Query 036150
Match_columns 77
No_of_seqs 119 out of 246
Neff 2.5
Searched_HMMs 46136
Date Fri Mar 29 09:55:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/036150.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/036150hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01780 Ribosomal_L37ae: Ribo 99.8 2.1E-20 4.6E-25 124.5 3.3 49 8-56 36-84 (90)
2 PRK03976 rpl37ae 50S ribosomal 99.8 4.5E-20 9.6E-25 123.0 4.9 48 8-55 37-84 (90)
3 TIGR00280 L37a ribosomal prote 99.8 4.3E-20 9.3E-25 123.4 4.6 49 8-56 36-84 (91)
4 PTZ00255 60S ribosomal protein 99.8 4.9E-20 1.1E-24 122.8 4.5 50 7-56 36-85 (90)
5 COG1997 RPL43A Ribosomal prote 99.7 1.9E-18 4.1E-23 115.9 2.0 47 6-52 34-80 (89)
6 KOG0402 60S ribosomal protein 99.6 2.8E-16 6.1E-21 106.2 1.6 49 9-57 38-86 (92)
7 PF12760 Zn_Tnp_IS1595: Transp 96.3 0.0029 6.3E-08 36.2 2.0 26 9-34 20-46 (46)
8 PHA00626 hypothetical protein 95.4 0.012 2.6E-07 37.5 2.1 33 9-41 2-39 (59)
9 PRK00432 30S ribosomal protein 95.2 0.01 2.2E-07 35.4 1.2 26 9-35 22-47 (50)
10 PRK00398 rpoP DNA-directed RNA 93.6 0.066 1.4E-06 30.4 2.1 29 7-35 3-31 (46)
11 TIGR03655 anti_R_Lar restricti 92.8 0.11 2.3E-06 30.4 2.3 28 8-35 2-36 (53)
12 PF07282 OrfB_Zn_ribbon: Putat 92.4 0.1 2.3E-06 30.9 1.9 29 7-35 28-56 (69)
13 PF08646 Rep_fac-A_C: Replicat 91.3 0.11 2.3E-06 34.6 1.2 36 8-44 19-56 (146)
14 PF08271 TF_Zn_Ribbon: TFIIB z 91.1 0.13 2.9E-06 28.8 1.3 30 8-37 1-31 (43)
15 PRK12366 replication factor A; 90.6 0.1 2.2E-06 43.5 0.8 26 7-34 532-557 (637)
16 COG0675 Transposase and inacti 89.2 0.27 5.9E-06 34.0 1.9 27 4-35 306-332 (364)
17 COG1998 RPS31 Ribosomal protei 89.1 0.18 3.9E-06 31.3 0.8 27 9-35 21-47 (51)
18 cd04476 RPA1_DBD_C RPA1_DBD_C: 89.1 0.18 3.8E-06 34.2 0.9 32 8-40 35-66 (166)
19 smart00661 RPOL9 RNA polymeras 87.4 0.46 1E-05 26.6 1.8 32 9-40 2-35 (52)
20 PRK09710 lar restriction allev 86.7 1 2.2E-05 28.9 3.2 31 4-34 3-36 (64)
21 PRK08402 replication factor A; 85.9 0.47 1E-05 37.5 1.7 27 8-34 213-239 (355)
22 PHA02942 putative transposase; 85.5 0.44 9.6E-06 37.4 1.3 29 6-35 324-352 (383)
23 PF09082 DUF1922: Domain of un 84.5 1.2 2.5E-05 28.9 2.7 31 5-37 1-31 (68)
24 PF11781 RRN7: RNA polymerase 82.2 0.96 2.1E-05 25.4 1.5 26 9-35 10-35 (36)
25 PF08273 Prim_Zn_Ribbon: Zinc- 81.7 1.5 3.3E-05 25.3 2.3 30 7-37 3-37 (40)
26 cd00729 rubredoxin_SM Rubredox 81.5 1.3 2.7E-05 24.4 1.7 15 25-39 2-16 (34)
27 PRK00464 nrdR transcriptional 81.4 1 2.2E-05 32.1 1.7 26 8-37 1-40 (154)
28 PRK07591 threonine synthase; V 80.3 0.91 2E-05 35.6 1.3 28 3-33 14-41 (421)
29 PRK14890 putative Zn-ribbon RN 79.1 1 2.2E-05 28.5 1.0 22 5-33 23-44 (59)
30 COG2888 Predicted Zn-ribbon RN 78.8 0.98 2.1E-05 28.9 0.8 22 5-33 25-46 (61)
31 TIGR01384 TFS_arch transcripti 78.7 3.8 8.3E-05 25.9 3.6 31 8-38 63-103 (104)
32 PRK08197 threonine synthase; V 77.9 1.5 3.2E-05 33.8 1.7 29 1-32 1-29 (394)
33 COG1571 Predicted DNA-binding 77.6 0.64 1.4E-05 38.3 -0.3 32 9-41 352-383 (421)
34 PF03367 zf-ZPR1: ZPR1 zinc-fi 77.2 3.6 7.7E-05 29.1 3.4 35 9-43 3-52 (161)
35 TIGR00617 rpa1 replication fac 75.5 0.99 2.1E-05 37.6 0.2 32 8-40 475-508 (608)
36 COG3677 Transposase and inacti 74.7 1.9 4.1E-05 29.6 1.4 31 8-38 31-66 (129)
37 PF01927 Mut7-C: Mut7-C RNAse 74.7 2.8 6.1E-05 28.5 2.3 33 7-39 91-138 (147)
38 cd00350 rubredoxin_like Rubred 74.4 2.2 4.7E-05 23.0 1.3 14 25-38 1-14 (33)
39 PRK00423 tfb transcription ini 74.0 1.8 4E-05 32.7 1.4 32 6-37 10-42 (310)
40 COG1592 Rubrerythrin [Energy p 74.0 1.8 3.8E-05 31.6 1.2 13 25-37 134-146 (166)
41 PF01096 TFIIS_C: Transcriptio 73.4 7.2 0.00016 21.7 3.4 27 9-35 2-38 (39)
42 PF00096 zf-C2H2: Zinc finger, 73.3 2.9 6.3E-05 19.8 1.5 12 26-37 1-12 (23)
43 PF13894 zf-C2H2_4: C2H2-type 73.2 2.6 5.7E-05 19.2 1.3 11 26-36 1-11 (24)
44 PF14353 CpXC: CpXC protein 72.6 6.3 0.00014 25.8 3.5 29 8-36 2-49 (128)
45 smart00440 ZnF_C2C2 C2C2 Zinc 72.1 9.9 0.00021 21.3 3.8 28 9-36 2-39 (40)
46 PRK00415 rps27e 30S ribosomal 72.0 5.4 0.00012 25.1 2.9 35 2-36 6-41 (59)
47 smart00778 Prim_Zn_Ribbon Zinc 71.8 2.3 5E-05 24.3 1.1 27 7-33 3-33 (37)
48 TIGR00340 zpr1_rel ZPR1-relate 71.8 3.4 7.3E-05 29.7 2.2 33 10-42 1-49 (163)
49 TIGR02098 MJ0042_CXXC MJ0042 f 71.5 2.1 4.5E-05 22.9 0.8 28 8-35 3-35 (38)
50 smart00834 CxxC_CXXC_SSSS Puta 71.0 5 0.00011 21.2 2.3 27 8-34 6-35 (41)
51 COG1594 RPB9 DNA-directed RNA 71.0 3.6 7.8E-05 27.7 2.1 29 8-36 3-33 (113)
52 PRK05978 hypothetical protein; 70.4 2 4.3E-05 30.8 0.7 26 8-36 34-63 (148)
53 PF03811 Zn_Tnp_IS1: InsA N-te 68.5 3.7 8E-05 23.1 1.5 24 8-31 6-35 (36)
54 PRK14892 putative transcriptio 68.4 4.4 9.6E-05 27.3 2.1 30 5-35 19-52 (99)
55 PF08772 NOB1_Zn_bind: Nin one 67.8 3 6.5E-05 26.8 1.1 17 9-25 26-42 (73)
56 PRK03681 hypA hydrogenase nick 67.5 3.1 6.6E-05 27.8 1.1 26 7-33 70-95 (114)
57 PF13717 zinc_ribbon_4: zinc-r 67.2 3.7 8E-05 22.7 1.3 28 8-35 3-35 (36)
58 PF07191 zinc-ribbons_6: zinc- 67.0 5.1 0.00011 25.9 2.1 33 8-42 2-34 (70)
59 PF08792 A2L_zn_ribbon: A2L zi 66.4 9 0.0002 21.1 2.7 28 8-35 4-31 (33)
60 PRK11823 DNA repair protein Ra 66.2 3.8 8.2E-05 32.6 1.6 24 6-33 6-29 (446)
61 PRK07218 replication factor A; 65.8 2.6 5.6E-05 34.3 0.6 27 8-42 298-324 (423)
62 PF13240 zinc_ribbon_2: zinc-r 65.5 1.6 3.5E-05 22.4 -0.4 22 9-34 1-22 (23)
63 PF05129 Elf1: Transcription e 64.4 13 0.00027 23.9 3.5 31 6-36 21-57 (81)
64 PF13719 zinc_ribbon_5: zinc-r 64.1 5.1 0.00011 22.1 1.5 29 7-35 2-35 (37)
65 PF01599 Ribosomal_S27: Riboso 63.9 7.2 0.00016 23.5 2.2 26 9-34 20-47 (47)
66 COG1405 SUA7 Transcription ini 63.6 5.3 0.00012 30.8 2.0 32 8-39 2-34 (285)
67 TIGR00310 ZPR1_znf ZPR1 zinc f 63.4 8.1 0.00018 28.3 2.8 35 8-42 1-51 (192)
68 PF13453 zf-TFIIB: Transcripti 62.6 14 0.00029 20.4 3.0 26 9-35 1-29 (41)
69 PLN00209 ribosomal protein S27 62.3 16 0.00034 24.7 3.8 34 3-36 32-66 (86)
70 PF10571 UPF0547: Uncharacteri 61.1 2.9 6.2E-05 22.1 0.1 23 9-35 2-24 (26)
71 TIGR00416 sms DNA repair prote 61.0 5.4 0.00012 32.0 1.7 23 7-33 7-29 (454)
72 PF09723 Zn-ribbon_8: Zinc rib 61.0 5.3 0.00012 22.4 1.2 14 8-21 27-40 (42)
73 PTZ00083 40S ribosomal protein 58.8 20 0.00043 24.1 3.8 34 3-36 31-65 (85)
74 cd01121 Sms Sms (bacterial rad 58.3 5 0.00011 31.5 1.0 21 9-33 2-22 (372)
75 PF11023 DUF2614: Protein of u 57.8 4.4 9.6E-05 28.5 0.6 24 7-34 69-94 (114)
76 PF12874 zf-met: Zinc-finger o 57.7 9.3 0.0002 18.3 1.6 12 26-37 1-12 (25)
77 PF04606 Ogr_Delta: Ogr/Delta- 56.6 14 0.00029 21.1 2.4 29 9-37 1-39 (47)
78 PF14311 DUF4379: Domain of un 56.4 7.3 0.00016 22.5 1.3 12 25-36 28-39 (55)
79 COG4640 Predicted membrane pro 55.7 4.5 9.8E-05 34.1 0.4 29 8-40 2-30 (465)
80 PRK06386 replication factor A; 55.5 5 0.00011 32.1 0.6 20 8-33 237-256 (358)
81 COG2051 RPS27A Ribosomal prote 55.2 26 0.00057 22.7 3.8 34 3-36 15-49 (67)
82 PRK04351 hypothetical protein; 54.8 13 0.00028 26.2 2.5 29 7-35 112-142 (149)
83 PF01667 Ribosomal_S27e: Ribos 54.8 11 0.00023 23.3 1.9 34 3-36 3-37 (55)
84 TIGR00100 hypA hydrogenase nic 54.4 7.4 0.00016 25.9 1.2 25 7-33 70-94 (115)
85 PRK04023 DNA polymerase II lar 54.4 5.4 0.00012 36.8 0.7 24 8-36 639-662 (1121)
86 TIGR02159 PA_CoA_Oxy4 phenylac 54.1 2.9 6.4E-05 29.3 -0.8 28 8-35 106-140 (146)
87 PRK11032 hypothetical protein; 53.0 8.3 0.00018 27.9 1.3 28 7-34 124-151 (160)
88 PF09862 DUF2089: Protein of u 52.2 17 0.00037 25.1 2.8 44 10-60 1-45 (113)
89 TIGR03831 YgiT_finger YgiT-typ 51.8 13 0.00027 19.8 1.7 19 18-36 25-43 (46)
90 PF06397 Desulfoferrod_N: Desu 51.7 11 0.00024 21.5 1.5 12 24-35 5-16 (36)
91 PF13465 zf-H2C2_2: Zinc-finge 51.7 12 0.00026 18.9 1.5 11 26-36 15-25 (26)
92 PRK07562 ribonucleotide-diphos 51.7 10 0.00022 35.2 2.0 28 6-34 1189-1216(1220)
93 COG1656 Uncharacterized conser 51.2 5.2 0.00011 29.5 0.1 30 7-36 97-141 (165)
94 PF07295 DUF1451: Protein of u 51.1 8.1 0.00017 27.3 1.0 28 7-34 112-139 (146)
95 PF15135 UPF0515: Uncharacteri 50.8 9.3 0.0002 30.5 1.4 33 6-38 131-168 (278)
96 PF10122 Mu-like_Com: Mu-like 50.2 7.6 0.00017 24.0 0.7 32 5-36 2-35 (51)
97 COG1198 PriA Primosomal protei 48.8 12 0.00026 32.7 1.9 28 7-34 444-471 (730)
98 PRK00241 nudC NADH pyrophospha 48.1 14 0.0003 27.6 1.9 27 8-34 100-126 (256)
99 TIGR02605 CxxC_CxxC_SSSS putat 47.7 12 0.00025 21.0 1.2 15 8-22 27-41 (52)
100 COG4888 Uncharacterized Zn rib 47.6 28 0.0006 24.3 3.2 36 6-41 21-62 (104)
101 PRK00564 hypA hydrogenase nick 47.3 7.3 0.00016 26.1 0.3 25 7-33 71-96 (117)
102 PRK06450 threonine synthase; V 46.2 11 0.00023 29.0 1.1 23 8-33 4-26 (338)
103 PHA00689 hypothetical protein 45.9 8.8 0.00019 24.5 0.5 16 6-21 16-31 (62)
104 COG1096 Predicted RNA-binding 45.8 16 0.00034 27.6 1.9 18 7-24 165-182 (188)
105 PF13912 zf-C2H2_6: C2H2-type 45.8 15 0.00033 17.8 1.3 11 26-36 2-12 (27)
106 PF00641 zf-RanBP: Zn-finger i 45.7 10 0.00023 19.5 0.7 12 24-35 3-14 (30)
107 PF08996 zf-DNA_Pol: DNA Polym 45.7 16 0.00035 25.9 1.9 27 7-33 18-53 (188)
108 PF06044 DRP: Dam-replacing fa 44.5 16 0.00036 28.7 1.9 34 8-41 32-82 (254)
109 PF14319 Zn_Tnp_IS91: Transpos 43.9 16 0.00034 24.3 1.5 30 5-34 40-69 (111)
110 COG4049 Uncharacterized protei 43.3 9.5 0.00021 24.7 0.4 11 6-16 16-26 (65)
111 PF08209 Sgf11: Sgf11 (transcr 43.3 14 0.0003 20.7 1.0 17 26-42 5-21 (33)
112 TIGR03844 cysteate_syn cysteat 43.2 12 0.00027 29.5 1.1 23 7-32 2-24 (398)
113 PF02150 RNA_POL_M_15KD: RNA p 42.6 20 0.00042 19.7 1.5 27 9-36 3-31 (35)
114 PF04071 zf-like: Cysteine-ric 42.5 16 0.00036 24.2 1.4 21 14-34 40-60 (86)
115 smart00659 RPOLCX RNA polymera 42.5 24 0.00052 20.4 1.9 27 8-36 3-30 (44)
116 smart00290 ZnF_UBP Ubiquitin C 41.9 20 0.00044 19.6 1.6 24 9-38 1-24 (50)
117 cd00974 DSRD Desulforedoxin (D 41.8 23 0.0005 18.8 1.7 13 24-36 3-15 (34)
118 PRK09678 DNA-binding transcrip 41.7 26 0.00057 22.4 2.2 30 8-37 2-41 (72)
119 smart00531 TFIIE Transcription 41.4 10 0.00022 25.8 0.3 29 7-35 99-133 (147)
120 TIGR00319 desulf_FeS4 desulfof 41.3 22 0.00048 18.8 1.6 14 23-36 5-18 (34)
121 PF01586 Basic: Myogenic Basic 41.0 9.4 0.0002 25.5 0.1 11 25-35 72-82 (86)
122 PF14354 Lar_restr_allev: Rest 40.5 41 0.00089 19.2 2.8 27 7-33 3-37 (61)
123 PRK12380 hydrogenase nickel in 39.7 17 0.00036 24.2 1.1 24 7-32 70-93 (113)
124 COG2158 Uncharacterized protei 39.5 18 0.00039 25.6 1.3 26 9-34 44-71 (112)
125 PLN03086 PRLI-interacting fact 39.1 15 0.00032 31.4 1.0 32 5-36 431-464 (567)
126 PRK14873 primosome assembly pr 38.8 21 0.00046 30.4 1.9 26 8-33 393-418 (665)
127 PF03107 C1_2: C1 domain; Int 38.8 11 0.00025 19.7 0.2 16 26-41 1-17 (30)
128 PRK03824 hypA hydrogenase nick 38.2 25 0.00054 24.0 1.8 15 24-38 69-83 (135)
129 PF01921 tRNA-synt_1f: tRNA sy 38.2 29 0.00064 28.0 2.5 28 8-35 175-209 (360)
130 PF05191 ADK_lid: Adenylate ki 38.0 25 0.00055 19.6 1.5 11 26-36 2-12 (36)
131 smart00547 ZnF_RBZ Zinc finger 37.8 12 0.00025 18.5 0.1 11 24-34 1-11 (26)
132 PF02892 zf-BED: BED zinc fing 37.1 24 0.00051 19.0 1.3 17 22-38 13-29 (45)
133 PRK14811 formamidopyrimidine-D 37.1 30 0.00065 25.9 2.2 25 9-34 237-264 (269)
134 PF03604 DNA_RNApol_7kD: DNA d 36.3 6 0.00013 21.9 -1.2 7 27-33 19-25 (32)
135 COG2956 Predicted N-acetylgluc 35.7 26 0.00056 29.2 1.9 22 8-33 355-376 (389)
136 smart00731 SprT SprT homologue 35.7 38 0.00083 22.7 2.4 29 7-35 112-143 (146)
137 PF05876 Terminase_GpA: Phage 35.0 29 0.00063 28.6 2.0 40 6-45 199-258 (557)
138 TIGR00595 priA primosomal prot 34.8 24 0.00051 28.7 1.5 30 7-36 222-251 (505)
139 PRK13945 formamidopyrimidine-D 34.7 34 0.00074 25.7 2.2 23 9-32 256-281 (282)
140 PF09332 Mcm10: Mcm10 replicat 34.5 16 0.00034 29.3 0.5 11 25-35 285-295 (344)
141 PF05899 Cupin_3: Protein of u 34.5 20 0.00044 21.7 0.9 17 20-36 6-22 (74)
142 PF09297 zf-NADH-PPase: NADH p 34.1 30 0.00065 18.1 1.4 25 10-34 6-30 (32)
143 PF13597 NRDD: Anaerobic ribon 34.1 30 0.00065 28.6 2.0 24 6-34 490-513 (546)
144 PRK06260 threonine synthase; V 34.0 18 0.00039 27.9 0.7 23 8-32 4-26 (397)
145 PF01807 zf-CHC2: CHC2 zinc fi 34.0 21 0.00045 22.8 0.9 36 4-42 31-69 (97)
146 cd01675 RNR_III Class III ribo 33.7 14 0.00031 30.4 0.1 27 4-34 515-541 (555)
147 COG1773 Rubredoxin [Energy pro 33.6 27 0.00057 21.7 1.3 11 25-35 3-13 (55)
148 smart00709 Zpr1 Duplicated dom 33.4 51 0.0011 23.4 2.8 35 9-43 2-51 (160)
149 PF12773 DZR: Double zinc ribb 33.4 9.2 0.0002 21.2 -0.8 30 8-38 13-42 (50)
150 TIGR01385 TFSII transcription 33.3 33 0.00071 26.7 2.0 28 8-35 259-296 (299)
151 PF01396 zf-C4_Topoisom: Topoi 33.1 54 0.0012 18.2 2.4 29 7-35 1-34 (39)
152 PRK08173 DNA topoisomerase III 33.1 24 0.00052 31.0 1.3 26 8-35 625-650 (862)
153 PF13913 zf-C2HC_2: zinc-finge 32.8 24 0.00052 18.0 0.8 10 27-36 4-13 (25)
154 PRK13130 H/ACA RNA-protein com 32.5 32 0.00069 21.2 1.5 23 6-34 4-26 (56)
155 PRK14810 formamidopyrimidine-D 32.3 40 0.00087 25.2 2.3 23 9-32 246-271 (272)
156 COG2260 Predicted Zn-ribbon RN 32.3 28 0.00062 22.1 1.3 21 8-34 6-26 (59)
157 PF13842 Tnp_zf-ribbon_2: DDE_ 32.2 30 0.00065 18.7 1.2 22 9-32 2-23 (32)
158 cd06968 NR_DBD_ROR DNA-binding 31.9 20 0.00044 23.4 0.6 30 3-33 1-30 (95)
159 TIGR03830 CxxCG_CxxCG_HTH puta 31.9 58 0.0013 20.4 2.7 17 22-38 28-44 (127)
160 PHA02998 RNA polymerase subuni 31.8 48 0.001 25.4 2.6 28 9-36 145-182 (195)
161 PRK08665 ribonucleotide-diphos 31.8 19 0.00041 31.2 0.5 25 9-35 726-750 (752)
162 PF04135 Nop10p: Nucleolar RNA 31.8 33 0.00072 21.0 1.5 24 5-34 3-26 (53)
163 COG3809 Uncharacterized protei 31.5 49 0.0011 22.6 2.4 29 8-36 2-32 (88)
164 PLN02569 threonine synthase 31.4 23 0.0005 29.0 0.9 26 3-32 45-71 (484)
165 PF07754 DUF1610: Domain of un 31.3 30 0.00064 18.3 1.0 20 13-32 4-23 (24)
166 PF00645 zf-PARP: Poly(ADP-rib 30.9 29 0.00063 21.0 1.1 18 27-44 9-26 (82)
167 PRK01103 formamidopyrimidine/5 30.6 49 0.0011 24.6 2.5 24 9-33 247-273 (274)
168 PF14803 Nudix_N_2: Nudix N-te 30.5 37 0.00081 18.8 1.4 25 10-34 3-31 (34)
169 PRK07111 anaerobic ribonucleos 30.2 23 0.00049 30.7 0.7 23 6-33 679-701 (735)
170 cd00730 rubredoxin Rubredoxin; 29.7 25 0.00055 20.9 0.7 12 25-36 1-12 (50)
171 PF09986 DUF2225: Uncharacteri 29.6 33 0.0007 24.9 1.4 14 25-38 48-61 (214)
172 TIGR00577 fpg formamidopyrimid 29.5 48 0.001 24.8 2.3 22 9-31 247-271 (272)
173 COG2023 RPR2 RNase P subunit R 29.1 66 0.0014 22.3 2.7 26 10-35 59-92 (105)
174 PF05907 DUF866: Eukaryotic pr 28.4 1.2E+02 0.0026 21.5 4.0 32 3-34 26-73 (161)
175 smart00355 ZnF_C2H2 zinc finge 28.4 19 0.00042 16.0 0.0 11 27-37 2-12 (26)
176 PF10263 SprT-like: SprT-like 28.3 52 0.0011 21.5 2.0 30 6-35 122-153 (157)
177 KOG1598 Transcription initiati 28.1 26 0.00056 30.0 0.7 37 9-45 2-39 (521)
178 PRK02935 hypothetical protein; 28.0 40 0.00087 23.7 1.5 23 7-33 70-94 (110)
179 PRK04338 N(2),N(2)-dimethylgua 27.4 18 0.0004 28.4 -0.3 32 4-35 220-254 (382)
180 TIGR00354 polC DNA polymerase, 26.8 33 0.00071 31.9 1.2 21 8-34 626-646 (1095)
181 PRK05580 primosome assembly pr 26.8 37 0.00081 28.5 1.4 27 8-34 391-417 (679)
182 PF03833 PolC_DP2: DNA polymer 26.4 22 0.00048 32.3 0.0 31 8-38 656-693 (900)
183 COG1996 RPC10 DNA-directed RNA 25.9 61 0.0013 19.6 1.9 29 7-35 6-34 (49)
184 smart00400 ZnF_CHCC zinc finge 25.8 36 0.00078 19.4 0.9 12 22-33 20-31 (55)
185 COG3357 Predicted transcriptio 25.5 25 0.00054 24.3 0.2 11 27-37 60-70 (97)
186 PF06353 DUF1062: Protein of u 25.1 38 0.00082 24.0 1.0 17 25-41 13-29 (142)
187 PF00301 Rubredoxin: Rubredoxi 25.1 56 0.0012 19.2 1.6 16 26-41 2-17 (47)
188 COG2401 ABC-type ATPase fused 24.9 33 0.00072 29.9 0.8 16 20-35 125-140 (593)
