Query 025050
Match_columns 258
No_of_seqs 183 out of 464
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 09:36:34 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025050.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025050hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2768 Translation initiation 100.0 1.6E-65 3.4E-70 453.2 11.8 197 50-250 16-212 (231)
2 PRK03988 translation initiatio 100.0 6.2E-54 1.3E-58 359.2 16.0 134 115-254 4-137 (138)
3 TIGR00311 aIF-2beta translatio 100.0 5.4E-53 1.2E-57 351.7 15.1 131 117-253 1-131 (133)
4 PRK12336 translation initiatio 100.0 1.3E-50 2.8E-55 356.4 15.5 131 116-252 1-131 (201)
5 smart00653 eIF2B_5 domain pres 100.0 8.9E-49 1.9E-53 317.1 13.5 109 141-249 2-110 (110)
6 PF01873 eIF-5_eIF-2B: Domain 100.0 4E-49 8.7E-54 325.3 11.0 120 131-250 4-124 (125)
7 COG1601 GCD7 Translation initi 100.0 5.2E-42 1.1E-46 291.1 7.4 135 113-252 3-138 (151)
8 KOG2767 Translation initiation 100.0 2.3E-33 5.1E-38 263.1 4.7 116 137-252 10-130 (400)
9 PF09526 DUF2387: Probable met 95.3 0.011 2.3E-07 45.1 2.0 38 213-251 3-41 (71)
10 TIGR02443 conserved hypothetic 95.1 0.015 3.2E-07 43.1 2.0 38 213-251 4-42 (59)
11 PF01253 SUI1: Translation ini 93.5 0.23 5E-06 38.0 5.8 57 156-216 19-79 (83)
12 PF14354 Lar_restr_allev: Rest 92.7 0.1 2.2E-06 37.2 2.6 28 221-248 5-37 (61)
13 PF01096 TFIIS_C: Transcriptio 90.7 0.27 5.8E-06 33.0 2.8 30 220-249 1-37 (39)
14 smart00440 ZnF_C2C2 C2C2 Zinc 89.4 0.51 1.1E-05 31.8 3.3 30 221-250 2-38 (40)
15 PRK00939 translation initiatio 89.1 0.74 1.6E-05 37.0 4.6 56 152-213 34-89 (99)
16 cd00474 SUI1_eIF1 The SUI1/eIF 88.1 0.93 2E-05 34.8 4.4 54 154-212 12-65 (77)
17 PRK09710 lar restriction allev 88.1 0.57 1.2E-05 35.3 3.1 32 221-252 8-39 (64)
18 TIGR03655 anti_R_Lar restricti 87.7 0.52 1.1E-05 33.3 2.6 31 221-252 3-38 (53)
19 PF08271 TF_Zn_Ribbon: TFIIB z 86.5 0.5 1.1E-05 31.9 1.8 30 221-252 2-31 (43)
20 TIGR01158 SUI1_rel translation 85.9 1.6 3.5E-05 35.1 4.8 52 152-208 35-86 (101)
21 PHA02998 RNA polymerase subuni 84.9 0.99 2.2E-05 40.4 3.4 81 163-251 87-182 (195)
22 COG4888 Uncharacterized Zn rib 84.5 0.76 1.6E-05 37.5 2.3 35 217-251 20-57 (104)
23 PF13719 zinc_ribbon_5: zinc-r 81.9 0.74 1.6E-05 30.5 1.1 30 219-250 2-35 (37)
24 COG2051 RPS27A Ribosomal prote 81.8 0.95 2.1E-05 34.4 1.8 29 219-249 19-47 (67)
25 TIGR01159 DRP1 density-regulat 81.2 3.7 8E-05 36.2 5.5 56 156-215 103-162 (173)
26 PF11331 DUF3133: Protein of u 80.7 0.92 2E-05 32.0 1.3 32 219-250 6-41 (46)
27 PF14803 Nudix_N_2: Nudix N-te 79.9 1.5 3.2E-05 29.0 2.0 28 221-249 2-31 (34)
28 COG0023 SUI1 Translation initi 79.9 5.1 0.00011 32.8 5.5 60 149-213 34-93 (104)
29 PF03833 PolC_DP2: DNA polymer 79.6 0.58 1.3E-05 50.0 0.0 29 220-257 656-684 (900)
30 PRK14892 putative transcriptio 78.7 1.5 3.1E-05 35.5 2.0 34 217-250 19-52 (99)
31 PF05129 Elf1: Transcription e 78.5 2 4.4E-05 33.3 2.7 36 217-252 20-58 (81)
32 TIGR02159 PA_CoA_Oxy4 phenylac 77.7 2.4 5.2E-05 36.2 3.2 55 196-250 63-140 (146)
33 PRK00415 rps27e 30S ribosomal 77.0 1.9 4.2E-05 32.0 2.1 29 219-249 11-39 (59)
34 PF04760 IF2_N: Translation in 76.7 2.8 6.1E-05 29.2 2.8 27 162-188 5-31 (54)
35 smart00401 ZnF_GATA zinc finge 76.4 1.3 2.9E-05 31.4 1.1 31 220-250 4-35 (52)
36 PF07191 zinc-ribbons_6: zinc- 76.4 2.2 4.9E-05 32.6 2.3 33 220-257 2-34 (70)
37 COG1997 RPL43A Ribosomal prote 76.0 2.4 5.3E-05 33.8 2.5 41 206-250 23-63 (89)
38 PF12760 Zn_Tnp_IS1595: Transp 75.8 2.6 5.7E-05 28.8 2.4 28 220-249 19-46 (46)
39 PF04216 FdhE: Protein involve 75.5 1.9 4.1E-05 39.9 2.2 31 220-250 173-207 (290)
40 cd04762 HTH_MerR-trunc Helix-T 75.0 9.1 0.0002 24.5 4.8 46 162-212 2-47 (49)
41 PF13453 zf-TFIIB: Transcripti 74.9 3.3 7.2E-05 27.6 2.7 28 221-249 1-28 (41)
42 PRK05580 primosome assembly pr 74.2 2 4.3E-05 44.6 2.1 37 219-257 381-425 (679)
43 TIGR00595 priA primosomal prot 73.9 2.3 4.9E-05 42.7 2.4 18 240-257 240-257 (505)
44 TIGR03826 YvyF flagellar opero 73.5 4 8.7E-05 34.7 3.4 22 161-182 47-68 (137)
45 PRK00420 hypothetical protein; 72.4 2.3 4.9E-05 35.2 1.6 27 219-249 23-49 (112)
46 PF05180 zf-DNL: DNL zinc fing 72.2 2.5 5.5E-05 31.9 1.7 31 220-250 5-39 (66)
47 cd00202 ZnF_GATA Zinc finger D 72.1 0.93 2E-05 32.6 -0.6 33 221-253 1-34 (54)
48 PRK08665 ribonucleotide-diphos 71.5 4.1 8.8E-05 43.2 3.7 41 205-250 688-750 (752)
49 PF01921 tRNA-synt_1f: tRNA sy 71.0 5.5 0.00012 38.9 4.2 38 215-252 170-211 (360)
50 TIGR01160 SUI1_MOF2 translatio 70.2 4.7 0.0001 33.2 3.0 60 151-215 34-98 (110)
51 PRK04023 DNA polymerase II lar 70.2 2.1 4.6E-05 46.7 1.3 29 220-257 627-655 (1121)
52 COG3529 Predicted nucleic-acid 69.5 0.93 2E-05 34.1 -1.1 39 213-252 5-44 (66)
53 TIGR01384 TFS_arch transcripti 69.3 6.2 0.00013 30.9 3.4 35 219-253 62-103 (104)
54 COG1198 PriA Primosomal protei 69.0 3.8 8.3E-05 43.3 2.8 39 219-257 435-479 (730)
55 PF13717 zinc_ribbon_4: zinc-r 68.0 2.6 5.6E-05 27.8 0.9 30 219-250 2-35 (36)
56 PRK03954 ribonuclease P protei 67.6 4.9 0.00011 33.6 2.6 32 220-251 65-104 (121)
57 PRK14714 DNA polymerase II lar 67.6 2.6 5.7E-05 47.0 1.3 30 219-257 667-696 (1337)
58 PRK03564 formate dehydrogenase 67.5 4.1 8.9E-05 39.0 2.5 31 219-249 187-221 (309)
59 TIGR00100 hypA hydrogenase nic 67.0 5.5 0.00012 32.5 2.8 51 173-235 40-102 (115)
60 PF00320 GATA: GATA zinc finge 66.2 2 4.4E-05 28.2 0.1 30 222-251 1-31 (36)
61 COG3478 Predicted nucleic-acid 66.1 4.9 0.00011 30.5 2.1 31 219-249 4-49 (68)
62 TIGR01385 TFSII transcription 65.1 6.2 0.00013 37.5 3.1 33 219-251 258-297 (299)
63 COG3058 FdhE Uncharacterized p 64.8 3 6.5E-05 39.7 1.0 35 220-254 186-239 (308)
64 PRK14873 primosome assembly pr 64.5 5 0.00011 41.9 2.6 38 219-257 383-426 (665)
65 PF09297 zf-NADH-PPase: NADH p 64.3 2.3 4.9E-05 27.1 0.0 28 219-249 3-30 (32)
66 PRK00241 nudC NADH pyrophospha 64.2 6.2 0.00013 36.3 2.9 36 211-249 91-126 (256)
67 COG1096 Predicted RNA-binding 63.9 5.2 0.00011 35.9 2.2 27 219-250 149-175 (188)
68 TIGR02098 MJ0042_CXXC MJ0042 f 63.8 3.3 7.3E-05 26.8 0.8 31 219-250 2-35 (38)
69 PRK07451 translation initiatio 63.8 9.4 0.0002 31.7 3.6 52 154-210 51-102 (115)
70 PLN00209 ribosomal protein S27 63.7 5.5 0.00012 31.6 2.1 29 219-249 36-64 (86)
71 PRK12496 hypothetical protein; 63.5 4.8 0.0001 34.8 1.9 31 228-258 115-148 (164)
72 PF12898 Stc1: Stc1 domain; I 63.4 8.6 0.00019 29.8 3.1 49 196-252 7-62 (84)
73 TIGR01562 FdhE formate dehydro 63.1 4.1 8.9E-05 38.8 1.6 26 105-130 85-112 (305)
74 PRK12380 hydrogenase nickel in 61.9 5.7 0.00012 32.3 2.0 57 173-250 40-96 (113)
75 PTZ00083 40S ribosomal protein 61.0 6.8 0.00015 31.1 2.2 29 219-249 35-63 (85)
76 PF09855 DUF2082: Nucleic-acid 60.9 8 0.00017 28.9 2.5 29 221-249 2-45 (64)
77 PF10058 DUF2296: Predicted in 60.9 5.8 0.00013 28.6 1.7 30 220-249 23-53 (54)
78 PF07282 OrfB_Zn_ribbon: Putat 60.9 5.5 0.00012 28.8 1.6 28 220-250 29-56 (69)
79 PF04194 PDCD2_C: Programmed c 60.9 1.5 3.2E-05 37.7 -1.7 18 163-180 60-77 (164)
80 COG2835 Uncharacterized conser 60.8 5.8 0.00013 29.6 1.7 33 215-250 4-36 (60)
81 PF12677 DUF3797: Domain of un 60.7 10 0.00022 27.3 2.8 32 216-248 10-46 (49)
82 PRK00564 hypA hydrogenase nick 60.3 7.9 0.00017 31.6 2.6 25 174-200 41-66 (117)
83 TIGR00100 hypA hydrogenase nic 60.3 6.2 0.00014 32.1 2.0 51 201-257 34-90 (115)
84 COG1163 DRG Predicted GTPase [ 59.4 10 0.00022 37.1 3.5 55 113-174 272-327 (365)
85 PF01927 Mut7-C: Mut7-C RNAse 58.6 9.7 0.00021 31.9 2.9 52 197-248 63-132 (147)
86 smart00531 TFIIE Transcription 58.4 8 0.00017 32.5 2.4 70 156-251 61-134 (147)
87 PF02150 RNA_POL_M_15KD: RNA p 57.5 8.5 0.00018 25.3 1.9 29 221-251 3-31 (35)
88 PF08792 A2L_zn_ribbon: A2L zi 57.4 12 0.00027 24.4 2.6 30 219-251 3-32 (33)
89 smart00834 CxxC_CXXC_SSSS Puta 57.3 5.8 0.00013 25.7 1.1 29 221-249 7-35 (41)
90 KOG3507 DNA-directed RNA polym 57.0 4.2 9E-05 30.4 0.4 28 220-251 21-48 (62)
91 TIGR00467 lysS_arch lysyl-tRNA 56.9 13 0.00028 37.8 4.0 70 181-252 112-202 (515)
92 PRK09019 translation initiatio 56.6 23 0.00049 29.2 4.6 53 154-211 44-96 (108)
93 PRK00398 rpoP DNA-directed RNA 56.5 9.7 0.00021 25.9 2.1 29 220-251 4-32 (46)
94 PF06322 Phage_NinH: Phage Nin 56.5 16 0.00034 27.6 3.3 37 161-204 17-53 (64)
95 PF12172 DUF35_N: Rubredoxin-l 56.5 7.6 0.00016 25.2 1.5 23 235-257 6-29 (37)
96 PRK00432 30S ribosomal protein 56.1 7.3 0.00016 27.6 1.5 28 219-250 20-47 (50)
97 PRK07562 ribonucleotide-diphos 55.0 8.4 0.00018 43.0 2.4 38 207-250 1180-1217(1220)
98 smart00661 RPOL9 RNA polymeras 54.6 8.2 0.00018 26.3 1.5 28 221-250 2-30 (52)
99 smart00659 RPOLCX RNA polymera 54.4 6.2 0.00013 27.3 0.9 26 221-250 4-29 (44)
100 PRK03681 hypA hydrogenase nick 54.3 11 0.00023 30.8 2.4 26 173-200 40-65 (114)
101 PF01667 Ribosomal_S27e: Ribos 53.9 4.5 9.8E-05 29.5 0.1 29 219-249 7-35 (55)
102 PF08274 PhnA_Zn_Ribbon: PhnA 53.8 7.8 0.00017 25.0 1.2 26 220-249 3-28 (30)
103 PF04032 Rpr2: RNAse P Rpr2/Rp 53.5 14 0.00031 27.4 2.8 29 220-248 47-85 (85)
104 PRK00762 hypA hydrogenase nick 53.4 13 0.00027 30.8 2.7 26 173-200 40-65 (124)
105 PRK06824 translation initiatio 52.3 19 0.00041 30.0 3.6 55 152-211 52-106 (118)
106 cd00674 LysRS_core_class_I cat 52.2 16 0.00034 35.4 3.6 89 163-252 89-204 (353)
107 PRK00564 hypA hydrogenase nick 51.6 10 0.00022 31.0 1.9 29 229-257 60-92 (117)
108 PRK03824 hypA hydrogenase nick 50.8 13 0.00027 31.2 2.3 15 220-234 108-122 (135)
109 PF00165 HTH_AraC: Bacterial r 50.6 23 0.00049 23.1 3.1 28 161-188 9-36 (42)
110 PF14205 Cys_rich_KTR: Cystein 50.1 8.8 0.00019 28.2 1.1 33 218-250 3-38 (55)
111 COG1594 RPB9 DNA-directed RNA 49.9 18 0.0004 29.5 3.1 34 219-252 72-112 (113)
112 cd04761 HTH_MerR-SF Helix-Turn 49.9 38 0.00082 22.1 4.2 45 162-211 2-46 (49)
113 PRK03681 hypA hydrogenase nick 49.8 12 0.00026 30.5 2.0 51 201-257 34-91 (114)
114 PF11781 RRN7: RNA polymerase 49.6 14 0.0003 24.6 1.9 26 221-250 10-35 (36)
115 PRK12380 hydrogenase nickel in 48.6 15 0.00033 29.8 2.5 20 219-238 86-105 (113)
116 KOG2703 C4-type Zn-finger prot 48.3 12 0.00026 37.4 2.1 32 219-250 258-297 (460)
117 PF03604 DNA_RNApol_7kD: DNA d 48.3 5 0.00011 26.1 -0.4 26 221-250 2-27 (32)
118 smart00647 IBR In Between Ring 47.8 29 0.00062 24.0 3.5 39 209-250 5-50 (64)
119 PRK13500 transcriptional activ 47.7 4.3 9.2E-05 37.5 -1.0 66 161-254 223-289 (312)
120 PRK03824 hypA hydrogenase nick 46.7 16 0.00034 30.7 2.3 63 172-250 39-117 (135)
121 PF13248 zf-ribbon_3: zinc-rib 46.7 8.8 0.00019 23.4 0.6 23 220-249 3-25 (26)
122 COG0375 HybF Zn finger protein 46.5 18 0.00039 30.1 2.6 18 222-239 89-106 (115)
123 PRK00762 hypA hydrogenase nick 46.1 17 0.00036 30.0 2.4 20 229-249 59-78 (124)
124 COG3677 Transposase and inacti 46.0 27 0.00058 29.2 3.6 43 214-257 25-70 (129)
125 PF13936 HTH_38: Helix-turn-he 45.8 21 0.00045 24.1 2.4 22 161-182 21-42 (44)
126 PF01396 zf-C4_Topoisom: Topoi 45.6 22 0.00047 23.8 2.4 30 220-251 2-35 (39)
127 COG2023 RPR2 RNase P subunit R 45.5 22 0.00048 29.2 2.9 32 220-251 57-93 (105)
128 PRK06556 vitamin B12-dependent 45.0 18 0.0004 39.5 3.0 42 204-250 909-950 (953)
129 PF04606 Ogr_Delta: Ogr/Delta- 44.9 21 0.00046 24.5 2.4 31 221-251 1-38 (47)
130 PF05077 DUF678: Protein of un 44.9 12 0.00026 29.0 1.2 12 238-249 55-66 (74)
131 PRK09678 DNA-binding transcrip 44.3 21 0.00045 27.3 2.4 32 221-253 3-42 (72)
132 cd03031 GRX_GRX_like Glutaredo 44.3 17 0.00037 31.0 2.2 78 145-250 59-143 (147)
133 PF01783 Ribosomal_L32p: Ribos 43.9 14 0.00031 26.5 1.4 8 219-226 26-33 (56)
134 PF07649 C1_3: C1-like domain; 43.2 9.6 0.00021 23.7 0.4 17 242-258 2-20 (30)
135 PRK11827 hypothetical protein; 42.1 14 0.0003 27.5 1.1 34 214-250 3-36 (60)
136 PF09723 Zn-ribbon_8: Zinc rib 42.0 14 0.0003 24.9 1.0 28 221-248 7-34 (42)
137 TIGR00373 conserved hypothetic 41.7 14 0.0003 31.7 1.2 61 120-188 43-104 (158)
138 COG5631 Predicted transcriptio 40.5 25 0.00054 31.5 2.7 71 117-192 53-130 (199)
139 COG0675 Transposase and inacti 39.5 17 0.00037 32.4 1.5 22 220-249 310-331 (364)
140 PF01155 HypA: Hydrogenase exp 39.3 17 0.00036 29.4 1.3 57 173-250 40-96 (113)
141 PF08535 KorB: KorB domain; I 39.0 27 0.00058 26.9 2.4 21 162-182 5-25 (93)
142 PF06107 DUF951: Bacterial pro 38.9 31 0.00067 25.5 2.5 30 223-252 14-43 (57)
143 TIGR00354 polC DNA polymerase, 38.8 16 0.00034 40.2 1.4 29 219-256 625-653 (1095)
144 KOG2768 Translation initiation 38.5 12 0.00026 34.5 0.4 21 14-34 20-40 (231)
145 PF14353 CpXC: CpXC protein 38.3 17 0.00037 29.4 1.2 19 236-254 34-52 (128)
146 PF06044 DRP: Dam-replacing fa 38.3 30 0.00066 32.4 3.0 52 201-252 12-65 (254)
147 COG2093 DNA-directed RNA polym 38.2 15 0.00033 27.7 0.8 11 221-231 20-30 (64)
148 PRK12286 rpmF 50S ribosomal pr 37.3 17 0.00037 26.5 1.0 24 216-247 24-47 (57)
149 TIGR01206 lysW lysine biosynth 37.2 18 0.0004 26.2 1.1 30 220-252 3-34 (54)
150 PF04423 Rad50_zn_hook: Rad50 37.1 21 0.00046 25.0 1.4 20 210-229 7-30 (54)
151 TIGR01391 dnaG DNA primase, ca 37.1 37 0.00081 33.2 3.6 31 220-250 35-65 (415)
152 COG5349 Uncharacterized protei 37.0 11 0.00025 31.8 0.0 23 219-249 21-49 (126)
153 TIGR01031 rpmF_bact ribosomal 36.8 17 0.00038 26.2 0.9 21 219-247 26-46 (55)
154 PF15494 SRCR_2: Scavenger rec 36.7 22 0.00048 27.6 1.6 15 236-250 84-98 (98)
155 PRK06266 transcription initiat 36.3 1E+02 0.0022 27.0 5.8 88 161-250 37-146 (178)
156 smart00497 IENR1 Intron encode 36.0 92 0.002 20.7 4.5 25 159-183 16-40 (53)
157 PHA02942 putative transposase; 35.8 23 0.0005 34.5 1.9 27 220-250 326-352 (383)
158 TIGR01566 ZF_HD_prot_N ZF-HD h 35.5 17 0.00037 26.5 0.7 16 236-251 32-47 (53)
159 PRK05667 dnaG DNA primase; Val 35.2 43 0.00093 34.5 3.8 33 218-250 34-67 (580)
160 PF09332 Mcm10: Mcm10 replicat 35.2 24 0.00052 34.3 1.9 40 218-257 251-302 (344)
161 PRK08332 ribonucleotide-diphos 35.1 41 0.0009 39.2 4.0 42 206-250 1691-1736(1740)
162 COG3741 HutG N-formylglutamate 35.0 6.1 0.00013 37.3 -2.1 64 156-219 63-129 (272)
163 TIGR03831 YgiT_finger YgiT-typ 34.0 41 0.00089 21.9 2.4 9 242-250 34-42 (46)
164 smart00422 HTH_MERR helix_turn 33.6 1.1E+02 0.0023 21.4 4.6 46 162-211 2-47 (70)
165 PHA00626 hypothetical protein 33.0 32 0.00068 25.6 1.8 30 221-250 2-33 (59)
166 PF05379 Peptidase_C23: Carlav 33.0 44 0.00095 26.3 2.7 63 163-234 7-70 (89)
167 PF00641 zf-RanBP: Zn-finger i 32.6 18 0.00038 22.4 0.4 25 221-252 6-30 (30)
168 PF03966 Trm112p: Trm112p-like 32.0 39 0.00085 24.7 2.2 12 217-228 5-16 (68)
169 KOG2907 RNA polymerase I trans 31.9 26 0.00057 29.3 1.3 31 220-250 75-112 (116)
170 PRK00750 lysK lysyl-tRNA synth 31.8 42 0.00091 33.9 3.0 33 219-252 175-211 (510)
171 PRK01310 hypothetical protein; 31.8 1E+02 0.0023 25.0 4.8 40 175-216 55-102 (104)
172 TIGR02609 doc_partner putative 31.7 1.9E+02 0.004 21.6 5.9 58 150-219 3-65 (74)
173 PRK12775 putative trifunctiona 31.7 38 0.00083 37.0 2.9 39 219-257 796-842 (1006)
174 COG1656 Uncharacterized conser 31.6 29 0.00063 30.6 1.7 70 170-249 52-139 (165)
175 PF14599 zinc_ribbon_6: Zinc-r 31.4 21 0.00045 26.5 0.6 13 219-231 48-60 (61)
176 PF12225 MTHFR_C: Methylene-te 31.3 25 0.00054 28.4 1.1 30 229-258 6-40 (97)
177 TIGR01764 excise DNA binding d 31.2 1.3E+02 0.0028 19.1 4.4 47 160-212 1-47 (49)
178 PF01155 HypA: Hydrogenase exp 30.8 48 0.001 26.8 2.7 18 221-238 88-105 (113)
179 PF06573 Churchill: Churchill 30.8 43 0.00093 27.8 2.4 36 214-249 22-67 (112)
180 PF08394 Arc_trans_TRASH: Arch 30.6 52 0.0011 22.2 2.4 28 222-249 1-32 (37)
181 PF13597 NRDD: Anaerobic ribon 30.5 86 0.0019 32.1 5.0 57 183-250 447-514 (546)
182 PF03811 Zn_Tnp_IS1: InsA N-te 30.1 48 0.001 22.0 2.2 28 219-246 5-35 (36)
183 COG0375 HybF Zn finger protein 29.8 36 0.00077 28.4 1.8 55 177-251 43-97 (115)
184 PF04216 FdhE: Protein involve 29.4 43 0.00093 31.0 2.5 36 219-254 211-252 (290)
185 smart00342 HTH_ARAC helix_turn 29.3 77 0.0017 21.9 3.3 28 161-188 51-79 (84)
186 PF14116 YyzF: YyzF-like prote 29.0 72 0.0016 22.6 3.0 40 205-249 3-42 (48)
187 PF05876 Terminase_GpA: Phage 29.0 45 0.00098 34.0 2.8 32 219-250 200-239 (557)
188 COG1545 Predicted nucleic-acid 28.9 29 0.00063 29.2 1.2 15 212-226 22-36 (140)
189 cd01106 HTH_TipAL-Mta Helix-Tu 28.7 1.1E+02 0.0024 23.7 4.4 46 162-211 2-47 (103)
190 PRK10219 DNA-binding transcrip 28.5 69 0.0015 24.6 3.2 27 162-188 23-49 (107)
191 TIGR01051 topA_bact DNA topois 28.0 53 0.0011 33.9 3.1 53 196-250 535-607 (610)
192 KOG3084 NADH pyrophosphatase I 27.8 53 0.0011 32.1 2.8 44 208-254 139-184 (345)
193 cd01279 HTH_HspR-like Helix-Tu 26.5 1.2E+02 0.0026 23.7 4.2 45 162-211 3-47 (98)
194 PRK04023 DNA polymerase II lar 26.4 41 0.00088 37.4 2.0 30 219-257 638-667 (1121)
195 PRK08402 replication factor A; 26.0 44 0.00094 32.5 1.9 48 196-253 196-243 (355)
196 PRK14973 DNA topoisomerase I; 25.7 40 0.00087 36.8 1.8 31 221-251 637-668 (936)
197 PF05315 ICEA: ICEA Protein; 25.6 47 0.001 30.6 2.0 64 171-234 45-116 (230)
198 PF12728 HTH_17: Helix-turn-he 25.6 1.7E+02 0.0038 19.4 4.4 47 161-213 2-48 (51)
199 PF13408 Zn_ribbon_recom: Reco 25.6 70 0.0015 21.7 2.5 31 218-248 4-34 (58)
200 COG1996 RPC10 DNA-directed RNA 25.5 31 0.00067 24.7 0.6 27 221-250 8-34 (49)
201 PRK06393 rpoE DNA-directed RNA 25.3 27 0.00059 26.3 0.4 10 221-230 19-28 (64)
202 PRK14704 anaerobic ribonucleos 25.3 75 0.0016 33.2 3.6 63 185-258 516-600 (618)
203 cd02983 P5_C P5 family, C-term 25.2 83 0.0018 25.8 3.2 42 177-218 71-117 (130)
204 PRK11511 DNA-binding transcrip 24.7 89 0.0019 25.2 3.3 28 161-188 26-53 (127)
205 KOG2422 Uncharacterized conser 24.4 88 0.0019 33.0 3.8 21 116-136 168-188 (665)
206 cd01896 DRG The developmentall 24.3 98 0.0021 27.5 3.8 95 120-228 92-189 (233)
207 PF04770 ZF-HD_dimer: ZF-HD pr 24.2 36 0.00078 25.4 0.8 16 236-251 36-51 (60)
208 PRK12366 replication factor A; 24.1 45 0.00099 34.7 1.8 30 219-253 532-561 (637)
209 COG1497 Predicted transcriptio 24.1 1.6E+02 0.0034 27.8 5.1 72 142-219 12-87 (260)
210 PRK06319 DNA topoisomerase I/S 24.0 1.1E+02 0.0023 33.2 4.5 32 220-251 593-627 (860)
211 PF10083 DUF2321: Uncharacteri 24.0 46 0.001 29.2 1.5 33 219-251 39-79 (158)
212 COG5595 Zn-ribbon-containing, 23.7 34 0.00074 31.5 0.7 80 165-251 155-250 (256)
213 COG5242 TFB4 RNA polymerase II 23.6 1.1E+02 0.0025 28.8 4.1 49 140-192 179-233 (296)
214 PF15288 zf-CCHC_6: Zinc knuck 23.2 39 0.00084 23.3 0.7 10 241-250 2-11 (40)
215 KOG2907 RNA polymerase I trans 23.1 31 0.00066 28.9 0.3 25 229-253 63-87 (116)
216 PRK07220 DNA topoisomerase I; 23.1 58 0.0012 34.5 2.3 29 220-248 636-665 (740)
217 KOG1814 Predicted E3 ubiquitin 23.1 74 0.0016 32.1 2.9 48 199-249 342-395 (445)
218 PF06677 Auto_anti-p27: Sjogre 23.0 88 0.0019 21.4 2.5 34 210-247 8-41 (41)
219 TIGR02827 RNR_anaer_Bdell anae 23.0 95 0.0021 32.3 3.8 45 199-250 502-556 (586)
220 cd01104 HTH_MlrA-CarA Helix-Tu 22.9 2.3E+02 0.0051 19.6 4.9 46 162-212 2-48 (68)
221 PF02591 DUF164: Putative zinc 22.8 51 0.0011 23.2 1.4 23 203-227 32-54 (56)
222 TIGR01562 FdhE formate dehydro 22.7 83 0.0018 30.1 3.1 14 241-254 225-238 (305)
223 PF04502 DUF572: Family of unk 22.6 56 0.0012 31.1 2.0 32 219-250 40-87 (324)
224 PF14446 Prok-RING_1: Prokaryo 22.5 41 0.00088 24.6 0.8 11 219-229 21-31 (54)
225 TIGR03829 YokU_near_AblA uncha 22.5 61 0.0013 25.9 1.9 11 240-250 35-45 (89)
226 cd04476 RPA1_DBD_C RPA1_DBD_C: 22.4 59 0.0013 27.3 1.9 26 219-249 34-60 (166)
227 smart00249 PHD PHD zinc finger 22.3 64 0.0014 20.2 1.7 23 221-249 1-23 (47)
228 PF08209 Sgf11: Sgf11 (transcr 22.1 34 0.00074 22.5 0.3 11 218-228 3-13 (33)
229 PF05451 Phytoreo_Pns: Phytore 22.1 35 0.00075 33.1 0.5 33 226-258 129-161 (344)
230 smart00342 HTH_ARAC helix_turn 21.8 1.3E+02 0.0028 20.7 3.3 27 162-188 3-29 (84)
231 PF11242 DUF2774: Protein of u 21.8 74 0.0016 24.0 2.1 44 161-204 14-57 (63)
232 PF09332 Mcm10: Mcm10 replicat 21.8 25 0.00054 34.2 -0.6 31 216-249 282-312 (344)
233 PRK06599 DNA topoisomerase I; 21.7 97 0.0021 32.4 3.6 30 221-250 587-619 (675)
234 KOG0481 DNA replication licens 21.7 1.9E+02 0.0042 30.5 5.6 132 117-252 24-173 (729)
235 PHA03112 IL-18 binding protein 20.9 78 0.0017 27.3 2.3 33 218-250 19-52 (141)
236 KOG1603 Copper chaperone [Inor 20.9 2.2E+02 0.0047 20.9 4.5 40 175-214 20-61 (73)
237 TIGR02605 CxxC_CxxC_SSSS putat 20.9 52 0.0011 22.5 1.0 8 241-248 27-34 (52)
238 PF09538 FYDLN_acid: Protein o 20.6 39 0.00085 27.6 0.4 29 220-252 10-38 (108)
239 PF14768 RPA_interact_C: Repli 20.6 1.9E+02 0.0042 22.0 4.2 52 197-249 23-79 (82)
240 PHA02893 hypothetical protein; 20.6 40 0.00086 26.9 0.4 10 240-249 69-78 (88)
241 KOG1779 40s ribosomal protein 20.5 55 0.0012 25.9 1.2 28 219-248 34-61 (84)
242 PRK13501 transcriptional activ 20.5 1.1E+02 0.0023 27.6 3.3 66 161-254 193-259 (290)
243 PRK08173 DNA topoisomerase III 20.4 68 0.0015 34.7 2.2 49 196-249 581-649 (862)
244 PRK11788 tetratricopeptide rep 20.2 47 0.001 30.3 0.9 28 206-233 339-382 (389)
245 COG1384 LysS Lysyl-tRNA synthe 20.2 1.5E+02 0.0032 30.7 4.4 76 175-252 106-206 (521)
246 PF11023 DUF2614: Protein of u 20.1 37 0.0008 28.3 0.2 26 219-249 69-94 (114)
No 1
>KOG2768 consensus Translation initiation factor 2, beta subunit (eIF-2beta) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.6e-65 Score=453.21 Aligned_cols=197 Identities=63% Similarity=0.979 Sum_probs=163.7
Q ss_pred cccccCccccccccccccCCCccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccHHHHHHHHHHHH
Q 025050 50 LSVSEGLESTFTGLKKKKKKPVESSLLNDEIGDAGDDLDGHVGEDDEADGSGGPRQRYPWEGSDRDYEYEELLGRVFNIL 129 (258)
Q Consensus 50 ~~~~~~~~~~~~~~KKKKKk~~~~~~~~~e~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~YeeLL~R~~~~L 129 (258)
.+++++++..+.++||||||++..+.++++...+.+..++...++.++ ...++..+|.|++++|.|++||.|+|++|
T Consensus 16 ~~~~~~l~~~~~~kKKKKkk~k~~s~~ee~~~~~~e~~~e~~~~~~e~---~~~~~~~~~~g~e~dy~Y~ElL~rvf~il 92 (231)
T KOG2768|consen 16 DEASERLDFLSLKKKKKKKKSKSLSALEEEDVNAGEFADEDKDPDKEV---RQNQQGVSWVGSEPDYTYYELLSRVFNIL 92 (231)
T ss_pred cchhhcccccccccccccCCCCchhhhHHHHHhccchhhhccChhhcc---ccccccccccccCCCccHHHHHHHHHHHH
Confidence 345556655556666666666544433333222222222111111111 13333499999999999999999999999
Q ss_pred hhcCCCcccccceeecCCCeEEEeCceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHH
Q 025050 130 RENNPELAGDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFE 209 (258)
Q Consensus 130 ~~~nP~~~~~~~R~~mp~pqV~reG~kKTvi~Nf~eI~k~L~R~pehv~kfl~~ELGt~gsid~~~rliikGrf~~k~ie 209 (258)
+++|||++|++.||.|+||||.|+| +||+|+||+|||+.|||+|+||++||++||||+||||+++||||+|+|++++||
T Consensus 93 reknpe~aGe~~k~v~~PPqvlReg-kkT~f~Nf~Dick~mhR~pdHv~~FLlAELgTsGSidg~~rLviKGrfq~kq~e 171 (231)
T KOG2768|consen 93 REKNPELAGEKRKFVMKPPQVLREG-KKTVFVNFADICKTMHRSPDHVMQFLLAELGTSGSIDGQQRLVIKGRFQQKQFE 171 (231)
T ss_pred HhcCchhcccccceeeCCHHHHhhc-cceeeeeHHHHHHHhccChHHHHHHHHHHhccccccCCCceEEEeccccHHHHH
Confidence 9999999999999999999999999 999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHhccccCCCCCCCceeEEcCceEEeeeccccCcc
Q 025050 210 GILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKVKAHI 250 (258)
Q Consensus 210 ~~L~~YI~eYVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~ 250 (258)
++||+||.+||+|.+|+||||.|+++||||||+|..||+++
T Consensus 172 ~VLRrYI~eyV~C~~CkSpdt~L~kenRLfFL~C~~cgs~~ 212 (231)
T KOG2768|consen 172 NVLRRYIKEYVTCKTCKSPDTILQKENRLFFLRCEKCGSRC 212 (231)
T ss_pred HHHHHHHHHheEeeecCChhHHhhhhcceEEEEecCCCCee
Confidence 99999999999999999999999999999999999999984
No 2
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=100.00 E-value=6.2e-54 Score=359.24 Aligned_cols=134 Identities=42% Similarity=0.766 Sum_probs=128.2
Q ss_pred CccHHHHHHHHHHHHhhcCCCcccccceeecCCCeEEEeCceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecCC
Q 025050 115 DYEYEELLGRVFNILRENNPELAGDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQ 194 (258)
Q Consensus 115 ~~~YeeLL~R~~~~L~~~nP~~~~~~~R~~mp~pqV~reG~kKTvi~Nf~eI~k~L~R~pehv~kfl~~ELGt~gsid~~ 194 (258)
+|+|++||+|||+.| |+..++.+||+||+|+|.++| +||+|+||.+||++|||+|+||++||++||||+|+|+ +
T Consensus 4 ~~~Y~~lL~R~~~~l----p~~~~~~~R~~~p~~~v~~eG-~kTvi~Nf~~I~~~L~R~~~hv~ky~~~ELgt~g~i~-~ 77 (138)
T PRK03988 4 YYDYEELLDRAYEKL----PEKVFKESRFEVPKPDVRIEG-NRTIIRNFKEIADRLNRDPKHVAKFLLKELGTAGNIE-G 77 (138)
T ss_pred ccCHHHHHHHHHHHC----ccccCCCcceeCCCCeEEEEc-CcEEEecHHHHHHHHCCCHHHHHHHHHHHhCCceeec-C
Confidence 689999999999999 777778899999999999999 7899999999999999999999999999999999996 5
Q ss_pred ceEEEEeecChHHHHHHHHHHHHhccccCCCCCCCceeEEcCceEEeeeccccCcccccc
Q 025050 195 QRLVVKGRFAPKNFEGILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKVKAHIQSYY 254 (258)
Q Consensus 195 ~rliikGrf~~k~ie~~L~~YI~eYVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~~~~~ 254 (258)
++|||+|+|++++|+++|++||++||+|++|+||||.|++++|+++++|+||||+++.-+
T Consensus 78 ~~lii~G~~~~~~i~~~L~~yI~~yVlC~~C~spdT~l~k~~r~~~l~C~ACGa~~~V~~ 137 (138)
T PRK03988 78 GRLILQGKFSPRVINEKIDRYVKEYVICPECGSPDTKLIKEGRIWVLKCEACGAETPVKP 137 (138)
T ss_pred CEEEEEEeeCHHHHHHHHHHHHHhcEECCCCCCCCcEEEEcCCeEEEEcccCCCCCcCCc
Confidence 899999999999999999999999999999999999999999999999999999998643
No 3
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=100.00 E-value=5.4e-53 Score=351.68 Aligned_cols=131 Identities=35% Similarity=0.687 Sum_probs=125.6
Q ss_pred cHHHHHHHHHHHHhhcCCCcccccceeecCCCeEEEeCceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecCCce
Q 025050 117 EYEELLGRVFNILRENNPELAGDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQR 196 (258)
Q Consensus 117 ~YeeLL~R~~~~L~~~nP~~~~~~~R~~mp~pqV~reG~kKTvi~Nf~eI~k~L~R~pehv~kfl~~ELGt~gsid~~~r 196 (258)
+|++||+|||+.| |+..++.+||+||+|+|.++| +||+|+||.+||++|||+|+||++||++||||+|++++ ++
T Consensus 1 ~Y~~lL~R~~~~l----~~~~~~~~R~~mP~~~v~~eG-~kTvi~Nf~~Ia~~L~R~~~~v~ky~~~ELgt~g~i~~-~r 74 (133)
T TIGR00311 1 DYEKLLERAIDQL----PDEVFETKRFEVPKAYIVIEG-NRTIIQNFREVAKALNRDEQHLLKYLLKELGTAGNLEG-GR 74 (133)
T ss_pred CHHHHHHHHHHHC----ccccCCCccccCCCceEEEEc-CcEEEecHHHHHHHHCCCHHHHHHHHHHHhCCCceecC-CE
Confidence 5999999999999 776677889999999999999 78999999999999999999999999999999999985 69
Q ss_pred EEEEeecChHHHHHHHHHHHHhccccCCCCCCCceeEEcCceEEeeeccccCccccc
Q 025050 197 LVVKGRFAPKNFEGILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKVKAHIQSY 253 (258)
Q Consensus 197 liikGrf~~k~ie~~L~~YI~eYVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~~~~ 253 (258)
|||+|+|++++|+++|++||++||+|++|+||||.|++++|+++++|+||||+++.-
T Consensus 75 lii~G~~~~~~i~~~L~~yI~~yVlC~~C~sPdT~l~k~~r~~~l~C~ACGa~~~v~ 131 (133)
T TIGR00311 75 LILQGKFTHFLLNERIEDYVRKYVICRECNRPDTRIIKEGRVSLLKCEACGAKAPLR 131 (133)
T ss_pred EEEEeecCHHHHHHHHHHHHhheEECCCCCCCCcEEEEeCCeEEEecccCCCCCccC
Confidence 999999999999999999999999999999999999999999999999999999863
No 4
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=100.00 E-value=1.3e-50 Score=356.41 Aligned_cols=131 Identities=40% Similarity=0.801 Sum_probs=126.9
Q ss_pred ccHHHHHHHHHHHHhhcCCCcccccceeecCCCeEEEeCceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecCCc
Q 025050 116 YEYEELLGRVFNILRENNPELAGDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQ 195 (258)
Q Consensus 116 ~~YeeLL~R~~~~L~~~nP~~~~~~~R~~mp~pqV~reG~kKTvi~Nf~eI~k~L~R~pehv~kfl~~ELGt~gsid~~~ 195 (258)
|+|++||+|||+.| |+..++.+||+||+|+|.++| +||+|+||.+||++|||+|+||++||++||||+|+|++ +
T Consensus 1 ~~Y~~lL~r~~~~l----~~~~~~~~R~~~p~~~v~~eG-~kT~i~N~~~i~~~l~R~~~~~~ky~~~ELgt~~~~~~-~ 74 (201)
T PRK12336 1 MDYESLLDRAMEVL----PEPTKSGERFSIPEPKIFIEG-KTTILTNFGEIADALNRDPDHLMKFLQRELGTAGKIEG-G 74 (201)
T ss_pred CCHHHHHHHHHHHC----CcccCCccceecCCceEEEEc-CcEEEecHHHHHHHHCCCHHHHHHHHHHHhCCcceecC-C
Confidence 57999999999999 888888899999999999999 89999999999999999999999999999999999986 5
Q ss_pred eEEEEeecChHHHHHHHHHHHHhccccCCCCCCCceeEEcCceEEeeeccccCcccc
Q 025050 196 RLVVKGRFAPKNFEGILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKVKAHIQS 252 (258)
Q Consensus 196 rliikGrf~~k~ie~~L~~YI~eYVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~~~ 252 (258)
+|||+|+|++++||++|++||++||+|++|+||||.|++++|+++++|.||||+++.
