Query 036389
Match_columns 198
No_of_seqs 170 out of 675
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 12:12:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036389.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036389hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01385 TFSII transcription 100.0 1.6E-47 3.6E-52 335.6 15.3 158 17-189 132-299 (299)
2 KOG1105 Transcription elongati 100.0 9.3E-44 2E-48 309.2 14.4 159 16-189 128-296 (296)
3 smart00510 TFS2M Domain in the 100.0 2.2E-30 4.7E-35 195.2 10.6 102 21-131 1-102 (102)
4 PF07500 TFIIS_M: Transcriptio 100.0 2.8E-30 6.1E-35 197.7 3.9 115 19-148 1-115 (115)
5 KOG1634 Predicted transcriptio 99.6 2.8E-15 6.1E-20 143.9 4.9 82 55-137 267-349 (778)
6 smart00440 ZnF_C2C2 C2C2 Zinc 99.1 3.5E-11 7.6E-16 76.1 2.8 30 158-187 1-39 (40)
7 PF01096 TFIIS_C: Transcriptio 99.1 6.4E-11 1.4E-15 74.5 2.2 30 158-187 1-39 (39)
8 COG1594 RPB9 DNA-directed RNA 98.9 8.9E-10 1.9E-14 84.5 2.8 35 155-189 70-113 (113)
9 KOG2906 RNA polymerase III sub 98.8 7.9E-10 1.7E-14 82.1 0.7 32 156-187 64-104 (105)
10 PHA02998 RNA polymerase subuni 98.7 9E-09 1.9E-13 84.2 2.7 32 156-187 142-182 (195)
11 TIGR01384 TFS_arch transcripti 98.7 1.1E-08 2.4E-13 76.7 2.8 34 155-188 60-102 (104)
12 KOG2691 RNA polymerase II subu 98.0 3.2E-06 7E-11 63.9 2.4 34 154-187 70-112 (113)
13 KOG2907 RNA polymerase I trans 97.5 3.7E-05 8E-10 58.7 1.5 33 155-187 72-113 (116)
14 PF13717 zinc_ribbon_4: zinc-r 95.7 0.011 2.5E-07 36.2 2.8 27 158-187 3-36 (36)
15 PF08271 TF_Zn_Ribbon: TFIIB z 95.2 0.016 3.4E-07 36.7 2.3 29 158-186 1-29 (43)
16 PF12760 Zn_Tnp_IS1595: Transp 94.9 0.021 4.5E-07 36.7 2.3 28 158-185 19-46 (46)
17 PF13719 zinc_ribbon_5: zinc-r 94.9 0.03 6.4E-07 34.5 2.8 28 158-188 3-37 (37)
18 TIGR02098 MJ0042_CXXC MJ0042 f 94.3 0.043 9.2E-07 33.5 2.6 28 158-188 3-37 (38)
19 COG4888 Uncharacterized Zn rib 94.3 0.041 8.9E-07 41.4 2.9 39 155-193 20-63 (104)
20 COG3478 Predicted nucleic-acid 94.0 0.037 8E-07 38.4 1.9 30 156-185 3-49 (68)
21 COG2051 RPS27A Ribosomal prote 94.0 0.047 1E-06 38.1 2.4 29 157-185 19-47 (67)
22 PF09855 DUF2082: Nucleic-acid 93.9 0.038 8.2E-07 38.4 1.9 28 158-185 1-45 (64)
23 PF08274 PhnA_Zn_Ribbon: PhnA 93.7 0.03 6.6E-07 33.2 1.0 28 158-187 3-30 (30)
24 PRK09678 DNA-binding transcrip 92.9 0.077 1.7E-06 37.7 2.1 38 157-194 1-47 (72)
25 PF04606 Ogr_Delta: Ogr/Delta- 91.8 0.15 3.2E-06 32.9 2.3 32 159-190 1-41 (47)
26 PF05180 zf-DNL: DNL zinc fing 91.3 0.15 3.1E-06 35.7 1.9 29 157-185 4-38 (66)
27 KOG1886 BAH domain proteins [T 91.2 0.15 3.2E-06 47.8 2.5 173 17-198 238-414 (464)
28 PRK00398 rpoP DNA-directed RNA 90.9 0.2 4.3E-06 32.0 2.2 28 157-185 3-30 (46)
29 PRK00415 rps27e 30S ribosomal 90.5 0.25 5.4E-06 33.8 2.5 30 157-186 11-40 (59)
30 PLN00209 ribosomal protein S27 90.2 0.48 1E-05 34.7 3.8 31 156-186 35-65 (86)
31 TIGR00311 aIF-2beta translatio 90.0 0.36 7.8E-06 38.1 3.4 30 156-185 96-127 (133)
32 PRK03988 translation initiatio 89.8 0.38 8.2E-06 38.2 3.4 30 156-185 101-132 (138)
33 TIGR00686 phnA alkylphosphonat 89.4 0.24 5.1E-06 37.8 1.8 30 158-189 3-32 (109)
34 PF05129 Elf1: Transcription e 89.2 0.39 8.4E-06 34.7 2.8 35 155-189 20-59 (81)
35 PTZ00083 40S ribosomal protein 89.1 0.69 1.5E-05 33.8 4.0 31 156-186 34-64 (85)
36 smart00653 eIF2B_5 domain pres 89.1 0.47 1E-05 36.2 3.3 30 156-185 79-110 (110)
37 PF11781 RRN7: RNA polymerase 88.5 0.32 7E-06 29.8 1.7 26 158-185 9-34 (36)
38 PF01873 eIF-5_eIF-2B: Domain 88.1 0.43 9.2E-06 37.2 2.6 28 158-185 94-123 (125)
39 TIGR02443 conserved hypothetic 87.9 0.74 1.6E-05 31.5 3.3 36 158-193 10-48 (59)
40 PRK10220 hypothetical protein; 87.6 0.41 8.9E-06 36.6 2.1 31 158-190 4-34 (111)
41 PF03604 DNA_RNApol_7kD: DNA d 87.4 0.22 4.8E-06 29.9 0.5 26 158-185 1-26 (32)
42 smart00659 RPOLCX RNA polymera 87.4 0.6 1.3E-05 29.9 2.5 26 157-185 2-28 (44)
43 PF09526 DUF2387: Probable met 87.2 0.64 1.4E-05 32.9 2.8 34 158-191 9-45 (71)
44 PF01667 Ribosomal_S27e: Ribos 87.2 0.41 9E-06 32.2 1.7 28 158-185 8-35 (55)
45 PF04216 FdhE: Protein involve 87.0 0.43 9.3E-06 41.8 2.3 38 157-194 172-215 (290)
46 PRK14892 putative transcriptio 86.8 0.6 1.3E-05 35.1 2.6 34 155-188 19-54 (99)
47 PHA00626 hypothetical protein 86.7 0.55 1.2E-05 31.8 2.1 28 159-186 2-33 (59)
48 PRK12336 translation initiatio 86.7 0.73 1.6E-05 38.6 3.4 30 156-185 97-128 (201)
49 PF13453 zf-TFIIB: Transcripti 85.7 0.72 1.6E-05 28.7 2.2 29 159-187 1-30 (41)
50 PF14354 Lar_restr_allev: Rest 85.7 0.82 1.8E-05 30.5 2.6 29 156-184 2-37 (61)
51 smart00531 TFIIE Transcription 85.0 1.4 3E-05 34.9 4.0 37 154-191 96-138 (147)
52 PRK05978 hypothetical protein; 84.9 0.48 1E-05 38.1 1.4 34 158-191 34-67 (148)
53 PRK09710 lar restriction allev 84.7 1.1 2.4E-05 31.1 2.8 37 156-192 5-43 (64)
54 PRK03564 formate dehydrogenase 82.5 0.92 2E-05 40.6 2.3 39 156-194 186-230 (309)
55 PRK00432 30S ribosomal protein 82.0 0.85 1.8E-05 30.0 1.4 29 157-187 20-48 (50)
56 TIGR03655 anti_R_Lar restricti 81.9 1.5 3.2E-05 28.8 2.6 29 158-186 2-36 (53)
57 PRK06266 transcription initiat 81.7 0.67 1.5E-05 38.1 1.0 36 154-189 114-149 (178)
58 PF09332 Mcm10: Mcm10 replicat 81.0 0.59 1.3E-05 42.5 0.5 30 154-185 249-294 (344)
59 TIGR00373 conserved hypothetic 78.1 1.9 4.1E-05 34.7 2.5 34 154-188 106-140 (158)
60 PF07282 OrfB_Zn_ribbon: Putat 77.9 1.5 3.3E-05 29.8 1.7 34 155-192 27-60 (69)
61 PF09538 FYDLN_acid: Protein o 77.9 1 2.3E-05 34.3 0.9 30 157-189 9-39 (108)
62 PF09723 Zn-ribbon_8: Zinc rib 77.8 1.4 3E-05 27.7 1.3 28 157-184 5-34 (42)
63 KOG3277 Uncharacterized conser 77.7 1.7 3.7E-05 35.3 2.1 31 156-186 78-114 (165)
64 PF06044 DRP: Dam-replacing fa 77.4 1.5 3.3E-05 38.1 1.9 30 156-186 30-63 (254)
65 TIGR01562 FdhE formate dehydro 77.0 1.6 3.4E-05 39.0 2.0 39 156-194 183-228 (305)
66 COG2888 Predicted Zn-ribbon RN 75.9 1.7 3.6E-05 29.8 1.4 31 154-184 24-58 (61)
67 COG1997 RPL43A Ribosomal prote 75.4 2.5 5.5E-05 31.1 2.3 32 155-187 33-64 (89)
68 PF09332 Mcm10: Mcm10 replicat 74.6 1.8 4E-05 39.3 1.7 33 154-187 282-315 (344)
69 TIGR02300 FYDLN_acid conserved 74.0 1.6 3.4E-05 34.3 1.0 30 157-189 9-39 (129)
70 PF11648 RIG-I_C-RD: C-termina 73.4 2 4.3E-05 33.2 1.5 15 174-188 58-72 (123)
71 PF07295 DUF1451: Protein of u 72.5 3.5 7.5E-05 33.0 2.7 32 154-186 109-140 (146)
72 KOG4274 Positive cofactor 2 (P 71.7 8.4 0.00018 37.4 5.4 61 21-97 9-69 (742)
73 PF02701 zf-Dof: Dof domain, z 70.3 1.4 3E-05 30.4 -0.0 33 156-188 4-42 (63)
74 PF05876 Terminase_GpA: Phage 69.6 3.2 6.9E-05 39.9 2.2 31 157-187 200-240 (557)
75 smart00661 RPOL9 RNA polymeras 69.1 4.1 8.9E-05 26.0 2.0 30 159-190 2-34 (52)
76 PRK14890 putative Zn-ribbon RN 68.9 3.6 7.8E-05 28.1 1.7 29 155-184 23-56 (59)
77 TIGR01206 lysW lysine biosynth 68.8 4.6 0.0001 27.0 2.2 31 157-188 2-34 (54)
78 TIGR00373 conserved hypothetic 68.8 9.8 0.00021 30.6 4.6 17 173-189 106-122 (158)
79 PF09297 zf-NADH-PPase: NADH p 68.7 4.6 0.0001 23.6 2.0 26 159-185 5-30 (32)
80 PRK06266 transcription initiat 67.7 11 0.00024 30.9 4.8 16 174-189 115-130 (178)
81 COG1996 RPC10 DNA-directed RNA 67.1 3.4 7.4E-05 27.2 1.3 30 155-185 4-33 (49)
82 PF10571 UPF0547: Uncharacteri 66.5 3.2 7E-05 23.6 1.0 24 159-187 2-25 (26)
83 PRK11827 hypothetical protein; 66.1 6.1 0.00013 27.0 2.4 40 156-197 7-46 (60)
84 smart00834 CxxC_CXXC_SSSS Puta 65.1 4.1 9E-05 24.6 1.4 28 157-184 5-34 (41)
85 PRK11032 hypothetical protein; 64.9 6.8 0.00015 31.9 2.9 32 154-186 121-152 (160)
86 TIGR02605 CxxC_CxxC_SSSS putat 64.9 4 8.7E-05 26.2 1.3 28 157-184 5-34 (52)
87 COG1656 Uncharacterized conser 64.6 3.8 8.2E-05 33.6 1.4 31 157-187 97-142 (165)
88 PF10080 DUF2318: Predicted me 64.2 4.6 0.0001 30.4 1.7 35 153-189 31-65 (102)
89 COG2824 PhnA Uncharacterized Z 64.0 5.6 0.00012 30.4 2.1 29 157-187 3-31 (112)
90 TIGR00100 hypA hydrogenase nic 63.2 5.2 0.00011 30.5 1.9 29 154-185 67-95 (115)
91 PF02172 KIX: KIX domain; Int 62.8 36 0.00079 24.6 6.1 67 19-91 10-76 (81)
92 COG2816 NPY1 NTP pyrophosphohy 62.8 5 0.00011 35.5 1.9 37 159-196 113-150 (279)
93 PF14122 YokU: YokU-like prote 62.5 5.1 0.00011 29.4 1.6 28 159-186 1-45 (87)
94 smart00401 ZnF_GATA zinc finge 62.4 3.3 7.1E-05 27.2 0.6 31 158-188 4-37 (52)
95 KOG3507 DNA-directed RNA polym 62.1 5 0.00011 27.4 1.4 30 154-185 17-46 (62)
96 COG5349 Uncharacterized protei 61.8 2.9 6.3E-05 32.6 0.2 35 158-192 22-56 (126)
97 PHA02540 61 DNA primase; Provi 61.1 7.5 0.00016 35.3 2.8 30 156-185 26-64 (337)
98 PRK12380 hydrogenase nickel in 59.8 6 0.00013 30.1 1.7 29 154-185 67-95 (113)
99 COG2023 RPR2 RNase P subunit R 58.3 10 0.00022 28.9 2.6 33 157-189 56-95 (105)
100 PF01927 Mut7-C: Mut7-C RNAse 58.3 6.6 0.00014 30.9 1.8 31 157-187 91-136 (147)
101 smart00778 Prim_Zn_Ribbon Zinc 57.7 8.3 0.00018 23.8 1.7 27 158-184 4-33 (37)
102 PF07754 DUF1610: Domain of un 57.7 5.7 0.00012 22.3 0.9 11 155-165 14-24 (24)
103 PRK03954 ribonuclease P protei 57.4 9.1 0.0002 29.8 2.3 33 156-188 63-105 (121)
104 PF04216 FdhE: Protein involve 56.8 6.7 0.00014 34.3 1.7 34 157-190 211-252 (290)
105 PRK14714 DNA polymerase II lar 56.8 6.8 0.00015 41.2 1.9 32 154-185 664-701 (1337)
106 KOG2593 Transcription initiati 56.3 5.5 0.00012 37.2 1.1 33 154-186 125-163 (436)
107 PF01780 Ribosomal_L37ae: Ribo 55.0 10 0.00022 28.1 2.1 31 155-186 33-63 (90)
108 TIGR00595 priA primosomal prot 53.1 19 0.00041 34.2 4.2 32 155-186 211-250 (505)
109 cd00202 ZnF_GATA Zinc finger D 53.1 3.1 6.7E-05 27.7 -0.8 30 159-188 1-33 (54)
110 PF00320 GATA: GATA zinc finge 51.9 3.3 7.2E-05 25.1 -0.7 28 160-187 1-31 (36)
111 TIGR00280 L37a ribosomal prote 51.6 14 0.00031 27.3 2.5 31 155-186 33-63 (91)
112 COG0675 Transposase and inacti 51.5 9.2 0.0002 32.7 1.7 26 155-186 307-332 (364)
113 PF15135 UPF0515: Uncharacteri 51.0 13 0.00027 32.6 2.4 15 174-188 153-167 (278)
114 COG3529 Predicted nucleic-acid 50.9 4.1 8.8E-05 28.1 -0.5 32 158-189 11-45 (66)
115 PF08792 A2L_zn_ribbon: A2L zi 50.6 20 0.00044 21.4 2.6 28 157-185 3-30 (33)
116 PF09606 Med15: ARC105 or Med1 50.1 27 0.0006 35.2 4.9 51 26-92 2-52 (799)
117 PHA02942 putative transposase; 48.5 12 0.00027 34.2 2.1 29 155-186 324-352 (383)
118 KOG0909 Peptide:N-glycanase [P 47.8 23 0.0005 33.4 3.7 107 76-190 86-208 (500)
119 PF06254 DUF1019: Protein of u 47.3 15 0.00032 27.1 1.9 50 67-116 12-61 (89)
120 PRK03681 hypA hydrogenase nick 46.9 13 0.00029 28.2 1.7 28 154-185 67-96 (114)
121 PF03811 Zn_Tnp_IS1: InsA N-te 46.9 27 0.00058 21.3 2.8 28 155-182 3-35 (36)
122 PF14949 ARF7EP_C: ARF7 effect 46.8 9.4 0.0002 28.9 0.9 14 157-170 74-87 (103)
123 PRK12286 rpmF 50S ribosomal pr 46.3 17 0.00038 24.4 2.0 25 154-184 24-48 (57)
124 KOG2767 Translation initiation 45.8 8.8 0.00019 35.1 0.7 29 157-185 96-127 (400)
125 PRK14715 DNA polymerase II lar 45.6 12 0.00025 39.9 1.6 32 154-192 671-702 (1627)
126 PTZ00255 60S ribosomal protein 45.1 21 0.00045 26.4 2.5 31 155-186 34-64 (90)
127 COG1281 Disulfide bond chapero 44.9 7.9 0.00017 34.4 0.3 73 104-195 198-285 (286)
128 PRK03824 hypA hydrogenase nick 44.6 15 0.00033 28.7 1.9 31 155-185 68-116 (135)
129 PLN03119 putative ADP-ribosyla 44.6 25 0.00054 34.3 3.5 25 158-183 24-50 (648)
130 PF13408 Zn_ribbon_recom: Reco 44.5 28 0.00061 22.2 2.9 29 155-183 3-33 (58)
131 COG2835 Uncharacterized conser 44.4 35 0.00075 23.4 3.3 40 156-197 7-46 (60)
132 PF01396 zf-C4_Topoisom: Topoi 44.4 21 0.00046 21.9 2.1 27 159-185 3-33 (39)
133 TIGR00354 polC DNA polymerase, 44.3 13 0.00028 38.3 1.6 25 154-185 622-646 (1095)
134 cd00674 LysRS_core_class_I cat 44.2 18 0.0004 32.9 2.5 29 157-186 169-202 (353)
135 PRK00564 hypA hydrogenase nick 42.9 12 0.00026 28.6 1.0 29 154-185 68-97 (117)
136 smart00647 IBR In Between Ring 42.8 17 0.00037 23.6 1.6 8 179-186 51-58 (64)
137 PF01807 zf-CHC2: CHC2 zinc fi 42.6 22 0.00048 26.0 2.3 32 155-186 31-64 (97)
138 PF14803 Nudix_N_2: Nudix N-te 42.3 29 0.00063 20.9 2.4 25 159-184 2-30 (34)
139 COG1645 Uncharacterized Zn-fin 42.2 16 0.00035 28.8 1.6 28 156-186 27-54 (131)
140 PF14311 DUF4379: Domain of un 42.2 12 0.00025 24.5 0.7 14 176-189 28-41 (55)
141 TIGR02159 PA_CoA_Oxy4 phenylac 41.8 8.9 0.00019 30.6 0.1 30 157-186 105-140 (146)
142 KOG2768 Translation initiation 41.4 13 0.00029 31.8 1.1 30 156-185 180-211 (231)
143 PRK04860 hypothetical protein; 40.9 14 0.0003 30.0 1.1 36 155-191 117-158 (160)
144 PRK00420 hypothetical protein; 40.5 18 0.00039 27.7 1.6 31 158-190 24-54 (112)
145 PRK05580 primosome assembly pr 39.9 36 0.00077 33.5 3.9 34 154-187 378-419 (679)
146 PF06397 Desulfoferrod_N: Desu 39.5 19 0.0004 22.2 1.2 14 173-186 3-16 (36)
147 COG4332 Uncharacterized protei 39.4 16 0.00035 30.5 1.3 18 172-189 45-62 (203)
148 KOG1779 40s ribosomal protein 39.4 37 0.00081 24.6 2.9 27 158-184 35-61 (84)
149 PF01921 tRNA-synt_1f: tRNA sy 38.8 16 0.00036 33.4 1.3 31 157-187 174-210 (360)
150 PF12773 DZR: Double zinc ribb 38.4 13 0.00028 23.5 0.4 33 155-189 10-46 (50)
151 PRK03976 rpl37ae 50S ribosomal 38.1 31 0.00067 25.5 2.5 31 155-186 34-64 (90)
152 smart00531 TFIIE Transcription 37.7 16 0.00034 28.8 0.9 18 172-189 95-112 (147)
153 PRK12495 hypothetical protein; 37.7 18 0.00038 31.1 1.3 30 154-186 39-68 (226)
154 PRK12496 hypothetical protein; 37.6 17 0.00036 29.4 1.1 25 158-186 128-153 (164)
155 COG4481 Uncharacterized protei 37.4 35 0.00075 23.1 2.4 27 163-189 19-47 (60)
156 PHA00616 hypothetical protein 37.0 9.9 0.00022 24.4 -0.3 10 157-166 1-10 (44)
157 TIGR01031 rpmF_bact ribosomal 36.5 31 0.00068 22.9 2.1 24 154-183 23-46 (55)
158 PRK04338 N(2),N(2)-dimethylgua 36.0 17 0.00038 33.2 1.1 33 157-191 244-276 (382)
159 PF10609 ParA: ParA/MinD ATPas 35.4 18 0.0004 26.1 0.9 48 110-166 27-74 (81)
160 PF10058 DUF2296: Predicted in 35.4 35 0.00075 22.7 2.2 29 156-184 21-52 (54)
161 cd00974 DSRD Desulforedoxin (D 35.2 24 0.00051 20.8 1.2 13 174-186 2-14 (34)
162 PLN03114 ADP-ribosylation fact 34.9 29 0.00063 32.0 2.3 26 158-184 23-50 (395)
163 PF03833 PolC_DP2: DNA polymer 34.7 13 0.00028 37.7 0.0 33 154-186 652-690 (900)
164 PF01155 HypA: Hydrogenase exp 34.7 14 0.0003 28.0 0.1 29 154-185 67-95 (113)
165 TIGR00319 desulf_FeS4 desulfof 34.4 25 0.00054 20.7 1.2 12 175-186 6-17 (34)
166 PF10263 SprT-like: SprT-like 33.3 28 0.00061 27.0 1.7 35 154-188 120-155 (157)
167 PF02150 RNA_POL_M_15KD: RNA p 32.5 45 0.00098 20.0 2.2 27 159-186 3-30 (35)
168 PF05207 zf-CSL: CSL zinc fing 32.2 47 0.001 22.0 2.4 26 155-184 16-48 (55)
169 PRK06599 DNA topoisomerase I; 31.8 71 0.0015 31.5 4.5 15 100-114 543-557 (675)
170 TIGR00515 accD acetyl-CoA carb 31.4 12 0.00026 33.1 -0.8 31 157-189 26-58 (285)
171 PLN03131 hypothetical protein; 31.2 54 0.0012 32.4 3.5 26 158-184 24-51 (705)
172 PF01412 ArfGap: Putative GTPa 30.6 25 0.00055 26.5 1.0 29 158-187 14-44 (116)
173 TIGR00467 lysS_arch lysyl-tRNA 30.2 40 0.00088 32.3 2.5 28 157-185 168-199 (515)
174 COG3677 Transposase and inacti 29.5 31 0.00067 26.9 1.3 33 154-187 27-64 (129)
175 PRK06319 DNA topoisomerase I/S 29.4 71 0.0015 32.5 4.2 26 156-181 591-618 (860)
176 PF00096 zf-C2H2: Zinc finger, 29.4 30 0.00065 17.9 0.9 7 178-184 2-8 (23)
177 TIGR00308 TRM1 tRNA(guanine-26 29.3 30 0.00064 31.7 1.4 35 157-191 233-267 (374)
178 KOG1222 Kinesin associated pro 29.2 1.3E+02 0.0029 29.3 5.7 86 24-111 302-391 (791)
179 PRK00241 nudC NADH pyrophospha 28.7 43 0.00094 28.9 2.3 28 159-187 101-128 (256)
180 PRK07219 DNA topoisomerase I; 28.7 75 0.0016 32.1 4.2 18 100-117 550-567 (822)
181 PF03966 Trm112p: Trm112p-like 28.6 53 0.0011 22.3 2.3 17 172-188 49-65 (68)
182 PF00628 PHD: PHD-finger; Int 28.6 50 0.0011 20.6 2.0 10 174-183 12-21 (51)
183 PRK00750 lysK lysyl-tRNA synth 28.5 46 0.001 31.7 2.6 29 157-186 175-209 (510)
184 KOG3214 Uncharacterized Zn rib 28.4 40 0.00087 25.5 1.7 34 154-187 20-58 (109)
185 PF03107 C1_2: C1 domain; Int 28.3 46 0.00099 19.1 1.6 22 158-183 1-22 (30)
186 COG1601 GCD7 Translation initi 28.1 14 0.00031 29.7 -0.8 29 157-185 105-135 (151)
187 PF06107 DUF951: Bacterial pro 28.1 49 0.0011 22.4 1.9 30 163-192 16-47 (57)
188 COG1096 Predicted RNA-binding 28.0 49 0.0011 27.7 2.3 26 157-185 149-174 (188)
189 PRK04023 DNA polymerase II lar 27.9 30 0.00066 35.9 1.3 32 152-183 633-670 (1121)
190 COG5595 Zn-ribbon-containing, 27.9 23 0.0005 30.1 0.4 30 162-191 195-233 (256)
191 PRK09521 exosome complex RNA-b 27.8 45 0.00097 27.2 2.1 26 158-186 150-176 (189)
192 smart00099 btg1 tob/btg1 famil 27.7 21 0.00044 27.3 0.0 62 57-120 27-92 (108)
193 PRK03564 formate dehydrogenase 27.3 54 0.0012 29.4 2.6 33 157-189 226-265 (309)
194 PF00684 DnaJ_CXXCXGXG: DnaJ c 27.2 88 0.0019 21.1 3.2 34 155-188 13-53 (66)
195 COG4049 Uncharacterized protei 27.2 27 0.00058 23.8 0.5 11 155-165 15-25 (65)
196 PF08209 Sgf11: Sgf11 (transcr 27.2 45 0.00097 20.0 1.5 12 175-186 3-14 (33)
197 PF10083 DUF2321: Uncharacteri 26.9 24 0.00052 28.7 0.3 31 155-185 37-77 (158)
198 COG1675 TFA1 Transcription ini 26.8 27 0.00059 28.8 0.6 32 154-186 110-142 (176)
199 PF01485 IBR: IBR domain; Int 26.5 34 0.00074 22.1 1.0 8 179-186 51-58 (64)
200 PF04676 CwfJ_C_2: Protein sim 26.1 51 0.0011 24.1 1.9 36 1-36 29-64 (98)
201 COG3058 FdhE Uncharacterized p 25.7 17 0.00037 32.4 -0.8 16 156-171 184-199 (308)
202 smart00731 SprT SprT homologue 25.7 72 0.0016 24.9 2.8 32 155-186 110-143 (146)
203 PF08273 Prim_Zn_Ribbon: Zinc- 25.0 82 0.0018 19.7 2.4 26 158-183 4-33 (40)
204 PRK13130 H/ACA RNA-protein com 24.9 45 0.00097 22.5 1.3 23 155-184 3-25 (56)
205 PF02005 TRM: N2,N2-dimethylgu 24.9 33 0.00072 31.4 0.9 35 155-191 238-274 (377)
206 KOG2462 C2H2-type Zn-finger pr 24.8 39 0.00085 29.9 1.3 17 155-171 128-144 (279)
207 COG4098 comFA Superfamily II D 24.8 35 0.00075 31.6 1.0 29 154-183 36-67 (441)
208 cd00350 rubredoxin_like Rubred 24.4 26 0.00056 20.6 0.1 16 156-171 16-31 (33)
209 PF05605 zf-Di19: Drought indu 24.3 23 0.00051 22.9 -0.2 29 156-185 1-40 (54)
210 COG0777 AccD Acetyl-CoA carbox 24.0 35 0.00077 30.3 0.8 33 155-189 26-60 (294)
211 COG5207 UBP14 Isopeptidase T [ 24.0 49 0.0011 32.2 1.8 44 154-197 428-499 (749)
212 TIGR01562 FdhE formate dehydro 23.7 68 0.0015 28.7 2.6 34 156-189 223-265 (305)
213 PF13894 zf-C2H2_4: C2H2-type 23.7 42 0.00091 16.9 0.8 7 158-164 1-7 (24)
214 PRK08173 DNA topoisomerase III 23.6 91 0.002 31.8 3.8 27 158-187 625-652 (862)
215 cd06891 PX_Vps17p The phosphoi 23.4 1.4E+02 0.003 23.7 4.1 41 2-42 85-125 (140)
216 PF15135 UPF0515: Uncharacteri 23.4 33 0.00071 30.1 0.5 31 155-185 153-183 (278)
217 smart00105 ArfGap Putative GTP 23.2 43 0.00093 25.1 1.1 24 159-183 5-30 (112)
218 PF00301 Rubredoxin: Rubredoxi 22.8 41 0.00089 21.7 0.8 16 155-170 32-47 (47)
219 PF08421 Methyltransf_13: Puta 22.7 61 0.0013 21.8 1.7 12 172-184 37-48 (62)
220 COG1198 PriA Primosomal protei 22.6 66 0.0014 32.3 2.5 72 107-185 386-471 (730)
221 PRK05654 acetyl-CoA carboxylas 22.4 22 0.00047 31.6 -0.8 31 157-189 27-59 (292)
222 PF09082 DUF1922: Domain of un 22.4 88 0.0019 22.0 2.4 29 157-189 3-32 (68)
223 PRK05508 methionine sulfoxide 22.3 1.4E+02 0.0031 23.1 3.8 32 154-185 30-88 (119)
224 COG5415 Predicted integral mem 22.2 44 0.00095 28.7 1.0 29 156-185 191-223 (251)
225 COG0484 DnaJ DnaJ-class molecu 22.1 68 0.0015 29.6 2.3 34 154-187 156-194 (371)
226 PF14237 DUF4339: Domain of un 21.9 65 0.0014 20.0 1.6 20 96-115 17-36 (45)
227 PF13901 DUF4206: Domain of un 21.9 50 0.0011 27.5 1.3 66 107-185 114-181 (202)
228 PF14446 Prok-RING_1: Prokaryo 21.9 57 0.0012 21.9 1.3 22 159-183 7-28 (54)
229 PRK05776 DNA topoisomerase I; 21.8 99 0.0021 30.6 3.5 79 100-188 548-637 (670)
230 cd00730 rubredoxin Rubredoxin; 21.8 31 0.00068 22.5 0.1 17 155-171 32-48 (50)
231 TIGR00244 transcriptional regu 21.7 2.7E+02 0.0058 22.4 5.4 37 24-72 63-99 (147)
232 CHL00174 accD acetyl-CoA carbo 21.6 22 0.00048 31.7 -0.9 31 157-189 38-70 (296)
233 PRK00085 recO DNA repair prote 21.6 40 0.00086 28.2 0.7 38 154-191 146-187 (247)
234 KOG2391 Vacuolar sorting prote 21.5 2.1E+02 0.0046 26.3 5.2 65 59-124 253-317 (365)
235 PF07742 BTG: BTG family; Int 21.5 47 0.001 25.5 1.0 57 57-113 27-87 (118)
236 PF05952 ComX: Bacillus compet 21.4 61 0.0013 21.9 1.4 30 84-118 3-32 (57)
237 PF13913 zf-C2HC_2: zinc-finge 21.3 42 0.0009 18.5 0.5 8 158-165 3-10 (25)
238 COG5189 SFP1 Putative transcri 21.3 48 0.001 30.2 1.2 17 172-188 388-410 (423)
239 TIGR03831 YgiT_finger YgiT-typ 21.2 60 0.0013 19.6 1.3 7 179-185 35-41 (46)
240 KOG1914 mRNA cleavage and poly 21.0 2E+02 0.0043 28.3 5.2 41 75-115 433-474 (656)
241 TIGR00357 methionine-R-sulfoxi 20.9 1.9E+02 0.004 22.9 4.3 13 154-166 37-49 (134)
242 COG3877 Uncharacterized protei 20.9 59 0.0013 25.0 1.4 53 62-115 61-119 (122)
243 PHA02325 hypothetical protein 20.9 39 0.00084 23.6 0.4 9 178-186 5-13 (72)
244 KOG2041 WD40 repeat protein [G 20.7 1.3E+02 0.0027 30.8 3.9 14 172-185 1150-1165(1189)
245 PF05443 ROS_MUCR: ROS/MUCR tr 20.7 46 0.001 26.2 0.8 13 175-187 71-83 (132)
246 COG2331 Uncharacterized protei 20.6 49 0.0011 23.9 0.8 13 174-186 10-22 (82)
247 PRK01402 hslO Hsp33-like chape 20.6 42 0.00091 30.3 0.6 41 154-195 273-327 (328)
248 COG3364 Zn-ribbon containing p 20.3 45 0.00098 25.4 0.7 15 157-171 20-34 (112)
249 PF04032 Rpr2: RNAse P Rpr2/Rp 20.0 59 0.0013 22.6 1.2 29 156-184 45-85 (85)
No 1
>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=100.00 E-value=1.6e-47 Score=335.58 Aligned_cols=158 Identities=30% Similarity=0.550 Sum_probs=145.2
Q ss_pred ccCCcHHHHHHHHHHHHHHhhhhhhccccchhhhhhcccChHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhcCCCCCH
Q 036389 17 VKCNDCIREIVRKNLYGALSKVSIEAAHDKNVIDQVKACNPIQVAISMESAMYEKWGRSSETYKFKYRRLLFNFNDPKNH 96 (198)
Q Consensus 17 ~~~~d~iR~k~r~~L~~aL~~~~~e~~~~~~~~~~~~~~~~~~~A~~IE~alf~~~~~~~~~Yk~k~Rsl~~NLkd~kNp 96 (198)
+.++|++|+++|++|++||.....+.+. .+++..+|.+||.+||..++.++.+|++++|||+|||||++||
T Consensus 132 ~~t~d~~Rdk~r~~L~~aL~~~~~~~~~---------~~~~~~lA~~iE~~~f~~~~~~~~~Yk~k~Rsl~~NLKd~kNp 202 (299)
T TIGR01385 132 AVTNDKVRDKCRELLYDALAKDSDHPPQ---------SIDPEAKAIQIEELKFNNLGTTEAAYKARYRSIYSNLRDKNNP 202 (299)
T ss_pred ccCCcHHHHHHHHHHHHHHhhcCCCCcc---------ccCHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHccCCCCH
Confidence 5799999999999999999975432222 2467789999999999999988889999999999999999999
Q ss_pred HHHHHhhcCCCCchhcccCCHHhhccHHHHHHHHHHhccccccccccccccc-CCCcccccceEcCCCCCCCceEe----
Q 036389 97 EFRKKVLLGDVKPETIVNMTAKEMASDKMQLWYENSRKGRAETNGRIFSGLV-SPKNIVYGICKCSRCGHKRMSFI---- 171 (198)
Q Consensus 97 ~Lr~~vl~G~isp~~lv~Ms~eELas~e~k~~~e~~~~~e~~~~~~l~~~~~-~~~~~~t~~~~C~~C~~~~~~~~---- 171 (198)
+||.+|++|+|+|++||.|+++||||+++|++++++.+ ++ |+++|+ ...++.|++|+|++||+++|+|+
T Consensus 203 ~Lr~~vl~G~i~p~~lv~Ms~eEmas~e~k~~~e~~~k-e~-----l~~~~~~~~~~~~t~~~~C~~C~~~~~~~~q~Qt 276 (299)
T TIGR01385 203 DLRHNVLTGEITPEKLATMTAEEMASAELKQEREEITK-EN-----LFEAQGAKIQKAVTDLFTCGKCKQKKCTYYQLQT 276 (299)
T ss_pred HHHHHHHcCCCCHHHHhcCCHHHcCCHHHHHHHHHHHH-HH-----HHHHHhhhhhcCCcccccCCCCCCccceEEEecc
Confidence 99999999999999999999999999999999999999 99 999988 44555899999999999999999
Q ss_pred -----ccceEEEeccCCCccccc
Q 036389 172 -----PLRRHITCLNCYQYWAST 189 (198)
Q Consensus 172 -----pmt~fv~C~~Cg~~W~~~ 189 (198)
|||+||+|.+|||+|+||
T Consensus 277 rsaDEpmT~f~~C~~Cg~~w~fc 299 (299)
T TIGR01385 277 RSADEPMTTFVTCEECGNRWKFC 299 (299)
T ss_pred cCCCCCCeEEEEcCCCCCeeeeC
Confidence 999999999999999998
No 2
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]
Probab=100.00 E-value=9.3e-44 Score=309.21 Aligned_cols=159 Identities=30% Similarity=0.572 Sum_probs=146.4
Q ss_pred cccCCcHHHHHHHHHHHHHHhhhhhhccccchhhhhhcccChHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhcCCCCC
Q 036389 16 VVKCNDCIREIVRKNLYGALSKVSIEAAHDKNVIDQVKACNPIQVAISMESAMYEKWGRSSETYKFKYRRLLFNFNDPKN 95 (198)
Q Consensus 16 ~~~~~d~iR~k~r~~L~~aL~~~~~e~~~~~~~~~~~~~~~~~~~A~~IE~alf~~~~~~~~~Yk~k~Rsl~~NLkd~kN 95 (198)
++.++|.+|++++++|++||..... ++...+++..+|.+||.+||..++.++.+|+.++||++|||+|++|
T Consensus 128 ~~~~~d~~r~k~~e~l~~al~~~~~---------~~~~~~~~~~~a~~iE~~~~~~~g~~~~kyK~r~RS~~~NLkd~~N 198 (296)
T KOG1105|consen 128 VPITNDPVRDKCRELLYAALTTEDD---------SRVTGADPLELAVQIEEAIFEKLGNTDSKYKNRYRSRVSNLKDKNN 198 (296)
T ss_pred CCCCCchHHHHHHHHHHHHhccccc---------ccccCCCHHHHHHHHHHHHHHHhCCCcHHHHHHHHHHhhccCCCCC
Confidence 3456899999999999999983211 1223566789999999999999999999999999999999999999
Q ss_pred HHHHHHhhcCCCCchhcccCCHHhhccHHHHHHHHHHhccccccccccccccc-CCCcccccceEcCCCCCCCceEe---
Q 036389 96 HEFRKKVLLGDVKPETIVNMTAKEMASDKMQLWYENSRKGRAETNGRIFSGLV-SPKNIVYGICKCSRCGHKRMSFI--- 171 (198)
Q Consensus 96 p~Lr~~vl~G~isp~~lv~Ms~eELas~e~k~~~e~~~~~e~~~~~~l~~~~~-~~~~~~t~~~~C~~C~~~~~~~~--- 171 (198)
|+||++||+|+|+|++|+.|+++||||++++++++++.+ ++ |+++|+ .+++++|+.|+|++|++++|+|+
T Consensus 199 p~LR~~vl~G~i~pe~la~mt~eEMaS~~lk~~~~k~~k-ea-----l~~~q~~~~~gt~td~fkcgkckk~~cty~q~Q 272 (296)
T KOG1105|consen 199 PDLRRNVLTGEISPERLATMTSEEMASEELKEERQKLTK-EA-----LREHQMAKIQGTQTDLFKCGKCKKKNCTYTQLQ 272 (296)
T ss_pred HHHHHHHhcCCCCHHHhccCChhhhccHHHHHHHHHHHH-HH-----HHHHhhcccccccccceeeccccccceeEEeec
Confidence 999999999999999999999999999999999999999 99 999999 67777999999999999999999
Q ss_pred ------ccceEEEeccCCCccccc
Q 036389 172 ------PLRRHITCLNCYQYWAST 189 (198)
Q Consensus 172 ------pmt~fv~C~~Cg~~W~~~ 189 (198)
||||||+|..||||||||
T Consensus 273 trs~DePmtTfv~C~ecgnrWkfc 296 (296)
T KOG1105|consen 273 TRSADEPMTTFVTCNECGNRWKFC 296 (296)
T ss_pred cCCCCCCcceeeeecccCCccccC
Confidence 999999999999999998
No 3
>smart00510 TFS2M Domain in the central regions of transcription elongation factor S-II (and elsewhere).
