Query 020131
Match_columns 330
No_of_seqs 185 out of 288
Neff 5.2
Searched_HMMs 46136
Date Fri Mar 29 07:15:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/020131.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/020131hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2593 Transcription initiati 100.0 1.6E-52 3.4E-57 411.8 13.0 302 1-330 112-436 (436)
2 PRK06266 transcription initiat 99.5 9.1E-15 2E-19 131.6 6.7 51 1-57 101-151 (178)
3 TIGR00373 conserved hypothetic 99.5 3.1E-14 6.7E-19 125.8 5.8 51 1-57 93-143 (158)
4 smart00531 TFIIE Transcription 99.4 6.5E-14 1.4E-18 122.1 4.8 58 1-59 83-140 (147)
5 COG1675 TFA1 Transcription ini 99.2 1.9E-11 4.2E-16 110.0 6.9 75 1-103 97-171 (176)
6 PF08271 TF_Zn_Ribbon: TFIIB z 97.6 2.7E-05 5.9E-10 54.6 1.4 33 18-56 1-33 (43)
7 PRK00398 rpoP DNA-directed RNA 97.5 3.4E-05 7.3E-10 54.8 0.5 34 16-56 2-35 (46)
8 PF05191 ADK_lid: Adenylate ki 97.1 0.00025 5.4E-09 48.4 1.4 34 18-56 2-35 (36)
9 PRK14526 adenylate kinase; Pro 96.8 0.0018 4E-08 59.7 5.2 63 17-100 122-184 (211)
10 PLN02674 adenylate kinase 96.7 0.0022 4.8E-08 60.7 5.3 62 17-99 158-219 (244)
11 TIGR02098 MJ0042_CXXC MJ0042 f 96.6 0.0015 3.2E-08 44.3 2.1 35 17-53 2-36 (38)
12 COG1996 RPC10 DNA-directed RNA 96.1 0.0022 4.7E-08 46.8 0.9 33 15-54 4-36 (49)
13 PF13717 zinc_ribbon_4: zinc-r 96.1 0.0047 1E-07 42.0 2.3 34 17-52 2-35 (36)
14 PRK00279 adk adenylate kinase; 95.9 0.015 3.3E-07 52.8 5.5 63 17-100 127-189 (215)
15 PF09538 FYDLN_acid: Protein o 95.8 0.0046 9.9E-08 52.0 1.8 31 17-55 9-39 (108)
16 smart00659 RPOLCX RNA polymera 95.8 0.0057 1.2E-07 43.5 1.9 30 17-54 2-31 (44)
17 smart00834 CxxC_CXXC_SSSS Puta 95.7 0.0031 6.7E-08 42.9 0.2 32 17-52 5-36 (41)
18 PF08274 PhnA_Zn_Ribbon: PhnA 95.5 0.0039 8.5E-08 41.1 0.2 26 19-52 4-29 (30)
19 TIGR01351 adk adenylate kinase 95.4 0.026 5.6E-07 51.1 5.3 63 17-100 124-186 (210)
20 PRK00420 hypothetical protein; 95.4 0.043 9.4E-07 46.5 6.0 66 16-100 22-88 (112)
21 cd00350 rubredoxin_like Rubred 95.2 0.0081 1.8E-07 39.9 1.0 27 17-52 1-27 (33)
22 PTZ00088 adenylate kinase 1; P 95.1 0.023 4.9E-07 53.2 4.0 68 17-100 130-202 (229)
23 TIGR02300 FYDLN_acid conserved 95.1 0.012 2.6E-07 50.9 1.9 30 17-54 9-38 (129)
24 PHA02768 hypothetical protein; 95.0 0.0082 1.8E-07 44.8 0.6 35 16-51 4-40 (55)
25 PF13719 zinc_ribbon_5: zinc-r 94.9 0.022 4.7E-07 38.9 2.4 34 17-52 2-35 (37)
26 PRK03824 hypA hydrogenase nick 94.7 0.0092 2E-07 51.8 0.2 40 13-52 66-117 (135)
27 PRK10220 hypothetical protein; 94.7 0.016 3.5E-07 48.8 1.5 30 19-56 5-34 (111)
28 TIGR00686 phnA alkylphosphonat 94.6 0.013 2.9E-07 49.2 0.9 29 19-55 4-32 (109)
29 PRK14530 adenylate kinase; Pro 94.6 0.063 1.4E-06 48.8 5.3 62 18-100 127-188 (215)
30 PLN02459 probable adenylate ki 94.5 0.056 1.2E-06 51.9 5.1 66 17-100 153-226 (261)
31 PF13240 zinc_ribbon_2: zinc-r 94.0 0.022 4.7E-07 35.2 0.7 23 19-52 1-23 (23)
32 TIGR01206 lysW lysine biosynth 93.8 0.019 4.2E-07 42.7 0.3 34 17-55 2-35 (54)
33 PF14353 CpXC: CpXC protein 93.7 0.018 4E-07 48.7 0.0 35 18-53 2-49 (128)
34 PF00301 Rubredoxin: Rubredoxi 93.7 0.019 4.1E-07 41.5 0.1 34 18-51 2-43 (47)
35 PF09723 Zn-ribbon_8: Zinc rib 93.6 0.033 7.1E-07 38.9 1.1 32 17-52 5-37 (42)
36 cd00730 rubredoxin Rubredoxin; 93.5 0.033 7.2E-07 40.7 1.1 36 17-52 1-44 (50)
37 TIGR02605 CxxC_CxxC_SSSS putat 93.3 0.026 5.6E-07 40.6 0.2 32 17-52 5-37 (52)
38 PF03604 DNA_RNApol_7kD: DNA d 93.1 0.026 5.7E-07 37.6 -0.0 29 18-54 1-29 (32)
39 PRK14529 adenylate kinase; Pro 93.1 0.11 2.4E-06 48.6 4.2 64 17-99 126-193 (223)
40 PF13248 zf-ribbon_3: zinc-rib 93.1 0.039 8.5E-07 34.8 0.8 25 17-52 2-26 (26)
41 PF05605 zf-Di19: Drought indu 92.4 0.086 1.9E-06 38.4 1.9 35 17-51 2-40 (54)
42 cd00729 rubredoxin_SM Rubredox 92.2 0.048 1E-06 36.6 0.4 28 17-53 2-29 (34)
43 COG1379 PHP family phosphoeste 91.8 0.047 1E-06 54.1 -0.0 29 19-53 248-276 (403)
44 TIGR00100 hypA hydrogenase nic 91.8 0.071 1.5E-06 45.0 1.0 32 12-52 65-96 (115)
45 COG2824 PhnA Uncharacterized Z 91.5 0.047 1E-06 45.9 -0.4 30 19-56 5-34 (112)
46 COG2331 Uncharacterized protei 91.2 0.081 1.8E-06 42.1 0.7 33 17-53 12-44 (82)
47 cd01410 SIRT7 SIRT7: Eukaryoti 90.7 0.2 4.4E-06 46.0 2.9 40 16-55 94-133 (206)
48 COG2888 Predicted Zn-ribbon RN 90.6 0.24 5.2E-06 37.6 2.7 8 17-24 27-34 (61)
49 PRK06450 threonine synthase; V 90.3 0.16 3.5E-06 50.1 2.0 30 17-56 3-32 (338)
50 COG1997 RPL43A Ribosomal prote 89.9 0.18 3.9E-06 41.0 1.6 30 16-52 34-63 (89)
51 PF10571 UPF0547: Uncharacteri 89.7 0.2 4.4E-06 31.8 1.4 23 19-52 2-24 (26)
52 PF13824 zf-Mss51: Zinc-finger 89.7 0.68 1.5E-05 34.6 4.4 26 19-54 1-26 (55)
53 cd01428 ADK Adenylate kinase ( 89.5 0.57 1.2E-05 40.9 4.7 54 18-100 126-179 (194)
54 PRK06260 threonine synthase; V 89.4 0.19 4.1E-06 50.4 1.8 30 17-55 3-32 (397)
55 PRK12380 hydrogenase nickel in 89.2 0.19 4E-06 42.4 1.3 31 13-52 66-96 (113)
56 TIGR00622 ssl1 transcription f 89.2 0.18 3.8E-06 42.9 1.1 27 17-54 1-27 (112)
57 PF01155 HypA: Hydrogenase exp 88.7 0.1 2.3E-06 43.7 -0.6 32 13-53 66-97 (113)
58 PRK00423 tfb transcription ini 88.7 0.22 4.7E-06 48.6 1.5 33 17-55 11-43 (310)
59 PRK07591 threonine synthase; V 88.7 0.22 4.8E-06 50.4 1.7 30 17-56 18-47 (421)
60 PRK14714 DNA polymerase II lar 88.6 0.21 4.6E-06 56.8 1.6 11 94-104 747-757 (1337)
61 TIGR03844 cysteate_syn cysteat 88.2 0.21 4.6E-06 50.4 1.2 29 17-55 2-30 (398)
62 PRK14138 NAD-dependent deacety 88.2 0.44 9.5E-06 45.0 3.2 39 16-55 118-156 (244)
63 PRK14890 putative Zn-ribbon RN 88.1 0.38 8.2E-06 36.5 2.2 31 17-54 7-37 (59)
64 PRK00564 hypA hydrogenase nick 87.9 0.19 4.1E-06 42.6 0.5 34 12-53 66-99 (117)
65 PF00096 zf-C2H2: Zinc finger, 87.3 0.27 5.9E-06 29.1 0.8 16 18-33 1-16 (23)
66 PRK03681 hypA hydrogenase nick 87.1 0.38 8.3E-06 40.5 1.9 33 12-52 65-97 (114)
67 PF07282 OrfB_Zn_ribbon: Putat 86.9 0.35 7.7E-06 36.4 1.5 33 17-56 28-60 (69)
68 PF13894 zf-C2H2_4: C2H2-type 86.8 0.32 7E-06 28.3 0.9 17 18-34 1-17 (24)
69 PRK00464 nrdR transcriptional 86.6 0.22 4.7E-06 44.4 0.2 38 17-58 28-65 (154)
70 PF02146 SIR2: Sir2 family; I 86.6 0.41 9E-06 42.5 1.9 38 17-55 105-142 (178)
71 PHA00732 hypothetical protein 86.4 0.47 1E-05 37.7 2.0 36 18-53 2-38 (79)
72 PF13465 zf-H2C2_2: Zinc-finge 86.4 0.53 1.2E-05 29.4 1.8 19 10-28 7-25 (26)
73 PHA00626 hypothetical protein 86.0 0.31 6.8E-06 36.7 0.7 33 19-54 2-35 (59)
74 PF11781 RRN7: RNA polymerase 85.6 0.36 7.8E-06 32.9 0.8 26 19-52 10-35 (36)
75 PRK00432 30S ribosomal protein 85.6 0.4 8.8E-06 34.9 1.1 28 17-52 20-47 (50)
76 PRK00762 hypA hydrogenase nick 85.4 0.37 8.1E-06 41.2 1.0 36 12-52 65-102 (124)
77 PF09986 DUF2225: Uncharacteri 85.2 0.25 5.5E-06 45.8 -0.1 39 16-54 4-60 (214)
78 PF06044 DRP: Dam-replacing fa 85.1 0.28 6.1E-06 46.8 0.1 35 17-55 31-66 (254)
79 PF01780 Ribosomal_L37ae: Ribo 85.0 0.22 4.7E-06 40.8 -0.6 30 16-52 34-63 (90)
80 PF04423 Rad50_zn_hook: Rad50 84.9 0.96 2.1E-05 32.9 2.8 33 44-98 22-54 (54)
81 PF11023 DUF2614: Protein of u 84.9 0.54 1.2E-05 40.0 1.7 33 16-57 68-100 (114)
82 TIGR00280 L37a ribosomal prote 84.8 0.33 7.1E-06 39.8 0.4 30 16-52 34-63 (91)
83 COG1645 Uncharacterized Zn-fin 84.8 0.45 9.6E-06 41.5 1.2 41 3-52 14-54 (131)
84 TIGR00375 conserved hypothetic 84.4 0.49 1.1E-05 47.7 1.5 28 19-53 242-269 (374)
85 PF08996 zf-DNA_Pol: DNA Polym 84.3 0.5 1.1E-05 42.9 1.4 38 15-52 16-55 (188)
86 cd01413 SIR2_Af2 SIR2_Af2: Arc 84.3 0.89 1.9E-05 42.2 3.0 38 16-55 112-149 (222)
87 PF09862 DUF2089: Protein of u 84.0 0.4 8.6E-06 40.8 0.5 26 20-56 1-26 (113)
88 PRK08197 threonine synthase; V 83.9 0.59 1.3E-05 46.8 1.8 30 16-55 6-35 (394)
89 PRK00481 NAD-dependent deacety 83.7 0.77 1.7E-05 43.0 2.4 35 16-55 121-155 (242)
90 PRK05452 anaerobic nitric oxid 83.5 0.4 8.6E-06 49.6 0.4 42 14-55 422-471 (479)
91 TIGR00570 cdk7 CDK-activating 83.4 1.4 3.1E-05 43.4 4.2 16 40-55 41-56 (309)
92 KOG2807 RNA polymerase II tran 83.4 0.51 1.1E-05 46.9 1.1 30 14-54 273-302 (378)
93 COG0675 Transposase and inacti 83.2 0.6 1.3E-05 43.8 1.5 29 17-57 309-337 (364)
94 PF07754 DUF1610: Domain of un 83.2 0.45 9.7E-06 29.9 0.4 8 42-49 16-23 (24)
95 PF12760 Zn_Tnp_IS1595: Transp 83.1 0.67 1.5E-05 32.8 1.3 33 11-50 12-45 (46)
96 cd01408 SIRT1 SIRT1: Eukaryoti 82.6 1.1 2.3E-05 42.1 2.9 39 16-55 115-153 (235)
97 PRK03976 rpl37ae 50S ribosomal 82.3 0.44 9.5E-06 39.0 0.2 30 16-52 35-64 (90)
98 PF10122 Mu-like_Com: Mu-like 81.9 0.37 8.1E-06 35.5 -0.4 33 16-54 3-36 (51)
99 cd01407 SIR2-fam SIR2 family o 81.9 1.2 2.7E-05 40.9 3.0 39 16-55 108-146 (218)
100 PTZ00255 60S ribosomal protein 81.9 0.57 1.2E-05 38.4 0.7 30 16-52 35-64 (90)
101 PF13453 zf-TFIIB: Transcripti 81.5 0.27 5.9E-06 33.9 -1.1 31 19-54 1-31 (41)
102 cd01409 SIRT4 SIRT4: Eukaryoti 81.2 1.2 2.7E-05 42.4 2.8 17 16-32 117-133 (260)
103 COG4530 Uncharacterized protei 81.1 0.83 1.8E-05 38.9 1.4 28 17-52 9-36 (129)
104 PLN02569 threonine synthase 81.0 0.78 1.7E-05 47.7 1.4 31 15-55 47-77 (484)
105 TIGR00515 accD acetyl-CoA carb 80.6 1.1 2.3E-05 43.7 2.2 32 16-53 25-56 (285)
106 CHL00174 accD acetyl-CoA carbo 80.4 1.1 2.3E-05 44.0 2.1 32 16-53 37-68 (296)
107 PHA00626 hypothetical protein 80.1 0.92 2E-05 34.2 1.2 15 15-29 21-35 (59)
108 COG1571 Predicted DNA-binding 80.1 0.92 2E-05 46.5 1.6 29 18-54 351-379 (421)
109 PRK05638 threonine synthase; V 80.0 0.94 2E-05 46.1 1.6 27 18-55 2-28 (442)
110 cd01411 SIR2H SIR2H: Uncharact 79.8 1.1 2.3E-05 41.8 1.8 33 16-55 117-149 (225)
111 PRK08329 threonine synthase; V 79.8 0.91 2E-05 44.8 1.4 27 18-55 2-28 (347)
112 PHA00733 hypothetical protein 79.2 1.3 2.8E-05 38.0 2.1 40 15-54 71-111 (128)
113 PRK04860 hypothetical protein; 79.2 1.7 3.6E-05 39.0 2.8 38 17-55 119-156 (160)
114 cd01412 SIRT5_Af1_CobB SIRT5_A 79.2 1.3 2.8E-05 40.9 2.1 37 16-56 108-144 (224)
115 smart00661 RPOL9 RNA polymeras 79.0 0.75 1.6E-05 32.6 0.4 30 19-53 2-31 (52)
116 PRK04351 hypothetical protein; 78.9 1.2 2.7E-05 39.4 1.8 33 17-54 112-144 (149)
117 COG5257 GCD11 Translation init 78.8 1.2 2.6E-05 44.7 1.9 28 14-53 54-83 (415)
118 smart00778 Prim_Zn_Ribbon Zinc 78.7 0.9 2E-05 31.3 0.7 27 19-50 5-33 (37)
119 PF05502 Dynactin_p62: Dynacti 78.7 1.2 2.6E-05 46.4 1.9 45 14-58 23-68 (483)
120 PF06827 zf-FPG_IleRS: Zinc fi 78.6 0.24 5.2E-06 31.9 -2.1 28 18-50 2-29 (30)
121 KOG2462 C2H2-type Zn-finger pr 78.5 1.3 2.7E-05 43.1 1.9 38 15-52 159-197 (279)
122 COG2260 Predicted Zn-ribbon RN 78.4 0.99 2.1E-05 34.2 0.9 25 17-54 5-29 (59)
123 PF07295 DUF1451: Protein of u 78.1 0.66 1.4E-05 41.0 -0.1 31 15-52 110-140 (146)
124 COG2176 PolC DNA polymerase II 78.0 0.88 1.9E-05 51.8 0.8 42 15-58 912-955 (1444)
125 PF04423 Rad50_zn_hook: Rad50 77.9 2 4.4E-05 31.2 2.4 31 5-36 9-39 (54)
126 PF03833 PolC_DP2: DNA polymer 77.6 0.73 1.6E-05 50.8 0.0 11 94-104 729-739 (900)
127 cd00296 SIR2 SIR2 superfamily 77.5 1.9 4.1E-05 39.2 2.7 38 16-57 112-149 (222)
128 smart00440 ZnF_C2C2 C2C2 Zinc 77.4 0.67 1.5E-05 32.1 -0.2 35 18-52 1-38 (40)
129 PRK05333 NAD-dependent deacety 77.2 2 4.4E-05 41.4 2.9 17 16-32 127-143 (285)
130 COG2888 Predicted Zn-ribbon RN 77.1 0.81 1.7E-05 34.8 0.1 32 18-56 10-41 (61)
131 PF02591 DUF164: Putative zinc 77.0 2.3 5E-05 31.1 2.5 35 17-52 22-56 (56)
132 PF12773 DZR: Double zinc ribb 76.8 1.3 2.9E-05 31.3 1.2 29 17-53 12-40 (50)
133 PF07191 zinc-ribbons_6: zinc- 76.8 0.99 2.1E-05 35.4 0.5 27 16-54 16-42 (70)
134 PF06397 Desulfoferrod_N: Desu 76.7 0.56 1.2E-05 32.2 -0.8 31 15-53 4-34 (36)
135 PRK05654 acetyl-CoA carboxylas 76.7 1.6 3.5E-05 42.6 2.1 33 15-53 25-57 (292)
136 PRK13130 H/ACA RNA-protein com 76.3 1.4 3.1E-05 33.0 1.3 25 17-54 5-29 (56)
137 COG1773 Rubredoxin [Energy pro 76.0 1.1 2.5E-05 33.5 0.7 34 17-50 3-44 (55)
138 TIGR01384 TFS_arch transcripti 76.0 1.7 3.7E-05 35.4 1.7 26 19-53 2-27 (104)
139 PRK11823 DNA repair protein Ra 75.8 1.6 3.6E-05 44.7 2.0 25 15-50 5-29 (446)
140 PF13912 zf-C2H2_6: C2H2-type 75.7 1.3 2.8E-05 27.2 0.7 17 18-34 2-18 (27)
141 PF14446 Prok-RING_1: Prokaryo 75.4 1.7 3.8E-05 32.4 1.5 29 16-53 4-32 (54)
142 PRK14890 putative Zn-ribbon RN 75.3 1.2 2.5E-05 33.9 0.6 33 15-51 23-57 (59)
143 PF04135 Nop10p: Nucleolar RNA 74.0 1.7 3.8E-05 32.2 1.2 25 17-54 3-29 (53)
144 COG1405 SUA7 Transcription ini 73.8 1.8 3.8E-05 42.2 1.6 31 18-54 2-32 (285)
145 TIGR03830 CxxCG_CxxCG_HTH puta 73.6 1.8 3.8E-05 35.8 1.3 16 41-56 30-45 (127)
146 smart00731 SprT SprT homologue 73.3 2.3 5E-05 36.8 2.0 35 16-54 111-145 (146)
147 TIGR00354 polC DNA polymerase, 72.8 2 4.3E-05 48.1 1.8 27 13-52 621-647 (1095)
148 PF05876 Terminase_GpA: Phage 72.7 1.8 3.9E-05 45.7 1.4 49 4-54 186-241 (557)
149 PRK12286 rpmF 50S ribosomal pr 72.6 2.3 4.9E-05 31.9 1.5 26 13-50 23-48 (57)
150 PHA02942 putative transposase; 72.3 2.4 5.1E-05 42.8 2.1 30 17-54 325-354 (383)
151 KOG0402 60S ribosomal protein 72.2 1.7 3.6E-05 35.3 0.8 31 15-52 34-64 (92)
152 TIGR00416 sms DNA repair prote 72.2 2.3 5.1E-05 43.7 2.1 25 15-50 5-29 (454)
153 COG0777 AccD Acetyl-CoA carbox 71.9 3.1 6.7E-05 40.6 2.6 75 14-117 25-101 (294)
154 PF15135 UPF0515: Uncharacteri 71.9 2.3 4.9E-05 41.0 1.7 33 15-53 153-185 (278)
155 smart00709 Zpr1 Duplicated dom 71.8 1.1 2.4E-05 40.1 -0.4 13 42-54 29-41 (160)
156 COG1326 Uncharacterized archae 71.8 3.1 6.8E-05 38.6 2.6 34 16-52 5-40 (201)
157 PRK02935 hypothetical protein; 71.7 1.8 3.8E-05 36.6 0.9 31 18-57 71-101 (110)
158 PTZ00410 NAD-dependent SIR2; P 71.6 3.5 7.6E-05 41.4 3.1 39 16-55 146-184 (349)
159 PRK05978 hypothetical protein; 71.5 1.9 4.1E-05 38.3 1.0 33 18-56 34-66 (148)
160 KOG3623 Homeobox transcription 71.0 2.3 4.9E-05 46.5 1.7 8 232-239 569-576 (1007)
161 PF10058 DUF2296: Predicted in 71.0 2.7 5.8E-05 31.1 1.6 35 13-50 18-52 (54)
162 PRK00415 rps27e 30S ribosomal 70.8 2 4.4E-05 32.6 0.9 30 19-54 13-42 (59)
163 PRK04023 DNA polymerase II lar 70.5 2.1 4.6E-05 48.1 1.4 12 15-26 624-635 (1121)
164 COG2051 RPS27A Ribosomal prote 69.9 2.2 4.7E-05 33.2 0.9 30 19-54 21-50 (67)