T Consensus 75 ~~ii~G~~~~~~i~~~l~~yi~~yV~C~~C~~pdT~l~k~~~~~~l~C~aCGa~~~v 131 (201)
T PRK12336 75 RAVFNGKFTEEDIQAAIDAYVDEYVICSECGLPDTRLVKEDRVLMLRCDACGAHRPV 131 (201)
T ss_pred EEEEEeeeCHHHHHHHHHHHHHheEECCCCCCCCcEEEEcCCeEEEEcccCCCCccc
Confidence 999999999999999999999999999999999999999999999999999999875
No 5
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=100.00 E-value=8.9e-49 Score=317.10 Aligned_cols=109 Identities=62% Similarity=1.086 Sum_probs=106.7
Q ss_pred ceeecCCCeEEEeCceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHHHHHHhcc
Q 025050 141 RRTVMRPPQVLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILRRYVNEYV 220 (258)
Q Consensus 141 ~R~~mp~pqV~reG~kKTvi~Nf~eI~k~L~R~pehv~kfl~~ELGt~gsid~~~rliikGrf~~k~ie~~L~~YI~eYV 220 (258)
+||+||+|+|.++|++||+|+||.|||++|||+|+||++||++||||+|+||++++|||+|+|++++||++|++||++||
T Consensus 2 ~R~~~p~~~v~~eG~~kTvi~Nf~~I~~~L~R~p~hv~kyl~~ELgt~g~id~~~rlii~G~~~~~~i~~~l~~yI~~yV 81 (110)
T smart00653 2 YRFKMPPPQVLREGKGKTVIVNFADIAKALNRPPDHVLKFLLAELGTQGSIDGKGRLIVNGRFTPKKLQDLLRRYIKEYV 81 (110)
T ss_pred CccccCCCeEEEEcCCeEEEEcHHHHHHHHCCCHHHHHHHHHHHhCCceeECCCCeEEEEEeeCHHHHHHHHHHHHHhcE
Confidence 69999999999999669999999999999999999999999999999999999889999999999999999999999999
Q ss_pred ccCCCCCCCceeEEcCceEEeeeccccCc
Q 025050 221 ICLGCKSPDTILSKENRLFFLRCEKVKAH 249 (258)
Q Consensus 221 lC~~C~sPdT~L~ke~rl~~l~C~aCGa~ 249 (258)
+|++|+||||.|++++|+++++|+||||+
T Consensus 82 lC~~C~spdT~l~k~~r~~~l~C~aCGa~ 110 (110)
T smart00653 82 LCPECGSPDTELIKENRLFFLKCEACGAR 110 (110)
T ss_pred ECCCCCCCCcEEEEeCCeEEEEccccCCC
Confidence 99999999999999999999999999985
No 6
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=100.00 E-value=4e-49 Score=325.31 Aligned_cols=120 Identities=50% Similarity=0.929 Sum_probs=111.8
Q ss_pred hcCCCc-ccccceeecCCCeEEEeCceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHH
Q 025050 131 ENNPEL-AGDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFE 209 (258)
Q Consensus 131 ~~nP~~-~~~~~R~~mp~pqV~reG~kKTvi~Nf~eI~k~L~R~pehv~kfl~~ELGt~gsid~~~rliikGrf~~k~ie 209 (258)
++||+. .++..||+||+|+|.++|++||+|+||.|||++|||+|+||++||++||||+|+||++++|||+|+|++++||
T Consensus 4 ~~np~~~~~~~~R~kmP~~~v~~eG~~KTvi~Nf~dI~~~L~R~p~~~~ky~~~ELgt~~~id~~~~lii~G~~~~~~i~ 83 (125)
T PF01873_consen 4 EKNPERSNSDKFRYKMPPPQVKIEGKKKTVIVNFVDICKALNRDPEHVLKYFGKELGTQGSIDGKGRLIINGRFSSKQIQ 83 (125)
T ss_dssp CSSTTTSCSSSSS-CCCT--EEEETSTEEEETTHHHHHHHHTSSHHHHHHHHHHHSSSEEEEETTTEEEEESSSSCCHHH
T ss_pred HhCcCcccCCCcceecCCCeEEEEccceeeeecHHHHHHHHCCCHHHHHHHHHHHHCCceEECCCCEEEEEEecCHHHHH
Confidence 457984 5565799999999999999999999999999999999999999999999999999988899999999999999
Q ss_pred HHHHHHHHhccccCCCCCCCceeEEcCceEEeeeccccCcc
Q 025050 210 GILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKVKAHI 250 (258)
Q Consensus 210 ~~L~~YI~eYVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~ 250 (258)
++|++||++||+|++|+||||.|++++|+++++|.||||++
T Consensus 84 ~~L~~fI~~yVlC~~C~spdT~l~k~~r~~~l~C~aCGa~~ 124 (125)
T PF01873_consen 84 DLLDKFIKEYVLCPECGSPDTELIKEGRLIFLKCKACGASR 124 (125)
T ss_dssp HHHHHHHCHHSSCTSTSSSSEEEEEETTCCEEEETTTSCEE
T ss_pred HHHHHHHHHEEEcCCCCCCccEEEEcCCEEEEEecccCCcC
Confidence 99999999999999999999999999999999999999986
No 7
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.2e-42 Score=291.10 Aligned_cols=135 Identities=42% Similarity=0.773 Sum_probs=128.4
Q ss_pred CCCccHHHHHHHHHHHHhhcCCCcccccc-eeecCCCeEEEeCceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceee
Q 025050 113 DRDYEYEELLGRVFNILRENNPELAGDRR-RTVMRPPQVLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSL 191 (258)
Q Consensus 113 ~~~~~YeeLL~R~~~~L~~~nP~~~~~~~-R~~mp~pqV~reG~kKTvi~Nf~eI~k~L~R~pehv~kfl~~ELGt~gsi 191 (258)
...+.|++||+|+|..| |+...... ||.||.|.|.++| ++|++.||.+||++|||+|+|+++||.+||||+|++
T Consensus 3 ~~~~~yeelLeR~~~~l----P~~~~~~~~R~~ip~~~i~~~g-~~Ti~~Nf~dia~~l~rDp~h~~k~l~kel~t~g~~ 77 (151)
T COG1601 3 EMEDDYEELLERAYSEL----PEKEVKNDERFRIPEPEINREG-NRTIIRNFGDIAEALNRDPEHLVKFLKKELGTAGSI 77 (151)
T ss_pred hhhhhHHHHHHHHHHhC----CccccccccceecCCcceeccc-chhHHHhHHHHHHHhcCCHHHHHHHHHHHhcccccc
Confidence 34578999999999766 99877655 9999999999999 999999999999999999999999999999999999
Q ss_pred cCCceEEEEeecChHHHHHHHHHHHHhccccCCCCCCCceeEEcCceEEeeeccccCcccc
Q 025050 192 DGQQRLVVKGRFAPKNFEGILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKVKAHIQS 252 (258)
Q Consensus 192 d~~~rliikGrf~~k~ie~~L~~YI~eYVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~~~ 252 (258)
|+.++|||+|+|++++|++.|++||..||.|++|+||||.|++++|+|+|+|.||||.++-
T Consensus 78 d~~~rlvl~g~f~~~~i~~~i~~yi~~yv~C~~c~s~dt~l~~~~R~~~l~c~acGa~~pv 138 (151)
T COG1601 78 DGKGRLVLQGKFSDSEIVNEIERYIAEYVKCKECGSPDTELIKEERLLFLKCEACGAIRPV 138 (151)
T ss_pred CCcceEEEEecccHHHHHHHHHHHHHheeEeccCCCCchhhhhhhhhHhhHHHHhCCcccc
Confidence 9988999999999999999999999999999999999999999999999999999999874
No 8
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=2.3e-33 Score=263.09 Aligned_cols=116 Identities=25% Similarity=0.443 Sum_probs=109.6
Q ss_pred ccccceeecCCCeEEEeCc---eeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecC-CceEEEEeecChHHHHHHH
Q 025050 137 AGDRRRTVMRPPQVLREGT---KKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDG-QQRLVVKGRFAPKNFEGIL 212 (258)
Q Consensus 137 ~~~~~R~~mp~pqV~reG~---kKTvi~Nf~eI~k~L~R~pehv~kfl~~ELGt~gsid~-~~rliikGrf~~k~ie~~L 212 (258)
....|||+||++|++.||+ +||+|+|+.|||++|+|+|-|+++||++|||+|++||. ++|+++||.|.+..||++|
T Consensus 10 ~D~FYRYKMPrl~aKvEGKGNGIKTvIvNm~eIakAL~RPp~Y~tKyFGcELGAQT~fd~kn~ryiVNG~Hd~~KLqdlL 89 (400)
T KOG2767|consen 10 RDPFYRYKMPRLQAKVEGKGNGIKTVIVNMVEIAKALGRPPLYPTKYFGCELGAQTKFDVKNGRYIVNGAHEASKLQDLL 89 (400)
T ss_pred cchhhhhccchhhhhccccCCCeeeeeecHHHHHHHhCCCCCcccccceeeccccccccccCCeeeecccccHHHHHHHH
Confidence 3457999999999999987 99999999999999999999999999999999999994 7999999999999999999
Q ss_pred HHHHHhccccCCCCCCCceeEEc-CceEEeeeccccCcccc
Q 025050 213 RRYVNEYVICLGCKSPDTILSKE-NRLFFLRCEKVKAHIQS 252 (258)
Q Consensus 213 ~~YI~eYVlC~~C~sPdT~L~ke-~rl~~l~C~aCGa~~~~ 252 (258)
+.||++||+|+.|.+|+|.|+.. +..+.+.|.|||.++..
T Consensus 90 dgFIkKFVlC~~C~NPETel~itk~q~i~~~CkACG~r~~~ 130 (400)
T KOG2767|consen 90 DGFIKKFVLCPSCENPETELIITKKQTISLKCKACGFRSDM 130 (400)
T ss_pred HHHHHHheeCcCCCCCceeEEecccchhhhHHHHcCCcccc
Confidence 99999999999999999999975 68889999999998764
No 9
>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=95.33 E-value=0.011 Score=45.07 Aligned_cols=38 Identities=24% Similarity=0.618 Sum_probs=31.6
Q ss_pred HHHHHhccccCCCCCCCceeE-EcCceEEeeeccccCccc
Q 025050 213 RRYVNEYVICLGCKSPDTILS-KENRLFFLRCEKVKAHIQ 251 (258)
Q Consensus 213 ~~YI~eYVlC~~C~sPdT~L~-ke~rl~~l~C~aCGa~~~ 251 (258)
+|||.- ..||.|++.||... +++.+-.+.|-+||.+..
T Consensus 3 krFIAG-a~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~ 41 (71)
T PF09526_consen 3 KRFIAG-AVCPKCQAMDTIMMWRENGVEYVECVECGYTER 41 (71)
T ss_pred ceEecC-ccCCCCcCccEEEEEEeCCceEEEecCCCCeec
Confidence 456655 78999999999886 688899999999998643
No 10
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=95.08 E-value=0.015 Score=43.08 Aligned_cols=38 Identities=26% Similarity=0.614 Sum_probs=31.4
Q ss_pred HHHHHhccccCCCCCCCceeE-EcCceEEeeeccccCccc
Q 025050 213 RRYVNEYVICLGCKSPDTILS-KENRLFFLRCEKVKAHIQ 251 (258)
Q Consensus 213 ~~YI~eYVlC~~C~sPdT~L~-ke~rl~~l~C~aCGa~~~ 251 (258)
+|||.- ..||.|+..||... +++.+-...|-.||.+-.
T Consensus 4 KRFIAG-A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~~ 42 (59)
T TIGR02443 4 KRFIAG-AVCPACSAQDTLAMWKENNIELVECVECGYQEQ 42 (59)
T ss_pred ceEecc-ccCCCCcCccEEEEEEeCCceEEEeccCCCccc
Confidence 456655 78999999999876 689999999999998643
No 11
>PF01253 SUI1: Translation initiation factor SUI1; InterPro: IPR001950 In Saccharomyces cerevisiae (Baker's yeast), SUI1 is a translation initiation factor that functions in concert with eIF-2 and the initiator tRNA-Met in directing the ribosome to the proper start site of translation []. SUI1 is a protein of 108 residues. Close homologs of SUI1 have been found [] in mammals, insects and plants. SUI1 is also evolutionary related to hypothetical proteins from Escherichia coli (yciH), Haemophilus influenzae (HI1225) and Methanococcus vannielii.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2OGH_A 1D1R_A 2IF1_A 2XZN_F 2XZM_F.
Probab=93.49 E-value=0.23 Score=37.97 Aligned_cols=57 Identities=9% Similarity=0.082 Sum_probs=42.7
Q ss_pred eeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeec----CCceEEEEeecChHHHHHHHHHHH
Q 025050 156 KKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLD----GQQRLVVKGRFAPKNFEGILRRYV 216 (258)
Q Consensus 156 kKTvi~Nf~eI~k~L~R~pehv~kfl~~ELGt~gsid----~~~rliikGrf~~k~ie~~L~~YI 216 (258)
.-|++.||. .-.=+++-+++.|...+|++||+. ....+.|+|.|...-.+-++.+|+
T Consensus 19 ~vT~V~gl~----~~~~d~~~lak~lkk~~ac~~sv~~~~~k~~~I~iQGd~~~~i~~~L~~~~~ 79 (83)
T PF01253_consen 19 FVTIVSGLE----LFGIDLKELAKELKKKFACGGSVTKDPGKGEEIQIQGDHRDEIKDLLVEKGG 79 (83)
T ss_dssp EEEEEES------STTSHHHHHHHHHHHHHTS-EEEEE-TTTSSEEEEESS-HHHHHHHHHHHCS
T ss_pred EEEEEECCc----ccccCHHHHHHHHHHhccCceEEeecCCCCCEEEECCcHHHHHHHHHHHhCC
Confidence 668899998 344578999999999999999993 245799999999887777777764
No 12
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=92.75 E-value=0.1 Score=37.22 Aligned_cols=28 Identities=21% Similarity=0.668 Sum_probs=21.8
Q ss_pred ccCCCCCCCceeEEcCce-----EEeeeccccC
Q 025050 221 ICLGCKSPDTILSKENRL-----FFLRCEKVKA 248 (258)
Q Consensus 221 lC~~C~sPdT~L~ke~rl-----~~l~C~aCGa 248 (258)
-||-|+++...+...... +++.|..||+
T Consensus 5 PCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 5 PCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 499997777666654333 8999999999
No 13
>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=90.70 E-value=0.27 Score=32.99 Aligned_cols=30 Identities=17% Similarity=0.448 Sum_probs=21.9
Q ss_pred cccCCCCCCCceeEE-------cCceEEeeeccccCc
Q 025050 220 VICLGCKSPDTILSK-------ENRLFFLRCEKVKAH 249 (258)
Q Consensus 220 VlC~~C~sPdT~L~k-------e~rl~~l~C~aCGa~ 249 (258)
+.||.|++.++...- +.-.+|..|..||.+
T Consensus 1 ~~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~ 37 (39)
T PF01096_consen 1 IKCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHR 37 (39)
T ss_dssp S--SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEE
T ss_pred CCCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCe
Confidence 469999999988873 245889999999975
No 14
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=89.36 E-value=0.51 Score=31.84 Aligned_cols=30 Identities=20% Similarity=0.397 Sum_probs=24.4
Q ss_pred ccCCCCCCCceeEE-------cCceEEeeeccccCcc
Q 025050 221 ICLGCKSPDTILSK-------ENRLFFLRCEKVKAHI 250 (258)
Q Consensus 221 lC~~C~sPdT~L~k-------e~rl~~l~C~aCGa~~ 250 (258)
.||.|++.+..+.. +.-.+|..|..||.+.
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w 38 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRW 38 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEe
Confidence 69999999988753 3458899999999764
No 15
>PRK00939 translation initiation factor Sui1; Reviewed
Probab=89.09 E-value=0.74 Score=37.03 Aligned_cols=56 Identities=16% Similarity=0.221 Sum_probs=42.7
Q ss_pred EeCceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHH
Q 025050 152 REGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILR 213 (258)
Q Consensus 152 reG~kKTvi~Nf~eI~k~L~R~pehv~kfl~~ELGt~gsid~~~rliikGrf~~k~ie~~L~ 213 (258)
+-|+.-|+|.||..- .-++.-+++.|...+|+.|++.+ +.+.|+|.|..... ++|.
T Consensus 34 ~~gK~VTiI~Gl~~~----~~~lk~l~k~lKk~~gcGgsvk~-~~I~iQGD~r~~v~-~~L~ 89 (99)
T PRK00939 34 RYGKEVTIIEGIDPK----DIDLKELAKKLKSKLACGGTVKD-GRIELQGDHRERVK-ELLI 89 (99)
T ss_pred CCCceEEEEeCCCCc----chhHHHHHHHHHHHhCCCceEEC-CEEEEeCcHHHHHH-HHHH
Confidence 445578999999642 12578899999999999999975 47999999876655 4443
No 16
>cd00474 SUI1_eIF1 The SUI1/eIF1 (eukaryotic initiation factor 1) fold is found in eukaryotes, archaea, and some bacteria and is thought to play an important role in accurate initiator codon recognition during translation initiation. This fold, which includes two antiparallel alpha helices packed against the same side of a five-strand beta sheet, is structurally similar to other RNA-binding domains suggesting that SUI1/eIF1 may bind RNA. Point mutations in the yeast eIF1 implicate the protein in maintaining accurate start-site selection but its mechanism of action is unknown.
Probab=88.10 E-value=0.93 Score=34.77 Aligned_cols=54 Identities=13% Similarity=0.092 Sum_probs=42.5
Q ss_pred CceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHH
Q 025050 154 GTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGIL 212 (258)
Q Consensus 154 G~kKTvi~Nf~eI~k~L~R~pehv~kfl~~ELGt~gsid~~~rliikGrf~~k~ie~~L 212 (258)
|+.-|+|.+|..-.. +++-+++.|...+|+.|++.+ +.+.|+|.+.....+-++
T Consensus 12 ~K~VT~I~Gl~~~~~----dlk~l~k~lKk~~~cggtv~~-~~I~lQGD~r~~v~~~L~ 65 (77)
T cd00474 12 GKTVTTVQGLDLEYA----DLKKLAKELKKKCACGGTVKD-EVIELQGDQRKKIKEFLI 65 (77)
T ss_pred CccEEEEECCCCchH----hHHHHHHHHHHHcCCCcEEec-CEEEEeCcHHHHHHHHHH
Confidence 447789999964222 789999999999999999985 599999998776554433
No 17
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=88.08 E-value=0.57 Score=35.27 Aligned_cols=32 Identities=13% Similarity=0.337 Sum_probs=27.0
Q ss_pred ccCCCCCCCceeEEcCceEEeeeccccCcccc
Q 025050 221 ICLGCKSPDTILSKENRLFFLRCEKVKAHIQS 252 (258)
Q Consensus 221 lC~~C~sPdT~L~ke~rl~~l~C~aCGa~~~~ 252 (258)
-||-|+-.+-.+.-.++.|+..|..||+..+-
T Consensus 8 PCPFCG~~~~~v~~~~g~~~v~C~~CgA~~~~ 39 (64)
T PRK09710 8 PCPFCGCPSVTVKAISGYYRAKCNGCESRTGY 39 (64)
T ss_pred CCCCCCCceeEEEecCceEEEEcCCCCcCccc
Confidence 49999998877777788889999999998653
No 18
>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=87.65 E-value=0.52 Score=33.27 Aligned_cols=31 Identities=23% Similarity=0.434 Sum_probs=22.0
Q ss_pred ccCCCCCCCceeEE-----cCceEEeeeccccCcccc
Q 025050 221 ICLGCKSPDTILSK-----ENRLFFLRCEKVKAHIQS 252 (258)
Q Consensus 221 lC~~C~sPdT~L~k-----e~rl~~l~C~aCGa~~~~ 252 (258)
-||-|++-+-.+.. +..-++ .|..||++.+.
T Consensus 3 PCPfCGg~~~~~~~~~~~~~~~~~~-~C~~Cga~~~~ 38 (53)
T TIGR03655 3 PCPFCGGADVYLRRGFDPLDLSHYF-ECSTCGASGPV 38 (53)
T ss_pred CCCCCCCcceeeEeccCCCCCEEEE-ECCCCCCCccc
Confidence 49999997765542 223333 99999999875
No 19
>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=86.50 E-value=0.5 Score=31.94 Aligned_cols=30 Identities=17% Similarity=0.288 Sum_probs=19.4
Q ss_pred ccCCCCCCCceeEEcCceEEeeeccccCcccc
Q 025050 221 ICLGCKSPDTILSKENRLFFLRCEKVKAHIQS 252 (258)
Q Consensus 221 lC~~C~sPdT~L~ke~rl~~l~C~aCGa~~~~ 252 (258)
.||.|++.. ++-+..--.+.|..||..-.-
T Consensus 2 ~Cp~Cg~~~--~~~D~~~g~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 2 KCPNCGSKE--IVFDPERGELVCPNCGLVLEE 31 (43)
T ss_dssp SBTTTSSSE--EEEETTTTEEEETTT-BBEE-
T ss_pred CCcCCcCCc--eEEcCCCCeEECCCCCCEeec
Confidence 599999977 344322236699999986543
No 20
>TIGR01158 SUI1_rel translation initation factor SUI1, putative, prokaryotic. This family of archaeal and bacterial proteins is homologous to the eukaryotic translation intiation factor SUI1 involved in directing the ribosome to the proper start site of translation by functioning in concert with eIF-2 and the initiator tRNA-Met.
Probab=85.86 E-value=1.6 Score=35.10 Aligned_cols=52 Identities=13% Similarity=0.156 Sum_probs=41.4
Q ss_pred EeCceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHH
Q 025050 152 REGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNF 208 (258)
Q Consensus 152 reG~kKTvi~Nf~eI~k~L~R~pehv~kfl~~ELGt~gsid~~~rliikGrf~~k~i 208 (258)
|-|+.-|+|.||..-. -+++-+++.|...+|+.|++. ++.+.|+|.|.....
T Consensus 35 r~gK~VTvV~Gl~~~~----~~l~~l~k~LKk~~gcGgtvk-~~~IeiQGD~~~~v~ 86 (101)
T TIGR01158 35 RKGKGVTIIEGLDLSD----IDLKELAKELKSKCGCGGTVK-DGVIEIQGDHRDRVK 86 (101)
T ss_pred CCCCEEEEEeCCcCch----hhHHHHHHHHHHHhcCCeeEe-CCEEEEeCcHHHHHH
Confidence 4566889999996322 357889999999999999997 459999999876554
No 21
>PHA02998 RNA polymerase subunit; Provisional
Probab=84.85 E-value=0.99 Score=40.38 Aligned_cols=81 Identities=21% Similarity=0.394 Sum_probs=48.5
Q ss_pred hHHHHHHhC---CChHHHHHHHHHhhc-----CceeecCCceEEEEeecChHHHHHHHHHHHHhccccCCCCCCCceeEE
Q 025050 163 FMDLCKTMH---RQPDHVMTFLLAELG-----TSGSLDGQQRLVVKGRFAPKNFEGILRRYVNEYVICLGCKSPDTILSK 234 (258)
Q Consensus 163 f~eI~k~L~---R~pehv~kfl~~ELG-----t~gsid~~~rliikGrf~~k~ie~~L~~YI~eYVlC~~C~sPdT~L~k 234 (258)
..+||..++ --...+++||+.-+- +.-.||.=. .+.-..-=+|+.. +.-|.||.|++.++...-
T Consensus 87 y~~lc~~ir~tng~eke~lry~lfgikcv~~~veydid~~~------d~~y~~yfnvlpk--kt~v~CPkCg~~~A~f~q 158 (195)
T PHA02998 87 YKDLCDMIRGTNGTEKEILRYLLFGIKCIKKGVEYDIDKIP------DVDYDDYFNVLDE--KYNTPCPNCKSKNTTPMM 158 (195)
T ss_pred HHHHHHHHHhcCCchHHHHHHHHHHHHHHhcCCccchhhcc------cccchhheeccCc--ccCCCCCCCCCCceEEEE
Confidence 567887764 346778888886553 333333200 0111111122221 135899999999987643
Q ss_pred -------cCceEEeeeccccCccc
Q 025050 235 -------ENRLFFLRCEKVKAHIQ 251 (258)
Q Consensus 235 -------e~rl~~l~C~aCGa~~~ 251 (258)
|.-..|.+|..||.+..
T Consensus 159 lQTRSADEPmT~FYkC~~CG~~wk 182 (195)
T PHA02998 159 IQTRAADEPPLVRHACRDCKKHFK 182 (195)
T ss_pred EeeccCCCCceEEEEcCCCCCccC
Confidence 34588999999998754
No 22
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=84.48 E-value=0.76 Score=37.53 Aligned_cols=35 Identities=11% Similarity=0.207 Sum_probs=28.1
Q ss_pred HhccccCCCCCCCce---eEEcCceEEeeeccccCccc
Q 025050 217 NEYVICLGCKSPDTI---LSKENRLFFLRCEKVKAHIQ 251 (258)
Q Consensus 217 ~eYVlC~~C~sPdT~---L~ke~rl~~l~C~aCGa~~~ 251 (258)
..+-.||-|+.-.-. +.+...+.++.|..||.+.+
T Consensus 20 ~k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFE 57 (104)
T ss_pred CceEecCccCCeeeeEEEEEecCceeEEEcccCcceEE
Confidence 456799999886544 66778899999999998754
No 23
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=81.95 E-value=0.74 Score=30.46 Aligned_cols=30 Identities=30% Similarity=0.655 Sum_probs=23.1
Q ss_pred ccccCCCCC----CCceeEEcCceEEeeeccccCcc
Q 025050 219 YVICLGCKS----PDTILSKENRLFFLRCEKVKAHI 250 (258)
Q Consensus 219 YVlC~~C~s----PdT~L~ke~rl~~l~C~aCGa~~ 250 (258)
.+.||.|+. |++.|...++ .++|..||+..
T Consensus 2 ~i~CP~C~~~f~v~~~~l~~~~~--~vrC~~C~~~f 35 (37)
T PF13719_consen 2 IITCPNCQTRFRVPDDKLPAGGR--KVRCPKCGHVF 35 (37)
T ss_pred EEECCCCCceEEcCHHHcccCCc--EEECCCCCcEe
Confidence 478999975 5667665555 79999999864
No 24
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=81.80 E-value=0.95 Score=34.36 Aligned_cols=29 Identities=17% Similarity=0.364 Sum_probs=23.7
Q ss_pred ccccCCCCCCCceeEEcCceEEeeeccccCc
Q 025050 219 YVICLGCKSPDTILSKENRLFFLRCEKVKAH 249 (258)
Q Consensus 219 YVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~ 249 (258)
+|.|+.|++--|.+..- -...+|..||..
T Consensus 19 ~VkCpdC~N~q~vFsha--st~V~C~~CG~~ 47 (67)
T COG2051 19 RVKCPDCGNEQVVFSHA--STVVTCLICGTT 47 (67)
T ss_pred EEECCCCCCEEEEeccC--ceEEEecccccE
Confidence 79999999988777664 346899999975
No 25
>TIGR01159 DRP1 density-regulated protein DRP1. This protein family shows weak but suggestive similarity to translation initiation factor SUI1 and its prokaryotic homologs.
Probab=81.22 E-value=3.7 Score=36.24 Aligned_cols=56 Identities=14% Similarity=0.207 Sum_probs=46.4
Q ss_pred eeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeec----CCceEEEEeecChHHHHHHHHHH
Q 025050 156 KKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLD----GQQRLVVKGRFAPKNFEGILRRY 215 (258)
Q Consensus 156 kKTvi~Nf~eI~k~L~R~pehv~kfl~~ELGt~gsid----~~~rliikGrf~~k~ie~~L~~Y 215 (258)
.-|+|.+|... .-++.-+.++|...+++.||+. +++.++|+|.|....++=++.+|
T Consensus 103 ~VT~V~GLe~f----~idlk~laK~lkkkfacG~SV~k~~~~~~eI~IQGD~~~~v~e~L~~~~ 162 (173)
T TIGR01159 103 FVTVIKGLETF----DIDLKKASKTFAQKFATGCSVSKSVTGKEEIVIQGDVMDDIEDYIHEKW 162 (173)
T ss_pred eEEEEeCCcCC----CcCHHHHHHHHHHHhCCCCccccCCCCCCEEEecCCHHHHHHHHHHHHc
Confidence 56899999742 4579999999999999998772 46799999999988887777776
No 26
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=80.71 E-value=0.92 Score=32.01 Aligned_cols=32 Identities=22% Similarity=0.485 Sum_probs=25.0
Q ss_pred ccccCCCC----CCCceeEEcCceEEeeeccccCcc
Q 025050 219 YVICLGCK----SPDTILSKENRLFFLRCEKVKAHI 250 (258)
Q Consensus 219 YVlC~~C~----sPdT~L~ke~rl~~l~C~aCGa~~ 250 (258)
||+|+.|. -|........+..-|+|-+|...-
T Consensus 6 Fv~C~~C~~lLqlP~~~~~~~k~~~klrCGaCs~vl 41 (46)
T PF11331_consen 6 FVVCSSCFELLQLPAKFSLSKKNQQKLRCGACSEVL 41 (46)
T ss_pred EeECccHHHHHcCCCccCCCccceeEEeCCCCceeE
Confidence 89999994 476666666668899999998653
No 27
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=79.90 E-value=1.5 Score=28.98 Aligned_cols=28 Identities=21% Similarity=0.311 Sum_probs=14.9
Q ss_pred ccCCCCCCCceeEE--cCceEEeeeccccCc
Q 025050 221 ICLGCKSPDTILSK--ENRLFFLRCEKVKAH 249 (258)
Q Consensus 221 lC~~C~sPdT~L~k--e~rl~~l~C~aCGa~ 249 (258)
-|+.|++|=+..+- ++| .-+.|.+||..