Probab=99.97 E-value=2.2e-30 Score=195.22 Aligned_cols=102 Identities=37% Similarity=0.651 Sum_probs=92.2
Q ss_pred cHHHHHHHHHHHHHHhhhhhhccccchhhhhhcccChHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhcCCCCCHHHHH
Q 036389 21 DCIREIVRKNLYGALSKVSIEAAHDKNVIDQVKACNPIQVAISMESAMYEKWGRSSETYKFKYRRLLFNFNDPKNHEFRK 100 (198)
Q Consensus 21 d~iR~k~r~~L~~aL~~~~~e~~~~~~~~~~~~~~~~~~~A~~IE~alf~~~~~~~~~Yk~k~Rsl~~NLkd~kNp~Lr~ 100 (198)
|++|++++++|+++|.......+. ..++..+|.+||.+||+.++..+++|++++|||+|||||++||+||.
T Consensus 1 d~~R~~~~~~L~~al~~~~~~~~~---------~~~~~~lA~~IE~~lf~~~~~~~~~Yk~k~Rsl~fNLkd~kN~~Lr~ 71 (102)
T smart00510 1 DKVRDKCQEMLYKALQKISDPEEI---------ELDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRR 71 (102)
T ss_pred ChHHHHHHHHHHHHHHhcCCCCcc---------cccHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHhcCCCCHHHHH
Confidence 689999999999999986543321 23578899999999999998888899999999999999999999999
Q ss_pred HhhcCCCCchhcccCCHHhhccHHHHHHHHH
Q 036389 101 KVLLGDVKPETIVNMTAKEMASDKMQLWYEN 131 (198)
Q Consensus 101 ~vl~G~isp~~lv~Ms~eELas~e~k~~~e~ 131 (198)
+|++|+|+|++||.||++||||+++|+++++
T Consensus 72 ~vl~G~i~p~~lv~Ms~~ElAs~elk~~~e~ 102 (102)
T smart00510 72 KVLNGEITPEKLATMTAEELASAELKEKREK 102 (102)
T ss_pred HHHcCCCCHHHHhcCCHHHcCCHHHHHHHhC
Confidence 9999999999999999999999999998863
No 4
>PF07500 TFIIS_M: Transcription factor S-II (TFIIS), central domain; InterPro: IPR003618 Transcription factor S-II (TFIIS) is a eukaryotic protein which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites. TFIIS shows DNA-binding activity only in the presence of RNA polymerase II []. It is widely distributed being found in mammals, Drosophila, yeast and in the archaebacteria Sulfolobus acidocaldarius []. S-II proteins have a relatively conserved C-terminal region but variable N-terminal region, and some members of this family are expressed in a tissue-specific manner [, ]. TFIIS is a modular factor that comprises an N-terminal domain I, a central domain II, and a C-terminal domain III []. The weakly conserved domain I forms a four-helix bundle and is not required for TFIIS activity. Domain II forms a three-helix bundle, and domain III adopts a zinc-ribbon fold with a thin protruding beta-hairpin. Domain II and the linker between domains II and III are required for Pol II binding, whereas domain III is essential for stimulation of RNA cleavage. TFIIS extends from the polymerase surface via a pore to the internal active site, spanning a distance of 100 Angstroms. 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. This domain is found in the central region of transcription elongation factor S-II and in several hypothetical proteins.; GO: 0006351 transcription, DNA-dependent; PDB: 3PO3_S 1ENW_A 3GTM_S 1Y1V_S 3NDQ_A 2DME_A.
Probab=99.96 E-value=2.8e-30 Score=197.71 Aligned_cols=115 Identities=37% Similarity=0.634 Sum_probs=103.4
Q ss_pred CCcHHHHHHHHHHHHHHhhhhhhccccchhhhhhcccChHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhcCCCCCHHH
Q 036389 19 CNDCIREIVRKNLYGALSKVSIEAAHDKNVIDQVKACNPIQVAISMESAMYEKWGRSSETYKFKYRRLLFNFNDPKNHEF 98 (198)
Q Consensus 19 ~~d~iR~k~r~~L~~aL~~~~~e~~~~~~~~~~~~~~~~~~~A~~IE~alf~~~~~~~~~Yk~k~Rsl~~NLkd~kNp~L 98 (198)
|++++|++++++|+++|.....+ .+ ....+..+|.+||.+||..|+.++..|++++|+|+|||||++||+|
T Consensus 1 ~~~~~R~k~~~~L~~~l~~~~~~-~~--------~~~~~~~lA~~IE~~lf~~~~~~~~~Y~~k~Rsl~~NLkd~~N~~L 71 (115)
T PF07500_consen 1 TNDKVRDKARKLLYKALQKRSDE-QD--------DPEDAKELAKEIEEALFDKFGSTSKKYKQKFRSLMFNLKDPKNPDL 71 (115)
T ss_dssp -TCHHHHHHHHHHHHHHHHCCCC-CC--------CTCCHHHHHHHHHHHHHHHHTSTSHHHHHHHHHHHHHHCSSTTCCH
T ss_pred CCcHHHHHHHHHHHHHHHhcCcc-cc--------chhHHHHHHHHHHHHHHHHHccCcHHHHHHHHHHHHHhccCCcHHH
Confidence 68999999999999999987544 12 1346789999999999999988889999999999999999999999
Q ss_pred HHHhhcCCCCchhcccCCHHhhccHHHHHHHHHHhccccccccccccccc
Q 036389 99 RKKVLLGDVKPETIVNMTAKEMASDKMQLWYENSRKGRAETNGRIFSGLV 148 (198)
Q Consensus 99 r~~vl~G~isp~~lv~Ms~eELas~e~k~~~e~~~~~e~~~~~~l~~~~~ 148 (198)
+.+|++|+|+|.+||+|+++||||+++|++++++.+ ++ +.++|+
T Consensus 72 ~~~il~g~i~p~~lv~ms~~Elas~e~k~~~e~~~~-~~-----l~~~~~ 115 (115)
T PF07500_consen 72 RRRILSGEISPEELVTMSPEELASEELKEEREKIRK-ES-----LKQSQM 115 (115)
T ss_dssp HHHHHHSSSTTCHHHHCTTTTTTTSCCCCCHCCHHH-HH-----HHHTB-
T ss_pred HHHHHcCCCCHHHHhcCCHHHhCCHHHHHHHHHHHH-HH-----HHHhhC
Confidence 999999999999999999999999999999999999 88 777664
No 5
>KOG1634 consensus Predicted transcription factor DATF1, contains PHD and TFS2M domains [Transcription]
Probab=99.55 E-value=2.8e-15 Score=143.90 Aligned_cols=82 Identities=33% Similarity=0.595 Sum_probs=75.9
Q ss_pred cChHHHHHHHHHHHHHHhC-CCcHHHHHHHHHHHHhcCCCCCHHHHHHhhcCCCCchhcccCCHHhhccHHHHHHHHHHh
Q 036389 55 CNPIQVAISMESAMYEKWG-RSSETYKFKYRRLLFNFNDPKNHEFRKKVLLGDVKPETIVNMTAKEMASDKMQLWYENSR 133 (198)
Q Consensus 55 ~~~~~~A~~IE~alf~~~~-~~~~~Yk~k~Rsl~~NLkd~kNp~Lr~~vl~G~isp~~lv~Ms~eELas~e~k~~~e~~~ 133 (198)
.+..-++..||.++|..|| +.+++|+.|+|+|+|||||++||.||.+|..|+|+|++|+.|+++|||+.++++|+++..
T Consensus 267 ~d~~ll~~~ie~el~~~fG~gvnkkY~ek~RsL~fNlKDkkN~~lre~v~~~ei~~e~Lv~msaeelAs~eL~~~rEek~ 346 (778)
T KOG1634|consen 267 QDPNLLLEKIEHELFVLFGLGVNKKYPEKLRSLLFNLKDKKNPELRERVMSGEISAERLVNMSAEELASPELAEWREEKA 346 (778)
T ss_pred cchhhHhhhhhhhceeccCCcccccchhhhhhhhhccccccchHHHHHHhhcccCHhhhccCCchhhcCchHHHHHHHHH
Confidence 3455677799999999999 788999999999999999999999999999999999999999999999999999999887
Q ss_pred cccc
Q 036389 134 KGRA 137 (198)
Q Consensus 134 ~~e~ 137 (198)
+ +.
T Consensus 347 e-e~ 349 (778)
T KOG1634|consen 347 E-EM 349 (778)
T ss_pred H-HH
Confidence 7 53
No 6
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=99.12 E-value=3.5e-11 Score=76.09 Aligned_cols=30 Identities=27% Similarity=0.939 Sum_probs=28.7
Q ss_pred eEcCCCCCCCceEe---------ccceEEEeccCCCccc
Q 036389 158 CKCSRCGHKRMSFI---------PLRRHITCLNCYQYWA 187 (198)
Q Consensus 158 ~~C~~C~~~~~~~~---------pmt~fv~C~~Cg~~W~ 187 (198)
++||+||++++.|+ |||+|+.|.+|||+|+
T Consensus 1 ~~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w~ 39 (40)
T smart00440 1 APCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRWR 39 (40)
T ss_pred CcCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEeC
Confidence 58999999999998 9999999999999997
No 7
>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=99.07 E-value=6.4e-11 Score=74.49 Aligned_cols=30 Identities=37% Similarity=0.997 Sum_probs=25.8
Q ss_pred eEcCCCCCCCceEe---------ccceEEEeccCCCccc
Q 036389 158 CKCSRCGHKRMSFI---------PLRRHITCLNCYQYWA 187 (198)
Q Consensus 158 ~~C~~C~~~~~~~~---------pmt~fv~C~~Cg~~W~ 187 (198)
++||+||++++.|+ |||.|+.|.+|||+|+
T Consensus 1 ~~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~wr 39 (39)
T PF01096_consen 1 IKCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRWR 39 (39)
T ss_dssp S--SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEEE
T ss_pred CCCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCeeC
Confidence 58999999999999 9999999999999996
No 8
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=98.89 E-value=8.9e-10 Score=84.54 Aligned_cols=35 Identities=29% Similarity=0.666 Sum_probs=32.2
Q ss_pred ccceEcCCCCCCCceEe---------ccceEEEeccCCCccccc
Q 036389 155 YGICKCSRCGHKRMSFI---------PLRRHITCLNCYQYWAST 189 (198)
Q Consensus 155 t~~~~C~~C~~~~~~~~---------pmt~fv~C~~Cg~~W~~~ 189 (198)
+..+.||+||++++.|+ |||+|++|..|||+|++.
T Consensus 70 ~~~~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~wre~ 113 (113)
T COG1594 70 TAKEKCPKCGNKEAYYWQLQTRSADEPETRFYKCTRCGYRWREY 113 (113)
T ss_pred cccccCCCCCCceeEEEeeehhccCCCceEEEEecccCCEeecC
Confidence 33689999999999999 999999999999999973
No 9
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=98.83 E-value=7.9e-10 Score=82.14 Aligned_cols=32 Identities=31% Similarity=0.915 Sum_probs=29.9
Q ss_pred cceEcCCCCCCCceEe---------ccceEEEeccCCCccc
Q 036389 156 GICKCSRCGHKRMSFI---------PLRRHITCLNCYQYWA 187 (198)
Q Consensus 156 ~~~~C~~C~~~~~~~~---------pmt~fv~C~~Cg~~W~ 187 (198)
...+||+||+.+++|+ |||+||.|.+|+|+|+
T Consensus 64 t~~~Cp~Cgh~rayF~qlQtRSADEPmT~FYkC~~C~~~Wr 104 (105)
T KOG2906|consen 64 TEATCPTCGHERAYFMQLQTRSADEPMTTFYKCCKCKHRWR 104 (105)
T ss_pred ccCcCCCCCCCceEEEEeeeccCCCcHhHhhhhhccccccc
Confidence 3359999999999999 9999999999999997
No 10
>PHA02998 RNA polymerase subunit; Provisional
Probab=98.69 E-value=9e-09 Score=84.16 Aligned_cols=32 Identities=19% Similarity=0.429 Sum_probs=30.1
Q ss_pred cceEcCCCCCCCceEe---------ccceEEEeccCCCccc
Q 036389 156 GICKCSRCGHKRMSFI---------PLRRHITCLNCYQYWA 187 (198)
Q Consensus 156 ~~~~C~~C~~~~~~~~---------pmt~fv~C~~Cg~~W~ 187 (198)
...+||+||+++++|+ |||+|+.|.+||++|+
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wk 182 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFK 182 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccC
Confidence 4479999999999999 9999999999999996
No 11
>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=98.68 E-value=1.1e-08 Score=76.65 Aligned_cols=34 Identities=29% Similarity=0.754 Sum_probs=30.9
Q ss_pred ccceEcCCCCCCCceEe---------ccceEEEeccCCCcccc
Q 036389 155 YGICKCSRCGHKRMSFI---------PLRRHITCLNCYQYWAS 188 (198)
Q Consensus 155 t~~~~C~~C~~~~~~~~---------pmt~fv~C~~Cg~~W~~ 188 (198)
+...+|++||++++.|+ |||+|++|.+|||+|+-
T Consensus 60 ~~~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~~ 102 (104)
T TIGR01384 60 TTRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWRE 102 (104)
T ss_pred cccCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeEe
Confidence 33579999999999998 99999999999999984
No 12
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=98.01 E-value=3.2e-06 Score=63.94 Aligned_cols=34 Identities=26% Similarity=0.745 Sum_probs=31.3
Q ss_pred cccceEcCCCCCCCceEe---------ccceEEEeccCCCccc
Q 036389 154 VYGICKCSRCGHKRMSFI---------PLRRHITCLNCYQYWA 187 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~~~~---------pmt~fv~C~~Cg~~W~ 187 (198)
.|..-.||+||++++-|+ -|+.|+.|.+|||+|.
T Consensus 70 rts~~~C~~C~~~eavffQ~~~~r~d~~m~l~yvC~~C~h~wt 112 (113)
T KOG2691|consen 70 RTSDKHCPKCGHREAVFFQAQTRRADEAMRLFYVCCSCGHRWT 112 (113)
T ss_pred ccccccCCccCCcceEEEecccccccceEEEEEEecccccccc
Confidence 566779999999999999 7999999999999995
No 13
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=97.53 E-value=3.7e-05 Score=58.71 Aligned_cols=33 Identities=30% Similarity=0.606 Sum_probs=28.6
Q ss_pred ccceEcCCCCCCCceEe---------ccceEEEeccCCCccc
Q 036389 155 YGICKCSRCGHKRMSFI---------PLRRHITCLNCYQYWA 187 (198)
Q Consensus 155 t~~~~C~~C~~~~~~~~---------pmt~fv~C~~Cg~~W~ 187 (198)
+-.-+||+||+.++.|. .-|+||+|.+|+++..
T Consensus 72 ~I~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k~~ 113 (116)
T KOG2907|consen 72 VIKHKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYKFT 113 (116)
T ss_pred chhccCcccCCchhhhhhhhcccccCCceEEEEcCccceeee
Confidence 33459999999999999 7799999999998764
No 14
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=95.71 E-value=0.011 Score=36.22 Aligned_cols=27 Identities=22% Similarity=0.682 Sum_probs=22.5
Q ss_pred eEcCCCCCCCceEe-------ccceEEEeccCCCccc
Q 036389 158 CKCSRCGHKRMSFI-------PLRRHITCLNCYQYWA 187 (198)
Q Consensus 158 ~~C~~C~~~~~~~~-------pmt~fv~C~~Cg~~W~ 187 (198)
+.|+.|+. .|. |-..-|.|.+|||.|.
T Consensus 3 i~Cp~C~~---~y~i~d~~ip~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 3 ITCPNCQA---KYEIDDEKIPPKGRKVRCSKCGHVFF 36 (36)
T ss_pred EECCCCCC---EEeCCHHHCCCCCcEEECCCCCCEeC
Confidence 68999975 466 6678999999999995
No 15
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=95.24 E-value=0.016 Score=36.67 Aligned_cols=29 Identities=38% Similarity=0.799 Sum_probs=22.6
Q ss_pred eEcCCCCCCCceEeccceEEEeccCCCcc
Q 036389 158 CKCSRCGHKRMSFIPLRRHITCLNCYQYW 186 (198)
Q Consensus 158 ~~C~~C~~~~~~~~pmt~fv~C~~Cg~~W 186 (198)
++||.||+....+-+++..+.|.+||.-.
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGLVL 29 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-BBE
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCCEe
Confidence 58999999883333999999999999643
No 16
>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=94.94 E-value=0.021 Score=36.68 Aligned_cols=28 Identities=21% Similarity=0.562 Sum_probs=23.6
Q ss_pred eEcCCCCCCCceEeccceEEEeccCCCc
Q 036389 158 CKCSRCGHKRMSFIPLRRHITCLNCYQY 185 (198)
Q Consensus 158 ~~C~~C~~~~~~~~pmt~fv~C~~Cg~~ 185 (198)
|.||+||+.+.+.......+.|..|+++
T Consensus 19 ~~CP~Cg~~~~~~~~~~~~~~C~~C~~q 46 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKTRGRYRCKACRKQ 46 (46)
T ss_pred CCCCCCCCeeeEEeCCCCeEECCCCCCc
Confidence 7899999996666666788999999975
No 17
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=94.90 E-value=0.03 Score=34.51 Aligned_cols=28 Identities=21% Similarity=0.578 Sum_probs=22.4
Q ss_pred eEcCCCCCCCceEe-------ccceEEEeccCCCcccc
Q 036389 158 CKCSRCGHKRMSFI-------PLRRHITCLNCYQYWAS 188 (198)
Q Consensus 158 ~~C~~C~~~~~~~~-------pmt~fv~C~~Cg~~W~~ 188 (198)
.+||.|+. .|. +-..-|.|.+|||.|.+
T Consensus 3 i~CP~C~~---~f~v~~~~l~~~~~~vrC~~C~~~f~v 37 (37)
T PF13719_consen 3 ITCPNCQT---RFRVPDDKLPAGGRKVRCPKCGHVFRV 37 (37)
T ss_pred EECCCCCc---eEEcCHHHcccCCcEEECCCCCcEeeC
Confidence 68999985 455 44679999999999974
No 18
>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=94.34 E-value=0.043 Score=33.52 Aligned_cols=28 Identities=21% Similarity=0.653 Sum_probs=22.0
Q ss_pred eEcCCCCCCCceEe-------ccceEEEeccCCCcccc
Q 036389 158 CKCSRCGHKRMSFI-------PLRRHITCLNCYQYWAS 188 (198)
Q Consensus 158 ~~C~~C~~~~~~~~-------pmt~fv~C~~Cg~~W~~ 188 (198)
+.||.|+.. |. +....|.|.+||+.|..
T Consensus 3 ~~CP~C~~~---~~v~~~~~~~~~~~v~C~~C~~~~~~ 37 (38)
T TIGR02098 3 IQCPNCKTS---FRVVDSQLGANGGKVRCGKCGHVWYA 37 (38)
T ss_pred EECCCCCCE---EEeCHHHcCCCCCEEECCCCCCEEEe
Confidence 689999975 44 34558999999999964
No 19
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=94.34 E-value=0.041 Score=41.41 Aligned_cols=39 Identities=28% Similarity=0.514 Sum_probs=31.9
Q ss_pred ccceEcCCCCCCCceEe-----ccceEEEeccCCCccccccccc
Q 036389 155 YGICKCSRCGHKRMSFI-----PLRRHITCLNCYQYWASTNPEI 193 (198)
Q Consensus 155 t~~~~C~~C~~~~~~~~-----pmt~fv~C~~Cg~~W~~~~~~~ 193 (198)
...|.||.||+.+..-. -+.-++.|.+||.+..+--+..
T Consensus 20 ~k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~ev~~l 63 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFECEVPEL 63 (104)
T ss_pred CceEecCccCCeeeeEEEEEecCceeEEEcccCcceEEEecccc
Confidence 34599999999998854 8889999999999987655544
No 20
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=93.99 E-value=0.037 Score=38.44 Aligned_cols=30 Identities=30% Similarity=0.505 Sum_probs=20.6
Q ss_pred cceEcCCCCCCCceEe--cc---------------ceEEEeccCCCc
Q 036389 156 GICKCSRCGHKRMSFI--PL---------------RRHITCLNCYQY 185 (198)
Q Consensus 156 ~~~~C~~C~~~~~~~~--pm---------------t~fv~C~~Cg~~ 185 (198)
.+++||+||.+...-- .+ -+.++|.+||-+
T Consensus 3 ~~~kCpKCgn~~~~ekei~~tg~~lskifdvq~n~f~~itCk~CgYt 49 (68)
T COG3478 3 NAFKCPKCGNTNYEEKEIAATGGGLSKIFDVQNNKFIVITCKNCGYT 49 (68)
T ss_pred ccccCCCcCCcchhhceeeccCCCcceeEEecccEEEEEEeccCCch
Confidence 4678999998754322 22 255799999965
No 21
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=93.98 E-value=0.047 Score=38.09 Aligned_cols=29 Identities=31% Similarity=0.683 Sum_probs=26.0
Q ss_pred ceEcCCCCCCCceEeccceEEEeccCCCc
Q 036389 157 ICKCSRCGHKRMSFIPLRRHITCLNCYQY 185 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~ 185 (198)
..+|+.|+...+-|--..+-|+|..||..
T Consensus 19 ~VkCpdC~N~q~vFshast~V~C~~CG~~ 47 (67)
T COG2051 19 RVKCPDCGNEQVVFSHASTVVTCLICGTT 47 (67)
T ss_pred EEECCCCCCEEEEeccCceEEEecccccE
Confidence 46999999999999977888999999975
No 22
>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=93.92 E-value=0.038 Score=38.35 Aligned_cols=28 Identities=25% Similarity=0.554 Sum_probs=20.6
Q ss_pred eEcCCCCCCCceEe---------------cc--ceEEEeccCCCc
Q 036389 158 CKCSRCGHKRMSFI---------------PL--RRHITCLNCYQY 185 (198)
Q Consensus 158 ~~C~~C~~~~~~~~---------------pm--t~fv~C~~Cg~~ 185 (198)
+.|+|||......- +. =+.++|.+||..
T Consensus 1 y~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~CGYT 45 (64)
T PF09855_consen 1 YKCPKCGNEEYESGEVRATGGGLSKIFDVQNKKFTTVSCTNCGYT 45 (64)
T ss_pred CCCCCCCCcceecceEEccCCeeEEEEEecCcEEEEEECCCCCCE
Confidence 47999999865443 22 356789999987
No 23
>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=93.73 E-value=0.03 Score=33.17 Aligned_cols=28 Identities=25% Similarity=0.600 Sum_probs=14.4
Q ss_pred eEcCCCCCCCceEeccceEEEeccCCCccc
Q 036389 158 CKCSRCGHKRMSFIPLRRHITCLNCYQYWA 187 (198)
Q Consensus 158 ~~C~~C~~~~~~~~pmt~fv~C~~Cg~~W~ 187 (198)
-+|+.|++..+. .....+.|..|||.|.
T Consensus 3 p~Cp~C~se~~y--~D~~~~vCp~C~~ew~ 30 (30)
T PF08274_consen 3 PKCPLCGSEYTY--EDGELLVCPECGHEWN 30 (30)
T ss_dssp ---TTT-----E--E-SSSEEETTTTEEE-
T ss_pred CCCCCCCCccee--ccCCEEeCCcccccCC
Confidence 479999988654 4455556999999993
No 24
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=92.89 E-value=0.077 Score=37.66 Aligned_cols=38 Identities=21% Similarity=0.422 Sum_probs=27.3
Q ss_pred ceEcCCCCCCCceEe-----cc--ceEEEec--cCCCcccccccccc
Q 036389 157 ICKCSRCGHKRMSFI-----PL--RRHITCL--NCYQYWASTNPEIR 194 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~-----pm--t~fv~C~--~Cg~~W~~~~~~~~ 194 (198)
|+.||.||...-.-. +. ..+..|. +||++|..-....+
T Consensus 1 mm~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF~t~es~s~ 47 (72)
T PRK09678 1 MFHCPLCQHAAHARTSRYITDTTKERYHQCQNVNCSATFITYESVQR 47 (72)
T ss_pred CccCCCCCCccEEEEChhcChhhheeeeecCCCCCCCEEEEEEEEEE
Confidence 589999999873222 32 3788999 79999987655433
No 25
>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=91.85 E-value=0.15 Score=32.93 Aligned_cols=32 Identities=28% Similarity=0.605 Sum_probs=23.8
Q ss_pred EcCCCCCCCceEe-----cc--ceEEEecc--CCCcccccc
Q 036389 159 KCSRCGHKRMSFI-----PL--RRHITCLN--CYQYWASTN 190 (198)
Q Consensus 159 ~C~~C~~~~~~~~-----pm--t~fv~C~~--Cg~~W~~~~ 190 (198)
.||.||.+-.... |. ..++.|.| ||++|....
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg~tfv~~~ 41 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSPLTRELYCQCTNPECGHTFVANL 41 (47)
T ss_pred CcCCCCCeeEEEEchhhCcceEEEEEEECCCcCCCEEEEEE
Confidence 5999999855444 22 37889998 999997654
No 26
>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=91.27 E-value=0.15 Score=35.69 Aligned_cols=29 Identities=17% Similarity=0.528 Sum_probs=22.3
Q ss_pred ceEcCCCCCCCceEe------ccceEEEeccCCCc
Q 036389 157 ICKCSRCGHKRMSFI------PLRRHITCLNCYQY 185 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~------pmt~fv~C~~Cg~~ 185 (198)
.|+|..|+.+...-+ --+++|+|.+|.++
T Consensus 4 ~FTC~~C~~Rs~~~~sk~aY~~GvViv~C~gC~~~ 38 (66)
T PF05180_consen 4 TFTCNKCGTRSAKMFSKQAYHKGVVIVQCPGCKNR 38 (66)
T ss_dssp EEEETTTTEEEEEEEEHHHHHTSEEEEE-TTS--E
T ss_pred EEEcCCCCCccceeeCHHHHhCCeEEEECCCCcce
Confidence 599999999987666 56799999999986
No 27
>KOG1886 consensus BAH domain proteins [Transcription]
Probab=91.23 E-value=0.15 Score=47.84 Aligned_cols=173 Identities=10% Similarity=-0.033 Sum_probs=104.4
Q ss_pred ccCCcHHHHHHHHHHHHHHhhhhhhccccc--hhhhhhcccChHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhcCCCC
Q 036389 17 VKCNDCIREIVRKNLYGALSKVSIEAAHDK--NVIDQVKACNPIQVAISMESAMYEKWGRSSETYKFKYRRLLFNFNDPK 94 (198)
Q Consensus 17 ~~~~d~iR~k~r~~L~~aL~~~~~e~~~~~--~~~~~~~~~~~~~~A~~IE~alf~~~~~~~~~Yk~k~Rsl~~NLkd~k 94 (198)
+.+++.-|+|++.-+..++.+...-..... +-........+......||.+.|+.+...-..|..+...|.++|+ .
