Query 017510
Match_columns 370
No_of_seqs 279 out of 986
Neff 6.3
Searched_HMMs 46136
Date Fri Mar 29 09:12:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/017510.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/017510hhsearch_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 1.1E-65 2.4E-70 497.1 24.6 292 7-361 3-299 (299)
2 KOG1105 Transcription elongati 100.0 1.2E-60 2.6E-65 456.1 22.2 288 8-361 2-296 (296)
3 smart00510 TFS2M Domain in the 100.0 3.7E-28 7.9E-33 201.4 9.7 101 190-297 1-101 (102)
4 PF07500 TFIIS_M: Transcriptio 99.9 9.6E-28 2.1E-32 202.8 5.6 115 188-309 1-115 (115)
5 smart00509 TFS2N Domain in the 99.7 1.8E-17 3.9E-22 130.1 5.6 74 8-84 1-74 (75)
6 cd00183 TFIIS_I N-terminal dom 99.6 2E-15 4.4E-20 118.7 5.4 72 10-84 5-76 (76)
7 smart00440 ZnF_C2C2 C2C2 Zinc 99.4 3.5E-13 7.7E-18 93.2 3.3 34 325-359 1-39 (40)
8 PF08711 Med26: TFIIS helical 99.4 2.5E-13 5.3E-18 99.5 2.4 52 33-84 1-53 (53)
9 PF01096 TFIIS_C: Transcriptio 99.3 5.4E-13 1.2E-17 91.8 3.3 34 325-359 1-39 (39)
10 KOG1634 Predicted transcriptio 99.3 6.9E-13 1.5E-17 140.5 5.1 83 223-305 268-351 (778)
11 COG1594 RPB9 DNA-directed RNA 99.2 8.3E-12 1.8E-16 105.4 3.3 40 321-361 69-113 (113)
12 KOG2906 RNA polymerase III sub 99.2 6.5E-12 1.4E-16 101.5 2.3 37 322-359 63-104 (105)
13 PHA02998 RNA polymerase subuni 99.1 8.5E-11 1.8E-15 104.8 3.5 36 323-359 142-182 (195)
14 TIGR01384 TFS_arch transcripti 99.0 1.4E-10 3E-15 96.3 4.0 38 322-360 60-102 (104)
15 KOG2691 RNA polymerase II subu 98.7 8.3E-09 1.8E-13 85.0 2.9 39 320-359 69-112 (113)
16 KOG2907 RNA polymerase I trans 98.6 1.4E-08 2.9E-13 84.5 0.8 38 321-359 71-113 (116)
17 PF11467 LEDGF: Lens epitheliu 96.7 0.0015 3.3E-08 54.7 3.6 78 2-84 1-80 (106)
18 KOG2821 RNA polymerase II tran 96.7 0.00076 1.7E-08 68.6 1.8 74 5-86 7-80 (433)
19 KOG1793 Uncharacterized conser 95.6 0.013 2.9E-07 58.9 4.4 55 31-85 235-292 (417)
20 PF09855 DUF2082: Nucleic-acid 95.1 0.017 3.7E-07 44.1 2.6 32 325-357 1-45 (64)
21 PF08274 PhnA_Zn_Ribbon: PhnA 94.9 0.013 2.8E-07 38.1 1.2 28 325-359 3-30 (30)
22 COG5139 Uncharacterized conser 94.6 0.04 8.6E-07 53.6 4.3 54 32-85 233-288 (397)
23 COG3478 Predicted nucleic-acid 94.2 0.03 6.6E-07 42.5 1.9 34 323-357 3-49 (68)
24 TIGR00686 phnA alkylphosphonat 93.7 0.039 8.4E-07 46.1 1.8 30 325-361 3-32 (109)
25 PF13719 zinc_ribbon_5: zinc-r 93.1 0.045 9.7E-07 37.1 1.1 34 324-360 2-37 (37)
26 COG4332 Uncharacterized protei 92.5 0.077 1.7E-06 48.3 2.1 49 311-361 6-62 (203)
27 TIGR02098 MJ0042_CXXC MJ0042 f 92.4 0.12 2.5E-06 34.9 2.4 35 324-360 2-37 (38)
28 PRK10220 hypothetical protein; 92.1 0.083 1.8E-06 44.2 1.7 31 325-362 4-34 (111)
29 PF13717 zinc_ribbon_4: zinc-r 92.1 0.079 1.7E-06 35.7 1.3 34 324-359 2-36 (36)
30 PRK09678 DNA-binding transcrip 91.8 0.16 3.5E-06 39.7 2.9 38 324-362 1-43 (72)
31 KOG3507 DNA-directed RNA polym 90.5 0.15 3.2E-06 38.1 1.4 32 319-357 15-46 (62)
32 PHA00626 hypothetical protein 90.5 0.2 4.3E-06 37.1 2.1 32 326-359 2-34 (59)
33 PF06044 DRP: Dam-replacing fa 89.9 0.15 3.2E-06 48.6 1.3 35 324-360 31-65 (254)
34 TIGR02443 conserved hypothetic 89.7 0.3 6.4E-06 36.6 2.5 34 325-361 10-44 (59)
35 PF04606 Ogr_Delta: Ogr/Delta- 89.3 0.36 7.7E-06 34.4 2.6 34 326-361 1-40 (47)
36 PF05129 Elf1: Transcription e 89.1 0.38 8.2E-06 38.4 2.9 45 323-370 21-67 (81)
37 PF11781 RRN7: RNA polymerase 88.6 0.31 6.8E-06 32.9 1.8 26 324-357 8-34 (36)
38 smart00659 RPOLCX RNA polymera 88.5 0.37 8.1E-06 34.0 2.2 27 324-357 2-28 (44)
39 PF03604 DNA_RNApol_7kD: DNA d 88.3 0.32 7E-06 32.0 1.7 26 325-357 1-26 (32)
40 COG4888 Uncharacterized Zn rib 88.3 0.45 9.7E-06 39.4 2.9 37 324-360 22-58 (104)
41 PF14353 CpXC: CpXC protein 87.7 0.57 1.2E-05 40.0 3.4 38 325-362 2-52 (128)
42 PLN02976 amine oxidase 87.0 0.74 1.6E-05 54.1 4.7 59 31-89 1303-1362(1713)
43 PF08271 TF_Zn_Ribbon: TFIIB z 86.9 0.63 1.4E-05 32.3 2.6 30 325-359 1-30 (43)
44 PF09526 DUF2387: Probable met 86.7 0.58 1.3E-05 36.4 2.6 33 325-361 9-43 (71)
45 PF12760 Zn_Tnp_IS1595: Transp 86.6 0.74 1.6E-05 32.4 2.9 28 325-357 19-46 (46)
46 COG2051 RPS27A Ribosomal prote 84.0 0.73 1.6E-05 35.3 1.9 30 323-357 18-47 (67)
47 KOG1886 BAH domain proteins [T 84.0 0.28 6.1E-06 50.8 -0.4 165 186-365 238-409 (464)
48 PF14354 Lar_restr_allev: Rest 81.7 1.6 3.5E-05 32.2 3.0 33 323-356 2-37 (61)
49 smart00661 RPOL9 RNA polymeras 80.8 1.3 2.8E-05 31.5 2.1 34 326-363 2-35 (52)
50 COG1997 RPL43A Ribosomal prote 79.9 1.6 3.5E-05 35.3 2.6 30 323-359 34-64 (89)
51 PF10571 UPF0547: Uncharacteri 78.6 0.96 2.1E-05 28.4 0.7 24 326-359 2-25 (26)
52 PRK00432 30S ribosomal protein 78.3 1.5 3.3E-05 31.7 1.9 29 324-359 20-48 (50)
53 PF13453 zf-TFIIB: Transcripti 77.8 2 4.4E-05 29.4 2.3 32 326-363 1-34 (41)
54 TIGR03655 anti_R_Lar restricti 77.2 3 6.6E-05 30.2 3.2 32 325-358 2-36 (53)
55 PF04216 FdhE: Protein involve 76.5 1.7 3.6E-05 42.5 2.1 37 323-360 171-209 (290)
56 COG4734 ArdA Antirestriction p 75.8 0.27 5.9E-06 44.2 -3.2 41 324-366 16-65 (193)
57 PF05180 zf-DNL: DNL zinc fing 75.1 1.4 3E-05 33.9 1.0 34 324-358 4-39 (66)
58 PF07282 OrfB_Zn_ribbon: Putat 74.1 2.1 4.6E-05 32.3 1.7 29 324-358 28-56 (69)
59 TIGR02300 FYDLN_acid conserved 73.3 2 4.3E-05 37.1 1.6 32 324-362 9-40 (129)
60 PRK00415 rps27e 30S ribosomal 73.0 3.1 6.7E-05 31.3 2.3 31 323-358 10-40 (59)
61 PF10080 DUF2318: Predicted me 72.7 2.5 5.4E-05 35.2 2.0 35 321-362 32-66 (102)
62 smart00531 TFIIE Transcription 72.5 3 6.4E-05 36.7 2.5 39 321-360 96-135 (147)
63 PRK03564 formate dehydrogenase 72.5 2.5 5.5E-05 41.9 2.3 37 323-360 186-224 (309)
64 COG2888 Predicted Zn-ribbon RN 72.4 2.3 5.1E-05 31.9 1.5 38 319-357 22-59 (61)
65 PF09723 Zn-ribbon_8: Zinc rib 71.5 3.7 8.1E-05 28.4 2.3 30 323-356 4-34 (42)
66 PF09538 FYDLN_acid: Protein o 70.8 2.7 5.9E-05 35.3 1.8 31 324-361 9-39 (108)
67 PRK05978 hypothetical protein; 70.7 2 4.3E-05 38.2 1.0 35 324-365 33-69 (148)
68 smart00834 CxxC_CXXC_SSSS Puta 69.9 4.3 9.3E-05 27.2 2.4 30 323-356 4-34 (41)
69 COG2824 PhnA Uncharacterized Z 69.4 2.9 6.2E-05 35.0 1.6 30 324-360 3-32 (112)
70 PF01667 Ribosomal_S27e: Ribos 68.4 3.1 6.7E-05 30.8 1.4 30 324-358 7-36 (55)
71 PF15135 UPF0515: Uncharacteri 68.3 5.1 0.00011 38.4 3.2 17 348-364 155-171 (278)
72 PF07295 DUF1451: Protein of u 66.7 4.5 9.8E-05 35.8 2.4 36 317-358 105-140 (146)
73 PRK09710 lar restriction allev 66.1 6.4 0.00014 30.1 2.8 35 323-360 5-39 (64)
74 PF01873 eIF-5_eIF-2B: Domain 66.1 6.6 0.00014 33.9 3.3 31 324-357 93-123 (125)
75 PTZ00083 40S ribosomal protein 65.6 5.2 0.00011 32.2 2.3 31 323-358 34-64 (85)
76 PLN00209 ribosomal protein S27 65.2 5.3 0.00011 32.2 2.3 31 323-358 35-65 (86)
77 PF08792 A2L_zn_ribbon: A2L zi 65.1 5.9 0.00013 26.2 2.1 30 323-358 2-31 (33)
78 PRK00398 rpoP DNA-directed RNA 64.6 4.3 9.3E-05 28.4 1.5 29 324-358 3-31 (46)
79 COG3677 Transposase and inacti 64.1 4.6 0.0001 34.9 2.0 38 321-360 27-65 (129)
80 COG1996 RPC10 DNA-directed RNA 63.5 4.6 9.9E-05 29.2 1.5 31 322-358 4-34 (49)
81 TIGR01206 lysW lysine biosynth 63.3 5.4 0.00012 29.4 1.9 33 324-360 2-34 (54)
82 PF03811 Zn_Tnp_IS1: InsA N-te 62.3 8.1 0.00017 26.1 2.4 32 322-354 3-35 (36)
83 PRK14892 putative transcriptio 62.0 6.7 0.00015 32.5 2.5 34 323-360 20-54 (99)
84 PRK03954 ribonuclease P protei 61.7 7.9 0.00017 33.3 2.9 37 323-360 63-105 (121)
85 COG1779 C4-type Zn-finger prot 61.3 8 0.00017 35.9 3.1 40 320-359 10-54 (201)
86 PRK03988 translation initiatio 60.9 7.4 0.00016 34.1 2.7 32 323-357 101-132 (138)
87 PF01780 Ribosomal_L37ae: Ribo 60.9 14 0.0003 30.2 4.0 29 323-358 34-63 (90)
88 PF09332 Mcm10: Mcm10 replicat 59.8 3.3 7.1E-05 41.7 0.3 10 348-357 285-294 (344)
89 TIGR01562 FdhE formate dehydro 58.6 4.8 0.0001 39.9 1.2 37 323-360 183-222 (305)
90 PF02701 zf-Dof: Dof domain, z 58.3 4.7 0.0001 30.6 0.8 41 323-364 4-46 (63)
91 KOG0909 Peptide:N-glycanase [P 58.1 9.4 0.0002 39.5 3.2 102 247-360 90-206 (500)
92 PRK14890 putative Zn-ribbon RN 57.9 9.7 0.00021 28.6 2.4 34 322-357 23-57 (59)
93 TIGR00373 conserved hypothetic 57.9 7.1 0.00015 34.8 2.1 34 321-359 106-139 (158)
94 KOG2879 Predicted E3 ubiquitin 57.0 5.5 0.00012 38.8 1.3 37 320-357 235-285 (298)
95 smart00653 eIF2B_5 domain pres 56.8 10 0.00022 32.0 2.7 32 323-357 79-110 (110)
96 PRK03976 rpl37ae 50S ribosomal 56.6 22 0.00047 29.1 4.4 30 323-358 35-64 (90)
97 PF01396 zf-C4_Topoisom: Topoi 56.5 13 0.00029 25.3 2.8 29 325-357 2-33 (39)
98 TIGR00280 L37a ribosomal prote 56.4 21 0.00046 29.2 4.4 30 323-358 34-63 (91)
99 PRK06266 transcription initiat 55.7 9.6 0.00021 34.7 2.6 35 321-360 114-148 (178)
100 PF05876 Terminase_GpA: Phage 55.7 7.5 0.00016 41.6 2.2 35 324-359 200-240 (557)
101 PF14726 RTTN_N: Rotatin, an a 55.7 11 0.00024 31.1 2.7 53 25-77 44-96 (98)
102 TIGR02605 CxxC_CxxC_SSSS putat 55.1 10 0.00022 26.9 2.2 30 323-356 4-34 (52)
103 PRK11032 hypothetical protein; 54.1 9.5 0.00021 34.3 2.2 35 318-358 118-152 (160)
104 PHA02942 putative transposase; 52.4 6.6 0.00014 40.0 1.1 27 324-358 325-352 (383)
105 PRK04338 N(2),N(2)-dimethylgua 50.8 7.8 0.00017 39.5 1.3 36 324-366 244-279 (382)
106 PF09332 Mcm10: Mcm10 replicat 50.5 4.4 9.6E-05 40.8 -0.5 37 320-362 281-318 (344)
107 PTZ00255 60S ribosomal protein 50.5 30 0.00064 28.3 4.3 29 323-358 35-64 (90)
108 TIGR00311 aIF-2beta translatio 49.6 14 0.0003 32.2 2.5 32 323-357 96-127 (133)
109 PF13248 zf-ribbon_3: zinc-rib 49.5 7.1 0.00015 24.1 0.5 23 325-357 3-25 (26)
110 PRK00420 hypothetical protein; 49.0 11 0.00023 32.1 1.6 29 324-359 23-51 (112)
111 COG0675 Transposase and inacti 48.7 20 0.00043 34.4 3.7 59 284-358 274-332 (364)
112 PF04032 Rpr2: RNAse P Rpr2/Rp 47.9 66 0.0014 24.9 6.0 33 323-356 45-85 (85)
113 PF07754 DUF1610: Domain of un 47.1 12 0.00025 23.1 1.2 12 321-332 13-24 (24)
114 PRK12495 hypothetical protein; 46.7 6.2 0.00013 37.2 -0.1 33 319-359 37-69 (226)
115 PF13240 zinc_ribbon_2: zinc-r 46.7 7.9 0.00017 23.4 0.4 6 351-356 16-21 (23)
116 KOG4274 Positive cofactor 2 (P 46.4 25 0.00055 37.6 4.2 66 190-269 9-74 (742)
117 PRK12336 translation initiatio 46.3 17 0.00036 33.8 2.7 32 323-357 97-128 (201)
118 TIGR02159 PA_CoA_Oxy4 phenylac 46.2 9.7 0.00021 33.7 1.0 34 324-359 105-141 (146)
119 PF14803 Nudix_N_2: Nudix N-te 45.6 19 0.00042 24.0 2.1 27 327-358 3-32 (34)
120 PF04216 FdhE: Protein involve 44.5 14 0.00031 35.9 2.0 41 322-362 209-252 (290)
121 TIGR00100 hypA hydrogenase nic 43.6 11 0.00024 31.8 1.0 30 320-357 66-95 (115)
122 PF11648 RIG-I_C-RD: C-termina 43.2 11 0.00023 32.3 0.8 13 348-360 60-72 (123)
123 TIGR00373 conserved hypothetic 42.7 11 0.00024 33.6 0.8 17 348-364 109-125 (158)
124 COG2023 RPR2 RNase P subunit R 42.6 13 0.00029 31.1 1.3 34 324-361 56-95 (105)
125 KOG3352 Cytochrome c oxidase, 42.6 17 0.00036 32.4 1.9 34 325-360 112-145 (153)
126 KOG1779 40s ribosomal protein 42.4 32 0.0007 27.3 3.3 57 285-356 5-61 (84)
127 PF01921 tRNA-synt_1f: tRNA sy 42.4 29 0.00062 35.3 3.8 56 291-360 153-211 (360)
128 PF12773 DZR: Double zinc ribb 41.6 14 0.00029 26.0 1.0 34 322-362 10-47 (50)
129 KOG3277 Uncharacterized conser 41.4 12 0.00027 33.4 0.9 36 323-359 78-115 (165)
130 PRK06266 transcription initiat 40.7 12 0.00027 34.0 0.9 17 348-364 117-133 (178)
131 COG1645 Uncharacterized Zn-fin 40.0 16 0.00034 31.9 1.3 32 321-360 25-56 (131)
132 PRK12380 hydrogenase nickel in 39.9 14 0.00029 31.2 0.9 29 320-356 66-94 (113)
133 COG4957 Predicted transcriptio 39.8 12 0.00027 32.7 0.6 14 347-360 75-88 (148)
134 PF11792 Baculo_LEF5_C: Baculo 38.2 6.6 0.00014 27.7 -1.0 25 330-356 13-42 (43)
135 PF14311 DUF4379: Domain of un 37.6 18 0.00038 26.2 1.1 14 348-361 28-41 (55)
136 COG3529 Predicted nucleic-acid 37.3 7.7 0.00017 29.3 -0.8 33 325-360 11-44 (66)
137 PF05443 ROS_MUCR: ROS/MUCR tr 37.1 15 0.00032 32.1 0.7 14 347-360 71-84 (132)
138 PRK03824 hypA hydrogenase nick 36.8 23 0.00049 30.8 1.8 11 322-332 68-78 (135)
139 smart00531 TFIIE Transcription 36.4 18 0.00038 31.7 1.1 17 348-364 99-115 (147)
140 PRK03681 hypA hydrogenase nick 36.0 15 0.00033 30.9 0.7 31 320-357 66-96 (114)
141 PF06397 Desulfoferrod_N: Desu 35.5 17 0.00038 24.6 0.7 12 348-359 6-17 (36)
142 PF01927 Mut7-C: Mut7-C RNAse 35.2 25 0.00054 30.8 1.9 33 324-357 91-133 (147)
143 COG4481 Uncharacterized protei 34.6 40 0.00087 25.0 2.5 27 329-359 18-45 (60)
144 COG2816 NPY1 NTP pyrophosphohy 34.4 20 0.00044 35.0 1.3 30 322-358 110-139 (279)
145 PF10058 DUF2296: Predicted in 34.4 25 0.00055 25.8 1.5 30 324-356 22-52 (54)
146 PRK00564 hypA hydrogenase nick 34.1 16 0.00034 31.0 0.4 31 320-357 67-97 (117)
147 COG1656 Uncharacterized conser 33.0 19 0.00042 32.5 0.8 38 322-359 95-142 (165)
148 PF06107 DUF951: Bacterial pro 32.9 46 0.00099 24.9 2.6 28 330-361 16-44 (57)
149 PF02172 KIX: KIX domain; Int 32.4 2E+02 0.0043 23.0 6.4 66 187-258 9-76 (81)
150 TIGR00515 accD acetyl-CoA carb 32.3 10 0.00022 37.2 -1.2 32 324-361 26-58 (285)
151 PF14690 zf-ISL3: zinc-finger 32.1 45 0.00098 22.9 2.5 12 325-336 3-14 (47)
152 COG2331 Uncharacterized protei 32.0 7 0.00015 30.9 -1.9 36 320-359 8-44 (82)
153 PF09297 zf-NADH-PPase: NADH p 31.8 28 0.00061 22.4 1.2 27 326-358 5-31 (32)
154 COG3809 Uncharacterized protei 31.2 38 0.00082 27.0 2.1 35 325-364 2-37 (88)
155 smart00401 ZnF_GATA zinc finge 31.1 21 0.00045 25.9 0.6 31 325-360 4-37 (52)
156 PRK03564 formate dehydrogenase 30.1 49 0.0011 32.9 3.1 41 321-362 223-266 (309)
157 COG1579 Zn-ribbon protein, pos 29.4 12 0.00026 35.9 -1.2 37 320-357 193-230 (239)
158 KOG3214 Uncharacterized Zn rib 28.7 38 0.00081 28.2 1.7 46 323-369 22-67 (109)
159 cd00674 LysRS_core_class_I cat 28.6 45 0.00098 33.7 2.7 32 324-360 169-204 (353)
160 CHL00174 accD acetyl-CoA carbo 28.5 13 0.00027 36.8 -1.3 34 323-361 37-70 (296)
161 PF13408 Zn_ribbon_recom: Reco 28.3 60 0.0013 23.0 2.7 32 322-356 3-34 (58)
162 PLN03119 putative ADP-ribosyla 27.7 78 0.0017 34.1 4.3 30 324-357 23-52 (648)
163 PRK05654 acetyl-CoA carboxylas 27.4 17 0.00037 35.7 -0.5 33 324-361 27-59 (292)
164 PRK12775 putative trifunctiona 27.4 40 0.00086 38.8 2.3 49 319-369 791-842 (1006)
165 TIGR01562 FdhE formate dehydro 26.2 58 0.0012 32.4 2.9 42 321-363 221-267 (305)
166 PRK14714 DNA polymerase II lar 25.7 31 0.00068 40.3 1.1 21 58-78 237-261 (1337)
167 smart00778 Prim_Zn_Ribbon Zinc 25.4 61 0.0013 22.0 2.0 29 325-356 4-33 (37)
168 PF14255 Cys_rich_CPXG: Cystei 25.4 79 0.0017 23.1 2.7 35 325-360 1-36 (52)
169 TIGR03830 CxxCG_CxxCG_HTH puta 25.1 46 0.001 27.6 1.8 12 348-359 31-42 (127)
170 PF02591 DUF164: Putative zinc 25.1 14 0.0003 26.9 -1.3 33 323-356 21-54 (56)
171 TIGR00319 desulf_FeS4 desulfof 24.8 38 0.00081 22.1 0.9 12 348-359 7-18 (34)
172 smart00731 SprT SprT homologue 24.8 60 0.0013 28.2 2.5 33 322-359 110-144 (146)
173 PF10122 Mu-like_Com: Mu-like 24.6 43 0.00093 24.5 1.2 30 324-360 4-36 (51)
174 KOG2593 Transcription initiati 24.3 50 0.0011 34.2 2.1 37 320-357 124-162 (436)
175 cd00974 DSRD Desulforedoxin (D 24.2 39 0.00085 22.0 0.9 12 348-359 4-15 (34)
176 PF03589 Antiterm: Antitermina 23.9 24 0.00052 28.9 -0.2 31 326-357 7-41 (95)
177 COG1198 PriA Primosomal protei 23.9 78 0.0017 35.2 3.6 17 274-290 386-402 (730)
178 PF05605 zf-Di19: Drought indu 23.8 17 0.00037 26.2 -1.0 34 323-357 1-40 (54)
179 COG4049 Uncharacterized protei 23.8 30 0.00064 25.9 0.3 11 348-358 17-27 (65)
180 COG3058 FdhE Uncharacterized p 23.1 33 0.00072 33.6 0.5 18 323-340 184-201 (308)
181 COG5415 Predicted integral mem 22.8 51 0.0011 31.1 1.7 34 322-357 190-223 (251)
182 TIGR01031 rpmF_bact ribosomal 22.8 50 0.0011 24.3 1.3 24 322-356 24-47 (55)
183 PRK00762 hypA hydrogenase nick 22.4 34 0.00074 29.3 0.4 30 320-355 66-99 (124)
184 PF01783 Ribosomal_L32p: Ribos 22.1 41 0.00089 24.7 0.8 22 323-355 25-46 (56)
185 PF08273 Prim_Zn_Ribbon: Zinc- 22.0 57 0.0012 22.5 1.4 30 325-356 4-34 (40)
186 COG1096 Predicted RNA-binding 21.9 63 0.0014 29.9 2.1 36 323-366 148-184 (188)
187 COG0777 AccD Acetyl-CoA carbox 21.9 29 0.00063 34.0 -0.1 35 321-361 25-60 (294)
188 KOG2462 C2H2-type Zn-finger pr 21.7 24 0.00053 34.4 -0.7 34 325-358 216-253 (279)
189 PF02005 TRM: N2,N2-dimethylgu 21.6 29 0.00063 35.4 -0.2 39 323-366 239-277 (377)
190 PRK04860 hypothetical protein; 21.6 27 0.00059 31.3 -0.3 40 323-363 118-158 (160)
191 PF14446 Prok-RING_1: Prokaryo 21.2 70 0.0015 23.6 1.8 24 324-356 5-29 (54)
192 PRK04351 hypothetical protein; 21.0 71 0.0015 28.3 2.2 33 323-361 111-145 (149)
193 PRK04179 rpl37e 50S ribosomal 20.7 46 0.00099 25.3 0.7 25 323-356 16-40 (62)
194 PF14599 zinc_ribbon_6: Zinc-r 20.6 34 0.00073 25.9 0.0 28 322-356 28-56 (61)
195 COG1571 Predicted DNA-binding 20.2 41 0.00089 34.9 0.5 28 323-359 349-378 (421)
196 PRK14873 primosome assembly pr 20.1 1E+02 0.0022 34.0 3.5 17 271-287 327-343 (665)
197 cd00202 ZnF_GATA Zinc finger D 20.1 25 0.00055 25.7 -0.7 32 326-361 1-34 (54)
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=1.1e-65 Score=497.13 Aligned_cols=292 Identities=29% Similarity=0.405 Sum_probs=222.0
Q ss_pred HHHHHHHHHHHHHHhhcCcccHHHHHHHHHHhhcCCCCHhhhhccCceeecccccCCCCHHHHHHHHHHHHHHHHHHHhh
Q 017510 7 ELCEAAKRRAETAASAEGELEEAQCIAALDQLHKSSITCQLLVSTQLVRHLLPLTKHPRQKIQDTASELILSWRSLFLEQ 86 (370)
Q Consensus 7 el~~~a~k~~~~a~~~~~~~~~~~~l~~L~~L~~~~it~e~L~~T~IG~~V~~Lrkh~~~~I~~~Ak~Li~~WK~~v~~~ 86 (370)
|+...++ ++++++.. + ++++||++|++|+.++||.++|++|+||++||+||||++++|+.+|+.||++||++|..+
T Consensus 3 ei~~~~k-~L~k~~~~--~-~~~~~l~~L~~L~~~~~t~~lL~~T~IG~~Vn~lrkh~~~~I~~lAk~li~~WK~~v~~~ 78 (299)
T TIGR01385 3 EVASHAK-ALDKNKSS--K-NVEQCLDILHQLKEFPPTEELLQETKVGVKVNKLRKHPNEDISKLAKKIIKSWKKVVDKN 78 (299)
T ss_pred HHHHHHH-HhhhhccC--C-CHHHHHHHHHHHhcCCCcHHHHhhCchhHHHHHHHcCCcHHHHHHHHHHHHHHHHHHhhh
Confidence 3444444 55665442 2 567899999999999999999999999999999999999999999999999999999876
Q ss_pred cCCCCCCCCcccccccccchhhhhcccCCCCchhhhhhhhhhHhHhhhcCCCCCCCcccccCcccccccccccCCcchhh
Q 017510 87 MKGDEENGSFAICGEIKSANVEIAKGKRQITSDEFEQALDVEVVKVRRVDQKGAPRSKKLVGSEFIVTEETNSLDNVDAE 166 (370)
Q Consensus 87 ~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~ 166 (370)
+... ....+.. .....++.++.+. +..++ +.+. +
T Consensus 79 k~~~--~~~~~~~--~~~~~~~~~~~~~-------~~~~~------------~~~~-----------------------~ 112 (299)
T TIGR01385 79 KSDH--PGGNPED--KTTVGESVNSVKQ-------EAKSQ------------SDKI-----------------------E 112 (299)
T ss_pred cccC--ccccccc--ccccCCCCCCCCc-------cccCC------------cccc-----------------------c
Confidence 3321 1100000 0000000000000 00000 0000 0
Q ss_pred hhhccCCCCcCCCcccccccCCChHHHHHHHHHHHHHHhhhcCCCchhhhhhcCCCChHHHHHHHHHHHHHhhCCCchhh
Q 017510 167 AIREEKPASAVVPQKLVSMIKCNDYFRERIREKLYKALSKVSGEVDEEVQDKLNGCDPIRVAITAESLMFEKWGHSFGTY 246 (370)
Q Consensus 167 ~~~~~~~~~~~~~p~~~~~~~t~d~vR~k~r~lL~~aL~~~~~~~~~~~~~~~~~~~~~~~A~~IE~~if~~~~~~~~~Y 246 (370)
......+...+.++..+..+.++|++|++||+|||+||.....+++ ..+++..+|.+||.+||..|+.+++.|
T Consensus 113 ~~~~~~~~~~~~~~~~~~~~~t~d~~Rdk~r~~L~~aL~~~~~~~~-------~~~~~~~lA~~iE~~~f~~~~~~~~~Y 185 (299)
T TIGR01385 113 QPKYVSSSPRNAKNDFVPTAVTNDKVRDKCRELLYDALAKDSDHPP-------QSIDPEAKAIQIEELKFNNLGTTEAAY 185 (299)
T ss_pred CCCCCCCcccccCCCCCCCccCCcHHHHHHHHHHHHHHhhcCCCCc-------cccCHHHHHHHHHHHHHHHcCCCcHHH
Confidence 0000000000112222334589999999999999999997543322 234677899999999999999888899
Q ss_pred hHHHHhHHhhcCCCCChHhhhchhcCCCChhhhcCCChhhcCChHHHHHHHHHHHHHhhcccCcccCCCCCCcccccccc
Q 017510 247 EVKYRSILFNLMDPENPDFRRKVLLGHVKPEALIKMSSEEMVSDGSRRLNQQIKKERASDRYLPWKGGYLGPIYHSTRYM 326 (370)
Q Consensus 247 k~k~Rsl~~NLKd~kNp~Lr~~vl~G~isp~~lv~Ms~eEmas~e~k~~r~~~~~e~l~~~~l~~~~~~~~~~~~t~~~~ 326 (370)
+++||||+|||||++||+||++||+|+|+|++||.|+++||||+++|++++++.+++|+++|+++..+ +.|++|+
T Consensus 186 k~k~Rsl~~NLKd~kNp~Lr~~vl~G~i~p~~lv~Ms~eEmas~e~k~~~e~~~ke~l~~~~~~~~~~-----~~t~~~~ 260 (299)
T TIGR01385 186 KARYRSIYSNLRDKNNPDLRHNVLTGEITPEKLATMTAEEMASAELKQEREEITKENLFEAQGAKIQK-----AVTDLFT 260 (299)
T ss_pred HHHHHHHHHHccCCCCHHHHHHHHcCCCCHHHHhcCCHHHcCCHHHHHHHHHHHHHHHHHHHhhhhhc-----CCccccc
Confidence 99999999999999999999999999999999999999999999999999999999999998776544 8999999
Q ss_pred ccCCCCcceEEEeeccccCCC-----ceeccCCCCcceeh
Q 017510 327 CGRCGHKKTTNHGNDQNSSAK-----RIKCLNCYQYWEST 361 (370)
Q Consensus 327 C~~C~~~~~~~~q~~Q~RsaD-----f~~C~~Cg~~w~~~ 361 (370)
|++||+++|+|+|+ |||||| ||+|.+|||+|+||
T Consensus 261 C~~C~~~~~~~~q~-QtrsaDEpmT~f~~C~~Cg~~w~fc 299 (299)
T TIGR01385 261 CGKCKQKKCTYYQL-QTRSADEPMTTFVTCEECGNRWKFC 299 (299)
T ss_pred CCCCCCccceEEEe-cccCCCCCCeEEEEcCCCCCeeeeC
Confidence 99999999999999 999999 99999999999999
No 2
>KOG1105 consensus Transcription elongation factor TFIIS/Cofactor of enhancer-binding protein Sp1 [Transcription]
Probab=100.00 E-value=1.2e-60 Score=456.07 Aligned_cols=288 Identities=28% Similarity=0.433 Sum_probs=222.0
Q ss_pred HHHHHHHHHHHH-HhhcCcccHHHHHHHHHHhhcCCCCHhhhhccCceeecc-cccCCCCHHHHHHHHHHHHHHHHHHHh
Q 017510 8 LCEAAKRRAETA-ASAEGELEEAQCIAALDQLHKSSITCQLLVSTQLVRHLL-PLTKHPRQKIQDTASELILSWRSLFLE 85 (370)
Q Consensus 8 l~~~a~k~~~~a-~~~~~~~~~~~~l~~L~~L~~~~it~e~L~~T~IG~~V~-~Lrkh~~~~I~~~Ak~Li~~WK~~v~~ 85 (370)
+++.++|+|+.. ...++ +..+.++++|.+|++++||.++|++|+||+.|| .|++|++++|+++|+.||+.||++|..