T Consensus 2 fC~~CG~~l~~~ip~gd~r-~R~vC~~Cg~I 31 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDR-ERLVCPACGFI 31 (34)
T ss_dssp B-TTT--B-EEE--TT-SS--EEEETTTTEE
T ss_pred ccccccChhhhhcCCCCCc-cceECCCCCCE
Confidence 49999999444444 444 47889999963
No 28
>COG0023 SUI1 Translation initiation factor 1 (eIF-1/SUI1) and related proteins [Translation, ribosomal structure and biogenesis]
Probab=79.86 E-value=5.1 Score=32.77 Aligned_cols=60 Identities=13% Similarity=0.176 Sum_probs=47.5
Q ss_pred eEEEeCceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHH
Q 025050 149 QVLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILR 213 (258)
Q Consensus 149 qV~reG~kKTvi~Nf~eI~k~L~R~pehv~kfl~~ELGt~gsid~~~rliikGrf~~k~ie~~L~ 213 (258)
+-.|-|+.-|+|.+|.. -.-+++-|++.|-+.+|+.|++-.+ ...|+|-|..+..+=++.
T Consensus 34 e~rr~gK~VTiI~Gld~----~~~dlk~Lak~LKk~cacGGtvk~~-~IeiQGdhr~~v~~~L~~ 93 (104)
T COG0023 34 ETRRKGKTVTIIEGLDL----KDIDLKKLAKELKKKCACGGTVKDG-EIEIQGDHRDKVKELLIK 93 (104)
T ss_pred EeecCCcEEEEEeCccc----chhhHHHHHHHHHHHcCCCceecCC-EEEEeChHHHHHHHHHHH
Confidence 33466778899999986 3346788999999999999999754 999999998876665543
No 29
>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=79.64 E-value=0.58 Score=50.03 Aligned_cols=29 Identities=31% Similarity=0.844 Sum_probs=0.0
Q ss_pred cccCCCCCCCceeEEcCceEEeeeccccCccccccccc
Q 025050 220 VICLGCKSPDTILSKENRLFFLRCEKVKAHIQSYYLCP 257 (258)
Q Consensus 220 VlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~~~~~~~~ 257 (258)
-.|+.|+.+ .++.+|..||+.+..+|.||
T Consensus 656 r~Cp~Cg~~---------t~~~~Cp~CG~~T~~~~~Cp 684 (900)
T PF03833_consen 656 RRCPKCGKE---------TFYNRCPECGSHTEPVYVCP 684 (900)
T ss_dssp --------------------------------------
T ss_pred ccCcccCCc---------chhhcCcccCCccccceecc
Confidence 479999865 57889999999999999998
No 30
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=78.66 E-value=1.5 Score=35.50 Aligned_cols=34 Identities=9% Similarity=0.243 Sum_probs=24.9
Q ss_pred HhccccCCCCCCCceeEEcCceEEeeeccccCcc
Q 025050 217 NEYVICLGCKSPDTILSKENRLFFLRCEKVKAHI 250 (258)
Q Consensus 217 ~eYVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~ 250 (258)
..++.||.|+++--.+.++.....+.|..||...
T Consensus 19 pt~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~ 52 (99)
T PRK14892 19 PKIFECPRCGKVSISVKIKKNIAIITCGNCGLYT 52 (99)
T ss_pred CcEeECCCCCCeEeeeecCCCcceEECCCCCCcc
Confidence 3679999999753333345567799999999754
No 31
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=78.48 E-value=2 Score=33.25 Aligned_cols=36 Identities=17% Similarity=0.315 Sum_probs=21.6
Q ss_pred HhccccCCCCCCCceeEE---cCceEEeeeccccCcccc
Q 025050 217 NEYVICLGCKSPDTILSK---ENRLFFLRCEKVKAHIQS 252 (258)
Q Consensus 217 ~eYVlC~~C~sPdT~L~k---e~rl~~l~C~aCGa~~~~ 252 (258)
..+-.||-|+...|.-++ +.++-.+.|..||...+.
T Consensus 20 ~~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~ 58 (81)
T PF05129_consen 20 PKVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQT 58 (81)
T ss_dssp SS----TTT--SS-EEEEEETTTTEEEEEESSS--EEEE
T ss_pred CceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEE
Confidence 356689999999888775 467999999999987653
No 32
>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=77.68 E-value=2.4 Score=36.20 Aligned_cols=55 Identities=22% Similarity=0.349 Sum_probs=36.8
Q ss_pred eEEEEeecChHHHHHHHHHHHHhc-------------------cccCCCCCCCceeEEc-Cc---eEEeeeccccCcc
Q 025050 196 RLVVKGRFAPKNFEGILRRYVNEY-------------------VICLGCKSPDTILSKE-NR---LFFLRCEKVKAHI 250 (258)
Q Consensus 196 rliikGrf~~k~ie~~L~~YI~eY-------------------VlC~~C~sPdT~L~ke-~r---l~~l~C~aCGa~~ 250 (258)
++.+.=..++.-|-.-=|+-+.+| |.||.|+|.+|.++-. +. --..+|.+|...+
T Consensus 63 ~i~~~p~Wt~d~it~~gr~~l~~~giapp~~~~~~~~~~~~~~~~cp~c~s~~t~~~s~fg~t~cka~~~c~~c~epf 140 (146)
T TIGR02159 63 STSLDPPWTTDWITEDAREKLREYGIAPPAGHYVVGVSPEPPSVQCPRCGSADTTITSIFGPTACKALYRCRACKEPF 140 (146)
T ss_pred eEeeCCCCChHHCCHHHHHHHHhcCccCCCccCCCcccCCCCCCcCCCCCCCCcEeecCCCChhhHHHhhhhhhCCcH
Confidence 445555555566655555555555 8999999999999975 21 1245899997654
No 33
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=76.98 E-value=1.9 Score=31.96 Aligned_cols=29 Identities=21% Similarity=0.468 Sum_probs=24.3
Q ss_pred ccccCCCCCCCceeEEcCceEEeeeccccCc
Q 025050 219 YVICLGCKSPDTILSKENRLFFLRCEKVKAH 249 (258)
Q Consensus 219 YVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~ 249 (258)
.|.|+.|.+.-|.+..-.. .+.|..||..
T Consensus 11 ~VkCp~C~n~q~vFsha~t--~V~C~~Cg~~ 39 (59)
T PRK00415 11 KVKCPDCGNEQVVFSHAST--VVRCLVCGKT 39 (59)
T ss_pred EEECCCCCCeEEEEecCCc--EEECcccCCC
Confidence 5999999999988887643 6899999975
No 34
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=76.67 E-value=2.8 Score=29.22 Aligned_cols=27 Identities=22% Similarity=0.372 Sum_probs=23.1
Q ss_pred ehHHHHHHhCCChHHHHHHHHHhhcCc
Q 025050 162 NFMDLCKTMHRQPDHVMTFLLAELGTS 188 (258)
Q Consensus 162 Nf~eI~k~L~R~pehv~kfl~~ELGt~ 188 (258)
.+.|+|+.|+.++..|++.|..++|..
T Consensus 5 ~V~elAk~l~v~~~~ii~~l~~~~Gi~ 31 (54)
T PF04760_consen 5 RVSELAKELGVPSKEIIKKLFKELGIM 31 (54)
T ss_dssp -TTHHHHHHSSSHHHHHHHH-HHHTS-
T ss_pred EHHHHHHHHCcCHHHHHHHHHHhCCcC
Confidence 467999999999999999999999998
No 35
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=76.44 E-value=1.3 Score=31.37 Aligned_cols=31 Identities=16% Similarity=0.180 Sum_probs=23.7
Q ss_pred cccCCCCCCCceeEEcCceE-EeeeccccCcc
Q 025050 220 VICLGCKSPDTILSKENRLF-FLRCEKVKAHI 250 (258)
Q Consensus 220 VlC~~C~sPdT~L~ke~rl~-~l~C~aCGa~~ 250 (258)
..|..|+..+|.+-+.+..- .+-|+|||-..
T Consensus 4 ~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~ 35 (52)
T smart00401 4 RSCSNCGTTETPLWRRGPSGNKTLCNACGLYY 35 (52)
T ss_pred CCcCCCCCCCCCccccCCCCCCcEeecccHHH
Confidence 46999999999998864322 47899999643
No 36
>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=76.35 E-value=2.2 Score=32.59 Aligned_cols=33 Identities=21% Similarity=0.542 Sum_probs=21.1
Q ss_pred cccCCCCCCCceeEEcCceEEeeeccccCccccccccc
Q 025050 220 VICLGCKSPDTILSKENRLFFLRCEKVKAHIQSYYLCP 257 (258)
Q Consensus 220 VlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~~~~~~~~ 257 (258)
.+||.|..| |...++ ..+|.+|+.....--+||
T Consensus 2 ~~CP~C~~~---L~~~~~--~~~C~~C~~~~~~~a~CP 34 (70)
T PF07191_consen 2 NTCPKCQQE---LEWQGG--HYHCEACQKDYKKEAFCP 34 (70)
T ss_dssp -B-SSS-SB---EEEETT--EEEETTT--EEEEEEE-T
T ss_pred CcCCCCCCc---cEEeCC--EEECccccccceecccCC
Confidence 479999988 777664 457999998887777787
No 37
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=76.02 E-value=2.4 Score=33.81 Aligned_cols=41 Identities=17% Similarity=0.374 Sum_probs=26.0
Q ss_pred HHHHHHHHHHHHhccccCCCCCCCceeEEcCceEEeeeccccCcc
Q 025050 206 KNFEGILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKVKAHI 250 (258)
Q Consensus 206 k~ie~~L~~YI~eYVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~ 250 (258)
..+..+.-.-...| .||.|+++ |.-..-.++| +|..||+..
T Consensus 23 rrv~~ie~~~~~~~-~Cp~C~~~-~VkR~a~GIW--~C~kCg~~f 63 (89)
T COG1997 23 RRVKEIEAQQRAKH-VCPFCGRT-TVKRIATGIW--KCRKCGAKF 63 (89)
T ss_pred HHHHHHHHHHhcCC-cCCCCCCc-ceeeeccCeE--EcCCCCCee
Confidence 33444444434444 69999999 4444456765 799999865
No 38
>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=75.79 E-value=2.6 Score=28.82 Aligned_cols=28 Identities=18% Similarity=0.369 Sum_probs=20.0
Q ss_pred cccCCCCCCCceeEEcCceEEeeeccccCc
Q 025050 220 VICLGCKSPDTILSKENRLFFLRCEKVKAH 249 (258)
Q Consensus 220 VlC~~C~sPdT~L~ke~rl~~l~C~aCGa~ 249 (258)
+.||.|++. ......+ ....+|.+|+..
T Consensus 19 ~~CP~Cg~~-~~~~~~~-~~~~~C~~C~~q 46 (46)
T PF12760_consen 19 FVCPHCGST-KHYRLKT-RGRYRCKACRKQ 46 (46)
T ss_pred CCCCCCCCe-eeEEeCC-CCeEECCCCCCc
Confidence 559999998 4444444 446799999863
No 39
>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=75.55 E-value=1.9 Score=39.90 Aligned_cols=31 Identities=19% Similarity=0.321 Sum_probs=16.5
Q ss_pred cccCCCCCC-CceeEEc-C--ceEEeeeccccCcc
Q 025050 220 VICLGCKSP-DTILSKE-N--RLFFLRCEKVKAHI 250 (258)
Q Consensus 220 VlC~~C~sP-dT~L~ke-~--rl~~l~C~aCGa~~ 250 (258)
-.||.|+|+ .-..++. . +.-+|+|.-||..-
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W 207 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEW 207 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EE
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCee
Confidence 589999996 4444443 3 56899999999764
No 40
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=74.99 E-value=9.1 Score=24.49 Aligned_cols=46 Identities=11% Similarity=0.142 Sum_probs=33.8
Q ss_pred ehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHH
Q 025050 162 NFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGIL 212 (258)
Q Consensus 162 Nf~eI~k~L~R~pehv~kfl~~ELGt~gsid~~~rliikGrf~~k~ie~~L 212 (258)
+..++|+.|+.++.+|.+|+........... +++. +|+..+|..++
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~g~~~~~~~~-~~~~----~~~~~ei~~~~ 47 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKEGKLKAIRTP-GGHR----RFPEEDLERLL 47 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcCCCCceeCC-CCce----ecCHHHHHHHH
Confidence 5789999999999999999988665443322 2333 37888887765
No 41
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=74.95 E-value=3.3 Score=27.63 Aligned_cols=28 Identities=11% Similarity=0.138 Sum_probs=20.1
Q ss_pred ccCCCCCCCceeEEcCceEEeeeccccCc
Q 025050 221 ICLGCKSPDTILSKENRLFFLRCEKVKAH 249 (258)
Q Consensus 221 lC~~C~sPdT~L~ke~rl~~l~C~aCGa~ 249 (258)
.||.|+.+ -....-..+..-.|.+||..
T Consensus 1 ~CP~C~~~-l~~~~~~~~~id~C~~C~G~ 28 (41)
T PF13453_consen 1 KCPRCGTE-LEPVRLGDVEIDVCPSCGGI 28 (41)
T ss_pred CcCCCCcc-cceEEECCEEEEECCCCCeE
Confidence 49999984 22233356889999999964
No 42
>PRK05580 primosome assembly protein PriA; Validated
Probab=74.23 E-value=2 Score=44.61 Aligned_cols=37 Identities=27% Similarity=0.555 Sum_probs=25.3
Q ss_pred ccccCCCCCC------CceeE--EcCceEEeeeccccCccccccccc
Q 025050 219 YVICLGCKSP------DTILS--KENRLFFLRCEKVKAHIQSYYLCP 257 (258)
Q Consensus 219 YVlC~~C~sP------dT~L~--ke~rl~~l~C~aCGa~~~~~~~~~ 257 (258)
||.|..|+.. +..|+ +..+ .+.|.-||.+.+.-..||
T Consensus 381 ~~~C~~Cg~~~~C~~C~~~l~~h~~~~--~l~Ch~Cg~~~~~~~~Cp 425 (679)
T PRK05580 381 FLLCRDCGWVAECPHCDASLTLHRFQR--RLRCHHCGYQEPIPKACP 425 (679)
T ss_pred ceEhhhCcCccCCCCCCCceeEECCCC--eEECCCCcCCCCCCCCCC
Confidence 5666666543 23344 3333 689999999998888898
No 43
>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=73.90 E-value=2.3 Score=42.68 Aligned_cols=18 Identities=28% Similarity=0.390 Sum_probs=16.6
Q ss_pred EeeeccccCccccccccc
Q 025050 240 FLRCEKVKAHIQSYYLCP 257 (258)
Q Consensus 240 ~l~C~aCGa~~~~~~~~~ 257 (258)
.|+|.-||.+.+.-..||
T Consensus 240 ~l~Ch~Cg~~~~~~~~Cp 257 (505)
T TIGR00595 240 KLRCHYCGYQEPIPKTCP 257 (505)
T ss_pred eEEcCCCcCcCCCCCCCC
Confidence 689999999999999998
No 44
>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=73.53 E-value=4 Score=34.73 Aligned_cols=22 Identities=5% Similarity=0.211 Sum_probs=20.0
Q ss_pred EehHHHHHHhCCChHHHHHHHH
Q 025050 161 VNFMDLCKTMHRQPDHVMTFLL 182 (258)
Q Consensus 161 ~Nf~eI~k~L~R~pehv~kfl~ 182 (258)
.|+.+|++++.-++++|.+||-
T Consensus 47 ati~eV~e~tgVs~~~I~~~Ir 68 (137)
T TIGR03826 47 ATVSEIVEETGVSEKLILKFIR 68 (137)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 5789999999999999999985
No 45
>PRK00420 hypothetical protein; Validated
Probab=72.41 E-value=2.3 Score=35.16 Aligned_cols=27 Identities=22% Similarity=0.266 Sum_probs=21.0
Q ss_pred ccccCCCCCCCceeEEcCceEEeeeccccCc
Q 025050 219 YVICLGCKSPDTILSKENRLFFLRCEKVKAH 249 (258)
Q Consensus 219 YVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~ 249 (258)
--.||.|++|=+.+ +++. ..|.+||..
T Consensus 23 ~~~CP~Cg~pLf~l-k~g~---~~Cp~Cg~~ 49 (112)
T PRK00420 23 SKHCPVCGLPLFEL-KDGE---VVCPVHGKV 49 (112)
T ss_pred cCCCCCCCCcceec-CCCc---eECCCCCCe
Confidence 35899999998887 5554 579999973
No 46
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=72.22 E-value=2.5 Score=31.89 Aligned_cols=31 Identities=13% Similarity=0.373 Sum_probs=23.7
Q ss_pred cccCCCCCCCceeEE----cCceEEeeeccccCcc
Q 025050 220 VICLGCKSPDTILSK----ENRLFFLRCEKVKAHI 250 (258)
Q Consensus 220 VlC~~C~sPdT~L~k----e~rl~~l~C~aCGa~~ 250 (258)
-+|..|+...+..+. +.++.+++|..|.+..
T Consensus 5 FTC~~C~~Rs~~~~sk~aY~~GvViv~C~gC~~~H 39 (66)
T PF05180_consen 5 FTCNKCGTRSAKMFSKQAYHKGVVIVQCPGCKNRH 39 (66)
T ss_dssp EEETTTTEEEEEEEEHHHHHTSEEEEE-TTS--EE
T ss_pred EEcCCCCCccceeeCHHHHhCCeEEEECCCCccee
Confidence 479999998888876 3799999999999764
No 47
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=72.06 E-value=0.93 Score=32.56 Aligned_cols=33 Identities=15% Similarity=0.137 Sum_probs=25.1
Q ss_pred ccCCCCCCCceeEEcCc-eEEeeeccccCccccc
Q 025050 221 ICLGCKSPDTILSKENR-LFFLRCEKVKAHIQSY 253 (258)
Q Consensus 221 lC~~C~sPdT~L~ke~r-l~~l~C~aCGa~~~~~ 253 (258)
.|..|+..+|-+-+.+. --..-|+|||-....|
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k~ 34 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKKH 34 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHhc
Confidence 59999999999988642 3356899999765443
No 48
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=71.52 E-value=4.1 Score=43.15 Aligned_cols=41 Identities=20% Similarity=0.301 Sum_probs=29.7
Q ss_pred hHHHHHHHHHHHHhc----------------------cccCCCCCCCceeEEcCceEEeeeccccCcc
Q 025050 205 PKNFEGILRRYVNEY----------------------VICLGCKSPDTILSKENRLFFLRCEKVKAHI 250 (258)
Q Consensus 205 ~k~ie~~L~~YI~eY----------------------VlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~ 250 (258)
+.+|-.+|.+|+..- ..||.|++ | |+.+.+ ...|.+||.+.
T Consensus 688 pDaI~kaL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~Cg~--~-l~~~~G--C~~C~~CG~sk 750 (752)
T PRK08665 688 PDAIAKVLEKHYLGGGKDVGAGNGTGSAGIEAPAPERGACPECGS--I-LEHEEG--CVVCHSCGYSK 750 (752)
T ss_pred HHHHHHHHHHHHHhccccccccccccccccccccCCCCCCCCCCc--c-cEECCC--CCcCCCCCCCC
Confidence 668888888876640 35999984 3 666656 45999999764
No 49
>PF01921 tRNA-synt_1f: tRNA synthetases class I (K); InterPro: IPR002904 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. Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and in a number of bacterial groups that include the alphaproteobacteria and spirochaetes[]. A refined crystal structures shows that the active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [].; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IRX_A.
Probab=70.99 E-value=5.5 Score=38.88 Aligned_cols=38 Identities=24% Similarity=0.355 Sum_probs=21.0
Q ss_pred HHHhccccCCCCCCCcee-EE-c--CceEEeeeccccCcccc
Q 025050 215 YVNEYVICLGCKSPDTIL-SK-E--NRLFFLRCEKVKAHIQS 252 (258)
Q Consensus 215 YI~eYVlC~~C~sPdT~L-~k-e--~rl~~l~C~aCGa~~~~ 252 (258)
|+==.++|+.|+..+|.= +. + +..+.-+|..||.+...
T Consensus 170 y~Pf~piC~~cGri~tt~v~~~d~~~~~v~Y~c~~cG~~g~~ 211 (360)
T PF01921_consen 170 YSPFLPICEKCGRIDTTEVTEYDPEGGTVTYRCEECGHEGEV 211 (360)
T ss_dssp --SEEEEETTTEE--EEEEEEE--SSSEEEEE--TTS---EE
T ss_pred eeeeeeeccccCCcccceeeEeecCCCEEEEEecCCCCEEEE
Confidence 333469999999976544 33 3 67888999999987643
No 50
>TIGR01160 SUI1_MOF2 translation initiation factor SUI1, eukaryotic. Alternate name: MOF2. A similar protein family (see TIGRFAMs model TIGR01158) is found in prokaryotes. The human proteins complements a yeast SUI1 mutatation.
Probab=70.18 E-value=4.7 Score=33.21 Aligned_cols=60 Identities=13% Similarity=0.165 Sum_probs=44.3
Q ss_pred EEeC-ceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecC----CceEEEEeecChHHHHHHHHHH
Q 025050 151 LREG-TKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDG----QQRLVVKGRFAPKNFEGILRRY 215 (258)
Q Consensus 151 ~reG-~kKTvi~Nf~eI~k~L~R~pehv~kfl~~ELGt~gsid~----~~rliikGrf~~k~ie~~L~~Y 215 (258)
.|-| +.-|+|.+|.+ .=+-.-+++.|.+.+|+.|++-. ++.+.|+|-|..+..+-+....
T Consensus 34 qR~grK~VTiI~Gl~~-----~~dlk~l~K~lKkk~~cGGsVk~~~~~~~~IelQGD~re~v~~~L~~~g 98 (110)
T TIGR01160 34 QRNGRKTLTTVQGLPK-----EYDLKKIVKALKKEFACNGTVIEDPEMGEVIQLQGDQRKNVCEFLISQG 98 (110)
T ss_pred EccCCccEEEEeccCC-----hHHHHHHHHHHHHHhCCCceEEeCCCCCCEEEEeCcHHHHHHHHHHHcC
Confidence 3445 36688888873 23456789999999999999953 3578999999887766666554
No 51
>PRK04023 DNA polymerase II large subunit; Validated
Probab=70.17 E-value=2.1 Score=46.74 Aligned_cols=29 Identities=31% Similarity=0.771 Sum_probs=22.7
Q ss_pred cccCCCCCCCceeEEcCceEEeeeccccCccccccccc
Q 025050 220 VICLGCKSPDTILSKENRLFFLRCEKVKAHIQSYYLCP 257 (258)
Q Consensus 220 VlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~~~~~~~~ 257 (258)
-.|+.|+.. .+..+|..||+.....|.||
T Consensus 627 RfCpsCG~~---------t~~frCP~CG~~Te~i~fCP 655 (1121)
T PRK04023 627 RKCPSCGKE---------TFYRRCPFCGTHTEPVYRCP 655 (1121)
T ss_pred ccCCCCCCc---------CCcccCCCCCCCCCcceeCc
Confidence 379999877 25678888888888888887
No 52
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=69.52 E-value=0.93 Score=34.05 Aligned_cols=39 Identities=26% Similarity=0.679 Sum_probs=32.0
Q ss_pred HHHHHhccccCCCCCCCcee-EEcCceEEeeeccccCcccc
Q 025050 213 RRYVNEYVICLGCKSPDTIL-SKENRLFFLRCEKVKAHIQS 252 (258)
Q Consensus 213 ~~YI~eYVlC~~C~sPdT~L-~ke~rl~~l~C~aCGa~~~~ 252 (258)
.|||.- -.||.|..-||.- -+++.+-...|-+||...++
T Consensus 5 KRFIAG-A~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~~~ 44 (66)
T COG3529 5 KRFIAG-AVCPACQAQDTLAMWRENNVEIVECVKCGHHMRE 44 (66)
T ss_pred hhhhcc-CCCcccchhhHHHHHHhcCCceEehhhcchHhhh
Confidence 567776 5699999999965 47899999999999987543
No 53
>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=69.30 E-value=6.2 Score=30.92 Aligned_cols=35 Identities=23% Similarity=0.374 Sum_probs=27.2
Q ss_pred ccccCCCCCCCceeEE-------cCceEEeeeccccCccccc
Q 025050 219 YVICLGCKSPDTILSK-------ENRLFFLRCEKVKAHIQSY 253 (258)
Q Consensus 219 YVlC~~C~sPdT~L~k-------e~rl~~l~C~aCGa~~~~~ 253 (258)
.+.|+.|++.+..+.- +.-.+|-.|..||.+-.-|
T Consensus 62 ~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~~~ 103 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWREY 103 (104)
T ss_pred cCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeEeC
Confidence 5899999999976652 3467899999999875543
No 54
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=68.96 E-value=3.8 Score=43.34 Aligned_cols=39 Identities=23% Similarity=0.363 Sum_probs=28.3
Q ss_pred ccccCCCCCC------CceeEEcCceEEeeeccccCccccccccc
Q 025050 219 YVICLGCKSP------DTILSKENRLFFLRCEKVKAHIQSYYLCP 257 (258)
Q Consensus 219 YVlC~~C~sP------dT~L~ke~rl~~l~C~aCGa~~~~~~~~~ 257 (258)
+|+|+.|+.. |..|+-...--.|+|.-||+....-.-||
T Consensus 435 ~l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp 479 (730)
T COG1198 435 LLLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCP 479 (730)
T ss_pred eeecccCCCcccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCC
Confidence 7888888753 33444433334789999999998888898
No 55
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=68.02 E-value=2.6 Score=27.81 Aligned_cols=30 Identities=23% Similarity=0.572 Sum_probs=20.5
Q ss_pred ccccCCCCC----CCceeEEcCceEEeeeccccCcc
Q 025050 219 YVICLGCKS----PDTILSKENRLFFLRCEKVKAHI 250 (258)
Q Consensus 219 YVlC~~C~s----PdT~L~ke~rl~~l~C~aCGa~~ 250 (258)
.|.|+.|+. ||..|--.++ .++|..||...
T Consensus 2 ~i~Cp~C~~~y~i~d~~ip~~g~--~v~C~~C~~~f 35 (36)
T PF13717_consen 2 IITCPNCQAKYEIDDEKIPPKGR--KVRCSKCGHVF 35 (36)
T ss_pred EEECCCCCCEEeCCHHHCCCCCc--EEECCCCCCEe
Confidence 478999975 3444433333 89999999864
No 56
>PRK03954 ribonuclease P protein component 4; Validated
Probab=67.60 E-value=4.9 Score=33.62 Aligned_cols=32 Identities=16% Similarity=0.342 Sum_probs=20.8
Q ss_pred cccCCCCCC-----CceeEEc-Cc--eEEeeeccccCccc
Q 025050 220 VICLGCKSP-----DTILSKE-NR--LFFLRCEKVKAHIQ 251 (258)
Q Consensus 220 VlC~~C~sP-----dT~L~ke-~r--l~~l~C~aCGa~~~ 251 (258)
-+|..|.++ ...+... ++ .+.+.|..||..+-
T Consensus 65 ~~CK~C~t~LiPG~n~~vRi~~~~~~~vvitCl~CG~~kR 104 (121)
T PRK03954 65 RYCKRCHSFLVPGVNARVRLRQKRMPHVVITCLECGHIMR 104 (121)
T ss_pred HHhhcCCCeeecCCceEEEEecCCcceEEEECccCCCEEe
Confidence 468888776 3333323 32 46889999998753
No 57
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=67.57 E-value=2.6 Score=47.01 Aligned_cols=30 Identities=27% Similarity=0.709 Sum_probs=19.5
Q ss_pred ccccCCCCCCCceeEEcCceEEeeeccccCccccccccc
Q 025050 219 YVICLGCKSPDTILSKENRLFFLRCEKVKAHIQSYYLCP 257 (258)
Q Consensus 219 YVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~~~~~~~~ 257 (258)
...||.|+.+- +...|..||++....|.||
T Consensus 667 ~rkCPkCG~~t---------~~~fCP~CGs~te~vy~CP 696 (1337)
T PRK14714 667 RRRCPSCGTET---------YENRCPDCGTHTEPVYVCP 696 (1337)
T ss_pred EEECCCCCCcc---------ccccCcccCCcCCCceeCc
Confidence 46788888752 1226777777766666666
No 58
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=67.48 E-value=4.1 Score=38.95 Aligned_cols=31 Identities=19% Similarity=0.412 Sum_probs=21.9
Q ss_pred ccccCCCCCCC-ceeEE---cCceEEeeeccccCc
Q 025050 219 YVICLGCKSPD-TILSK---ENRLFFLRCEKVKAH 249 (258)
Q Consensus 219 YVlC~~C~sPd-T~L~k---e~rl~~l~C~aCGa~ 249 (258)
--.||.|+|+= ..+++ .++.-+|+|.-||..
T Consensus 187 ~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~te 221 (309)
T PRK03564 187 RQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESE 221 (309)
T ss_pred CCCCCCCCCcchhheeeccCCCCceEEEcCCCCCc
Confidence 37899999964 44443 356778888888764
No 59
>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=67.00 E-value=5.5 Score=32.46 Aligned_cols=51 Identities=12% Similarity=0.278 Sum_probs=28.6
Q ss_pred ChHHHHHHHHHhhcCceeecCCceEEEEe-----------e-cChHHHHHHHHHHHHhccccCCCCCCCceeEEc
Q 025050 173 QPDHVMTFLLAELGTSGSLDGQQRLVVKG-----------R-FAPKNFEGILRRYVNEYVICLGCKSPDTILSKE 235 (258)
Q Consensus 173 ~pehv~kfl~~ELGt~gsid~~~rliikG-----------r-f~~k~ie~~L~~YI~eYVlC~~C~sPdT~L~ke 235 (258)
+|+.|.-.| . +-+.|++-.+-+|.|.= . |.... .+..||.|+|+++.++.-
T Consensus 40 ~p~~L~faf-~-~~~~~t~~ega~L~I~~~p~~~~C~~Cg~~~~~~~----------~~~~CP~Cgs~~~~i~~G 102 (115)
T TIGR00100 40 NPSQLQFAF-E-VVREGTVAEGAKLNIEDEPVECECEDCSEEVSPEI----------DLYRCPKCHGIMLQVRAG 102 (115)
T ss_pred CHHHHHHHH-H-HHhCCCccCCCEEEEEeeCcEEEcccCCCEEecCC----------cCccCcCCcCCCcEEecC
Confidence 365554444 3 34667775556787751 1 11111 156688888887777653
No 60
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=66.17 E-value=2 Score=28.20 Aligned_cols=30 Identities=13% Similarity=0.182 Sum_probs=18.0
Q ss_pred cCCCCCCCceeEEcCc-eEEeeeccccCccc
Q 025050 222 CLGCKSPDTILSKENR-LFFLRCEKVKAHIQ 251 (258)
Q Consensus 222 C~~C~sPdT~L~ke~r-l~~l~C~aCGa~~~ 251 (258)
|..|+..+|.+-+.+. --..-|++||-...
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~~k 31 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLYYK 31 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHHHH
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHHHH
Confidence 8899999999988532 22338999996543
No 61
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=66.08 E-value=4.9 Score=30.54 Aligned_cols=31 Identities=23% Similarity=0.469 Sum_probs=22.2
Q ss_pred ccccCCCCCCCc----------eeEE-----cCceEEeeeccccCc
Q 025050 219 YVICLGCKSPDT----------ILSK-----ENRLFFLRCEKVKAH 249 (258)
Q Consensus 219 YVlC~~C~sPdT----------~L~k-----e~rl~~l~C~aCGa~ 249 (258)
+-.||.|++-+- .|.+ .++.+...|..||.+
T Consensus 4 ~~kCpKCgn~~~~ekei~~tg~~lskifdvq~n~f~~itCk~CgYt 49 (68)
T COG3478 4 AFKCPKCGNTNYEEKEIAATGGGLSKIFDVQNNKFIVITCKNCGYT 49 (68)
T ss_pred cccCCCcCCcchhhceeeccCCCcceeEEecccEEEEEEeccCCch
Confidence 445999998652 2322 367888999999976
No 62
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=65.08 E-value=6.2 Score=37.47 Aligned_cols=33 Identities=21% Similarity=0.406 Sum_probs=25.8
Q ss_pred ccccCCCCCCCceeEE-------cCceEEeeeccccCccc
Q 025050 219 YVICLGCKSPDTILSK-------ENRLFFLRCEKVKAHIQ 251 (258)
Q Consensus 219 YVlC~~C~sPdT~L~k-------e~rl~~l~C~aCGa~~~ 251 (258)
-+.|+.|+..++.+.. +.=..|..|..||.+..
T Consensus 258 ~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w~ 297 (299)
T TIGR01385 258 LFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRWK 297 (299)
T ss_pred cccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCeee
Confidence 4899999999987753 23377999999998643
No 63
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=64.76 E-value=3 Score=39.74 Aligned_cols=35 Identities=23% Similarity=0.447 Sum_probs=25.0
Q ss_pred cccCCCCC-CCceeEEc----CceEEeeec--------------cccCcccccc
Q 025050 220 VICLGCKS-PDTILSKE----NRLFFLRCE--------------KVKAHIQSYY 254 (258)
Q Consensus 220 VlC~~C~s-PdT~L~ke----~rl~~l~C~--------------aCGa~~~~~~ 254 (258)
-.||.|+| |=+.++.. .++-|++|. +||.+..+-|
T Consensus 186 ~~CPvCGS~PvaSmV~~g~~~~GlRYL~CslC~teW~~VR~KC~nC~~t~~l~y 239 (308)
T COG3058 186 QYCPVCGSMPVASMVQIGETEQGLRYLHCSLCETEWHYVRVKCSNCEQSKKLHY 239 (308)
T ss_pred ccCCCcCCCCcceeeeecCccccchhhhhhhHHHHHHHHHHHhccccccCCccc
Confidence 47999999 67888874 367777654 5666666554
No 64
>PRK14873 primosome assembly protein PriA; Provisional
Probab=64.55 E-value=5 Score=41.90 Aligned_cols=38 Identities=21% Similarity=0.391 Sum_probs=23.1
Q ss_pred ccccCCCCCC------CceeEEcCceEEeeeccccCccccccccc
Q 025050 219 YVICLGCKSP------DTILSKENRLFFLRCEKVKAHIQSYYLCP 257 (258)
Q Consensus 219 YVlC~~C~sP------dT~L~ke~rl~~l~C~aCGa~~~~~~~~~ 257 (258)
++.|..|+.+ +..|+-...--.++|.-||... .-+.||
T Consensus 383 ~l~C~~Cg~~~~C~~C~~~L~~h~~~~~l~Ch~CG~~~-~p~~Cp 426 (665)
T PRK14873 383 SLACARCRTPARCRHCTGPLGLPSAGGTPRCRWCGRAA-PDWRCP 426 (665)
T ss_pred eeEhhhCcCeeECCCCCCceeEecCCCeeECCCCcCCC-cCccCC
Confidence 5666655543 2333332112268999999976 578898
No 65
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=64.26 E-value=2.3 Score=27.06 Aligned_cols=28 Identities=18% Similarity=0.341 Sum_probs=14.9
Q ss_pred ccccCCCCCCCceeEEcCceEEeeeccccCc
Q 025050 219 YVICLGCKSPDTILSKENRLFFLRCEKVKAH 249 (258)
Q Consensus 219 YVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~ 249 (258)
.=.|+.|++|-+ +... =+.++|.+||..
T Consensus 3 ~rfC~~CG~~t~-~~~~--g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 3 HRFCGRCGAPTK-PAPG--GWARRCPSCGHE 30 (32)
T ss_dssp TSB-TTT--BEE-E-SS--SS-EEESSSS-E
T ss_pred CcccCcCCcccc-CCCC--cCEeECCCCcCE
Confidence 346999999843 3332 358899999975
No 66
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=64.17 E-value=6.2 Score=36.29 Aligned_cols=36 Identities=19% Similarity=0.391 Sum_probs=26.7
Q ss_pred HHHHHHHhccccCCCCCCCceeEEcCceEEeeeccccCc
Q 025050 211 ILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKVKAH 249 (258)
Q Consensus 211 ~L~~YI~eYVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~ 249 (258)
.|-.|-..+--|+.|++| |.... .+ +.+.|.+||..