T Consensus 238 ~~t~~~~~~k~~g~~~~~v~~~~~~~s~~~~~~~~~~~~p~~~v~~~~~le~~s~~s~a~d~~~~~~~~~~l~~~~k--~ 315 (464)
T KOG1886|consen 238 LLTGRSDRDKVLGKLLEVVWQNSCSTSEAKPAGDQGSLWPNPSVSPCGALEQPSHASLAKDLESYLGLRETLVLLLK--G 315 (464)
T ss_pred CCCCcccccccccccchhhccccccccccCCCcccccCCCCcccchhhhhhhhhhhhHhhhhhhhhhhhhHHHhhhc--c
Confidence 467899999999999999965543222210 000001123356778899999999887666789999999999998 5
Q ss_pred CHHHHHHhhcCC-CCchhcccCCHHhhccHHHHHHHHHHhcccccccccccccccCCCcc-cccceEcCCCCCCCceEec
Q 036389 95 NHEFRKKVLLGD-VKPETIVNMTAKEMASDKMQLWYENSRKGRAETNGRIFSGLVSPKNI-VYGICKCSRCGHKRMSFIP 172 (198)
Q Consensus 95 Np~Lr~~vl~G~-isp~~lv~Ms~eELas~e~k~~~e~~~~~e~~~~~~l~~~~~~~~~~-~t~~~~C~~C~~~~~~~~p 172 (198)
---|+.+.++|. +.|+..+.|.+-++-+...-..-.+..- .- .....+...-+ ..-...|+ |.+-.|.++-
T Consensus 316 ~~~l~~~~ln~~~~~~e~~~~l~~p~~p~~~~~~~~~~~~~-d~-----~~~l~~~~~~~~~~~~~~~g-~~~~~~~~~~ 388 (464)
T KOG1886|consen 316 QALLKPEPLNPGETKPEPKQELHPPSFPDGQSSPSSMKLND-DD-----YDGLCVGLELTAGSLYLYCG-QEGLICAGHL 388 (464)
T ss_pred hhhhccccCCCcccCchhhhhccCCCCCCCccCccccccCc-hh-----HHHHHHhhhhhccchhhhcc-cccceecccc
Confidence 567888889994 8899888887665554431000000000 00 00000000000 01112343 5555566661
Q ss_pred cceEEEeccCCCcccccccccccccC
Q 036389 173 LRRHITCLNCYQYWASTNPEIRVLPI 198 (198)
Q Consensus 173 mt~fv~C~~Cg~~W~~~~~~~~~~~~ 198 (198)
---..-|..|+.+|...|...+++++
T Consensus 389 ~~~~~~~v~~~~~a~~~~~~~~~~~~ 414 (464)
T KOG1886|consen 389 PCPMLPEVKLSPVAAVHREGLLLAPS 414 (464)
T ss_pred CCCCCCCcCcccccccchhhhcccce
Confidence 11223478899999999999888775
No 28
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=90.89 E-value=0.2 Score=31.99 Aligned_cols=28 Identities=25% Similarity=0.581 Sum_probs=21.8
Q ss_pred ceEcCCCCCCCceEeccceEEEeccCCCc
Q 036389 157 ICKCSRCGHKRMSFIPLRRHITCLNCYQY 185 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~ 185 (198)
.|+|+.||.. ..+.+.+.-++|..||++
T Consensus 3 ~y~C~~CG~~-~~~~~~~~~~~Cp~CG~~ 30 (46)
T PRK00398 3 EYKCARCGRE-VELDEYGTGVRCPYCGYR 30 (46)
T ss_pred EEECCCCCCE-EEECCCCCceECCCCCCe
Confidence 4899999984 445566668899999987
No 29
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=90.50 E-value=0.25 Score=33.76 Aligned_cols=30 Identities=27% Similarity=0.649 Sum_probs=26.7
Q ss_pred ceEcCCCCCCCceEeccceEEEeccCCCcc
Q 036389 157 ICKCSRCGHKRMSFIPLRRHITCLNCYQYW 186 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~W 186 (198)
..+|+.|+...+-|.-..+-|.|..||..-
T Consensus 11 ~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L 40 (59)
T PRK00415 11 KVKCPDCGNEQVVFSHASTVVRCLVCGKTL 40 (59)
T ss_pred EEECCCCCCeEEEEecCCcEEECcccCCCc
Confidence 369999999999999888899999999864
No 30
>PLN00209 ribosomal protein S27; Provisional
Probab=90.15 E-value=0.48 Score=34.71 Aligned_cols=31 Identities=19% Similarity=0.330 Sum_probs=27.2
Q ss_pred cceEcCCCCCCCceEeccceEEEeccCCCcc
Q 036389 156 GICKCSRCGHKRMSFIPLRRHITCLNCYQYW 186 (198)
Q Consensus 156 ~~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~W 186 (198)
-..+|+.|+...+-|.-..+-|.|..||..-
T Consensus 35 m~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L 65 (86)
T PLN00209 35 MDVKCQGCFNITTVFSHSQTVVVCGSCQTVL 65 (86)
T ss_pred EEEECCCCCCeeEEEecCceEEEccccCCEe
Confidence 3469999999999999889999999999753
No 31
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=90.00 E-value=0.36 Score=38.10 Aligned_cols=30 Identities=17% Similarity=0.359 Sum_probs=25.8
Q ss_pred cceEcCCCCCCCceEe--ccceEEEeccCCCc
Q 036389 156 GICKCSRCGHKRMSFI--PLRRHITCLNCYQY 185 (198)
Q Consensus 156 ~~~~C~~C~~~~~~~~--pmt~fv~C~~Cg~~ 185 (198)
.-..|+.|+.+.+.+. .-..|..|..||.+
T Consensus 96 ~yVlC~~C~sPdT~l~k~~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 96 KYVICRECNRPDTRIIKEGRVSLLKCEACGAK 127 (133)
T ss_pred heEECCCCCCCCcEEEEeCCeEEEecccCCCC
Confidence 3479999999999998 56678999999985
No 32
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=89.82 E-value=0.38 Score=38.19 Aligned_cols=30 Identities=20% Similarity=0.416 Sum_probs=26.4
Q ss_pred cceEcCCCCCCCceEe--ccceEEEeccCCCc
Q 036389 156 GICKCSRCGHKRMSFI--PLRRHITCLNCYQY 185 (198)
Q Consensus 156 ~~~~C~~C~~~~~~~~--pmt~fv~C~~Cg~~ 185 (198)
.-..|+.||++.+.+. .-+.|..|..||.+
T Consensus 101 ~yVlC~~C~spdT~l~k~~r~~~l~C~ACGa~ 132 (138)
T PRK03988 101 EYVICPECGSPDTKLIKEGRIWVLKCEACGAE 132 (138)
T ss_pred hcEECCCCCCCCcEEEEcCCeEEEEcccCCCC
Confidence 3479999999999998 66789999999986
No 33
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=89.42 E-value=0.24 Score=37.82 Aligned_cols=30 Identities=17% Similarity=0.538 Sum_probs=22.8
Q ss_pred eEcCCCCCCCceEeccceEEEeccCCCccccc
Q 036389 158 CKCSRCGHKRMSFIPLRRHITCLNCYQYWAST 189 (198)
Q Consensus 158 ~~C~~C~~~~~~~~pmt~fv~C~~Cg~~W~~~ 189 (198)
-.||+|++..++ ++-..+.|..|||.|.-.
T Consensus 3 p~CP~C~seytY--~dg~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 3 PPCPKCNSEYTY--HDGTQLICPSCLYEWNEN 32 (109)
T ss_pred CcCCcCCCcceE--ecCCeeECcccccccccc
Confidence 479999987443 555567899999999654
No 34
>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=89.16 E-value=0.39 Score=34.69 Aligned_cols=35 Identities=14% Similarity=0.384 Sum_probs=20.8
Q ss_pred ccceEcCCCCCCCceEe-----ccceEEEeccCCCccccc
Q 036389 155 YGICKCSRCGHKRMSFI-----PLRRHITCLNCYQYWAST 189 (198)
Q Consensus 155 t~~~~C~~C~~~~~~~~-----pmt~fv~C~~Cg~~W~~~ 189 (198)
...|.||-|++.++--. -.+-.+.|..||..|.+.
T Consensus 20 ~~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~ 59 (81)
T PF05129_consen 20 PKVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTK 59 (81)
T ss_dssp SS----TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE
T ss_pred CceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEc
Confidence 46699999997766554 678999999999998765
No 35
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=89.14 E-value=0.69 Score=33.82 Aligned_cols=31 Identities=19% Similarity=0.376 Sum_probs=27.2
Q ss_pred cceEcCCCCCCCceEeccceEEEeccCCCcc
Q 036389 156 GICKCSRCGHKRMSFIPLRRHITCLNCYQYW 186 (198)
Q Consensus 156 ~~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~W 186 (198)
-..+|+.|+...+-|.-..+-|.|..||..-
T Consensus 34 m~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L 64 (85)
T PTZ00083 34 MDVKCPGCSQITTVFSHAQTVVLCGGCSSQL 64 (85)
T ss_pred EEEECCCCCCeeEEEecCceEEEccccCCEe
Confidence 4469999999999999888999999999753
No 36
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=89.07 E-value=0.47 Score=36.21 Aligned_cols=30 Identities=20% Similarity=0.440 Sum_probs=26.0
Q ss_pred cceEcCCCCCCCceEe--ccceEEEeccCCCc
Q 036389 156 GICKCSRCGHKRMSFI--PLRRHITCLNCYQY 185 (198)
Q Consensus 156 ~~~~C~~C~~~~~~~~--pmt~fv~C~~Cg~~ 185 (198)
.-..|+.|+++.+.+. .-+.|..|..||.+
T Consensus 79 ~yVlC~~C~spdT~l~k~~r~~~l~C~aCGa~ 110 (110)
T smart00653 79 EYVLCPECGSPDTELIKENRLFFLKCEACGAR 110 (110)
T ss_pred hcEECCCCCCCCcEEEEeCCeEEEEccccCCC
Confidence 3479999999999998 56789999999974
No 37
>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=88.54 E-value=0.32 Score=29.84 Aligned_cols=26 Identities=23% Similarity=0.476 Sum_probs=22.4
Q ss_pred eEcCCCCCCCceEeccceEEEeccCCCc
Q 036389 158 CKCSRCGHKRMSFIPLRRHITCLNCYQY 185 (198)
Q Consensus 158 ~~C~~C~~~~~~~~pmt~fv~C~~Cg~~ 185 (198)
++|+.|+.+ .|.+---|+.|..|||.
T Consensus 9 ~~C~~C~~~--~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 9 EPCPVCGSR--WFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CcCCCCCCe--EeEccCCEEEhhhCceE
Confidence 579999999 67788888999999985
No 38
>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=88.13 E-value=0.43 Score=37.25 Aligned_cols=28 Identities=21% Similarity=0.497 Sum_probs=25.2
Q ss_pred eEcCCCCCCCceEe--ccceEEEeccCCCc
Q 036389 158 CKCSRCGHKRMSFI--PLRRHITCLNCYQY 185 (198)
Q Consensus 158 ~~C~~C~~~~~~~~--pmt~fv~C~~Cg~~ 185 (198)
..|+.|+++++.+. --..|..|..||.+
T Consensus 94 VlC~~C~spdT~l~k~~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 94 VLCPECGSPDTELIKEGRLIFLKCKACGAS 123 (125)
T ss_dssp SSCTSTSSSSEEEEEETTCCEEEETTTSCE
T ss_pred EEcCCCCCCccEEEEcCCEEEEEecccCCc
Confidence 68999999999998 66799999999975
No 39
>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=87.90 E-value=0.74 Score=31.45 Aligned_cols=36 Identities=11% Similarity=0.321 Sum_probs=27.4
Q ss_pred eEcCCCCCCCceEe---ccceEEEeccCCCccccccccc
Q 036389 158 CKCSRCGHKRMSFI---PLRRHITCLNCYQYWASTNPEI 193 (198)
Q Consensus 158 ~~C~~C~~~~~~~~---pmt~fv~C~~Cg~~W~~~~~~~ 193 (198)
..||+|+.-..--. --.-.++|..||++-......+
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~~~~~~~~ 48 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGYQEQQKDQSV 48 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCCccccCCccc
Confidence 58999999877544 4447899999999877665544
No 40
>PRK10220 hypothetical protein; Provisional
Probab=87.59 E-value=0.41 Score=36.58 Aligned_cols=31 Identities=16% Similarity=0.503 Sum_probs=23.4
Q ss_pred eEcCCCCCCCceEeccceEEEeccCCCcccccc
Q 036389 158 CKCSRCGHKRMSFIPLRRHITCLNCYQYWASTN 190 (198)
Q Consensus 158 ~~C~~C~~~~~~~~pmt~fv~C~~Cg~~W~~~~ 190 (198)
-.||+|++.-++ +....+.|..|||.|.-..
T Consensus 4 P~CP~C~seytY--~d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 4 PHCPKCNSEYTY--EDNGMYICPECAHEWNDAE 34 (111)
T ss_pred CcCCCCCCcceE--cCCCeEECCcccCcCCccc
Confidence 479999986432 5555688999999997554
No 41
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=87.42 E-value=0.22 Score=29.86 Aligned_cols=26 Identities=23% Similarity=0.545 Sum_probs=15.5
Q ss_pred eEcCCCCCCCceEeccceEEEeccCCCc
Q 036389 158 CKCSRCGHKRMSFIPLRRHITCLNCYQY 185 (198)
Q Consensus 158 ~~C~~C~~~~~~~~pmt~fv~C~~Cg~~ 185 (198)
+.|+.||..-- .....-+.|.+||+|
T Consensus 1 Y~C~~Cg~~~~--~~~~~~irC~~CG~R 26 (32)
T PF03604_consen 1 YICGECGAEVE--LKPGDPIRCPECGHR 26 (32)
T ss_dssp EBESSSSSSE---BSTSSTSSBSSSS-S
T ss_pred CCCCcCCCeeE--cCCCCcEECCcCCCe
Confidence 46888887643 322334688888887
No 42
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=87.38 E-value=0.6 Score=29.90 Aligned_cols=26 Identities=23% Similarity=0.547 Sum_probs=18.7
Q ss_pred ceEcCCCCCCCceEe-ccceEEEeccCCCc
Q 036389 157 ICKCSRCGHKRMSFI-PLRRHITCLNCYQY 185 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~-pmt~fv~C~~Cg~~ 185 (198)
.|.|+.||.. +. ....-+.|.+||++
T Consensus 2 ~Y~C~~Cg~~---~~~~~~~~irC~~CG~r 28 (44)
T smart00659 2 IYICGECGRE---NEIKSKDVVRCRECGYR 28 (44)
T ss_pred EEECCCCCCE---eecCCCCceECCCCCce
Confidence 3788999874 22 34566889999987
No 43
>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=87.22 E-value=0.64 Score=32.86 Aligned_cols=34 Identities=12% Similarity=0.320 Sum_probs=26.4
Q ss_pred eEcCCCCCCCceEe---ccceEEEeccCCCccccccc
Q 036389 158 CKCSRCGHKRMSFI---PLRRHITCLNCYQYWASTNP 191 (198)
Q Consensus 158 ~~C~~C~~~~~~~~---pmt~fv~C~~Cg~~W~~~~~ 191 (198)
..||+|+.-..-.+ --.-.++|..||++-.....
T Consensus 9 a~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~~~~~ 45 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRENGVEYVECVECGYTERQPDQ 45 (71)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEecCCCCeeccCCc
Confidence 58999999886444 34789999999998765554
No 44
>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=87.15 E-value=0.41 Score=32.23 Aligned_cols=28 Identities=21% Similarity=0.519 Sum_probs=20.7
Q ss_pred eEcCCCCCCCceEeccceEEEeccCCCc
Q 036389 158 CKCSRCGHKRMSFIPLRRHITCLNCYQY 185 (198)
Q Consensus 158 ~~C~~C~~~~~~~~pmt~fv~C~~Cg~~ 185 (198)
.+|+.|+...+-|.-..+-|.|..||..
T Consensus 8 VkCp~C~~~q~vFSha~t~V~C~~Cg~~ 35 (55)
T PF01667_consen 8 VKCPGCYNIQTVFSHAQTVVKCVVCGTV 35 (55)
T ss_dssp EE-TTT-SEEEEETT-SS-EE-SSSTSE
T ss_pred EECCCCCCeeEEEecCCeEEEcccCCCE
Confidence 6999999999998888888999999975
No 45
>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=87.03 E-value=0.43 Score=41.81 Aligned_cols=38 Identities=18% Similarity=0.364 Sum_probs=20.8
Q ss_pred ceEcCCCCCCCceEe----c--cceEEEeccCCCcccccccccc
Q 036389 157 ICKCSRCGHKRMSFI----P--LRRHITCLNCYQYWASTNPEIR 194 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~----p--mt~fv~C~~Cg~~W~~~~~~~~ 194 (198)
.-.||-||+.-..-. + -..|..|.-||+.|.|-|-.|.
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp 215 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCP 215 (290)
T ss_dssp -SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-T
T ss_pred CCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCc
Confidence 358999999855444 2 3699999999999999886653
No 46
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=86.84 E-value=0.6 Score=35.09 Aligned_cols=34 Identities=35% Similarity=0.513 Sum_probs=23.9
Q ss_pred ccceEcCCCCCCCceEe--ccceEEEeccCCCcccc
Q 036389 155 YGICKCSRCGHKRMSFI--PLRRHITCLNCYQYWAS 188 (198)
Q Consensus 155 t~~~~C~~C~~~~~~~~--pmt~fv~C~~Cg~~W~~ 188 (198)
...|.|+.||....... -.+.++.|.+||.....
T Consensus 19 pt~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 19 PKIFECPRCGKVSISVKIKKNIAIITCGNCGLYTEF 54 (99)
T ss_pred CcEeECCCCCCeEeeeecCCCcceEECCCCCCccCE
Confidence 56899999995322211 34679999999987543
No 47
>PHA00626 hypothetical protein
Probab=86.73 E-value=0.55 Score=31.82 Aligned_cols=28 Identities=18% Similarity=0.450 Sum_probs=18.6
Q ss_pred EcCCCCCCCceEe----ccceEEEeccCCCcc
Q 036389 159 KCSRCGHKRMSFI----PLRRHITCLNCYQYW 186 (198)
Q Consensus 159 ~C~~C~~~~~~~~----pmt~fv~C~~Cg~~W 186 (198)
.||+||+....-. --..-|.|..||.++
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~f 33 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYND 33 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCee
Confidence 5888988754432 224556699999764
No 48
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=86.68 E-value=0.73 Score=38.61 Aligned_cols=30 Identities=20% Similarity=0.408 Sum_probs=26.4
Q ss_pred cceEcCCCCCCCceEe--ccceEEEeccCCCc
Q 036389 156 GICKCSRCGHKRMSFI--PLRRHITCLNCYQY 185 (198)
Q Consensus 156 ~~~~C~~C~~~~~~~~--pmt~fv~C~~Cg~~ 185 (198)
.-..|+.|+.+.+.+. .-+.|..|..||.+
T Consensus 97 ~yV~C~~C~~pdT~l~k~~~~~~l~C~aCGa~ 128 (201)
T PRK12336 97 EYVICSECGLPDTRLVKEDRVLMLRCDACGAH 128 (201)
T ss_pred heEECCCCCCCCcEEEEcCCeEEEEcccCCCC
Confidence 3479999999999999 67889999999975
No 49
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=85.70 E-value=0.72 Score=28.68 Aligned_cols=29 Identities=28% Similarity=0.544 Sum_probs=21.0
Q ss_pred EcCCCCCCCceEe-ccceEEEeccCCCccc
Q 036389 159 KCSRCGHKRMSFI-PLRRHITCLNCYQYWA 187 (198)
Q Consensus 159 ~C~~C~~~~~~~~-pmt~fv~C~~Cg~~W~ 187 (198)
+||+|+..-..+. +-.....|.+||--|-
T Consensus 1 ~CP~C~~~l~~~~~~~~~id~C~~C~G~W~ 30 (41)
T PF13453_consen 1 KCPRCGTELEPVRLGDVEIDVCPSCGGIWF 30 (41)
T ss_pred CcCCCCcccceEEECCEEEEECCCCCeEEc
Confidence 5999998644444 4456666999999983
No 50
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=85.70 E-value=0.82 Score=30.47 Aligned_cols=29 Identities=17% Similarity=0.396 Sum_probs=21.9
Q ss_pred cceEcCCCCCCCceEe-c-c-----ceEEEeccCCC
Q 036389 156 GICKCSRCGHKRMSFI-P-L-----RRHITCLNCYQ 184 (198)
Q Consensus 156 ~~~~C~~C~~~~~~~~-p-m-----t~fv~C~~Cg~ 184 (198)
.+..||-||.....+. . . ..+|.|.+||.
T Consensus 2 ~LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 3568999977776666 1 1 18899999997
No 51
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=85.02 E-value=1.4 Score=34.92 Aligned_cols=37 Identities=22% Similarity=0.477 Sum_probs=24.4
Q ss_pred cccceEcCCCCCCCceEe------ccceEEEeccCCCccccccc
Q 036389 154 VYGICKCSRCGHKRMSFI------PLRRHITCLNCYQYWASTNP 191 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~~~~------pmt~fv~C~~Cg~~W~~~~~ 191 (198)
....|.||.||.+-. |. .++..++|.+||..-...+.
T Consensus 96 ~~~~Y~Cp~C~~~y~-~~ea~~~~d~~~~f~Cp~Cg~~l~~~dn 138 (147)
T smart00531 96 NNAYYKCPNCQSKYT-FLEANQLLDMDGTFTCPRCGEELEEDDN 138 (147)
T ss_pred CCcEEECcCCCCEee-HHHHHHhcCCCCcEECCCCCCEEEEcCc
Confidence 356799999984422 22 23444889999987655443
No 52
>PRK05978 hypothetical protein; Provisional
Probab=84.93 E-value=0.48 Score=38.08 Aligned_cols=34 Identities=18% Similarity=0.439 Sum_probs=27.8
Q ss_pred eEcCCCCCCCceEeccceEEEeccCCCccccccc
Q 036389 158 CKCSRCGHKRMSFIPLRRHITCLNCYQYWASTNP 191 (198)
Q Consensus 158 ~~C~~C~~~~~~~~pmt~fv~C~~Cg~~W~~~~~ 191 (198)
-+||+||+-+..-.-.+.--+|..||..+.+-+.
T Consensus 34 grCP~CG~G~LF~g~Lkv~~~C~~CG~~~~~~~a 67 (148)
T PRK05978 34 GRCPACGEGKLFRAFLKPVDHCAACGEDFTHHRA 67 (148)
T ss_pred CcCCCCCCCcccccccccCCCccccCCccccCCc
Confidence 4899999998765566777789999999887654
No 53
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=84.67 E-value=1.1 Score=31.12 Aligned_cols=37 Identities=16% Similarity=0.290 Sum_probs=28.8
Q ss_pred cceEcCCCCCCCceEe-cc-ceEEEeccCCCcccccccc
Q 036389 156 GICKCSRCGHKRMSFI-PL-RRHITCLNCYQYWASTNPE 192 (198)
Q Consensus 156 ~~~~C~~C~~~~~~~~-pm-t~fv~C~~Cg~~W~~~~~~ 192 (198)
+.-.||-||....... +- ..+|.|..||.+|.+-.++
T Consensus 5 ~lKPCPFCG~~~~~v~~~~g~~~v~C~~CgA~~~~~~te 43 (64)
T PRK09710 5 NVKPCPFCGCPSVTVKAISGYYRAKCNGCESRTGYGGSE 43 (64)
T ss_pred cccCCCCCCCceeEEEecCceEEEEcCCCCcCcccccCH
Confidence 3458999999999888 33 3459999999998776543
No 54
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=82.51 E-value=0.92 Score=40.61 Aligned_cols=39 Identities=21% Similarity=0.354 Sum_probs=30.1
Q ss_pred cceEcCCCCCCCceE-e-----ccceEEEeccCCCcccccccccc
Q 036389 156 GICKCSRCGHKRMSF-I-----PLRRHITCLNCYQYWASTNPEIR 194 (198)
Q Consensus 156 ~~~~C~~C~~~~~~~-~-----pmt~fv~C~~Cg~~W~~~~~~~~ 194 (198)
..-.||-||+.-..- . .--.|..|.-|++.|.|-|-.|.
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~ 230 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCS 230 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCC
Confidence 456899999997432 2 33589999999999999886653
No 55
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=81.99 E-value=0.85 Score=29.97 Aligned_cols=29 Identities=21% Similarity=0.247 Sum_probs=21.8
Q ss_pred ceEcCCCCCCCceEeccceEEEeccCCCccc
Q 036389 157 ICKCSRCGHKRMSFIPLRRHITCLNCYQYWA 187 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~W~ 187 (198)
.-.||+||.. ...+......|..||-.+.
T Consensus 20 ~~fCP~Cg~~--~m~~~~~r~~C~~Cgyt~~ 48 (50)
T PRK00432 20 NKFCPRCGSG--FMAEHLDRWHCGKCGYTEF 48 (50)
T ss_pred cCcCcCCCcc--hheccCCcEECCCcCCEEe
Confidence 3489999985 2237778889999998753
No 56
>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=81.90 E-value=1.5 Score=28.81 Aligned_cols=29 Identities=21% Similarity=0.395 Sum_probs=20.6
Q ss_pred eEcCCCCCCCceEe------ccceEEEeccCCCcc
Q 036389 158 CKCSRCGHKRMSFI------PLRRHITCLNCYQYW 186 (198)
Q Consensus 158 ~~C~~C~~~~~~~~------pmt~fv~C~~Cg~~W 186 (198)
-.||-||+..-.+. .-+.++.|..||..=
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~ 36 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECSTCGASG 36 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECCCCCCCc
Confidence 47999999877554 223344899999863
No 57
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=81.74 E-value=0.67 Score=38.15 Aligned_cols=36 Identities=11% Similarity=0.154 Sum_probs=25.6
Q ss_pred cccceEcCCCCCCCceEeccceEEEeccCCCccccc
Q 036389 154 VYGICKCSRCGHKRMSFIPLRRHITCLNCYQYWAST 189 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~W~~~ 189 (198)
....|.||.|+.+-+..-.|...++|.+||..-...
T Consensus 114 ~~~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~~~ 149 (178)
T PRK06266 114 NNMFFFCPNCHIRFTFDEAMEYGFRCPQCGEMLEEY 149 (178)
T ss_pred CCCEEECCCCCcEEeHHHHhhcCCcCCCCCCCCeec
Confidence 356799999994422222888889999999875443
No 58
>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=81.03 E-value=0.59 Score=42.45 Aligned_cols=30 Identities=20% Similarity=0.574 Sum_probs=16.0
Q ss_pred cccceEcCCCCCCCceEe----------------ccceEEEeccCCCc
Q 036389 154 VYGICKCSRCGHKRMSFI----------------PLRRHITCLNCYQY 185 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~~~~----------------pmt~fv~C~~Cg~~ 185 (198)
.-..+.|..|+ .+.|. -...|+.|.+||+|
T Consensus 249 k~kav~C~~C~--yt~~~~~~~C~~~~H~l~~~~a~KRFFkC~~C~~R 294 (344)
T PF09332_consen 249 KCKAVTCKQCK--YTAFKPSDRCKEEGHPLKWHDAVKRFFKCKDCGNR 294 (344)
T ss_dssp EEEEEEETTT----EESS--HHHHHTT--EEEEEEE-EEEE-T-TS-E
T ss_pred EEEEEEcCCCC--CcccCcchhHHhcCCceEEeeeeeeeEECCCCCCe
Confidence 45667888884 22222 44678888888887
No 59
>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=78.09 E-value=1.9 Score=34.74 Aligned_cols=34 Identities=15% Similarity=0.276 Sum_probs=24.6
Q ss_pred cccceEcCCCCCCCceEe-ccceEEEeccCCCcccc
Q 036389 154 VYGICKCSRCGHKRMSFI-PLRRHITCLNCYQYWAS 188 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~~~~-pmt~fv~C~~Cg~~W~~ 188 (198)
....|.||.|+.+ -+|. -|..-++|.+||..-.+
T Consensus 106 ~~~~Y~Cp~c~~r-~tf~eA~~~~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 106 NNMFFICPNMCVR-FTFNEAMELNFTCPRCGAMLDY 140 (158)
T ss_pred CCCeEECCCCCcE-eeHHHHHHcCCcCCCCCCEeee
Confidence 3567999999943 2222 77788999999987443
No 60
>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=77.91 E-value=1.5 Score=29.81 Aligned_cols=34 Identities=29% Similarity=0.499 Sum_probs=25.8
Q ss_pred ccceEcCCCCCCCceEeccceEEEeccCCCcccccccc
Q 036389 155 YGICKCSRCGHKRMSFIPLRRHITCLNCYQYWASTNPE 192 (198)
Q Consensus 155 t~~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~W~~~~~~ 192 (198)
|+. .|+.||...-. .+....++|.+||..| .+|.
T Consensus 27 TSq-~C~~CG~~~~~-~~~~r~~~C~~Cg~~~--~rD~ 60 (69)
T PF07282_consen 27 TSQ-TCPRCGHRNKK-RRSGRVFTCPNCGFEM--DRDV 60 (69)
T ss_pred Ccc-CccCccccccc-ccccceEEcCCCCCEE--CcHH
Confidence 444 89999998777 5556677899999885 5554
No 61
>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=77.85 E-value=1 Score=34.25 Aligned_cols=30 Identities=30% Similarity=0.661 Sum_probs=22.0
Q ss_pred ceEcCCCCCCCceEeccc-eEEEeccCCCccccc
Q 036389 157 ICKCSRCGHKRMSFIPLR-RHITCLNCYQYWAST 189 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~pmt-~fv~C~~Cg~~W~~~ 189 (198)
.-.|+.||.+ ||.+. .-++|-.||..|-..
T Consensus 9 KR~Cp~CG~k---FYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 9 KRTCPSCGAK---FYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cccCCCCcch---hccCCCCCccCCCCCCccCcc
Confidence 3589999965 77221 335699999999766
No 62
>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=77.83 E-value=1.4 Score=27.67 Aligned_cols=28 Identities=21% Similarity=0.644 Sum_probs=20.4
Q ss_pred ceEcCCCCCCCceEeccce--EEEeccCCC
Q 036389 157 ICKCSRCGHKRMSFIPLRR--HITCLNCYQ 184 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~pmt~--fv~C~~Cg~ 184 (198)
.|+|..||..--...||.. -+.|-.||.
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EEEeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 4788888876666666654 777888886
No 63
>KOG3277 consensus Uncharacterized conserved protein [Function unknown]
Probab=77.69 E-value=1.7 Score=35.28 Aligned_cols=31 Identities=13% Similarity=0.231 Sum_probs=25.5
Q ss_pred cceEcCCCCCCCceE------eccceEEEeccCCCcc
Q 036389 156 GICKCSRCGHKRMSF------IPLRRHITCLNCYQYW 186 (198)
Q Consensus 156 ~~~~C~~C~~~~~~~------~pmt~fv~C~~Cg~~W 186 (198)
-.|+|..|+.+...- +--|++|+|..|.++-
T Consensus 78 l~yTCkvCntRs~ktisk~AY~~GvVivqC~gC~~~H 114 (165)
T KOG3277|consen 78 LAYTCKVCNTRSTKTISKQAYEKGVVIVQCPGCKNHH 114 (165)
T ss_pred EEEEeeccCCccccccChhhhhCceEEEECCCCccce
Confidence 459999999997743 3789999999999763
No 64
>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=77.43 E-value=1.5 Score=38.05 Aligned_cols=30 Identities=30% Similarity=0.693 Sum_probs=13.6
Q ss_pred cceEcCCCCCCCceEe----ccceEEEeccCCCcc
Q 036389 156 GICKCSRCGHKRMSFI----PLRRHITCLNCYQYW 186 (198)
Q Consensus 156 ~~~~C~~C~~~~~~~~----pmt~fv~C~~Cg~~W 186 (198)
.-+.||.||...-.-+ |.-.|+ |.+|++.+
T Consensus 30 ~n~yCP~Cg~~~L~~f~NN~PVaDF~-C~~C~eey 63 (254)
T PF06044_consen 30 ENMYCPNCGSKPLSKFENNRPVADFY-CPNCNEEY 63 (254)
T ss_dssp HH---TTT--SS-EE--------EEE--TTT--EE
T ss_pred HCCcCCCCCChhHhhccCCCccceeE-CCCCchHH
Confidence 3469999999966655 999998 99999875
No 65
>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=77.01 E-value=1.6 Score=39.04 Aligned_cols=39 Identities=18% Similarity=0.417 Sum_probs=29.5
Q ss_pred cceEcCCCCCCCceEe-------ccceEEEeccCCCcccccccccc
Q 036389 156 GICKCSRCGHKRMSFI-------PLRRHITCLNCYQYWASTNPEIR 194 (198)
Q Consensus 156 ~~~~C~~C~~~~~~~~-------pmt~fv~C~~Cg~~W~~~~~~~~ 194 (198)
..-.||-||+.-..-. .--.|..|.-|+..|.|-|--|.