165 PF09855 DUF2082: Nucleic-acid 69.7 1.5 3.2E-05 33.7 -0.0 34 18-51 1-45 (64)
166 TIGR01405 polC_Gram_pos DNA po 69.7 1.9 4.2E-05 49.6 0.9 41 16-58 682-724 (1213)
167 PHA00616 hypothetical protein 69.4 1.3 2.8E-05 31.7 -0.3 15 18-32 2-16 (44)
168 PTZ00408 NAD-dependent deacety 69.4 3.5 7.6E-05 39.0 2.5 33 17-54 117-151 (242)
169 PF03966 Trm112p: Trm112p-like 69.3 1.5 3.3E-05 33.3 0.0 36 16-51 6-62 (68)
170 COG1503 eRF1 Peptide chain rel 68.8 2 4.4E-05 43.9 0.8 38 13-54 323-360 (411)
171 PF12171 zf-C2H2_jaz: Zinc-fin 68.5 3 6.6E-05 25.9 1.3 18 18-35 2-19 (27)
172 cd04476 RPA1_DBD_C RPA1_DBD_C: 68.5 1.8 3.9E-05 38.0 0.2 28 17-52 34-61 (166)
173 COG1867 TRM1 N2,N2-dimethylgua 68.3 13 0.00028 37.8 6.2 26 17-50 240-265 (380)
174 COG0846 SIR2 NAD-dependent pro 68.2 3.9 8.5E-05 39.1 2.5 37 16-53 121-158 (250)
175 COG4049 Uncharacterized protei 67.5 1.9 4.1E-05 32.7 0.2 13 16-28 16-28 (65)
176 PRK08402 replication factor A; 67.5 2.8 6E-05 42.1 1.4 28 16-50 211-238 (355)
177 PRK00448 polC DNA polymerase I 67.5 2.2 4.9E-05 49.8 0.8 40 16-59 907-950 (1437)
178 PRK14892 putative transcriptio 67.2 2.8 6.1E-05 34.8 1.2 37 15-56 19-56 (99)
179 PRK14714 DNA polymerase II lar 67.1 2.7 5.9E-05 48.3 1.4 11 44-54 711-721 (1337)
180 PF09332 Mcm10: Mcm10 replicat 66.9 1.3 2.8E-05 44.3 -1.0 31 15-52 283-313 (344)
181 TIGR00340 zpr1_rel ZPR1-relate 66.6 1.5 3.3E-05 39.4 -0.6 32 20-53 1-39 (163)
182 COG1327 Predicted transcriptio 66.4 6.2 0.00014 35.3 3.2 22 17-38 28-49 (156)
183 PRK08579 anaerobic ribonucleos 65.8 3.1 6.7E-05 44.8 1.4 29 12-51 563-591 (625)
184 COG3809 Uncharacterized protei 65.5 1.8 4E-05 34.8 -0.2 32 18-54 2-33 (88)
185 PRK00464 nrdR transcriptional 65.4 1.8 4E-05 38.5 -0.3 15 43-57 29-43 (154)
186 PRK14715 DNA polymerase II lar 65.4 3.3 7.1E-05 48.0 1.6 27 14-53 671-697 (1627)
187 PRK12366 replication factor A; 65.2 3.4 7.3E-05 44.4 1.6 26 17-51 532-557 (637)
188 KOG3078 Adenylate kinase [Nucl 64.5 10 0.00022 36.2 4.5 64 17-101 138-201 (235)
189 TIGR00354 polC DNA polymerase, 64.4 3.1 6.6E-05 46.7 1.1 37 13-58 1008-1044(1095)
190 cd01121 Sms Sms (bacterial rad 64.3 3.5 7.5E-05 41.5 1.4 22 18-50 1-22 (372)
191 PRK04023 DNA polymerase II lar 64.2 3.8 8.2E-05 46.2 1.8 11 16-26 637-647 (1121)
192 TIGR00155 pqiA_fam integral me 64.1 2.8 6.1E-05 42.6 0.7 32 18-54 14-45 (403)
193 KOG2907 RNA polymerase I trans 63.8 5.6 0.00012 34.0 2.3 40 14-53 71-113 (116)
194 PF06750 DiS_P_DiS: Bacterial 63.8 1.6 3.5E-05 35.5 -0.9 36 18-53 34-69 (92)
195 PF14311 DUF4379: Domain of un 63.7 4.9 0.00011 29.2 1.7 32 13-48 24-55 (55)
196 PF14803 Nudix_N_2: Nudix N-te 63.5 2.2 4.8E-05 28.8 -0.1 29 19-51 2-31 (34)
197 TIGR00155 pqiA_fam integral me 63.2 4.5 9.7E-05 41.2 2.0 27 19-55 217-243 (403)
198 KOG3623 Homeobox transcription 63.2 3.7 8E-05 44.9 1.4 37 17-54 281-321 (1007)
199 PF02318 FYVE_2: FYVE-type zin 63.2 5.8 0.00013 33.3 2.3 30 16-53 53-82 (118)
200 TIGR02159 PA_CoA_Oxy4 phenylac 63.2 1.8 3.8E-05 38.2 -0.8 36 18-55 106-143 (146)
201 PRK15103 paraquat-inducible me 62.5 2.8 6.1E-05 42.8 0.4 33 18-55 11-43 (419)
202 TIGR00310 ZPR1_znf ZPR1 zinc f 62.3 2.3 4.9E-05 39.2 -0.3 13 42-54 30-42 (192)
203 PRK12495 hypothetical protein; 61.6 8 0.00017 36.6 3.2 46 3-57 28-73 (226)
204 COG5189 SFP1 Putative transcri 61.5 3.1 6.7E-05 41.5 0.4 38 15-52 347-408 (423)
205 PF09845 DUF2072: Zn-ribbon co 61.5 3.8 8.2E-05 35.8 0.9 33 18-57 2-34 (131)
206 KOG3507 DNA-directed RNA polym 60.9 5.4 0.00012 30.4 1.5 34 13-54 16-49 (62)
207 PF04216 FdhE: Protein involve 60.7 3.8 8.3E-05 39.4 0.9 11 43-53 198-208 (290)
208 KOG2462 C2H2-type Zn-finger pr 60.7 5.6 0.00012 38.7 2.0 35 16-52 186-225 (279)
209 TIGR01384 TFS_arch transcripti 60.7 2.9 6.2E-05 34.0 0.1 39 16-54 61-102 (104)
210 PF13913 zf-C2HC_2: zinc-finge 60.7 5.7 0.00012 24.7 1.4 17 18-34 3-19 (25)
211 TIGR01031 rpmF_bact ribosomal 60.3 4.9 0.00011 29.8 1.2 25 14-50 23-47 (55)
212 COG3877 Uncharacterized protei 60.0 3.8 8.2E-05 34.8 0.6 28 17-55 6-33 (122)
213 cd00817 ValRS_core catalytic c 59.5 4.4 9.6E-05 40.5 1.2 33 12-56 135-167 (382)
214 KOG2923 Uncharacterized conser 59.5 7 0.00015 30.2 2.0 40 10-52 13-54 (67)
215 COG4888 Uncharacterized Zn rib 59.4 2.8 6E-05 35.1 -0.2 38 16-57 21-61 (104)
216 COG3364 Zn-ribbon containing p 59.1 4.7 0.0001 33.9 1.1 33 17-56 2-34 (112)
217 PRK11893 methionyl-tRNA synthe 59.0 4.5 9.7E-05 41.4 1.1 41 11-57 116-156 (511)
218 KOG3576 Ovo and related transc 58.8 5.3 0.00011 37.7 1.4 49 4-52 104-155 (267)
219 TIGR00320 dfx_rbo desulfoferro 58.2 5.9 0.00013 34.1 1.6 32 15-54 5-36 (125)
220 COG3091 SprT Zn-dependent meta 58.1 6 0.00013 35.4 1.6 39 14-54 114-152 (156)
221 PF14353 CpXC: CpXC protein 57.8 9.3 0.0002 32.1 2.7 35 4-39 26-60 (128)
222 COG3677 Transposase and inacti 57.7 4.5 9.7E-05 34.9 0.7 37 18-56 31-67 (129)
223 PF14354 Lar_restr_allev: Rest 57.6 3.9 8.4E-05 30.0 0.3 33 18-50 4-37 (61)
224 PF12874 zf-met: Zinc-finger o 57.6 5.2 0.00011 23.9 0.8 17 18-34 1-17 (25)
225 PRK09263 anaerobic ribonucleos 57.4 6.1 0.00013 43.1 1.9 32 12-50 636-667 (711)
226 PRK14715 DNA polymerase II lar 57.4 4.7 0.0001 46.8 1.0 36 13-58 1538-1573(1627)
227 PRK15103 paraquat-inducible me 57.4 6.4 0.00014 40.3 1.9 25 19-54 223-247 (419)
228 TIGR03655 anti_R_Lar restricti 56.9 4.1 8.9E-05 29.6 0.3 35 19-54 3-38 (53)
229 cd03361 TOPRIM_TopoIA_RevGyr T 56.9 7.2 0.00016 34.9 2.0 45 19-104 79-123 (170)
230 COG1198 PriA Primosomal protei 56.7 3.6 7.8E-05 45.1 -0.0 12 18-29 445-456 (730)
231 PF03119 DNA_ligase_ZBD: NAD-d 56.6 4.8 0.0001 25.9 0.6 14 44-57 1-14 (28)
232 COG1545 Predicted nucleic-acid 56.5 5.3 0.00012 34.8 1.0 26 16-52 28-53 (140)
233 PF13597 NRDD: Anaerobic ribon 56.3 4.9 0.00011 42.4 0.9 28 12-51 486-513 (546)
234 PF04438 zf-HIT: HIT zinc fing 56.2 5 0.00011 26.3 0.6 16 15-30 11-26 (30)
235 COG1198 PriA Primosomal protei 55.5 9.9 0.00021 41.7 3.1 10 42-51 475-484 (730)
236 PRK08271 anaerobic ribonucleos 55.5 7.5 0.00016 41.9 2.1 28 12-50 561-588 (623)
237 smart00355 ZnF_C2H2 zinc finge 55.3 6.3 0.00014 22.7 0.9 15 18-32 1-15 (26)
238 PF06689 zf-C4_ClpX: ClpX C4-t 55.2 1.5 3.2E-05 30.6 -2.2 29 18-48 2-30 (41)
239 PF01783 Ribosomal_L32p: Ribos 55.2 7.5 0.00016 28.8 1.5 23 15-49 24-46 (56)
240 PRK14704 anaerobic ribonucleos 55.2 7.1 0.00015 42.0 1.9 28 12-51 554-581 (618)
241 TIGR00630 uvra excinuclease AB 54.9 6.3 0.00014 44.3 1.5 34 16-50 249-282 (924)
242 COG0375 HybF Zn finger protein 54.9 6 0.00013 33.8 1.1 33 12-53 65-97 (115)
243 PTZ00409 Sir2 (Silent Informat 54.8 8.8 0.00019 37.0 2.3 38 16-54 136-176 (271)
244 PRK07218 replication factor A; 53.9 6.1 0.00013 40.6 1.1 22 17-51 297-318 (423)
245 PF15135 UPF0515: Uncharacteri 53.6 4.5 9.7E-05 39.0 0.1 35 18-54 133-167 (278)
246 COG4640 Predicted membrane pro 53.2 11 0.00025 38.6 2.8 25 19-54 3-27 (465)
247 PF01667 Ribosomal_S27e: Ribos 52.8 7 0.00015 29.3 1.0 31 18-54 8-38 (55)
248 PRK11827 hypothetical protein; 52.7 10 0.00022 28.8 1.9 26 17-49 8-33 (60)
249 KOG4317 Predicted Zn-finger pr 52.7 7.9 0.00017 38.6 1.6 13 17-29 19-31 (383)
250 PRK07111 anaerobic ribonucleos 52.4 7.7 0.00017 42.5 1.7 27 12-50 675-701 (735)
251 PRK14559 putative protein seri 51.9 6.7 0.00015 42.4 1.1 12 17-28 15-26 (645)
252 PF09963 DUF2197: Uncharacteri 51.7 5.5 0.00012 30.0 0.3 37 18-54 3-43 (56)
253 PRK14559 putative protein seri 51.7 7 0.00015 42.3 1.2 25 19-54 29-53 (645)
254 PRK12267 methionyl-tRNA synthe 51.5 8.2 0.00018 41.3 1.7 39 12-57 120-158 (648)
255 TIGR00108 eRF peptide chain re 51.2 6.9 0.00015 39.9 1.0 37 15-54 322-358 (409)
256 PRK12722 transcriptional activ 51.0 9.6 0.00021 35.2 1.8 31 17-52 134-164 (187)
257 COG3357 Predicted transcriptio 51.0 4.7 0.0001 33.3 -0.2 31 18-55 59-89 (97)
258 smart00734 ZnF_Rad18 Rad18-lik 50.6 9.1 0.0002 24.1 1.1 19 19-37 3-21 (26)
259 KOG2817 Predicted E3 ubiquitin 50.5 12 0.00025 38.3 2.4 40 14-53 331-385 (394)
260 COG1594 RPB9 DNA-directed RNA 50.4 4.6 0.0001 34.1 -0.3 38 17-54 72-112 (113)
261 PF03833 PolC_DP2: DNA polymer 50.3 5.3 0.00011 44.3 0.0 39 15-53 653-691 (900)
262 TIGR00613 reco DNA repair prot 50.2 5.4 0.00012 36.7 0.1 31 17-51 147-177 (241)
263 PLN00209 ribosomal protein S27 50.1 8.1 0.00018 31.5 1.0 30 19-54 38-67 (86)
264 PRK12860 transcriptional activ 49.8 10 0.00023 35.0 1.8 30 17-51 134-163 (189)
265 PLN03086 PRLI-interacting fact 49.7 21 0.00047 38.1 4.4 37 16-53 477-515 (567)
266 smart00132 LIM Zinc-binding do 49.6 4 8.7E-05 26.2 -0.7 35 19-53 1-38 (39)
267 COG3677 Transposase and inacti 49.6 7.3 0.00016 33.6 0.8 15 15-29 51-65 (129)
268 PF01096 TFIIS_C: Transcriptio 49.3 6.6 0.00014 26.9 0.4 17 12-28 23-39 (39)
269 PF14205 Cys_rich_KTR: Cystein 49.2 7.2 0.00016 29.2 0.6 35 17-56 4-42 (55)
270 PF09297 zf-NADH-PPase: NADH p 49.1 4 8.8E-05 26.6 -0.7 26 19-51 5-30 (32)
271 PF01807 zf-CHC2: CHC2 zinc fi 48.8 5.6 0.00012 32.3 -0.1 31 16-50 32-62 (97)
272 KOG1842 FYVE finger-containing 48.2 9.9 0.00022 39.4 1.6 37 14-59 177-213 (505)
273 COG5349 Uncharacterized protei 48.1 7.8 0.00017 33.5 0.7 33 18-56 22-54 (126)
274 COG5151 SSL1 RNA polymerase II 48.1 7 0.00015 38.9 0.5 30 14-54 305-334 (421)
275 KOG2879 Predicted E3 ubiquitin 47.9 11 0.00023 37.0 1.7 13 42-54 276-288 (298)
276 COG0068 HypF Hydrogenase matur 47.8 5.8 0.00013 43.3 -0.2 18 17-34 123-140 (750)
277 PF08209 Sgf11: Sgf11 (transcr 47.7 11 0.00023 25.4 1.2 12 42-53 4-15 (33)
278 PF08792 A2L_zn_ribbon: A2L zi 47.3 11 0.00023 25.3 1.1 15 14-28 18-32 (33)
279 COG1998 RPS31 Ribosomal protei 47.1 8 0.00017 28.5 0.5 29 16-52 18-47 (51)
280 COG5216 Uncharacterized conser 47.0 11 0.00023 28.9 1.2 32 17-52 22-54 (67)
281 PTZ00083 40S ribosomal protein 46.8 9.9 0.00022 30.9 1.1 30 19-54 37-66 (85)
282 PHA02998 RNA polymerase subuni 46.6 4.9 0.00011 37.0 -0.8 38 17-54 143-183 (195)
283 PRK05580 primosome assembly pr 46.6 16 0.00035 39.5 3.0 27 19-52 392-418 (679)
284 PF01363 FYVE: FYVE zinc finge 46.2 7 0.00015 29.2 0.1 31 17-56 9-39 (69)
285 PRK12495 hypothetical protein; 46.2 9.6 0.00021 36.1 1.0 15 39-53 39-53 (226)
286 PF06906 DUF1272: Protein of u 46.1 8.7 0.00019 29.0 0.6 13 42-54 41-53 (57)
287 PLN03086 PRLI-interacting fact 45.7 13 0.00028 39.7 2.0 35 17-52 453-487 (567)
288 TIGR00244 transcriptional regu 45.5 6.1 0.00013 35.2 -0.4 22 17-38 28-49 (147)
289 PRK14873 primosome assembly pr 45.4 7.1 0.00015 42.3 0.1 28 17-51 392-419 (665)
290 KOG2846 Predicted membrane pro 45.2 8.4 0.00018 38.4 0.5 34 13-52 216-252 (328)
291 TIGR01562 FdhE formate dehydro 45.1 13 0.00028 36.7 1.8 9 19-27 186-194 (305)
292 PRK00635 excinuclease ABC subu 45.0 12 0.00027 44.9 1.9 34 16-50 243-276 (1809)
293 PRK00349 uvrA excinuclease ABC 44.9 11 0.00025 42.4 1.6 34 16-50 251-284 (943)
294 PRK11088 rrmA 23S rRNA methylt 44.9 12 0.00027 35.2 1.6 25 17-50 2-26 (272)
295 COG0423 GRS1 Glycyl-tRNA synth 44.9 14 0.00031 39.1 2.1 36 18-53 89-140 (558)
296 TIGR00595 priA primosomal prot 44.4 7.1 0.00015 40.7 -0.1 27 19-52 224-250 (505)
297 PRK04338 N(2),N(2)-dimethylgua 44.3 11 0.00024 38.0 1.2 29 17-53 244-272 (382)
298 PRK00085 recO DNA repair prote 44.1 9.8 0.00021 35.1 0.7 29 17-49 149-177 (247)
299 PF01921 tRNA-synt_1f: tRNA sy 44.0 2.9 6.3E-05 42.1 -2.9 37 18-56 175-213 (360)
300 PF04564 U-box: U-box domain; 44.0 21 0.00045 27.4 2.5 37 16-54 3-51 (73)
301 PHA02540 61 DNA primase; Provi 43.4 13 0.00028 37.2 1.5 34 17-50 27-63 (337)
302 smart00504 Ubox Modified RING 43.3 15 0.00032 26.5 1.5 28 23-53 19-46 (63)
303 KOG0703 Predicted GTPase-activ 43.3 9.6 0.00021 37.4 0.6 43 2-52 13-55 (287)
304 PRK03564 formate dehydrogenase 43.1 15 0.00031 36.5 1.8 9 19-27 189-197 (309)
305 PF10609 ParA: ParA/MinD ATPas 42.8 11 0.00024 30.2 0.8 13 16-28 64-76 (81)
306 PLN02224 methionine-tRNA ligas 42.8 14 0.00031 39.7 1.8 39 12-57 185-223 (616)
307 PF02150 RNA_POL_M_15KD: RNA p 42.6 5.4 0.00012 26.9 -0.9 28 19-52 3-30 (35)
308 PF04641 Rtf2: Rtf2 RING-finge 42.5 23 0.00049 33.7 3.0 37 14-54 110-162 (260)
309 COG0498 ThrC Threonine synthas 42.5 15 0.00033 37.7 1.9 31 17-56 5-35 (411)
310 TIGR00467 lysS_arch lysyl-tRNA 42.3 8.7 0.00019 40.4 0.1 34 19-56 170-204 (515)
311 PRK14873 primosome assembly pr 41.9 23 0.00049 38.5 3.2 23 16-51 409-431 (665)
312 COG5109 Uncharacterized conser 41.8 17 0.00036 36.4 2.0 38 15-53 334-387 (396)
313 PRK05580 primosome assembly pr 41.8 7.9 0.00017 41.8 -0.3 23 17-51 408-430 (679)
314 PRK00750 lysK lysyl-tRNA synth 41.8 6.4 0.00014 41.2 -1.0 35 19-56 177-213 (510)
315 TIGR00595 priA primosomal prot 41.7 15 0.00032 38.3 1.8 25 16-52 239-263 (505)
316 TIGR02827 RNR_anaer_Bdell anae 41.5 12 0.00027 40.0 1.1 29 12-51 527-555 (586)
317 PF06221 zf-C2HC5: Putative zi 40.8 9.7 0.00021 28.7 0.2 29 18-54 19-47 (57)
318 PLN02842 nucleotide kinase 40.8 35 0.00075 36.1 4.2 58 17-99 121-178 (505)
319 PF08273 Prim_Zn_Ribbon: Zinc- 40.0 10 0.00023 26.5 0.2 28 19-50 5-34 (40)
320 PF08646 Rep_fac-A_C: Replicat 40.0 13 0.00027 31.9 0.8 29 16-52 17-47 (146)
321 PRK00241 nudC NADH pyrophospha 39.9 10 0.00022 36.2 0.1 31 17-54 99-129 (256)
322 KOG2691 RNA polymerase II subu 39.7 9.4 0.0002 32.4 -0.1 30 18-53 74-112 (113)
323 COG1655 Uncharacterized protei 39.7 12 0.00026 35.8 0.6 18 16-33 18-35 (267)
324 COG1656 Uncharacterized conser 39.6 15 0.00033 33.3 1.2 37 16-52 96-140 (165)
325 TIGR03826 YvyF flagellar opero 38.7 8.3 0.00018 33.8 -0.6 26 19-54 5-30 (137)
326 COG4307 Uncharacterized protei 38.4 9.6 0.00021 37.3 -0.2 26 17-53 3-28 (349)
327 PF10005 DUF2248: Uncharacteri 38.1 16 0.00034 36.8 1.2 27 20-57 2-28 (343)
328 PF14787 zf-CCHC_5: GAG-polypr 37.9 15 0.00033 25.3 0.7 11 19-29 4-14 (36)
329 PF07818 HCNGP: HCNGP-like pro 37.8 35 0.00075 28.1 3.0 19 236-254 76-94 (96)
330 COG1779 C4-type Zn-finger prot 37.7 6.2 0.00013 36.8 -1.6 35 17-53 14-54 (201)
331 COG2995 PqiA Uncharacterized p 37.6 12 0.00026 38.3 0.3 36 16-56 17-52 (418)