189 PF08274 PhnA_Zn_Ribbon: PhnA 24.6 55 0.0012 17.9 1.4 26 9-35 4-29 (30)
190 PRK00762 hypA hydrogenase nick 24.5 35 0.00076 23.0 0.7 25 7-32 70-99 (124)
191 smart00614 ZnF_BED BED zinc fi 24.5 51 0.0011 18.6 1.3 13 27-39 20-32 (50)
192 cd00674 LysRS_core_class_I cat 24.4 1.2E+02 0.0025 24.2 3.7 27 8-35 170-202 (353)
193 COG1545 Predicted nucleic-acid 24.3 42 0.00092 23.1 1.1 9 27-35 31-39 (140)
194 PF02977 CarbpepA_inh: Carboxy 23.9 13 0.00029 22.6 -1.3 30 13-42 8-39 (46)
195 PF14952 zf-tcix: Putative tre 23.9 30 0.00065 20.9 0.3 11 23-33 9-19 (44)
196 KOG4167 Predicted DNA-binding 23.3 13 0.00028 33.7 -1.9 14 22-35 789-802 (907)
197 TIGR01391 dnaG DNA primase, ca 23.1 42 0.00092 26.5 1.0 32 9-42 36-70 (415)
198 PRK08270 anaerobic ribonucleos 22.5 35 0.00076 29.1 0.5 23 7-34 626-648 (656)
199 COG5034 TNG2 Chromatin remodel 22.5 24 0.00052 28.1 -0.4 33 2-34 229-270 (271)
200 cd01411 SIR2H SIR2H: Uncharact 22.4 39 0.00085 24.4 0.7 27 6-32 117-143 (225)
201 PRK14714 DNA polymerase II lar 22.2 47 0.001 31.5 1.3 11 25-35 692-702 (1337)
202 PF13397 DUF4109: Domain of un 21.7 44 0.00095 23.1 0.8 11 24-34 49-59 (105)
203 PF09943 DUF2175: Uncharacteri 21.2 51 0.0011 22.6 1.0 15 25-39 2-16 (101)
204 PRK14714 DNA polymerase II lar 21.2 41 0.0009 31.9 0.7 23 7-35 667-689 (1337)
205 PRK14704 anaerobic ribonucleos 21.2 42 0.0009 28.6 0.7 21 7-33 559-580 (618)
206 TIGR00308 TRM1 tRNA(guanine-26 20.6 32 0.0007 27.2 -0.1 31 4-34 209-242 (374)
207 PRK01110 rpmF 50S ribosomal pr 20.1 81 0.0017 19.3 1.6 15 8-22 28-42 (60)
208 PRK08329 threonine synthase; V 20.0 47 0.001 25.3 0.7 21 8-32 2-22 (347)
No 1
>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=99.80 E-value=2.1e-20 Score=124.55 Aligned_cols=49 Identities=35% Similarity=0.480 Sum_probs=42.4
Q ss_pred eeeCCCCceeeEEeEEEEEeeCCCCcEEeCcccccccccccccHHHHHh
Q 036150 8 LRRKRTKKYAVKRKAVGIWSCKYCGKVKAGALNAATLAAFTALPAAAAA 56 (77)
Q Consensus 8 ~~~~~CGK~~VKR~AVGIWkCkkCgkt~AGGAYtp~Tpag~s~~~~~~~ 56 (77)
..||.|||++|||+++|||+|++||++||||||+|+||++...+.+-.-
T Consensus 36 y~Cp~Cgk~~vkR~a~GIW~C~~C~~~~AGGAy~~~T~~~~t~~~~i~r 84 (90)
T PF01780_consen 36 YTCPFCGKTSVKRVATGIWKCKKCGKKFAGGAYTPSTPAAKTVKRAIRR 84 (90)
T ss_dssp BEESSSSSSEEEEEETTEEEETTTTEEEE-BSSSSS-HHHHHHHHHHHH
T ss_pred CcCCCCCCceeEEeeeEEeecCCCCCEEeCCCccccchHHHHHHHHHHH
Confidence 4699999999999999999999999999999999999999877665443
No 2
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=99.80 E-value=4.5e-20 Score=123.00 Aligned_cols=48 Identities=27% Similarity=0.388 Sum_probs=43.2
Q ss_pred eeeCCCCceeeEEeEEEEEeeCCCCcEEeCcccccccccccccHHHHH
Q 036150 8 LRRKRTKKYAVKRKAVGIWSCKYCGKVKAGALNAATLAAFTALPAAAA 55 (77)
Q Consensus 8 ~~~~~CGK~~VKR~AVGIWkCkkCgkt~AGGAYtp~Tpag~s~~~~~~ 55 (77)
..||.|||++|||+++|||+|++||++||||||+|+||++.....+-+
T Consensus 37 y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGGAy~~~T~~~~t~~~~ir 84 (90)
T PRK03976 37 HVCPVCGRPKVKRVGTGIWECRKCGAKFAGGAYTPETPAGKTVTRAIR 84 (90)
T ss_pred ccCCCCCCCceEEEEEEEEEcCCCCCEEeCCccccccchhhhHHHHHH
Confidence 469999999999999999999999999999999999999987554433
No 3
>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=99.80 E-value=4.3e-20 Score=123.39 Aligned_cols=49 Identities=27% Similarity=0.398 Sum_probs=43.5
Q ss_pred eeeCCCCceeeEEeEEEEEeeCCCCcEEeCcccccccccccccHHHHHh
Q 036150 8 LRRKRTKKYAVKRKAVGIWSCKYCGKVKAGALNAATLAAFTALPAAAAA 56 (77)
Q Consensus 8 ~~~~~CGK~~VKR~AVGIWkCkkCgkt~AGGAYtp~Tpag~s~~~~~~~ 56 (77)
..||.|||++|||+++|||+|++||++||||||+|+||++.....+-+-
T Consensus 36 y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGGAy~p~T~~~~t~~~~irr 84 (91)
T TIGR00280 36 YVCPFCGKKTVKRGSTGIWTCRKCGAKFAGGAYTPVTPAGKTVRKTIRR 84 (91)
T ss_pred ccCCCCCCCceEEEeeEEEEcCCCCCEEeCCccccccchhHHHHHHHHH
Confidence 4699999999999999999999999999999999999999875544433
No 4
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=99.80 E-value=4.9e-20 Score=122.81 Aligned_cols=50 Identities=34% Similarity=0.428 Sum_probs=44.0
Q ss_pred eeeeCCCCceeeEEeEEEEEeeCCCCcEEeCcccccccccccccHHHHHh
Q 036150 7 VLRRKRTKKYAVKRKAVGIWSCKYCGKVKAGALNAATLAAFTALPAAAAA 56 (77)
Q Consensus 7 ~~~~~~CGK~~VKR~AVGIWkCkkCgkt~AGGAYtp~Tpag~s~~~~~~~ 56 (77)
-..||.|||++|||+++|||+|++||++||||||+|+||+++....+-.-
T Consensus 36 ~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGGAy~~~T~~~~t~~~~irr 85 (90)
T PTZ00255 36 KYFCPFCGKHAVKRQAVGIWRCKGCKKTVAGGAWTLSTPAASTVRSTIRR 85 (90)
T ss_pred CccCCCCCCCceeeeeeEEEEcCCCCCEEeCCccccccchhHHHHHHHHH
Confidence 34699999999999999999999999999999999999999875544433
No 5
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=99.72 E-value=1.9e-18 Score=115.89 Aligned_cols=47 Identities=30% Similarity=0.398 Sum_probs=42.9
Q ss_pred eeeeeCCCCceeeEEeEEEEEeeCCCCcEEeCcccccccccccccHH
Q 036150 6 RVLRRKRTKKYAVKRKAVGIWSCKYCGKVKAGALNAATLAAFTALPA 52 (77)
Q Consensus 6 ~~~~~~~CGK~~VKR~AVGIWkCkkCgkt~AGGAYtp~Tpag~s~~~ 52 (77)
..-.||-||++.|||+++|||.|++||++||||||+|+||+++...-
T Consensus 34 ~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~fAGgay~P~t~~~k~~~~ 80 (89)
T COG1997 34 AKHVCPFCGRTTVKRIATGIWKCRKCGAKFAGGAYTPVTPAGKAVKR 80 (89)
T ss_pred cCCcCCCCCCcceeeeccCeEEcCCCCCeeccccccccchHHHHHHH
Confidence 34579999999999999999999999999999999999999987643
No 6
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=99.59 E-value=2.8e-16 Score=106.15 Aligned_cols=49 Identities=41% Similarity=0.550 Sum_probs=43.8
Q ss_pred eeCCCCceeeEEeEEEEEeeCCCCcEEeCcccccccccccccHHHHHhh
Q 036150 9 RRKRTKKYAVKRKAVGIWSCKYCGKVKAGALNAATLAAFTALPAAAAAL 57 (77)
Q Consensus 9 ~~~~CGK~~VKR~AVGIWkCkkCgkt~AGGAYtp~Tpag~s~~~~~~~~ 57 (77)
.|+-|||+.|||++||||.|+.|++++|||||+.+||++.+.+.+-+-|
T Consensus 38 ~CsfCGK~~vKR~AvGiW~C~~C~kv~agga~~~~t~aa~t~rs~irrl 86 (92)
T KOG0402|consen 38 TCSFCGKKTVKRKAVGIWKCGSCKKVVAGGAYTVTTAAAATVRSTIRRL 86 (92)
T ss_pred hhhhcchhhhhhhceeEEecCCccceeccceEEeccchhHHHHHHHHHH
Confidence 4788999999999999999999999999999999999988877655443
No 7
>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=96.33 E-value=0.0029 Score=36.22 Aligned_cols=26 Identities=23% Similarity=0.295 Sum_probs=22.8
Q ss_pred eeCCCCceeeEEeEE-EEEeeCCCCcE
Q 036150 9 RRKRTKKYAVKRKAV-GIWSCKYCGKV 34 (77)
Q Consensus 9 ~~~~CGK~~VKR~AV-GIWkCkkCgkt 34 (77)
.||+||..++.+... +.|+|++|++.
T Consensus 20 ~CP~Cg~~~~~~~~~~~~~~C~~C~~q 46 (46)
T PF12760_consen 20 VCPHCGSTKHYRLKTRGRYRCKACRKQ 46 (46)
T ss_pred CCCCCCCeeeEEeCCCCeEECCCCCCc
Confidence 499999998888877 99999999873
No 8
>PHA00626 hypothetical protein
Probab=95.41 E-value=0.012 Score=37.51 Aligned_cols=33 Identities=9% Similarity=0.150 Sum_probs=27.1
Q ss_pred eeCCCCceeeEEeE-----EEEEeeCCCCcEEeCcccc
Q 036150 9 RRKRTKKYAVKRKA-----VGIWSCKYCGKVKAGALNA 41 (77)
Q Consensus 9 ~~~~CGK~~VKR~A-----VGIWkCkkCgkt~AGGAYt 41 (77)
.||+||...|.|-+ ..-.+|+.||+.+.-.|+-
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~~~~ 39 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSKDAFG 39 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeechhhhh
Confidence 58999998777743 4789999999999887764
No 9
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=95.18 E-value=0.01 Score=35.40 Aligned_cols=26 Identities=19% Similarity=0.395 Sum_probs=22.3
Q ss_pred eeCCCCceeeEEeEEEEEeeCCCCcEE
Q 036150 9 RRKRTKKYAVKRKAVGIWSCKYCGKVK 35 (77)
Q Consensus 9 ~~~~CGK~~VKR~AVGIWkCkkCgkt~ 35 (77)
.||+||.. +-....+.|+|++||.+.
T Consensus 22 fCP~Cg~~-~m~~~~~r~~C~~Cgyt~ 47 (50)
T PRK00432 22 FCPRCGSG-FMAEHLDRWHCGKCGYTE 47 (50)
T ss_pred cCcCCCcc-hheccCCcEECCCcCCEE
Confidence 58999997 777777999999999875
No 10
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=93.55 E-value=0.066 Score=30.36 Aligned_cols=29 Identities=17% Similarity=0.174 Sum_probs=22.9
Q ss_pred eeeeCCCCceeeEEeEEEEEeeCCCCcEE
Q 036150 7 VLRRKRTKKYAVKRKAVGIWSCKYCGKVK 35 (77)
Q Consensus 7 ~~~~~~CGK~~VKR~AVGIWkCkkCgkt~ 35 (77)
..+|+|||..-..-...+.++|..||..+
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYRI 31 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCeE
Confidence 46899999986555555689999999765
No 11
>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=92.77 E-value=0.11 Score=30.43 Aligned_cols=28 Identities=18% Similarity=0.205 Sum_probs=22.3
Q ss_pred eeeCCCCceee-EE------eEEEEEeeCCCCcEE
Q 036150 8 LRRKRTKKYAV-KR------KAVGIWSCKYCGKVK 35 (77)
Q Consensus 8 ~~~~~CGK~~V-KR------~AVGIWkCkkCgkt~ 35 (77)
+.||-||...+ .| ...|+|+|..||...
T Consensus 2 kPCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~ 36 (53)
T TIGR03655 2 KPCPFCGGADVYLRRGFDPLDLSHYFECSTCGASG 36 (53)
T ss_pred CCCCCCCCcceeeEeccCCCCCEEEEECCCCCCCc
Confidence 57999998876 55 467899999999763
No 12
>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=92.40 E-value=0.1 Score=30.88 Aligned_cols=29 Identities=21% Similarity=0.356 Sum_probs=25.1
Q ss_pred eeeeCCCCceeeEEeEEEEEeeCCCCcEE
Q 036150 7 VLRRKRTKKYAVKRKAVGIWSCKYCGKVK 35 (77)
Q Consensus 7 ~~~~~~CGK~~VKR~AVGIWkCkkCgkt~ 35 (77)
--.||+||...-++....+|.|..||.++
T Consensus 28 Sq~C~~CG~~~~~~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 28 SQTCPRCGHRNKKRRSGRVFTCPNCGFEM 56 (69)
T ss_pred ccCccCcccccccccccceEEcCCCCCEE
Confidence 34689999998888888999999999874
No 13
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=91.31 E-value=0.11 Score=34.64 Aligned_cols=36 Identities=19% Similarity=0.294 Sum_probs=24.2
Q ss_pred eeeC--CCCceeeEEeEEEEEeeCCCCcEEeCccccccc
Q 036150 8 LRRK--RTKKYAVKRKAVGIWSCKYCGKVKAGALNAATL 44 (77)
Q Consensus 8 ~~~~--~CGK~~VKR~AVGIWkCkkCgkt~AGGAYtp~T 44 (77)
.-|| .|+|. |.....|.|.|.+|++.+.---|..-+
T Consensus 19 ~aC~~~~C~kK-v~~~~~~~y~C~~C~~~~~~~~~ry~l 56 (146)
T PF08646_consen 19 PACPNEKCNKK-VTENGDGSYRCEKCNKTVENPKYRYRL 56 (146)
T ss_dssp EE-TSTTTS-B--EEETTTEEEETTTTEEESS-EEEEEE
T ss_pred CCCCCccCCCE-eecCCCcEEECCCCCCcCCCeeEEEEE
Confidence 3589 99985 555577999999999998665555533
No 14
>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=91.08 E-value=0.13 Score=28.80 Aligned_cols=30 Identities=20% Similarity=0.277 Sum_probs=22.7
Q ss_pred eeeCCCCcee-eEEeEEEEEeeCCCCcEEeC
Q 036150 8 LRRKRTKKYA-VKRKAVGIWSCKYCGKVKAG 37 (77)
Q Consensus 8 ~~~~~CGK~~-VKR~AVGIWkCkkCgkt~AG 37 (77)
.+||+||... +--...|-..|..||.++.-
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGLVLEE 31 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-BBEE-
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCCEeec
Confidence 3699999987 44457899999999988754
No 15
>PRK12366 replication factor A; Reviewed
Probab=90.65 E-value=0.1 Score=43.46 Aligned_cols=26 Identities=23% Similarity=0.565 Sum_probs=21.4
Q ss_pred eeeeCCCCceeeEEeEEEEEeeCCCCcE
Q 036150 7 VLRRKRTKKYAVKRKAVGIWSCKYCGKV 34 (77)
Q Consensus 7 ~~~~~~CGK~~VKR~AVGIWkCkkCgkt 34 (77)
.-+||+|.|.-++ .-|.|.|.+|+++
T Consensus 532 y~aCp~CnkKv~~--~~g~~~C~~c~~~ 557 (637)
T PRK12366 532 LYLCPNCRKRVEE--VDGEYICEFCGEV 557 (637)
T ss_pred EecccccCeEeEc--CCCcEECCCCCCC
Confidence 3689999886553 5699999999998
No 16
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=89.22 E-value=0.27 Score=34.01 Aligned_cols=27 Identities=22% Similarity=0.436 Sum_probs=21.8
Q ss_pred eeeeeeeCCCCceeeEEeEEEEEeeCCCCcEE
Q 036150 4 YYRVLRRKRTKKYAVKRKAVGIWSCKYCGKVK 35 (77)
Q Consensus 4 ~~~~~~~~~CGK~~VKR~AVGIWkCkkCgkt~ 35 (77)
+|---.|+.||. ...+.|.|..||.++
T Consensus 306 ~~tS~~C~~cg~-----~~~r~~~C~~cg~~~ 332 (364)
T COG0675 306 YYTSKTCPCCGH-----LSGRLFKCPRCGFVH 332 (364)
T ss_pred CCCcccccccCC-----ccceeEECCCCCCee
Confidence 444457999999 668999999999874
No 17
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=89.10 E-value=0.18 Score=31.35 Aligned_cols=27 Identities=19% Similarity=0.337 Sum_probs=16.8
Q ss_pred eeCCCCceeeEEeEEEEEeeCCCCcEE
Q 036150 9 RRKRTKKYAVKRKAVGIWSCKYCGKVK 35 (77)
Q Consensus 9 ~~~~CGK~~VKR~AVGIWkCkkCgkt~ 35 (77)
.|||||--.+-=.---=|.|.+||+|-
T Consensus 21 ~CPrCG~gvfmA~H~dR~~CGkCgyTe 47 (51)
T COG1998 21 FCPRCGPGVFMADHKDRWACGKCGYTE 47 (51)
T ss_pred cCCCCCCcchhhhcCceeEeccccceE
Confidence 489999432211111259999999874
No 18
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=89.08 E-value=0.18 Score=34.17 Aligned_cols=32 Identities=19% Similarity=0.272 Sum_probs=23.2
Q ss_pred eeeCCCCceeeEEeEEEEEeeCCCCcEEeCccc
Q 036150 8 LRRKRTKKYAVKRKAVGIWSCKYCGKVKAGALN 40 (77)
Q Consensus 8 ~~~~~CGK~~VKR~AVGIWkCkkCgkt~AGGAY 40 (77)
..||+|+|. |.-...|.|.|.+|++.+.---|
T Consensus 35 ~aC~~C~kk-v~~~~~~~~~C~~C~~~~~~~~~ 66 (166)
T cd04476 35 PACPGCNKK-VVEEGNGTYRCEKCNKSVPNPEY 66 (166)
T ss_pred ccccccCcc-cEeCCCCcEECCCCCCcCCCccE
Confidence 469999986 44444489999999998743333
No 19
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=87.44 E-value=0.46 Score=26.56 Aligned_cols=32 Identities=9% Similarity=0.226 Sum_probs=24.5
Q ss_pred eeCCCCceeeEEeEEE--EEeeCCCCcEEeCccc
Q 036150 9 RRKRTKKYAVKRKAVG--IWSCKYCGKVKAGALN 40 (77)
Q Consensus 9 ~~~~CGK~~VKR~AVG--IWkCkkCgkt~AGGAY 40 (77)
-||+||..-..+..-+ .|.|..||+.+--.+.
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYEEPIEQK 35 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCeEECCCc
Confidence 3799999776665433 8999999998877665
No 20
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=86.72 E-value=1 Score=28.92 Aligned_cols=31 Identities=23% Similarity=0.164 Sum_probs=23.0
Q ss_pred eeeeeeeCCCCceeeEEeEEE---EEeeCCCCcE
Q 036150 4 YYRVLRRKRTKKYAVKRKAVG---IWSCKYCGKV 34 (77)
Q Consensus 4 ~~~~~~~~~CGK~~VKR~AVG---IWkCkkCgkt 34 (77)
|--+.-||.||...+.=++.| +|.|++|+..
T Consensus 3 ~d~lKPCPFCG~~~~~v~~~~g~~~v~C~~CgA~ 36 (64)
T PRK09710 3 YDNVKPCPFCGCPSVTVKAISGYYRAKCNGCESR 36 (64)
T ss_pred cccccCCCCCCCceeEEEecCceEEEEcCCCCcC
Confidence 445678999999986655444 5679999873
No 21
>PRK08402 replication factor A; Reviewed
Probab=85.89 E-value=0.47 Score=37.52 Aligned_cols=27 Identities=19% Similarity=0.278 Sum_probs=21.7
Q ss_pred eeeCCCCceeeEEeEEEEEeeCCCCcE
Q 036150 8 LRRKRTKKYAVKRKAVGIWSCKYCGKV 34 (77)
Q Consensus 8 ~~~~~CGK~~VKR~AVGIWkCkkCgkt 34 (77)
.+||+|.|.-+.-...|-|.|..|+++
T Consensus 213 ~aCp~CnKkv~~~~~~~~~~Ce~~~~v 239 (355)
T PRK08402 213 DACPECRRKVDYDPATDTWICPEHGEV 239 (355)
T ss_pred ecCCCCCeEEEEecCCCCEeCCCCCCc
Confidence 589999885554567799999999863
No 22
>PHA02942 putative transposase; Provisional
Probab=85.46 E-value=0.44 Score=37.44 Aligned_cols=29 Identities=14% Similarity=0.221 Sum_probs=22.4
Q ss_pred eeeeeCCCCceeeEEeEEEEEeeCCCCcEE
Q 036150 6 RVLRRKRTKKYAVKRKAVGIWSCKYCGKVK 35 (77)
Q Consensus 6 ~~~~~~~CGK~~VKR~AVGIWkCkkCgkt~ 35 (77)
---.||+||... ++....+|.|..||.+.
T Consensus 324 TSq~Cs~CG~~~-~~l~~r~f~C~~CG~~~ 352 (383)
T PHA02942 324 SSVSCPKCGHKM-VEIAHRYFHCPSCGYEN 352 (383)
T ss_pred CCccCCCCCCcc-CcCCCCEEECCCCCCEe
Confidence 345799999754 45566799999999975
No 23
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=84.51 E-value=1.2 Score=28.88 Aligned_cols=31 Identities=23% Similarity=0.478 Sum_probs=24.2
Q ss_pred eeeeeeCCCCceeeEEeEEEEEeeCCCCcEEeC
Q 036150 5 YRVLRRKRTKKYAVKRKAVGIWSCKYCGKVKAG 37 (77)
Q Consensus 5 ~~~~~~~~CGK~~VKR~AVGIWkCkkCgkt~AG 37 (77)
|-+.|| .||+..+-+..+--=+| .||+++-=
T Consensus 1 ylifrC-~Cgr~lya~e~~kTkkC-~CG~~l~v 31 (68)
T PF09082_consen 1 YLIFRC-DCGRYLYAKEGAKTKKC-VCGKTLKV 31 (68)
T ss_dssp EEEEEE-TTS--EEEETT-SEEEE-TTTEEEE-
T ss_pred CEEEEe-cCCCEEEecCCcceeEe-cCCCeeee
Confidence 668899 79999999999999999 99998753
No 24
>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=82.19 E-value=0.96 Score=25.38 Aligned_cols=26 Identities=15% Similarity=0.226 Sum_probs=22.6
Q ss_pred eeCCCCceeeEEeEEEEEeeCCCCcEE
Q 036150 9 RRKRTKKYAVKRKAVGIWSCKYCGKVK 35 (77)
Q Consensus 9 ~~~~CGK~~VKR~AVGIWkCkkCgkt~ 35 (77)
+|+.|+.. .-+..-|-+-|..||-+.