T Consensus 183 ~~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~C~ 228 (305)
T TIGR01562 183 SRTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRVKCS 228 (305)
T ss_pred CCCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCccCC
Confidence 3459999999975322 22479999999999999886653
No 66
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=75.88 E-value=1.7 Score=29.84 Aligned_cols=31 Identities=19% Similarity=0.349 Sum_probs=21.0
Q ss_pred cccceEcCCCCCCCceEe----ccceEEEeccCCC
Q 036389 154 VYGICKCSRCGHKRMSFI----PLRRHITCLNCYQ 184 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~~~~----pmt~fv~C~~Cg~ 184 (198)
....|.||.||.-...-- -.-+-|+|-+||-
T Consensus 24 ~~v~F~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CGF 58 (61)
T COG2888 24 TAVKFPCPNCGEVEIYRCAKCRKLGNPYRCPKCGF 58 (61)
T ss_pred ceeEeeCCCCCceeeehhhhHHHcCCceECCCcCc
Confidence 456799999996432221 4556677999984
No 67
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=75.43 E-value=2.5 Score=31.09 Aligned_cols=32 Identities=19% Similarity=0.274 Sum_probs=23.0
Q ss_pred ccceEcCCCCCCCceEeccceEEEeccCCCccc
Q 036389 155 YGICKCSRCGHKRMSFIPLRRHITCLNCYQYWA 187 (198)
Q Consensus 155 t~~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~W~ 187 (198)
-+...||.|+.. +-=.-.+-.-.|..||..|.
T Consensus 33 ~~~~~Cp~C~~~-~VkR~a~GIW~C~kCg~~fA 64 (89)
T COG1997 33 RAKHVCPFCGRT-TVKRIATGIWKCRKCGAKFA 64 (89)
T ss_pred hcCCcCCCCCCc-ceeeeccCeEEcCCCCCeec
Confidence 345789999988 33336677778999998763
No 68
>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=74.59 E-value=1.8 Score=39.30 Aligned_cols=33 Identities=33% Similarity=0.751 Sum_probs=16.7
Q ss_pred cccceEcCCCCCCCceEeccceEEEeccCCCc-cc
Q 036389 154 VYGICKCSRCGHKRMSFIPLRRHITCLNCYQY-WA 187 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~-W~ 187 (198)
.--.|+|+.||.+-++|..+- ...|.+||.. |.
T Consensus 282 ~KRFFkC~~C~~Rt~sl~r~P-~~~C~~Cg~~~we 315 (344)
T PF09332_consen 282 VKRFFKCKDCGNRTISLERLP-KKHCSNCGSSKWE 315 (344)
T ss_dssp E-EEEE-T-TS-EEEESSSS---S--TTT-S---E
T ss_pred eeeeEECCCCCCeeeecccCC-CCCCCcCCcCcee
Confidence 446799999999988776221 2589999964 53
No 69
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=74.01 E-value=1.6 Score=34.35 Aligned_cols=30 Identities=23% Similarity=0.314 Sum_probs=22.5
Q ss_pred ceEcCCCCCCCceEecc-ceEEEeccCCCccccc
Q 036389 157 ICKCSRCGHKRMSFIPL-RRHITCLNCYQYWAST 189 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~pm-t~fv~C~~Cg~~W~~~ 189 (198)
...|+.||.+ ||.+ ..-++|..||..|...
T Consensus 9 Kr~Cp~cg~k---FYDLnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 9 KRICPNTGSK---FYDLNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred cccCCCcCcc---ccccCCCCccCCCcCCccCcc
Confidence 3589999965 7733 3556799999999655
No 70
>PF11648 RIG-I_C-RD: C-terminal domain of RIG-I; InterPro: IPR021673 This family of proteins represents the regulatory domain RD of RIG-I, a protein which initiates a signalling cascade that provides essential antiviral protection for the host. The RD domain binds viral RNA, activating the RIG-I ATPase by RNA-dependent dimerisation. The structure of RD contains a zinc-binding domain and is thought to confer ligand specificity []. ; GO: 0016817 hydrolase activity, acting on acid anhydrides; PDB: 2RQB_A 3GA3_A 2W4R_D 3EQT_A 2RQA_A 2RMJ_A 3NCU_A 2QFD_C 2QFB_D 3TMI_A ....
Probab=73.45 E-value=2 Score=33.23 Aligned_cols=15 Identities=40% Similarity=0.824 Sum_probs=11.9
Q ss_pred ceEEEeccCCCcccc
Q 036389 174 RRHITCLNCYQYWAS 188 (198)
Q Consensus 174 t~fv~C~~Cg~~W~~ 188 (198)
.-.+.|.+||+.|++
T Consensus 58 ~~~I~C~~C~~~wG~ 72 (123)
T PF11648_consen 58 NGKIHCKNCGQDWGI 72 (123)
T ss_dssp EEEEEETSTSBEEEE
T ss_pred CCEEEcCCCChHhhh
Confidence 345789999999975
No 71
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=72.51 E-value=3.5 Score=33.02 Aligned_cols=32 Identities=28% Similarity=0.459 Sum_probs=26.5
Q ss_pred cccceEcCCCCCCCceEeccceEEEeccCCCcc
Q 036389 154 VYGICKCSRCGHKRMSFIPLRRHITCLNCYQYW 186 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~W 186 (198)
..|.+.|-+||..-..+.| +..--|.+||+.-
T Consensus 109 g~G~l~C~~Cg~~~~~~~~-~~l~~Cp~C~~~~ 140 (146)
T PF07295_consen 109 GPGTLVCENCGHEVELTHP-ERLPPCPKCGHTE 140 (146)
T ss_pred cCceEecccCCCEEEecCC-CcCCCCCCCCCCe
Confidence 5788999999999777666 4577899999974
No 72
>KOG4274 consensus Positive cofactor 2 (PC2), subunit of a multiprotein coactivator of RNA polymerase II [Transcription]
Probab=71.70 E-value=8.4 Score=37.45 Aligned_cols=61 Identities=23% Similarity=0.259 Sum_probs=46.4
Q ss_pred cHHHHHHHHHHHHHHhhhhhhccccchhhhhhcccChHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhcCCCCCHH
Q 036389 21 DCIREIVRKNLYGALSKVSIEAAHDKNVIDQVKACNPIQVAISMESAMYEKWGRSSETYKFKYRRLLFNFNDPKNHE 97 (198)
Q Consensus 21 d~iR~k~r~~L~~aL~~~~~e~~~~~~~~~~~~~~~~~~~A~~IE~alf~~~~~~~~~Yk~k~Rsl~~NLkd~kNp~ 97 (198)
-+.|.++...|.++|.+.-... ..-|..+|+.+|.+.. +..+|-..+--|+.+++|-.|..
T Consensus 9 ~kFRq~vIsried~l~~n~q~~---------------~k~a~~mE~hVF~K~~-tkDEYl~lvAkli~h~~d~s~~k 69 (742)
T KOG4274|consen 9 PKFRQHVISRIEDELRKNGQAH---------------SKSAKDMESHVFLKAK-TKDEYLSLVAKLIIHFRDISNKK 69 (742)
T ss_pred HHHHHHHHHHhhhhhhhhhhcc---------------CcchHHHHHHHHHhhh-hHHHHHHHHHHHHHHHHhhhhhh
Confidence 4679999999999998743222 2347889999998764 45689999999999999766543
No 73
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 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 consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=70.32 E-value=1.4 Score=30.41 Aligned_cols=33 Identities=27% Similarity=0.741 Sum_probs=24.6
Q ss_pred cceEcCCCCCCCceEe-----cc-ceEEEeccCCCcccc
Q 036389 156 GICKCSRCGHKRMSFI-----PL-RRHITCLNCYQYWAS 188 (198)
Q Consensus 156 ~~~~C~~C~~~~~~~~-----pm-t~fv~C~~Cg~~W~~ 188 (198)
...+||+|++..+.|. .+ ---+.|..|...|..
T Consensus 4 ~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~rywT~ 42 (63)
T PF02701_consen 4 QPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRRYWTH 42 (63)
T ss_pred cCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHHHHHh
Confidence 3469999999998876 22 233559999999964
No 74
>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=69.57 E-value=3.2 Score=39.88 Aligned_cols=31 Identities=19% Similarity=0.443 Sum_probs=24.9
Q ss_pred ceEcCCCCCCCceEe----------ccceEEEeccCCCccc
Q 036389 157 ICKCSRCGHKRMSFI----------PLRRHITCLNCYQYWA 187 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~----------pmt~fv~C~~Cg~~W~ 187 (198)
..+||.||....--+ |.+..+.|..||..|.
T Consensus 200 ~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~ 240 (557)
T PF05876_consen 200 YVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIE 240 (557)
T ss_pred EccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCC
Confidence 468999999866432 6789999999999874
No 75
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=69.06 E-value=4.1 Score=25.98 Aligned_cols=30 Identities=20% Similarity=0.419 Sum_probs=19.1
Q ss_pred EcCCCCCCCceEe-cc--ceEEEeccCCCcccccc
Q 036389 159 KCSRCGHKRMSFI-PL--RRHITCLNCYQYWASTN 190 (198)
Q Consensus 159 ~C~~C~~~~~~~~-pm--t~fv~C~~Cg~~W~~~~ 190 (198)
-|+.||.- -|. .. ..++.|..||+.++...
T Consensus 2 FCp~Cg~~--l~~~~~~~~~~~vC~~Cg~~~~~~~ 34 (52)
T smart00661 2 FCPKCGNM--LIPKEGKEKRRFVCRKCGYEEPIEQ 34 (52)
T ss_pred CCCCCCCc--cccccCCCCCEEECCcCCCeEECCC
Confidence 48888873 222 11 23677999998877643
No 76
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=68.91 E-value=3.6 Score=28.10 Aligned_cols=29 Identities=21% Similarity=0.408 Sum_probs=21.0
Q ss_pred ccceEcCCCCCCCceEe-----ccceEEEeccCCC
Q 036389 155 YGICKCSRCGHKRMSFI-----PLRRHITCLNCYQ 184 (198)
Q Consensus 155 t~~~~C~~C~~~~~~~~-----pmt~fv~C~~Cg~ 184 (198)
...|.||.||.. .-|+ -.-.-|+|-+||-
T Consensus 23 ~~~F~CPnCG~~-~I~RC~~CRk~~~~Y~CP~CGF 56 (59)
T PRK14890 23 AVKFLCPNCGEV-IIYRCEKCRKQSNPYTCPKCGF 56 (59)
T ss_pred cCEeeCCCCCCe-eEeechhHHhcCCceECCCCCC
Confidence 567999999874 2233 5567788999984
No 77
>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=68.83 E-value=4.6 Score=27.01 Aligned_cols=31 Identities=19% Similarity=0.503 Sum_probs=21.6
Q ss_pred ceEcCCCCCCCceEe-cc-ceEEEeccCCCcccc
Q 036389 157 ICKCSRCGHKRMSFI-PL-RRHITCLNCYQYWAS 188 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~-pm-t~fv~C~~Cg~~W~~ 188 (198)
+|.||.||+. ..+- ++ -..|.|..||.....
T Consensus 2 ~~~CP~CG~~-iev~~~~~GeiV~Cp~CGaeleV 34 (54)
T TIGR01206 2 QFECPDCGAE-IELENPELGELVICDECGAELEV 34 (54)
T ss_pred ccCCCCCCCE-EecCCCccCCEEeCCCCCCEEEE
Confidence 5899999983 2222 33 468899999987543
No 78
>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=68.80 E-value=9.8 Score=30.56 Aligned_cols=17 Identities=12% Similarity=0.122 Sum_probs=14.3
Q ss_pred cceEEEeccCCCccccc
Q 036389 173 LRRHITCLNCYQYWAST 189 (198)
Q Consensus 173 mt~fv~C~~Cg~~W~~~ 189 (198)
-..||.|.+|+.+|-|-
T Consensus 106 ~~~~Y~Cp~c~~r~tf~ 122 (158)
T TIGR00373 106 NNMFFICPNMCVRFTFN 122 (158)
T ss_pred CCCeEECCCCCcEeeHH
Confidence 35899999999999663
No 79
>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=68.69 E-value=4.6 Score=23.62 Aligned_cols=26 Identities=27% Similarity=0.491 Sum_probs=12.8
Q ss_pred EcCCCCCCCceEeccceEEEeccCCCc
Q 036389 159 KCSRCGHKRMSFIPLRRHITCLNCYQY 185 (198)
Q Consensus 159 ~C~~C~~~~~~~~pmt~fv~C~~Cg~~ 185 (198)
-|++||+. +...+--.--.|..||+.
T Consensus 5 fC~~CG~~-t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 5 FCGRCGAP-TKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp B-TTT--B-EEE-SSSS-EEESSSS-E
T ss_pred ccCcCCcc-ccCCCCcCEeECCCCcCE
Confidence 48888876 344455556667777764
No 80
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=67.75 E-value=11 Score=30.92 Aligned_cols=16 Identities=19% Similarity=0.362 Sum_probs=13.8
Q ss_pred ceEEEeccCCCccccc
Q 036389 174 RRHITCLNCYQYWAST 189 (198)
Q Consensus 174 t~fv~C~~Cg~~W~~~ 189 (198)
..||.|.+||.+|-|-
T Consensus 115 ~~~Y~Cp~C~~rytf~ 130 (178)
T PRK06266 115 NMFFFCPNCHIRFTFD 130 (178)
T ss_pred CCEEECCCCCcEEeHH
Confidence 4799999999999764
No 81
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=67.06 E-value=3.4 Score=27.18 Aligned_cols=30 Identities=30% Similarity=0.528 Sum_probs=20.8
Q ss_pred ccceEcCCCCCCCceEeccceEEEeccCCCc
Q 036389 155 YGICKCSRCGHKRMSFIPLRRHITCLNCYQY 185 (198)
Q Consensus 155 t~~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~ 185 (198)
+..+.|.+||..- .-.--+.-+.|..||++
T Consensus 4 ~~~Y~C~~Cg~~~-~~~~~~~~irCp~Cg~r 33 (49)
T COG1996 4 MMEYKCARCGREV-ELDQETRGIRCPYCGSR 33 (49)
T ss_pred eEEEEhhhcCCee-ehhhccCceeCCCCCcE
Confidence 4567888888764 21245677888888887
No 82
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=66.49 E-value=3.2 Score=23.59 Aligned_cols=24 Identities=25% Similarity=0.675 Sum_probs=13.6
Q ss_pred EcCCCCCCCceEeccceEEEeccCCCccc
Q 036389 159 KCSRCGHKRMSFIPLRRHITCLNCYQYWA 187 (198)
Q Consensus 159 ~C~~C~~~~~~~~pmt~fv~C~~Cg~~W~ 187 (198)
+||.|+..- | ..-..|..||+.|.
T Consensus 2 ~CP~C~~~V----~-~~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAEV----P-ESAKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCCc----h-hhcCcCCCCCCCCc
Confidence 466666552 1 23344777777764
No 83
>PRK11827 hypothetical protein; Provisional
Probab=66.05 E-value=6.1 Score=27.04 Aligned_cols=40 Identities=20% Similarity=0.274 Sum_probs=29.5
Q ss_pred cceEcCCCCCCCceEeccceEEEeccCCCccccccccccccc
Q 036389 156 GICKCSRCGHKRMSFIPLRRHITCLNCYQYWASTNPEIRVLP 197 (198)
Q Consensus 156 ~~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~W~~~~~~~~~~~ 197 (198)
+...||.|++.- .|.....-..|..||-.+-. ++.|-||+
T Consensus 7 eILaCP~ckg~L-~~~~~~~~Lic~~~~laYPI-~dgIPVlL 46 (60)
T PRK11827 7 EIIACPVCNGKL-WYNQEKQELICKLDNLAFPL-RDGIPVLL 46 (60)
T ss_pred hheECCCCCCcC-eEcCCCCeEECCccCeeccc-cCCccccC
Confidence 457899999864 45555666779999988876 66676664
No 84
>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=65.11 E-value=4.1 Score=24.60 Aligned_cols=28 Identities=25% Similarity=0.553 Sum_probs=18.5
Q ss_pred ceEcCCCCCCCceEecc--ceEEEeccCCC
Q 036389 157 ICKCSRCGHKRMSFIPL--RRHITCLNCYQ 184 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~pm--t~fv~C~~Cg~ 184 (198)
.|+|+.||..--...++ ...+.|-.||.
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EEEcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 47888888754433443 34667888886
No 85
>PRK11032 hypothetical protein; Provisional
Probab=64.92 E-value=6.8 Score=31.90 Aligned_cols=32 Identities=22% Similarity=0.391 Sum_probs=24.8
Q ss_pred cccceEcCCCCCCCceEeccceEEEeccCCCcc
Q 036389 154 VYGICKCSRCGHKRMSFIPLRRHITCLNCYQYW 186 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~W 186 (198)
.-|.+.|.+||..-+.|.|.. .--|.+||+.-
T Consensus 121 g~G~LvC~~Cg~~~~~~~p~~-i~pCp~C~~~~ 152 (160)
T PRK11032 121 GLGNLVCEKCHHHLAFYTPEV-LPLCPKCGHDQ 152 (160)
T ss_pred ecceEEecCCCCEEEecCCCc-CCCCCCCCCCe
Confidence 468899999999977766543 34599999974
No 86
>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=64.86 E-value=4 Score=26.22 Aligned_cols=28 Identities=25% Similarity=0.597 Sum_probs=19.4
Q ss_pred ceEcCCCCCCCceEeccc--eEEEeccCCC
Q 036389 157 ICKCSRCGHKRMSFIPLR--RHITCLNCYQ 184 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~pmt--~fv~C~~Cg~ 184 (198)
.|+|..||..--.+.++. ..+.|-.||.
T Consensus 5 ey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 5 EYRCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEEeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 488999987544444544 3567999997
No 87
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=64.63 E-value=3.8 Score=33.56 Aligned_cols=31 Identities=16% Similarity=0.570 Sum_probs=23.9
Q ss_pred ceEcCCCCCCCceEe--------------ccceEEEeccCCCc-cc
Q 036389 157 ICKCSRCGHKRMSFI--------------PLRRHITCLNCYQY-WA 187 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~--------------pmt~fv~C~~Cg~~-W~ 187 (198)
.-.|+.|++.-.... ....|+.|.+||.- |+
T Consensus 97 ~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~ 142 (165)
T COG1656 97 FSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYWK 142 (165)
T ss_pred cccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccccC
Confidence 458999998755444 56789999999975 64
No 88
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=64.23 E-value=4.6 Score=30.43 Aligned_cols=35 Identities=14% Similarity=0.332 Sum_probs=27.2
Q ss_pred ccccceEcCCCCCCCceEeccceEEEeccCCCccccc
Q 036389 153 IVYGICKCSRCGHKRMSFIPLRRHITCLNCYQYWAST 189 (198)
Q Consensus 153 ~~t~~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~W~~~ 189 (198)
..+..-.|.-| ....|+---..+.|.+||.+|...
T Consensus 31 ~~va~daCeiC--~~~GY~q~g~~lvC~~C~~~~~~~ 65 (102)
T PF10080_consen 31 YRVAFDACEIC--GPKGYYQEGDQLVCKNCGVRFNLP 65 (102)
T ss_pred EEEEEEecccc--CCCceEEECCEEEEecCCCEEehh
Confidence 35566689999 456777667888999999999654
No 89
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=64.01 E-value=5.6 Score=30.39 Aligned_cols=29 Identities=17% Similarity=0.683 Sum_probs=21.1
Q ss_pred ceEcCCCCCCCceEeccceEEEeccCCCccc
Q 036389 157 ICKCSRCGHKRMSFIPLRRHITCLNCYQYWA 187 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~W~ 187 (198)
+-.||+|+.. -+|...+ .+.|..|+|.|.
T Consensus 3 lp~cp~c~sE-ytYed~~-~~~cpec~~ew~ 31 (112)
T COG2824 3 LPPCPKCNSE-YTYEDGG-QLICPECAHEWN 31 (112)
T ss_pred CCCCCccCCc-eEEecCc-eEeCchhccccc
Confidence 3479999876 2334555 556999999997
No 90
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=63.21 E-value=5.2 Score=30.48 Aligned_cols=29 Identities=21% Similarity=0.442 Sum_probs=21.2
Q ss_pred cccceEcCCCCCCCceEeccceEEEeccCCCc
Q 036389 154 VYGICKCSRCGHKRMSFIPLRRHITCLNCYQY 185 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~ 185 (198)
....+.|..|| ..|.+...++.|..||..
T Consensus 67 ~p~~~~C~~Cg---~~~~~~~~~~~CP~Cgs~ 95 (115)
T TIGR00100 67 EPVECECEDCS---EEVSPEIDLYRCPKCHGI 95 (115)
T ss_pred eCcEEEcccCC---CEEecCCcCccCcCCcCC
Confidence 45678999999 334454567889999963
No 91
>PF02172 KIX: KIX domain; InterPro: IPR003101 The nuclear factor CREB activates transcription of target genes in part through direct interactions with the KIX domain of the coactivator CBP in a phosphorylation-dependent manner []. This provides a model for activator:coactivator interactions. The KIX domain of CBP also binds to transactivation domains of other nuclear factors including Myb and Jun.; GO: 0003712 transcription cofactor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2KWF_A 1KDX_A 2LQH_A 2LQI_A 1SB0_A 2AGH_B.
Probab=62.84 E-value=36 Score=24.56 Aligned_cols=67 Identities=19% Similarity=0.232 Sum_probs=43.0
Q ss_pred CCcHHHHHHHHHHHHHHhhhhhhccccchhhhhhcccChHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhcC
Q 036389 19 CNDCIREIVRKNLYGALSKVSIEAAHDKNVIDQVKACNPIQVAISMESAMYEKWGRSSETYKFKYRRLLFNFN 91 (198)
Q Consensus 19 ~~d~iR~k~r~~L~~aL~~~~~e~~~~~~~~~~~~~~~~~~~A~~IE~alf~~~~~~~~~Yk~k~Rsl~~NLk 91 (198)
-+..+|+..+..|..++........-.+ .++ .+....|..||..+|... .+..+|-..+-..++.++
T Consensus 10 vt~~lR~hlV~KLv~aI~P~pdp~a~~d---~rm--~~l~~yarkvE~~~fe~A-~sreeYY~llA~kiy~iq 76 (81)
T PF02172_consen 10 VTPDLRNHLVHKLVQAIFPTPDPNAMND---PRM--KNLIEYARKVEKDMFETA-QSREEYYHLLAEKIYKIQ 76 (81)
T ss_dssp T-HHHHHHHHHHHHHHHS-SSSCCCCCS---HHH--HHHHHHHHHHHHHHHHC--SSHHHHHHHHHHHHHHHH
T ss_pred cCHHHHHHHHHHHHHhhCCCCChhhhhh---HHH--HHHHHHHHHHHHHHHHHh-ccHHHHHHHHHHHHHHHH
Confidence 4578999999999888876421111000 111 134688999999999874 345678888777777774
No 92
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=62.79 E-value=5 Score=35.52 Aligned_cols=37 Identities=24% Similarity=0.395 Sum_probs=24.7
Q ss_pred EcCCCCCCCceEeccceEEEeccCCCc-ccccccccccc
Q 036389 159 KCSRCGHKRMSFIPLRRHITCLNCYQY-WASTNPEIRVL 196 (198)
Q Consensus 159 ~C~~C~~~~~~~~pmt~fv~C~~Cg~~-W~~~~~~~~~~ 196 (198)
-|++||++ +....--.-..|.+||+. +=-..|.|=||
T Consensus 113 FCg~CG~~-~~~~~~g~~~~C~~cg~~~fPR~dP~vIv~ 150 (279)
T COG2816 113 FCGRCGTK-TYPREGGWARVCPKCGHEHFPRIDPCVIVA 150 (279)
T ss_pred CCCCCCCc-CccccCceeeeCCCCCCccCCCCCCeEEEE
Confidence 59999987 444455566779999987 33344555444
No 93
>PF14122 YokU: YokU-like protein
Probab=62.49 E-value=5.1 Score=29.37 Aligned_cols=28 Identities=32% Similarity=0.689 Sum_probs=19.9
Q ss_pred EcCCCCCCCce------Ee-----------ccceEEEeccCCCcc
Q 036389 159 KCSRCGHKRMS------FI-----------PLRRHITCLNCYQYW 186 (198)
Q Consensus 159 ~C~~C~~~~~~------~~-----------pmt~fv~C~~Cg~~W 186 (198)
+|.-||+.++. |+ ++|--+.|.+||-.+
T Consensus 1 ~C~wC~~~~a~~~~~tvyWeLpdGtraIeI~~tP~i~C~~CgmvY 45 (87)
T PF14122_consen 1 KCEWCGSEEASESESTVYWELPDGTRAIEITDTPAIICSNCGMVY 45 (87)
T ss_pred CcccccCcccccccceEEEEcCCCceEEEecCCceeeecCCCcEE
Confidence 47778876442 22 888889999999643
No 94
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=62.42 E-value=3.3 Score=27.22 Aligned_cols=31 Identities=26% Similarity=0.639 Sum_probs=24.9
Q ss_pred eEcCCCCCCCceEe---ccceEEEeccCCCcccc
Q 036389 158 CKCSRCGHKRMSFI---PLRRHITCLNCYQYWAS 188 (198)
Q Consensus 158 ~~C~~C~~~~~~~~---pmt~fv~C~~Cg~~W~~ 188 (198)
..|..|+...+... |.-.-+.|+.||-+|+-
T Consensus 4 ~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k 37 (52)
T smart00401 4 RSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKK 37 (52)
T ss_pred CCcCCCCCCCCCccccCCCCCCcEeecccHHHHH
Confidence 47999999888776 66556779999999864
No 95
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=62.08 E-value=5 Score=27.44 Aligned_cols=30 Identities=23% Similarity=0.420 Sum_probs=22.8
Q ss_pred cccceEcCCCCCCCceEeccceEEEeccCCCc
Q 036389 154 VYGICKCSRCGHKRMSFIPLRRHITCLNCYQY 185 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~ 185 (198)
.+-.+.|+.||+...- -.+.-+.|..||+|
T Consensus 17 ~~miYiCgdC~~en~l--k~~D~irCReCG~R 46 (62)
T KOG3507|consen 17 ATMIYICGDCGQENTL--KRGDVIRCRECGYR 46 (62)
T ss_pred ccEEEEeccccccccc--cCCCcEehhhcchH
Confidence 5777899999988542 33556789999987
No 96
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=61.76 E-value=2.9 Score=32.64 Aligned_cols=35 Identities=23% Similarity=0.455 Sum_probs=24.8
Q ss_pred eEcCCCCCCCceEeccceEEEeccCCCcccccccc
Q 036389 158 CKCSRCGHKRMSFIPLRRHITCLNCYQYWASTNPE 192 (198)
Q Consensus 158 ~~C~~C~~~~~~~~pmt~fv~C~~Cg~~W~~~~~~ 192 (198)
-.||+||+-+-.--=.+.--.|..||....|-+++
T Consensus 22 grCP~CGeGrLF~gFLK~~p~C~aCG~dyg~~~a~ 56 (126)
T COG5349 22 GRCPRCGEGRLFRGFLKVVPACEACGLDYGFADAD 56 (126)
T ss_pred CCCCCCCCchhhhhhcccCchhhhccccccCCccc
Confidence 37999999865322233444699999999988754
No 97
>PHA02540 61 DNA primase; Provisional
Probab=61.13 E-value=7.5 Score=35.26 Aligned_cols=30 Identities=20% Similarity=0.386 Sum_probs=25.1
Q ss_pred cceEcCCCCC-----CCceEe--ccce--EEEeccCCCc
Q 036389 156 GICKCSRCGH-----KRMSFI--PLRR--HITCLNCYQY 185 (198)
Q Consensus 156 ~~~~C~~C~~-----~~~~~~--pmt~--fv~C~~Cg~~ 185 (198)
=.+.||=|+. ++.+|+ |-.. |+.|-+||..
T Consensus 26 ~~~~CPf~~ds~~~~~kpsF~V~p~k~~~~yhCFgCGa~ 64 (337)
T PHA02540 26 YNFRCPICGDSQKDKNKARGWIYEKKDGGVFKCHNCGYH 64 (337)
T ss_pred EEecCCCCCCccccCcCCcEEEeccCCceEEEecCCCCC
Confidence 4789999998 456777 9998 9999999964
No 98
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=59.84 E-value=6 Score=30.06 Aligned_cols=29 Identities=14% Similarity=0.222 Sum_probs=20.9
Q ss_pred cccceEcCCCCCCCceEeccceEEEeccCCCc
Q 036389 154 VYGICKCSRCGHKRMSFIPLRRHITCLNCYQY 185 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~ 185 (198)
....+.|+.|| ..|.+...++.|..||..
T Consensus 67 vp~~~~C~~Cg---~~~~~~~~~~~CP~Cgs~ 95 (113)
T PRK12380 67 KPAQAWCWDCS---QVVEIHQHDAQCPHCHGE 95 (113)
T ss_pred eCcEEEcccCC---CEEecCCcCccCcCCCCC
Confidence 45678999999 334444566779999953
No 99
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=58.27 E-value=10 Score=28.86 Aligned_cols=33 Identities=21% Similarity=0.340 Sum_probs=23.6
Q ss_pred ceEcCCCCCC-----CceEe--ccceEEEeccCCCccccc
Q 036389 157 ICKCSRCGHK-----RMSFI--PLRRHITCLNCYQYWAST 189 (198)
Q Consensus 157 ~~~C~~C~~~-----~~~~~--pmt~fv~C~~Cg~~W~~~ 189 (198)
...|.+|... +|... --..-++|+.||.--+|.
T Consensus 56 R~~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~~R~p 95 (105)
T COG2023 56 RTICKKCYTPLVPGKNARVRLRKGRVVVTCLECGTIRRYP 95 (105)
T ss_pred HHhccccCcccccCcceEEEEcCCeEEEEecCCCcEEEec
Confidence 4689999873 44444 333889999999876553
No 100
>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=58.26 E-value=6.6 Score=30.95 Aligned_cols=31 Identities=16% Similarity=0.574 Sum_probs=22.1
Q ss_pred ceEcCCCCCCCceEe--------------ccceEEEeccCCCc-cc
Q 036389 157 ICKCSRCGHKRMSFI--------------PLRRHITCLNCYQY-WA 187 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~--------------pmt~fv~C~~Cg~~-W~ 187 (198)
.-.|+.|++.-.... +...|..|..||+- |.
T Consensus 91 ~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~ 136 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWE 136 (147)
T ss_pred CCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecc
Confidence 458999999533322 44679999999974 53
No 101
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=57.67 E-value=8.3 Score=23.80 Aligned_cols=27 Identities=22% Similarity=0.349 Sum_probs=18.9
Q ss_pred eEcCCCCCCCceEe---ccceEEEeccCCC
Q 036389 158 CKCSRCGHKRMSFI---PLRRHITCLNCYQ 184 (198)
Q Consensus 158 ~~C~~C~~~~~~~~---pmt~fv~C~~Cg~ 184 (198)
..||.||++.-.-+ ..+--..|..||.
T Consensus 4 ~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred cCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 47999999766555 4555566888874
No 102
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=57.67 E-value=5.7 Score=22.30 Aligned_cols=11 Identities=27% Similarity=0.628 Sum_probs=9.2
Q ss_pred ccceEcCCCCC
Q 036389 155 YGICKCSRCGH 165 (198)
Q Consensus 155 t~~~~C~~C~~ 165 (198)
...|.||+||.
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 56799999984
No 103
>PRK03954 ribonuclease P protein component 4; Validated
Probab=57.37 E-value=9.1 Score=29.76 Aligned_cols=33 Identities=24% Similarity=0.386 Sum_probs=23.2
Q ss_pred cceEcCCCCCC-----CceEe----cc-ceEEEeccCCCcccc
Q 036389 156 GICKCSRCGHK-----RMSFI----PL-RRHITCLNCYQYWAS 188 (198)
Q Consensus 156 ~~~~C~~C~~~-----~~~~~----pm-t~fv~C~~Cg~~W~~ 188 (198)
-...|.+|+.. .++.. ++ ...++|+.||+.-+|
T Consensus 63 KR~~CK~C~t~LiPG~n~~vRi~~~~~~~vvitCl~CG~~kR~ 105 (121)
T PRK03954 63 KRRYCKRCHSFLVPGVNARVRLRQKRMPHVVITCLECGHIMRY 105 (121)
T ss_pred HHHHhhcCCCeeecCCceEEEEecCCcceEEEECccCCCEEee
Confidence 34679999765 44444 32 478899999997665
No 104
>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=56.83 E-value=6.7 Score=34.30 Aligned_cols=34 Identities=26% Similarity=0.585 Sum_probs=20.1
Q ss_pred ceEcCCCCCCCceEe--------ccceEEEeccCCCcccccc
Q 036389 157 ICKCSRCGHKRMSFI--------PLRRHITCLNCYQYWASTN 190 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~--------pmt~fv~C~~Cg~~W~~~~ 190 (198)
..+|+.||..+-.-+ |.-...+|..||..+|.-+
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 345667776665322 7677788999999998755
No 105
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=56.77 E-value=6.8 Score=41.22 Aligned_cols=32 Identities=19% Similarity=0.388 Sum_probs=21.4
Q ss_pred cccceEcCCCCCCCceEe------ccceEEEeccCCCc
Q 036389 154 VYGICKCSRCGHKRMSFI------PLRRHITCLNCYQY 185 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~~~~------pmt~fv~C~~Cg~~ 185 (198)
.-+.++||+||..--..+ +++.-+.|.+||..