T Consensus 91 ~l~~w~~~~~fC~~CG~~-~~~~~-~~-~~~~C~~c~~~ 126 (256)
T PRK00241 91 QLAEFYRSHRFCGYCGHP-MHPSK-TE-WAMLCPHCRER 126 (256)
T ss_pred HHHHHhhcCccccccCCC-CeecC-Cc-eeEECCCCCCE
Confidence 466788889999999998 44332 33 46889999964
No 67
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=63.90 E-value=5.2 Score=35.91 Aligned_cols=27 Identities=30% Similarity=0.748 Sum_probs=21.8
Q ss_pred ccccCCCCCCCceeEEcCceEEeeeccccCcc
Q 025050 219 YVICLGCKSPDTILSKENRLFFLRCEKVKAHI 250 (258)
Q Consensus 219 YVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~ 250 (258)
|-+|+.|+.+ |+++++ .|+|..||++-
T Consensus 149 ~A~CsrC~~~---L~~~~~--~l~Cp~Cg~tE 175 (188)
T COG1096 149 YARCSRCRAP---LVKKGN--MLKCPNCGNTE 175 (188)
T ss_pred EEEccCCCcc---eEEcCc--EEECCCCCCEE
Confidence 7889999965 777544 89999999864
No 68
>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=63.78 E-value=3.3 Score=26.83 Aligned_cols=31 Identities=23% Similarity=0.280 Sum_probs=19.6
Q ss_pred ccccCCCCCC---CceeEEcCceEEeeeccccCcc
Q 025050 219 YVICLGCKSP---DTILSKENRLFFLRCEKVKAHI 250 (258)
Q Consensus 219 YVlC~~C~sP---dT~L~ke~rl~~l~C~aCGa~~ 250 (258)
.+.||.|+.- +....-.++. .++|..||+..
T Consensus 2 ~~~CP~C~~~~~v~~~~~~~~~~-~v~C~~C~~~~ 35 (38)
T TIGR02098 2 RIQCPNCKTSFRVVDSQLGANGG-KVRCGKCGHVW 35 (38)
T ss_pred EEECCCCCCEEEeCHHHcCCCCC-EEECCCCCCEE
Confidence 3789999872 2222222222 68999999864
No 69
>PRK07451 translation initiation factor Sui1; Validated
Probab=63.77 E-value=9.4 Score=31.70 Aligned_cols=52 Identities=19% Similarity=0.319 Sum_probs=38.5
Q ss_pred CceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHH
Q 025050 154 GTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEG 210 (258)
Q Consensus 154 G~kKTvi~Nf~eI~k~L~R~pehv~kfl~~ELGt~gsid~~~rliikGrf~~k~ie~ 210 (258)
|+.-|+|.+|..-.. +-.-|++.|-..+|+.|++.+ +.+.|+|.|..+..+-
T Consensus 51 GK~VTvV~Gl~~~~~----dlk~LaK~LK~k~gcGGtvkd-~~IelQGD~r~~v~~~ 102 (115)
T PRK07451 51 GKTVTVITGFQHKPE----TLAKLLKQLKTQCGSGGTVKD-NTIEIQGDHRQKILEI 102 (115)
T ss_pred CCeEEEEeCCCCCHH----HHHHHHHHHHHHhcCCceEcC-CEEEEcCcHHHHHHHH
Confidence 346789999863222 246688999999999999964 4899999987654443
No 70
>PLN00209 ribosomal protein S27; Provisional
Probab=63.65 E-value=5.5 Score=31.64 Aligned_cols=29 Identities=24% Similarity=0.500 Sum_probs=24.3
Q ss_pred ccccCCCCCCCceeEEcCceEEeeeccccCc
Q 025050 219 YVICLGCKSPDTILSKENRLFFLRCEKVKAH 249 (258)
Q Consensus 219 YVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~ 249 (258)
.|.|+.|.+.-|.+..-.. .+.|..||..
T Consensus 36 ~VkCp~C~n~q~VFShA~t--~V~C~~Cg~~ 64 (86)
T PLN00209 36 DVKCQGCFNITTVFSHSQT--VVVCGSCQTV 64 (86)
T ss_pred EEECCCCCCeeEEEecCce--EEEccccCCE
Confidence 5999999999998887643 6899999974
No 71
>PRK12496 hypothetical protein; Provisional
Probab=63.50 E-value=4.8 Score=34.78 Aligned_cols=31 Identities=19% Similarity=0.127 Sum_probs=20.8
Q ss_pred CCceeEEcCceEEeeeccccCccccc---ccccC
Q 025050 228 PDTILSKENRLFFLRCEKVKAHIQSY---YLCPI 258 (258)
Q Consensus 228 PdT~L~ke~rl~~l~C~aCGa~~~~~---~~~~~ 258 (258)
..|.=+++.+.|-.+|.+||...+.. -.||+
T Consensus 115 ~~~~~i~~~~~w~~~C~gC~~~~~~~~~~~~C~~ 148 (164)
T PRK12496 115 IKTKGIKKVIKWRKVCKGCKKKYPEDYPDDVCEI 148 (164)
T ss_pred cccccchhheeeeEECCCCCccccCCCCCCcCCC
Confidence 33444456677888888888877643 34875
No 72
>PF12898 Stc1: Stc1 domain; InterPro: IPR024630 The domain contains 8 conserved cysteines that may bind to zinc. In S. pombe, proteins containing the domain act as protein linkers, which link the chromatin modifying CLRC complex to RNAi by tethering it to the RITS complex. This domain has a slightly different arrangement of its CxxC pairs from the LIM domain, hence it is not part of that family []. The tandem zinc-finger structure could mediate protein-protein interactions.
Probab=63.43 E-value=8.6 Score=29.80 Aligned_cols=49 Identities=12% Similarity=0.232 Sum_probs=34.7
Q ss_pred eEEEEeecChHHHHHHHHHHHHh-------ccccCCCCCCCceeEEcCceEEeeeccccCcccc
Q 025050 196 RLVVKGRFAPKNFEGILRRYVNE-------YVICLGCKSPDTILSKENRLFFLRCEKVKAHIQS 252 (258)
Q Consensus 196 rliikGrf~~k~ie~~L~~YI~e-------YVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~~~ 252 (258)
...-.+.|+..|++.+-..-... ++.|..|-+..+ .-+.|..||-..++
T Consensus 7 ~~k~~~~FS~~Ql~~~~~~~~~~~~~~~~~~i~C~~ct~~q~--------~El~C~~C~~~k~l 62 (84)
T PF12898_consen 7 KWKPLSAFSKNQLEKLRKQIRANRVDPANSGIRCRECTGGQV--------VELTCSPCGKTKPL 62 (84)
T ss_pred eECChHHcCHHHHHHHHHHHhhccCccCCCCCCCccCCCCCc--------CcCEeccCCCCcCH
Confidence 34445789999988776655555 799999976532 23489999977664
No 73
>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=63.12 E-value=4.1 Score=38.85 Aligned_cols=26 Identities=12% Similarity=-0.004 Sum_probs=19.1
Q ss_pred CCCCCC--CCCCCccHHHHHHHHHHHHh
Q 025050 105 QRYPWE--GSDRDYEYEELLGRVFNILR 130 (258)
Q Consensus 105 ~~~~~~--~~~~~~~YeeLL~R~~~~L~ 130 (258)
+..|.. ...++..+.++|.++.+.|+
T Consensus 85 g~PpL~~~~~~~d~~w~~~l~~LL~~l~ 112 (305)
T TIGR01562 85 GMPPLDYDLLVREGAWLPWLDALLAGYP 112 (305)
T ss_pred CCCCCChhhcccCHHHHHHHHHHHHHhc
Confidence 344554 34667788999999999995
No 74
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=61.93 E-value=5.7 Score=32.30 Aligned_cols=57 Identities=12% Similarity=0.198 Sum_probs=35.8
Q ss_pred ChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHHHHHHhccccCCCCCCCceeEEcCceEEeeeccccCcc
Q 025050 173 QPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKVKAHI 250 (258)
Q Consensus 173 ~pehv~kfl~~ELGt~gsid~~~rliikGrf~~k~ie~~L~~YI~eYVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~ 250 (258)
.|+.|.-.| ++-+.|++-.+-+|.|.- +.--+.|+.|+. ...... ++..|..||+..
T Consensus 40 ~pe~L~f~f--~~~~~~T~~egA~L~I~~--------------vp~~~~C~~Cg~---~~~~~~--~~~~CP~Cgs~~ 96 (113)
T PRK12380 40 EESAVRFSF--EIVCHGTVAQGCDLHIVY--------------KPAQAWCWDCSQ---VVEIHQ--HDAQCPHCHGER 96 (113)
T ss_pred CHHHHHHHH--HHHhCCCccCCCEEEEEe--------------eCcEEEcccCCC---EEecCC--cCccCcCCCCCC
Confidence 466665555 355777776666888852 334578999992 222222 244599999764
No 75
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=60.96 E-value=6.8 Score=31.09 Aligned_cols=29 Identities=24% Similarity=0.531 Sum_probs=24.2
Q ss_pred ccccCCCCCCCceeEEcCceEEeeeccccCc
Q 025050 219 YVICLGCKSPDTILSKENRLFFLRCEKVKAH 249 (258)
Q Consensus 219 YVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~ 249 (258)
.|.|+.|.+.-|.+..-.. .+.|..||..
T Consensus 35 ~VkCp~C~n~q~VFShA~t--~V~C~~Cg~~ 63 (85)
T PTZ00083 35 DVKCPGCSQITTVFSHAQT--VVLCGGCSSQ 63 (85)
T ss_pred EEECCCCCCeeEEEecCce--EEEccccCCE
Confidence 5999999999998887643 6889999974
No 76
>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=60.93 E-value=8 Score=28.92 Aligned_cols=29 Identities=17% Similarity=0.351 Sum_probs=21.0
Q ss_pred ccCCCCCCCcee----------EE-----cCceEEeeeccccCc
Q 025050 221 ICLGCKSPDTIL----------SK-----ENRLFFLRCEKVKAH 249 (258)
Q Consensus 221 lC~~C~sPdT~L----------~k-----e~rl~~l~C~aCGa~ 249 (258)
.||.|++-+... .+ .++.+.+.|..||.+
T Consensus 2 ~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~CGYT 45 (64)
T PF09855_consen 2 KCPKCGNEEYESGEVRATGGGLSKIFDVQNKKFTTVSCTNCGYT 45 (64)
T ss_pred CCCCCCCcceecceEEccCCeeEEEEEecCcEEEEEECCCCCCE
Confidence 599999876543 11 246678899999987
No 77
>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=60.92 E-value=5.8 Score=28.57 Aligned_cols=30 Identities=27% Similarity=0.411 Sum_probs=23.2
Q ss_pred cccCCCCCCCcee-EEcCceEEeeeccccCc
Q 025050 220 VICLGCKSPDTIL-SKENRLFFLRCEKVKAH 249 (258)
Q Consensus 220 VlC~~C~sPdT~L-~ke~rl~~l~C~aCGa~ 249 (258)
++|+.|++.+=.. ..+..-+.-+|-.||+.
T Consensus 23 LIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 23 LICSKCFSHNGLAPKEEFEEIQYRCPYCGAL 53 (54)
T ss_pred EECcccchhhcccccccCCceEEEcCCCCCc
Confidence 5899999987555 45666668899999974
No 78
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=60.90 E-value=5.5 Score=28.81 Aligned_cols=28 Identities=14% Similarity=0.437 Sum_probs=20.7
Q ss_pred cccCCCCCCCceeEEcCceEEeeeccccCcc
Q 025050 220 VICLGCKSPDTILSKENRLFFLRCEKVKAHI 250 (258)
Q Consensus 220 VlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~ 250 (258)
-+|+.|+...-. ...+| ...|..||...
T Consensus 29 q~C~~CG~~~~~-~~~~r--~~~C~~Cg~~~ 56 (69)
T PF07282_consen 29 QTCPRCGHRNKK-RRSGR--VFTCPNCGFEM 56 (69)
T ss_pred cCccCccccccc-ccccc--eEEcCCCCCEE
Confidence 469999998766 33344 67899999763
No 79
>PF04194 PDCD2_C: Programmed cell death protein 2, C-terminal putative domain ; InterPro: IPR007320 PDCD2 is localized predominantly in the cytosol of cells situated at the opposite pole of the germinal centre from the centroblasts as well as in cells in the mantle zone. It has been shown to interact with BCL6, an evolutionarily conserved Kruppel-type zinc finger protein that functions as a strong transcriptional repressor and is required for germinal centre development. The rat homologue, Rp8, is associated with programmed cell death in thymocytes.; GO: 0005737 cytoplasm
Probab=60.89 E-value=1.5 Score=37.68 Aligned_cols=18 Identities=28% Similarity=0.805 Sum_probs=11.8
Q ss_pred hHHHHHHhCCChHHHHHH
Q 025050 163 FMDLCKTMHRQPDHVMTF 180 (258)
Q Consensus 163 f~eI~k~L~R~pehv~kf 180 (258)
|....++|.|.|++|++|
T Consensus 60 f~~F~~rl~~~P~QvlRY 77 (164)
T PF04194_consen 60 FLKFQKRLSRNPEQVLRY 77 (164)
T ss_pred HHHHHHHHhcCCCeEEEE
Confidence 555556666777777776
No 80
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=60.81 E-value=5.8 Score=29.55 Aligned_cols=33 Identities=27% Similarity=0.514 Sum_probs=23.8
Q ss_pred HHHhccccCCCCCCCceeEEcCceEEeeeccccCcc
Q 025050 215 YVNEYVICLGCKSPDTILSKENRLFFLRCEKVKAHI 250 (258)
Q Consensus 215 YI~eYVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~ 250 (258)
.+-+-+-||.|+.| -.+..+++ .|.|..||-.-
T Consensus 4 ~LLeiLaCP~~kg~-L~~~~~~~--~L~c~~~~~aY 36 (60)
T COG2835 4 RLLEILACPVCKGP-LVYDEEKQ--ELICPRCKLAY 36 (60)
T ss_pred hhheeeeccCcCCc-ceEeccCC--EEEecccCcee
Confidence 44566899999999 44444555 78999998643
No 81
>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=60.68 E-value=10 Score=27.26 Aligned_cols=32 Identities=25% Similarity=0.453 Sum_probs=22.8
Q ss_pred HHhccccCCCCCC-----CceeEEcCceEEeeeccccC
Q 025050 216 VNEYVICLGCKSP-----DTILSKENRLFFLRCEKVKA 248 (258)
Q Consensus 216 I~eYVlC~~C~sP-----dT~L~ke~rl~~l~C~aCGa 248 (258)
..+|+.||.|++- +-.|+.+...|.-.|. ||-
T Consensus 10 ~~kY~~Cp~CGN~~vGngEG~liV~edtfkRtCk-CGf 46 (49)
T PF12677_consen 10 SNKYCKCPKCGNDKVGNGEGTLIVEEDTFKRTCK-CGF 46 (49)
T ss_pred hhhhccCcccCCcEeecCcceEEEeccceeeeec-ccc
Confidence 4458999999874 5567777677777774 553
No 82
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=60.34 E-value=7.9 Score=31.64 Aligned_cols=25 Identities=8% Similarity=-0.060 Sum_probs=13.9
Q ss_pred hHHHHHHHHHhhcCcee-ecCCceEEEE
Q 025050 174 PDHVMTFLLAELGTSGS-LDGQQRLVVK 200 (258)
Q Consensus 174 pehv~kfl~~ELGt~gs-id~~~rliik 200 (258)
|+.|.-.| .. -+.|+ +-.+-+|.|.
T Consensus 41 pe~L~faf-~~-~~~~T~~~ega~L~Ie 66 (117)
T PRK00564 41 KSLFVSAF-ET-FREESLVCKDAILDIV 66 (117)
T ss_pred HHHHHHHH-HH-HhcCCcccCCCEEEEE
Confidence 55444333 33 46677 6555577775
No 83
>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=60.33 E-value=6.2 Score=32.12 Aligned_cols=51 Identities=18% Similarity=0.391 Sum_probs=32.1
Q ss_pred eecC---hHHHHHHHHHHHHhccccCCCCCCCceeEEcCceEEeeeccccCcccc---ccccc
Q 025050 201 GRFA---PKNFEGILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKVKAHIQS---YYLCP 257 (258)
Q Consensus 201 Grf~---~k~ie~~L~~YI~eYVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~~~---~~~~~ 257 (258)
|.++ +..|+-.+.-+.+.. .| -++.|..+.--...+|..||..... ++.||
T Consensus 34 G~ls~V~p~~L~faf~~~~~~t-~~-----ega~L~I~~~p~~~~C~~Cg~~~~~~~~~~~CP 90 (115)
T TIGR00100 34 GELSCVNPSQLQFAFEVVREGT-VA-----EGAKLNIEDEPVECECEDCSEEVSPEIDLYRCP 90 (115)
T ss_pred ccccccCHHHHHHHHHHHhCCC-cc-----CCCEEEEEeeCcEEEcccCCCEEecCCcCccCc
Confidence 5544 666666666543332 11 2466776655557899999988754 67798
No 84
>COG1163 DRG Predicted GTPase [General function prediction only]
Probab=59.44 E-value=10 Score=37.11 Aligned_cols=55 Identities=22% Similarity=0.443 Sum_probs=37.4
Q ss_pred CCCccHHHHHHHHHHHHhhcCCCcc-cccceeecCCCeEEEeCceeEEEEehHHHHHHhCCCh
Q 025050 113 DRDYEYEELLGRVFNILRENNPELA-GDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTMHRQP 174 (258)
Q Consensus 113 ~~~~~YeeLL~R~~~~L~~~nP~~~-~~~~R~~mp~pqV~reG~kKTvi~Nf~eI~k~L~R~p 174 (258)
.++++-++|++++|..|.--. =+. .....-..++|.|.|.| ....|+|..|||+-
T Consensus 272 ~~~~nld~L~e~i~~~L~liR-VYtK~~g~~pd~~~PlIlr~G------sTV~Dvc~~IH~~l 327 (365)
T COG1163 272 KKGINLDELKERIWDVLGLIR-VYTKPPGEEPDFDEPLILRRG------STVGDVCRKIHRDL 327 (365)
T ss_pred ccCCCHHHHHHHHHHhhCeEE-EEecCCCCCCCCCCCeEEeCC------CcHHHHHHHHHHHH
Confidence 445678999999999992100 000 01122345789999999 46899999999964
No 85
>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=58.61 E-value=9.7 Score=31.93 Aligned_cols=52 Identities=21% Similarity=0.445 Sum_probs=36.4
Q ss_pred EEEEeecChHHHHHHHHHHH-----Hh-ccccCCCCCCCceeEEc------------CceEEeeeccccC
Q 025050 197 LVVKGRFAPKNFEGILRRYV-----NE-YVICLGCKSPDTILSKE------------NRLFFLRCEKVKA 248 (258)
Q Consensus 197 liikGrf~~k~ie~~L~~YI-----~e-YVlC~~C~sPdT~L~ke------------~rl~~l~C~aCGa 248 (258)
+.|...-..+|+..++++|= +. +-.|+.|.++=..+.++ .---|-+|..||.
T Consensus 63 ~li~~~~~~~QL~ev~~~~~l~~~~~~~~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~k 132 (147)
T PF01927_consen 63 ILIRSDDPEEQLREVLERFGLKLRLDPIFSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGK 132 (147)
T ss_pred EEEcCCCHHHHHHHHHHHcCCccccCCCCCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCC
Confidence 45667777889999988874 22 67999999964444443 1113889999985
No 86
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=58.38 E-value=8 Score=32.50 Aligned_cols=70 Identities=17% Similarity=0.269 Sum_probs=45.6
Q ss_pred eeEEE-EehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHHHHHHhccccCCCCCCCceeEE
Q 025050 156 KKTVF-VNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILRRYVNEYVICLGCKSPDTILSK 234 (258)
Q Consensus 156 kKTvi-~Nf~eI~k~L~R~pehv~kfl~~ELGt~gsid~~~rliikGrf~~k~ie~~L~~YI~eYVlC~~C~sPdT~L~k 234 (258)
..+.| .|+..|..+|...-.++.+=|..+|--..+- .+..||.|+.-=|.+.-
T Consensus 61 ~~~yw~i~y~~~~~vik~r~~~~~~~L~~~l~~e~~~--------------------------~~Y~Cp~C~~~y~~~ea 114 (147)
T smart00531 61 YRYYWYINYDTLLDVVKYKLDKMRKRLEDKLEDETNN--------------------------AYYKCPNCQSKYTFLEA 114 (147)
T ss_pred EEEEEEecHHHHHHHHHHHHHHHHHHHHHHHhcccCC--------------------------cEEECcCCCCEeeHHHH
Confidence 45566 9999999999988888888887777543221 36789999843332211
Q ss_pred ---cCceEEeeeccccCccc
Q 025050 235 ---ENRLFFLRCEKVKAHIQ 251 (258)
Q Consensus 235 ---e~rl~~l~C~aCGa~~~ 251 (258)
.+---...|..||+.-.
T Consensus 115 ~~~~d~~~~f~Cp~Cg~~l~ 134 (147)
T smart00531 115 NQLLDMDGTFTCPRCGEELE 134 (147)
T ss_pred HHhcCCCCcEECCCCCCEEE
Confidence 00011278999997643
No 87
>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=57.49 E-value=8.5 Score=25.27 Aligned_cols=29 Identities=10% Similarity=0.195 Sum_probs=16.6
Q ss_pred ccCCCCCCCceeEEcCceEEeeeccccCccc
Q 025050 221 ICLGCKSPDTILSKENRLFFLRCEKVKAHIQ 251 (258)
Q Consensus 221 lC~~C~sPdT~L~ke~rl~~l~C~aCGa~~~ 251 (258)
-||.|++.=..-....... .|..||..-+
T Consensus 3 FCp~C~nlL~p~~~~~~~~--~C~~C~Y~~~ 31 (35)
T PF02150_consen 3 FCPECGNLLYPKEDKEKRV--ACRTCGYEEP 31 (35)
T ss_dssp BETTTTSBEEEEEETTTTE--EESSSS-EEE
T ss_pred eCCCCCccceEcCCCccCc--CCCCCCCccC
Confidence 5999998532211122222 9999998654
No 88
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=57.41 E-value=12 Score=24.35 Aligned_cols=30 Identities=17% Similarity=0.325 Sum_probs=21.3
Q ss_pred ccccCCCCCCCceeEEcCceEEeeeccccCccc
Q 025050 219 YVICLGCKSPDTILSKENRLFFLRCEKVKAHIQ 251 (258)
Q Consensus 219 YVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~~ 251 (258)
..+|+.|+++--.. ++.. .+.|.-||+..+
T Consensus 3 ~~~C~~C~~~~i~~-~~~~--~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 3 LKKCSKCGGNGIVN-KEDD--YEVCIFCGSSFP 32 (33)
T ss_pred ceEcCCCCCCeEEE-ecCC--eEEcccCCcEee
Confidence 46899999987222 4444 578999998764
No 89
>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=57.31 E-value=5.8 Score=25.68 Aligned_cols=29 Identities=17% Similarity=0.292 Sum_probs=20.9
Q ss_pred ccCCCCCCCceeEEcCceEEeeeccccCc
Q 025050 221 ICLGCKSPDTILSKENRLFFLRCEKVKAH 249 (258)
Q Consensus 221 lC~~C~sPdT~L~ke~rl~~l~C~aCGa~ 249 (258)
.|+.|+..=+.+..-..--...|-.||+.
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~ 35 (41)
T smart00834 7 RCEDCGHTFEVLQKISDDPLATCPECGGD 35 (41)
T ss_pred EcCCCCCEEEEEEecCCCCCCCCCCCCCc
Confidence 69999987666665322346789999984
No 90
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=56.96 E-value=4.2 Score=30.39 Aligned_cols=28 Identities=25% Similarity=0.565 Sum_probs=21.1
Q ss_pred cccCCCCCCCceeEEcCceEEeeeccccCccc
Q 025050 220 VICLGCKSPDTILSKENRLFFLRCEKVKAHIQ 251 (258)
Q Consensus 220 VlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~~ 251 (258)
-+|..|++-+|.=.++ .++|.-||.+-+
T Consensus 21 YiCgdC~~en~lk~~D----~irCReCG~RIl 48 (62)
T KOG3507|consen 21 YICGDCGQENTLKRGD----VIRCRECGYRIL 48 (62)
T ss_pred EEeccccccccccCCC----cEehhhcchHHH
Confidence 3699999988754333 679999998753
No 91
>TIGR00467 lysS_arch lysyl-tRNA synthetase, archaeal and spirochete. This model represents the lysyl-tRNA synthetases that are class I amino-acyl tRNA synthetases. It includes archaeal and spirochete examples of the enzyme. All other known examples are class IIc amino-acyl tRNA synthetases and seem to form a separate orthologous set.
Probab=56.94 E-value=13 Score=37.81 Aligned_cols=70 Identities=21% Similarity=0.391 Sum_probs=44.7
Q ss_pred HHHhhcCceeecCCceEEEEeecCh---------HHHHHHHHHHHHh---------ccccCCCCCCCceeEE-c--CceE
Q 025050 181 LLAELGTSGSLDGQQRLVVKGRFAP---------KNFEGILRRYVNE---------YVICLGCKSPDTILSK-E--NRLF 239 (258)
Q Consensus 181 l~~ELGt~gsid~~~rliikGrf~~---------k~ie~~L~~YI~e---------YVlC~~C~sPdT~L~k-e--~rl~ 239 (258)
++.+||..-.+-.+..+.=+|+|.. ..|.++|..|... .++|+.|+.-.|.++. + ..+.
T Consensus 112 ~l~~~gi~~e~~s~te~Y~sG~~~~~i~~~L~~~~~I~~il~~~~~~~~~~~~~P~~pic~~cGrv~~~~~~~~~~~~v~ 191 (515)
T TIGR00467 112 SLPVLGINPEFIRASKQYTSGLYASQIKIALDHRKEISEILNEYRTSKLEENWYPISVFCENCGRDTTTVNNYDNEYSIE 191 (515)
T ss_pred HHHHcCCeEEEEEHHHhhhcCChHHHHHHHHHhHHHHHHHHHHhcCCccCCCceeeeeecCCcCccCceEEEecCCceEE
Confidence 3455666443333445555677754 4667777777742 3699999999886663 2 3454
Q ss_pred EeeeccccCcccc
Q 025050 240 FLRCEKVKAHIQS 252 (258)
Q Consensus 240 ~l~C~aCGa~~~~ 252 (258)
+ +|. ||.....
T Consensus 192 Y-~c~-cG~~g~~ 202 (515)
T TIGR00467 192 Y-SCE-CGNQESV 202 (515)
T ss_pred E-EcC-CCCEEEE
Confidence 5 896 9987654
No 92
>PRK09019 translation initiation factor Sui1; Validated
Probab=56.58 E-value=23 Score=29.16 Aligned_cols=53 Identities=9% Similarity=0.019 Sum_probs=38.8
Q ss_pred CceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHH
Q 025050 154 GTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGI 211 (258)
Q Consensus 154 G~kKTvi~Nf~eI~k~L~R~pehv~kfl~~ELGt~gsid~~~rliikGrf~~k~ie~~ 211 (258)
|+.-|+|..|..-... -+-|++.|-..+|+-|++-+ +.+.|+|.|.....+-+
T Consensus 44 GK~VTiI~Gl~~~~~d----lk~l~K~lKkk~gcGGtvk~-~~IelQGD~r~~v~~~L 96 (108)
T PRK09019 44 GKGVCLITGLDLDDAE----LKKLAAELKKKCGCGGAVKD-GVIEIQGDKRDLLKSLL 96 (108)
T ss_pred CCeEEEEeCCcCCHHH----HHHHHHHHHHHhcCCCeEEc-CEEEEcCcHHHHHHHHH
Confidence 4466899988511111 45688999999999999974 58999999876654433
No 93
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=56.53 E-value=9.7 Score=25.88 Aligned_cols=29 Identities=17% Similarity=0.241 Sum_probs=18.9
Q ss_pred cccCCCCCCCceeEEcCceEEeeeccccCccc
Q 025050 220 VICLGCKSPDTILSKENRLFFLRCEKVKAHIQ 251 (258)
Q Consensus 220 VlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~~ 251 (258)
..|+.|+.. +..+...-.++|..||+...
T Consensus 4 y~C~~CG~~---~~~~~~~~~~~Cp~CG~~~~ 32 (46)
T PRK00398 4 YKCARCGRE---VELDEYGTGVRCPYCGYRIL 32 (46)
T ss_pred EECCCCCCE---EEECCCCCceECCCCCCeEE
Confidence 468999873 33333222689999997654
No 94
>PF06322 Phage_NinH: Phage NinH protein; InterPro: IPR010454 This entry is represented by Bacteriophage 933W, NinH. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=56.53 E-value=16 Score=27.58 Aligned_cols=37 Identities=14% Similarity=0.227 Sum_probs=31.0
Q ss_pred EehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecC
Q 025050 161 VNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFA 204 (258)
Q Consensus 161 ~Nf~eI~k~L~R~pehv~kfl~~ELGt~gsid~~~rliikGrf~ 204 (258)
-|..++|..|+-.-..|.+|.. -.++...+|+||.+.
T Consensus 17 GnqtEvaR~l~c~R~TVrKY~~-------D~~a~~HaIvNgvLM 53 (64)
T PF06322_consen 17 GNQTEVARRLGCNRATVRKYSR-------DKDAKRHAIVNGVLM 53 (64)
T ss_pred CcHHHHHHHhcccHHHHHHHhc-------ccccceEEEEcCEEE
Confidence 4899999999999999999974 345567889998875
No 95
>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=56.50 E-value=7.6 Score=25.20 Aligned_cols=23 Identities=30% Similarity=0.558 Sum_probs=11.8
Q ss_pred cCceEEeeeccccCc-cccccccc
Q 025050 235 ENRLFFLRCEKVKAH-IQSYYLCP 257 (258)
Q Consensus 235 e~rl~~l~C~aCGa~-~~~~~~~~ 257 (258)
++||+..+|.+||.. .+.-..||
T Consensus 6 ~~~l~~~rC~~Cg~~~~pPr~~Cp 29 (37)
T PF12172_consen 6 EGRLLGQRCRDCGRVQFPPRPVCP 29 (37)
T ss_dssp TT-EEEEE-TTT--EEES--SEET
T ss_pred CCEEEEEEcCCCCCEecCCCcCCC
Confidence 468899999999987 33334454
No 96
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=56.06 E-value=7.3 Score=27.61 Aligned_cols=28 Identities=18% Similarity=0.294 Sum_probs=19.2
Q ss_pred ccccCCCCCCCceeEEcCceEEeeeccccCcc
Q 025050 219 YVICLGCKSPDTILSKENRLFFLRCEKVKAHI 250 (258)
Q Consensus 219 YVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~ 250 (258)
.-.||.|++- .|..... .++|..||.+-
T Consensus 20 ~~fCP~Cg~~--~m~~~~~--r~~C~~Cgyt~ 47 (50)
T PRK00432 20 NKFCPRCGSG--FMAEHLD--RWHCGKCGYTE 47 (50)
T ss_pred cCcCcCCCcc--hheccCC--cEECCCcCCEE
Confidence 4579999984 4444332 46899999763
No 97
>PRK07562 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=55.04 E-value=8.4 Score=43.04 Aligned_cols=38 Identities=18% Similarity=0.418 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHhccccCCCCCCCceeEEcCceEEeeeccccCcc
Q 025050 207 NFEGILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKVKAHI 250 (258)
Q Consensus 207 ~ie~~L~~YI~eYVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~ 250 (258)
..+..+..| +=..|+.|++ +.|++.+. .++|..||+++
T Consensus 1180 ~~~a~~~g~--~g~~c~~cg~--~~~vrngt--c~~c~~cg~t~ 1217 (1220)
T PRK07562 1180 RAEAKMQGY--TGEACSECGN--FTLVRNGT--CLKCDTCGSTT 1217 (1220)
T ss_pred hhHHHhCCC--CCCcCCCcCC--eEEEeCCe--eeeccccCCCC
Confidence 344555556 5677999996 67888766 78999999976
No 98
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=54.60 E-value=8.2 Score=26.27 Aligned_cols=28 Identities=21% Similarity=0.309 Sum_probs=17.0
Q ss_pred ccCCCCCCCceeEEcC-ceEEeeeccccCcc
Q 025050 221 ICLGCKSPDTILSKEN-RLFFLRCEKVKAHI 250 (258)
Q Consensus 221 lC~~C~sPdT~L~ke~-rl~~l~C~aCGa~~ 250 (258)
.||.|++.= +.++. .-..+.|..||...
T Consensus 2 FCp~Cg~~l--~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 2 FCPKCGNML--IPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCCcc--ccccCCCCCEEECCcCCCeE
Confidence 499999832 22222 11266899999753
No 99
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=54.43 E-value=6.2 Score=27.30 Aligned_cols=26 Identities=27% Similarity=0.519 Sum_probs=18.6
Q ss_pred ccCCCCCCCceeEEcCceEEeeeccccCcc
Q 025050 221 ICLGCKSPDTILSKENRLFFLRCEKVKAHI 250 (258)
Q Consensus 221 lC~~C~sPdT~L~ke~rl~~l~C~aCGa~~ 250 (258)
+|..|+..-+. . ..--++|..||++-
T Consensus 4 ~C~~Cg~~~~~-~---~~~~irC~~CG~rI 29 (44)
T smart00659 4 ICGECGRENEI-K---SKDVVRCRECGYRI 29 (44)
T ss_pred ECCCCCCEeec-C---CCCceECCCCCceE
Confidence 69999985432 2 33468999999864
No 100
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=54.33 E-value=11 Score=30.76 Aligned_cols=26 Identities=12% Similarity=0.147 Sum_probs=15.4
Q ss_pred ChHHHHHHHHHhhcCceeecCCceEEEE
Q 025050 173 QPDHVMTFLLAELGTSGSLDGQQRLVVK 200 (258)
Q Consensus 173 ~pehv~kfl~~ELGt~gsid~~~rliik 200 (258)
.|+.|.-.|- +-+.|++-.+-+|.|.
T Consensus 40 ~p~~L~f~f~--~~~~~t~~egA~L~i~ 65 (114)
T PRK03681 40 ETSSLAFCFD--LVCRGTVAEGCKLHLE 65 (114)
T ss_pred CHHHHHHHHH--HHhCCCccCCCEEEEE
Confidence 3555554443 3466777656688775
No 101
>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=53.89 E-value=4.5 Score=29.53 Aligned_cols=29 Identities=24% Similarity=0.481 Sum_probs=18.5
Q ss_pred ccccCCCCCCCceeEEcCceEEeeeccccCc
Q 025050 219 YVICLGCKSPDTILSKENRLFFLRCEKVKAH 249 (258)
Q Consensus 219 YVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~ 249 (258)
-|.|+.|.+.-|.+..-. ..+.|..||..
T Consensus 7 ~VkCp~C~~~q~vFSha~--t~V~C~~Cg~~ 35 (55)
T PF01667_consen 7 DVKCPGCYNIQTVFSHAQ--TVVKCVVCGTV 35 (55)
T ss_dssp EEE-TTT-SEEEEETT-S--S-EE-SSSTSE
T ss_pred EEECCCCCCeeEEEecCC--eEEEcccCCCE
Confidence 489999999887766543 36789999974
No 102
>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=53.83 E-value=7.8 Score=24.97 Aligned_cols=26 Identities=23% Similarity=0.404 Sum_probs=13.0
Q ss_pred cccCCCCCCCceeEEcCceEEeeeccccCc
Q 025050 220 VICLGCKSPDTILSKENRLFFLRCEKVKAH 249 (258)
Q Consensus 220 VlC~~C~sPdT~L~ke~rl~~l~C~aCGa~ 249 (258)
-.|+.|+|..|- .++. .+.|..||+.
T Consensus 3 p~Cp~C~se~~y--~D~~--~~vCp~C~~e 28 (30)
T PF08274_consen 3 PKCPLCGSEYTY--EDGE--LLVCPECGHE 28 (30)
T ss_dssp ---TTT-----E--E-SS--SEEETTTTEE
T ss_pred CCCCCCCCccee--ccCC--EEeCCccccc
Confidence 469999999998 4444 5789999874
No 103
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=53.48 E-value=14 Score=27.44 Aligned_cols=29 Identities=21% Similarity=0.512 Sum_probs=17.1
Q ss_pred cccCCCCC---CC-ce-eEEc-----CceEEeeeccccC
Q 025050 220 VICLGCKS---PD-TI-LSKE-----NRLFFLRCEKVKA 248 (258)
Q Consensus 220 VlC~~C~s---Pd-T~-L~ke-----~rl~~l~C~aCGa 248 (258)
-+|..|++ |- |. +... ++.+...|..||.
T Consensus 47 ~~Ck~C~~~liPG~~~~vri~~~~~~~~~l~~~C~~C~~ 85 (85)
T PF04032_consen 47 TICKKCGSLLIPGVNCSVRIRKKKKKKNFLVYTCLNCGH 85 (85)
T ss_dssp TB-TTT--B--CTTTEEEEEE---SSS-EEEEEETTTTE
T ss_pred ccccCCCCEEeCCCccEEEEEecCCCCCEEEEEccccCC
Confidence 58999998 42 22 2223 5788999999984
No 104
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=53.38 E-value=13 Score=30.78 Aligned_cols=26 Identities=19% Similarity=0.409 Sum_probs=16.2
Q ss_pred ChHHHHHHHHHhhcCceeecCCceEEEE
Q 025050 173 QPDHVMTFLLAELGTSGSLDGQQRLVVK 200 (258)
Q Consensus 173 ~pehv~kfl~~ELGt~gsid~~~rliik 200 (258)
.|+.|.-.|- +-+.|++-.+-.|.|.