T Consensus 10 ~C~~C~~~-~~~~~dG~~yC~~cG~~~ 35 (36)
T PF11781_consen 10 PCPVCGSR-WFYSDDGFYYCDRCGHQS 35 (36)
T ss_pred cCCCCCCe-EeEccCCEEEhhhCceEc
Confidence 48899999 888899999999999763
No 25
>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=81.72 E-value=1.5 Score=25.32 Aligned_cols=30 Identities=23% Similarity=0.490 Sum_probs=14.9
Q ss_pred eeeeCCCCce-eeE----EeEEEEEeeCCCCcEEeC
Q 036150 7 VLRRKRTKKY-AVK----RKAVGIWSCKYCGKVKAG 37 (77)
Q Consensus 7 ~~~~~~CGK~-~VK----R~AVGIWkCkkCgkt~AG 37 (77)
-..||+||-. +.+ +...|-|.|..|+. .+|
T Consensus 3 h~pCP~CGG~DrFri~~d~~~~G~~~C~~C~~-~~G 37 (40)
T PF08273_consen 3 HGPCPICGGKDRFRIFDDKDGRGTWICRQCGG-DAG 37 (40)
T ss_dssp EE--TTTT-TTTEEEETT----S-EEETTTTB-E--
T ss_pred CCCCCCCcCccccccCcCcccCCCEECCCCCC-cCC
Confidence 3468999865 344 34569999999965 443
No 26
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=81.46 E-value=1.3 Score=24.40 Aligned_cols=15 Identities=33% Similarity=1.101 Sum_probs=13.0
Q ss_pred EEeeCCCCcEEeCcc
Q 036150 25 IWSCKYCGKVKAGAL 39 (77)
Q Consensus 25 IWkCkkCgkt~AGGA 39 (77)
+|.|..||+++-|..
T Consensus 2 ~~~C~~CG~i~~g~~ 16 (34)
T cd00729 2 VWVCPVCGYIHEGEE 16 (34)
T ss_pred eEECCCCCCEeECCc
Confidence 699999999998753
No 27
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=81.42 E-value=1 Score=32.13 Aligned_cols=26 Identities=23% Similarity=0.406 Sum_probs=19.2
Q ss_pred eeeCCCCcee--------------eEEeEEEEEeeCCCCcEEeC
Q 036150 8 LRRKRTKKYA--------------VKRKAVGIWSCKYCGKVKAG 37 (77)
Q Consensus 8 ~~~~~CGK~~--------------VKR~AVGIWkCkkCgkt~AG 37 (77)
++||-||... |+|. -+|..||++|.+
T Consensus 1 m~cp~c~~~~~~~~~s~~~~~~~~~~~~----~~c~~c~~~f~~ 40 (154)
T PRK00464 1 MRCPFCGHPDTRVIDSRPAEDGNAIRRR----RECLACGKRFTT 40 (154)
T ss_pred CcCCCCCCCCCEeEeccccCCCCceeee----eeccccCCcceE
Confidence 4799999533 4444 799999999863
No 28
>PRK07591 threonine synthase; Validated
Probab=80.32 E-value=0.91 Score=35.58 Aligned_cols=28 Identities=14% Similarity=0.060 Sum_probs=21.0
Q ss_pred ceeeeeeeCCCCceeeEEeEEEEEeeCCCCc
Q 036150 3 SYYRVLRRKRTKKYAVKRKAVGIWSCKYCGK 33 (77)
Q Consensus 3 ~~~~~~~~~~CGK~~VKR~AVGIWkCkkCgk 33 (77)
+|+..|+|.+||+.-=-- .+|.|..||-
T Consensus 14 ~~~~~l~C~~Cg~~~~~~---~~~~C~~cg~ 41 (421)
T PRK07591 14 GPAVALKCRECGAEYPLG---PIHVCEECFG 41 (421)
T ss_pred cceeEEEeCCCCCcCCCC---CCccCCCCCC
Confidence 677789999999884211 2399999973
No 29
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=79.10 E-value=1 Score=28.50 Aligned_cols=22 Identities=14% Similarity=0.217 Sum_probs=14.7
Q ss_pred eeeeeeCCCCceeeEEeEEEEEeeCCCCc
Q 036150 5 YRVLRRKRTKKYAVKRKAVGIWSCKYCGK 33 (77)
Q Consensus 5 ~~~~~~~~CGK~~VKR~AVGIWkCkkCgk 33 (77)
+-...|||||+.-|. .|.+|.+
T Consensus 23 ~~~F~CPnCG~~~I~-------RC~~CRk 44 (59)
T PRK14890 23 AVKFLCPNCGEVIIY-------RCEKCRK 44 (59)
T ss_pred cCEeeCCCCCCeeEe-------echhHHh
Confidence 345679999987544 4666654
No 30
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=78.83 E-value=0.98 Score=28.94 Aligned_cols=22 Identities=18% Similarity=0.332 Sum_probs=14.5
Q ss_pred eeeeeeCCCCceeeEEeEEEEEeeCCCCc
Q 036150 5 YRVLRRKRTKKYAVKRKAVGIWSCKYCGK 33 (77)
Q Consensus 5 ~~~~~~~~CGK~~VKR~AVGIWkCkkCgk 33 (77)
|-+.-|||||+.. ||.|.+|-+
T Consensus 25 ~v~F~CPnCGe~~-------I~Rc~~CRk 46 (61)
T COG2888 25 AVKFPCPNCGEVE-------IYRCAKCRK 46 (61)
T ss_pred eeEeeCCCCCcee-------eehhhhHHH
Confidence 4567799999764 555555543
No 31
>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=78.70 E-value=3.8 Score=25.95 Aligned_cols=31 Identities=13% Similarity=0.192 Sum_probs=22.1
Q ss_pred eeeCCCCceeeEEe----------EEEEEeeCCCCcEEeCc
Q 036150 8 LRRKRTKKYAVKRK----------AVGIWSCKYCGKVKAGA 38 (77)
Q Consensus 8 ~~~~~CGK~~VKR~----------AVGIWkCkkCgkt~AGG 38 (77)
.+||+||+..+--. .+=++.|.+|+++|-.+
T Consensus 63 ~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~~~ 103 (104)
T TIGR01384 63 VECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWREY 103 (104)
T ss_pred CCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeEeC
Confidence 47888988874222 45688898899887654
No 32
>PRK08197 threonine synthase; Validated
Probab=77.90 E-value=1.5 Score=33.80 Aligned_cols=29 Identities=21% Similarity=0.187 Sum_probs=21.5
Q ss_pred CcceeeeeeeCCCCceeeEEeEEEEEeeCCCC
Q 036150 1 MVSYYRVLRRKRTKKYAVKRKAVGIWSCKYCG 32 (77)
Q Consensus 1 ~~~~~~~~~~~~CGK~~VKR~AVGIWkCkkCg 32 (77)
|.++...|+|.+||+.-= .-.-+|.| +||
T Consensus 1 ~~~~~~~~~C~~Cg~~~~--~~~~~~~C-~cg 29 (394)
T PRK08197 1 PFSYVSHLECSKCGETYD--ADQVHNLC-KCG 29 (394)
T ss_pred CCceeeEEEECCCCCCCC--CCCcceec-CCC
Confidence 567888899999998742 11237999 896
No 33
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=77.55 E-value=0.64 Score=38.28 Aligned_cols=32 Identities=22% Similarity=0.270 Sum_probs=23.7
Q ss_pred eeCCCCceeeEEeEEEEEeeCCCCcEEeCcccc
Q 036150 9 RRKRTKKYAVKRKAVGIWSCKYCGKVKAGALNA 41 (77)
Q Consensus 9 ~~~~CGK~~VKR~AVGIWkCkkCgkt~AGGAYt 41 (77)
+||.||+. ||=.+-+=|+|++||+++-.-...
T Consensus 352 ~Cp~Cg~~-m~S~G~~g~rC~kCg~~~~~~~~~ 383 (421)
T COG1571 352 VCPRCGGR-MKSAGRNGFRCKKCGTRARETLIK 383 (421)
T ss_pred CCCccCCc-hhhcCCCCcccccccccCCccccc
Confidence 68899875 444444469999999998776655
No 34
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=77.23 E-value=3.6 Score=29.11 Aligned_cols=35 Identities=17% Similarity=0.316 Sum_probs=20.6
Q ss_pred eeCCCCceeeEEe-EEEE----------EeeCCCCcEE----eCcccccc
Q 036150 9 RRKRTKKYAVKRK-AVGI----------WSCKYCGKVK----AGALNAAT 43 (77)
Q Consensus 9 ~~~~CGK~~VKR~-AVGI----------WkCkkCgkt~----AGGAYtp~ 43 (77)
.||+||+..+.|. -+-| +.|.+||++. .||+..|.
T Consensus 3 ~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~ev~~~~~~~~~ 52 (161)
T PF03367_consen 3 LCPNCGENGTTRILLTDIPYFKEVIIMSFECEHCGYKNNEVKSGGQIQPK 52 (161)
T ss_dssp E-TTTSSCCEEEEEEEEETTTEEEEEEEEE-TTT--EEEEEEEECSS-SS
T ss_pred cCCCCCCCcEEEEEEEcCCCCceEEEEEeECCCCCCEeeeEEECccCCCC
Confidence 5999999864443 4455 8999999864 46666553
No 35
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=75.53 E-value=0.99 Score=37.61 Aligned_cols=32 Identities=22% Similarity=0.231 Sum_probs=22.8
Q ss_pred eeeCC--CCceeeEEeEEEEEeeCCCCcEEeCccc
Q 036150 8 LRRKR--TKKYAVKRKAVGIWSCKYCGKVKAGALN 40 (77)
Q Consensus 8 ~~~~~--CGK~~VKR~AVGIWkCkkCgkt~AGGAY 40 (77)
--||+ |.|. |....-|.|.|.+|++.+.-=-|
T Consensus 475 ~ACp~~~CnKK-V~~~~~g~~~CekC~~~~~~~~~ 508 (608)
T TIGR00617 475 RACPSEDCNKK-VVDQGDGTYRCEKCNKNFAEFKY 508 (608)
T ss_pred ccCChhhCCCc-cccCCCCCEECCCCCCCCCCccE
Confidence 35776 9886 44455699999999987654333
No 36
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=74.75 E-value=1.9 Score=29.65 Aligned_cols=31 Identities=23% Similarity=0.337 Sum_probs=23.2
Q ss_pred eeeCCCCceeeEEeE-----EEEEeeCCCCcEEeCc
Q 036150 8 LRRKRTKKYAVKRKA-----VGIWSCKYCGKVKAGA 38 (77)
Q Consensus 8 ~~~~~CGK~~VKR~A-----VGIWkCkkCgkt~AGG 38 (77)
..||.|+...++|.+ .-=|+|+.|+++|.-=
T Consensus 31 ~~cP~C~s~~~~k~g~~~~~~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 31 VNCPRCKSSNVVKIGGIRRGHQRYKCKSCGSTFTVE 66 (129)
T ss_pred CcCCCCCccceeeECCccccccccccCCcCcceeee
Confidence 468999988866554 3358999999998643
No 37
>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=74.67 E-value=2.8 Score=28.49 Aligned_cols=33 Identities=24% Similarity=0.463 Sum_probs=23.1
Q ss_pred eeeeCCCCcee--eEEeEE-------------EEEeeCCCCcEEeCcc
Q 036150 7 VLRRKRTKKYA--VKRKAV-------------GIWSCKYCGKVKAGAL 39 (77)
Q Consensus 7 ~~~~~~CGK~~--VKR~AV-------------GIWkCkkCgkt~AGGA 39 (77)
.-||+.|+..- |.+..+ -.|.|.+||+.+=.|.
T Consensus 91 ~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~Gs 138 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWEGS 138 (147)
T ss_pred CCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecccc
Confidence 35888888752 333322 3899999999987664
No 38
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=74.44 E-value=2.2 Score=22.99 Aligned_cols=14 Identities=29% Similarity=0.812 Sum_probs=11.9
Q ss_pred EEeeCCCCcEEeCc
Q 036150 25 IWSCKYCGKVKAGA 38 (77)
Q Consensus 25 IWkCkkCgkt~AGG 38 (77)
+|.|+.||++.-+.
T Consensus 1 ~~~C~~CGy~y~~~ 14 (33)
T cd00350 1 KYVCPVCGYIYDGE 14 (33)
T ss_pred CEECCCCCCEECCC
Confidence 59999999997765
No 39
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=74.03 E-value=1.8 Score=32.72 Aligned_cols=32 Identities=19% Similarity=0.170 Sum_probs=25.8
Q ss_pred eeeeeCCCCcee-eEEeEEEEEeeCCCCcEEeC
Q 036150 6 RVLRRKRTKKYA-VKRKAVGIWSCKYCGKVKAG 37 (77)
Q Consensus 6 ~~~~~~~CGK~~-VKR~AVGIWkCkkCgkt~AG 37 (77)
+.++||+||.+. |.-...|-.-|..||.++.-
T Consensus 10 ~~~~Cp~Cg~~~iv~d~~~Ge~vC~~CG~Vl~e 42 (310)
T PRK00423 10 EKLVCPECGSDKLIYDYERGEIVCADCGLVIEE 42 (310)
T ss_pred cCCcCcCCCCCCeeEECCCCeEeecccCCcccc
Confidence 346899999854 56678999999999997753
No 40
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=73.95 E-value=1.8 Score=31.58 Aligned_cols=13 Identities=38% Similarity=1.262 Sum_probs=12.7
Q ss_pred EEeeCCCCcEEeC
Q 036150 25 IWSCKYCGKVKAG 37 (77)
Q Consensus 25 IWkCkkCgkt~AG 37 (77)
||.|+.||+++.|
T Consensus 134 ~~vC~vCGy~~~g 146 (166)
T COG1592 134 VWVCPVCGYTHEG 146 (166)
T ss_pred EEEcCCCCCcccC
Confidence 9999999999998
No 41
>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=73.36 E-value=7.2 Score=21.74 Aligned_cols=27 Identities=11% Similarity=0.145 Sum_probs=17.5
Q ss_pred eeCCCCceeeEEe----------EEEEEeeCCCCcEE
Q 036150 9 RRKRTKKYAVKRK----------AVGIWSCKYCGKVK 35 (77)
Q Consensus 9 ~~~~CGK~~VKR~----------AVGIWkCkkCgkt~ 35 (77)
.||+||....--. .+=+-.|.+||++|
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~w 38 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRW 38 (39)
T ss_dssp --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEE
T ss_pred CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCee
Confidence 5888988763322 26788999999876
No 42
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=73.35 E-value=2.9 Score=19.77 Aligned_cols=12 Identities=33% Similarity=0.913 Sum_probs=9.6
Q ss_pred EeeCCCCcEEeC
Q 036150 26 WSCKYCGKVKAG 37 (77)
Q Consensus 26 WkCkkCgkt~AG 37 (77)
|.|..|++.|.-
T Consensus 1 y~C~~C~~~f~~ 12 (23)
T PF00096_consen 1 YKCPICGKSFSS 12 (23)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCCCCCccCC
Confidence 679999998853
No 43
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=73.22 E-value=2.6 Score=19.17 Aligned_cols=11 Identities=36% Similarity=0.920 Sum_probs=7.5
Q ss_pred EeeCCCCcEEe
Q 036150 26 WSCKYCGKVKA 36 (77)
Q Consensus 26 WkCkkCgkt~A 36 (77)
|.|..|++++.
T Consensus 1 ~~C~~C~~~~~ 11 (24)
T PF13894_consen 1 FQCPICGKSFR 11 (24)
T ss_dssp EE-SSTS-EES
T ss_pred CCCcCCCCcCC
Confidence 78999998875
No 44
>PF14353 CpXC: CpXC protein
Probab=72.62 E-value=6.3 Score=25.77 Aligned_cols=29 Identities=10% Similarity=0.208 Sum_probs=20.0
Q ss_pred eeeCCCCceeeEEe--EEE-----------------EEeeCCCCcEEe
Q 036150 8 LRRKRTKKYAVKRK--AVG-----------------IWSCKYCGKVKA 36 (77)
Q Consensus 8 ~~~~~CGK~~VKR~--AVG-----------------IWkCkkCgkt~A 36 (77)
+.||+||+.-.... .+- .+.|.+||+++.
T Consensus 2 itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~ 49 (128)
T PF14353_consen 2 ITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFR 49 (128)
T ss_pred cCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCcee
Confidence 57888888754333 222 689999999875
No 45
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=72.07 E-value=9.9 Score=21.34 Aligned_cols=28 Identities=14% Similarity=0.274 Sum_probs=20.4
Q ss_pred eeCCCCceeeE------E----eEEEEEeeCCCCcEEe
Q 036150 9 RRKRTKKYAVK------R----KAVGIWSCKYCGKVKA 36 (77)
Q Consensus 9 ~~~~CGK~~VK------R----~AVGIWkCkkCgkt~A 36 (77)
.||+||...+- | -.+=++.|.+|++++-
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w~ 39 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRWR 39 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEeC
Confidence 58899987643 2 1356899999998863
No 46
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=71.98 E-value=5.4 Score=25.09 Aligned_cols=35 Identities=23% Similarity=0.271 Sum_probs=28.3
Q ss_pred cceeeeeeeCCCCcee-eEEeEEEEEeeCCCCcEEe
Q 036150 2 VSYYRVLRRKRTKKYA-VKRKAVGIWSCKYCGKVKA 36 (77)
Q Consensus 2 ~~~~~~~~~~~CGK~~-VKR~AVGIWkCkkCgkt~A 36 (77)
-|||--.+||.|++.. |=-.+.-.=.|..||.+.+
T Consensus 6 ~S~F~~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~ 41 (59)
T PRK00415 6 RSRFLKVKCPDCGNEQVVFSHASTVVRCLVCGKTLA 41 (59)
T ss_pred CCeEEEEECCCCCCeEEEEecCCcEEECcccCCCcc
Confidence 4788889999999997 4455667779999999873
No 47
>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=71.80 E-value=2.3 Score=24.29 Aligned_cols=27 Identities=19% Similarity=0.434 Sum_probs=18.7
Q ss_pred eeeeCCCCce-eeE---EeEEEEEeeCCCCc
Q 036150 7 VLRRKRTKKY-AVK---RKAVGIWSCKYCGK 33 (77)
Q Consensus 7 ~~~~~~CGK~-~VK---R~AVGIWkCkkCgk 33 (77)
-..||+||-. +.+ +...|-|.|..|+.
T Consensus 3 ~~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 3 HGPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred ccCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 3468999754 332 33569999999974
No 48
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=71.79 E-value=3.4 Score=29.67 Aligned_cols=33 Identities=12% Similarity=0.150 Sum_probs=22.2
Q ss_pred eCCCCceeeEEe------------EEEEEeeCCCCcE----EeCccccc
Q 036150 10 RKRTKKYAVKRK------------AVGIWSCKYCGKV----KAGALNAA 42 (77)
Q Consensus 10 ~~~CGK~~VKR~------------AVGIWkCkkCgkt----~AGGAYtp 42 (77)
||+||+..+++. -.==+.|.+||++ ..||...|
T Consensus 1 CP~Cg~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~ev~~~~~~~p 49 (163)
T TIGR00340 1 CPVCGSRTLKAVTYDYDIPYFGKIMLSTYICEKCGYRSTDVYQLEEKEP 49 (163)
T ss_pred CCCCCCcceEeeeEeccCCCcceEEEEEEECCCCCCchhheeEcCCcCC
Confidence 799998765552 2234899999986 35665544
No 49
>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=71.48 E-value=2.1 Score=22.94 Aligned_cols=28 Identities=25% Similarity=0.316 Sum_probs=17.9
Q ss_pred eeeCCCCcee-eEE----eEEEEEeeCCCCcEE
Q 036150 8 LRRKRTKKYA-VKR----KAVGIWSCKYCGKVK 35 (77)
Q Consensus 8 ~~~~~CGK~~-VKR----~AVGIWkCkkCgkt~ 35 (77)
+.||||++.- |.- ..-+-=.|.+|+..|
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~ 35 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVW 35 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCCCEEECCCCCCEE
Confidence 6899999842 221 112245799999876
No 50
>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=71.04 E-value=5 Score=21.24 Aligned_cols=27 Identities=15% Similarity=0.150 Sum_probs=17.9
Q ss_pred eeeCCCCceeeEEeE---EEEEeeCCCCcE
Q 036150 8 LRRKRTKKYAVKRKA---VGIWSCKYCGKV 34 (77)
Q Consensus 8 ~~~~~CGK~~VKR~A---VGIWkCkkCgkt 34 (77)
.+|++||+.--.... -.+-.|..||..
T Consensus 6 y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~ 35 (41)
T smart00834 6 YRCEDCGHTFEVLQKISDDPLATCPECGGD 35 (41)
T ss_pred EEcCCCCCEEEEEEecCCCCCCCCCCCCCc
Confidence 489999995422232 347789999863
No 51
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=70.97 E-value=3.6 Score=27.73 Aligned_cols=29 Identities=17% Similarity=0.265 Sum_probs=23.4
Q ss_pred eeeCCCCceeeEEe--EEEEEeeCCCCcEEe
Q 036150 8 LRRKRTKKYAVKRK--AVGIWSCKYCGKVKA 36 (77)
Q Consensus 8 ~~~~~CGK~~VKR~--AVGIWkCkkCgkt~A 36 (77)
.-||+||-.=+-|. ..+++.|++||+..-
T Consensus 3 ~FCp~Cgsll~p~~~~~~~~l~C~kCgye~~ 33 (113)
T COG1594 3 RFCPKCGSLLYPKKDDEGGKLVCRKCGYEEE 33 (113)
T ss_pred cccCCccCeeEEeEcCCCcEEECCCCCcchh
Confidence 35899999987776 467999999998754
No 52
>PRK05978 hypothetical protein; Provisional
Probab=70.36 E-value=2 Score=30.78 Aligned_cols=26 Identities=19% Similarity=0.239 Sum_probs=19.7
Q ss_pred eeeCCCCceeeEEeEEEEE----eeCCCCcEEe
Q 036150 8 LRRKRTKKYAVKRKAVGIW----SCKYCGKVKA 36 (77)
Q Consensus 8 ~~~~~CGK~~VKR~AVGIW----kCkkCgkt~A 36 (77)
.||||||+-++=| |.. +|..||..+.
T Consensus 34 grCP~CG~G~LF~---g~Lkv~~~C~~CG~~~~ 63 (148)
T PRK05978 34 GRCPACGEGKLFR---AFLKPVDHCAACGEDFT 63 (148)
T ss_pred CcCCCCCCCcccc---cccccCCCccccCCccc
Confidence 4899999999855 333 5999998763
No 53
>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=68.50 E-value=3.7 Score=23.15 Aligned_cols=24 Identities=25% Similarity=0.524 Sum_probs=19.3
Q ss_pred eeeCCCCcee-eEEeEEE-----EEeeCCC
Q 036150 8 LRRKRTKKYA-VKRKAVG-----IWSCKYC 31 (77)
Q Consensus 8 ~~~~~CGK~~-VKR~AVG-----IWkCkkC 31 (77)
+.||.|+.+. |+|.+-+ -|.|+.|
T Consensus 6 v~CP~C~s~~~v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 6 VHCPRCQSTEGVKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eeCCCCCCCCcceeCCCCCCCCEeEecCcC
Confidence 6799999999 9997543 5777777
No 54
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=68.36 E-value=4.4 Score=27.26 Aligned_cols=30 Identities=23% Similarity=0.541 Sum_probs=22.1
Q ss_pred eeeeeeCCCCceee----EEeEEEEEeeCCCCcEE
Q 036150 5 YRVLRRKRTKKYAV----KRKAVGIWSCKYCGKVK 35 (77)
Q Consensus 5 ~~~~~~~~CGK~~V----KR~AVGIWkCkkCgkt~ 35 (77)
..+..|||||...| +| ..+.=.|..||.-+
T Consensus 19 pt~f~CP~Cge~~v~v~~~k-~~~h~~C~~CG~y~ 52 (99)
T PRK14892 19 PKIFECPRCGKVSISVKIKK-NIAIITCGNCGLYT 52 (99)
T ss_pred CcEeECCCCCCeEeeeecCC-CcceEECCCCCCcc
Confidence 45778999996555 23 67788899998753
No 55
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=67.75 E-value=3 Score=26.81 Aligned_cols=17 Identities=18% Similarity=0.204 Sum_probs=8.9
Q ss_pred eeCCCCceeeEEeEEEE
Q 036150 9 RRKRTKKYAVKRKAVGI 25 (77)
Q Consensus 9 ~~~~CGK~~VKR~AVGI 25 (77)
-||+||...++|+++-+
T Consensus 26 FCp~CGn~TL~rvsvsv 42 (73)
T PF08772_consen 26 FCPKCGNATLKRVSVSV 42 (73)
T ss_dssp S-SSS--S--EEEE-B-
T ss_pred eCcccCCCcceEEEEEE
Confidence 48999999999999865
No 56
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=67.45 E-value=3.1 Score=27.79 Aligned_cols=26 Identities=12% Similarity=0.227 Sum_probs=16.3
Q ss_pred eeeeCCCCceeeEEeEEEEEeeCCCCc
Q 036150 7 VLRRKRTKKYAVKRKAVGIWSCKYCGK 33 (77)
Q Consensus 7 ~~~~~~CGK~~VKR~AVGIWkCkkCgk 33 (77)
..+|++||+.- ......++.|.+||.
