG~~~tl~r 98 (123)
+||-|+.. +.+ ..||.||+. .++.
T Consensus 410 ~Ch~Cg~~~~~~-~~Cp~Cg~~-~l~~ 434 (679)
T PRK05580 410 RCHHCGYQEPIP-KACPECGST-DLVP 434 (679)
T ss_pred ECCCCcCCCCCC-CCCCCCcCC-eeEE
Confidence 57777766 333 579999988 4443
No 122
>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=70.54 E-value=2.5 Score=29.09 Aligned_cols=25 Identities=8% Similarity=0.098 Sum_probs=14.3
Q ss_pred eeccccCCcccccCccccccCCCCCe
Q 033276 70 IVDKCLKLFSSPFPLVICIKSNHEIR 95 (123)
Q Consensus 70 vl~rC~gC~k~~~~~~fCp~CG~~~t 95 (123)
.+ .|.+|.+.-...-+||.||.++.
T Consensus 17 ~~-~C~~C~~~~~~~a~CPdC~~~Le 41 (70)
T PF07191_consen 17 HY-HCEACQKDYKKEAFCPDCGQPLE 41 (70)
T ss_dssp EE-EETTT--EEEEEEE-TTT-SB-E
T ss_pred EE-ECccccccceecccCCCcccHHH
Confidence 46 88888876233478999999943
No 123
>PRK07218 replication factor A; Provisional
Probab=70.35 E-value=2.1 Score=37.74 Aligned_cols=50 Identities=12% Similarity=0.143 Sum_probs=29.8
Q ss_pred HHHHHHHHHhCceeeCCCC--CcceeeeEEeeccccCCcccccCccccccCCCC
Q 033276 42 YAMQNVILQMGLRLLAPGG--MQIRQLHRYIVDKCLKLFSSPFPLVICIKSNHE 93 (123)
Q Consensus 42 yAmQNVllqlGL~l~sv~g--~~I~~v~~wvl~rC~gC~k~~~~~~fCp~CG~~ 93 (123)
..+.+.+..-|..-+.+.| -.|++-.-... ||+.|.|. ..+..||.||..
T Consensus 267 ~~I~e~~~~~g~~~Vev~G~Iv~i~~gsgli~-rCP~C~r~-v~~~~C~~hG~v 318 (423)
T PRK07218 267 LKIREAVERGGIFDVELVGNIISVRDGSGLIE-RCPECGRV-IQKGQCRSHGAV 318 (423)
T ss_pred cchhhhhccCCcceEEEEEEEEEeccCCccee-cCcCcccc-ccCCcCCCCCCc
Confidence 3455544433332133434 23445556777 99999998 223689999954
No 124
>COG4640 Predicted membrane protein [Function unknown]
Probab=70.04 E-value=2.3 Score=38.10 Aligned_cols=24 Identities=25% Similarity=0.239 Sum_probs=18.3
Q ss_pred cccCCccc-ccCccccccCCCCCee
Q 033276 73 KCLKLFSS-PFPLVICIKSNHEIRI 96 (123)
Q Consensus 73 rC~gC~k~-~~~~~fCp~CG~~~tl 96 (123)
-|+-|++- ...-.+||.||++.+-
T Consensus 3 fC~kcG~qk~Ed~~qC~qCG~~~t~ 27 (465)
T COG4640 3 FCPKCGSQKAEDDVQCTQCGHKFTS 27 (465)
T ss_pred cccccccccccccccccccCCcCCc
Confidence 69999966 4444669999999643
No 125
>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=70.03 E-value=2.7 Score=32.03 Aligned_cols=22 Identities=9% Similarity=0.084 Sum_probs=17.1
Q ss_pred cccCCccc--ccC--ccccccCCCCC
Q 033276 73 KCLKLFSS--PFP--LVICIKSNHEI 94 (123)
Q Consensus 73 rC~gC~k~--~~~--~~fCp~CG~~~ 94 (123)
.|+.|++. ++. -..||+||...
T Consensus 11 ~Cp~cg~kFYDLnk~p~vcP~cg~~~ 36 (129)
T TIGR02300 11 ICPNTGSKFYDLNRRPAVSPYTGEQF 36 (129)
T ss_pred cCCCcCccccccCCCCccCCCcCCcc
Confidence 79999986 433 37899999873
No 126
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=69.56 E-value=5.2 Score=33.91 Aligned_cols=21 Identities=14% Similarity=0.295 Sum_probs=18.8
Q ss_pred cccCCccc-ccCccccccCCCC
Q 033276 73 KCLKLFSS-PFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~-~~~~~fCp~CG~~ 93 (123)
.|.-|... ...+.-||.||+.
T Consensus 212 ~CslC~teW~~~R~~C~~Cg~~ 233 (305)
T TIGR01562 212 SCSLCATEWHYVRVKCSHCEES 233 (305)
T ss_pred EcCCCCCcccccCccCCCCCCC
Confidence 59999988 8889999999986
No 127
>PRK14873 primosome assembly protein PriA; Provisional
Probab=69.13 E-value=3.8 Score=37.91 Aligned_cols=20 Identities=10% Similarity=0.082 Sum_probs=9.4
Q ss_pred cccCCcccccCccccccCCCC
Q 033276 73 KCLKLFSSPFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~~~~~~fCp~CG~~ 93 (123)
+||-|+.... -..||.||++
T Consensus 412 ~Ch~CG~~~~-p~~Cp~Cgs~ 431 (665)
T PRK14873 412 RCRWCGRAAP-DWRCPRCGSD 431 (665)
T ss_pred ECCCCcCCCc-CccCCCCcCC
Confidence 4444444311 2356666665
No 128
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=68.75 E-value=2.6 Score=35.98 Aligned_cols=27 Identities=22% Similarity=0.335 Sum_probs=21.0
Q ss_pred eEEeeccccCCccc------ccCccccccCCCCCe
Q 033276 67 HRYIVDKCLKLFSS------PFPLVICIKSNHEIR 95 (123)
Q Consensus 67 ~~wvl~rC~gC~k~------~~~~~fCp~CG~~~t 95 (123)
--|.. |++|+.. ......||+||+...
T Consensus 26 ~lw~K--Cp~c~~~~y~~eL~~n~~vcp~c~~h~r 58 (294)
T COG0777 26 GLWTK--CPSCGEMLYRKELESNLKVCPKCGHHMR 58 (294)
T ss_pred CceeE--CCCccceeeHHHHHhhhhcccccCcccc
Confidence 46876 9999986 244788999999843
No 129
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=68.68 E-value=2.2 Score=25.22 Aligned_cols=21 Identities=29% Similarity=0.388 Sum_probs=15.7
Q ss_pred cccCCccc---c-------cCccccccCCCC
Q 033276 73 KCLKLFSS---P-------FPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~---~-------~~~~fCp~CG~~ 93 (123)
+|+.|.+. + ..+.-||+||+.
T Consensus 4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~ 34 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHV 34 (37)
T ss_pred ECCCCCceEEcCHHHcccCCcEEECCCCCcE
Confidence 79999875 2 226789999986
No 130
>COG0267 RpmG Ribosomal protein L33 [Translation, ribosomal structure and biogenesis]
Probab=68.68 E-value=4 Score=26.38 Aligned_cols=29 Identities=7% Similarity=0.085 Sum_probs=20.1
Q ss_pred EEeeccccCCc-cc---------c----cCccccccCCCCCeeeE
Q 033276 68 RYIVDKCLKLF-SS---------P----FPLVICIKSNHEIRISP 98 (123)
Q Consensus 68 ~wvl~rC~gC~-k~---------~----~~~~fCp~CG~~~tl~r 98 (123)
.-.+ .|.+|. +. . .-+.|||+|+.. |+.|
T Consensus 5 kI~L-~ct~c~g~nY~t~kN~r~~~~rLelkKycp~~~kh-tlhk 47 (50)
T COG0267 5 KIKL-ACTACTSRNYTTTKNKRNKPERLELKKYCPVCRKH-TLHK 47 (50)
T ss_pred eEEE-EEeccCCeeEEEeeccCCCcceEEEEecCcccccE-EEEe
Confidence 3456 888888 21 1 126899999999 7765
No 131
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=68.57 E-value=6.2 Score=23.75 Aligned_cols=8 Identities=25% Similarity=0.484 Sum_probs=6.3
Q ss_pred ccccCCCC
Q 033276 86 ICIKSNHE 93 (123)
Q Consensus 86 fCp~CG~~ 93 (123)
-||+||++
T Consensus 2 ~Cp~C~~~ 9 (40)
T smart00440 2 PCPKCGNR 9 (40)
T ss_pred cCCCCCCC
Confidence 48888877
No 132
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=68.53 E-value=3 Score=42.22 Aligned_cols=28 Identities=18% Similarity=0.183 Sum_probs=20.2
Q ss_pred EEeeccccCCccc---ccCccccccCCCCCeee
Q 033276 68 RYIVDKCLKLFSS---PFPLVICIKSNHEIRIS 97 (123)
Q Consensus 68 ~wvl~rC~gC~k~---~~~~~fCp~CG~~~tl~ 97 (123)
+=.+ || .|++. .+-..-||+||+++.|+
T Consensus 1540 rQ~~-RC-kC~~kyRR~PL~G~C~kCGg~~ilT 1570 (1627)
T PRK14715 1540 RQEF-RC-KCGAKYRRVPLKGKCPKCGSKLILT 1570 (1627)
T ss_pred ccce-ee-cCCCccccCCCCCcCcccCCeEEEE
Confidence 3457 99 99975 33357899999996443
No 133
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=68.27 E-value=4.5 Score=37.74 Aligned_cols=58 Identities=19% Similarity=0.232 Sum_probs=31.7
Q ss_pred HHHHHHHHh--CceeeCCCCCcceeeeEEeeccccCCccc-cc----CccccccCCCCCeeeEEEEEeeEEEEEe
Q 033276 43 AMQNVILQM--GLRLLAPGGMQIRQLHRYIVDKCLKLFSS-PF----PLVICIKSNHEIRISPVFMLILICLYIQ 110 (123)
Q Consensus 43 AmQNVllql--GL~l~sv~g~~I~~v~~wvl~rC~gC~k~-~~----~~~fCp~CG~~~tl~rV~~~~~~~~~~~ 110 (123)
|+.++.+.+ +|...++. -.+++|..|+.. .. ....||+||++ --.++.+.-=++=|+.
T Consensus 620 a~~~lv~~~~~~i~Y~~in---------~~~~~C~~CG~~Ge~~~~~~~~~CP~CG~~-~~~~~~v~~Ri~GYl~ 684 (711)
T PRK09263 620 ALEAVWDYSYDRVGYLGTN---------TPIDECYECGFTGEFECTEKGFTCPKCGNH-DPKTVSVTRRTCGYLG 684 (711)
T ss_pred HHHHHHHHHHHCCCeEEeC---------CCCcccCCCCCCccccCCCCCCcCcCCCCC-CCcceeEEEeeccccC
Confidence 666665553 44444442 234699999975 21 13679999986 2223333333333553
No 134
>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=68.08 E-value=1.7 Score=28.96 Aligned_cols=30 Identities=10% Similarity=0.057 Sum_probs=20.8
Q ss_pred eEEeeccccCCccc--ccCccccccCCCCCeee
Q 033276 67 HRYIVDKCLKLFSS--PFPLVICIKSNHEIRIS 97 (123)
Q Consensus 67 ~~wvl~rC~gC~k~--~~~~~fCp~CG~~~tl~ 97 (123)
+.-.+ .|+-|..- ..-...||+||+.++.|
T Consensus 23 ~ICSf-ECTFC~~C~e~~l~~~CPNCgGelv~R 54 (57)
T PF06906_consen 23 YICSF-ECTFCADCAETMLNGVCPNCGGELVRR 54 (57)
T ss_pred eEEeE-eCcccHHHHHHHhcCcCcCCCCccccC
Confidence 34456 78888765 33368899999996544
No 135
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=68.00 E-value=5.8 Score=33.78 Aligned_cols=21 Identities=19% Similarity=0.211 Sum_probs=18.8
Q ss_pred cccCCccc-ccCccccccCCCC
Q 033276 73 KCLKLFSS-PFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~-~~~~~fCp~CG~~ 93 (123)
.|.-|... ...+.-||.||+.
T Consensus 214 ~CslC~teW~~~R~~C~~Cg~~ 235 (309)
T PRK03564 214 HCNLCESEWHVVRVKCSNCEQS 235 (309)
T ss_pred EcCCCCCcccccCccCCCCCCC
Confidence 59999988 8889999999986
No 136
>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=67.98 E-value=1.3 Score=29.33 Aligned_cols=21 Identities=24% Similarity=0.298 Sum_probs=16.7
Q ss_pred cccCCccc-ccCcccc-ccCCCC
Q 033276 73 KCLKLFSS-PFPLVIC-IKSNHE 93 (123)
Q Consensus 73 rC~gC~k~-~~~~~fC-p~CG~~ 93 (123)
-|+-|++. ++++.|| +.|+..
T Consensus 5 HC~~CG~~Ip~~~~fCS~~C~~~ 27 (59)
T PF09889_consen 5 HCPVCGKPIPPDESFCSPKCREE 27 (59)
T ss_pred cCCcCCCcCCcchhhhCHHHHHH
Confidence 48888887 7788899 688765
No 137
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=67.83 E-value=1.7 Score=41.82 Aligned_cols=20 Identities=15% Similarity=0.150 Sum_probs=0.0
Q ss_pred cccCCcccccCccccccCCCC
Q 033276 73 KCLKLFSSPFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~~~~~~fCp~CG~~ 93 (123)
+|+.|++. .....||.||++
T Consensus 657 ~Cp~Cg~~-t~~~~Cp~CG~~ 676 (900)
T PF03833_consen 657 RCPKCGKE-TFYNRCPECGSH 676 (900)
T ss_dssp ---------------------
T ss_pred cCcccCCc-chhhcCcccCCc
Confidence 56666654 112335555555
No 138
>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=67.70 E-value=2.8 Score=41.40 Aligned_cols=22 Identities=23% Similarity=0.199 Sum_probs=18.1
Q ss_pred eccccCCccc------------ccCccccccCCCC
Q 033276 71 VDKCLKLFSS------------PFPLVICIKSNHE 93 (123)
Q Consensus 71 l~rC~gC~k~------------~~~~~fCp~CG~~ 93 (123)
| +|+.|+.. |++.+-||+||.+
T Consensus 684 y-~c~~c~~~ef~~~~~~~sg~dlp~k~cp~c~~~ 717 (1213)
T TIGR01405 684 Y-LCPNCKYSEFITDGSVGSGFDLPDKDCPKCGAP 717 (1213)
T ss_pred c-cCcccccccccccccccccccCccccCcccccc
Confidence 7 99999873 3566789999988
No 139
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=67.50 E-value=3.3 Score=41.60 Aligned_cols=22 Identities=23% Similarity=0.212 Sum_probs=18.1
Q ss_pred eccccCCccc------------ccCccccccCCCC
Q 033276 71 VDKCLKLFSS------------PFPLVICIKSNHE 93 (123)
Q Consensus 71 l~rC~gC~k~------------~~~~~fCp~CG~~ 93 (123)
| +|+.|+.. |.+-+-||+||.|
T Consensus 915 Y-~Cp~Cky~Ef~~d~svgsGfDLpdK~CPkCg~p 948 (1444)
T COG2176 915 Y-LCPECKYSEFIDDGSVGSGFDLPDKDCPKCGTP 948 (1444)
T ss_pred c-cCCCCceeeeecCCCcCCCCCCCCCCCCcCCCc
Confidence 6 99999864 2556889999999
No 140
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=67.26 E-value=2.9 Score=42.07 Aligned_cols=22 Identities=23% Similarity=0.238 Sum_probs=17.8
Q ss_pred eccccCCccc------------ccCccccccCCCC
Q 033276 71 VDKCLKLFSS------------PFPLVICIKSNHE 93 (123)
Q Consensus 71 l~rC~gC~k~------------~~~~~fCp~CG~~ 93 (123)
| +|+.|+.. |++.+-||+||.+
T Consensus 909 y-~C~~C~~~ef~~~~~~~sG~Dlpdk~Cp~Cg~~ 942 (1437)
T PRK00448 909 Y-VCPNCKYSEFFTDGSVGSGFDLPDKDCPKCGTK 942 (1437)
T ss_pred c-cCcccccccccccccccccccCccccCcccccc
Confidence 6 99999875 2456789999998
No 141
>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=66.70 E-value=1.6 Score=28.29 Aligned_cols=14 Identities=7% Similarity=0.176 Sum_probs=10.0
Q ss_pred ccCccccccCCCCC
Q 033276 81 PFPLVICIKSNHEI 94 (123)
Q Consensus 81 ~~~~~fCp~CG~~~ 94 (123)
...+.||+.||.++
T Consensus 45 ~~~r~FC~~CGs~l 58 (92)
T PF04828_consen 45 GVERYFCPTCGSPL 58 (92)
T ss_dssp SCEEEEETTT--EE
T ss_pred cCcCcccCCCCCee
Confidence 56689999999994
No 142
>PRK05978 hypothetical protein; Provisional
Probab=66.55 E-value=2.8 Score=32.25 Aligned_cols=28 Identities=11% Similarity=0.201 Sum_probs=20.4
Q ss_pred EEeeccccCCcccc------cCccccccCCCCCee
Q 033276 68 RYIVDKCLKLFSSP------FPLVICIKSNHEIRI 96 (123)
Q Consensus 68 ~wvl~rC~gC~k~~------~~~~fCp~CG~~~tl 96 (123)
-+.. ||+.|++-. .-.+.||.||.+...
T Consensus 31 Gl~g-rCP~CG~G~LF~g~Lkv~~~C~~CG~~~~~ 64 (148)
T PRK05978 31 GFRG-RCPACGEGKLFRAFLKPVDHCAACGEDFTH 64 (148)
T ss_pred HHcC-cCCCCCCCcccccccccCCCccccCCcccc
Confidence 3556 999999751 236889999998433
No 143
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=66.15 E-value=3.4 Score=32.96 Aligned_cols=27 Identities=15% Similarity=0.142 Sum_probs=22.4
Q ss_pred cccCCccc-ccCccccccCCCCCeeeEE
Q 033276 73 KCLKLFSS-PFPLVICIKSNHEIRISPV 99 (123)
Q Consensus 73 rC~gC~k~-~~~~~fCp~CG~~~tl~rV 99 (123)
+|..|+.+ ....-.||.||+--|++..
T Consensus 356 ~c~~cg~~~~~~~~~c~~c~~~~~~~~~ 383 (389)
T PRK11788 356 RCRNCGFTARTLYWHCPSCKAWETIKPI 383 (389)
T ss_pred ECCCCCCCCccceeECcCCCCccCcCCc
Confidence 79999998 6667899999998777654
No 144
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=66.07 E-value=4.2 Score=27.91 Aligned_cols=26 Identities=19% Similarity=0.379 Sum_probs=19.6
Q ss_pred EEeeccccCCccc------ccCccccccCCCC
Q 033276 68 RYIVDKCLKLFSS------PFPLVICIKSNHE 93 (123)
Q Consensus 68 ~wvl~rC~gC~k~------~~~~~fCp~CG~~ 93 (123)
+|..-+|++|+.. ..+...|+.||.-
T Consensus 16 ~Fl~VkCpdC~N~q~vFshast~V~C~~CG~~ 47 (67)
T COG2051 16 RFLRVKCPDCGNEQVVFSHASTVVTCLICGTT 47 (67)
T ss_pred eEEEEECCCCCCEEEEeccCceEEEecccccE
Confidence 3444489999986 3557899999975
No 145
>PLN02569 threonine synthase
Probab=65.76 E-value=6.1 Score=35.10 Aligned_cols=54 Identities=13% Similarity=0.057 Sum_probs=34.8
Q ss_pred eEEecccHHHHHHHHHhCceeeCCCCCcceeeeEEeeccccCCccc-c--cCccccccCCCCC
Q 033276 35 VACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSS-P--FPLVICIKSNHEI 94 (123)
Q Consensus 35 va~vTdDyAmQNVllqlGL~l~sv~g~~I~~v~~wvl~rC~gC~k~-~--~~~~fCp~CG~~~ 94 (123)
..-.|.|-++|-++++ +... +. ..+.-...+.+ +|..|++. + .....| .||..+
T Consensus 18 ~~~~~~~~~~~~~~~~-~~~~-~~--~~~~~~~~~~l-~C~~Cg~~y~~~~~~~~C-~cgg~l 74 (484)
T PLN02569 18 ATKFTADENIRDEARR-GPPA-PP--DEFSAKYVPFL-ECPLTGEKYSLDEVVYRS-KSGGLL 74 (484)
T ss_pred ccccCcchhhhhhhhh-cCCC-CC--ccccccccccc-EeCCCCCcCCCccccccC-CCCCeE
Confidence 4568899999999998 2211 11 22222223358 99999987 3 334679 699875
No 146
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=65.26 E-value=6.8 Score=27.95 Aligned_cols=42 Identities=10% Similarity=0.072 Sum_probs=26.1
Q ss_pred EeeccccCCccc------ccCccccccCCCCC---eeeEEEEEeeEEEEEe
Q 033276 69 YIVDKCLKLFSS------PFPLVICIKSNHEI---RISPVFMLILICLYIQ 110 (123)
Q Consensus 69 wvl~rC~gC~k~------~~~~~fCp~CG~~~---tl~rV~~~~~~~~~~~ 110 (123)
|..-+|++|+++ ..+...|..||..+ |=-|...+-|-+.+-|
T Consensus 33 Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~PTGGKa~l~~gc~fr~k 83 (85)
T PTZ00083 33 FMDVKCPGCSQITTVFSHAQTVVLCGGCSSQLCQPTGGKAKLTEGCSFRRK 83 (85)
T ss_pred EEEEECCCCCCeeEEEecCceEEEccccCCEeeccCCCCeEecCCceEEec
Confidence 333489999987 24568999999763 2334444444444433
No 147
>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=65.14 E-value=6.3 Score=34.09 Aligned_cols=38 Identities=18% Similarity=0.281 Sum_probs=16.9
Q ss_pred cceeeeEEeeccccCCccc-----ccCccccccCCCCCeeeEEEEE
Q 033276 62 QIRQLHRYIVDKCLKLFSS-----PFPLVICIKSNHEIRISPVFML 102 (123)
Q Consensus 62 ~I~~v~~wvl~rC~gC~k~-----~~~~~fCp~CG~~~tl~rV~~~ 102 (123)
.++-+++|- +|..|+.. ..|..-|++||+. --.|++|.
T Consensus 278 ~~~a~KRFF--kC~~C~~Rt~sl~r~P~~~C~~Cg~~-~wer~~M~ 320 (344)
T PF09332_consen 278 WHDAVKRFF--KCKDCGNRTISLERLPKKHCSNCGSS-KWERTGML 320 (344)
T ss_dssp EEEEE-EEE--E-T-TS-EEEESSSS--S--TTT-S----EEE---
T ss_pred EeeeeeeeE--ECCCCCCeeeecccCCCCCCCcCCcC-ceeehhhh
Confidence 445567775 59999973 4677899999998 78888863
No 148
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=65.11 E-value=3.5 Score=28.68 Aligned_cols=20 Identities=15% Similarity=-0.111 Sum_probs=15.0
Q ss_pred cccCCccc----ccC--ccccccCCC
Q 033276 73 KCLKLFSS----PFP--LVICIKSNH 92 (123)
Q Consensus 73 rC~gC~k~----~~~--~~fCp~CG~ 92 (123)
.|+-|+.. ... .++||+|+=
T Consensus 3 ~CPCCg~~Tl~~~~~~~ydIC~VC~W 28 (78)
T PF14206_consen 3 PCPCCGYYTLEERGEGTYDICPVCFW 28 (78)
T ss_pred cCCCCCcEEeccCCCcCceECCCCCc
Confidence 79999975 222 779999983
No 149
>PRK04860 hypothetical protein; Provisional
Probab=64.60 E-value=8.8 Score=29.59 Aligned_cols=55 Identities=7% Similarity=0.144 Sum_probs=33.3
Q ss_pred cHHHHHHHHH-hCceeeCCCCCccee--eeEEeeccccCCccc-------c-----cCccccccCCCCCeee
Q 033276 41 DYAMQNVILQ-MGLRLLAPGGMQIRQ--LHRYIVDKCLKLFSS-------P-----FPLVICIKSNHEIRIS 97 (123)
Q Consensus 41 DyAmQNVllq-lGL~l~sv~g~~I~~--v~~wvl~rC~gC~k~-------~-----~~~~fCp~CG~~~tl~ 97 (123)
|-.=|-++.+ +|++........|.. .+.|.| +|. |.+. . ...-.|..||.++...
T Consensus 87 g~ewk~lm~~v~g~~~r~~h~~~~~~~~~~~~~Y-~C~-C~~~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 87 GKEWQWMMESVLGVPARRTHQFEVQSVRGKTFPY-RCK-CQEHQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred CHHHHHHHHHhcCCCCcccCCCcCCccccCEEEE-EcC-CCCeeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 5555677776 476333333223332 457999 997 9542 1 3347899999995443
No 150
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=64.46 E-value=4.4 Score=34.71 Aligned_cols=26 Identities=15% Similarity=0.031 Sum_probs=21.4
Q ss_pred cccCCccc-ccCccccccCCCCCeeeE
Q 033276 73 KCLKLFSS-PFPLVICIKSNHEIRISP 98 (123)
Q Consensus 73 rC~gC~k~-~~~~~fCp~CG~~~tl~r 98 (123)
+|..|+.. +.....||.||.=.|+..
T Consensus 2 ~c~~cg~~~~~~~g~cp~c~~w~~~~e 28 (372)
T cd01121 2 VCSECGYVSPKWLGKCPECGEWNTLVE 28 (372)
T ss_pred CCCCCCCCCCCccEECcCCCCceeeee
Confidence 89999988 667788999998777766
No 151
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=64.21 E-value=4.3 Score=31.22 Aligned_cols=27 Identities=7% Similarity=0.085 Sum_probs=22.4
Q ss_pred cccCCccc--cc--CccccccCCCCCeeeEEE
Q 033276 73 KCLKLFSS--PF--PLVICIKSNHEIRISPVF 100 (123)
Q Consensus 73 rC~gC~k~--~~--~~~fCp~CG~~~tl~rV~ 100 (123)
+|..|+.. +. ....||.||+. -.||||
T Consensus 151 ~~~~~g~~~~~~~~~~~~c~~~~~~-e~rkva 181 (189)
T PRK09521 151 MCSRCRTPLVKKGENELKCPNCGNI-ETRKLS 181 (189)
T ss_pred EccccCCceEECCCCEEECCCCCCE-Eeeccc
Confidence 79999986 32 46899999988 889998
No 152
>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=63.96 E-value=3.5 Score=26.72 Aligned_cols=10 Identities=20% Similarity=0.481 Sum_probs=9.1
Q ss_pred ccccccCCCC
Q 033276 84 LVICIKSNHE 93 (123)
Q Consensus 84 ~~fCp~CG~~ 93 (123)
...||+|||.
T Consensus 13 Y~~Cp~CGN~ 22 (49)
T PF12677_consen 13 YCKCPKCGND 22 (49)
T ss_pred hccCcccCCc
Confidence 5789999999
No 153
>COG4031 Predicted metal-binding protein [General function prediction only]
Probab=63.90 E-value=3.6 Score=33.73 Aligned_cols=19 Identities=16% Similarity=0.520 Sum_probs=16.5
Q ss_pred cccCCccc-ccCccccccCCCC
Q 033276 73 KCLKLFSS-PFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~-~~~~~fCp~CG~~ 93 (123)
+| -|+.. +.+ .||+.||.+
T Consensus 2 ~C-rCG~~l~~p-~~Cl~Cg~~ 21 (227)
T COG4031 2 IC-RCGAELSSP-AFCLNCGRR 21 (227)
T ss_pred cc-ccCCccccc-chhcccCCc
Confidence 68 89988 666 999999987
No 154
>PRK11823 DNA repair protein RadA; Provisional
Probab=63.82 E-value=4.9 Score=35.01 Aligned_cols=30 Identities=13% Similarity=0.050 Sum_probs=25.0
Q ss_pred EEeeccccCCccc-ccCccccccCCCCCeeeE
Q 033276 68 RYIVDKCLKLFSS-PFPLVICIKSNHEIRISP 98 (123)
Q Consensus 68 ~wvl~rC~gC~k~-~~~~~fCp~CG~~~tl~r 98 (123)
+-.| +|..|+.. ....-.||.||.-.|+..
T Consensus 5 ~~~y-~C~~Cg~~~~~~~g~Cp~C~~w~t~~e 35 (446)
T PRK11823 5 KTAY-VCQECGAESPKWLGRCPECGAWNTLVE 35 (446)
T ss_pred CCeE-ECCcCCCCCcccCeeCcCCCCccceee
Confidence 4568 99999988 767788999998877766
No 155
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=63.62 E-value=4.1 Score=21.67 Aligned_cols=21 Identities=10% Similarity=0.029 Sum_probs=17.2
Q ss_pred cccCCccc-ccCccccccCCCC
Q 033276 73 KCLKLFSS-PFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~-~~~~~fCp~CG~~ 93 (123)
.|.+|... ...+..|..||.+
T Consensus 4 ~C~~C~~~N~~~~~~C~~C~~p 25 (26)
T smart00547 4 ECPACTFLNFASRSKCFACGAP 25 (26)
T ss_pred cCCCCCCcChhhhccccccCCc
Confidence 68999877 5667889999976
No 156
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=63.43 E-value=7.9 Score=28.17 Aligned_cols=35 Identities=14% Similarity=0.069 Sum_probs=20.9
Q ss_pred EEeecccc--CCccc---c-cCccccccCCCCC--eeeEEEEE
Q 033276 68 RYIVDKCL--KLFSS---P-FPLVICIKSNHEI--RISPVFML 102 (123)
Q Consensus 68 ~wvl~rC~--gC~k~---~-~~~~fCp~CG~~~--tl~rV~~~ 102 (123)
.|-|..|+ .|++. . ...-+|++||... ...|..+.