T Consensus 664 EV~~rkCPkCG~~t~~~fCP~CGs~te~vy~CPsCGae 701 (1337)
T PRK14714 664 EVGRRRCPSCGTETYENRCPDCGTHTEPVYVCPDCGAE 701 (1337)
T ss_pred EEEEEECCCCCCccccccCcccCCcCCCceeCccCCCc
Confidence 446689999998532222 45556688888875
No 106
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=56.26 E-value=5.5 Score=37.19 Aligned_cols=33 Identities=21% Similarity=0.283 Sum_probs=25.4
Q ss_pred cccceEcCCCCCCCceEe------ccceEEEeccCCCcc
Q 036389 154 VYGICKCSRCGHKRMSFI------PLRRHITCLNCYQYW 186 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~~~~------pmt~fv~C~~Cg~~W 186 (198)
....|.||-|+..-...- ++|..+.|.+||-.-
T Consensus 125 ~~~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gel 163 (436)
T KOG2593|consen 125 NVAGYVCPNCQKKYTSLEALQLLDNETGEFHCENCGGEL 163 (436)
T ss_pred ccccccCCccccchhhhHHHHhhcccCceEEEecCCCch
Confidence 345699999998744443 779999999999653
No 107
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=54.99 E-value=10 Score=28.08 Aligned_cols=31 Identities=16% Similarity=0.378 Sum_probs=21.6
Q ss_pred ccceEcCCCCCCCceEeccceEEEeccCCCcc
Q 036389 155 YGICKCSRCGHKRMSFIPLRRHITCLNCYQYW 186 (198)
Q Consensus 155 t~~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~W 186 (198)
...+.||.||..... .-.+-.-.|..||..|
T Consensus 33 ~~ky~Cp~Cgk~~vk-R~a~GIW~C~~C~~~~ 63 (90)
T PF01780_consen 33 HAKYTCPFCGKTSVK-RVATGIWKCKKCGKKF 63 (90)
T ss_dssp HS-BEESSSSSSEEE-EEETTEEEETTTTEEE
T ss_pred hCCCcCCCCCCceeE-EeeeEEeecCCCCCEE
Confidence 345799999988622 2556667899998775
No 108
>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=53.09 E-value=19 Score=34.19 Aligned_cols=32 Identities=19% Similarity=0.233 Sum_probs=16.7
Q ss_pred ccceEcCCCCCC-CceEe--ccce-----EEEeccCCCcc
Q 036389 155 YGICKCSRCGHK-RMSFI--PLRR-----HITCLNCYQYW 186 (198)
Q Consensus 155 t~~~~C~~C~~~-~~~~~--pmt~-----fv~C~~Cg~~W 186 (198)
.....|..||.. +|... |||. ...|..||++-
T Consensus 211 a~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~ 250 (505)
T TIGR00595 211 SKNLLCRSCGYILCCPNCDVSLTYHKKEGKLRCHYCGYQE 250 (505)
T ss_pred CCeeEhhhCcCccCCCCCCCceEEecCCCeEEcCCCcCcC
Confidence 344566666654 22222 4443 46677777653
No 109
>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=53.08 E-value=3.1 Score=27.65 Aligned_cols=30 Identities=30% Similarity=0.761 Sum_probs=23.9
Q ss_pred EcCCCCCCCceEe---ccceEEEeccCCCcccc
Q 036389 159 KCSRCGHKRMSFI---PLRRHITCLNCYQYWAS 188 (198)
Q Consensus 159 ~C~~C~~~~~~~~---pmt~fv~C~~Cg~~W~~ 188 (198)
.|..|+..++... |...-.-|+.||-+|+-
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~k 33 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWKK 33 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHHh
Confidence 3888999888766 76667789999998864
No 110
>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=51.90 E-value=3.3 Score=25.07 Aligned_cols=28 Identities=29% Similarity=0.666 Sum_probs=16.5
Q ss_pred cCCCCCCCceEe---ccceEEEeccCCCccc
Q 036389 160 CSRCGHKRMSFI---PLRRHITCLNCYQYWA 187 (198)
Q Consensus 160 C~~C~~~~~~~~---pmt~fv~C~~Cg~~W~ 187 (198)
|..|+..++... |.-....|+.||-+|+
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 677887776544 6555558999998875
No 111
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=51.64 E-value=14 Score=27.33 Aligned_cols=31 Identities=23% Similarity=0.327 Sum_probs=23.0
Q ss_pred ccceEcCCCCCCCceEeccceEEEeccCCCcc
Q 036389 155 YGICKCSRCGHKRMSFIPLRRHITCLNCYQYW 186 (198)
Q Consensus 155 t~~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~W 186 (198)
...+.|+.||... --...+-...|..||..|
T Consensus 33 ~a~y~CpfCgk~~-vkR~a~GIW~C~~C~~~~ 63 (91)
T TIGR00280 33 KAKYVCPFCGKKT-VKRGSTGIWTCRKCGAKF 63 (91)
T ss_pred hcCccCCCCCCCc-eEEEeeEEEEcCCCCCEE
Confidence 3458999999543 333778888999999875
No 112
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=51.51 E-value=9.2 Score=32.66 Aligned_cols=26 Identities=31% Similarity=0.603 Sum_probs=19.9
Q ss_pred ccceEcCCCCCCCceEeccceEEEeccCCCcc
Q 036389 155 YGICKCSRCGHKRMSFIPLRRHITCLNCYQYW 186 (198)
Q Consensus 155 t~~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~W 186 (198)
.+.-.|+.||. .....+.|.+||+.|
T Consensus 307 ~tS~~C~~cg~------~~~r~~~C~~cg~~~ 332 (364)
T COG0675 307 YTSKTCPCCGH------LSGRLFKCPRCGFVH 332 (364)
T ss_pred CCcccccccCC------ccceeEECCCCCCee
Confidence 33358999999 445667899999875
No 113
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=51.04 E-value=13 Score=32.64 Aligned_cols=15 Identities=13% Similarity=0.467 Sum_probs=12.3
Q ss_pred ceEEEeccCCCcccc
Q 036389 174 RRHITCLNCYQYWAS 188 (198)
Q Consensus 174 t~fv~C~~Cg~~W~~ 188 (198)
--++.|.+|+|.|+-
T Consensus 153 ~aef~C~~C~h~F~G 167 (278)
T PF15135_consen 153 IAEFHCPKCRHNFRG 167 (278)
T ss_pred eeeeecccccccchh
Confidence 368899999999873
No 114
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=50.92 E-value=4.1 Score=28.09 Aligned_cols=32 Identities=13% Similarity=0.351 Sum_probs=23.8
Q ss_pred eEcCCCCCCCceEe---ccceEEEeccCCCccccc
Q 036389 158 CKCSRCGHKRMSFI---PLRRHITCLNCYQYWAST 189 (198)
Q Consensus 158 ~~C~~C~~~~~~~~---pmt~fv~C~~Cg~~W~~~ 189 (198)
..||.|+.-.+--+ .-.-.|.|..||+.-+..
T Consensus 11 A~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~~~~ 45 (66)
T COG3529 11 AVCPACQAQDTLAMWRENNVEIVECVKCGHHMREA 45 (66)
T ss_pred CCCcccchhhHHHHHHhcCCceEehhhcchHhhhc
Confidence 48999987765433 667789999999875443
No 115
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=50.62 E-value=20 Score=21.40 Aligned_cols=28 Identities=25% Similarity=0.508 Sum_probs=19.4
Q ss_pred ceEcCCCCCCCceEeccceEEEeccCCCc
Q 036389 157 ICKCSRCGHKRMSFIPLRRHITCLNCYQY 185 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~ 185 (198)
...|..||+....+ --.-...|..||..
T Consensus 3 ~~~C~~C~~~~i~~-~~~~~~~C~~Cg~~ 30 (33)
T PF08792_consen 3 LKKCSKCGGNGIVN-KEDDYEVCIFCGSS 30 (33)
T ss_pred ceEcCCCCCCeEEE-ecCCeEEcccCCcE
Confidence 45788999887554 34456668888864
No 116
>PF09606 Med15: ARC105 or Med15 subunit of Mediator complex non-fungal; InterPro: IPR019087 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. The proteins in this entry represent subunit Med15 of the Mediator complex. They contain a single copy of the approximately 70 residue ARC105 domain. The ARC105 domain of the ARC-Mediator co-activator is a three-helix bundle with marked similarity to the KIX domain. The sterol regulatory element binding protein (SREBP) family of transcription activators use the ARC105 subunit to activate target genes in the regulation of cholesterol and fatty acid homeostasis. In addition, ARC105 is a critical transducer of gene activation signals that control early metazoan development []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex; PDB: 2GUT_A.
Probab=50.10 E-value=27 Score=35.24 Aligned_cols=51 Identities=22% Similarity=0.277 Sum_probs=36.0
Q ss_pred HHHHHHHHHHhhhhhhccccchhhhhhcccChHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhcCC
Q 036389 26 IVRKNLYGALSKVSIEAAHDKNVIDQVKACNPIQVAISMESAMYEKWGRSSETYKFKYRRLLFNFND 92 (198)
Q Consensus 26 k~r~~L~~aL~~~~~e~~~~~~~~~~~~~~~~~~~A~~IE~alf~~~~~~~~~Yk~k~Rsl~~NLkd 92 (198)
+|...|.++|.+..... ..-|.++|+++|.+.. +..+|-..+--|+.+++|
T Consensus 2 ~vi~~ie~a~~~~~~~~---------------~k~a~emE~hvF~Ka~-tkdEYl~~varli~h~r~ 52 (799)
T PF09606_consen 2 KVISKIEEAMRKNGQNT---------------PKSAREMENHVFQKAK-TKDEYLSLVARLILHIRD 52 (799)
T ss_dssp HHHHHHHHHHHHH-------------------SS-HHHHHHHHHHH-S-SHHHHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHhCCCC---------------CCCHHHHHHHHHHhhc-cHHHHHHHHHHHHHHHHH
Confidence 57777888887643222 2337899999998863 567999999999998885
No 117
>PHA02942 putative transposase; Provisional
Probab=48.51 E-value=12 Score=34.21 Aligned_cols=29 Identities=28% Similarity=0.544 Sum_probs=20.5
Q ss_pred ccceEcCCCCCCCceEeccceEEEeccCCCcc
Q 036389 155 YGICKCSRCGHKRMSFIPLRRHITCLNCYQYW 186 (198)
Q Consensus 155 t~~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~W 186 (198)
|+ -.|+.||...- .+....+.|.+||..+
T Consensus 324 TS-q~Cs~CG~~~~--~l~~r~f~C~~CG~~~ 352 (383)
T PHA02942 324 SS-VSCPKCGHKMV--EIAHRYFHCPSCGYEN 352 (383)
T ss_pred CC-ccCCCCCCccC--cCCCCEEECCCCCCEe
Confidence 44 38999998653 1233467899999875
No 118
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=47.77 E-value=23 Score=33.41 Aligned_cols=107 Identities=11% Similarity=0.128 Sum_probs=61.8
Q ss_pred cHHHHHHHHHHHHhcCCCCCHHHHHHhhcCCCCchhcccCCHHhhcc-HHHHHHHH-HHhcccccccccccccccCCCcc
Q 036389 76 SETYKFKYRRLLFNFNDPKNHEFRKKVLLGDVKPETIVNMTAKEMAS-DKMQLWYE-NSRKGRAETNGRIFSGLVSPKNI 153 (198)
Q Consensus 76 ~~~Yk~k~Rsl~~NLkd~kNp~Lr~~vl~G~isp~~lv~Ms~eELas-~e~k~~~e-~~~~~e~~~~~~l~~~~~~~~~~ 153 (198)
+..+-+.+|+-...+--=.||.|....+ ..|+.++|..+..++|+- +..+..+. -++- +- ..-++.+. -.
T Consensus 86 ~~~Fle~l~~~sqhvlvYEDP~lq~~Al-s~iPvdEL~~kA~ekla~~eg~ki~kdy~i~l-eL---L~WFKq~F---F~ 157 (500)
T KOG0909|consen 86 TNAFLEVLRSYSQHVLVYEDPVLQAKAL-STIPVDELKEKASEKLAKAEGEKIYKDYLIKL-EL---LNWFKQDF---FK 157 (500)
T ss_pred chHHHHHHHHhccCceeecCHHHHHHHH-hcCCHHHHHHHHHHhhcccchhhhhcchHHHH-HH---HHHHHHhh---he
Confidence 3567777787777777667888855444 467778888888888885 22111111 1110 00 00111111 00
Q ss_pred cccceEcCCCCCCCceEe----cc----------ceEEEeccCCCcccccc
Q 036389 154 VYGICKCSRCGHKRMSFI----PL----------RRHITCLNCYQYWASTN 190 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~~~~----pm----------t~fv~C~~Cg~~W~~~~ 190 (198)
=-+.-.|++||+.--.-. |. .-.+.|..||+.=+|-|
T Consensus 158 WvN~PpC~~CG~et~~~l~~~~p~eeE~~~Ga~rVEiy~C~~C~~~~RFPR 208 (500)
T KOG0909|consen 158 WVNNPPCNKCGGETSSGLGNQPPNEEEKKFGAGRVEIYKCNRCGTETRFPR 208 (500)
T ss_pred ecCCCCcccccccccccccCCCCchhHhhcCCceEEEEEecCCCCcccCcc
Confidence 123458999999864222 22 23578999999888865
No 119
>PF06254 DUF1019: Protein of unknown function (DUF1019); InterPro: IPR009364 This entry is represented by Bacteriophage phi-80, CII. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 3C4R_C.
Probab=47.25 E-value=15 Score=27.13 Aligned_cols=50 Identities=16% Similarity=0.135 Sum_probs=31.6
Q ss_pred HHHHHhCCCcHHHHHHHHHHHHhcCCCCCHHHHHHhhcCCCCchhcccCC
Q 036389 67 AMYEKWGRSSETYKFKYRRLLFNFNDPKNHEFRKKVLLGDVKPETIVNMT 116 (198)
Q Consensus 67 alf~~~~~~~~~Yk~k~Rsl~~NLkd~kNp~Lr~~vl~G~isp~~lv~Ms 116 (198)
.||-++.+.++.|+.+++.|.-.+...-=++++.+|.+|.-...-|+.+-
T Consensus 12 ~iFRwl~~ds~~~~~~~~~L~PAI~aAlP~E~rarl~~~~~~~~~la~~~ 61 (89)
T PF06254_consen 12 KIFRWLDNDSPAYREKIMQLSPAILAALPPERRARLSSGDSTMYLLASAA 61 (89)
T ss_dssp HHHHHHH--SHHHHHHHHHHHHHHHHHS-HHHHHHHHCTT-HHH------
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHHHHhCCHHHHhhccCCCCchhhhhHhH
Confidence 56877777778999999988777776666789999888866555566554
No 120
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=46.93 E-value=13 Score=28.22 Aligned_cols=28 Identities=25% Similarity=0.624 Sum_probs=19.8
Q ss_pred cccceEcCCCCCCCceEecc-c-eEEEeccCCCc
Q 036389 154 VYGICKCSRCGHKRMSFIPL-R-RHITCLNCYQY 185 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~~~~pm-t-~fv~C~~Cg~~ 185 (198)
....+.|..||. ++|. . .++.|..||..
T Consensus 67 ~p~~~~C~~Cg~----~~~~~~~~~~~CP~Cgs~ 96 (114)
T PRK03681 67 QEAECWCETCQQ----YVTLLTQRVRRCPQCHGD 96 (114)
T ss_pred eCcEEEcccCCC----eeecCCccCCcCcCcCCC
Confidence 456789999994 4443 2 34779999953
No 121
>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=46.88 E-value=27 Score=21.32 Aligned_cols=28 Identities=21% Similarity=0.454 Sum_probs=18.7
Q ss_pred ccceEcCCCCCCCceEe----cc-ceEEEeccC
Q 036389 155 YGICKCSRCGHKRMSFI----PL-RRHITCLNC 182 (198)
Q Consensus 155 t~~~~C~~C~~~~~~~~----pm-t~fv~C~~C 182 (198)
+-...||.|++.+-.+. |- ..-|.|..|
T Consensus 3 ~i~v~CP~C~s~~~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 3 KIDVHCPRCQSTEGVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred cEeeeCCCCCCCCcceeCCCCCCCCEeEecCcC
Confidence 44578999999885555 32 355667666
No 122
>PF14949 ARF7EP_C: ARF7 effector protein C-terminus
Probab=46.77 E-value=9.4 Score=28.89 Aligned_cols=14 Identities=21% Similarity=0.721 Sum_probs=11.6
Q ss_pred ceEcCCCCCCCceE
Q 036389 157 ICKCSRCGHKRMSF 170 (198)
Q Consensus 157 ~~~C~~C~~~~~~~ 170 (198)
-|.|++||+++|..
T Consensus 74 ~~PC~~C~S~KCG~ 87 (103)
T PF14949_consen 74 HYPCPKCGSRKCGP 87 (103)
T ss_pred cccCCCCCCCccCh
Confidence 48899999999753
No 123
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=46.31 E-value=17 Score=24.42 Aligned_cols=25 Identities=28% Similarity=0.757 Sum_probs=19.3
Q ss_pred cccceEcCCCCCCCceEeccceEEEeccCCC
Q 036389 154 VYGICKCSRCGHKRMSFIPLRRHITCLNCYQ 184 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~~~~pmt~fv~C~~Cg~ 184 (198)
......|+.||..+ ..+..|.+||.
T Consensus 24 ~~~l~~C~~CG~~~------~~H~vC~~CG~ 48 (57)
T PRK12286 24 APGLVECPNCGEPK------LPHRVCPSCGY 48 (57)
T ss_pred CCcceECCCCCCcc------CCeEECCCCCc
Confidence 46778999999975 44677888983
No 124
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=45.80 E-value=8.8 Score=35.13 Aligned_cols=29 Identities=17% Similarity=0.438 Sum_probs=24.7
Q ss_pred ceEcCCCCCCCceEe---ccceEEEeccCCCc
Q 036389 157 ICKCSRCGHKRMSFI---PLRRHITCLNCYQY 185 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~---pmt~fv~C~~Cg~~ 185 (198)
...|+.|+.+.+.+. --|.-..|.-||.+
T Consensus 96 FVlC~~C~NPETel~itk~q~i~~~CkACG~r 127 (400)
T KOG2767|consen 96 FVLCPSCENPETELIITKKQTISLKCKACGFR 127 (400)
T ss_pred heeCcCCCCCceeEEecccchhhhHHHHcCCc
Confidence 368999999999999 34677889999976
No 125
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=45.63 E-value=12 Score=39.90 Aligned_cols=32 Identities=19% Similarity=0.298 Sum_probs=25.4
Q ss_pred cccceEcCCCCCCCceEeccceEEEeccCCCcccccccc
Q 036389 154 VYGICKCSRCGHKRMSFIPLRRHITCLNCYQYWASTNPE 192 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~W~~~~~~ 192 (198)
+-+.++||+||.. |.+..|..||.++......
T Consensus 671 ei~~~~Cp~Cg~~-------~~~~~Cp~CG~~~~~~~~~ 702 (1627)
T PRK14715 671 EIAFFKCPKCGKV-------GLYHVCPFCGTRVELKPYA 702 (1627)
T ss_pred EEEeeeCCCCCCc-------cccccCcccCCcccCCCcc
Confidence 5678999999986 6778899999887655443
No 126
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=45.08 E-value=21 Score=26.40 Aligned_cols=31 Identities=16% Similarity=0.224 Sum_probs=22.6
Q ss_pred ccceEcCCCCCCCceEeccceEEEeccCCCcc
Q 036389 155 YGICKCSRCGHKRMSFIPLRRHITCLNCYQYW 186 (198)
Q Consensus 155 t~~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~W 186 (198)
...+.|+-||... --...+-...|..||..|
T Consensus 34 ~a~y~CpfCgk~~-vkR~a~GIW~C~~C~~~~ 64 (90)
T PTZ00255 34 HAKYFCPFCGKHA-VKRQAVGIWRCKGCKKTV 64 (90)
T ss_pred hCCccCCCCCCCc-eeeeeeEEEEcCCCCCEE
Confidence 3458999999543 333677888999999864
No 127
>COG1281 Disulfide bond chaperones of the HSP33 family [Posttranslational modification, protein turnover, chaperones]
Probab=44.94 E-value=7.9 Score=34.36 Aligned_cols=73 Identities=18% Similarity=0.262 Sum_probs=45.9
Q ss_pred cCCCCchhcccCCHHhhccHHHHHHHHHHhcccccccccccccccCCCcccccceEcCCCCCCCceEe------------
Q 036389 104 LGDVKPETIVNMTAKEMASDKMQLWYENSRKGRAETNGRIFSGLVSPKNIVYGICKCSRCGHKRMSFI------------ 171 (198)
Q Consensus 104 ~G~isp~~lv~Ms~eELas~e~k~~~e~~~~~e~~~~~~l~~~~~~~~~~~t~~~~C~~C~~~~~~~~------------ 171 (198)
-..|+...+..|++++|...= .- + ...++.+- ..-.|+|+ |...++.-.
T Consensus 198 ~~ti~~~~~~~~~~e~ll~rL--------~~-e--~~v~ile~-------~~v~f~C~-CSrEr~~~aL~~lg~eEi~~m 258 (286)
T COG1281 198 LPTITEEELFGLPAEELLYRL--------FH-E--EGVQLLEP-------QPVEFRCS-CSRERVAAALLSLGKEELEDM 258 (286)
T ss_pred hccccHHHHcCCCHHHHHHHH--------hc-c--ccccccCC-------ccceEEcC-CCHHHHHHHHHhcCHHHHHHH
Confidence 455777777777777765432 11 1 00012211 23468998 777665433
Q ss_pred ---ccceEEEeccCCCccccccccccc
Q 036389 172 ---PLRRHITCLNCYQYWASTNPEIRV 195 (198)
Q Consensus 172 ---pmt~fv~C~~Cg~~W~~~~~~~~~ 195 (198)
.-..-|+|.=||+.+.|...+|--
T Consensus 259 ~eedg~iev~C~FC~~~Y~f~~~ei~~ 285 (286)
T COG1281 259 LEEDGGIEVTCEFCGTKYLFDEEEIEE 285 (286)
T ss_pred HhcCCCeEEEeeccCCEEecCHHHHhc
Confidence 447899999999999999988754
No 128
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=44.65 E-value=15 Score=28.69 Aligned_cols=31 Identities=26% Similarity=0.579 Sum_probs=19.9
Q ss_pred ccceEcCCCCCCCceE----------------ecc--ceEEEeccCCCc
Q 036389 155 YGICKCSRCGHKRMSF----------------IPL--RRHITCLNCYQY 185 (198)
Q Consensus 155 t~~~~C~~C~~~~~~~----------------~pm--t~fv~C~~Cg~~ 185 (198)
-..+.|+.||..-..- .|- ..++.|..||..
T Consensus 68 p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 68 EAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred ceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCC
Confidence 4678999999432110 022 467789999964
No 129
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=44.63 E-value=25 Score=34.31 Aligned_cols=25 Identities=16% Similarity=0.693 Sum_probs=20.4
Q ss_pred eEcCCCCCCCceEe--ccceEEEeccCC
Q 036389 158 CKCSRCGHKRMSFI--PLRRHITCLNCY 183 (198)
Q Consensus 158 ~~C~~C~~~~~~~~--pmt~fv~C~~Cg 183 (198)
-.|..||.....|. ..-+|+ |..|.
T Consensus 24 k~CADCgs~~P~WASiNlGIFI-Ci~CS 50 (648)
T PLN03119 24 RRCINCNSLGPQYVCTTFWTFV-CMACS 50 (648)
T ss_pred CccccCCCCCCCceeeccceEE-eccch
Confidence 48999999998888 566776 88886
No 130
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=44.47 E-value=28 Score=22.19 Aligned_cols=29 Identities=28% Similarity=0.458 Sum_probs=19.9
Q ss_pred ccceEcCCCCCCCceEe--ccceEEEeccCC
Q 036389 155 YGICKCSRCGHKRMSFI--PLRRHITCLNCY 183 (198)
Q Consensus 155 t~~~~C~~C~~~~~~~~--pmt~fv~C~~Cg 183 (198)
++...|+.||..-.... --..++.|.++-
T Consensus 3 ~g~l~C~~CG~~m~~~~~~~~~~yy~C~~~~ 33 (58)
T PF13408_consen 3 SGLLRCGHCGSKMTRRKRKGKYRYYRCSNRR 33 (58)
T ss_pred CCcEEcccCCcEeEEEECCCCceEEEcCCCc
Confidence 67899999998755544 234677777543
No 131
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=44.42 E-value=35 Score=23.39 Aligned_cols=40 Identities=20% Similarity=0.385 Sum_probs=29.6
Q ss_pred cceEcCCCCCCCceEeccceEEEeccCCCccccccccccccc
Q 036389 156 GICKCSRCGHKRMSFIPLRRHITCLNCYQYWASTNPEIRVLP 197 (198)
Q Consensus 156 ~~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~W~~~~~~~~~~~ 197 (198)
+..-||-|+++ -.|..-..-..|..|+ +|+=-++.|-+|+
T Consensus 7 eiLaCP~~kg~-L~~~~~~~~L~c~~~~-~aYpI~dGIPvlL 46 (60)
T COG2835 7 EILACPVCKGP-LVYDEEKQELICPRCK-LAYPIRDGIPVLL 46 (60)
T ss_pred eeeeccCcCCc-ceEeccCCEEEecccC-ceeecccCccccC
Confidence 45789999999 4455777777899997 5666677776664
No 132
>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=44.40 E-value=21 Score=21.94 Aligned_cols=27 Identities=26% Similarity=0.559 Sum_probs=18.5
Q ss_pred EcCCCCCCCceEe-ccceEEEecc---CCCc
Q 036389 159 KCSRCGHKRMSFI-PLRRHITCLN---CYQY 185 (198)
Q Consensus 159 ~C~~C~~~~~~~~-pmt~fv~C~~---Cg~~ 185 (198)
.||.||+.-..-. .-..|+.|.+ |.+.
T Consensus 3 ~CP~Cg~~lv~r~~k~g~F~~Cs~yP~C~~~ 33 (39)
T PF01396_consen 3 KCPKCGGPLVLRRGKKGKFLGCSNYPECKYT 33 (39)
T ss_pred CCCCCCceeEEEECCCCCEEECCCCCCcCCe
Confidence 6999995433322 5559999987 7764
No 133
>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=44.25 E-value=13 Score=38.29 Aligned_cols=25 Identities=28% Similarity=0.681 Sum_probs=21.7
Q ss_pred cccceEcCCCCCCCceEeccceEEEeccCCCc
Q 036389 154 VYGICKCSRCGHKRMSFIPLRRHITCLNCYQY 185 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~ 185 (198)
+.++++|++||.. |.+..|.+||.+
T Consensus 622 ev~~RKCPkCG~y-------Tlk~rCP~CG~~ 646 (1095)
T TIGR00354 622 EIAIRKCPQCGKE-------SFWLKCPVCGEL 646 (1095)
T ss_pred EEEEEECCCCCcc-------cccccCCCCCCc
Confidence 6688999999987 777889999976
No 134
>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=44.25 E-value=18 Score=32.88 Aligned_cols=29 Identities=17% Similarity=0.414 Sum_probs=19.9
Q ss_pred ceEcCCCCCCCceEe-----ccceEEEeccCCCcc
Q 036389 157 ICKCSRCGHKRMSFI-----PLRRHITCLNCYQYW 186 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~-----pmt~fv~C~~Cg~~W 186 (198)
+-.|++||.-.+... .-|..|.| .|||.-
T Consensus 169 ~p~c~~cg~~~~~v~~~d~~~~~v~y~c-~cG~~g 202 (353)
T cd00674 169 MPYCEKCGKDTTTVEAYDAKAGTVTYKC-ECGHEE 202 (353)
T ss_pred eeecCCcCcceeEEEEEeCCCCeEEEEc-CCCCEE
Confidence 458999994333332 46788899 599863
No 135
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=42.94 E-value=12 Score=28.59 Aligned_cols=29 Identities=24% Similarity=0.423 Sum_probs=19.2
Q ss_pred cccceEcCCCCCCCceEeccc-eEEEeccCCCc
Q 036389 154 VYGICKCSRCGHKRMSFIPLR-RHITCLNCYQY 185 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~~~~pmt-~fv~C~~Cg~~ 185 (198)
....+.|..||. .|.+.. .|..|..||..
T Consensus 68 vp~~~~C~~Cg~---~~~~~~~~~~~CP~Cgs~ 97 (117)
T PRK00564 68 EKVELECKDCSH---VFKPNALDYGVCEKCHSK 97 (117)
T ss_pred cCCEEEhhhCCC---ccccCCccCCcCcCCCCC
Confidence 456789999992 233333 45569999964
No 136
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=42.77 E-value=17 Score=23.59 Aligned_cols=8 Identities=38% Similarity=1.364 Sum_probs=4.3
Q ss_pred eccCCCcc
Q 036389 179 CLNCYQYW 186 (198)
Q Consensus 179 C~~Cg~~W 186 (198)
|..|+..|
T Consensus 51 C~~C~~~~ 58 (64)
T smart00647 51 CFRCKVPW 58 (64)
T ss_pred CCCCCCcC
Confidence 45555555
No 137
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=42.55 E-value=22 Score=26.00 Aligned_cols=32 Identities=25% Similarity=0.411 Sum_probs=19.4
Q ss_pred ccceEcCCCCCCCceEe--ccceEEEeccCCCcc
Q 036389 155 YGICKCSRCGHKRMSFI--PLRRHITCLNCYQYW 186 (198)
Q Consensus 155 t~~~~C~~C~~~~~~~~--pmt~fv~C~~Cg~~W 186 (198)
.-...||-|+.+.-+++ |-+..+.|-.||..+
T Consensus 31 ~~~~~CPfH~d~~pS~~i~~~k~~~~Cf~Cg~~G 64 (97)
T PF01807_consen 31 EYRCLCPFHDDKTPSFSINPDKNRFKCFGCGKGG 64 (97)
T ss_dssp EEEE--SSS--SS--EEEETTTTEEEETTT--EE
T ss_pred eEEEECcCCCCCCCceEEECCCCeEEECCCCCCC
Confidence 34678999998876666 888899999999765
No 138
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=42.30 E-value=29 Score=20.90 Aligned_cols=25 Identities=28% Similarity=0.660 Sum_probs=11.1
Q ss_pred EcCCCCCCCceEe-c---cceEEEeccCCC
Q 036389 159 KCSRCGHKRMSFI-P---LRRHITCLNCYQ 184 (198)
Q Consensus 159 ~C~~C~~~~~~~~-p---mt~fv~C~~Cg~ 184 (198)
-|+.||+. ..+. | -..-..|..||.
T Consensus 2 fC~~CG~~-l~~~ip~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 2 FCPQCGGP-LERRIPEGDDRERLVCPACGF 30 (34)
T ss_dssp B-TTT--B--EEE--TT-SS-EEEETTTTE
T ss_pred ccccccCh-hhhhcCCCCCccceECCCCCC
Confidence 37888887 4444 3 234445777773
No 139
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=42.23 E-value=16 Score=28.80 Aligned_cols=28 Identities=18% Similarity=0.337 Sum_probs=20.8
Q ss_pred cceEcCCCCCCCceEeccceEEEeccCCCcc
Q 036389 156 GICKCSRCGHKRMSFIPLRRHITCLNCYQYW 186 (198)
Q Consensus 156 ~~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~W 186 (198)
-..+||+||.+--. -|--|.|-.||++-
T Consensus 27 L~~hCp~Cg~PLF~---KdG~v~CPvC~~~~ 54 (131)
T COG1645 27 LAKHCPKCGTPLFR---KDGEVFCPVCGYRE 54 (131)
T ss_pred HHhhCcccCCccee---eCCeEECCCCCceE
Confidence 34699999987544 46667799999764
No 140
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=42.19 E-value=12 Score=24.50 Aligned_cols=14 Identities=21% Similarity=0.712 Sum_probs=8.9
Q ss_pred EEEeccCCCccccc
Q 036389 176 HITCLNCYQYWAST 189 (198)
Q Consensus 176 fv~C~~Cg~~W~~~ 189 (198)
.-.|..|||.|+.+
T Consensus 28 ~W~C~~Cgh~w~~~ 41 (55)
T PF14311_consen 28 WWKCPKCGHEWKAS 41 (55)
T ss_pred EEECCCCCCeeEcc
Confidence 34577777777643
No 141
>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=41.78 E-value=8.9 Score=30.60 Aligned_cols=30 Identities=20% Similarity=0.595 Sum_probs=23.7
Q ss_pred ceEcCCCCCCCceEe------ccceEEEeccCCCcc
Q 036389 157 ICKCSRCGHKRMSFI------PLRRHITCLNCYQYW 186 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~------pmt~fv~C~~Cg~~W 186 (198)
...||+||+..+.-. +=.-.+.|..|..-+
T Consensus 105 ~~~cp~c~s~~t~~~s~fg~t~cka~~~c~~c~epf 140 (146)
T TIGR02159 105 SVQCPRCGSADTTITSIFGPTACKALYRCRACKEPF 140 (146)
T ss_pred CCcCCCCCCCCcEeecCCCChhhHHHhhhhhhCCcH
Confidence 379999999999887 335778899998654
No 142
>KOG2768 consensus Translation initiation factor 2, beta subunit (eIF-2beta) [Translation, ribosomal structure and biogenesis]
Probab=41.39 E-value=13 Score=31.76 Aligned_cols=30 Identities=13% Similarity=0.299 Sum_probs=24.7
Q ss_pred cceEcCCCCCCCceEe-c-cceEEEeccCCCc
Q 036389 156 GICKCSRCGHKRMSFI-P-LRRHITCLNCYQY 185 (198)
Q Consensus 156 ~~~~C~~C~~~~~~~~-p-mt~fv~C~~Cg~~ 185 (198)
.-..|-.|++..+... . --.|..|..||.+
T Consensus 180 eyV~C~~CkSpdt~L~kenRLfFL~C~~cgs~ 211 (231)
T KOG2768|consen 180 EYVTCKTCKSPDTILQKENRLFFLRCEKCGSR 211 (231)
T ss_pred HheEeeecCChhHHhhhhcceEEEEecCCCCe
Confidence 4568999999998877 3 3478999999988
No 143
>PRK04860 hypothetical protein; Provisional
Probab=40.93 E-value=14 Score=29.98 Aligned_cols=36 Identities=11% Similarity=0.226 Sum_probs=25.2
Q ss_pred ccceEcCCCCCCCceEe------ccceEEEeccCCCccccccc
Q 036389 155 YGICKCSRCGHKRMSFI------PLRRHITCLNCYQYWASTNP 191 (198)
Q Consensus 155 t~~~~C~~C~~~~~~~~------pmt~fv~C~~Cg~~W~~~~~ 191 (198)
+=.|.|. |+....... --+..+.|..|+....+.++
T Consensus 117 ~~~Y~C~-C~~~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~~ 158 (160)
T PRK04860 117 TFPYRCK-CQEHQLTVRRHNRVVRGEAVYRCRRCGETLVFKGE 158 (160)
T ss_pred EEEEEcC-CCCeeCHHHHHHHHhcCCccEECCCCCceeEEecc
Confidence 4569998 988333223 23567899999999887654
No 144
>PRK00420 hypothetical protein; Validated
Probab=40.52 E-value=18 Score=27.73 Aligned_cols=31 Identities=13% Similarity=0.328 Sum_probs=21.6
Q ss_pred eEcCCCCCCCceEeccceEEEeccCCCcccccc
Q 036389 158 CKCSRCGHKRMSFIPLRRHITCLNCYQYWASTN 190 (198)
Q Consensus 158 ~~C~~C~~~~~~~~pmt~fv~C~~Cg~~W~~~~ 190 (198)
-.||.||.+-..+ -..-+.|.+||..-....