T Consensus 40 ~pe~L~faf~--~~~~gT~~egA~L~I~ 65 (124)
T PRK00762 40 NPEQLRFMLD--VLAEGTIAEDADLIVE 65 (124)
T ss_pred CHHHHHHHHH--HHhCCCCcCCCEEEEE
Confidence 4666665553 3466777655677775
No 105
>PRK06824 translation initiation factor Sui1; Validated
Probab=52.25 E-value=19 Score=30.03 Aligned_cols=55 Identities=18% Similarity=0.198 Sum_probs=40.3
Q ss_pred EeCceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHH
Q 025050 152 REGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGI 211 (258)
Q Consensus 152 reG~kKTvi~Nf~eI~k~L~R~pehv~kfl~~ELGt~gsid~~~rliikGrf~~k~ie~~ 211 (258)
|-|+.-|+|..|..-... -.-|++.|-..+|+.|++-+ +.+.|+|.|.....+-+
T Consensus 52 r~gK~VTvI~Gl~~~~~d----lk~l~K~LKkk~gcGGtvkd-~~IeiQGD~r~~v~~~L 106 (118)
T PRK06824 52 RGGKTVTVITGVPLAEDA----LKELAKELKRRCGTGGTLKD-GVIEIQGDHVELLLAEL 106 (118)
T ss_pred CCCceEEEEeCCcCCHHH----HHHHHHHHHHHhcCCceEec-CEEEEcCcHHHHHHHHH
Confidence 346677899998622222 35688999999999999964 59999999876655433
No 106
>cd00674 LysRS_core_class_I catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity.
Probab=52.16 E-value=16 Score=35.44 Aligned_cols=89 Identities=16% Similarity=0.249 Sum_probs=51.8
Q ss_pred hHHHHHHhCCChHHHHHH------HHHhhcCceeecCCceEEEEeecChH---------HHHHHHHHHHHh---------
Q 025050 163 FMDLCKTMHRQPDHVMTF------LLAELGTSGSLDGQQRLVVKGRFAPK---------NFEGILRRYVNE--------- 218 (258)
Q Consensus 163 f~eI~k~L~R~pehv~kf------l~~ELGt~gsid~~~rliikGrf~~k---------~ie~~L~~YI~e--------- 218 (258)
+..|+.--...|+++..| ++..||.+--+=..-.+--+|+|.+. .|.++|..|...
T Consensus 89 i~~ip~p~g~~~~~~d~~~~~f~~~l~~lgi~~d~~~~T~~y~~g~~~~~i~~~L~~~~~I~~i~~~~~~~~~~~~~~P~ 168 (353)
T cd00674 89 LSSVPDPFGCCESYAEHFERPFEESLEKLGIEVEFISQSQMYKSGLYDENILIALEKRDEIMAILNEYRGRELQETWYPF 168 (353)
T ss_pred chhchhhcCCCHHHHHHHHHHHHHHHHHcCCeeeeeecCCchhhchHHHHHHHHHHHCChHHHHHHHhcCCccCCCceee
Confidence 344444444445544444 34456664333233455566777653 566777777664
Q ss_pred ccccCCCCCCCceeEE-c--CceEEeeeccccCcccc
Q 025050 219 YVICLGCKSPDTILSK-E--NRLFFLRCEKVKAHIQS 252 (258)
Q Consensus 219 YVlC~~C~sPdT~L~k-e--~rl~~l~C~aCGa~~~~ 252 (258)
.++|+.|+...|.++. + .+.+.-+|. ||.....
T Consensus 169 ~p~c~~cg~~~~~v~~~d~~~~~v~y~c~-cG~~g~~ 204 (353)
T cd00674 169 MPYCEKCGKDTTTVEAYDAKAGTVTYKCE-CGHEETV 204 (353)
T ss_pred eeecCCcCcceeEEEEEeCCCCeEEEEcC-CCCEEEE
Confidence 3799999976666653 3 344444895 9987643
No 107
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=51.56 E-value=10 Score=31.00 Aligned_cols=29 Identities=24% Similarity=0.414 Sum_probs=19.9
Q ss_pred CceeEEcCceEEeeeccccCcccc---ccc-cc
Q 025050 229 DTILSKENRLFFLRCEKVKAHIQS---YYL-CP 257 (258)
Q Consensus 229 dT~L~ke~rl~~l~C~aCGa~~~~---~~~-~~ 257 (258)
++.|..+.--...+|..||..... .|+ ||
T Consensus 60 ga~L~Ie~vp~~~~C~~Cg~~~~~~~~~~~~CP 92 (117)
T PRK00564 60 DAILDIVDEKVELECKDCSHVFKPNALDYGVCE 92 (117)
T ss_pred CCEEEEEecCCEEEhhhCCCccccCCccCCcCc
Confidence 556666655557889999987644 244 88
No 108
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=50.78 E-value=13 Score=31.20 Aligned_cols=15 Identities=33% Similarity=0.541 Sum_probs=7.3
Q ss_pred cccCCCCCCCceeEE
Q 025050 220 VICLGCKSPDTILSK 234 (258)
Q Consensus 220 VlC~~C~sPdT~L~k 234 (258)
..||.|+|+++.+..
T Consensus 108 ~~CP~Cgs~~~~i~~ 122 (135)
T PRK03824 108 LKCPKCGSRDFEIVK 122 (135)
T ss_pred cCCcCCCCCCcEEec
Confidence 345555555544443
No 109
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=50.62 E-value=23 Score=23.12 Aligned_cols=28 Identities=14% Similarity=0.265 Sum_probs=23.2
Q ss_pred EehHHHHHHhCCChHHHHHHHHHhhcCc
Q 025050 161 VNFMDLCKTMHRQPDHVMTFLLAELGTS 188 (258)
Q Consensus 161 ~Nf~eI~k~L~R~pehv~kfl~~ELGt~ 188 (258)
..+.+||..++=++.|+.+-|..++|.+
T Consensus 9 ~~l~~iA~~~g~S~~~f~r~Fk~~~g~t 36 (42)
T PF00165_consen 9 LTLEDIAEQAGFSPSYFSRLFKKETGMT 36 (42)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHTSS-
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHCcC
Confidence 3589999999999999999999999975
No 110
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=50.09 E-value=8.8 Score=28.16 Aligned_cols=33 Identities=24% Similarity=0.553 Sum_probs=22.0
Q ss_pred hccccCCCCCCC-ceeEEcC--ceEEeeeccccCcc
Q 025050 218 EYVICLGCKSPD-TILSKEN--RLFFLRCEKVKAHI 250 (258)
Q Consensus 218 eYVlC~~C~sPd-T~L~ke~--rl~~l~C~aCGa~~ 250 (258)
+.++||.|++.- +.+..+. .-|-|-|..|...+
T Consensus 3 ~Wi~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~Et 38 (55)
T PF14205_consen 3 EWILCPICGNKTRLKIREDTVLKNFPLYCPKCKQET 38 (55)
T ss_pred eEEECCCCCCccceeeecCceeccccccCCCCCceE
Confidence 578999999753 3443443 34577888887654
No 111
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=49.92 E-value=18 Score=29.52 Aligned_cols=34 Identities=15% Similarity=0.326 Sum_probs=25.1
Q ss_pred ccccCCCCCCCceeEE-------cCceEEeeeccccCcccc
Q 025050 219 YVICLGCKSPDTILSK-------ENRLFFLRCEKVKAHIQS 252 (258)
Q Consensus 219 YVlC~~C~sPdT~L~k-------e~rl~~l~C~aCGa~~~~ 252 (258)
=+.||.|++-+=.+.- +.-..|-+|..||.+--.
T Consensus 72 ~~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~wre 112 (113)
T COG1594 72 KEKCPKCGNKEAYYWQLQTRSADEPETRFYKCTRCGYRWRE 112 (113)
T ss_pred cccCCCCCCceeEEEeeehhccCCCceEEEEecccCCEeec
Confidence 3789999998755542 234779999999987543
No 112
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=49.89 E-value=38 Score=22.10 Aligned_cols=45 Identities=11% Similarity=0.105 Sum_probs=32.9
Q ss_pred ehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHH
Q 025050 162 NFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGI 211 (258)
Q Consensus 162 Nf~eI~k~L~R~pehv~kfl~~ELGt~gsid~~~rliikGrf~~k~ie~~ 211 (258)
+..++|+.++-++..|-.|....+..+ ...++++. +|+..+|..+
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~~g~l~~-~~~~~~~~----~y~~~~v~~l 46 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYERIGLLSP-ARTEGGYR----LYSDADLERL 46 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHHCCCCCC-CcCCCCCE----EeCHHHHHHh
Confidence 468999999999999999988887663 33332332 4788877765
No 113
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=49.76 E-value=12 Score=30.49 Aligned_cols=51 Identities=16% Similarity=0.213 Sum_probs=30.6
Q ss_pred eecC---hHHHHHHHHHHHHhccccCCCCCCCceeEEcCceEEeeeccccCcccc----ccccc
Q 025050 201 GRFA---PKNFEGILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKVKAHIQS----YYLCP 257 (258)
Q Consensus 201 Grf~---~k~ie~~L~~YI~eYVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~~~----~~~~~ 257 (258)
|.++ +..|+-.+.-+.+.- + | -+..|..+.--...+|..||...+. |+.||
T Consensus 34 G~ls~V~p~~L~f~f~~~~~~t-~---~--egA~L~i~~~p~~~~C~~Cg~~~~~~~~~~~~CP 91 (114)
T PRK03681 34 GAFSCVETSSLAFCFDLVCRGT-V---A--EGCKLHLEEQEAECWCETCQQYVTLLTQRVRRCP 91 (114)
T ss_pred cCccccCHHHHHHHHHHHhCCC-c---c--CCCEEEEEeeCcEEEcccCCCeeecCCccCCcCc
Confidence 6655 666666666543322 2 2 2456666544446788899888755 25588
No 114
>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=49.59 E-value=14 Score=24.56 Aligned_cols=26 Identities=19% Similarity=0.474 Sum_probs=18.1
Q ss_pred ccCCCCCCCceeEEcCceEEeeeccccCcc
Q 025050 221 ICLGCKSPDTILSKENRLFFLRCEKVKAHI 250 (258)
Q Consensus 221 lC~~C~sPdT~L~ke~rl~~l~C~aCGa~~ 250 (258)
.|+.|++- ....+++ +..|..||...
T Consensus 10 ~C~~C~~~--~~~~~dG--~~yC~~cG~~~ 35 (36)
T PF11781_consen 10 PCPVCGSR--WFYSDDG--FYYCDRCGHQS 35 (36)
T ss_pred cCCCCCCe--EeEccCC--EEEhhhCceEc
Confidence 69999998 4444445 45688888753
No 115
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=48.60 E-value=15 Score=29.79 Aligned_cols=20 Identities=15% Similarity=0.315 Sum_probs=15.3
Q ss_pred ccccCCCCCCCceeEEcCce
Q 025050 219 YVICLGCKSPDTILSKENRL 238 (258)
Q Consensus 219 YVlC~~C~sPdT~L~ke~rl 238 (258)
+..||.|+|+++.++.-..+
T Consensus 86 ~~~CP~Cgs~~~~i~~G~El 105 (113)
T PRK12380 86 DAQCPHCHGERLRVDTGDSL 105 (113)
T ss_pred CccCcCCCCCCcEEccCCeE
Confidence 45699999999998864433
No 116
>KOG2703 consensus C4-type Zn-finger protein [General function prediction only]
Probab=48.29 E-value=12 Score=37.43 Aligned_cols=32 Identities=16% Similarity=0.416 Sum_probs=24.3
Q ss_pred ccccCCCCCC-CceeEEcC-------ceEEeeeccccCcc
Q 025050 219 YVICLGCKSP-DTILSKEN-------RLFFLRCEKVKAHI 250 (258)
Q Consensus 219 YVlC~~C~sP-dT~L~ke~-------rl~~l~C~aCGa~~ 250 (258)
--.||.|..| +|.|.--+ =+....|.+||.++
T Consensus 258 ~t~Cp~C~~pcet~Mk~~~IPhFkeVIiMst~Cd~CGyks 297 (460)
T KOG2703|consen 258 PTTCPSCTAPCETNMKLTDIPHFKEVIIMSTVCDRCGYKS 297 (460)
T ss_pred cCCCCCCCCchhccceeccCCcceeEEEEeecccccCCcc
Confidence 3469999999 89886522 34567899999876
No 117
>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=48.26 E-value=5 Score=26.15 Aligned_cols=26 Identities=27% Similarity=0.537 Sum_probs=17.0
Q ss_pred ccCCCCCCCceeEEcCceEEeeeccccCcc
Q 025050 221 ICLGCKSPDTILSKENRLFFLRCEKVKAHI 250 (258)
Q Consensus 221 lC~~C~sPdT~L~ke~rl~~l~C~aCGa~~ 250 (258)
+|..|+.... |.... .++|..||.+-
T Consensus 2 ~C~~Cg~~~~-~~~~~---~irC~~CG~RI 27 (32)
T PF03604_consen 2 ICGECGAEVE-LKPGD---PIRCPECGHRI 27 (32)
T ss_dssp BESSSSSSE--BSTSS---TSSBSSSS-SE
T ss_pred CCCcCCCeeE-cCCCC---cEECCcCCCeE
Confidence 6899998766 32222 36999999874
No 118
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=47.82 E-value=29 Score=23.98 Aligned_cols=39 Identities=18% Similarity=0.331 Sum_probs=25.3
Q ss_pred HHHHHHHHHh---ccccC--CCCCCCceeEEc--CceEEeeeccccCcc
Q 025050 209 EGILRRYVNE---YVICL--GCKSPDTILSKE--NRLFFLRCEKVKAHI 250 (258)
Q Consensus 209 e~~L~~YI~e---YVlC~--~C~sPdT~L~ke--~rl~~l~C~aCGa~~ 250 (258)
+-++++||+. +.-|| .|... +... .....+.|..||...
T Consensus 5 ~~~~~~~i~~~~~~~~CP~~~C~~~---~~~~~~~~~~~v~C~~C~~~f 50 (64)
T smart00647 5 RLLLESYVESNPDLKWCPAPDCSAA---IIVTEEEGCNRVTCPKCGFSF 50 (64)
T ss_pred HHHHHHHHhcCCCccCCCCCCCcce---EEecCCCCCCeeECCCCCCeE
Confidence 3456777764 77899 89653 3332 245578898888654
No 119
>PRK13500 transcriptional activator RhaR; Provisional
Probab=47.68 E-value=4.3 Score=37.49 Aligned_cols=66 Identities=11% Similarity=0.192 Sum_probs=52.7
Q ss_pred EehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHHHHHHhccccCCCCCC-CceeEEcCceE
Q 025050 161 VNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILRRYVNEYVICLGCKSP-DTILSKENRLF 239 (258)
Q Consensus 161 ~Nf~eI~k~L~R~pehv~kfl~~ELGt~gsid~~~rliikGrf~~k~ie~~L~~YI~eYVlC~~C~sP-dT~L~ke~rl~ 239 (258)
..+.++|+.++-+|.|+.++|-...|.+ ...||.++.+|..|..- .|.+ -+
T Consensus 223 isl~~lA~~~~iS~~~L~r~FK~~tG~T-----------------------~~~yi~~~RL~~A~~LL~~t~~-----sI 274 (312)
T PRK13500 223 FALDKFCDEASCSERVLRQQFRQQTGMT-----------------------INQYLRQVRVCHAQYLLQHSRL-----LI 274 (312)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHCcC-----------------------HHHHHHHHHHHHHHHHHHcCCC-----CH
Confidence 5789999999999999999999999996 46788888998888654 3322 33
Q ss_pred EeeeccccCcccccc
Q 025050 240 FLRCEKVKAHIQSYY 254 (258)
Q Consensus 240 ~l~C~aCGa~~~~~~ 254 (258)
.-.+..||-...+|+
T Consensus 275 ~eIA~~~GF~d~s~F 289 (312)
T PRK13500 275 SDISTECGFEDSNYF 289 (312)
T ss_pred HHHHHHhCCCCHHHH
Confidence 456788888888775
No 120
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=46.72 E-value=16 Score=30.66 Aligned_cols=63 Identities=19% Similarity=0.267 Sum_probs=36.5
Q ss_pred CChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHHHHHHhccccCCCCCCCcee----------------EEc
Q 025050 172 RQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILRRYVNEYVICLGCKSPDTIL----------------SKE 235 (258)
Q Consensus 172 R~pehv~kfl~~ELGt~gsid~~~rliikGrf~~k~ie~~L~~YI~eYVlC~~C~sPdT~L----------------~ke 235 (258)
-.|+.+...| ..+ +.|++-.+-+|.|.- +.-...|+.|+..-+.- +-+
T Consensus 39 V~pe~L~faf-e~l-~~gt~~ega~L~i~~--------------~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~ 102 (135)
T PRK03824 39 VDKEIVEFAL-NEL-LKGTILEGAEIIFEE--------------EEAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPE 102 (135)
T ss_pred hhHHHHHHHH-HHH-HcCCcccCCEEEEEe--------------cceEEECCCCCCEEeccccccccccccccccccccc
Confidence 3455555444 334 456665455888853 33578999999432211 011
Q ss_pred CceEEeeeccccCcc
Q 025050 236 NRLFFLRCEKVKAHI 250 (258)
Q Consensus 236 ~rl~~l~C~aCGa~~ 250 (258)
---++++|..||+..
T Consensus 103 ~~~~~~~CP~Cgs~~ 117 (135)
T PRK03824 103 VVHAFLKCPKCGSRD 117 (135)
T ss_pred ccccCcCCcCCCCCC
Confidence 113567899999875
No 121
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=46.66 E-value=8.8 Score=23.39 Aligned_cols=23 Identities=17% Similarity=0.504 Sum_probs=15.5
Q ss_pred cccCCCCCCCceeEEcCceEEeeeccccCc
Q 025050 220 VICLGCKSPDTILSKENRLFFLRCEKVKAH 249 (258)
Q Consensus 220 VlC~~C~sPdT~L~ke~rl~~l~C~aCGa~ 249 (258)
+.|+.|+.+ +..+ ..-|..||+.
T Consensus 3 ~~Cp~Cg~~---~~~~----~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAE---IDPD----AKFCPNCGAK 25 (26)
T ss_pred CCCcccCCc---CCcc----cccChhhCCC
Confidence 679999884 2222 4468888874
No 122
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=46.50 E-value=18 Score=30.08 Aligned_cols=18 Identities=22% Similarity=0.433 Sum_probs=12.7
Q ss_pred cCCCCCCCceeEEcCceE
Q 025050 222 CLGCKSPDTILSKENRLF 239 (258)
Q Consensus 222 C~~C~sPdT~L~ke~rl~ 239 (258)
||.|+|++..+..-+.++
T Consensus 89 CP~C~s~~~~i~~G~el~ 106 (115)
T COG0375 89 CPKCGSINLRIIGGDELI 106 (115)
T ss_pred CCCCCCCceEEecCCeeE
Confidence 888888887777655443
No 123
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=46.13 E-value=17 Score=30.02 Aligned_cols=20 Identities=20% Similarity=0.134 Sum_probs=14.5
Q ss_pred CceeEEcCceEEeeeccccCc
Q 025050 229 DTILSKENRLFFLRCEKVKAH 249 (258)
Q Consensus 229 dT~L~ke~rl~~l~C~aCGa~ 249 (258)
++.|..+.--...+| .||+.
T Consensus 59 gA~L~I~~vp~~~~C-~Cg~~ 78 (124)
T PRK00762 59 DADLIVEMIPVEIEC-ECGYE 78 (124)
T ss_pred CCEEEEEecCeeEEe-eCcCc
Confidence 567776654457889 99987
No 124
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=45.99 E-value=27 Score=29.20 Aligned_cols=43 Identities=19% Similarity=0.264 Sum_probs=29.6
Q ss_pred HHHHhccccCCCCCCCceeEEc---CceEEeeeccccCccccccccc
Q 025050 214 RYVNEYVICLGCKSPDTILSKE---NRLFFLRCEKVKAHIQSYYLCP 257 (258)
Q Consensus 214 ~YI~eYVlC~~C~sPdT~L~ke---~rl~~l~C~aCGa~~~~~~~~~ 257 (258)
+....-+.||-|++.. ..... .+.---+|..||..+..-+.-|
T Consensus 25 ~~~~~~~~cP~C~s~~-~~k~g~~~~~~qRyrC~~C~~tf~~~~~~~ 70 (129)
T COG3677 25 RMQITKVNCPRCKSSN-VVKIGGIRRGHQRYKCKSCGSTFTVETGSP 70 (129)
T ss_pred hhhcccCcCCCCCccc-eeeECCccccccccccCCcCcceeeeccCc
Confidence 3444558999999999 33332 2355668999999988766443
No 125
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=45.84 E-value=21 Score=24.09 Aligned_cols=22 Identities=18% Similarity=0.247 Sum_probs=16.6
Q ss_pred EehHHHHHHhCCChHHHHHHHH
Q 025050 161 VNFMDLCKTMHRQPDHVMTFLL 182 (258)
Q Consensus 161 ~Nf~eI~k~L~R~pehv~kfl~ 182 (258)
..+.+||+.|+|++.-|.++|-
T Consensus 21 ~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 21 MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp --HHHHHHHTT--HHHHHHHHH
T ss_pred CCHHHHHHHHCcCcHHHHHHHh
Confidence 5689999999999999998875
No 126
>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=45.61 E-value=22 Score=23.78 Aligned_cols=30 Identities=27% Similarity=0.543 Sum_probs=18.9
Q ss_pred cccCCCCCCCceeEE-cCceEEeeecc---ccCccc
Q 025050 220 VICLGCKSPDTILSK-ENRLFFLRCEK---VKAHIQ 251 (258)
Q Consensus 220 VlC~~C~sPdT~L~k-e~rl~~l~C~a---CGa~~~ 251 (258)
+.||.|+++ -.+.. ..+ .|+-|.. |..+..
T Consensus 2 ~~CP~Cg~~-lv~r~~k~g-~F~~Cs~yP~C~~~~~ 35 (39)
T PF01396_consen 2 EKCPKCGGP-LVLRRGKKG-KFLGCSNYPECKYTEP 35 (39)
T ss_pred cCCCCCCce-eEEEECCCC-CEEECCCCCCcCCeEe
Confidence 579999943 22222 234 7899987 776554
No 127
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=45.48 E-value=22 Score=29.22 Aligned_cols=32 Identities=16% Similarity=0.363 Sum_probs=21.6
Q ss_pred cccCCCCCC---C--ceeEEcCceEEeeeccccCccc
Q 025050 220 VICLGCKSP---D--TILSKENRLFFLRCEKVKAHIQ 251 (258)
Q Consensus 220 VlC~~C~sP---d--T~L~ke~rl~~l~C~aCGa~~~ 251 (258)
-+|+.|.+| - -.....+......|..||..+-
T Consensus 57 ~~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~~R 93 (105)
T COG2023 57 TICKKCYTPLVPGKNARVRLRKGRVVVTCLECGTIRR 93 (105)
T ss_pred HhccccCcccccCcceEEEEcCCeEEEEecCCCcEEE
Confidence 369999994 2 2222244447899999998653
No 128
>PRK06556 vitamin B12-dependent ribonucleotide reductase; Validated
Probab=45.04 E-value=18 Score=39.54 Aligned_cols=42 Identities=12% Similarity=0.249 Sum_probs=27.5
Q ss_pred ChHHHHHHHHHHHHhccccCCCCCCCceeEEcCceEEeeeccccCcc
Q 025050 204 APKNFEGILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKVKAHI 250 (258)
Q Consensus 204 ~~k~ie~~L~~YI~eYVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~ 250 (258)
++..+-.....+--.--+|++|+ |.+++.+. ...|+.||+++
T Consensus 909 ~~~~~~~~~~~~~~~~~~c~~c~---~~~~~~g~--c~~c~~cg~t~ 950 (953)
T PRK06556 909 SSTELLELQLGEAADAPLCPTCG---TKMVRNGS--CYVCEGCGSTS 950 (953)
T ss_pred ccHHHHHHhhcccccCCcCCCcc---CeeeECCc--eEeccCCCCCC
Confidence 33333333444444456788885 78877766 56899999986
No 129
>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=44.92 E-value=21 Score=24.53 Aligned_cols=31 Identities=19% Similarity=0.394 Sum_probs=22.5
Q ss_pred ccCCCCCCCceeEE-----cCceEEeeecc--ccCccc
Q 025050 221 ICLGCKSPDTILSK-----ENRLFFLRCEK--VKAHIQ 251 (258)
Q Consensus 221 lC~~C~sPdT~L~k-----e~rl~~l~C~a--CGa~~~ 251 (258)
.||.|+++=..-.. .-|-++..|.. ||++..
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg~tfv 38 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSPLTRELYCQCTNPECGHTFV 38 (47)
T ss_pred CcCCCCCeeEEEEchhhCcceEEEEEEECCCcCCCEEE
Confidence 49999998644432 23667899998 998764
No 130
>PF05077 DUF678: Protein of unknown function (DUF678); InterPro: IPR007769 This family contains poxvirus proteins belonging to the A19 family. The proteins are of unknown function.
Probab=44.90 E-value=12 Score=29.01 Aligned_cols=12 Identities=17% Similarity=0.163 Sum_probs=9.8
Q ss_pred eEEeeeccccCc
Q 025050 238 LFFLRCEKVKAH 249 (258)
Q Consensus 238 l~~l~C~aCGa~ 249 (258)
--.|+|.|||+.
T Consensus 55 ~~tLsCsACGS~ 66 (74)
T PF05077_consen 55 GNTLSCSACGSE 66 (74)
T ss_pred CCeEeehhcccc
Confidence 347899999986
No 131
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=44.34 E-value=21 Score=27.33 Aligned_cols=32 Identities=16% Similarity=0.403 Sum_probs=23.3
Q ss_pred ccCCCCCCCceeEEc------CceEEeeec--cccCccccc
Q 025050 221 ICLGCKSPDTILSKE------NRLFFLRCE--KVKAHIQSY 253 (258)
Q Consensus 221 lC~~C~sPdT~L~ke------~rl~~l~C~--aCGa~~~~~ 253 (258)
.||.|+++. .+..- -+-.+-.|. .||.++..|
T Consensus 3 ~CP~Cg~~a-~irtSr~~s~~~~~~Y~qC~N~eCg~tF~t~ 42 (72)
T PRK09678 3 HCPLCQHAA-HARTSRYITDTTKERYHQCQNVNCSATFITY 42 (72)
T ss_pred cCCCCCCcc-EEEEChhcChhhheeeeecCCCCCCCEEEEE
Confidence 699999999 33331 244578898 999988765
No 132
>cd03031 GRX_GRX_like Glutaredoxin (GRX) family, GRX-like domain containing protein subfamily; composed of uncharacterized eukaryotic proteins containing a GRX-like domain having only one conserved cysteine, aligning to the C-terminal cysteine of the CXXC motif of GRXs. This subfamily is predominantly composed of plant proteins. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins via a redox active CXXC motif using a similar dithiol mechanism employed by TRXs. GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. Proteins containing only the C-terminal cysteine are generally redox inactive.
Probab=44.34 E-value=17 Score=30.98 Aligned_cols=78 Identities=15% Similarity=0.379 Sum_probs=46.7
Q ss_pred cCCCeEEEeCceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCce-e--ec--CCceEEEEeecChHHHHHHHHHHHHhc
Q 025050 145 MRPPQVLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSG-S--LD--GQQRLVVKGRFAPKNFEGILRRYVNEY 219 (258)
Q Consensus 145 mp~pqV~reG~kKTvi~Nf~eI~k~L~R~pehv~kfl~~ELGt~g-s--id--~~~rliikGrf~~k~ie~~L~~YI~eY 219 (258)
...|||.+.| ..|-...+|-+ ||.+-+ |.+.| ..+.... . =+ |+ ..|
T Consensus 59 ~tvPqVFI~G---~~IGG~del~~-L~e~G~-L~~lL-~~~~~~~~~~~C~~Cgg----------------------~rf 110 (147)
T cd03031 59 VSLPRVFVDG---RYLGGAEEVLR-LNESGE-LRKLL-KGIRARAGGGVCEGCGG----------------------ARF 110 (147)
T ss_pred CCCCEEEECC---EEEecHHHHHH-HHHcCC-HHHHH-hhcccccCCCCCCCCCC----------------------cCe
Confidence 3679999999 25677777765 554433 33333 3321111 1 12 12 148
Q ss_pred cccCCCCCCCceeEEc--CceEEeeeccccCcc
Q 025050 220 VICLGCKSPDTILSKE--NRLFFLRCEKVKAHI 250 (258)
Q Consensus 220 VlC~~C~sPdT~L~ke--~rl~~l~C~aCGa~~ 250 (258)
|.|..|+..--.+..+ +...+++|..|....
T Consensus 111 v~C~~C~Gs~k~~~~~~~~~~~~~rC~~Cneng 143 (147)
T cd03031 111 VPCSECNGSCKVFAENATAAGGFLRCPECNENG 143 (147)
T ss_pred EECCCCCCcceEEeccCcccccEEECCCCCccc
Confidence 9999998776555554 245589999998653
No 133
>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=43.91 E-value=14 Score=26.49 Aligned_cols=8 Identities=38% Similarity=0.887 Sum_probs=4.1
Q ss_pred ccccCCCC
Q 025050 219 YVICLGCK 226 (258)
Q Consensus 219 YVlC~~C~ 226 (258)
.|.|+.|+
T Consensus 26 l~~c~~cg 33 (56)
T PF01783_consen 26 LVKCPNCG 33 (56)
T ss_dssp EEESSSSS
T ss_pred eeeeccCC
Confidence 34555555
No 134
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=43.22 E-value=9.6 Score=23.71 Aligned_cols=17 Identities=29% Similarity=0.733 Sum_probs=6.4
Q ss_pred eeccccCccc--ccccccC
Q 025050 242 RCEKVKAHIQ--SYYLCPI 258 (258)
Q Consensus 242 ~C~aCGa~~~--~~~~~~~ 258 (258)
.|.+||.... .+|.|++
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~ 20 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSE 20 (30)
T ss_dssp --TTTS----S--EEE-TT
T ss_pred cCCcCCCcCCCCceEECcc
Confidence 5778887776 4777763
No 135
>PRK11827 hypothetical protein; Provisional
Probab=42.06 E-value=14 Score=27.45 Aligned_cols=34 Identities=18% Similarity=0.264 Sum_probs=21.7
Q ss_pred HHHHhccccCCCCCCCceeEEcCceEEeeeccccCcc
Q 025050 214 RYVNEYVICLGCKSPDTILSKENRLFFLRCEKVKAHI 250 (258)
Q Consensus 214 ~YI~eYVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~ 250 (258)
..+-+-+.||.|+.+=. +..+.. .|.|.+||-..
T Consensus 3 ~~LLeILaCP~ckg~L~-~~~~~~--~Lic~~~~laY 36 (60)
T PRK11827 3 HRLLEIIACPVCNGKLW-YNQEKQ--ELICKLDNLAF 36 (60)
T ss_pred hHHHhheECCCCCCcCe-EcCCCC--eEECCccCeec
Confidence 34456789999998643 333322 46799998543
No 136
>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=41.96 E-value=14 Score=24.93 Aligned_cols=28 Identities=14% Similarity=0.209 Sum_probs=21.1
Q ss_pred ccCCCCCCCceeEEcCceEEeeeccccC
Q 025050 221 ICLGCKSPDTILSKENRLFFLRCEKVKA 248 (258)
Q Consensus 221 lC~~C~sPdT~L~ke~rl~~l~C~aCGa 248 (258)
.|..|+..-..+..-..--...|.+||+
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 5889998877777633355788999998
No 137
>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=41.73 E-value=14 Score=31.69 Aligned_cols=61 Identities=15% Similarity=0.205 Sum_probs=38.9
Q ss_pred HHHHHHHHHHhhcCCCcccccceeecCCCeEEEeCceeEEE-EehHHHHHHhCCChHHHHHHHHHhhcCc
Q 025050 120 ELLGRVFNILRENNPELAGDRRRTVMRPPQVLREGTKKTVF-VNFMDLCKTMHRQPDHVMTFLLAELGTS 188 (258)
Q Consensus 120 eLL~R~~~~L~~~nP~~~~~~~R~~mp~pqV~reG~kKTvi-~Nf~eI~k~L~R~pehv~kfl~~ELGt~ 188 (258)
.-+.|+...|.+++ ++.- .| ... ...|.....| .|..+|.++|...-..+.+=|..+|--.
T Consensus 43 ~~VRk~L~~L~e~~--Lv~~-~r--~r~---~~~gw~~Y~w~i~~~~i~d~Ik~~~~~~~~~lk~~l~~e 104 (158)
T TIGR00373 43 NEVRKALYALYDAG--LADY-KR--RKD---DETGWYEYTWRINYEKALDVLKRKLEETAKKLREKLEFE 104 (158)
T ss_pred HHHHHHHHHHHHCC--Ccee-ee--eee---cCCCcEEEEEEeCHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 55777777886543 3321 11 111 1125466666 8999999999998888887777766543
No 138
>COG5631 Predicted transcription regulator, contains HTH domain (MarR family) [Transcription]
Probab=40.52 E-value=25 Score=31.45 Aligned_cols=71 Identities=23% Similarity=0.389 Sum_probs=45.1
Q ss_pred cHHHHHHHHHHHHhhcCCC-cccccceeecCCCeEE------EeCceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCce
Q 025050 117 EYEELLGRVFNILRENNPE-LAGDRRRTVMRPPQVL------REGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSG 189 (258)
Q Consensus 117 ~YeeLL~R~~~~L~~~nP~-~~~~~~R~~mp~pqV~------reG~kKTvi~Nf~eI~k~L~R~pehv~kfl~~ELGt~g 189 (258)
..+.-|.|+|+-...=.-. ++... -|.+.+|.+. ..|+-| -+.|||.+|||+.-|+..|-+..|-..|
T Consensus 53 EvEyaL~~ay~Af~rW~vrCmAaag-~~~ls~~e~l~lH~irhrdR~K----~laDic~~ln~eDth~itYslrKL~k~g 127 (199)
T COG5631 53 EVEYALMRAYEAFGRWQVRCMAAAG-EFSLSGPENLLLHIIRHRDRPK----SLADICQMLNREDTHNITYSLRKLLKGG 127 (199)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhc-CCCCcchHHHHHHHHhhcCchh----hHHHHHHHhccccchhHHHHHHHHHhcc
Confidence 4677888888766321000 11111 1233344332 223333 3899999999999999999999998888
Q ss_pred eec
Q 025050 190 SLD 192 (258)
Q Consensus 190 sid 192 (258)
-|.
T Consensus 128 Lit 130 (199)
T COG5631 128 LIT 130 (199)
T ss_pred cee
Confidence 886
No 139
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=39.46 E-value=17 Score=32.38 Aligned_cols=22 Identities=18% Similarity=0.505 Sum_probs=16.8
Q ss_pred cccCCCCCCCceeEEcCceEEeeeccccCc
Q 025050 220 VICLGCKSPDTILSKENRLFFLRCEKVKAH 249 (258)
Q Consensus 220 VlC~~C~sPdT~L~ke~rl~~l~C~aCGa~ 249 (258)
+.|+.|+. ...| ...|..||..
T Consensus 310 ~~C~~cg~------~~~r--~~~C~~cg~~ 331 (364)
T COG0675 310 KTCPCCGH------LSGR--LFKCPRCGFV 331 (364)
T ss_pred ccccccCC------ccce--eEECCCCCCe
Confidence 68999999 3344 4689999975
No 140
>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=39.34 E-value=17 Score=29.44 Aligned_cols=57 Identities=14% Similarity=0.259 Sum_probs=28.4
Q ss_pred ChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHHHHHHhccccCCCCCCCceeEEcCceEEeeeccccCcc
Q 025050 173 QPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKVKAHI 250 (258)
Q Consensus 173 ~pehv~kfl~~ELGt~gsid~~~rliikGrf~~k~ie~~L~~YI~eYVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~ 250 (258)
.|+.|.-.|. .-+.|++-.+-+|.|.- +.--+.|..|+..-+ .+. +...|..||+..