T Consensus 15 ~~~Y~aC~~~~C~kKv~~~~~~~y~C~~C~~~~~~~~~ry~l~ 57 (146)
T PF08646_consen 15 NWYYPACPNEKCNKKVTENGDGSYRCEKCNKTVENPKYRYRLS 57 (146)
T ss_dssp TTEEEE-TSTTTS-B-EEETTTEEEETTTTEEESS-EEEEEEE
T ss_pred CcEECCCCCccCCCEeecCCCcEEECCCCCCcCCCeeEEEEEE
Confidence 46666999 99986 2 2356999999762 34444433
No 157
>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=63.27 E-value=2.9 Score=27.50 Aligned_cols=26 Identities=12% Similarity=-0.026 Sum_probs=20.1
Q ss_pred cCccccccCCCCCeeeEEEEEeeEEEE
Q 033276 82 FPLVICIKSNHEIRISPVFMLILICLY 108 (123)
Q Consensus 82 ~~~~fCp~CG~~~tl~rV~~~~~~~~~ 108 (123)
+....||.||+. ..++|....|...|
T Consensus 5 p~~~~CP~C~~~-~~T~v~~~~g~~t~ 30 (73)
T PF10601_consen 5 PVRIYCPYCQQQ-VQTRVEYKSGTMTY 30 (73)
T ss_pred ceeeECCCCCCE-EEEEEEEEeChHHH
Confidence 345889999999 89999877765544
No 158
>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=63.26 E-value=3.1 Score=24.20 Aligned_cols=21 Identities=33% Similarity=0.456 Sum_probs=10.7
Q ss_pred cccCCccc----ccCccccccCCCC
Q 033276 73 KCLKLFSS----PFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~----~~~~~fCp~CG~~ 93 (123)
.|+-|... +.....||.||+.
T Consensus 4 ~Cp~C~se~~y~D~~~~vCp~C~~e 28 (30)
T PF08274_consen 4 KCPLCGSEYTYEDGELLVCPECGHE 28 (30)
T ss_dssp --TTT-----EE-SSSEEETTTTEE
T ss_pred CCCCCCCcceeccCCEEeCCccccc
Confidence 57777754 5556778888765
No 159
>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=63.16 E-value=5.6 Score=26.67 Aligned_cols=11 Identities=9% Similarity=0.220 Sum_probs=9.0
Q ss_pred ccccccCCCCC
Q 033276 84 LVICIKSNHEI 94 (123)
Q Consensus 84 ~~fCp~CG~~~ 94 (123)
...|++||.++
T Consensus 78 ~~~C~vC~k~l 88 (109)
T PF10367_consen 78 STKCSVCGKPL 88 (109)
T ss_pred CCCccCcCCcC
Confidence 46699999995
No 160
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=62.77 E-value=4.3 Score=35.49 Aligned_cols=24 Identities=13% Similarity=0.234 Sum_probs=19.5
Q ss_pred eeccccCCccc-ccCccccccCCCCC
Q 033276 70 IVDKCLKLFSS-PFPLVICIKSNHEI 94 (123)
Q Consensus 70 vl~rC~gC~k~-~~~~~fCp~CG~~~ 94 (123)
.. .|+.|... +..+..||.||+.+
T Consensus 221 l~-~C~~Cd~l~~~~~a~CpRC~~~L 245 (419)
T PRK15103 221 LR-SCSCCTAILPADQPVCPRCHTKG 245 (419)
T ss_pred CC-cCCCCCCCCCCCCCCCCCCCCcC
Confidence 44 69999988 55566899999985
No 161
>COG4469 CoiA Competence protein CoiA-like family, contains a predicted nuclease domain [General function prediction only]
Probab=62.56 E-value=3.5 Score=35.86 Aligned_cols=14 Identities=7% Similarity=0.304 Sum_probs=10.9
Q ss_pred ccccccCCCCCeee
Q 033276 84 LVICIKSNHEIRIS 97 (123)
Q Consensus 84 ~~fCp~CG~~~tl~ 97 (123)
+-|||.||+++.|+
T Consensus 25 ~ffCPaC~~~l~lK 38 (342)
T COG4469 25 RFFCPACGSQLILK 38 (342)
T ss_pred ccccCCCCCeeeee
Confidence 46999999996444
No 162
>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=62.49 E-value=4.3 Score=35.24 Aligned_cols=23 Identities=13% Similarity=0.391 Sum_probs=18.4
Q ss_pred cccCCccc--ccCccccccCCCCCe
Q 033276 73 KCLKLFSS--PFPLVICIKSNHEIR 95 (123)
Q Consensus 73 rC~gC~k~--~~~~~fCp~CG~~~t 95 (123)
.|+.|... +..+-.||.||+.+.
T Consensus 217 ~C~~Cd~~~~~~~~a~CpRC~~~L~ 241 (403)
T TIGR00155 217 SCSACHTTILPAQEPVCPRCSTPLY 241 (403)
T ss_pred cCCCCCCccCCCCCcCCcCCCCccc
Confidence 69999986 444667999999853
No 163
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=61.79 E-value=3.9 Score=30.40 Aligned_cols=26 Identities=19% Similarity=0.278 Sum_probs=18.8
Q ss_pred EEeeccccCCccc-c----cC------ccccccCCCCC
Q 033276 68 RYIVDKCLKLFSS-P----FP------LVICIKSNHEI 94 (123)
Q Consensus 68 ~wvl~rC~gC~k~-~----~~------~~fCp~CG~~~ 94 (123)
.-.| .|+.|++. . +. .-.||.||.++
T Consensus 97 ~~~Y-~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 97 NAYY-KCPNCQSKYTFLEANQLLDMDGTFTCPRCGEEL 133 (147)
T ss_pred CcEE-ECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEE
Confidence 4478 99999975 1 11 15799999984
No 164
>PRK04023 DNA polymerase II large subunit; Validated
Probab=61.78 E-value=4.3 Score=39.97 Aligned_cols=20 Identities=15% Similarity=0.034 Sum_probs=9.1
Q ss_pred cccCCcccccCccccccCCCC
Q 033276 73 KCLKLFSSPFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~~~~~~fCp~CG~~ 93 (123)
+|+.|++. ....+||+||.+
T Consensus 628 fCpsCG~~-t~~frCP~CG~~ 647 (1121)
T PRK04023 628 KCPSCGKE-TFYRRCPFCGTH 647 (1121)
T ss_pred cCCCCCCc-CCcccCCCCCCC
Confidence 55555554 122345555443
No 165
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=61.41 E-value=9 Score=29.53 Aligned_cols=33 Identities=21% Similarity=0.232 Sum_probs=23.2
Q ss_pred eEEeeccccCCccc-c--------------cCccccccCCCCCeeeEEEEE
Q 033276 67 HRYIVDKCLKLFSS-P--------------FPLVICIKSNHEIRISPVFML 102 (123)
Q Consensus 67 ~~wvl~rC~gC~k~-~--------------~~~~fCp~CG~~~tl~rV~~~ 102 (123)
++|-| +|. ++.. + ....-||.||+. .++|.-+.
T Consensus 2 I~y~L-~C~-~gH~FEgWF~ss~~fd~Q~~~glv~CP~Cgs~-~V~K~lmA 49 (148)
T PF06676_consen 2 IVYDL-RCE-NGHEFEGWFRSSAAFDRQQARGLVSCPVCGST-EVSKALMA 49 (148)
T ss_pred eeEEE-ecC-CCCccceecCCHHHHHHHHHcCCccCCCCCCC-eEeeecCC
Confidence 57888 887 4433 1 246789999999 78776554
No 166
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=61.26 E-value=5.3 Score=31.04 Aligned_cols=57 Identities=7% Similarity=-0.112 Sum_probs=31.1
Q ss_pred EEecccHHHHHHHHHhCceeeCCCCCcce-eeeEEeeccccCCccc-c-----cCccccccCCCCC
Q 033276 36 ACITGDYAMQNVILQMGLRLLAPGGMQIR-QLHRYIVDKCLKLFSS-P-----FPLVICIKSNHEI 94 (123)
Q Consensus 36 a~vTdDyAmQNVllqlGL~l~sv~g~~I~-~v~~wvl~rC~gC~k~-~-----~~~~fCp~CG~~~ 94 (123)
-.+|.+.+.+.+..++---+..+. .++. ....=-| .|+.|++. . ...-.||.||+.+
T Consensus 83 w~l~~~~i~d~ik~~~~~~~~klk-~~l~~e~~~~~Y-~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L 146 (178)
T PRK06266 83 WKPELEKLPEIIKKKKMEELKKLK-EQLEEEENNMFF-FCPNCHIRFTFDEAMEYGFRCPQCGEML 146 (178)
T ss_pred EEeCHHHHHHHHHHHHHHHHHHHH-HHhhhccCCCEE-ECCCCCcEEeHHHHhhcCCcCCCCCCCC
Confidence 346777777766666522111111 1111 1112346 89999875 1 2235599999984
No 167
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=61.00 E-value=4.9 Score=29.51 Aligned_cols=17 Identities=6% Similarity=-0.029 Sum_probs=12.9
Q ss_pred ccCccccccCCCCCeee
Q 033276 81 PFPLVICIKSNHEIRIS 97 (123)
Q Consensus 81 ~~~~~fCp~CG~~~tl~ 97 (123)
...+.|||.||.++.-+
T Consensus 66 ~~~r~FC~~CGs~l~~~ 82 (133)
T COG3791 66 SAGRGFCPTCGSPLFWR 82 (133)
T ss_pred CCCCeecccCCCceEEe
Confidence 34578999999996444
No 168
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=60.72 E-value=2.7 Score=27.30 Aligned_cols=22 Identities=14% Similarity=0.295 Sum_probs=18.1
Q ss_pred ccccccCCCCCeeeEEEEEeeEE
Q 033276 84 LVICIKSNHEIRISPVFMLILIC 106 (123)
Q Consensus 84 ~~fCp~CG~~~tl~rV~~~~~~~ 106 (123)
..+||.||+. ..++|....|..
T Consensus 3 ~i~Cp~C~~~-~~T~v~~~~g~~ 24 (67)
T smart00714 3 QLFCPRCQNN-VTTRVETETGVC 24 (67)
T ss_pred ceECCCCCCE-EEEEEEEEeChH
Confidence 4689999999 899998777653
No 169
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=60.59 E-value=3.9 Score=24.33 Aligned_cols=8 Identities=13% Similarity=0.347 Sum_probs=3.5
Q ss_pred cccccCCC
Q 033276 85 VICIKSNH 92 (123)
Q Consensus 85 ~fCp~CG~ 92 (123)
+.||.||+
T Consensus 20 d~C~~C~G 27 (41)
T PF13453_consen 20 DVCPSCGG 27 (41)
T ss_pred EECCCCCe
Confidence 33444443
No 170
>PHA02942 putative transposase; Provisional
Probab=60.11 E-value=12 Score=32.11 Aligned_cols=40 Identities=15% Similarity=0.076 Sum_probs=21.6
Q ss_pred HHHHhCceeeCCCCCcceeeeEEeeccccCCccc-c-cC--ccccccCCCC
Q 033276 47 VILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSS-P-FP--LVICIKSNHE 93 (123)
Q Consensus 47 VllqlGL~l~sv~g~~I~~v~~wvl~rC~gC~k~-~-~~--~~fCp~CG~~ 93 (123)
-+...|+.|+.++-..-. . .|+.|+.. . .. .-.||.||..
T Consensus 308 KA~~~G~~Vv~V~p~yTS------q-~Cs~CG~~~~~l~~r~f~C~~CG~~ 351 (383)
T PHA02942 308 QAKKHGMIVEFVNPSYSS------V-SCPKCGHKMVEIAHRYFHCPSCGYE 351 (383)
T ss_pred HHHHhCCEEEEECCCCCC------c-cCCCCCCccCcCCCCEEECCCCCCE
Confidence 444556666655432212 3 68888765 2 11 2357888764
No 171
>KOG3084 consensus NADH pyrophosphatase I of the Nudix family of hydrolases [Replication, recombination and repair]
Probab=59.70 E-value=4.5 Score=35.20 Aligned_cols=7 Identities=29% Similarity=0.192 Sum_probs=4.1
Q ss_pred ccCCccc
Q 033276 74 CLKLFSS 80 (123)
Q Consensus 74 C~gC~k~ 80 (123)
|++|+..
T Consensus 153 Cp~CG~~ 159 (345)
T KOG3084|consen 153 CPGCGSP 159 (345)
T ss_pred CcccCCC
Confidence 6666654
No 172
>PF14949 ARF7EP_C: ARF7 effector protein C-terminus
Probab=59.67 E-value=5 Score=29.32 Aligned_cols=15 Identities=20% Similarity=0.408 Sum_probs=11.3
Q ss_pred cccCCcccccCccccccCCCC
Q 033276 73 KCLKLFSSPFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~~~~~~fCp~CG~~ 93 (123)
-|+|||-+ ||+||+.
T Consensus 69 ~C~GC~~P------C~~C~S~ 83 (103)
T PF14949_consen 69 DCPGCHYP------CPKCGSR 83 (103)
T ss_pred CCCCcccc------CCCCCCC
Confidence 58888843 8888875
No 173
>COG1328 NrdD Oxygen-sensitive ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]
Probab=59.37 E-value=6.8 Score=36.85 Aligned_cols=62 Identities=18% Similarity=0.093 Sum_probs=39.0
Q ss_pred cccHHHHHHHHH---hCceeeCCCCCcceeeeEEeeccccCCccc-ccCccccccCCCCCeeeEEEEEeeEEEEEeeCC
Q 033276 39 TGDYAMQNVILQ---MGLRLLAPGGMQIRQLHRYIVDKCLKLFSS-PFPLVICIKSNHEIRISPVFMLILICLYIQVDT 113 (123)
Q Consensus 39 TdDyAmQNVllq---lGL~l~sv~g~~I~~v~~wvl~rC~gC~k~-~~~~~fCp~CG~~~tl~rV~~~~~~~~~~~~~~ 113 (123)
.+-=|++|+.+. .++.+.+.. ..| +.|..|+.. ......||+||++ - |.+.-=++=|++...
T Consensus 615 ~~~eal~~l~k~~~~~ri~Y~~~n-~~i--------~~C~~cg~~~~~~~~~Cp~CG~~-d---ve~~~Ri~GYl~~~~ 680 (700)
T COG1328 615 ADPEALMDLTKYIYKTRIGYWGYT-TPI--------SVCNRCGYSGEGLRTRCPKCGSE-D---VEVFSRITGYLQNPS 680 (700)
T ss_pred CCHHHHHHHHHHHHhcCcceEecC-CCc--------eeeccCCcccccccccCCCCCCc-c---ceeeeeecccccCcc
Confidence 345678887663 355555553 222 379999987 4322339999988 3 666666666776443
No 174
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=58.66 E-value=7.7 Score=29.03 Aligned_cols=22 Identities=14% Similarity=0.246 Sum_probs=14.5
Q ss_pred cccCccccccCCCCCeeeEEEEEe
Q 033276 80 SPFPLVICIKSNHEIRISPVFMLI 103 (123)
Q Consensus 80 ~~~~~~fCp~CG~~~tl~rV~~~~ 103 (123)
++.....||+||.+ +.-+.++-
T Consensus 45 ie~G~t~CP~Cg~~--~e~~fvva 66 (115)
T COG1885 45 IEVGSTSCPKCGEP--FESAFVVA 66 (115)
T ss_pred EecccccCCCCCCc--cceeEEEe
Confidence 35556779999998 34444443
No 175
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=58.45 E-value=5.7 Score=32.68 Aligned_cols=60 Identities=18% Similarity=0.186 Sum_probs=32.1
Q ss_pred eEEecccHHHHHHHHHhCce-eeCCCCCcceeeeEEeeccccCCccc-c------cCcc----ccccCCCCCeeeEEEEE
Q 033276 35 VACITGDYAMQNVILQMGLR-LLAPGGMQIRQLHRYIVDKCLKLFSS-P------FPLV----ICIKSNHEIRISPVFML 102 (123)
Q Consensus 35 va~vTdDyAmQNVllqlGL~-l~sv~g~~I~~v~~wvl~rC~gC~k~-~------~~~~----fCp~CG~~~tl~rV~~~ 102 (123)
..++|. -+.|.-.+.|.+ ++.++|. -+.. +|..|+.. + .... -||.||.+ .+|+=-|.
T Consensus 94 ~~iiTQ--NiD~Lhe~AGs~~Vi~lHGs------l~~~-~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~-~lrP~VV~ 163 (250)
T COG0846 94 LRIITQ--NIDGLHERAGSKNVIELHGS------LKRV-RCSKCGNQYYDEDVIKFIEDGLIPRCPKCGGP-VLRPDVVW 163 (250)
T ss_pred eEEEec--ccchHHHHcCCCcEEEeccc------eeee-EeCCCcCccchhhhhhhcccCCCCcCccCCCc-cccCCEEE
Confidence 456663 123445555543 3444542 4556 99999765 2 1112 39999996 34443333
Q ss_pred ee
Q 033276 103 IL 104 (123)
Q Consensus 103 ~~ 104 (123)
-|
T Consensus 164 fG 165 (250)
T COG0846 164 FG 165 (250)
T ss_pred eC
Confidence 33
No 176
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=58.10 E-value=10 Score=23.10 Aligned_cols=23 Identities=26% Similarity=0.306 Sum_probs=18.8
Q ss_pred cccCCCCCeeeEEEEEeeEEEEE
Q 033276 87 CIKSNHEIRISPVFMLILICLYI 109 (123)
Q Consensus 87 Cp~CG~~~tl~rV~~~~~~~~~~ 109 (123)
|..||++++=....+.+++-+|.
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~ 23 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYY 23 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEE
Confidence 78899998888888888877764
No 177
>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=57.94 E-value=8.5 Score=33.10 Aligned_cols=26 Identities=19% Similarity=0.359 Sum_probs=19.7
Q ss_pred EEeeccccCCccc-c-----cCccccccCCCCC
Q 033276 68 RYIVDKCLKLFSS-P-----FPLVICIKSNHEI 94 (123)
Q Consensus 68 ~wvl~rC~gC~k~-~-----~~~~fCp~CG~~~ 94 (123)
-|++ .|+.|+.. . .....||.||.+.
T Consensus 231 g~v~-~C~~c~~~~~~~~~~~~~~~C~~c~~~~ 262 (374)
T TIGR00308 231 GYTY-HCSRCLHNKPVNGISQRKGRCKECGGEY 262 (374)
T ss_pred eeEE-ECCCcccccccccccCCCCCCCCCCCcc
Confidence 5788 99999865 2 2346899999873
No 178
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=57.76 E-value=4.6 Score=35.97 Aligned_cols=29 Identities=14% Similarity=0.230 Sum_probs=22.7
Q ss_pred EEeeccccCCccc-cc-CccccccCCCCCeeeE
Q 033276 68 RYIVDKCLKLFSS-PF-PLVICIKSNHEIRISP 98 (123)
Q Consensus 68 ~wvl~rC~gC~k~-~~-~~~fCp~CG~~~tl~r 98 (123)
.|+. |+.|... +. .+..||.||+++-.+|
T Consensus 219 ~~~~--C~~C~~~~~~~~~~~CpRC~~~Ly~rr 249 (418)
T COG2995 219 GLRS--CLCCHYILPHDAEPRCPRCGSKLYVRR 249 (418)
T ss_pred ccee--cccccccCCHhhCCCCCCCCChhhccC
Confidence 5555 9999988 43 5788999999976555
No 179
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=57.73 E-value=6.4 Score=23.86 Aligned_cols=15 Identities=13% Similarity=0.237 Sum_probs=11.2
Q ss_pred CccccccCCCCCeee
Q 033276 83 PLVICIKSNHEIRIS 97 (123)
Q Consensus 83 ~~~fCp~CG~~~tl~ 97 (123)
.+.+|+.||++.+.+
T Consensus 4 g~l~C~~CG~~m~~~ 18 (58)
T PF13408_consen 4 GLLRCGHCGSKMTRR 18 (58)
T ss_pred CcEEcccCCcEeEEE
Confidence 457899999995543
No 180
>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=57.66 E-value=6 Score=25.98 Aligned_cols=21 Identities=19% Similarity=0.415 Sum_probs=13.5
Q ss_pred cccCCccc------ccCccccccCCCC
Q 033276 73 KCLKLFSS------PFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~------~~~~~fCp~CG~~ 93 (123)
+|++|+++ ......|..||..
T Consensus 9 kCp~C~~~q~vFSha~t~V~C~~Cg~~ 35 (55)
T PF01667_consen 9 KCPGCYNIQTVFSHAQTVVKCVVCGTV 35 (55)
T ss_dssp E-TTT-SEEEEETT-SS-EE-SSSTSE
T ss_pred ECCCCCCeeEEEecCCeEEEcccCCCE
Confidence 89999986 2456899999986
No 181
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=57.64 E-value=4.6 Score=40.01 Aligned_cols=30 Identities=10% Similarity=0.020 Sum_probs=21.8
Q ss_pred ceeeeEEeeccccCCccc-ccCccccccCCCC
Q 033276 63 IRQLHRYIVDKCLKLFSS-PFPLVICIKSNHE 93 (123)
Q Consensus 63 I~~v~~wvl~rC~gC~k~-~~~~~fCp~CG~~ 93 (123)
..-+..=+. ||..|+.. .....+||.||++
T Consensus 687 ~vPvY~tIK-rC~dcg~q~~~~~~~cP~Cgs~ 717 (1187)
T COG1110 687 YVPVYDTIK-RCRDCGEQFVDSEDKCPRCGSR 717 (1187)
T ss_pred eEehHHHHH-HHhhcCceeccccccCCCCCCc
Confidence 334444567 99999998 3335699999996
No 182
>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=57.28 E-value=7.5 Score=27.86 Aligned_cols=20 Identities=15% Similarity=0.090 Sum_probs=14.8
Q ss_pred CccccccCCCCCeeeEEEEEe
Q 033276 83 PLVICIKSNHEIRISPVFMLI 103 (123)
Q Consensus 83 ~~~fCp~CG~~~tl~rV~~~~ 103 (123)
.+.+||.||.. .++|+++-|
T Consensus 34 ~ky~Cp~Cgk~-~vkR~a~GI 53 (90)
T PF01780_consen 34 AKYTCPFCGKT-SVKRVATGI 53 (90)
T ss_dssp S-BEESSSSSS-EEEEEETTE
T ss_pred CCCcCCCCCCc-eeEEeeeEE
Confidence 35789999999 788887533
No 183
>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=57.20 E-value=6.6 Score=34.44 Aligned_cols=29 Identities=14% Similarity=-0.011 Sum_probs=24.2
Q ss_pred EeeccccCCccc-ccCccccccCCCCCeeeE
Q 033276 69 YIVDKCLKLFSS-PFPLVICIKSNHEIRISP 98 (123)
Q Consensus 69 wvl~rC~gC~k~-~~~~~fCp~CG~~~tl~r 98 (123)
-.| +|..|+.. +...-.||.||+=.|+..
T Consensus 6 ~~y-~C~~Cg~~~~~~~g~Cp~C~~w~t~~~ 35 (454)
T TIGR00416 6 SKF-VCQHCGADSPKWQGKCPACHAWNTITE 35 (454)
T ss_pred CeE-ECCcCCCCCccccEECcCCCCccccch
Confidence 468 99999988 767788999998777776
No 184
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=56.81 E-value=6.3 Score=25.45 Aligned_cols=24 Identities=17% Similarity=0.458 Sum_probs=19.7
Q ss_pred cccCCccc-ccCccccccCCCCCeee
Q 033276 73 KCLKLFSS-PFPLVICIKSNHEIRIS 97 (123)
Q Consensus 73 rC~gC~k~-~~~~~fCp~CG~~~tl~ 97 (123)
.|.-|+.. +..-.-|-+||+. .|+
T Consensus 16 ICrkC~ARnp~~A~~CRKCg~~-~LR 40 (48)
T PRK04136 16 ICMRCNARNPWRATKCRKCGYK-NLR 40 (48)
T ss_pred chhcccCCCCccccccccCCCC-CcC
Confidence 89999987 6666889999987 565
No 185
>PHA00626 hypothetical protein
Probab=56.70 E-value=8.1 Score=25.92 Aligned_cols=8 Identities=25% Similarity=0.410 Sum_probs=5.4
Q ss_pred ccccCCCC
Q 033276 86 ICIKSNHE 93 (123)
Q Consensus 86 fCp~CG~~ 93 (123)
.||.||+.
T Consensus 2 ~CP~CGS~ 9 (59)
T PHA00626 2 SCPKCGSG 9 (59)
T ss_pred CCCCCCCc
Confidence 47777775
No 186
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=56.59 E-value=5.6 Score=34.77 Aligned_cols=24 Identities=8% Similarity=0.121 Sum_probs=18.0
Q ss_pred cccCCccc-c------cCccccccCCCCCee
Q 033276 73 KCLKLFSS-P------FPLVICIKSNHEIRI 96 (123)
Q Consensus 73 rC~gC~k~-~------~~~~fCp~CG~~~tl 96 (123)
.|+.|... . ..+-.||.||+++..
T Consensus 12 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~~ 42 (419)
T PRK15103 12 LCPQCDMLVALPRLEHGQKAACPRCGTTLTV 42 (419)
T ss_pred cCCCCCceeecCCCCCCCeeECCCCCCCCcC
Confidence 79999976 2 125679999999643
No 187
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=56.49 E-value=5.4 Score=32.45 Aligned_cols=21 Identities=10% Similarity=0.078 Sum_probs=14.0
Q ss_pred cccCCccc-c--cC--ccccccCCCC
Q 033276 73 KCLKLFSS-P--FP--LVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~-~--~~--~~fCp~CG~~ 93 (123)
.|+.|+.. . .. +..||.||..
T Consensus 101 fC~~CG~~~~~~~~~~~~~C~~c~~~ 126 (256)
T PRK00241 101 FCGYCGHPMHPSKTEWAMLCPHCRER 126 (256)
T ss_pred cccccCCCCeecCCceeEECCCCCCE
Confidence 58888876 2 22 4568888865
No 188
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=56.35 E-value=8.1 Score=27.82 Aligned_cols=17 Identities=6% Similarity=0.157 Sum_probs=9.4
Q ss_pred ccccccCCCCCeeeEEEE
Q 033276 84 LVICIKSNHEIRISPVFM 101 (123)
Q Consensus 84 ~~fCp~CG~~~tl~rV~~ 101 (123)
+..||.||.+ +++|++.
T Consensus 35 ~~~Cp~C~~~-~VkR~a~ 51 (89)
T COG1997 35 KHVCPFCGRT-TVKRIAT 51 (89)
T ss_pred CCcCCCCCCc-ceeeecc
Confidence 3456666666 5555553
No 189
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=56.32 E-value=7.2 Score=34.32 Aligned_cols=23 Identities=9% Similarity=0.063 Sum_probs=17.3
Q ss_pred eeccccCCccc-ccCc-------------------cccccCCCC
Q 033276 70 IVDKCLKLFSS-PFPL-------------------VICIKSNHE 93 (123)
Q Consensus 70 vl~rC~gC~k~-~~~~-------------------~fCp~CG~~ 93 (123)
++ +|..|+.+ ++.. -.||.||.+
T Consensus 425 ~~-~c~~c~~~yd~~~g~~~~~~~~gt~~~~lp~~~~cp~c~~~ 467 (479)
T PRK05452 425 RM-QCSVCQWIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSLG 467 (479)
T ss_pred eE-EECCCCeEECCCCCCcccCCCCCCChhhCCCCCcCcCCCCc
Confidence 46 89999987 5432 269999976
No 190
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=56.05 E-value=9.4 Score=32.79 Aligned_cols=26 Identities=19% Similarity=0.363 Sum_probs=19.7
Q ss_pred EEeeccccCCccc---c-cCccccccCCCCC
Q 033276 68 RYIVDKCLKLFSS---P-FPLVICIKSNHEI 94 (123)
Q Consensus 68 ~wvl~rC~gC~k~---~-~~~~fCp~CG~~~ 94 (123)
-|++ +|+.|+.. . .....||.||++.
T Consensus 242 g~~~-~C~~c~~~~~~~~~~~~~C~~c~~~~ 271 (382)
T PRK04338 242 GYVY-YCPKCLYREEVEGLPPEECPVCGGKF 271 (382)
T ss_pred eeEE-ECCCCCcEEEecCCCCCCCCCCCCcc
Confidence 5788 99999975 1 2346799999873
No 191
>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=55.43 E-value=6.6 Score=29.19 Aligned_cols=22 Identities=27% Similarity=0.209 Sum_probs=17.7
Q ss_pred cccCCccc----ccCccccccCCCCC
Q 033276 73 KCLKLFSS----PFPLVICIKSNHEI 94 (123)
Q Consensus 73 rC~gC~k~----~~~~~fCp~CG~~~ 94 (123)
.|+.|... +.....||.||++=
T Consensus 4 ~CP~C~seytY~dg~~~iCpeC~~EW 29 (109)
T TIGR00686 4 PCPKCNSEYTYHDGTQLICPSCLYEW 29 (109)
T ss_pred cCCcCCCcceEecCCeeECccccccc
Confidence 68999865 56678999999983
No 192
>PRK08197 threonine synthase; Validated
Probab=55.25 E-value=9.2 Score=32.42 Aligned_cols=24 Identities=17% Similarity=0.254 Sum_probs=17.7
Q ss_pred eeccccCCccc-cc--CccccccCCCCCe
Q 033276 70 IVDKCLKLFSS-PF--PLVICIKSNHEIR 95 (123)
Q Consensus 70 vl~rC~gC~k~-~~--~~~fCp~CG~~~t 95 (123)
.+ +|..|++. +. ....| .||.++.