T Consensus 70 ~~~C~~Cg~~~-~~~~~~~~~CP~Cgs 95 (114)
T PRK03681 70 ECWCETCQQYV-TLLTQRVRRCPQCHG 95 (114)
T ss_pred EEEcccCCCee-ecCCccCCcCcCcCC
Confidence 46788898642 222234577988883
No 57
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=67.25 E-value=3.7 Score=22.71 Aligned_cols=28 Identities=14% Similarity=0.176 Sum_probs=18.3
Q ss_pred eeeCCCCcee-e----EEeEEEEEeeCCCCcEE
Q 036150 8 LRRKRTKKYA-V----KRKAVGIWSCKYCGKVK 35 (77)
Q Consensus 8 ~~~~~CGK~~-V----KR~AVGIWkCkkCgkt~ 35 (77)
++||||++.- | -+.....=+|.+|+.+|
T Consensus 3 i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 5788998752 1 12333456899999876
No 58
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=66.97 E-value=5.1 Score=25.92 Aligned_cols=33 Identities=12% Similarity=0.228 Sum_probs=19.0
Q ss_pred eeeCCCCceeeEEeEEEEEeeCCCCcEEeCccccc
Q 036150 8 LRRKRTKKYAVKRKAVGIWSCKYCGKVKAGALNAA 42 (77)
Q Consensus 8 ~~~~~CGK~~VKR~AVGIWkCkkCgkt~AGGAYtp 42 (77)
+.||.|... |.++. |..+|..|.+-+-==|+=|
T Consensus 2 ~~CP~C~~~-L~~~~-~~~~C~~C~~~~~~~a~CP 34 (70)
T PF07191_consen 2 NTCPKCQQE-LEWQG-GHYHCEACQKDYKKEAFCP 34 (70)
T ss_dssp -B-SSS-SB-EEEET-TEEEETTT--EEEEEEE-T
T ss_pred CcCCCCCCc-cEEeC-CEEECccccccceecccCC
Confidence 457888877 66666 7888888887665555444
No 59
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=66.42 E-value=9 Score=21.12 Aligned_cols=28 Identities=14% Similarity=0.265 Sum_probs=22.8
Q ss_pred eeeCCCCceeeEEeEEEEEeeCCCCcEE
Q 036150 8 LRRKRTKKYAVKRKAVGIWSCKYCGKVK 35 (77)
Q Consensus 8 ~~~~~CGK~~VKR~AVGIWkCkkCgkt~ 35 (77)
.+|+.|+...+--.--++-.|..|+.++
T Consensus 4 ~~C~~C~~~~i~~~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 4 KKCSKCGGNGIVNKEDDYEVCIFCGSSF 31 (33)
T ss_pred eEcCCCCCCeEEEecCCeEEcccCCcEe
Confidence 4678899888776777899999999876
No 60
>PRK11823 DNA repair protein RadA; Provisional
Probab=66.24 E-value=3.8 Score=32.64 Aligned_cols=24 Identities=17% Similarity=0.188 Sum_probs=20.0
Q ss_pred eeeeeCCCCceeeEEeEEEEEeeCCCCc
Q 036150 6 RVLRRKRTKKYAVKRKAVGIWSCKYCGK 33 (77)
Q Consensus 6 ~~~~~~~CGK~~VKR~AVGIWkCkkCgk 33 (77)
...+|.+||-..-|.. |+|..|+.
T Consensus 6 ~~y~C~~Cg~~~~~~~----g~Cp~C~~ 29 (446)
T PRK11823 6 TAYVCQECGAESPKWL----GRCPECGA 29 (446)
T ss_pred CeEECCcCCCCCcccC----eeCcCCCC
Confidence 4568999999998874 99999963
No 61
>PRK07218 replication factor A; Provisional
Probab=65.80 E-value=2.6 Score=34.28 Aligned_cols=27 Identities=19% Similarity=0.185 Sum_probs=20.3
Q ss_pred eeeCCCCceeeEEeEEEEEeeCCCCcEEeCccccc
Q 036150 8 LRRKRTKKYAVKRKAVGIWSCKYCGKVKAGALNAA 42 (77)
Q Consensus 8 ~~~~~CGK~~VKR~AVGIWkCkkCgkt~AGGAYtp 42 (77)
-|||+|+|.--+ |.|+.||++ -|-|.+
T Consensus 298 ~rCP~C~r~v~~------~~C~~hG~v--e~~~dl 324 (423)
T PRK07218 298 ERCPECGRVIQK------GQCRSHGAV--EGEDDL 324 (423)
T ss_pred ecCcCccccccC------CcCCCCCCc--CCeeee
Confidence 589999987533 999999987 444544
No 62
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=65.55 E-value=1.6 Score=22.37 Aligned_cols=22 Identities=14% Similarity=0.166 Sum_probs=11.0
Q ss_pred eeCCCCceeeEEeEEEEEeeCCCCcE
Q 036150 9 RRKRTKKYAVKRKAVGIWSCKYCGKV 34 (77)
Q Consensus 9 ~~~~CGK~~VKR~AVGIWkCkkCgkt 34 (77)
+||+||+.--.-.- -|..||..
T Consensus 1 ~Cp~CG~~~~~~~~----fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIEDDAK----FCPNCGTP 22 (23)
T ss_pred CCcccCCCCCCcCc----chhhhCCc
Confidence 36777765422211 26666653
No 63
>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=64.44 E-value=13 Score=23.87 Aligned_cols=31 Identities=29% Similarity=0.552 Sum_probs=16.9
Q ss_pred eeeeeCCCC-ceee--EE---eEEEEEeeCCCCcEEe
Q 036150 6 RVLRRKRTK-KYAV--KR---KAVGIWSCKYCGKVKA 36 (77)
Q Consensus 6 ~~~~~~~CG-K~~V--KR---~AVGIWkCkkCgkt~A 36 (77)
.+..||.|+ +.+| +. ..+|+=+|+.||..+.
T Consensus 21 ~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~ 57 (81)
T PF05129_consen 21 KVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQ 57 (81)
T ss_dssp S----TTT--SS-EEEEEETTTTEEEEEESSS--EEE
T ss_pred ceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEE
Confidence 467899999 5442 22 3799999999987764
No 64
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=64.15 E-value=5.1 Score=22.07 Aligned_cols=29 Identities=17% Similarity=0.265 Sum_probs=20.0
Q ss_pred eeeeCCCCce-eeEE----eEEEEEeeCCCCcEE
Q 036150 7 VLRRKRTKKY-AVKR----KAVGIWSCKYCGKVK 35 (77)
Q Consensus 7 ~~~~~~CGK~-~VKR----~AVGIWkCkkCgkt~ 35 (77)
.++||||+.. +|-- ..-+.=+|.+|+.+|
T Consensus 2 ~i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 2 IITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EEECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 3689999875 2322 344566899999887
No 65
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=63.94 E-value=7.2 Score=23.49 Aligned_cols=26 Identities=15% Similarity=0.162 Sum_probs=15.5
Q ss_pred eeC--CCCceeeEEeEEEEEeeCCCCcE
Q 036150 9 RRK--RTKKYAVKRKAVGIWSCKYCGKV 34 (77)
Q Consensus 9 ~~~--~CGK~~VKR~AVGIWkCkkCgkt 34 (77)
.|| +||.--+-=.-..=|.|.+|+.|
T Consensus 20 ~CP~~~CG~GvFMA~H~dR~~CGKCg~T 47 (47)
T PF01599_consen 20 ECPSPRCGAGVFMAEHKDRHYCGKCGYT 47 (47)
T ss_dssp E-TSTTTTSSSEEEE-SSEEEETTTSS-
T ss_pred cCCCcccCCceEeeecCCCccCCCcccC
Confidence 356 78875433333456899999875
No 66
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=63.57 E-value=5.3 Score=30.84 Aligned_cols=32 Identities=19% Similarity=0.263 Sum_probs=25.9
Q ss_pred eeeCCCCceeeEE-eEEEEEeeCCCCcEEeCcc
Q 036150 8 LRRKRTKKYAVKR-KAVGIWSCKYCGKVKAGAL 39 (77)
Q Consensus 8 ~~~~~CGK~~VKR-~AVGIWkCkkCgkt~AGGA 39 (77)
..||+||-+.+-+ ..-|=|.|..||-++--..
T Consensus 2 ~~CpeCg~~~~~~d~~~ge~VC~~CG~Vi~~~~ 34 (285)
T COG1405 2 MSCPECGSTNIITDYERGEIVCADCGLVLEDSL 34 (285)
T ss_pred CCCCCCCCccceeeccCCeEEeccCCEEecccc
Confidence 4699999997555 4789999999998876544
No 67
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=63.36 E-value=8.1 Score=28.32 Aligned_cols=35 Identities=17% Similarity=0.151 Sum_probs=22.6
Q ss_pred eeeCCCCceeeEE-eEEE-----------EEeeCCCCcE----EeCccccc
Q 036150 8 LRRKRTKKYAVKR-KAVG-----------IWSCKYCGKV----KAGALNAA 42 (77)
Q Consensus 8 ~~~~~CGK~~VKR-~AVG-----------IWkCkkCgkt----~AGGAYtp 42 (77)
+.||+||+...-| .-+- =+.|.+||++ ..||+..|
T Consensus 1 ~~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~ev~~~g~~~p 51 (192)
T TIGR00310 1 IDCPSCGGECETVMKTVNDIPYFGEVLETSTICEHCGYRSNDVKTLGAKEP 51 (192)
T ss_pred CcCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCCCccceeEECCCCCC
Confidence 4699998653222 2333 4899999986 45666655
No 68
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=62.59 E-value=14 Score=20.39 Aligned_cols=26 Identities=23% Similarity=0.349 Sum_probs=18.1
Q ss_pred eeCCCCceeeEE---eEEEEEeeCCCCcEE
Q 036150 9 RRKRTKKYAVKR---KAVGIWSCKYCGKVK 35 (77)
Q Consensus 9 ~~~~CGK~~VKR---~AVGIWkCkkCgkt~ 35 (77)
.||+|+.. |.. ..+=|..|.+|+=.+
T Consensus 1 ~CP~C~~~-l~~~~~~~~~id~C~~C~G~W 29 (41)
T PF13453_consen 1 KCPRCGTE-LEPVRLGDVEIDVCPSCGGIW 29 (41)
T ss_pred CcCCCCcc-cceEEECCEEEEECCCCCeEE
Confidence 37889874 333 356799999997544
No 69
>PLN00209 ribosomal protein S27; Provisional
Probab=62.33 E-value=16 Score=24.68 Aligned_cols=34 Identities=15% Similarity=0.265 Sum_probs=28.5
Q ss_pred ceeeeeeeCCCCcee-eEEeEEEEEeeCCCCcEEe
Q 036150 3 SYYRVLRRKRTKKYA-VKRKAVGIWSCKYCGKVKA 36 (77)
Q Consensus 3 ~~~~~~~~~~CGK~~-VKR~AVGIWkCkkCgkt~A 36 (77)
|||--.+||.|++.. |==.|.-.=.|..||.+.+
T Consensus 32 S~Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~ 66 (86)
T PLN00209 32 SFFMDVKCQGCFNITTVFSHSQTVVVCGSCQTVLC 66 (86)
T ss_pred CEEEEEECCCCCCeeEEEecCceEEEccccCCEee
Confidence 788889999999996 5555777789999999874
No 70
>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=61.12 E-value=2.9 Score=22.14 Aligned_cols=23 Identities=13% Similarity=0.046 Sum_probs=15.3
Q ss_pred eeCCCCceeeEEeEEEEEeeCCCCcEE
Q 036150 9 RRKRTKKYAVKRKAVGIWSCKYCGKVK 35 (77)
Q Consensus 9 ~~~~CGK~~VKR~AVGIWkCkkCgkt~ 35 (77)
+||+|++.- .+..=.|..||+.|
T Consensus 2 ~CP~C~~~V----~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEV----PESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCc----hhhcCcCCCCCCCC
Confidence 477887753 34445688888776
No 71
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=61.00 E-value=5.4 Score=31.97 Aligned_cols=23 Identities=13% Similarity=0.151 Sum_probs=19.6
Q ss_pred eeeeCCCCceeeEEeEEEEEeeCCCCc
Q 036150 7 VLRRKRTKKYAVKRKAVGIWSCKYCGK 33 (77)
Q Consensus 7 ~~~~~~CGK~~VKR~AVGIWkCkkCgk 33 (77)
+.+|.+||-..-|.. |+|..|+.
T Consensus 7 ~y~C~~Cg~~~~~~~----g~Cp~C~~ 29 (454)
T TIGR00416 7 KFVCQHCGADSPKWQ----GKCPACHA 29 (454)
T ss_pred eEECCcCCCCCcccc----EECcCCCC
Confidence 568999999998874 99999963
No 72
>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=60.98 E-value=5.3 Score=22.42 Aligned_cols=14 Identities=14% Similarity=0.102 Sum_probs=10.9
Q ss_pred eeeCCCCceeeEEe
Q 036150 8 LRRKRTKKYAVKRK 21 (77)
Q Consensus 8 ~~~~~CGK~~VKR~ 21 (77)
..||+||...++|+
T Consensus 27 ~~CP~Cg~~~~~r~ 40 (42)
T PF09723_consen 27 VPCPECGSTEVRRV 40 (42)
T ss_pred CcCCCCCCCceEEe
Confidence 46888888888875
No 73
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=58.80 E-value=20 Score=24.12 Aligned_cols=34 Identities=18% Similarity=0.258 Sum_probs=28.5
Q ss_pred ceeeeeeeCCCCcee-eEEeEEEEEeeCCCCcEEe
Q 036150 3 SYYRVLRRKRTKKYA-VKRKAVGIWSCKYCGKVKA 36 (77)
Q Consensus 3 ~~~~~~~~~~CGK~~-VKR~AVGIWkCkkCgkt~A 36 (77)
|||--.+||.|++.. |==.|.-.=.|..|+.+.+
T Consensus 31 S~Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~ 65 (85)
T PTZ00083 31 SYFMDVKCPGCSQITTVFSHAQTVVLCGGCSSQLC 65 (85)
T ss_pred CeEEEEECCCCCCeeEEEecCceEEEccccCCEee
Confidence 788889999999996 5556777789999999874
No 74
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=58.32 E-value=5 Score=31.50 Aligned_cols=21 Identities=19% Similarity=0.222 Sum_probs=18.1
Q ss_pred eeCCCCceeeEEeEEEEEeeCCCCc
Q 036150 9 RRKRTKKYAVKRKAVGIWSCKYCGK 33 (77)
Q Consensus 9 ~~~~CGK~~VKR~AVGIWkCkkCgk 33 (77)
+|.|||...-|.. |+|..|+.
T Consensus 2 ~c~~cg~~~~~~~----g~cp~c~~ 22 (372)
T cd01121 2 VCSECGYVSPKWL----GKCPECGE 22 (372)
T ss_pred CCCCCCCCCCCcc----EECcCCCC
Confidence 6899999998875 99999974
No 75
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=57.84 E-value=4.4 Score=28.53 Aligned_cols=24 Identities=17% Similarity=0.292 Sum_probs=19.0
Q ss_pred eeeeCCCCcee--eEEeEEEEEeeCCCCcE
Q 036150 7 VLRRKRTKKYA--VKRKAVGIWSCKYCGKV 34 (77)
Q Consensus 7 ~~~~~~CGK~~--VKR~AVGIWkCkkCgkt 34 (77)
..+||||+|.. +.|+- .|-.|+..
T Consensus 69 ~V~CP~C~K~TKmLGr~D----~CM~C~~p 94 (114)
T PF11023_consen 69 QVECPNCGKQTKMLGRVD----ACMHCKEP 94 (114)
T ss_pred eeECCCCCChHhhhchhh----ccCcCCCc
Confidence 46799999997 88873 78888764
No 76
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=57.71 E-value=9.3 Score=18.28 Aligned_cols=12 Identities=25% Similarity=0.703 Sum_probs=10.2
Q ss_pred EeeCCCCcEEeC
Q 036150 26 WSCKYCGKVKAG 37 (77)
Q Consensus 26 WkCkkCgkt~AG 37 (77)
|.|+-|++++..
T Consensus 1 ~~C~~C~~~f~s 12 (25)
T PF12874_consen 1 FYCDICNKSFSS 12 (25)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCCCCCCcCC
Confidence 789999998864
No 77
>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=56.63 E-value=14 Score=21.14 Aligned_cols=29 Identities=21% Similarity=0.287 Sum_probs=21.0
Q ss_pred eeCCCCceeeEEeEEE--------EEeeCC--CCcEEeC
Q 036150 9 RRKRTKKYAVKRKAVG--------IWSCKY--CGKVKAG 37 (77)
Q Consensus 9 ~~~~CGK~~VKR~AVG--------IWkCkk--Cgkt~AG 37 (77)
+||.||.....|.+.. ...|.. ||.+|..
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg~tfv~ 39 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSPLTRELYCQCTNPECGHTFVA 39 (47)
T ss_pred CcCCCCCeeEEEEchhhCcceEEEEEEECCCcCCCEEEE
Confidence 5899999887776543 467776 8887754
No 78
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=56.41 E-value=7.3 Score=22.47 Aligned_cols=12 Identities=33% Similarity=0.950 Sum_probs=9.8
Q ss_pred EEeeCCCCcEEe
Q 036150 25 IWSCKYCGKVKA 36 (77)
Q Consensus 25 IWkCkkCgkt~A 36 (77)
-|+|.+||..+-
T Consensus 28 ~W~C~~Cgh~w~ 39 (55)
T PF14311_consen 28 WWKCPKCGHEWK 39 (55)
T ss_pred EEECCCCCCeeE
Confidence 599999987764
No 79
>COG4640 Predicted membrane protein [Function unknown]
Probab=55.71 E-value=4.5 Score=34.13 Aligned_cols=29 Identities=10% Similarity=0.111 Sum_probs=22.3
Q ss_pred eeeCCCCceeeEEeEEEEEeeCCCCcEEeCccc
Q 036150 8 LRRKRTKKYAVKRKAVGIWSCKYCGKVKAGALN 40 (77)
Q Consensus 8 ~~~~~CGK~~VKR~AVGIWkCkkCgkt~AGGAY 40 (77)
+-||+||+.+-. +=-+|+.||..+.++-=
T Consensus 2 ~fC~kcG~qk~E----d~~qC~qCG~~~t~~~s 30 (465)
T COG4640 2 KFCPKCGSQKAE----DDVQCTQCGHKFTSRQS 30 (465)
T ss_pred Cccccccccccc----ccccccccCCcCCchhh
Confidence 469999987644 44459999999999853
No 80
>PRK06386 replication factor A; Reviewed
Probab=55.46 E-value=5 Score=32.14 Aligned_cols=20 Identities=15% Similarity=0.042 Sum_probs=16.7
Q ss_pred eeeCCCCceeeEEeEEEEEeeCCCCc
Q 036150 8 LRRKRTKKYAVKRKAVGIWSCKYCGK 33 (77)
Q Consensus 8 ~~~~~CGK~~VKR~AVGIWkCkkCgk 33 (77)
-|||+|+|.--+ |.|+.||+
T Consensus 237 ~rCP~C~R~l~~------g~C~~HG~ 256 (358)
T PRK06386 237 TKCSVCNKIIED------GVCKDHPD 256 (358)
T ss_pred ecCcCCCeEccC------CcCCCCCC
Confidence 589999987554 89999997
No 81
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=55.19 E-value=26 Score=22.70 Aligned_cols=34 Identities=21% Similarity=0.286 Sum_probs=26.3
Q ss_pred ceeeeeeeCCCCcee-eEEeEEEEEeeCCCCcEEe
Q 036150 3 SYYRVLRRKRTKKYA-VKRKAVGIWSCKYCGKVKA 36 (77)
Q Consensus 3 ~~~~~~~~~~CGK~~-VKR~AVGIWkCkkCgkt~A 36 (77)
|+|--.+||+|+-.. |=-.+.=.=.|..||.+.+
T Consensus 15 s~Fl~VkCpdC~N~q~vFshast~V~C~~CG~~l~ 49 (67)
T COG2051 15 SRFLRVKCPDCGNEQVVFSHASTVVTCLICGTTLA 49 (67)
T ss_pred ceEEEEECCCCCCEEEEeccCceEEEecccccEEE
Confidence 556667999999986 4445666779999999876
No 82
>PRK04351 hypothetical protein; Provisional
Probab=54.82 E-value=13 Score=26.16 Aligned_cols=29 Identities=10% Similarity=0.191 Sum_probs=21.8
Q ss_pred eeeeCCCCce--eeEEeEEEEEeeCCCCcEE
Q 036150 7 VLRRKRTKKY--AVKRKAVGIWSCKYCGKVK 35 (77)
Q Consensus 7 ~~~~~~CGK~--~VKR~AVGIWkCkkCgkt~ 35 (77)
+.+|.+||.. ..+|..+--..|+.|+-+.
T Consensus 112 ~Y~C~~Cg~~~~r~Rr~n~~~yrCg~C~g~L 142 (149)
T PRK04351 112 LYECQSCGQQYLRKRRINTKRYRCGKCRGKL 142 (149)
T ss_pred EEECCCCCCEeeeeeecCCCcEEeCCCCcEe
Confidence 5788899984 4667777778999998543
No 83
>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=54.78 E-value=11 Score=23.32 Aligned_cols=34 Identities=24% Similarity=0.376 Sum_probs=21.0
Q ss_pred ceeeeeeeCCCCceeeE-EeEEEEEeeCCCCcEEe
Q 036150 3 SYYRVLRRKRTKKYAVK-RKAVGIWSCKYCGKVKA 36 (77)
Q Consensus 3 ~~~~~~~~~~CGK~~VK-R~AVGIWkCkkCgkt~A 36 (77)
|||--.+||.|++..+- =.+.-.=.|..|+.+.+
T Consensus 3 S~Fm~VkCp~C~~~q~vFSha~t~V~C~~Cg~~L~ 37 (55)
T PF01667_consen 3 SYFMDVKCPGCYNIQTVFSHAQTVVKCVVCGTVLA 37 (55)
T ss_dssp --EEEEE-TTT-SEEEEETT-SS-EE-SSSTSEEE
T ss_pred ccEEEEECCCCCCeeEEEecCCeEEEcccCCCEec
Confidence 78888899999999743 33555668999999874
No 84
>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=54.43 E-value=7.4 Score=25.91 Aligned_cols=25 Identities=8% Similarity=0.204 Sum_probs=15.3
Q ss_pred eeeeCCCCceeeEEeEEEEEeeCCCCc
Q 036150 7 VLRRKRTKKYAVKRKAVGIWSCKYCGK 33 (77)
Q Consensus 7 ~~~~~~CGK~~VKR~AVGIWkCkkCgk 33 (77)
+.+|++||+.--... -.+.|.+||-
T Consensus 70 ~~~C~~Cg~~~~~~~--~~~~CP~Cgs 94 (115)
T TIGR00100 70 ECECEDCSEEVSPEI--DLYRCPKCHG 94 (115)
T ss_pred EEEcccCCCEEecCC--cCccCcCCcC
Confidence 467888886532211 1477888873
No 85
>PRK04023 DNA polymerase II large subunit; Validated
Probab=54.39 E-value=5.4 Score=36.79 Aligned_cols=24 Identities=17% Similarity=0.257 Sum_probs=17.8
Q ss_pred eeeCCCCceeeEEeEEEEEeeCCCCcEEe
Q 036150 8 LRRKRTKKYAVKRKAVGIWSCKYCGKVKA 36 (77)
Q Consensus 8 ~~~~~CGK~~VKR~AVGIWkCkkCgkt~A 36 (77)
.+||+||+. ...||.|.+|+....