332 cd00674 LysRS_core_class_I cat 37.5 7.8 0.00017 38.9 -1.1 33 19-55 171-205 (353)
333 PF09334 tRNA-synt_1g: tRNA sy 37.1 17 0.00037 36.7 1.3 38 15-53 118-160 (391)
334 PF06677 Auto_anti-p27: Sjogre 37.0 26 0.00056 24.6 1.8 12 43-54 18-29 (41)
335 PF13397 DUF4109: Domain of un 36.9 20 0.00043 30.3 1.4 39 16-57 27-65 (105)
336 COG4888 Uncharacterized Zn rib 36.7 15 0.00033 30.8 0.7 15 40-54 20-34 (104)
337 KOG2893 Zn finger protein [Gen 36.7 15 0.00033 35.5 0.8 34 19-53 12-45 (341)
338 PF11789 zf-Nse: Zinc-finger o 36.3 42 0.00091 24.9 3.0 29 20-49 27-55 (57)
339 COG4068 Uncharacterized protei 36.3 1.1E+02 0.0023 23.5 5.1 18 80-97 37-54 (64)
340 COG2093 DNA-directed RNA polym 36.0 16 0.00034 28.2 0.6 22 19-51 6-27 (64)
341 PRK09401 reverse gyrase; Revie 35.5 21 0.00045 41.3 1.8 25 19-54 680-704 (1176)
342 PRK09710 lar restriction allev 35.5 9.7 0.00021 29.4 -0.6 33 19-55 8-40 (64)
343 PRK04011 peptide chain release 35.4 20 0.00044 36.6 1.5 37 15-54 326-362 (411)
344 COG0178 UvrA Excinuclease ATPa 35.1 17 0.00038 40.5 1.0 34 16-50 244-277 (935)
345 PF14206 Cys_rich_CPCC: Cystei 34.6 13 0.00029 29.6 0.1 28 18-51 2-29 (78)
346 COG5415 Predicted integral mem 34.5 17 0.00038 34.3 0.8 35 12-52 187-224 (251)
347 COG1066 Sms Predicted ATP-depe 34.4 22 0.00047 36.9 1.5 24 16-50 6-29 (456)
348 PF14369 zf-RING_3: zinc-finge 34.2 16 0.00034 24.7 0.3 32 17-54 2-33 (35)
349 PRK06386 replication factor A; 34.1 19 0.00041 36.4 1.0 22 16-50 235-256 (358)
350 PRK01110 rpmF 50S ribosomal pr 34.0 33 0.00072 25.9 2.1 24 14-50 24-47 (60)
351 COG1110 Reverse gyrase [DNA re 33.8 16 0.00035 41.7 0.5 26 19-55 696-721 (1187)
352 TIGR00617 rpa1 replication fac 33.7 26 0.00056 37.6 2.1 29 16-52 473-503 (608)
353 PRK07225 DNA-directed RNA poly 33.7 34 0.00074 36.8 2.9 39 5-50 531-570 (605)
354 KOG1598 Transcription initiati 33.6 19 0.00041 38.1 0.9 31 19-55 2-32 (521)
355 PRK03564 formate dehydrogenase 33.5 18 0.00038 35.9 0.7 27 13-50 208-234 (309)
356 PRK14894 glycyl-tRNA synthetas 33.4 19 0.0004 38.3 0.9 27 18-53 89-116 (539)
357 cd00162 RING RING-finger (Real 32.8 39 0.00084 21.7 2.1 34 17-52 12-45 (45)
358 KOG4317 Predicted Zn-finger pr 32.7 18 0.0004 36.1 0.7 14 15-28 5-21 (383)
359 PF01927 Mut7-C: Mut7-C RNAse 32.5 24 0.00053 30.6 1.3 39 14-52 88-134 (147)
360 PRK03918 chromosome segregatio 32.5 68 0.0015 35.1 5.1 12 44-55 437-448 (880)
361 PF04475 DUF555: Protein of un 32.3 14 0.0003 30.9 -0.2 15 39-53 44-58 (102)
362 PF08746 zf-RING-like: RING-li 32.3 53 0.0011 23.0 2.8 34 14-48 8-43 (43)
363 TIGR02487 NrdD anaerobic ribon 31.9 26 0.00055 37.4 1.6 29 12-51 519-547 (579)
364 COG2816 NPY1 NTP pyrophosphohy 31.9 18 0.00039 35.4 0.5 35 17-58 111-145 (279)
365 TIGR00398 metG methionyl-tRNA 31.9 22 0.00048 36.8 1.1 19 13-31 116-134 (530)
366 smart00064 FYVE Protein presen 31.4 30 0.00066 25.6 1.5 32 17-57 10-41 (68)
367 COG4031 Predicted metal-bindin 31.2 22 0.00048 33.1 0.9 9 43-51 13-21 (227)
368 KOG3454 U1 snRNP-specific prot 30.8 92 0.002 28.3 4.7 54 42-102 3-58 (165)
369 PF13878 zf-C2H2_3: zinc-finge 30.7 18 0.00039 25.1 0.2 15 18-32 14-28 (41)
370 TIGR03670 rpoB_arch DNA-direct 30.4 41 0.0009 36.2 2.9 40 5-51 525-565 (599)
371 COG2835 Uncharacterized conser 30.1 32 0.00069 26.3 1.4 26 17-49 8-33 (60)
372 PRK10220 hypothetical protein; 30.0 24 0.00053 30.0 0.9 18 14-31 17-34 (111)
373 PF12647 RNHCP: RNHCP domain; 29.7 18 0.00038 29.9 0.0 34 16-54 3-36 (92)
374 COG3813 Uncharacterized protei 29.7 22 0.00048 28.3 0.5 14 42-55 41-54 (84)
375 COG4391 Uncharacterized protei 29.5 28 0.0006 26.8 1.0 14 16-29 47-60 (62)
376 cd00065 FYVE FYVE domain; Zinc 29.5 30 0.00065 24.6 1.2 30 18-56 3-32 (57)
377 COG1241 MCM2 Predicted ATPase 29.5 16 0.00034 39.9 -0.4 33 13-48 125-157 (682)
378 smart00401 ZnF_GATA zinc finge 29.4 34 0.00075 24.8 1.5 35 16-53 2-36 (52)
379 PF14471 DUF4428: Domain of un 29.3 11 0.00024 27.5 -1.1 30 19-52 1-30 (51)
380 CHL00174 accD acetyl-CoA carbo 29.1 53 0.0011 32.4 3.2 27 17-45 57-86 (296)
381 PF11672 DUF3268: Protein of u 29.1 26 0.00055 29.4 0.8 35 18-52 3-41 (102)
382 smart00507 HNHc HNH nucleases. 29.0 18 0.0004 24.2 -0.0 11 18-28 11-21 (52)
383 PF12660 zf-TFIIIC: Putative z 28.8 30 0.00065 28.4 1.2 17 17-33 55-71 (99)
384 PF08882 Acetone_carb_G: Aceto 28.7 28 0.0006 29.7 1.0 10 17-26 74-83 (112)
385 PF12172 DUF35_N: Rubredoxin-l 28.7 32 0.00069 22.9 1.1 25 16-51 10-34 (37)
386 COG3880 Modulator of heat shoc 28.6 85 0.0018 28.7 4.1 35 17-58 74-108 (176)
387 TIGR01562 FdhE formate dehydro 28.5 38 0.00082 33.5 2.1 28 13-51 206-233 (305)
388 PF14255 Cys_rich_CPXG: Cystei 28.5 25 0.00055 25.9 0.6 33 18-55 1-37 (52)
389 TIGR03831 YgiT_finger YgiT-typ 28.4 28 0.0006 23.5 0.8 14 14-27 29-42 (46)
390 COG1040 ComFC Predicted amidop 28.4 18 0.0004 33.8 -0.1 27 18-55 25-51 (225)
391 COG1651 DsbG Protein-disulfide 28.2 19 0.00042 32.9 -0.0 22 16-38 92-113 (244)
392 PF07503 zf-HYPF: HypF finger; 28.2 16 0.00034 24.9 -0.5 15 16-30 20-34 (35)
393 TIGR00319 desulf_FeS4 desulfof 28.1 32 0.00069 22.6 1.0 15 15-29 5-19 (34)
394 PF07975 C1_4: TFIIH C1-like d 27.9 27 0.00059 25.7 0.7 31 15-49 19-50 (51)
395 PF01286 XPA_N: XPA protein N- 27.7 42 0.0009 22.8 1.5 25 18-49 4-28 (34)
396 PF06170 DUF983: Protein of un 27.6 16 0.00035 29.5 -0.5 13 20-32 11-23 (86)
397 TIGR00686 phnA alkylphosphonat 27.6 32 0.00068 29.2 1.2 18 14-31 16-33 (109)
398 KOG3113 Uncharacterized conser 27.6 46 0.001 32.4 2.4 37 13-54 107-159 (293)
399 KOG2324 Prolyl-tRNA synthetase 27.5 35 0.00076 34.9 1.6 32 17-53 227-259 (457)
400 KOG2703 C4-type Zn-finger prot 27.4 18 0.00039 37.2 -0.4 52 9-60 31-86 (460)
401 cd00974 DSRD Desulforedoxin (D 27.3 34 0.00073 22.5 1.0 14 16-29 3-16 (34)
402 KOG3993 Transcription factor ( 27.2 25 0.00054 36.5 0.6 14 15-28 293-306 (500)
403 COG1885 Uncharacterized protei 27.0 20 0.00044 30.3 -0.1 14 40-53 47-60 (115)
404 KOG3854 SPRT-like metalloprote 27.0 23 0.00049 37.1 0.2 38 17-58 408-445 (505)
405 COG2995 PqiA Uncharacterized p 26.9 48 0.001 34.1 2.5 28 17-54 220-247 (418)
406 PRK05654 acetyl-CoA carboxylas 26.9 58 0.0013 31.9 3.0 22 17-38 46-70 (292)
407 PF09889 DUF2116: Uncharacteri 26.7 28 0.0006 26.4 0.6 12 44-55 5-16 (59)
408 KOG3039 Uncharacterized conser 26.7 53 0.0011 32.0 2.6 48 16-67 220-283 (303)
409 PF02005 TRM: N2,N2-dimethylgu 26.7 21 0.00045 36.1 -0.1 33 16-54 239-271 (377)
410 PF10013 DUF2256: Uncharacteri 26.6 29 0.00064 24.7 0.7 21 14-34 5-25 (42)
411 TIGR00396 leuS_bact leucyl-tRN 26.5 43 0.00093 37.3 2.3 38 10-54 145-182 (842)
412 smart00350 MCM minichromosome 26.4 26 0.00055 36.5 0.5 34 14-50 34-69 (509)
413 TIGR00201 comF comF family pro 25.8 31 0.00067 30.9 0.8 23 20-53 1-23 (190)
414 TIGR00382 clpX endopeptidase C 25.6 34 0.00074 35.1 1.2 29 18-49 8-36 (413)
415 TIGR01054 rgy reverse gyrase. 25.6 35 0.00076 39.5 1.4 25 19-54 680-704 (1171)
416 COG0333 RpmF Ribosomal protein 25.4 41 0.00089 25.4 1.3 23 16-50 26-48 (57)
417 TIGR00308 TRM1 tRNA(guanine-26 25.4 30 0.00066 34.9 0.8 31 17-53 233-263 (374)
418 PF05741 zf-nanos: Nanos RNA b 25.4 28 0.0006 26.1 0.4 10 17-26 33-42 (55)
419 KOG4021 Mitochondrial ribosoma 25.3 35 0.00076 32.0 1.1 75 17-115 108-184 (239)
420 COG1933 Archaeal DNA polymeras 25.1 27 0.00058 33.6 0.3 35 14-57 164-198 (253)
421 PF09538 FYDLN_acid: Protein o 25.0 38 0.00082 28.5 1.2 16 15-30 24-39 (108)
422 PRK09678 DNA-binding transcrip 24.9 37 0.0008 26.7 1.0 39 18-56 2-43 (72)
423 PF14319 Zn_Tnp_IS91: Transpos 24.6 43 0.00092 28.1 1.4 32 14-52 39-70 (111)
424 PF13901 DUF4206: Domain of un 24.6 46 0.00099 30.6 1.8 31 16-52 151-182 (202)
425 TIGR03829 YokU_near_AblA uncha 24.5 44 0.00095 27.4 1.4 23 14-36 32-54 (89)
426 PHA02325 hypothetical protein 24.5 31 0.00067 26.8 0.5 11 18-28 4-14 (72)
427 PF10083 DUF2321: Uncharacteri 24.5 62 0.0014 29.2 2.5 40 19-58 41-84 (158)
428 smart00451 ZnF_U1 U1-like zinc 24.3 42 0.0009 21.4 1.1 11 18-28 4-14 (35)
429 TIGR00618 sbcc exonuclease Sbc 24.3 61 0.0013 36.8 3.0 37 16-55 500-537 (1042)
430 PRK11088 rrmA 23S rRNA methylt 24.2 31 0.00067 32.4 0.6 13 42-54 2-14 (272)
431 TIGR01391 dnaG DNA primase, ca 24.1 41 0.0009 34.2 1.5 29 17-50 34-63 (415)
432 PF11494 Ta0938: Ta0938; Inte 24.1 25 0.00055 29.4 -0.0 36 16-53 13-48 (105)
433 PF05129 Elf1: Transcription e 24.1 30 0.00065 27.6 0.4 11 41-51 21-31 (81)
434 TIGR00310 ZPR1_znf ZPR1 zinc f 23.8 38 0.00081 31.3 1.0 23 16-38 29-51 (192)
435 PRK02625 rpoC1 DNA-directed RN 23.4 37 0.0008 36.8 1.0 19 176-194 237-255 (627)
436 PRK05342 clpX ATP-dependent pr 23.3 43 0.00093 34.2 1.4 32 14-48 6-37 (412)
437 PF01412 ArfGap: Putative GTPa 23.2 24 0.00051 29.5 -0.4 32 18-54 14-45 (116)
438 COG4338 Uncharacterized protei 23.2 25 0.00055 25.9 -0.2 16 16-31 11-26 (54)
439 PF04981 NMD3: NMD3 family ; 23.2 39 0.00084 31.6 1.0 14 41-54 34-47 (236)
440 TIGR00515 accD acetyl-CoA carb 23.1 46 0.00099 32.5 1.5 27 17-45 45-74 (285)
441 COG1571 Predicted DNA-binding 23.0 37 0.00081 35.0 0.9 13 17-29 367-379 (421)
442 PRK07219 DNA topoisomerase I; 22.9 34 0.00074 38.0 0.6 32 17-54 669-700 (822)
443 PRK03922 hypothetical protein; 22.8 28 0.0006 29.7 -0.0 14 40-53 47-60 (113)
444 PRK00133 metG methionyl-tRNA s 22.8 33 0.00071 37.0 0.5 16 14-29 120-135 (673)
445 PF10276 zf-CHCC: Zinc-finger 22.7 34 0.00074 23.9 0.4 11 17-27 29-39 (40)
446 smart00709 Zpr1 Duplicated dom 22.7 41 0.00088 30.1 1.0 33 16-48 28-60 (160)
447 PRK00390 leuS leucyl-tRNA synt 22.5 53 0.0011 36.4 2.0 39 9-55 147-185 (805)
448 PF12756 zf-C2H2_2: C2H2 type 22.4 43 0.00093 25.6 1.0 19 17-35 50-68 (100)
449 TIGR00340 zpr1_rel ZPR1-relate 22.1 42 0.0009 30.2 0.9 22 16-37 27-48 (163)
450 PHA02565 49 recombination endo 22.0 29 0.00063 31.3 -0.1 42 14-56 17-69 (157)
451 PF01396 zf-C4_Topoisom: Topoi 22.0 38 0.00082 23.2 0.5 14 44-57 3-16 (39)
452 PHA02562 46 endonuclease subun 22.0 1.3E+02 0.0028 31.0 4.7 14 42-55 284-297 (562)
453 PF04810 zf-Sec23_Sec24: Sec23 21.9 38 0.00082 23.2 0.5 30 19-51 4-33 (40)
454 PF05207 zf-CSL: CSL zinc fing 21.7 46 0.001 24.5 1.0 34 16-52 17-50 (55)
455 KOG2906 RNA polymerase III sub 21.6 21 0.00045 29.9 -1.0 37 17-53 65-104 (105)
456 PF10186 Atg14: UV radiation r 21.6 30 0.00065 32.3 -0.1 18 19-49 1-18 (302)
457 PRK00893 aspartate carbamoyltr 21.5 32 0.00069 30.8 0.1 38 17-54 105-146 (152)
458 PF06054 CoiA: Competence prot 21.5 46 0.00099 33.5 1.2 18 40-57 28-45 (375)
459 TIGR00311 aIF-2beta translatio 21.4 31 0.00067 30.1 -0.0 44 3-51 84-127 (133)
460 PF09567 RE_MamI: MamI restric 21.3 38 0.00082 33.0 0.5 29 18-57 83-111 (314)
461 smart00105 ArfGap Putative GTP 21.0 33 0.00072 28.5 0.1 30 19-53 5-34 (112)
462 COG5222 Uncharacterized conser 21.0 53 0.0011 32.8 1.5 25 22-50 292-318 (427)
463 KOG0978 E3 ubiquitin ligase in 20.8 69 0.0015 35.2 2.4 38 17-54 643-690 (698)
464 PRK10996 thioredoxin 2; Provis 20.8 39 0.00086 28.7 0.5 31 18-54 3-34 (139)
465 TIGR02387 rpoC1_cyan DNA-direc 20.8 45 0.00098 36.1 1.0 20 175-194 229-248 (619)
466 KOG1088 Uncharacterized conser 20.7 47 0.001 28.7 0.9 15 16-30 97-111 (124)
467 PF14447 Prok-RING_4: Prokaryo 20.7 40 0.00088 25.3 0.5 11 19-29 41-51 (55)
468 PF11238 DUF3039: Protein of u 20.7 21 0.00046 27.1 -1.0 14 17-30 44-57 (58)
469 PF02197 RIIa: Regulatory subu 20.3 79 0.0017 21.6 1.8 14 232-245 24-37 (38)
470 KOG4602 Nanos and related prot 20.2 41 0.00089 32.8 0.5 11 17-27 268-278 (318)
471 COG1328 NrdD Oxygen-sensitive 20.2 44 0.00095 36.7 0.8 28 13-51 637-664 (700)
472 PTZ00303 phosphatidylinositol 20.1 51 0.0011 37.0 1.2 36 18-57 461-496 (1374)
473 KOG1779 40s ribosomal protein 20.1 40 0.00086 27.2 0.3 30 19-54 36-65 (84)
474 KOG2683 Sirtuin 4 and related 20.1 75 0.0016 30.9 2.2 39 18-56 158-225 (305)
No 1
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=100.00 E-value=1.6e-52 Score=411.77 Aligned_cols=302 Identities=36% Similarity=0.612 Sum_probs=248.7
Q ss_pred ChhHHHHHHhhcCCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccchhhhhhcCCCCChhHHHHHHHHHH
Q 020131 1 MRKKLKDELECKNTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESDKLAAQEGGDGDDNARRRRREKLK 80 (330)
Q Consensus 1 Mrk~Le~~l~~~~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~~~~~~e~~~g~~na~r~~~e~~k 80 (330)
||||||+++++.+++++|+||+|+++||.|||++||++.++.|+|.+||++|+++++++++. ..+
T Consensus 112 m~krled~~~d~t~~~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelveDe~~~~~~---------------e~~ 176 (436)
T KOG2593|consen 112 MRKRLEDRLRDDTNVAGYVCPNCQKKYTSLEALQLLDNETGEFHCENCGGELVEDENKLPSK---------------ESR 176 (436)
T ss_pred HHHHHHHHhhhccccccccCCccccchhhhHHHHhhcccCceEEEecCCCchhcccccCchH---------------HHH
Confidence 89999999999999999999999999999999999999999999999999999999987732 224
Q ss_pred HHHHHHHHhHHHHHHHHHhhcCcC-------------CCCCCcHHHHHHHHHhhcccCCCCCCCCCCCCCCCCCCCCCCC
Q 020131 81 DLLQKLEVHLKPLMEQINRVKDLD-------------VPEFGTLQAWEARASAAGRAANGDSSSNDPNKSSQGYGGTPMP 147 (330)
Q Consensus 81 ~~l~r~n~QlkpI~~~Lk~id~i~-------------iP~f~~~~aw~~~a~~~~r~~~g~~~~~~~s~~~~a~~g~pm~ 147 (330)
.+++|||.|+.||+++|+++++|. +|.|+++.+|..+.+.+++. +|+.++.+.+++.|+|+++||+
T Consensus 177 ~~l~~~~~Q~~pi~d~Lk~~e~i~~l~~~~n~~~~~~~p~~~~~~~~~~~~a~~a~~-~G~~~~~d~~rs~G~~~s~~~~ 255 (436)
T KOG2593|consen 177 TALNRLMEQLEPIIDLLKELEGIKPLAPPQNEPKDTPIPALESFLALQADTAKAASE-NGGLNPDDASRSQGGYGSTPMV 255 (436)
T ss_pred HHHHHHHHHHHHHHHHHHHhhccccccccccCCccCcCccccccccccccchhhhhh-ccCCCCCchhhcCCCCCCCcce
Confidence 778999999999999999999965 88999999999885555554 4777777888889999999999
Q ss_pred CCCCceEEEEeeCCCcccccccccccCCCCCCCCchhhhccccccccccccccccccCCCCCCCCCCCCcccCCchhhhh
Q 020131 148 FLGDTKVEVAFSGAEGKQVDVKSETDSTPQKVLPPWMIKQGMNLTKEQRGEVKQESKMDGSSATGGLSDDKKSTVEDDKA 227 (330)
Q Consensus 148 ~lg~~~v~V~ls~~~~~~e~ek~a~~~~~qnaLP~Wm~~Stv~l~~e~~G~vk~e~~~~~~~~~~~~k~~~k~~~~~~~~ 227 (330)
+.+.+.++|++ +.. +++ +....+.||.||+||++|||.++..+.|++..++..+.+-..+...++.+ ...