T Consensus 2 ~~e~~~r~ak~l~~~~~~-~n~~~~ld~l~~L~~~pvt~ell~~Tr~g~~vn~~~Kk~~n~ev~~~ak~Lik~Wkk~~~~ 80 (296)
T KOG1105|consen 2 LEEEALRAAKALEKDKQS-KNVEAALDLLKRLKKIPVTLELLQETRTGMGVNEVLKKHKNEEVRSLAKKLIKSWKKLVDK 80 (296)
T ss_pred ccHHHHHHHHHHHhhccc-ccHHHHHHHHHHHHhcccHHHHHHHhhHHHHHHHHHHhCCCHHHHHHHHHHHHHHHHHhhc
Confidence 456666666665 22344 378999999999999999999999999999999 777899999999999999999999987
Q ss_pred hcCCCCCCCCcccccccccchhhhhcccCCCCchhhhhhhhhhHhHhhhcCCCCCCCcccccCcccccccccccCCcchh
Q 017510 86 QMKGDEENGSFAICGEIKSANVEIAKGKRQITSDEFEQALDVEVVKVRRVDQKGAPRSKKLVGSEFIVTEETNSLDNVDA 165 (370)
Q Consensus 86 ~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~ 165 (370)
.+... ..+.... ..|+.. +..+ ++++. .+..+. .+ ..
T Consensus 81 ~~~~~-k~~~~~~----------~~p~~~---~~~~----~s~~~-----~~~ks~----~~--------------~~-- 117 (296)
T KOG1105|consen 81 SPGRE-KSGDNKS----------HDPGEA---SSKS----PSGAK-----QPEKSR----GD--------------SK-- 117 (296)
T ss_pred ccccc-cCccccC----------CCCCcC---CcCC----ccCCC-----Cccccc----cc--------------cc--
Confidence 51111 0110000 011100 0000 00000 000000 00 00
Q ss_pred hhhhccCCCCcCCCcccccccCCChHHHHHHHHHHHHHHhhhcCCCchhhhhhcCCCChHHHHHHHHHHHHHhhCCCchh
Q 017510 166 EAIREEKPASAVVPQKLVSMIKCNDYFRERIREKLYKALSKVSGEVDEEVQDKLNGCDPIRVAITAESLMFEKWGHSFGT 245 (370)
Q Consensus 166 ~~~~~~~~~~~~~~p~~~~~~~t~d~vR~k~r~lL~~aL~~~~~~~~~~~~~~~~~~~~~~~A~~IE~~if~~~~~~~~~ 245 (370)
..++.+..+| .+.++|++|++|++|||+||... .+ .....+++..+|.+||.+||..++.++++
T Consensus 118 -----~~~~~~~~~~----~~~~~d~~r~k~~e~l~~al~~~-----~~--~~~~~~~~~~~a~~iE~~~~~~~g~~~~k 181 (296)
T KOG1105|consen 118 -----RDKHSGSKDP----VPITNDPVRDKCRELLYAALTTE-----DD--SRVTGADPLELAVQIEEAIFEKLGNTDSK 181 (296)
T ss_pred -----cccccCcCCC----CCCCCchHHHHHHHHHHHHhccc-----cc--ccccCCCHHHHHHHHHHHHHHHhCCCcHH
Confidence 0000000111 24568999999999999999842 11 12245677899999999999999999999
Q ss_pred hhHHHHhHHhhcCCCCChHhhhchhcCCCChhhhcCCChhhcCChHHHHHHHHHHHHHhhcccCcccCCCCCCccccccc
Q 017510 246 YEVKYRSILFNLMDPENPDFRRKVLLGHVKPEALIKMSSEEMVSDGSRRLNQQIKKERASDRYLPWKGGYLGPIYHSTRY 325 (370)
Q Consensus 246 Yk~k~Rsl~~NLKd~kNp~Lr~~vl~G~isp~~lv~Ms~eEmas~e~k~~r~~~~~e~l~~~~l~~~~~~~~~~~~t~~~ 325 (370)
|+++|||++|||+|++||+||++||+|+|+|++|+.|+++||||++++++++++.+++|++||++..++ ++||.|
T Consensus 182 yK~r~RS~~~NLkd~~Np~LR~~vl~G~i~pe~la~mt~eEMaS~~lk~~~~k~~keal~~~q~~~~~g-----t~td~f 256 (296)
T KOG1105|consen 182 YKNRYRSRVSNLKDKNNPDLRRNVLTGEISPERLATMTSEEMASEELKEERQKLTKEALREHQMAKIQG-----TQTDLF 256 (296)
T ss_pred HHHHHHHHhhccCCCCCHHHHHHHhcCCCCHHHhccCChhhhccHHHHHHHHHHHHHHHHHHhhccccc-----ccccce
Confidence 999999999999999999999999999999999999999999999999999999999999999875544 999999
Q ss_pred cccCCCCcceEEEeeccccCCC-----ceeccCCCCcceeh
Q 017510 326 MCGRCGHKKTTNHGNDQNSSAK-----RIKCLNCYQYWEST 361 (370)
Q Consensus 326 ~C~~C~~~~~~~~q~~Q~RsaD-----f~~C~~Cg~~w~~~ 361 (370)
+|++|++++|+|+|+ ||||+| ||+|.+|||+||||
T Consensus 257 kcgkckk~~cty~q~-Qtrs~DePmtTfv~C~ecgnrWkfc 296 (296)
T KOG1105|consen 257 KCGKCKKKNCTYTQL-QTRSADEPMTTFVTCNECGNRWKFC 296 (296)
T ss_pred eeccccccceeEEee-ccCCCCCCcceeeeecccCCccccC
Confidence 999999999999999 999999 99999999999999
No 3
>smart00510 TFS2M Domain in the central regions of transcription elongation factor S-II (and elsewhere).
Probab=99.95 E-value=3.7e-28 Score=201.36 Aligned_cols=101 Identities=42% Similarity=0.675 Sum_probs=91.6
Q ss_pred hHHHHHHHHHHHHHHhhhcCCCchhhhhhcCCCChHHHHHHHHHHHHHhhCCCchhhhHHHHhHHhhcCCCCChHhhhch
Q 017510 190 DYFRERIREKLYKALSKVSGEVDEEVQDKLNGCDPIRVAITAESLMFEKWGHSFGTYEVKYRSILFNLMDPENPDFRRKV 269 (370)
Q Consensus 190 d~vR~k~r~lL~~aL~~~~~~~~~~~~~~~~~~~~~~~A~~IE~~if~~~~~~~~~Yk~k~Rsl~~NLKd~kNp~Lr~~v 269 (370)
|++|++|+++|+++|..+...++. ..++..+|.+||.+||+.|+.++++|++++|||+|||||++||+||++|
T Consensus 1 d~~R~~~~~~L~~al~~~~~~~~~-------~~~~~~lA~~IE~~lf~~~~~~~~~Yk~k~Rsl~fNLkd~kN~~Lr~~v 73 (102)
T smart00510 1 DKVRDKCQEMLYKALQKISDPEEI-------ELDPTELAVQIEAEMFSEFGTTDKKYKNKYRSLYFNLKDKKNPDLRRKV 73 (102)
T ss_pred ChHHHHHHHHHHHHHHhcCCCCcc-------cccHHHHHHHHHHHHHHHcCCCcHHHHHHHHHHHHHhcCCCCHHHHHHH
Confidence 579999999999999986544321 2356789999999999999888889999999999999999999999999
Q ss_pred hcCCCChhhhcCCChhhcCChHHHHHHH
Q 017510 270 LLGHVKPEALIKMSSEEMVSDGSRRLNQ 297 (370)
Q Consensus 270 l~G~isp~~lv~Ms~eEmas~e~k~~r~ 297 (370)
|+|+|+|++||.||++||||+++|++++
T Consensus 74 l~G~i~p~~lv~Ms~~ElAs~elk~~~e 101 (102)
T smart00510 74 LNGEITPEKLATMTAEELASAELKEKRE 101 (102)
T ss_pred HcCCCCHHHHhcCCHHHcCCHHHHHHHh
Confidence 9999999999999999999999999886
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=99.94 E-value=9.6e-28 Score=202.83 Aligned_cols=115 Identities=39% Similarity=0.682 Sum_probs=104.2
Q ss_pred CChHHHHHHHHHHHHHHhhhcCCCchhhhhhcCCCChHHHHHHHHHHHHHhhCCCchhhhHHHHhHHhhcCCCCChHhhh
Q 017510 188 CNDYFRERIREKLYKALSKVSGEVDEEVQDKLNGCDPIRVAITAESLMFEKWGHSFGTYEVKYRSILFNLMDPENPDFRR 267 (370)
Q Consensus 188 t~d~vR~k~r~lL~~aL~~~~~~~~~~~~~~~~~~~~~~~A~~IE~~if~~~~~~~~~Yk~k~Rsl~~NLKd~kNp~Lr~ 267 (370)
|++++|++|+++|+++|...... .+ ...++..+|.+||.+||..|+.++..|++++|+|+|||||++||+||.
T Consensus 1 ~~~~~R~k~~~~L~~~l~~~~~~-~~------~~~~~~~lA~~IE~~lf~~~~~~~~~Y~~k~Rsl~~NLkd~~N~~L~~ 73 (115)
T PF07500_consen 1 TNDKVRDKARKLLYKALQKRSDE-QD------DPEDAKELAKEIEEALFDKFGSTSKKYKQKFRSLMFNLKDPKNPDLRR 73 (115)
T ss_dssp -TCHHHHHHHHHHHHHHHHCCCC-CC------CTCCHHHHHHHHHHHHHHHHTSTSHHHHHHHHHHHHHHCSSTTCCHHH
T ss_pred CCcHHHHHHHHHHHHHHHhcCcc-cc------chhHHHHHHHHHHHHHHHHHccCcHHHHHHHHHHHHHhccCCcHHHHH
Confidence 57899999999999999986543 11 234677999999999999998888999999999999999999999999
Q ss_pred chhcCCCChhhhcCCChhhcCChHHHHHHHHHHHHHhhcccC
Q 017510 268 KVLLGHVKPEALIKMSSEEMVSDGSRRLNQQIKKERASDRYL 309 (370)
Q Consensus 268 ~vl~G~isp~~lv~Ms~eEmas~e~k~~r~~~~~e~l~~~~l 309 (370)
+|++|.|+|.+||.|+++||||+++|++++++.+++++++||
T Consensus 74 ~il~g~i~p~~lv~ms~~Elas~e~k~~~e~~~~~~l~~~~~ 115 (115)
T PF07500_consen 74 RILSGEISPEELVTMSPEELASEELKEEREKIRKESLKQSQM 115 (115)
T ss_dssp HHHHSSSTTCHHHHCTTTTTTTSCCCCCHCCHHHHHHHHTB-
T ss_pred HHHcCCCCHHHHhcCCHHHhCCHHHHHHHHHHHHHHHHHhhC
Confidence 999999999999999999999999999999999999999864
No 5
>smart00509 TFS2N Domain in the N-terminus of transcription elongation factor S-II (and elsewhere).
Probab=99.70 E-value=1.8e-17 Score=130.10 Aligned_cols=74 Identities=34% Similarity=0.509 Sum_probs=66.3
Q ss_pred HHHHHHHHHHHHHhhcCcccHHHHHHHHHHhhcCCCCHhhhhccCceeecccccCCCCHHHHHHHHHHHHHHHHHHH
Q 017510 8 LCEAAKRRAETAASAEGELEEAQCIAALDQLHKSSITCQLLVSTQLVRHLLPLTKHPRQKIQDTASELILSWRSLFL 84 (370)
Q Consensus 8 l~~~a~k~~~~a~~~~~~~~~~~~l~~L~~L~~~~it~e~L~~T~IG~~V~~Lrkh~~~~I~~~Ak~Li~~WK~~v~ 84 (370)
||+.+++..+.+.. ++++++|+++|++|+.++||.++|++|+||+.||.||+|++++|+.+|+.||+.||++|+
T Consensus 1 ~~~~~k~~~k~~~~---~~~~~~~l~~L~~L~~~~~t~~~L~~T~iG~~v~~Lrkh~~~~I~~~A~~Li~~WK~~v~ 74 (75)
T smart00509 1 LLRAAKKLDKVANN---GKEVSRCLDILKKLKKLPITVDLLEETRIGKKVNGLRKHKNEEIRKLAKKLIKSWKKLVY 74 (75)
T ss_pred ChHHHHHHHHHhcC---CCCHHHHHHHHHHHhcCCCCHHHHHHCcHHHHHHHHHcCCcHHHHHHHHHHHHHHHHHhc
Confidence 46777777777632 336889999999999999999999999999999999999999999999999999999985
No 6
>cd00183 TFIIS_I N-terminal domain (domain I) of transcription elongation factor S-II (TFIIS); similar to a domain found in elongin A and CRSP70; likely to be involved in transcription; domain I from TFIIS interacts with RNA polymerase II holoenzyme
Probab=99.58 E-value=2e-15 Score=118.75 Aligned_cols=72 Identities=31% Similarity=0.422 Sum_probs=62.0
Q ss_pred HHHHHHHHHHHhhcCcccHHHHHHHHHHhhcCCCCHhhhhccCceeecccccCCCCHHHHHHHHHHHHHHHHHHH
Q 017510 10 EAAKRRAETAASAEGELEEAQCIAALDQLHKSSITCQLLVSTQLVRHLLPLTKHPRQKIQDTASELILSWRSLFL 84 (370)
Q Consensus 10 ~~a~k~~~~a~~~~~~~~~~~~l~~L~~L~~~~it~e~L~~T~IG~~V~~Lrkh~~~~I~~~Ak~Li~~WK~~v~ 84 (370)
..+++.++.... + ++.+.|+++|+.|+.++||.++|++|+||+.||+||+|++++|+.+|+.||++||++|+
T Consensus 5 ~r~~~~l~~~~~--~-~~~~~~~~~L~~L~~~~it~~~L~~T~iG~~V~~Lrkh~~~~i~~~A~~Lv~~Wk~~v~ 76 (76)
T cd00183 5 LRAKKKLEKKDS--N-EEVSRLLDLLRLLKKLPLTVEILKETRIGKKVNSLRKHSNEKIRKLAKALIKSWKKLVD 76 (76)
T ss_pred HHHHHHhhcccc--C-CCHHHHHHHHHHHhcCCCCHHHHHHCCHHHHHHHHHcCCcHHHHHHHHHHHHHHHHhcC
Confidence 344445554432 2 37889999999999999999999999999999999999999999999999999999873
No 7
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=99.37 E-value=3.5e-13 Score=93.25 Aligned_cols=34 Identities=29% Similarity=0.609 Sum_probs=32.8
Q ss_pred ccccCCCCcceEEEeeccccCCC-----ceeccCCCCcce
Q 017510 325 YMCGRCGHKKTTNHGNDQNSSAK-----RIKCLNCYQYWE 359 (370)
Q Consensus 325 ~~C~~C~~~~~~~~q~~Q~RsaD-----f~~C~~Cg~~w~ 359 (370)
++||+||++++.|+|+ |+|||| ||+|.+|||+|+
T Consensus 1 ~~Cp~C~~~~a~~~q~-Q~RsaDE~mT~fy~C~~C~~~w~ 39 (40)
T smart00440 1 APCPKCGNREATFFQL-QTRSADEPMTVFYVCTKCGHRWR 39 (40)
T ss_pred CcCCCCCCCeEEEEEE-cccCCCCCCeEEEEeCCCCCEeC
Confidence 4799999999999999 999999 999999999997
No 8
>PF08711 Med26: TFIIS helical bundle-like domain; InterPro: IPR017923 Transcription factor IIS (TFIIS) is a transcription elongation factor that increases the overall transcription rate of RNA polymerase II by reactivating transcription elongation complexes that have arrested transcription. The three structural domains of TFIIS are conserved from yeast to human. The 80 or so N-terminal residues form a protein interaction domain containing a conserved motif, which has been called the LW motif because of the invariant leucine and tryptophan residues it contains. Although the N-terminal domain is not needed for transcriptional activity, a similar sequence has been identified in other transcription factors and proteins that are predominantly nuclear localized [, ]: MED26 (also known as CRSP70 and ARC70), a subunit of the Mediator complex, which is required for the activity of the enhancer-binding protein Sp1. Elongin A, a subunit of a transcription elongation factor previously known as SIII. It increases the rate of transcription by suppressing transient pausing of the elongation complex. PPP1R10, a nuclear regulatory subunit of protein phosphatase 1 that was previously known as p99, FB19 or PNUTS. PIBP, a small hypothetical protein that could be a phosphoinositide binding protein. IWS1, which is thought to function in both transcription initiation and elongation. The TFIIS N-terminal domain is a compact four-helix bundle. The hydrophobic core residues of helices 2, 3, and 4 are well conserved among TFIIS domains, although helix 1 is less conserved []. ; GO: 0003677 DNA binding, 0006351 transcription, DNA-dependent, 0005634 nucleus; PDB: 1EO0_A 3OAK_A 3NFQ_B 3O8Z_A 1WJT_A 2XPL_A 2XPO_A 2XPP_A 2XPN_A.
Probab=99.36 E-value=2.5e-13 Score=99.48 Aligned_cols=52 Identities=35% Similarity=0.463 Sum_probs=47.4
Q ss_pred HHHHHhhcCCCCHhhhhccCceeecccccCC-CCHHHHHHHHHHHHHHHHHHH
Q 017510 33 AALDQLHKSSITCQLLVSTQLVRHLLPLTKH-PRQKIQDTASELILSWRSLFL 84 (370)
Q Consensus 33 ~~L~~L~~~~it~e~L~~T~IG~~V~~Lrkh-~~~~I~~~Ak~Li~~WK~~v~ 84 (370)
++|+.|..+|||.++|++|+||++|+.|++| .+++|+.+|+.||++||++|+
T Consensus 1 ~iL~~L~~l~it~~~L~~T~IGk~V~~l~k~~~~~~i~~~A~~Li~~Wk~~v~ 53 (53)
T PF08711_consen 1 EILKVLEKLPITVELLKSTGIGKAVNKLRKHSENPEIRKLAKELIKKWKRIVD 53 (53)
T ss_dssp HHHHHHHCSS-SHHHHHHHSHHHHHHHHHHCTS-HHHHHHHHHHHHHHHHHH-
T ss_pred CHHHHhhcCCCCHHHHHhCChhHHHHHHHcCCCCHHHHHHHHHHHHHHhHhcC
Confidence 5799999999999999999999999999999 999999999999999999874
No 9
>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=99.35 E-value=5.4e-13 Score=91.83 Aligned_cols=34 Identities=32% Similarity=0.667 Sum_probs=30.0
Q ss_pred ccccCCCCcceEEEeeccccCCC-----ceeccCCCCcce
Q 017510 325 YMCGRCGHKKTTNHGNDQNSSAK-----RIKCLNCYQYWE 359 (370)
Q Consensus 325 ~~C~~C~~~~~~~~q~~Q~RsaD-----f~~C~~Cg~~w~ 359 (370)
++||+||++++.|+|+ |+|||| ||.|.+|||+|+
T Consensus 1 ~~Cp~Cg~~~a~~~~~-Q~rsaDE~~T~fy~C~~C~~~wr 39 (39)
T PF01096_consen 1 IKCPKCGHNEAVFFQI-QTRSADEPMTLFYVCCNCGHRWR 39 (39)
T ss_dssp S--SSS-SSEEEEEEE-SSSSSSSSSEEEEEESSSTEEEE
T ss_pred CCCcCCCCCeEEEEEe-eccCCCCCCeEEEEeCCCCCeeC
Confidence 5799999999999999 999999 999999999996
No 10
>KOG1634 consensus Predicted transcription factor DATF1, contains PHD and TFS2M domains [Transcription]
Probab=99.34 E-value=6.9e-13 Score=140.53 Aligned_cols=83 Identities=33% Similarity=0.501 Sum_probs=76.6
Q ss_pred ChHHHHHHHHHHHHHhhC-CCchhhhHHHHhHHhhcCCCCChHhhhchhcCCCChhhhcCCChhhcCChHHHHHHHHHHH
Q 017510 223 DPIRVAITAESLMFEKWG-HSFGTYEVKYRSILFNLMDPENPDFRRKVLLGHVKPEALIKMSSEEMVSDGSRRLNQQIKK 301 (370)
Q Consensus 223 ~~~~~A~~IE~~if~~~~-~~~~~Yk~k~Rsl~~NLKd~kNp~Lr~~vl~G~isp~~lv~Ms~eEmas~e~k~~r~~~~~ 301 (370)
++..++..||..+|..|+ +.+.+|+.|+|+|+|||||++||.||.+|..|+|+|++|+.|+++|||+.++.+++++..+
T Consensus 268 d~~ll~~~ie~el~~~fG~gvnkkY~ek~RsL~fNlKDkkN~~lre~v~~~ei~~e~Lv~msaeelAs~eL~~~rEek~e 347 (778)
T KOG1634|consen 268 DPNLLLEKIEHELFVLFGLGVNKKYPEKLRSLLFNLKDKKNPELRERVMSGEISAERLVNMSAEELASPELAEWREEKAE 347 (778)
T ss_pred chhhHhhhhhhhceeccCCcccccchhhhhhhhhccccccchHHHHHHhhcccCHhhhccCCchhhcCchHHHHHHHHHH
Confidence 444677899999999998 7789999999999999999999999999999999999999999999999999999999887
Q ss_pred HHhh
Q 017510 302 ERAS 305 (370)
Q Consensus 302 e~l~ 305 (370)
+.+.
T Consensus 348 e~~~ 351 (778)
T KOG1634|consen 348 EMNE 351 (778)
T ss_pred HHHh
Confidence 6544
No 11
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=99.20 E-value=8.3e-12 Score=105.44 Aligned_cols=40 Identities=28% Similarity=0.527 Sum_probs=36.8
Q ss_pred ccccccccCCCCcceEEEeeccccCCC-----ceeccCCCCcceeh
Q 017510 321 HSTRYMCGRCGHKKTTNHGNDQNSSAK-----RIKCLNCYQYWEST 361 (370)
Q Consensus 321 ~t~~~~C~~C~~~~~~~~q~~Q~RsaD-----f~~C~~Cg~~w~~~ 361 (370)
.+..+.||+||++++.|+|+ |+|||| ||+|..|||+|++.