T Consensus 40 ~pe~L~f~f~--~~~~~T~~e~a~L~Ie~--------------~p~~~~C~~Cg~~~~---~~~--~~~~CP~Cgs~~ 96 (113)
T PF01155_consen 40 EPEALRFAFE--VLAEGTILEGAELEIEE--------------VPARARCRDCGHEFE---PDE--FDFSCPRCGSPD 96 (113)
T ss_dssp -HHHHHHHHH--HHHCCSTTTT-EEEEEE--------------E--EEEETTTS-EEE---CHH--CCHH-SSSSSS-
T ss_pred CHHHHHHHHH--HHhCCCCccCCEEEEEe--------------cCCcEECCCCCCEEe---cCC--CCCCCcCCcCCC
Confidence 3666554443 33456776666887743 233578888875311 111 114588888864
No 141
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=39.02 E-value=27 Score=26.86 Aligned_cols=21 Identities=14% Similarity=0.211 Sum_probs=16.7
Q ss_pred ehHHHHHHhCCChHHHHHHHH
Q 025050 162 NFMDLCKTMHRQPDHVMTFLL 182 (258)
Q Consensus 162 Nf~eI~k~L~R~pehv~kfl~ 182 (258)
+-.+||+.|.|++.||.+||.
T Consensus 5 tq~eIA~~lGks~s~Vs~~l~ 25 (93)
T PF08535_consen 5 TQEEIAKRLGKSRSWVSNHLA 25 (93)
T ss_dssp -HHHHHHHTT--HHHHHHHHG
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 357999999999999999987
No 142
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=38.93 E-value=31 Score=25.49 Aligned_cols=30 Identities=13% Similarity=0.143 Sum_probs=24.9
Q ss_pred CCCCCCCceeEEcCceEEeeeccccCcccc
Q 025050 223 LGCKSPDTILSKENRLFFLRCEKVKAHIQS 252 (258)
Q Consensus 223 ~~C~sPdT~L~ke~rl~~l~C~aCGa~~~~ 252 (258)
+-|++-+=.+.+-+--+-++|..||..-++
T Consensus 14 HPCG~~~Wei~R~GaDikikC~gCg~~iml 43 (57)
T PF06107_consen 14 HPCGSNEWEIIRIGADIKIKCLGCGRQIML 43 (57)
T ss_pred CCCCCCEEEEEEccCcEEEEECCCCCEEEE
Confidence 459998888888887789999999987653
No 143
>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=38.77 E-value=16 Score=40.19 Aligned_cols=29 Identities=21% Similarity=0.484 Sum_probs=23.8
Q ss_pred ccccCCCCCCCceeEEcCceEEeeeccccCcccccccc
Q 025050 219 YVICLGCKSPDTILSKENRLFFLRCEKVKAHIQSYYLC 256 (258)
Q Consensus 219 YVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~~~~~~~ 256 (258)
.-.||.|+.. .+..+|..||++...-|.|
T Consensus 625 ~RKCPkCG~y---------Tlk~rCP~CG~~Te~~~pc 653 (1095)
T TIGR00354 625 IRKCPQCGKE---------SFWLKCPVCGELTEQLYYG 653 (1095)
T ss_pred EEECCCCCcc---------cccccCCCCCCccccccce
Confidence 3579999876 5688999999998888877
No 144
>KOG2768 consensus Translation initiation factor 2, beta subunit (eIF-2beta) [Translation, ribosomal structure and biogenesis]
Probab=38.46 E-value=12 Score=34.51 Aligned_cols=21 Identities=38% Similarity=0.278 Sum_probs=14.9
Q ss_pred hccCCCCCcccccccccccCC
Q 025050 14 AELAPFDPTKKKKKKKVVIQD 34 (258)
Q Consensus 14 ~dl~~fd~~kKKKkkK~~~~d 34 (258)
..|..|++.|||||||.....
T Consensus 20 ~~l~~~~~~kKKKKkk~k~~s 40 (231)
T KOG2768|consen 20 ERLDFLSLKKKKKKKKSKSLS 40 (231)
T ss_pred hcccccccccccccCCCCchh
Confidence 457788887777777776553
No 145
>PF14353 CpXC: CpXC protein
Probab=38.29 E-value=17 Score=29.41 Aligned_cols=19 Identities=21% Similarity=0.448 Sum_probs=11.5
Q ss_pred CceEEeeeccccCcccccc
Q 025050 236 NRLFFLRCEKVKAHIQSYY 254 (258)
Q Consensus 236 ~rl~~l~C~aCGa~~~~~~ 254 (258)
+.++...|..||+...+-|
T Consensus 34 g~l~~~~CP~Cg~~~~~~~ 52 (128)
T PF14353_consen 34 GSLFSFTCPSCGHKFRLEY 52 (128)
T ss_pred CCcCEEECCCCCCceecCC
Confidence 4566666666666665544
No 146
>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=38.26 E-value=30 Score=32.43 Aligned_cols=52 Identities=15% Similarity=0.268 Sum_probs=25.5
Q ss_pred eecChHHHHHHH-HHHHHhccccCCCCCCCceeEE-cCceEEeeeccccCcccc
Q 025050 201 GRFAPKNFEGIL-RRYVNEYVICLGCKSPDTILSK-ENRLFFLRCEKVKAHIQS 252 (258)
Q Consensus 201 Grf~~k~ie~~L-~~YI~eYVlC~~C~sPdT~L~k-e~rl~~l~C~aCGa~~~~ 252 (258)
|-.+..|+-.+| ..++.+.+.||.|++.-..=.. ...+--..|..|+...++
T Consensus 12 ~YkS~sQ~aRVltE~Wv~~n~yCP~Cg~~~L~~f~NN~PVaDF~C~~C~eeyEL 65 (254)
T PF06044_consen 12 GYKSNSQIARVLTEDWVAENMYCPNCGSKPLSKFENNRPVADFYCPNCNEEYEL 65 (254)
T ss_dssp HTTT-TTHHHHHHHHHHHHH---TTT--SS-EE--------EEE-TTT--EEEE
T ss_pred hccChhhhhHHHHHHHHHHCCcCCCCCChhHhhccCCCccceeECCCCchHHhh
Confidence 344566666666 6799999999999998544444 446778899999976554
No 147
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=38.24 E-value=15 Score=27.69 Aligned_cols=11 Identities=45% Similarity=0.770 Sum_probs=9.2
Q ss_pred ccCCCCCCCce
Q 025050 221 ICLGCKSPDTI 231 (258)
Q Consensus 221 lC~~C~sPdT~ 231 (258)
+||.|+|+++.
T Consensus 20 ~CP~Cgs~~~t 30 (64)
T COG2093 20 ICPVCGSTDLT 30 (64)
T ss_pred cCCCCCCcccc
Confidence 59999999764
No 148
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=37.32 E-value=17 Score=26.49 Aligned_cols=24 Identities=25% Similarity=0.463 Sum_probs=15.5
Q ss_pred HHhccccCCCCCCCceeEEcCceEEeeecccc
Q 025050 216 VNEYVICLGCKSPDTILSKENRLFFLRCEKVK 247 (258)
Q Consensus 216 I~eYVlC~~C~sPdT~L~ke~rl~~l~C~aCG 247 (258)
+...|.|+.|+++- +--..|..||
T Consensus 24 ~~~l~~C~~CG~~~--------~~H~vC~~CG 47 (57)
T PRK12286 24 APGLVECPNCGEPK--------LPHRVCPSCG 47 (57)
T ss_pred CCcceECCCCCCcc--------CCeEECCCCC
Confidence 34567788887762 3355677777
No 149
>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=37.17 E-value=18 Score=26.17 Aligned_cols=30 Identities=20% Similarity=0.418 Sum_probs=19.4
Q ss_pred cccCCCCCCCceeEEcC--ceEEeeeccccCcccc
Q 025050 220 VICLGCKSPDTILSKEN--RLFFLRCEKVKAHIQS 252 (258)
Q Consensus 220 VlC~~C~sPdT~L~ke~--rl~~l~C~aCGa~~~~ 252 (258)
..||.|+.. |.... +=-.+.|..||+.-..
T Consensus 3 ~~CP~CG~~---iev~~~~~GeiV~Cp~CGaeleV 34 (54)
T TIGR01206 3 FECPDCGAE---IELENPELGELVICDECGAELEV 34 (54)
T ss_pred cCCCCCCCE---EecCCCccCCEEeCCCCCCEEEE
Confidence 379999982 33221 1235699999997554
No 150
>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=37.09 E-value=21 Score=24.96 Aligned_cols=20 Identities=30% Similarity=0.619 Sum_probs=11.6
Q ss_pred HHHHHHHHhcc----ccCCCCCCC
Q 025050 210 GILRRYVNEYV----ICLGCKSPD 229 (258)
Q Consensus 210 ~~L~~YI~eYV----lC~~C~sPd 229 (258)
..+.+||.+.- .||.|++|=
T Consensus 7 ~~~~k~i~~l~~~~~~CPlC~r~l 30 (54)
T PF04423_consen 7 EELKKYIEELKEAKGCCPLCGRPL 30 (54)
T ss_dssp HHHHHHHHHHTT-SEE-TTT--EE
T ss_pred HHHHHHHHHHhcCCCcCCCCCCCC
Confidence 34566666665 999999873
No 151
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=37.08 E-value=37 Score=33.20 Aligned_cols=31 Identities=16% Similarity=0.085 Sum_probs=20.2
Q ss_pred cccCCCCCCCceeEEcCceEEeeeccccCcc
Q 025050 220 VICLGCKSPDTILSKENRLFFLRCEKVKAHI 250 (258)
Q Consensus 220 VlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~ 250 (258)
..||-|.--...+.....--+-+|-+||...
T Consensus 35 ~~CPfh~ek~pSf~v~~~k~~~~Cf~Cg~~G 65 (415)
T TIGR01391 35 GLCPFHHEKTPSFSVSPEKQFYHCFGCGAGG 65 (415)
T ss_pred eeCCCCCCCCCeEEEEcCCCcEEECCCCCCC
Confidence 4899996544456554222356899999864
No 152
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.98 E-value=11 Score=31.78 Aligned_cols=23 Identities=35% Similarity=0.642 Sum_probs=15.4
Q ss_pred ccccCCCCCCCceeEEcCceE--E----eeeccccCc
Q 025050 219 YVICLGCKSPDTILSKENRLF--F----LRCEKVKAH 249 (258)
Q Consensus 219 YVlC~~C~sPdT~L~ke~rl~--~----l~C~aCGa~ 249 (258)
.-.||.|+. +||| | -.|.|||-.
T Consensus 21 ~grCP~CGe--------GrLF~gFLK~~p~C~aCG~d 49 (126)
T COG5349 21 RGRCPRCGE--------GRLFRGFLKVVPACEACGLD 49 (126)
T ss_pred cCCCCCCCC--------chhhhhhcccCchhhhcccc
Confidence 357999984 4444 2 359999964
No 153
>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=36.81 E-value=17 Score=26.18 Aligned_cols=21 Identities=24% Similarity=0.501 Sum_probs=11.4
Q ss_pred ccccCCCCCCCceeEEcCceEEeeecccc
Q 025050 219 YVICLGCKSPDTILSKENRLFFLRCEKVK 247 (258)
Q Consensus 219 YVlC~~C~sPdT~L~ke~rl~~l~C~aCG 247 (258)
.|.|+.|+.+ .+--..|..||
T Consensus 26 l~~C~~cG~~--------~~~H~vc~~cG 46 (55)
T TIGR01031 26 LVVCPNCGEF--------KLPHRVCPSCG 46 (55)
T ss_pred ceECCCCCCc--------ccCeeECCccC
Confidence 4566666654 23344566666
No 154
>PF15494 SRCR_2: Scavenger receptor cysteine-rich domain
Probab=36.67 E-value=22 Score=27.58 Aligned_cols=15 Identities=13% Similarity=0.346 Sum_probs=12.9
Q ss_pred CceEEeeeccccCcc
Q 025050 236 NRLFFLRCEKVKAHI 250 (258)
Q Consensus 236 ~rl~~l~C~aCGa~~ 250 (258)
++++.|+|.+||.+.
T Consensus 84 ~~vVsL~C~~CG~r~ 98 (98)
T PF15494_consen 84 GSVVSLQCSDCGKRT 98 (98)
T ss_pred CCEEEEECcccCCcC
Confidence 579999999999863
No 155
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=36.27 E-value=1e+02 Score=27.02 Aligned_cols=88 Identities=14% Similarity=0.200 Sum_probs=55.1
Q ss_pred EehHHHHHHhCCChHHHHHHH--HHhhcCceee---c-CCceEEEEeecChHHHHHHHHHHH----------------Hh
Q 025050 161 VNFMDLCKTMHRQPDHVMTFL--LAELGTSGSL---D-GQQRLVVKGRFAPKNFEGILRRYV----------------NE 218 (258)
Q Consensus 161 ~Nf~eI~k~L~R~pehv~kfl--~~ELGt~gsi---d-~~~rliikGrf~~k~ie~~L~~YI----------------~e 218 (258)
..-.+||..|+-....|-+-| +.|-|.-..- + +.|++..-=+++..++.++|..=+ ..
T Consensus 37 ~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~r~r~~~~Gr~~y~w~l~~~~i~d~ik~~~~~~~~klk~~l~~e~~~~ 116 (178)
T PRK06266 37 VTDEEIAEQTGIKLNTVRKILYKLYDARLADYKREKDEETNWYTYTWKPELEKLPEIIKKKKMEELKKLKEQLEEEENNM 116 (178)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEeeeeccCCCcEEEEEEeCHHHHHHHHHHHHHHHHHHHHHHhhhccCCC
Confidence 568999999999999888755 4555554422 2 345666655676666666554321 23
Q ss_pred ccccCCCCCCCceeEEcCceEEeeeccccCcc
Q 025050 219 YVICLGCKSPDTILSKENRLFFLRCEKVKAHI 250 (258)
Q Consensus 219 YVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~ 250 (258)
|-.||.|+.-=|.+.--+ +.-.|..||+.-
T Consensus 117 ~Y~Cp~C~~rytf~eA~~--~~F~Cp~Cg~~L 146 (178)
T PRK06266 117 FFFCPNCHIRFTFDEAME--YGFRCPQCGEML 146 (178)
T ss_pred EEECCCCCcEEeHHHHhh--cCCcCCCCCCCC
Confidence 667888885434333211 256788888753
No 156
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=35.98 E-value=92 Score=20.74 Aligned_cols=25 Identities=12% Similarity=0.195 Sum_probs=23.2
Q ss_pred EEEehHHHHHHhCCChHHHHHHHHH
Q 025050 159 VFVNFMDLCKTMHRQPDHVMTFLLA 183 (258)
Q Consensus 159 vi~Nf~eI~k~L~R~pehv~kfl~~ 183 (258)
.|..+.+.|+.|+.+..+|.+++-.
T Consensus 16 ~f~S~~eAa~~lg~~~~~I~~~~~~ 40 (53)
T smart00497 16 EFSSIREAAKYLGISHSSISKYLNT 40 (53)
T ss_pred EecCHHHHHHHhCCCHHHHHHHHhC
Confidence 6999999999999999999999875
No 157
>PHA02942 putative transposase; Provisional
Probab=35.80 E-value=23 Score=34.47 Aligned_cols=27 Identities=19% Similarity=0.438 Sum_probs=19.5
Q ss_pred cccCCCCCCCceeEEcCceEEeeeccccCcc
Q 025050 220 VICLGCKSPDTILSKENRLFFLRCEKVKAHI 250 (258)
Q Consensus 220 VlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~ 250 (258)
-+||.|+.....+ .+| ...|..||...
T Consensus 326 q~Cs~CG~~~~~l--~~r--~f~C~~CG~~~ 352 (383)
T PHA02942 326 VSCPKCGHKMVEI--AHR--YFHCPSCGYEN 352 (383)
T ss_pred ccCCCCCCccCcC--CCC--EEECCCCCCEe
Confidence 5799999866432 345 57899999864
No 158
>TIGR01566 ZF_HD_prot_N ZF-HD homeobox protein Cys/His-rich dimerization domain. This model describes a 54-residue domain found in the N-terminal region of plant proteins, the vast majority of which contain a ZF-HD class homeobox domain toward the C-terminus. The region between the two domains typically is rich in low complexity sequence. The companion ZF-HD homeobox domain is described in model TIGR01565.
Probab=35.53 E-value=17 Score=26.48 Aligned_cols=16 Identities=19% Similarity=0.204 Sum_probs=12.2
Q ss_pred CceEEeeeccccCccc
Q 025050 236 NRLFFLRCEKVKAHIQ 251 (258)
Q Consensus 236 ~rl~~l~C~aCGa~~~ 251 (258)
+..-.|+|.|||..|-
T Consensus 32 ~~~~al~CaACgCHRn 47 (53)
T TIGR01566 32 GDPESLTCAACGCHRN 47 (53)
T ss_pred CCCcceeeeecCcccc
Confidence 3345899999998874
No 159
>PRK05667 dnaG DNA primase; Validated
Probab=35.23 E-value=43 Score=34.53 Aligned_cols=33 Identities=15% Similarity=0.169 Sum_probs=21.8
Q ss_pred hcc-ccCCCCCCCceeEEcCceEEeeeccccCcc
Q 025050 218 EYV-ICLGCKSPDTILSKENRLFFLRCEKVKAHI 250 (258)
Q Consensus 218 eYV-lC~~C~sPdT~L~ke~rl~~l~C~aCGa~~ 250 (258)
.|+ .||-|.--...+.....--+-+|-+||+..
T Consensus 34 ~~~~~CPfH~ektpSf~V~~~k~~~~CF~Cg~~G 67 (580)
T PRK05667 34 NYKGLCPFHDEKTPSFTVSPDKQFYHCFGCGAGG 67 (580)
T ss_pred ceeecCCCCCCCCCceEEECCCCeEEECCCCCCC
Confidence 344 799996544466664333367899999864
No 160
>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=35.21 E-value=24 Score=34.34 Aligned_cols=40 Identities=23% Similarity=0.324 Sum_probs=21.4
Q ss_pred hccccCCCCCCCc-----------eeEE-cCceEEeeeccccCccccccccc
Q 025050 218 EYVICLGCKSPDT-----------ILSK-ENRLFFLRCEKVKAHIQSYYLCP 257 (258)
Q Consensus 218 eYVlC~~C~sPdT-----------~L~k-e~rl~~l~C~aCGa~~~~~~~~~ 257 (258)
..|.|.+|...-- .|.. +.---|.+|..||.+.-+|+.-|
T Consensus 251 kav~C~~C~yt~~~~~~~C~~~~H~l~~~~a~KRFFkC~~C~~Rt~sl~r~P 302 (344)
T PF09332_consen 251 KAVTCKQCKYTAFKPSDRCKEEGHPLKWHDAVKRFFKCKDCGNRTISLERLP 302 (344)
T ss_dssp EEEEETTT--EESS--HHHHHTT--EEEEEEE-EEEE-T-TS-EEEESSSS-
T ss_pred EEEEcCCCCCcccCcchhHHhcCCceEEeeeeeeeEECCCCCCeeeecccCC
Confidence 4789999963211 1222 22233889999999998887655
No 161
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=35.10 E-value=41 Score=39.19 Aligned_cols=42 Identities=19% Similarity=0.261 Sum_probs=28.2
Q ss_pred HHH-HHHHHHHHHhccccCCCCCCCceeE---EcCceEEeeeccccCcc
Q 025050 206 KNF-EGILRRYVNEYVICLGCKSPDTILS---KENRLFFLRCEKVKAHI 250 (258)
Q Consensus 206 k~i-e~~L~~YI~eYVlC~~C~sPdT~L~---ke~rl~~l~C~aCGa~~ 250 (258)
..+ ..+|.+++ .-+-||.|++++-.|+ .+.+ ...|..||-+.
T Consensus 1691 ~~~~~~~~~~~~-~~~~cp~c~~~~~~~~~~~~~~g--c~~c~~cg~s~ 1736 (1740)
T PRK08332 1691 DGIPEEKIRELL-GVVYCPVCYEKEGKLVELRMESG--CATCPVCGWSK 1736 (1740)
T ss_pred hhHHHHHHHHHh-ccCCCCCCCCCCCcceeeEecCC--ceeCCCCCCcc
Confidence 335 56666665 3345999999975554 4566 56899999653
No 162
>COG3741 HutG N-formylglutamate amidohydrolase [Amino acid transport and metabolism]
Probab=35.04 E-value=6.1 Score=37.27 Aligned_cols=64 Identities=20% Similarity=0.332 Sum_probs=50.7
Q ss_pred eeEEEEehHHHHHHhCCChHHHHHH---HHHhhcCceeecCCceEEEEeecChHHHHHHHHHHHHhc
Q 025050 156 KKTVFVNFMDLCKTMHRQPDHVMTF---LLAELGTSGSLDGQQRLVVKGRFAPKNFEGILRRYVNEY 219 (258)
Q Consensus 156 kKTvi~Nf~eI~k~L~R~pehv~kf---l~~ELGt~gsid~~~rliikGrf~~k~ie~~L~~YI~eY 219 (258)
.-++-.||.-.+--+||+|.++.-| --..||+...+|+.+.++--|+.+..++..-|..|-+=|
T Consensus 63 A~~l~A~fsR~~vDvNR~p~~~~l~~~~~ttGL~~~~~fdge~l~~~g~~~~~~e~~~Rle~~~~PY 129 (272)
T COG3741 63 ATLLRANFSRAVVDVNREPDGASLYPGRVTTGLGPVTTFDGEPLYIYGGAPTPAEALARLETLWKPY 129 (272)
T ss_pred chhhhccccceeEecCCCCCCCcCccccccCCccccccccCccccccCCCCCHHHHHHHHHHhhccH
Confidence 4455566666666789999999888 446788999999998999988999999998887775543
No 163
>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=34.01 E-value=41 Score=21.88 Aligned_cols=9 Identities=11% Similarity=0.338 Sum_probs=7.0
Q ss_pred eeccccCcc
Q 025050 242 RCEKVKAHI 250 (258)
Q Consensus 242 ~C~aCGa~~ 250 (258)
.|..||..-
T Consensus 34 ~C~~CGE~~ 42 (46)
T TIGR03831 34 VCPQCGEEY 42 (46)
T ss_pred ccccCCCEe
Confidence 599999753
No 164
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=33.56 E-value=1.1e+02 Score=21.44 Aligned_cols=46 Identities=7% Similarity=-0.018 Sum_probs=32.5
Q ss_pred ehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHH
Q 025050 162 NFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGI 211 (258)
Q Consensus 162 Nf~eI~k~L~R~pehv~kfl~~ELGt~gsid~~~rliikGrf~~k~ie~~ 211 (258)
+..++|+.++.+|.+|..|....+-.+..-+.+++. +|+..+|..+
T Consensus 2 s~~eva~~~gvs~~tlr~~~~~gli~~~~~~~~g~r----~y~~~dl~~l 47 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYERIGLLPPPIRTEGGYR----LYSDEDLERL 47 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCCCCCCCccCCCCCE----ecCHHHHHHH
Confidence 468999999999999999987666554312223322 5888888755
No 165
>PHA00626 hypothetical protein
Probab=32.99 E-value=32 Score=25.59 Aligned_cols=30 Identities=17% Similarity=0.092 Sum_probs=17.2
Q ss_pred ccCCCCCCCceeEEc--CceEEeeeccccCcc
Q 025050 221 ICLGCKSPDTILSKE--NRLFFLRCEKVKAHI 250 (258)
Q Consensus 221 lC~~C~sPdT~L~ke--~rl~~l~C~aCGa~~ 250 (258)
.||.|+|-+-..-.. +.----+|..||...
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~f 33 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYND 33 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCee
Confidence 699999865433111 101134788888653
No 166
>PF05379 Peptidase_C23: Carlavirus endopeptidase ; InterPro: IPR008041 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C23 (clan CA). The type example is Carlavirus (apple stem pitting virus) endopeptidase, this thought to play a role in the post-translational cleavage of the high molecular weight primary translation products of the virus.; GO: 0003968 RNA-directed RNA polymerase activity, 0016817 hydrolase activity, acting on acid anhydrides
Probab=32.99 E-value=44 Score=26.28 Aligned_cols=63 Identities=14% Similarity=0.274 Sum_probs=43.2
Q ss_pred hHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEee-cChHHHHHHHHHHHHhccccCCCCCCCceeEE
Q 025050 163 FMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGR-FAPKNFEGILRRYVNEYVICLGCKSPDTILSK 234 (258)
Q Consensus 163 f~eI~k~L~R~pehv~kfl~~ELGt~gsid~~~rliikGr-f~~k~ie~~L~~YI~eYVlC~~C~sPdT~L~k 234 (258)
+.-||++|+|.+..|++.|....+.. +- +-+..|. ++..+++.++.- |=+|-.|......++-
T Consensus 7 i~AiA~aL~R~~~dVl~Vl~~~~~~~--~~---~~l~~G~Gl~l~~le~~f~~----F~I~A~v~~~g~~~~l 70 (89)
T PF05379_consen 7 IRAIAEALGRREQDVLAVLSRKCGEE--LL---EELWSGEGLDLEDLEELFEL----FDICAHVNFGGETFVL 70 (89)
T ss_pred hHHHHHHhCCCHHHHHHHHHhccCHH--HH---HHHHcCCCcCHHHHHHHHHH----cCeEEEEEECCEEEEE
Confidence 46799999999999999999988852 21 2233344 667777766655 4778777655544443
No 167
>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=32.61 E-value=18 Score=22.44 Aligned_cols=25 Identities=20% Similarity=0.239 Sum_probs=13.5
Q ss_pred ccCCCCCCCceeEEcCceEEeeeccccCcccc
Q 025050 221 ICLGCKSPDTILSKENRLFFLRCEKVKAHIQS 252 (258)
Q Consensus 221 lC~~C~sPdT~L~ke~rl~~l~C~aCGa~~~~ 252 (258)
.|+.|.. .|...-.+|.+||+.+++
T Consensus 6 ~C~~C~~-------~N~~~~~~C~~C~~~rp~ 30 (30)
T PF00641_consen 6 KCPSCTF-------MNPASRSKCVACGAPRPG 30 (30)
T ss_dssp EETTTTE-------EEESSSSB-TTT--BTTB
T ss_pred cCCCCcC-------CchHHhhhhhCcCCCCcC
Confidence 5666642 123345789999998874
No 168
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=31.95 E-value=39 Score=24.70 Aligned_cols=12 Identities=33% Similarity=0.744 Sum_probs=8.7
Q ss_pred HhccccCCCCCC
Q 025050 217 NEYVICLGCKSP 228 (258)
Q Consensus 217 ~eYVlC~~C~sP 228 (258)
-++..||.|++|
T Consensus 5 lniL~Cp~ck~p 16 (68)
T PF03966_consen 5 LNILACPVCKGP 16 (68)
T ss_dssp CGTBB-TTTSSB
T ss_pred HhhhcCCCCCCc
Confidence 457889999994
No 169
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=31.91 E-value=26 Score=29.28 Aligned_cols=31 Identities=23% Similarity=0.478 Sum_probs=24.3
Q ss_pred cccCCCCCCCceeE----E---cCceEEeeeccccCcc
Q 025050 220 VICLGCKSPDTILS----K---ENRLFFLRCEKVKAHI 250 (258)
Q Consensus 220 VlC~~C~sPdT~L~----k---e~rl~~l~C~aCGa~~ 250 (258)
-.||.|+.++-.+. | |+...|-.|..|+.+.
T Consensus 75 ~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k~ 112 (116)
T KOG2907|consen 75 HKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYKF 112 (116)
T ss_pred ccCcccCCchhhhhhhhcccccCCceEEEEcCccceee
Confidence 37999999875443 3 5789999999999764
No 170
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=31.77 E-value=42 Score=33.93 Aligned_cols=33 Identities=18% Similarity=0.194 Sum_probs=22.9
Q ss_pred ccccCCCCCCCceeEE--c--CceEEeeeccccCcccc
Q 025050 219 YVICLGCKSPDTILSK--E--NRLFFLRCEKVKAHIQS 252 (258)
Q Consensus 219 YVlC~~C~sPdT~L~k--e--~rl~~l~C~aCGa~~~~ 252 (258)
.++|+.|+.-.|..+. + .+.+.-.|. ||.....
T Consensus 175 ~pic~~cg~~~~~~~~~~d~~~~~v~y~~~-cG~~~~~ 211 (510)
T PRK00750 175 LPICPKCGKVLTTPVISYDAEAGTVTYDCE-CGHEGEV 211 (510)
T ss_pred eeeCCCCCccceEEEEEEeCCCCEEEEEcC-CCCEEEE
Confidence 4799999999987763 2 333333786 9987643
No 171
>PRK01310 hypothetical protein; Validated
Probab=31.75 E-value=1e+02 Score=24.97 Aligned_cols=40 Identities=23% Similarity=0.471 Sum_probs=30.1
Q ss_pred HHHHHHHHHhhcCc--------eeecCCceEEEEeecChHHHHHHHHHHH
Q 025050 175 DHVMTFLLAELGTS--------GSLDGQQRLVVKGRFAPKNFEGILRRYV 216 (258)
Q Consensus 175 ehv~kfl~~ELGt~--------gsid~~~rliikGrf~~k~ie~~L~~YI 216 (258)
++|++||...||+. |.-...-.+.|.| +++++...|..++
T Consensus 55 ~ali~~LA~~l~v~ks~I~iv~G~tsR~K~v~I~~--~~~~l~~~l~~~~ 102 (104)
T PRK01310 55 RALIELLAKALGVPKSSVRLLSGATSRLKQLRIDG--DPEDLGEALRALT 102 (104)
T ss_pred HHHHHHHHHHhCCChhhEEEEecCCCCceEEEEeC--CHHHHHHHHHHHh
Confidence 68999999999973 2223345677777 7888888888775
No 172
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=31.72 E-value=1.9e+02 Score=21.64 Aligned_cols=58 Identities=21% Similarity=0.248 Sum_probs=36.3
Q ss_pred EEEeCceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeec-CCceEEEEeecC----hHHHHHHHHHHHHhc
Q 025050 150 VLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLD-GQQRLVVKGRFA----PKNFEGILRRYVNEY 219 (258)
Q Consensus 150 V~reG~kKTvi~Nf~eI~k~L~R~pehv~kfl~~ELGt~gsid-~~~rliikGrf~----~k~ie~~L~~YI~eY 219 (258)
|.+-|+...|.. |..++.-+.-.-|..-.+. .++.++|.=.-. ...|..++++.+++|
T Consensus 3 i~k~GNS~~vtI------------Pk~i~~~lgl~~Gd~v~v~~~~~~iii~~~~~~~~~~~~~~~~~~~~~~~y 65 (74)
T TIGR02609 3 IRKVGNSLVVTL------------PKEVLESLGLKEGDTLYVDEEEGGLKLKRFDEGKELEKKMQMAVERAMSKY 65 (74)
T ss_pred EEEECCeeEEEE------------CHHHHHHcCcCCCCEEEEEEECCEEEEEECCCCccHHHHHHHHHHHHHHHH
Confidence 566675544433 7777777777778777775 356788874333 344445566666665
No 173
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=31.68 E-value=38 Score=37.05 Aligned_cols=39 Identities=23% Similarity=0.532 Sum_probs=28.2
Q ss_pred ccccCCCCCC---CceeEE-cCceEEeeeccccCccc----cccccc
Q 025050 219 YVICLGCKSP---DTILSK-ENRLFFLRCEKVKAHIQ----SYYLCP 257 (258)
Q Consensus 219 YVlC~~C~sP---dT~L~k-e~rl~~l~C~aCGa~~~----~~~~~~ 257 (258)
--.||.|+.| +..++- -+.-+.-+|..||..+. .|-.||
T Consensus 796 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 842 (1006)
T PRK12775 796 VATCPKCHRPLEGDEEYVCCATSELQWRCDDCGKVSEGFAFPYGMCP 842 (1006)
T ss_pred CccCcccCCCCCCCceeEEecCcceeeehhhhccccccccCCcCcCc
Confidence 4589999998 334442 45667889999998764 466787
No 174
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=31.56 E-value=29 Score=30.61 Aligned_cols=70 Identities=21% Similarity=0.379 Sum_probs=40.2
Q ss_pred hCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHHHH------HHhccccCCCCCCCceeEEcC---c---
Q 025050 170 MHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILRRY------VNEYVICLGCKSPDTILSKEN---R--- 237 (258)
Q Consensus 170 L~R~pehv~kfl~~ELGt~gsid~~~rliikGrf~~k~ie~~L~~Y------I~eYVlC~~C~sPdT~L~ke~---r--- 237 (258)
|-|+-+.+-++ -+|..+-+ |.-....+|+-.+|.++ --++-.||.|+.+=-.+.++. +
T Consensus 52 lTRDr~L~~r~---k~g~~~i~-------i~~~s~~~Ql~e~~~~~~l~~~~~~e~~RCp~CN~~L~~vs~eev~~~Vp~ 121 (165)
T COG1656 52 LTRDRELYKRA---KLGIKAIL-------IRSDSIEEQLAEFLARLGLKPRLFPEFSRCPECNGELEKVSREEVKEKVPE 121 (165)
T ss_pred EeccHHHHHHh---hccCceEE-------EeCCCHHHHHHHHHHHhccchhcccccccCcccCCEeccCcHHHHhhccch
Confidence 44666555554 55554433 33334456666664432 134889999987754444432 1
Q ss_pred ------eEEeeeccccCc
Q 025050 238 ------LFFLRCEKVKAH 249 (258)
Q Consensus 238 ------l~~l~C~aCGa~ 249 (258)
--|.+|..||..
T Consensus 122 ~~~~~~~~f~~C~~Cgki 139 (165)
T COG1656 122 KVYRNYEEFYRCPKCGKI 139 (165)
T ss_pred hhhhcccceeECCCCccc
Confidence 127889999963
No 175
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=31.44 E-value=21 Score=26.51 Aligned_cols=13 Identities=31% Similarity=0.301 Sum_probs=5.3
Q ss_pred ccccCCCCCCCce
Q 025050 219 YVICLGCKSPDTI 231 (258)
Q Consensus 219 YVlC~~C~sPdT~ 231 (258)
+..|+.|+|.+|.
T Consensus 48 g~KC~~C~SYNT~ 60 (61)
T PF14599_consen 48 GHKCSHCGSYNTR 60 (61)
T ss_dssp ----TTTS---EE
T ss_pred hhcCCCCCCcccC
Confidence 6889999999985
No 176
>PF12225 MTHFR_C: Methylene-tetrahydrofolate reductase C terminal; InterPro: IPR022026 This family is found in bacteria and archaea, and is approximately 100 amino acids in length. There is a conserved NGPCGG sequence motif. This family is the C-terminal of methylene-tetrahydrofolate reductase. This protein reduces FAD using the reducing equivalents from reduced FAD, subsequently reduces tetrahydrofolate. The C-terminal of MTHFR contains the FAD binding site and is the catalytic portion of the enzyme.
Probab=31.25 E-value=25 Score=28.39 Aligned_cols=30 Identities=23% Similarity=0.617 Sum_probs=21.5
Q ss_pred CceeE---EcCceEEeeeccccCccccc--ccccC
Q 025050 229 DTILS---KENRLFFLRCEKVKAHIQSY--YLCPI 258 (258)
Q Consensus 229 dT~L~---ke~rl~~l~C~aCGa~~~~~--~~~~~ 258 (258)
||.++ +.-+.|.-.|.+||.-.-.+ |+||+
T Consensus 6 ~t~f~g~~~~~~~~~~~C~~CG~C~L~~TggiCP~ 40 (97)
T PF12225_consen 6 NTLFIGVEREVKVFLERCRACGDCVLGDTGGICPM 40 (97)
T ss_pred CcccccceeeccchhccCCCCCCcccccccccCcc
Confidence 44444 34578888899999877665 68886
No 177
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=31.17 E-value=1.3e+02 Score=19.09 Aligned_cols=47 Identities=11% Similarity=0.147 Sum_probs=31.0
Q ss_pred EEehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHH
Q 025050 160 FVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGIL 212 (258)
Q Consensus 160 i~Nf~eI~k~L~R~pehv~kfl~~ELGt~gsid~~~rliikGrf~~k~ie~~L 212 (258)
|.++.++|+.|+-++..|.+++..-.- ++...|+ + -+|....|+..|
T Consensus 1 ~lt~~e~a~~lgis~~ti~~~~~~g~i-~~~~~g~-~----~~~~~~~l~~~~ 47 (49)
T TIGR01764 1 YLTVEEAAEYLGVSKDTVYRLIHEGEL-PAYRVGR-H----YRIPREDVDEYL 47 (49)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHcCCC-CeEEeCC-e----EEEeHHHHHHHH
Confidence 357899999999999999999865322 2222232 2 235666666554
No 178
>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=30.80 E-value=48 Score=26.77 Aligned_cols=18 Identities=33% Similarity=0.623 Sum_probs=11.7
Q ss_pred ccCCCCCCCceeEEcCce
Q 025050 221 ICLGCKSPDTILSKENRL 238 (258)
Q Consensus 221 lC~~C~sPdT~L~ke~rl 238 (258)
.||.|+|++..++.-..+
T Consensus 88 ~CP~Cgs~~~~i~~G~el 105 (113)
T PF01155_consen 88 SCPRCGSPDVEIISGREL 105 (113)
T ss_dssp H-SSSSSS-EEEEESS-E
T ss_pred CCcCCcCCCcEEccCCeE
Confidence 399999999888765444
No 179
>PF06573 Churchill: Churchill protein; InterPro: IPR009508 This family consists of several eukaryotic Churchill proteins. This protein contains a novel zinc binding region that mediates FGF signalling during neural development. The slow induction by FGF of a transcription factor (Churchill) in the neural plate in turn induces expression of Sip1 (Smad interacting protein-1), which inhibits mesodermal genes and sensitizes cells to later neural inducing factors [].; GO: 0008270 zinc ion binding, 0007275 multicellular organismal development, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2JOX_A.