T Consensus 256 ~~~~t~~~v~~-~d~--neD--~~~e~k~~~~~P~W~~~sti~~~~~~~ge~~~da~~t~~~~~~~~~dd~~-----s~~ 325 (436)
T KOG2593|consen 256 EEFETDNEVNL-GDD--NED--AVEEKKSQKILPEWLAKSTIGGTEAQDGEMALDAVVTESGEGSRNPDDNK-----SEM 325 (436)
T ss_pred eeeecccceec-ccc--ccc--hhhhhhhhhcCChHHHhcccccchhhccchhhhhhhhcccccccCCCcch-----hHH
Confidence 99988888887 443 222 34567789999999999999999988998888776655311112222222 122
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCCCCCCCCccccccccccccccccCCCCCcccccccc---ccCCcc
Q 020131 228 SLQDEYIRAYYAALLKKQQELDEAAKNQQESSNTPISDGLSGASSNRQVGMKSKREEVEGDDDVDWEEAPV---AGTTSE 304 (330)
Q Consensus 228 ~~~ee~l~aYyAal~k~q~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~g~k~k~~~~~~~~~~ew~~~~~---~~~~~~ 304 (330)
+.-+.|+++|||.|+.+++..++.+.+++++....+++.+.+..+.|+|+||+||+|++ |++|+||+.++ .|+..-
T Consensus 326 ~~~d~~~~~~~a~~ke~~e~~~~~n~~es~~e~~~~di~~~~~~~~~~~~~~~k~eeEe-D~~~e~e~~~sv~v~g~~~p 404 (436)
T KOG2593|consen 326 SAHDAYYKAYYAALKEEEELSEEENQDESEEEEPTSDIESATDESARQVYMKSKREEEE-DEDVEWEETASVAVNGRPLP 404 (436)
T ss_pred HHHHHHHHHHHHHHhhhhhhhhhccccccccCcccccccccccHHHHHhhhccchhhhc-cchhhcccCcchhhcCCCCC
Confidence 45689999999999999999999999999998888899999999999999999999875 68999999888 444444
Q ss_pred cccccccc--ccccccCC-----CCCcccccCC
Q 020131 305 SFKVHDLN--VEAEASAE-----DEDDIDWEEG 330 (330)
Q Consensus 305 ~~~~~d~~--~~~~~~~~-----~~d~~~w~~~ 330 (330)
-|+| |+| |++....+ +.|++||+++
T Consensus 405 ~~~v-d~~~~~~~m~~~eke~~~~~~~~d~ed~ 436 (436)
T KOG2593|consen 405 LSQV-DLNMVVTAMTPSEKENYIEGDQDDDEDD 436 (436)
T ss_pred cccc-ccchhhhhcCchhccccccccccccccC
Confidence 5787 888 66655443 5688999975
No 2
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=99.54 E-value=9.1e-15 Score=131.63 Aligned_cols=51 Identities=31% Similarity=0.630 Sum_probs=47.7
Q ss_pred ChhHHHHHHhhcCCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccch
Q 020131 1 MRKKLKDELECKNTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESD 57 (330)
Q Consensus 1 Mrk~Le~~l~~~~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~ 57 (330)
|+++|+.+++++.++++|+||+|+++|||+||+++ +|+||.||++|++.++
T Consensus 101 ~~~klk~~l~~e~~~~~Y~Cp~C~~rytf~eA~~~------~F~Cp~Cg~~L~~~dn 151 (178)
T PRK06266 101 ELKKLKEQLEEEENNMFFFCPNCHIRFTFDEAMEY------GFRCPQCGEMLEEYDN 151 (178)
T ss_pred HHHHHHHHhhhccCCCEEECCCCCcEEeHHHHhhc------CCcCCCCCCCCeeccc
Confidence 46899999999999999999999999999999986 8999999999998765
No 3
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=99.49 E-value=3.1e-14 Score=125.82 Aligned_cols=51 Identities=31% Similarity=0.587 Sum_probs=47.9
Q ss_pred ChhHHHHHHhhcCCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccch
Q 020131 1 MRKKLKDELECKNTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESD 57 (330)
Q Consensus 1 Mrk~Le~~l~~~~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~ 57 (330)
|.++|+.+++++.++++|+||+|+++|||+||+++ +|+||.||++|++.++
T Consensus 93 ~~~~lk~~l~~e~~~~~Y~Cp~c~~r~tf~eA~~~------~F~Cp~Cg~~L~~~dn 143 (158)
T TIGR00373 93 TAKKLREKLEFETNNMFFICPNMCVRFTFNEAMEL------NFTCPRCGAMLDYLDN 143 (158)
T ss_pred HHHHHHHHHhhccCCCeEECCCCCcEeeHHHHHHc------CCcCCCCCCEeeeccC
Confidence 46789999999999999999999999999999997 8999999999998876
No 4
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=99.45 E-value=6.5e-14 Score=122.06 Aligned_cols=58 Identities=40% Similarity=0.800 Sum_probs=54.0
Q ss_pred ChhHHHHHHhhcCCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccchhh
Q 020131 1 MRKKLKDELECKNTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESDKL 59 (330)
Q Consensus 1 Mrk~Le~~l~~~~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~~~ 59 (330)
|+++|+.+++++.++.+|+||+|+.+|+++||+.+.|+ ++.|.||+||++|++.++..
T Consensus 83 ~~~~L~~~l~~e~~~~~Y~Cp~C~~~y~~~ea~~~~d~-~~~f~Cp~Cg~~l~~~dn~~ 140 (147)
T smart00531 83 MRKRLEDKLEDETNNAYYKCPNCQSKYTFLEANQLLDM-DGTFTCPRCGEELEEDDNSE 140 (147)
T ss_pred HHHHHHHHHhcccCCcEEECcCCCCEeeHHHHHHhcCC-CCcEECCCCCCEEEEcCchh
Confidence 68999999999999999999999999999999999997 67899999999999987753
No 5
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=99.22 E-value=1.9e-11 Score=110.00 Aligned_cols=75 Identities=32% Similarity=0.646 Sum_probs=60.3
Q ss_pred ChhHHHHHHhhcCCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccchhhhhhcCCCCChhHHHHHHHHHH
Q 020131 1 MRKKLKDELECKNTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESDKLAAQEGGDGDDNARRRRREKLK 80 (330)
Q Consensus 1 Mrk~Le~~l~~~~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~~~~~~e~~~g~~na~r~~~e~~k 80 (330)
|.++|+..++..+++.+|+||+|+.+|||.+|+.+ +|.||.||+.|++.++.
T Consensus 97 ~le~Lk~~le~~~~~~~y~C~~~~~r~sfdeA~~~------~F~Cp~Cg~~L~~~d~s---------------------- 148 (176)
T COG1675 97 ILEKLKRKLEKETENNYYVCPNCHVKYSFDEAMEL------GFTCPKCGEDLEEYDSS---------------------- 148 (176)
T ss_pred HHHHHHHHHHhhccCCceeCCCCCCcccHHHHHHh------CCCCCCCCchhhhccch----------------------
Confidence 46889999999999999999999999999999999 89999999999887652
Q ss_pred HHHHHHHHhHHHHHHHHHhhcCc
Q 020131 81 DLLQKLEVHLKPLMEQINRVKDL 103 (330)
Q Consensus 81 ~~l~r~n~QlkpI~~~Lk~id~i 103 (330)
..+..+...++.|...|.+....
T Consensus 149 ~~i~~l~~~i~~l~~~l~~~~~~ 171 (176)
T COG1675 149 EEIEELESELDELEEELERNDKL 171 (176)
T ss_pred HHHHHHHHHHHHHHHHHhccccc
Confidence 23455555555566666555443
No 6
>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=97.59 E-value=2.7e-05 Score=54.56 Aligned_cols=33 Identities=27% Similarity=0.540 Sum_probs=26.5
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccc
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAES 56 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~ 56 (330)
|+||+|+.++. ++|+.++.|.|+.||..|.+..
T Consensus 1 m~Cp~Cg~~~~------~~D~~~g~~vC~~CG~Vl~e~~ 33 (43)
T PF08271_consen 1 MKCPNCGSKEI------VFDPERGELVCPNCGLVLEENI 33 (43)
T ss_dssp ESBTTTSSSEE------EEETTTTEEEETTT-BBEE-TT
T ss_pred CCCcCCcCCce------EEcCCCCeEECCCCCCEeeccc
Confidence 79999999884 6678889999999999996543
No 7
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=97.46 E-value=3.4e-05 Score=54.79 Aligned_cols=34 Identities=21% Similarity=0.532 Sum_probs=27.0
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAES 56 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~ 56 (330)
..|+||+||..|++.+ ....++||+||+++....
T Consensus 2 ~~y~C~~CG~~~~~~~-------~~~~~~Cp~CG~~~~~~~ 35 (46)
T PRK00398 2 AEYKCARCGREVELDE-------YGTGVRCPYCGYRILFKE 35 (46)
T ss_pred CEEECCCCCCEEEECC-------CCCceECCCCCCeEEEcc
Confidence 4699999999998733 223699999999998644
No 8
>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=97.08 E-value=0.00025 Score=48.42 Aligned_cols=34 Identities=38% Similarity=0.754 Sum_probs=27.8
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccc
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAES 56 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~ 56 (330)
++||.||+.|.. .++|....-+|+.||++|+...
T Consensus 2 r~C~~Cg~~Yh~-----~~~pP~~~~~Cd~cg~~L~qR~ 35 (36)
T PF05191_consen 2 RICPKCGRIYHI-----EFNPPKVEGVCDNCGGELVQRK 35 (36)
T ss_dssp EEETTTTEEEET-----TTB--SSTTBCTTTTEBEBEEG
T ss_pred cCcCCCCCcccc-----ccCCCCCCCccCCCCCeeEeCC
Confidence 689999999986 6787777889999999998754
No 9
>PRK14526 adenylate kinase; Provisional
Probab=96.82 E-value=0.0018 Score=59.68 Aligned_cols=63 Identities=29% Similarity=0.556 Sum_probs=51.3
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccchhhhhhcCCCCChhHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESDKLAAQEGGDGDDNARRRRREKLKDLLQKLEVHLKPLMEQ 96 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~~~~~~e~~~g~~na~r~~~e~~k~~l~r~n~QlkpI~~~ 96 (330)
..+||.||..|.. .+.|....-.|+.|++.|+...++. .+.++.+|..+..++.||+++
T Consensus 122 R~~~~~~g~~y~~-----~~~pp~~~~~~~~~~~~l~~R~DD~----------------~e~i~~Rl~~y~~~t~pv~~~ 180 (211)
T PRK14526 122 RRICKSCNNIFNI-----YTLPTKEKGICDVCKGDLYQRKDDK----------------EESLKTRLQEYKLQTKPLIEF 180 (211)
T ss_pred CCcccccCCcccc-----ccCCCCccCcCCCCCCeeeccCCCC----------------HHHHHHHHHHHHHhhhHHHHH
Confidence 4689999999997 4666666679999999998766642 246678999999999999999
Q ss_pred HHhh
Q 020131 97 INRV 100 (330)
Q Consensus 97 Lk~i 100 (330)
++..
T Consensus 181 y~~~ 184 (211)
T PRK14526 181 YSKC 184 (211)
T ss_pred HHhc
Confidence 9864
No 10
>PLN02674 adenylate kinase
Probab=96.74 E-value=0.0022 Score=60.74 Aligned_cols=62 Identities=18% Similarity=0.276 Sum_probs=50.8
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccchhhhhhcCCCCChhHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESDKLAAQEGGDGDDNARRRRREKLKDLLQKLEVHLKPLMEQ 96 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~~~~~~e~~~g~~na~r~~~e~~k~~l~r~n~QlkpI~~~ 96 (330)
.++||.||+.|.. .++|....-+|..||.+|+...++.+ +.++.+|..|+.+..||+++
T Consensus 158 R~~~~~~g~~yn~-----~~~pp~~~~~~~~~g~~L~~R~DD~~----------------e~i~~RL~~Y~~~t~pv~~~ 216 (244)
T PLN02674 158 RWIHPSSGRTYHT-----KFAPPKVPGVDDVTGEPLIQRKDDTA----------------AVLKSRLEAFHKQTEPVIDY 216 (244)
T ss_pred cccccccCCcccc-----ccCCCcccCcccccCCccccCCCCCH----------------HHHHHHHHHHHHHhHHHHHH
Confidence 4789999999997 46665555679999999987766422 46678999999999999999
Q ss_pred HHh
Q 020131 97 INR 99 (330)
Q Consensus 97 Lk~ 99 (330)
+++
T Consensus 217 Y~~ 219 (244)
T PLN02674 217 YAK 219 (244)
T ss_pred HHh
Confidence 987
No 11
>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=96.57 E-value=0.0015 Score=44.29 Aligned_cols=35 Identities=20% Similarity=0.545 Sum_probs=26.5
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
.+.||+|+..|..-+..-. .....+.|++||+.+.
T Consensus 2 ~~~CP~C~~~~~v~~~~~~--~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 2 RIQCPNCKTSFRVVDSQLG--ANGGKVRCGKCGHVWY 36 (38)
T ss_pred EEECCCCCCEEEeCHHHcC--CCCCEEECCCCCCEEE
Confidence 4789999999997654432 3334799999999884
No 12
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=96.12 E-value=0.0022 Score=46.78 Aligned_cols=33 Identities=21% Similarity=0.625 Sum_probs=25.2
Q ss_pred CCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 15 VQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 15 ~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
...|+|-+||+.|+.+.+ +....|++||+.+..
T Consensus 4 ~~~Y~C~~Cg~~~~~~~~-------~~~irCp~Cg~rIl~ 36 (49)
T COG1996 4 MMEYKCARCGREVELDQE-------TRGIRCPYCGSRILV 36 (49)
T ss_pred eEEEEhhhcCCeeehhhc-------cCceeCCCCCcEEEE
Confidence 358999999999943322 246999999998754
No 13
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=96.06 E-value=0.0047 Score=42.03 Aligned_cols=34 Identities=26% Similarity=0.665 Sum_probs=27.2
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
...||+|+++|...|.. |-+....++|+.||+.+
T Consensus 2 ~i~Cp~C~~~y~i~d~~--ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 2 IITCPNCQAKYEIDDEK--IPPKGRKVRCSKCGHVF 35 (36)
T ss_pred EEECCCCCCEEeCCHHH--CCCCCcEEECCCCCCEe
Confidence 46899999999987665 44556689999999864
No 14
>PRK00279 adk adenylate kinase; Reviewed
Probab=95.85 E-value=0.015 Score=52.80 Aligned_cols=63 Identities=24% Similarity=0.516 Sum_probs=50.6
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccchhhhhhcCCCCChhHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESDKLAAQEGGDGDDNARRRRREKLKDLLQKLEVHLKPLMEQ 96 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~~~~~~e~~~g~~na~r~~~e~~k~~l~r~n~QlkpI~~~ 96 (330)
..+||.||..|.. .++|....=.|..||..|+...++. .+.++.+|..|..++.||+++
T Consensus 127 R~~~~~~g~~~~~-----~~~~p~~~~~~~~~~~~l~~r~dd~----------------~~~i~~Rl~~y~~~~~~i~~~ 185 (215)
T PRK00279 127 RRICPACGRTYHV-----KFNPPKVEGKCDVCGEELIQRADDN----------------EETVRKRLEVYHKQTAPLIDY 185 (215)
T ss_pred CcccCccCCcccc-----cCCCCCCcCcCcCCCCcccCCCCCC----------------HHHHHHHHHHHHHhhHHHHHH
Confidence 4689999999987 4666656678999999997765432 245678899999999999999
Q ss_pred HHhh
Q 020131 97 INRV 100 (330)
Q Consensus 97 Lk~i 100 (330)
++..
T Consensus 186 y~~~ 189 (215)
T PRK00279 186 YKKK 189 (215)
T ss_pred HHhC
Confidence 9875
No 15
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=95.84 E-value=0.0046 Score=52.00 Aligned_cols=31 Identities=29% Similarity=0.802 Sum_probs=23.9
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAE 55 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~ 55 (330)
-.+||.||+||=. .....-+||+||+.+...
T Consensus 9 KR~Cp~CG~kFYD--------Lnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 9 KRTCPSCGAKFYD--------LNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred cccCCCCcchhcc--------CCCCCccCCCCCCccCcc
Confidence 4689999999954 333457899999998653
No 16
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=95.82 E-value=0.0057 Score=43.54 Aligned_cols=30 Identities=27% Similarity=0.675 Sum_probs=24.8
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
.|+|..||..|+.. ..+..+|++||+.+..
T Consensus 2 ~Y~C~~Cg~~~~~~--------~~~~irC~~CG~rIly 31 (44)
T smart00659 2 IYICGECGRENEIK--------SKDVVRCRECGYRILY 31 (44)
T ss_pred EEECCCCCCEeecC--------CCCceECCCCCceEEE
Confidence 69999999999853 2357999999998865
No 17
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=95.68 E-value=0.0031 Score=42.93 Aligned_cols=32 Identities=28% Similarity=0.797 Sum_probs=24.5
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
.|.|+.||..|+.+....- ...-.||.||.++
T Consensus 5 ~y~C~~Cg~~fe~~~~~~~----~~~~~CP~Cg~~~ 36 (41)
T smart00834 5 EYRCEDCGHTFEVLQKISD----DPLATCPECGGDV 36 (41)
T ss_pred EEEcCCCCCEEEEEEecCC----CCCCCCCCCCCcc
Confidence 5999999999997544322 2367899999965
No 18
>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=95.53 E-value=0.0039 Score=41.05 Aligned_cols=26 Identities=27% Similarity=0.727 Sum_probs=15.1
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
.||.|+..|+. .+...|+|+.|+.++
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 69999999997 334579999999876
No 19
>TIGR01351 adk adenylate kinases. Adenylate kinase (EC 2.7.4.3) converts ATP + AMP to ADP + ADP, that is, uses ATP as a phosphate donor for AMP. Most members of this family are known or believed to be adenylate kinase. However, some members accept other nucleotide triphosphates as donors, may be unable to use ATP, and may fail to complement adenylate kinase mutants. An example of a nucleoside-triphosphate--adenylate kinase (EC 2.7.4.10) is a GTP:AMP phosphotransferase. This family is designated subfamily rather than equivalog for this reason.