T Consensus 69 ~~~~~~CpkCg~~ea~y~~~-QtRsaDEp~T~Fy~C~~Cg~~wre~ 113 (113)
T COG1594 69 PTAKEKCPKCGNKEAYYWQL-QTRSADEPETRFYKCTRCGYRWREY 113 (113)
T ss_pred ccccccCCCCCCceeEEEee-ehhccCCCceEEEEecccCCEeecC
Confidence 34479999999999999999 999999 99999999999973
No 12
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=99.19 E-value=6.5e-12 Score=101.51 Aligned_cols=37 Identities=32% Similarity=0.630 Sum_probs=34.8
Q ss_pred cccccccCCCCcceEEEeeccccCCC-----ceeccCCCCcce
Q 017510 322 STRYMCGRCGHKKTTNHGNDQNSSAK-----RIKCLNCYQYWE 359 (370)
Q Consensus 322 t~~~~C~~C~~~~~~~~q~~Q~RsaD-----f~~C~~Cg~~w~ 359 (370)
.....||+||+.+++|+|+ |||||| ||.|.+|+|+|+
T Consensus 63 ~t~~~Cp~Cgh~rayF~ql-QtRSADEPmT~FYkC~~C~~~Wr 104 (105)
T KOG2906|consen 63 QTEATCPTCGHERAYFMQL-QTRSADEPMTTFYKCCKCKHRWR 104 (105)
T ss_pred hccCcCCCCCCCceEEEEe-eeccCCCcHhHhhhhhccccccc
Confidence 3468899999999999999 999999 999999999997
No 13
>PHA02998 RNA polymerase subunit; Provisional
Probab=99.06 E-value=8.5e-11 Score=104.80 Aligned_cols=36 Identities=28% Similarity=0.456 Sum_probs=34.4
Q ss_pred ccccccCCCCcceEEEeeccccCCC-----ceeccCCCCcce
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSAK-----RIKCLNCYQYWE 359 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~RsaD-----f~~C~~Cg~~w~ 359 (370)
...+||+||+++++|+|+ |||||| ||+|.+|||+|+
T Consensus 142 t~v~CPkCg~~~A~f~ql-QTRSADEPmT~FYkC~~CG~~wk 182 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMI-QTRAADEPPLVRHACRDCKKHFK 182 (195)
T ss_pred cCCCCCCCCCCceEEEEE-eeccCCCCceEEEEcCCCCCccC
Confidence 458999999999999999 999999 999999999996
No 14
>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=99.05 E-value=1.4e-10 Score=96.25 Aligned_cols=38 Identities=34% Similarity=0.626 Sum_probs=35.4
Q ss_pred cccccccCCCCcceEEEeeccccCCC-----ceeccCCCCccee
Q 017510 322 STRYMCGRCGHKKTTNHGNDQNSSAK-----RIKCLNCYQYWES 360 (370)
Q Consensus 322 t~~~~C~~C~~~~~~~~q~~Q~RsaD-----f~~C~~Cg~~w~~ 360 (370)
+..+.|++||++++.|+|+ |+|||| ||+|.+|||+|+-
T Consensus 60 ~~~~~Cp~Cg~~~a~f~~~-Q~RsadE~~T~fy~C~~C~~~w~~ 102 (104)
T TIGR01384 60 TTRVECPKCGHKEAYYWLL-QTRRADEPETRFYKCTKCGYVWRE 102 (104)
T ss_pred cccCCCCCCCCCeeEEEEe-ccCCCCCCcEEEEEeCCCCCeeEe
Confidence 3468999999999999999 999999 9999999999984
No 15
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=98.70 E-value=8.3e-09 Score=84.98 Aligned_cols=39 Identities=23% Similarity=0.560 Sum_probs=36.0
Q ss_pred cccccccccCCCCcceEEEeeccccCCC-----ceeccCCCCcce
Q 017510 320 YHSTRYMCGRCGHKKTTNHGNDQNSSAK-----RIKCLNCYQYWE 359 (370)
Q Consensus 320 ~~t~~~~C~~C~~~~~~~~q~~Q~RsaD-----f~~C~~Cg~~w~ 359 (370)
..|....||+||++++.|+|. |+|.+| ||.|.+|||+|.
T Consensus 69 Prts~~~C~~C~~~eavffQ~-~~~r~d~~m~l~yvC~~C~h~wt 112 (113)
T KOG2691|consen 69 PRTSDKHCPKCGHREAVFFQA-QTRRADEAMRLFYVCCSCGHRWT 112 (113)
T ss_pred CccccccCCccCCcceEEEec-ccccccceEEEEEEecccccccc
Confidence 345779999999999999999 999999 999999999995
No 16
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=98.58 E-value=1.4e-08 Score=84.48 Aligned_cols=38 Identities=26% Similarity=0.502 Sum_probs=34.6
Q ss_pred ccccccccCCCCcceEEEeeccccCCC-----ceeccCCCCcce
Q 017510 321 HSTRYMCGRCGHKKTTNHGNDQNSSAK-----RIKCLNCYQYWE 359 (370)
Q Consensus 321 ~t~~~~C~~C~~~~~~~~q~~Q~RsaD-----f~~C~~Cg~~w~ 359 (370)
.+-.-+||+||+.++.|+.+ |+|||| ||+|.+|++++.
T Consensus 71 a~I~~kCpkCghe~m~Y~T~-QlRSADEGQTVFYTC~kC~~k~~ 113 (116)
T KOG2907|consen 71 AVIKHKCPKCGHEEMSYHTL-QLRSADEGQTVFYTCPKCKYKFT 113 (116)
T ss_pred cchhccCcccCCchhhhhhh-hcccccCCceEEEEcCccceeee
Confidence 34567899999999999999 999999 999999999875
No 17
>PF11467 LEDGF: Lens epithelium-derived growth factor (LEDGF) ; InterPro: IPR021567 LEDGF is a chromatin-associated protein that protects cells from stress-induced apoptosis. It is the binding partner of HIV-1 integrase in human cells. The integrase binding domain (IBD) of LEDGF is a compact right-handed bundle composed of five alpha-helices. The residues essential for the interaction with the integrase are present in the inter-helical loop regions of the bundle structure. ; PDB: 3F9K_K 3HPG_G 3U88_C 3HPH_H 2B4J_D 1Z9E_A.
Probab=96.73 E-value=0.0015 Score=54.70 Aligned_cols=78 Identities=29% Similarity=0.466 Sum_probs=55.8
Q ss_pred hhhHHHHHHHHHHHHHHHHhhcCcccHHHHHHHHHHhhcCCCCHhhhh-ccCceeecccccCC-CCHHHHHHHHHHHHHH
Q 017510 2 EKEVMELCEAAKRRAETAASAEGELEEAQCIAALDQLHKSSITCQLLV-STQLVRHLLPLTKH-PRQKIQDTASELILSW 79 (370)
Q Consensus 2 e~e~~el~~~a~k~~~~a~~~~~~~~~~~~l~~L~~L~~~~it~e~L~-~T~IG~~V~~Lrkh-~~~~I~~~Ak~Li~~W 79 (370)
|+.|.+|----+-++.. + -++..+|+++|.+|..+++|.-+|+ .+.+..++++||+. .+..|.+.|..|+.+.
T Consensus 1 E~~L~~l~~~Ik~~L~~----~-~~Dv~kcL~~LdeL~~l~vT~~mL~kn~e~V~TlkklRrY~gn~~Ir~KA~~lYnkf 75 (106)
T PF11467_consen 1 ERRLQELHSEIKSSLKV----D-NPDVKKCLKALDELKSLQVTSLMLQKNPECVETLKKLRRYKGNQQIRKKATELYNKF 75 (106)
T ss_dssp HHHHHHHHHHHHHTCET----T-EE-HHHHHHHHHHHHTS---HHHHTTTHHHHHHHHHHTT-TT-HHHHHHHHHHHHHH
T ss_pred ChhHHHHHHHHHHHHcC----C-CCCHHHHHHHHHHHhccCCCHHHHHhCHHHHHHHHHHHHhhccHHHHHHHHHHHHHH
Confidence 45566665533333221 2 2389999999999999999998665 56688899999997 6789999999999999
Q ss_pred HHHHH
Q 017510 80 RSLFL 84 (370)
Q Consensus 80 K~~v~ 84 (370)
|.++.
T Consensus 76 K~~f~ 80 (106)
T PF11467_consen 76 KSLFL 80 (106)
T ss_dssp HHHHH
T ss_pred HHHhC
Confidence 99996
No 18
>KOG2821 consensus RNA polymerase II transcription elongation factor Elongin/SIII, subunit elongin A [Transcription]
Probab=96.69 E-value=0.00076 Score=68.60 Aligned_cols=74 Identities=18% Similarity=0.236 Sum_probs=63.9
Q ss_pred HHHHHHHHHHHHHHHHhhcCcccHHHHHHHHHHhhcCCCCHhhhhccCceeecccccCCCCHHHHHHHHHHHHHHHHHHH
Q 017510 5 VMELCEAAKRRAETAASAEGELEEAQCIAALDQLHKSSITCQLLVSTQLVRHLLPLTKHPRQKIQDTASELILSWRSLFL 84 (370)
Q Consensus 5 ~~el~~~a~k~~~~a~~~~~~~~~~~~l~~L~~L~~~~it~e~L~~T~IG~~V~~Lrkh~~~~I~~~Ak~Li~~WK~~v~ 84 (370)
.++.++.++..++.. + +..+++..|..|.++|+++++|.+|++|+.|+.|++|. .+..+|..|+..||++|.
T Consensus 7 ~l~~Vr~lQ~~l~~~-----~-dpkR~lk~I~~ls~lP~~~k~l~Et~~~k~l~~L~k~~--~~g~~~~Dl~~~WK~~v~ 78 (433)
T KOG2821|consen 7 GLGAVRKLQARLENR-----I-DPKRLLKRIQKLSNLPHLFKHLLETGKGKTLNSLRKIS--HVGKLAFDLVALWKDLVL 78 (433)
T ss_pred hHHHHHHHHHHHHhC-----c-cHHHHHHHHHHhccchHHHHHHHHhhhhHHHHHHHHhh--cccccccchHHHHHHhcc
Confidence 566666666666655 2 56899999999999999999999999999999999998 699999999999999996
Q ss_pred hh
Q 017510 85 EQ 86 (370)
Q Consensus 85 ~~ 86 (370)
..
T Consensus 79 ~d 80 (433)
T KOG2821|consen 79 VD 80 (433)
T ss_pred cc
Confidence 43
No 19
>KOG1793 consensus Uncharacterized conserved protein [Function unknown]
Probab=95.63 E-value=0.013 Score=58.92 Aligned_cols=55 Identities=24% Similarity=0.344 Sum_probs=48.6
Q ss_pred HHHHHHHhhcCCCCH-hhhhccCceeecccccCCCC--HHHHHHHHHHHHHHHHHHHh
Q 017510 31 CIAALDQLHKSSITC-QLLVSTQLVRHLLPLTKHPR--QKIQDTASELILSWRSLFLE 85 (370)
Q Consensus 31 ~l~~L~~L~~~~it~-e~L~~T~IG~~V~~Lrkh~~--~~I~~~Ak~Li~~WK~~v~~ 85 (370)
=..+|..|.+++|-. ++|+..+||++|=.|.+|+. .+++.+|..||..|-.-|..
T Consensus 235 r~~ll~iL~dlpi~~~E~Lk~SGlGkvVmflsks~ket~~nkrlA~kLI~eWsRpI~~ 292 (417)
T KOG1793|consen 235 RKSLLDILNDLPIDKREHLKESGLGKVVMFLSKSPKETKENKRLANKLINEWSRPIFK 292 (417)
T ss_pred HHHHHHHHhcCCcchHHHHHhcCCCeEEEEEecCCccchHHHHHHHHHHHHhhccccC
Confidence 346788888999988 99999999999999999964 78999999999999987763
No 20
>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=95.12 E-value=0.017 Score=44.09 Aligned_cols=32 Identities=22% Similarity=0.577 Sum_probs=24.0
Q ss_pred ccccCCCCcceEEEeeccc-------------cCCCceeccCCCCc
Q 017510 325 YMCGRCGHKKTTNHGNDQN-------------SSAKRIKCLNCYQY 357 (370)
Q Consensus 325 ~~C~~C~~~~~~~~q~~Q~-------------RsaDf~~C~~Cg~~ 357 (370)
+.|+|||+.....-++ |. +.--+++|.+||+.
T Consensus 1 y~C~KCg~~~~e~~~v-~~tgg~~skiFdvq~~~f~~v~C~~CGYT 45 (64)
T PF09855_consen 1 YKCPKCGNEEYESGEV-RATGGGLSKIFDVQNKKFTTVSCTNCGYT 45 (64)
T ss_pred CCCCCCCCcceecceE-EccCCeeEEEEEecCcEEEEEECCCCCCE
Confidence 4799999988777766 42 22228999999996
No 21
>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=94.90 E-value=0.013 Score=38.07 Aligned_cols=28 Identities=29% Similarity=0.711 Sum_probs=15.6
Q ss_pred ccccCCCCcceEEEeeccccCCCceeccCCCCcce
Q 017510 325 YMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYWE 359 (370)
Q Consensus 325 ~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w~ 359 (370)
-+|+.|+...++.... .+.|..|||.|.
T Consensus 3 p~Cp~C~se~~y~D~~-------~~vCp~C~~ew~ 30 (30)
T PF08274_consen 3 PKCPLCGSEYTYEDGE-------LLVCPECGHEWN 30 (30)
T ss_dssp ---TTT-----EE-SS-------SEEETTTTEEE-
T ss_pred CCCCCCCCcceeccCC-------EEeCCcccccCC
Confidence 3799999988874444 889999999993
No 22
>COG5139 Uncharacterized conserved protein [Function unknown]
Probab=94.62 E-value=0.04 Score=53.63 Aligned_cols=54 Identities=20% Similarity=0.324 Sum_probs=46.3
Q ss_pred HHHHHHhhcCCCCHhhhhccCceeecccccC--CCCHHHHHHHHHHHHHHHHHHHh
Q 017510 32 IAALDQLHKSSITCQLLVSTQLVRHLLPLTK--HPRQKIQDTASELILSWRSLFLE 85 (370)
Q Consensus 32 l~~L~~L~~~~it~e~L~~T~IG~~V~~Lrk--h~~~~I~~~Ak~Li~~WK~~v~~ 85 (370)
-.+|..|..+||-.++|++.+||+.|=.... ...++|+.+|+.||..|-.-|..
T Consensus 233 ksL~dvL~~lpI~tEHL~eSgvGrIV~FYtiskk~e~~v~r~A~~LV~eWtrpIik 288 (397)
T COG5139 233 KSLLDVLKTLPIHTEHLVESGVGRIVYFYTISKKEEKEVRRSAKALVQEWTRPIIK 288 (397)
T ss_pred HHHHHHHhhCCchHHHhhhcCCceEEEEEecCCcccHHHHHHHHHHHHHhhccccC
Confidence 3567788899999999999999999977764 46789999999999999887753
No 23
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=94.19 E-value=0.03 Score=42.46 Aligned_cols=34 Identities=21% Similarity=0.529 Sum_probs=24.9
Q ss_pred ccccccCCCCcceEEEeeccccCC------C-------ceeccCCCCc
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSA------K-------RIKCLNCYQY 357 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~Rsa------D-------f~~C~~Cg~~ 357 (370)
..++||+||.++..--++ +.-.. | -++|.+||..
T Consensus 3 ~~~kCpKCgn~~~~ekei-~~tg~~lskifdvq~n~f~~itCk~CgYt 49 (68)
T COG3478 3 NAFKCPKCGNTNYEEKEI-AATGGGLSKIFDVQNNKFIVITCKNCGYT 49 (68)
T ss_pred ccccCCCcCCcchhhcee-eccCCCcceeEEecccEEEEEEeccCCch
Confidence 356799999988776666 54322 2 6799999985
No 24
>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=93.66 E-value=0.039 Score=46.15 Aligned_cols=30 Identities=23% Similarity=0.693 Sum_probs=24.5
Q ss_pred ccccCCCCcceEEEeeccccCCCceeccCCCCcceeh
Q 017510 325 YMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYWEST 361 (370)
Q Consensus 325 ~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w~~~ 361 (370)
-.||+|++.-++-.+. .+.|..|||.|.--
T Consensus 3 p~CP~C~seytY~dg~-------~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGT-------QLICPSCLYEWNEN 32 (109)
T ss_pred CcCCcCCCcceEecCC-------eeECcccccccccc
Confidence 4699999887776555 89999999999754
No 25
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=93.07 E-value=0.045 Score=37.08 Aligned_cols=34 Identities=12% Similarity=0.523 Sum_probs=23.0
Q ss_pred cccccCCCCc-ceEEEeeccccCCC-ceeccCCCCccee
Q 017510 324 RYMCGRCGHK-KTTNHGNDQNSSAK-RIKCLNCYQYWES 360 (370)
Q Consensus 324 ~~~C~~C~~~-~~~~~q~~Q~RsaD-f~~C~~Cg~~w~~ 360 (370)
.++||.|+.. +..-. |.+.+. -|.|.+|+|.|.+
T Consensus 2 ~i~CP~C~~~f~v~~~---~l~~~~~~vrC~~C~~~f~v 37 (37)
T PF13719_consen 2 IITCPNCQTRFRVPDD---KLPAGGRKVRCPKCGHVFRV 37 (37)
T ss_pred EEECCCCCceEEcCHH---HcccCCcEEECCCCCcEeeC
Confidence 4689999753 11112 334444 9999999999975
No 26
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=92.48 E-value=0.077 Score=48.26 Aligned_cols=49 Identities=22% Similarity=0.383 Sum_probs=37.8
Q ss_pred ccCCCCCCccccccccccCCCCcceE-----EEeeccccCCC---ceeccCCCCcceeh
Q 017510 311 WKGGYLGPIYHSTRYMCGRCGHKKTT-----NHGNDQNSSAK---RIKCLNCYQYWEST 361 (370)
Q Consensus 311 ~~~~~~~~~~~t~~~~C~~C~~~~~~-----~~q~~Q~RsaD---f~~C~~Cg~~w~~~ 361 (370)
|+.. +..++.-...|++||..+.+ |.--+|.+--| .|.|.+|.+.|.+.
T Consensus 6 WtIt--p~~~pq~~k~C~~Cg~kr~f~cSg~fRvNAq~K~LDvWlIYkC~~Cd~tWN~~ 62 (203)
T COG4332 6 WTIT--PVGAPQPAKRCNSCGVKRAFTCSGKFRVNAQGKVLDVWLIYKCTHCDYTWNIS 62 (203)
T ss_pred EEec--cccCChhhhhCcccCCcceeeecCcEEEcCCCcEEEEEEEEEeeccCCccchh
Confidence 5555 55566677899999998765 34446888888 99999999999974
No 27
>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=92.41 E-value=0.12 Score=34.85 Aligned_cols=35 Identities=20% Similarity=0.517 Sum_probs=22.7
Q ss_pred cccccCCCCcceEEEeeccccCCC-ceeccCCCCccee
Q 017510 324 RYMCGRCGHKKTTNHGNDQNSSAK-RIKCLNCYQYWES 360 (370)
Q Consensus 324 ~~~C~~C~~~~~~~~q~~Q~RsaD-f~~C~~Cg~~w~~ 360 (370)
.+.||.|+..- +.+-.+...++ .+.|.+||+.|+.
T Consensus 2 ~~~CP~C~~~~--~v~~~~~~~~~~~v~C~~C~~~~~~ 37 (38)
T TIGR02098 2 RIQCPNCKTSF--RVVDSQLGANGGKVRCGKCGHVWYA 37 (38)
T ss_pred EEECCCCCCEE--EeCHHHcCCCCCEEECCCCCCEEEe
Confidence 47899998751 12111222233 7999999999974
No 28
>PRK10220 hypothetical protein; Provisional
Probab=92.15 E-value=0.083 Score=44.24 Aligned_cols=31 Identities=19% Similarity=0.551 Sum_probs=24.6
Q ss_pred ccccCCCCcceEEEeeccccCCCceeccCCCCcceehh
Q 017510 325 YMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYWESTT 362 (370)
Q Consensus 325 ~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w~~~~ 362 (370)
-.||+|+..-++-.+- .+.|..|+|.|.--.
T Consensus 4 P~CP~C~seytY~d~~-------~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 4 PHCPKCNSEYTYEDNG-------MYICPECAHEWNDAE 34 (111)
T ss_pred CcCCCCCCcceEcCCC-------eEECCcccCcCCccc
Confidence 4699999877665544 889999999998643
No 29
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=92.11 E-value=0.079 Score=35.71 Aligned_cols=34 Identities=15% Similarity=0.391 Sum_probs=22.2
Q ss_pred cccccCCCCcceEEEeeccccCCC-ceeccCCCCcce
Q 017510 324 RYMCGRCGHKKTTNHGNDQNSSAK-RIKCLNCYQYWE 359 (370)
Q Consensus 324 ~~~C~~C~~~~~~~~q~~Q~RsaD-f~~C~~Cg~~w~ 359 (370)
.+.|++|+..-. +-.- +++..- -+.|.+|||.|+
T Consensus 2 ~i~Cp~C~~~y~-i~d~-~ip~~g~~v~C~~C~~~f~ 36 (36)
T PF13717_consen 2 IITCPNCQAKYE-IDDE-KIPPKGRKVRCSKCGHVFF 36 (36)
T ss_pred EEECCCCCCEEe-CCHH-HCCCCCcEEECCCCCCEeC
Confidence 478999975311 1122 444333 899999999995
No 30
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=91.82 E-value=0.16 Score=39.68 Aligned_cols=38 Identities=16% Similarity=0.382 Sum_probs=24.4
Q ss_pred cccccCCCCcceEEEeeccc--cCCC-ceecc--CCCCcceehh
Q 017510 324 RYMCGRCGHKKTTNHGNDQN--SSAK-RIKCL--NCYQYWESTT 362 (370)
Q Consensus 324 ~~~C~~C~~~~~~~~q~~Q~--RsaD-f~~C~--~Cg~~w~~~~ 362 (370)
++.||.||..- .....-+. ...+ |+.|. +||++|..-.
T Consensus 1 mm~CP~Cg~~a-~irtSr~~s~~~~~~Y~qC~N~eCg~tF~t~e 43 (72)
T PRK09678 1 MFHCPLCQHAA-HARTSRYITDTTKERYHQCQNVNCSATFITYE 43 (72)
T ss_pred CccCCCCCCcc-EEEEChhcChhhheeeeecCCCCCCCEEEEEE
Confidence 57899999986 22221000 0122 99999 8999998643
No 31
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=90.51 E-value=0.15 Score=38.11 Aligned_cols=32 Identities=28% Similarity=0.665 Sum_probs=26.5
Q ss_pred ccccccccccCCCCcceEEEeeccccCCCceeccCCCCc
Q 017510 319 IYHSTRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQY 357 (370)
Q Consensus 319 ~~~t~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~ 357 (370)
+..+-.+-|+.||+.+.- .+.|-+.|.+||||
T Consensus 15 r~~~miYiCgdC~~en~l-------k~~D~irCReCG~R 46 (62)
T KOG3507|consen 15 RTATMIYICGDCGQENTL-------KRGDVIRCRECGYR 46 (62)
T ss_pred CcccEEEEeccccccccc-------cCCCcEehhhcchH
Confidence 456778999999998752 47788999999997
No 32
>PHA00626 hypothetical protein
Probab=90.46 E-value=0.2 Score=37.10 Aligned_cols=32 Identities=16% Similarity=0.391 Sum_probs=21.7
Q ss_pred cccCCCCcceEEEeeccccC-CCceeccCCCCcce
Q 017510 326 MCGRCGHKKTTNHGNDQNSS-AKRIKCLNCYQYWE 359 (370)
Q Consensus 326 ~C~~C~~~~~~~~q~~Q~Rs-aDf~~C~~Cg~~w~ 359 (370)
.||+||+.+..--- ..|- ..-|.|..||+++.
T Consensus 2 ~CP~CGS~~Ivrcg--~cr~~snrYkCkdCGY~ft 34 (59)
T PHA00626 2 SCPKCGSGNIAKEK--TMRGWSDDYVCCDCGYNDS 34 (59)
T ss_pred CCCCCCCceeeeec--eecccCcceEcCCCCCeec
Confidence 59999997655311 2333 33889999998764
No 33
>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=89.90 E-value=0.15 Score=48.59 Aligned_cols=35 Identities=29% Similarity=0.587 Sum_probs=14.6
Q ss_pred cccccCCCCcceEEEeeccccCCCceeccCCCCccee
Q 017510 324 RYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYWES 360 (370)
Q Consensus 324 ~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w~~ 360 (370)
.+-||.||+....-+.- -.+.|||+ |.+|++.+..
T Consensus 31 n~yCP~Cg~~~L~~f~N-N~PVaDF~-C~~C~eeyEL 65 (254)
T PF06044_consen 31 NMYCPNCGSKPLSKFEN-NRPVADFY-CPNCNEEYEL 65 (254)
T ss_dssp H---TTT--SS-EE---------EEE--TTT--EEEE
T ss_pred CCcCCCCCChhHhhccC-CCccceeE-CCCCchHHhh
Confidence 46799999998887777 78899988 9999987643
No 34
>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=89.66 E-value=0.3 Score=36.63 Aligned_cols=34 Identities=15% Similarity=0.356 Sum_probs=23.5
Q ss_pred ccccCCCCcceEEEeeccccCCC-ceeccCCCCcceeh
Q 017510 325 YMCGRCGHKKTTNHGNDQNSSAK-RIKCLNCYQYWEST 361 (370)
Q Consensus 325 ~~C~~C~~~~~~~~q~~Q~RsaD-f~~C~~Cg~~w~~~ 361 (370)
..||+|+.-..- ++ +.-..+ +++|..|||+-..-
T Consensus 10 A~CP~C~~~Dtl--~~-~~e~~~e~vECv~Cg~~~~~~ 44 (59)
T TIGR02443 10 AVCPACSAQDTL--AM-WKENNIELVECVECGYQEQQK 44 (59)
T ss_pred ccCCCCcCccEE--EE-EEeCCceEEEeccCCCccccC
Confidence 579999887654 22 322233 99999999986553
No 35
>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=89.35 E-value=0.36 Score=34.35 Aligned_cols=34 Identities=26% Similarity=0.521 Sum_probs=23.0
Q ss_pred cccCCCCcceEEEeeccccCCC----ceeccC--CCCcceeh
Q 017510 326 MCGRCGHKKTTNHGNDQNSSAK----RIKCLN--CYQYWEST 361 (370)
Q Consensus 326 ~C~~C~~~~~~~~q~~Q~RsaD----f~~C~~--Cg~~w~~~ 361 (370)
.||.||.+-....-. + -+.+ |+.|.| |||+|..-
T Consensus 1 ~CP~Cg~~a~ir~S~-~-~s~~~~~~Y~qC~N~~Cg~tfv~~ 40 (47)
T PF04606_consen 1 RCPHCGSKARIRTSR-Q-LSPLTRELYCQCTNPECGHTFVAN 40 (47)
T ss_pred CcCCCCCeeEEEEch-h-hCcceEEEEEEECCCcCCCEEEEE
Confidence 599999875433222 1 1333 999998 99999764
No 36
>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=89.09 E-value=0.38 Score=38.38 Aligned_cols=45 Identities=16% Similarity=0.313 Sum_probs=22.5
Q ss_pred ccccccCCCCcceEEEeeccccCCC--ceeccCCCCcceehhhcccCCCC
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSAK--RIKCLNCYQYWESTTALYGLLPV 370 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~RsaD--f~~C~~Cg~~w~~~~~~~~~~~~ 370 (370)
..|.||-|++.++.--.+ - +... .+.|..||..|.+- .-|.+.||
T Consensus 21 ~~F~CPfC~~~~sV~v~i-d-kk~~~~~~~C~~Cg~~~~~~-i~~L~epi 67 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKI-D-KKEGIGILSCRVCGESFQTK-INPLSEPI 67 (81)
T ss_dssp S----TTT--SS-EEEEE-E-TTTTEEEEEESSS--EEEEE---SS--TT
T ss_pred ceEcCCcCCCCCeEEEEE-E-ccCCEEEEEecCCCCeEEEc-cCccCccc
Confidence 479999999888877766 2 2222 99999999998764 33444443
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=88.62 E-value=0.31 Score=32.89 Aligned_cols=26 Identities=23% Similarity=0.350 Sum_probs=20.1
Q ss_pred cccccCCCCcceEEEeeccccCCC-ceeccCCCCc
Q 017510 324 RYMCGRCGHKKTTNHGNDQNSSAK-RIKCLNCYQY 357 (370)
Q Consensus 324 ~~~C~~C~~~~~~~~q~~Q~RsaD-f~~C~~Cg~~ 357 (370)
.+.|+.|+.+ ++. +.| |+.|..|||.