T Consensus 639 frCP~CG~~-----Te~i~fCP~CG~~~~ 662 (1121)
T PRK04023 639 RRCPFCGTH-----TEPVYRCPRCGIEVE 662 (1121)
T ss_pred ccCCCCCCC-----CCcceeCccccCcCC
Confidence 478888877 457888888877644
No 86
>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=54.08 E-value=2.9 Score=29.30 Aligned_cols=28 Identities=11% Similarity=0.288 Sum_probs=22.6
Q ss_pred eeeCCCCceeeEEeE-------EEEEeeCCCCcEE
Q 036150 8 LRRKRTKKYAVKRKA-------VGIWSCKYCGKVK 35 (77)
Q Consensus 8 ~~~~~CGK~~VKR~A-------VGIWkCkkCgkt~ 35 (77)
.+||+||....++.+ --+|.|+.|.+-|
T Consensus 106 ~~cp~c~s~~t~~~s~fg~t~cka~~~c~~c~epf 140 (146)
T TIGR02159 106 VQCPRCGSADTTITSIFGPTACKALYRCRACKEPF 140 (146)
T ss_pred CcCCCCCCCCcEeecCCCChhhHHHhhhhhhCCcH
Confidence 689999999888874 3589999997644
No 87
>PRK11032 hypothetical protein; Provisional
Probab=52.97 E-value=8.3 Score=27.92 Aligned_cols=28 Identities=14% Similarity=0.113 Sum_probs=16.9
Q ss_pred eeeeCCCCceeeEEeEEEEEeeCCCCcE
Q 036150 7 VLRRKRTKKYAVKRKAVGIWSCKYCGKV 34 (77)
Q Consensus 7 ~~~~~~CGK~~VKR~AVGIWkCkkCgkt 34 (77)
+|+|.|||....--...=|=-|.+||.+
T Consensus 124 ~LvC~~Cg~~~~~~~p~~i~pCp~C~~~ 151 (160)
T PRK11032 124 NLVCEKCHHHLAFYTPEVLPLCPKCGHD 151 (160)
T ss_pred eEEecCCCCEEEecCCCcCCCCCCCCCC
Confidence 4667777766544455556666666643
No 88
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=52.21 E-value=17 Score=25.08 Aligned_cols=44 Identities=18% Similarity=0.203 Sum_probs=27.8
Q ss_pred eCCCCce-eeEEeEEEEEeeCCCCcEEeCcccccccccccccHHHHHhhhhh
Q 036150 10 RKRTKKY-AVKRKAVGIWSCKYCGKVKAGALNAATLAAFTALPAAAAALLTF 60 (77)
Q Consensus 10 ~~~CGK~-~VKR~AVGIWkCkkCgkt~AGGAYtp~Tpag~s~~~~~~~~~~~ 60 (77)
||.||.. .|.|. +|..|+-++-|.=..+. -..-++-+-.|+..|
T Consensus 1 CPvCg~~l~vt~l-----~C~~C~t~i~G~F~l~~--~~~L~~E~~~Fi~~F 45 (113)
T PF09862_consen 1 CPVCGGELVVTRL-----KCPSCGTEIEGEFELPW--FARLSPEQLEFIKLF 45 (113)
T ss_pred CCCCCCceEEEEE-----EcCCCCCEEEeeeccch--hhcCCHHHHHHHHHH
Confidence 7899987 46664 89999999987533321 222234555555554
No 89
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=51.82 E-value=13 Score=19.79 Aligned_cols=19 Identities=21% Similarity=0.396 Sum_probs=13.7
Q ss_pred eEEeEEEEEeeCCCCcEEe
Q 036150 18 VKRKAVGIWSCKYCGKVKA 36 (77)
Q Consensus 18 VKR~AVGIWkCkkCgkt~A 36 (77)
+.-..+--|.|..||..+-
T Consensus 25 ~~i~~vp~~~C~~CGE~~~ 43 (46)
T TIGR03831 25 IVIENVPALVCPQCGEEYL 43 (46)
T ss_pred EEEeCCCccccccCCCEee
Confidence 3334567899999998764
No 90
>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=51.74 E-value=11 Score=21.53 Aligned_cols=12 Identities=25% Similarity=0.977 Sum_probs=7.6
Q ss_pred EEEeeCCCCcEE
Q 036150 24 GIWSCKYCGKVK 35 (77)
Q Consensus 24 GIWkCkkCgkt~ 35 (77)
.|++|+.||..+
T Consensus 5 ~~YkC~~CGniV 16 (36)
T PF06397_consen 5 EFYKCEHCGNIV 16 (36)
T ss_dssp EEEE-TTT--EE
T ss_pred cEEEccCCCCEE
Confidence 589999999876
No 91
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=51.73 E-value=12 Score=18.92 Aligned_cols=11 Identities=45% Similarity=1.241 Sum_probs=8.9
Q ss_pred EeeCCCCcEEe
Q 036150 26 WSCKYCGKVKA 36 (77)
Q Consensus 26 WkCkkCgkt~A 36 (77)
.+|+.|++.|.
T Consensus 15 ~~C~~C~k~F~ 25 (26)
T PF13465_consen 15 YKCPYCGKSFS 25 (26)
T ss_dssp EEESSSSEEES
T ss_pred CCCCCCcCeeC
Confidence 68999998874
No 92
>PRK07562 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=51.68 E-value=10 Score=35.17 Aligned_cols=28 Identities=14% Similarity=0.334 Sum_probs=23.5
Q ss_pred eeeeeCCCCceeeEEeEEEEEeeCCCCcE
Q 036150 6 RVLRRKRTKKYAVKRKAVGIWSCKYCGKV 34 (77)
Q Consensus 6 ~~~~~~~CGK~~VKR~AVGIWkCkkCgkt 34 (77)
.=--|++||...|.|.+ +-|+|..||-+
T Consensus 1189 ~g~~c~~cg~~~~vrng-tc~~c~~cg~t 1216 (1220)
T PRK07562 1189 TGEACSECGNFTLVRNG-TCLKCDTCGST 1216 (1220)
T ss_pred CCCcCCCcCCeEEEeCC-eeeeccccCCC
Confidence 33459999999999998 57999999975
No 93
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=51.23 E-value=5.2 Score=29.48 Aligned_cols=30 Identities=23% Similarity=0.342 Sum_probs=21.2
Q ss_pred eeeeCCCCce--ee-------------EEeEEEEEeeCCCCcEEe
Q 036150 7 VLRRKRTKKY--AV-------------KRKAVGIWSCKYCGKVKA 36 (77)
Q Consensus 7 ~~~~~~CGK~--~V-------------KR~AVGIWkCkkCgkt~A 36 (77)
.-|||.|+-. +| .|...-.|.|.+||+.+=
T Consensus 97 ~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW 141 (165)
T COG1656 97 FSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYW 141 (165)
T ss_pred cccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCccccc
Confidence 4588888865 23 344555999999999853
No 94
>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=51.12 E-value=8.1 Score=27.34 Aligned_cols=28 Identities=14% Similarity=0.207 Sum_probs=16.5
Q ss_pred eeeeCCCCceeeEEeEEEEEeeCCCCcE
Q 036150 7 VLRRKRTKKYAVKRKAVGIWSCKYCGKV 34 (77)
Q Consensus 7 ~~~~~~CGK~~VKR~AVGIWkCkkCgkt 34 (77)
.++|.|||....--...=|=.|.+||.+
T Consensus 112 ~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~ 139 (146)
T PF07295_consen 112 TLVCENCGHEVELTHPERLPPCPKCGHT 139 (146)
T ss_pred eEecccCCCEEEecCCCcCCCCCCCCCC
Confidence 4667777766433334446677777653
No 95
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=50.85 E-value=9.3 Score=30.48 Aligned_cols=33 Identities=21% Similarity=0.322 Sum_probs=25.3
Q ss_pred eeeeeCCCCce-----eeEEeEEEEEeeCCCCcEEeCc
Q 036150 6 RVLRRKRTKKY-----AVKRKAVGIWSCKYCGKVKAGA 38 (77)
Q Consensus 6 ~~~~~~~CGK~-----~VKR~AVGIWkCkkCgkt~AGG 38 (77)
+|-||-+|.|. .=|=-+.|-.+|.+|+.+|-|=
T Consensus 131 eVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~G~ 168 (278)
T PF15135_consen 131 EVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFRGF 168 (278)
T ss_pred ccccccccccccCCCccccccceeeeecccccccchhh
Confidence 56788888875 1233478899999999999874
No 96
>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=50.18 E-value=7.6 Score=23.98 Aligned_cols=32 Identities=16% Similarity=0.222 Sum_probs=22.9
Q ss_pred eeeeeeCCCCceeeE--EeEEEEEeeCCCCcEEe
Q 036150 5 YRVLRRKRTKKYAVK--RKAVGIWSCKYCGKVKA 36 (77)
Q Consensus 5 ~~~~~~~~CGK~~VK--R~AVGIWkCkkCgkt~A 36 (77)
++-+||++|+|.=.+ -....==+|.+|+...-
T Consensus 2 ~~eiRC~~CnklLa~~g~~~~leIKCpRC~tiN~ 35 (51)
T PF10122_consen 2 LKEIRCGHCNKLLAKAGEVIELEIKCPRCKTINH 35 (51)
T ss_pred CcceeccchhHHHhhhcCccEEEEECCCCCccce
Confidence 466899999998655 23445669999987643
No 97
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=48.83 E-value=12 Score=32.70 Aligned_cols=28 Identities=25% Similarity=0.452 Sum_probs=23.2
Q ss_pred eeeeCCCCceeeEEeEEEEEeeCCCCcE
Q 036150 7 VLRRKRTKKYAVKRKAVGIWSCKYCGKV 34 (77)
Q Consensus 7 ~~~~~~CGK~~VKR~AVGIWkCkkCgkt 34 (77)
+.+||||+..=+--+..|+=.|..||+.
T Consensus 444 v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~ 471 (730)
T COG1198 444 IAECPNCDSPLTLHKATGQLRCHYCGYQ 471 (730)
T ss_pred cccCCCCCcceEEecCCCeeEeCCCCCC
Confidence 5788899888777777799999999986
No 98
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=48.08 E-value=14 Score=27.55 Aligned_cols=27 Identities=11% Similarity=-0.068 Sum_probs=20.3
Q ss_pred eeeCCCCceeeEEeEEEEEeeCCCCcE
Q 036150 8 LRRKRTKKYAVKRKAVGIWSCKYCGKV 34 (77)
Q Consensus 8 ~~~~~CGK~~VKR~AVGIWkCkkCgkt 34 (77)
--|++||.....+..--.-.|.+|+..
T Consensus 100 ~fC~~CG~~~~~~~~~~~~~C~~c~~~ 126 (256)
T PRK00241 100 RFCGYCGHPMHPSKTEWAMLCPHCRER 126 (256)
T ss_pred ccccccCCCCeecCCceeEECCCCCCE
Confidence 358999998766666666789998864
No 99
>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=47.71 E-value=12 Score=21.02 Aligned_cols=15 Identities=7% Similarity=-0.079 Sum_probs=11.0
Q ss_pred eeeCCCCceeeEEeE
Q 036150 8 LRRKRTKKYAVKRKA 22 (77)
Q Consensus 8 ~~~~~CGK~~VKR~A 22 (77)
..||+||...++|.-
T Consensus 27 ~~CP~Cg~~~~~r~~ 41 (52)
T TIGR02605 27 ATCPECGGEKLRRLL 41 (52)
T ss_pred CCCCCCCCCceeEEe
Confidence 458888887777763
No 100
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=47.56 E-value=28 Score=24.32 Aligned_cols=36 Identities=19% Similarity=0.287 Sum_probs=26.6
Q ss_pred eeeeeCCCCceee-----E-EeEEEEEeeCCCCcEEeCcccc
Q 036150 6 RVLRRKRTKKYAV-----K-RKAVGIWSCKYCGKVKAGALNA 41 (77)
Q Consensus 6 ~~~~~~~CGK~~V-----K-R~AVGIWkCkkCgkt~AGGAYt 41 (77)
+...||+||+.+| | -...|.=.|+.||..+.--.-.
T Consensus 21 k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~ev~~ 62 (104)
T COG4888 21 KTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFECEVPE 62 (104)
T ss_pred ceEecCccCCeeeeEEEEEecCceeEEEcccCcceEEEeccc
Confidence 4567999999864 3 3478889999999877654433
No 101
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=47.32 E-value=7.3 Score=26.08 Aligned_cols=25 Identities=20% Similarity=0.247 Sum_probs=13.6
Q ss_pred eeeeCCCCcee-eEEeEEEEEeeCCCCc
Q 036150 7 VLRRKRTKKYA-VKRKAVGIWSCKYCGK 33 (77)
Q Consensus 7 ~~~~~~CGK~~-VKR~AVGIWkCkkCgk 33 (77)
..+|++||+.- +. .....+|.+||-
T Consensus 71 ~~~C~~Cg~~~~~~--~~~~~~CP~Cgs 96 (117)
T PRK00564 71 ELECKDCSHVFKPN--ALDYGVCEKCHS 96 (117)
T ss_pred EEEhhhCCCccccC--CccCCcCcCCCC
Confidence 35777787542 22 123345777763
No 102
>PRK06450 threonine synthase; Validated
Probab=46.21 E-value=11 Score=29.00 Aligned_cols=23 Identities=22% Similarity=0.276 Sum_probs=17.3
Q ss_pred eeeCCCCceeeEEeEEEEEeeCCCCc
Q 036150 8 LRRKRTKKYAVKRKAVGIWSCKYCGK 33 (77)
Q Consensus 8 ~~~~~CGK~~VKR~AVGIWkCkkCgk 33 (77)
|+|.+||+.. . ..-.|.|..||-
T Consensus 4 ~~C~~Cg~~~-~--~~~~~~C~~cg~ 26 (338)
T PRK06450 4 EVCMKCGKER-E--SIYEIRCKKCGG 26 (338)
T ss_pred eEECCcCCcC-C--CcccccCCcCCC
Confidence 7899999985 2 133599999974
No 103
>PHA00689 hypothetical protein
Probab=45.94 E-value=8.8 Score=24.51 Aligned_cols=16 Identities=25% Similarity=0.343 Sum_probs=13.1
Q ss_pred eeeeeCCCCceeeEEe
Q 036150 6 RVLRRKRTKKYAVKRK 21 (77)
Q Consensus 6 ~~~~~~~CGK~~VKR~ 21 (77)
|...|++|||+.++.+
T Consensus 16 ravtckrcgktglrwe 31 (62)
T PHA00689 16 RAVTCKRCGKTGLRWE 31 (62)
T ss_pred ceeehhhccccCceee
Confidence 5677899999988876
No 104
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=45.83 E-value=16 Score=27.56 Aligned_cols=18 Identities=11% Similarity=0.104 Sum_probs=9.4
Q ss_pred eeeeCCCCceeeEEeEEE
Q 036150 7 VLRRKRTKKYAVKRKAVG 24 (77)
Q Consensus 7 ~~~~~~CGK~~VKR~AVG 24 (77)
-|+|||||.+-.+..|++
T Consensus 165 ~l~Cp~Cg~tEkRKia~~ 182 (188)
T COG1096 165 MLKCPNCGNTEKRKIAKD 182 (188)
T ss_pred EEECCCCCCEEeeeeccc
Confidence 455555555555544443
No 105
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=45.82 E-value=15 Score=17.84 Aligned_cols=11 Identities=36% Similarity=0.975 Sum_probs=8.6
Q ss_pred EeeCCCCcEEe
Q 036150 26 WSCKYCGKVKA 36 (77)
Q Consensus 26 WkCkkCgkt~A 36 (77)
-.|..|+++|.
T Consensus 2 ~~C~~C~~~F~ 12 (27)
T PF13912_consen 2 FECDECGKTFS 12 (27)
T ss_dssp EEETTTTEEES
T ss_pred CCCCccCCccC
Confidence 47888988874
No 106
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=45.71 E-value=10 Score=19.55 Aligned_cols=12 Identities=33% Similarity=0.988 Sum_probs=9.6
Q ss_pred EEEeeCCCCcEE
Q 036150 24 GIWSCKYCGKVK 35 (77)
Q Consensus 24 GIWkCkkCgkt~ 35 (77)
|-|.|..|...=
T Consensus 3 g~W~C~~C~~~N 14 (30)
T PF00641_consen 3 GDWKCPSCTFMN 14 (30)
T ss_dssp SSEEETTTTEEE
T ss_pred cCccCCCCcCCc
Confidence 679999998653
No 107
>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.
Probab=45.68 E-value=16 Score=25.86 Aligned_cols=27 Identities=11% Similarity=0.022 Sum_probs=15.7
Q ss_pred eeeeCCCCceeeE---------EeEEEEEeeCCCCc
Q 036150 7 VLRRKRTKKYAVK---------RKAVGIWSCKYCGK 33 (77)
Q Consensus 7 ~~~~~~CGK~~VK---------R~AVGIWkCkkCgk 33 (77)
.++||.|++...= ......|.|.+|+.
T Consensus 18 ~~~C~~C~~~~~f~g~~~~~~~~~~~~~~~C~~C~~ 53 (188)
T PF08996_consen 18 KLTCPSCGTEFEFPGVFEEDGDDVSPSGLQCPNCST 53 (188)
T ss_dssp EEE-TTT--EEEE-SSS--SSEEEETTEEEETTT--
T ss_pred EeECCCCCCCccccccccCCccccccCcCcCCCCCC
Confidence 5789999987532 23455899999998
No 108
>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=44.48 E-value=16 Score=28.71 Aligned_cols=34 Identities=9% Similarity=0.138 Sum_probs=17.6
Q ss_pred eeeCCCCceeeEEe----EEEEEeeCCCC-------------cEEeCcccc
Q 036150 8 LRRKRTKKYAVKRK----AVGIWSCKYCG-------------KVKAGALNA 41 (77)
Q Consensus 8 ~~~~~CGK~~VKR~----AVGIWkCkkCg-------------kt~AGGAYt 41 (77)
.-|||||...+.+- -|.=..|..|+ +++.+|||.
T Consensus 32 ~yCP~Cg~~~L~~f~NN~PVaDF~C~~C~eeyELKSk~~~l~~~I~dGAY~ 82 (254)
T PF06044_consen 32 MYCPNCGSKPLSKFENNRPVADFYCPNCNEEYELKSKKKKLSNKINDGAYH 82 (254)
T ss_dssp ---TTT--SS-EE--------EEE-TTT--EEEEEEEESS--SEEEEEEHH
T ss_pred CcCCCCCChhHhhccCCCccceeECCCCchHHhhhhhccccCCcccCccHH
Confidence 45899999877664 36678888886 467888885
No 109
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=43.90 E-value=16 Score=24.31 Aligned_cols=30 Identities=10% Similarity=0.182 Sum_probs=22.1
Q ss_pred eeeeeeCCCCceeeEEeEEEEEeeCCCCcE
Q 036150 5 YRVLRRKRTKKYAVKRKAVGIWSCKYCGKV 34 (77)
Q Consensus 5 ~~~~~~~~CGK~~VKR~AVGIWkCkkCgkt 34 (77)
+.+.+|++||...+--.+-+==.|.+|+..
T Consensus 40 ~~~~~C~~Cg~~~~~~~SCk~R~CP~C~~~ 69 (111)
T PF14319_consen 40 FHRYRCEDCGHEKIVYNSCKNRHCPSCQAK 69 (111)
T ss_pred cceeecCCCCceEEecCcccCcCCCCCCCh
Confidence 346788888888877777777778888754
No 110
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=43.35 E-value=9.5 Score=24.72 Aligned_cols=11 Identities=27% Similarity=0.214 Sum_probs=8.6
Q ss_pred eeeeeCCCCce
Q 036150 6 RVLRRKRTKKY 16 (77)
Q Consensus 6 ~~~~~~~CGK~ 16 (77)
..||||+||+.
T Consensus 16 ~~lrCPRC~~~ 26 (65)
T COG4049 16 EFLRCPRCGMV 26 (65)
T ss_pred eeeeCCchhHH
Confidence 36899999864
No 111
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=43.35 E-value=14 Score=20.69 Aligned_cols=17 Identities=29% Similarity=0.507 Sum_probs=12.1
Q ss_pred EeeCCCCcEEeCccccc
Q 036150 26 WSCKYCGKVKAGALNAA 42 (77)
Q Consensus 26 WkCkkCgkt~AGGAYtp 42 (77)
-.|..|++.++.+-|.|
T Consensus 5 ~~C~nC~R~v~a~RfA~ 21 (33)
T PF08209_consen 5 VECPNCGRPVAASRFAP 21 (33)
T ss_dssp EE-TTTSSEEEGGGHHH
T ss_pred EECCCCcCCcchhhhHH
Confidence 46888888888877765
No 112
>TIGR03844 cysteate_syn cysteate synthase. Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M.
Probab=43.21 E-value=12 Score=29.47 Aligned_cols=23 Identities=17% Similarity=0.059 Sum_probs=17.3
Q ss_pred eeeeCCCCceeeEEeEEEEEeeCCCC
Q 036150 7 VLRRKRTKKYAVKRKAVGIWSCKYCG 32 (77)
Q Consensus 7 ~~~~~~CGK~~VKR~AVGIWkCkkCg 32 (77)
.|+|.+||+.- . .. ..|.|..|+
T Consensus 2 ~l~C~~Cg~~~-~-~~-~~~~C~~c~ 24 (398)
T TIGR03844 2 TLRCPGCGEVL-P-DH-YTLSCPLDC 24 (398)
T ss_pred EEEeCCCCCcc-C-Cc-cccCCCCCC
Confidence 57999999885 3 33 379998886
No 113
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=42.55 E-value=20 Score=19.74 Aligned_cols=27 Identities=11% Similarity=0.294 Sum_probs=16.8
Q ss_pred eeCCCCceeeEEeEE--EEEeeCCCCcEEe
Q 036150 9 RRKRTKKYAVKRKAV--GIWSCKYCGKVKA 36 (77)
Q Consensus 9 ~~~~CGK~~VKR~AV--GIWkCkkCgkt~A 36 (77)
-||.||..=+-+... -+ .|+.|++..-
T Consensus 3 FCp~C~nlL~p~~~~~~~~-~C~~C~Y~~~ 31 (35)
T PF02150_consen 3 FCPECGNLLYPKEDKEKRV-ACRTCGYEEP 31 (35)
T ss_dssp BETTTTSBEEEEEETTTTE-EESSSS-EEE
T ss_pred eCCCCCccceEcCCCccCc-CCCCCCCccC
Confidence 378888875444321 13 6999998764
No 114
>PF04071 zf-like: Cysteine-rich small domain; InterPro: IPR007212 This is a probable metal-binding domain. It is found in a probable precorrin-3B C17-methyltransferase from Methanobacterium thermoautotrophicum, that catalyses the methylation of C-17 in precorrin-3B to form precorrin-4.
Probab=42.49 E-value=16 Score=24.18 Aligned_cols=21 Identities=14% Similarity=0.604 Sum_probs=12.9
Q ss_pred CceeeEEeEEEEEeeCCCCcE
Q 036150 14 KKYAVKRKAVGIWSCKYCGKV 34 (77)
Q Consensus 14 GK~~VKR~AVGIWkCkkCgkt 34 (77)
|.....+.+..||.|..|...
T Consensus 40 G~~~~~~~G~~vw~C~~C~~~ 60 (86)
T PF04071_consen 40 GNFIYTKNGSKVWDCSDCTLP 60 (86)
T ss_pred ccEEEcCCCCeeeECccCCCc
Confidence 443343333449999999753
No 115
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=42.47 E-value=24 Score=20.41 Aligned_cols=27 Identities=15% Similarity=0.262 Sum_probs=18.0
Q ss_pred eeeCCCCcee-eEEeEEEEEeeCCCCcEEe
Q 036150 8 LRRKRTKKYA-VKRKAVGIWSCKYCGKVKA 36 (77)
Q Consensus 8 ~~~~~CGK~~-VKR~AVGIWkCkkCgkt~A 36 (77)
.+|.+||..- ++ .-+-=+|+.||..+-
T Consensus 3 Y~C~~Cg~~~~~~--~~~~irC~~CG~rIl 30 (44)
T smart00659 3 YICGECGRENEIK--SKDVVRCRECGYRIL 30 (44)
T ss_pred EECCCCCCEeecC--CCCceECCCCCceEE
Confidence 4688888863 44 235568888887663
No 116
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=41.94 E-value=20 Score=19.65 Aligned_cols=24 Identities=29% Similarity=0.689 Sum_probs=17.4
Q ss_pred eeCCCCceeeEEeEEEEEeeCCCCcEEeCc
Q 036150 9 RRKRTKKYAVKRKAVGIWSCKYCGKVKAGA 38 (77)
Q Consensus 9 ~~~~CGK~~VKR~AVGIWkCkkCgkt~AGG 38 (77)
||.+|+... .+|.|-.|++..-|-
T Consensus 1 ~C~~C~~~~------~l~~CL~C~~~~c~~ 24 (50)
T smart00290 1 RCSVCGTIE------NLWLCLTCGQVGCGR 24 (50)
T ss_pred CcccCCCcC------CeEEecCCCCcccCC
Confidence 466777544 499999998877543
No 117
>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=41.82 E-value=23 Score=18.82 Aligned_cols=13 Identities=23% Similarity=0.994 Sum_probs=10.7
Q ss_pred EEEeeCCCCcEEe
Q 036150 24 GIWSCKYCGKVKA 36 (77)
Q Consensus 24 GIWkCkkCgkt~A 36 (77)
.|++|+.||..+.