T Consensus 7 ~~-~C~~Cg~~~~~~~~~~~C-~cg~~l~ 33 (394)
T PRK08197 7 HL-ECSKCGETYDADQVHNLC-KCGKPLL 33 (394)
T ss_pred EE-EECCCCCCCCCCCcceec-CCCCeeE
Confidence 58 99999998 32 23569 8998843
No 193
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=54.90 E-value=5.9 Score=38.05 Aligned_cols=23 Identities=17% Similarity=0.313 Sum_probs=19.2
Q ss_pred eeccccCCccc----ccCccccccCCCC
Q 033276 70 IVDKCLKLFSS----PFPLVICIKSNHE 93 (123)
Q Consensus 70 vl~rC~gC~k~----~~~~~fCp~CG~~ 93 (123)
-+ ||--|+++ ..+...||.||.+
T Consensus 821 ~~-~~~~~~~~~~~~~~~~~~~~~~~~~ 847 (1006)
T PRK12775 821 QW-RCDDCGKVSEGFAFPYGMCPACGGK 847 (1006)
T ss_pred ee-ehhhhccccccccCCcCcCcccccc
Confidence 46 89999987 5677899999987
No 194
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=54.75 E-value=6.2 Score=23.40 Aligned_cols=10 Identities=10% Similarity=0.112 Sum_probs=8.4
Q ss_pred cccccCCCCC
Q 033276 85 VICIKSNHEI 94 (123)
Q Consensus 85 ~fCp~CG~~~ 94 (123)
..||.||++.
T Consensus 3 ~~Cp~Cg~~~ 12 (47)
T PF14690_consen 3 PRCPHCGSPS 12 (47)
T ss_pred ccCCCcCCCc
Confidence 5799999994
No 195
>COG0384 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]
Probab=54.54 E-value=9.4 Score=32.07 Aligned_cols=49 Identities=14% Similarity=-0.027 Sum_probs=27.7
Q ss_pred ccHHHHHHHHHhCceeeCCCCCcceeeeEEeeccccCCcccccCccccccCCCCCeee
Q 033276 40 GDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSSPFPLVICIKSNHEIRIS 97 (123)
Q Consensus 40 dDyAmQNVllqlGL~l~sv~g~~I~~v~~wvl~rC~gC~k~~~~~~fCp~CG~~~tl~ 97 (123)
+|-.||+++.++|+.--.---+.=.. ..|++ | +.++...=|-|||+ |+=
T Consensus 32 sd~~MQ~IA~e~n~SET~Fv~~~~~~-~~~rl-R------~FTP~~Evpf~GHa-Tlg 80 (291)
T COG0384 32 SDEQMQAIAREFNLSETAFVLPPDDP-ADARL-R------IFTPTTEVPFAGHA-TLG 80 (291)
T ss_pred CHHHHHHHHHHhCCceeEEEcCCCCc-CceEE-E------EeCCCcccccCCCH-HHH
Confidence 78999999999999643311000011 34555 2 21222334559999 543
No 196
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=54.26 E-value=5.2 Score=29.61 Aligned_cols=20 Identities=15% Similarity=0.170 Sum_probs=10.6
Q ss_pred ccCCccc-ccCccccccCCCC
Q 033276 74 CLKLFSS-PFPLVICIKSNHE 93 (123)
Q Consensus 74 C~gC~k~-~~~~~fCp~CG~~ 93 (123)
|+.|+.. ..++..||.||..
T Consensus 1 CPvCg~~l~vt~l~C~~C~t~ 21 (113)
T PF09862_consen 1 CPVCGGELVVTRLKCPSCGTE 21 (113)
T ss_pred CCCCCCceEEEEEEcCCCCCE
Confidence 5555554 4445555555544
No 197
>PRK12366 replication factor A; Reviewed
Probab=54.11 E-value=16 Score=33.48 Aligned_cols=26 Identities=12% Similarity=0.006 Sum_probs=18.8
Q ss_pred eEEeeccccCCccc-c--cCccccccCCCC
Q 033276 67 HRYIVDKCLKLFSS-P--FPLVICIKSNHE 93 (123)
Q Consensus 67 ~~wvl~rC~gC~k~-~--~~~~fCp~CG~~ 93 (123)
.-|-. +|+.|.|. . ...-.||+||..
T Consensus 529 ~~~y~-aCp~CnkKv~~~~g~~~C~~c~~~ 557 (637)
T PRK12366 529 KIILY-LCPNCRKRVEEVDGEYICEFCGEV 557 (637)
T ss_pred CEEEe-cccccCeEeEcCCCcEECCCCCCC
Confidence 34555 99999987 2 234579999975
No 198
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=53.60 E-value=10 Score=22.36 Aligned_cols=21 Identities=24% Similarity=0.268 Sum_probs=15.3
Q ss_pred cccCCccc---c-------cCccccccCCCC
Q 033276 73 KCLKLFSS---P-------FPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~---~-------~~~~fCp~CG~~ 93 (123)
+|+.|.+. + ..+.-|++||+.
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 78889875 1 125789999975
No 199
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=53.50 E-value=7.9 Score=29.50 Aligned_cols=26 Identities=19% Similarity=0.262 Sum_probs=18.7
Q ss_pred cCccccccCCCCCeeeEEEEEeeEEEEEeeCCccceeecc
Q 033276 82 FPLVICIKSNHEIRISPVFMLILICLYIQVDTEMPCLLHY 121 (123)
Q Consensus 82 ~~~~fCp~CG~~~tl~rV~~~~~~~~~~~~~~~~~~~~~~ 121 (123)
|.-.-||.||.|+ .+-||++=|-.|-
T Consensus 26 ML~~hCp~Cg~PL--------------F~KdG~v~CPvC~ 51 (131)
T COG1645 26 MLAKHCPKCGTPL--------------FRKDGEVFCPVCG 51 (131)
T ss_pred HHHhhCcccCCcc--------------eeeCCeEECCCCC
Confidence 3446799999994 3478888776553
No 200
>PRK00504 rpmG 50S ribosomal protein L33; Validated
Probab=52.83 E-value=7.9 Score=24.81 Aligned_cols=29 Identities=14% Similarity=0.229 Sum_probs=20.5
Q ss_pred EEeeccccCCccc------c--------cCccccccCCCCCeeeE
Q 033276 68 RYIVDKCLKLFSS------P--------FPLVICIKSNHEIRISP 98 (123)
Q Consensus 68 ~wvl~rC~gC~k~------~--------~~~~fCp~CG~~~tl~r 98 (123)
.-.+ .|..|... . .-+.|||.|+.. |+.+
T Consensus 5 ~i~L-~C~~c~~rnY~t~KNk~~~~~rLelkKycp~c~kh-tlhk 47 (50)
T PRK00504 5 KITL-ACTECKSRNYTTTKNKKNTPERLELKKFCPRCNKH-TLHK 47 (50)
T ss_pred EEEE-EEcCCCCccEeEcCCCCCCCceEEEECcCCCCCCe-Eeee
Confidence 3457 89998853 0 116899999999 7754
No 201
>PLN00209 ribosomal protein S27; Provisional
Probab=52.77 E-value=11 Score=27.03 Aligned_cols=25 Identities=20% Similarity=0.405 Sum_probs=19.0
Q ss_pred EeeccccCCccc------ccCccccccCCCC
Q 033276 69 YIVDKCLKLFSS------PFPLVICIKSNHE 93 (123)
Q Consensus 69 wvl~rC~gC~k~------~~~~~fCp~CG~~ 93 (123)
|..-+|++|+++ ......|..||..
T Consensus 34 Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~ 64 (86)
T PLN00209 34 FMDVKCQGCFNITTVFSHSQTVVVCGSCQTV 64 (86)
T ss_pred EEEEECCCCCCeeEEEecCceEEEccccCCE
Confidence 333489999987 2456899999986
No 202
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 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 RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=52.31 E-value=8.2 Score=21.39 Aligned_cols=21 Identities=19% Similarity=0.293 Sum_probs=14.9
Q ss_pred cccCCccc-ccCccccccCCCC
Q 033276 73 KCLKLFSS-PFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~-~~~~~fCp~CG~~ 93 (123)
.|..|... ......|-.||.+
T Consensus 6 ~C~~C~~~N~~~~~~C~~C~~~ 27 (30)
T PF00641_consen 6 KCPSCTFMNPASRSKCVACGAP 27 (30)
T ss_dssp EETTTTEEEESSSSB-TTT--B
T ss_pred cCCCCcCCchHHhhhhhCcCCC
Confidence 68999987 6677889999976
No 203
>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=51.99 E-value=8.5 Score=26.63 Aligned_cols=23 Identities=22% Similarity=0.150 Sum_probs=17.4
Q ss_pred cccCCccc---ccCccccccCCCCCe
Q 033276 73 KCLKLFSS---PFPLVICIKSNHEIR 95 (123)
Q Consensus 73 rC~gC~k~---~~~~~fCp~CG~~~t 95 (123)
.|+-|+.. ......||.||+...
T Consensus 2 fC~~Cg~~l~~~~~~~~C~~C~~~~~ 27 (104)
T TIGR01384 2 FCPKCGSLMTPKNGVYVCPSCGYEKE 27 (104)
T ss_pred CCcccCcccccCCCeEECcCCCCccc
Confidence 58999987 235788999997633
No 204
>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=51.96 E-value=5 Score=31.43 Aligned_cols=35 Identities=9% Similarity=-0.064 Sum_probs=22.6
Q ss_pred EeeccccCCccc-cc-----------CccccccCCCCCeeeEEEEEeeEE
Q 033276 69 YIVDKCLKLFSS-PF-----------PLVICIKSNHEIRISPVFMLILIC 106 (123)
Q Consensus 69 wvl~rC~gC~k~-~~-----------~~~fCp~CG~~~tl~rV~~~~~~~ 106 (123)
+.. +|..|.+. +. ....||.||+. +|.--|..|+.
T Consensus 94 ~~~-~C~~C~~~~~~~~~~~~~~~~~~~p~C~~Cgg~--lrP~VV~FgE~ 140 (206)
T cd01410 94 FIE-VCKSCGPEYVRDDVVETRGDKETGRRCHACGGI--LKDTIVDFGER 140 (206)
T ss_pred Ccc-cCCCCCCccchHHHHHHhhcCCCCCcCCCCcCc--cCCcEEECCCC
Confidence 456 99999976 21 12359999987 55555555553
No 205
>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=51.37 E-value=7.6 Score=29.49 Aligned_cols=24 Identities=8% Similarity=0.173 Sum_probs=17.1
Q ss_pred eeccccCCccc-c-----cCccccccCCCCC
Q 033276 70 IVDKCLKLFSS-P-----FPLVICIKSNHEI 94 (123)
Q Consensus 70 vl~rC~gC~k~-~-----~~~~fCp~CG~~~ 94 (123)
-| .|+.|++. . ...-.||.||+.+
T Consensus 109 ~Y-~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~L 138 (158)
T TIGR00373 109 FF-ICPNMCVRFTFNEAMELNFTCPRCGAML 138 (158)
T ss_pred eE-ECCCCCcEeeHHHHHHcCCcCCCCCCEe
Confidence 46 89999965 1 2235599999983
No 206
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=50.93 E-value=8.1 Score=26.59 Aligned_cols=16 Identities=13% Similarity=0.148 Sum_probs=9.7
Q ss_pred cccCCCCC-eeeEEEEE
Q 033276 87 CIKSNHEI-RISPVFML 102 (123)
Q Consensus 87 Cp~CG~~~-tl~rV~~~ 102 (123)
||+||+.- -.+-++.+
T Consensus 7 CpKCgn~~~~ekei~~t 23 (68)
T COG3478 7 CPKCGNTNYEEKEIAAT 23 (68)
T ss_pred CCCcCCcchhhceeecc
Confidence 99999752 23344444
No 207
>COG5270 PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis]
Probab=50.28 E-value=12 Score=30.38 Aligned_cols=30 Identities=13% Similarity=-0.025 Sum_probs=22.4
Q ss_pred eEEeeccccCCcccccCccccccCCCCCeeeE
Q 033276 67 HRYIVDKCLKLFSSPFPLVICIKSNHEIRISP 98 (123)
Q Consensus 67 ~~wvl~rC~gC~k~~~~~~fCp~CG~~~tl~r 98 (123)
+-|+| .|..|.=+ .....|+.||+.++.-|
T Consensus 11 k~~iy-WCe~cNlP-l~~~~c~~cg~~~~~l~ 40 (202)
T COG5270 11 KFPIY-WCEKCNLP-LLGRRCSVCGSKVEELR 40 (202)
T ss_pred cccee-ehhhCCCc-cccccccccCCcceEEE
Confidence 57999 99999844 44577999998754433
No 208
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=49.97 E-value=13 Score=24.59 Aligned_cols=21 Identities=19% Similarity=0.338 Sum_probs=16.1
Q ss_pred cccCCcccccCccccccCCCC
Q 033276 73 KCLKLFSSPFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~~~~~~fCp~CG~~ 93 (123)
.|..|++...+...|+.||.-
T Consensus 29 ~c~~cG~~~l~Hrvc~~cg~Y 49 (57)
T COG0333 29 VCPNCGEYKLPHRVCLKCGYY 49 (57)
T ss_pred eccCCCCcccCceEcCCCCCc
Confidence 788888776666788888865
No 209
>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=49.73 E-value=12 Score=22.70 Aligned_cols=10 Identities=10% Similarity=0.285 Sum_probs=7.8
Q ss_pred ccccccCCCC
Q 033276 84 LVICIKSNHE 93 (123)
Q Consensus 84 ~~fCp~CG~~ 93 (123)
...||+||+.
T Consensus 18 g~~CP~Cg~~ 27 (46)
T PF12760_consen 18 GFVCPHCGST 27 (46)
T ss_pred CCCCCCCCCe
Confidence 3569999986
No 210
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=49.58 E-value=14 Score=37.81 Aligned_cols=31 Identities=13% Similarity=0.161 Sum_probs=23.3
Q ss_pred eeeEEeeccccCCcccccCccccccCCCCCeee
Q 033276 65 QLHRYIVDKCLKLFSSPFPLVICIKSNHEIRIS 97 (123)
Q Consensus 65 ~v~~wvl~rC~gC~k~~~~~~fCp~CG~~~tl~ 97 (123)
++.--.. +|+.|++. .....||.||.++-+.
T Consensus 669 ~vei~~~-~Cp~Cg~~-~~~~~Cp~CG~~~~~~ 699 (1627)
T PRK14715 669 DIEIAFF-KCPKCGKV-GLYHVCPFCGTRVELK 699 (1627)
T ss_pred eEEEEee-eCCCCCCc-cccccCcccCCcccCC
Confidence 6667778 99999998 2346699999884333
No 211
>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=49.54 E-value=26 Score=20.23 Aligned_cols=13 Identities=23% Similarity=0.652 Sum_probs=7.8
Q ss_pred ccCccccccCCCC
Q 033276 81 PFPLVICIKSNHE 93 (123)
Q Consensus 81 ~~~~~fCp~CG~~ 93 (123)
+.+..+|+.||..
T Consensus 29 ~vp~~~C~~CGE~ 41 (46)
T TIGR03831 29 NVPALVCPQCGEE 41 (46)
T ss_pred CCCccccccCCCE
Confidence 4455666666655
No 212
>PRK13764 ATPase; Provisional
Probab=49.51 E-value=15 Score=33.84 Aligned_cols=30 Identities=17% Similarity=0.131 Sum_probs=27.1
Q ss_pred CceeEEecccHHHHHHHHHhCceeeCCCCC
Q 033276 32 ESTVACITGDYAMQNVILQMGLRLLAPGGM 61 (123)
Q Consensus 32 ~~~va~vTdDyAmQNVllqlGL~l~sv~g~ 61 (123)
+..+.++|.|+.+..+|+..||+++.+..+
T Consensus 101 ~~~~~lvT~D~~l~~~A~~~GI~V~~l~~~ 130 (602)
T PRK13764 101 ELGATLVTSDRVQAEVARAKGIDVIYLKPE 130 (602)
T ss_pred HcCCEEEeCCHHHHHHHHHcCCEEEEeCCC
Confidence 457899999999999999999999998764
No 213
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=49.36 E-value=7.3 Score=25.13 Aligned_cols=11 Identities=18% Similarity=0.171 Sum_probs=3.9
Q ss_pred EeeccccCCccc
Q 033276 69 YIVDKCLKLFSS 80 (123)
Q Consensus 69 wvl~rC~gC~k~ 80 (123)
-+| +|+.|...
T Consensus 20 ~~y-~C~~C~~~ 30 (51)
T PF07975_consen 20 SRY-RCPKCKNH 30 (51)
T ss_dssp EEE---TTTT--
T ss_pred CeE-ECCCCCCc
Confidence 445 66666553
No 214
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=48.45 E-value=17 Score=27.95 Aligned_cols=27 Identities=22% Similarity=0.322 Sum_probs=18.0
Q ss_pred cccccCCCC-CeeeEEEEEeeEEEEEeeCC
Q 033276 85 VICIKSNHE-IRISPVFMLILICLYIQVDT 113 (123)
Q Consensus 85 ~fCp~CG~~-~tl~rV~~~~~~~~~~~~~~ 113 (123)
.-||.||.. +|+.++.-.+- .-||-||
T Consensus 29 ~~c~~c~~~f~~~e~~~~~~i--~VIKRDG 56 (154)
T PRK00464 29 RECLACGKRFTTFERVELVPL--LVIKKDG 56 (154)
T ss_pred eeccccCCcceEeEeccCccc--EEEecCC
Confidence 568888843 46666665552 4688888
No 215
>PRK05638 threonine synthase; Validated
Probab=48.39 E-value=12 Score=32.31 Aligned_cols=26 Identities=19% Similarity=0.255 Sum_probs=18.2
Q ss_pred eeccccCCccc-c-cCccccccCCCCCeee
Q 033276 70 IVDKCLKLFSS-P-FPLVICIKSNHEIRIS 97 (123)
Q Consensus 70 vl~rC~gC~k~-~-~~~~fCp~CG~~~tl~ 97 (123)
++ +|..|++. + .....| .||+++.+.
T Consensus 1 ~l-~C~~Cg~~~~~~~~~~C-~c~~~l~~~ 28 (442)
T PRK05638 1 KM-KCPKCGREYNSYIPPFC-ICGELLEII 28 (442)
T ss_pred Ce-EeCCCCCCCCCCCceec-CCCCcEEEE
Confidence 36 89999988 3 233679 899875443
No 216
>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=48.15 E-value=9.4 Score=22.70 Aligned_cols=21 Identities=19% Similarity=0.227 Sum_probs=15.7
Q ss_pred cccCCccc----ccCccccccCCCC
Q 033276 73 KCLKLFSS----PFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~----~~~~~fCp~CG~~ 93 (123)
+|.-|... +..+.+|..||+.
T Consensus 10 ~C~~C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 10 PCPVCGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred cCCCCCCeEeEccCCEEEhhhCceE
Confidence 58888875 4557888888875
No 217
>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=48.07 E-value=9.8 Score=25.16 Aligned_cols=29 Identities=7% Similarity=0.040 Sum_probs=20.8
Q ss_pred EEeeccccCCccc--ccCccccccCCCCCeeeE
Q 033276 68 RYIVDKCLKLFSS--PFPLVICIKSNHEIRISP 98 (123)
Q Consensus 68 ~wvl~rC~gC~k~--~~~~~fCp~CG~~~tl~r 98 (123)
...+ |.-|++. ..-+..|..||.+...+|
T Consensus 14 tH~~--CrRCG~~syH~qK~~CasCGyp~~kkr 44 (55)
T PF01907_consen 14 THTL--CRRCGRRSYHIQKKTCASCGYPAAKKR 44 (55)
T ss_dssp SEEE---TTTSSEEEETTTTEETTTBTTTSSS-
T ss_pred cEee--ecccCCeeeecCCCcccccCCCccccc
Confidence 4554 9999987 677899999998854443
No 218
>PF00471 Ribosomal_L33: Ribosomal protein L33; InterPro: IPR001705 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L33 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L33 has been shown to be on the surface of 50S subunit. L33 belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, , ], groups: Eubacterial L33. Algal and plant chloroplast L33. Cyanelle L33. L33 is a small protein of 49 to 66 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3PIO_1 3PIP_1 3PYT_3 3MS1_3 3F1F_6 3F1H_6 3MRZ_3 3PYO_3 3D5B_6 3D5D_6 ....
Probab=48.04 E-value=10 Score=24.00 Aligned_cols=14 Identities=7% Similarity=0.247 Sum_probs=11.4
Q ss_pred ccccccCCCCCeeeE
Q 033276 84 LVICIKSNHEIRISP 98 (123)
Q Consensus 84 ~~fCp~CG~~~tl~r 98 (123)
+.|||.|+.. |+.+
T Consensus 32 kKycp~~~kh-tlhk 45 (48)
T PF00471_consen 32 KKYCPRCRKH-TLHK 45 (48)
T ss_dssp EEEETSSSSE-EEEE
T ss_pred eccCCCCCCE-ecEE
Confidence 6899999999 6653
No 219
>PRK10220 hypothetical protein; Provisional
Probab=47.73 E-value=11 Score=28.11 Aligned_cols=22 Identities=32% Similarity=0.437 Sum_probs=17.6
Q ss_pred cccCCccc----ccCccccccCCCCC
Q 033276 73 KCLKLFSS----PFPLVICIKSNHEI 94 (123)
Q Consensus 73 rC~gC~k~----~~~~~fCp~CG~~~ 94 (123)
.|+.|... +.....||.||++=
T Consensus 5 ~CP~C~seytY~d~~~~vCpeC~hEW 30 (111)
T PRK10220 5 HCPKCNSEYTYEDNGMYICPECAHEW 30 (111)
T ss_pred cCCCCCCcceEcCCCeEECCcccCcC
Confidence 68888864 56678999999873
No 220
>TIGR02820 formald_GSH S-(hydroxymethyl)glutathione synthase. The formation of S-(hydroxymethyl)glutathione synthase from glutathione and formaldehyde occurs naturally, but this enzyme speeds its formation in some species as part of a pathway of formaldehyde detoxification.
Probab=47.70 E-value=8.1 Score=30.63 Aligned_cols=14 Identities=7% Similarity=0.176 Sum_probs=11.2
Q ss_pred ccCccccccCCCCC
Q 033276 81 PFPLVICIKSNHEI 94 (123)
Q Consensus 81 ~~~~~fCp~CG~~~ 94 (123)
...+.|||.||+++
T Consensus 86 ~~~R~FC~~CGS~L 99 (182)
T TIGR02820 86 TIQRHACKGCGTHM 99 (182)
T ss_pred CEEeecCCCCCCcc
Confidence 34578999999994
No 221
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=47.29 E-value=8 Score=28.15 Aligned_cols=11 Identities=18% Similarity=0.431 Sum_probs=8.5
Q ss_pred ccccccCCCCC
Q 033276 84 LVICIKSNHEI 94 (123)
Q Consensus 84 ~~fCp~CG~~~ 94 (123)
..|||.||+-+
T Consensus 2 m~FCp~Cgsll 12 (113)
T COG1594 2 MRFCPKCGSLL 12 (113)
T ss_pred ccccCCccCee
Confidence 36899999873
No 222
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=47.19 E-value=8.9 Score=28.33 Aligned_cols=12 Identities=8% Similarity=0.418 Sum_probs=9.4
Q ss_pred cccccCCCCCee
Q 033276 85 VICIKSNHEIRI 96 (123)
Q Consensus 85 ~fCp~CG~~~tl 96 (123)
.|||.|||-+.+
T Consensus 2 ~FCP~Cgn~Liv 13 (105)
T KOG2906|consen 2 LFCPTCGNMLIV 13 (105)
T ss_pred cccCCCCCEEEE
Confidence 699999997543
No 223
>COG1412 Uncharacterized proteins of PilT N-term./Vapc superfamily [General function prediction only]
Probab=46.82 E-value=23 Score=26.86 Aligned_cols=30 Identities=10% Similarity=0.194 Sum_probs=26.8
Q ss_pred eeEEecccHHHHHHHHHhCceeeCCCCCcc
Q 033276 34 TVACITGDYAMQNVILQMGLRLLAPGGMQI 63 (123)
Q Consensus 34 ~va~vTdDyAmQNVllqlGL~l~sv~g~~I 63 (123)
.+++.|.|-.+..-|+..|++++.+.|+..
T Consensus 99 ~~iVaTnD~eLk~rlr~~GIPvi~lr~r~~ 128 (136)
T COG1412 99 RYIVATNDKELKRRLRENGIPVITLRQRKL 128 (136)
T ss_pred CEEEEeCCHHHHHHHHHcCCCEEEEeCCeE
Confidence 589999999999999999999999986543
No 224
>PRK06386 replication factor A; Reviewed
Probab=46.42 E-value=12 Score=32.37 Aligned_cols=23 Identities=17% Similarity=0.206 Sum_probs=18.0
Q ss_pred EEeeccccCCccc-ccCccccccCCCC
Q 033276 68 RYIVDKCLKLFSS-PFPLVICIKSNHE 93 (123)
Q Consensus 68 ~wvl~rC~gC~k~-~~~~~fCp~CG~~ 93 (123)
.-.. |||.|.|. . ..+||.||..
T Consensus 234 gli~-rCP~C~R~l~--~g~C~~HG~v 257 (358)
T PRK06386 234 RIFT-KCSVCNKIIE--DGVCKDHPDA 257 (358)
T ss_pred EeEe-cCcCCCeEcc--CCcCCCCCCC
Confidence 3445 99999998 5 3689999954
No 225
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=46.31 E-value=12 Score=33.10 Aligned_cols=25 Identities=16% Similarity=0.126 Sum_probs=19.3
Q ss_pred EEeeccccCCccc----ccCccccccCCCC
Q 033276 68 RYIVDKCLKLFSS----PFPLVICIKSNHE 93 (123)
Q Consensus 68 ~wvl~rC~gC~k~----~~~~~fCp~CG~~ 93 (123)
-|++ .|..|+++ ......||.||..
T Consensus 238 g~~~-~c~~cg~~~~~~~~~~~~c~~Cg~~ 266 (380)
T COG1867 238 GYIY-HCSRCGEIVGSFREVDEKCPHCGGK 266 (380)
T ss_pred CcEE-EcccccceecccccccccCCccccc
Confidence 3668 99999744 4557889999975
No 226
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=45.86 E-value=14 Score=23.43 Aligned_cols=21 Identities=19% Similarity=0.048 Sum_probs=13.0
Q ss_pred cccCCcc-c---ccCccccccCCCC
Q 033276 73 KCLKLFS-S---PFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k-~---~~~~~fCp~CG~~ 93 (123)
.|+-|+. . ...+..|++||..
T Consensus 22 fCP~Cg~~~m~~~~~r~~C~~Cgyt 46 (50)
T PRK00432 22 FCPRCGSGFMAEHLDRWHCGKCGYT 46 (50)
T ss_pred cCcCCCcchheccCCcEECCCcCCE
Confidence 4666666 3 3456667777754
No 227
>PTZ00157 60S ribosomal protein L36a; Provisional
Probab=45.85 E-value=14 Score=26.31 Aligned_cols=17 Identities=18% Similarity=0.161 Sum_probs=14.6
Q ss_pred ccccccCCCCCeeeEEEE
Q 033276 84 LVICIKSNHEIRISPVFM 101 (123)
Q Consensus 84 ~~fCp~CG~~~tl~rV~~ 101 (123)
+-|||.|+.. |..+|+-
T Consensus 9 ~tyC~~C~kH-t~HkV~q 25 (84)
T PTZ00157 9 KTYCKKCGKH-TSHKVSQ 25 (84)
T ss_pred cccCcCCCCC-ccEEEEE
Confidence 5799999999 8888873
No 228
>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=45.73 E-value=11 Score=32.65 Aligned_cols=22 Identities=14% Similarity=0.202 Sum_probs=16.8
Q ss_pred cccCCccc---c----cCccccccCCCCC
Q 033276 73 KCLKLFSS---P----FPLVICIKSNHEI 94 (123)
Q Consensus 73 rC~gC~k~---~----~~~~fCp~CG~~~ 94 (123)
+|+.|... + ..+-.||.||+++
T Consensus 15 ~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L 43 (403)
T TIGR00155 15 LCSQCDMLVALPRIESGQKAACPRCGTTL 43 (403)
T ss_pred eCCCCCCcccccCCCCCCeeECCCCCCCC
Confidence 79999975 1 2245799999995
No 229
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=45.73 E-value=13 Score=26.55 Aligned_cols=25 Identities=20% Similarity=0.384 Sum_probs=18.4
Q ss_pred EeeccccCCccc------ccCccccccCCCC
Q 033276 69 YIVDKCLKLFSS------PFPLVICIKSNHE 93 (123)
Q Consensus 69 wvl~rC~gC~k~------~~~~~fCp~CG~~ 93 (123)
|+.-+|+||+++ -..-..|+.|+.-
T Consensus 32 Fm~VkC~gc~~iT~vfSHaqtvVvc~~c~~i 62 (84)
T KOG1779|consen 32 FMDVKCPGCFKITTVFSHAQTVVVCEGCSTI 62 (84)
T ss_pred EEEEEcCCceEEEEEeecCceEEEcCCCceE
Confidence 333489999997 2446889999865
No 230
>PRK00595 rpmG 50S ribosomal protein L33; Validated
Probab=45.62 E-value=12 Score=24.02 Aligned_cols=29 Identities=0% Similarity=-0.266 Sum_probs=20.4
Q ss_pred EEeeccccCCccc------c--------cCccccccCCCCCeeeE
Q 033276 68 RYIVDKCLKLFSS------P--------FPLVICIKSNHEIRISP 98 (123)
Q Consensus 68 ~wvl~rC~gC~k~------~--------~~~~fCp~CG~~~tl~r 98 (123)
.-.+ .|.+|... . .-+.|||.|+.. |+.+
T Consensus 8 ~i~L-~ct~c~~~nY~t~Kn~k~~~~rL~lkKycp~~~kh-tlhk 50 (53)
T PRK00595 8 KIKL-ESTEGTGRFYTTTKNKRNTPEKLELKKYDPVLRKH-VLHK 50 (53)
T ss_pred EEEE-EecCCCCEEEEEccCCCCCCCceEEECcCCCCCCE-EeEE
Confidence 4567 88888743 1 116899999999 6654
No 231
>TIGR02387 rpoC1_cyan DNA-directed RNA polymerase, gamma subunit. The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''.