T Consensus 8 ~~~C~~C~~~---~~~-----~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 8 NEPCPVCGSR---WFY-----SDDGFYYCDRCGHQ 34 (36)
T ss_pred CCcCCCCCCe---EeE-----ccCCEEEhhhCceE
Confidence 4679999998 332 346 9999999985
No 38
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=88.54 E-value=0.37 Score=33.99 Aligned_cols=27 Identities=30% Similarity=0.794 Sum_probs=20.0
Q ss_pred cccccCCCCcceEEEeeccccCCCceeccCCCCc
Q 017510 324 RYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQY 357 (370)
Q Consensus 324 ~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~ 357 (370)
.|.|++||.. +.+ .+.|-+.|.+|||+
T Consensus 2 ~Y~C~~Cg~~----~~~---~~~~~irC~~CG~r 28 (44)
T smart00659 2 IYICGECGRE----NEI---KSKDVVRCRECGYR 28 (44)
T ss_pred EEECCCCCCE----eec---CCCCceECCCCCce
Confidence 4789999984 222 25568999999987
No 39
>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=88.28 E-value=0.32 Score=32.01 Aligned_cols=26 Identities=31% Similarity=0.856 Sum_probs=17.4
Q ss_pred ccccCCCCcceEEEeeccccCCCceeccCCCCc
Q 017510 325 YMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQY 357 (370)
Q Consensus 325 ~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~ 357 (370)
+.|++||...- + ...|-+.|.+||||
T Consensus 1 Y~C~~Cg~~~~----~---~~~~~irC~~CG~R 26 (32)
T PF03604_consen 1 YICGECGAEVE----L---KPGDPIRCPECGHR 26 (32)
T ss_dssp EBESSSSSSE-----B---STSSTSSBSSSS-S
T ss_pred CCCCcCCCeeE----c---CCCCcEECCcCCCe
Confidence 46888887654 2 34567889999987
No 40
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=88.26 E-value=0.45 Score=39.36 Aligned_cols=37 Identities=27% Similarity=0.588 Sum_probs=27.5
Q ss_pred cccccCCCCcceEEEeeccccCCCceeccCCCCccee
Q 017510 324 RYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYWES 360 (370)
Q Consensus 324 ~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w~~ 360 (370)
.|.||.||+-+.....+.-+-..-+..|.+||.++.+
T Consensus 22 ~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~ 58 (104)
T COG4888 22 TFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFEC 58 (104)
T ss_pred eEecCccCCeeeeEEEEEecCceeEEEcccCcceEEE
Confidence 5999999999888655511112229999999998876
No 41
>PF14353 CpXC: CpXC protein
Probab=87.66 E-value=0.57 Score=39.97 Aligned_cols=38 Identities=16% Similarity=0.359 Sum_probs=25.4
Q ss_pred ccccCCCCc-ceEEEeecc----------ccCCC--ceeccCCCCcceehh
Q 017510 325 YMCGRCGHK-KTTNHGNDQ----------NSSAK--RIKCLNCYQYWESTT 362 (370)
Q Consensus 325 ~~C~~C~~~-~~~~~q~~Q----------~RsaD--f~~C~~Cg~~w~~~~ 362 (370)
++||.||+. ...+++.+= ..+++ .++|.+||+....-+
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~ 52 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEY 52 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCC
Confidence 689999886 444554412 11223 899999999987643
No 42
>PLN02976 amine oxidase
Probab=87.04 E-value=0.74 Score=54.12 Aligned_cols=59 Identities=15% Similarity=0.184 Sum_probs=50.2
Q ss_pred HHHHHHHhhcCCCCHhhhhccCceeec-ccccCCCCHHHHHHHHHHHHHHHHHHHhhcCC
Q 017510 31 CIAALDQLHKSSITCQLLVSTQLVRHL-LPLTKHPRQKIQDTASELILSWRSLFLEQMKG 89 (370)
Q Consensus 31 ~l~~L~~L~~~~it~e~L~~T~IG~~V-~~Lrkh~~~~I~~~Ak~Li~~WK~~v~~~~~~ 89 (370)
+...|+-|--++..+..|+..+||++| +++.-|.+++|+.+|..|+..|..++...+..
T Consensus 1303 ~~~~~~ll~~~~~d~~a~r~sg~~~~~k~~~~~h~~~~~r~~a~~~~~~w~~~~~~~~~~ 1362 (1713)
T PLN02976 1303 LRHCVRLLVLVSTDLLAVRLSGIGKTVKEKVCVHTSRDIRAIASQLVSVWLEVFRREKAS 1362 (1713)
T ss_pred HHHHHHHHhhcchhHHHHHhccchHHHHhhhhhcccHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 445566666667777888999999999 99999999999999999999999999877653
No 43
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=86.91 E-value=0.63 Score=32.31 Aligned_cols=30 Identities=27% Similarity=0.533 Sum_probs=19.7
Q ss_pred ccccCCCCcceEEEeeccccCCCceeccCCCCcce
Q 017510 325 YMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYWE 359 (370)
Q Consensus 325 ~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w~ 359 (370)
+.||.||+.. .++.- ....+.|.+||.-..
T Consensus 1 m~Cp~Cg~~~-~~~D~----~~g~~vC~~CG~Vl~ 30 (43)
T PF08271_consen 1 MKCPNCGSKE-IVFDP----ERGELVCPNCGLVLE 30 (43)
T ss_dssp ESBTTTSSSE-EEEET----TTTEEEETTT-BBEE
T ss_pred CCCcCCcCCc-eEEcC----CCCeEECCCCCCEee
Confidence 5799999988 44432 112678999997543
No 44
>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=86.70 E-value=0.58 Score=36.44 Aligned_cols=33 Identities=15% Similarity=0.368 Sum_probs=22.7
Q ss_pred ccccCCCCcceE-EEeeccccCCC-ceeccCCCCcceeh
Q 017510 325 YMCGRCGHKKTT-NHGNDQNSSAK-RIKCLNCYQYWEST 361 (370)
Q Consensus 325 ~~C~~C~~~~~~-~~q~~Q~RsaD-f~~C~~Cg~~w~~~ 361 (370)
..||+|+.-..- ++.- ..+ +++|..|||+-..-
T Consensus 9 a~CP~C~~~D~i~~~~e----~~ve~vECV~CGy~e~~~ 43 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRE----NGVEYVECVECGYTERQP 43 (71)
T ss_pred ccCCCCcCccEEEEEEe----CCceEEEecCCCCeeccC
Confidence 579999987643 2221 223 99999999986543
No 45
>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=86.64 E-value=0.74 Score=32.44 Aligned_cols=28 Identities=21% Similarity=0.677 Sum_probs=20.3
Q ss_pred ccccCCCCcceEEEeeccccCCCceeccCCCCc
Q 017510 325 YMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQY 357 (370)
Q Consensus 325 ~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~ 357 (370)
+.||+||+. .++.+ . ..-.+.|..|+++
T Consensus 19 ~~CP~Cg~~--~~~~~-~--~~~~~~C~~C~~q 46 (46)
T PF12760_consen 19 FVCPHCGST--KHYRL-K--TRGRYRCKACRKQ 46 (46)
T ss_pred CCCCCCCCe--eeEEe-C--CCCeEECCCCCCc
Confidence 789999998 33433 2 2238999999975
No 46
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=84.01 E-value=0.73 Score=35.32 Aligned_cols=30 Identities=23% Similarity=0.531 Sum_probs=24.5
Q ss_pred ccccccCCCCcceEEEeeccccCCCceeccCCCCc
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQY 357 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~ 357 (370)
-..+||.|++..+.|.-. |+ .|+|..||..
T Consensus 18 l~VkCpdC~N~q~vFsha-st----~V~C~~CG~~ 47 (67)
T COG2051 18 LRVKCPDCGNEQVVFSHA-ST----VVTCLICGTT 47 (67)
T ss_pred EEEECCCCCCEEEEeccC-ce----EEEecccccE
Confidence 467999999999988654 44 7999999965
No 47
>KOG1886 consensus BAH domain proteins [Transcription]
Probab=84.00 E-value=0.28 Score=50.75 Aligned_cols=165 Identities=10% Similarity=-0.016 Sum_probs=105.4
Q ss_pred cCCChHHHHHHHHHHHHHHhhhcCCCchhhhhh----cCCCChHHHHHHHHHHHHHhhCCCchhhhHHHHhHHhhcCCCC
Q 017510 186 IKCNDYFRERIREKLYKALSKVSGEVDEEVQDK----LNGCDPIRVAITAESLMFEKWGHSFGTYEVKYRSILFNLMDPE 261 (370)
Q Consensus 186 ~~t~d~vR~k~r~lL~~aL~~~~~~~~~~~~~~----~~~~~~~~~A~~IE~~if~~~~~~~~~Yk~k~Rsl~~NLKd~k 261 (370)
..+++.-|+|++.-++.++...+.-....-... .-..+.......||...|+.+..+...|..+...|.++|| .
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 467899999999999999955432221110000 1122456778899999999987777899999999999998 5
Q ss_pred ChHhhhchhcC-CCChhhhcCCChhhcCChHHHHHHHHHHHHHhhcccCcccCCCCCCccccccccccCCCCcceEEEee
Q 017510 262 NPDFRRKVLLG-HVKPEALIKMSSEEMVSDGSRRLNQQIKKERASDRYLPWKGGYLGPIYHSTRYMCGRCGHKKTTNHGN 340 (370)
Q Consensus 262 Np~Lr~~vl~G-~isp~~lv~Ms~eEmas~e~k~~r~~~~~e~l~~~~l~~~~~~~~~~~~t~~~~C~~C~~~~~~~~q~ 340 (370)
---|+.+.++| ++.|+..+.|.+-++-....-..-.+. ... . .....-+.-.|..|=+.-|+-.++
T Consensus 316 ~~~l~~~~ln~~~~~~e~~~~l~~p~~p~~~~~~~~~~~-----~~d------~--~~~l~~~~~~~~~~~~~~~g~~~~ 382 (464)
T KOG1886|consen 316 QALLKPEPLNPGETKPEPKQELHPPSFPDGQSSPSSMKL-----NDD------D--YDGLCVGLELTAGSLYLYCGQEGL 382 (464)
T ss_pred hhhhccccCCCcccCchhhhhccCCCCCCCccCcccccc-----Cch------h--HHHHHHhhhhhccchhhhcccccc
Confidence 56788899998 499999999877666554321100000 000 0 001122344555555555555555
Q ss_pred ccccCCC--ceeccCCCCcceehhhcc
Q 017510 341 DQNSSAK--RIKCLNCYQYWESTTALY 365 (370)
Q Consensus 341 ~Q~RsaD--f~~C~~Cg~~w~~~~~~~ 365 (370)
+|.-..+ ..-|..|+.+|..-+..-
T Consensus 383 ~~~~~~~~~~~~~v~~~~~a~~~~~~~ 409 (464)
T KOG1886|consen 383 ICAGHLPCPMLPEVKLSPVAAVHREGL 409 (464)
T ss_pred eeccccCCCCCCCcCcccccccchhhh
Confidence 4555555 777888998888766543
No 48
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=81.66 E-value=1.6 Score=32.22 Aligned_cols=33 Identities=15% Similarity=0.348 Sum_probs=23.9
Q ss_pred ccccccCCCCcceEEEeeccccCCC---ceeccCCCC
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSAK---RIKCLNCYQ 356 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~RsaD---f~~C~~Cg~ 356 (370)
....||-||.....+.+. -....+ +|.|.+||.
T Consensus 2 ~LkPCPFCG~~~~~~~~~-~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 2 ELKPCPFCGSADVLIRQD-EGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCcCCCCCCCcceEeecc-cCCCCCCEEEEEcCCCCC
Confidence 467899998888877765 322222 788999997
No 49
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=80.77 E-value=1.3 Score=31.53 Aligned_cols=34 Identities=18% Similarity=0.391 Sum_probs=20.6
Q ss_pred cccCCCCcceEEEeeccccCCCceeccCCCCcceehhh
Q 017510 326 MCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYWESTTA 363 (370)
Q Consensus 326 ~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w~~~~~ 363 (370)
-||.||.. .|... .....++.|..||+.|+.-..
T Consensus 2 FCp~Cg~~--l~~~~--~~~~~~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 2 FCPKCGNM--LIPKE--GKEKRRFVCRKCGYEEPIEQK 35 (52)
T ss_pred CCCCCCCc--ccccc--CCCCCEEECCcCCCeEECCCc
Confidence 39999882 12211 011127889999998887443
No 50
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=79.89 E-value=1.6 Score=35.28 Aligned_cols=30 Identities=27% Similarity=0.528 Sum_probs=22.2
Q ss_pred ccccccCCCCcceEEEeeccccCCC-ceeccCCCCcce
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSAK-RIKCLNCYQYWE 359 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~RsaD-f~~C~~Cg~~w~ 359 (370)
+...||.|+.. +.. |.+- ...|..||+.|.
T Consensus 34 ~~~~Cp~C~~~--~Vk-----R~a~GIW~C~kCg~~fA 64 (89)
T COG1997 34 AKHVCPFCGRT--TVK-----RIATGIWKCRKCGAKFA 64 (89)
T ss_pred cCCcCCCCCCc--cee-----eeccCeEEcCCCCCeec
Confidence 46789999998 222 4444 999999997764
No 51
>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=78.57 E-value=0.96 Score=28.36 Aligned_cols=24 Identities=25% Similarity=0.573 Sum_probs=14.9
Q ss_pred cccCCCCcceEEEeeccccCCCceeccCCCCcce
Q 017510 326 MCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYWE 359 (370)
Q Consensus 326 ~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w~ 359 (370)
.||.|+..=-. +--.|..|||.|.
T Consensus 2 ~CP~C~~~V~~----------~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAEVPE----------SAKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCCchh----------hcCcCCCCCCCCc
Confidence 47777654322 1345888888874
No 52
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=78.28 E-value=1.5 Score=31.71 Aligned_cols=29 Identities=24% Similarity=0.397 Sum_probs=20.3
Q ss_pred cccccCCCCcceEEEeeccccCCCceeccCCCCcce
Q 017510 324 RYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYWE 359 (370)
Q Consensus 324 ~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w~ 359 (370)
...||+||.. +.-. +.|.+.|..||..+.
T Consensus 20 ~~fCP~Cg~~---~m~~----~~~r~~C~~Cgyt~~ 48 (50)
T PRK00432 20 NKFCPRCGSG---FMAE----HLDRWHCGKCGYTEF 48 (50)
T ss_pred cCcCcCCCcc---hhec----cCCcEECCCcCCEEe
Confidence 4479999975 2222 237889999998764
No 53
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=77.81 E-value=2 Score=29.43 Aligned_cols=32 Identities=22% Similarity=0.451 Sum_probs=21.1
Q ss_pred cccCCCCcceEEEeeccccCCC--ceeccCCCCcceehhh
Q 017510 326 MCGRCGHKKTTNHGNDQNSSAK--RIKCLNCYQYWESTTA 363 (370)
Q Consensus 326 ~C~~C~~~~~~~~q~~Q~RsaD--f~~C~~Cg~~w~~~~~ 363 (370)
+||+|+.. ..-..+ .+ ...|..||-.|---.+
T Consensus 1 ~CP~C~~~-l~~~~~-----~~~~id~C~~C~G~W~d~~e 34 (41)
T PF13453_consen 1 KCPRCGTE-LEPVRL-----GDVEIDVCPSCGGIWFDAGE 34 (41)
T ss_pred CcCCCCcc-cceEEE-----CCEEEEECCCCCeEEccHHH
Confidence 59999873 322221 33 7889999999964433
No 54
>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=77.18 E-value=3 Score=30.21 Aligned_cols=32 Identities=16% Similarity=0.240 Sum_probs=20.9
Q ss_pred ccccCCCCcceEEEeeccccCCC---ceeccCCCCcc
Q 017510 325 YMCGRCGHKKTTNHGNDQNSSAK---RIKCLNCYQYW 358 (370)
Q Consensus 325 ~~C~~C~~~~~~~~q~~Q~RsaD---f~~C~~Cg~~w 358 (370)
..||-||+....+.-- ...-| ++.|..||..=
T Consensus 2 kPCPfCGg~~~~~~~~--~~~~~~~~~~~C~~Cga~~ 36 (53)
T TIGR03655 2 KPCPFCGGADVYLRRG--FDPLDLSHYFECSTCGASG 36 (53)
T ss_pred CCCCCCCCcceeeEec--cCCCCCEEEEECCCCCCCc
Confidence 5799999976655321 12222 66899999863
No 55
>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=76.46 E-value=1.7 Score=42.46 Aligned_cols=37 Identities=22% Similarity=0.441 Sum_probs=17.3
Q ss_pred ccccccCCCCcc-eEEEeeccccCCC-ceeccCCCCccee
Q 017510 323 TRYMCGRCGHKK-TTNHGNDQNSSAK-RIKCLNCYQYWES 360 (370)
Q Consensus 323 ~~~~C~~C~~~~-~~~~q~~Q~RsaD-f~~C~~Cg~~w~~ 360 (370)
..-.||-||+.- ..+..- ..+++- |..|.-||+.|.|
T Consensus 171 ~~g~CPvCGs~P~~s~l~~-~~~~G~R~L~Cs~C~t~W~~ 209 (290)
T PF04216_consen 171 QRGYCPVCGSPPVLSVLRG-GEREGKRYLHCSLCGTEWRF 209 (290)
T ss_dssp T-SS-TTT---EEEEEEE-------EEEEEETTT--EEE-
T ss_pred cCCcCCCCCCcCceEEEec-CCCCccEEEEcCCCCCeeee
Confidence 346899999974 344433 333233 9999999999998
No 56
>COG4734 ArdA Antirestriction protein [General function prediction only]
Probab=75.81 E-value=0.27 Score=44.17 Aligned_cols=41 Identities=34% Similarity=0.487 Sum_probs=35.6
Q ss_pred cccccCCCCcceEEEeeccccCCC---------ceeccCCCCcceehhhccc
Q 017510 324 RYMCGRCGHKKTTNHGNDQNSSAK---------RIKCLNCYQYWESTTALYG 366 (370)
Q Consensus 324 ~~~C~~C~~~~~~~~q~~Q~RsaD---------f~~C~~Cg~~w~~~~~~~~ 366 (370)
.+.|=.||+--+.++|. +||+| +|.|.+|.-+|.-|+.+-+
T Consensus 16 ~y~~y~~gsi~t~~fqe--~vsaml~~srfPnvmVkCpnceg~~e~Ct~~~~ 65 (193)
T COG4734 16 TYHKYNCGSIFTKWFQE--TVSAMLFDSRFPNVMVKCPNCEGFYEACTALHA 65 (193)
T ss_pred hcceeeccccccHHHHH--HHHHHHHhhcCccceeeccchhhHHHHHHhhcC
Confidence 46788999999999997 68887 8999999999999998643
No 57
>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=75.05 E-value=1.4 Score=33.85 Aligned_cols=34 Identities=18% Similarity=0.561 Sum_probs=22.0
Q ss_pred cccccCCCCcceEEEeeccccCCC--ceeccCCCCcc
Q 017510 324 RYMCGRCGHKKTTNHGNDQNSSAK--RIKCLNCYQYW 358 (370)
Q Consensus 324 ~~~C~~C~~~~~~~~q~~Q~RsaD--f~~C~~Cg~~w 358 (370)
.|+|..|+.+....+-- |.-... ++.|..|.++-
T Consensus 4 ~FTC~~C~~Rs~~~~sk-~aY~~GvViv~C~gC~~~H 39 (66)
T PF05180_consen 4 TFTCNKCGTRSAKMFSK-QAYHKGVVIVQCPGCKNRH 39 (66)
T ss_dssp EEEETTTTEEEEEEEEH-HHHHTSEEEEE-TTS--EE
T ss_pred EEEcCCCCCccceeeCH-HHHhCCeEEEECCCCccee
Confidence 58999999987765544 332223 99999999874
No 58
>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=74.11 E-value=2.1 Score=32.35 Aligned_cols=29 Identities=31% Similarity=0.675 Sum_probs=21.7
Q ss_pred cccccCCCCcceEEEeeccccCCCceeccCCCCcc
Q 017510 324 RYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYW 358 (370)
Q Consensus 324 ~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w 358 (370)
...|+.||...-. .++...+.|.+||..|
T Consensus 28 Sq~C~~CG~~~~~------~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 28 SQTCPRCGHRNKK------RRSGRVFTCPNCGFEM 56 (69)
T ss_pred ccCccCccccccc------ccccceEEcCCCCCEE
Confidence 3569999998665 2333488999999875
No 59
>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=73.27 E-value=2 Score=37.12 Aligned_cols=32 Identities=6% Similarity=0.069 Sum_probs=24.8
Q ss_pred cccccCCCCcceEEEeeccccCCCceeccCCCCcceehh
Q 017510 324 RYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYWESTT 362 (370)
Q Consensus 324 ~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w~~~~ 362 (370)
...|+.||. .||.+ . | +-++|..||..|...+
T Consensus 9 Kr~Cp~cg~---kFYDL-n-k--~p~vcP~cg~~~~~~~ 40 (129)
T TIGR02300 9 KRICPNTGS---KFYDL-N-R--RPAVSPYTGEQFPPEE 40 (129)
T ss_pred cccCCCcCc---ccccc-C-C--CCccCCCcCCccCcch
Confidence 567999985 47887 3 3 5788999999997653
No 60
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=72.96 E-value=3.1 Score=31.27 Aligned_cols=31 Identities=19% Similarity=0.535 Sum_probs=24.8
Q ss_pred ccccccCCCCcceEEEeeccccCCCceeccCCCCcc
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYW 358 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w 358 (370)
-+.+|+.|++-.+.|.-. |+ -|.|..||..-
T Consensus 10 ~~VkCp~C~n~q~vFsha-~t----~V~C~~Cg~~L 40 (59)
T PRK00415 10 LKVKCPDCGNEQVVFSHA-ST----VVRCLVCGKTL 40 (59)
T ss_pred EEEECCCCCCeEEEEecC-Cc----EEECcccCCCc
Confidence 468999999998888644 33 89999999864
No 61
>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=72.73 E-value=2.5 Score=35.22 Aligned_cols=35 Identities=17% Similarity=0.315 Sum_probs=26.0
Q ss_pred ccccccccCCCCcceEEEeeccccCCCceeccCCCCcceehh
Q 017510 321 HSTRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYWESTT 362 (370)
Q Consensus 321 ~t~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w~~~~ 362 (370)
.+..-.|.-| ....|+|. .|.++|.+||.+|..-+
T Consensus 32 ~va~daCeiC--~~~GY~q~-----g~~lvC~~C~~~~~~~~ 66 (102)
T PF10080_consen 32 RVAFDACEIC--GPKGYYQE-----GDQLVCKNCGVRFNLPT 66 (102)
T ss_pred EEEEEecccc--CCCceEEE-----CCEEEEecCCCEEehhh
Confidence 3455579999 45566665 45999999999997644
No 62
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=72.54 E-value=3 Score=36.68 Aligned_cols=39 Identities=23% Similarity=0.391 Sum_probs=23.0
Q ss_pred ccccccccCCCCcceEEEeeccccCCC-ceeccCCCCccee
Q 017510 321 HSTRYMCGRCGHKKTTNHGNDQNSSAK-RIKCLNCYQYWES 360 (370)
Q Consensus 321 ~t~~~~C~~C~~~~~~~~q~~Q~RsaD-f~~C~~Cg~~w~~ 360 (370)
....|.||.||.+ -++......-+.| .++|.+||..-..
T Consensus 96 ~~~~Y~Cp~C~~~-y~~~ea~~~~d~~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 96 NNAYYKCPNCQSK-YTFLEANQLLDMDGTFTCPRCGEELEE 135 (147)
T ss_pred CCcEEECcCCCCE-eeHHHHHHhcCCCCcEECCCCCCEEEE
Confidence 3467999999843 2233320111223 5899999987544
No 63
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=72.48 E-value=2.5 Score=41.87 Aligned_cols=37 Identities=19% Similarity=0.438 Sum_probs=26.4
Q ss_pred ccccccCCCCcce-EEEeeccccCCC-ceeccCCCCccee
Q 017510 323 TRYMCGRCGHKKT-TNHGNDQNSSAK-RIKCLNCYQYWES 360 (370)
Q Consensus 323 ~~~~C~~C~~~~~-~~~q~~Q~RsaD-f~~C~~Cg~~w~~ 360 (370)
..-.||-||+.-+ .+... ....+- |..|.-|++.|.|
T Consensus 186 ~~~~CPvCGs~P~~s~v~~-~~~~G~RyL~CslC~teW~~ 224 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQI-GTTQGLRYLHCNLCESEWHV 224 (309)
T ss_pred CCCCCCCCCCcchhheeec-cCCCCceEEEcCCCCCcccc
Confidence 4678999999854 33333 222222 9999999999997
No 64
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=72.39 E-value=2.3 Score=31.94 Aligned_cols=38 Identities=13% Similarity=0.313 Sum_probs=22.6
Q ss_pred ccccccccccCCCCcceEEEeeccccCCCceeccCCCCc
Q 017510 319 IYHSTRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQY 357 (370)
Q Consensus 319 ~~~t~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~ 357 (370)
...-..|.||.||.-...--+. =.+-+.-|+|.+||..
T Consensus 22 ~e~~v~F~CPnCGe~~I~Rc~~-CRk~g~~Y~Cp~CGF~ 59 (61)
T COG2888 22 GETAVKFPCPNCGEVEIYRCAK-CRKLGNPYRCPKCGFE 59 (61)
T ss_pred CCceeEeeCCCCCceeeehhhh-HHHcCCceECCCcCcc
Confidence 3444679999999643222221 1122238999999963
No 65
>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=71.52 E-value=3.7 Score=28.38 Aligned_cols=30 Identities=27% Similarity=0.617 Sum_probs=21.1
Q ss_pred ccccccCCCCcceEEEeeccccCC-CceeccCCCC
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSA-KRIKCLNCYQ 356 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~Rsa-Df~~C~~Cg~ 356 (370)
=.|+|..||+.-..+.-+ +. +-+.|..||.
T Consensus 4 Yey~C~~Cg~~fe~~~~~----~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 4 YEYRCEECGHEFEVLQSI----SEDDPVPCPECGS 34 (42)
T ss_pred EEEEeCCCCCEEEEEEEc----CCCCCCcCCCCCC
Confidence 468999999754444333 33 4999999997
No 66
>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=70.80 E-value=2.7 Score=35.32 Aligned_cols=31 Identities=19% Similarity=0.432 Sum_probs=24.1
Q ss_pred cccccCCCCcceEEEeeccccCCCceeccCCCCcceeh
Q 017510 324 RYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYWEST 361 (370)
Q Consensus 324 ~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w~~~ 361 (370)
...|+.||. .||.+ . | +-++|..||..|---
T Consensus 9 KR~Cp~CG~---kFYDL-n-k--~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 9 KRTCPSCGA---KFYDL-N-K--DPIVCPKCGTEFPPE 39 (108)
T ss_pred cccCCCCcc---hhccC-C-C--CCccCCCCCCccCcc
Confidence 567999985 58888 3 3 567799999999754
No 67
>PRK05978 hypothetical protein; Provisional
Probab=70.68 E-value=2 Score=38.15 Aligned_cols=35 Identities=23% Similarity=0.268 Sum_probs=26.8
Q ss_pred cccccCCCCcceE--EEeeccccCCCceeccCCCCcceehhhcc
Q 017510 324 RYMCGRCGHKKTT--NHGNDQNSSAKRIKCLNCYQYWESTTALY 365 (370)
Q Consensus 324 ~~~C~~C~~~~~~--~~q~~Q~RsaDf~~C~~Cg~~w~~~~~~~ 365 (370)
.-+||+||+-+.. |..+ --.|..||..+.+-.+-|
T Consensus 33 ~grCP~CG~G~LF~g~Lkv-------~~~C~~CG~~~~~~~a~D 69 (148)
T PRK05978 33 RGRCPACGEGKLFRAFLKP-------VDHCAACGEDFTHHRADD 69 (148)
T ss_pred cCcCCCCCCCccccccccc-------CCCccccCCccccCCccc
Confidence 4679999998774 5555 567999999988765544
No 68
>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=69.91 E-value=4.3 Score=27.23 Aligned_cols=30 Identities=30% Similarity=0.522 Sum_probs=19.7
Q ss_pred ccccccCCCCcceEEEeeccccC-CCceeccCCCC
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSS-AKRIKCLNCYQ 356 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~Rs-aDf~~C~~Cg~ 356 (370)
=.|+|+.||.. |..+ +..+ .+...|..||.