T Consensus 24 ~~CP~Cg~pLf~l--k~g~~~Cp~Cg~~~~v~~ 54 (112)
T PRK00420 24 KHCPVCGLPLFEL--KDGEVVCPVHGKVYIVKS 54 (112)
T ss_pred CCCCCCCCcceec--CCCceECCCCCCeeeecc
Confidence 5899999764443 345677999998655443
No 145
>PRK05580 primosome assembly protein PriA; Validated
Probab=39.85 E-value=36 Score=33.55 Aligned_cols=34 Identities=21% Similarity=0.401 Sum_probs=20.4
Q ss_pred cccceEcCCCCCC-CceEe--ccc-----eEEEeccCCCccc
Q 036389 154 VYGICKCSRCGHK-RMSFI--PLR-----RHITCLNCYQYWA 187 (198)
Q Consensus 154 ~t~~~~C~~C~~~-~~~~~--pmt-----~fv~C~~Cg~~W~ 187 (198)
-...+.|..||.. +|... ||| ....|..||++..
T Consensus 378 y~~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~ 419 (679)
T PRK05580 378 YAPFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEP 419 (679)
T ss_pred CCCceEhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCCC
Confidence 3456677777754 23333 444 4467888887644
No 146
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=39.48 E-value=19 Score=22.16 Aligned_cols=14 Identities=14% Similarity=0.273 Sum_probs=8.0
Q ss_pred cceEEEeccCCCcc
Q 036389 173 LRRHITCLNCYQYW 186 (198)
Q Consensus 173 mt~fv~C~~Cg~~W 186 (198)
+..||.|..|||--
T Consensus 3 ~~~~YkC~~CGniV 16 (36)
T PF06397_consen 3 KGEFYKCEHCGNIV 16 (36)
T ss_dssp TTEEEE-TTT--EE
T ss_pred cccEEEccCCCCEE
Confidence 34688999999854
No 147
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.40 E-value=16 Score=30.50 Aligned_cols=18 Identities=17% Similarity=0.457 Sum_probs=15.8
Q ss_pred ccceEEEeccCCCccccc
Q 036389 172 PLRRHITCLNCYQYWAST 189 (198)
Q Consensus 172 pmt~fv~C~~Cg~~W~~~ 189 (198)
..=-.|.|.+|.++|.++
T Consensus 45 DvWlIYkC~~Cd~tWN~~ 62 (203)
T COG4332 45 DVWLIYKCTHCDYTWNIS 62 (203)
T ss_pred EEEEEEEeeccCCccchh
Confidence 667889999999999875
No 148
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=39.35 E-value=37 Score=24.57 Aligned_cols=27 Identities=22% Similarity=0.508 Sum_probs=22.8
Q ss_pred eEcCCCCCCCceEeccceEEEeccCCC
Q 036389 158 CKCSRCGHKRMSFIPLRRHITCLNCYQ 184 (198)
Q Consensus 158 ~~C~~C~~~~~~~~pmt~fv~C~~Cg~ 184 (198)
.+|++|-.--+-|.-..+-|.|.+|+-
T Consensus 35 VkC~gc~~iT~vfSHaqtvVvc~~c~~ 61 (84)
T KOG1779|consen 35 VKCPGCFKITTVFSHAQTVVVCEGCST 61 (84)
T ss_pred EEcCCceEEEEEeecCceEEEcCCCce
Confidence 699999998888887777888999874
No 149
>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=38.78 E-value=16 Score=33.40 Aligned_cols=31 Identities=16% Similarity=0.349 Sum_probs=19.0
Q ss_pred ceEcCCCCC-CCceEe-----ccceEEEeccCCCccc
Q 036389 157 ICKCSRCGH-KRMSFI-----PLRRHITCLNCYQYWA 187 (198)
Q Consensus 157 ~~~C~~C~~-~~~~~~-----pmt~fv~C~~Cg~~W~ 187 (198)
.-.|++||. ..+... --|..|.|..|||+-.
T Consensus 174 ~piC~~cGri~tt~v~~~d~~~~~v~Y~c~~cG~~g~ 210 (360)
T PF01921_consen 174 LPICEKCGRIDTTEVTEYDPEGGTVTYRCEECGHEGE 210 (360)
T ss_dssp EEEETTTEE--EEEEEEE--SSSEEEEE--TTS---E
T ss_pred eeeccccCCcccceeeEeecCCCEEEEEecCCCCEEE
Confidence 468999999 455444 5678999999999743
No 150
>PF12773 DZR: Double zinc ribbon
Probab=38.44 E-value=13 Score=23.53 Aligned_cols=33 Identities=21% Similarity=0.264 Sum_probs=19.1
Q ss_pred ccceEcCCCCCCCceEeccceEEEeccCCCc----cccc
Q 036389 155 YGICKCSRCGHKRMSFIPLRRHITCLNCYQY----WAST 189 (198)
Q Consensus 155 t~~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~----W~~~ 189 (198)
.+.-.|+.||..-. .+-...+.|.+||.. |+||
T Consensus 10 ~~~~fC~~CG~~l~--~~~~~~~~C~~Cg~~~~~~~~fC 46 (50)
T PF12773_consen 10 DDAKFCPHCGTPLP--PPDQSKKICPNCGAENPPNAKFC 46 (50)
T ss_pred ccccCChhhcCChh--hccCCCCCCcCCcCCCcCCcCcc
Confidence 34456777776644 223345668888764 5555
No 151
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=38.05 E-value=31 Score=25.49 Aligned_cols=31 Identities=16% Similarity=0.270 Sum_probs=22.4
Q ss_pred ccceEcCCCCCCCceEeccceEEEeccCCCcc
Q 036389 155 YGICKCSRCGHKRMSFIPLRRHITCLNCYQYW 186 (198)
Q Consensus 155 t~~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~W 186 (198)
...+.|+.|+... --...+-...|..||..|
T Consensus 34 ~a~y~CpfCgk~~-vkR~a~GIW~C~~C~~~~ 64 (90)
T PRK03976 34 RAKHVCPVCGRPK-VKRVGTGIWECRKCGAKF 64 (90)
T ss_pred hcCccCCCCCCCc-eEEEEEEEEEcCCCCCEE
Confidence 3458999996443 333778888999999875
No 152
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=37.72 E-value=16 Score=28.82 Aligned_cols=18 Identities=17% Similarity=0.288 Sum_probs=15.1
Q ss_pred ccceEEEeccCCCccccc
Q 036389 172 PLRRHITCLNCYQYWAST 189 (198)
Q Consensus 172 pmt~fv~C~~Cg~~W~~~ 189 (198)
....||.|.+||.+|.|-
T Consensus 95 ~~~~~Y~Cp~C~~~y~~~ 112 (147)
T smart00531 95 TNNAYYKCPNCQSKYTFL 112 (147)
T ss_pred cCCcEEECcCCCCEeeHH
Confidence 456799999999999874
No 153
>PRK12495 hypothetical protein; Provisional
Probab=37.72 E-value=18 Score=31.06 Aligned_cols=30 Identities=20% Similarity=0.420 Sum_probs=21.6
Q ss_pred cccceEcCCCCCCCceEeccceEEEeccCCCcc
Q 036389 154 VYGICKCSRCGHKRMSFIPLRRHITCLNCYQYW 186 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~W 186 (198)
....+.|+.||..--.| .--+.|..|+...
T Consensus 39 tmsa~hC~~CG~PIpa~---pG~~~Cp~CQ~~~ 68 (226)
T PRK12495 39 TMTNAHCDECGDPIFRH---DGQEFCPTCQQPV 68 (226)
T ss_pred ccchhhcccccCcccCC---CCeeECCCCCCcc
Confidence 56778999999985533 3445599998764
No 154
>PRK12496 hypothetical protein; Provisional
Probab=37.60 E-value=17 Score=29.44 Aligned_cols=25 Identities=24% Similarity=0.371 Sum_probs=17.1
Q ss_pred eEcCCCCCCCceEeccc-eEEEeccCCCcc
Q 036389 158 CKCSRCGHKRMSFIPLR-RHITCLNCYQYW 186 (198)
Q Consensus 158 ~~C~~C~~~~~~~~pmt-~fv~C~~Cg~~W 186 (198)
++|++||.. ||.. .+-.|..||+.-
T Consensus 128 ~~C~gC~~~----~~~~~~~~~C~~CG~~~ 153 (164)
T PRK12496 128 KVCKGCKKK----YPEDYPDDVCEICGSPV 153 (164)
T ss_pred EECCCCCcc----ccCCCCCCcCCCCCChh
Confidence 789999943 3322 334699999864
No 155
>COG4481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.44 E-value=35 Score=23.09 Aligned_cols=27 Identities=30% Similarity=0.511 Sum_probs=18.3
Q ss_pred CCCCCceEe--ccceEEEeccCCCccccc
Q 036389 163 CGHKRMSFI--PLRRHITCLNCYQYWAST 189 (198)
Q Consensus 163 C~~~~~~~~--pmt~fv~C~~Cg~~W~~~ 189 (198)
||.+.-... .|..-..|.+|||.--..
T Consensus 19 Cg~NrwkIiRvGaDIkikC~nC~h~vm~p 47 (60)
T COG4481 19 CGTNRWKIIRVGADIKIKCENCGHSVMMP 47 (60)
T ss_pred cccceEEEEEecCcEEEEecCCCcEEEec
Confidence 555443333 888999999999864333
No 156
>PHA00616 hypothetical protein
Probab=37.04 E-value=9.9 Score=24.41 Aligned_cols=10 Identities=40% Similarity=1.072 Sum_probs=6.7
Q ss_pred ceEcCCCCCC
Q 036389 157 ICKCSRCGHK 166 (198)
Q Consensus 157 ~~~C~~C~~~ 166 (198)
+++|++||..
T Consensus 1 pYqC~~CG~~ 10 (44)
T PHA00616 1 MYQCLRCGGI 10 (44)
T ss_pred CCccchhhHH
Confidence 3677777764
No 157
>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=36.52 E-value=31 Score=22.92 Aligned_cols=24 Identities=25% Similarity=0.562 Sum_probs=18.4
Q ss_pred cccceEcCCCCCCCceEeccceEEEeccCC
Q 036389 154 VYGICKCSRCGHKRMSFIPLRRHITCLNCY 183 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~~~~pmt~fv~C~~Cg 183 (198)
......|+.||+. ..-+..|.+||
T Consensus 23 ~p~l~~C~~cG~~------~~~H~vc~~cG 46 (55)
T TIGR01031 23 APTLVVCPNCGEF------KLPHRVCPSCG 46 (55)
T ss_pred CCcceECCCCCCc------ccCeeECCccC
Confidence 4677899999985 45566788888
No 158
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=36.03 E-value=17 Score=33.21 Aligned_cols=33 Identities=15% Similarity=0.306 Sum_probs=24.2
Q ss_pred ceEcCCCCCCCceEeccceEEEeccCCCccccccc
Q 036389 157 ICKCSRCGHKRMSFIPLRRHITCLNCYQYWASTNP 191 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~W~~~~~ 191 (198)
.++|..|+.+.....+ .--.|..||.+|..+-|
T Consensus 244 ~~~C~~c~~~~~~~~~--~~~~C~~c~~~~~~~GP 276 (382)
T PRK04338 244 VYYCPKCLYREEVEGL--PPEECPVCGGKFGTAGP 276 (382)
T ss_pred EEECCCCCcEEEecCC--CCCCCCCCCCcceeccc
Confidence 6789999987665442 22369999999887665
No 159
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=35.42 E-value=18 Score=26.09 Aligned_cols=48 Identities=23% Similarity=0.258 Sum_probs=24.5
Q ss_pred hhcccCCHHhhccHHHHHHHHHHhcccccccccccccccCCCcccccceEcCCCCCC
Q 036389 110 ETIVNMTAKEMASDKMQLWYENSRKGRAETNGRIFSGLVSPKNIVYGICKCSRCGHK 166 (198)
Q Consensus 110 ~~lv~Ms~eELas~e~k~~~e~~~~~e~~~~~~l~~~~~~~~~~~t~~~~C~~C~~~ 166 (198)
..++--+|+++|..+.++.-.-.++ -. +.-.- -.++ -+-|.|+.||++
T Consensus 27 g~ivVTTPq~la~~dv~r~~~~~~~-~~-----vpilG-vVEN--Ms~~~Cp~Cg~~ 74 (81)
T PF10609_consen 27 GAIVVTTPQELALADVRRAIDMFRK-LN-----VPILG-VVEN--MSYFVCPHCGER 74 (81)
T ss_dssp EEEEEE-CCC--HHHHHHHHHHHHC-TT------EEEE-EEEC--T-EEE-TTT--E
T ss_pred eEEEEeCCHHHHHHHHHHHHHHHHh-cC-----CCcEE-EEEC--CCccCCCCCCCe
Confidence 3456678999999888877666666 22 11110 2222 456999999975
No 160
>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=35.37 E-value=35 Score=22.66 Aligned_cols=29 Identities=17% Similarity=0.132 Sum_probs=21.1
Q ss_pred cceEcCCCCCCCceEe---ccceEEEeccCCC
Q 036389 156 GICKCSRCGHKRMSFI---PLRRHITCLNCYQ 184 (198)
Q Consensus 156 ~~~~C~~C~~~~~~~~---pmt~fv~C~~Cg~ 184 (198)
-...|++|.+-.-.+. +..+.+.|..||.
T Consensus 21 ~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 21 YALICSKCFSHNGLAPKEEFEEIQYRCPYCGA 52 (54)
T ss_pred eeEECcccchhhcccccccCCceEEEcCCCCC
Confidence 3467999988777663 5555777999985
No 161
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=35.16 E-value=24 Score=20.83 Aligned_cols=13 Identities=15% Similarity=0.166 Sum_probs=10.1
Q ss_pred ceEEEeccCCCcc
Q 036389 174 RRHITCLNCYQYW 186 (198)
Q Consensus 174 t~fv~C~~Cg~~W 186 (198)
-.||.|..||+--
T Consensus 2 ~~~ykC~~CGniv 14 (34)
T cd00974 2 LEVYKCEICGNIV 14 (34)
T ss_pred CcEEEcCCCCcEE
Confidence 4688899998864
No 162
>PLN03114 ADP-ribosylation factor GTPase-activating protein AGD10; Provisional
Probab=34.93 E-value=29 Score=31.97 Aligned_cols=26 Identities=19% Similarity=0.581 Sum_probs=20.4
Q ss_pred eEcCCCCCCCceEe--ccceEEEeccCCC
Q 036389 158 CKCSRCGHKRMSFI--PLRRHITCLNCYQ 184 (198)
Q Consensus 158 ~~C~~C~~~~~~~~--pmt~fv~C~~Cg~ 184 (198)
-.|-.||.+.-.|. +.-+|+ |+.|..
T Consensus 23 k~CaDCga~nPtWASvn~GIFL-Cl~CSG 50 (395)
T PLN03114 23 KICFDCNAKNPTWASVTYGIFL-CIDCSA 50 (395)
T ss_pred CcCccCCCCCCCceeeccceee-hhhhhH
Confidence 47999999998888 555666 888863
No 163
>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=34.72 E-value=13 Score=37.70 Aligned_cols=33 Identities=18% Similarity=0.372 Sum_probs=0.0
Q ss_pred cccceEcCCCCCCCceEe------ccceEEEeccCCCcc
Q 036389 154 VYGICKCSRCGHKRMSFI------PLRRHITCLNCYQYW 186 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~~~~------pmt~fv~C~~Cg~~W 186 (198)
..+.++|+.||..--... +++..+.|..||+.-
T Consensus 652 ei~~r~Cp~Cg~~t~~~~Cp~CG~~T~~~~~Cp~C~~~~ 690 (900)
T PF03833_consen 652 EIGRRRCPKCGKETFYNRCPECGSHTEPVYVCPDCGIEV 690 (900)
T ss_dssp ---------------------------------------
T ss_pred eeecccCcccCCcchhhcCcccCCccccceecccccccc
Confidence 557889999998733322 566777888888763
No 164
>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=34.72 E-value=14 Score=27.98 Aligned_cols=29 Identities=31% Similarity=0.690 Sum_probs=18.6
Q ss_pred cccceEcCCCCCCCceEeccceEEEeccCCCc
Q 036389 154 VYGICKCSRCGHKRMSFIPLRRHITCLNCYQY 185 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~ 185 (198)
....+.|..||.. |.|-...+.|..||..
T Consensus 67 ~p~~~~C~~Cg~~---~~~~~~~~~CP~Cgs~ 95 (113)
T PF01155_consen 67 VPARARCRDCGHE---FEPDEFDFSCPRCGSP 95 (113)
T ss_dssp E--EEEETTTS-E---EECHHCCHH-SSSSSS
T ss_pred cCCcEECCCCCCE---EecCCCCCCCcCCcCC
Confidence 4567899999864 5555555779999976
No 165
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=34.40 E-value=25 Score=20.68 Aligned_cols=12 Identities=17% Similarity=0.288 Sum_probs=9.4
Q ss_pred eEEEeccCCCcc
Q 036389 175 RHITCLNCYQYW 186 (198)
Q Consensus 175 ~fv~C~~Cg~~W 186 (198)
.||.|..||+--
T Consensus 6 ~~ykC~~Cgniv 17 (34)
T TIGR00319 6 QVYKCEVCGNIV 17 (34)
T ss_pred cEEEcCCCCcEE
Confidence 488899998864
No 166
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=33.31 E-value=28 Score=26.97 Aligned_cols=35 Identities=17% Similarity=0.373 Sum_probs=25.0
Q ss_pred cccceEcCCCCCCCceEe-ccceEEEeccCCCcccc
Q 036389 154 VYGICKCSRCGHKRMSFI-PLRRHITCLNCYQYWAS 188 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~~~~-pmt~fv~C~~Cg~~W~~ 188 (198)
..-.+.|+.|+..-.... -.+..+.|..||..+.+
T Consensus 120 ~~~~~~C~~C~~~~~r~~~~~~~~~~C~~C~~~l~~ 155 (157)
T PF10263_consen 120 KKYVYRCPSCGREYKRHRRSKRKRYRCGRCGGPLVQ 155 (157)
T ss_pred cceEEEcCCCCCEeeeecccchhhEECCCCCCEEEE
Confidence 467799999998755444 33456889999976643
No 167
>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=32.49 E-value=45 Score=20.01 Aligned_cols=27 Identities=22% Similarity=0.364 Sum_probs=13.4
Q ss_pred EcCCCCCCCceEe-ccceEEEeccCCCcc
Q 036389 159 KCSRCGHKRMSFI-PLRRHITCLNCYQYW 186 (198)
Q Consensus 159 ~C~~C~~~~~~~~-pmt~fv~C~~Cg~~W 186 (198)
-||.||.--.--. ..+.. .|.+||...
T Consensus 3 FCp~C~nlL~p~~~~~~~~-~C~~C~Y~~ 30 (35)
T PF02150_consen 3 FCPECGNLLYPKEDKEKRV-ACRTCGYEE 30 (35)
T ss_dssp BETTTTSBEEEEEETTTTE-EESSSS-EE
T ss_pred eCCCCCccceEcCCCccCc-CCCCCCCcc
Confidence 4777776421111 33333 788887643
No 168
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 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 probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=32.16 E-value=47 Score=21.97 Aligned_cols=26 Identities=27% Similarity=0.529 Sum_probs=17.5
Q ss_pred ccceEcCCCCCCCceEe-------ccceEEEeccCCC
Q 036389 155 YGICKCSRCGHKRMSFI-------PLRRHITCLNCYQ 184 (198)
Q Consensus 155 t~~~~C~~C~~~~~~~~-------pmt~fv~C~~Cg~ 184 (198)
+=.+.| |||.. |. -....|.|..|.-
T Consensus 16 ~~~y~C-RCG~~---f~i~e~~l~~~~~iv~C~sCSL 48 (55)
T PF05207_consen 16 VYSYPC-RCGGE---FEISEEDLEEGEVIVQCDSCSL 48 (55)
T ss_dssp EEEEEE-TTSSE---EEEEHHHHHCT--EEEETTTTE
T ss_pred EEEEcC-CCCCE---EEEcchhccCcCEEEECCCCcc
Confidence 345789 89988 44 3457889998864
No 169
>PRK06599 DNA topoisomerase I; Validated
Probab=31.81 E-value=71 Score=31.49 Aligned_cols=15 Identities=7% Similarity=0.184 Sum_probs=11.0
Q ss_pred HHhhcCCCCchhccc
Q 036389 100 KKVLLGDVKPETIVN 114 (198)
Q Consensus 100 ~~vl~G~isp~~lv~ 114 (198)
..|..|+.++++++.
T Consensus 543 ~~I~~G~~~~~~~l~ 557 (675)
T PRK06599 543 DEIAEGKKDWKPVLR 557 (675)
T ss_pred HHHHcCCCCHHHHHH
Confidence 457788888877765
No 170
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=31.39 E-value=12 Score=33.13 Aligned_cols=31 Identities=26% Similarity=0.582 Sum_probs=21.9
Q ss_pred ceEcCCCCCCCceEe-cc-ceEEEeccCCCccccc
Q 036389 157 ICKCSRCGHKRMSFI-PL-RRHITCLNCYQYWAST 189 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~-pm-t~fv~C~~Cg~~W~~~ 189 (198)
-.+|+.|+.- -|. .. ..+..|.+|||.++.+
T Consensus 26 ~~~c~~c~~~--~~~~~l~~~~~vc~~c~~h~rl~ 58 (285)
T TIGR00515 26 WTKCPKCGQV--LYTKELERNLEVCPKCDHHMRMD 58 (285)
T ss_pred eeECCCCcch--hhHHHHHhhCCCCCCCCCcCcCC
Confidence 5689999864 344 23 4567899999988753
No 171
>PLN03131 hypothetical protein; Provisional
Probab=31.16 E-value=54 Score=32.38 Aligned_cols=26 Identities=23% Similarity=0.687 Sum_probs=20.7
Q ss_pred eEcCCCCCCCceEe--ccceEEEeccCCC
Q 036389 158 CKCSRCGHKRMSFI--PLRRHITCLNCYQ 184 (198)
Q Consensus 158 ~~C~~C~~~~~~~~--pmt~fv~C~~Cg~ 184 (198)
-.|..|+.....|. ..-+|+ |..|..
T Consensus 24 k~CADCga~~P~WASiNlGIFI-Ci~CSG 51 (705)
T PLN03131 24 RRCINCNSLGPQFVCTNFWTFI-CMTCSG 51 (705)
T ss_pred CccccCCCCCCCeeEeccceEE-chhchh
Confidence 48999999998888 555666 998863
No 172
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=30.56 E-value=25 Score=26.49 Aligned_cols=29 Identities=21% Similarity=0.549 Sum_probs=17.5
Q ss_pred eEcCCCCCCCceEe--ccceEEEeccCCCccc
Q 036389 158 CKCSRCGHKRMSFI--PLRRHITCLNCYQYWA 187 (198)
Q Consensus 158 ~~C~~C~~~~~~~~--pmt~fv~C~~Cg~~W~ 187 (198)
-.|.-||....+|. ..-+|+ |..|..-.+
T Consensus 14 ~~CaDCg~~~p~w~s~~~Gifl-C~~Cag~HR 44 (116)
T PF01412_consen 14 KVCADCGAPNPTWASLNYGIFL-CLECAGIHR 44 (116)
T ss_dssp TB-TTT-SBS--EEETTTTEEE--HHHHHHHH
T ss_pred CcCCCCCCCCCCEEEeecChhh-hHHHHHHHH
Confidence 48999999999999 444665 999875443
No 173
>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=30.24 E-value=40 Score=32.26 Aligned_cols=28 Identities=18% Similarity=0.490 Sum_probs=20.1
Q ss_pred ceEcCCCCCCCceEe----ccceEEEeccCCCc
Q 036389 157 ICKCSRCGHKRMSFI----PLRRHITCLNCYQY 185 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~----pmt~fv~C~~Cg~~ 185 (198)
.-.|++||.-.++.. --|+.|.| .|||.
T Consensus 168 ~pic~~cGrv~~~~~~~~~~~~v~Y~c-~cG~~ 199 (515)
T TIGR00467 168 SVFCENCGRDTTTVNNYDNEYSIEYSC-ECGNQ 199 (515)
T ss_pred eeecCCcCccCceEEEecCCceEEEEc-CCCCE
Confidence 458999999755433 22788889 49985
No 174
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=29.49 E-value=31 Score=26.87 Aligned_cols=33 Identities=15% Similarity=0.437 Sum_probs=24.0
Q ss_pred cccceEcCCCCCCCceEe--cc---ceEEEeccCCCccc
Q 036389 154 VYGICKCSRCGHKRMSFI--PL---RRHITCLNCYQYWA 187 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~~~~--pm---t~fv~C~~Cg~~W~ 187 (198)
...+..||.|++.. .+. +- -.-+.|..||..|-
T Consensus 27 ~~~~~~cP~C~s~~-~~k~g~~~~~~qRyrC~~C~~tf~ 64 (129)
T COG3677 27 QITKVNCPRCKSSN-VVKIGGIRRGHQRYKCKSCGSTFT 64 (129)
T ss_pred hcccCcCCCCCccc-eeeECCccccccccccCCcCccee
Confidence 45667999999988 444 22 45678999998874
No 175
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=29.42 E-value=71 Score=32.49 Aligned_cols=26 Identities=19% Similarity=0.420 Sum_probs=14.4
Q ss_pred cceEcCCCCCCCceEe--ccceEEEecc
Q 036389 156 GICKCSRCGHKRMSFI--PLRRHITCLN 181 (198)
Q Consensus 156 ~~~~C~~C~~~~~~~~--pmt~fv~C~~ 181 (198)
+...||+||+...... ..-.|+-|.+
T Consensus 591 ~~~~CP~Cg~~~L~~k~gr~G~Fl~Cs~ 618 (860)
T PRK06319 591 TEIDCPKCHKGKLVKIWAKNRYFYGCSE 618 (860)
T ss_pred cCcccCCCCCcceeEEecCCCceeeccC
Confidence 3468999986433322 3334555544
No 176
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=29.37 E-value=30 Score=17.90 Aligned_cols=7 Identities=29% Similarity=0.738 Sum_probs=3.1
Q ss_pred EeccCCC
Q 036389 178 TCLNCYQ 184 (198)
Q Consensus 178 ~C~~Cg~ 184 (198)
.|..||.
T Consensus 2 ~C~~C~~ 8 (23)
T PF00096_consen 2 KCPICGK 8 (23)
T ss_dssp EETTTTE
T ss_pred CCCCCCC
Confidence 3444444
No 177
>TIGR00308 TRM1 tRNA(guanine-26,N2-N2) methyltransferase. This enzyme is responsible for two methylations of a characteristic guanine of most tRNA molecules. The activity has been demonstrated for eukaryotic and archaeal proteins, which are active when expressed in E. coli, a species that lacks this enzyme. At least one Eubacterium, Aquifex aeolicus, has an ortholog, as do all completed archaeal genomes.
Probab=29.30 E-value=30 Score=31.69 Aligned_cols=35 Identities=26% Similarity=0.428 Sum_probs=22.9
Q ss_pred ceEcCCCCCCCceEeccceEEEeccCCCccccccc
Q 036389 157 ICKCSRCGHKRMSFIPLRRHITCLNCYQYWASTNP 191 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~W~~~~~ 191 (198)
.++|+.|+.+...-......-.|..||.+|..+-|
T Consensus 233 v~~C~~c~~~~~~~~~~~~~~~C~~c~~~~~~~GP 267 (374)
T TIGR00308 233 TYHCSRCLHNKPVNGISQRKGRCKECGGEYHLAGP 267 (374)
T ss_pred EEECCCcccccccccccCCCCCCCCCCCcceeecC
Confidence 67899998775432111123459999998876655
No 178
>KOG1222 consensus Kinesin associated protein KAP [Intracellular trafficking, secretion, and vesicular transport]
Probab=29.17 E-value=1.3e+02 Score=29.27 Aligned_cols=86 Identities=14% Similarity=0.136 Sum_probs=57.8
Q ss_pred HHHHHHHHHHHHhhhhhhcccc-c---hhhhhhcccChHHHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhcCCCCCHHHH
Q 036389 24 REIVRKNLYGALSKVSIEAAHD-K---NVIDQVKACNPIQVAISMESAMYEKWGRSSETYKFKYRRLLFNFNDPKNHEFR 99 (198)
Q Consensus 24 R~k~r~~L~~aL~~~~~e~~~~-~---~~~~~~~~~~~~~~A~~IE~alf~~~~~~~~~Yk~k~Rsl~~NLkd~kNp~Lr 99 (198)
|.++..+|.+||.....+.--. - .-.+...+......+..|-..+-..|+....+-++-.-.|+|||. =...||
T Consensus 302 rkniV~mLVKaLdr~n~~Ll~lv~~FLkKLSIf~eNK~~M~~~~iveKL~klfp~~h~dL~~~tl~LlfNlS--FD~glr 379 (791)
T KOG1222|consen 302 RKNIVAMLVKALDRSNSSLLTLVIKFLKKLSIFDENKIVMEQNGIVEKLLKLFPIQHPDLRKATLMLLFNLS--FDSGLR 379 (791)
T ss_pred HHhHHHHHHHHHcccchHHHHHHHHHHHHhhhhccchHHHHhccHHHHHHHhcCCCCHHHHHHHHHHhhhcc--cccccc
Confidence 5678888988887542111000 0 001122233345667777788888888777888999999999999 566799
Q ss_pred HHhhcCCCCchh
Q 036389 100 KKVLLGDVKPET 111 (198)
Q Consensus 100 ~~vl~G~isp~~ 111 (198)
.++..|-+-|.-
T Consensus 380 ~KMv~~GllP~l 391 (791)
T KOG1222|consen 380 PKMVNGGLLPHL 391 (791)
T ss_pred HHHhhccchHHH
Confidence 999999887753
No 179
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=28.72 E-value=43 Score=28.90 Aligned_cols=28 Identities=21% Similarity=0.501 Sum_probs=18.9
Q ss_pred EcCCCCCCCceEeccceEEEeccCCCccc
Q 036389 159 KCSRCGHKRMSFIPLRRHITCLNCYQYWA 187 (198)
Q Consensus 159 ~C~~C~~~~~~~~pmt~fv~C~~Cg~~W~ 187 (198)
.|++||++- ....-..-..|..||+...
T Consensus 101 fC~~CG~~~-~~~~~~~~~~C~~c~~~~y 128 (256)
T PRK00241 101 FCGYCGHPM-HPSKTEWAMLCPHCRERYY 128 (256)
T ss_pred cccccCCCC-eecCCceeEECCCCCCEEC
Confidence 799999873 3334444566888987654
No 180
>PRK07219 DNA topoisomerase I; Validated
Probab=28.66 E-value=75 Score=32.12 Aligned_cols=18 Identities=17% Similarity=0.222 Sum_probs=12.9
Q ss_pred HHhhcCCCCchhcccCCH
Q 036389 100 KKVLLGDVKPETIVNMTA 117 (198)
Q Consensus 100 ~~vl~G~isp~~lv~Ms~ 117 (198)
..|..|+++.++++.-.-
T Consensus 550 ~~I~~G~~~~~~~l~~~~ 567 (822)
T PRK07219 550 QAIEDGKKKKEDVTEESR 567 (822)
T ss_pred HHHHcCCCCHHHHHHHHH
Confidence 567788888888766533
No 181
>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=28.59 E-value=53 Score=22.34 Aligned_cols=17 Identities=12% Similarity=0.397 Sum_probs=11.5
Q ss_pred ccceEEEeccCCCcccc
Q 036389 172 PLRRHITCLNCYQYWAS 188 (198)
Q Consensus 172 pmt~fv~C~~Cg~~W~~ 188 (198)
.+.--..|.+||+.+-.