Probab=45.23 E-value=7.6 Score=36.17 Aligned_cols=30 Identities=13% Similarity=0.114 Sum_probs=22.2
Q ss_pred eeEEeeccccCCccc---ccCccccccCCCCCeeeEE
Q 033276 66 LHRYIVDKCLKLFSS---PFPLVICIKSNHEIRISPV 99 (123)
Q Consensus 66 v~~wvl~rC~gC~k~---~~~~~fCp~CG~~~tl~rV 99 (123)
++.|.- +|++. .....||+.||-+.|..||
T Consensus 59 ~k~~eC----~CGkyk~~~~~~~~C~~CgvE~t~s~v 91 (619)
T TIGR02387 59 SKDWEC----HCGKYKRVRHRGIVCERCGVEVTESRV 91 (619)
T ss_pred CcCcEE----eCCCccccCcCCcCCCCCCCEEchhhh
Confidence 567776 66655 4446899999998887776
No 232
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=44.61 E-value=19 Score=22.50 Aligned_cols=8 Identities=13% Similarity=0.140 Sum_probs=4.1
Q ss_pred ccccCCCC
Q 033276 86 ICIKSNHE 93 (123)
Q Consensus 86 fCp~CG~~ 93 (123)
-||-||++
T Consensus 5 PCPFCG~~ 12 (61)
T PF14354_consen 5 PCPFCGSA 12 (61)
T ss_pred CCCCCCCc
Confidence 35555544
No 233
>PRK08402 replication factor A; Reviewed
Probab=44.54 E-value=33 Score=29.60 Aligned_cols=32 Identities=16% Similarity=0.165 Sum_probs=21.6
Q ss_pred EeeccccCCccc-c----cCccccccCC--CCCeeeEEEE
Q 033276 69 YIVDKCLKLFSS-P----FPLVICIKSN--HEIRISPVFM 101 (123)
Q Consensus 69 wvl~rC~gC~k~-~----~~~~fCp~CG--~~~tl~rV~~ 101 (123)
|.. +|+.|.|. . ...-.|+.|| .+.-+.++++
T Consensus 211 ~y~-aCp~CnKkv~~~~~~~~~~Ce~~~~v~p~~ryil~~ 249 (355)
T PRK08402 211 VYD-ACPECRRKVDYDPATDTWICPEHGEVEPIKITILDF 249 (355)
T ss_pred eEe-cCCCCCeEEEEecCCCCEeCCCCCCcCcceeEEEEE
Confidence 655 99999987 3 2356899999 5533334443
No 234
>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=44.33 E-value=9.6 Score=32.59 Aligned_cols=27 Identities=15% Similarity=0.101 Sum_probs=19.8
Q ss_pred ccccCCccc-ccCccccccCCCCCeeeEE
Q 033276 72 DKCLKLFSS-PFPLVICIKSNHEIRISPV 99 (123)
Q Consensus 72 ~rC~gC~k~-~~~~~fCp~CG~~~tl~rV 99 (123)
+.|..|+.. ..-...||.||+. -++|.
T Consensus 83 ~~C~~CGa~V~~~e~~Cp~C~St-nI~r~ 110 (314)
T PF09567_consen 83 GKCNNCGANVSRLEESCPNCGST-NIKRK 110 (314)
T ss_pred hhhccccceeeehhhcCCCCCcc-ccccc
Confidence 378999987 4445789999998 55543
No 235
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=44.25 E-value=19 Score=21.73 Aligned_cols=14 Identities=29% Similarity=0.539 Sum_probs=9.0
Q ss_pred cccccCCCCCeeeEE
Q 033276 85 VICIKSNHEIRISPV 99 (123)
Q Consensus 85 ~fCp~CG~~~tl~rV 99 (123)
..||+||-. .|..|
T Consensus 2 hlcpkcgvg-vl~pv 15 (36)
T PF09151_consen 2 HLCPKCGVG-VLEPV 15 (36)
T ss_dssp -B-TTTSSS-BEEEE
T ss_pred ccCCccCce-EEEEe
Confidence 469999988 55554
No 236
>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=44.18 E-value=35 Score=25.96 Aligned_cols=51 Identities=20% Similarity=0.205 Sum_probs=32.4
Q ss_pred eEEecccHHHHHHHHHhCce---eeCCCCCcceeeeEEeeccccCCccc-c-------cCccccccCCCCC
Q 033276 35 VACITGDYAMQNVILQMGLR---LLAPGGMQIRQLHRYIVDKCLKLFSS-P-------FPLVICIKSNHEI 94 (123)
Q Consensus 35 va~vTdDyAmQNVllqlGL~---l~sv~g~~I~~v~~wvl~rC~gC~k~-~-------~~~~fCp~CG~~~ 94 (123)
..++|.- +-|...+.|.+ ++-++|.- ... +|..|.+. + .....||.||+.+
T Consensus 83 ~~iiTqN--iD~L~~~ag~~~~~v~~lHG~~------~~~-~C~~C~~~~~~~~~~~~~~~p~C~~C~~~l 144 (222)
T cd00296 83 KRIITQN--VDGLHERAGSRRNRVIELHGSL------DRV-RCTSCGKEYPRDEVLEREKPPRCPKCGGLL 144 (222)
T ss_pred ceEEecC--hHHHHHHhCCCcCcEEEecCCC------Ccc-EECCCCCCcchhhhhhccCCCCCCCCCCcc
Confidence 4677753 34566677775 66677631 224 89999865 2 1345699999884
No 237
>PRK08329 threonine synthase; Validated
Probab=44.12 E-value=15 Score=30.67 Aligned_cols=25 Identities=12% Similarity=0.230 Sum_probs=17.4
Q ss_pred eccccCCccc-c-cCccccccCCCCCeee
Q 033276 71 VDKCLKLFSS-P-FPLVICIKSNHEIRIS 97 (123)
Q Consensus 71 l~rC~gC~k~-~-~~~~fCp~CG~~~tl~ 97 (123)
+ +|..|++. + .....| .||.++.+.
T Consensus 2 l-~C~~Cg~~~~~~~~~~C-~c~~~l~~~ 28 (347)
T PRK08329 2 L-RCTKCGRTYEEKFKLRC-DCGGTLLVE 28 (347)
T ss_pred c-CcCCCCCCcCCCCceec-CCCCcEEEE
Confidence 6 89999988 3 233579 699874333
No 238
>COG2405 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=44.10 E-value=18 Score=28.46 Aligned_cols=29 Identities=24% Similarity=0.330 Sum_probs=24.9
Q ss_pred Ccee-EEecccHHHHHHHHHhCceeeCCCC
Q 033276 32 ESTV-ACITGDYAMQNVILQMGLRLLAPGG 60 (123)
Q Consensus 32 ~~~v-a~vTdDyAmQNVllqlGL~l~sv~g 60 (123)
+.++ -+++||+.=.|+|..|||++.++-|
T Consensus 85 e~~ad~Ll~Ddr~aR~~A~~lgL~V~GtlG 114 (157)
T COG2405 85 ELKADLLLMDDRDARNVAKSLGLKVTGTLG 114 (157)
T ss_pred HcCCCeeeeccHHHHHHHHHcCCeeeehhH
Confidence 3455 7899999999999999999998755
No 239
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=44.01 E-value=12 Score=24.59 Aligned_cols=19 Identities=5% Similarity=-0.200 Sum_probs=13.3
Q ss_pred cccCCcccccCccccccCCC
Q 033276 73 KCLKLFSSPFPLVICIKSNH 92 (123)
Q Consensus 73 rC~gC~k~~~~~~fCp~CG~ 92 (123)
.|..|+....+...|| ||.
T Consensus 29 ~c~~cg~~~~pH~vc~-cG~ 47 (60)
T PRK01110 29 VDKTTGEYHLPHHVSP-KGY 47 (60)
T ss_pred EcCCCCceeccceecC-Ccc
Confidence 6888887745556688 883
No 240
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=43.91 E-value=26 Score=25.18 Aligned_cols=20 Identities=10% Similarity=0.054 Sum_probs=14.6
Q ss_pred CccccccCCCCCeeeEEEEEe
Q 033276 83 PLVICIKSNHEIRISPVFMLI 103 (123)
Q Consensus 83 ~~~fCp~CG~~~tl~rV~~~~ 103 (123)
.+..||.||.. .++|+++-|
T Consensus 34 a~y~CpfCgk~-~vkR~a~GI 53 (91)
T TIGR00280 34 AKYVCPFCGKK-TVKRGSTGI 53 (91)
T ss_pred cCccCCCCCCC-ceEEEeeEE
Confidence 35778888876 788887544
No 241
>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=43.79 E-value=7.7 Score=37.58 Aligned_cols=27 Identities=19% Similarity=0.342 Sum_probs=0.0
Q ss_pred eeEEeeccccCCcccccCccccccCCCC
Q 033276 66 LHRYIVDKCLKLFSSPFPLVICIKSNHE 93 (123)
Q Consensus 66 v~~wvl~rC~gC~k~~~~~~fCp~CG~~ 93 (123)
..+|.. +|+.|+....+..+||.||..
T Consensus 663 ~~t~~~-~Cp~CG~~T~~~~~Cp~C~~~ 689 (900)
T PF03833_consen 663 KETFYN-RCPECGSHTEPVYVCPDCGIE 689 (900)
T ss_dssp ----------------------------
T ss_pred Ccchhh-cCcccCCccccceeccccccc
Confidence 346777 888888763334555555555
No 242
>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=43.57 E-value=14 Score=23.72 Aligned_cols=26 Identities=31% Similarity=0.416 Sum_probs=18.6
Q ss_pred eEEeeccccCCccc----c-----cCccccccCCCC
Q 033276 67 HRYIVDKCLKLFSS----P-----FPLVICIKSNHE 93 (123)
Q Consensus 67 ~~wvl~rC~gC~k~----~-----~~~~fCp~CG~~ 93 (123)
.++.+ .|..|+.. + .-.-.||.||.-
T Consensus 19 ~r~aL-IC~~C~~hNGla~~~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 19 NRYAL-ICSKCFSHNGLAPKEEFEEIQYRCPYCGAL 53 (54)
T ss_pred CceeE-ECcccchhhcccccccCCceEEEcCCCCCc
Confidence 37889 99999975 1 124569999863
No 243
>TIGR01023 rpmG_bact ribosomal protein L33, bacterial type. This model describes bacterial ribosomal protein L33 and its chloroplast and mitochondrial equivalents.
Probab=43.46 E-value=14 Score=23.90 Aligned_cols=29 Identities=7% Similarity=-0.039 Sum_probs=20.5
Q ss_pred EEeeccccCCccc------c--------cCccccccCCCCCeeeE
Q 033276 68 RYIVDKCLKLFSS------P--------FPLVICIKSNHEIRISP 98 (123)
Q Consensus 68 ~wvl~rC~gC~k~------~--------~~~~fCp~CG~~~tl~r 98 (123)
.-.+ .|.+|... . .-+.|||.|+.. |+.+
T Consensus 9 ~i~L-~ct~c~~~nY~t~Kn~~~~~~kL~lkKycp~~~kh-tlhk 51 (54)
T TIGR01023 9 LIRL-VCTACTGINYTTTKNRRNKPEKLELRKYCPVCRKH-VLHK 51 (54)
T ss_pred EEEE-EecCCCCCCEEEcCCCCCCCCceEEECcCCCCCCe-EeEE
Confidence 4567 89999642 1 116899999999 6654
No 244
>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=43.39 E-value=7.2 Score=24.32 Aligned_cols=10 Identities=10% Similarity=0.195 Sum_probs=5.3
Q ss_pred cccccCCCCC
Q 033276 85 VICIKSNHEI 94 (123)
Q Consensus 85 ~fCp~CG~~~ 94 (123)
.-||.||.++
T Consensus 21 ~~CPlC~r~l 30 (54)
T PF04423_consen 21 GCCPLCGRPL 30 (54)
T ss_dssp EE-TTT--EE
T ss_pred CcCCCCCCCC
Confidence 3799999874
No 245
>PRK05767 rpl44e 50S ribosomal protein L44e; Validated
Probab=43.32 E-value=16 Score=26.38 Aligned_cols=17 Identities=12% Similarity=-0.009 Sum_probs=14.6
Q ss_pred ccccccCCCCCeeeEEEE
Q 033276 84 LVICIKSNHEIRISPVFM 101 (123)
Q Consensus 84 ~~fCp~CG~~~tl~rV~~ 101 (123)
+-|||.|+.. |..+|+-
T Consensus 8 ~tyCp~CkkH-t~HkV~q 24 (92)
T PRK05767 8 RTYCPYCKTH-TEHEVEK 24 (92)
T ss_pred cccCcCCCCc-ccEEEEE
Confidence 5799999999 8888873
No 246
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=43.23 E-value=14 Score=26.85 Aligned_cols=29 Identities=17% Similarity=0.195 Sum_probs=18.6
Q ss_pred cccccCCCCCeeeEEEEEeeEEEEEeeCCcccee
Q 033276 85 VICIKSNHEIRISPVFMLILICLYIQVDTEMPCL 118 (123)
Q Consensus 85 ~fCp~CG~~~tl~rV~~~~~~~~~~~~~~~~~~~ 118 (123)
..||.||.++.|.+ +.-+|=+.-++-|.+
T Consensus 3 ~~CpYCg~~~~l~~-----~~~iYg~~~~~~~~~ 31 (102)
T PF11672_consen 3 IICPYCGGPAELVD-----GSEIYGHRYDDGPYL 31 (102)
T ss_pred cccCCCCCeeEEcc-----cchhcCccCCCCcee
Confidence 57999999976655 344455554455554
No 247
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=43.17 E-value=4 Score=26.57 Aligned_cols=22 Identities=14% Similarity=0.167 Sum_probs=15.1
Q ss_pred cccCCccc-ccCccccccCCCCC
Q 033276 73 KCLKLFSS-PFPLVICIKSNHEI 94 (123)
Q Consensus 73 rC~gC~k~-~~~~~fCp~CG~~~ 94 (123)
-|..|-.. -...++||+||.++
T Consensus 23 LCl~CLt~ml~~s~~C~iC~~~L 45 (50)
T PF03854_consen 23 LCLNCLTLMLSRSDRCPICGKPL 45 (50)
T ss_dssp EEHHHHHHT-SSSSEETTTTEE-
T ss_pred HHHHHHHHHhccccCCCcccCcC
Confidence 46777766 33458999999873
No 248
>PF11648 RIG-I_C-RD: C-terminal domain of RIG-I; InterPro: IPR021673 This family of proteins represents the regulatory domain RD of RIG-I, a protein which initiates a signalling cascade that provides essential antiviral protection for the host. The RD domain binds viral RNA, activating the RIG-I ATPase by RNA-dependent dimerisation. The structure of RD contains a zinc-binding domain and is thought to confer ligand specificity []. ; GO: 0016817 hydrolase activity, acting on acid anhydrides; PDB: 2RQB_A 3GA3_A 2W4R_D 3EQT_A 2RQA_A 2RMJ_A 3NCU_A 2QFD_C 2QFB_D 3TMI_A ....
Probab=43.16 E-value=20 Score=26.23 Aligned_cols=27 Identities=19% Similarity=0.460 Sum_probs=18.8
Q ss_pred cCccccccCCCCCeeeEEEEEeeEEEEEeeCC-ccceee
Q 033276 82 FPLVICIKSNHEIRISPVFMLILICLYIQVDT-EMPCLL 119 (123)
Q Consensus 82 ~~~~fCp~CG~~~tl~rV~~~~~~~~~~~~~~-~~~~~~ 119 (123)
..+.+|..||+.. ...++-.| ++|||+
T Consensus 58 ~~~I~C~~C~~~w-----------G~~m~yk~~~LP~L~ 85 (123)
T PF11648_consen 58 NGKIHCKNCGQDW-----------GIMMKYKGVELPCLK 85 (123)
T ss_dssp EEEEEETSTSBEE-----------EEEEEETTEEEEEE-
T ss_pred CCEEEcCCCChHh-----------hhheEECCccccEEE
Confidence 4468899999982 33555666 899986
No 249
>PRK05417 glutathione-dependent formaldehyde-activating enzyme; Provisional
Probab=43.13 E-value=10 Score=30.14 Aligned_cols=17 Identities=6% Similarity=0.192 Sum_probs=12.5
Q ss_pred cCccccccCCCCCeeeEE
Q 033276 82 FPLVICIKSNHEIRISPV 99 (123)
Q Consensus 82 ~~~~fCp~CG~~~tl~rV 99 (123)
..+.|||.||.++ -.+.
T Consensus 91 i~R~FC~~CGS~L-~~~~ 107 (191)
T PRK05417 91 IQRHACKECGVHM-YGRI 107 (191)
T ss_pred eEeeeCCCCCCcc-cccc
Confidence 4578999999994 4443
No 250
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=42.98 E-value=26 Score=25.09 Aligned_cols=20 Identities=10% Similarity=0.074 Sum_probs=14.8
Q ss_pred CccccccCCCCCeeeEEEEEe
Q 033276 83 PLVICIKSNHEIRISPVFMLI 103 (123)
Q Consensus 83 ~~~fCp~CG~~~tl~rV~~~~ 103 (123)
.+..||.||.. .++|+++=|
T Consensus 35 a~y~CpfCgk~-~vkR~a~GI 54 (90)
T PTZ00255 35 AKYFCPFCGKH-AVKRQAVGI 54 (90)
T ss_pred CCccCCCCCCC-ceeeeeeEE
Confidence 45778888877 788887633
No 251
>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional
Probab=42.97 E-value=9.7 Score=35.53 Aligned_cols=30 Identities=13% Similarity=0.114 Sum_probs=21.8
Q ss_pred eeEEeeccccCCccc---ccCccccccCCCCCeeeEE
Q 033276 66 LHRYIVDKCLKLFSS---PFPLVICIKSNHEIRISPV 99 (123)
Q Consensus 66 v~~wvl~rC~gC~k~---~~~~~fCp~CG~~~tl~rV 99 (123)
++.|.- +|++. .....||+.||-+.|-.||
T Consensus 66 ~k~~eC----~CGkyk~~~~~~~~C~~CgvE~t~s~v 98 (627)
T PRK02625 66 SKDWEC----HCGKYKRVRHRGIVCERCGVEVTESRV 98 (627)
T ss_pred ccCcEE----eCCCccccCcCCcCCCCCCcEecchhh
Confidence 567776 66655 3446899999998777665
No 252
>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=42.62 E-value=18 Score=28.86 Aligned_cols=43 Identities=14% Similarity=0.243 Sum_probs=26.6
Q ss_pred eeCCCCCcceeeeEEeeccccCCccc-cc----------CccccccCCCCCeeeEEEEEeeEE
Q 033276 55 LLAPGGMQIRQLHRYIVDKCLKLFSS-PF----------PLVICIKSNHEIRISPVFMLILIC 106 (123)
Q Consensus 55 l~sv~g~~I~~v~~wvl~rC~gC~k~-~~----------~~~fCp~CG~~~tl~rV~~~~~~~ 106 (123)
++.++|. -+.. +|..|.+. +. ..-.||.||+. ||.--|..|+.
T Consensus 107 V~elHG~------l~~~-~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cgg~--lrP~Vv~FGE~ 160 (235)
T cd01408 107 IIEAHGS------FATA-HCIKCKHKYPGDWMREDIFNQEVPKCPRCGGL--VKPDIVFFGES 160 (235)
T ss_pred EEEeCcC------CCcc-ccccCCCcCCHHHHHHHHhCCCCccCCCCCCC--ccCcEEECCCC
Confidence 5555553 2345 99999986 31 12359999977 55555555553
No 253
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=42.61 E-value=11 Score=25.22 Aligned_cols=8 Identities=38% Similarity=0.638 Sum_probs=6.9
Q ss_pred ccccCCCC
Q 033276 86 ICIKSNHE 93 (123)
Q Consensus 86 fCp~CG~~ 93 (123)
-||+||+.
T Consensus 2 ~C~KCg~~ 9 (64)
T PF09855_consen 2 KCPKCGNE 9 (64)
T ss_pred CCCCCCCc
Confidence 49999987
No 254
>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=42.11 E-value=18 Score=31.17 Aligned_cols=27 Identities=11% Similarity=0.090 Sum_probs=17.4
Q ss_pred eEEeeccccCCccc--c----cCccccccCCCCC
Q 033276 67 HRYIVDKCLKLFSS--P----FPLVICIKSNHEI 94 (123)
Q Consensus 67 ~~wvl~rC~gC~k~--~----~~~~fCp~CG~~~ 94 (123)
.-|++ .|++|... . ..+..||.||++.
T Consensus 237 ~G~v~-~C~~C~~~~~~~~~~~~~~~c~~cg~~~ 269 (377)
T PF02005_consen 237 LGYVY-YCPSCGYREEVKGLQKLKSKCPECGSKL 269 (377)
T ss_dssp EEEEE-EETTT--EECCT-GCC--CEETTT-SCC
T ss_pred eeEEE-ECCCccccccccCccccCCcCCCCCCcc
Confidence 47999 99999953 1 1137899999995
No 255
>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=42.09 E-value=25 Score=26.33 Aligned_cols=35 Identities=17% Similarity=0.144 Sum_probs=21.6
Q ss_pred EEeeccccCCccc-c----------cCccccccCCCCCeeeEEEEEeeE
Q 033276 68 RYIVDKCLKLFSS-P----------FPLVICIKSNHEIRISPVFMLILI 105 (123)
Q Consensus 68 ~wvl~rC~gC~k~-~----------~~~~fCp~CG~~~tl~rV~~~~~~ 105 (123)
-+.. +|..|++. + .....||.||+. +|.=-|..|+
T Consensus 103 l~~~-~C~~C~~~~~~~~~~~~~~~~~~~~C~~C~~~--lrp~vv~fgE 148 (178)
T PF02146_consen 103 LFRL-RCSKCGKEYDREDIVDSIDEEEPPRCPKCGGL--LRPDVVLFGE 148 (178)
T ss_dssp EEEE-EETTTSBEEEGHHHHHHHHTTSSCBCTTTSCB--EEEEE--BTS
T ss_pred hcee-eecCCCccccchhhcccccccccccccccCcc--CCCCeeecCC
Confidence 4566 99999985 1 223579999996 4443333343
No 256
>PF15616 TerY-C: TerY-C metal binding domain
Probab=41.58 E-value=16 Score=27.70 Aligned_cols=22 Identities=18% Similarity=-0.014 Sum_probs=17.2
Q ss_pred cccCCccc----ccCccccccCCCCCe
Q 033276 73 KCLKLFSS----PFPLVICIKSNHEIR 95 (123)
Q Consensus 73 rC~gC~k~----~~~~~fCp~CG~~~t 95 (123)
.| +|+++ .+....||-||+...
T Consensus 91 ~C-~CGkl~Ci~g~~~~~CPwCg~~g~ 116 (131)
T PF15616_consen 91 VC-GCGKLFCIDGEGEVTCPWCGNEGS 116 (131)
T ss_pred Ee-cCCCEEEeCCCCCEECCCCCCeee
Confidence 47 89998 455789999999853
No 257
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=41.17 E-value=31 Score=24.69 Aligned_cols=20 Identities=15% Similarity=0.157 Sum_probs=14.3
Q ss_pred CccccccCCCCCeeeEEEEEe
Q 033276 83 PLVICIKSNHEIRISPVFMLI 103 (123)
Q Consensus 83 ~~~fCp~CG~~~tl~rV~~~~ 103 (123)
.+..||.||.. .++|+++=|
T Consensus 35 a~y~CpfCgk~-~vkR~a~GI 54 (90)
T PRK03976 35 AKHVCPVCGRP-KVKRVGTGI 54 (90)
T ss_pred cCccCCCCCCC-ceEEEEEEE
Confidence 35678888777 788877544
No 258
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=40.88 E-value=22 Score=22.87 Aligned_cols=23 Identities=17% Similarity=-0.081 Sum_probs=13.2
Q ss_pred ccccCCCCCeeeEEEEEeeEEEEE
Q 033276 86 ICIKSNHEIRISPVFMLILICLYI 109 (123)
Q Consensus 86 fCp~CG~~~tl~rV~~~~~~~~~~ 109 (123)
.||.||.++ -.-+-.+.|.--||
T Consensus 2 ~CPyCge~~-~~~iD~s~~~Q~yi 24 (52)
T PF14255_consen 2 QCPYCGEPI-EILIDPSAGDQEYI 24 (52)
T ss_pred CCCCCCCee-EEEEecCCCCeeEE
Confidence 489999884 33444444443343
No 259
>COG5134 Uncharacterized conserved protein [Function unknown]
Probab=40.85 E-value=20 Score=30.08 Aligned_cols=52 Identities=19% Similarity=0.261 Sum_probs=35.2
Q ss_pred CCCCcceeeeEEeeccccCCccc-ccC-----------------------ccccccCCCCCeeeEEEEEeeEEEEEeeCC
Q 033276 58 PGGMQIRQLHRYIVDKCLKLFSS-PFP-----------------------LVICIKSNHEIRISPVFMLILICLYIQVDT 113 (123)
Q Consensus 58 v~g~~I~~v~~wvl~rC~gC~k~-~~~-----------------------~~fCp~CG~~~tl~rV~~~~~~~~~~~~~~ 113 (123)
+.|--|+=.--|-. ||..|... +-. ...||-||+++-+|.= -|+++|+-+-|
T Consensus 30 prglSiRL~TPF~~-RCL~C~~YI~K~~rfNavkE~~~dK~y~~~kiYRf~I~C~~C~n~i~~RTD---PkN~~YV~EsG 105 (272)
T COG5134 30 PRGLSIRLETPFPV-RCLNCENYIQKGTRFNAVKEEIGDKSYYTTKIYRFSIKCHLCSNPIDVRTD---PKNTEYVVESG 105 (272)
T ss_pred cccceEEeccCcce-eecchhhhhhcccchhHHHHHhcccccceeEEEEEEEEccCCCCceeeecC---CCCceEEEecC
Confidence 34555666667888 99999865 211 1359999999654433 37888887666
No 260
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=40.75 E-value=19 Score=31.73 Aligned_cols=70 Identities=17% Similarity=0.212 Sum_probs=43.2
Q ss_pred EEecccHHHHHHHHHhCceeeCCCCCcceeeeEEeeccccCCccc-ccC-ccccccCCCCCeeeEEEEEeeEEEEEeeCC
Q 033276 36 ACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSS-PFP-LVICIKSNHEIRISPVFMLILICLYIQVDT 113 (123)
Q Consensus 36 a~vTdDyAmQNVllqlGL~l~sv~g~~I~~v~~wvl~rC~gC~k~-~~~-~~fCp~CG~~~tl~rV~~~~~~~~~~~~~~ 113 (123)
-..|-||++--=+.++++.+..--++.-- --+|.+ .=.-=++. ..+ ..||.+||-+ |+.-|
T Consensus 42 p~e~~tv~~e~~~~~~~~p~f~~~~r~pp-hl~w~~-~V~~~gek~l~p~VHfCd~Cd~P---------------I~IYG 104 (389)
T KOG2932|consen 42 PTETVTVACEDHLVLADLPVFKGIGRVPP-HLTWIK-PVGRRGEKQLGPRVHFCDRCDFP---------------IAIYG 104 (389)
T ss_pred CcceeeeccchhhhhcCCchhcccccCCC-ceeeee-ecccccccccCcceEeecccCCc---------------ceeee
Confidence 35667888888888888887754333332 246777 22222222 223 6899999999 45556
Q ss_pred -ccceeecccC
Q 033276 114 -EMPCLLHYHC 123 (123)
Q Consensus 114 -~~~~~~~~~~ 123 (123)
-||| +|..|
T Consensus 105 RmIPC-kHvFC 114 (389)
T KOG2932|consen 105 RMIPC-KHVFC 114 (389)
T ss_pred ccccc-chhhh
Confidence 6788 44443
No 261
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=40.60 E-value=25 Score=26.32 Aligned_cols=20 Identities=25% Similarity=0.391 Sum_probs=15.1
Q ss_pred CccccccCCCCCeeeEEEEEeeEEEEEeeCC
Q 033276 83 PLVICIKSNHEIRISPVFMLILICLYIQVDT 113 (123)
Q Consensus 83 ~~~fCp~CG~~~tl~rV~~~~~~~~~~~~~~ 113 (123)
....||+||+. +.||.|.-+
T Consensus 72 s~~~C~~C~~~-----------eavffQ~~~ 91 (113)
T KOG2691|consen 72 SDKHCPKCGHR-----------EAVFFQAQT 91 (113)
T ss_pred ccccCCccCCc-----------ceEEEeccc
Confidence 35779999988 567888744
No 262
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=40.48 E-value=16 Score=32.61 Aligned_cols=27 Identities=11% Similarity=0.180 Sum_probs=19.8
Q ss_pred EEeeccccCCccc-c------cCccccccCCCCCe
Q 033276 68 RYIVDKCLKLFSS-P------FPLVICIKSNHEIR 95 (123)
Q Consensus 68 ~wvl~rC~gC~k~-~------~~~~fCp~CG~~~t 95 (123)
--.. +|+.|.-. + ...-+||.||+.++
T Consensus 16 ~~~~-~C~eCd~~~~~P~l~~~q~A~CPRC~~~l~ 49 (418)
T COG2995 16 GHLI-LCPECDMLVSLPRLDSGQSAYCPRCGHTLT 49 (418)
T ss_pred ccee-cCCCCCceeccccCCCCCcccCCCCCCccc
Confidence 3456 89999975 2 23679999999854
No 263
>TIGR00201 comF comF family protein. This protein is found in species that do (Bacillus subtilis, Haemophilus influenzae) or do not (E. coli, Borrelia burgdorferi) have described systems for natural transformation with exogenous DNA. It is involved in competence for transformation in Bacillus subtilis.