T Consensus 4 Y~y~C~~Cg~~---fe~~-~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 4 YEYRCEDCGHT---FEVL-QKISDDPLATCPECGG 34 (41)
T ss_pred EEEEcCCCCCE---EEEE-EecCCCCCCCCCCCCC
Confidence 36899999873 2222 3222 33888999997
No 69
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=69.42 E-value=2.9 Score=35.05 Aligned_cols=30 Identities=20% Similarity=0.578 Sum_probs=20.9
Q ss_pred cccccCCCCcceEEEeeccccCCCceeccCCCCccee
Q 017510 324 RYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYWES 360 (370)
Q Consensus 324 ~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w~~ 360 (370)
+-.||+|...- +|..- ..+.|..|+|.|.-
T Consensus 3 lp~cp~c~sEy-tYed~------~~~~cpec~~ew~~ 32 (112)
T COG2824 3 LPPCPKCNSEY-TYEDG------GQLICPECAHEWNE 32 (112)
T ss_pred CCCCCccCCce-EEecC------ceEeCchhcccccc
Confidence 35699997643 33332 26789999999984
No 70
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=68.36 E-value=3.1 Score=30.85 Aligned_cols=30 Identities=23% Similarity=0.401 Sum_probs=20.2
Q ss_pred cccccCCCCcceEEEeeccccCCCceeccCCCCcc
Q 017510 324 RYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYW 358 (370)
Q Consensus 324 ~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w 358 (370)
+.+|+.|++..+.|... |+ -|.|..||..-
T Consensus 7 ~VkCp~C~~~q~vFSha-~t----~V~C~~Cg~~L 36 (55)
T PF01667_consen 7 DVKCPGCYNIQTVFSHA-QT----VVKCVVCGTVL 36 (55)
T ss_dssp EEE-TTT-SEEEEETT--SS-----EE-SSSTSEE
T ss_pred EEECCCCCCeeEEEecC-Ce----EEEcccCCCEe
Confidence 57999999998888655 54 79999999753
No 71
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=68.28 E-value=5.1 Score=38.44 Aligned_cols=17 Identities=12% Similarity=0.528 Sum_probs=14.3
Q ss_pred ceeccCCCCcceehhhc
Q 017510 348 RIKCLNCYQYWESTTAL 364 (370)
Q Consensus 348 f~~C~~Cg~~w~~~~~~ 364 (370)
+|.|.+|+|.|+-+...
T Consensus 155 ef~C~~C~h~F~G~~qm 171 (278)
T PF15135_consen 155 EFHCPKCRHNFRGFAQM 171 (278)
T ss_pred eeecccccccchhhhhc
Confidence 99999999999976443
No 72
>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=66.71 E-value=4.5 Score=35.82 Aligned_cols=36 Identities=22% Similarity=0.510 Sum_probs=26.6
Q ss_pred CCccccccccccCCCCcceEEEeeccccCCCceeccCCCCcc
Q 017510 317 GPIYHSTRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYW 358 (370)
Q Consensus 317 ~~~~~t~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w 358 (370)
+.....+.+.|-+||+.-..+.-- + .-.|.+||+.-
T Consensus 105 GE~~g~G~l~C~~Cg~~~~~~~~~-~-----l~~Cp~C~~~~ 140 (146)
T PF07295_consen 105 GEVVGPGTLVCENCGHEVELTHPE-R-----LPPCPKCGHTE 140 (146)
T ss_pred CcEecCceEecccCCCEEEecCCC-c-----CCCCCCCCCCe
Confidence 345667899999999987665422 2 77899999863
No 73
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=66.13 E-value=6.4 Score=30.06 Aligned_cols=35 Identities=26% Similarity=0.296 Sum_probs=26.2
Q ss_pred ccccccCCCCcceEEEeeccccCCCceeccCCCCccee
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYWES 360 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w~~ 360 (370)
....||-||.......+. +-.-++.|..||-.|-+
T Consensus 5 ~lKPCPFCG~~~~~v~~~---~g~~~v~C~~CgA~~~~ 39 (64)
T PRK09710 5 NVKPCPFCGCPSVTVKAI---SGYYRAKCNGCESRTGY 39 (64)
T ss_pred cccCCCCCCCceeEEEec---CceEEEEcCCCCcCccc
Confidence 357899999998887752 11117999999998766
No 74
>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=66.10 E-value=6.6 Score=33.86 Aligned_cols=31 Identities=23% Similarity=0.423 Sum_probs=23.3
Q ss_pred cccccCCCCcceEEEeeccccCCCceeccCCCCc
Q 017510 324 RYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQY 357 (370)
Q Consensus 324 ~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~ 357 (370)
-..|+.|++..+.+.-- ...=|..|..||.+
T Consensus 93 yVlC~~C~spdT~l~k~---~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 93 YVLCPECGSPDTELIKE---GRLIFLKCKACGAS 123 (125)
T ss_dssp HSSCTSTSSSSEEEEEE---TTCCEEEETTTSCE
T ss_pred EEEcCCCCCCccEEEEc---CCEEEEEecccCCc
Confidence 47799999999877643 11119999999975
No 75
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=65.60 E-value=5.2 Score=32.17 Aligned_cols=31 Identities=19% Similarity=0.337 Sum_probs=26.1
Q ss_pred ccccccCCCCcceEEEeeccccCCCceeccCCCCcc
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYW 358 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w 358 (370)
-+.+|+.|++-.+.|... |+ -|.|..||..-
T Consensus 34 m~VkCp~C~n~q~VFShA-~t----~V~C~~Cg~~L 64 (85)
T PTZ00083 34 MDVKCPGCSQITTVFSHA-QT----VVLCGGCSSQL 64 (85)
T ss_pred EEEECCCCCCeeEEEecC-ce----EEEccccCCEe
Confidence 568999999999998876 65 79999999764
No 76
>PLN00209 ribosomal protein S27; Provisional
Probab=65.17 E-value=5.3 Score=32.22 Aligned_cols=31 Identities=19% Similarity=0.312 Sum_probs=26.0
Q ss_pred ccccccCCCCcceEEEeeccccCCCceeccCCCCcc
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYW 358 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w 358 (370)
-..+|+.|++-.+.|... |+ -|.|..||..-
T Consensus 35 m~VkCp~C~n~q~VFShA-~t----~V~C~~Cg~~L 65 (86)
T PLN00209 35 MDVKCQGCFNITTVFSHS-QT----VVVCGSCQTVL 65 (86)
T ss_pred EEEECCCCCCeeEEEecC-ce----EEEccccCCEe
Confidence 568999999999998766 65 79999999754
No 77
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=65.08 E-value=5.9 Score=26.20 Aligned_cols=30 Identities=20% Similarity=0.494 Sum_probs=21.9
Q ss_pred ccccccCCCCcceEEEeeccccCCCceeccCCCCcc
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYW 358 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w 358 (370)
+...|..|++....+. -.|++.|..||...
T Consensus 2 ~~~~C~~C~~~~i~~~------~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 2 NLKKCSKCGGNGIVNK------EDDYEVCIFCGSSF 31 (33)
T ss_pred CceEcCCCCCCeEEEe------cCCeEEcccCCcEe
Confidence 4578999999986642 12389999999753
No 78
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=64.64 E-value=4.3 Score=28.44 Aligned_cols=29 Identities=24% Similarity=0.599 Sum_probs=16.3
Q ss_pred cccccCCCCcceEEEeeccccCCCceeccCCCCcc
Q 017510 324 RYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYW 358 (370)
Q Consensus 324 ~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w 358 (370)
.|.|++||..-. +.+. . .-++|..||++.
T Consensus 3 ~y~C~~CG~~~~-~~~~---~--~~~~Cp~CG~~~ 31 (46)
T PRK00398 3 EYKCARCGREVE-LDEY---G--TGVRCPYCGYRI 31 (46)
T ss_pred EEECCCCCCEEE-ECCC---C--CceECCCCCCeE
Confidence 477888876322 2221 0 146788888753
No 79
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=64.10 E-value=4.6 Score=34.94 Aligned_cols=38 Identities=21% Similarity=0.367 Sum_probs=28.8
Q ss_pred ccccccccCCCCcceEEEeeccccCCC-ceeccCCCCccee
Q 017510 321 HSTRYMCGRCGHKKTTNHGNDQNSSAK-RIKCLNCYQYWES 360 (370)
Q Consensus 321 ~t~~~~C~~C~~~~~~~~q~~Q~RsaD-f~~C~~Cg~~w~~ 360 (370)
...+..||.|++.. ..-.+..+.++ -|.|..|+..|.-
T Consensus 27 ~~~~~~cP~C~s~~--~~k~g~~~~~~qRyrC~~C~~tf~~ 65 (129)
T COG3677 27 QITKVNCPRCKSSN--VVKIGGIRRGHQRYKCKSCGSTFTV 65 (129)
T ss_pred hcccCcCCCCCccc--eeeECCccccccccccCCcCcceee
Confidence 45678899999988 33444666667 8999999998854
No 80
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=63.52 E-value=4.6 Score=29.24 Aligned_cols=31 Identities=29% Similarity=0.664 Sum_probs=21.4
Q ss_pred cccccccCCCCcceEEEeeccccCCCceeccCCCCcc
Q 017510 322 STRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYW 358 (370)
Q Consensus 322 t~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w 358 (370)
+..+.|.+||..- .++ | -.+.+.|..||++-
T Consensus 4 ~~~Y~C~~Cg~~~---~~~-~--~~~~irCp~Cg~rI 34 (49)
T COG1996 4 MMEYKCARCGREV---ELD-Q--ETRGIRCPYCGSRI 34 (49)
T ss_pred eEEEEhhhcCCee---ehh-h--ccCceeCCCCCcEE
Confidence 4568999998765 222 2 22388999999973
No 81
>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=63.32 E-value=5.4 Score=29.44 Aligned_cols=33 Identities=18% Similarity=0.421 Sum_probs=22.3
Q ss_pred cccccCCCCcceEEEeeccccCCCceeccCCCCccee
Q 017510 324 RYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYWES 360 (370)
Q Consensus 324 ~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w~~ 360 (370)
+|.||.||..- .+... .+ +..+.|..||-....
T Consensus 2 ~~~CP~CG~~i-ev~~~--~~-GeiV~Cp~CGaeleV 34 (54)
T TIGR01206 2 QFECPDCGAEI-ELENP--EL-GELVICDECGAELEV 34 (54)
T ss_pred ccCCCCCCCEE-ecCCC--cc-CCEEeCCCCCCEEEE
Confidence 58999999832 22111 23 449999999987654
No 82
>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=62.29 E-value=8.1 Score=26.09 Aligned_cols=32 Identities=22% Similarity=0.625 Sum_probs=22.5
Q ss_pred cccccccCCCCcceEEEeeccccCCC-ceeccCC
Q 017510 322 STRYMCGRCGHKKTTNHGNDQNSSAK-RIKCLNC 354 (370)
Q Consensus 322 t~~~~C~~C~~~~~~~~q~~Q~RsaD-f~~C~~C 354 (370)
+-.+.||+|++..-.|.-= +..++- -|.|..|
T Consensus 3 ~i~v~CP~C~s~~~v~k~G-~~~~G~qryrC~~C 35 (36)
T PF03811_consen 3 KIDVHCPRCQSTEGVKKNG-KSPSGHQRYRCKDC 35 (36)
T ss_pred cEeeeCCCCCCCCcceeCC-CCCCCCEeEecCcC
Confidence 3468899999998555533 444443 8889888
No 83
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=62.04 E-value=6.7 Score=32.50 Aligned_cols=34 Identities=29% Similarity=0.502 Sum_probs=21.9
Q ss_pred ccccccCCCCcceEEEeeccccCCC-ceeccCCCCccee
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSAK-RIKCLNCYQYWES 360 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~RsaD-f~~C~~Cg~~w~~ 360 (370)
..|.||.||....... + .| .- .+.|.+||.....
T Consensus 20 t~f~CP~Cge~~v~v~-~--~k-~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 20 KIFECPRCGKVSISVK-I--KK-NIAIITCGNCGLYTEF 54 (99)
T ss_pred cEeECCCCCCeEeeee-c--CC-CcceEECCCCCCccCE
Confidence 4799999996433221 1 12 11 8899999987543
No 84
>PRK03954 ribonuclease P protein component 4; Validated
Probab=61.75 E-value=7.9 Score=33.27 Aligned_cols=37 Identities=24% Similarity=0.423 Sum_probs=25.4
Q ss_pred ccccccCCCCc-----ceEEEeeccccCCC-ceeccCCCCccee
Q 017510 323 TRYMCGRCGHK-----KTTNHGNDQNSSAK-RIKCLNCYQYWES 360 (370)
Q Consensus 323 ~~~~C~~C~~~-----~~~~~q~~Q~RsaD-f~~C~~Cg~~w~~ 360 (370)
-..-|.+|+.. ++++... ..+... .++|+.||+.-+|
T Consensus 63 KR~~CK~C~t~LiPG~n~~vRi~-~~~~~~vvitCl~CG~~kR~ 105 (121)
T PRK03954 63 KRRYCKRCHSFLVPGVNARVRLR-QKRMPHVVITCLECGHIMRY 105 (121)
T ss_pred HHHHhhcCCCeeecCCceEEEEe-cCCcceEEEECccCCCEEee
Confidence 35669999875 5665543 322234 8899999998776
No 85
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=61.32 E-value=8 Score=35.93 Aligned_cols=40 Identities=18% Similarity=0.091 Sum_probs=22.5
Q ss_pred cccccccccCCCCcceEEEeeccccCCC-----ceeccCCCCcce
Q 017510 320 YHSTRYMCGRCGHKKTTNHGNDQNSSAK-----RIKCLNCYQYWE 359 (370)
Q Consensus 320 ~~t~~~~C~~C~~~~~~~~q~~Q~RsaD-----f~~C~~Cg~~w~ 359 (370)
..+....||-||+.=.....+--+-.=. .+.|-+||+|..
T Consensus 10 ~~~~~~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~ 54 (201)
T COG1779 10 EFETRIDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGYRST 54 (201)
T ss_pred eeeeeecCCcccceeeEEEeeecCCccceEEEEEEEccccCCccc
Confidence 4566889999999100000000000111 789999999864
No 86
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=60.89 E-value=7.4 Score=34.13 Aligned_cols=32 Identities=22% Similarity=0.402 Sum_probs=23.7
Q ss_pred ccccccCCCCcceEEEeeccccCCCceeccCCCCc
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQY 357 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~ 357 (370)
.-..|+.|++..+.+.- ..| .-|..|..||.+
T Consensus 101 ~yVlC~~C~spdT~l~k--~~r-~~~l~C~ACGa~ 132 (138)
T PRK03988 101 EYVICPECGSPDTKLIK--EGR-IWVLKCEACGAE 132 (138)
T ss_pred hcEECCCCCCCCcEEEE--cCC-eEEEEcccCCCC
Confidence 35789999999988753 211 129999999986
No 87
>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=60.87 E-value=14 Score=30.17 Aligned_cols=29 Identities=28% Similarity=0.658 Sum_probs=21.1
Q ss_pred ccccccCCCCcceEEEeeccccCCC-ceeccCCCCcc
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSAK-RIKCLNCYQYW 358 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~RsaD-f~~C~~Cg~~w 358 (370)
..+.||.||...+. |-+- ...|..||..|
T Consensus 34 ~ky~Cp~Cgk~~vk-------R~a~GIW~C~~C~~~~ 63 (90)
T PF01780_consen 34 AKYTCPFCGKTSVK-------RVATGIWKCKKCGKKF 63 (90)
T ss_dssp S-BEESSSSSSEEE-------EEETTEEEETTTTEEE
T ss_pred CCCcCCCCCCceeE-------EeeeEEeecCCCCCEE
Confidence 35889999998743 2333 89999999765
No 88
>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=59.77 E-value=3.3 Score=41.70 Aligned_cols=10 Identities=30% Similarity=0.634 Sum_probs=6.8
Q ss_pred ceeccCCCCc
Q 017510 348 RIKCLNCYQY 357 (370)
Q Consensus 348 f~~C~~Cg~~ 357 (370)
||.|.+||+|
T Consensus 285 FFkC~~C~~R 294 (344)
T PF09332_consen 285 FFKCKDCGNR 294 (344)
T ss_dssp EEE-T-TS-E
T ss_pred eEECCCCCCe
Confidence 9999999999
No 89
>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=58.63 E-value=4.8 Score=39.87 Aligned_cols=37 Identities=19% Similarity=0.501 Sum_probs=24.9
Q ss_pred ccccccCCCCcceE-EEeeccc-cCCC-ceeccCCCCccee
Q 017510 323 TRYMCGRCGHKKTT-NHGNDQN-SSAK-RIKCLNCYQYWES 360 (370)
Q Consensus 323 ~~~~C~~C~~~~~~-~~q~~Q~-RsaD-f~~C~~Cg~~w~~ 360 (370)
..-.||-||+.-+. +... .. ..+- |..|.-|+..|.|
T Consensus 183 ~~~~CPvCGs~P~~s~~~~-~~~~~G~RyL~CslC~teW~~ 222 (305)
T TIGR01562 183 SRTLCPACGSPPVASMVRQ-GGKETGLRYLSCSLCATEWHY 222 (305)
T ss_pred CCCcCCCCCChhhhhhhcc-cCCCCCceEEEcCCCCCcccc
Confidence 35589999998643 2222 11 1122 9999999999987
No 90
>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=58.29 E-value=4.7 Score=30.55 Aligned_cols=41 Identities=27% Similarity=0.530 Sum_probs=27.3
Q ss_pred ccccccCCCCcceEEEeeccccCCC--ceeccCCCCcceehhhc
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSAK--RIKCLNCYQYWESTTAL 364 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~RsaD--f~~C~~Cg~~w~~~~~~ 364 (370)
....||+|++.++.|-=- -.-+.. -+.|..|...|..-+.+
T Consensus 4 ~~~~CPRC~S~nTKFcYy-NNy~~~QPR~~Ck~C~rywT~GG~l 46 (63)
T PF02701_consen 4 QPLPCPRCDSTNTKFCYY-NNYNLSQPRYFCKSCRRYWTHGGTL 46 (63)
T ss_pred cCCCCCCcCCCCCEEEee-cCCCCCCcchhhHHHHHHHHhccee
Confidence 357899999987764322 222222 56799999999765543
No 91
>KOG0909 consensus Peptide:N-glycanase [Posttranslational modification, protein turnover, chaperones]
Probab=58.14 E-value=9.4 Score=39.50 Aligned_cols=102 Identities=22% Similarity=0.326 Sum_probs=56.1
Q ss_pred hHHHHhHHhhcCCCCChHhhhchhcCCCChhhhcCCChhhcCC-hHHHHHHH-HHH--HHHhhccc-CcccCCCCCCccc
Q 017510 247 EVKYRSILFNLMDPENPDFRRKVLLGHVKPEALIKMSSEEMVS-DGSRRLNQ-QIK--KERASDRY-LPWKGGYLGPIYH 321 (370)
Q Consensus 247 k~k~Rsl~~NLKd~kNp~Lr~~vl~G~isp~~lv~Ms~eEmas-~e~k~~r~-~~~--~e~l~~~~-l~~~~~~~~~~~~ 321 (370)
-..+|+-+..+--=.||.|....++ -|+.++|..|..++++- +..+..+. .+. --.-++.+ .-|.
T Consensus 90 le~l~~~sqhvlvYEDP~lq~~Als-~iPvdEL~~kA~ekla~~eg~ki~kdy~i~leLL~WFKq~FF~Wv--------- 159 (500)
T KOG0909|consen 90 LEVLRSYSQHVLVYEDPVLQAKALS-TIPVDELKEKASEKLAKAEGEKIYKDYLIKLELLNWFKQDFFKWV--------- 159 (500)
T ss_pred HHHHHHhccCceeecCHHHHHHHHh-cCCHHHHHHHHHHhhcccchhhhhcchHHHHHHHHHHHHhhheec---------
Confidence 3344444444443468887665543 57779999999999885 22222221 111 11112222 1132
Q ss_pred cccccccCCCCcceEEEeeccccC------CC----ceeccCCCCccee
Q 017510 322 STRYMCGRCGHKKTTNHGNDQNSS------AK----RIKCLNCYQYWES 360 (370)
Q Consensus 322 t~~~~C~~C~~~~~~~~q~~Q~Rs------aD----f~~C~~Cg~~w~~ 360 (370)
+...|.+||+.--+-.+- |--. ++ .|.|..||+.=+|
T Consensus 160 -N~PpC~~CG~et~~~l~~-~~p~eeE~~~Ga~rVEiy~C~~C~~~~RF 206 (500)
T KOG0909|consen 160 -NNPPCNKCGGETSSGLGN-QPPNEEEKKFGAGRVEIYKCNRCGTETRF 206 (500)
T ss_pred -CCCCcccccccccccccC-CCCchhHhhcCCceEEEEEecCCCCcccC
Confidence 457799999876422221 2111 22 8999999998776
No 92
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=57.89 E-value=9.7 Score=28.62 Aligned_cols=34 Identities=15% Similarity=0.435 Sum_probs=21.0
Q ss_pred cccccccCCCCcceEEEeeccccCCC-ceeccCCCCc
Q 017510 322 STRYMCGRCGHKKTTNHGNDQNSSAK-RIKCLNCYQY 357 (370)
Q Consensus 322 t~~~~C~~C~~~~~~~~q~~Q~RsaD-f~~C~~Cg~~ 357 (370)
-..|.||.||... -|+=. .=|..- -|+|.+||..
T Consensus 23 ~~~F~CPnCG~~~-I~RC~-~CRk~~~~Y~CP~CGF~ 57 (59)
T PRK14890 23 AVKFLCPNCGEVI-IYRCE-KCRKQSNPYTCPKCGFE 57 (59)
T ss_pred cCEeeCCCCCCee-Eeech-hHHhcCCceECCCCCCc
Confidence 4589999998731 12211 223222 8999999964
No 93
>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=57.88 E-value=7.1 Score=34.83 Aligned_cols=34 Identities=12% Similarity=0.282 Sum_probs=22.1
Q ss_pred ccccccccCCCCcceEEEeeccccCCCceeccCCCCcce
Q 017510 321 HSTRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYWE 359 (370)
Q Consensus 321 ~t~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w~ 359 (370)
....|.||+|+ .+-+|.+. . + ..++|.+||..-.
T Consensus 106 ~~~~Y~Cp~c~-~r~tf~eA-~--~-~~F~Cp~Cg~~L~ 139 (158)
T TIGR00373 106 NNMFFICPNMC-VRFTFNEA-M--E-LNFTCPRCGAMLD 139 (158)
T ss_pred CCCeEECCCCC-cEeeHHHH-H--H-cCCcCCCCCCEee
Confidence 44679999998 33343333 2 1 2678999998643
No 94
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=57.02 E-value=5.5 Score=38.78 Aligned_cols=37 Identities=19% Similarity=0.262 Sum_probs=28.3
Q ss_pred cccccccccCCCCcceEEEeecc-cc------------CCC-ceeccCCCCc
Q 017510 320 YHSTRYMCGRCGHKKTTNHGNDQ-NS------------SAK-RIKCLNCYQY 357 (370)
Q Consensus 320 ~~t~~~~C~~C~~~~~~~~q~~Q-~R------------saD-f~~C~~Cg~~ 357 (370)
+.|+...|+.||..-+--+++ | =+ --| .++|..||..
T Consensus 235 ~~t~~~~C~~Cg~~PtiP~~~-~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~ 285 (298)
T KOG2879|consen 235 TGTSDTECPVCGEPPTIPHVI-GKCGHIYCYYCIATSRLWDASFTCPLCGEN 285 (298)
T ss_pred cccCCceeeccCCCCCCCeee-ccccceeehhhhhhhhcchhhcccCccCCC
Confidence 566789999999999998988 5 22 224 7789999864
No 95
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=56.81 E-value=10 Score=31.98 Aligned_cols=32 Identities=22% Similarity=0.395 Sum_probs=23.2
Q ss_pred ccccccCCCCcceEEEeeccccCCCceeccCCCCc
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQY 357 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~ 357 (370)
.-..|+.|++..+.+.-- ...-|..|..||.+
T Consensus 79 ~yVlC~~C~spdT~l~k~---~r~~~l~C~aCGa~ 110 (110)
T smart00653 79 EYVLCPECGSPDTELIKE---NRLFFLKCEACGAR 110 (110)
T ss_pred hcEECCCCCCCCcEEEEe---CCeEEEEccccCCC
Confidence 357899999999776542 11119999999974
No 96
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=56.56 E-value=22 Score=29.06 Aligned_cols=30 Identities=23% Similarity=0.581 Sum_probs=21.4
Q ss_pred ccccccCCCCcceEEEeeccccCCCceeccCCCCcc
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYW 358 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w 358 (370)
..+.|+.|+...+.-.-. ..+.|..||..|
T Consensus 35 a~y~CpfCgk~~vkR~a~------GIW~C~~C~~~~ 64 (90)
T PRK03976 35 AKHVCPVCGRPKVKRVGT------GIWECRKCGAKF 64 (90)
T ss_pred cCccCCCCCCCceEEEEE------EEEEcCCCCCEE
Confidence 368899998766543222 278999999875
No 97
>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=56.50 E-value=13 Score=25.26 Aligned_cols=29 Identities=24% Similarity=0.455 Sum_probs=19.6
Q ss_pred ccccCCCCcceEEEeeccccCCCceeccC---CCCc
Q 017510 325 YMCGRCGHKKTTNHGNDQNSSAKRIKCLN---CYQY 357 (370)
Q Consensus 325 ~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~---Cg~~ 357 (370)
..||.||+ ...+. +.|.+-|+-|.+ |.+.
T Consensus 2 ~~CP~Cg~---~lv~r-~~k~g~F~~Cs~yP~C~~~ 33 (39)
T PF01396_consen 2 EKCPKCGG---PLVLR-RGKKGKFLGCSNYPECKYT 33 (39)
T ss_pred cCCCCCCc---eeEEE-ECCCCCEEECCCCCCcCCe
Confidence 46999993 22333 556666999987 8765
No 98
>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=56.36 E-value=21 Score=29.16 Aligned_cols=30 Identities=23% Similarity=0.613 Sum_probs=21.0
Q ss_pred ccccccCCCCcceEEEeeccccCCCceeccCCCCcc
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYW 358 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w 358 (370)
..+.||.||...+.-.- ...+.|..||..|
T Consensus 34 a~y~CpfCgk~~vkR~a------~GIW~C~~C~~~~ 63 (91)
T TIGR00280 34 AKYVCPFCGKKTVKRGS------TGIWTCRKCGAKF 63 (91)
T ss_pred cCccCCCCCCCceEEEe------eEEEEcCCCCCEE
Confidence 36889999976543221 1278999999875
No 99
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=55.74 E-value=9.6 Score=34.73 Aligned_cols=35 Identities=17% Similarity=0.421 Sum_probs=21.8
Q ss_pred ccccccccCCCCcceEEEeeccccCCCceeccCCCCccee
Q 017510 321 HSTRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYWES 360 (370)
Q Consensus 321 ~t~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w~~ 360 (370)
....|.||+|+. +-+|... - . ..|+|..||..-.+
T Consensus 114 ~~~~Y~Cp~C~~-rytf~eA-~--~-~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 114 NNMFFFCPNCHI-RFTFDEA-M--E-YGFRCPQCGEMLEE 148 (178)
T ss_pred CCCEEECCCCCc-EEeHHHH-h--h-cCCcCCCCCCCCee
Confidence 346799999983 3333322 1 1 16789999986543
No 100
>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=55.71 E-value=7.5 Score=41.60 Aligned_cols=35 Identities=20% Similarity=0.346 Sum_probs=24.7
Q ss_pred cccccCCCCcceE-EEeeccccC---CC--ceeccCCCCcce
Q 017510 324 RYMCGRCGHKKTT-NHGNDQNSS---AK--RIKCLNCYQYWE 359 (370)
Q Consensus 324 ~~~C~~C~~~~~~-~~q~~Q~Rs---aD--f~~C~~Cg~~w~ 359 (370)
...||.||+...- |.++ +--. .+ +|.|..||..|.