Probab=30.78 E-value=43 Score=27.83 Aligned_cols=36 Identities=19% Similarity=0.463 Sum_probs=19.3
Q ss_pred HHHHhccccCCCCCCCceeEEc------C----ceEEeeeccccCc
Q 025050 214 RYVNEYVICLGCKSPDTILSKE------N----RLFFLRCEKVKAH 249 (258)
Q Consensus 214 ~YI~eYVlC~~C~sPdT~L~ke------~----rl~~l~C~aCGa~ 249 (258)
.|+-.|+-|..|++-|-.++.+ + =.|-..|..|+..
T Consensus 22 SyllN~~~Ca~C~krdfv~i~nk~~~eedgeEivTY~HvC~nC~Hv 67 (112)
T PF06573_consen 22 SYLLNFVGCASCQKRDFVLISNKSIEEEDGEEIVTYDHVCKNCHHV 67 (112)
T ss_dssp --TTTB---SSS--SS-EEEEEEEEEEETTEEEEEEEEEETTT--E
T ss_pred ceeeechhhhccCCCCcEEEecccccccCCcEEEEeeeccCccceE
Confidence 3677899999999999777642 2 2567889999864
No 180
>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=30.65 E-value=52 Score=22.24 Aligned_cols=28 Identities=14% Similarity=0.498 Sum_probs=19.9
Q ss_pred cCCCCCCC---c-eeEEcCceEEeeeccccCc
Q 025050 222 CLGCKSPD---T-ILSKENRLFFLRCEKVKAH 249 (258)
Q Consensus 222 C~~C~sPd---T-~L~ke~rl~~l~C~aCGa~ 249 (258)
|.-|+++= - .+...|++|+.=|..|-+.
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC~tC~~~ 32 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCCPTCLSQ 32 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEECHHHHHH
Confidence 66788762 2 2334789999999999654
No 181
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=30.52 E-value=86 Score=32.06 Aligned_cols=57 Identities=19% Similarity=0.292 Sum_probs=28.1
Q ss_pred HhhcCceeecCCceEEEEeecChHHHHHHHHHHHHh-----------ccccCCCCCCCceeEEcCceEEeeeccccCcc
Q 025050 183 AELGTSGSLDGQQRLVVKGRFAPKNFEGILRRYVNE-----------YVICLGCKSPDTILSKENRLFFLRCEKVKAHI 250 (258)
Q Consensus 183 ~ELGt~gsid~~~rliikGrf~~k~ie~~L~~YI~e-----------YVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~ 250 (258)
..+-+.|.|- .+.+--+.+++.+++++++=.+. +-+|+.|+.-.. . .-.|..||++.
T Consensus 447 ~~~~~GG~I~---hv~l~e~~n~~al~~lv~~~~~~~~i~Y~~in~~~~~C~~CG~~~~------~--~~~CP~CGs~~ 514 (546)
T PF13597_consen 447 QKLYTGGHIF---HVELGEKPNPEALEKLVRYAMENTGIPYFTINPPIDICPDCGYIGG------E--GDKCPKCGSEN 514 (546)
T ss_dssp HTTSTTB--E---EEE----T-HHHHHHHHHHHHH--H-SEEEEE--EEEETTT---S----------EEE-CCC----
T ss_pred ccccCCceEE---EEEcCCCCCHHHHHHHHHHHHHhCCCCeEEEecCcccccCCCcCCC------C--CCCCCCCCCcc
Confidence 3455566663 44454456788999988887772 347999996432 2 56799999984
No 182
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=30.06 E-value=48 Score=22.02 Aligned_cols=28 Identities=21% Similarity=0.418 Sum_probs=17.5
Q ss_pred ccccCCCCCCCceeEE---cCceEEeeeccc
Q 025050 219 YVICLGCKSPDTILSK---ENRLFFLRCEKV 246 (258)
Q Consensus 219 YVlC~~C~sPdT~L~k---e~rl~~l~C~aC 246 (258)
.|.||.|.|.+-...- .++----+|..|
T Consensus 5 ~v~CP~C~s~~~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 5 DVHCPRCQSTEGVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eeeCCCCCCCCcceeCCCCCCCCEeEecCcC
Confidence 5899999997643321 124445567776
No 183
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=29.78 E-value=36 Score=28.35 Aligned_cols=55 Identities=20% Similarity=0.331 Sum_probs=33.6
Q ss_pred HHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHHHHHHhccccCCCCCCCceeEEcCceEEeeeccccCccc
Q 025050 177 VMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKVKAHIQ 251 (258)
Q Consensus 177 v~kfl~~ELGt~gsid~~~rliikGrf~~k~ie~~L~~YI~eYVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~~ 251 (258)
.++|-+ +.-+.|++-.+.+++|. ++.-.-.|..|.-+ +..+.- ...|..||+.+.
T Consensus 43 ~l~FaF-ev~~egT~aega~l~Ie--------------~~p~~~~C~~C~~~---~~~e~~--~~~CP~C~s~~~ 97 (115)
T COG0375 43 ALRFAF-EVVAEGTIAEGAELHIE--------------EEPAECWCLDCGQE---VELEEL--DYRCPKCGSINL 97 (115)
T ss_pred HHHHHH-HHHhccCcccCCEEEEE--------------EeccEEEeccCCCe---ecchhh--eeECCCCCCCce
Confidence 344444 45556777656688883 45556789999443 333322 222999998653
No 184
>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=29.43 E-value=43 Score=30.98 Aligned_cols=36 Identities=17% Similarity=0.193 Sum_probs=20.1
Q ss_pred ccccCCCCCCCceeE----E--cCceEEeeeccccCcccccc
Q 025050 219 YVICLGCKSPDTILS----K--ENRLFFLRCEKVKAHIQSYY 254 (258)
Q Consensus 219 YVlC~~C~sPdT~L~----k--e~rl~~l~C~aCGa~~~~~~ 254 (258)
-+.|+.|++.+-.-. . +...-.-.|..||+-.+.++
T Consensus 211 R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK~vd 252 (290)
T PF04216_consen 211 RIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLKTVD 252 (290)
T ss_dssp TTS-TTT---SS-EEE--------SEEEEEETTTTEEEEEEE
T ss_pred CCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHHHHh
Confidence 578999988764422 2 24567889999998666554
No 185
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=29.33 E-value=77 Score=21.94 Aligned_cols=28 Identities=4% Similarity=0.052 Sum_probs=25.8
Q ss_pred EehHHHHHHhCC-ChHHHHHHHHHhhcCc
Q 025050 161 VNFMDLCKTMHR-QPDHVMTFLLAELGTS 188 (258)
Q Consensus 161 ~Nf~eI~k~L~R-~pehv~kfl~~ELGt~ 188 (258)
.++.+||..++= ++.|+.+.|....|.+
T Consensus 51 ~~~~~ia~~~g~~s~~~f~r~Fk~~~g~s 79 (84)
T smart00342 51 LSVTEIALRVGFSSQSYFSRAFKKLFGVT 79 (84)
T ss_pred CCHHHHHHHhCCCChHHHHHHHHHHHCcC
Confidence 579999999999 9999999999999875
No 186
>PF14116 YyzF: YyzF-like protein
Probab=29.01 E-value=72 Score=22.62 Aligned_cols=40 Identities=23% Similarity=0.314 Sum_probs=27.6
Q ss_pred hHHHHHHHHHHHHhccccCCCCCCCceeEEcCceEEeeeccccCc
Q 025050 205 PKNFEGILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKVKAH 249 (258)
Q Consensus 205 ~k~ie~~L~~YI~eYVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~ 249 (258)
.++|+-.|+.||++|=. .|+..-..+..-.-.+|.-|+..
T Consensus 3 ~EHie~AiD~~Vde~e~-----aP~i~~l~~~~~~~~~C~~C~~~ 42 (48)
T PF14116_consen 3 EEHIELAIDDFVDEYEQ-----APDIEKLEEVEKLPTTCEYCDQP 42 (48)
T ss_pred HHHHHHHHHHHHHhhcc-----CCCeEeccccCCCCCcchhhCCC
Confidence 46899999999999864 56665555544445677777543
No 187
>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=28.97 E-value=45 Score=34.02 Aligned_cols=32 Identities=22% Similarity=0.414 Sum_probs=22.7
Q ss_pred ccccCCCCCCCce----eEEc----CceEEeeeccccCcc
Q 025050 219 YVICLGCKSPDTI----LSKE----NRLFFLRCEKVKAHI 250 (258)
Q Consensus 219 YVlC~~C~sPdT~----L~ke----~rl~~l~C~aCGa~~ 250 (258)
||-||.|+-.-.. |.=+ .....+.|..||..-
T Consensus 200 ~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i 239 (557)
T PF05876_consen 200 YVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEI 239 (557)
T ss_pred EccCCCCCCCccccccceeecCCCCccceEEECCCCcCCC
Confidence 8999999876442 2212 246789999999864
No 188
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=28.88 E-value=29 Score=29.21 Aligned_cols=15 Identities=20% Similarity=0.184 Sum_probs=7.1
Q ss_pred HHHHHHhccccCCCC
Q 025050 212 LRRYVNEYVICLGCK 226 (258)
Q Consensus 212 L~~YI~eYVlC~~C~ 226 (258)
|+++---...|+.|+
T Consensus 22 l~~~kl~g~kC~~CG 36 (140)
T COG1545 22 LKEGKLLGTKCKKCG 36 (140)
T ss_pred hhhCcEEEEEcCCCC
Confidence 333333445555554
No 189
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=28.72 E-value=1.1e+02 Score=23.72 Aligned_cols=46 Identities=7% Similarity=0.010 Sum_probs=34.4
Q ss_pred ehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHH
Q 025050 162 NFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGI 211 (258)
Q Consensus 162 Nf~eI~k~L~R~pehv~kfl~~ELGt~gsid~~~rliikGrf~~k~ie~~ 211 (258)
++.++|+.++-+|.+|-.|....+..+...+++|+ -.|+..+|+.+
T Consensus 2 ti~eva~~~gvs~~tlR~ye~~Gll~~~~~~~~g~----R~y~~~di~~l 47 (103)
T cd01106 2 TVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENGY----RLYTEEDLERL 47 (103)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCCCCCCCccCCCCc----eeeCHHHHHHH
Confidence 57899999999999999998776665554444432 24888888776
No 190
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=28.48 E-value=69 Score=24.60 Aligned_cols=27 Identities=7% Similarity=-0.101 Sum_probs=25.4
Q ss_pred ehHHHHHHhCCChHHHHHHHHHhhcCc
Q 025050 162 NFMDLCKTMHRQPDHVMTFLLAELGTS 188 (258)
Q Consensus 162 Nf~eI~k~L~R~pehv~kfl~~ELGt~ 188 (258)
++.+||+.++-++.|+.+.|...+|.+
T Consensus 23 ~~~~lA~~~~~S~~~l~r~f~~~~g~s 49 (107)
T PRK10219 23 NIDVVAKKSGYSKWYLQRMFRTVTHQT 49 (107)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHCcC
Confidence 789999999999999999999999985
No 191
>TIGR01051 topA_bact DNA topoisomerase I, bacterial. This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events.
Probab=28.03 E-value=53 Score=33.90 Aligned_cols=53 Identities=21% Similarity=0.202 Sum_probs=29.5
Q ss_pred eEEEEeecChHHHHHHHHHHHHhcc----------------ccCCCCCCCceeEEcC-ceEEeeecc---ccCcc
Q 025050 196 RLVVKGRFAPKNFEGILRRYVNEYV----------------ICLGCKSPDTILSKEN-RLFFLRCEK---VKAHI 250 (258)
Q Consensus 196 rliikGrf~~k~ie~~L~~YI~eYV----------------lC~~C~sPdT~L~ke~-rl~~l~C~a---CGa~~ 250 (258)
..|-.|+.+..++-+-+..||...| .||.|+++ .+.+.+ +--|..|.. |+...
T Consensus 535 ~~I~~G~~~~~~~l~~~~~~~~~~v~~~~~~~~~~~~~~~~~CP~Cg~~--~~~~~~~~gkf~gCs~y~~C~~~~ 607 (610)
T TIGR01051 535 DEIAEGKAEWKPVLKNFYTGFSSKVKKLRNMRIIVDFKTSQDCPLCGRP--MVVKLGKYGPFLACSNFPECKYTK 607 (610)
T ss_pred HHHHcCCCCHHHHHHHHHHHHHHHHHHhhhcccccccccCCCCCCCCCe--eEEEecCCCceeeCCCCCCCCCCC
Confidence 4455577776666555555544332 49999874 232221 113678877 66443
No 192
>KOG3084 consensus NADH pyrophosphatase I of the Nudix family of hydrolases [Replication, recombination and repair]
Probab=27.79 E-value=53 Score=32.05 Aligned_cols=44 Identities=25% Similarity=0.459 Sum_probs=28.0
Q ss_pred HHHHHHHHHHhccccCCCCCCCceeEEcCceEEeeec--cccCcccccc
Q 025050 208 FEGILRRYVNEYVICLGCKSPDTILSKENRLFFLRCE--KVKAHIQSYY 254 (258)
Q Consensus 208 ie~~L~~YI~eYVlC~~C~sPdT~L~ke~rl~~l~C~--aCGa~~~~~~ 254 (258)
.-..+-.++..|-.||.|++|- ..+.-++ -++|. .|-+..-.||
T Consensus 139 ~ars~l~W~skykFCp~CG~~t-kp~e~g~--k~~Cs~~~C~~~n~~yP 184 (345)
T KOG3084|consen 139 VARSLLDWVSKYKFCPGCGSPT-KPEEAGT--KLQCSDETCPSCNVIYP 184 (345)
T ss_pred HHHHHHHHHHHhccCcccCCCc-ccccCCc--cceeecccCCcCCeecc
Confidence 3455667899999999999984 3322222 34555 6665555555
No 193
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=26.52 E-value=1.2e+02 Score=23.65 Aligned_cols=45 Identities=13% Similarity=0.228 Sum_probs=32.0
Q ss_pred ehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHH
Q 025050 162 NFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGI 211 (258)
Q Consensus 162 Nf~eI~k~L~R~pehv~kfl~~ELGt~gsid~~~rliikGrf~~k~ie~~ 211 (258)
++.++|+.++-++.+|-.|....|..+..-.++.| .|+..+|..+
T Consensus 3 ~i~eva~~~gVs~~tLR~ye~~Gli~p~r~~~g~R-----~Ys~~dv~~l 47 (98)
T cd01279 3 PISVAAELLGIHPQTLRVYDRLGLVSPARTNGGGR-----RYSNNDLELL 47 (98)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCCCCCCCcCCCCCe-----eECHHHHHHH
Confidence 78999999999999999998777666522222322 2677766654
No 194
>PRK04023 DNA polymerase II large subunit; Validated
Probab=26.42 E-value=41 Score=37.38 Aligned_cols=30 Identities=23% Similarity=0.468 Sum_probs=18.3
Q ss_pred ccccCCCCCCCceeEEcCceEEeeeccccCccccccccc
Q 025050 219 YVICLGCKSPDTILSKENRLFFLRCEKVKAHIQSYYLCP 257 (258)
Q Consensus 219 YVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~~~~~~~~ 257 (258)
+-.||.|+.. |..+ .+|..||.....| -||
T Consensus 638 ~frCP~CG~~-Te~i-------~fCP~CG~~~~~y-~CP 667 (1121)
T PRK04023 638 YRRCPFCGTH-TEPV-------YRCPRCGIEVEED-ECE 667 (1121)
T ss_pred cccCCCCCCC-CCcc-------eeCccccCcCCCC-cCC
Confidence 5799999998 2221 2566666655543 354
No 195
>PRK08402 replication factor A; Reviewed
Probab=25.96 E-value=44 Score=32.54 Aligned_cols=48 Identities=15% Similarity=0.137 Sum_probs=28.3
Q ss_pred eEEEEeecChHHHHHHHHHHHHhccccCCCCCCCceeEEcCceEEeeeccccCccccc
Q 025050 196 RLVVKGRFAPKNFEGILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKVKAHIQSY 253 (258)
Q Consensus 196 rliikGrf~~k~ie~~L~~YI~eYVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~~~~ 253 (258)
-+.|.|.+.. |.. .+ -|-.||+|+. .++.+..--.-+|..||...+.|
T Consensus 196 ~v~v~g~Iv~--i~~---~~--~y~aCp~CnK---kv~~~~~~~~~~Ce~~~~v~p~~ 243 (355)
T PRK08402 196 FVEVRGTIAK--VYR---VL--VYDACPECRR---KVDYDPATDTWICPEHGEVEPIK 243 (355)
T ss_pred EEEEEEEEEE--Eec---Ce--eEecCCCCCe---EEEEecCCCCEeCCCCCCcCcce
Confidence 3677776554 111 33 3999999976 44422111134899999766655
No 196
>PRK14973 DNA topoisomerase I; Provisional
Probab=25.66 E-value=40 Score=36.84 Aligned_cols=31 Identities=10% Similarity=0.111 Sum_probs=20.4
Q ss_pred ccCCCCCCCceeEEcCc-eEEeeeccccCccc
Q 025050 221 ICLGCKSPDTILSKENR-LFFLRCEKVKAHIQ 251 (258)
Q Consensus 221 lC~~C~sPdT~L~ke~r-l~~l~C~aCGa~~~ 251 (258)
.|+.|++|--.+.+.+| =+|+-|..|.+..+
T Consensus 637 ~Cp~CG~p~~~~~r~Gr~g~fl~CP~C~~~~~ 668 (936)
T PRK14973 637 VCPIHHLNHVRLIRKGARPWDIGCPLCSHIES 668 (936)
T ss_pred CCCCCCCCceEEeecCCCcccccCccccchhh
Confidence 58888888444445553 46788888876543
No 197
>PF05315 ICEA: ICEA Protein; InterPro: IPR007979 This family consists of several ICEA proteins from Helicobacter pylori, infection of which causes gastritis and peptic ulcer disease, and the bacteria is classified as a definite carcinogen of gastric cancer. ICEA1 is speculated to be associated with peptic ulcer disease and may have endonuclease activity [].
Probab=25.64 E-value=47 Score=30.58 Aligned_cols=64 Identities=17% Similarity=0.264 Sum_probs=48.1
Q ss_pred CCChHHHHHHHHHhhcCceeecC-CceEEEEeecChHHHHHHHHHHHHhc------cccCCCCCC-CceeEE
Q 025050 171 HRQPDHVMTFLLAELGTSGSLDG-QQRLVVKGRFAPKNFEGILRRYVNEY------VICLGCKSP-DTILSK 234 (258)
Q Consensus 171 ~R~pehv~kfl~~ELGt~gsid~-~~rliikGrf~~k~ie~~L~~YI~eY------VlC~~C~sP-dT~L~k 234 (258)
.|.-..|.+++--|++-.-+-.. =.++.++|--+...|+.-||.=|+.| |+|..|++. +|.|..
T Consensus 45 cR~~SsLak~y~lEfdk~~~~gnsId~IRLnG~n~~~~fnq~Ir~dIk~~yk~q~Cvm~g~~g~sent~iei 116 (230)
T PF05315_consen 45 CRSSSSLAKEYILEFDKRQTSGNSIDRIRLNGFNTEKVFNQNIRQDIKNYYKQQCCVMCGVRGNSENTKIEI 116 (230)
T ss_pred cCCchHHHHHhhcccccccCCCccHHHHHHcCcCchhhhhhHHHHHHHHHHHhcCeeeecccCCCccceeee
Confidence 47788888888888875322211 14889999999999999999888877 788888665 577765
No 198
>PF12728 HTH_17: Helix-turn-helix domain
Probab=25.61 E-value=1.7e+02 Score=19.43 Aligned_cols=47 Identities=9% Similarity=0.121 Sum_probs=30.2
Q ss_pred EehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHH
Q 025050 161 VNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILR 213 (258)
Q Consensus 161 ~Nf~eI~k~L~R~pehv~kfl~~ELGt~gsid~~~rliikGrf~~k~ie~~L~ 213 (258)
.+..|+|+.|+-++..|.+++-...--.-. .|. ++ +|..++|++.|.
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g~i~~~~-~g~-~~----~~~~~~l~~~~~ 48 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQGKIPPFK-IGR-KW----RIPKSDLDRWLE 48 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCCCeEE-eCC-EE----EEeHHHHHHHHH
Confidence 478999999999999999998654222211 111 22 356666666554
No 199
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=25.55 E-value=70 Score=21.69 Aligned_cols=31 Identities=19% Similarity=0.404 Sum_probs=22.3
Q ss_pred hccccCCCCCCCceeEEcCceEEeeeccccC
Q 025050 218 EYVICLGCKSPDTILSKENRLFFLRCEKVKA 248 (258)
Q Consensus 218 eYVlC~~C~sPdT~L~ke~rl~~l~C~aCGa 248 (258)
..|.|+.|+++=|.-...++-.+.+|..+-.
T Consensus 4 g~l~C~~CG~~m~~~~~~~~~~yy~C~~~~~ 34 (58)
T PF13408_consen 4 GLLRCGHCGSKMTRRKRKGKYRYYRCSNRRR 34 (58)
T ss_pred CcEEcccCCcEeEEEECCCCceEEEcCCCcC
Confidence 3589999999977755555556788877643
No 200
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=25.46 E-value=31 Score=24.70 Aligned_cols=27 Identities=19% Similarity=0.330 Sum_probs=18.2
Q ss_pred ccCCCCCCCceeEEcCceEEeeeccccCcc
Q 025050 221 ICLGCKSPDTILSKENRLFFLRCEKVKAHI 250 (258)
Q Consensus 221 lC~~C~sPdT~L~ke~rl~~l~C~aCGa~~ 250 (258)
.|..|+..-..+... -.++|.-||++.
T Consensus 8 ~C~~Cg~~~~~~~~~---~~irCp~Cg~rI 34 (49)
T COG1996 8 KCARCGREVELDQET---RGIRCPYCGSRI 34 (49)
T ss_pred EhhhcCCeeehhhcc---CceeCCCCCcEE
Confidence 588888876333332 256899999874
No 201
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=25.33 E-value=27 Score=26.28 Aligned_cols=10 Identities=20% Similarity=0.199 Sum_probs=5.4
Q ss_pred ccCCCCCCCc
Q 025050 221 ICLGCKSPDT 230 (258)
Q Consensus 221 lC~~C~sPdT 230 (258)
.||.|+|.+|
T Consensus 19 ~Cp~Cgs~~~ 28 (64)
T PRK06393 19 TCPVHGDEKT 28 (64)
T ss_pred cCCCCCCCcC
Confidence 4555555553
No 202
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=25.32 E-value=75 Score=33.17 Aligned_cols=63 Identities=16% Similarity=0.314 Sum_probs=0.0
Q ss_pred hcCceeecCCceEEEEeec--ChHHHHHHHHHHHH----------hccccCCCCCCCceeEEcCceEEeeeccccCc---
Q 025050 185 LGTSGSLDGQQRLVVKGRF--APKNFEGILRRYVN----------EYVICLGCKSPDTILSKENRLFFLRCEKVKAH--- 249 (258)
Q Consensus 185 LGt~gsid~~~rliikGrf--~~k~ie~~L~~YI~----------eYVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~--- 249 (258)
+-+.|.|. .+.+-|.. +++.++++++..-+ .+-.|+.|+. .-.+. -.|..||++
T Consensus 516 ~~~GG~I~---hv~l~~~~~~n~~Al~~lvk~~~~~~i~Y~sin~~~~~C~~CGy-~g~~~-------~~CP~CG~~d~~ 584 (618)
T PRK14704 516 LCNGGHIT---YIELDGAAMHNKKALKQIVQAMAEHGVGYGSINHPVDRCKCCSY-HGVIG-------NECPSCGNEDEA 584 (618)
T ss_pred ccCCeEEE---EEEECCccCCCHHHHHHHHHHHHhcCCceEEeCCCCeecCCCCC-CCCcC-------ccCcCCCCCCcc
Q ss_pred ------ccccccc-cC
Q 025050 250 ------IQSYYLC-PI 258 (258)
Q Consensus 250 ------~~~~~~~-~~ 258 (258)
|--=||. |+
T Consensus 585 ~~~v~~Ri~GYl~~pv 600 (618)
T PRK14704 585 NIERIRRITGYLVGDM 600 (618)
T ss_pred hhHHHHHHHhHhcCch
No 203
>cd02983 P5_C P5 family, C-terminal redox inactive TRX-like domain; P5 is a protein disulfide isomerase (PDI)-related protein with a domain structure of aa'b (where a and a' are redox active TRX domains and b is a redox inactive TRX-like domain). Like PDI, P5 is located in the endoplasmic reticulum (ER) and displays both isomerase and chaperone activities, which are independent of each other. Compared to PDI, the isomerase and chaperone activities of P5 are lower. The first cysteine in the CXXC motif of both redox active domains in P5 is necessary for isomerase activity. The P5 gene was first isolated as an amplified gene from a hydroxyurea-resistant hamster cell line. The zebrafish P5 homolog has been implicated to play a critical role in establishing left/right asymmetries in the embryonic midline. The C-terminal domain is likely involved in substrate binding, similar to the b and b' domains of PDI.
Probab=25.19 E-value=83 Score=25.81 Aligned_cols=42 Identities=17% Similarity=0.287 Sum_probs=26.8
Q ss_pred HHHHHHH-hhcCcee--ecC-CceEE-EEeecChHHHHHHHHHHHHh
Q 025050 177 VMTFLLA-ELGTSGS--LDG-QQRLV-VKGRFAPKNFEGILRRYVNE 218 (258)
Q Consensus 177 v~kfl~~-ELGt~gs--id~-~~rli-ikGrf~~k~ie~~L~~YI~e 218 (258)
+++||+- +-+.+.- ++. ++++. ..|.|+.+.|...+..|+.-
T Consensus 71 ~~~~fgl~~~~~P~v~i~~~~~~KY~~~~~~~t~e~i~~Fv~~~l~G 117 (130)
T cd02983 71 LEEALNIGGFGYPAMVAINFRKMKFATLKGSFSEDGINEFLRELSYG 117 (130)
T ss_pred HHHHcCCCccCCCEEEEEecccCccccccCccCHHHHHHHHHHHHcC
Confidence 6666652 2233322 232 23777 88999999998888888764
No 204
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=24.72 E-value=89 Score=25.22 Aligned_cols=28 Identities=14% Similarity=0.173 Sum_probs=25.6
Q ss_pred EehHHHHHHhCCChHHHHHHHHHhhcCc
Q 025050 161 VNFMDLCKTMHRQPDHVMTFLLAELGTS 188 (258)
Q Consensus 161 ~Nf~eI~k~L~R~pehv~kfl~~ELGt~ 188 (258)
.++.+||+.++-.|.|+.+.|..++|.+
T Consensus 26 ~sl~~lA~~~g~S~~~l~r~Fk~~~G~s 53 (127)
T PRK11511 26 LSLEKVSERSGYSKWHLQRMFKKETGHS 53 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence 3578999999999999999999999985
No 205
>KOG2422 consensus Uncharacterized conserved protein [Function unknown]
Probab=24.35 E-value=88 Score=32.96 Aligned_cols=21 Identities=14% Similarity=0.205 Sum_probs=15.2
Q ss_pred ccHHHHHHHHHHHHhhcCCCc
Q 025050 116 YEYEELLGRVFNILRENNPEL 136 (258)
Q Consensus 116 ~~YeeLL~R~~~~L~~~nP~~ 136 (258)
-.|..-+.++|.-.+.-||+.
T Consensus 168 r~l~~k~~k~~v~~~~lnpdt 188 (665)
T KOG2422|consen 168 RSLGSKSCKLFVDFKKLNPDT 188 (665)
T ss_pred hhHHHHHHHHHHhhhccCCCc
Confidence 357788888886666778874
No 206
>cd01896 DRG The developmentally regulated GTP-binding protein (DRG) subfamily is an uncharacterized member of the Obg family, an evolutionary branch of GTPase superfamily proteins. GTPases act as molecular switches regulating diverse cellular processes. DRG2 and DRG1 comprise the DRG subfamily in eukaryotes. In view of their widespread expression in various tissues and high conservation among distantly related species in eukaryotes and archaea, DRG proteins may regulate fundamental cellular processes. It is proposed that the DRG subfamily proteins play their physiological roles through RNA binding.
Probab=24.32 E-value=98 Score=27.53 Aligned_cols=95 Identities=12% Similarity=0.113 Sum_probs=63.3
Q ss_pred HHHHHHHHHHhhcCCCcccccceeecCCCeEEEeCceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEE
Q 025050 120 ELLGRVFNILRENNPELAGDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVV 199 (258)
Q Consensus 120 eLL~R~~~~L~~~nP~~~~~~~R~~mp~pqV~reG~kKTvi~Nf~eI~k~L~R~pehv~kfl~~ELGt~gsid~~~rlii 199 (258)
..++++.+.|.... -|+.-++|+|...+ +.+-=.++.--.+..+=+.+.+.+ ++.|.|.. +..+.|
T Consensus 92 ~~~~~~~~~l~~~g-------i~l~~~~~~v~~~~-~~~ggi~~~~~~~~~~~~~~~v~~-~l~~~~i~-----~~~v~~ 157 (233)
T cd01896 92 GHREILERELEGVG-------IRLNKRPPNITIKK-KKKGGINITSTVPLTKLDEKTIKA-ILREYKIH-----NADVLI 157 (233)
T ss_pred hHHHHHHHHHHHcC-------ceecCCCCeEEEEE-EecCCEEEeccCCCCCCCHHHHHH-HHHHhCee-----eEEEEE
Confidence 35666677774321 14556778888876 333233333345566667777777 66788885 456789
Q ss_pred EeecChHHHHHHHH---HHHHhccccCCCCCC
Q 025050 200 KGRFAPKNFEGILR---RYVNEYVICLGCKSP 228 (258)
Q Consensus 200 kGrf~~k~ie~~L~---~YI~eYVlC~~C~sP 228 (258)
.|..+.++|.++|. .|+...+....|-..
T Consensus 158 ~~~~~~~~~~~~~~~~~~y~p~iiV~NK~Dl~ 189 (233)
T cd01896 158 REDITVDDLIDVIEGNRVYIPCLYVYNKIDLI 189 (233)
T ss_pred ccCCCHHHHHHHHhCCceEeeEEEEEECccCC
Confidence 99999999999997 677777777777543
No 207
>PF04770 ZF-HD_dimer: ZF-HD protein dimerisation region; InterPro: IPR006456 The homeodomain (HD) is a 60-amino acid DNA-binding domain found in many transcription factors. HD-containing proteins are found in diverse organisms such as humans, Drosophila, nematode worms, and plants, where they play important roles in development. Zinc-finger-homeodomain (ZF- HD) subfamily proteins have only been identified in plants, and likely play plant specific roles. ZF-HD proteins are expressed predominantly or exclusively in floral tissue, indicating a likely regulatory role during floral development []. The ZF-HD class of homeodomain proteins may also be involved in the photosynthesis-related mesophyll-specific gene expression of phosphoenolpyruvate carboxylase in C4 species [] and in pathogen signaling and plant defense mechanisms []. These proteins share three domains of high sequence similarity: the homeodomain (II) located at the carboxy-terminus, and two other segments (Ia and Ib) located in the amino-terminal part. These N-terminal domains contain five conserved cysteine residues and at least three conserved histidine residues whose spacing ressembles zinc-binding domains involved in dimerization of transcription factors. Although the two domains contain at least eight potential zinc-binding amino-acids, the unique spacing of the conserved cysteine and histidine residues within domain Ib suggests that both domains form one rather than two zinc finger structures. The two conserved motifs Ia and Ib constitute a dimerization domain which is sufficient for the formation of homo- and heterodimers []. This entry represents the N-terminal Cysteine/Histidine-rich dimerization domain. The companion ZF-HD homeobox domain is described in IPR006455 from INTERPRO.