Probab=40.22 E-value=15 Score=27.95 Aligned_cols=21 Identities=10% Similarity=0.022 Sum_probs=16.3
Q ss_pred ccCCccc-ccCccccccCCCCC
Q 033276 74 CLKLFSS-PFPLVICIKSNHEI 94 (123)
Q Consensus 74 C~gC~k~-~~~~~fCp~CG~~~ 94 (123)
|.+|++. .....+|+.|+.++
T Consensus 1 C~~C~~~~~~~~~~C~~C~~~~ 22 (190)
T TIGR00201 1 CSLCGRPYQSVHALCRQCGSWR 22 (190)
T ss_pred CCccccccccccCCchhhCCcc
Confidence 8899987 33457899999874
No 264
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=39.66 E-value=16 Score=24.73 Aligned_cols=21 Identities=10% Similarity=0.200 Sum_probs=18.1
Q ss_pred cccCCccc--ccCccccccCCC-C
Q 033276 73 KCLKLFSS--PFPLVICIKSNH-E 93 (123)
Q Consensus 73 rC~gC~k~--~~~~~fCp~CG~-~ 93 (123)
+|.-|++. ...+..|..||. +
T Consensus 19 ~CrRCG~~syh~qK~~CasCGygp 42 (62)
T PRK04179 19 RCRRCGRHSYNVRKKYCAACGFGR 42 (62)
T ss_pred hhcccCcccccccccchhhcCCCc
Confidence 59999987 667899999998 5
No 265
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=39.36 E-value=18 Score=23.91 Aligned_cols=20 Identities=15% Similarity=0.273 Sum_probs=14.0
Q ss_pred cccCCccc-ccCccccccCCCCC
Q 033276 73 KCLKLFSS-PFPLVICIKSNHEI 94 (123)
Q Consensus 73 rC~gC~k~-~~~~~fCp~CG~~~ 94 (123)
.|.+||-. +. -=||.||.++
T Consensus 29 I~~~~f~~~rY--ngCPfC~~~~ 49 (55)
T PF14447_consen 29 ICDNCFPGERY--NGCPFCGTPF 49 (55)
T ss_pred eeccccChhhc--cCCCCCCCcc
Confidence 56777755 33 4599999883
No 266
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=39.26 E-value=18 Score=32.61 Aligned_cols=28 Identities=14% Similarity=-0.024 Sum_probs=21.5
Q ss_pred EeeccccCCccc-ccCccccccCCCCCeee
Q 033276 69 YIVDKCLKLFSS-PFPLVICIKSNHEIRIS 97 (123)
Q Consensus 69 wvl~rC~gC~k~-~~~~~fCp~CG~~~tl~ 97 (123)
=.| .|..|+.. +....-||.||.=.|+.
T Consensus 6 t~f-~C~~CG~~s~KW~GkCp~Cg~Wns~v 34 (456)
T COG1066 6 TAF-VCQECGYVSPKWLGKCPACGAWNTLV 34 (456)
T ss_pred cEE-EcccCCCCCccccccCCCCCCccceE
Confidence 356 99999998 77778899999544443
No 267
>CHL00018 rpoC1 RNA polymerase beta' subunit
Probab=39.04 E-value=10 Score=35.54 Aligned_cols=31 Identities=16% Similarity=-0.032 Sum_probs=22.1
Q ss_pred eeEEeeccccCCccc---c---cCccccccCCCCCeeeEEE
Q 033276 66 LHRYIVDKCLKLFSS---P---FPLVICIKSNHEIRISPVF 100 (123)
Q Consensus 66 v~~wvl~rC~gC~k~---~---~~~~fCp~CG~~~tl~rV~ 100 (123)
++.|.- +|++. . ....||+.||-+.|..||.
T Consensus 64 ~k~~~C----~CGkyk~~~~~~~~~~~C~~CgVE~t~s~vR 100 (663)
T CHL00018 64 IKSGIC----ACGNYRVIGDEKEDPKFCEQCGVEFTDSRVR 100 (663)
T ss_pred CcCCEE----eCCCccccCccccCCCccCCcCCEechhhhh
Confidence 566766 66655 3 3457999999998877763
No 268
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=38.36 E-value=7.9 Score=34.18 Aligned_cols=39 Identities=18% Similarity=0.148 Sum_probs=29.8
Q ss_pred CCCcceeeeEEeeccccCCccc-ccCccccccCCCCCeeeEEE
Q 033276 59 GGMQIRQLHRYIVDKCLKLFSS-PFPLVICIKSNHEIRISPVF 100 (123)
Q Consensus 59 ~g~~I~~v~~wvl~rC~gC~k~-~~~~~fCp~CG~~~tl~rV~ 100 (123)
-|.+|++ +-.| ||+.|+.. ..-.--||.|..=-|++++.
T Consensus 345 vge~l~~--~~~Y-RC~~CGF~a~~l~W~CPsC~~W~TikPir 384 (389)
T COG2956 345 VGEQLRR--KPRY-RCQNCGFTAHTLYWHCPSCRAWETIKPIR 384 (389)
T ss_pred HHHHHhh--cCCc-eecccCCcceeeeeeCCCcccccccCCcc
Confidence 3667776 7788 99999977 55556799999876777654
No 269
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=38.17 E-value=17 Score=28.21 Aligned_cols=21 Identities=14% Similarity=0.064 Sum_probs=14.3
Q ss_pred cccCCcccccCccccccCCCC
Q 033276 73 KCLKLFSSPFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~~~~~~fCp~CG~~ 93 (123)
.|+.|+......-+||.||..
T Consensus 311 ~C~~cg~~~~r~~~C~~cg~~ 331 (364)
T COG0675 311 TCPCCGHLSGRLFKCPRCGFV 331 (364)
T ss_pred cccccCCccceeEECCCCCCe
Confidence 788888731223678888874
No 270
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=38.06 E-value=21 Score=24.40 Aligned_cols=13 Identities=15% Similarity=0.266 Sum_probs=9.5
Q ss_pred cccccCCCCCeee
Q 033276 85 VICIKSNHEIRIS 97 (123)
Q Consensus 85 ~fCp~CG~~~tl~ 97 (123)
..||.||++..++
T Consensus 2 m~CP~Cg~~a~ir 14 (72)
T PRK09678 2 FHCPLCQHAAHAR 14 (72)
T ss_pred ccCCCCCCccEEE
Confidence 3699999995333
No 271
>PF02639 DUF188: Uncharacterized BCR, YaiI/YqxD family COG1671; InterPro: IPR003791 This entry describes proteins of unknown function.
Probab=37.90 E-value=43 Score=24.91 Aligned_cols=29 Identities=28% Similarity=0.477 Sum_probs=26.2
Q ss_pred EEecccHHHHHHHHHhCceeeCCCCCcce
Q 033276 36 ACITGDYAMQNVILQMGLRLLAPGGMQIR 64 (123)
Q Consensus 36 a~vTdDyAmQNVllqlGL~l~sv~g~~I~ 64 (123)
.++|.||.+-..++.-|..++++.|....
T Consensus 54 iVITqDigLA~~~l~Kga~vl~~rG~~yt 82 (130)
T PF02639_consen 54 IVITQDIGLASLLLAKGAYVLNPRGKEYT 82 (130)
T ss_pred EEEECCHHHHHHHHHCCCEEECCCCCCCC
Confidence 78999999999999999999999987543
No 272
>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=37.30 E-value=18 Score=31.05 Aligned_cols=16 Identities=6% Similarity=0.100 Sum_probs=11.7
Q ss_pred cCccccccCCCCCeee
Q 033276 82 FPLVICIKSNHEIRIS 97 (123)
Q Consensus 82 ~~~~fCp~CG~~~tl~ 97 (123)
...-+||.||.++.++
T Consensus 28 ~~~~~CP~C~~~v~lk 43 (375)
T PF06054_consen 28 KGKYFCPGCGEPVILK 43 (375)
T ss_pred CCcEECCCCCCeeEEE
Confidence 3457899999996554
No 273
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=37.24 E-value=6.6 Score=25.56 Aligned_cols=24 Identities=17% Similarity=0.400 Sum_probs=20.0
Q ss_pred cccCCccc-ccCccccccCCCCCeee
Q 033276 73 KCLKLFSS-PFPLVICIKSNHEIRIS 97 (123)
Q Consensus 73 rC~gC~k~-~~~~~fCp~CG~~~tl~ 97 (123)
.|.-|+.. ++.-.-|-+||++ .|+
T Consensus 16 IC~rC~Arnp~~A~kCRkC~~k-~LR 40 (50)
T COG1552 16 ICRRCYARNPPRATKCRKCGYK-NLR 40 (50)
T ss_pred HHHHhcCCCCcchhHHhhccCC-Ccc
Confidence 79999988 6667889999998 665
No 274
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=37.21 E-value=33 Score=22.42 Aligned_cols=36 Identities=8% Similarity=-0.014 Sum_probs=20.9
Q ss_pred eeeCCCCCcceeeeEEeeccccCCcc--c---ccCccccccCCCC
Q 033276 54 RLLAPGGMQIRQLHRYIVDKCLKLFS--S---PFPLVICIKSNHE 93 (123)
Q Consensus 54 ~l~sv~g~~I~~v~~wvl~rC~gC~k--~---~~~~~fCp~CG~~ 93 (123)
.+..+++.++++ -.. .|+-|+. . ...+.-|-+||.-
T Consensus 6 ~yY~v~~~kv~r---k~~-~CPrCG~gvfmA~H~dR~~CGkCgyT 46 (51)
T COG1998 6 KYYEVDDEKVKR---KNR-FCPRCGPGVFMADHKDRWACGKCGYT 46 (51)
T ss_pred eEEEEcCCcEEE---ccc-cCCCCCCcchhhhcCceeEeccccce
Confidence 344555544333 334 6777773 2 3557778888864
No 275
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=37.14 E-value=14 Score=23.54 Aligned_cols=20 Identities=15% Similarity=0.109 Sum_probs=13.1
Q ss_pred ccc--CCccc-----ccCccccccCCC
Q 033276 73 KCL--KLFSS-----PFPLVICIKSNH 92 (123)
Q Consensus 73 rC~--gC~k~-----~~~~~fCp~CG~ 92 (123)
.|+ .|+.- ...+..|-+||.
T Consensus 20 ~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 20 ECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp E-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred cCCCcccCCceEeeecCCCccCCCccc
Confidence 787 77652 456888888884
No 276
>CHL00104 rpl33 ribosomal protein L33
Probab=37.10 E-value=19 Score=24.39 Aligned_cols=14 Identities=14% Similarity=0.161 Sum_probs=11.8
Q ss_pred ccccccCCCCCeeeE
Q 033276 84 LVICIKSNHEIRISP 98 (123)
Q Consensus 84 ~~fCp~CG~~~tl~r 98 (123)
+.|||.|... |+.+
T Consensus 49 kKycp~c~kH-tlhk 62 (66)
T CHL00104 49 KKFCPYCYKH-TIHK 62 (66)
T ss_pred ECcCCCCCCE-eeEe
Confidence 6899999999 7764
No 277
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=36.68 E-value=20 Score=25.84 Aligned_cols=21 Identities=10% Similarity=0.259 Sum_probs=13.2
Q ss_pred cccCCccccc--------CccccccCCCC
Q 033276 73 KCLKLFSSPF--------PLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~~~--------~~~fCp~CG~~ 93 (123)
.|+-|+.... ....||+||.-
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 5777774311 35678888765
No 278
>TIGR02642 phage_xxxx uncharacterized phage protein. This uncharacterized protein is found in prophage regions of Shewanella oneidensis MR-1, Vibrio vulnificus YJ016, Yersinia pseudotuberculosis IP 32953, and Aeromonas hydrophila ATCC7966. It appears to have regions of sequence similarity to phage lambda antitermination protein Q.
Probab=36.40 E-value=81 Score=25.09 Aligned_cols=27 Identities=15% Similarity=0.063 Sum_probs=18.2
Q ss_pred eeccccCCccc-c--cCccccccCCCCCeee
Q 033276 70 IVDKCLKLFSS-P--FPLVICIKSNHEIRIS 97 (123)
Q Consensus 70 vl~rC~gC~k~-~--~~~~fCp~CG~~~tl~ 97 (123)
.. .|+.|.-. . .+..-||.|++....+
T Consensus 99 ~~-~C~~C~G~G~~i~~~~~C~~C~G~G~v~ 128 (186)
T TIGR02642 99 SC-KCPRCRGTGLIQRRQRECDTCAGTGRFR 128 (186)
T ss_pred CC-cCCCCCCeeEEecCCCCCCCCCCccEEe
Confidence 45 79999865 2 2236799999974433
No 279
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=36.13 E-value=21 Score=25.98 Aligned_cols=25 Identities=16% Similarity=0.390 Sum_probs=15.0
Q ss_pred eeEEeeccccCCcccccC--------ccccccCCC
Q 033276 66 LHRYIVDKCLKLFSSPFP--------LVICIKSNH 92 (123)
Q Consensus 66 v~~wvl~rC~gC~k~~~~--------~~fCp~CG~ 92 (123)
++.||+ |+.|+.+++. ..-|..||.
T Consensus 77 I~~yVl--C~~C~spdT~l~k~~r~~~l~C~aCGa 109 (110)
T smart00653 77 IKEYVL--CPECGSPDTELIKENRLFFLKCEACGA 109 (110)
T ss_pred HHhcEE--CCCCCCCCcEEEEeCCeEEEEccccCC
Confidence 556776 8888876211 234777775
No 280
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=35.96 E-value=21 Score=26.94 Aligned_cols=27 Identities=19% Similarity=0.384 Sum_probs=16.7
Q ss_pred eeEEeeccccCCcccc--------cCccccccCCCCC
Q 033276 66 LHRYIVDKCLKLFSSP--------FPLVICIKSNHEI 94 (123)
Q Consensus 66 v~~wvl~rC~gC~k~~--------~~~~fCp~CG~~~ 94 (123)
++.|++ |+.|+.++ ....-|..||...
T Consensus 99 I~~yVl--C~~C~spdT~l~k~~r~~~l~C~ACGa~~ 133 (138)
T PRK03988 99 VKEYVI--CPECGSPDTKLIKEGRIWVLKCEACGAET 133 (138)
T ss_pred HHhcEE--CCCCCCCCcEEEEcCCeEEEEcccCCCCC
Confidence 455666 88888762 1134577787763
No 281
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=35.82 E-value=23 Score=26.66 Aligned_cols=27 Identities=15% Similarity=0.407 Sum_probs=16.8
Q ss_pred eeEEeeccccCCccccc-----C---ccccccCCCCC
Q 033276 66 LHRYIVDKCLKLFSSPF-----P---LVICIKSNHEI 94 (123)
Q Consensus 66 v~~wvl~rC~gC~k~~~-----~---~~fCp~CG~~~ 94 (123)
++.|++ |+.|+.+++ . ..-|..||+.-
T Consensus 94 I~~yVl--C~~C~sPdT~l~k~~r~~~l~C~ACGa~~ 128 (133)
T TIGR00311 94 VRKYVI--CRECNRPDTRIIKEGRVSLLKCEACGAKA 128 (133)
T ss_pred HhheEE--CCCCCCCCcEEEEeCCeEEEecccCCCCC
Confidence 556776 888887621 1 23588888763
No 282
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=35.75 E-value=18 Score=35.95 Aligned_cols=31 Identities=19% Similarity=0.171 Sum_probs=22.3
Q ss_pred eeEEeeccccCCccc---ccCccccccCCCCCeeeEEE
Q 033276 66 LHRYIVDKCLKLFSS---PFPLVICIKSNHEIRISPVF 100 (123)
Q Consensus 66 v~~wvl~rC~gC~k~---~~~~~fCp~CG~~~tl~rV~ 100 (123)
++.|.- +|++. .....+|++||-++|..||.
T Consensus 55 ~kd~eC----~Cgkyk~~~~~~~~C~~cgve~~~~~vr 88 (1156)
T PRK00566 55 TKDYEC----LCGKYKRVRYKGIICERCGVEVTRSKVR 88 (1156)
T ss_pred ccCcEE----eCccccccCcCCcCCCCCCceeeechhh
Confidence 456655 77765 34458999999998887764
No 283
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=35.58 E-value=35 Score=27.73 Aligned_cols=12 Identities=17% Similarity=0.304 Sum_probs=8.0
Q ss_pred CccccccCCCCC
Q 033276 83 PLVICIKSNHEI 94 (123)
Q Consensus 83 ~~~fCp~CG~~~ 94 (123)
...|||.||+++
T Consensus 98 ~~~fC~~CG~~~ 109 (256)
T PRK00241 98 SHRFCGYCGHPM 109 (256)
T ss_pred cCccccccCCCC
Confidence 356777777774
No 284
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.34 E-value=9.9 Score=26.91 Aligned_cols=25 Identities=16% Similarity=0.224 Sum_probs=15.3
Q ss_pred cccCCcccccCccccccCCCCCeeeE
Q 033276 73 KCLKLFSSPFPLVICIKSNHEIRISP 98 (123)
Q Consensus 73 rC~gC~k~~~~~~fCp~CG~~~tl~r 98 (123)
-|..|-.. .-...||.||+++..|.
T Consensus 31 FCadCae~-~l~g~CPnCGGelv~RP 55 (84)
T COG3813 31 FCADCAEN-RLHGLCPNCGGELVARP 55 (84)
T ss_pred hhHhHHHH-hhcCcCCCCCchhhcCc
Confidence 34455443 22367999999965443
No 285
>PRK07217 replication factor A; Reviewed
Probab=35.31 E-value=22 Score=30.53 Aligned_cols=24 Identities=13% Similarity=0.174 Sum_probs=18.3
Q ss_pred EEeeccccC--CcccccCccccccCCCC
Q 033276 68 RYIVDKCLK--LFSSPFPLVICIKSNHE 93 (123)
Q Consensus 68 ~wvl~rC~g--C~k~~~~~~fCp~CG~~ 93 (123)
..++ ||+. |.|. ..+..||.||..
T Consensus 186 glI~-rCP~~~C~Rv-l~~g~C~~HG~v 211 (311)
T PRK07217 186 GLIK-RCPEEDCTRV-LQNGRCSEHGKV 211 (311)
T ss_pred CCee-cCCccccCcc-ccCCCCCCCCCc
Confidence 4556 9999 9998 233689999954
No 286
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=35.23 E-value=34 Score=27.08 Aligned_cols=24 Identities=17% Similarity=0.121 Sum_probs=16.4
Q ss_pred eeccccCCccc-c------cCccccccCCCCC
Q 033276 70 IVDKCLKLFSS-P------FPLVICIKSNHEI 94 (123)
Q Consensus 70 vl~rC~gC~k~-~------~~~~fCp~CG~~~ 94 (123)
.+ +|..|.+. + ....-||.||+.+
T Consensus 122 ~~-~C~~C~~~~~~~~~~~~~~p~C~~Cgg~l 152 (242)
T PRK00481 122 RA-RCTKCGQTYDLDEYLKPEPPRCPKCGGIL 152 (242)
T ss_pred ce-eeCCCCCCcChhhhccCCCCCCCCCCCcc
Confidence 35 89999875 2 1223499999873
No 287
>PF12387 Peptidase_C74: Pestivirus NS2 peptidase; InterPro: IPR022120 The pestivirus NS2 peptidase is responsible for single cleavage between NS2 and NS3 of the Bovine viral diarrhea virus 1 polyprotein, a cleavage that is correlated with cytopathogenicity []. The peptidase is activated by its interaction with 'J-domain protein interacting with viral protein' - Jiv. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0004252 serine-type endopeptidase activity, 0016817 hydrolase activity, acting on acid anhydrides, 0017111 nucleoside-triphosphatase activity, 0070008 serine-type exopeptidase activity
Probab=35.10 E-value=17 Score=29.48 Aligned_cols=23 Identities=13% Similarity=0.075 Sum_probs=16.2
Q ss_pred cccCCcccccCccccccCCCCCe
Q 033276 73 KCLKLFSSPFPLVICIKSNHEIR 95 (123)
Q Consensus 73 rC~gC~k~~~~~~fCp~CG~~~t 95 (123)
.|+-|-..+-....||+||....
T Consensus 164 lCtvCe~r~w~g~~CPKCGr~G~ 186 (200)
T PF12387_consen 164 LCTVCEGREWKGGNCPKCGRHGK 186 (200)
T ss_pred EEeeeecCccCCCCCCcccCCCC
Confidence 58888766444566999997643
No 288
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.08 E-value=14 Score=30.52 Aligned_cols=28 Identities=18% Similarity=0.186 Sum_probs=22.6
Q ss_pred cccCCccc----ccCccccccCCCCCeeeEEE
Q 033276 73 KCLKLFSS----PFPLVICIKSNHEIRISPVF 100 (123)
Q Consensus 73 rC~gC~k~----~~~~~fCp~CG~~~tl~rV~ 100 (123)
.|.+|... ....++||+|-.+++..+|-
T Consensus 69 FCWpClyqWl~~~~~~~~cPVCK~~Vs~~~vv 100 (230)
T KOG0823|consen 69 FCWPCLYQWLQTRPNSKECPVCKAEVSIDTVV 100 (230)
T ss_pred eehHHHHHHHhhcCCCeeCCccccccccceEE
Confidence 69999976 46689999999997776664
No 289
>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=35.01 E-value=32 Score=26.76 Aligned_cols=39 Identities=21% Similarity=0.260 Sum_probs=24.5
Q ss_pred HHHhCce-eeCCCCCcceeeeEEeeccccCCccc-cc----------CccccccCCCC
Q 033276 48 ILQMGLR-LLAPGGMQIRQLHRYIVDKCLKLFSS-PF----------PLVICIKSNHE 93 (123)
Q Consensus 48 llqlGL~-l~sv~g~~I~~v~~wvl~rC~gC~k~-~~----------~~~fCp~CG~~ 93 (123)
-.+.|.+ ++.++|. -..+ +|..|.+. +. ....||.||+.
T Consensus 92 ~~~aG~~~v~elHG~------~~~~-~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~ 142 (218)
T cd01407 92 HQRAGSPKVIELHGS------LFRV-RCTKCGKEYPRDELQADIDREEVPRCPKCGGL 142 (218)
T ss_pred HHHcCCCCEEECcCC------cCcc-eeCCCcCCCcHHHHhHhhccCCCCcCCCCCCc
Confidence 4445553 6666663 2335 89999876 21 12469999987
No 290
>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=34.58 E-value=12 Score=28.47 Aligned_cols=20 Identities=15% Similarity=0.100 Sum_probs=16.0
Q ss_pred cccCCccc--ccCccccccCCC
Q 033276 73 KCLKLFSS--PFPLVICIKSNH 92 (123)
Q Consensus 73 rC~gC~k~--~~~~~fCp~CG~ 92 (123)
.|+.|++. ......||.|..
T Consensus 5 nC~~CgklF~~~~~~iCp~C~~ 26 (137)
T TIGR03826 5 NCPKCGRLFVKTGRDVCPSCYE 26 (137)
T ss_pred cccccchhhhhcCCccCHHHhH
Confidence 69999998 346688999985
No 291
>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=34.53 E-value=28 Score=27.51 Aligned_cols=23 Identities=9% Similarity=-0.050 Sum_probs=16.3
Q ss_pred eeccccCCccc-c----cCccccccCCCC
Q 033276 70 IVDKCLKLFSS-P----FPLVICIKSNHE 93 (123)
Q Consensus 70 vl~rC~gC~k~-~----~~~~fCp~CG~~ 93 (123)
.. +|..|.+. + .....||.||+.
T Consensus 118 ~~-~C~~C~~~~~~~~~~~~p~C~~Cgg~ 145 (225)
T cd01411 118 RI-YCTVCGKTVDWEEYLKSPYHAKCGGV 145 (225)
T ss_pred ee-EeCCCCCccchhhcCCCCCCCCCCCE
Confidence 35 89999876 2 112569999976
No 292
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=34.39 E-value=19 Score=31.05 Aligned_cols=12 Identities=8% Similarity=-0.064 Sum_probs=10.4
Q ss_pred cCccccccCCCC
Q 033276 82 FPLVICIKSNHE 93 (123)
Q Consensus 82 ~~~~fCp~CG~~ 93 (123)
..+.+||+||++
T Consensus 183 e~~~~CPvCGS~ 194 (308)
T COG3058 183 ESRQYCPVCGSM 194 (308)
T ss_pred cccccCCCcCCC
Confidence 567899999988
No 293
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=33.98 E-value=22 Score=30.16 Aligned_cols=21 Identities=24% Similarity=0.187 Sum_probs=16.3
Q ss_pred cccCCccc-----ccCccccccCCCC
Q 033276 73 KCLKLFSS-----PFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~-----~~~~~fCp~CG~~ 93 (123)
-|..|+.. ...+..||+||+.
T Consensus 113 FCg~CG~~~~~~~~g~~~~C~~cg~~ 138 (279)
T COG2816 113 FCGRCGTKTYPREGGWARVCPKCGHE 138 (279)
T ss_pred CCCCCCCcCccccCceeeeCCCCCCc
Confidence 48899876 2347889999987
No 294
>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=33.51 E-value=22 Score=26.34 Aligned_cols=8 Identities=25% Similarity=0.472 Sum_probs=5.4
Q ss_pred cccCCccc
Q 033276 73 KCLKLFSS 80 (123)
Q Consensus 73 rC~gC~k~ 80 (123)
||..|...
T Consensus 93 RC~~CN~~ 100 (147)
T PF01927_consen 93 RCPKCNGP 100 (147)
T ss_pred ccCCCCcE
Confidence 77777654
No 295
>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=33.10 E-value=18 Score=27.40 Aligned_cols=10 Identities=20% Similarity=0.322 Sum_probs=8.3
Q ss_pred cccccCCCCC
Q 033276 85 VICIKSNHEI 94 (123)
Q Consensus 85 ~fCp~CG~~~ 94 (123)
.-||.||+.-
T Consensus 106 ~~cp~c~s~~ 115 (146)
T TIGR02159 106 VQCPRCGSAD 115 (146)
T ss_pred CcCCCCCCCC
Confidence 6799999883
No 296
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=33.06 E-value=21 Score=24.12 Aligned_cols=21 Identities=10% Similarity=0.178 Sum_probs=18.4
Q ss_pred cccCCccc--ccCccccccCCCC
Q 033276 73 KCLKLFSS--PFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~--~~~~~fCp~CG~~ 93 (123)
+|.-|++. ...+..|..||-+
T Consensus 18 ~CRRCGr~syhv~k~~CaaCGfg 40 (61)
T COG2126 18 RCRRCGRRSYHVRKKYCAACGFG 40 (61)
T ss_pred hhhhccchheeeccceecccCCC
Confidence 79999987 6678999999977
No 297
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=33.05 E-value=26 Score=27.72 Aligned_cols=28 Identities=18% Similarity=0.146 Sum_probs=17.6
Q ss_pred ccccccCCCCCeeeEEEEEeeEEEEEeeCC
Q 033276 84 LVICIKSNHEIRISPVFMLILICLYIQVDT 113 (123)
Q Consensus 84 ~~fCp~CG~~~tl~rV~~~~~~~~~~~~~~ 113 (123)
...||+||+..+-++|. .|-.-.++.|.
T Consensus 5 ~~~CPvC~~~F~~~~vr--s~~~r~~~~d~ 32 (214)
T PF09986_consen 5 KITCPVCGKEFKTKKVR--SGKIRVIRRDS 32 (214)
T ss_pred ceECCCCCCeeeeeEEE--cCCceEeeecC
Confidence 46799999996666554 33333345554
No 298
>cd03361 TOPRIM_TopoIA_RevGyr TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to the ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=32.92 E-value=36 Score=25.94 Aligned_cols=25 Identities=16% Similarity=0.110 Sum_probs=18.7
Q ss_pred EEeeccccCCccc-ccCccccccCCCC
Q 033276 68 RYIVDKCLKLFSS-PFPLVICIKSNHE 93 (123)
Q Consensus 68 ~wvl~rC~gC~k~-~~~~~fCp~CG~~ 93 (123)
.+.. +|.+|++. +.....||+||++
T Consensus 75 ~~~~-~c~pc~~lF~~~~~~cp~c~~~ 100 (170)
T cd03361 75 DSIK-RCRDCGYQFTEDSDKCPRCGSE 100 (170)
T ss_pred eEee-ccCCcccccccccccCCcCCCc
Confidence 3345 79999887 5455689999976
No 299
>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=32.44 E-value=18 Score=23.46 Aligned_cols=13 Identities=23% Similarity=0.424 Sum_probs=9.8
Q ss_pred ccccCCCCCeeeE
Q 033276 86 ICIKSNHEIRISP 98 (123)
Q Consensus 86 fCp~CG~~~tl~r 98 (123)
.||.||..+.+..