T Consensus 200 ~vpCPhCg~~~~l~~~~l-~w~~~~~~~~a~y~C~~Cg~~i~ 240 (557)
T PF05876_consen 200 YVPCPHCGEEQVLEWENL-KWDKGEAPETARYVCPHCGCEIE 240 (557)
T ss_pred EccCCCCCCCccccccce-eecCCCCccceEEECCCCcCCCC
Confidence 4689999987554 4555 3221 22 999999999885
No 101
>PF14726 RTTN_N: Rotatin, an armadillo repeat protein, centriole functioning
Probab=55.67 E-value=11 Score=31.13 Aligned_cols=53 Identities=25% Similarity=0.244 Sum_probs=44.4
Q ss_pred cccHHHHHHHHHHhhcCCCCHhhhhccCceeecccccCCCCHHHHHHHHHHHH
Q 017510 25 ELEEAQCIAALDQLHKSSITCQLLVSTQLVRHLLPLTKHPRQKIQDTASELIL 77 (370)
Q Consensus 25 ~~~~~~~l~~L~~L~~~~it~e~L~~T~IG~~V~~Lrkh~~~~I~~~Ak~Li~ 77 (370)
++..++++++|.+|-+.+....+|+.-+.-..+.+||++-++..+...-.|++
T Consensus 44 ~~~~~~VL~Ll~~L~~~~~a~~~l~~iG~~~fL~klr~~~~~~~~~~id~il~ 96 (98)
T PF14726_consen 44 VPMKEEVLALLLRLLKSPYAAQILRDIGAVRFLSKLRPNVEPNLQAEIDEILD 96 (98)
T ss_pred CccHHHHHHHHHHHHhCcHHHHHHHHccHHHHHHHHHhcCCHHHHHHHHHHHh
Confidence 44889999999999999999999998776677899999988877777666654
No 102
>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=55.11 E-value=10 Score=26.92 Aligned_cols=30 Identities=27% Similarity=0.543 Sum_probs=19.3
Q ss_pred ccccccCCCCcceEEEeeccccCCC-ceeccCCCC
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSAK-RIKCLNCYQ 356 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~RsaD-f~~C~~Cg~ 356 (370)
=.|+|..||+.--.+.-+ +.+ ...|..||.
T Consensus 4 Yey~C~~Cg~~fe~~~~~----~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 4 YEYRCTACGHRFEVLQKM----SDDPLATCPECGG 34 (52)
T ss_pred EEEEeCCCCCEeEEEEec----CCCCCCCCCCCCC
Confidence 368999999643322211 223 788999997
No 103
>PRK11032 hypothetical protein; Provisional
Probab=54.07 E-value=9.5 Score=34.33 Aligned_cols=35 Identities=14% Similarity=0.264 Sum_probs=26.4
Q ss_pred CccccccccccCCCCcceEEEeeccccCCCceeccCCCCcc
Q 017510 318 PIYHSTRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYW 358 (370)
Q Consensus 318 ~~~~t~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w 358 (370)
..+.-+.+.|-+||+.-+.|+-- + .--|.+||+.-
T Consensus 118 Evvg~G~LvC~~Cg~~~~~~~p~-~-----i~pCp~C~~~~ 152 (160)
T PRK11032 118 EVVGLGNLVCEKCHHHLAFYTPE-V-----LPLCPKCGHDQ 152 (160)
T ss_pred eeeecceEEecCCCCEEEecCCC-c-----CCCCCCCCCCe
Confidence 34556889999999988776533 3 67799999863
No 104
>PHA02942 putative transposase; Provisional
Probab=52.38 E-value=6.6 Score=40.03 Aligned_cols=27 Identities=30% Similarity=0.560 Sum_probs=19.4
Q ss_pred cccccCCCCcceEEEeeccccCCC-ceeccCCCCcc
Q 017510 324 RYMCGRCGHKKTTNHGNDQNSSAK-RIKCLNCYQYW 358 (370)
Q Consensus 324 ~~~C~~C~~~~~~~~q~~Q~RsaD-f~~C~~Cg~~w 358 (370)
.-.|+.||+.... . .+ .+.|.+||+.+
T Consensus 325 Sq~Cs~CG~~~~~---l-----~~r~f~C~~CG~~~ 352 (383)
T PHA02942 325 SVSCPKCGHKMVE---I-----AHRYFHCPSCGYEN 352 (383)
T ss_pred CccCCCCCCccCc---C-----CCCEEECCCCCCEe
Confidence 3679999986421 1 22 89999999865
No 105
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=50.85 E-value=7.8 Score=39.49 Aligned_cols=36 Identities=17% Similarity=0.352 Sum_probs=27.6
Q ss_pred cccccCCCCcceEEEeeccccCCCceeccCCCCcceehhhccc
Q 017510 324 RYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYWESTTALYG 366 (370)
Q Consensus 324 ~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w~~~~~~~~ 366 (370)
.+.|..|+.+....... .-.|..||.+|...+.+|.
T Consensus 244 ~~~C~~c~~~~~~~~~~-------~~~C~~c~~~~~~~GPlW~ 279 (382)
T PRK04338 244 VYYCPKCLYREEVEGLP-------PEECPVCGGKFGTAGPLWL 279 (382)
T ss_pred EEECCCCCcEEEecCCC-------CCCCCCCCCcceecccccc
Confidence 57899999876643322 3469999999999999885
No 106
>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=50.54 E-value=4.4 Score=40.78 Aligned_cols=37 Identities=24% Similarity=0.556 Sum_probs=18.4
Q ss_pred cccccccccCCCCcceEEEeeccccCCCceeccCCCCc-ceehh
Q 017510 320 YHSTRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQY-WESTT 362 (370)
Q Consensus 320 ~~t~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~-w~~~~ 362 (370)
+.--.|+|+.|+++-++|..+ . ...|.+||.. |.=++
T Consensus 281 a~KRFFkC~~C~~Rt~sl~r~-P-----~~~C~~Cg~~~wer~~ 318 (344)
T PF09332_consen 281 AVKRFFKCKDCGNRTISLERL-P-----KKHCSNCGSSKWERTG 318 (344)
T ss_dssp EE-EEEE-T-TS-EEEESSSS--------S--TTT-S---EEE-
T ss_pred eeeeeEECCCCCCeeeecccC-C-----CCCCCcCCcCceeehh
Confidence 344578999999998887655 4 3579999954 77554
No 107
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=50.53 E-value=30 Score=28.26 Aligned_cols=29 Identities=24% Similarity=0.619 Sum_probs=21.1
Q ss_pred ccccccCCCCcceEEEeeccccCCC-ceeccCCCCcc
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSAK-RIKCLNCYQYW 358 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~RsaD-f~~C~~Cg~~w 358 (370)
..+.||.||...+. |.+- .+.|..||..|
T Consensus 35 a~y~CpfCgk~~vk-------R~a~GIW~C~~C~~~~ 64 (90)
T PTZ00255 35 AKYFCPFCGKHAVK-------RQAVGIWRCKGCKKTV 64 (90)
T ss_pred CCccCCCCCCCcee-------eeeeEEEEcCCCCCEE
Confidence 36889999976543 2232 78999999875
No 108
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=49.58 E-value=14 Score=32.20 Aligned_cols=32 Identities=19% Similarity=0.404 Sum_probs=23.6
Q ss_pred ccccccCCCCcceEEEeeccccCCCceeccCCCCc
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQY 357 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~ 357 (370)
.-..|+.|++..+.+.- ..| .-|..|..||.+
T Consensus 96 ~yVlC~~C~sPdT~l~k--~~r-~~~l~C~ACGa~ 127 (133)
T TIGR00311 96 KYVICRECNRPDTRIIK--EGR-VSLLKCEACGAK 127 (133)
T ss_pred heEECCCCCCCCcEEEE--eCC-eEEEecccCCCC
Confidence 45789999999988653 211 118899999976
No 109
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=49.55 E-value=7.1 Score=24.13 Aligned_cols=23 Identities=26% Similarity=0.602 Sum_probs=13.2
Q ss_pred ccccCCCCcceEEEeeccccCCCceeccCCCCc
Q 017510 325 YMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQY 357 (370)
Q Consensus 325 ~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~ 357 (370)
..|+.||... ..|+-.|.+||.+
T Consensus 3 ~~Cp~Cg~~~----------~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEI----------DPDAKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcC----------CcccccChhhCCC
Confidence 4578887621 2224457777764
No 110
>PRK00420 hypothetical protein; Validated
Probab=48.99 E-value=11 Score=32.07 Aligned_cols=29 Identities=14% Similarity=0.219 Sum_probs=20.8
Q ss_pred cccccCCCCcceEEEeeccccCCCceeccCCCCcce
Q 017510 324 RYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYWE 359 (370)
Q Consensus 324 ~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w~ 359 (370)
...||.||..-..+.+- -+.|.+||....
T Consensus 23 ~~~CP~Cg~pLf~lk~g-------~~~Cp~Cg~~~~ 51 (112)
T PRK00420 23 SKHCPVCGLPLFELKDG-------EVVCPVHGKVYI 51 (112)
T ss_pred cCCCCCCCCcceecCCC-------ceECCCCCCeee
Confidence 36799999765554443 677999998544
No 111
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=48.65 E-value=20 Score=34.38 Aligned_cols=59 Identities=20% Similarity=0.174 Sum_probs=33.2
Q ss_pred hhhcCChHHHHHHHHHHHHHhhcccCcccCCCCCCccccccccccCCCCcceEEEeeccccCCCceeccCCCCcc
Q 017510 284 SEEMVSDGSRRLNQQIKKERASDRYLPWKGGYLGPIYHSTRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYW 358 (370)
Q Consensus 284 ~eEmas~e~k~~r~~~~~e~l~~~~l~~~~~~~~~~~~t~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w 358 (370)
...+..-.+.+.++.++.++-. --++.... ....+...|+.||. . +...+.|.+||+.|
T Consensus 274 ~~~i~~~~~~~~~~~l~yka~~-~~~~v~~~----~~~~tS~~C~~cg~-------~----~~r~~~C~~cg~~~ 332 (364)
T COG0675 274 RRSISDWAFGELRRQLEYKAEW-GGIVVKVV----PPYYTSKTCPCCGH-------L----SGRLFKCPRCGFVH 332 (364)
T ss_pred cccHhhhhHHHHHHHHHHHHHh-CCeEEEEC----CCCCCcccccccCC-------c----cceeEECCCCCCee
Confidence 4444444466666666666554 21222111 11233477999999 1 22278899999864
No 112
>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=47.85 E-value=66 Score=24.90 Aligned_cols=33 Identities=24% Similarity=0.596 Sum_probs=18.1
Q ss_pred ccccccCCCC-----cceEEEeecc-ccCCC--ceeccCCCC
Q 017510 323 TRYMCGRCGH-----KKTTNHGNDQ-NSSAK--RIKCLNCYQ 356 (370)
Q Consensus 323 ~~~~C~~C~~-----~~~~~~q~~Q-~RsaD--f~~C~~Cg~ 356 (370)
...-|.+||. ..+++... . ...++ .++|..|||
T Consensus 45 kr~~Ck~C~~~liPG~~~~vri~-~~~~~~~~l~~~C~~C~~ 85 (85)
T PF04032_consen 45 KRTICKKCGSLLIPGVNCSVRIR-KKKKKKNFLVYTCLNCGH 85 (85)
T ss_dssp CCTB-TTT--B--CTTTEEEEEE----SSS-EEEEEETTTTE
T ss_pred hcccccCCCCEEeCCCccEEEEE-ecCCCCCEEEEEccccCC
Confidence 4567999998 34544433 1 12334 999999996
No 113
>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=47.14 E-value=12 Score=23.14 Aligned_cols=12 Identities=25% Similarity=0.896 Sum_probs=9.1
Q ss_pred ccccccccCCCC
Q 017510 321 HSTRYMCGRCGH 332 (370)
Q Consensus 321 ~t~~~~C~~C~~ 332 (370)
....|.||+||.
T Consensus 13 ~~v~f~CPnCG~ 24 (24)
T PF07754_consen 13 QAVPFPCPNCGF 24 (24)
T ss_pred cCceEeCCCCCC
Confidence 346799999984
No 114
>PRK12495 hypothetical protein; Provisional
Probab=46.72 E-value=6.2 Score=37.21 Aligned_cols=33 Identities=24% Similarity=0.369 Sum_probs=22.6
Q ss_pred ccccccccccCCCCcceEEEeeccccCCCceeccCCCCcce
Q 017510 319 IYHSTRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYWE 359 (370)
Q Consensus 319 ~~~t~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w~ 359 (370)
+.....+.|+.||..=-.|-- -+.|..|+...-
T Consensus 37 gatmsa~hC~~CG~PIpa~pG--------~~~Cp~CQ~~~~ 69 (226)
T PRK12495 37 GATMTNAHCDECGDPIFRHDG--------QEFCPTCQQPVT 69 (226)
T ss_pred hcccchhhcccccCcccCCCC--------eeECCCCCCccc
Confidence 345567999999987553311 567999987643
No 115
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=46.67 E-value=7.9 Score=23.44 Aligned_cols=6 Identities=50% Similarity=1.137 Sum_probs=3.6
Q ss_pred ccCCCC
Q 017510 351 CLNCYQ 356 (370)
Q Consensus 351 C~~Cg~ 356 (370)
|.+||+
T Consensus 16 C~~CG~ 21 (23)
T PF13240_consen 16 CPNCGT 21 (23)
T ss_pred hhhhCC
Confidence 666665
No 116
>KOG4274 consensus Positive cofactor 2 (PC2), subunit of a multiprotein coactivator of RNA polymerase II [Transcription]
Probab=46.39 E-value=25 Score=37.62 Aligned_cols=66 Identities=20% Similarity=0.215 Sum_probs=49.3
Q ss_pred hHHHHHHHHHHHHHHhhhcCCCchhhhhhcCCCChHHHHHHHHHHHHHhhCCCchhhhHHHHhHHhhcCCCCChHhhhch
Q 017510 190 DYFRERIREKLYKALSKVSGEVDEEVQDKLNGCDPIRVAITAESLMFEKWGHSFGTYEVKYRSILFNLMDPENPDFRRKV 269 (370)
Q Consensus 190 d~vR~k~r~lL~~aL~~~~~~~~~~~~~~~~~~~~~~~A~~IE~~if~~~~~~~~~Yk~k~Rsl~~NLKd~kNp~Lr~~v 269 (370)
-++|.+++.-|.++|.... -++ ..-|..+|+++|.... +..+|-..+--||.+++|-.|..-...|
T Consensus 9 ~kFRq~vIsried~l~~n~----q~~---------~k~a~~mE~hVF~K~~-tkDEYl~lvAkli~h~~d~s~~ksq~sv 74 (742)
T KOG4274|consen 9 PKFRQHVISRIEDELRKNG----QAH---------SKSAKDMESHVFLKAK-TKDEYLSLVAKLIIHFRDISNKKSQASV 74 (742)
T ss_pred HHHHHHHHHHhhhhhhhhh----hcc---------CcchHHHHHHHHHhhh-hHHHHHHHHHHHHHHHHhhhhhhhhhhh
Confidence 4789999999999998621 111 2567899999998864 4569999999999999987764433333
No 117
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=46.31 E-value=17 Score=33.81 Aligned_cols=32 Identities=19% Similarity=0.437 Sum_probs=23.7
Q ss_pred ccccccCCCCcceEEEeeccccCCCceeccCCCCc
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQY 357 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~ 357 (370)
.-..|+.|++..+.+.- .. ..-|..|..||.+
T Consensus 97 ~yV~C~~C~~pdT~l~k--~~-~~~~l~C~aCGa~ 128 (201)
T PRK12336 97 EYVICSECGLPDTRLVK--ED-RVLMLRCDACGAH 128 (201)
T ss_pred heEECCCCCCCCcEEEE--cC-CeEEEEcccCCCC
Confidence 45789999999988753 21 1118899999976
No 118
>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=46.16 E-value=9.7 Score=33.66 Aligned_cols=34 Identities=26% Similarity=0.516 Sum_probs=24.6
Q ss_pred cccccCCCCcceEEEeeccccCCC---ceeccCCCCcce
Q 017510 324 RYMCGRCGHKKTTNHGNDQNSSAK---RIKCLNCYQYWE 359 (370)
Q Consensus 324 ~~~C~~C~~~~~~~~q~~Q~RsaD---f~~C~~Cg~~w~ 359 (370)
...||+||+.++...- |=.|.- .|.|..|.+-|-
T Consensus 105 ~~~cp~c~s~~t~~~s--~fg~t~cka~~~c~~c~epf~ 141 (146)
T TIGR02159 105 SVQCPRCGSADTTITS--IFGPTACKALYRCRACKEPFE 141 (146)
T ss_pred CCcCCCCCCCCcEeec--CCCChhhHHHhhhhhhCCcHh
Confidence 4799999999887542 333433 888999987653
No 119
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=45.60 E-value=19 Score=23.96 Aligned_cols=27 Identities=22% Similarity=0.554 Sum_probs=14.1
Q ss_pred ccCCCCcceEEEeeccccCCC---ceeccCCCCcc
Q 017510 327 CGRCGHKKTTNHGNDQNSSAK---RIKCLNCYQYW 358 (370)
Q Consensus 327 C~~C~~~~~~~~q~~Q~RsaD---f~~C~~Cg~~w 358 (370)
|+.||+. ..+ .+-.+| -..|..||.-.
T Consensus 3 C~~CG~~-l~~----~ip~gd~r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 3 CPQCGGP-LER----RIPEGDDRERLVCPACGFIH 32 (34)
T ss_dssp -TTT--B--EE----E--TT-SS-EEEETTTTEEE
T ss_pred cccccCh-hhh----hcCCCCCccceECCCCCCEE
Confidence 9999988 222 233556 78899998643
No 120
>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=44.50 E-value=14 Score=35.93 Aligned_cols=41 Identities=17% Similarity=0.315 Sum_probs=20.2
Q ss_pred cccccccCCCCcceEEEeeccc-cCCC--ceeccCCCCcceehh
Q 017510 322 STRYMCGRCGHKKTTNHGNDQN-SSAK--RIKCLNCYQYWESTT 362 (370)
Q Consensus 322 t~~~~C~~C~~~~~~~~q~~Q~-RsaD--f~~C~~Cg~~w~~~~ 362 (370)
-....|+.||+.+..-+...-. .... ..+|..||..+|.-.
T Consensus 209 ~~R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK~vd 252 (290)
T PF04216_consen 209 FVRIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLKTVD 252 (290)
T ss_dssp --TTS-TTT---SS-EEE--------SEEEEEETTTTEEEEEEE
T ss_pred ecCCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHHHHh
Confidence 3467899998875542222011 1111 889999999999754
No 121
>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=43.64 E-value=11 Score=31.81 Aligned_cols=30 Identities=13% Similarity=0.400 Sum_probs=19.7
Q ss_pred cccccccccCCCCcceEEEeeccccCCCceeccCCCCc
Q 017510 320 YHSTRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQY 357 (370)
Q Consensus 320 ~~t~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~ 357 (370)
.....+.|..||. ...+.+. ++.|..||..
T Consensus 66 ~~p~~~~C~~Cg~-~~~~~~~-------~~~CP~Cgs~ 95 (115)
T TIGR00100 66 DEPVECECEDCSE-EVSPEID-------LYRCPKCHGI 95 (115)
T ss_pred eeCcEEEcccCCC-EEecCCc-------CccCcCCcCC
Confidence 4557899999992 1222222 7789999953
No 122
>PF11648 RIG-I_C-RD: C-terminal domain of RIG-I; InterPro: IPR021673 This family of proteins represents the regulatory domain RD of RIG-I, a protein which initiates a signalling cascade that provides essential antiviral protection for the host. The RD domain binds viral RNA, activating the RIG-I ATPase by RNA-dependent dimerisation. The structure of RD contains a zinc-binding domain and is thought to confer ligand specificity []. ; GO: 0016817 hydrolase activity, acting on acid anhydrides; PDB: 2RQB_A 3GA3_A 2W4R_D 3EQT_A 2RQA_A 2RMJ_A 3NCU_A 2QFD_C 2QFB_D 3TMI_A ....
Probab=43.24 E-value=11 Score=32.34 Aligned_cols=13 Identities=46% Similarity=1.012 Sum_probs=11.5
Q ss_pred ceeccCCCCccee
Q 017510 348 RIKCLNCYQYWES 360 (370)
Q Consensus 348 f~~C~~Cg~~w~~ 360 (370)
.+.|.+||+.|-.
T Consensus 60 ~I~C~~C~~~wG~ 72 (123)
T PF11648_consen 60 KIHCKNCGQDWGI 72 (123)
T ss_dssp EEEETSTSBEEEE
T ss_pred EEEcCCCChHhhh
Confidence 6889999999976
No 123
>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=42.66 E-value=11 Score=33.64 Aligned_cols=17 Identities=18% Similarity=0.204 Sum_probs=14.8
Q ss_pred ceeccCCCCcceehhhc
Q 017510 348 RIKCLNCYQYWESTTAL 364 (370)
Q Consensus 348 f~~C~~Cg~~w~~~~~~ 364 (370)
||.|.+|+.+|.|-.|+
T Consensus 109 ~Y~Cp~c~~r~tf~eA~ 125 (158)
T TIGR00373 109 FFICPNMCVRFTFNEAM 125 (158)
T ss_pred eEECCCCCcEeeHHHHH
Confidence 99999999999886654
No 124
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=42.62 E-value=13 Score=31.06 Aligned_cols=34 Identities=18% Similarity=0.453 Sum_probs=23.6
Q ss_pred cccccCCCCc-----ceEEEeeccccCCC-ceeccCCCCcceeh
Q 017510 324 RYMCGRCGHK-----KTTNHGNDQNSSAK-RIKCLNCYQYWEST 361 (370)
Q Consensus 324 ~~~C~~C~~~-----~~~~~q~~Q~RsaD-f~~C~~Cg~~w~~~ 361 (370)
...|.+|+.. ++.+. .|++- -++|..||+.-+|-
T Consensus 56 R~~CkkC~t~Lvpg~n~rvR----~~~~~v~vtC~~CG~~~R~p 95 (105)
T COG2023 56 RTICKKCYTPLVPGKNARVR----LRKGRVVVTCLECGTIRRYP 95 (105)
T ss_pred HHhccccCcccccCcceEEE----EcCCeEEEEecCCCcEEEec
Confidence 4569999884 33332 34443 99999999987773
No 125
>KOG3352 consensus Cytochrome c oxidase, subunit Vb/COX4 [Energy production and conversion]
Probab=42.56 E-value=17 Score=32.45 Aligned_cols=34 Identities=15% Similarity=0.332 Sum_probs=25.5
Q ss_pred ccccCCCCcceEEEeeccccCCCceeccCCCCccee
Q 017510 325 YMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYWES 360 (370)
Q Consensus 325 ~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w~~ 360 (370)
+=| -|........=+ |.+.++-..|.+|||-++.
T Consensus 112 VGC-~c~eD~~~V~Wm-wl~Kge~~rc~eCG~~fkL 145 (153)
T KOG3352|consen 112 VGC-GCEEDSHAVVWM-WLEKGETQRCPECGHYFKL 145 (153)
T ss_pred Eee-cccCCCcceEEE-EEEcCCcccCCcccceEEe
Confidence 447 688877775555 7788886679999998763
No 126
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=42.37 E-value=32 Score=27.34 Aligned_cols=57 Identities=16% Similarity=0.285 Sum_probs=34.7
Q ss_pred hhcCChHHHHHHHHHHHHHhhcccCcccCCCCCCccccccccccCCCCcceEEEeeccccCCCceeccCCCC
Q 017510 285 EEMVSDGSRRLNQQIKKERASDRYLPWKGGYLGPIYHSTRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQ 356 (370)
Q Consensus 285 eEmas~e~k~~r~~~~~e~l~~~~l~~~~~~~~~~~~t~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~ 356 (370)
.||+-...+++..+.+.+.|-++ +...- ...+|+.|-+--+.|.-. || -|.|.+|+-
T Consensus 5 ~dllhPs~e~e~r~hK~krLvq~---------~nsyF-m~VkC~gc~~iT~vfSHa-qt----vVvc~~c~~ 61 (84)
T KOG1779|consen 5 KDLLHPSPEKEKRKHKLKRLVQS---------PNSYF-MDVKCPGCFKITTVFSHA-QT----VVVCEGCST 61 (84)
T ss_pred hhhcCCCHHHHhhhhhhhhheeC---------CCceE-EEEEcCCceEEEEEeecC-ce----EEEcCCCce
Confidence 34554544554445555555444 11222 358999998888888665 65 778888864
No 127
>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=42.36 E-value=29 Score=35.26 Aligned_cols=56 Identities=18% Similarity=0.392 Sum_probs=26.5
Q ss_pred HHHHHHHHHHHHHhhcccCcccCCCCCCccccccccccCCCC-cceEEEeeccccCCC--ceeccCCCCccee
Q 017510 291 GSRRLNQQIKKERASDRYLPWKGGYLGPIYHSTRYMCGRCGH-KKTTNHGNDQNSSAK--RIKCLNCYQYWES 360 (370)
Q Consensus 291 e~k~~r~~~~~e~l~~~~l~~~~~~~~~~~~t~~~~C~~C~~-~~~~~~q~~Q~RsaD--f~~C~~Cg~~w~~ 360 (370)
+.++...+...+.+.+.+.| =.--|++||. ..+..... .-.++ .|.|..|||+-..
T Consensus 153 ~I~~Il~~~~~~~~~~~y~P------------f~piC~~cGri~tt~v~~~--d~~~~~v~Y~c~~cG~~g~~ 211 (360)
T PF01921_consen 153 EIREILNEYRGRERPETYSP------------FLPICEKCGRIDTTEVTEY--DPEGGTVTYRCEECGHEGEV 211 (360)
T ss_dssp HHHHHHHHHHHHT--TT--S------------EEEEETTTEE--EEEEEEE----SSSEEEEE--TTS---EE
T ss_pred HHHHHHHHhcCcCCCCCeee------------eeeeccccCCcccceeeEe--ecCCCEEEEEecCCCCEEEE
Confidence 34455555555555555433 1456999998 44444443 11233 9999999998654
No 128
>PF12773 DZR: Double zinc ribbon
Probab=41.61 E-value=14 Score=26.03 Aligned_cols=34 Identities=18% Similarity=0.338 Sum_probs=21.1
Q ss_pred cccccccCCCCcceEEEeeccccCCCceeccCCCCc----ceehh
Q 017510 322 STRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQY----WESTT 362 (370)
Q Consensus 322 t~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~----w~~~~ 362 (370)
.+...|+.||..-....+ ..+.|..||.. |+||.
T Consensus 10 ~~~~fC~~CG~~l~~~~~-------~~~~C~~Cg~~~~~~~~fC~ 47 (50)
T PF12773_consen 10 DDAKFCPHCGTPLPPPDQ-------SKKICPNCGAENPPNAKFCP 47 (50)
T ss_pred ccccCChhhcCChhhccC-------CCCCCcCCcCCCcCCcCccC
Confidence 345668888876551111 16778888864 66664
No 129
>KOG3277 consensus Uncharacterized conserved protein [Function unknown]
Probab=41.40 E-value=12 Score=33.37 Aligned_cols=36 Identities=19% Similarity=0.422 Sum_probs=26.1
Q ss_pred ccccccCCCCcceEEEeeccccCCC--ceeccCCCCcce
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSAK--RIKCLNCYQYWE 359 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~RsaD--f~~C~~Cg~~w~ 359 (370)
-.|.|..|+.+...-+-. |.-.-. ||+|..|.+...
T Consensus 78 l~yTCkvCntRs~ktisk-~AY~~GvVivqC~gC~~~Hl 115 (165)
T KOG3277|consen 78 LAYTCKVCNTRSTKTISK-QAYEKGVVIVQCPGCKNHHL 115 (165)
T ss_pred EEEEeeccCCccccccCh-hhhhCceEEEECCCCcccee
Confidence 359999999987754444 433333 999999998744
No 130
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=40.74 E-value=12 Score=34.00 Aligned_cols=17 Identities=24% Similarity=0.372 Sum_probs=14.8
Q ss_pred ceeccCCCCcceehhhc
Q 017510 348 RIKCLNCYQYWESTTAL 364 (370)
Q Consensus 348 f~~C~~Cg~~w~~~~~~ 364 (370)
||.|.+||.+|.|-.|.