T Consensus 3 ~~ykC~~CGniv~ 15 (34)
T cd00974 3 EVYKCEICGNIVE 15 (34)
T ss_pred cEEEcCCCCcEEE
Confidence 4789999998884
No 118
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=41.68 E-value=26 Score=22.41 Aligned_cols=30 Identities=13% Similarity=0.185 Sum_probs=22.2
Q ss_pred eeeCCCCceeeEEeEE--------EEEeeC--CCCcEEeC
Q 036150 8 LRRKRTKKYAVKRKAV--------GIWSCK--YCGKVKAG 37 (77)
Q Consensus 8 ~~~~~CGK~~VKR~AV--------GIWkCk--kCgkt~AG 37 (77)
++||.||....-|.+- =...|. .||.+|.-
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF~t 41 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDTTKERYHQCQNVNCSATFIT 41 (72)
T ss_pred ccCCCCCCccEEEEChhcChhhheeeeecCCCCCCCEEEE
Confidence 5799999887555432 357898 89998864
No 119
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=41.44 E-value=10 Score=25.82 Aligned_cols=29 Identities=17% Similarity=0.307 Sum_probs=17.8
Q ss_pred eeeeCCCCceeeEEeE------EEEEeeCCCCcEE
Q 036150 7 VLRRKRTKKYAVKRKA------VGIWSCKYCGKVK 35 (77)
Q Consensus 7 ~~~~~~CGK~~VKR~A------VGIWkCkkCgkt~ 35 (77)
+..||||++.----.+ .|--.|..||..+
T Consensus 99 ~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l 133 (147)
T smart00531 99 YYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEEL 133 (147)
T ss_pred EEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEE
Confidence 4578999865211111 3448899998765
No 120
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=41.33 E-value=22 Score=18.84 Aligned_cols=14 Identities=21% Similarity=0.831 Sum_probs=11.4
Q ss_pred EEEEeeCCCCcEEe
Q 036150 23 VGIWSCKYCGKVKA 36 (77)
Q Consensus 23 VGIWkCkkCgkt~A 36 (77)
..|++|+.||..+.
T Consensus 5 ~~~ykC~~Cgniv~ 18 (34)
T TIGR00319 5 GQVYKCEVCGNIVE 18 (34)
T ss_pred CcEEEcCCCCcEEE
Confidence 35899999998884
No 121
>PF01586 Basic: Myogenic Basic domain; InterPro: IPR002546 This basic domain is found in the MyoD family of muscle specific proteins that control muscle development. The bHLH region of the MyoD family includes the basic domain and the Helix-loop-helix (HLH) motif. The bHLH region mediates specific DNA binding []. With 12 residues of the basic domain involved in DNA binding []. The basic domain forms an extended alpha helix in the structure.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0007517 muscle organ development, 0005634 nucleus; PDB: 1MDY_C.
Probab=41.02 E-value=9.4 Score=25.47 Aligned_cols=11 Identities=36% Similarity=1.274 Sum_probs=0.9
Q ss_pred EEeeCCCCcEE
Q 036150 25 IWSCKYCGKVK 35 (77)
Q Consensus 25 IWkCkkCgkt~ 35 (77)
+|-||-|++|-
T Consensus 72 ~WACKaCKRKt 82 (86)
T PF01586_consen 72 LWACKACKRKT 82 (86)
T ss_dssp -------S---
T ss_pred HHHhHhhhccC
Confidence 79999999874
No 122
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=40.52 E-value=41 Score=19.21 Aligned_cols=27 Identities=15% Similarity=0.154 Sum_probs=17.6
Q ss_pred eeeeCCCCceeeEEeEEEEE--------eeCCCCc
Q 036150 7 VLRRKRTKKYAVKRKAVGIW--------SCKYCGK 33 (77)
Q Consensus 7 ~~~~~~CGK~~VKR~AVGIW--------kCkkCgk 33 (77)
+..||-||...+.-.....+ .|..||.
T Consensus 3 LkPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 3 LKPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CcCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 56799999887554433221 2888876
No 123
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=39.74 E-value=17 Score=24.22 Aligned_cols=24 Identities=8% Similarity=-0.024 Sum_probs=14.1
Q ss_pred eeeeCCCCceeeEEeEEEEEeeCCCC
Q 036150 7 VLRRKRTKKYAVKRKAVGIWSCKYCG 32 (77)
Q Consensus 7 ~~~~~~CGK~~VKR~AVGIWkCkkCg 32 (77)
+.+|++||+.--... -.+.|.+||
T Consensus 70 ~~~C~~Cg~~~~~~~--~~~~CP~Cg 93 (113)
T PRK12380 70 QAWCWDCSQVVEIHQ--HDAQCPHCH 93 (113)
T ss_pred EEEcccCCCEEecCC--cCccCcCCC
Confidence 467888885532211 234588887
No 124
>COG2158 Uncharacterized protein containing a Zn-finger-like domain [General function prediction only]
Probab=39.49 E-value=18 Score=25.58 Aligned_cols=26 Identities=19% Similarity=0.418 Sum_probs=17.0
Q ss_pred eeCCCCceeeEEeEEE--EEeeCCCCcE
Q 036150 9 RRKRTKKYAVKRKAVG--IWSCKYCGKV 34 (77)
Q Consensus 9 ~~~~CGK~~VKR~AVG--IWkCkkCgkt 34 (77)
-|-|++-...++..-| ||.|..|.-.
T Consensus 44 pc~~~~~gewi~~~~G~~VwSC~dC~~i 71 (112)
T COG2158 44 PCENEELGEWISDSNGRKVWSCSDCHWI 71 (112)
T ss_pred cccccccCceeEcCCCCEEeecccccee
Confidence 3455555555555556 9999999643
No 125
>PLN03086 PRLI-interacting factor K; Provisional
Probab=39.09 E-value=15 Score=31.41 Aligned_cols=32 Identities=13% Similarity=0.096 Sum_probs=26.0
Q ss_pred eeeeeeCC--CCceeeEEeEEEEEeeCCCCcEEe
Q 036150 5 YRVLRRKR--TKKYAVKRKAVGIWSCKYCGKVKA 36 (77)
Q Consensus 5 ~~~~~~~~--CGK~~VKR~AVGIWkCkkCgkt~A 36 (77)
|....||+ ||..-.++.----|+|..|++.+.
T Consensus 431 r~~V~Cp~~~Cg~v~~r~el~~H~~C~~Cgk~f~ 464 (567)
T PLN03086 431 RHNVVCPHDGCGIVLRVEEAKNHVHCEKCGQAFQ 464 (567)
T ss_pred CcceeCCcccccceeeccccccCccCCCCCCccc
Confidence 34566885 999888888888999999999873
No 126
>PRK14873 primosome assembly protein PriA; Provisional
Probab=38.76 E-value=21 Score=30.39 Aligned_cols=26 Identities=23% Similarity=0.406 Sum_probs=10.3
Q ss_pred eeeCCCCceeeEEeEEEEEeeCCCCc
Q 036150 8 LRRKRTKKYAVKRKAVGIWSCKYCGK 33 (77)
Q Consensus 8 ~~~~~CGK~~VKR~AVGIWkCkkCgk 33 (77)
.+||||+-.=+-....+.=+|..||+
T Consensus 393 ~~C~~C~~~L~~h~~~~~l~Ch~CG~ 418 (665)
T PRK14873 393 ARCRHCTGPLGLPSAGGTPRCRWCGR 418 (665)
T ss_pred eECCCCCCceeEecCCCeeECCCCcC
Confidence 34444443322222333444444444
No 127
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=38.76 E-value=11 Score=19.70 Aligned_cols=16 Identities=19% Similarity=0.509 Sum_probs=9.8
Q ss_pred EeeCCCCcEEeCc-ccc
Q 036150 26 WSCKYCGKVKAGA-LNA 41 (77)
Q Consensus 26 WkCkkCgkt~AGG-AYt 41 (77)
|+|.-|++++-|- .|.
T Consensus 1 ~~C~~C~~~~~~~~~Y~ 17 (30)
T PF03107_consen 1 FWCDVCRRKIDGFYFYH 17 (30)
T ss_pred CCCCCCCCCcCCCEeEE
Confidence 5666666666665 443
No 128
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=38.21 E-value=25 Score=24.04 Aligned_cols=15 Identities=20% Similarity=0.570 Sum_probs=12.6
Q ss_pred EEEeeCCCCcEEeCc
Q 036150 24 GIWSCKYCGKVKAGA 38 (77)
Q Consensus 24 GIWkCkkCgkt~AGG 38 (77)
..|.|..||+.+.-.
T Consensus 69 ~~~~C~~CG~~~~~~ 83 (135)
T PRK03824 69 AVLKCRNCGNEWSLK 83 (135)
T ss_pred eEEECCCCCCEEecc
Confidence 789999999888764
No 129
>PF01921 tRNA-synt_1f: tRNA synthetases class I (K); InterPro: IPR002904 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and in a number of bacterial groups that include the alphaproteobacteria and spirochaetes[]. A refined crystal structures shows that the active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [].; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IRX_A.
Probab=38.15 E-value=29 Score=28.01 Aligned_cols=28 Identities=11% Similarity=0.278 Sum_probs=15.4
Q ss_pred eeeCCCCc-eeeEEeEEE------EEeeCCCCcEE
Q 036150 8 LRRKRTKK-YAVKRKAVG------IWSCKYCGKVK 35 (77)
Q Consensus 8 ~~~~~CGK-~~VKR~AVG------IWkCkkCgkt~ 35 (77)
-.|++||| +.++=..+- -++|..||...
T Consensus 175 piC~~cGri~tt~v~~~d~~~~~v~Y~c~~cG~~g 209 (360)
T PF01921_consen 175 PICEKCGRIDTTEVTEYDPEGGTVTYRCEECGHEG 209 (360)
T ss_dssp EEETTTEE--EEEEEEE--SSSEEEEE--TTS---
T ss_pred eeccccCCcccceeeEeecCCCEEEEEecCCCCEE
Confidence 35899999 455444443 69999999864
No 130
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=37.96 E-value=25 Score=19.55 Aligned_cols=11 Identities=27% Similarity=0.800 Sum_probs=8.5
Q ss_pred EeeCCCCcEEe
Q 036150 26 WSCKYCGKVKA 36 (77)
Q Consensus 26 WkCkkCgkt~A 36 (77)
|.|.+||+++-
T Consensus 2 r~C~~Cg~~Yh 12 (36)
T PF05191_consen 2 RICPKCGRIYH 12 (36)
T ss_dssp EEETTTTEEEE
T ss_pred cCcCCCCCccc
Confidence 67889988753
No 131
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=37.80 E-value=12 Score=18.48 Aligned_cols=11 Identities=36% Similarity=1.054 Sum_probs=8.3
Q ss_pred EEEeeCCCCcE
Q 036150 24 GIWSCKYCGKV 34 (77)
Q Consensus 24 GIWkCkkCgkt 34 (77)
|-|.|..|+..
T Consensus 1 g~W~C~~C~~~ 11 (26)
T smart00547 1 GDWECPACTFL 11 (26)
T ss_pred CcccCCCCCCc
Confidence 56999998753
No 132
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 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 predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=37.06 E-value=24 Score=19.05 Aligned_cols=17 Identities=41% Similarity=0.649 Sum_probs=10.1
Q ss_pred EEEEEeeCCCCcEEeCc
Q 036150 22 AVGIWSCKYCGKVKAGA 38 (77)
Q Consensus 22 AVGIWkCkkCgkt~AGG 38 (77)
.....+|+.|++++.++
T Consensus 13 ~~~~a~C~~C~~~~~~~ 29 (45)
T PF02892_consen 13 DKKKAKCKYCGKVIKYS 29 (45)
T ss_dssp CSS-EEETTTTEE----
T ss_pred CcCeEEeCCCCeEEeeC
Confidence 34678999999999986
No 133
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=37.06 E-value=30 Score=25.92 Aligned_cols=25 Identities=20% Similarity=0.376 Sum_probs=17.6
Q ss_pred eeCCCCceeeEEeEE---EEEeeCCCCcE
Q 036150 9 RRKRTKKYAVKRKAV---GIWSCKYCGKV 34 (77)
Q Consensus 9 ~~~~CGK~~VKR~AV---GIWkCkkCgkt 34 (77)
.||+||.. |+|..+ +.|-|..|-+.
T Consensus 237 pC~~Cg~~-I~~~~~~gR~ty~Cp~CQ~~ 264 (269)
T PRK14811 237 PCPRCGTP-IEKIVVGGRGTHFCPQCQPL 264 (269)
T ss_pred CCCcCCCe-eEEEEECCCCcEECCCCcCC
Confidence 58899855 555554 48999999653
No 134
>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=36.28 E-value=6 Score=21.86 Aligned_cols=7 Identities=43% Similarity=1.270 Sum_probs=3.0
Q ss_pred eeCCCCc
Q 036150 27 SCKYCGK 33 (77)
Q Consensus 27 kCkkCgk 33 (77)
+|+.||.
T Consensus 19 rC~~CG~ 25 (32)
T PF03604_consen 19 RCPECGH 25 (32)
T ss_dssp SBSSSS-
T ss_pred ECCcCCC
Confidence 4555543
No 135
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=35.73 E-value=26 Score=29.17 Aligned_cols=22 Identities=23% Similarity=0.394 Sum_probs=17.2
Q ss_pred eeeCCCCceeeEEeEEEEEeeCCCCc
Q 036150 8 LRRKRTKKYAVKRKAVGIWSCKYCGK 33 (77)
Q Consensus 8 ~~~~~CGK~~VKR~AVGIWkCkkCgk 33 (77)
.||.|||-..- +=-|+|.+|++
T Consensus 355 YRC~~CGF~a~----~l~W~CPsC~~ 376 (389)
T COG2956 355 YRCQNCGFTAH----TLYWHCPSCRA 376 (389)
T ss_pred ceecccCCcce----eeeeeCCCccc
Confidence 37999998653 35799999985
No 136
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=35.67 E-value=38 Score=22.73 Aligned_cols=29 Identities=24% Similarity=0.382 Sum_probs=17.9
Q ss_pred eeeeCCCCcee--eEEeE-EEEEeeCCCCcEE
Q 036150 7 VLRRKRTKKYA--VKRKA-VGIWSCKYCGKVK 35 (77)
Q Consensus 7 ~~~~~~CGK~~--VKR~A-VGIWkCkkCgkt~ 35 (77)
+.+|.+|+... ++|.- +....|++|+-.+
T Consensus 112 ~y~C~~C~~~~~~~rr~~~~~~y~C~~C~g~l 143 (146)
T smart00731 112 PYRCTGCGQRYLRVRRSNNVSRYRCGKCGGKL 143 (146)
T ss_pred EEECCCCCCCCceEccccCcceEEcCCCCCEE
Confidence 45677787753 44432 2677888887654
No 137
>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=34.97 E-value=29 Score=28.62 Aligned_cols=40 Identities=15% Similarity=0.092 Sum_probs=30.6
Q ss_pred eeeeeCCCCceeeEE-----------eEEEEEeeCCCCcEEe---------Ccccccccc
Q 036150 6 RVLRRKRTKKYAVKR-----------KAVGIWSCKYCGKVKA---------GALNAATLA 45 (77)
Q Consensus 6 ~~~~~~~CGK~~VKR-----------~AVGIWkCkkCgkt~A---------GGAYtp~Tp 45 (77)
-.+.||+||...+=+ ...-.+.|.+||..+- .|-|.++-|
T Consensus 199 ~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e~~k~~m~~~G~Wv~~~~ 258 (557)
T PF05876_consen 199 YYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEEHDKRRMVRRGRWVATNP 258 (557)
T ss_pred EEccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCHHHHhhccCCeEEEeccc
Confidence 357899999875322 2346789999998775 799999888
No 138
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=34.84 E-value=24 Score=28.66 Aligned_cols=30 Identities=23% Similarity=0.407 Sum_probs=17.1
Q ss_pred eeeeCCCCceeeEEeEEEEEeeCCCCcEEe
Q 036150 7 VLRRKRTKKYAVKRKAVGIWSCKYCGKVKA 36 (77)
Q Consensus 7 ~~~~~~CGK~~VKR~AVGIWkCkkCgkt~A 36 (77)
+.+||||+-.=+--...+.=+|..||++..
T Consensus 222 ~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~ 251 (505)
T TIGR00595 222 ILCCPNCDVSLTYHKKEGKLRCHYCGYQEP 251 (505)
T ss_pred ccCCCCCCCceEEecCCCeEEcCCCcCcCC
Confidence 456677764433333445556777776654
No 139
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=34.72 E-value=34 Score=25.66 Aligned_cols=23 Identities=13% Similarity=0.316 Sum_probs=16.5
Q ss_pred eeCCCCceeeEEeEE---EEEeeCCCC
Q 036150 9 RRKRTKKYAVKRKAV---GIWSCKYCG 32 (77)
Q Consensus 9 ~~~~CGK~~VKR~AV---GIWkCkkCg 32 (77)
.||+||.. |++..+ +.|-|..|-
T Consensus 256 pC~~Cg~~-I~~~~~~gR~t~~CP~CQ 281 (282)
T PRK13945 256 PCRKCGTP-IERIKLAGRSTHWCPNCQ 281 (282)
T ss_pred CCCcCCCe-eEEEEECCCccEECCCCc
Confidence 58899964 555544 488899885
No 140
>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=34.51 E-value=16 Score=29.34 Aligned_cols=11 Identities=36% Similarity=1.017 Sum_probs=5.3
Q ss_pred EEeeCCCCcEE
Q 036150 25 IWSCKYCGKVK 35 (77)
Q Consensus 25 IWkCkkCgkt~ 35 (77)
-|+|+.|++..
T Consensus 285 FFkC~~C~~Rt 295 (344)
T PF09332_consen 285 FFKCKDCGNRT 295 (344)
T ss_dssp EEE-T-TS-EE
T ss_pred eEECCCCCCee
Confidence 47777777653
No 141
>PF05899 Cupin_3: Protein of unknown function (DUF861); InterPro: IPR008579 The function of the proteins in this entry are unknown. They contain the conserved barrel domain of the 'cupin' superfamily and members are specific to plants and bacteria.; PDB: 1RC6_A 3MYX_A 1O5U_A 2K9Z_A 1LKN_A 3ES4_A 1SFN_B 3BCW_A.
Probab=34.51 E-value=20 Score=21.68 Aligned_cols=17 Identities=18% Similarity=0.337 Sum_probs=12.1
Q ss_pred EeEEEEEeeCCCCcEEe
Q 036150 20 RKAVGIWSCKYCGKVKA 36 (77)
Q Consensus 20 R~AVGIWkCkkCgkt~A 36 (77)
+..+|||+|......+.
T Consensus 6 ~~~~g~w~~~pg~~~~~ 22 (74)
T PF05899_consen 6 VFSAGVWECTPGKFPWP 22 (74)
T ss_dssp SEEEEEEEEECEEEEEE
T ss_pred CEEEEEEEECCceeEee
Confidence 35679999988665443
No 142
>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=34.11 E-value=30 Score=18.13 Aligned_cols=25 Identities=16% Similarity=0.133 Sum_probs=12.2
Q ss_pred eCCCCceeeEEeEEEEEeeCCCCcE
Q 036150 10 RKRTKKYAVKRKAVGIWSCKYCGKV 34 (77)
Q Consensus 10 ~~~CGK~~VKR~AVGIWkCkkCgkt 34 (77)
|++||...+.-.+---=.|..|+..
T Consensus 6 C~~CG~~t~~~~~g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 6 CGRCGAPTKPAPGGWARRCPSCGHE 30 (32)
T ss_dssp -TTT--BEEE-SSSS-EEESSSS-E
T ss_pred cCcCCccccCCCCcCEeECCCCcCE
Confidence 6777777666555444467777754
No 143
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=34.11 E-value=30 Score=28.59 Aligned_cols=24 Identities=13% Similarity=0.005 Sum_probs=12.1
Q ss_pred eeeeeCCCCceeeEEeEEEEEeeCCCCcE
Q 036150 6 RVLRRKRTKKYAVKRKAVGIWSCKYCGKV 34 (77)
Q Consensus 6 ~~~~~~~CGK~~VKR~AVGIWkCkkCgkt 34 (77)
.+-.|++||.... +-++|.+||..
T Consensus 490 ~~~~C~~CG~~~~-----~~~~CP~CGs~ 513 (546)
T PF13597_consen 490 PIDICPDCGYIGG-----EGDKCPKCGSE 513 (546)
T ss_dssp -EEEETTT---S-------EEE-CCC---
T ss_pred CcccccCCCcCCC-----CCCCCCCCCCc
Confidence 3568999998653 47999999987
No 144
>PRK06260 threonine synthase; Validated
Probab=34.05 E-value=18 Score=27.94 Aligned_cols=23 Identities=26% Similarity=0.366 Sum_probs=15.8
Q ss_pred eeeCCCCceeeEEeEEEEEeeCCCC
Q 036150 8 LRRKRTKKYAVKRKAVGIWSCKYCG 32 (77)
Q Consensus 8 ~~~~~CGK~~VKR~AVGIWkCkkCg 32 (77)
|+|.+||+.-= .-.-.|.|..|+
T Consensus 4 ~~C~~cg~~~~--~~~~~~~Cp~cg 26 (397)
T PRK06260 4 LKCIECGKEYD--PDEIIYTCPECG 26 (397)
T ss_pred EEECCCCCCCC--CCCccccCCCCC
Confidence 88999998731 112368898896
No 145
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=34.02 E-value=21 Score=22.82 Aligned_cols=36 Identities=19% Similarity=0.250 Sum_probs=17.1
Q ss_pred eeeeeeeCCCCce--eeEEe-EEEEEeeCCCCcEEeCccccc
Q 036150 4 YYRVLRRKRTKKY--AVKRK-AVGIWSCKYCGKVKAGALNAA 42 (77)
Q Consensus 4 ~~~~~~~~~CGK~--~VKR~-AVGIWkCkkCgkt~AGGAYtp 42 (77)
.|+ .+||.|+-. ++.=. .-|+|+|-.||+ .|.+..+
T Consensus 31 ~~~-~~CPfH~d~~pS~~i~~~k~~~~Cf~Cg~--~Gd~i~~ 69 (97)
T PF01807_consen 31 EYR-CLCPFHDDKTPSFSINPDKNRFKCFGCGK--GGDVIDF 69 (97)
T ss_dssp EEE-E--SSS--SS--EEEETTTTEEEETTT----EE-HHHH
T ss_pred eEE-EECcCCCCCCCceEEECCCCeEEECCCCC--CCcHHhH
Confidence 344 458888754 22221 348999999995 4555544
No 146
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=33.74 E-value=14 Score=30.44 Aligned_cols=27 Identities=11% Similarity=0.119 Sum_probs=19.3
Q ss_pred eeeeeeeCCCCceeeEEeEEEEEeeCCCCcE
Q 036150 4 YYRVLRRKRTKKYAVKRKAVGIWSCKYCGKV 34 (77)
Q Consensus 4 ~~~~~~~~~CGK~~VKR~AVGIWkCkkCgkt 34 (77)
+..+..|++||.... +. .|+|.+||..
T Consensus 515 ~~p~~~C~~CG~~~~-~~---~~~CP~CGs~ 541 (555)
T cd01675 515 NTPIDICNDCGYIGE-GE---GFKCPKCGSE 541 (555)
T ss_pred ecCCccCCCCCCCCc-CC---CCCCcCCCCc
Confidence 345678999998543 22 4999999964
No 147
>COG1773 Rubredoxin [Energy production and conversion]
Probab=33.64 E-value=27 Score=21.72 Aligned_cols=11 Identities=45% Similarity=1.192 Sum_probs=9.3
Q ss_pred EEeeCCCCcEE
Q 036150 25 IWSCKYCGKVK 35 (77)
Q Consensus 25 IWkCkkCgkt~ 35 (77)
-|+|+-||.++
T Consensus 3 ~~~C~~CG~vY 13 (55)
T COG1773 3 RWRCSVCGYVY 13 (55)
T ss_pred ceEecCCceEe
Confidence 49999999875
No 148
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=33.40 E-value=51 Score=23.43 Aligned_cols=35 Identities=14% Similarity=0.258 Sum_probs=21.9
Q ss_pred eeCCCCceeeEE-----------eEEEEEeeCCCCcEE----eCcccccc
Q 036150 9 RRKRTKKYAVKR-----------KAVGIWSCKYCGKVK----AGALNAAT 43 (77)
Q Consensus 9 ~~~~CGK~~VKR-----------~AVGIWkCkkCgkt~----AGGAYtp~ 43 (77)
.||+||+...-| +-.==..|.+||++. .||+..|.