Probab=95.43 E-value=0.026 Score=51.11 Aligned_cols=63 Identities=21% Similarity=0.332 Sum_probs=48.3
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccchhhhhhcCCCCChhHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESDKLAAQEGGDGDDNARRRRREKLKDLLQKLEVHLKPLMEQ 96 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~~~~~~e~~~g~~na~r~~~e~~k~~l~r~n~QlkpI~~~ 96 (330)
.++||.||..|.. .++|....-.|..|+..|+...++. .+.++.+|..|+.++.||+++
T Consensus 124 R~~~~~~g~~y~~-----~~~~p~~~~~~~~~~~~l~~R~dD~----------------~e~i~~Rl~~y~~~~~~v~~~ 182 (210)
T TIGR01351 124 RRICPSCGRVYHL-----KFNPPKVPGCDDCTGELLIQREDDT----------------EEVVKKRLEVYKEQTEPLIDY 182 (210)
T ss_pred CCccCCcCCcccc-----ccCCCccCCcCcccCCccccCCCCC----------------HHHHHHHHHHHHHhhHHHHHH
Confidence 4789999999975 3444444567999999997655432 135678899999999999999
Q ss_pred HHhh
Q 020131 97 INRV 100 (330)
Q Consensus 97 Lk~i 100 (330)
++.-
T Consensus 183 y~~~ 186 (210)
T TIGR01351 183 YKKR 186 (210)
T ss_pred HHhC
Confidence 9874
No 20
>PRK00420 hypothetical protein; Validated
Probab=95.36 E-value=0.043 Score=46.49 Aligned_cols=66 Identities=20% Similarity=0.340 Sum_probs=40.9
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccchhhhhhcCCCCChhHHH-HHHHHHHHHHHHHHHhHHHHH
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESDKLAAQEGGDGDDNARR-RRREKLKDLLQKLEVHLKPLM 94 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~~~~~~e~~~g~~na~r-~~~e~~k~~l~r~n~QlkpI~ 94 (330)
....||.||.-+. -...|...||.||..+.-..... +++ .....++.....++..|.-|+
T Consensus 22 l~~~CP~Cg~pLf--------~lk~g~~~Cp~Cg~~~~v~~~ee-----------~~~~~~~~~~~~~~~il~~ki~~L~ 82 (112)
T PRK00420 22 LSKHCPVCGLPLF--------ELKDGEVVCPVHGKVYIVKSDEE-----------EKKVESKETLKEVEEVLIEKINYLA 82 (112)
T ss_pred ccCCCCCCCCcce--------ecCCCceECCCCCCeeeeccHHH-----------HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4578999996543 22457899999999886543321 111 112233455566677777777
Q ss_pred HHHHhh
Q 020131 95 EQINRV 100 (330)
Q Consensus 95 ~~Lk~i 100 (330)
..|..-
T Consensus 83 ~kL~~e 88 (112)
T PRK00420 83 KKLKED 88 (112)
T ss_pred HhCccc
Confidence 666655
No 21
>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=95.22 E-value=0.0081 Score=39.93 Aligned_cols=27 Identities=26% Similarity=0.814 Sum_probs=21.7
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
.|+|+.||..|.... ..+.||.||..=
T Consensus 1 ~~~C~~CGy~y~~~~---------~~~~CP~Cg~~~ 27 (33)
T cd00350 1 KYVCPVCGYIYDGEE---------APWVCPVCGAPK 27 (33)
T ss_pred CEECCCCCCEECCCc---------CCCcCcCCCCcH
Confidence 389999999987533 369999999854
No 22
>PTZ00088 adenylate kinase 1; Provisional
Probab=95.13 E-value=0.023 Score=53.20 Aligned_cols=68 Identities=24% Similarity=0.407 Sum_probs=47.1
Q ss_pred eeecCCCCccccHHHHH-hhcC-C-CCCCeeccCCCc--cccccchhhhhhcCCCCChhHHHHHHHHHHHHHHHHHHhHH
Q 020131 17 EYICPNCQRRYNALDAL-RLVS-L-EDDSFHCENCNG--ELVAESDKLAAQEGGDGDDNARRRRREKLKDLLQKLEVHLK 91 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~-~Lld-~-~~~~F~C~~Cg~--eL~~~~~~~~~~e~~~g~~na~r~~~e~~k~~l~r~n~Qlk 91 (330)
..+||.||..|...-+. +-++ | ....-.|..||. .|+...++. -+.++.+|..++.+..
T Consensus 130 Rr~~~~~g~~y~~~~~~~~~~~~pp~~~~~~c~~~~~~~~l~~R~DD~----------------~e~i~~Rl~~Y~~~t~ 193 (229)
T PTZ00088 130 RRICNTCNRNFNIAHIRSDPYDMPPILPPADCEGCKGNPKLQKRSDDT----------------EEIVAHRLNTYESTNS 193 (229)
T ss_pred CcCCCccCCcceecccccccccCCCCCCCCcccccCCcccccCCCCCC----------------HHHHHHHHHHHHHHhH
Confidence 37899999999864221 1111 1 111237999996 677655532 2456788999999999
Q ss_pred HHHHHHHhh
Q 020131 92 PLMEQINRV 100 (330)
Q Consensus 92 pI~~~Lk~i 100 (330)
||+++++..
T Consensus 194 pl~~~y~~~ 202 (229)
T PTZ00088 194 PIIQFFKNE 202 (229)
T ss_pred HHHHHHHHc
Confidence 999999876
No 23
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=95.10 E-value=0.012 Score=50.89 Aligned_cols=30 Identities=17% Similarity=0.341 Sum_probs=23.3
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
-++||.||+||=.| ....-+||+||+.+..
T Consensus 9 Kr~Cp~cg~kFYDL--------nk~p~vcP~cg~~~~~ 38 (129)
T TIGR02300 9 KRICPNTGSKFYDL--------NRRPAVSPYTGEQFPP 38 (129)
T ss_pred cccCCCcCcccccc--------CCCCccCCCcCCccCc
Confidence 47899999999552 2346899999999754
No 24
>PHA02768 hypothetical protein; Provisional
Probab=95.02 E-value=0.0082 Score=44.80 Aligned_cols=35 Identities=20% Similarity=0.404 Sum_probs=27.4
Q ss_pred CeeecCCCCccccHHHHHhh--cCCCCCCeeccCCCcc
Q 020131 16 QEYICPNCQRRYNALDALRL--VSLEDDSFHCENCNGE 51 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~L--ld~~~~~F~C~~Cg~e 51 (330)
-+|.||.||++|+..+++.. .... -.|.|..|+-.
T Consensus 4 ~~y~C~~CGK~Fs~~~~L~~H~r~H~-k~~kc~~C~k~ 40 (55)
T PHA02768 4 LGYECPICGEIYIKRKSMITHLRKHN-TNLKLSNCKRI 40 (55)
T ss_pred cccCcchhCCeeccHHHHHHHHHhcC-CcccCCcccce
Confidence 47999999999999998853 1222 37999999964
No 25
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=94.91 E-value=0.022 Score=38.86 Aligned_cols=34 Identities=26% Similarity=0.650 Sum_probs=25.9
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
.-.||+|+++|..-+.. |......++|+.|++..
T Consensus 2 ~i~CP~C~~~f~v~~~~--l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 2 IITCPNCQTRFRVPDDK--LPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EEECCCCCceEEcCHHH--cccCCcEEECCCCCcEe
Confidence 35799999999976553 23445689999999875
No 26
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=94.73 E-value=0.0092 Score=51.75 Aligned_cols=40 Identities=15% Similarity=0.357 Sum_probs=27.5
Q ss_pred CCCCeeecCCCCccccHHHHHhhc----------CCC--CCCeeccCCCccc
Q 020131 13 NTVQEYICPNCQRRYNALDALRLV----------SLE--DDSFHCENCNGEL 52 (330)
Q Consensus 13 ~~~~~Y~CP~C~~~YT~lDA~~Ll----------d~~--~~~F~C~~Cg~eL 52 (330)
..+..|.|+.||..|+..++..-| .|. ...|.||.||+.-
T Consensus 66 ~~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~ 117 (135)
T PRK03824 66 EEEAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRD 117 (135)
T ss_pred ecceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCC
Confidence 445789999999999987532221 221 2357899999763
No 27
>PRK10220 hypothetical protein; Provisional
Probab=94.66 E-value=0.016 Score=48.80 Aligned_cols=30 Identities=27% Similarity=0.713 Sum_probs=24.5
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAES 56 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~ 56 (330)
.||.|+..||+.| ...|.||.|++++...+
T Consensus 5 ~CP~C~seytY~d--------~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 5 HCPKCNSEYTYED--------NGMYICPECAHEWNDAE 34 (111)
T ss_pred cCCCCCCcceEcC--------CCeEECCcccCcCCccc
Confidence 5999999999743 24699999999997654
No 28
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=94.60 E-value=0.013 Score=49.19 Aligned_cols=29 Identities=28% Similarity=0.652 Sum_probs=23.7
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCcccccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAE 55 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~ 55 (330)
-||.|+..||+.| ...|.||.|++++...
T Consensus 4 ~CP~C~seytY~d--------g~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 4 PCPKCNSEYTYHD--------GTQLICPSCLYEWNEN 32 (109)
T ss_pred cCCcCCCcceEec--------CCeeECcccccccccc
Confidence 4999999999742 3469999999999653
No 29
>PRK14530 adenylate kinase; Provisional
Probab=94.57 E-value=0.063 Score=48.76 Aligned_cols=62 Identities=24% Similarity=0.629 Sum_probs=48.0
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccchhhhhhcCCCCChhHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESDKLAAQEGGDGDDNARRRRREKLKDLLQKLEVHLKPLMEQI 97 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~~~~~~e~~~g~~na~r~~~e~~k~~l~r~n~QlkpI~~~L 97 (330)
..||.|+..|.. .+.|....=.|..||..|+...++. .+.++.+|..+..+..||++++
T Consensus 127 ~~~~~~g~~~~~-----~~~~p~~~~~~~~~~~rl~~R~dD~----------------~e~i~~Rl~~y~~~~~~v~~~y 185 (215)
T PRK14530 127 RVCPDCGANYHV-----EFNQPEEEGVCDECGGELIQRDDDT----------------EETVRERLDVFEENTEPVIEHY 185 (215)
T ss_pred CcCcccCCcccc-----CCCCCcccccCcccCCcccCCCCCC----------------HHHHHHHHHHHHHHHHHHHHHH
Confidence 689999999975 3444444457999999997765532 2467889999999999999999
Q ss_pred Hhh
Q 020131 98 NRV 100 (330)
Q Consensus 98 k~i 100 (330)
+.-
T Consensus 186 ~~~ 188 (215)
T PRK14530 186 RDQ 188 (215)
T ss_pred HhC
Confidence 873
No 30
>PLN02459 probable adenylate kinase
Probab=94.54 E-value=0.056 Score=51.91 Aligned_cols=66 Identities=20% Similarity=0.369 Sum_probs=48.2
Q ss_pred eeecCCCCccccHHHHH--------hhcCCCCCCeeccCCCccccccchhhhhhcCCCCChhHHHHHHHHHHHHHHHHHH
Q 020131 17 EYICPNCQRRYNALDAL--------RLVSLEDDSFHCENCNGELVAESDKLAAQEGGDGDDNARRRRREKLKDLLQKLEV 88 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~--------~Lld~~~~~F~C~~Cg~eL~~~~~~~~~~e~~~g~~na~r~~~e~~k~~l~r~n~ 88 (330)
.++||.||..|...-+. ..++|.. --|+.|+..|+...++.+ +.++.+|..|+.
T Consensus 153 R~~~~~~g~~Yn~~~~~~~~~~~~~~~~~~p~--~~~~~~~~~L~~R~DD~~----------------e~i~kRL~~Y~~ 214 (261)
T PLN02459 153 RRICSECGKNFNVADIDLKGEDGRPGIVMPPL--LPPPECASKLITRADDTE----------------EVVKARLRVYKE 214 (261)
T ss_pred cccccccCccccccccccccccccccccCCCC--CCCcccccccccCCCCCH----------------HHHHHHHHHHHH
Confidence 47899999999864322 1234321 236789999987666422 456788999999
Q ss_pred hHHHHHHHHHhh
Q 020131 89 HLKPLMEQINRV 100 (330)
Q Consensus 89 QlkpI~~~Lk~i 100 (330)
++.||+++++..
T Consensus 215 ~t~pv~~~Y~~~ 226 (261)
T PLN02459 215 ESQPVEDFYRKR 226 (261)
T ss_pred HhHHHHHHHHhc
Confidence 999999999875
No 31
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=94.00 E-value=0.022 Score=35.19 Aligned_cols=23 Identities=43% Similarity=1.057 Sum_probs=17.2
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
+||+||+.... ...| |++||++|
T Consensus 1 ~Cp~CG~~~~~----------~~~f-C~~CG~~l 23 (23)
T PF13240_consen 1 YCPNCGAEIED----------DAKF-CPNCGTPL 23 (23)
T ss_pred CCcccCCCCCC----------cCcc-hhhhCCcC
Confidence 59999998754 1234 99999876
No 32
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=93.82 E-value=0.019 Score=42.65 Aligned_cols=34 Identities=21% Similarity=0.583 Sum_probs=25.2
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAE 55 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~ 55 (330)
.|.||.|+..++.-+... .....|+.||..|+-.
T Consensus 2 ~~~CP~CG~~iev~~~~~-----GeiV~Cp~CGaeleVv 35 (54)
T TIGR01206 2 QFECPDCGAEIELENPEL-----GELVICDECGAELEVV 35 (54)
T ss_pred ccCCCCCCCEEecCCCcc-----CCEEeCCCCCCEEEEE
Confidence 479999999987633221 2468999999999653
No 33
>PF14353 CpXC: CpXC protein
Probab=93.73 E-value=0.018 Score=48.70 Aligned_cols=35 Identities=20% Similarity=0.547 Sum_probs=23.0
Q ss_pred eecCCCCccccHHHHHhhc-------------CCCCCCeeccCCCcccc
Q 020131 18 YICPNCQRRYNALDALRLV-------------SLEDDSFHCENCNGELV 53 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Ll-------------d~~~~~F~C~~Cg~eL~ 53 (330)
..||.|+..|.+ +++.++ +-.-..|.||.||....
T Consensus 2 itCP~C~~~~~~-~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~ 49 (128)
T PF14353_consen 2 ITCPHCGHEFEF-EVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFR 49 (128)
T ss_pred cCCCCCCCeeEE-EEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCcee
Confidence 369999998865 223333 33334689999997654
No 34
>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=93.69 E-value=0.019 Score=41.46 Aligned_cols=34 Identities=24% Similarity=0.502 Sum_probs=21.4
Q ss_pred eecCCCCccccHHHHHh--------hcCCCCCCeeccCCCcc
Q 020131 18 YICPNCQRRYNALDALR--------LVSLEDDSFHCENCNGE 51 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~--------Lld~~~~~F~C~~Cg~e 51 (330)
|+|+.|+..|....-.. .|+-....|+||.|+..
T Consensus 2 y~C~~CgyvYd~~~Gd~~~~i~pGt~F~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 2 YQCPVCGYVYDPEKGDPENGIPPGTPFEDLPDDWVCPVCGAP 43 (47)
T ss_dssp EEETTTSBEEETTTBBGGGTB-TT--GGGS-TT-B-TTTSSB
T ss_pred cCCCCCCEEEcCCcCCcccCcCCCCCHHHCCCCCcCcCCCCc
Confidence 89999999998654321 12222457999999976
No 35
>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=93.58 E-value=0.033 Score=38.94 Aligned_cols=32 Identities=34% Similarity=0.889 Sum_probs=24.0
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCc-cc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNG-EL 52 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~-eL 52 (330)
.|+|+.||..|..+-- ++- ...-.||.||+ .+
T Consensus 5 ey~C~~Cg~~fe~~~~---~~~-~~~~~CP~Cg~~~~ 37 (42)
T PF09723_consen 5 EYRCEECGHEFEVLQS---ISE-DDPVPCPECGSTEV 37 (42)
T ss_pred EEEeCCCCCEEEEEEE---cCC-CCCCcCCCCCCCce
Confidence 5999999999986432 222 34789999999 55
No 36
>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=93.53 E-value=0.033 Score=40.69 Aligned_cols=36 Identities=19% Similarity=0.396 Sum_probs=23.3
Q ss_pred eeecCCCCccccHHHHH--hh------cCCCCCCeeccCCCccc
Q 020131 17 EYICPNCQRRYNALDAL--RL------VSLEDDSFHCENCNGEL 52 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~--~L------ld~~~~~F~C~~Cg~eL 52 (330)
.|+|..||..|....=. .- |.-....|+||.||..-
T Consensus 1 ~y~C~~CgyiYd~~~Gd~~~~i~pGt~f~~Lp~~w~CP~C~a~K 44 (50)
T cd00730 1 KYECRICGYIYDPAEGDPDEGIPPGTPFEDLPDDWVCPVCGAGK 44 (50)
T ss_pred CcCCCCCCeEECCCCCCcccCcCCCCCHhHCCCCCCCCCCCCcH
Confidence 38999999999853211 00 11112379999999764
No 37
>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=93.28 E-value=0.026 Score=40.57 Aligned_cols=32 Identities=38% Similarity=0.830 Sum_probs=23.1
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCc-cc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNG-EL 52 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~-eL 52 (330)
.|+|+.|+.+|..+- .++- ...-.||.||. .+
T Consensus 5 ey~C~~Cg~~fe~~~---~~~~-~~~~~CP~Cg~~~~ 37 (52)
T TIGR02605 5 EYRCTACGHRFEVLQ---KMSD-DPLATCPECGGEKL 37 (52)
T ss_pred EEEeCCCCCEeEEEE---ecCC-CCCCCCCCCCCCce
Confidence 599999999999752 2221 23567999998 44
No 38
>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=93.12 E-value=0.026 Score=37.65 Aligned_cols=29 Identities=24% Similarity=0.705 Sum_probs=20.5
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
|+|..||+.++. .+ ....+|++||..+..
T Consensus 1 Y~C~~Cg~~~~~-------~~-~~~irC~~CG~RIly 29 (32)
T PF03604_consen 1 YICGECGAEVEL-------KP-GDPIRCPECGHRILY 29 (32)
T ss_dssp EBESSSSSSE-B-------ST-SSTSSBSSSS-SEEB
T ss_pred CCCCcCCCeeEc-------CC-CCcEECCcCCCeEEE
Confidence 899999999981 22 235899999987643
No 39
>PRK14529 adenylate kinase; Provisional
Probab=93.11 E-value=0.11 Score=48.59 Aligned_cols=64 Identities=17% Similarity=0.224 Sum_probs=44.6
Q ss_pred eeecCCCCccccHHHHHhhcCC-CCCCeeccCCCccccccchhhhhhcCCCCChhHHHHHHHHHHHHHHHHHHh---HHH
Q 020131 17 EYICPNCQRRYNALDALRLVSL-EDDSFHCENCNGELVAESDKLAAQEGGDGDDNARRRRREKLKDLLQKLEVH---LKP 92 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~-~~~~F~C~~Cg~eL~~~~~~~~~~e~~~g~~na~r~~~e~~k~~l~r~n~Q---lkp 92 (330)
..+||.|+..|.-.- +.| ....-.|+.||++|+...|+.. -+.++.+|..|+++ +.|
T Consensus 126 R~~c~~~~~~~~~~~----~~~p~~~~~~cd~~~~~l~~R~DD~~---------------ee~i~~Rl~~y~~~~~~~~~ 186 (223)
T PRK14529 126 RRLCKNDNNHPNNIF----IDAIKPDGDVCRVCGGELSTRADDQD---------------EEAINKRHDIYYDTETGTLA 186 (223)
T ss_pred CccccccCCcccccc----cCCCcccCCcCcCcCCccccCCCCCc---------------HHHHHHHHHHHHHcccccch
Confidence 367999988776522 222 2223489999999988776421 13567889999998 568
Q ss_pred HHHHHHh
Q 020131 93 LMEQINR 99 (330)
Q Consensus 93 I~~~Lk~ 99 (330)
|++++++
T Consensus 187 ~~~~y~~ 193 (223)
T PRK14529 187 AAYFFKD 193 (223)
T ss_pred HHHHHhh
Confidence 8899985
No 40
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=93.10 E-value=0.039 Score=34.77 Aligned_cols=25 Identities=40% Similarity=0.988 Sum_probs=18.2
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
..+||+||+.-.. +.-.|++||.+|
T Consensus 2 ~~~Cp~Cg~~~~~-----------~~~fC~~CG~~L 26 (26)
T PF13248_consen 2 EMFCPNCGAEIDP-----------DAKFCPNCGAKL 26 (26)
T ss_pred cCCCcccCCcCCc-----------ccccChhhCCCC
Confidence 3579999995422 345799999886
No 41
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=92.37 E-value=0.086 Score=38.41 Aligned_cols=35 Identities=17% Similarity=0.583 Sum_probs=23.9
Q ss_pred eeecCCCCccccHHHHHhhcC----CCCCCeeccCCCcc
Q 020131 17 EYICPNCQRRYNALDALRLVS----LEDDSFHCENCNGE 51 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld----~~~~~F~C~~Cg~e 51 (330)
.|.||.|++.|+.-.-...+. .....+.||.|...