T Consensus 117 ~Y~Cp~C~~rytf~eA~ 133 (178)
T PRK06266 117 FFFCPNCHIRFTFDEAM 133 (178)
T ss_pred EEECCCCCcEEeHHHHh
Confidence 99999999999886653
No 131
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=39.99 E-value=16 Score=31.90 Aligned_cols=32 Identities=19% Similarity=0.324 Sum_probs=22.1
Q ss_pred ccccccccCCCCcceEEEeeccccCCCceeccCCCCccee
Q 017510 321 HSTRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYWES 360 (370)
Q Consensus 321 ~t~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w~~ 360 (370)
..-..+||+||-.--.+.- -|.|..||++...
T Consensus 25 kML~~hCp~Cg~PLF~KdG--------~v~CPvC~~~~~~ 56 (131)
T COG1645 25 KMLAKHCPKCGTPLFRKDG--------EVFCPVCGYREVV 56 (131)
T ss_pred HHHHhhCcccCCcceeeCC--------eEECCCCCceEEE
Confidence 4456889999976543211 6789999987654
No 132
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=39.87 E-value=14 Score=31.20 Aligned_cols=29 Identities=21% Similarity=0.541 Sum_probs=18.5
Q ss_pred cccccccccCCCCcceEEEeeccccCCCceeccCCCC
Q 017510 320 YHSTRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQ 356 (370)
Q Consensus 320 ~~t~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~ 356 (370)
.....+.|+.||+.-. ..+. |+.|..||.
T Consensus 66 ~vp~~~~C~~Cg~~~~-~~~~-------~~~CP~Cgs 94 (113)
T PRK12380 66 YKPAQAWCWDCSQVVE-IHQH-------DAQCPHCHG 94 (113)
T ss_pred eeCcEEEcccCCCEEe-cCCc-------CccCcCCCC
Confidence 3457899999992211 1112 667999995
No 133
>COG4957 Predicted transcriptional regulator [Transcription]
Probab=39.83 E-value=12 Score=32.71 Aligned_cols=14 Identities=29% Similarity=0.387 Sum_probs=11.7
Q ss_pred CceeccCCCCccee
Q 017510 347 KRIKCLNCYQYWES 360 (370)
Q Consensus 347 Df~~C~~Cg~~w~~ 360 (370)
||.+|++||..||.
T Consensus 75 D~IicLEDGkkfKS 88 (148)
T COG4957 75 DYIICLEDGKKFKS 88 (148)
T ss_pred CeEEEeccCcchHH
Confidence 38999999998875
No 134
>PF11792 Baculo_LEF5_C: Baculoviridae late expression factor 5 C-terminal domain; InterPro: IPR021758 This C-terminal domain is likely to be a zinc-binding domain.
Probab=38.24 E-value=6.6 Score=27.65 Aligned_cols=25 Identities=28% Similarity=0.408 Sum_probs=17.3
Q ss_pred CCCcceEEEeeccccCCC-----ceeccCCCC
Q 017510 330 CGHKKTTNHGNDQNSSAK-----RIKCLNCYQ 356 (370)
Q Consensus 330 C~~~~~~~~q~~Q~RsaD-----f~~C~~Cg~ 356 (370)
|.+.=. .... |+|++| +-.|..||.
T Consensus 13 C~H~f~-~~E~-Q~RAGDE~VSfI~~C~~C~~ 42 (43)
T PF11792_consen 13 CKHKFV-TIEK-QLRAGDEAVSFIKYCQKCGQ 42 (43)
T ss_pred ceeeee-ehhh-hhcccchHHHHHHHHHHhCC
Confidence 655544 3344 999999 456888885
No 135
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=37.57 E-value=18 Score=26.23 Aligned_cols=14 Identities=29% Similarity=0.805 Sum_probs=11.6
Q ss_pred ceeccCCCCcceeh
Q 017510 348 RIKCLNCYQYWEST 361 (370)
Q Consensus 348 f~~C~~Cg~~w~~~ 361 (370)
...|..|||.|+..
T Consensus 28 ~W~C~~Cgh~w~~~ 41 (55)
T PF14311_consen 28 WWKCPKCGHEWKAS 41 (55)
T ss_pred EEECCCCCCeeEcc
Confidence 67899999999863
No 136
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=37.34 E-value=7.7 Score=29.29 Aligned_cols=33 Identities=15% Similarity=0.415 Sum_probs=21.0
Q ss_pred ccccCCCCcceEEEeeccccCC-CceeccCCCCccee
Q 017510 325 YMCGRCGHKKTTNHGNDQNSSA-KRIKCLNCYQYWES 360 (370)
Q Consensus 325 ~~C~~C~~~~~~~~q~~Q~Rsa-Df~~C~~Cg~~w~~ 360 (370)
..||.|.--.+ .|+ |.-.. +.++|..|||.-+.
T Consensus 11 A~CP~C~~~Dt--l~m-W~En~ve~vECV~CG~~~~~ 44 (66)
T COG3529 11 AVCPACQAQDT--LAM-WRENNVEIVECVKCGHHMRE 44 (66)
T ss_pred CCCcccchhhH--HHH-HHhcCCceEehhhcchHhhh
Confidence 56999965443 233 42222 39999999987543
No 137
>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=37.14 E-value=15 Score=32.06 Aligned_cols=14 Identities=29% Similarity=0.719 Sum_probs=8.4
Q ss_pred CceeccCCCCccee
Q 017510 347 KRIKCLNCYQYWES 360 (370)
Q Consensus 347 Df~~C~~Cg~~w~~ 360 (370)
|+++|+.||..++.
T Consensus 71 d~i~clecGk~~k~ 84 (132)
T PF05443_consen 71 DYIICLECGKKFKT 84 (132)
T ss_dssp S-EE-TBT--EESB
T ss_pred CeeEEccCCcccch
Confidence 49999999998876
No 138
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=36.82 E-value=23 Score=30.83 Aligned_cols=11 Identities=27% Similarity=0.833 Sum_probs=9.0
Q ss_pred cccccccCCCC
Q 017510 322 STRYMCGRCGH 332 (370)
Q Consensus 322 t~~~~C~~C~~ 332 (370)
-..+.|+.||.
T Consensus 68 p~~~~C~~CG~ 78 (135)
T PRK03824 68 EAVLKCRNCGN 78 (135)
T ss_pred ceEEECCCCCC
Confidence 36799999993
No 139
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=36.45 E-value=18 Score=31.74 Aligned_cols=17 Identities=29% Similarity=0.409 Sum_probs=14.8
Q ss_pred ceeccCCCCcceehhhc
Q 017510 348 RIKCLNCYQYWESTTAL 364 (370)
Q Consensus 348 f~~C~~Cg~~w~~~~~~ 364 (370)
||.|.+||.+|.|-.+.
T Consensus 99 ~Y~Cp~C~~~y~~~ea~ 115 (147)
T smart00531 99 YYKCPNCQSKYTFLEAN 115 (147)
T ss_pred EEECcCCCCEeeHHHHH
Confidence 99999999999986554
No 140
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=36.00 E-value=15 Score=30.91 Aligned_cols=31 Identities=13% Similarity=0.307 Sum_probs=19.4
Q ss_pred cccccccccCCCCcceEEEeeccccCCCceeccCCCCc
Q 017510 320 YHSTRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQY 357 (370)
Q Consensus 320 ~~t~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~ 357 (370)
.....+.|..||+ ++.. ..+ .++.|..||..
T Consensus 66 ~~p~~~~C~~Cg~----~~~~-~~~--~~~~CP~Cgs~ 96 (114)
T PRK03681 66 EQEAECWCETCQQ----YVTL-LTQ--RVRRCPQCHGD 96 (114)
T ss_pred eeCcEEEcccCCC----eeec-CCc--cCCcCcCcCCC
Confidence 3456899999994 3322 101 14779999953
No 141
>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=35.48 E-value=17 Score=24.57 Aligned_cols=12 Identities=33% Similarity=0.492 Sum_probs=7.2
Q ss_pred ceeccCCCCcce
Q 017510 348 RIKCLNCYQYWE 359 (370)
Q Consensus 348 f~~C~~Cg~~w~ 359 (370)
||.|..|||--.
T Consensus 6 ~YkC~~CGniVe 17 (36)
T PF06397_consen 6 FYKCEHCGNIVE 17 (36)
T ss_dssp EEE-TTT--EEE
T ss_pred EEEccCCCCEEE
Confidence 899999998643
No 142
>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=35.22 E-value=25 Score=30.76 Aligned_cols=33 Identities=12% Similarity=0.263 Sum_probs=19.5
Q ss_pred cccccCCCCcceEEEeecccc---------CCC-ceeccCCCCc
Q 017510 324 RYMCGRCGHKKTTNHGNDQNS---------SAK-RIKCLNCYQY 357 (370)
Q Consensus 324 ~~~C~~C~~~~~~~~q~~Q~R---------saD-f~~C~~Cg~~ 357 (370)
.-.|+.|++.=....-- +.+ ..| |+.|..||.-
T Consensus 91 ~sRC~~CN~~L~~v~~~-~v~~~vp~~v~~~~~~f~~C~~C~ki 133 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKE-EVKDRVPPYVYETYDEFWRCPGCGKI 133 (147)
T ss_pred CCccCCCCcEeeechhh-ccccccCccccccCCeEEECCCCCCE
Confidence 56899999832211111 111 112 9999999975
No 143
>COG4481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.57 E-value=40 Score=25.03 Aligned_cols=27 Identities=30% Similarity=0.458 Sum_probs=18.9
Q ss_pred CCCCcceEEEeeccccCCC-ceeccCCCCcce
Q 017510 329 RCGHKKTTNHGNDQNSSAK-RIKCLNCYQYWE 359 (370)
Q Consensus 329 ~C~~~~~~~~q~~Q~RsaD-f~~C~~Cg~~w~ 359 (370)
-||-++-....+ .|| -..|.+|||.--
T Consensus 18 ~Cg~NrwkIiRv----GaDIkikC~nC~h~vm 45 (60)
T COG4481 18 ACGTNRWKIIRV----GADIKIKCENCGHSVM 45 (60)
T ss_pred ccccceEEEEEe----cCcEEEEecCCCcEEE
Confidence 466655555544 688 899999999643
No 144
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=34.41 E-value=20 Score=35.04 Aligned_cols=30 Identities=37% Similarity=0.762 Sum_probs=19.5
Q ss_pred cccccccCCCCcceEEEeeccccCCCceeccCCCCcc
Q 017510 322 STRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYW 358 (370)
Q Consensus 322 t~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w 358 (370)
+.+| ||+||++.....+ ..-..|.+|||..
T Consensus 110 ~~RF-Cg~CG~~~~~~~~------g~~~~C~~cg~~~ 139 (279)
T COG2816 110 SHRF-CGRCGTKTYPREG------GWARVCPKCGHEH 139 (279)
T ss_pred hCcC-CCCCCCcCccccC------ceeeeCCCCCCcc
Confidence 3455 9999987543221 1266799999874
No 145
>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=34.37 E-value=25 Score=25.80 Aligned_cols=30 Identities=13% Similarity=0.414 Sum_probs=20.7
Q ss_pred cccccCCCCcceEEEeeccccCCC-ceeccCCCC
Q 017510 324 RYMCGRCGHKKTTNHGNDQNSSAK-RIKCLNCYQ 356 (370)
Q Consensus 324 ~~~C~~C~~~~~~~~q~~Q~RsaD-f~~C~~Cg~ 356 (370)
...|++|.+.+..+... .-.. .|+|..||+
T Consensus 22 aLIC~~C~~hNGla~~~---~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 22 ALICSKCFSHNGLAPKE---EFEEIQYRCPYCGA 52 (54)
T ss_pred eEECcccchhhcccccc---cCCceEEEcCCCCC
Confidence 45699999887766421 1112 889999986
No 146
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=34.06 E-value=16 Score=30.98 Aligned_cols=31 Identities=16% Similarity=0.327 Sum_probs=18.6
Q ss_pred cccccccccCCCCcceEEEeeccccCCCceeccCCCCc
Q 017510 320 YHSTRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQY 357 (370)
Q Consensus 320 ~~t~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~ 357 (370)
.....+.|..||+. +.. . .-.|..|..||..
T Consensus 67 ~vp~~~~C~~Cg~~----~~~-~--~~~~~~CP~Cgs~ 97 (117)
T PRK00564 67 DEKVELECKDCSHV----FKP-N--ALDYGVCEKCHSK 97 (117)
T ss_pred ecCCEEEhhhCCCc----ccc-C--CccCCcCcCCCCC
Confidence 34567899999932 221 0 0015569999964
No 147
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=32.99 E-value=19 Score=32.49 Aligned_cols=38 Identities=13% Similarity=0.378 Sum_probs=22.1
Q ss_pred cccccccCCCCcceEEEee---c-----cccCCC-ceeccCCCCc-ce
Q 017510 322 STRYMCGRCGHKKTTNHGN---D-----QNSSAK-RIKCLNCYQY-WE 359 (370)
Q Consensus 322 t~~~~C~~C~~~~~~~~q~---~-----Q~RsaD-f~~C~~Cg~~-w~ 359 (370)
-..-.||.|+..=....-- + --+..+ |+.|.+||.- |+
T Consensus 95 ~e~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~ 142 (165)
T COG1656 95 PEFSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYWK 142 (165)
T ss_pred cccccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccccC
Confidence 3467899998752221110 0 112333 9999999975 54
No 148
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=32.94 E-value=46 Score=24.90 Aligned_cols=28 Identities=29% Similarity=0.455 Sum_probs=18.1
Q ss_pred CCCcceEEEeeccccCCC-ceeccCCCCcceeh
Q 017510 330 CGHKKTTNHGNDQNSSAK-RIKCLNCYQYWEST 361 (370)
Q Consensus 330 C~~~~~~~~q~~Q~RsaD-f~~C~~Cg~~w~~~ 361 (370)
||.+.=....+ .|| -+.|..||+.--.-
T Consensus 16 CG~~~Wei~R~----GaDikikC~gCg~~imlp 44 (57)
T PF06107_consen 16 CGSNEWEIIRI----GADIKIKCLGCGRQIMLP 44 (57)
T ss_pred CCCCEEEEEEc----cCcEEEEECCCCCEEEEe
Confidence 66644433333 678 78899999975443
No 149
>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=32.42 E-value=2e+02 Score=22.98 Aligned_cols=66 Identities=18% Similarity=0.179 Sum_probs=43.0
Q ss_pred CCChHHHHHHHHHHHHHHhhhcCCC--chhhhhhcCCCChHHHHHHHHHHHHHhhCCCchhhhHHHHhHHhhcC
Q 017510 187 KCNDYFRERIREKLYKALSKVSGEV--DEEVQDKLNGCDPIRVAITAESLMFEKWGHSFGTYEVKYRSILFNLM 258 (370)
Q Consensus 187 ~t~d~vR~k~r~lL~~aL~~~~~~~--~~~~~~~~~~~~~~~~A~~IE~~if~~~~~~~~~Yk~k~Rsl~~NLK 258 (370)
.-+..+|+..+..|..++-...+.. .+..+ .+....|..||..+|..- .+..+|-..+--.+++++
T Consensus 9 ~vt~~lR~hlV~KLv~aI~P~pdp~a~~d~rm-----~~l~~yarkvE~~~fe~A-~sreeYY~llA~kiy~iq 76 (81)
T PF02172_consen 9 SVTPDLRNHLVHKLVQAIFPTPDPNAMNDPRM-----KNLIEYARKVEKDMFETA-QSREEYYHLLAEKIYKIQ 76 (81)
T ss_dssp CT-HHHHHHHHHHHHHHHS-SSSCCCCCSHHH-----HHHHHHHHHHHHHHHHC--SSHHHHHHHHHHHHHHHH
T ss_pred HcCHHHHHHHHHHHHHhhCCCCChhhhhhHHH-----HHHHHHHHHHHHHHHHHh-ccHHHHHHHHHHHHHHHH
Confidence 4457899999999999987531110 01111 133589999999999875 344678877777777764
No 150
>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=32.32 E-value=10 Score=37.25 Aligned_cols=32 Identities=16% Similarity=0.293 Sum_probs=21.9
Q ss_pred cccccCCCCcceEEE-eeccccCCCceeccCCCCcceeh
Q 017510 324 RYMCGRCGHKKTTNH-GNDQNSSAKRIKCLNCYQYWEST 361 (370)
Q Consensus 324 ~~~C~~C~~~~~~~~-q~~Q~RsaDf~~C~~Cg~~w~~~ 361 (370)
..+|+.|+.- .|. ++ ..+|+.|.+|||.++..
T Consensus 26 ~~~c~~c~~~--~~~~~l----~~~~~vc~~c~~h~rl~ 58 (285)
T TIGR00515 26 WTKCPKCGQV--LYTKEL----ERNLEVCPKCDHHMRMD 58 (285)
T ss_pred eeECCCCcch--hhHHHH----HhhCCCCCCCCCcCcCC
Confidence 7899999863 221 11 11288999999998863
No 151
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=32.12 E-value=45 Score=22.85 Aligned_cols=12 Identities=25% Similarity=0.634 Sum_probs=9.3
Q ss_pred ccccCCCCcceE
Q 017510 325 YMCGRCGHKKTT 336 (370)
Q Consensus 325 ~~C~~C~~~~~~ 336 (370)
..||.||+....
T Consensus 3 ~~Cp~Cg~~~~~ 14 (47)
T PF14690_consen 3 PRCPHCGSPSVH 14 (47)
T ss_pred ccCCCcCCCceE
Confidence 469999987744
No 152
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.04 E-value=7 Score=30.90 Aligned_cols=36 Identities=19% Similarity=0.434 Sum_probs=27.4
Q ss_pred cccccccccCCCCcceEEEeeccccCCC-ceeccCCCCcce
Q 017510 320 YHSTRYMCGRCGHKKTTNHGNDQNSSAK-RIKCLNCYQYWE 359 (370)
Q Consensus 320 ~~t~~~~C~~C~~~~~~~~q~~Q~RsaD-f~~C~~Cg~~w~ 359 (370)
+++=.+.|-.||++... + |.=..| +.+|..||-+.+
T Consensus 8 MPtY~Y~c~~cg~~~dv---v-q~~~ddplt~ce~c~a~~k 44 (82)
T COG2331 8 MPTYSYECTECGNRFDV---V-QAMTDDPLTTCEECGARLK 44 (82)
T ss_pred ccceEEeecccchHHHH---H-HhcccCccccChhhChHHH
Confidence 56778999999987544 3 544666 999999998654
No 153
>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=31.79 E-value=28 Score=22.39 Aligned_cols=27 Identities=30% Similarity=0.732 Sum_probs=12.1
Q ss_pred cccCCCCcceEEEeeccccCCCceeccCCCCcc
Q 017510 326 MCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYW 358 (370)
Q Consensus 326 ~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w 358 (370)
-|++||..-....-- + --.|..||+.-
T Consensus 5 fC~~CG~~t~~~~~g-~-----~r~C~~Cg~~~ 31 (32)
T PF09297_consen 5 FCGRCGAPTKPAPGG-W-----ARRCPSCGHEH 31 (32)
T ss_dssp B-TTT--BEEE-SSS-S------EEESSSS-EE
T ss_pred ccCcCCccccCCCCc-C-----EeECCCCcCEe
Confidence 399998864332111 1 55688888753
No 154
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.21 E-value=38 Score=27.04 Aligned_cols=35 Identities=23% Similarity=0.405 Sum_probs=23.9
Q ss_pred ccccCCCCcceEEEeeccccCCC-ceeccCCCCcceehhhc
Q 017510 325 YMCGRCGHKKTTNHGNDQNSSAK-RIKCLNCYQYWESTTAL 364 (370)
Q Consensus 325 ~~C~~C~~~~~~~~q~~Q~RsaD-f~~C~~Cg~~w~~~~~~ 364 (370)
..||.|+-. .++ -.||.- |-.|..|+--|--=++|
T Consensus 2 llCP~C~v~----l~~-~~rs~vEiD~CPrCrGVWLDrGEL 37 (88)
T COG3809 2 LLCPICGVE----LVM-SVRSGVEIDYCPRCRGVWLDRGEL 37 (88)
T ss_pred cccCcCCce----eee-eeecCceeeeCCccccEeecchhH
Confidence 469999742 233 346665 88999999999655443
No 155
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=31.13 E-value=21 Score=25.89 Aligned_cols=31 Identities=23% Similarity=0.578 Sum_probs=22.4
Q ss_pred ccccCCCCcceEEEeeccccCCC---ceeccCCCCccee
Q 017510 325 YMCGRCGHKKTTNHGNDQNSSAK---RIKCLNCYQYWES 360 (370)
Q Consensus 325 ~~C~~C~~~~~~~~q~~Q~RsaD---f~~C~~Cg~~w~~ 360 (370)
..|..|+-..+..+ |.+. -+.|..||-+|+-
T Consensus 4 ~~C~~C~~~~T~~W-----R~g~~g~~~LCnaCgl~~~k 37 (52)
T smart00401 4 RSCSNCGTTETPLW-----RRGPSGNKTLCNACGLYYKK 37 (52)
T ss_pred CCcCCCCCCCCCcc-----ccCCCCCCcEeecccHHHHH
Confidence 57999997666533 3333 5889999999875
No 156
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=30.05 E-value=49 Score=32.95 Aligned_cols=41 Identities=22% Similarity=0.402 Sum_probs=28.3
Q ss_pred ccccccccCCCCc-ceEEEeeccccCCC--ceeccCCCCcceehh
Q 017510 321 HSTRYMCGRCGHK-KTTNHGNDQNSSAK--RIKCLNCYQYWESTT 362 (370)
Q Consensus 321 ~t~~~~C~~C~~~-~~~~~q~~Q~RsaD--f~~C~~Cg~~w~~~~ 362 (370)
...+.+|+.||+. +-.|+.+ -...+. ..+|..|+..+|.-+
T Consensus 223 ~~~R~~C~~Cg~~~~l~y~~~-~~~~~~~r~e~C~~C~~YlK~~~ 266 (309)
T PRK03564 223 HVVRVKCSNCEQSGKLHYWSL-DSEQAAVKAESCGDCGTYLKILY 266 (309)
T ss_pred cccCccCCCCCCCCceeeeee-cCCCcceEeeecccccccceecc
Confidence 4457899999986 4456655 222222 688999999999853
No 157
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=29.38 E-value=12 Score=35.88 Aligned_cols=37 Identities=16% Similarity=0.296 Sum_probs=24.8
Q ss_pred cccccccccCCCCcceEEEeeccccCCC-ceeccCCCCc
Q 017510 320 YHSTRYMCGRCGHKKTTNHGNDQNSSAK-RIKCLNCYQY 357 (370)
Q Consensus 320 ~~t~~~~C~~C~~~~~~~~q~~Q~RsaD-f~~C~~Cg~~ 357 (370)
.+...-.|+.|+-.=..-+.. .+|-.| .|.|..||--
T Consensus 193 vpl~g~~C~GC~m~l~~~~~~-~V~~~d~iv~CP~CgRI 230 (239)
T COG1579 193 VPLEGRVCGGCHMKLPSQTLS-KVRKKDEIVFCPYCGRI 230 (239)
T ss_pred EeecCCcccCCeeeecHHHHH-HHhcCCCCccCCccchH
Confidence 455567799998653322222 456677 9999999953
No 158
>KOG3214 consensus Uncharacterized Zn ribbon-containing protein [Function unknown]
Probab=28.73 E-value=38 Score=28.23 Aligned_cols=46 Identities=24% Similarity=0.416 Sum_probs=30.3
Q ss_pred ccccccCCCCcceEEEeeccccCCCceeccCCCCcceehhhcccCCC
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYWESTTALYGLLP 369 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w~~~~~~~~~~~ 369 (370)
.+|.|+-|.+-+..-.-+.-.+.-.|.-|..|+..|. |+.-|-+-|
T Consensus 22 t~FnClfcnHek~v~~~~Dk~~~iG~~sC~iC~esFq-t~it~Lsep 67 (109)
T KOG3214|consen 22 TQFNCLFCNHEKSVSCTLDKKHNIGKASCRICEESFQ-TTITALSEP 67 (109)
T ss_pred eeeccCccccccceeeeehhhcCcceeeeeehhhhhc-cchHhhccc
Confidence 4799999988765544442334444999999998875 344443433
No 159
>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=28.62 E-value=45 Score=33.72 Aligned_cols=32 Identities=31% Similarity=0.531 Sum_probs=19.6
Q ss_pred cccccCCCCcceEEEeeccccCCC----ceeccCCCCccee
Q 017510 324 RYMCGRCGHKKTTNHGNDQNSSAK----RIKCLNCYQYWES 360 (370)
Q Consensus 324 ~~~C~~C~~~~~~~~q~~Q~RsaD----f~~C~~Cg~~w~~ 360 (370)
.-.|++||.-.+.... ...| .|.| .|||.-..
T Consensus 169 ~p~c~~cg~~~~~v~~----~d~~~~~v~y~c-~cG~~g~~ 204 (353)
T cd00674 169 MPYCEKCGKDTTTVEA----YDAKAGTVTYKC-ECGHEETV 204 (353)
T ss_pred eeecCCcCcceeEEEE----EeCCCCeEEEEc-CCCCEEEE
Confidence 4569999933333322 2333 7789 69997544
No 160
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=28.55 E-value=13 Score=36.84 Aligned_cols=34 Identities=15% Similarity=0.134 Sum_probs=22.0
Q ss_pred ccccccCCCCcceEEEeeccccCCCceeccCCCCcceeh
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYWEST 361 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w~~~ 361 (370)
-..+|+.|+.-- +..++ ...++.|.+|||.++..
T Consensus 37 lw~kc~~C~~~~-~~~~l----~~~~~vcp~c~~h~rlt 70 (296)
T CHL00174 37 LWVQCENCYGLN-YKKFL----KSKMNICEQCGYHLKMS 70 (296)
T ss_pred CeeECCCccchh-hHHHH----HHcCCCCCCCCCCcCCC
Confidence 378999998631 11111 11178999999988764
No 161
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=28.29 E-value=60 Score=22.98 Aligned_cols=32 Identities=28% Similarity=0.541 Sum_probs=20.3
Q ss_pred cccccccCCCCcceEEEeeccccCCCceeccCCCC
Q 017510 322 STRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQ 356 (370)
Q Consensus 322 t~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~ 356 (370)
++.+.|+.||..-.. +. +++.-.+|.|.++-.
T Consensus 3 ~g~l~C~~CG~~m~~--~~-~~~~~~yy~C~~~~~ 34 (58)
T PF13408_consen 3 SGLLRCGHCGSKMTR--RK-RKGKYRYYRCSNRRR 34 (58)
T ss_pred CCcEEcccCCcEeEE--EE-CCCCceEEEcCCCcC
Confidence 467899999987444 22 332223888887643
No 162
>PLN03119 putative ADP-ribosylation factor GTPase-activating protein AGD14; Provisional
Probab=27.74 E-value=78 Score=34.13 Aligned_cols=30 Identities=13% Similarity=0.274 Sum_probs=20.6
Q ss_pred cccccCCCCcceEEEeeccccCCCceeccCCCCc
Q 017510 324 RYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQY 357 (370)
Q Consensus 324 ~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~ 357 (370)
--.|..|+.....|.-+ .--.+.|.+|...
T Consensus 23 Nk~CADCgs~~P~WASi----NlGIFICi~CSGI 52 (648)
T PLN03119 23 NRRCINCNSLGPQYVCT----TFWTFVCMACSGI 52 (648)
T ss_pred CCccccCCCCCCCceee----ccceEEeccchhh
Confidence 35699999988776543 1126779999754
No 163
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=27.44 E-value=17 Score=35.75 Aligned_cols=33 Identities=18% Similarity=0.307 Sum_probs=21.9
Q ss_pred cccccCCCCcceEEEeeccccCCCceeccCCCCcceeh
Q 017510 324 RYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYWEST 361 (370)
Q Consensus 324 ~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w~~~ 361 (370)
..+|+.|+.. .|.. +. ..++..|..|||.++..