Probab=24.16 E-value=36 Score=25.42 Aligned_cols=16 Identities=19% Similarity=0.277 Sum_probs=13.0
Q ss_pred CceEEeeeccccCccc
Q 025050 236 NRLFFLRCEKVKAHIQ 251 (258)
Q Consensus 236 ~rl~~l~C~aCGa~~~ 251 (258)
+..-.|+|.|||..|-
T Consensus 36 g~~~al~CaACgCHRn 51 (60)
T PF04770_consen 36 GTPEALKCAACGCHRN 51 (60)
T ss_pred CCcccceecccCcchh
Confidence 4567899999998874
No 208
>PRK12366 replication factor A; Reviewed
Probab=24.11 E-value=45 Score=34.67 Aligned_cols=30 Identities=13% Similarity=0.262 Sum_probs=19.2
Q ss_pred ccccCCCCCCCceeEEcCceEEeeeccccCccccc
Q 025050 219 YVICLGCKSPDTILSKENRLFFLRCEKVKAHIQSY 253 (258)
Q Consensus 219 YVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~~~~ 253 (258)
|-.||+|+. .++..++ .-+|..||...+.|
T Consensus 532 y~aCp~Cnk---Kv~~~~g--~~~C~~c~~~~p~~ 561 (637)
T PRK12366 532 LYLCPNCRK---RVEEVDG--EYICEFCGEVEPNE 561 (637)
T ss_pred EecccccCe---EeEcCCC--cEECCCCCCCCCcE
Confidence 778999865 3333333 24699999875554
No 209
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=24.08 E-value=1.6e+02 Score=27.84 Aligned_cols=72 Identities=19% Similarity=0.244 Sum_probs=47.0
Q ss_pred eeecCCCeEEEeCceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecCC--ceEEEEeecChHHHHHH--HHHHHH
Q 025050 142 RTVMRPPQVLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQ--QRLVVKGRFAPKNFEGI--LRRYVN 217 (258)
Q Consensus 142 R~~mp~pqV~reG~kKTvi~Nf~eI~k~L~R~pehv~kfl~~ELGt~gsid~~--~rliikGrf~~k~ie~~--L~~YI~ 217 (258)
||.+-.-...+++. ++-.|||+.|.-.|+-|..|| ++|=..|-|+.. ++|.|.-+=-..-++++ ||+|++
T Consensus 12 ~fqIL~ei~~~qp~-----v~q~eIA~~lgiT~QaVsehi-K~Lv~eG~i~~~gR~~Y~iTkkG~e~l~~~~~dlr~f~~ 85 (260)
T COG1497 12 RFQILSEIAVRQPR-----VKQKEIAKKLGITLQAVSEHI-KELVKEGLIEKEGRGEYEITKKGAEWLLEQLSDLRRFSE 85 (260)
T ss_pred HHHHHHHHHHhCCC-----CCHHHHHHHcCCCHHHHHHHH-HHHHhccceeecCCeeEEEehhHHHHHHHHHHHHHHHHH
Confidence 44444444445553 567899999999999999886 678888989853 45666544333333322 577877
Q ss_pred hc
Q 025050 218 EY 219 (258)
Q Consensus 218 eY 219 (258)
+-
T Consensus 86 ev 87 (260)
T COG1497 86 EV 87 (260)
T ss_pred HH
Confidence 63
No 210
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=24.02 E-value=1.1e+02 Score=33.20 Aligned_cols=32 Identities=13% Similarity=0.359 Sum_probs=20.9
Q ss_pred cccCCCCCCCceeEEcCceEEeeecc---ccCccc
Q 025050 220 VICLGCKSPDTILSKENRLFFLRCEK---VKAHIQ 251 (258)
Q Consensus 220 VlC~~C~sPdT~L~ke~rl~~l~C~a---CGa~~~ 251 (258)
..||.|++....+..-..=.|+.|.. |..+++
T Consensus 593 ~~CP~Cg~~~L~~k~gr~G~Fl~Cs~yP~C~~t~~ 627 (860)
T PRK06319 593 IDCPKCHKGKLVKIWAKNRYFYGCSEYPECDYKTS 627 (860)
T ss_pred cccCCCCCcceeEEecCCCceeeccCCccccccCC
Confidence 46999998877665432234888866 765544
No 211
>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=23.95 E-value=46 Score=29.20 Aligned_cols=33 Identities=15% Similarity=0.272 Sum_probs=22.0
Q ss_pred ccccCCCCCC-CceeEEcCceEE-------eeeccccCccc
Q 025050 219 YVICLGCKSP-DTILSKENRLFF-------LRCEKVKAHIQ 251 (258)
Q Consensus 219 YVlC~~C~sP-dT~L~ke~rl~~-------l~C~aCGa~~~ 251 (258)
-..||.|+.| .=.+..++-+.+ --|..||...|
T Consensus 39 I~~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpyP 79 (158)
T PF10083_consen 39 ITSCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPYP 79 (158)
T ss_pred HHHCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCCc
Confidence 3579999887 344555544433 47999998755
No 212
>COG5595 Zn-ribbon-containing, possibly nucleic-acid-binding protein [General function prediction only]
Probab=23.68 E-value=34 Score=31.47 Aligned_cols=80 Identities=19% Similarity=0.328 Sum_probs=56.6
Q ss_pred HHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHHH-------------H-HHhccccCCCCCCCc
Q 025050 165 DLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILRR-------------Y-VNEYVICLGCKSPDT 230 (258)
Q Consensus 165 eI~k~L~R~pehv~kfl~~ELGt~gsid~~~rliikGrf~~k~ie~~L~~-------------Y-I~eYVlC~~C~sPdT 230 (258)
.-|+.|.-.-..+-++.++|+.-. +..|.++||...+.||..+.. | =+.|--||.|+.- =
T Consensus 155 qacdqlqmnga~leq~al~eIsd~-----dSdLsk~Gr~l~~rIek~t~iptyYylyrVgGnSlAqek~r~CPsC~k~-W 228 (256)
T COG5595 155 QACDQLQMNGAVLEQQALAEISDL-----DSDLSKHGRYLSKRIEKCTGIPTYYYLYRVGGNSLAQEKYRCCPSCGKD-W 228 (256)
T ss_pred HHHHHHHhhhHHHHHHHHHHHhcc-----cchHHHHHHHHHHHHHHHhCCCceEEEEEecCchhhhhccCCCCccccc-c
Confidence 368888888888888888888653 347888899999999987653 1 1456789999852 1
Q ss_pred eeEEc--CceEEeeeccccCccc
Q 025050 231 ILSKE--NRLFFLRCEKVKAHIQ 251 (258)
Q Consensus 231 ~L~ke--~rl~~l~C~aCGa~~~ 251 (258)
. .++ -.+|..+|..|--.+-
T Consensus 229 q-lk~~i~d~fhfkcd~crlvsn 250 (256)
T COG5595 229 Q-LKNPIFDTFHFKCDTCRLVSN 250 (256)
T ss_pred e-eccchhhheeeecccceeecc
Confidence 1 122 2578899999965443
No 213
>COG5242 TFB4 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 [Transcription / DNA replication, recombination, and repair]
Probab=23.60 E-value=1.1e+02 Score=28.77 Aligned_cols=49 Identities=18% Similarity=0.285 Sum_probs=37.0
Q ss_pred cceeecCCCeEEEeCceeEEEEehHHHHHHhC------CChHHHHHHHHHhhcCceeec
Q 025050 140 RRRTVMRPPQVLREGTKKTVFVNFMDLCKTMH------RQPDHVMTFLLAELGTSGSLD 192 (258)
Q Consensus 140 ~~R~~mp~pqV~reG~kKTvi~Nf~eI~k~L~------R~pehv~kfl~~ELGt~gsid 192 (258)
..++.+|--.+.+.|+.++ +.+-|++-+ -+|+-+++||+.-|++.|++-
T Consensus 179 Aqk~~ipI~v~~i~g~s~f----l~Q~~daTgG~Yl~ve~~eGllqyL~~~lf~d~~lr 233 (296)
T COG5242 179 AQKFGIPISVFSIFGNSKF----LLQCCDATGGDYLTVEDTEGLLQYLLSLLFTDGELR 233 (296)
T ss_pred hhhcCCceEEEEecCccHH----HHHHhhccCCeeEeecCchhHHHHHHHHhcCCCCcc
Confidence 3578888888888885343 456666654 468999999999999988763
No 214
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=23.16 E-value=39 Score=23.30 Aligned_cols=10 Identities=20% Similarity=0.491 Sum_probs=7.5
Q ss_pred eeeccccCcc
Q 025050 241 LRCEKVKAHI 250 (258)
Q Consensus 241 l~C~aCGa~~ 250 (258)
++|.+||+..
T Consensus 2 ~kC~~CG~~G 11 (40)
T PF15288_consen 2 VKCKNCGAFG 11 (40)
T ss_pred cccccccccc
Confidence 5788888754
No 215
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=23.15 E-value=31 Score=28.87 Aligned_cols=25 Identities=20% Similarity=0.295 Sum_probs=20.2
Q ss_pred CceeEEcCceEEeeeccccCccccc
Q 025050 229 DTILSKENRLFFLRCEKVKAHIQSY 253 (258)
Q Consensus 229 dT~L~ke~rl~~l~C~aCGa~~~~~ 253 (258)
++...+++-++-.+|..||+.-|+|
T Consensus 63 e~~~~~~ga~I~~kCpkCghe~m~Y 87 (116)
T KOG2907|consen 63 ENESSADGAVIKHKCPKCGHEEMSY 87 (116)
T ss_pred cccccccccchhccCcccCCchhhh
Confidence 4445556778899999999999987
No 216
>PRK07220 DNA topoisomerase I; Validated
Probab=23.13 E-value=58 Score=34.51 Aligned_cols=29 Identities=14% Similarity=0.226 Sum_probs=19.9
Q ss_pred cccCCCCCCCceeEEcC-ceEEeeeccccC
Q 025050 220 VICLGCKSPDTILSKEN-RLFFLRCEKVKA 248 (258)
Q Consensus 220 VlC~~C~sPdT~L~ke~-rl~~l~C~aCGa 248 (258)
..|+.|+.+...+.+.+ +-||+.|..|..
T Consensus 636 ~~Cp~Cg~~~~k~~~~g~~~~~~~Cp~C~~ 665 (740)
T PRK07220 636 KVCEAHGLNHIRIINGGKRPWDLGCPQCNF 665 (740)
T ss_pred CCCCCCCCceEEEEecCCccceeeCCCCCC
Confidence 36999988765444443 346789988875
No 217
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.08 E-value=74 Score=32.07 Aligned_cols=48 Identities=17% Similarity=0.432 Sum_probs=36.0
Q ss_pred EEeecChHHHHHHHHHHHHhcc------ccCCCCCCCceeEEcCceEEeeeccccCc
Q 025050 199 VKGRFAPKNFEGILRRYVNEYV------ICLGCKSPDTILSKENRLFFLRCEKVKAH 249 (258)
Q Consensus 199 ikGrf~~k~ie~~L~~YI~eYV------lC~~C~sPdT~L~ke~rl~~l~C~aCGa~ 249 (258)
+.-|+-...|+.++.+|..+-+ .||+|+. .+.|..+---++|..||.-
T Consensus 342 le~Ryg~rvve~~vn~~lsekwl~~N~krCP~C~v---~IEr~eGCnKM~C~~c~~~ 395 (445)
T KOG1814|consen 342 LEKRYGKRVVEELVNDFLSEKWLESNSKRCPKCKV---VIERSEGCNKMHCTKCGTY 395 (445)
T ss_pred HHHHhhHHHHHHHHHHHHHHHHHHhcCCCCCcccc---eeecCCCccceeecccccc
Confidence 3345566688888888888543 5999975 4677667778999999975
No 218
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=22.96 E-value=88 Score=21.40 Aligned_cols=34 Identities=18% Similarity=0.358 Sum_probs=19.5
Q ss_pred HHHHHHHHhccccCCCCCCCceeEEcCceEEeeecccc
Q 025050 210 GILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKVK 247 (258)
Q Consensus 210 ~~L~~YI~eYVlC~~C~sPdT~L~ke~rl~~l~C~aCG 247 (258)
-+|+-|-----.|+.|+.|=.. .+++++ .|-+|+
T Consensus 8 ~LL~G~~ML~~~Cp~C~~PL~~-~k~g~~---~Cv~C~ 41 (41)
T PF06677_consen 8 YLLQGWTMLDEHCPDCGTPLMR-DKDGKI---YCVSCG 41 (41)
T ss_pred HHHHhHhHhcCccCCCCCeeEE-ecCCCE---ECCCCC
Confidence 3445555555679999755333 133444 577775
No 219
>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=22.96 E-value=95 Score=32.33 Aligned_cols=45 Identities=20% Similarity=0.445 Sum_probs=31.0
Q ss_pred EEeecChHHHHHHHHHHHHh----------ccccCCCCCCCceeEEcCceEEeeeccccCcc
Q 025050 199 VKGRFAPKNFEGILRRYVNE----------YVICLGCKSPDTILSKENRLFFLRCEKVKAHI 250 (258)
Q Consensus 199 ikGrf~~k~ie~~L~~YI~e----------YVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~ 250 (258)
+-.+.+++.+++++++=.+. +-+|+.|+... +++ .-.|..||+..
T Consensus 502 l~e~~n~ea~~~lv~~~~~~~i~Y~tin~~~siC~~CGy~~------g~~-~~~CP~CGs~~ 556 (586)
T TIGR02827 502 LEESLSEDGYRKLLRVAADTGCNYFCFNIKITICNDCHHID------KRT-LHRCPVCGSAN 556 (586)
T ss_pred cCCCCCHHHHHHHHHHHHhcCCceEEeCCCCeecCCCCCcC------CCc-CCcCcCCCCcc
Confidence 43456889999998876553 56799999731 221 36899999654
No 220
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=22.91 E-value=2.3e+02 Score=19.63 Aligned_cols=46 Identities=7% Similarity=0.114 Sum_probs=30.4
Q ss_pred ehHHHHHHhCCChHHHHHHHHHhhcCcee-ecCCceEEEEeecChHHHHHHH
Q 025050 162 NFMDLCKTMHRQPDHVMTFLLAELGTSGS-LDGQQRLVVKGRFAPKNFEGIL 212 (258)
Q Consensus 162 Nf~eI~k~L~R~pehv~kfl~~ELGt~gs-id~~~rliikGrf~~k~ie~~L 212 (258)
.+.|+|+.+.-++..|-+|... .|.... -+.+++ -.|+..+|+.+.
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~-~g~~~~~r~~~~~----r~yt~~~v~~l~ 48 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERR-YGLPAPQRTDGGH----RLYSEADVARLR 48 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh-CCCCCCCcCCCCC----eecCHHHHHHHH
Confidence 4689999999999999998754 344332 222211 247888887653
No 221
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=22.85 E-value=51 Score=23.15 Aligned_cols=23 Identities=26% Similarity=0.684 Sum_probs=14.7
Q ss_pred cChHHHHHHHHHHHHhccccCCCCC
Q 025050 203 FAPKNFEGILRRYVNEYVICLGCKS 227 (258)
Q Consensus 203 f~~k~ie~~L~~YI~eYVlC~~C~s 227 (258)
.++..++.+... ++-|.|+.|+.
T Consensus 32 l~~~~~~~i~~~--~~i~~Cp~CgR 54 (56)
T PF02591_consen 32 LPPQELNEIRKG--DEIVFCPNCGR 54 (56)
T ss_pred cCHHHHHHHHcC--CCeEECcCCCc
Confidence 355666666555 66777777764
No 222
>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=22.72 E-value=83 Score=30.11 Aligned_cols=14 Identities=14% Similarity=0.487 Sum_probs=7.3
Q ss_pred eeeccccCcccccc
Q 025050 241 LRCEKVKAHIQSYY 254 (258)
Q Consensus 241 l~C~aCGa~~~~~~ 254 (258)
++|-.||+...+-|
T Consensus 225 ~~C~~Cg~~~~l~y 238 (305)
T TIGR01562 225 VKCSHCEESKHLAY 238 (305)
T ss_pred ccCCCCCCCCceee
Confidence 45555555555433
No 223
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=22.58 E-value=56 Score=31.08 Aligned_cols=32 Identities=25% Similarity=0.661 Sum_probs=19.5
Q ss_pred ccccCCCCCC---CceeE--Ec---C------ce--EEeeeccccCcc
Q 025050 219 YVICLGCKSP---DTILS--KE---N------RL--FFLRCEKVKAHI 250 (258)
Q Consensus 219 YVlC~~C~sP---dT~L~--ke---~------rl--~~l~C~aCGa~~ 250 (258)
-|.|.+|+.+ -|.+- |+ + ++ |+++|..|++..
T Consensus 40 ~i~C~~C~~~I~kG~rFNA~Ke~v~~E~Yls~~I~rF~~kC~~C~~~i 87 (324)
T PF04502_consen 40 NIWCNTCGEYIYKGVRFNARKEKVGNEKYLSTPIYRFYIKCPRCSNEI 87 (324)
T ss_pred cCcCCCCccccccceeeeeeeEecCCCccccceEEEEEEEcCCCCCEE
Confidence 3889999876 12221 11 1 23 578999998753
No 224
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=22.55 E-value=41 Score=24.56 Aligned_cols=11 Identities=36% Similarity=0.923 Sum_probs=9.2
Q ss_pred ccccCCCCCCC
Q 025050 219 YVICLGCKSPD 229 (258)
Q Consensus 219 YVlC~~C~sPd 229 (258)
-|.|+.|+.|=
T Consensus 21 iVvCp~Cgapy 31 (54)
T PF14446_consen 21 IVVCPECGAPY 31 (54)
T ss_pred EEECCCCCCcc
Confidence 58999999883
No 225
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=22.51 E-value=61 Score=25.86 Aligned_cols=11 Identities=9% Similarity=0.304 Sum_probs=7.8
Q ss_pred EeeeccccCcc
Q 025050 240 FLRCEKVKAHI 250 (258)
Q Consensus 240 ~l~C~aCGa~~ 250 (258)
.+.|..||..-
T Consensus 35 a~~C~~CGe~y 45 (89)
T TIGR03829 35 SISCSHCGMEY 45 (89)
T ss_pred cccccCCCcEe
Confidence 35788888653
No 226
>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=22.42 E-value=59 Score=27.28 Aligned_cols=26 Identities=35% Similarity=0.754 Sum_probs=19.0
Q ss_pred ccccCCCCCCCceeEEcC-ceEEeeeccccCc
Q 025050 219 YVICLGCKSPDTILSKEN-RLFFLRCEKVKAH 249 (258)
Q Consensus 219 YVlC~~C~sPdT~L~ke~-rl~~l~C~aCGa~ 249 (258)
|.-|+.|+.. +...+ + .-.|..|+..
T Consensus 34 Y~aC~~C~kk---v~~~~~~--~~~C~~C~~~ 60 (166)
T cd04476 34 YPACPGCNKK---VVEEGNG--TYRCEKCNKS 60 (166)
T ss_pred EccccccCcc---cEeCCCC--cEECCCCCCc
Confidence 9999999873 33332 3 4679999987
No 227
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=22.13 E-value=34 Score=22.47 Aligned_cols=11 Identities=45% Similarity=1.071 Sum_probs=7.3
Q ss_pred hccccCCCCCC
Q 025050 218 EYVICLGCKSP 228 (258)
Q Consensus 218 eYVlC~~C~sP 228 (258)
.||.|+.|+.+
T Consensus 3 ~~~~C~nC~R~ 13 (33)
T PF08209_consen 3 PYVECPNCGRP 13 (33)
T ss_dssp -EEE-TTTSSE
T ss_pred CeEECCCCcCC
Confidence 57899999864
No 229
>PF05451 Phytoreo_Pns: Phytoreovirus nonstructural protein Pns10/11; InterPro: IPR008777 This family consists of Phytoreovirus nonstructural proteins Pns10 and Pns11. Genome segment S11 of Rice gall dwarf virus (RGDV), a Phytoreovirus, encodes a putative protein of 40 kDa that exhibits approximately 37% homology at the amino acid level to the nonstructural proteins Pns10 of rice dwarf and wound tumour viruses, which are other members of this genus [].
Probab=22.08 E-value=35 Score=33.09 Aligned_cols=33 Identities=24% Similarity=0.357 Sum_probs=23.3
Q ss_pred CCCCceeEEcCceEEeeeccccCcccccccccC
Q 025050 226 KSPDTILSKENRLFFLRCEKVKAHIQSYYLCPI 258 (258)
Q Consensus 226 ~sPdT~L~ke~rl~~l~C~aCGa~~~~~~~~~~ 258 (258)
+.|=|..+...=+--|+|+-||+.--+||.|++
T Consensus 129 k~P~s~~i~~~~~k~l~~dv~gs~yDsfYYC~~ 161 (344)
T PF05451_consen 129 KRPLSMFIIHYIAKSLRIDVVGSSYDSFYYCSS 161 (344)
T ss_pred CCcchHHHHHHHHHHcCceeecCcccceEEcCc
Confidence 455554443322336899999999999999985
No 230
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=21.84 E-value=1.3e+02 Score=20.75 Aligned_cols=27 Identities=26% Similarity=0.491 Sum_probs=24.4
Q ss_pred ehHHHHHHhCCChHHHHHHHHHhhcCc
Q 025050 162 NFMDLCKTMHRQPDHVMTFLLAELGTS 188 (258)
Q Consensus 162 Nf~eI~k~L~R~pehv~kfl~~ELGt~ 188 (258)
++.+||..++-++.++.+.|....|.+
T Consensus 3 ~~~~la~~~~~s~~~l~~~f~~~~~~s 29 (84)
T smart00342 3 TLEDLAEALGMSPRHLQRLFKKETGTT 29 (84)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHhCcC
Confidence 578999999999999999999888874
No 231
>PF11242 DUF2774: Protein of unknown function (DUF2774); InterPro: IPR021404 This entry is represented by Bacteriophage T4, Gp24.3; it is a family of uncharacterised viral proteins.
Probab=21.82 E-value=74 Score=23.99 Aligned_cols=44 Identities=9% Similarity=0.242 Sum_probs=31.4
Q ss_pred EehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecC
Q 025050 161 VNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFA 204 (258)
Q Consensus 161 ~Nf~eI~k~L~R~pehv~kfl~~ELGt~gsid~~~rliikGrf~ 204 (258)
.||.+||+.|.-.|..+.++...--++--.+......+..-+|.
T Consensus 14 ~~FveIAr~~~i~a~e~a~~w~~Ve~Ak~kfk~rEkVVYRKr~~ 57 (63)
T PF11242_consen 14 LSFVEIARKIGITAKEVAKAWAEVETAKEKFKTREKVVYRKRLI 57 (63)
T ss_pred CcHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccCceeeehhhc
Confidence 68999999999999999998876555544444334555555543
No 232
>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=21.80 E-value=25 Score=34.23 Aligned_cols=31 Identities=23% Similarity=0.458 Sum_probs=16.6
Q ss_pred HHhccccCCCCCCCceeEEcCceEEeeeccccCc
Q 025050 216 VNEYVICLGCKSPDTILSKENRLFFLRCEKVKAH 249 (258)
Q Consensus 216 I~eYVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~ 249 (258)
++.|..|..|+.--|.| .|+=..+|..||..
T Consensus 282 ~KRFFkC~~C~~Rt~sl---~r~P~~~C~~Cg~~ 312 (344)
T PF09332_consen 282 VKRFFKCKDCGNRTISL---ERLPKKHCSNCGSS 312 (344)
T ss_dssp E-EEEE-T-TS-EEEES---SSS--S--TTT-S-
T ss_pred eeeeEECCCCCCeeeec---ccCCCCCCCcCCcC
Confidence 45789999999986655 46667899999975
No 233
>PRK06599 DNA topoisomerase I; Validated
Probab=21.73 E-value=97 Score=32.39 Aligned_cols=30 Identities=23% Similarity=0.352 Sum_probs=16.9
Q ss_pred ccCCCCCCCceeEEcCceEEeeecc---ccCcc
Q 025050 221 ICLGCKSPDTILSKENRLFFLRCEK---VKAHI 250 (258)
Q Consensus 221 lC~~C~sPdT~L~ke~rl~~l~C~a---CGa~~ 250 (258)
.||.|+.-+..+.+...--|+.|.. |+...
T Consensus 587 ~CP~C~~~~l~~k~~k~g~F~~Cs~~p~C~~~~ 619 (675)
T PRK06599 587 TCPKCGGGPLVLKLGKNGKFLGCSGYPECKYTK 619 (675)
T ss_pred cccccCCCcceEEecCCCceeeCCCCCccCCCC
Confidence 6999965454443221112778854 76543
No 234
>KOG0481 consensus DNA replication licensing factor, MCM5 component [Replication, recombination and repair]
Probab=21.67 E-value=1.9e+02 Score=30.51 Aligned_cols=132 Identities=13% Similarity=0.188 Sum_probs=77.6
Q ss_pred cHHHHHHHHHHHHhhcCCCcccccceeecCCCeEEEeCceeEEEEeh-------HHHHHHhCCChHHHHHHHHHh-----
Q 025050 117 EYEELLGRVFNILRENNPELAGDRRRTVMRPPQVLREGTKKTVFVNF-------MDLCKTMHRQPDHVMTFLLAE----- 184 (258)
Q Consensus 117 ~YeeLL~R~~~~L~~~nP~~~~~~~R~~mp~pqV~reG~kKTvi~Nf-------~eI~k~L~R~pehv~kfl~~E----- 184 (258)
.|+.++.++-+.++.-+-+- .-.||-.+..-. ..| ...+-+|+ .+++..|++.|...+..|..-
T Consensus 24 ~~~~v~~~fkefir~f~~~~-~f~Yrd~L~~N~--~~~-~y~L~v~le~L~~fdedl~~~L~~~P~~~lp~fEeAa~~Va 99 (729)
T KOG0481|consen 24 RKSQVKTKFKEFIRQFRTGT-DFKYRDQLKRNY--NLG-EYSLEVELEDLISFDEDLADKLSKQPADHLPLFEEAAKEVA 99 (729)
T ss_pred cHHHHHHHHHHHHHHhcccc-ccchHHHHHhcc--ccc-ceEEEEEHHHhhccchHHHHHHHhChHhHHHHHHHHHHHHH
Confidence 57888888777775322110 011232222211 113 34444555 368999999999888887654
Q ss_pred --h---cCceee-cCCceEEEEeecChHHHHHHHHHHHHhccccCCCCCCCceeEEcCceEEeeeccccCcccc
Q 025050 185 --L---GTSGSL-DGQQRLVVKGRFAPKNFEGILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKVKAHIQS 252 (258)
Q Consensus 185 --L---Gt~gsi-d~~~rliikGrf~~k~ie~~L~~YI~eYVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~~~ 252 (258)
+ +.+|-= --+=+++++-.-.+-.|..+=-.+|..-|.=+.=--.-..+.-+-.-+++.|..|-++++.
T Consensus 100 d~i~~~~~~~E~~~~d~Qv~L~sda~p~~iR~l~s~~vsklVki~GIiiaAS~v~~kat~l~l~CrnC~~t~~~ 173 (729)
T KOG0481|consen 100 DEITRPRPSGEEVLHDIQVLLTSDANPISIRQLKSDHVSKLVKISGIIIAASAVSAKATRLSLVCRNCRHTRPN 173 (729)
T ss_pred hhhcCCCcCCCccceeeEEEEecCCCcccHhHhhhHhhhhheeeccEEEEeeeeeecceEEEEEeccccccccc
Confidence 2 222200 0124788888888888999988999888866543222222222334458888888888754
No 235
>PHA03112 IL-18 binding protein; Provisional
Probab=20.94 E-value=78 Score=27.30 Aligned_cols=33 Identities=21% Similarity=0.426 Sum_probs=22.9
Q ss_pred hccccCCCCCCCcee-EEcCceEEeeeccccCcc
Q 025050 218 EYVICLGCKSPDTIL-SKENRLFFLRCEKVKAHI 250 (258)
Q Consensus 218 eYVlC~~C~sPdT~L-~ke~rl~~l~C~aCGa~~ 250 (258)
.||-|..=+.+.-.+ .+++..+.++|.||+...
T Consensus 19 ~~~~c~~~r~~~i~vp~k~~~~vvL~C~gcs~fp 52 (141)
T PHA03112 19 SYVDCVKTRDVNIYIPTKETEKVVLECRGCSYFP 52 (141)
T ss_pred ccccCcccccceEEcccCCCCEEEEEEECccCCC
Confidence 356666666655444 357888999999997644
No 236
>KOG1603 consensus Copper chaperone [Inorganic ion transport and metabolism]
Probab=20.92 E-value=2.2e+02 Score=20.88 Aligned_cols=40 Identities=28% Similarity=0.382 Sum_probs=32.1
Q ss_pred HHHHHHHHHhhc-Cceeec-CCceEEEEeecChHHHHHHHHH
Q 025050 175 DHVMTFLLAELG-TSGSLD-GQQRLVVKGRFAPKNFEGILRR 214 (258)
Q Consensus 175 ehv~kfl~~ELG-t~gsid-~~~rliikGrf~~k~ie~~L~~ 214 (258)
..|.+.|..--| -+..+| +++++++.|.+.+..|...|++
T Consensus 20 ~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~k 61 (73)
T KOG1603|consen 20 RKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLKK 61 (73)
T ss_pred HHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHHh
Confidence 367777777777 456667 4789999999999999999887
No 237
>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=20.88 E-value=52 Score=22.46 Aligned_cols=8 Identities=13% Similarity=0.426 Sum_probs=4.4
Q ss_pred eeeccccC
Q 025050 241 LRCEKVKA 248 (258)
Q Consensus 241 l~C~aCGa 248 (258)
..|-.||+
T Consensus 27 ~~CP~Cg~ 34 (52)
T TIGR02605 27 ATCPECGG 34 (52)
T ss_pred CCCCCCCC
Confidence 44555555
No 238
>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=20.65 E-value=39 Score=27.58 Aligned_cols=29 Identities=21% Similarity=0.355 Sum_probs=20.7
Q ss_pred cccCCCCCCCceeEEcCceEEeeeccccCcccc
Q 025050 220 VICLGCKSPDTILSKENRLFFLRCEKVKAHIQS 252 (258)
Q Consensus 220 VlC~~C~sPdT~L~ke~rl~~l~C~aCGa~~~~ 252 (258)
-+|++|+.-=-.|-|. -+.|-.||+..+.
T Consensus 10 R~Cp~CG~kFYDLnk~----PivCP~CG~~~~~ 38 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNKD----PIVCPKCGTEFPP 38 (108)
T ss_pred ccCCCCcchhccCCCC----CccCCCCCCccCc
Confidence 3799998766666662 3569999987654
No 239
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=20.61 E-value=1.9e+02 Score=22.02 Aligned_cols=52 Identities=13% Similarity=0.211 Sum_probs=38.1
Q ss_pred EEEEee---cChHHHHHHHHHHHHhccccCCCCCCCceeEEcC--ceEEeeeccccCc
Q 025050 197 LVVKGR---FAPKNFEGILRRYVNEYVICLGCKSPDTILSKEN--RLFFLRCEKVKAH 249 (258)
Q Consensus 197 liikGr---f~~k~ie~~L~~YI~eYVlC~~C~sPdT~L~ke~--rl~~l~C~aCGa~ 249 (258)
+.|+.. .+...|+..|..=+.+.-.= -...|.-.+.-.. .-+++.|.+|+..
T Consensus 23 l~l~~~~~~~tl~~l~~~L~~~~~~H~~~-C~~~p~F~v~~~~~~~~L~~~C~~Cd~~ 79 (82)
T PF14768_consen 23 LRLNTQQDELTLEELRQLLEEAVTEHSDR-CSSTPQFSVEPGFGESSLYMSCEACDFL 79 (82)
T ss_pred cEEecCCCCCCHHHHHHHHHHHHHHHHHh-CCCCCEEEEecCCCchhheeECCCCCcc
Confidence 666666 88999999999888876654 1456766666532 3779999999864
No 240
>PHA02893 hypothetical protein; Provisional
Probab=20.61 E-value=40 Score=26.87 Aligned_cols=10 Identities=10% Similarity=0.355 Sum_probs=6.4
Q ss_pred EeeeccccCc
Q 025050 240 FLRCEKVKAH 249 (258)
Q Consensus 240 ~l~C~aCGa~ 249 (258)
.|+|.|||+.
T Consensus 69 tL~CaACGS~ 78 (88)
T PHA02893 69 NIKCIACGSS 78 (88)
T ss_pred ceeehhhchh
Confidence 4667777764
No 241
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=20.53 E-value=55 Score=25.86 Aligned_cols=28 Identities=29% Similarity=0.542 Sum_probs=19.6
Q ss_pred ccccCCCCCCCceeEEcCceEEeeeccccC
Q 025050 219 YVICLGCKSPDTILSKENRLFFLRCEKVKA 248 (258)
Q Consensus 219 YVlC~~C~sPdT~L~ke~rl~~l~C~aCGa 248 (258)
||.|+.|...-|.+.--.- .+.|..|+-
T Consensus 34 ~VkC~gc~~iT~vfSHaqt--vVvc~~c~~ 61 (84)
T KOG1779|consen 34 DVKCPGCFKITTVFSHAQT--VVVCEGCST 61 (84)
T ss_pred EEEcCCceEEEEEeecCce--EEEcCCCce
Confidence 7999999887777665422 466777763
No 242
>PRK13501 transcriptional activator RhaR; Provisional
Probab=20.50 E-value=1.1e+02 Score=27.57 Aligned_cols=66 Identities=11% Similarity=0.199 Sum_probs=48.7
Q ss_pred EehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHHHHHHhccccCCCCCC-CceeEEcCceE
Q 025050 161 VNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILRRYVNEYVICLGCKSP-DTILSKENRLF 239 (258)
Q Consensus 161 ~Nf~eI~k~L~R~pehv~kfl~~ELGt~gsid~~~rliikGrf~~k~ie~~L~~YI~eYVlC~~C~sP-dT~L~ke~rl~ 239 (258)
.++.++|.+++-+|.|+.+.|-.++|.+ .-.||+++.+-..|... .|.+ -+
T Consensus 193 ~sl~~lA~~~~lS~~~l~r~Fk~~~G~T-----------------------~~qyi~~~Ri~~A~~LL~~t~~-----sI 244 (290)
T PRK13501 193 FDMADFCHKNQLVERSLKQLFRQQTGMS-----------------------ISHYLRQIRLCHAKCLLRGSEH-----RI 244 (290)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHCcC-----------------------HHHHHHHHHHHHHHHHHHcCCC-----CH
Confidence 3799999999999999999999999986 34677777766666442 2322 23
Q ss_pred EeeeccccCcccccc
Q 025050 240 FLRCEKVKAHIQSYY 254 (258)
Q Consensus 240 ~l~C~aCGa~~~~~~ 254 (258)
.-.|..||-...+|+
T Consensus 245 ~eIA~~~GF~~~s~F 259 (290)
T PRK13501 245 SDIAARCGFEDSNYF 259 (290)
T ss_pred HHHHHHhCCCCHHHH
Confidence 456777777777765
No 243
>PRK08173 DNA topoisomerase III; Validated
Probab=20.40 E-value=68 Score=34.72 Aligned_cols=49 Identities=14% Similarity=0.371 Sum_probs=31.2
Q ss_pred eEEEEeecChHHHHHHHHHHHHhc--------------------cccCCCCCCCceeEEcCceEEeeeccccCc
Q 025050 196 RLVVKGRFAPKNFEGILRRYVNEY--------------------VICLGCKSPDTILSKENRLFFLRCEKVKAH 249 (258)
Q Consensus 196 rliikGrf~~k~ie~~L~~YI~eY--------------------VlC~~C~sPdT~L~ke~rl~~l~C~aCGa~ 249 (258)
..|-+|..+..++-+-+..||... ..||.|++. +...++ ...|..|+..
T Consensus 581 ~~I~~G~~~~~~f~~~i~~~~~~~v~~~~~~~~~~~~~~~~~~~~~CP~Cg~~---~~~~~~--~~~Cs~C~f~ 649 (862)
T PRK08173 581 SQIERGKLSRDAFMQEIAQMTQQIVKRAKEYDSDTIPGDYATLQTPCPNCGGV---VKENYR--RFACTKCDFS 649 (862)
T ss_pred HHHHcCCCCHHHHHHHHHHHHHHHHHHHHhhhhcccccccccccccCCccccc---ccccCc--eeEcCCCCcc
Confidence 456668888777776666665432 249999874 322223 3688888744
No 244
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=20.18 E-value=47 Score=30.34 Aligned_cols=28 Identities=21% Similarity=0.401 Sum_probs=17.6
Q ss_pred HHHHHHHHHHHHh----------------ccccCCCCCCCceeE
Q 025050 206 KNFEGILRRYVNE----------------YVICLGCKSPDTILS 233 (258)
Q Consensus 206 k~ie~~L~~YI~e----------------YVlC~~C~sPdT~L~ 233 (258)
..++.++++.|.- |-.||.|++.+|..-
T Consensus 339 ~~~~~~~~~~~~~~p~~~c~~cg~~~~~~~~~c~~c~~~~~~~~ 382 (389)
T PRK11788 339 LLLRDLVGEQLKRKPRYRCRNCGFTARTLYWHCPSCKAWETIKP 382 (389)
T ss_pred HHHHHHHHHHHhCCCCEECCCCCCCCccceeECcCCCCccCcCC
Confidence 4467777766532 346777777777643
No 245
>COG1384 LysS Lysyl-tRNA synthetase (class I) [Translation, ribosomal structure and biogenesis]
Probab=20.17 E-value=1.5e+02 Score=30.71 Aligned_cols=76 Identities=20% Similarity=0.304 Sum_probs=45.4
Q ss_pred HHHHHHHHHhhcCceeec----CCceEEEEeecCh---------HHHHHHHHHHHHh---------ccccCCCCCCCc-e
Q 025050 175 DHVMTFLLAELGTSGSLD----GQQRLVVKGRFAP---------KNFEGILRRYVNE---------YVICLGCKSPDT-I 231 (258)
Q Consensus 175 ehv~kfl~~ELGt~gsid----~~~rliikGrf~~---------k~ie~~L~~YI~e---------YVlC~~C~sPdT-~ 231 (258)
+|.++=|...|..-| |+ .+..+.=+|.|.. ..|..+|..|-.. -++|+.|+..+| .
T Consensus 106 ~hf~~~f~~~l~~~G-i~~E~~s~se~Yk~G~~~~~i~~ale~rdeI~~il~~~~~~~~~e~~~P~~piC~kcGri~~t~ 184 (521)
T COG1384 106 EHFLRPFEEFLDEFG-IEVEFVSATELYKSGLYDEAIRIALERRDEIMEILNEYRGRELEEDWSPFMPICEKCGRILTTP 184 (521)
T ss_pred HHHHHHHHHHHHhcC-CceEEEEhHHhhhcccHHHHHHHHHhhHHHHHHHHHHhcCCcccCCceeccccccccCCcceeE
Confidence 455555555555444 32 2334445566654 4677777777666 479999999654 4
Q ss_pred eEE-cCc-eEEeeeccccCcccc
Q 025050 232 LSK-ENR-LFFLRCEKVKAHIQS 252 (258)
Q Consensus 232 L~k-e~r-l~~l~C~aCGa~~~~ 252 (258)
++. +.. .+.-+|+ ||+...+
T Consensus 185 v~~~d~~~~v~Y~Ce-~Gh~g~v 206 (521)
T COG1384 185 VIEWDGEGTVEYRCE-CGHEGEV 206 (521)
T ss_pred EEEecCCceEEEEec-CCcccee
Confidence 443 443 6677886 6876543
No 246
>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=20.14 E-value=37 Score=28.32 Aligned_cols=26 Identities=23% Similarity=0.520 Sum_probs=17.1
Q ss_pred ccccCCCCCCCceeEEcCceEEeeeccccCc
Q 025050 219 YVICLGCKSPDTILSKENRLFFLRCEKVKAH 249 (258)
Q Consensus 219 YVlC~~C~sPdT~L~ke~rl~~l~C~aCGa~ 249 (258)
.|.||+|+.+---|-+.. .|--|+..
T Consensus 69 ~V~CP~C~K~TKmLGr~D-----~CM~C~~p 94 (114)
T PF11023_consen 69 QVECPNCGKQTKMLGRVD-----ACMHCKEP 94 (114)
T ss_pred eeECCCCCChHhhhchhh-----ccCcCCCc
Confidence 488999998744444432 57777753
Done!