T Consensus 2 ~f~CP~C~~~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~ 40 (54)
T PF05605_consen 2 SFTCPYCGKGFSESSLVEHCEDEHRSESKNVVCPICSSR 40 (54)
T ss_pred CcCCCCCCCccCHHHHHHHHHhHCcCCCCCccCCCchhh
Confidence 699999999666544333322 13457999999864
No 42
>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=92.23 E-value=0.048 Score=36.63 Aligned_cols=28 Identities=18% Similarity=0.472 Sum_probs=21.3
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
.|+|+.||..|...+ + ...||.||.+-.
T Consensus 2 ~~~C~~CG~i~~g~~------~---p~~CP~Cg~~~~ 29 (34)
T cd00729 2 VWVCPVCGYIHEGEE------A---PEKCPICGAPKE 29 (34)
T ss_pred eEECCCCCCEeECCc------C---CCcCcCCCCchH
Confidence 699999998886532 1 358999998653
No 43
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=91.85 E-value=0.047 Score=54.10 Aligned_cols=29 Identities=31% Similarity=0.848 Sum_probs=26.4
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
-|.+|.++|+..+|..+ .++||.||+.+.
T Consensus 248 AC~rC~t~y~le~A~~~------~wrCpkCGg~ik 276 (403)
T COG1379 248 ACSRCYTRYSLEEAKSL------RWRCPKCGGKIK 276 (403)
T ss_pred HHHHhhhccCcchhhhh------cccCcccccchh
Confidence 39999999999999998 899999999664
No 44
>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=91.79 E-value=0.071 Score=44.99 Aligned_cols=32 Identities=22% Similarity=0.616 Sum_probs=24.4
Q ss_pred cCCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 12 KNTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 12 ~~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
+.-+....|+.|+..|...+ ..|.||.||+.-
T Consensus 65 ~~~p~~~~C~~Cg~~~~~~~---------~~~~CP~Cgs~~ 96 (115)
T TIGR00100 65 EDEPVECECEDCSEEVSPEI---------DLYRCPKCHGIM 96 (115)
T ss_pred EeeCcEEEcccCCCEEecCC---------cCccCcCCcCCC
Confidence 34456789999999887632 258999999865
No 45
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=91.49 E-value=0.047 Score=45.93 Aligned_cols=30 Identities=27% Similarity=0.637 Sum_probs=24.7
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAES 56 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~ 56 (330)
.||.|+..|++.|.. .|.||.|..++.+..
T Consensus 5 ~cp~c~sEytYed~~--------~~~cpec~~ew~~~~ 34 (112)
T COG2824 5 PCPKCNSEYTYEDGG--------QLICPECAHEWNENE 34 (112)
T ss_pred CCCccCCceEEecCc--------eEeCchhcccccccc
Confidence 599999999986543 499999999997543
No 46
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=91.23 E-value=0.081 Score=42.08 Aligned_cols=33 Identities=27% Similarity=0.698 Sum_probs=26.8
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
.|.|..|+.+|+.+.++.- || .-.|+.||+.|.
T Consensus 12 ~Y~c~~cg~~~dvvq~~~d-dp---lt~ce~c~a~~k 44 (82)
T COG2331 12 SYECTECGNRFDVVQAMTD-DP---LTTCEECGARLK 44 (82)
T ss_pred EEeecccchHHHHHHhccc-Cc---cccChhhChHHH
Confidence 6999999999988777764 33 458999999873
No 47
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=90.69 E-value=0.2 Score=46.05 Aligned_cols=40 Identities=20% Similarity=0.410 Sum_probs=28.1
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAE 55 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~ 55 (330)
....|+.|+..|...+....+.......+|+.||+.|..+
T Consensus 94 ~~~~C~~C~~~~~~~~~~~~~~~~~~~p~C~~Cgg~lrP~ 133 (206)
T cd01410 94 FIEVCKSCGPEYVRDDVVETRGDKETGRRCHACGGILKDT 133 (206)
T ss_pred CcccCCCCCCccchHHHHHHhhcCCCCCcCCCCcCccCCc
Confidence 3567999999998776654332222357899999988543
No 48
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=90.56 E-value=0.24 Score=37.62 Aligned_cols=8 Identities=50% Similarity=1.543 Sum_probs=3.9
Q ss_pred eeecCCCC
Q 020131 17 EYICPNCQ 24 (330)
Q Consensus 17 ~Y~CP~C~ 24 (330)
.|.||+||
T Consensus 27 ~F~CPnCG 34 (61)
T COG2888 27 KFPCPNCG 34 (61)
T ss_pred EeeCCCCC
Confidence 34455555
No 49
>PRK06450 threonine synthase; Validated
Probab=90.27 E-value=0.16 Score=50.11 Aligned_cols=30 Identities=17% Similarity=0.542 Sum_probs=23.1
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAES 56 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~ 56 (330)
.|+|++||++|.. . ..+.|+.||++|...-
T Consensus 3 ~~~C~~Cg~~~~~-------~---~~~~C~~cg~~l~~~~ 32 (338)
T PRK06450 3 KEVCMKCGKERES-------I---YEIRCKKCGGPFEILI 32 (338)
T ss_pred eeEECCcCCcCCC-------c---ccccCCcCCCEeEEee
Confidence 4899999999942 1 1479999999986543
No 50
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=89.91 E-value=0.18 Score=41.04 Aligned_cols=30 Identities=23% Similarity=0.774 Sum_probs=22.6
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
+-|.||.|++. +. -++ .++.+.|..||..+
T Consensus 34 ~~~~Cp~C~~~-~V---kR~---a~GIW~C~kCg~~f 63 (89)
T COG1997 34 AKHVCPFCGRT-TV---KRI---ATGIWKCRKCGAKF 63 (89)
T ss_pred cCCcCCCCCCc-ce---eee---ccCeEEcCCCCCee
Confidence 46999999998 21 122 34789999999877
No 51
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=89.69 E-value=0.2 Score=31.84 Aligned_cols=23 Identities=22% Similarity=0.735 Sum_probs=18.5
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
.||.|++.... ..-.|+.||..+
T Consensus 2 ~CP~C~~~V~~-----------~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPE-----------SAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchh-----------hcCcCCCCCCCC
Confidence 59999998844 367899999876
No 52
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=89.68 E-value=0.68 Score=34.64 Aligned_cols=26 Identities=23% Similarity=0.717 Sum_probs=20.8
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
.||.|+... +..-.|.||.||-+.--
T Consensus 1 ~Cpv~~~~~----------~~~v~~~Cp~cGipthc 26 (55)
T PF13824_consen 1 LCPVCKKDL----------PAHVNFECPDCGIPTHC 26 (55)
T ss_pred CCCCCcccc----------ccccCCcCCCCCCcCcc
Confidence 499999986 44558999999988844
No 53
>cd01428 ADK Adenylate kinase (ADK) catalyzes the reversible phosphoryl transfer from adenosine triphosphates (ATP) to adenosine monophosphates (AMP) and to yield adenosine diphosphates (ADP). This enzyme is required for the biosynthesis of ADP and is essential for homeostasis of adenosine phosphates.
Probab=89.49 E-value=0.57 Score=40.95 Aligned_cols=54 Identities=24% Similarity=0.338 Sum_probs=42.8
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccchhhhhhcCCCCChhHHHHHHHHHHHHHHHHHHhHHHHHHHH
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESDKLAAQEGGDGDDNARRRRREKLKDLLQKLEVHLKPLMEQI 97 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~~~~~~e~~~g~~na~r~~~e~~k~~l~r~n~QlkpI~~~L 97 (330)
..||.|+..|.. ..|+.|+.+|....+... +.++.++..|+.+..||++++
T Consensus 126 ~~~~~~~~~~~~-------------~~~~~~~~~l~~r~dd~~----------------~~i~~R~~~y~~~~~~i~~~~ 176 (194)
T cd01428 126 RICPVSGRVYHL-------------GKDDVTGEPLSQRSDDNE----------------ETIKKRLEVYKEQTAPLIDYY 176 (194)
T ss_pred CcCCCcCCcCCc-------------CCCcccCCccccCCCCCH----------------HHHHHHHHHHHHhHHHHHHHH
Confidence 469999999977 679999999986543211 355788999999999999999
Q ss_pred Hhh
Q 020131 98 NRV 100 (330)
Q Consensus 98 k~i 100 (330)
++.
T Consensus 177 ~~~ 179 (194)
T cd01428 177 KKK 179 (194)
T ss_pred HhC
Confidence 973
No 54
>PRK06260 threonine synthase; Validated
Probab=89.41 E-value=0.19 Score=50.37 Aligned_cols=30 Identities=23% Similarity=0.656 Sum_probs=23.1
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAE 55 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~ 55 (330)
.|+|++||++|.. ....+.||.||+.|...
T Consensus 3 ~~~C~~cg~~~~~---------~~~~~~Cp~cg~~l~~~ 32 (397)
T PRK06260 3 WLKCIECGKEYDP---------DEIIYTCPECGGLLEVI 32 (397)
T ss_pred EEEECCCCCCCCC---------CCccccCCCCCCeEEEE
Confidence 5899999999963 11247899999988554
No 55
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=89.21 E-value=0.19 Score=42.37 Aligned_cols=31 Identities=19% Similarity=0.485 Sum_probs=23.1
Q ss_pred CCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 13 NTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 13 ~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
.-+..+.|+.|+..|...+ ..|.||.||+.=
T Consensus 66 ~vp~~~~C~~Cg~~~~~~~---------~~~~CP~Cgs~~ 96 (113)
T PRK12380 66 YKPAQAWCWDCSQVVEIHQ---------HDAQCPHCHGER 96 (113)
T ss_pred eeCcEEEcccCCCEEecCC---------cCccCcCCCCCC
Confidence 3456789999998887632 257899999753
No 56
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=89.15 E-value=0.18 Score=42.86 Aligned_cols=27 Identities=30% Similarity=0.819 Sum_probs=23.5
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
+|.||+|+.+|-. | ...|+.||-.|+-
T Consensus 1 GY~CPrC~skvC~-----L------P~~CpiCgLtLVs 27 (112)
T TIGR00622 1 GYFCPQCRAKVCE-----L------PVECPICGLTLIL 27 (112)
T ss_pred CccCCCCCCCccC-----C------CCcCCcCCCEEec
Confidence 5999999999965 4 5789999999975
No 57
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=88.67 E-value=0.1 Score=43.75 Aligned_cols=32 Identities=19% Similarity=0.514 Sum_probs=20.7
Q ss_pred CCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 13 NTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 13 ~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
.-+..+.|+.|+..|+..+ ..|.||.||+.-.
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~---------~~~~CP~Cgs~~~ 97 (113)
T PF01155_consen 66 EVPARARCRDCGHEFEPDE---------FDFSCPRCGSPDV 97 (113)
T ss_dssp EE--EEEETTTS-EEECHH---------CCHH-SSSSSS-E
T ss_pred ecCCcEECCCCCCEEecCC---------CCCCCcCCcCCCc
Confidence 3456789999999998522 2488999999753
No 58
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=88.67 E-value=0.22 Score=48.62 Aligned_cols=33 Identities=18% Similarity=0.594 Sum_probs=25.7
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAE 55 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~ 55 (330)
.++||.||.. . -.+|+..|...|..||..|.+.
T Consensus 11 ~~~Cp~Cg~~-~-----iv~d~~~Ge~vC~~CG~Vl~e~ 43 (310)
T PRK00423 11 KLVCPECGSD-K-----LIYDYERGEIVCADCGLVIEEN 43 (310)
T ss_pred CCcCcCCCCC-C-----eeEECCCCeEeecccCCccccc
Confidence 4789999962 2 2456788999999999988653
No 59
>PRK07591 threonine synthase; Validated
Probab=88.66 E-value=0.22 Score=50.45 Aligned_cols=30 Identities=27% Similarity=0.578 Sum_probs=23.6
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAES 56 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~ 56 (330)
.|+|++||++|.. + . .+.|+.||+.|...-
T Consensus 18 ~l~C~~Cg~~~~~-------~--~-~~~C~~cg~~l~~~y 47 (421)
T PRK07591 18 ALKCRECGAEYPL-------G--P-IHVCEECFGPLEVAY 47 (421)
T ss_pred EEEeCCCCCcCCC-------C--C-CccCCCCCCeEEEEe
Confidence 6999999999963 1 1 389999999986543
No 60
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=88.65 E-value=0.21 Score=56.79 Aligned_cols=11 Identities=27% Similarity=0.486 Sum_probs=7.1
Q ss_pred HHHHHhhcCcC
Q 020131 94 MEQINRVKDLD 104 (330)
Q Consensus 94 ~~~Lk~id~i~ 104 (330)
++.||-|+++.
T Consensus 747 ~~~~KgVkgl~ 757 (1337)
T PRK14714 747 FDLLKGVKGLT 757 (1337)
T ss_pred ccccccceecc
Confidence 46677776664
No 61
>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=88.24 E-value=0.21 Score=50.44 Aligned_cols=29 Identities=28% Similarity=0.455 Sum_probs=22.2
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAE 55 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~ 55 (330)
.|+|++||++|. .. . .+.|+.|++.|...
T Consensus 2 ~l~C~~Cg~~~~-~~---~------~~~C~~c~g~l~~~ 30 (398)
T TIGR03844 2 TLRCPGCGEVLP-DH---Y------TLSCPLDCGLLRAE 30 (398)
T ss_pred EEEeCCCCCccC-Cc---c------ccCCCCCCCceEEe
Confidence 489999999995 11 1 47899999888654
No 62
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=88.16 E-value=0.44 Score=44.98 Aligned_cols=39 Identities=28% Similarity=0.744 Sum_probs=28.8
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAE 55 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~ 55 (330)
..+.|..|++.|+..+..+.+... ..-+|+.||++|...
T Consensus 118 ~~~~C~~C~~~~~~~~~~~~~~~~-~~p~Cp~Cgg~lrP~ 156 (244)
T PRK14138 118 EEYYCVRCGKRYTVEDVIEKLEKS-DVPRCDDCSGLIRPN 156 (244)
T ss_pred CeeEECCCCCcccHHHHHHHHhcC-CCCCCCCCCCeECCC
Confidence 356799999999988777643321 246899999988653
No 63
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=88.12 E-value=0.38 Score=36.47 Aligned_cols=31 Identities=19% Similarity=0.478 Sum_probs=16.3
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
..+|..|+......+- --.|.||+||..++.
T Consensus 7 ~~~CtSCg~~i~~~~~-------~~~F~CPnCG~~~I~ 37 (59)
T PRK14890 7 PPKCTSCGIEIAPREK-------AVKFLCPNCGEVIIY 37 (59)
T ss_pred CccccCCCCcccCCCc-------cCEeeCCCCCCeeEe
Confidence 3466677665443221 124777777766443
No 64
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=87.86 E-value=0.19 Score=42.57 Aligned_cols=34 Identities=24% Similarity=0.485 Sum_probs=23.5
Q ss_pred cCCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 12 KNTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 12 ~~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
+.-+..+.|+.|+..|+..+- ..++||.||+.-.
T Consensus 66 e~vp~~~~C~~Cg~~~~~~~~--------~~~~CP~Cgs~~~ 99 (117)
T PRK00564 66 VDEKVELECKDCSHVFKPNAL--------DYGVCEKCHSKNV 99 (117)
T ss_pred EecCCEEEhhhCCCccccCCc--------cCCcCcCCCCCce
Confidence 345668999999988865211 1245999998753
No 65
>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=87.34 E-value=0.27 Score=29.15 Aligned_cols=16 Identities=31% Similarity=0.920 Sum_probs=12.8
Q ss_pred eecCCCCccccHHHHH
Q 020131 18 YICPNCQRRYNALDAL 33 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~ 33 (330)
|.||.|++.|+....+
T Consensus 1 y~C~~C~~~f~~~~~l 16 (23)
T PF00096_consen 1 YKCPICGKSFSSKSNL 16 (23)
T ss_dssp EEETTTTEEESSHHHH
T ss_pred CCCCCCCCccCCHHHH
Confidence 7899999999865544
No 66
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=87.15 E-value=0.38 Score=40.51 Aligned_cols=33 Identities=24% Similarity=0.631 Sum_probs=22.7
Q ss_pred cCCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 12 KNTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 12 ~~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
+.-+..+.|+.|+..|...+ ...|.||.||+.-
T Consensus 65 ~~~p~~~~C~~Cg~~~~~~~--------~~~~~CP~Cgs~~ 97 (114)
T PRK03681 65 EEQEAECWCETCQQYVTLLT--------QRVRRCPQCHGDM 97 (114)
T ss_pred EeeCcEEEcccCCCeeecCC--------ccCCcCcCcCCCC
Confidence 34456789999998775410 1137899999764
No 67
>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=86.92 E-value=0.35 Score=36.45 Aligned_cols=33 Identities=27% Similarity=0.622 Sum_probs=24.2
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAES 56 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~ 56 (330)
+=.||.||..-.. ......|.|+.||..+-.+.
T Consensus 28 Sq~C~~CG~~~~~-------~~~~r~~~C~~Cg~~~~rD~ 60 (69)
T PF07282_consen 28 SQTCPRCGHRNKK-------RRSGRVFTCPNCGFEMDRDV 60 (69)
T ss_pred ccCccCccccccc-------ccccceEEcCCCCCEECcHH
Confidence 4469999998776 22334799999999975443
No 68
>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=86.78 E-value=0.32 Score=28.31 Aligned_cols=17 Identities=29% Similarity=0.903 Sum_probs=11.5
Q ss_pred eecCCCCccccHHHHHh
Q 020131 18 YICPNCQRRYNALDALR 34 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~ 34 (330)
|.|+.|+.+|.....+.
T Consensus 1 ~~C~~C~~~~~~~~~l~ 17 (24)
T PF13894_consen 1 FQCPICGKSFRSKSELR 17 (24)
T ss_dssp EE-SSTS-EESSHHHHH
T ss_pred CCCcCCCCcCCcHHHHH
Confidence 78999999888766654
No 69
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=86.61 E-value=0.22 Score=44.41 Aligned_cols=38 Identities=16% Similarity=0.351 Sum_probs=19.3
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccchh
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESDK 58 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~~ 58 (330)
+|.||+||.+|+.++-..++- ..+--+-|.....+..+
T Consensus 28 ~~~c~~c~~~f~~~e~~~~~~----i~VIKRDG~~v~Fd~~K 65 (154)
T PRK00464 28 RRECLACGKRFTTFERVELVP----LLVIKKDGRREPFDREK 65 (154)
T ss_pred eeeccccCCcceEeEeccCcc----cEEEecCCcCCCcCHHH
Confidence 466666666666555444421 24445555555444443
No 70
>PF02146 SIR2: Sir2 family; InterPro: IPR003000 These sequences represent the Sirtuin (Sir2-related) family of NAD+-dependent deacetylases. This family of enzymes is broadly conserved from bacteria to humans. In yeast, Sir2 proteins form complexes with other proteins to silence chromatin by accessing histones and deacetylating them. Sir2 proteins have been proposed to play a role in silencing, chromosome stability and ageing []. The bacterial enzyme CobB, an homologue of Sir2, is a phosphoribosyltransferase []. An in vitro ADP ribosyltransferase activity has also been associated with human members of this family []. Sir2-like enzymes employ NAD+ as a cosubstrate in deacetylation reactions [] and catalyse a reaction in which the cleavage of NAD(+)and histone and/or protein deacetylation are coupled to the formation of O-acetyl-ADP-ribose, a novel metabolite. The dependence of the reaction on both NAD(+) and the generation of this potential second messenger offers new clues to understanding the function and regulation of nuclear, cytoplasmic and mitochondrial Sir2-like enzymes []. Silent Information Regulator protein of Saccharomyces cerevisiae (Sir2) is one of several factors critical for silencing at least three loci. Among them, it is unique because it silences the rDNA as well as the mating type loci and telomeres []. Sir2 interacts in a complex with itself and with Sir3 and Sir4, two proteins that are able to interact with nucleosomes. In addition Sir2 also interacts with ubiquitination factors and/or complexes []. Homologues of Sir2 share a core domain including the GAG and NID motifs and a putative C4 Zinc finger. The regions containing these three conserved motifs are individually essential for Sir2 silencing function, as are the four cysteins []. In addition, the conserved residues HG next to the putative Zn finger have been shown to be essential for the ADP ribosyltransferase activity []. ; GO: 0008270 zinc ion binding, 0070403 NAD+ binding, 0006476 protein deacetylation; PDB: 1S5P_A 3PKI_E 3PKJ_F 3K35_A 1ICI_A 1M2K_A 1M2G_A 1M2N_B 1M2H_A 1M2J_A ....
Probab=86.55 E-value=0.41 Score=42.49 Aligned_cols=38 Identities=24% Similarity=0.623 Sum_probs=28.6
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAE 55 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~ 55 (330)
..+|..|++.|...+....+... ..-.|+.||+.|..+
T Consensus 105 ~~~C~~C~~~~~~~~~~~~~~~~-~~~~C~~C~~~lrp~ 142 (178)
T PF02146_consen 105 RLRCSKCGKEYDREDIVDSIDEE-EPPRCPKCGGLLRPD 142 (178)
T ss_dssp EEEETTTSBEEEGHHHHHHHHTT-SSCBCTTTSCBEEEE
T ss_pred eeeecCCCccccchhhccccccc-ccccccccCccCCCC
Confidence 57899999999987766544332 245999999988664
No 71
>PHA00732 hypothetical protein
Probab=86.44 E-value=0.47 Score=37.68 Aligned_cols=36 Identities=25% Similarity=0.423 Sum_probs=26.8
Q ss_pred eecCCCCccccHHHHHhhcCC-CCCCeeccCCCcccc
Q 020131 18 YICPNCQRRYNALDALRLVSL-EDDSFHCENCNGELV 53 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~-~~~~F~C~~Cg~eL~ 53 (330)
|.|+.|++.|+....+..--. .-..+.|+.||....