T Consensus 27 ~~~c~~c~~~--~~~~--~l-~~~~~vc~~c~~h~rl~ 59 (292)
T PRK05654 27 WTKCPSCGQV--LYRK--EL-EANLNVCPKCGHHMRIS 59 (292)
T ss_pred eeECCCccch--hhHH--HH-HhcCCCCCCCCCCeeCC
Confidence 7899999863 1211 10 11277899999998864
No 164
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=27.40 E-value=40 Score=38.79 Aligned_cols=49 Identities=18% Similarity=0.322 Sum_probs=25.5
Q ss_pred ccccccccccCCCCcceEEEeeccccCCC---ceeccCCCCcceehhhcccCCC
Q 017510 319 IYHSTRYMCGRCGHKKTTNHGNDQNSSAK---RIKCLNCYQYWESTTALYGLLP 369 (370)
Q Consensus 319 ~~~t~~~~C~~C~~~~~~~~q~~Q~RsaD---f~~C~~Cg~~w~~~~~~~~~~~ 369 (370)
...|+-..||+|++.--.--. ..=.|| .+.|..||....=...-||.-|
T Consensus 791 ~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 842 (1006)
T PRK12775 791 GAETGVATCPKCHRPLEGDEE--YVCCATSELQWRCDDCGKVSEGFAFPYGMCP 842 (1006)
T ss_pred cccCCCccCcccCCCCCCCce--eEEecCcceeeehhhhccccccccCCcCcCc
Confidence 357888999999976221100 011223 5555556655444444444433
No 165
>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=26.19 E-value=58 Score=32.37 Aligned_cols=42 Identities=21% Similarity=0.381 Sum_probs=28.4
Q ss_pred ccccccccCCCCcc-eEEEeecccc--CCC--ceeccCCCCcceehhh
Q 017510 321 HSTRYMCGRCGHKK-TTNHGNDQNS--SAK--RIKCLNCYQYWESTTA 363 (370)
Q Consensus 321 ~t~~~~C~~C~~~~-~~~~q~~Q~R--saD--f~~C~~Cg~~w~~~~~ 363 (370)
...+.+|+.||+.+ -.|+.+ -.. .+- ..+|..|+..+|.-+.
T Consensus 221 ~~~R~~C~~Cg~~~~l~y~~~-e~~~~~~~~r~e~C~~C~~YlK~~~~ 267 (305)
T TIGR01562 221 HYVRVKCSHCEESKHLAYLSL-EHDAEKAVLKAETCDSCQGYLKILYQ 267 (305)
T ss_pred cccCccCCCCCCCCceeeEee-cCCCCCcceEEeeccccccchhhhcc
Confidence 44578899998864 446655 321 122 6689999999998544
No 166
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=25.67 E-value=31 Score=40.26 Aligned_cols=21 Identities=14% Similarity=-0.042 Sum_probs=13.3
Q ss_pred ccccCC----CCHHHHHHHHHHHHH
Q 017510 58 LPLTKH----PRQKIQDTASELILS 78 (370)
Q Consensus 58 ~~Lrkh----~~~~I~~~Ak~Li~~ 78 (370)
|.+|-. -.+.|...|+.|++.
T Consensus 237 N~~RGG~~LVlaEGi~~Ka~Ki~k~ 261 (1337)
T PRK14714 237 NSLRGGMCLVLAEGIALKAPKIQKY 261 (1337)
T ss_pred ccccceeeheehhhHhhhcHHHHHH
Confidence 555543 245677888877765
No 167
>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=25.42 E-value=61 Score=22.01 Aligned_cols=29 Identities=17% Similarity=0.394 Sum_probs=17.7
Q ss_pred ccccCCCCcceEEEeeccccCCC-ceeccCCCC
Q 017510 325 YMCGRCGHKKTTNHGNDQNSSAK-RIKCLNCYQ 356 (370)
Q Consensus 325 ~~C~~C~~~~~~~~q~~Q~RsaD-f~~C~~Cg~ 356 (370)
..||.||.+.-+-+. .+... -+.|..||.
T Consensus 4 ~pCP~CGG~DrFr~~---d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 4 GPCPNCGGSDRFRFD---DKDGRGTWFCSVCGA 33 (37)
T ss_pred cCCCCCCCccccccc---cCCCCcCEEeCCCCC
Confidence 579999986554322 12223 566888864
No 168
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=25.37 E-value=79 Score=23.11 Aligned_cols=35 Identities=17% Similarity=0.293 Sum_probs=25.8
Q ss_pred ccccCCCCcceEEEeeccccCCC-ceeccCCCCccee
Q 017510 325 YMCGRCGHKKTTNHGNDQNSSAK-RIKCLNCYQYWES 360 (370)
Q Consensus 325 ~~C~~C~~~~~~~~q~~Q~RsaD-f~~C~~Cg~~w~~ 360 (370)
+.||-||+........ ..+..+ +--|-.|-+-|.|
T Consensus 1 i~CPyCge~~~~~iD~-s~~~Q~yiEDC~vCC~PI~~ 36 (52)
T PF14255_consen 1 IQCPYCGEPIEILIDP-SAGDQEYIEDCQVCCRPIEV 36 (52)
T ss_pred CCCCCCCCeeEEEEec-CCCCeeEEeehhhcCCccEE
Confidence 4799999998887776 334444 5568889887766
No 169
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=25.08 E-value=46 Score=27.62 Aligned_cols=12 Identities=17% Similarity=0.196 Sum_probs=9.4
Q ss_pred ceeccCCCCcce
Q 017510 348 RIKCLNCYQYWE 359 (370)
Q Consensus 348 f~~C~~Cg~~w~ 359 (370)
.+.|..||..+.
T Consensus 31 ~~~C~~CGe~~~ 42 (127)
T TIGR03830 31 GWYCPACGEELL 42 (127)
T ss_pred eeECCCCCCEEE
Confidence 677999998754
No 170
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=25.06 E-value=14 Score=26.92 Aligned_cols=33 Identities=18% Similarity=0.335 Sum_probs=20.7
Q ss_pred ccccccCCCCcceEEEeeccccCCC-ceeccCCCC
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSAK-RIKCLNCYQ 356 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~RsaD-f~~C~~Cg~ 356 (370)
..-.|..|+-.=..-... ..+.+| .+.|.+||-
T Consensus 21 ~~~~C~gC~~~l~~~~~~-~i~~~~~i~~Cp~CgR 54 (56)
T PF02591_consen 21 EGGTCSGCHMELPPQELN-EIRKGDEIVFCPNCGR 54 (56)
T ss_pred eCCccCCCCEEcCHHHHH-HHHcCCCeEECcCCCc
Confidence 445799997542221111 456667 999999984
No 171
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=24.77 E-value=38 Score=22.07 Aligned_cols=12 Identities=33% Similarity=0.431 Sum_probs=10.1
Q ss_pred ceeccCCCCcce
Q 017510 348 RIKCLNCYQYWE 359 (370)
Q Consensus 348 f~~C~~Cg~~w~ 359 (370)
||.|..||+.-.
T Consensus 7 ~ykC~~Cgniv~ 18 (34)
T TIGR00319 7 VYKCEVCGNIVE 18 (34)
T ss_pred EEEcCCCCcEEE
Confidence 899999998754
No 172
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=24.77 E-value=60 Score=28.21 Aligned_cols=33 Identities=24% Similarity=0.492 Sum_probs=24.4
Q ss_pred cccccccCCCCcceEEEeeccccCCC--ceeccCCCCcce
Q 017510 322 STRYMCGRCGHKKTTNHGNDQNSSAK--RIKCLNCYQYWE 359 (370)
Q Consensus 322 t~~~~C~~C~~~~~~~~q~~Q~RsaD--f~~C~~Cg~~w~ 359 (370)
+-.+.|.+|+...- - +.|+-+ .|.|..||....
T Consensus 110 ~~~y~C~~C~~~~~----~-~rr~~~~~~y~C~~C~g~l~ 144 (146)
T smart00731 110 KYPYRCTGCGQRYL----R-VRRSNNVSRYRCGKCGGKLI 144 (146)
T ss_pred eEEEECCCCCCCCc----e-EccccCcceEEcCCCCCEEE
Confidence 45789999997643 2 567766 899999997654
No 173
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=24.64 E-value=43 Score=24.48 Aligned_cols=30 Identities=27% Similarity=0.492 Sum_probs=15.9
Q ss_pred cccccCCCCc--ce-EEEeeccccCCCceeccCCCCccee
Q 017510 324 RYMCGRCGHK--KT-TNHGNDQNSSAKRIKCLNCYQYWES 360 (370)
Q Consensus 324 ~~~C~~C~~~--~~-~~~q~~Q~RsaDf~~C~~Cg~~w~~ 360 (370)
.++|+.|++- ++ .|..+ -+.|..||.--.+
T Consensus 4 eiRC~~CnklLa~~g~~~~l-------eIKCpRC~tiN~~ 36 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIEL-------EIKCPRCKTINHV 36 (51)
T ss_pred ceeccchhHHHhhhcCccEE-------EEECCCCCccceE
Confidence 4667777664 21 24444 4567777654433
No 174
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=24.34 E-value=50 Score=34.24 Aligned_cols=37 Identities=24% Similarity=0.415 Sum_probs=24.5
Q ss_pred cccccccccCCCCcceEEEeeccccCCC--ceeccCCCCc
Q 017510 320 YHSTRYMCGRCGHKKTTNHGNDQNSSAK--RIKCLNCYQY 357 (370)
Q Consensus 320 ~~t~~~~C~~C~~~~~~~~q~~Q~RsaD--f~~C~~Cg~~ 357 (370)
+....|.||.|...=...--+ |.=..+ +|.|.+||--
T Consensus 124 t~~~~Y~Cp~C~kkyt~Lea~-~L~~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 124 TNVAGYVCPNCQKKYTSLEAL-QLLDNETGEFHCENCGGE 162 (436)
T ss_pred cccccccCCccccchhhhHHH-HhhcccCceEEEecCCCc
Confidence 344579999998754443333 444443 8999999864
No 175
>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=24.20 E-value=39 Score=22.02 Aligned_cols=12 Identities=33% Similarity=0.415 Sum_probs=10.3
Q ss_pred ceeccCCCCcce
Q 017510 348 RIKCLNCYQYWE 359 (370)
Q Consensus 348 f~~C~~Cg~~w~ 359 (370)
||.|..||+.-.
T Consensus 4 ~ykC~~CGniv~ 15 (34)
T cd00974 4 VYKCEICGNIVE 15 (34)
T ss_pred EEEcCCCCcEEE
Confidence 899999998754
No 176
>PF03589 Antiterm: Antitermination protein; InterPro: IPR003222 This entry consists of antitermination proteins found in bacteriophages, such as protein Q from phage lambda, and some bacterial homologues. Protein Q positively regulates expression of the phage late gene operon by binding to the bacterial host RNA polymerase (RNAP) and modifying it. The modified RNAP transcribes through termination sites that otherwise prevent expression of the regulated genes [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=23.90 E-value=24 Score=28.92 Aligned_cols=31 Identities=19% Similarity=0.347 Sum_probs=25.6
Q ss_pred cccCCCCcceEEEeeccccCC-C---ceeccCCCCc
Q 017510 326 MCGRCGHKKTTNHGNDQNSSA-K---RIKCLNCYQY 357 (370)
Q Consensus 326 ~C~~C~~~~~~~~q~~Q~Rsa-D---f~~C~~Cg~~ 357 (370)
.|.+|+.+....-.. |++-. . |-+|..||.+
T Consensus 7 ~c~~c~g~g~al~~~-~s~~~~G~pvfk~c~rcgg~ 41 (95)
T PF03589_consen 7 SCRRCAGDGAALDMK-QSKAQFGVPVFKDCERCGGR 41 (95)
T ss_pred CcCccCCcceeccHH-HhHhccCCchhhhhhhhcCC
Confidence 588999998777777 88877 4 8899999875
No 177
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=23.85 E-value=78 Score=35.20 Aligned_cols=17 Identities=18% Similarity=0.305 Sum_probs=12.8
Q ss_pred CChhhhcCCChhhcCCh
Q 017510 274 VKPEALIKMSSEEMVSD 290 (370)
Q Consensus 274 isp~~lv~Ms~eEmas~ 290 (370)
++.-.+++|..+.+...
T Consensus 386 ~p~v~iiDmr~e~~~~~ 402 (730)
T COG1198 386 LPRVEIIDMRKEPLETG 402 (730)
T ss_pred CCcceEEeccccccccC
Confidence 55567889998888774
No 178
>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=23.78 E-value=17 Score=26.21 Aligned_cols=34 Identities=15% Similarity=0.429 Sum_probs=21.0
Q ss_pred ccccccCCCCcceEEEee---ccccCCC---ceeccCCCCc
Q 017510 323 TRYMCGRCGHKKTTNHGN---DQNSSAK---RIKCLNCYQY 357 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~---~Q~RsaD---f~~C~~Cg~~ 357 (370)
+.|.||=|+. ......+ .+....+ .|.|.-|..+
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 5444443 1222222 7889988864
No 179
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=23.77 E-value=30 Score=25.89 Aligned_cols=11 Identities=18% Similarity=0.630 Sum_probs=6.6
Q ss_pred ceeccCCCCcc
Q 017510 348 RIKCLNCYQYW 358 (370)
Q Consensus 348 f~~C~~Cg~~w 358 (370)
|+.|..||.-|
T Consensus 17 ~lrCPRC~~~F 27 (65)
T COG4049 17 FLRCPRCGMVF 27 (65)
T ss_pred eeeCCchhHHH
Confidence 66666666443
No 180
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=23.09 E-value=33 Score=33.64 Aligned_cols=18 Identities=22% Similarity=0.477 Sum_probs=13.5
Q ss_pred ccccccCCCCcceEEEee
Q 017510 323 TRYMCGRCGHKKTTNHGN 340 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~ 340 (370)
..--||-||+.-+.-+-+
T Consensus 184 ~~~~CPvCGS~PvaSmV~ 201 (308)
T COG3058 184 SRQYCPVCGSMPVASMVQ 201 (308)
T ss_pred ccccCCCcCCCCcceeee
Confidence 456799999987765554
No 181
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=22.84 E-value=51 Score=31.10 Aligned_cols=34 Identities=15% Similarity=0.370 Sum_probs=22.7
Q ss_pred cccccccCCCCcceEEEeeccccCCCceeccCCCCc
Q 017510 322 STRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQY 357 (370)
Q Consensus 322 t~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~ 357 (370)
--...|+.|.+.+.-|.-- ....|-|.|.+|.|.
T Consensus 190 ~~alIC~~C~hhngl~~~~--ek~~~efiC~~Cn~~ 223 (251)
T COG5415 190 FKALICPQCHHHNGLYRLA--EKPIIEFICPHCNHK 223 (251)
T ss_pred hhhhccccccccccccccc--cccchheecccchhh
Confidence 3457899998887666533 123335779999764
No 182
>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=22.79 E-value=50 Score=24.29 Aligned_cols=24 Identities=29% Similarity=0.570 Sum_probs=16.6
Q ss_pred cccccccCCCCcceEEEeeccccCCCceeccCCCC
Q 017510 322 STRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQ 356 (370)
Q Consensus 322 t~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~ 356 (370)
.....|+.||...-. ...|..||.
T Consensus 24 p~l~~C~~cG~~~~~-----------H~vc~~cG~ 47 (55)
T TIGR01031 24 PTLVVCPNCGEFKLP-----------HRVCPSCGY 47 (55)
T ss_pred CcceECCCCCCcccC-----------eeECCccCe
Confidence 456779999985443 455888883
No 183
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=22.43 E-value=34 Score=29.26 Aligned_cols=30 Identities=20% Similarity=0.420 Sum_probs=17.5
Q ss_pred cccccccccCCCCcceEEEeeccccCCC----ceeccCCC
Q 017510 320 YHSTRYMCGRCGHKKTTNHGNDQNSSAK----RIKCLNCY 355 (370)
Q Consensus 320 ~~t~~~~C~~C~~~~~~~~q~~Q~RsaD----f~~C~~Cg 355 (370)
.....+.| .||+. +.+ ....-+ |+.|..||
T Consensus 66 ~vp~~~~C-~Cg~~----~~~-~~~~~~~~~~~~~CP~Cg 99 (124)
T PRK00762 66 MIPVEIEC-ECGYE----GVV-DEDEIDHYAAVIECPVCG 99 (124)
T ss_pred ecCeeEEe-eCcCc----ccc-cccchhccccCCcCcCCC
Confidence 45578999 99943 211 101111 36799999
No 184
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=22.12 E-value=41 Score=24.71 Aligned_cols=22 Identities=23% Similarity=0.501 Sum_probs=16.5
Q ss_pred ccccccCCCCcceEEEeeccccCCCceeccCCC
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCY 355 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg 355 (370)
....|+.||. +.+- ...|.+||
T Consensus 25 ~l~~c~~cg~----~~~~-------H~vc~~cG 46 (56)
T PF01783_consen 25 NLVKCPNCGE----PKLP-------HRVCPSCG 46 (56)
T ss_dssp SEEESSSSSS----EEST-------TSBCTTTB
T ss_pred ceeeeccCCC----Eecc-------cEeeCCCC
Confidence 6788999995 4444 66788897
No 185
>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=22.04 E-value=57 Score=22.54 Aligned_cols=30 Identities=20% Similarity=0.428 Sum_probs=13.5
Q ss_pred ccccCCCCcceEE-EeeccccCCCceeccCCCC
Q 017510 325 YMCGRCGHKKTTN-HGNDQNSSAKRIKCLNCYQ 356 (370)
Q Consensus 325 ~~C~~C~~~~~~~-~q~~Q~RsaDf~~C~~Cg~ 356 (370)
..||.|+.+.-.- +.- ..... -+.|..|+.
T Consensus 4 ~pCP~CGG~DrFri~~d-~~~~G-~~~C~~C~~ 34 (40)
T PF08273_consen 4 GPCPICGGKDRFRIFDD-KDGRG-TWICRQCGG 34 (40)
T ss_dssp E--TTTT-TTTEEEETT-----S--EEETTTTB
T ss_pred CCCCCCcCccccccCcC-cccCC-CEECCCCCC
Confidence 4699998865443 322 11111 666999943
No 186
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=21.93 E-value=63 Score=29.86 Aligned_cols=36 Identities=25% Similarity=0.456 Sum_probs=23.9
Q ss_pred ccccccCCCCcceEEEeeccccCCCceeccCCCCccee-hhhccc
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYWES-TTALYG 366 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w~~-~~~~~~ 366 (370)
-...|.+|++.-.. ..+...|.+||+.-+= |...|+
T Consensus 148 I~A~CsrC~~~L~~--------~~~~l~Cp~Cg~tEkRKia~~y~ 184 (188)
T COG1096 148 IYARCSRCRAPLVK--------KGNMLKCPNCGNTEKRKIAKDYG 184 (188)
T ss_pred EEEEccCCCcceEE--------cCcEEECCCCCCEEeeeeccccc
Confidence 35789999986443 2226789999998543 554444
No 187
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=21.88 E-value=29 Score=34.00 Aligned_cols=35 Identities=14% Similarity=0.261 Sum_probs=23.8
Q ss_pred ccccccccCCCCcceEE-EeeccccCCCceeccCCCCcceeh
Q 017510 321 HSTRYMCGRCGHKKTTN-HGNDQNSSAKRIKCLNCYQYWEST 361 (370)
Q Consensus 321 ~t~~~~C~~C~~~~~~~-~q~~Q~RsaDf~~C~~Cg~~w~~~ 361 (370)
..-..+||.|++- .| ..+ -.++..|.+|||..+..
T Consensus 25 e~lw~KCp~c~~~--~y~~eL----~~n~~vcp~c~~h~ri~ 60 (294)
T COG0777 25 EGLWTKCPSCGEM--LYRKEL----ESNLKVCPKCGHHMRIS 60 (294)
T ss_pred CCceeECCCccce--eeHHHH----HhhhhcccccCcccccC
Confidence 4467899999862 22 222 12388899999988764
No 188
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=21.70 E-value=24 Score=34.40 Aligned_cols=34 Identities=21% Similarity=0.488 Sum_probs=0.0
Q ss_pred ccccCCCCcceEEEee---ccccCCC-ceeccCCCCcc
Q 017510 325 YMCGRCGHKKTTNHGN---DQNSSAK-RIKCLNCYQYW 358 (370)
Q Consensus 325 ~~C~~C~~~~~~~~q~---~Q~RsaD-f~~C~~Cg~~w 358 (370)
|.|+-|+..=+--.-+ .||-|.| -|.|.+||..|
T Consensus 216 F~C~hC~kAFADRSNLRAHmQTHS~~K~~qC~~C~KsF 253 (279)
T KOG2462|consen 216 FSCPHCGKAFADRSNLRAHMQTHSDVKKHQCPRCGKSF 253 (279)
T ss_pred ccCCcccchhcchHHHHHHHHhhcCCccccCcchhhHH
No 189
>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=21.64 E-value=29 Score=35.38 Aligned_cols=39 Identities=21% Similarity=0.425 Sum_probs=22.6
Q ss_pred ccccccCCCCcceEEEeeccccCCCceeccCCCCcceehhhccc
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQYWESTTALYG 366 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~~w~~~~~~~~ 366 (370)
-.+.|..|+.++...... .. -..|..||.+|...+.+|.
T Consensus 239 ~v~~C~~C~~~~~~~~~~--~~---~~~c~~cg~~~~~~GPlWl 277 (377)
T PF02005_consen 239 YVYYCPSCGYREEVKGLQ--KL---KSKCPECGSKLHISGPLWL 277 (377)
T ss_dssp EEEEETTT--EECCT-GC--C-----CEETTT-SCCCEEEEEE-
T ss_pred EEEECCCccccccccCcc--cc---CCcCCCCCCccceecCccc
Confidence 368899995442211110 00 2789999999999988874
No 190
>PRK04860 hypothetical protein; Provisional
Probab=21.63 E-value=27 Score=31.33 Aligned_cols=40 Identities=15% Similarity=0.324 Sum_probs=23.5
Q ss_pred ccccccCCCCcceEEEeeccccCCC-ceeccCCCCcceehhh
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSAK-RIKCLNCYQYWESTTA 363 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~RsaD-f~~C~~Cg~~w~~~~~ 363 (370)
=.|.|. |+.....+.....+-.+. .|.|..|+..+.+-.+
T Consensus 118 ~~Y~C~-C~~~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~~~ 158 (160)
T PRK04860 118 FPYRCK-CQEHQLTVRRHNRVVRGEAVYRCRRCGETLVFKGE 158 (160)
T ss_pred EEEEcC-CCCeeCHHHHHHHHhcCCccEECCCCCceeEEecc
Confidence 358998 987222111110011123 7999999999887654
No 191
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=21.19 E-value=70 Score=23.64 Aligned_cols=24 Identities=25% Similarity=0.569 Sum_probs=15.2
Q ss_pred cccccCCCCcceEEEeecccc-CCCceeccCCCC
Q 017510 324 RYMCGRCGHKKTTNHGNDQNS-SAKRIKCLNCYQ 356 (370)
Q Consensus 324 ~~~C~~C~~~~~~~~q~~Q~R-saDf~~C~~Cg~ 356 (370)
...|.-||.+ .. ..|.|.|..||-
T Consensus 5 ~~~C~~Cg~~---------~~~~dDiVvCp~Cga 29 (54)
T PF14446_consen 5 GCKCPVCGKK---------FKDGDDIVVCPECGA 29 (54)
T ss_pred CccChhhCCc---------ccCCCCEEECCCCCC
Confidence 3567777753 23 233888888884
No 192
>PRK04351 hypothetical protein; Provisional
Probab=20.95 E-value=71 Score=28.29 Aligned_cols=33 Identities=21% Similarity=0.492 Sum_probs=23.3
Q ss_pred ccccccCCCCcceEEEeeccccCCC--ceeccCCCCcceeh
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSAK--RIKCLNCYQYWEST 361 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~RsaD--f~~C~~Cg~~w~~~ 361 (370)
=.+.|.+||+. |.- + |+-| -|.|..|+.+-.+-
T Consensus 111 y~Y~C~~Cg~~---~~r--~-Rr~n~~~yrCg~C~g~L~~~ 145 (149)
T PRK04351 111 YLYECQSCGQQ---YLR--K-RRINTKRYRCGKCRGKLKLI 145 (149)
T ss_pred EEEECCCCCCE---eee--e-eecCCCcEEeCCCCcEeeec
Confidence 36899999852 221 2 5566 89999999887654
No 193
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=20.69 E-value=46 Score=25.29 Aligned_cols=25 Identities=28% Similarity=0.626 Sum_probs=18.4
Q ss_pred ccccccCCCCcceEEEeeccccCCCceeccCCCC
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSAKRIKCLNCYQ 356 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~RsaDf~~C~~Cg~ 356 (370)
....|.+||.+ .|+-. --+|-.||+
T Consensus 16 tHt~CrRCG~~--syh~q-------K~~CasCGy 40 (62)
T PRK04179 16 THIRCRRCGRH--SYNVR-------KKYCAACGF 40 (62)
T ss_pred ccchhcccCcc--ccccc-------ccchhhcCC
Confidence 46789999987 44432 457999997
No 194
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=20.64 E-value=34 Score=25.88 Aligned_cols=28 Identities=25% Similarity=0.487 Sum_probs=14.2
Q ss_pred cccccccCCCCc-ceEEEeeccccCCCceeccCCCC
Q 017510 322 STRYMCGRCGHK-KTTNHGNDQNSSAKRIKCLNCYQ 356 (370)
Q Consensus 322 t~~~~C~~C~~~-~~~~~q~~Q~RsaDf~~C~~Cg~ 356 (370)
.-.+.|-.|+.+ .+.|+-+ ...|..||-
T Consensus 28 ~v~IlCNDC~~~s~v~fH~l-------g~KC~~C~S 56 (61)
T PF14599_consen 28 KVWILCNDCNAKSEVPFHFL-------GHKCSHCGS 56 (61)
T ss_dssp EEEEEESSS--EEEEE--TT-----------TTTS-
T ss_pred EEEEECCCCCCccceeeeHh-------hhcCCCCCC
Confidence 356889999886 5556666 678888873
No 195
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=20.16 E-value=41 Score=34.85 Aligned_cols=28 Identities=29% Similarity=0.600 Sum_probs=19.2
Q ss_pred ccccccCCCCcceEEEeeccccCCC--ceeccCCCCcce
Q 017510 323 TRYMCGRCGHKKTTNHGNDQNSSAK--RIKCLNCYQYWE 359 (370)
Q Consensus 323 ~~~~C~~C~~~~~~~~q~~Q~RsaD--f~~C~~Cg~~w~ 359 (370)
..-.||+||.+- -|+. -|.|..||.+..
T Consensus 349 ~~p~Cp~Cg~~m---------~S~G~~g~rC~kCg~~~~ 378 (421)
T COG1571 349 VNPVCPRCGGRM---------KSAGRNGFRCKKCGTRAR 378 (421)
T ss_pred cCCCCCccCCch---------hhcCCCCcccccccccCC
Confidence 345799998753 2333 788999998754
No 196
>PRK14873 primosome assembly protein PriA; Provisional
Probab=20.14 E-value=1e+02 Score=33.96 Aligned_cols=17 Identities=6% Similarity=-0.093 Sum_probs=10.7
Q ss_pred cCCCChhhhcCCChhhc
Q 017510 271 LGHVKPEALIKMSSEEM 287 (370)
Q Consensus 271 ~G~isp~~lv~Ms~eEm 287 (370)
...++.-+++.|..+++
T Consensus 327 ~~~~P~v~~vd~~~~~~ 343 (665)
T PRK14873 327 RARAPRVRALGDSGLAL 343 (665)
T ss_pred cCCCCeEEEEeCchhhh
Confidence 34455567888876544
No 197
>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=20.13 E-value=25 Score=25.71 Aligned_cols=32 Identities=25% Similarity=0.641 Sum_probs=21.6
Q ss_pred cccCCCCcceEEEeeccccCCC--ceeccCCCCcceeh
Q 017510 326 MCGRCGHKKTTNHGNDQNSSAK--RIKCLNCYQYWEST 361 (370)
Q Consensus 326 ~C~~C~~~~~~~~q~~Q~RsaD--f~~C~~Cg~~w~~~ 361 (370)
.|..|+-.++.. |.|..+ -..|+.||-+|+--
T Consensus 1 ~C~~C~~~~Tp~----WR~g~~~~~~LCNaCgl~~~k~ 34 (54)
T cd00202 1 ACSNCGTTTTPL----WRRGPSGGSTLCNACGLYWKKH 34 (54)
T ss_pred CCCCCCCCCCcc----cccCCCCcchHHHHHHHHHHhc
Confidence 388888866642 333332 77899999988653
Done!