T Consensus 4 ~CP~CG~~iev~~ 16 (54)
T TIGR01206 4 ECPDCGAEIELEN 16 (54)
T ss_pred CCCCCCCEEecCC
Confidence 5999999876643
No 300
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=32.41 E-value=32 Score=27.58 Aligned_cols=33 Identities=12% Similarity=0.134 Sum_probs=20.3
Q ss_pred eeccccCCccc-cc----------CccccccCCCCCeeeEEEEEeeE
Q 033276 70 IVDKCLKLFSS-PF----------PLVICIKSNHEIRISPVFMLILI 105 (123)
Q Consensus 70 vl~rC~gC~k~-~~----------~~~fCp~CG~~~tl~rV~~~~~~ 105 (123)
.. +|..|.+. +. ..-.||.||+. ++.=-|..|+
T Consensus 119 ~~-~C~~C~~~~~~~~~~~~~~~~~~p~Cp~Cgg~--lrP~Vv~FgE 162 (244)
T PRK14138 119 EY-YCVRCGKRYTVEDVIEKLEKSDVPRCDDCSGL--IRPNIVFFGE 162 (244)
T ss_pred ee-EECCCCCcccHHHHHHHHhcCCCCCCCCCCCe--ECCCEEECCC
Confidence 45 89999876 31 12359999986 4443334444
No 301
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=32.39 E-value=19 Score=27.01 Aligned_cols=10 Identities=40% Similarity=0.534 Sum_probs=7.2
Q ss_pred ccccccCCCC
Q 033276 84 LVICIKSNHE 93 (123)
Q Consensus 84 ~~fCp~CG~~ 93 (123)
+..||+|||+
T Consensus 74 ~~kCpkCghe 83 (116)
T KOG2907|consen 74 KHKCPKCGHE 83 (116)
T ss_pred hccCcccCCc
Confidence 4568888876
No 302
>PRK08764 ferredoxin; Provisional
Probab=31.99 E-value=55 Score=23.90 Aligned_cols=41 Identities=12% Similarity=0.201 Sum_probs=25.2
Q ss_pred cccHHHHHHHHHhCceeeCCCCCc----ceeeeEEeeccccCCcc
Q 033276 39 TGDYAMQNVILQMGLRLLAPGGMQ----IRQLHRYIVDKCLKLFS 79 (123)
Q Consensus 39 TdDyAmQNVllqlGL~l~sv~g~~----I~~v~~wvl~rC~gC~k 79 (123)
..+-.+|+++..||+...+..... ..++..+..++|.+|++
T Consensus 48 ~G~c~lq~~a~~~gv~~~~~~~~~~~~~~~~~~~~~~~~Ci~C~~ 92 (135)
T PRK08764 48 GGDAGARALAQVLGVPARPYDRSRGTHKLPQVAWIVEADCIGCTK 92 (135)
T ss_pred CCHHHHHHHHHHhCCCccccccccCCCCCCeeEEECcccCcCcch
Confidence 456679999999999866543211 11222222238988886
No 303
>PRK14289 chaperone protein DnaJ; Provisional
Probab=31.76 E-value=69 Score=27.29 Aligned_cols=26 Identities=15% Similarity=0.078 Sum_probs=17.8
Q ss_pred eeccccCCccc-ccCccccccCCCCCee
Q 033276 70 IVDKCLKLFSS-PFPLVICIKSNHEIRI 96 (123)
Q Consensus 70 vl~rC~gC~k~-~~~~~fCp~CG~~~tl 96 (123)
.. .|+.|.-. .....+|+.|++..++
T Consensus 197 ~~-~C~~C~G~G~~~~~~C~~C~G~g~v 223 (386)
T PRK14289 197 QS-TCPTCNGEGKIIKKKCKKCGGEGIV 223 (386)
T ss_pred EE-ecCCCCccccccCcCCCCCCCCcEE
Confidence 44 67777766 4456789999987443
No 304
>PF14353 CpXC: CpXC protein
Probab=31.57 E-value=21 Score=25.45 Aligned_cols=11 Identities=18% Similarity=0.459 Sum_probs=8.8
Q ss_pred ccccccCCCCC
Q 033276 84 LVICIKSNHEI 94 (123)
Q Consensus 84 ~~fCp~CG~~~ 94 (123)
.-.||.||...
T Consensus 38 ~~~CP~Cg~~~ 48 (128)
T PF14353_consen 38 SFTCPSCGHKF 48 (128)
T ss_pred EEECCCCCCce
Confidence 35699999993
No 305
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=31.48 E-value=22 Score=25.69 Aligned_cols=26 Identities=8% Similarity=0.054 Sum_probs=20.6
Q ss_pred eEEeeccccCCccc--ccCccccccCCCCC
Q 033276 67 HRYIVDKCLKLFSS--PFPLVICIKSNHEI 94 (123)
Q Consensus 67 ~~wvl~rC~gC~k~--~~~~~fCp~CG~~~ 94 (123)
+...+ |.-|++. ...+..|..||.+.
T Consensus 14 ktHtl--CrRCG~~syH~qK~~CasCGyps 41 (91)
T PTZ00073 14 KTHTL--CRRCGKRSFHVQKKRCASCGYPS 41 (91)
T ss_pred cCcch--hcccCccccccccccchhcCCch
Confidence 45554 9999987 66788999999873
No 306
>PTZ00408 NAD-dependent deacetylase; Provisional
Probab=31.05 E-value=26 Score=28.31 Aligned_cols=36 Identities=11% Similarity=0.065 Sum_probs=23.0
Q ss_pred EeeccccCCccc-ccC------ccccccCCCCCeeeEEEEEeeE
Q 033276 69 YIVDKCLKLFSS-PFP------LVICIKSNHEIRISPVFMLILI 105 (123)
Q Consensus 69 wvl~rC~gC~k~-~~~------~~fCp~CG~~~tl~rV~~~~~~ 105 (123)
+.. +|..|.+. +.. ...||.||....+|.=-|..|+
T Consensus 116 ~~~-~C~~C~~~~~~~~~~~~~~p~C~~Cg~~g~lrP~vV~FGE 158 (242)
T PTZ00408 116 LKV-RCTATGHVFDWTEDVVHGSSRCKCCGCVGTLRPHIVWFGE 158 (242)
T ss_pred ceE-EECCCCcccCchhhhhcCCCccccCCCCCCCCCCEEEcCC
Confidence 446 89999976 311 2459999943246665555666
No 307
>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=30.97 E-value=27 Score=31.02 Aligned_cols=21 Identities=10% Similarity=0.153 Sum_probs=12.6
Q ss_pred cccCCcccccCccccccCCCCCeee
Q 033276 73 KCLKLFSSPFPLVICIKSNHEIRIS 97 (123)
Q Consensus 73 rC~gC~k~~~~~~fCp~CG~~~tl~ 97 (123)
.|..|+.+ ..||.|+.++|.+
T Consensus 215 ~C~~Cg~~----~~C~~C~~~l~~h 235 (505)
T TIGR00595 215 LCRSCGYI----LCCPNCDVSLTYH 235 (505)
T ss_pred EhhhCcCc----cCCCCCCCceEEe
Confidence 67777765 3366666665443
No 308
>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=30.86 E-value=27 Score=27.02 Aligned_cols=34 Identities=9% Similarity=0.150 Sum_probs=18.3
Q ss_pred CCCcceeeeEEeeccccCCccc---c-----------cCccccccCCCC
Q 033276 59 GGMQIRQLHRYIVDKCLKLFSS---P-----------FPLVICIKSNHE 93 (123)
Q Consensus 59 ~g~~I~~v~~wvl~rC~gC~k~---~-----------~~~~fCp~CG~~ 93 (123)
+..|-+....+.+ +|++|++. + .....||+|++.
T Consensus 7 d~erf~~c~~l~~-~C~~C~~~~~f~g~~~~~~~~~~~~~~~C~~C~~~ 54 (188)
T PF08996_consen 7 DEERFKDCEPLKL-TCPSCGTEFEFPGVFEEDGDDVSPSGLQCPNCSTP 54 (188)
T ss_dssp -TTTTTT---EEE-E-TTT--EEEE-SSS--SSEEEETTEEEETTT--B
T ss_pred HHHHhcCCCceEe-ECCCCCCCccccccccCCccccccCcCcCCCCCCc
Confidence 4567778889999 99999986 1 225679999985
No 309
>PRK07418 acetolactate synthase 3 catalytic subunit; Reviewed
Probab=30.77 E-value=25 Score=31.45 Aligned_cols=21 Identities=14% Similarity=0.257 Sum_probs=17.6
Q ss_pred cccCCccc-ccCccccccCCCC
Q 033276 73 KCLKLFSS-PFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~-~~~~~fCp~CG~~ 93 (123)
.|+.|... +...+||+.||.+
T Consensus 594 ~~~~~~~~~~~~~~f~~~~g~~ 615 (616)
T PRK07418 594 YCSNCGAKNPSTHRFCPECGTK 615 (616)
T ss_pred cCCCCCCcCccccccchhhCCC
Confidence 49999984 6667999999987
No 310
>cd03472 Rieske_RO_Alpha_BPDO_like Rieske non-heme iron oxygenase (RO) family, Biphenyl dioxygenase (BPDO)-like subfamily, N-terminal Rieske domain of the oxygenase alpha subunit; composed of the oxygenase alpha subunits of BPDO and similar proteins including cumene dioxygenase (CumDO), nitrobenzene dioxygenase (NBDO), alkylbenzene dioxygenase (AkbDO) and dibenzofuran 4,4a-dioxygenase (DFDO). ROs comprise a large class of aromatic ring-hydroxylating dioxygenases that enable microorganisms to tolerate and utilize aromatic compounds for growth. The oxygenase alpha subunit contains an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. BPDO degrades biphenyls and polychlorinated biphenyls (PCB's) while CumDO degrades cumene (isopropylbenzene), an aromatic hydrocarbon that is i
Probab=30.73 E-value=74 Score=22.99 Aligned_cols=93 Identities=15% Similarity=0.193 Sum_probs=55.4
Q ss_pred CceeccCCCCceeEEe-ccc---HHHHHHHHHhCceeeCCC-C--Ccce-eeeEEeeccccCCccc-ccCcccc--ccCC
Q 033276 23 QSWMLRSLSESTVACI-TGD---YAMQNVILQMGLRLLAPG-G--MQIR-QLHRYIVDKCLKLFSS-PFPLVIC--IKSN 91 (123)
Q Consensus 23 ~~WIt~~~~~~~va~v-TdD---yAmQNVllqlGL~l~sv~-g--~~I~-~v~~wvl~rC~gC~k~-~~~~~fC--p~CG 91 (123)
+...+.......++++ +.| ||++|+--|.|..+..-. + ..|. -...|.+|.--.|-+. .....|. -.+.
T Consensus 22 g~~~~~~~~~~~i~l~r~~~g~i~A~~n~C~Hrg~~L~~g~~g~~~~i~CP~Hgw~fd~~G~~~~~P~~~~~~~~~~~~~ 101 (128)
T cd03472 22 GDYLTTYMGEDPVIVVRQKDGSIRVFLNQCRHRGMRICRSDAGNAKAFTCTYHGWAYDTAGNLVNVPFEKEAFCDGLDKA 101 (128)
T ss_pred CCEEEEEECCceEEEEECCCCCEEEEhhhCcCCCCeeeccCCCCcCEEECCcCCeEECCCcCEEeccCcccccccCCCHH
Confidence 3344443334445444 445 999999999999876422 1 1232 3457888665666655 2222343 2233
Q ss_pred CCCeeeEEEEEe-eEEEEEeeCCccc
Q 033276 92 HEIRISPVFMLI-LICLYIQVDTEMP 116 (123)
Q Consensus 92 ~~~tl~rV~~~~-~~~~~~~~~~~~~ 116 (123)
.. .|+++.|.+ +.-|||.-|.+-|
T Consensus 102 ~~-~l~~~~v~~~~g~vfv~~~~~~~ 126 (128)
T cd03472 102 DW-GPLQARVETYKGLIFANWDAEAP 126 (128)
T ss_pred HC-CCcceeEeEECCEEEEEcCCCCC
Confidence 33 678888775 6678888887654
No 311
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=30.72 E-value=32 Score=25.03 Aligned_cols=16 Identities=19% Similarity=0.175 Sum_probs=14.1
Q ss_pred ccccccCCCCCeeeEEE
Q 033276 84 LVICIKSNHEIRISPVF 100 (123)
Q Consensus 84 ~~fCp~CG~~~tl~rV~ 100 (123)
+-+||.|... |+..|+
T Consensus 8 ~tyCp~Ckkh-T~H~V~ 23 (94)
T COG1631 8 RTYCPYCKKH-TIHKVE 23 (94)
T ss_pred eecCcccccc-eeeeee
Confidence 5789999999 898886
No 312
>PRK14873 primosome assembly protein PriA; Provisional
Probab=30.72 E-value=27 Score=32.39 Aligned_cols=26 Identities=8% Similarity=0.209 Sum_probs=17.0
Q ss_pred EEeeccccCCcccccCccccccCCCCCeeeE
Q 033276 68 RYIVDKCLKLFSSPFPLVICIKSNHEIRISP 98 (123)
Q Consensus 68 ~wvl~rC~gC~k~~~~~~fCp~CG~~~tl~r 98 (123)
.-.+ .|..|+.. -.||+|+.++|+++
T Consensus 381 ap~l-~C~~Cg~~----~~C~~C~~~L~~h~ 406 (665)
T PRK14873 381 VPSL-ACARCRTP----ARCRHCTGPLGLPS 406 (665)
T ss_pred CCee-EhhhCcCe----eECCCCCCceeEec
Confidence 3456 78888865 44777777766543
No 313
>COG1040 ComFC Predicted amidophosphoribosyltransferases [General function prediction only]
Probab=30.64 E-value=12 Score=29.88 Aligned_cols=22 Identities=14% Similarity=0.223 Sum_probs=17.5
Q ss_pred cccCCccc-ccCccccccCCCCC
Q 033276 73 KCLKLFSS-PFPLVICIKSNHEI 94 (123)
Q Consensus 73 rC~gC~k~-~~~~~fCp~CG~~~ 94 (123)
.|.+|++. +....+||.||.++
T Consensus 26 ~C~~C~~~~~~~~~~C~~C~~~l 48 (225)
T COG1040 26 LCSGCQADLPLIGNLCPLCGLPL 48 (225)
T ss_pred cChhhhhchhHHHhhhHhhhChh
Confidence 79999987 44334999999994
No 314
>PRK12495 hypothetical protein; Provisional
Probab=30.31 E-value=27 Score=28.89 Aligned_cols=21 Identities=10% Similarity=0.070 Sum_probs=16.0
Q ss_pred cccCCccc---ccCccccccCCCC
Q 033276 73 KCLKLFSS---PFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~---~~~~~fCp~CG~~ 93 (123)
.|..|+.. -+...|||.|+..
T Consensus 44 hC~~CG~PIpa~pG~~~Cp~CQ~~ 67 (226)
T PRK12495 44 HCDECGDPIFRHDGQEFCPTCQQP 67 (226)
T ss_pred hcccccCcccCCCCeeECCCCCCc
Confidence 78888886 2456889999866
No 315
>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=30.12 E-value=21 Score=28.05 Aligned_cols=24 Identities=17% Similarity=0.173 Sum_probs=17.0
Q ss_pred EeeccccCCccc-cc---------CccccccCCCC
Q 033276 69 YIVDKCLKLFSS-PF---------PLVICIKSNHE 93 (123)
Q Consensus 69 wvl~rC~gC~k~-~~---------~~~fCp~CG~~ 93 (123)
+.+ +|..|.+. +. ....||.||+.
T Consensus 112 ~~~-~C~~C~~~~~~~~~~~~~~~~~p~C~~Cgg~ 145 (222)
T cd01413 112 QTA-YCVNCGSKYDLEEVKYAKKHEVPRCPKCGGI 145 (222)
T ss_pred Ccc-eECCCCCCcchhHHHHhccCCCCcCCCCCCc
Confidence 345 89999886 21 12469999987
No 316
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=29.88 E-value=31 Score=20.57 Aligned_cols=19 Identities=16% Similarity=0.392 Sum_probs=12.1
Q ss_pred cccCCcccccCccccccCCC
Q 033276 73 KCLKLFSSPFPLVICIKSNH 92 (123)
Q Consensus 73 rC~gC~k~~~~~~fCp~CG~ 92 (123)
+|..|.+.. ..-+|..||+
T Consensus 1 ~C~~C~~~~-~l~~CL~C~~ 19 (50)
T smart00290 1 RCSVCGTIE-NLWLCLTCGQ 19 (50)
T ss_pred CcccCCCcC-CeEEecCCCC
Confidence 577777652 2567777774
No 317
>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=29.82 E-value=49 Score=19.57 Aligned_cols=18 Identities=11% Similarity=-0.044 Sum_probs=13.1
Q ss_pred CCcceeeeEEeeccccCCc
Q 033276 60 GMQIRQLHRYIVDKCLKLF 78 (123)
Q Consensus 60 g~~I~~v~~wvl~rC~gC~ 78 (123)
...+.+.++.++ +|+.|.
T Consensus 30 ~~~V~e~~~~~y-~C~~C~ 47 (47)
T PF13005_consen 30 KPEVTEHVRHKY-ACPCCG 47 (47)
T ss_pred ceEEEEEEeceE-ECCCCC
Confidence 455667778888 888874
No 318
>PHA02325 hypothetical protein
Probab=29.66 E-value=25 Score=24.35 Aligned_cols=11 Identities=27% Similarity=0.380 Sum_probs=8.9
Q ss_pred CccccccCCCC
Q 033276 83 PLVICIKSNHE 93 (123)
Q Consensus 83 ~~~fCp~CG~~ 93 (123)
....||+||..
T Consensus 2 ~~k~CPkC~A~ 12 (72)
T PHA02325 2 DTKICPKCGAR 12 (72)
T ss_pred CccccCccCCE
Confidence 45789999976
No 319
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=29.28 E-value=37 Score=28.43 Aligned_cols=25 Identities=16% Similarity=0.238 Sum_probs=17.4
Q ss_pred eEEeeccccCCccc--ccCccccccCCCC
Q 033276 67 HRYIVDKCLKLFSS--PFPLVICIKSNHE 93 (123)
Q Consensus 67 ~~wvl~rC~gC~k~--~~~~~fCp~CG~~ 93 (123)
..=.| .|+-|..+ ..+ ..||.||.+
T Consensus 252 v~~Gy-vCs~Clsi~C~~p-~~C~~Cgt~ 278 (279)
T TIGR00627 252 VSIGF-VCSVCLSVLCQYT-PICKTCKTA 278 (279)
T ss_pred ccceE-ECCCccCCcCCCC-CCCCCCCCC
Confidence 33447 88888877 444 479999875
No 320
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=29.24 E-value=20 Score=36.59 Aligned_cols=30 Identities=13% Similarity=0.188 Sum_probs=21.5
Q ss_pred eeEEeeccccCCccc---ccCccccccCCCCCeeeEE
Q 033276 66 LHRYIVDKCLKLFSS---PFPLVICIKSNHEIRISPV 99 (123)
Q Consensus 66 v~~wvl~rC~gC~k~---~~~~~fCp~CG~~~tl~rV 99 (123)
++.|.- +|+|. .....+|++||-++|..||
T Consensus 57 ~kd~eC----~CGKyk~~~~~g~~C~~CGVEvt~s~v 89 (1460)
T PRK14906 57 TKDWEC----ACGKYKRIRFKGIVCERCGVEVTRAKV 89 (1460)
T ss_pred ccCcEE----eCccccccCcCCeEcCCCCcEecchHH
Confidence 456665 67765 3345799999999887766
No 321
>COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]
Probab=29.04 E-value=39 Score=31.25 Aligned_cols=71 Identities=20% Similarity=0.230 Sum_probs=40.8
Q ss_pred EEecccHHHHHHHHHhCceeeCCCCCcceeeeEEeeccccCCccc--ccCccccccCCCCCeeeEEEEEee---------
Q 033276 36 ACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSS--PFPLVICIKSNHEIRISPVFMLIL--------- 104 (123)
Q Consensus 36 a~vTdDyAmQNVllqlGL~l~sv~g~~I~~v~~wvl~rC~gC~k~--~~~~~fCp~CG~~~tl~rV~~~~~--------- 104 (123)
|..-.||----=|.|.- -. .+-..+ =+. +|..|++. -..+-.| .||+++-+.-+.=++-
T Consensus 104 a~ye~dfe~i~~leqyh-----ya-s~k~~v--a~w-~c~~cg~~iean~kp~c-~cg~~~~~~ei~gs~pasrf~i~el 173 (593)
T COG2401 104 ATYEEDFEFIAELEQYH-----YA-SQKEKV--ALW-RCEKCGTIIEANTKPEC-KCGSHVHILEIKGSTPASRFLIVEL 173 (593)
T ss_pred hhHHHHHHHHHHHHHhh-----hc-cccceE--EEE-ecchhchhhhhcCCccc-CCCCceEEEEeecCCcchheeeeeh
Confidence 56667776443344421 11 111233 334 99999997 3446789 9999865554432221
Q ss_pred ---------EEEEEeeCCccc
Q 033276 105 ---------ICLYIQVDTEMP 116 (123)
Q Consensus 105 ---------~~~~~~~~~~~~ 116 (123)
+--|+.+|.-||
T Consensus 174 ~~r~~yep~i~ayvrvdppip 194 (593)
T COG2401 174 VKREEYEPRILAYVRVDPPIP 194 (593)
T ss_pred hcCCcCCcceEEEEecCCCch
Confidence 234777777777
No 322
>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=28.56 E-value=96 Score=28.77 Aligned_cols=47 Identities=17% Similarity=0.321 Sum_probs=27.9
Q ss_pred HHHHHhCcee-----eCCCCCcceeeeEEeeccccCCcc-c-ccCccccccCCCCC
Q 033276 46 NVILQMGLRL-----LAPGGMQIRQLHRYIVDKCLKLFS-S-PFPLVICIKSNHEI 94 (123)
Q Consensus 46 NVllqlGL~l-----~sv~g~~I~~v~~wvl~rC~gC~k-~-~~~~~fCp~CG~~~ 94 (123)
+-+.++||++ +.-.|.-|-++..-+. .=..=.. . .++ ..||.||+++
T Consensus 349 ~~i~~~~i~iGD~V~V~raGdVIP~i~~vv~-~~r~~~~~~~~~P-~~CP~C~s~l 402 (652)
T TIGR00575 349 DEIEELDIRIGDTVVVRKAGDVIPKVVRVLL-EKRTGSERPIRFP-THCPSCGSPL 402 (652)
T ss_pred HHHHHcCCCCCCEEEEEecCCcCceeeeecc-ccCCCCCCCCCCC-CCCCCCCCEe
Confidence 3467788764 2235888888877554 2111111 1 334 5899999994
No 323
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=28.44 E-value=30 Score=27.18 Aligned_cols=14 Identities=7% Similarity=0.384 Sum_probs=12.3
Q ss_pred ccccccCCCCCeee
Q 033276 84 LVICIKSNHEIRIS 97 (123)
Q Consensus 84 ~~fCp~CG~~~tl~ 97 (123)
..||..||++.+||
T Consensus 89 ~r~CARCGGrv~lr 102 (169)
T KOG3799|consen 89 TRFCARCGGRVSLR 102 (169)
T ss_pred hhHHHhcCCeeeec
Confidence 58999999998877
No 324
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=28.29 E-value=31 Score=28.21 Aligned_cols=11 Identities=18% Similarity=0.313 Sum_probs=8.9
Q ss_pred ccccccCCCCC
Q 033276 84 LVICIKSNHEI 94 (123)
Q Consensus 84 ~~fCp~CG~~~ 94 (123)
.+-||.||+++
T Consensus 244 g~pCprCG~~I 254 (272)
T PRK14810 244 GEPCLNCKTPI 254 (272)
T ss_pred CCcCCCCCCee
Confidence 46799999884
No 325
>PTZ00410 NAD-dependent SIR2; Provisional
Probab=27.87 E-value=63 Score=28.00 Aligned_cols=35 Identities=9% Similarity=0.199 Sum_probs=21.4
Q ss_pred EeeccccCCccc-cc----------CccccccCCCCCeeeEEEEEeeEE
Q 033276 69 YIVDKCLKLFSS-PF----------PLVICIKSNHEIRISPVFMLILIC 106 (123)
Q Consensus 69 wvl~rC~gC~k~-~~----------~~~fCp~CG~~~tl~rV~~~~~~~ 106 (123)
+.. +|..|.+. +. ....||.||+. +|.=-|..|+.
T Consensus 146 ~~~-~C~~C~~~~~~~~~~~~~~~~~vP~C~~CgG~--lRPdVVlFGE~ 191 (349)
T PTZ00410 146 SAA-SCIECHTPYDIEQAYLEARSGKVPHCSTCGGI--VKPDVVFFGEN 191 (349)
T ss_pred Cee-EeCCCCCCcchhHHHHHhhcCCCCCCCCCCCc--cCCcEEecCCc
Confidence 345 89999975 31 12359999986 44444445554
No 326
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=27.73 E-value=42 Score=22.05 Aligned_cols=20 Identities=10% Similarity=0.057 Sum_probs=13.2
Q ss_pred ccCCccc--ccCccccccCCCC
Q 033276 74 CLKLFSS--PFPLVICIKSNHE 93 (123)
Q Consensus 74 C~gC~k~--~~~~~fCp~CG~~ 93 (123)
|+-|.+. ....-.||.||-+
T Consensus 2 Cpv~~~~~~~~v~~~Cp~cGip 23 (55)
T PF13824_consen 2 CPVCKKDLPAHVNFECPDCGIP 23 (55)
T ss_pred CCCCccccccccCCcCCCCCCc
Confidence 6667663 1234569999987
No 327
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=27.60 E-value=17 Score=24.76 Aligned_cols=21 Identities=24% Similarity=0.496 Sum_probs=17.1
Q ss_pred cccCCccc---------ccCccccccCCCC
Q 033276 73 KCLKLFSS---------PFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~---------~~~~~fCp~CG~~ 93 (123)
.|++|... ..+...|-+||+.
T Consensus 12 ~CP~C~~~Dtl~mW~En~ve~vECV~CG~~ 41 (66)
T COG3529 12 VCPACQAQDTLAMWRENNVEIVECVKCGHH 41 (66)
T ss_pred CCcccchhhHHHHHHhcCCceEehhhcchH
Confidence 79999975 2457899999987
No 328
>PF07131 DUF1382: Protein of unknown function (DUF1382); InterPro: IPR009814 This entry is represented by Bacteriophage lambda, Xis. This entry overlaps with IPR009750, both representing lambda Xis. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several hypothetical Escherichia coli and Bacteriophage lambda-like proteins of around 60 residues in length. The function of this family is unknown.
Probab=27.54 E-value=49 Score=22.34 Aligned_cols=17 Identities=18% Similarity=0.464 Sum_probs=14.5
Q ss_pred HHHHHHHHhCceeeCCC
Q 033276 43 AMQNVILQMGLRLLAPG 59 (123)
Q Consensus 43 AmQNVllqlGL~l~sv~ 59 (123)
-|-|.|.|.||+|+++.
T Consensus 14 E~A~~La~~GIRFVpiP 30 (61)
T PF07131_consen 14 EMAHSLAHIGIRFVPIP 30 (61)
T ss_pred HHHHHHHHcCceeeccc
Confidence 46789999999999863
No 329
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=27.40 E-value=11 Score=26.61 Aligned_cols=21 Identities=10% Similarity=0.205 Sum_probs=11.6
Q ss_pred cccCCccc--ccCccccccCCCC
Q 033276 73 KCLKLFSS--PFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~--~~~~~fCp~CG~~ 93 (123)
.|..|+.. .+..+-||.|+++
T Consensus 38 vCr~CyEYErkeg~q~CpqCkt~ 60 (80)
T PF14569_consen 38 VCRPCYEYERKEGNQVCPQCKTR 60 (80)
T ss_dssp --HHHHHHHHHTS-SB-TTT--B
T ss_pred cchhHHHHHhhcCcccccccCCC
Confidence 56677765 5677999999977
No 330
>PRK12267 methionyl-tRNA synthetase; Reviewed
Probab=27.26 E-value=94 Score=28.19 Aligned_cols=57 Identities=12% Similarity=0.142 Sum_probs=32.1
Q ss_pred HHHHHHHHhCceeeCCCCCcceeeeEEeeccccCCccc-ccC----ccccccCCCCCeeeEEEEEeeEEEEEee
Q 033276 43 AMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSS-PFP----LVICIKSNHEIRISPVFMLILICLYIQV 111 (123)
Q Consensus 43 AmQNVllqlGL~l~sv~g~~I~~v~~wvl~rC~gC~k~-~~~----~~fCp~CG~~~tl~rV~~~~~~~~~~~~ 111 (123)
.+|.+..+|= . .| .|. .+.+...+|..|.+. +.. ...||.||+++..+.. ...|++.