T Consensus 2 y~C~~Cgk~F~s~s~Lk~H~r~~H~~~~C~~CgKsF~ 38 (79)
T PHA00732 2 FKCPICGFTTVTLFALKQHARRNHTLTKCPVCNKSYR 38 (79)
T ss_pred ccCCCCCCccCCHHHHHHHhhcccCCCccCCCCCEeC
Confidence 889999999998777664321 123579999998774
No 72
>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=86.39 E-value=0.53 Score=29.41 Aligned_cols=19 Identities=21% Similarity=0.726 Sum_probs=14.3
Q ss_pred hhcCCCCeeecCCCCcccc
Q 020131 10 ECKNTVQEYICPNCQRRYN 28 (330)
Q Consensus 10 ~~~~~~~~Y~CP~C~~~YT 28 (330)
+.=+....|.||.|+++|+
T Consensus 7 ~~H~~~k~~~C~~C~k~F~ 25 (26)
T PF13465_consen 7 RTHTGEKPYKCPYCGKSFS 25 (26)
T ss_dssp HHHSSSSSEEESSSSEEES
T ss_pred hhcCCCCCCCCCCCcCeeC
Confidence 3344556799999999985
No 73
>PHA00626 hypothetical protein
Probab=86.00 E-value=0.31 Score=36.67 Aligned_cols=33 Identities=21% Similarity=0.483 Sum_probs=19.5
Q ss_pred ecCCCCcc-ccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 19 ICPNCQRR-YNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 19 ~CP~C~~~-YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
.||+||+. ..-.-..... ...|+|+.||....-
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~---snrYkCkdCGY~ft~ 35 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGW---SDDYVCCDCGYNDSK 35 (59)
T ss_pred CCCCCCCceeeeeceeccc---CcceEcCCCCCeech
Confidence 58888884 3322222221 247899999877643
No 74
>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=85.60 E-value=0.36 Score=32.93 Aligned_cols=26 Identities=27% Similarity=0.750 Sum_probs=20.4
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
.|+.|+.++- ...+|.|.|..||+..
T Consensus 10 ~C~~C~~~~~--------~~~dG~~yC~~cG~~~ 35 (36)
T PF11781_consen 10 PCPVCGSRWF--------YSDDGFYYCDRCGHQS 35 (36)
T ss_pred cCCCCCCeEe--------EccCCEEEhhhCceEc
Confidence 4999999843 3456889999999875
No 75
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=85.59 E-value=0.4 Score=34.95 Aligned_cols=28 Identities=29% Similarity=0.662 Sum_probs=19.5
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
.-.||+||.. +| +. ..+.|.|..||...
T Consensus 20 ~~fCP~Cg~~--~m-~~-----~~~r~~C~~Cgyt~ 47 (50)
T PRK00432 20 NKFCPRCGSG--FM-AE-----HLDRWHCGKCGYTE 47 (50)
T ss_pred cCcCcCCCcc--hh-ec-----cCCcEECCCcCCEE
Confidence 4479999986 21 11 22589999999764
No 76
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=85.44 E-value=0.37 Score=41.17 Aligned_cols=36 Identities=14% Similarity=0.239 Sum_probs=23.2
Q ss_pred cCCCCeeecCCCCccccHHH--HHhhcCCCCCCeeccCCCccc
Q 020131 12 KNTVQEYICPNCQRRYNALD--ALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 12 ~~~~~~Y~CP~C~~~YT~lD--A~~Lld~~~~~F~C~~Cg~eL 52 (330)
+.-+..+.| .|+..|+..+ ...+ -| .|.||.||+.-
T Consensus 65 ~~vp~~~~C-~Cg~~~~~~~~~~~~~-~~---~~~CP~Cgs~~ 102 (124)
T PRK00762 65 EMIPVEIEC-ECGYEGVVDEDEIDHY-AA---VIECPVCGNKR 102 (124)
T ss_pred EecCeeEEe-eCcCcccccccchhcc-cc---CCcCcCCCCCC
Confidence 344567899 9999987643 1111 11 37899999644
No 77
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=85.19 E-value=0.25 Score=45.83 Aligned_cols=39 Identities=13% Similarity=0.535 Sum_probs=25.7
Q ss_pred CeeecCCCCccccHHHHHh----hcCCCC--------------CCeeccCCCccccc
Q 020131 16 QEYICPNCQRRYNALDALR----LVSLED--------------DSFHCENCNGELVA 54 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~----Lld~~~--------------~~F~C~~Cg~eL~~ 54 (330)
+.+.||.|++.|+...+.. ++..++ ...+||+||.--..
T Consensus 4 k~~~CPvC~~~F~~~~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~ 60 (214)
T PF09986_consen 4 KKITCPVCGKEFKTKKVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFE 60 (214)
T ss_pred CceECCCCCCeeeeeEEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCcccc
Confidence 3689999999999876654 111110 12389999976643
No 78
>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=85.08 E-value=0.28 Score=46.83 Aligned_cols=35 Identities=34% Similarity=0.728 Sum_probs=14.0
Q ss_pred eeecCCCCccc-cHHHHHhhcCCCCCCeeccCCCcccccc
Q 020131 17 EYICPNCQRRY-NALDALRLVSLEDDSFHCENCNGELVAE 55 (330)
Q Consensus 17 ~Y~CP~C~~~Y-T~lDA~~Lld~~~~~F~C~~Cg~eL~~~ 55 (330)
.+.||+||..+ +......=+ ..|.|+.|+.+-+--
T Consensus 31 n~yCP~Cg~~~L~~f~NN~PV----aDF~C~~C~eeyELK 66 (254)
T PF06044_consen 31 NMYCPNCGSKPLSKFENNRPV----ADFYCPNCNEEYELK 66 (254)
T ss_dssp H---TTT--SS-EE------------EEE-TTT--EEEEE
T ss_pred CCcCCCCCChhHhhccCCCcc----ceeECCCCchHHhhh
Confidence 36799999994 344433322 379999999876543
No 79
>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=84.99 E-value=0.22 Score=40.78 Aligned_cols=30 Identities=20% Similarity=0.715 Sum_probs=21.5
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
..|.||.|++.--- --..|.+.|..|+..+
T Consensus 34 ~ky~Cp~Cgk~~vk-------R~a~GIW~C~~C~~~~ 63 (90)
T PF01780_consen 34 AKYTCPFCGKTSVK-------RVATGIWKCKKCGKKF 63 (90)
T ss_dssp S-BEESSSSSSEEE-------EEETTEEEETTTTEEE
T ss_pred CCCcCCCCCCceeE-------EeeeEEeecCCCCCEE
Confidence 46999999986411 1134789999999776
No 80
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=84.91 E-value=0.96 Score=32.90 Aligned_cols=33 Identities=24% Similarity=0.550 Sum_probs=19.0
Q ss_pred eccCCCccccccchhhhhhcCCCCChhHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 020131 44 HCENCNGELVAESDKLAAQEGGDGDDNARRRRREKLKDLLQKLEVHLKPLMEQIN 98 (330)
Q Consensus 44 ~C~~Cg~eL~~~~~~~~~~e~~~g~~na~r~~~e~~k~~l~r~n~QlkpI~~~Lk 98 (330)
.||.|+.+|..+. + +.++.++..+++-|-+.|+
T Consensus 22 ~CPlC~r~l~~e~---------------------~-~~li~~~~~~i~~~~~~lk 54 (54)
T PF04423_consen 22 CCPLCGRPLDEEH---------------------R-QELIKKYKSEIEELPEKLK 54 (54)
T ss_dssp E-TTT--EE-HHH---------------------H-HHHHHHHHHHHHHHHH---
T ss_pred cCCCCCCCCCHHH---------------------H-HHHHHHHHHHHHhhhhccC
Confidence 9999999995421 1 4677888888887776653
No 81
>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=84.86 E-value=0.54 Score=39.97 Aligned_cols=33 Identities=24% Similarity=0.554 Sum_probs=23.9
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccch
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESD 57 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~ 57 (330)
...+||+|++.--.+ .. .-.|.+|+++|.-+.+
T Consensus 68 v~V~CP~C~K~TKmL---Gr------~D~CM~C~~pLTLd~~ 100 (114)
T PF11023_consen 68 VQVECPNCGKQTKML---GR------VDACMHCKEPLTLDPS 100 (114)
T ss_pred eeeECCCCCChHhhh---ch------hhccCcCCCcCccCch
Confidence 357899999975431 11 2379999999987665
No 82
>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=84.78 E-value=0.33 Score=39.82 Aligned_cols=30 Identities=20% Similarity=0.727 Sum_probs=21.4
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
.-|.||.|++.- +- -...|.+.|..|+..+
T Consensus 34 a~y~CpfCgk~~----vk---R~a~GIW~C~~C~~~~ 63 (91)
T TIGR00280 34 AKYVCPFCGKKT----VK---RGSTGIWTCRKCGAKF 63 (91)
T ss_pred cCccCCCCCCCc----eE---EEeeEEEEcCCCCCEE
Confidence 469999998642 11 1234779999999876
No 83
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=84.77 E-value=0.45 Score=41.48 Aligned_cols=41 Identities=24% Similarity=0.453 Sum_probs=30.0
Q ss_pred hHHHHHHhhcCCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 3 KKLKDELECKNTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 3 k~Le~~l~~~~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
|+|-..|...-.--.+.||.||.= ||- -+|...||+||...
T Consensus 14 k~iA~lLl~GAkML~~hCp~Cg~P--------LF~-KdG~v~CPvC~~~~ 54 (131)
T COG1645 14 KKIAELLLQGAKMLAKHCPKCGTP--------LFR-KDGEVFCPVCGYRE 54 (131)
T ss_pred HHHHHHHHhhhHHHHhhCcccCCc--------cee-eCCeEECCCCCceE
Confidence 566666666555557899999963 555 56899999999544
No 84
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=84.41 E-value=0.49 Score=47.73 Aligned_cols=28 Identities=25% Similarity=0.557 Sum_probs=25.2
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
.|-.|+..|+..++..+ ..+|| ||.+|+
T Consensus 242 ~c~~C~~~~~~~~~~~~------~~~Cp-CG~~i~ 269 (374)
T TIGR00375 242 ACEACGEPAVSEDAETA------CANCP-CGGRIK 269 (374)
T ss_pred hhcccCCcCCchhhhhc------CCCCC-CCCcce
Confidence 59999999999999888 79999 998875
No 85
>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=84.30 E-value=0.5 Score=42.95 Aligned_cols=38 Identities=18% Similarity=0.541 Sum_probs=20.3
Q ss_pred CCeeecCCCCccccHHHHHhhcC--CCCCCeeccCCCccc
Q 020131 15 VQEYICPNCQRRYNALDALRLVS--LEDDSFHCENCNGEL 52 (330)
Q Consensus 15 ~~~Y~CP~C~~~YT~lDA~~Lld--~~~~~F~C~~Cg~eL 52 (330)
+-.+.||.|+..|.+..+..--. .....+.|+.|+..+
T Consensus 16 ~l~~~C~~C~~~~~f~g~~~~~~~~~~~~~~~C~~C~~~~ 55 (188)
T PF08996_consen 16 PLKLTCPSCGTEFEFPGVFEEDGDDVSPSGLQCPNCSTPL 55 (188)
T ss_dssp -EEEE-TTT--EEEE-SSS--SSEEEETTEEEETTT--B-
T ss_pred ceEeECCCCCCCccccccccCCccccccCcCcCCCCCCcC
Confidence 44689999999999877765111 123479999999954
No 86
>cd01413 SIR2_Af2 SIR2_Af2: Archaeal and prokaryotic group which includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus solfataricus ssSir2, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The Sir2 homolog from the archaea Sulfolobus solftaricus deacetylates the non-specific DNA protein Alba to mediate transcription repression.
Probab=84.28 E-value=0.89 Score=42.18 Aligned_cols=38 Identities=21% Similarity=0.515 Sum_probs=27.2
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAE 55 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~ 55 (330)
..+.|..|+..|...++..... ....+|+.||+.|..+
T Consensus 112 ~~~~C~~C~~~~~~~~~~~~~~--~~~p~C~~Cgg~lrP~ 149 (222)
T cd01413 112 QTAYCVNCGSKYDLEEVKYAKK--HEVPRCPKCGGIIRPD 149 (222)
T ss_pred CcceECCCCCCcchhHHHHhcc--CCCCcCCCCCCccCCC
Confidence 3578999999999776632221 1246899999998653
No 87
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=83.99 E-value=0.4 Score=40.80 Aligned_cols=26 Identities=27% Similarity=0.713 Sum_probs=21.0
Q ss_pred cCCCCccccHHHHHhhcCCCCCCeeccCCCccccccc
Q 020131 20 CPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAES 56 (330)
Q Consensus 20 CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~ 56 (330)
||.||..... ..++|+.|++.+.-.-
T Consensus 1 CPvCg~~l~v-----------t~l~C~~C~t~i~G~F 26 (113)
T PF09862_consen 1 CPVCGGELVV-----------TRLKCPSCGTEIEGEF 26 (113)
T ss_pred CCCCCCceEE-----------EEEEcCCCCCEEEeee
Confidence 9999988764 4799999999996443
No 88
>PRK08197 threonine synthase; Validated
Probab=83.90 E-value=0.59 Score=46.82 Aligned_cols=30 Identities=23% Similarity=0.572 Sum_probs=22.4
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAE 55 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~ 55 (330)
..|+|++||++|... ...+.| .||++|.-.
T Consensus 6 ~~~~C~~Cg~~~~~~---------~~~~~C-~cg~~l~~~ 35 (394)
T PRK08197 6 SHLECSKCGETYDAD---------QVHNLC-KCGKPLLVR 35 (394)
T ss_pred eEEEECCCCCCCCCC---------Ccceec-CCCCeeEEE
Confidence 369999999999631 124789 799998554
No 89
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=83.72 E-value=0.77 Score=42.98 Aligned_cols=35 Identities=23% Similarity=0.578 Sum_probs=25.6
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAE 55 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~ 55 (330)
..+.|..|+..|...+.... ....|+.||+.|...
T Consensus 121 ~~~~C~~C~~~~~~~~~~~~-----~~p~C~~Cgg~lrP~ 155 (242)
T PRK00481 121 LRARCTKCGQTYDLDEYLKP-----EPPRCPKCGGILRPD 155 (242)
T ss_pred CceeeCCCCCCcChhhhccC-----CCCCCCCCCCccCCC
Confidence 35789999999986654421 245699999998654
No 90
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=83.49 E-value=0.4 Score=49.57 Aligned_cols=42 Identities=21% Similarity=0.309 Sum_probs=27.4
Q ss_pred CCCeeecCCCCccccHHHHH--hhcCC------CCCCeeccCCCcccccc
Q 020131 14 TVQEYICPNCQRRYNALDAL--RLVSL------EDDSFHCENCNGELVAE 55 (330)
Q Consensus 14 ~~~~Y~CP~C~~~YT~lDA~--~Lld~------~~~~F~C~~Cg~eL~~~ 55 (330)
....|+|+.|+..|....-. .-+-| ....|.||.||..-..+
T Consensus 422 ~~~~~~c~~c~~~yd~~~g~~~~~~~~gt~~~~lp~~~~cp~c~~~k~~f 471 (479)
T PRK05452 422 LGPRMQCSVCQWIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSLGKDVF 471 (479)
T ss_pred CCCeEEECCCCeEECCCCCCcccCCCCCCChhhCCCCCcCcCCCCcHHHh
Confidence 45689999999999875221 11111 12368999999875433
No 91
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=83.40 E-value=1.4 Score=43.41 Aligned_cols=16 Identities=25% Similarity=0.482 Sum_probs=12.7
Q ss_pred CCCeeccCCCcccccc
Q 020131 40 DDSFHCENCNGELVAE 55 (330)
Q Consensus 40 ~~~F~C~~Cg~eL~~~ 55 (330)
.+...||.|+.+|...
T Consensus 41 ~~~~~CP~C~~~lrk~ 56 (309)
T TIGR00570 41 RGSGSCPECDTPLRKN 56 (309)
T ss_pred CCCCCCCCCCCccchh
Confidence 3567999999998654
No 92
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=83.38 E-value=0.51 Score=46.88 Aligned_cols=30 Identities=30% Similarity=0.763 Sum_probs=25.5
Q ss_pred CCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 14 TVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 14 ~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
...+|+||+|++++-. | .-.||.|+..|+-
T Consensus 273 ~~~Gy~CP~CkakvCs-----L------P~eCpiC~ltLVs 302 (378)
T KOG2807|consen 273 SGGGYFCPQCKAKVCS-----L------PIECPICSLTLVS 302 (378)
T ss_pred ccCceeCCcccCeeec-----C------CccCCccceeEec
Confidence 4568999999999976 3 5789999999975
No 93
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=83.22 E-value=0.6 Score=43.76 Aligned_cols=29 Identities=24% Similarity=0.573 Sum_probs=21.1
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccch
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESD 57 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~ 57 (330)
+=.||.||. ++ ...|.|+.||...-.+.+
T Consensus 309 S~~C~~cg~----------~~--~r~~~C~~cg~~~~rD~n 337 (364)
T COG0675 309 SKTCPCCGH----------LS--GRLFKCPRCGFVHDRDVN 337 (364)
T ss_pred cccccccCC----------cc--ceeEECCCCCCeehhhHH
Confidence 346999999 22 357999999999855433
No 94
>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=83.17 E-value=0.45 Score=29.90 Aligned_cols=8 Identities=50% Similarity=1.373 Sum_probs=5.3
Q ss_pred CeeccCCC
Q 020131 42 SFHCENCN 49 (330)
Q Consensus 42 ~F~C~~Cg 49 (330)
.|.||+||
T Consensus 16 ~f~CPnCG 23 (24)
T PF07754_consen 16 PFPCPNCG 23 (24)
T ss_pred eEeCCCCC
Confidence 46677776
No 95
>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=83.13 E-value=0.67 Score=32.76 Aligned_cols=33 Identities=18% Similarity=0.572 Sum_probs=21.2
Q ss_pred hcCCCCeeecCCCCcc-ccHHHHHhhcCCCCCCeeccCCCc
Q 020131 11 CKNTVQEYICPNCQRR-YNALDALRLVSLEDDSFHCENCNG 50 (330)
Q Consensus 11 ~~~~~~~Y~CP~C~~~-YT~lDA~~Lld~~~~~F~C~~Cg~ 50 (330)
.-.=..+++||.||.. +.. +=+ .+.|.|..|+.
T Consensus 12 ~~RW~~g~~CP~Cg~~~~~~-----~~~--~~~~~C~~C~~ 45 (46)
T PF12760_consen 12 EIRWPDGFVCPHCGSTKHYR-----LKT--RGRYRCKACRK 45 (46)
T ss_pred HhcCCCCCCCCCCCCeeeEE-----eCC--CCeEECCCCCC
Confidence 3334457899999984 222 211 35799999985
No 96
>cd01408 SIRT1 SIRT1: Eukaryotic group (class1) which includes human sirtuins SIRT1-3 and yeast Hst1-4; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The nuclear SIRT1 has been shown to target the p53 tumor suppressor protein for deacetylation to suppress DNA damage, and the cytoplasmic SIRT2 homolog has been shown to target alpha-tubulin for deacetylation for the maintenance of cell integrity.
Probab=82.61 E-value=1.1 Score=42.10 Aligned_cols=39 Identities=15% Similarity=0.348 Sum_probs=26.3
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAE 55 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~ 55 (330)
..+.|..|+..|........+... ...+|+.||+.|..+
T Consensus 115 ~~~~C~~C~~~~~~~~~~~~~~~~-~~p~C~~Cgg~lrP~ 153 (235)
T cd01408 115 ATAHCIKCKHKYPGDWMREDIFNQ-EVPKCPRCGGLVKPD 153 (235)
T ss_pred CccccccCCCcCCHHHHHHHHhCC-CCccCCCCCCCccCc
Confidence 457899999999864433332211 246899999988643
No 97
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=82.33 E-value=0.44 Score=39.02 Aligned_cols=30 Identities=20% Similarity=0.665 Sum_probs=21.2
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
.-|.||.|++.--- -...|.+.|..|+..+
T Consensus 35 a~y~CpfCgk~~vk-------R~a~GIW~C~~C~~~~ 64 (90)
T PRK03976 35 AKHVCPVCGRPKVK-------RVGTGIWECRKCGAKF 64 (90)
T ss_pred cCccCCCCCCCceE-------EEEEEEEEcCCCCCEE
Confidence 46999999754211 1234679999999877
No 98
>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=81.94 E-value=0.37 Score=35.50 Aligned_cols=33 Identities=18% Similarity=0.480 Sum_probs=23.8
Q ss_pred CeeecCCCCccccH-HHHHhhcCCCCCCeeccCCCccccc
Q 020131 16 QEYICPNCQRRYNA-LDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~-lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
+.+.|+.|++..-- -++..+ ..+||+|++.-..
T Consensus 3 ~eiRC~~CnklLa~~g~~~~l------eIKCpRC~tiN~~ 36 (51)
T PF10122_consen 3 KEIRCGHCNKLLAKAGEVIEL------EIKCPRCKTINHV 36 (51)
T ss_pred cceeccchhHHHhhhcCccEE------EEECCCCCccceE
Confidence 46899999987644 234444 7999999987643
No 99
>cd01407 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.