T Consensus 2 ~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~ev~~~~~~~p~ 51 (160)
T smart00709 2 DCPSCGGNGTTRMLLTSIPYFREVIIMSFECEHCGYRNNEVKSGGAIEPK 51 (160)
T ss_pred cCCCCCCCCEEEEEEecCCCcceEEEEEEECCCCCCccceEEECcccCCC
Confidence 489997654322 223348999999863 56665553
No 149
>PF12773 DZR: Double zinc ribbon
Probab=33.36 E-value=9.2 Score=21.22 Aligned_cols=30 Identities=10% Similarity=-0.007 Sum_probs=19.4
Q ss_pred eeeCCCCceeeEEeEEEEEeeCCCCcEEeCc
Q 036150 8 LRRKRTKKYAVKRKAVGIWSCKYCGKVKAGA 38 (77)
Q Consensus 8 ~~~~~CGK~~VKR~AVGIWkCkkCgkt~AGG 38 (77)
..+++||..-. +.-...+.|.+|+..+..+
T Consensus 13 ~fC~~CG~~l~-~~~~~~~~C~~Cg~~~~~~ 42 (50)
T PF12773_consen 13 KFCPHCGTPLP-PPDQSKKICPNCGAENPPN 42 (50)
T ss_pred cCChhhcCChh-hccCCCCCCcCCcCCCcCC
Confidence 45777777654 4444567888888765433
No 150
>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=33.26 E-value=33 Score=26.75 Aligned_cols=28 Identities=18% Similarity=0.342 Sum_probs=20.6
Q ss_pred eeeCCCCceeeE------E----eEEEEEeeCCCCcEE
Q 036150 8 LRRKRTKKYAVK------R----KAVGIWSCKYCGKVK 35 (77)
Q Consensus 8 ~~~~~CGK~~VK------R----~AVGIWkCkkCgkt~ 35 (77)
+.|++||+..+- | --+-++.|..||..|
T Consensus 259 ~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w 296 (299)
T TIGR01385 259 FTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRW 296 (299)
T ss_pred ccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCee
Confidence 679999988652 2 126688999999865
No 151
>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=33.12 E-value=54 Score=18.19 Aligned_cols=29 Identities=17% Similarity=0.266 Sum_probs=19.3
Q ss_pred eeeeCCCCceeeEEeEE--EEEeeCC---CCcEE
Q 036150 7 VLRRKRTKKYAVKRKAV--GIWSCKY---CGKVK 35 (77)
Q Consensus 7 ~~~~~~CGK~~VKR~AV--GIWkCkk---Cgkt~ 35 (77)
|-.||.||..=|.|.+- =.|.|.. |..+.
T Consensus 1 ~~~CP~Cg~~lv~r~~k~g~F~~Cs~yP~C~~~~ 34 (39)
T PF01396_consen 1 VEKCPKCGGPLVLRRGKKGKFLGCSNYPECKYTE 34 (39)
T ss_pred CcCCCCCCceeEEEECCCCCEEECCCCCCcCCeE
Confidence 34689999876666633 3678865 66553
No 152
>PRK08173 DNA topoisomerase III; Validated
Probab=33.10 E-value=24 Score=30.98 Aligned_cols=26 Identities=8% Similarity=0.083 Sum_probs=19.0
Q ss_pred eeeCCCCceeeEEeEEEEEeeCCCCcEE
Q 036150 8 LRRKRTKKYAVKRKAVGIWSCKYCGKVK 35 (77)
Q Consensus 8 ~~~~~CGK~~VKR~AVGIWkCkkCgkt~ 35 (77)
-.||+||+.-+++ -+-|.|..|+.++
T Consensus 625 ~~CP~Cg~~~~~~--~~~~~Cs~C~f~~ 650 (862)
T PRK08173 625 TPCPNCGGVVKEN--YRRFACTKCDFSI 650 (862)
T ss_pred ccCCccccccccc--CceeEcCCCCccc
Confidence 4699999864433 3449999998765
No 153
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=32.78 E-value=24 Score=17.99 Aligned_cols=10 Identities=30% Similarity=0.869 Sum_probs=7.5
Q ss_pred eeCCCCcEEe
Q 036150 27 SCKYCGKVKA 36 (77)
Q Consensus 27 kCkkCgkt~A 36 (77)
.|..||++|.
T Consensus 4 ~C~~CgR~F~ 13 (25)
T PF13913_consen 4 PCPICGRKFN 13 (25)
T ss_pred cCCCCCCEEC
Confidence 4788888874
No 154
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=32.47 E-value=32 Score=21.18 Aligned_cols=23 Identities=22% Similarity=0.580 Sum_probs=16.9
Q ss_pred eeeeeCCCCceeeEEeEEEEEeeCCCCcE
Q 036150 6 RVLRRKRTKKYAVKRKAVGIWSCKYCGKV 34 (77)
Q Consensus 6 ~~~~~~~CGK~~VKR~AVGIWkCkkCgkt 34 (77)
++-.|++||...+|- .|..||..
T Consensus 4 ~mr~C~~CgvYTLk~------~CP~CG~~ 26 (56)
T PRK13130 4 KIRKCPKCGVYTLKE------ICPVCGGK 26 (56)
T ss_pred cceECCCCCCEEccc------cCcCCCCC
Confidence 566789999999854 37777754
No 155
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=32.34 E-value=40 Score=25.21 Aligned_cols=23 Identities=22% Similarity=0.345 Sum_probs=16.6
Q ss_pred eeCCCCceeeEEeEEE---EEeeCCCC
Q 036150 9 RRKRTKKYAVKRKAVG---IWSCKYCG 32 (77)
Q Consensus 9 ~~~~CGK~~VKR~AVG---IWkCkkCg 32 (77)
.||+|| ..|+|..+| -|-|..|-
T Consensus 246 pCprCG-~~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 246 PCLNCK-TPIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred cCCCCC-CeeEEEEECCCccEECcCCc
Confidence 578998 566666654 77888874
No 156
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=32.25 E-value=28 Score=22.09 Aligned_cols=21 Identities=24% Similarity=0.637 Sum_probs=16.6
Q ss_pred eeeCCCCceeeEEeEEEEEeeCCCCcE
Q 036150 8 LRRKRTKKYAVKRKAVGIWSCKYCGKV 34 (77)
Q Consensus 8 ~~~~~CGK~~VKR~AVGIWkCkkCgkt 34 (77)
-+|++||...+| + +|..||..
T Consensus 6 rkC~~cg~YTLk-e-----~Cp~CG~~ 26 (59)
T COG2260 6 RKCPKCGRYTLK-E-----KCPVCGGD 26 (59)
T ss_pred hcCcCCCceeec-c-----cCCCCCCc
Confidence 368899999998 3 58889854
No 157
>PF13842 Tnp_zf-ribbon_2: DDE_Tnp_1-like zinc-ribbon
Probab=32.16 E-value=30 Score=18.73 Aligned_cols=22 Identities=23% Similarity=0.428 Sum_probs=17.0
Q ss_pred eeCCCCceeeEEeEEEEEeeCCCC
Q 036150 9 RRKRTKKYAVKRKAVGIWSCKYCG 32 (77)
Q Consensus 9 ~~~~CGK~~VKR~AVGIWkCkkCg 32 (77)
|++-|-+.++++. =.|.|..|+
T Consensus 2 rC~vC~~~k~rk~--T~~~C~~C~ 23 (32)
T PF13842_consen 2 RCKVCSKKKRRKD--TRYMCSKCD 23 (32)
T ss_pred CCeECCcCCccce--eEEEccCCC
Confidence 5677888777776 579999997
No 158
>cd06968 NR_DBD_ROR DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. DNA-binding domain of Retinoid-related orphan receptors (RORs) is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. ROR interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. RORS are key regulators of many physiological processes during embryonic development. RORs bind as monomers to specific ROR response elements (ROREs) consisting of the consensus core motif AGGTCA preceded by a 5-bp A/T-rich sequence. There are three subtypes of retinoid-related orphan receptors (RORs), alpha, beta, and gamma, which differ only in N-terminal sequence and are distributed in distinct tissues. RORalpha plays a key role in the development of the cerebellum particularly in the regulation of the maturation and survival of Purkinje cells. RORbe
Probab=31.94 E-value=20 Score=23.39 Aligned_cols=30 Identities=17% Similarity=0.248 Sum_probs=22.2
Q ss_pred ceeeeeeeCCCCceeeEEeEEEEEeeCCCCc
Q 036150 3 SYYRVLRRKRTKKYAVKRKAVGIWSCKYCGK 33 (77)
Q Consensus 3 ~~~~~~~~~~CGK~~VKR~AVGIWkCkkCgk 33 (77)
+|..+..|.-||....- .-.|.|.|..|.-
T Consensus 1 ~~~~~~~C~VCg~~~~g-~hyGv~sC~aC~~ 30 (95)
T cd06968 1 AQIEVIPCKICGDKSSG-IHYGVITCEGCKG 30 (95)
T ss_pred CCccccCCcccCCcCcc-eEECceeehhhHH
Confidence 46667788889876644 4588899988864
No 159
>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=31.90 E-value=58 Score=20.45 Aligned_cols=17 Identities=29% Similarity=0.653 Sum_probs=13.5
Q ss_pred EEEEEeeCCCCcEEeCc
Q 036150 22 AVGIWSCKYCGKVKAGA 38 (77)
Q Consensus 22 AVGIWkCkkCgkt~AGG 38 (77)
.+-.|.|..||..+...
T Consensus 28 ~~~~~~C~~CGe~~~~~ 44 (127)
T TIGR03830 28 GVPGWYCPACGEELLDP 44 (127)
T ss_pred eeeeeECCCCCCEEEcH
Confidence 56789999999987543
No 160
>PHA02998 RNA polymerase subunit; Provisional
Probab=31.83 E-value=48 Score=25.38 Aligned_cols=28 Identities=18% Similarity=0.209 Sum_probs=20.2
Q ss_pred eeCCCCceeeE------Ee----EEEEEeeCCCCcEEe
Q 036150 9 RRKRTKKYAVK------RK----AVGIWSCKYCGKVKA 36 (77)
Q Consensus 9 ~~~~CGK~~VK------R~----AVGIWkCkkCgkt~A 36 (77)
+||+||....- |. .+--.+|..||+.|-
T Consensus 145 ~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wk 182 (195)
T PHA02998 145 PCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFK 182 (195)
T ss_pred CCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccC
Confidence 57999988654 22 256779999998764
No 161
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=31.81 E-value=19 Score=31.16 Aligned_cols=25 Identities=20% Similarity=0.399 Sum_probs=19.8
Q ss_pred eeCCCCceeeEEeEEEEEeeCCCCcEE
Q 036150 9 RRKRTKKYAVKRKAVGIWSCKYCGKVK 35 (77)
Q Consensus 9 ~~~~CGK~~VKR~AVGIWkCkkCgkt~ 35 (77)
.||.||. .+.++. |=..|+.||+..
T Consensus 726 ~Cp~Cg~-~l~~~~-GC~~C~~CG~sk 750 (752)
T PRK08665 726 ACPECGS-ILEHEE-GCVVCHSCGYSK 750 (752)
T ss_pred CCCCCCc-ccEECC-CCCcCCCCCCCC
Confidence 5999994 566665 888999999854
No 162
>PF04135 Nop10p: Nucleolar RNA-binding protein, Nop10p family; InterPro: IPR007264 H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs. More than 100 mammalian H/ACA RNAs form an equal number of ribonucleoproteins (RNPs) by associating with the same four core proteins: Cbf5, Gar1, Nhp2 and Nop10. The function of these H/ACA RNPs is essential for biogenesis of the ribosome, splicing of precursor mRNAs (pre-mRNAs), maintenance of telomeres and probably for additional cellular processes []. Recent crystal structures of archaeal H/ACA protein complexes show how the same four proteins accommodate >100 distinct but related H/ACA RNAs []. The complex contains a stable core composed of Cbf5 and Nop10, to which Gar1 and Nhp2 subsequently bind, the complex interacts with snoRNAs []. In eukaryotes Nop10 is a nucleolar protein that is specifically associated with H/ACA snoRNAs. It is essential for normal 18S rRNA production and rRNA pseudouridylation by the ribonucleoprotein particles containing H/ACA snoRNAs (H/ACA snoRNPs). Nop10 is probably necessary for the stability of these RNPs [].; PDB: 2RFK_B 3LWR_B 2HVY_C 3HAX_C 3MQK_B 3LWO_B 3LWV_B 3HAY_C 3HJY_B 2EY4_E ....
Probab=31.77 E-value=33 Score=20.99 Aligned_cols=24 Identities=25% Similarity=0.602 Sum_probs=18.2
Q ss_pred eeeeeeCCCCceeeEEeEEEEEeeCCCCcE
Q 036150 5 YRVLRRKRTKKYAVKRKAVGIWSCKYCGKV 34 (77)
Q Consensus 5 ~~~~~~~~CGK~~VKR~AVGIWkCkkCgkt 34 (77)
|.+.+|++|+...+| . +|.+||..
T Consensus 3 ~~~r~c~~~~~YTLk-~-----~cp~cG~~ 26 (53)
T PF04135_consen 3 YYIRKCPGCRVYTLK-D-----KCPPCGGP 26 (53)
T ss_dssp EEEEECTTTCEEESS-S-----BBTTTSSB
T ss_pred cccccCCCCCcEeCC-C-----ccCCCCCC
Confidence 445689999988888 2 68888764
No 163
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.52 E-value=49 Score=22.58 Aligned_cols=29 Identities=24% Similarity=0.102 Sum_probs=23.6
Q ss_pred eeeCCCCcee--eEEeEEEEEeeCCCCcEEe
Q 036150 8 LRRKRTKKYA--VKRKAVGIWSCKYCGKVKA 36 (77)
Q Consensus 8 ~~~~~CGK~~--VKR~AVGIWkCkkCgkt~A 36 (77)
|-||+|+-.- +-|..|-|=.|..|.-++-
T Consensus 2 llCP~C~v~l~~~~rs~vEiD~CPrCrGVWL 32 (88)
T COG3809 2 LLCPICGVELVMSVRSGVEIDYCPRCRGVWL 32 (88)
T ss_pred cccCcCCceeeeeeecCceeeeCCccccEee
Confidence 5699999884 5677889999999986654
No 164
>PLN02569 threonine synthase
Probab=31.36 E-value=23 Score=28.96 Aligned_cols=26 Identities=15% Similarity=0.192 Sum_probs=19.2
Q ss_pred ceeeeeeeCCCCcee-eEEeEEEEEeeCCCC
Q 036150 3 SYYRVLRRKRTKKYA-VKRKAVGIWSCKYCG 32 (77)
Q Consensus 3 ~~~~~~~~~~CGK~~-VKR~AVGIWkCkkCg 32 (77)
+|..-|+|.+||+.- +.. -+|.| .||
T Consensus 45 ~~~~~l~C~~Cg~~y~~~~---~~~~C-~cg 71 (484)
T PLN02569 45 KYVPFLECPLTGEKYSLDE---VVYRS-KSG 71 (484)
T ss_pred ccccccEeCCCCCcCCCcc---ccccC-CCC
Confidence 466679999999874 332 37999 796
No 165
>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=31.32 E-value=30 Score=18.31 Aligned_cols=20 Identities=20% Similarity=0.471 Sum_probs=8.6
Q ss_pred CCceeeEEeEEEEEeeCCCC
Q 036150 13 TKKYAVKRKAVGIWSCKYCG 32 (77)
Q Consensus 13 CGK~~VKR~AVGIWkCkkCg 32 (77)
||..-.-|+-.=...|.+||
T Consensus 4 C~~~i~~r~~~v~f~CPnCG 23 (24)
T PF07754_consen 4 CGRPIAPREQAVPFPCPNCG 23 (24)
T ss_pred CCCcccCcccCceEeCCCCC
Confidence 44443334423344555554
No 166
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=30.89 E-value=29 Score=20.97 Aligned_cols=18 Identities=28% Similarity=0.224 Sum_probs=14.0
Q ss_pred eeCCCCcEEeCccccccc
Q 036150 27 SCKYCGKVKAGALNAATL 44 (77)
Q Consensus 27 kCkkCgkt~AGGAYtp~T 44 (77)
+|++|+++++=|...+-.
T Consensus 9 ~Ck~C~~~I~kg~lRiG~ 26 (82)
T PF00645_consen 9 KCKGCKKKIAKGELRIGK 26 (82)
T ss_dssp BETTTSCBE-TTSEEEEE
T ss_pred cCcccCCcCCCCCEEEEE
Confidence 699999999988877643
No 167
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=30.60 E-value=49 Score=24.58 Aligned_cols=24 Identities=17% Similarity=0.364 Sum_probs=17.3
Q ss_pred eeCCCCceeeEEeEE---EEEeeCCCCc
Q 036150 9 RRKRTKKYAVKRKAV---GIWSCKYCGK 33 (77)
Q Consensus 9 ~~~~CGK~~VKR~AV---GIWkCkkCgk 33 (77)
.||+||.. |+|+-+ +.|-|..|-+
T Consensus 247 pC~~Cg~~-I~~~~~~gR~t~~CP~CQ~ 273 (274)
T PRK01103 247 PCRRCGTP-IEKIKQGGRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCe-eEEEEECCCCcEECcCCCC
Confidence 48999865 555544 5899999865
No 168
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=30.52 E-value=37 Score=18.84 Aligned_cols=25 Identities=20% Similarity=0.303 Sum_probs=13.1
Q ss_pred eCCCCceeeEEeEEE----EEeeCCCCcE
Q 036150 10 RKRTKKYAVKRKAVG----IWSCKYCGKV 34 (77)
Q Consensus 10 ~~~CGK~~VKR~AVG----IWkCkkCgkt 34 (77)
||+||..-..|+-.| =+.|..||.+
T Consensus 3 C~~CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 3 CPQCGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp -TTT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred cccccChhhhhcCCCCCccceECCCCCCE
Confidence 788888865555433 3778888865
No 169
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=30.19 E-value=23 Score=30.66 Aligned_cols=23 Identities=26% Similarity=0.274 Sum_probs=17.1
Q ss_pred eeeeeCCCCceeeEEeEEEEEeeCCCCc
Q 036150 6 RVLRRKRTKKYAVKRKAVGIWSCKYCGK 33 (77)
Q Consensus 6 ~~~~~~~CGK~~VKR~AVGIWkCkkCgk 33 (77)
.+-+|++||-..... |.|.+||.
T Consensus 679 ~~~~C~~CG~~~~~~-----~~CP~CG~ 701 (735)
T PRK07111 679 PVDRCPVCGYLGVIE-----DKCPKCGS 701 (735)
T ss_pred CCeecCCCCCCCCcC-----ccCcCCCC
Confidence 456899999654422 99999995
No 170
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=29.71 E-value=25 Score=20.90 Aligned_cols=12 Identities=25% Similarity=0.899 Sum_probs=10.0
Q ss_pred EEeeCCCCcEEe
Q 036150 25 IWSCKYCGKVKA 36 (77)
Q Consensus 25 IWkCkkCgkt~A 36 (77)
.|.|..||++.-
T Consensus 1 ~y~C~~CgyiYd 12 (50)
T cd00730 1 KYECRICGYIYD 12 (50)
T ss_pred CcCCCCCCeEEC
Confidence 489999999865
No 171
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=29.63 E-value=33 Score=24.95 Aligned_cols=14 Identities=29% Similarity=0.895 Sum_probs=7.0
Q ss_pred EEeeCCCCcEEeCc
Q 036150 25 IWSCKYCGKVKAGA 38 (77)
Q Consensus 25 IWkCkkCgkt~AGG 38 (77)
||.|.+||+.+.-.
T Consensus 48 V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 48 VWVCPHCGYAAFEE 61 (214)
T ss_pred EEECCCCCCccccc
Confidence 45555555544433
No 172
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=29.50 E-value=48 Score=24.76 Aligned_cols=22 Identities=23% Similarity=0.466 Sum_probs=15.0
Q ss_pred eeCCCCceeeEEeEEE---EEeeCCC
Q 036150 9 RRKRTKKYAVKRKAVG---IWSCKYC 31 (77)
Q Consensus 9 ~~~~CGK~~VKR~AVG---IWkCkkC 31 (77)
.||+||.. |+|..+| .|-|..|
T Consensus 247 pC~~Cg~~-I~~~~~~gR~t~~CP~C 271 (272)
T TIGR00577 247 PCRRCGTP-IEKIKVGGRGTHFCPQC 271 (272)
T ss_pred CCCCCCCe-eEEEEECCCCCEECCCC
Confidence 47889855 5555554 7778777
No 173
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=29.06 E-value=66 Score=22.26 Aligned_cols=26 Identities=23% Similarity=0.363 Sum_probs=17.0
Q ss_pred eCCCCc------eeeEEeEE--EEEeeCCCCcEE
Q 036150 10 RKRTKK------YAVKRKAV--GIWSCKYCGKVK 35 (77)
Q Consensus 10 ~~~CGK------~~VKR~AV--GIWkCkkCgkt~ 35 (77)
||+|.. ..--|.-. =+|.|..||...
T Consensus 59 CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~~ 92 (105)
T COG2023 59 CKKCYTPLVPGKNARVRLRKGRVVVTCLECGTIR 92 (105)
T ss_pred ccccCcccccCcceEEEEcCCeEEEEecCCCcEE
Confidence 677765 23334433 489999999764
No 174
>PF05907 DUF866: Eukaryotic protein of unknown function (DUF866); InterPro: IPR008584 This family consists of a number of hypothetical eukaryotic proteins of unknown function with an average length of around 165 residues.; PDB: 1ZSO_B.
Probab=28.43 E-value=1.2e+02 Score=21.48 Aligned_cols=32 Identities=16% Similarity=0.340 Sum_probs=17.6
Q ss_pred ceeeeeeeCCCCceeeEE----------------eEEEEEeeCCCCcE
Q 036150 3 SYYRVLRRKRTKKYAVKR----------------KAVGIWSCKYCGKV 34 (77)
Q Consensus 3 ~~~~~~~~~~CGK~~VKR----------------~AVGIWkCkkCgkt 34 (77)
.||--+.|.+||-..=|. .|-=+|+|+.|++.
T Consensus 26 ~~~fkvkCt~CgE~~~k~V~i~~~e~~e~~gsrG~aNfv~KCk~C~re 73 (161)
T PF05907_consen 26 EWFFKVKCTSCGEVHPKWVYINRFEKHEIPGSRGTANFVMKCKFCKRE 73 (161)
T ss_dssp -EEEEEEETTSS--EEEEEEE-TT-BEE-TTSS-EESEEE--SSSS--
T ss_pred EEEEEEEECCCCCccCcceEeecceEEecCCCccceEeEecCcCcCCc
Confidence 366678899998654333 34447999999874
No 175
>smart00355 ZnF_C2H2 zinc finger.
Probab=28.41 E-value=19 Score=16.04 Aligned_cols=11 Identities=45% Similarity=0.890 Sum_probs=7.5
Q ss_pred eeCCCCcEEeC
Q 036150 27 SCKYCGKVKAG 37 (77)
Q Consensus 27 kCkkCgkt~AG 37 (77)
.|..|++.+..
T Consensus 2 ~C~~C~~~f~~ 12 (26)
T smart00355 2 RCPECGKVFKS 12 (26)
T ss_pred CCCCCcchhCC
Confidence 57778777653
No 176
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=28.27 E-value=52 Score=21.51 Aligned_cols=30 Identities=17% Similarity=0.263 Sum_probs=18.2
Q ss_pred eeeeeCCCCceeeEEe--EEEEEeeCCCCcEE
Q 036150 6 RVLRRKRTKKYAVKRK--AVGIWSCKYCGKVK 35 (77)
Q Consensus 6 ~~~~~~~CGK~~VKR~--AVGIWkCkkCgkt~ 35 (77)
.+.+|++|+..-.++. ...=..|+.|+-.+
T Consensus 122 ~~~~C~~C~~~~~r~~~~~~~~~~C~~C~~~l 153 (157)
T PF10263_consen 122 YVYRCPSCGREYKRHRRSKRKRYRCGRCGGPL 153 (157)
T ss_pred eEEEcCCCCCEeeeecccchhhEECCCCCCEE
Confidence 3567888886643332 23346788887544
No 177
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=28.15 E-value=26 Score=29.99 Aligned_cols=37 Identities=24% Similarity=0.255 Sum_probs=29.6
Q ss_pred eeCCCCceeeEEe-EEEEEeeCCCCcEEeCcccccccc
Q 036150 9 RRKRTKKYAVKRK-AVGIWSCKYCGKVKAGALNAATLA 45 (77)
Q Consensus 9 ~~~~CGK~~VKR~-AVGIWkCkkCgkt~AGGAYtp~Tp 45 (77)
+|+|||+..+.|. +.|==.|..||.+.=--++.-+..