T Consensus 104 ~v~~~~~~L~----~-kG-~IY-~~~~~~~yc~~~~~~l~~~~l~~~~~c~~cg~~~e~~~~-----~~~f~~l 165 (648)
T PRK12267 104 VVQKIFEKLY----E-QG-DIY-KGEYEGWYCVSCETFFTESQLVDGGKCPDCGREVELVKE-----ESYFFRM 165 (648)
T ss_pred HHHHHHHHHH----H-CC-CEE-EeeEEEeecCCCCccCChHHhccCCcCCCCCCcCeEEec-----ceEEEEc
Confidence 4566666551 0 22 233 334444389999987 321 1579999999543332 3556553
No 331
>PRK03922 hypothetical protein; Provisional
Probab=27.21 E-value=47 Score=24.90 Aligned_cols=14 Identities=29% Similarity=0.418 Sum_probs=11.2
Q ss_pred cccCccccccCCCC
Q 033276 80 SPFPLVICIKSNHE 93 (123)
Q Consensus 80 ~~~~~~fCp~CG~~ 93 (123)
++.....||.||.+
T Consensus 45 ievG~~~cP~cge~ 58 (113)
T PRK03922 45 VEVGLTICPKCGEP 58 (113)
T ss_pred EecCcccCCCCCCc
Confidence 45666889999998
No 332
>KOG3022 consensus Predicted ATPase, nucleotide-binding [Cell cycle control, cell division, chromosome partitioning]
Probab=27.17 E-value=80 Score=27.21 Aligned_cols=45 Identities=18% Similarity=0.239 Sum_probs=27.6
Q ss_pred eEEecc--cHHHHHHHHHhCceeeCCCCCcceeeeEEeeccccCCccc-ccCccccccCCCCC
Q 033276 35 VACITG--DYAMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSS-PFPLVICIKSNHEI 94 (123)
Q Consensus 35 va~vTd--DyAmQNVllqlGL~l~sv~g~~I~~v~~wvl~rC~gC~k~-~~~~~fCp~CG~~~ 94 (123)
++++|+ +.|+|-|.+.+++ . +-.+++-... + +|.+-.||+||+.+
T Consensus 185 AviVTTPQ~vAl~Dv~K~i~f--c-----~K~~I~ilGv--------VENMs~f~Cp~C~~~~ 232 (300)
T KOG3022|consen 185 AVIVTTPQEVALQDVRKEIDF--C-----RKAGIPILGV--------VENMSGFVCPKCGHST 232 (300)
T ss_pred eEEEeCchhhhhHHHHhhhhh--h-----hhcCCceEEE--------EeccccccCCCCCCcc
Confidence 567775 7888888877542 1 1111222222 3 67788899999884
No 333
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=27.11 E-value=56 Score=25.69 Aligned_cols=39 Identities=13% Similarity=0.117 Sum_probs=26.7
Q ss_pred cccCCccc-----c----------cCccccccCCCC-CeeeEEEEEeeEEEEEeeCC
Q 033276 73 KCLKLFSS-----P----------FPLVICIKSNHE-IRISPVFMLILICLYIQVDT 113 (123)
Q Consensus 73 rC~gC~k~-----~----------~~~~fCp~CG~~-~tl~rV~~~~~~~~~~~~~~ 113 (123)
+|+-|+.. | --+..|+.||.. +|..|+...+. +-||-||
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFTTfE~~El~~~--~VvKkdg 56 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFTTFERAELRPL--IVVKKDG 56 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccchhheeeeccc--eEECcCC
Confidence 79999865 1 015789999976 46677765543 3578777
No 334
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=27.11 E-value=38 Score=25.10 Aligned_cols=20 Identities=20% Similarity=0.318 Sum_probs=15.4
Q ss_pred cccCCccc--ccCccccccCCCC
Q 033276 73 KCLKLFSS--PFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~--~~~~~fCp~CG~~ 93 (123)
.|+-|+.. ..+ ..||+||-.
T Consensus 3 ~CPrC~skvC~LP-~~CpiCgLt 24 (112)
T TIGR00622 3 FCPQCRAKVCELP-VECPICGLT 24 (112)
T ss_pred cCCCCCCCccCCC-CcCCcCCCE
Confidence 78899865 555 679999855
No 335
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=26.91 E-value=37 Score=26.83 Aligned_cols=21 Identities=10% Similarity=0.222 Sum_probs=9.8
Q ss_pred CCCCcceeeeEEeeccccCCcc
Q 033276 58 PGGMQIRQLHRYIVDKCLKLFS 79 (123)
Q Consensus 58 v~g~~I~~v~~wvl~rC~gC~k 79 (123)
+++..+++-+.|.+ +|.+|+.
T Consensus 107 pdT~l~k~~~~~~l-~C~aCGa 127 (201)
T PRK12336 107 PDTRLVKEDRVLML-RCDACGA 127 (201)
T ss_pred CCcEEEEcCCeEEE-EcccCCC
Confidence 34444444444555 5555554
No 336
>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=26.89 E-value=29 Score=20.90 Aligned_cols=10 Identities=10% Similarity=-0.021 Sum_probs=8.1
Q ss_pred cccccCCCCC
Q 033276 85 VICIKSNHEI 94 (123)
Q Consensus 85 ~fCp~CG~~~ 94 (123)
.-||.||++-
T Consensus 4 ~pCP~CGG~D 13 (37)
T smart00778 4 GPCPNCGGSD 13 (37)
T ss_pred cCCCCCCCcc
Confidence 4599999984
No 337
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=26.60 E-value=14 Score=32.74 Aligned_cols=34 Identities=18% Similarity=0.274 Sum_probs=22.0
Q ss_pred eeeEEeeccccCCccc----c--cCccccccCCCCCeeeEE
Q 033276 65 QLHRYIVDKCLKLFSS----P--FPLVICIKSNHEIRISPV 99 (123)
Q Consensus 65 ~v~~wvl~rC~gC~k~----~--~~~~fCp~CG~~~tl~rV 99 (123)
++-+|-+..|..|++. + ..+--||+||+. ..+-|
T Consensus 240 ~LGKY~~TAC~rC~t~y~le~A~~~~wrCpkCGg~-ikKGV 279 (403)
T COG1379 240 RLGKYHLTACSRCYTRYSLEEAKSLRWRCPKCGGK-IKKGV 279 (403)
T ss_pred cccchhHHHHHHhhhccCcchhhhhcccCcccccc-hhhhH
Confidence 3444544489999965 1 224679999997 44433
No 338
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=26.58 E-value=44 Score=25.29 Aligned_cols=31 Identities=13% Similarity=0.151 Sum_probs=22.2
Q ss_pred CcceeeeEEeeccccCCcccccCccccccCCCCC
Q 033276 61 MQIRQLHRYIVDKCLKLFSSPFPLVICIKSNHEI 94 (123)
Q Consensus 61 ~~I~~v~~wvl~rC~gC~k~~~~~~fCp~CG~~~ 94 (123)
..+..+..| .|.-|..--...++||.||.-+
T Consensus 90 ~pv~~~~~W---~Cv~C~~~Y~GeK~C~~C~tGi 120 (128)
T PF11682_consen 90 DPVPRKTDW---HCVMCGNHYHGEKYCPKCGTGI 120 (128)
T ss_pred CCCCcCceE---EEecCCCccCcCEecCCCCCcc
Confidence 334455566 7899998734468999999874
No 339
>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=26.24 E-value=47 Score=18.22 Aligned_cols=10 Identities=20% Similarity=0.222 Sum_probs=5.1
Q ss_pred cccccCCCCC
Q 033276 85 VICIKSNHEI 94 (123)
Q Consensus 85 ~fCp~CG~~~ 94 (123)
+-||.||+.+
T Consensus 2 ~~C~rC~~~~ 11 (30)
T PF06827_consen 2 EKCPRCWNYI 11 (30)
T ss_dssp SB-TTT--BB
T ss_pred CcCccCCCcc
Confidence 4599999984
No 340
>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=26.20 E-value=35 Score=27.71 Aligned_cols=20 Identities=10% Similarity=0.188 Sum_probs=13.9
Q ss_pred ccccCCCCCeeeEEEEEeeEEE
Q 033276 86 ICIKSNHEIRISPVFMLILICL 107 (123)
Q Consensus 86 fCp~CG~~~tl~rV~~~~~~~~ 107 (123)
.||.||+. ||.=-|..|+.+
T Consensus 171 ~C~~Cgg~--lrP~VV~FGE~l 190 (260)
T cd01409 171 ECERCGGV--LKPDVVFFGENV 190 (260)
T ss_pred CCCCCCCE--ECCCEEECCCCC
Confidence 59999965 666666666643
No 341
>PF00609 DAGK_acc: Diacylglycerol kinase accessory domain; InterPro: IPR000756 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 []. Diacylglycerol (DAG) is a second messenger that acts as a protein kinase C activator. The DAG kinase domain is assumed to be an accessory domain. Upon cell stimulation, DAG kinase converts DAG into phosphatidate, initiating the resynthesis of phosphatidylinositols and attenuating protein kinase C activity. It catalyses the reaction: ATP + 1,2-diacylglycerol = ADP + 1,2-diacylglycerol 3-phosphate. The enzyme is stimulated by calcium and phosphatidylserine and phosphorylated by protein kinase C. This domain is always associated with IPR001206 from INTERPRO.; GO: 0004143 diacylglycerol kinase activity, 0007205 activation of protein kinase C activity by G-protein coupled receptor protein signaling pathway
Probab=26.15 E-value=56 Score=24.30 Aligned_cols=9 Identities=44% Similarity=0.379 Sum_probs=7.9
Q ss_pred EEEEeeCCc
Q 033276 106 CLYIQVDTE 114 (123)
Q Consensus 106 ~~~~~~~~~ 114 (123)
.+|+|+|||
T Consensus 152 ~~~~QvDGE 160 (161)
T PF00609_consen 152 KVPFQVDGE 160 (161)
T ss_pred ceeEEeCCC
Confidence 569999998
No 342
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=26.10 E-value=50 Score=24.32 Aligned_cols=14 Identities=29% Similarity=0.306 Sum_probs=10.3
Q ss_pred cccCccccccCCCC
Q 033276 80 SPFPLVICIKSNHE 93 (123)
Q Consensus 80 ~~~~~~fCp~CG~~ 93 (123)
++.....||.||.+
T Consensus 43 IevG~~~cP~Cge~ 56 (102)
T PF04475_consen 43 IEVGDTICPKCGEE 56 (102)
T ss_pred EecCcccCCCCCCc
Confidence 34556779999988
No 343
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=25.86 E-value=45 Score=20.75 Aligned_cols=11 Identities=9% Similarity=-0.161 Sum_probs=8.7
Q ss_pred cccccCCCCCe
Q 033276 85 VICIKSNHEIR 95 (123)
Q Consensus 85 ~fCp~CG~~~t 95 (123)
+-||.||++..
T Consensus 2 kPCPfCGg~~~ 12 (53)
T TIGR03655 2 KPCPFCGGADV 12 (53)
T ss_pred CCCCCCCCcce
Confidence 45999999854
No 344
>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=25.57 E-value=32 Score=28.97 Aligned_cols=15 Identities=13% Similarity=0.284 Sum_probs=5.4
Q ss_pred ccccccCCCCCeeeEE
Q 033276 84 LVICIKSNHEIRISPV 99 (123)
Q Consensus 84 ~~fCp~CG~~~tl~rV 99 (123)
-.+||.||+. .|.+.
T Consensus 31 n~yCP~Cg~~-~L~~f 45 (254)
T PF06044_consen 31 NMYCPNCGSK-PLSKF 45 (254)
T ss_dssp H---TTT--S-S-EE-
T ss_pred CCcCCCCCCh-hHhhc
Confidence 3678888888 55543
No 345
>PRK10445 endonuclease VIII; Provisional
Probab=25.57 E-value=41 Score=27.33 Aligned_cols=11 Identities=18% Similarity=0.147 Sum_probs=8.4
Q ss_pred ccccccCCCCC
Q 033276 84 LVICIKSNHEI 94 (123)
Q Consensus 84 ~~fCp~CG~~~ 94 (123)
.+-||.||.++
T Consensus 235 g~~Cp~Cg~~I 245 (263)
T PRK10445 235 GEACERCGGII 245 (263)
T ss_pred CCCCCCCCCEe
Confidence 46699999884
No 346
>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=25.57 E-value=30 Score=22.56 Aligned_cols=25 Identities=8% Similarity=0.095 Sum_probs=16.9
Q ss_pred cccCCccc--cc-----CccccccCCCCCeee
Q 033276 73 KCLKLFSS--PF-----PLVICIKSNHEIRIS 97 (123)
Q Consensus 73 rC~gC~k~--~~-----~~~fCp~CG~~~tl~ 97 (123)
||..|.+. .. -..-||.||.-..++
T Consensus 6 RC~~CnklLa~~g~~~~leIKCpRC~tiN~~~ 37 (51)
T PF10122_consen 6 RCGHCNKLLAKAGEVIELEIKCPRCKTINHVR 37 (51)
T ss_pred eccchhHHHhhhcCccEEEEECCCCCccceEe
Confidence 89999987 21 134699999654333
No 347
>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=25.54 E-value=36 Score=24.48 Aligned_cols=19 Identities=21% Similarity=0.221 Sum_probs=14.1
Q ss_pred cccCCccc-c---cCccccccCC
Q 033276 73 KCLKLFSS-P---FPLVICIKSN 91 (123)
Q Consensus 73 rC~gC~k~-~---~~~~fCp~CG 91 (123)
.|..|..+ . ....-||+||
T Consensus 5 AC~~C~~I~~~~qf~~~gCpnC~ 27 (98)
T cd07973 5 ACLLCSLIKTEDQFERDGCPNCE 27 (98)
T ss_pred hhccCCcccccccccCCCCCCCc
Confidence 69999987 2 2345799995
No 348
>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=25.51 E-value=7 Score=30.71 Aligned_cols=34 Identities=18% Similarity=0.167 Sum_probs=19.3
Q ss_pred CCCcceeeeEEe----eccccCCcccccCccccccCCCCC
Q 033276 59 GGMQIRQLHRYI----VDKCLKLFSSPFPLVICIKSNHEI 94 (123)
Q Consensus 59 ~g~~I~~v~~wv----l~rC~gC~k~~~~~~fCp~CG~~~ 94 (123)
+|..|..-..|- .+.|..|++. ...-||.|++++
T Consensus 12 NGH~~t~~~~~~p~~~~~fC~kCG~~--tI~~Cp~C~~~I 49 (158)
T PF10083_consen 12 NGHVITDSYDKNPELREKFCSKCGAK--TITSCPNCSTPI 49 (158)
T ss_pred CccccccccccCchHHHHHHHHhhHH--HHHHCcCCCCCC
Confidence 455554433332 2357788865 224588888884
No 349
>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=25.50 E-value=48 Score=28.87 Aligned_cols=27 Identities=22% Similarity=0.176 Sum_probs=19.6
Q ss_pred eEEeeccccCCccc-c--------cCccccccCCCCC
Q 033276 67 HRYIVDKCLKLFSS-P--------FPLVICIKSNHEI 94 (123)
Q Consensus 67 ~~wvl~rC~gC~k~-~--------~~~~fCp~CG~~~ 94 (123)
.++.+ ||..|+.. . ....+||.||.++
T Consensus 317 ~r~~~-rc~~c~~~~~~~~~~~~~~~~~~~~~~~~~~ 352 (403)
T TIGR03676 317 IRVTF-KCPNCGYEEEKTVKPEEGDKSEACPKCGSEL 352 (403)
T ss_pred eeEEE-EcCCCCcceeeecccccccccccCcccCccc
Confidence 35788 99999875 1 1125799999884
No 350
>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=25.43 E-value=23 Score=22.24 Aligned_cols=15 Identities=20% Similarity=0.390 Sum_probs=11.2
Q ss_pred ccCccccccCCCCCe
Q 033276 81 PFPLVICIKSNHEIR 95 (123)
Q Consensus 81 ~~~~~fCp~CG~~~t 95 (123)
+.+...||.||-+.+
T Consensus 5 ~lp~K~C~~C~rpf~ 19 (42)
T PF10013_consen 5 NLPSKICPVCGRPFT 19 (42)
T ss_pred cCCCCcCcccCCcch
Confidence 455688999998854
No 351
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=25.13 E-value=69 Score=23.70 Aligned_cols=13 Identities=31% Similarity=0.715 Sum_probs=9.7
Q ss_pred ccccccCCCCCeee
Q 033276 84 LVICIKSNHEIRIS 97 (123)
Q Consensus 84 ~~fCp~CG~~~tl~ 97 (123)
+-.||.||+. ++.
T Consensus 22 ~FtCp~Cghe-~vs 34 (104)
T COG4888 22 TFTCPRCGHE-KVS 34 (104)
T ss_pred eEecCccCCe-eee
Confidence 4569999998 443
No 352
>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=25.11 E-value=73 Score=24.71 Aligned_cols=39 Identities=13% Similarity=0.083 Sum_probs=25.2
Q ss_pred cccCCccc-----c-----c-----CccccccCCCC-CeeeEEEEEeeEEEEEeeCC
Q 033276 73 KCLKLFSS-----P-----F-----PLVICIKSNHE-IRISPVFMLILICLYIQVDT 113 (123)
Q Consensus 73 rC~gC~k~-----~-----~-----~~~fCp~CG~~-~tl~rV~~~~~~~~~~~~~~ 113 (123)
+||-|+.. + . -+..|+.||.. +|..|+..... .-||.||
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFTTyErve~~~l--~ViKkdG 56 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFTTFERAELLPP--TVIKQDG 56 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccceeeecccccc--EEEcCCC
Confidence 78999874 1 1 15789999976 45666654332 2578887
No 353
>PRK14289 chaperone protein DnaJ; Provisional
Probab=25.10 E-value=1.2e+02 Score=25.89 Aligned_cols=31 Identities=6% Similarity=0.006 Sum_probs=19.7
Q ss_pred eeeeEEeeccccCCccc----ccCccccccCCCCC
Q 033276 64 RQLHRYIVDKCLKLFSS----PFPLVICIKSNHEI 94 (123)
Q Consensus 64 ~~v~~wvl~rC~gC~k~----~~~~~fCp~CG~~~ 94 (123)
++++-.....|..|.-. ......||.|+...
T Consensus 147 ~~i~~~r~~~C~~C~G~G~~~~~~~~~C~~C~G~G 181 (386)
T PRK14289 147 KKFKVKKYVPCSHCHGTGAEGNNGSETCPTCKGSG 181 (386)
T ss_pred EEEEEEeecccCCCCCCCCCCCCCCCcCCCCcCeE
Confidence 33333333368888654 34468899999884
No 354
>KOG0856 consensus Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones]
Probab=24.91 E-value=53 Score=25.61 Aligned_cols=45 Identities=9% Similarity=0.029 Sum_probs=32.5
Q ss_pred HHHHhCceeeCCCCCcceeeeEEeeccccCCccc--ccCccccccCCCC
Q 033276 47 VILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSS--PFPLVICIKSNHE 93 (123)
Q Consensus 47 VllqlGL~l~sv~g~~I~~v~~wvl~rC~gC~k~--~~~~~fCp~CG~~ 93 (123)
|+++.|..--.. |.-.+.-..=+| .|-+|.+. ....+|...||=|
T Consensus 32 v~RekgTE~p~t-Gey~~~~e~GvY-~C~~C~~pLykS~tKfdsgcGWP 78 (146)
T KOG0856|consen 32 VLREKGTERPGT-GEYTKHFEEGVY-VCAGCGTPLYKSTTKFDSGCGWP 78 (146)
T ss_pred hhHhhcccCCCC-cccccccCCceE-EEeecCCccccccccccCCCCCc
Confidence 677887643322 444444566789 99999998 6777999999965
No 355
>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=24.75 E-value=62 Score=25.11 Aligned_cols=24 Identities=21% Similarity=0.180 Sum_probs=17.0
Q ss_pred EeeccccCCccc-cc-------CccccccCCCC
Q 033276 69 YIVDKCLKLFSS-PF-------PLVICIKSNHE 93 (123)
Q Consensus 69 wvl~rC~gC~k~-~~-------~~~fCp~CG~~ 93 (123)
..+ +|..|.+. .. ....||.||+.
T Consensus 108 ~~~-~C~~C~~~~~~~~~~~~~~~p~C~~Cgg~ 139 (224)
T cd01412 108 FRV-RCSSCGYVGENNEEIPEEELPRCPKCGGL 139 (224)
T ss_pred Ccc-ccCCCCCCCCcchhhhccCCCCCCCCCCc
Confidence 346 89999986 21 12469999987
No 356
>PRK13795 hypothetical protein; Provisional
Probab=24.75 E-value=79 Score=29.03 Aligned_cols=32 Identities=19% Similarity=-0.003 Sum_probs=23.3
Q ss_pred eeEEeeccccCCcccccCccccccCCCCCeeeEEEE
Q 033276 66 LHRYIVDKCLKLFSSPFPLVICIKSNHEIRISPVFM 101 (123)
Q Consensus 66 v~~wvl~rC~gC~k~~~~~~fCp~CG~~~tl~rV~~ 101 (123)
-+.|++ .|..|.-+ .-...|..||++ + ++|.+
T Consensus 8 ~~~~~~-wc~~cn~p-~~~~~c~~c~~~-~-~~~~~ 39 (636)
T PRK13795 8 GKDHIY-WCEKCNVP-LLGKKCGICGKE-G-FKVRL 39 (636)
T ss_pred cceeEE-EcccCCCe-eccccccccCCC-c-eEeec
Confidence 457899 99999865 222459999999 4 66654
No 357
>KOG3475 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=24.29 E-value=25 Score=25.40 Aligned_cols=32 Identities=9% Similarity=0.079 Sum_probs=22.9
Q ss_pred eeeeEEeeccccCCccc--ccCccccccCCCCCeee
Q 033276 64 RQLHRYIVDKCLKLFSS--PFPLVICIKSNHEIRIS 97 (123)
Q Consensus 64 ~~v~~wvl~rC~gC~k~--~~~~~fCp~CG~~~tl~ 97 (123)
++-+...+ |.-|++. ..-+.-|..||.|.-.+
T Consensus 11 r~nkshtl--C~RCG~~syH~QKstC~~CGYpaak~ 44 (92)
T KOG3475|consen 11 RHNKSHTL--CRRCGRRSYHIQKSTCSSCGYPAAKK 44 (92)
T ss_pred ccccchHH--HHHhCchhhhhhcccccccCCcchhc
Confidence 34445555 9999987 56678899999994433
No 358
>PRK04011 peptide chain release factor 1; Provisional
Probab=24.28 E-value=53 Score=28.61 Aligned_cols=26 Identities=27% Similarity=0.379 Sum_probs=19.8
Q ss_pred EEeeccccCCccc---------ccCccccccCCCCC
Q 033276 68 RYIVDKCLKLFSS---------PFPLVICIKSNHEI 94 (123)
Q Consensus 68 ~wvl~rC~gC~k~---------~~~~~fCp~CG~~~ 94 (123)
++.+ +|+.|+.. ......||.||.++
T Consensus 326 r~~~-~c~~c~~~~~~~~~~~~~~~~~~c~~~~~~~ 360 (411)
T PRK04011 326 RVTY-KCPNCGYEEEKTVKRREELPEKTCPKCGSEL 360 (411)
T ss_pred eEEE-EcCCCCcceeeecccccccccccCcccCccc
Confidence 5788 99999875 12356899999883
No 359
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=24.25 E-value=40 Score=20.62 Aligned_cols=10 Identities=10% Similarity=-0.084 Sum_probs=5.6
Q ss_pred cccccCCCCC
Q 033276 85 VICIKSNHEI 94 (123)
Q Consensus 85 ~fCp~CG~~~ 94 (123)
.-||.||.+.
T Consensus 4 ~pCP~CGG~D 13 (40)
T PF08273_consen 4 GPCPICGGKD 13 (40)
T ss_dssp E--TTTT-TT
T ss_pred CCCCCCcCcc
Confidence 4599999984
No 360
>cd00817 ValRS_core catalytic core domain of valyl-tRNA synthetases. Valine amino-acyl tRNA synthetase (ValRS) catalytic core domain. This enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. ValRS has an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids.
Probab=24.16 E-value=1.9e+02 Score=24.45 Aligned_cols=45 Identities=22% Similarity=0.321 Sum_probs=29.4
Q ss_pred cceeeeEEeeccccCCcccccCccccccCCCCCeeeEEEEEeeEEEEEeeC
Q 033276 62 QIRQLHRYIVDKCLKLFSSPFPLVICIKSNHEIRISPVFMLILICLYIQVD 112 (123)
Q Consensus 62 ~I~~v~~wvl~rC~gC~k~~~~~~fCp~CG~~~tl~rV~~~~~~~~~~~~~ 112 (123)
.|-+-..-++ .|+.|.+.-...+.|..||+++. ...-...|++..
T Consensus 132 ~iy~~~~~~~-yc~~~~t~l~~~evc~~cg~~~~-----~~~~~qwf~~l~ 176 (382)
T cd00817 132 LIYRDNRLVN-WCPKLRTAISDIEVCSRSGDVIE-----PLLKPQWFVKVK 176 (382)
T ss_pred CEEeeeeEEe-ecCCcCCCCCcchhcccCCCeEE-----EEecCeeEEehH
Confidence 3555566778 99999988223466999998832 233455666643
No 361
>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=24.15 E-value=46 Score=27.12 Aligned_cols=12 Identities=17% Similarity=0.196 Sum_probs=9.1
Q ss_pred ccccccCCCCCe
Q 033276 84 LVICIKSNHEIR 95 (123)
Q Consensus 84 ~~fCp~CG~~~t 95 (123)
.+-||.||.++.
T Consensus 245 g~pC~~Cg~~I~ 256 (272)
T TIGR00577 245 GEPCRRCGTPIE 256 (272)
T ss_pred CCCCCCCCCeeE
Confidence 467999998843
No 362
>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=24.14 E-value=54 Score=29.56 Aligned_cols=29 Identities=24% Similarity=0.393 Sum_probs=21.5
Q ss_pred eeEEeeccccCCccc-cc---------------CccccccCCCCCe
Q 033276 66 LHRYIVDKCLKLFSS-PF---------------PLVICIKSNHEIR 95 (123)
Q Consensus 66 v~~wvl~rC~gC~k~-~~---------------~~~fCp~CG~~~t 95 (123)
.++|-. .|+.|+.. .+ .+..||.||..+.
T Consensus 196 qr~~~v-pCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~ 240 (557)
T PF05876_consen 196 QRRYYV-PCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIE 240 (557)
T ss_pred ceEEEc-cCCCCCCCccccccceeecCCCCccceEEECCCCcCCCC
Confidence 458988 99999975 11 2457999998754
No 363
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=24.05 E-value=41 Score=30.11 Aligned_cols=32 Identities=22% Similarity=0.236 Sum_probs=20.8
Q ss_pred cceeeeEEee--ccccCCccc-ccC---ccccccCCCC
Q 033276 62 QIRQLHRYIV--DKCLKLFSS-PFP---LVICIKSNHE 93 (123)
Q Consensus 62 ~I~~v~~wvl--~rC~gC~k~-~~~---~~fCp~CG~~ 93 (123)
+|.++-+|.. .+|+-|++. ... .--||+||..
T Consensus 339 ~v~~l~~~~~~~p~Cp~Cg~~m~S~G~~g~rC~kCg~~ 376 (421)
T COG1571 339 QVLKLARYERVNPVCPRCGGRMKSAGRNGFRCKKCGTR 376 (421)
T ss_pred EEEEeeeeEEcCCCCCccCCchhhcCCCCccccccccc
Confidence 4444444543 379999987 221 3569999976
No 364
>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=23.98 E-value=43 Score=20.24 Aligned_cols=21 Identities=19% Similarity=0.137 Sum_probs=8.8
Q ss_pred cccC--Cccc---c--cCc--cccccCCCC
Q 033276 73 KCLK--LFSS---P--FPL--VICIKSNHE 93 (123)
Q Consensus 73 rC~g--C~k~---~--~~~--~fCp~CG~~ 93 (123)
.|+. |... + ... ..|+.||..
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 5766 7765 1 112 567777765
No 365
>PTZ00409 Sir2 (Silent Information Regulator) protein; Provisional
Probab=23.97 E-value=36 Score=28.02 Aligned_cols=33 Identities=12% Similarity=0.190 Sum_probs=19.4
Q ss_pred EeeccccCCccc-ccC--------------ccccccCCCCCeeeEEEEEeeE
Q 033276 69 YIVDKCLKLFSS-PFP--------------LVICIKSNHEIRISPVFMLILI 105 (123)
Q Consensus 69 wvl~rC~gC~k~-~~~--------------~~fCp~CG~~~tl~rV~~~~~~ 105 (123)
+.. +|..|++. +.. ...|| ||+. +|.=-|..|+
T Consensus 136 ~~~-~C~~C~~~~~~~~~~~~~~~~~~~~~~P~C~-Cgg~--lrP~VV~FGE 183 (271)
T PTZ00409 136 FEA-RCCTCRKTIQLNKIMLQKTSHFMHQLPPECP-CGGI--FKPNVILFGE 183 (271)
T ss_pred Ccc-eeCCCCCCcccCHHHHhhhhhhccCCCCCCC-CCCc--ccCcEEEeCC
Confidence 456 99999865 210 13599 9976 4443334444
No 366
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=23.91 E-value=42 Score=27.43 Aligned_cols=12 Identities=17% Similarity=0.202 Sum_probs=9.3
Q ss_pred ccccccCCCCCe
Q 033276 84 LVICIKSNHEIR 95 (123)
Q Consensus 84 ~~fCp~CG~~~t 95 (123)
.+-||.||.++.
T Consensus 235 g~pC~~Cg~~I~ 246 (269)
T PRK14811 235 GQPCPRCGTPIE 246 (269)
T ss_pred cCCCCcCCCeeE
Confidence 467999998843
No 367
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=23.80 E-value=39 Score=18.26 Aligned_cols=10 Identities=30% Similarity=0.464 Sum_probs=7.9
Q ss_pred ccccccCCCC
Q 033276 84 LVICIKSNHE 93 (123)
Q Consensus 84 ~~fCp~CG~~ 93 (123)
..-||.||..