T Consensus 49 i~eg~L~Cp~c~r~YPI 65 (68)
T PF03966_consen 49 IVEGELICPECGREYPI 65 (68)
T ss_dssp TTTTEEEETTTTEEEEE
T ss_pred ccCCEEEcCCCCCEEeC
Confidence 66667777777766543
No 182
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=28.56 E-value=50 Score=20.62 Aligned_cols=10 Identities=30% Similarity=0.663 Sum_probs=4.5
Q ss_pred ceEEEeccCC
Q 036389 174 RRHITCLNCY 183 (198)
Q Consensus 174 t~fv~C~~Cg 183 (198)
...+.|..|+
T Consensus 12 ~~~i~C~~C~ 21 (51)
T PF00628_consen 12 GDMIQCDSCN 21 (51)
T ss_dssp SSEEEBSTTS
T ss_pred CCeEEcCCCC
Confidence 3444444444
No 183
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=28.46 E-value=46 Score=31.68 Aligned_cols=29 Identities=17% Similarity=0.353 Sum_probs=20.9
Q ss_pred ceEcCCCCCCCceEe------ccceEEEeccCCCcc
Q 036389 157 ICKCSRCGHKRMSFI------PLRRHITCLNCYQYW 186 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~------pmt~fv~C~~Cg~~W 186 (198)
.-.|++||.-.++-. ..|+.|.|. |||..
T Consensus 175 ~pic~~cg~~~~~~~~~~d~~~~~v~y~~~-cG~~~ 209 (510)
T PRK00750 175 LPICPKCGKVLTTPVISYDAEAGTVTYDCE-CGHEG 209 (510)
T ss_pred eeeCCCCCccceEEEEEEeCCCCEEEEEcC-CCCEE
Confidence 458999999876543 446777775 99864
No 184
>KOG3214 consensus Uncharacterized Zn ribbon-containing protein [Function unknown]
Probab=28.43 E-value=40 Score=25.54 Aligned_cols=34 Identities=15% Similarity=0.296 Sum_probs=26.7
Q ss_pred cccceEcCCCCCCCceEe-----ccceEEEeccCCCccc
Q 036389 154 VYGICKCSRCGHKRMSFI-----PLRRHITCLNCYQYWA 187 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~~~~-----pmt~fv~C~~Cg~~W~ 187 (198)
-...|.|+-|++.+.--. -+.-+..|..|+..+.
T Consensus 20 ldt~FnClfcnHek~v~~~~Dk~~~iG~~sC~iC~esFq 58 (109)
T KOG3214|consen 20 LDTQFNCLFCNHEKSVSCTLDKKHNIGKASCRICEESFQ 58 (109)
T ss_pred hheeeccCccccccceeeeehhhcCcceeeeeehhhhhc
Confidence 356799999999875433 7788999999998753
No 185
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=28.29 E-value=46 Score=19.07 Aligned_cols=22 Identities=27% Similarity=0.612 Sum_probs=13.2
Q ss_pred eEcCCCCCCCceEeccceEEEeccCC
Q 036389 158 CKCSRCGHKRMSFIPLRRHITCLNCY 183 (198)
Q Consensus 158 ~~C~~C~~~~~~~~pmt~fv~C~~Cg 183 (198)
|.|.-|+..--.+ . ||+|..|+
T Consensus 1 ~~C~~C~~~~~~~---~-~Y~C~~c~ 22 (30)
T PF03107_consen 1 FWCDVCRRKIDGF---Y-FYHCSECC 22 (30)
T ss_pred CCCCCCCCCcCCC---E-eEEeCCCC
Confidence 3566775553332 2 78887776
No 186
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=28.08 E-value=14 Score=29.73 Aligned_cols=29 Identities=24% Similarity=0.550 Sum_probs=23.6
Q ss_pred ceEcCCCCCCCceEe--ccceEEEeccCCCc
Q 036389 157 ICKCSRCGHKRMSFI--PLRRHITCLNCYQY 185 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~--pmt~fv~C~~Cg~~ 185 (198)
-..|+.||+..+.+. --.-|.+|..||..
T Consensus 105 yv~C~~c~s~dt~l~~~~R~~~l~c~acGa~ 135 (151)
T COG1601 105 YVKCKECGSPDTELIKEERLLFLKCEACGAI 135 (151)
T ss_pred eeEeccCCCCchhhhhhhhhHhhHHHHhCCc
Confidence 368999999999888 55678889999964
No 187
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=28.07 E-value=49 Score=22.44 Aligned_cols=30 Identities=23% Similarity=0.480 Sum_probs=21.1
Q ss_pred CCCCCceEe--ccceEEEeccCCCcccccccc
Q 036389 163 CGHKRMSFI--PLRRHITCLNCYQYWASTNPE 192 (198)
Q Consensus 163 C~~~~~~~~--pmt~fv~C~~Cg~~W~~~~~~ 192 (198)
||+..=... .|..-+.|..||+.-=..|.+
T Consensus 16 CG~~~Wei~R~GaDikikC~gCg~~imlpR~~ 47 (57)
T PF06107_consen 16 CGSNEWEIIRIGADIKIKCLGCGRQIMLPRSK 47 (57)
T ss_pred CCCCEEEEEEccCcEEEEECCCCCEEEEeHHH
Confidence 666544444 888889999999976555543
No 188
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=28.00 E-value=49 Score=27.70 Aligned_cols=26 Identities=27% Similarity=0.611 Sum_probs=18.7
Q ss_pred ceEcCCCCCCCceEeccceEEEeccCCCc
Q 036389 157 ICKCSRCGHKRMSFIPLRRHITCLNCYQY 185 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~ 185 (198)
...|.+|++.-.. --....|-+||++
T Consensus 149 ~A~CsrC~~~L~~---~~~~l~Cp~Cg~t 174 (188)
T COG1096 149 YARCSRCRAPLVK---KGNMLKCPNCGNT 174 (188)
T ss_pred EEEccCCCcceEE---cCcEEECCCCCCE
Confidence 3589999876433 4566779999986
No 189
>PRK04023 DNA polymerase II large subunit; Validated
Probab=27.91 E-value=30 Score=35.87 Aligned_cols=32 Identities=16% Similarity=0.213 Sum_probs=0.0
Q ss_pred cccccceEcCCCCCCCceEe------ccceEEEeccCC
Q 036389 152 NIVYGICKCSRCGHKRMSFI------PLRRHITCLNCY 183 (198)
Q Consensus 152 ~~~t~~~~C~~C~~~~~~~~------pmt~fv~C~~Cg 183 (198)
+..+..|+|+.||......+ -...-++|.+||
T Consensus 633 G~~t~~frCP~CG~~Te~i~fCP~CG~~~~~y~CPKCG 670 (1121)
T PRK04023 633 GKETFYRRCPFCGTHTEPVYRCPRCGIEVEEDECEKCG 670 (1121)
T ss_pred CCcCCcccCCCCCCCCCcceeCccccCcCCCCcCCCCC
No 190
>COG5595 Zn-ribbon-containing, possibly nucleic-acid-binding protein [General function prediction only]
Probab=27.87 E-value=23 Score=30.12 Aligned_cols=30 Identities=20% Similarity=0.523 Sum_probs=19.2
Q ss_pred CCCCCCceEe---------ccceEEEeccCCCccccccc
Q 036389 162 RCGHKRMSFI---------PLRRHITCLNCYQYWASTNP 191 (198)
Q Consensus 162 ~C~~~~~~~~---------pmt~fv~C~~Cg~~W~~~~~ 191 (198)
+|-+.+++|+ --...--|..||+.|.+-+|
T Consensus 195 k~t~iptyYylyrVgGnSlAqek~r~CPsC~k~Wqlk~~ 233 (256)
T COG5595 195 KCTGIPTYYYLYRVGGNSLAQEKYRCCPSCGKDWQLKNP 233 (256)
T ss_pred HHhCCCceEEEEEecCchhhhhccCCCCcccccceeccc
Confidence 5777777777 22344456778888877654
No 191
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=27.84 E-value=45 Score=27.24 Aligned_cols=26 Identities=27% Similarity=0.566 Sum_probs=20.1
Q ss_pred eEcCCCCCCCceEeccc-eEEEeccCCCcc
Q 036389 158 CKCSRCGHKRMSFIPLR-RHITCLNCYQYW 186 (198)
Q Consensus 158 ~~C~~C~~~~~~~~pmt-~fv~C~~Cg~~W 186 (198)
..|++||..- .|.. +...|.+||++-
T Consensus 150 a~~~~~g~~~---~~~~~~~~~c~~~~~~e 176 (189)
T PRK09521 150 AMCSRCRTPL---VKKGENELKCPNCGNIE 176 (189)
T ss_pred EEccccCCce---EECCCCEEECCCCCCEE
Confidence 4688898874 4777 788999999763
No 192
>smart00099 btg1 tob/btg1 family. The tob/btg1 is a family of proteins that inhibit cell proliferation.
Probab=27.65 E-value=21 Score=27.29 Aligned_cols=62 Identities=11% Similarity=0.078 Sum_probs=45.3
Q ss_pred hHHHHHHHHHHHHHHhCC----CcHHHHHHHHHHHHhcCCCCCHHHHHHhhcCCCCchhcccCCHHhh
Q 036389 57 PIQVAISMESAMYEKWGR----SSETYKFKYRRLLFNFNDPKNHEFRKKVLLGDVKPETIVNMTAKEM 120 (198)
Q Consensus 57 ~~~~A~~IE~alf~~~~~----~~~~Yk~k~Rsl~~NLkd~kNp~Lr~~vl~G~isp~~lv~Ms~eEL 120 (198)
+..++.++++.|.+.|.+ .+...-+.+|.|.-| ++..|-|...-..--|+.++|..+=|.||
T Consensus 27 v~~F~~~L~~~L~~~y~~HWyP~~P~kGqayRCIrIn--~~~Dp~l~~Aa~~sGl~~~~l~~~LP~el 92 (108)
T smart00099 27 VEIFAEKLTRLLKEKYKNHWYPEKPYKGSGFRCIRIN--QKVDPVIEQACKESGLDIDDLGGNLPKEL 92 (108)
T ss_pred HHHHHHHHHHHHHHHHhcCCCCCCCCCCcceEEEEEC--CcCCHHHHHHHHHhCCCHHHHHHhCCccc
Confidence 578999999999998854 234556778889888 66888887776666677777665544444
No 193
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=27.29 E-value=54 Score=29.44 Aligned_cols=33 Identities=21% Similarity=0.463 Sum_probs=22.3
Q ss_pred ceEcCCCCCCCc-eEe------ccceEEEeccCCCccccc
Q 036389 157 ICKCSRCGHKRM-SFI------PLRRHITCLNCYQYWAST 189 (198)
Q Consensus 157 ~~~C~~C~~~~~-~~~------pmt~fv~C~~Cg~~W~~~ 189 (198)
..+|+.||+.+- .|+ +--.--+|..|+..+|.-
T Consensus 226 R~~C~~Cg~~~~l~y~~~~~~~~~~r~e~C~~C~~YlK~~ 265 (309)
T PRK03564 226 RVKCSNCEQSGKLHYWSLDSEQAAVKAESCGDCGTYLKIL 265 (309)
T ss_pred CccCCCCCCCCceeeeeecCCCcceEeeecccccccceec
Confidence 457888887543 343 334557899999998874
No 194
>PF00684 DnaJ_CXXCXGXG: DnaJ central domain; InterPro: IPR001305 The hsp70 chaperone machine performs many diverse roles in the cell, including folding of nascent proteins, translocation of polypeptides across organelle membranes, coordinating responses to stress, and targeting selected proteins for degradation. DnaJ is a member of the hsp40 family of molecular chaperones, which is also called the J-protein family, the members of which regulate the activity of hsp70s. DnaJ (hsp40) binds to DnaK (hsp70) and stimulates its ATPase activity, generating the ADP-bound state of DnaK, which interacts stably with the polypeptide substrate []. Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation []. DnaJ consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acid residues, a glycine and phenylalanine-rich domain ('G/F' domain), a central cysteine rich domain (CR-type zinc finger) containing four repeats of a CXXCXGXG motif which can coordinate two zinc atom and a C-terminal domain (CTD) []. This entry represents the central cysteine-rich (CR) domain of DnaJ proteins. This central cysteine rich domain (CR-type zinc finger) has an overall V-shaped extended beta-hairpin topology and contains four repeats of the motif CXXCXGXG where X is any amino acid. The isolated cysteine rich domain folds in zinc dependent fashion. Each set of two repeats binds one unit of zinc. Although this domain has been implicated in substrate binding, no evidence of specific interaction between the isolated DnaJ cysteine rich domain and various hydrophobic peptides has been found [].; GO: 0031072 heat shock protein binding, 0051082 unfolded protein binding; PDB: 1NLT_A 2CTT_A 1EXK_A.
Probab=27.22 E-value=88 Score=21.08 Aligned_cols=34 Identities=15% Similarity=0.179 Sum_probs=22.7
Q ss_pred ccceEcCCCCCCCceEe-------ccceEEEeccCCCcccc
Q 036389 155 YGICKCSRCGHKRMSFI-------PLRRHITCLNCYQYWAS 188 (198)
Q Consensus 155 t~~~~C~~C~~~~~~~~-------pmt~fv~C~~Cg~~W~~ 188 (198)
....+|+.|++.-.... .+.+..+|..|+-+=++
T Consensus 13 ~~~~~C~~C~G~G~~~~~~~~~~~~~~~~~~C~~C~G~G~~ 53 (66)
T PF00684_consen 13 KKPKTCPQCNGSGQVTRRQQTPGGVFQMQQTCPKCGGTGKI 53 (66)
T ss_dssp TT-EE-TTSSSSSEEEEEEESSSTTEEEEEE-TTTSSSSEE
T ss_pred CCCcCCcCCCCeeEEEEEEeCCCeEEEEEEECCCCcceeeE
Confidence 55679999999987766 45677889999765433
No 195
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=27.17 E-value=27 Score=23.84 Aligned_cols=11 Identities=36% Similarity=0.972 Sum_probs=9.1
Q ss_pred ccceEcCCCCC
Q 036389 155 YGICKCSRCGH 165 (198)
Q Consensus 155 t~~~~C~~C~~ 165 (198)
...++||+||.
T Consensus 15 E~~lrCPRC~~ 25 (65)
T COG4049 15 EEFLRCPRCGM 25 (65)
T ss_pred ceeeeCCchhH
Confidence 56789999984
No 196
>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=27.17 E-value=45 Score=20.03 Aligned_cols=12 Identities=25% Similarity=0.451 Sum_probs=6.0
Q ss_pred eEEEeccCCCcc
Q 036389 175 RHITCLNCYQYW 186 (198)
Q Consensus 175 ~fv~C~~Cg~~W 186 (198)
.+|+|.+|+..-
T Consensus 3 ~~~~C~nC~R~v 14 (33)
T PF08209_consen 3 PYVECPNCGRPV 14 (33)
T ss_dssp -EEE-TTTSSEE
T ss_pred CeEECCCCcCCc
Confidence 456666666543
No 197
>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=26.88 E-value=24 Score=28.70 Aligned_cols=31 Identities=19% Similarity=0.389 Sum_probs=19.7
Q ss_pred ccceEcCCCCCCCc-eEe---------ccceEEEeccCCCc
Q 036389 155 YGICKCSRCGHKRM-SFI---------PLRRHITCLNCYQY 185 (198)
Q Consensus 155 t~~~~C~~C~~~~~-~~~---------pmt~fv~C~~Cg~~ 185 (198)
...-.||.|+..=- .|+ +...---|.+||+.
T Consensus 37 ~tI~~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkp 77 (158)
T PF10083_consen 37 KTITSCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKP 77 (158)
T ss_pred HHHHHCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCC
Confidence 34457888887532 233 44444569999997
No 198
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=26.78 E-value=27 Score=28.82 Aligned_cols=32 Identities=25% Similarity=0.438 Sum_probs=22.2
Q ss_pred cccceEcCCCCCCCceEe-ccceEEEeccCCCcc
Q 036389 154 VYGICKCSRCGHKRMSFI-PLRRHITCLNCYQYW 186 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~~~~-pmt~fv~C~~Cg~~W 186 (198)
....|.|+.|.-+ -+|- .|..-++|..||.--
T Consensus 110 ~~~~y~C~~~~~r-~sfdeA~~~~F~Cp~Cg~~L 142 (176)
T COG1675 110 ENNYYVCPNCHVK-YSFDEAMELGFTCPKCGEDL 142 (176)
T ss_pred cCCceeCCCCCCc-ccHHHHHHhCCCCCCCCchh
Confidence 4567999766544 3343 777778899999753
No 199
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=26.46 E-value=34 Score=22.06 Aligned_cols=8 Identities=38% Similarity=1.439 Sum_probs=4.2
Q ss_pred eccCCCcc
Q 036389 179 CLNCYQYW 186 (198)
Q Consensus 179 C~~Cg~~W 186 (198)
|..|+..|
T Consensus 51 C~~C~~~~ 58 (64)
T PF01485_consen 51 CFKCGEPW 58 (64)
T ss_dssp CSSSTSES
T ss_pred ccccCccc
Confidence 44555555
No 200
>PF04676 CwfJ_C_2: Protein similar to CwfJ C-terminus 2; InterPro: IPR006767 This group of sequences contain a conserved C-terminal domain which is found in the Schizosaccharomyces pombe (Fission yeast) protein Cwf19 (Q09909 from SWISSPROT) and its homologues. Cwf19 is part of the Cdc5p complex involved in mRNA splicing []. This domain is found in association with IPR006768 from INTERPRO, which is generally N-terminal and adjacent to this domain.
Probab=26.09 E-value=51 Score=24.13 Aligned_cols=36 Identities=25% Similarity=0.254 Sum_probs=20.7
Q ss_pred CeEEEecCCCCCCCccccCCcHHHHHHHHHHHHHHh
Q 036389 1 YIHVIFSTNVPKASKVVKCNDCIREIVRKNLYGALS 36 (198)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~d~iR~k~r~~L~~aL~ 36 (198)
|+||+|+.+..-+..+.....=-++=.|+.|+..|.
T Consensus 29 Yf~V~~~~~~~~~~vie~~~~f~~qFgReVla~lL~ 64 (98)
T PF04676_consen 29 YFHVEFPDGKGYAHVIEDEERFPLQFGREVLAGLLN 64 (98)
T ss_pred EEEEEEeCCCEEEEECCcCCccCcchHHHHHHHHhC
Confidence 899999977622211111111124677788887664
No 201
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=25.70 E-value=17 Score=32.37 Aligned_cols=16 Identities=19% Similarity=0.447 Sum_probs=12.6
Q ss_pred cceEcCCCCCCCceEe
Q 036389 156 GICKCSRCGHKRMSFI 171 (198)
Q Consensus 156 ~~~~C~~C~~~~~~~~ 171 (198)
..-.||-||+.-+.-+
T Consensus 184 ~~~~CPvCGS~PvaSm 199 (308)
T COG3058 184 SRQYCPVCGSMPVASM 199 (308)
T ss_pred ccccCCCcCCCCccee
Confidence 4558999999977655
No 202
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=25.67 E-value=72 Score=24.85 Aligned_cols=32 Identities=16% Similarity=0.326 Sum_probs=23.7
Q ss_pred ccceEcCCCCCCCceEe--ccceEEEeccCCCcc
Q 036389 155 YGICKCSRCGHKRMSFI--PLRRHITCLNCYQYW 186 (198)
Q Consensus 155 t~~~~C~~C~~~~~~~~--pmt~fv~C~~Cg~~W 186 (198)
+-.++|.+|+...-+.. .-+..+.|..||.+-
T Consensus 110 ~~~y~C~~C~~~~~~~rr~~~~~~y~C~~C~g~l 143 (146)
T smart00731 110 KYPYRCTGCGQRYLRVRRSNNVSRYRCGKCGGKL 143 (146)
T ss_pred eEEEECCCCCCCCceEccccCcceEEcCCCCCEE
Confidence 45789999998765444 334788999999764
No 203
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=25.02 E-value=82 Score=19.67 Aligned_cols=26 Identities=27% Similarity=0.427 Sum_probs=13.7
Q ss_pred eEcCCCCCCCceE-ec---cceEEEeccCC
Q 036389 158 CKCSRCGHKRMSF-IP---LRRHITCLNCY 183 (198)
Q Consensus 158 ~~C~~C~~~~~~~-~p---mt~fv~C~~Cg 183 (198)
-.||.|+++.-.- ++ -+--..|..|+
T Consensus 4 ~pCP~CGG~DrFri~~d~~~~G~~~C~~C~ 33 (40)
T PF08273_consen 4 GPCPICGGKDRFRIFDDKDGRGTWICRQCG 33 (40)
T ss_dssp E--TTTT-TTTEEEETT----S-EEETTTT
T ss_pred CCCCCCcCccccccCcCcccCCCEECCCCC
Confidence 4799999887655 42 24455588884
No 204
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=24.95 E-value=45 Score=22.46 Aligned_cols=23 Identities=30% Similarity=0.566 Sum_probs=13.1
Q ss_pred ccceEcCCCCCCCceEeccceEEEeccCCC
Q 036389 155 YGICKCSRCGHKRMSFIPLRRHITCLNCYQ 184 (198)
Q Consensus 155 t~~~~C~~C~~~~~~~~pmt~fv~C~~Cg~ 184 (198)
+.+-+|+.||.. |..-.|-.||.
T Consensus 3 s~mr~C~~CgvY-------TLk~~CP~CG~ 25 (56)
T PRK13130 3 SKIRKCPKCGVY-------TLKEICPVCGG 25 (56)
T ss_pred ccceECCCCCCE-------EccccCcCCCC
Confidence 445567766653 33555666664
No 205
>PF02005 TRM: N2,N2-dimethylguanosine tRNA methyltransferase; InterPro: IPR002905 This enzyme 2.1.1.32 from EC uses S-adenosyl-L-methionine to methylate tRNA: S-AdoMet + tRNA = S-adenosyl-L-homocysteine + tRNA containing N2-methylguanine The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs []. The enzyme is found in both eukaryotes and archaea [].; GO: 0003723 RNA binding, 0004809 tRNA (guanine-N2-)-methyltransferase activity, 0008033 tRNA processing; PDB: 2YTZ_B 2DUL_A 2EJU_A 2EJT_A 3AXT_A 3AXS_A.
Probab=24.93 E-value=33 Score=31.44 Aligned_cols=35 Identities=20% Similarity=0.370 Sum_probs=20.7
Q ss_pred ccceEcCCCCCCCceEe--ccceEEEeccCCCccccccc
Q 036389 155 YGICKCSRCGHKRMSFI--PLRRHITCLNCYQYWASTNP 191 (198)
Q Consensus 155 t~~~~C~~C~~~~~~~~--pmt~fv~C~~Cg~~W~~~~~ 191 (198)
--.++|..|+.++...- +.. ..|..||.+|...-|
T Consensus 238 G~v~~C~~C~~~~~~~~~~~~~--~~c~~cg~~~~~~GP 274 (377)
T PF02005_consen 238 GYVYYCPSCGYREEVKGLQKLK--SKCPECGSKLHISGP 274 (377)
T ss_dssp EEEEEETTT--EECCT-GCC----CEETTT-SCCCEEEE
T ss_pred eEEEECCCccccccccCccccC--CcCCCCCCccceecC
Confidence 35689999975422111 222 789999999987765
No 206
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=24.83 E-value=39 Score=29.90 Aligned_cols=17 Identities=24% Similarity=0.419 Sum_probs=9.1
Q ss_pred ccceEcCCCCCCCceEe
Q 036389 155 YGICKCSRCGHKRMSFI 171 (198)
Q Consensus 155 t~~~~C~~C~~~~~~~~ 171 (198)
-+.++|+.||....++.
T Consensus 128 ~~r~~c~eCgk~ysT~s 144 (279)
T KOG2462|consen 128 HPRYKCPECGKSYSTSS 144 (279)
T ss_pred CCceecccccccccccc
Confidence 34555666655555444
No 207
>COG4098 comFA Superfamily II DNA/RNA helicase required for DNA uptake (late competence protein) [DNA replication, recombination, and repair]
Probab=24.83 E-value=35 Score=31.64 Aligned_cols=29 Identities=31% Similarity=0.817 Sum_probs=21.6
Q ss_pred cccceEcCCCCCCCceEe---ccceEEEeccCC
Q 036389 154 VYGICKCSRCGHKRMSFI---PLRRHITCLNCY 183 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~~~~---pmt~fv~C~~Cg 183 (198)
..+.+.|.+||...-.++ |.--+| |.+|-
T Consensus 36 ~~gk~~C~RC~~~~~~~~~~lp~~~~Y-Cr~Cl 67 (441)
T COG4098 36 ENGKYRCNRCGNTHIELFAKLPCGCLY-CRNCL 67 (441)
T ss_pred ccCcEEehhcCCcchhhhcccccceEe-ehhhh
Confidence 567899999997766555 777555 87774
No 208
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=24.43 E-value=26 Score=20.60 Aligned_cols=16 Identities=25% Similarity=0.540 Sum_probs=12.1
Q ss_pred cceEcCCCCCCCceEe
Q 036389 156 GICKCSRCGHKRMSFI 171 (198)
Q Consensus 156 ~~~~C~~C~~~~~~~~ 171 (198)
....||.||..+..|.
T Consensus 16 ~~~~CP~Cg~~~~~F~ 31 (33)
T cd00350 16 APWVCPVCGAPKDKFE 31 (33)
T ss_pred CCCcCcCCCCcHHHcE
Confidence 4578999998876653
No 209
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=24.29 E-value=23 Score=22.93 Aligned_cols=29 Identities=21% Similarity=0.480 Sum_probs=18.9
Q ss_pred cceEcCCCCCCCceEe----------cc-ceEEEeccCCCc
Q 036389 156 GICKCSRCGHKRMSFI----------PL-RRHITCLNCYQY 185 (198)
Q Consensus 156 ~~~~C~~C~~~~~~~~----------pm-t~fv~C~~Cg~~ 185 (198)
+.|+||=|+. .-... +. ..-|.|.-|..+
T Consensus 1 ~~f~CP~C~~-~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~ 40 (54)
T PF05605_consen 1 DSFTCPYCGK-GFSESSLVEHCEDEHRSESKNVVCPICSSR 40 (54)
T ss_pred CCcCCCCCCC-ccCHHHHHHHHHhHCcCCCCCccCCCchhh
Confidence 3588999988 54433 22 335788888864
No 210
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=23.98 E-value=35 Score=30.32 Aligned_cols=33 Identities=21% Similarity=0.337 Sum_probs=25.0
Q ss_pred ccceEcCCCCCCCceEe--ccceEEEeccCCCccccc
Q 036389 155 YGICKCSRCGHKRMSFI--PLRRHITCLNCYQYWAST 189 (198)
Q Consensus 155 t~~~~C~~C~~~~~~~~--pmt~fv~C~~Cg~~W~~~ 189 (198)
.-..+||.|+. .-|. =++.+..|.+|||..+.+
T Consensus 26 ~lw~KCp~c~~--~~y~~eL~~n~~vcp~c~~h~ri~ 60 (294)
T COG0777 26 GLWTKCPSCGE--MLYRKELESNLKVCPKCGHHMRIS 60 (294)
T ss_pred CceeECCCccc--eeeHHHHHhhhhcccccCcccccC
Confidence 45679999986 4566 456677899999987765
No 211
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=23.96 E-value=49 Score=32.17 Aligned_cols=44 Identities=30% Similarity=0.451 Sum_probs=36.3
Q ss_pred cccceEcCCCCCCCceEe---------------------------ccceEEEeccCCCcccccc-ccccccc
Q 036389 154 VYGICKCSRCGHKRMSFI---------------------------PLRRHITCLNCYQYWASTN-PEIRVLP 197 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~~~~---------------------------pmt~fv~C~~Cg~~W~~~~-~~~~~~~ 197 (198)
..+...|..|+.-+.+|- |-|.-++|-+|+..-+.++ |.+.+||
T Consensus 428 ~e~rlsC~~C~~v~ySye~~~~i~i~le~n~E~~di~~~v~a~f~pdtiE~~CenCk~K~~a~~k~~~kslP 499 (749)
T COG5207 428 VERRLSCSGCMDVSYSYESMLMICIFLEGNDEPQDIRKSVEAFFLPDTIEWSCENCKGKKKASRKPFIKSLP 499 (749)
T ss_pred hcceecccccccccccccceEEEEeecccCcchhhHHHHHHheECccceeeehhhhcCcccccccchhhccC
Confidence 456789999998887776 8899999999999888877 6666666
No 212
>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=23.72 E-value=68 Score=28.71 Aligned_cols=34 Identities=24% Similarity=0.503 Sum_probs=21.9
Q ss_pred cceEcCCCCCCCce-Ee---c-----cceEEEeccCCCccccc
Q 036389 156 GICKCSRCGHKRMS-FI---P-----LRRHITCLNCYQYWAST 189 (198)
Q Consensus 156 ~~~~C~~C~~~~~~-~~---p-----mt~fv~C~~Cg~~W~~~ 189 (198)
...+|+.||+.+-- |+ + --.--+|..|+..+|.-
T Consensus 223 ~R~~C~~Cg~~~~l~y~~~e~~~~~~~~r~e~C~~C~~YlK~~ 265 (305)
T TIGR01562 223 VRVKCSHCEESKHLAYLSLEHDAEKAVLKAETCDSCQGYLKIL 265 (305)
T ss_pred cCccCCCCCCCCceeeEeecCCCCCcceEEeeccccccchhhh
Confidence 34578888876542 33 1 23445799999888864
No 213
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=23.66 E-value=42 Score=16.88 Aligned_cols=7 Identities=43% Similarity=1.345 Sum_probs=2.8
Q ss_pred eEcCCCC
Q 036389 158 CKCSRCG 164 (198)
Q Consensus 158 ~~C~~C~ 164 (198)
|+|+.|+
T Consensus 1 ~~C~~C~ 7 (24)
T PF13894_consen 1 FQCPICG 7 (24)
T ss_dssp EE-SSTS
T ss_pred CCCcCCC
Confidence 3455544
No 214
>PRK08173 DNA topoisomerase III; Validated
Probab=23.58 E-value=91 Score=31.82 Aligned_cols=27 Identities=22% Similarity=0.434 Sum_probs=17.9
Q ss_pred eEcCCCCCCCceEeccceEEEeccCCCc-cc
Q 036389 158 CKCSRCGHKRMSFIPLRRHITCLNCYQY-WA 187 (198)
Q Consensus 158 ~~C~~C~~~~~~~~pmt~fv~C~~Cg~~-W~ 187 (198)
..||+||+.- .--..++.|.+|+.. |+
T Consensus 625 ~~CP~Cg~~~---~~~~~~~~Cs~C~f~~~~ 652 (862)
T PRK08173 625 TPCPNCGGVV---KENYRRFACTKCDFSISK 652 (862)
T ss_pred ccCCcccccc---cccCceeEcCCCCcccch
Confidence 5799999742 111234789999865 75
No 215
>cd06891 PX_Vps17p The phosphoinositide binding Phox Homology domain of yeast sorting nexin Vps17p. The PX domain is a phosphoinositide (PI) binding module present in many proteins with diverse functions. Sorting nexins (SNXs) make up the largest group among PX domain containing proteins. They are involved in regulating membrane traffic and protein sorting in the endosomal system. The PX domain of SNXs binds PIs and targets the protein to PI-enriched membranes. SNXs differ from each other in PI-binding specificity and affinity, and the presence of other protein-protein interaction domains, which help determine subcellular localization and specific function in the endocytic pathway. Vsp17p forms a dimer with Vps5p, the yeast counterpart of human SNX1, and is part of the retromer complex that mediates the transport of the carboxypeptidase Y receptor Vps10p from endosomes to Golgi. Similar to Vps5p and SNX1, Vps17p harbors a Bin/Amphiphysin/Rvs (BAR) domain, which detects membrane curvatur
Probab=23.43 E-value=1.4e+02 Score=23.70 Aligned_cols=41 Identities=10% Similarity=0.020 Sum_probs=32.8
Q ss_pred eEEEecCCCCCCCccccCCcHHHHHHHHHHHHHHhhhhhhc
Q 036389 2 IHVIFSTNVPKASKVVKCNDCIREIVRKNLYGALSKVSIEA 42 (198)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~d~iR~k~r~~L~~aL~~~~~e~ 42 (198)
.-++.|+-|++++.....+++-+.+-+..|..-|..+..++
T Consensus 85 ~~~iVPplP~k~~~~~~~~~E~~~~rr~~LqrfL~RV~~hP 125 (140)
T cd06891 85 PETFVPALPLPSTSYGSNNEEDARKLKANLQRWFNRVCSDP 125 (140)
T ss_pred CCcEeCCCCCccccCCCCCHHHHHHHHHHHHHHHHHHhCCh
Confidence 34788999999988778888888888888888888765544
No 216
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=23.43 E-value=33 Score=30.12 Aligned_cols=31 Identities=19% Similarity=0.477 Sum_probs=24.5
Q ss_pred ccceEcCCCCCCCceEeccceEEEeccCCCc
Q 036389 155 YGICKCSRCGHKRMSFIPLRRHITCLNCYQY 185 (198)
Q Consensus 155 t~~~~C~~C~~~~~~~~pmt~fv~C~~Cg~~ 185 (198)
-+.|.|++|+..=..|-.|-.---|..||+.