T Consensus 2 ~C~~C~~s~fe~d~a~g~~~C~~CG~v~E~~~ivsev~ 39 (521)
T KOG1598|consen 2 VCKNCGGSNFERDEATGNLYCTACGTVLEYNNIVAEVT 39 (521)
T ss_pred cCCCCCCCCcccccccCCceeccccceeeccceeEEee
Confidence 6999999997665 899999999998876666655433
No 178
>PRK02935 hypothetical protein; Provisional
Probab=28.04 E-value=40 Score=23.74 Aligned_cols=23 Identities=17% Similarity=0.322 Sum_probs=16.1
Q ss_pred eeeeCCCCcee--eEEeEEEEEeeCCCCc
Q 036150 7 VLRRKRTKKYA--VKRKAVGIWSCKYCGK 33 (77)
Q Consensus 7 ~~~~~~CGK~~--VKR~AVGIWkCkkCgk 33 (77)
.+.||||+|.. ..|+- .|-.|++
T Consensus 70 qV~CP~C~K~TKmLGrvD----~CM~C~~ 94 (110)
T PRK02935 70 QVICPSCEKPTKMLGRVD----ACMHCNQ 94 (110)
T ss_pred eeECCCCCchhhhcccee----ecCcCCC
Confidence 35899999984 45543 5777775
No 179
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=27.44 E-value=18 Score=28.43 Aligned_cols=32 Identities=22% Similarity=0.522 Sum_probs=16.6
Q ss_pred eeeeeeeCCCCceeeEEe--EEE-EEeeCCCCcEE
Q 036150 4 YYRVLRRKRTKKYAVKRK--AVG-IWSCKYCGKVK 35 (77)
Q Consensus 4 ~~~~~~~~~CGK~~VKR~--AVG-IWkCkkCgkt~ 35 (77)
||||.-|-.=|..+.++. -.| |++|..|+...
T Consensus 220 y~Rv~vrv~~~~~~~~~~~~~~g~~~~C~~c~~~~ 254 (382)
T PRK04338 220 YYRVFLKVERGAKKADKALENLGYVYYCPKCLYRE 254 (382)
T ss_pred EEEEEEEEecCHHHHHHHHHhceeEEECCCCCcEE
Confidence 667655544443333221 135 77777777643
No 180
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=26.82 E-value=33 Score=31.91 Aligned_cols=21 Identities=19% Similarity=0.392 Sum_probs=16.1
Q ss_pred eeeCCCCceeeEEeEEEEEeeCCCCcE
Q 036150 8 LRRKRTKKYAVKRKAVGIWSCKYCGKV 34 (77)
Q Consensus 8 ~~~~~CGK~~VKR~AVGIWkCkkCgkt 34 (77)
-+||+||+..++. .|.+||..
T Consensus 626 RKCPkCG~yTlk~------rCP~CG~~ 646 (1095)
T TIGR00354 626 RKCPQCGKESFWL------KCPVCGEL 646 (1095)
T ss_pred EECCCCCcccccc------cCCCCCCc
Confidence 4688999988875 58888865
No 181
>PRK05580 primosome assembly protein PriA; Validated
Probab=26.77 E-value=37 Score=28.52 Aligned_cols=27 Identities=11% Similarity=0.138 Sum_probs=10.9
Q ss_pred eeeCCCCceeeEEeEEEEEeeCCCCcE
Q 036150 8 LRRKRTKKYAVKRKAVGIWSCKYCGKV 34 (77)
Q Consensus 8 ~~~~~CGK~~VKR~AVGIWkCkkCgkt 34 (77)
++||||+-.=+--...+.=.|..||++
T Consensus 391 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~~ 417 (679)
T PRK05580 391 AECPHCDASLTLHRFQRRLRCHHCGYQ 417 (679)
T ss_pred cCCCCCCCceeEECCCCeEECCCCcCC
Confidence 455555543222122333344444443
No 182
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=26.37 E-value=22 Score=32.33 Aligned_cols=31 Identities=16% Similarity=0.296 Sum_probs=0.0
Q ss_pred eeeCCCCceeeEEeE--E-----EEEeeCCCCcEEeCc
Q 036150 8 LRRKRTKKYAVKRKA--V-----GIWSCKYCGKVKAGA 38 (77)
Q Consensus 8 ~~~~~CGK~~VKR~A--V-----GIWkCkkCgkt~AGG 38 (77)
-+||+||+.+.+... - =+|.|..|+..+-.+
T Consensus 656 r~Cp~Cg~~t~~~~Cp~CG~~T~~~~~Cp~C~~~~~~~ 693 (900)
T PF03833_consen 656 RRCPKCGKETFYNRCPECGSHTEPVYVCPDCGIEVEED 693 (900)
T ss_dssp --------------------------------------
T ss_pred ccCcccCCcchhhcCcccCCccccceeccccccccCcc
Confidence 367888888877665 2 367888888776544
No 183
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=25.90 E-value=61 Score=19.63 Aligned_cols=29 Identities=17% Similarity=0.276 Sum_probs=13.8
Q ss_pred eeeeCCCCceeeEEeEEEEEeeCCCCcEE
Q 036150 7 VLRRKRTKKYAVKRKAVGIWSCKYCGKVK 35 (77)
Q Consensus 7 ~~~~~~CGK~~VKR~AVGIWkCkkCgkt~ 35 (77)
+.+|-+||+.--.=+...-=.|..||..+
T Consensus 6 ~Y~C~~Cg~~~~~~~~~~~irCp~Cg~rI 34 (49)
T COG1996 6 EYKCARCGREVELDQETRGIRCPYCGSRI 34 (49)
T ss_pred EEEhhhcCCeeehhhccCceeCCCCCcEE
Confidence 34566666654212222333566666554
No 184
>smart00400 ZnF_CHCC zinc finger.
Probab=25.78 E-value=36 Score=19.45 Aligned_cols=12 Identities=25% Similarity=0.647 Sum_probs=9.9
Q ss_pred EEEEEeeCCCCc
Q 036150 22 AVGIWSCKYCGK 33 (77)
Q Consensus 22 AVGIWkCkkCgk 33 (77)
.-++|+|-.||+
T Consensus 20 ~kn~~~Cf~cg~ 31 (55)
T smart00400 20 DKQFFHCFGCGA 31 (55)
T ss_pred CCCEEEEeCCCC
Confidence 358999999984
No 185
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=25.52 E-value=25 Score=24.31 Aligned_cols=11 Identities=36% Similarity=0.652 Sum_probs=8.8
Q ss_pred eeCCCCcEEeC
Q 036150 27 SCKYCGKVKAG 37 (77)
Q Consensus 27 kCkkCgkt~AG 37 (77)
.|++||+.|-.
T Consensus 60 ~CkkCGfef~~ 70 (97)
T COG3357 60 RCKKCGFEFRD 70 (97)
T ss_pred hhcccCccccc
Confidence 69999998754
No 186
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=25.08 E-value=38 Score=23.96 Aligned_cols=17 Identities=18% Similarity=0.413 Sum_probs=12.7
Q ss_pred EEeeCCCCcEEeCcccc
Q 036150 25 IWSCKYCGKVKAGALNA 41 (77)
Q Consensus 25 IWkCkkCgkt~AGGAYt 41 (77)
|.+|.+|++|+==.-|.
T Consensus 13 IYrC~~C~~TwN~ti~e 29 (142)
T PF06353_consen 13 IYRCEKCDYTWNMTIFE 29 (142)
T ss_pred EEEcccCcCccccceEe
Confidence 77999999987554444
No 187
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=25.05 E-value=56 Score=19.21 Aligned_cols=16 Identities=25% Similarity=0.573 Sum_probs=11.5
Q ss_pred EeeCCCCcEEeCcccc
Q 036150 26 WSCKYCGKVKAGALNA 41 (77)
Q Consensus 26 WkCkkCgkt~AGGAYt 41 (77)
|+|..||++.---.=.
T Consensus 2 y~C~~CgyvYd~~~Gd 17 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKGD 17 (47)
T ss_dssp EEETTTSBEEETTTBB
T ss_pred cCCCCCCEEEcCCcCC
Confidence 8999999886544433
No 188
>COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]
Probab=24.94 E-value=33 Score=29.88 Aligned_cols=16 Identities=31% Similarity=1.124 Sum_probs=13.0
Q ss_pred EeEEEEEeeCCCCcEE
Q 036150 20 RKAVGIWSCKYCGKVK 35 (77)
Q Consensus 20 R~AVGIWkCkkCgkt~ 35 (77)
..-|.||.|.+||..+
T Consensus 125 k~~va~w~c~~cg~~i 140 (593)
T COG2401 125 KEKVALWRCEKCGTII 140 (593)
T ss_pred cceEEEEecchhchhh
Confidence 4557899999999765
No 189
>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=24.62 E-value=55 Score=17.88 Aligned_cols=26 Identities=12% Similarity=0.113 Sum_probs=13.1
Q ss_pred eeCCCCceeeEEeEEEEEeeCCCCcEE
Q 036150 9 RRKRTKKYAVKRKAVGIWSCKYCGKVK 35 (77)
Q Consensus 9 ~~~~CGK~~VKR~AVGIWkCkkCgkt~ 35 (77)
.||.|+..-.- .--.|+.|..|+..+
T Consensus 4 ~Cp~C~se~~y-~D~~~~vCp~C~~ew 29 (30)
T PF08274_consen 4 KCPLCGSEYTY-EDGELLVCPECGHEW 29 (30)
T ss_dssp --TTT-----E-E-SSSEEETTTTEEE
T ss_pred CCCCCCCccee-ccCCEEeCCcccccC
Confidence 46777766544 444688898888765
No 190
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=24.53 E-value=35 Score=23.02 Aligned_cols=25 Identities=16% Similarity=0.364 Sum_probs=13.2
Q ss_pred eeeeCCCCcee-eEEeE---EE-EEeeCCCC
Q 036150 7 VLRRKRTKKYA-VKRKA---VG-IWSCKYCG 32 (77)
Q Consensus 7 ~~~~~~CGK~~-VKR~A---VG-IWkCkkCg 32 (77)
+.+| +||+.. +.... .. .+.|..||
T Consensus 70 ~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cg 99 (124)
T PRK00762 70 EIEC-ECGYEGVVDEDEIDHYAAVIECPVCG 99 (124)
T ss_pred eEEe-eCcCcccccccchhccccCCcCcCCC
Confidence 4678 888662 11010 01 26788887
No 191
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=24.49 E-value=51 Score=18.58 Aligned_cols=13 Identities=46% Similarity=1.004 Sum_probs=10.6
Q ss_pred eeCCCCcEEeCcc
Q 036150 27 SCKYCGKVKAGAL 39 (77)
Q Consensus 27 kCkkCgkt~AGGA 39 (77)
.|+.|++++....
T Consensus 20 ~C~~C~~~l~~~~ 32 (50)
T smart00614 20 KCKYCGKKLSRSS 32 (50)
T ss_pred EecCCCCEeeeCC
Confidence 6999999997543
No 192
>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=24.41 E-value=1.2e+02 Score=24.15 Aligned_cols=27 Identities=19% Similarity=0.306 Sum_probs=18.2
Q ss_pred eeeCCCCceeeEEeEE------EEEeeCCCCcEE
Q 036150 8 LRRKRTKKYAVKRKAV------GIWSCKYCGKVK 35 (77)
Q Consensus 8 ~~~~~CGK~~VKR~AV------GIWkCkkCgkt~ 35 (77)
-.|++||+..+.-+.+ =.|.| +||...
T Consensus 170 p~c~~cg~~~~~v~~~d~~~~~v~y~c-~cG~~g 202 (353)
T cd00674 170 PYCEKCGKDTTTVEAYDAKAGTVTYKC-ECGHEE 202 (353)
T ss_pred eecCCcCcceeEEEEEeCCCCeEEEEc-CCCCEE
Confidence 4699999876544433 35888 588753
No 193
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=24.29 E-value=42 Score=23.06 Aligned_cols=9 Identities=56% Similarity=1.287 Sum_probs=6.4
Q ss_pred eeCCCCcEE
Q 036150 27 SCKYCGKVK 35 (77)
Q Consensus 27 kCkkCgkt~ 35 (77)
+|++||+++
T Consensus 31 kC~~CG~v~ 39 (140)
T COG1545 31 KCKKCGRVY 39 (140)
T ss_pred EcCCCCeEE
Confidence 577777765
No 194
>PF02977 CarbpepA_inh: Carboxypeptidase A inhibitor; InterPro: IPR004231 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. This family is represented by the well-characterised metallocarboxypeptidase A inhibitor (MCPI) from potatoes, which belongs to the MEROPS inhibitor family I37, clan IE. It inhibits metallopeptidases belonging to MEROPS peptidase family M14, carboxypeptidase A. In Russet Burbank potatoes, it is a mixture of approximately equal amounts of two polypeptide chains containing 38 or 39 amino acid residues. The chains differ in their amino terminal sequence only [] and are resistant to fragmentation by proteases []. The structure of the complex between bovine carboxypeptidase A and the 39-amino-acid carboxypeptidase A inhibitor from potatoes has been determined at 2.5-A resolution []. The potato inhibitor is synthesised as a precursor, having a 29 residue N-terminal signal peptide, a 27 residue pro-peptide, the 39 residue mature inhibitor region and a 7 residue C-terminal extension. The 7 residue C-terminal extension is involved in inhibitor inactivation and may be required for targeting to the vacuole where the mature active inhibitor accumulates []. The N-terminal region and the mature inhibitor are weakly related to other solananaceous proteins found in this entry, from potato, tomato and henbane, which have been incorrectly described as metallocarboxipeptidase inhibitors [].; GO: 0008191 metalloendopeptidase inhibitor activity; PDB: 4CPA_I 1H20_A 2HLG_A.
Probab=23.91 E-value=13 Score=22.64 Aligned_cols=30 Identities=23% Similarity=0.417 Sum_probs=18.3
Q ss_pred CCce-eeEEeEEEEEeeCCC-CcEEeCccccc
Q 036150 13 TKKY-AVKRKAVGIWSCKYC-GKVKAGALNAA 42 (77)
Q Consensus 13 CGK~-~VKR~AVGIWkCkkC-gkt~AGGAYtp 42 (77)
|+|. +..-...|||-|.-| +.+..+|-|+-
T Consensus 8 Cn~~C~t~sDC~g~tlC~~C~k~~~t~~g~~~ 39 (46)
T PF02977_consen 8 CNKYCNTNSDCSGITLCQWCWKLKKTCGGYVG 39 (46)
T ss_dssp TT-B-SSSCCCTTSSSS-EE-CCCEBCC--EE
T ss_pred cCCccccCccccceeehHHHHhcccCCCCccc
Confidence 4444 334456799999999 88888777654
No 195
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=23.90 E-value=30 Score=20.88 Aligned_cols=11 Identities=45% Similarity=1.033 Sum_probs=9.0
Q ss_pred EEEEeeCCCCc
Q 036150 23 VGIWSCKYCGK 33 (77)
Q Consensus 23 VGIWkCkkCgk 33 (77)
-||=+|.+||-
T Consensus 9 RGirkCp~CGt 19 (44)
T PF14952_consen 9 RGIRKCPKCGT 19 (44)
T ss_pred hccccCCcCcC
Confidence 38999999974
No 196
>KOG4167 consensus Predicted DNA-binding protein, contains SANT and ELM2 domains [Transcription]
Probab=23.32 E-value=13 Score=33.70 Aligned_cols=14 Identities=50% Similarity=1.137 Sum_probs=12.6
Q ss_pred EEEEEeeCCCCcEE
Q 036150 22 AVGIWSCKYCGKVK 35 (77)
Q Consensus 22 AVGIWkCkkCgkt~ 35 (77)
+.||..|+.|+|+|
T Consensus 789 ~~giFpCreC~kvF 802 (907)
T KOG4167|consen 789 PTGIFPCRECGKVF 802 (907)
T ss_pred CCceeehHHHHHHH
Confidence 48999999999986
No 197
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=23.07 E-value=42 Score=26.47 Aligned_cols=32 Identities=13% Similarity=0.168 Sum_probs=20.2
Q ss_pred eeCCCCce--eeE-EeEEEEEeeCCCCcEEeCccccc
Q 036150 9 RRKRTKKY--AVK-RKAVGIWSCKYCGKVKAGALNAA 42 (77)
Q Consensus 9 ~~~~CGK~--~VK-R~AVGIWkCkkCgkt~AGGAYtp 42 (77)
.||-|+.. ++. -..-|+|+|-.||. .|.+...
T Consensus 36 ~CPfh~ek~pSf~v~~~k~~~~Cf~Cg~--~Gd~i~f 70 (415)
T TIGR01391 36 LCPFHHEKTPSFSVSPEKQFYHCFGCGA--GGDAIKF 70 (415)
T ss_pred eCCCCCCCCCeEEEEcCCCcEEECCCCC--CCCHHHH
Confidence 47878653 222 23568999999997 4554443
No 198
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=22.54 E-value=35 Score=29.14 Aligned_cols=23 Identities=13% Similarity=0.137 Sum_probs=17.1
Q ss_pred eeeeCCCCceeeEEeEEEEEeeCCCCcE
Q 036150 7 VLRRKRTKKYAVKRKAVGIWSCKYCGKV 34 (77)
Q Consensus 7 ~~~~~~CGK~~VKR~AVGIWkCkkCgkt 34 (77)
+-.|++||... .+ .|.|.+||..
T Consensus 626 ~~~C~~CG~~~-g~----~~~CP~CG~~ 648 (656)
T PRK08270 626 FSICPKHGYLS-GE----HEFCPKCGEE 648 (656)
T ss_pred CcccCCCCCcC-CC----CCCCcCCcCc
Confidence 45799999742 22 4999999964
No 199
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=22.48 E-value=24 Score=28.10 Aligned_cols=33 Identities=30% Similarity=0.534 Sum_probs=19.1
Q ss_pred cceeeeeee--CCCCceeeEEeEE-------EEEeeCCCCcE
Q 036150 2 VSYYRVLRR--KRTKKYAVKRKAV-------GIWSCKYCGKV 34 (77)
Q Consensus 2 ~~~~~~~~~--~~CGK~~VKR~AV-------GIWkCkkCgkt 34 (77)
|||=...-| +||...=+-=..| |+|.|+.|.+.
T Consensus 229 vSyGqMVaCDn~nCkrEWFH~~CVGLk~pPKG~WYC~eCk~~ 270 (271)
T COG5034 229 VSYGQMVACDNANCKREWFHLECVGLKEPPKGKWYCPECKKA 270 (271)
T ss_pred cccccceecCCCCCchhheeccccccCCCCCCcEeCHHhHhc
Confidence 344444443 4666553333333 68999999864
No 200
>cd01411 SIR2H SIR2H: Uncharacterized prokaryotic Sir2 homologs from several gram positive bacterial species and Fusobacteria; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=22.43 E-value=39 Score=24.39 Aligned_cols=27 Identities=11% Similarity=-0.093 Sum_probs=17.8
Q ss_pred eeeeeCCCCceeeEEeEEEEEeeCCCC
Q 036150 6 RVLRRKRTKKYAVKRKAVGIWSCKYCG 32 (77)
Q Consensus 6 ~~~~~~~CGK~~VKR~AVGIWkCkkCg 32 (77)
..++|.+|++.--.....-+-.|..||
T Consensus 117 ~~~~C~~C~~~~~~~~~~~~p~C~~Cg 143 (225)
T cd01411 117 YRIYCTVCGKTVDWEEYLKSPYHAKCG 143 (225)
T ss_pred CeeEeCCCCCccchhhcCCCCCCCCCC
Confidence 447899998754333333468899996
No 201
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=22.25 E-value=47 Score=31.52 Aligned_cols=11 Identities=27% Similarity=0.860 Sum_probs=6.3
Q ss_pred EEeeCCCCcEE
Q 036150 25 IWSCKYCGKVK 35 (77)
Q Consensus 25 IWkCkkCgkt~ 35 (77)
+++|.+||..+
T Consensus 692 vy~CPsCGaev 702 (1337)
T PRK14714 692 VYVCPDCGAEV 702 (1337)
T ss_pred ceeCccCCCcc
Confidence 44666666654
No 202
>PF13397 DUF4109: Domain of unknown function (DUF4109)
Probab=21.71 E-value=44 Score=23.10 Aligned_cols=11 Identities=36% Similarity=1.138 Sum_probs=9.4
Q ss_pred EEEeeCCCCcE
Q 036150 24 GIWSCKYCGKV 34 (77)
Q Consensus 24 GIWkCkkCgkt 34 (77)
-.|.|+.||..
T Consensus 49 ~~WeC~~cG~~ 59 (105)
T PF13397_consen 49 ATWECPRCGLP 59 (105)
T ss_pred CceeCCCCCCc
Confidence 47999999976
No 203
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=21.22 E-value=51 Score=22.65 Aligned_cols=15 Identities=33% Similarity=0.760 Sum_probs=12.7
Q ss_pred EEeeCCCCcEEeCcc
Q 036150 25 IWSCKYCGKVKAGAL 39 (77)
Q Consensus 25 IWkCkkCgkt~AGGA 39 (77)
.|+|--||+.+-.|-
T Consensus 2 kWkC~iCg~~I~~gq 16 (101)
T PF09943_consen 2 KWKCYICGKPIYEGQ 16 (101)
T ss_pred ceEEEecCCeeeecc
Confidence 599999999887773
No 204
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=21.21 E-value=41 Score=31.87 Aligned_cols=23 Identities=17% Similarity=0.213 Sum_probs=17.5
Q ss_pred eeeeCCCCceeeEEeEEEEEeeCCCCcEE
Q 036150 7 VLRRKRTKKYAVKRKAVGIWSCKYCGKVK 35 (77)
Q Consensus 7 ~~~~~~CGK~~VKR~AVGIWkCkkCgkt~ 35 (77)
..+||+||..... ..|.+||...
T Consensus 667 ~rkCPkCG~~t~~------~fCP~CGs~t 689 (1337)
T PRK14714 667 RRRCPSCGTETYE------NRCPDCGTHT 689 (1337)
T ss_pred EEECCCCCCcccc------ccCcccCCcC
Confidence 4689999997543 3899999774
No 205
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=21.20 E-value=42 Score=28.61 Aligned_cols=21 Identities=38% Similarity=0.487 Sum_probs=16.0
Q ss_pred eeeeCCCCceeeEEeEEEE-EeeCCCCc
Q 036150 7 VLRRKRTKKYAVKRKAVGI-WSCKYCGK 33 (77)
Q Consensus 7 ~~~~~~CGK~~VKR~AVGI-WkCkkCgk 33 (77)
+-+|++||.... | |+|.+||.
T Consensus 559 ~~~C~~CGy~g~------~~~~CP~CG~ 580 (618)
T PRK14704 559 VDRCKCCSYHGV------IGNECPSCGN 580 (618)
T ss_pred CeecCCCCCCCC------cCccCcCCCC
Confidence 457999997432 3 99999995
No 206
>TIGR00308 TRM1 tRNA(guanine-26,N2-N2) methyltransferase. This enzyme is responsible for two methylations of a characteristic guanine of most tRNA molecules. The activity has been demonstrated for eukaryotic and archaeal proteins, which are active when expressed in E. coli, a species that lacks this enzyme. At least one Eubacterium, Aquifex aeolicus, has an ortholog, as do all completed archaeal genomes.
Probab=20.58 E-value=32 Score=27.20 Aligned_cols=31 Identities=19% Similarity=0.459 Sum_probs=14.5
Q ss_pred eeeeeeeCCCCceeeEEe--EEE-EEeeCCCCcE
Q 036150 4 YYRVLRRKRTKKYAVKRK--AVG-IWSCKYCGKV 34 (77)
Q Consensus 4 ~~~~~~~~~CGK~~VKR~--AVG-IWkCkkCgkt 34 (77)
||||.-|-.=|....++. -.| +|+|..|+..
T Consensus 209 y~Rv~vrv~~~~~~~~~~~~~~g~v~~C~~c~~~ 242 (374)
T TIGR00308 209 YVRVYVKVKRSAIRADKVMESTGYTYHCSRCLHN 242 (374)
T ss_pred EEEEEEEEecCHHHHHHHHHhceeEEECCCcccc
Confidence 666654443332222221 124 6777777553
No 207
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=20.11 E-value=81 Score=19.27 Aligned_cols=15 Identities=20% Similarity=0.240 Sum_probs=10.1
Q ss_pred eeeCCCCceeeEEeE
Q 036150 8 LRRKRTKKYAVKRKA 22 (77)
Q Consensus 8 ~~~~~CGK~~VKR~A 22 (77)
..|+|||...+-...
T Consensus 28 ~~c~~cg~~~~pH~v 42 (60)
T PRK01110 28 SVDKTTGEYHLPHHV 42 (60)
T ss_pred eEcCCCCceecccee
Confidence 457788877766554
No 208
>PRK08329 threonine synthase; Validated
Probab=20.05 E-value=47 Score=25.29 Aligned_cols=21 Identities=24% Similarity=0.479 Sum_probs=14.8
Q ss_pred eeeCCCCceeeEEeEEEEEeeCCCC
Q 036150 8 LRRKRTKKYAVKRKAVGIWSCKYCG 32 (77)
Q Consensus 8 ~~~~~CGK~~VKR~AVGIWkCkkCg 32 (77)
|+|.+||+.-= ...- |.| .|+
T Consensus 2 l~C~~Cg~~~~--~~~~-~~C-~c~ 22 (347)
T PRK08329 2 LRCTKCGRTYE--EKFK-LRC-DCG 22 (347)
T ss_pred cCcCCCCCCcC--CCCc-eec-CCC
Confidence 78999998752 2223 899 796
Done!