T Consensus 2 l~~C~~CgR~ 11 (25)
T PF13913_consen 2 LVPCPICGRK 11 (25)
T ss_pred CCcCCCCCCE
Confidence 3569999976
No 368
>PF03850 Tfb4: Transcription factor Tfb4; InterPro: IPR004600 Members of this family are part of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. The core-TFIIH basal transcription factor complex has six subunits, this is the p34 subunit.; GO: 0006281 DNA repair, 0006355 regulation of transcription, DNA-dependent, 0000439 core TFIIH complex
Probab=23.60 E-value=40 Score=27.95 Aligned_cols=25 Identities=16% Similarity=-0.029 Sum_probs=16.7
Q ss_pred eeEEeeccccCCccc---ccCccccccCC
Q 033276 66 LHRYIVDKCLKLFSS---PFPLVICIKSN 91 (123)
Q Consensus 66 v~~wvl~rC~gC~k~---~~~~~fCp~CG 91 (123)
+..-.+ .|.-|..+ .+....||.||
T Consensus 249 ~vd~g~-vCsvCLsIfc~~p~~~~C~tC~ 276 (276)
T PF03850_consen 249 VVDIGY-VCSVCLSIFCEFPDGGICPTCG 276 (276)
T ss_pred ccccee-EchhhhhhhhCCCCCCCCCCCC
Confidence 334467 88888887 33345799987
No 369
>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=23.40 E-value=45 Score=28.61 Aligned_cols=31 Identities=16% Similarity=0.113 Sum_probs=16.5
Q ss_pred HHHHHHHHhCceeeCCCCCcceeeeEEeeccccCCccc
Q 033276 43 AMQNVILQMGLRLLAPGGMQIRQLHRYIVDKCLKLFSS 80 (123)
Q Consensus 43 AmQNVllqlGL~l~sv~g~~I~~v~~wvl~rC~gC~k~ 80 (123)
..|.+.++|- . .| .|.+ +.|..-.|..|.+.
T Consensus 99 ~v~~i~~~L~----~-~G-~I~~-~~~~~~Yc~~~e~f 129 (391)
T PF09334_consen 99 FVQEIFKRLY----D-NG-YIYK-REYEGWYCPSCERF 129 (391)
T ss_dssp HHHHHHHHHH----H-TT-SEEE-EEEEEEEETTTTEE
T ss_pred HHHHHHHHHH----h-cC-ceee-cccceeEecCcCcc
Confidence 3566666642 1 23 2333 34443388888876
No 370
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=23.25 E-value=44 Score=27.19 Aligned_cols=11 Identities=18% Similarity=0.202 Sum_probs=8.9
Q ss_pred ccccccCCCCC
Q 033276 84 LVICIKSNHEI 94 (123)
Q Consensus 84 ~~fCp~CG~~~ 94 (123)
.+-||.||.++
T Consensus 245 g~pC~~Cg~~I 255 (274)
T PRK01103 245 GEPCRRCGTPI 255 (274)
T ss_pred CCCCCCCCCee
Confidence 46799999884
No 371
>PRK05333 NAD-dependent deacetylase; Provisional
Probab=23.16 E-value=76 Score=25.93 Aligned_cols=8 Identities=13% Similarity=0.173 Sum_probs=7.1
Q ss_pred ccccCCCC
Q 033276 86 ICIKSNHE 93 (123)
Q Consensus 86 fCp~CG~~ 93 (123)
.||.||+.
T Consensus 181 ~C~~Cgg~ 188 (285)
T PRK05333 181 ACPACGGI 188 (285)
T ss_pred CCCCCCCc
Confidence 59999987
No 372
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=23.04 E-value=33 Score=26.92 Aligned_cols=21 Identities=14% Similarity=0.274 Sum_probs=14.3
Q ss_pred cccCCccc-c----------cCccccccCCCC
Q 033276 73 KCLKLFSS-P----------FPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~-~----------~~~~fCp~CG~~ 93 (123)
+|-.|+.. + .....||+||+.
T Consensus 2 iCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~v 33 (208)
T PF04161_consen 2 ICIECGHPVKSLYRQYSPGNIRLTKCPNCGKV 33 (208)
T ss_pred EeccCCCcchhhhhccCCCcEEEeeccccCCc
Confidence 68888865 2 123679999875
No 373
>PRK00124 hypothetical protein; Validated
Probab=23.04 E-value=1.2e+02 Score=23.41 Aligned_cols=40 Identities=23% Similarity=0.339 Sum_probs=30.6
Q ss_pred CceeccCCCCceeEEecccHHHHHHHHHhCceeeCCCCCcc
Q 033276 23 QSWMLRSLSESTVACITGDYAMQNVILQMGLRLLAPGGMQI 63 (123)
Q Consensus 23 ~~WIt~~~~~~~va~vTdDyAmQNVllqlGL~l~sv~g~~I 63 (123)
+.||-.... ..-.++|.||.+--.++.-|..++++.|+..
T Consensus 58 D~~Iv~~~~-~gDiVIT~Di~LAa~~l~Kga~vl~prG~~y 97 (151)
T PRK00124 58 DNEIVQLAE-KGDIVITQDYGLAALALEKGAIVLNPRGYIY 97 (151)
T ss_pred HHHHHHhCC-CCCEEEeCCHHHHHHHHHCCCEEECCCCcCC
Confidence 455543322 2248899999999999999999999998654
No 374
>PF01020 Ribosomal_L40e: Ribosomal L40e family; InterPro: IPR001975 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family contains the L40 ribosomal protein from both archaea and eukaryotes. Bovine ribosomal protein L40 has been identified as a secondary RNA binding protein []. L40 is fused to a ubiquitin protein [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 3IZS_p 3IZR_p 2AYJ_A 4A1B_K 4A19_K 4A18_K 4A1D_K.
Probab=23.00 E-value=79 Score=20.71 Aligned_cols=25 Identities=24% Similarity=0.440 Sum_probs=14.6
Q ss_pred cccCCccc-ccCcccccc--CCCCCeee
Q 033276 73 KCLKLFSS-PFPLVICIK--SNHEIRIS 97 (123)
Q Consensus 73 rC~gC~k~-~~~~~fCp~--CG~~~tl~ 97 (123)
.|..|+.. ++.-..|-+ ||+...|+
T Consensus 19 ICrkCyarl~~~A~nCRKkkCGhsn~LR 46 (52)
T PF01020_consen 19 ICRKCYARLPPRATNCRKKKCGHSNNLR 46 (52)
T ss_dssp EETTT--EE-TTSSS-TSSSCTS-S-EE
T ss_pred ecccccCcCCCCccceecccCCCCcccC
Confidence 89999987 666678988 99653454
No 375
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=22.97 E-value=35 Score=21.59 Aligned_cols=11 Identities=18% Similarity=0.443 Sum_probs=8.6
Q ss_pred ccccCCCCCee
Q 033276 86 ICIKSNHEIRI 96 (123)
Q Consensus 86 fCp~CG~~~tl 96 (123)
.|++||+++.+
T Consensus 1 ~C~iCg~kigl 11 (51)
T PF14471_consen 1 KCAICGKKIGL 11 (51)
T ss_pred CCCcccccccc
Confidence 39999999644
No 376
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=22.90 E-value=40 Score=24.63 Aligned_cols=21 Identities=24% Similarity=0.262 Sum_probs=15.5
Q ss_pred cccCCccc--c--cC-ccccccCCCC
Q 033276 73 KCLKLFSS--P--FP-LVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~--~--~~-~~fCp~CG~~ 93 (123)
+|..|+.. + .. -.-||+|-+.
T Consensus 60 ~CkkCGfef~~~~ik~pSRCP~CKSE 85 (97)
T COG3357 60 RCKKCGFEFRDDKIKKPSRCPKCKSE 85 (97)
T ss_pred hhcccCccccccccCCcccCCcchhh
Confidence 89999977 2 11 2469999988
No 377
>smart00532 LIGANc Ligase N family.
Probab=22.71 E-value=47 Score=29.43 Aligned_cols=47 Identities=15% Similarity=0.271 Sum_probs=27.9
Q ss_pred HHHHHHhCcee-----eCCCCCcceeeeEEeeccccCCcc--c-ccCccccccCCCCC
Q 033276 45 QNVILQMGLRL-----LAPGGMQIRQLHRYIVDKCLKLFS--S-PFPLVICIKSNHEI 94 (123)
Q Consensus 45 QNVllqlGL~l-----~sv~g~~I~~v~~wvl~rC~gC~k--~-~~~~~fCp~CG~~~ 94 (123)
++-+.++||++ +.-.|.-|-++-.-+. . .--.. . .++ .+||.||+++
T Consensus 355 ~~~i~~~~i~iGd~V~V~raGdVIP~I~~vv~-~-~r~~~~~~~~~P-~~CP~C~s~l 409 (441)
T smart00532 355 EDEIEEKDIRIGDTVVVRKAGDVIPKVVGVVK-E-KRPGDEREIEMP-THCPSCGSEL 409 (441)
T ss_pred HHHHHHcCCCCCCEEEEEECCCcCcceeeccc-c-cCCCCCccCcCC-CCCCCCCCEe
Confidence 34467788864 2335888888766443 1 11111 1 234 7899999994
No 378
>COG1138 CcmF Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]
Probab=22.70 E-value=40 Score=31.75 Aligned_cols=18 Identities=22% Similarity=0.344 Sum_probs=15.0
Q ss_pred eEEecccHHHHHHHHHhC
Q 033276 35 VACITGDYAMQNVILQMG 52 (123)
Q Consensus 35 va~vTdDyAmQNVllqlG 52 (123)
-+.+|+||++|||+.+=.
T Consensus 59 ~afv~~DFSv~yVa~nS~ 76 (648)
T COG1138 59 YAFVVSDFSVQYVAQNSN 76 (648)
T ss_pred HHHHhccHHHHHHHHhcc
Confidence 367899999999999843
No 379
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 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. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=22.65 E-value=40 Score=22.33 Aligned_cols=22 Identities=23% Similarity=0.250 Sum_probs=14.2
Q ss_pred eeccccCCccc-cc------CccccccCCC
Q 033276 70 IVDKCLKLFSS-PF------PLVICIKSNH 92 (123)
Q Consensus 70 vl~rC~gC~k~-~~------~~~fCp~CG~ 92 (123)
.. .|..|.+. +. ...+||+|+.
T Consensus 41 ~v-~Cg~C~~~~~~~~~~c~~~~~C~~C~~ 69 (71)
T PF05495_consen 41 RV-ICGKCRTEQPIDEYSCGADYFCPICGL 69 (71)
T ss_dssp EE-EETTT--EEES-SBTT--SEEETTTTE
T ss_pred Ce-ECCCCCCccChhhhhcCCCccCcCcCC
Confidence 45 79999987 32 2469999985
No 380
>TIGR00269 conserved hypothetical protein TIGR00269.
Probab=22.62 E-value=39 Score=23.72 Aligned_cols=17 Identities=18% Similarity=0.254 Sum_probs=7.2
Q ss_pred cccCCcccccCccccccC
Q 033276 73 KCLKLFSSPFPLVICIKS 90 (123)
Q Consensus 73 rC~gC~k~~~~~~fCp~C 90 (123)
+|.-|+.+ .+.+.|..|
T Consensus 82 ~C~~CG~p-ss~~iC~~C 98 (104)
T TIGR00269 82 RCERCGEP-TSGRICKAC 98 (104)
T ss_pred cCCcCcCc-CCccccHhh
Confidence 45555543 222344444
No 381
>PRK14276 chaperone protein DnaJ; Provisional
Probab=22.53 E-value=1.2e+02 Score=25.81 Aligned_cols=35 Identities=17% Similarity=0.091 Sum_probs=20.7
Q ss_pred cccCCccc----ccCccccccCCCCCeeeEEEEEeeEEEE
Q 033276 73 KCLKLFSS----PFPLVICIKSNHEIRISPVFMLILICLY 108 (123)
Q Consensus 73 rC~gC~k~----~~~~~fCp~CG~~~tl~rV~~~~~~~~~ 108 (123)
.|..|.-. ......|+.|+... ...+...++...+
T Consensus 148 ~C~~C~G~G~~~~~~~~~C~~C~G~G-~~~~~~~~~~G~~ 186 (380)
T PRK14276 148 TCHTCNGSGAKPGTSPVTCGKCHGSG-VITVDTQTPLGMM 186 (380)
T ss_pred cCCCCcCcccCCCCCCccCCCCCCee-EEEEEEecCCceE
Confidence 58877654 23346799999884 3344444444433
No 382
>PF02132 RecR: RecR protein; InterPro: IPR023628 The bacterial protein RecR seems to play a role in a recombinational process of DNA repair []. It may act with RecF and RecO. RecR's structure consists of a N-terminal helix-hairpin-helix (HhH) motif, followed by a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif []. This entry represents the C4-type zinc finger.; PDB: 1VDD_D 2V1C_B.
Probab=22.49 E-value=5.6 Score=23.90 Aligned_cols=28 Identities=11% Similarity=0.007 Sum_probs=14.1
Q ss_pred eeeeEEeeccccCCcccccCccccccCCCC
Q 033276 64 RQLHRYIVDKCLKLFSSPFPLVICIKSNHE 93 (123)
Q Consensus 64 ~~v~~wvl~rC~gC~k~~~~~~fCp~CG~~ 93 (123)
.+++.-+. .|.-|+... ....|++|-++
T Consensus 11 ~~~~~~i~-~C~~C~nls-e~~~C~IC~d~ 38 (41)
T PF02132_consen 11 KEAKENIK-FCSICGNLS-EEDPCEICSDP 38 (41)
T ss_dssp HHHHHH-E-E-SSS--EE-SSSS-HHHH-T
T ss_pred HHHHHcCC-ccCCCCCcC-CCCcCcCCCCC
Confidence 34445566 899999882 13579999776
No 383
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated
Probab=22.45 E-value=56 Score=30.21 Aligned_cols=28 Identities=25% Similarity=0.123 Sum_probs=18.4
Q ss_pred cccCCccc-c----cCccccccCCCCCeeeEEE
Q 033276 73 KCLKLFSS-P----FPLVICIKSNHEIRISPVF 100 (123)
Q Consensus 73 rC~gC~k~-~----~~~~fCp~CG~~~tl~rV~ 100 (123)
.|..|+.. . ....+|+.|++...+.+|.
T Consensus 546 vC~~CG~~~~~~~~~~~~~C~~C~~~~~i~~v~ 578 (605)
T PRK07225 546 VCAKCGMIAIYDKKRNRKYCPICGEETDIYPVE 578 (605)
T ss_pred eecCcCcceehhcccCceeecccCCCCceeecc
Confidence 78889886 1 2345699998754555554
No 384
>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=22.40 E-value=63 Score=19.10 Aligned_cols=20 Identities=20% Similarity=0.182 Sum_probs=12.0
Q ss_pred cccCCccc--ccCccccccCCC
Q 033276 73 KCLKLFSS--PFPLVICIKSNH 92 (123)
Q Consensus 73 rC~gC~k~--~~~~~fCp~CG~ 92 (123)
+|.-|++. .....+|..|+.
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~ 22 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNR 22 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSC
T ss_pred eCcCCCCcCCCCCeEEcCCCCh
Confidence 36666665 344567777764
No 385
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=22.28 E-value=48 Score=27.17 Aligned_cols=11 Identities=27% Similarity=0.223 Sum_probs=8.8
Q ss_pred ccccccCCCCC
Q 033276 84 LVICIKSNHEI 94 (123)
Q Consensus 84 ~~fCp~CG~~~ 94 (123)
.+-||.||.++
T Consensus 254 g~pC~~Cg~~I 264 (282)
T PRK13945 254 GKPCRKCGTPI 264 (282)
T ss_pred cCCCCcCCCee
Confidence 46799999884
No 386
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 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 PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=22.19 E-value=45 Score=21.95 Aligned_cols=39 Identities=18% Similarity=0.251 Sum_probs=22.6
Q ss_pred CccccccCCCCCeeeEEEEEeeEEEEEee-CCccceeecccC
Q 033276 83 PLVICIKSNHEIRISPVFMLILICLYIQV-DTEMPCLLHYHC 123 (123)
Q Consensus 83 ~~~fCp~CG~~~tl~rV~~~~~~~~~~~~-~~~~~~~~~~~~ 123 (123)
.+--|..|+.+ +.+=.+.+|.-+.-.. ++.+|.-.|..|
T Consensus 6 ~Ra~Ck~C~~~--I~kg~lRiG~~~~~~~~~~~~~~W~H~~C 45 (82)
T PF00645_consen 6 GRAKCKGCKKK--IAKGELRIGKIVPSPEGDGDIPKWYHWDC 45 (82)
T ss_dssp STEBETTTSCB--E-TTSEEEEEEEEETTSSCEEEEEEEHHH
T ss_pred CCccCcccCCc--CCCCCEEEEEEecccccCCCCCceECccc
Confidence 45557777754 3344445555544433 368888888766
No 387
>PF02348 CTP_transf_3: Cytidylyltransferase; InterPro: IPR003329 Synonym(s): CMP-N-acetylneuraminic acid synthetase Acylneuraminate cytidylyltransferase (2.7.7.43 from EC) (CMP-NeuAc synthetase) catalyzes the reaction of CTP and NeuAc to form CMP-NeuAc, which is the nucleotide sugar donor used by sialyltransferases []. The outer membrane lipooligosaccharides of some microorganisms contain terminal sialic acid attached to N-acetyllactosamine and so this modification may be important in pathogenesis.; GO: 0009103 lipopolysaccharide biosynthetic process; PDB: 3K8D_C 1VH1_B 3K8E_C 1QWJ_A 3EWI_A 1VIC_B 3DUV_A 1VH3_C 3TQD_A 2Y6P_C ....
Probab=22.03 E-value=1.3e+02 Score=22.34 Aligned_cols=28 Identities=14% Similarity=0.348 Sum_probs=22.2
Q ss_pred ceeEEecccHHHHHHHHHhCceeeCCCC
Q 033276 33 STVACITGDYAMQNVILQMGLRLLAPGG 60 (123)
Q Consensus 33 ~~va~vTdDyAmQNVllqlGL~l~sv~g 60 (123)
.++++-|||-.+.+++.+.|.++.-..+
T Consensus 41 d~IvVaTd~~~i~~~~~~~g~~v~~~~~ 68 (217)
T PF02348_consen 41 DEIVVATDDEEIDDIAEEYGAKVIFRRG 68 (217)
T ss_dssp SEEEEEESSHHHHHHHHHTTSEEEE--T
T ss_pred CeEEEeCCCHHHHHHHHHcCCeeEEcCh
Confidence 4689999999999999999977764433
No 388
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=21.80 E-value=42 Score=23.13 Aligned_cols=11 Identities=9% Similarity=0.313 Sum_probs=8.9
Q ss_pred cccccCCCCCe
Q 033276 85 VICIKSNHEIR 95 (123)
Q Consensus 85 ~fCp~CG~~~t 95 (123)
+||..||-|++
T Consensus 1 k~CQSCGMPl~ 11 (81)
T PF12674_consen 1 KFCQSCGMPLS 11 (81)
T ss_pred CcCCcCcCccC
Confidence 48999999954
No 389
>PF11062 DUF2863: Protein of unknown function (DUF2863); InterPro: IPR021292 This bacterial family of proteins have no known function.
Probab=21.79 E-value=40 Score=30.01 Aligned_cols=20 Identities=25% Similarity=0.519 Sum_probs=15.4
Q ss_pred cCccccccCCCCCeeeEEEEEeeEEEEEeeCCc
Q 033276 82 FPLVICIKSNHEIRISPVFMLILICLYIQVDTE 114 (123)
Q Consensus 82 ~~~~fCp~CG~~~tl~rV~~~~~~~~~~~~~~~ 114 (123)
.+-+||..||.|+ |=..+||
T Consensus 362 f~~E~CdDCGaPl-------------ypd~~GE 381 (398)
T PF11062_consen 362 FPPEFCDDCGAPL-------------YPDPEGE 381 (398)
T ss_pred CCchhcccCCCCC-------------CCCCCcc
Confidence 3458999999995 7777774
No 390
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=21.41 E-value=18 Score=21.75 Aligned_cols=22 Identities=14% Similarity=0.037 Sum_probs=15.3
Q ss_pred cccCCccc-ccCccccccCCCCC
Q 033276 73 KCLKLFSS-PFPLVICIKSNHEI 94 (123)
Q Consensus 73 rC~gC~k~-~~~~~fCp~CG~~~ 94 (123)
.|..|... -.....||.|..++
T Consensus 25 ~C~~C~~~~~~~~~~CP~Cr~~i 47 (50)
T PF13920_consen 25 FCEECAERLLKRKKKCPICRQPI 47 (50)
T ss_dssp EEHHHHHHHHHTTSBBTTTTBB-
T ss_pred HHHHHhHHhcccCCCCCcCChhh
Confidence 57777765 33567899998883
No 391
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=21.09 E-value=1.1e+02 Score=20.34 Aligned_cols=31 Identities=16% Similarity=0.170 Sum_probs=13.7
Q ss_pred eeeeEEeeccccCCccc-c----cCccccccCCCCCee
Q 033276 64 RQLHRYIVDKCLKLFSS-P----FPLVICIKSNHEIRI 96 (123)
Q Consensus 64 ~~v~~wvl~rC~gC~k~-~----~~~~fCp~CG~~~tl 96 (123)
+..+.|++ |-.|.+. . .-..-|+.||+=.|.
T Consensus 25 ~~~~v~Il--CNDC~~~s~v~fH~lg~KC~~C~SYNT~ 60 (61)
T PF14599_consen 25 RNKKVWIL--CNDCNAKSEVPFHFLGHKCSHCGSYNTR 60 (61)
T ss_dssp ---EEEEE--ESSS--EEEEE--TT----TTTS---EE
T ss_pred hCCEEEEE--CCCCCCccceeeeHhhhcCCCCCCcccC
Confidence 34457777 9999986 2 234669999975443
No 392
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=20.95 E-value=32 Score=23.31 Aligned_cols=29 Identities=14% Similarity=0.115 Sum_probs=21.5
Q ss_pred eeeEEeeccccCCccc----ccCccccccCCCCC
Q 033276 65 QLHRYIVDKCLKLFSS----PFPLVICIKSNHEI 94 (123)
Q Consensus 65 ~v~~wvl~rC~gC~k~----~~~~~fCp~CG~~~ 94 (123)
+-..-+| .|--|+.. ...-..|..||+.+
T Consensus 15 r~~~miY-iCgdC~~en~lk~~D~irCReCG~RI 47 (62)
T KOG3507|consen 15 RTATMIY-ICGDCGQENTLKRGDVIRCRECGYRI 47 (62)
T ss_pred CcccEEE-EeccccccccccCCCcEehhhcchHH
Confidence 4456788 99999976 23446799999884
No 393
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=20.74 E-value=48 Score=27.59 Aligned_cols=28 Identities=14% Similarity=0.046 Sum_probs=19.1
Q ss_pred eeeeEEeeccccCCc----cc-----ccCccccccCCC
Q 033276 64 RQLHRYIVDKCLKLF----SS-----PFPLVICIKSNH 92 (123)
Q Consensus 64 ~~v~~wvl~rC~gC~----k~-----~~~~~fCp~CG~ 92 (123)
+.+--|.. ||-.|+ .. -..+..||+||.
T Consensus 188 h~LvIqg~-rCg~c~i~~h~~c~qty~q~~~~cphc~d 224 (235)
T KOG4718|consen 188 HCLVIQGI-RCGSCNIQYHRGCIQTYLQRRDICPHCGD 224 (235)
T ss_pred HHHhheee-ccCcccchhhhHHHHHHhcccCcCCchhc
Confidence 34556788 999993 22 133789999984
No 394
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=20.72 E-value=54 Score=27.56 Aligned_cols=17 Identities=12% Similarity=0.157 Sum_probs=10.9
Q ss_pred ceeeeEEeeccccCCccc
Q 033276 63 IRQLHRYIVDKCLKLFSS 80 (123)
Q Consensus 63 I~~v~~wvl~rC~gC~k~ 80 (123)
||-.-=|-. +|.+|+..
T Consensus 33 VRf~~Pf~i-~C~~C~~~ 49 (324)
T PF04502_consen 33 VRFMMPFNI-WCNTCGEY 49 (324)
T ss_pred EEEcCCccC-cCCCCccc
Confidence 344445667 88888764
No 395
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=20.69 E-value=53 Score=22.26 Aligned_cols=21 Identities=19% Similarity=0.303 Sum_probs=15.5
Q ss_pred cccCCccc---------ccCccccccCCCC
Q 033276 73 KCLKLFSS---------PFPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~---------~~~~~fCp~CG~~ 93 (123)
.|+.|... +.....|-.||+.
T Consensus 10 ~CP~C~~~D~i~~~~e~~ve~vECV~CGy~ 39 (71)
T PF09526_consen 10 VCPKCQAMDTIMMWRENGVEYVECVECGYT 39 (71)
T ss_pred cCCCCcCccEEEEEEeCCceEEEecCCCCe
Confidence 78888875 1346789999976
No 396
>PRK00076 recR recombination protein RecR; Reviewed
Probab=20.68 E-value=41 Score=26.94 Aligned_cols=38 Identities=11% Similarity=0.044 Sum_probs=26.0
Q ss_pred ceeeeEEeeccccCCcccccCccccccCCCCCeeeEEEEE
Q 033276 63 IRQLHRYIVDKCLKLFSSPFPLVICIKSNHEIRISPVFML 102 (123)
Q Consensus 63 I~~v~~wvl~rC~gC~k~~~~~~fCp~CG~~~tl~rV~~~ 102 (123)
|..+++-+. .|.-|+.... ...|+.|-++.+=+.+=|+
T Consensus 46 i~~~~~~i~-~C~~C~~lse-~~~C~IC~d~~Rd~~~icV 83 (196)
T PRK00076 46 LEEAKEKIK-HCSVCGNLTE-QDPCEICSDPRRDQSLICV 83 (196)
T ss_pred HHHHHHcCC-cCCCCCCcCC-CCcCCCCCCCCCCCCEEEE
Confidence 455667777 9999998822 2669999999433443333
No 397
>TIGR02386 rpoC_TIGR DNA-directed RNA polymerase, beta' subunit, predominant form. Bacteria have a single DNA-directed RNA polymerase, with required subunits that include alpha, beta, and beta-prime. This model describes the predominant architecture of the beta-prime subunit in most bacteria. This model excludes from among the bacterial mostly sequences from the cyanobacteria, where RpoC is replaced by two tandem genes homologous to it but also encoding an additional domain.
Probab=20.61 E-value=50 Score=33.02 Aligned_cols=31 Identities=16% Similarity=0.154 Sum_probs=22.0
Q ss_pred eeeEEeeccccCCccc---ccCccccccCCCCCeeeEE
Q 033276 65 QLHRYIVDKCLKLFSS---PFPLVICIKSNHEIRISPV 99 (123)
Q Consensus 65 ~v~~wvl~rC~gC~k~---~~~~~fCp~CG~~~tl~rV 99 (123)
-++.|.- +|+|. .....+|+.||-+.|..||
T Consensus 46 p~k~~ec----~Cgkyk~~~~~~~~C~~Cgve~t~~~v 79 (1140)
T TIGR02386 46 PTKDWEC----YCGKYKKIRYKGVVCERCGVEVTESKV 79 (1140)
T ss_pred CccCcee----ccccccccCcCCcCCCCCCCCcccchh
Confidence 3566766 67765 3345799999999887764
No 398
>COG1671 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.37 E-value=1.4e+02 Score=23.35 Aligned_cols=42 Identities=21% Similarity=0.460 Sum_probs=31.4
Q ss_pred CCCCceeccCCCCceeEEecccHHHHHHHHHhCceeeCCCCCc
Q 033276 20 CSEQSWMLRSLSESTVACITGDYAMQNVILQMGLRLLAPGGMQ 62 (123)
Q Consensus 20 ~~~~~WIt~~~~~~~va~vTdDyAmQNVllqlGL~l~sv~g~~ 62 (123)
|.-+.||-.- ....-.++|.|+.+--.++..|..++++.|+.
T Consensus 54 DaaD~~Iv~~-a~~gDlVVT~Di~LA~~ll~kg~~v~~prGr~ 95 (150)
T COG1671 54 DAADDWIVNL-AEKGDLVVTADIPLASLLLDKGAAVLNPRGRL 95 (150)
T ss_pred chHHHHHHHh-CCCCCEEEECchHHHHHHHhcCCEEECCCCcc
Confidence 3345566422 12334889999999999999999999999864
No 399
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=20.25 E-value=53 Score=27.23 Aligned_cols=21 Identities=14% Similarity=0.169 Sum_probs=14.8
Q ss_pred cccCCccc----c--cCccccccCCCC
Q 033276 73 KCLKLFSS----P--FPLVICIKSNHE 93 (123)
Q Consensus 73 rC~gC~k~----~--~~~~fCp~CG~~ 93 (123)
+|+.|+.. + ....+|..||.=
T Consensus 13 ~Cp~Cg~~~iv~d~~~Ge~vC~~CG~V 39 (310)
T PRK00423 13 VCPECGSDKLIYDYERGEIVCADCGLV 39 (310)
T ss_pred cCcCCCCCCeeEECCCCeEeecccCCc
Confidence 78888863 2 345788888863
No 400
>PRK14290 chaperone protein DnaJ; Provisional
Probab=20.06 E-value=1.5e+02 Score=25.04 Aligned_cols=24 Identities=17% Similarity=0.228 Sum_probs=17.2
Q ss_pred cccCCccc-ccCccccccCCCCCee
Q 033276 73 KCLKLFSS-PFPLVICIKSNHEIRI 96 (123)
Q Consensus 73 rC~gC~k~-~~~~~fCp~CG~~~tl 96 (123)
.|..|.-. ...+..|+.|.+..++
T Consensus 193 ~C~~C~G~G~~~~~~C~~C~G~g~v 217 (365)
T PRK14290 193 TCRTCGGRGRIPEEKCPRCNGTGTV 217 (365)
T ss_pred eCCCCCCceeEccCCCCCCCCceeE
Confidence 78888766 4556779999877443
Done!