T Consensus 153 ~aef~C~~C~h~F~G~~qm~v~sPCy~C~~~ 183 (278)
T PF15135_consen 153 IAEFHCPKCRHNFRGFAQMGVPSPCYGCGNP 183 (278)
T ss_pred eeeeecccccccchhhhhcCCCCCccCCCCc
Confidence 5779999999887777777777778888874
No 217
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=23.25 E-value=43 Score=25.10 Aligned_cols=24 Identities=29% Similarity=0.807 Sum_probs=18.8
Q ss_pred EcCCCCCCCceEe--ccceEEEeccCC
Q 036389 159 KCSRCGHKRMSFI--PLRRHITCLNCY 183 (198)
Q Consensus 159 ~C~~C~~~~~~~~--pmt~fv~C~~Cg 183 (198)
.|..|+.+...|. ..-+|+ |..|.
T Consensus 5 ~CaDC~~~~p~w~s~~~Gifv-C~~Cs 30 (112)
T smart00105 5 KCFDCGAPNPTWASVNLGVFL-CIECS 30 (112)
T ss_pred cccCCCCCCCCcEEeccceeE-hHHhH
Confidence 6889999888887 556666 88775
No 218
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=22.85 E-value=41 Score=21.71 Aligned_cols=16 Identities=25% Similarity=0.540 Sum_probs=10.3
Q ss_pred ccceEcCCCCCCCceE
Q 036389 155 YGICKCSRCGHKRMSF 170 (198)
Q Consensus 155 t~~~~C~~C~~~~~~~ 170 (198)
-+.+.||.|+..|-.|
T Consensus 32 p~~w~CP~C~a~K~~F 47 (47)
T PF00301_consen 32 PDDWVCPVCGAPKSDF 47 (47)
T ss_dssp -TT-B-TTTSSBGGGE
T ss_pred CCCCcCcCCCCccccC
Confidence 3558999999988654
No 219
>PF08421 Methyltransf_13: Putative zinc binding domain; InterPro: IPR013630 This domain is found at the N terminus of bacterial methyltransferases. ; PDB: 4E2X_A 3NDJ_A 3NDI_A 4E32_A 4E33_A 4E31_A 4E2Y_A 4E2W_A 4E2Z_A 4E30_A.
Probab=22.71 E-value=61 Score=21.76 Aligned_cols=12 Identities=33% Similarity=0.744 Sum_probs=5.9
Q ss_pred ccceEEEeccCCC
Q 036389 172 PLRRHITCLNCYQ 184 (198)
Q Consensus 172 pmt~fv~C~~Cg~ 184 (198)
|+..++ |..||.
T Consensus 37 pL~l~~-C~~Cgl 48 (62)
T PF08421_consen 37 PLDLYV-CEDCGL 48 (62)
T ss_dssp EEEEEE-ETTT--
T ss_pred CCEEEE-CCCCCc
Confidence 555544 666664
No 220
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=22.62 E-value=66 Score=32.26 Aligned_cols=72 Identities=11% Similarity=0.259 Sum_probs=36.8
Q ss_pred CCchhcccCCHHhhcc-----HH-HHHHHHHHhcccccccccccccccCCCcccccceEcCCCCCC----Cc----eEec
Q 036389 107 VKPETIVNMTAKEMAS-----DK-MQLWYENSRKGRAETNGRIFSGLVSPKNIVYGICKCSRCGHK----RM----SFIP 172 (198)
Q Consensus 107 isp~~lv~Ms~eELas-----~e-~k~~~e~~~~~e~~~~~~l~~~~~~~~~~~t~~~~C~~C~~~----~~----~~~p 172 (198)
++.-.+++|..+.+.. .. +++.++.+.+ .. +.-++- .-.| -.....|+.||.. .| +|.-
T Consensus 386 ~p~v~iiDmr~e~~~~~~~lS~~Ll~~i~~~l~~-ge--Q~llfl---nRRG-ys~~l~C~~Cg~v~~Cp~Cd~~lt~H~ 458 (730)
T COG1198 386 LPRVEIIDMRKEPLETGRSLSPALLEAIRKTLER-GE--QVLLFL---NRRG-YAPLLLCRDCGYIAECPNCDSPLTLHK 458 (730)
T ss_pred CCcceEEeccccccccCccCCHHHHHHHHHHHhc-CC--eEEEEE---ccCC-ccceeecccCCCcccCCCCCcceEEec
Confidence 5567788999888877 34 4444444444 21 111211 1123 2334566666642 22 2224
Q ss_pred cceEEEeccCCCc
Q 036389 173 LRRHITCLNCYQY 185 (198)
Q Consensus 173 mt~fv~C~~Cg~~ 185 (198)
-+....|.-||++
T Consensus 459 ~~~~L~CH~Cg~~ 471 (730)
T COG1198 459 ATGQLRCHYCGYQ 471 (730)
T ss_pred CCCeeEeCCCCCC
Confidence 4456667777765
No 221
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=22.43 E-value=22 Score=31.60 Aligned_cols=31 Identities=23% Similarity=0.473 Sum_probs=21.7
Q ss_pred ceEcCCCCCCCceEe-cc-ceEEEeccCCCccccc
Q 036389 157 ICKCSRCGHKRMSFI-PL-RRHITCLNCYQYWAST 189 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~-pm-t~fv~C~~Cg~~W~~~ 189 (198)
-.+|+.|+.- -|. .. ..+..|.+|||.++.+
T Consensus 27 ~~~c~~c~~~--~~~~~l~~~~~vc~~c~~h~rl~ 59 (292)
T PRK05654 27 WTKCPSCGQV--LYRKELEANLNVCPKCGHHMRIS 59 (292)
T ss_pred eeECCCccch--hhHHHHHhcCCCCCCCCCCeeCC
Confidence 6799999873 333 22 2456799999988754
No 222
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=22.41 E-value=88 Score=21.96 Aligned_cols=29 Identities=21% Similarity=0.542 Sum_probs=17.1
Q ss_pred ceEcCCCCCCCceEe-ccceEEEeccCCCccccc
Q 036389 157 ICKCSRCGHKRMSFI-PLRRHITCLNCYQYWAST 189 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~-pmt~fv~C~~Cg~~W~~~ 189 (198)
.|.| +||. ..|. ..+.-=+| .||.+-+.-
T Consensus 3 ifrC-~Cgr--~lya~e~~kTkkC-~CG~~l~vk 32 (68)
T PF09082_consen 3 IFRC-DCGR--YLYAKEGAKTKKC-VCGKTLKVK 32 (68)
T ss_dssp EEEE-TTS----EEEETT-SEEEE-TTTEEEE--
T ss_pred EEEe-cCCC--EEEecCCcceeEe-cCCCeeeee
Confidence 4888 6875 3555 55555678 999886653
No 223
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=22.26 E-value=1.4e+02 Score=23.14 Aligned_cols=32 Identities=31% Similarity=0.581 Sum_probs=22.8
Q ss_pred cccceEcCCCCCCCc----eEe-----------------------ccceEEEeccCCCc
Q 036389 154 VYGICKCSRCGHKRM----SFI-----------------------PLRRHITCLNCYQY 185 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~----~~~-----------------------pmt~fv~C~~Cg~~ 185 (198)
..+.|.|..||..-= .|- -+++-|.|.+||.-
T Consensus 30 ~~G~Y~C~~Cg~pLF~S~~KfdSg~GWPSF~~~i~~~v~~~~D~~~~RtEv~C~~C~~H 88 (119)
T PRK05508 30 EKGTYVCKQCGAPLYRSEDKFKSGCGWPSFDDEIKGAVKRIPDADGRRTEIVCANCGGH 88 (119)
T ss_pred CCeEEEecCCCCccccccccccCCCCCcccCcccccceEEEecCCCcEEEEEeCCCCCc
Confidence 578999999997521 111 33688999999854
No 224
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=22.25 E-value=44 Score=28.69 Aligned_cols=29 Identities=24% Similarity=0.620 Sum_probs=22.4
Q ss_pred cceEcCCCCCCCceEe----ccceEEEeccCCCc
Q 036389 156 GICKCSRCGHKRMSFI----PLRRHITCLNCYQY 185 (198)
Q Consensus 156 ~~~~C~~C~~~~~~~~----pmt~fv~C~~Cg~~ 185 (198)
-...|+.|....--|. |...|| |.+|.+-
T Consensus 191 ~alIC~~C~hhngl~~~~ek~~~efi-C~~Cn~~ 223 (251)
T COG5415 191 KALICPQCHHHNGLYRLAEKPIIEFI-CPHCNHK 223 (251)
T ss_pred hhhccccccccccccccccccchhee-cccchhh
Confidence 4568999998877776 777555 9999863
No 225
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=22.12 E-value=68 Score=29.57 Aligned_cols=34 Identities=15% Similarity=0.176 Sum_probs=25.1
Q ss_pred cccceEcCCCCCCCceEe-c----cceEEEeccCCCccc
Q 036389 154 VYGICKCSRCGHKRMSFI-P----LRRHITCLNCYQYWA 187 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~~~~-p----mt~fv~C~~Cg~~W~ 187 (198)
-|+.-+|+.|++.-.... . +....+|..|+-+=+
T Consensus 156 gt~~~tC~tC~G~G~v~~~~~~g~~~~~~~C~~C~G~G~ 194 (371)
T COG0484 156 GTDPKTCPTCNGSGQVRTVQRTGFFSFQQTCPTCNGTGK 194 (371)
T ss_pred CCCCCcCCCCCCcCeEEEEEeeeEEEEEEECCCCcccee
Confidence 356779999999877666 4 667788998875533
No 226
>PF14237 DUF4339: Domain of unknown function (DUF4339)
Probab=21.93 E-value=65 Score=19.96 Aligned_cols=20 Identities=30% Similarity=0.599 Sum_probs=16.8
Q ss_pred HHHHHHhhcCCCCchhcccC
Q 036389 96 HEFRKKVLLGDVKPETIVNM 115 (198)
Q Consensus 96 p~Lr~~vl~G~isp~~lv~M 115 (198)
.+|+.-+-+|+|++..||--
T Consensus 17 ~el~~l~~~g~i~~~tlvw~ 36 (45)
T PF14237_consen 17 EELRQLISSGEIDPDTLVWK 36 (45)
T ss_pred HHHHHHHHcCCCCCCCeEeC
Confidence 47888899999999998753
No 227
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=21.92 E-value=50 Score=27.47 Aligned_cols=66 Identities=14% Similarity=0.365 Sum_probs=39.4
Q ss_pred CCchhcccCCHHhhccHHHHHHHHHHhccccccccccccccc-CCCcccccceEcCCCCCCCceEe-ccceEEEeccCCC
Q 036389 107 VKPETIVNMTAKEMASDKMQLWYENSRKGRAETNGRIFSGLV-SPKNIVYGICKCSRCGHKRMSFI-PLRRHITCLNCYQ 184 (198)
Q Consensus 107 isp~~lv~Ms~eELas~e~k~~~e~~~~~e~~~~~~l~~~~~-~~~~~~t~~~~C~~C~~~~~~~~-pmt~fv~C~~Cg~ 184 (198)
.|..+|+....-+|+.. +++..+...+ - +..... ..+| |.|.-|++.+.-|- ...+-+.|..|+.
T Consensus 114 YSl~DL~~v~~G~L~~~-L~~l~~~~~~-H------V~~C~lC~~kG-----fiCe~C~~~~~IfPF~~~~~~~C~~C~~ 180 (202)
T PF13901_consen 114 YSLADLVQVKSGQLLPQ-LEKLVQFAEK-H------VYSCELCQQKG-----FICEICNSDDIIFPFQIDTTVRCPKCKS 180 (202)
T ss_pred EcHHHHHHHhhchHHHH-HHHHHHHHHH-H------HHHhHHHHhCC-----CCCccCCCCCCCCCCCCCCeeeCCcCcc
Confidence 55666666655555442 3333333333 1 234444 5555 89999998855554 5557888999985
Q ss_pred c
Q 036389 185 Y 185 (198)
Q Consensus 185 ~ 185 (198)
-
T Consensus 181 v 181 (202)
T PF13901_consen 181 V 181 (202)
T ss_pred c
Confidence 3
No 228
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=21.90 E-value=57 Score=21.85 Aligned_cols=22 Identities=36% Similarity=0.798 Sum_probs=9.8
Q ss_pred EcCCCCCCCceEeccceEEEeccCC
Q 036389 159 KCSRCGHKRMSFIPLRRHITCLNCY 183 (198)
Q Consensus 159 ~C~~C~~~~~~~~pmt~fv~C~~Cg 183 (198)
.|+.||.+ |.|-...|.|..||
T Consensus 7 ~C~~Cg~~---~~~~dDiVvCp~Cg 28 (54)
T PF14446_consen 7 KCPVCGKK---FKDGDDIVVCPECG 28 (54)
T ss_pred cChhhCCc---ccCCCCEEECCCCC
Confidence 44444443 22334445555554
No 229
>PRK05776 DNA topoisomerase I; Provisional
Probab=21.78 E-value=99 Score=30.57 Aligned_cols=79 Identities=13% Similarity=0.264 Sum_probs=39.7
Q ss_pred HHhhcCCCCchhcccCCHHhhccHHHHHHHHHHhccccccccccccccc-CCCcccccceEcCCCCCCCc-----eEe-c
Q 036389 100 KKVLLGDVKPETIVNMTAKEMASDKMQLWYENSRKGRAETNGRIFSGLV-SPKNIVYGICKCSRCGHKRM-----SFI-P 172 (198)
Q Consensus 100 ~~vl~G~isp~~lv~Ms~eELas~e~k~~~e~~~~~e~~~~~~l~~~~~-~~~~~~t~~~~C~~C~~~~~-----~~~-p 172 (198)
..|..|+++.++++.-.-+.+ .+.+.+..+.+.+ +.+... .... .+....||+||+.-| .+. .
T Consensus 548 d~I~~G~~~~~~vl~~~~~~~-~~~~~~~~~~~~~--------i~~~l~~~~~~-~~~~~~Cp~Cg~~l~~~~~~~~~~~ 617 (670)
T PRK05776 548 EMIRTGKATREEVIEEAKETL-NKLLEEFKKNKDE--------IGEELAKALGL-IKPVGKCKICGREAYKDGLCKYHYE 617 (670)
T ss_pred HHHHcCCCCHHHHHHHHHHHH-HHHHHHHHHHHHH--------HHHHHHhhccC-cCCCCcCCCCCCccccCceEEeccc
Confidence 567788888877766444333 2233333322222 111110 1111 222368999998652 222 2
Q ss_pred c-ceEEEecc---CCCcccc
Q 036389 173 L-RRHITCLN---CYQYWAS 188 (198)
Q Consensus 173 m-t~fv~C~~---Cg~~W~~ 188 (198)
. ..|+-|.+ |.+..-+
T Consensus 618 ~~~~f~~c~~~p~c~~~~~~ 637 (670)
T PRK05776 618 AKKRLVKAYEEWKERTGYDH 637 (670)
T ss_pred CCccceecCCCccccCCCCc
Confidence 2 35888885 7765433
No 230
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=21.78 E-value=31 Score=22.54 Aligned_cols=17 Identities=24% Similarity=0.415 Sum_probs=13.3
Q ss_pred ccceEcCCCCCCCceEe
Q 036389 155 YGICKCSRCGHKRMSFI 171 (198)
Q Consensus 155 t~~~~C~~C~~~~~~~~ 171 (198)
-+.+.||.|+..|..|.
T Consensus 32 p~~w~CP~C~a~K~~F~ 48 (50)
T cd00730 32 PDDWVCPVCGAGKDDFE 48 (50)
T ss_pred CCCCCCCCCCCcHHHcE
Confidence 35589999999887663
No 231
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=21.67 E-value=2.7e+02 Score=22.41 Aligned_cols=37 Identities=14% Similarity=0.095 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHhhhhhhccccchhhhhhcccChHHHHHHHHHHHHHHh
Q 036389 24 REIVRKNLYGALSKVSIEAAHDKNVIDQVKACNPIQVAISMESAMYEKW 72 (198)
Q Consensus 24 R~k~r~~L~~aL~~~~~e~~~~~~~~~~~~~~~~~~~A~~IE~alf~~~ 72 (198)
|+|.+..|..|+.+..... .....++..||..|.+..
T Consensus 63 r~Kl~~gl~~Ac~KRpVs~------------e~ie~~v~~Ie~~l~~~~ 99 (147)
T TIGR00244 63 REKLLRGMVRACEKRPVSF------------DDLEHAINHIEAQLRAQG 99 (147)
T ss_pred HHHHHHHHHHHhcCCCCCH------------HHHHHHHHHHHHHHHHcC
Confidence 8999999999999864211 123678899999998765
No 232
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=21.63 E-value=22 Score=31.69 Aligned_cols=31 Identities=16% Similarity=0.320 Sum_probs=22.2
Q ss_pred ceEcCCCCCCCceEe-cc-ceEEEeccCCCccccc
Q 036389 157 ICKCSRCGHKRMSFI-PL-RRHITCLNCYQYWAST 189 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~-pm-t~fv~C~~Cg~~W~~~ 189 (198)
-.+|+.|+.- -|. .. ..+..|.+|||..+.+
T Consensus 38 w~kc~~C~~~--~~~~~l~~~~~vcp~c~~h~rlt 70 (296)
T CHL00174 38 WVQCENCYGL--NYKKFLKSKMNICEQCGYHLKMS 70 (296)
T ss_pred eeECCCccch--hhHHHHHHcCCCCCCCCCCcCCC
Confidence 5789999864 333 44 4567899999987754
No 233
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=21.59 E-value=40 Score=28.22 Aligned_cols=38 Identities=18% Similarity=0.277 Sum_probs=26.2
Q ss_pred cccceEcCCCCCCCc--eEeccceEEEeccCC--Cccccccc
Q 036389 154 VYGICKCSRCGHKRM--SFIPLRRHITCLNCY--QYWASTNP 191 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~--~~~pmt~fv~C~~Cg--~~W~~~~~ 191 (198)
.-+...|..||+... +|.|..-.+.|..|+ +.+..+..
T Consensus 146 ~p~l~~C~~Cg~~~~~~~f~~~~gg~~c~~c~~~~~~~l~~~ 187 (247)
T PRK00085 146 GLDLDHCAVCGAPGDHRYFSPKEGGAVCSECGDPYAIKLLPL 187 (247)
T ss_pred ccchhhHhcCCCCCCceEEecccCCcccccccCccccccCcc
Confidence 345568999998754 333888888899996 34444443
No 234
>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=21.50 E-value=2.1e+02 Score=26.27 Aligned_cols=65 Identities=12% Similarity=0.086 Sum_probs=45.8
Q ss_pred HHHHHHHHHHHHHhCCCcHHHHHHHHHHHHhcCCCCCHHHHHHhhcCCCCchhcccCCHHhhccHH
Q 036389 59 QVAISMESAMYEKWGRSSETYKFKYRRLLFNFNDPKNHEFRKKVLLGDVKPETIVNMTAKEMASDK 124 (198)
Q Consensus 59 ~~A~~IE~alf~~~~~~~~~Yk~k~Rsl~~NLkd~kNp~Lr~~vl~G~isp~~lv~Ms~eELas~e 124 (198)
..-..||..+...-.+ ..-|+.|.|.-+.-+++-.+.+.-..+..+.---++++...+.|+|-++
T Consensus 253 ~~~etLEqq~~~L~~n-iDIL~~k~~eal~~~~n~~~~~~D~~~~~~~~l~kq~l~~~A~d~aieD 317 (365)
T KOG2391|consen 253 AMKETLEQQLQSLQKN-IDILKSKVREALEKAENLEALDIDEAIECTAPLYKQILECYALDLAIED 317 (365)
T ss_pred HHHHHHHHHHHHHHhh-hHHHHHHHHHHHhhhccCcCCCchhhhhccchHHHHHHHhhhhhhHHHH
Confidence 4445677777654322 3579999999555555555666667777777777888999999999885
No 235
>PF07742 BTG: BTG family; InterPro: IPR002087 Anti-proliferative proteins have been shown to include mammalian and avian protein BTG1 (which appears to be involved in negative regulation of cell proliferation) and rat/mouse NGF-inducible protein PC3/TIS21 (BTG2) [, , ]. These proteins have from 158 to 363 amino acid residues, that are highly similar and include 3 conserved cysteine residues. BTG2 seems to have a signal sequence; while the other proteins may lack such a domain. The sequence of the N-terminal half of these proteins is well conserved.; PDB: 3DJU_B 3E9V_A 2Z15_D 2D5R_B 3DJN_B.
Probab=21.46 E-value=47 Score=25.53 Aligned_cols=57 Identities=12% Similarity=0.123 Sum_probs=36.2
Q ss_pred hHHHHHHHHHHHHHHhCC----CcHHHHHHHHHHHHhcCCCCCHHHHHHhhcCCCCchhcc
Q 036389 57 PIQVAISMESAMYEKWGR----SSETYKFKYRRLLFNFNDPKNHEFRKKVLLGDVKPETIV 113 (198)
Q Consensus 57 ~~~~A~~IE~alf~~~~~----~~~~Yk~k~Rsl~~NLkd~kNp~Lr~~vl~G~isp~~lv 113 (198)
+..++..+++.|...|.+ .+...-+-+|.|..|=..+..|.|.+.-..-.|+.++|.
T Consensus 27 ~~~F~~~L~~~L~~ry~~HW~P~~P~kGsayRcIrin~~~~~Dp~l~~Aa~~sgl~~~~l~ 87 (118)
T PF07742_consen 27 VDRFAEELENLLCERYKGHWYPENPSKGSAYRCIRINPGHKMDPVLEQAAKESGLSYEDLR 87 (118)
T ss_dssp HHHHHHHHHHHHHHHHTTS--TTSTTTTHHHH-EEES--SSB-HHHHHHHHHTT--HHHHH
T ss_pred HHHHHHHHHHHHHHHHhCCCCCCCCCCCCceEEEEEcCCCCCCHHHHHHHHHhCCCHHHHH
Confidence 578999999999999864 234455678888777545577888776555555555554
No 236
>PF05952 ComX: Bacillus competence pheromone ComX; InterPro: IPR009233 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. Natural genetic competence in Bacillus subtilis is controlled by quorum-sensing (QS). The ComP- ComA two-component system detects the signalling molecule ComX, and this signal is transduced by a conserved phosphotransfer mechanism. ComX is synthesised as an inactive precursor and is then cleaved and modified by ComQ before export to the extracellular environment [].
Probab=21.44 E-value=61 Score=21.95 Aligned_cols=30 Identities=13% Similarity=0.294 Sum_probs=22.2
Q ss_pred HHHHHhcCCCCCHHHHHHhhcCCCCchhcccCCHH
Q 036389 84 RRLLFNFNDPKNHEFRKKVLLGDVKPETIVNMTAK 118 (198)
Q Consensus 84 Rsl~~NLkd~kNp~Lr~~vl~G~isp~~lv~Ms~e 118 (198)
..++..|- +||++..+|.+|+.+ |+..+..
T Consensus 3 Q~iV~YLv--~nPevl~kl~~g~as---LIGv~~~ 32 (57)
T PF05952_consen 3 QEIVNYLV--QNPEVLEKLKEGEAS---LIGVDKD 32 (57)
T ss_pred HHHHHHHH--HChHHHHHHHcCCee---EecCCHH
Confidence 34566666 899999999999876 4555544
No 237
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=21.28 E-value=42 Score=18.55 Aligned_cols=8 Identities=38% Similarity=1.149 Sum_probs=4.0
Q ss_pred eEcCCCCC
Q 036389 158 CKCSRCGH 165 (198)
Q Consensus 158 ~~C~~C~~ 165 (198)
.+|+.||.
T Consensus 3 ~~C~~CgR 10 (25)
T PF13913_consen 3 VPCPICGR 10 (25)
T ss_pred CcCCCCCC
Confidence 44555553
No 238
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=21.27 E-value=48 Score=30.24 Aligned_cols=17 Identities=12% Similarity=0.366 Sum_probs=14.7
Q ss_pred ccceE------EEeccCCCcccc
Q 036389 172 PLRRH------ITCLNCYQYWAS 188 (198)
Q Consensus 172 pmt~f------v~C~~Cg~~W~~ 188 (198)
||..| |.|-.|++|+|=
T Consensus 388 ~~~~F~~~~KPYrCevC~KRYKN 410 (423)
T COG5189 388 KMNIFSAKDKPYRCEVCDKRYKN 410 (423)
T ss_pred ccccccccCCceeccccchhhcc
Confidence 78888 899999999873
No 239
>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=21.20 E-value=60 Score=19.61 Aligned_cols=7 Identities=29% Similarity=0.781 Sum_probs=3.1
Q ss_pred eccCCCc
Q 036389 179 CLNCYQY 185 (198)
Q Consensus 179 C~~Cg~~ 185 (198)
|.+||..
T Consensus 35 C~~CGE~ 41 (46)
T TIGR03831 35 CPQCGEE 41 (46)
T ss_pred cccCCCE
Confidence 4444443
No 240
>KOG1914 consensus mRNA cleavage and polyadenylation factor I complex, subunit RNA14 [RNA processing and modification]
Probab=20.97 E-value=2e+02 Score=28.33 Aligned_cols=41 Identities=24% Similarity=0.391 Sum_probs=36.0
Q ss_pred CcHHHHHHHHHHHHhcCCCCCH-HHHHHhhcCCCCchhcccC
Q 036389 75 SSETYKFKYRRLLFNFNDPKNH-EFRKKVLLGDVKPETIVNM 115 (198)
Q Consensus 75 ~~~~Yk~k~Rsl~~NLkd~kNp-~Lr~~vl~G~isp~~lv~M 115 (198)
.+..|..++-..+.+|.|.+|. .|.++++...++|++...|
T Consensus 433 d~p~yv~~YldfL~~lNdd~N~R~LFEr~l~s~l~~~ks~~I 474 (656)
T KOG1914|consen 433 DSPEYVLKYLDFLSHLNDDNNARALFERVLTSVLSADKSKEI 474 (656)
T ss_pred CChHHHHHHHHHHHHhCcchhHHHHHHHHHhccCChhhhHHH
Confidence 4579999999999999998887 8999999999998877665
No 241
>TIGR00357 methionine-R-sulfoxide reductase. This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested.
Probab=20.93 E-value=1.9e+02 Score=22.92 Aligned_cols=13 Identities=31% Similarity=0.424 Sum_probs=11.2
Q ss_pred cccceEcCCCCCC
Q 036389 154 VYGICKCSRCGHK 166 (198)
Q Consensus 154 ~t~~~~C~~C~~~ 166 (198)
..+.|.|..||..
T Consensus 37 ~~G~Y~C~~Cg~p 49 (134)
T TIGR00357 37 EEGIYVDITCGEP 49 (134)
T ss_pred CCeEEEccCCCCc
Confidence 5889999999975
No 242
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.87 E-value=59 Score=24.98 Aligned_cols=53 Identities=17% Similarity=0.269 Sum_probs=30.2
Q ss_pred HHHHHHHHHHhCCCcHHHHHHHHHHHHhcCCCCCH------HHHHHhhcCCCCchhcccC
Q 036389 62 ISMESAMYEKWGRSSETYKFKYRRLLFNFNDPKNH------EFRKKVLLGDVKPETIVNM 115 (198)
Q Consensus 62 ~~IE~alf~~~~~~~~~Yk~k~Rsl~~NLkd~kNp------~Lr~~vl~G~isp~~lv~M 115 (198)
.+||+.+-..|.....+.-.-+|.+-+|- |..|+ ++...|-.|+|+|++-+.|
T Consensus 61 KEvEr~lg~sYptvR~kld~vlramgy~p-~~e~~~~i~~~~i~~qle~Gei~peeA~~~ 119 (122)
T COG3877 61 KEVERELGISYPTVRTKLDEVLRAMGYNP-DSENSVNIGKKKIIDQLEKGEISPEEAIKM 119 (122)
T ss_pred HHHHHHHCCccHHHHHHHHHHHHHcCCCC-CCCChhhhhHHHHHHHHHcCCCCHHHHHHH
Confidence 46777765554333333333334333332 22333 4788899999999987655
No 243
>PHA02325 hypothetical protein
Probab=20.87 E-value=39 Score=23.61 Aligned_cols=9 Identities=33% Similarity=1.077 Sum_probs=6.6
Q ss_pred EeccCCCcc
Q 036389 178 TCLNCYQYW 186 (198)
Q Consensus 178 ~C~~Cg~~W 186 (198)
+|.+||.+|
T Consensus 5 ~CPkC~A~W 13 (72)
T PHA02325 5 ICPKCGARW 13 (72)
T ss_pred ccCccCCEe
Confidence 477777777
No 244
>KOG2041 consensus WD40 repeat protein [General function prediction only]
Probab=20.72 E-value=1.3e+02 Score=30.76 Aligned_cols=14 Identities=21% Similarity=0.546 Sum_probs=11.6
Q ss_pred ccc--eEEEeccCCCc
Q 036389 172 PLR--RHITCLNCYQY 185 (198)
Q Consensus 172 pmt--~fv~C~~Cg~~ 185 (198)
|.| +|-.|..|.|+
T Consensus 1150 pIt~~~fWlC~~CkH~ 1165 (1189)
T KOG2041|consen 1150 PITDNIFWLCPRCKHR 1165 (1189)
T ss_pred ccccceEEEccccccc
Confidence 665 79999999886
No 245
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=20.66 E-value=46 Score=26.21 Aligned_cols=13 Identities=31% Similarity=0.703 Sum_probs=4.9
Q ss_pred eEEEeccCCCccc
Q 036389 175 RHITCLNCYQYWA 187 (198)
Q Consensus 175 ~fv~C~~Cg~~W~ 187 (198)
.+++|+.||+.+|
T Consensus 71 d~i~clecGk~~k 83 (132)
T PF05443_consen 71 DYIICLECGKKFK 83 (132)
T ss_dssp S-EE-TBT--EES
T ss_pred CeeEEccCCcccc
Confidence 4555666665544
No 246
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.59 E-value=49 Score=23.88 Aligned_cols=13 Identities=15% Similarity=0.465 Sum_probs=10.0
Q ss_pred ceEEEeccCCCcc
Q 036389 174 RRHITCLNCYQYW 186 (198)
Q Consensus 174 t~fv~C~~Cg~~W 186 (198)
|.-|.|.+|||+.
T Consensus 10 tY~Y~c~~cg~~~ 22 (82)
T COG2331 10 TYSYECTECGNRF 22 (82)
T ss_pred ceEEeecccchHH
Confidence 4567899999875
No 247
>PRK01402 hslO Hsp33-like chaperonin; Reviewed
Probab=20.58 E-value=42 Score=30.26 Aligned_cols=41 Identities=22% Similarity=0.459 Sum_probs=32.0
Q ss_pred cccceEcCCCCCCCceEe----------c----cceEEEeccCCCccccccccccc
Q 036389 154 VYGICKCSRCGHKRMSFI----------P----LRRHITCLNCYQYWASTNPEIRV 195 (198)
Q Consensus 154 ~t~~~~C~~C~~~~~~~~----------p----mt~fv~C~~Cg~~W~~~~~~~~~ 195 (198)
..-.|.|+ |...++.=. - -..-|+|.=||..+.|++.+|.|
T Consensus 273 ~~v~f~C~-CSrerv~~~L~~Lg~~El~~mie~g~iev~CeFC~~~Y~f~~~el~~ 327 (328)
T PRK01402 273 QPVIARCS-CSREKIAGVLKGFSAEERADMVEDGKISVTCEFCSRVYRFDPAEVGV 327 (328)
T ss_pred cccceeCC-CCHHHHHHHHHhcCHHHHHHHHhCCCEEEEeeCCCCEEEeCHHHhCc
Confidence 45668998 877665433 2 25789999999999999999876
No 248
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=20.33 E-value=45 Score=25.37 Aligned_cols=15 Identities=20% Similarity=0.986 Sum_probs=12.6
Q ss_pred ceEcCCCCCCCceEe
Q 036389 157 ICKCSRCGHKRMSFI 171 (198)
Q Consensus 157 ~~~C~~C~~~~~~~~ 171 (198)
+--||+||.++-.|.
T Consensus 20 l~GCp~CG~nkF~yv 34 (112)
T COG3364 20 LSGCPKCGCNKFLYV 34 (112)
T ss_pred HccCccccchheEec
Confidence 346999999998887
No 249
>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=20.03 E-value=59 Score=22.56 Aligned_cols=29 Identities=31% Similarity=0.485 Sum_probs=16.6
Q ss_pred cceEcCCCCCC-----CceEe-------ccceEEEeccCCC
Q 036389 156 GICKCSRCGHK-----RMSFI-------PLRRHITCLNCYQ 184 (198)
Q Consensus 156 ~~~~C~~C~~~-----~~~~~-------pmt~fv~C~~Cg~ 184 (198)
...-|.+||.- .++.. --...++|..|||
T Consensus 45 kr~~Ck~C~~~liPG~~~~vri~~~~~~~~~l~~~C~~C~~ 85 (85)
T PF04032_consen 45 KRTICKKCGSLLIPGVNCSVRIRKKKKKKNFLVYTCLNCGH 85 (85)
T ss_dssp CCTB-TTT--B--CTTTEEEEEE---SSS-EEEEEETTTTE
T ss_pred hcccccCCCCEEeCCCccEEEEEecCCCCCEEEEEccccCC
Confidence 34589999973 23333 2347789999996
Done!