Probab=81.92 E-value=1.2 Score=40.89 Aligned_cols=39 Identities=18% Similarity=0.454 Sum_probs=27.1
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAE 55 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~ 55 (330)
..+.|..|+..|...+....+.. ...-.|+.||+.|...
T Consensus 108 ~~~~C~~C~~~~~~~~~~~~~~~-~~~p~C~~Cg~~lrP~ 146 (218)
T cd01407 108 FRVRCTKCGKEYPRDELQADIDR-EEVPRCPKCGGLLRPD 146 (218)
T ss_pred CcceeCCCcCCCcHHHHhHhhcc-CCCCcCCCCCCccCCC
Confidence 35789999999987654322221 1256899999998654
No 100
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=81.89 E-value=0.57 Score=38.36 Aligned_cols=30 Identities=20% Similarity=0.681 Sum_probs=21.3
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
.-|.||.|++.- +--...|.+.|..|+..+
T Consensus 35 a~y~CpfCgk~~-------vkR~a~GIW~C~~C~~~~ 64 (90)
T PTZ00255 35 AKYFCPFCGKHA-------VKRQAVGIWRCKGCKKTV 64 (90)
T ss_pred CCccCCCCCCCc-------eeeeeeEEEEcCCCCCEE
Confidence 469999998532 111234789999999877
No 101
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=81.52 E-value=0.27 Score=33.92 Aligned_cols=31 Identities=26% Similarity=0.594 Sum_probs=21.1
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
.||+|+.... ...+-+ -....|+.|++.+..
T Consensus 1 ~CP~C~~~l~---~~~~~~--~~id~C~~C~G~W~d 31 (41)
T PF13453_consen 1 KCPRCGTELE---PVRLGD--VEIDVCPSCGGIWFD 31 (41)
T ss_pred CcCCCCcccc---eEEECC--EEEEECCCCCeEEcc
Confidence 5999998543 333311 235789999999964
No 102
>cd01409 SIRT4 SIRT4: Eukaryotic and prokaryotic group (class2) which includes human sirtuin SIRT4 and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=81.24 E-value=1.2 Score=42.36 Aligned_cols=17 Identities=18% Similarity=0.444 Sum_probs=13.1
Q ss_pred CeeecCCCCccccHHHH
Q 020131 16 QEYICPNCQRRYNALDA 32 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA 32 (330)
..+.|+.|+++|.....
T Consensus 117 ~~~~C~~C~~~~~~~~~ 133 (260)
T cd01409 117 HRVVCLSCGFRTPRAEL 133 (260)
T ss_pred CEEEeCCCcCccCHHHH
Confidence 35789999999985443
No 103
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=81.14 E-value=0.83 Score=38.91 Aligned_cols=28 Identities=14% Similarity=0.262 Sum_probs=21.4
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
--+||.|+++|-.| .....+||+||...
T Consensus 9 KridPetg~KFYDL--------NrdPiVsPytG~s~ 36 (129)
T COG4530 9 KRIDPETGKKFYDL--------NRDPIVSPYTGKSY 36 (129)
T ss_pred cccCccccchhhcc--------CCCccccCcccccc
Confidence 46899999999552 23468999999765
No 104
>PLN02569 threonine synthase
Probab=80.96 E-value=0.78 Score=47.67 Aligned_cols=31 Identities=19% Similarity=0.314 Sum_probs=23.2
Q ss_pred CCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccccc
Q 020131 15 VQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAE 55 (330)
Q Consensus 15 ~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~ 55 (330)
..+++|+.|+++|... ...|.| .||+.|...
T Consensus 47 ~~~l~C~~Cg~~y~~~---------~~~~~C-~cgg~l~~~ 77 (484)
T PLN02569 47 VPFLECPLTGEKYSLD---------EVVYRS-KSGGLLDVR 77 (484)
T ss_pred ccccEeCCCCCcCCCc---------cccccC-CCCCeEEEe
Confidence 4468999999999642 125899 699999543
No 105
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=80.59 E-value=1.1 Score=43.69 Aligned_cols=32 Identities=19% Similarity=0.365 Sum_probs=26.3
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
-..+||.|+...-..+.... .+.||.||+-+.
T Consensus 25 ~~~~c~~c~~~~~~~~l~~~------~~vc~~c~~h~r 56 (285)
T TIGR00515 25 VWTKCPKCGQVLYTKELERN------LEVCPKCDHHMR 56 (285)
T ss_pred CeeECCCCcchhhHHHHHhh------CCCCCCCCCcCc
Confidence 47899999999888776665 589999999764
No 106
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=80.36 E-value=1.1 Score=44.03 Aligned_cols=32 Identities=22% Similarity=0.177 Sum_probs=26.3
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
-..+||.|+...-..+.... .+.||.||+-+.
T Consensus 37 lw~kc~~C~~~~~~~~l~~~------~~vcp~c~~h~r 68 (296)
T CHL00174 37 LWVQCENCYGLNYKKFLKSK------MNICEQCGYHLK 68 (296)
T ss_pred CeeECCCccchhhHHHHHHc------CCCCCCCCCCcC
Confidence 36799999999888776665 589999999764
No 107
>PHA00626 hypothetical protein
Probab=80.14 E-value=0.92 Score=34.21 Aligned_cols=15 Identities=20% Similarity=0.684 Sum_probs=13.5
Q ss_pred CCeeecCCCCccccH
Q 020131 15 VQEYICPNCQRRYNA 29 (330)
Q Consensus 15 ~~~Y~CP~C~~~YT~ 29 (330)
++.|+||.||..||-
T Consensus 21 snrYkCkdCGY~ft~ 35 (59)
T PHA00626 21 SDDYVCCDCGYNDSK 35 (59)
T ss_pred CcceEcCCCCCeech
Confidence 468999999999996
No 108
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=80.10 E-value=0.92 Score=46.47 Aligned_cols=29 Identities=24% Similarity=0.744 Sum_probs=21.6
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
=+||.||.+-.. --.++|+|+.||.....
T Consensus 351 p~Cp~Cg~~m~S--------~G~~g~rC~kCg~~~~~ 379 (421)
T COG1571 351 PVCPRCGGRMKS--------AGRNGFRCKKCGTRARE 379 (421)
T ss_pred CCCCccCCchhh--------cCCCCcccccccccCCc
Confidence 379999998543 22348999999998743
No 109
>PRK05638 threonine synthase; Validated
Probab=80.04 E-value=0.94 Score=46.13 Aligned_cols=27 Identities=33% Similarity=0.728 Sum_probs=20.9
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCCcccccc
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAE 55 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~ 55 (330)
|+|+.||++|.. .. .+.| .||+.|...
T Consensus 2 l~C~~Cg~~~~~----~~------~~~C-~c~~~l~~~ 28 (442)
T PRK05638 2 MKCPKCGREYNS----YI------PPFC-ICGELLEII 28 (442)
T ss_pred eEeCCCCCCCCC----CC------ceec-CCCCcEEEE
Confidence 799999999962 11 3789 899998654
No 110
>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=79.84 E-value=1.1 Score=41.83 Aligned_cols=33 Identities=18% Similarity=0.382 Sum_probs=24.4
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAE 55 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~ 55 (330)
....|..|+..|...+... ...|+.||++|..+
T Consensus 117 ~~~~C~~C~~~~~~~~~~~-------~p~C~~Cgg~lrP~ 149 (225)
T cd01411 117 YRIYCTVCGKTVDWEEYLK-------SPYHAKCGGVIRPD 149 (225)
T ss_pred CeeEeCCCCCccchhhcCC-------CCCCCCCCCEeCCC
Confidence 3578999999998644321 36899999998654
No 111
>PRK08329 threonine synthase; Validated
Probab=79.81 E-value=0.91 Score=44.76 Aligned_cols=27 Identities=33% Similarity=1.020 Sum_probs=20.7
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCCcccccc
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAE 55 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~ 55 (330)
|+|++||++|.. .. .++| .||.+|...
T Consensus 2 l~C~~Cg~~~~~----~~------~~~C-~c~~~l~~~ 28 (347)
T PRK08329 2 LRCTKCGRTYEE----KF------KLRC-DCGGTLLVE 28 (347)
T ss_pred cCcCCCCCCcCC----CC------ceec-CCCCcEEEE
Confidence 789999999962 11 3789 699998654
No 112
>PHA00733 hypothetical protein
Probab=79.23 E-value=1.3 Score=38.04 Aligned_cols=40 Identities=25% Similarity=0.595 Sum_probs=28.5
Q ss_pred CCeeecCCCCccccHHHHHhh-cCCCCCCeeccCCCccccc
Q 020131 15 VQEYICPNCQRRYNALDALRL-VSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 15 ~~~Y~CP~C~~~YT~lDA~~L-ld~~~~~F~C~~Cg~eL~~ 54 (330)
...|.|+.|++.|...-.+.. .-.....|.|+.|+.....
T Consensus 71 ~kPy~C~~Cgk~Fss~s~L~~H~r~h~~~~~C~~CgK~F~~ 111 (128)
T PHA00733 71 VSPYVCPLCLMPFSSSVSLKQHIRYTEHSKVCPVCGKEFRN 111 (128)
T ss_pred CCCccCCCCCCcCCCHHHHHHHHhcCCcCccCCCCCCccCC
Confidence 457999999999997665532 1111346999999987744
No 113
>PRK04860 hypothetical protein; Provisional
Probab=79.19 E-value=1.7 Score=38.96 Aligned_cols=38 Identities=24% Similarity=0.527 Sum_probs=26.0
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAE 55 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~ 55 (330)
.|.|+ |+..+..+-.-.-+=-....|.|..|+..|..-
T Consensus 119 ~Y~C~-C~~~~~~~rrH~ri~~g~~~YrC~~C~~~l~~~ 156 (160)
T PRK04860 119 PYRCK-CQEHQLTVRRHNRVVRGEAVYRCRRCGETLVFK 156 (160)
T ss_pred EEEcC-CCCeeCHHHHHHHHhcCCccEECCCCCceeEEe
Confidence 59998 988666554444322223369999999999753
No 114
>cd01412 SIRT5_Af1_CobB SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. CobB is a bacterial sirtuin that deacetylates acetyl-CoA synthetase at an active site lysine to stimulate its enzymatic activity.
Probab=79.17 E-value=1.3 Score=40.88 Aligned_cols=37 Identities=19% Similarity=0.395 Sum_probs=26.1
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAES 56 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~ 56 (330)
....|..|+.+|....... .....+|+.||+.|..+.
T Consensus 108 ~~~~C~~C~~~~~~~~~~~----~~~~p~C~~Cgg~lrp~V 144 (224)
T cd01412 108 FRVRCSSCGYVGENNEEIP----EEELPRCPKCGGLLRPGV 144 (224)
T ss_pred CccccCCCCCCCCcchhhh----ccCCCCCCCCCCccCCce
Confidence 4578999999997753221 123578999999886543
No 115
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=78.95 E-value=0.75 Score=32.64 Aligned_cols=30 Identities=23% Similarity=0.573 Sum_probs=19.0
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
.||.||......+... ...|.|+.||....
T Consensus 2 FCp~Cg~~l~~~~~~~-----~~~~vC~~Cg~~~~ 31 (52)
T smart00661 2 FCPKCGNMLIPKEGKE-----KRRFVCRKCGYEEP 31 (52)
T ss_pred CCCCCCCccccccCCC-----CCEEECCcCCCeEE
Confidence 5999999443322111 12699999997653
No 116
>PRK04351 hypothetical protein; Provisional
Probab=78.87 E-value=1.2 Score=39.35 Aligned_cols=33 Identities=27% Similarity=0.759 Sum_probs=25.4
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
.|.|..|+..|-- . +-+++ ..++|-.|++.|..
T Consensus 112 ~Y~C~~Cg~~~~r--~-Rr~n~--~~yrCg~C~g~L~~ 144 (149)
T PRK04351 112 LYECQSCGQQYLR--K-RRINT--KRYRCGKCRGKLKL 144 (149)
T ss_pred EEECCCCCCEeee--e-eecCC--CcEEeCCCCcEeee
Confidence 5999999988743 2 33444 57999999999975
No 117
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=78.77 E-value=1.2 Score=44.69 Aligned_cols=28 Identities=36% Similarity=0.838 Sum_probs=21.6
Q ss_pred CCCeeecCCCCc--cccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 14 TVQEYICPNCQR--RYNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 14 ~~~~Y~CP~C~~--~YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
+-..|+||.|.. .|+. .-.|++||.+..
T Consensus 54 d~~i~kC~~c~~~~~y~~------------~~~C~~cg~~~~ 83 (415)
T COG5257 54 DAKIYKCPECYRPECYTT------------EPKCPNCGAETE 83 (415)
T ss_pred cCceEeCCCCCCCccccc------------CCCCCCCCCCcc
Confidence 456899999996 5554 679999997653
No 118
>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=78.75 E-value=0.9 Score=31.29 Aligned_cols=27 Identities=30% Similarity=0.738 Sum_probs=18.8
Q ss_pred ecCCCCc--cccHHHHHhhcCCCCCCeeccCCCc
Q 020131 19 ICPNCQR--RYNALDALRLVSLEDDSFHCENCNG 50 (330)
Q Consensus 19 ~CP~C~~--~YT~lDA~~Lld~~~~~F~C~~Cg~ 50 (330)
-||.|+- +|.+.+.. ..+.|.|..|+.
T Consensus 5 pCP~CGG~DrFr~~d~~-----g~G~~~C~~Cg~ 33 (37)
T smart00778 5 PCPNCGGSDRFRFDDKD-----GRGTWFCSVCGA 33 (37)
T ss_pred CCCCCCCccccccccCC-----CCcCEEeCCCCC
Confidence 4999998 56543322 247899999974
No 119
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=78.68 E-value=1.2 Score=46.38 Aligned_cols=45 Identities=22% Similarity=0.501 Sum_probs=31.7
Q ss_pred CCCeeecCCCCccccHHHHHhhcC-CCCCCeeccCCCccccccchh
Q 020131 14 TVQEYICPNCQRRYNALDALRLVS-LEDDSFHCENCNGELVAESDK 58 (330)
Q Consensus 14 ~~~~Y~CP~C~~~YT~lDA~~Lld-~~~~~F~C~~Cg~eL~~~~~~ 58 (330)
....|+||+|--.|..-+|...-. -...=|.||.|.+.|.-....
T Consensus 23 Ei~~~yCp~CL~~~p~~e~~~~~nrC~r~Cf~CP~C~~~L~~~~~~ 68 (483)
T PF05502_consen 23 EIDSYYCPNCLFEVPSSEARSEKNRCSRNCFDCPICFSPLSVRASD 68 (483)
T ss_pred ccceeECccccccCChhhheeccceeccccccCCCCCCcceeEecc
Confidence 445899999999999888832211 122359999999999665443
No 120
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=78.64 E-value=0.24 Score=31.91 Aligned_cols=28 Identities=18% Similarity=0.540 Sum_probs=15.4
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCCc
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCNG 50 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~ 50 (330)
.+||+|+..........- ..|.|++|..
T Consensus 2 ~~C~rC~~~~~~~~~~~r-----~~~~C~rCq~ 29 (30)
T PF06827_consen 2 EKCPRCWNYIEDIGINGR-----STYLCPRCQK 29 (30)
T ss_dssp SB-TTT--BBEEEEETTE-----EEEE-TTTCC
T ss_pred CcCccCCCcceEeEecCC-----CCeECcCCcC
Confidence 479999988765433222 4689999863
No 121
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=78.53 E-value=1.3 Score=43.10 Aligned_cols=38 Identities=18% Similarity=0.555 Sum_probs=22.4
Q ss_pred CCeeecCCCCccccHHHHHhh-cCCCCCCeeccCCCccc
Q 020131 15 VQEYICPNCQRRYNALDALRL-VSLEDDSFHCENCNGEL 52 (330)
Q Consensus 15 ~~~Y~CP~C~~~YT~lDA~~L-ld~~~~~F~C~~Cg~eL 52 (330)
+..+.|+.|++.|..|=|+.. |---+-.+.|..||.-.
T Consensus 159 ~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaF 197 (279)
T KOG2462|consen 159 KKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAF 197 (279)
T ss_pred cccccCCCCCceeeehHHHhhHhhccCCCcccccccccc
Confidence 456777777777777766643 11112356666666543
No 122
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=78.45 E-value=0.99 Score=34.19 Aligned_cols=25 Identities=32% Similarity=0.793 Sum_probs=19.0
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
.++||.|+ +||. .=.|+.||+....
T Consensus 5 ~rkC~~cg-~YTL------------ke~Cp~CG~~t~~ 29 (59)
T COG2260 5 IRKCPKCG-RYTL------------KEKCPVCGGDTKV 29 (59)
T ss_pred hhcCcCCC-ceee------------cccCCCCCCcccc
Confidence 57899977 5765 3579999988753
No 123
>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=78.11 E-value=0.66 Score=41.00 Aligned_cols=31 Identities=23% Similarity=0.484 Sum_probs=23.5
Q ss_pred CCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 15 VQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 15 ~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
.-.|+|.+||....+..+..| -.||.||+.-
T Consensus 110 ~G~l~C~~Cg~~~~~~~~~~l-------~~Cp~C~~~~ 140 (146)
T PF07295_consen 110 PGTLVCENCGHEVELTHPERL-------PPCPKCGHTE 140 (146)
T ss_pred CceEecccCCCEEEecCCCcC-------CCCCCCCCCe
Confidence 346999999999887554443 5799999865
No 124
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=78.00 E-value=0.88 Score=51.84 Aligned_cols=42 Identities=19% Similarity=0.404 Sum_probs=26.1
Q ss_pred CCeeecCCCCccccHH--HHHhhcCCCCCCeeccCCCccccccchh
Q 020131 15 VQEYICPNCQRRYNAL--DALRLVSLEDDSFHCENCNGELVAESDK 58 (330)
Q Consensus 15 ~~~Y~CP~C~~~YT~l--DA~~Lld~~~~~F~C~~Cg~eL~~~~~~ 58 (330)
...|+||.|+..=-+. -+..=+|.. .=.||.||++|.-+.-.
T Consensus 912 ~PHY~Cp~Cky~Ef~~d~svgsGfDLp--dK~CPkCg~pl~kDG~d 955 (1444)
T COG2176 912 PPHYLCPECKYSEFIDDGSVGSGFDLP--DKDCPKCGTPLKKDGHD 955 (1444)
T ss_pred CccccCCCCceeeeecCCCcCCCCCCC--CCCCCcCCCccccCCCC
Confidence 4589999998632121 233333332 34899999999765443
No 125
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=77.92 E-value=2 Score=31.19 Aligned_cols=31 Identities=26% Similarity=0.455 Sum_probs=18.0
Q ss_pred HHHHHhhcCCCCeeecCCCCccccHHHHHhhc
Q 020131 5 LKDELECKNTVQEYICPNCQRRYNALDALRLV 36 (330)
Q Consensus 5 Le~~l~~~~~~~~Y~CP~C~~~YT~lDA~~Ll 36 (330)
++..+..-..... .||.|++.|+......|+
T Consensus 9 ~~k~i~~l~~~~~-~CPlC~r~l~~e~~~~li 39 (54)
T PF04423_consen 9 LKKYIEELKEAKG-CCPLCGRPLDEEHRQELI 39 (54)
T ss_dssp HHHHHHHHTT-SE-E-TTT--EE-HHHHHHHH
T ss_pred HHHHHHHHhcCCC-cCCCCCCCCCHHHHHHHH
Confidence 4444555555556 999999999998887664
No 126
>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=77.57 E-value=0.73 Score=50.76 Aligned_cols=11 Identities=27% Similarity=0.465 Sum_probs=0.0
Q ss_pred HHHHHhhcCcC
Q 020131 94 MEQINRVKDLD 104 (330)
Q Consensus 94 ~~~Lk~id~i~ 104 (330)
++.||-|+++.
T Consensus 729 ~~~~KGVkgl~ 739 (900)
T PF03833_consen 729 PDELKGVKGLT 739 (900)
T ss_dssp -----------
T ss_pred hhhhhhHHhhh
Confidence 55666666654
No 127
>cd00296 SIR2 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer. Also included in this superfamily is a group of uncharacterized Sir2-like proteins which lack certain key catalytic
Probab=77.52 E-value=1.9 Score=39.18 Aligned_cols=38 Identities=21% Similarity=0.529 Sum_probs=28.8
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccch
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESD 57 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~ 57 (330)
....|..|+..|...+...- ....+|+.||+.|+....
T Consensus 112 ~~~~C~~C~~~~~~~~~~~~----~~~p~C~~C~~~l~p~v~ 149 (222)
T cd00296 112 DRVRCTSCGKEYPRDEVLER----EKPPRCPKCGGLLRPDVV 149 (222)
T ss_pred CccEECCCCCCcchhhhhhc----cCCCCCCCCCCcccCceE
Confidence 35679999999987766543 236889999999976543
No 128
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=77.44 E-value=0.67 Score=32.12 Aligned_cols=35 Identities=20% Similarity=0.402 Sum_probs=20.0
Q ss_pred eecCCCCcccc---HHHHHhhcCCCCCCeeccCCCccc
Q 020131 18 YICPNCQRRYN---ALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 18 Y~CP~C~~~YT---~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
+.||.|+..-. .+..-.-=.|++--|.|..||..+
T Consensus 1 ~~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w 38 (40)
T smart00440 1 APCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRW 38 (40)
T ss_pred CcCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEe
Confidence 46899986533 221111112345568999998765
No 129
>PRK05333 NAD-dependent deacetylase; Provisional
Probab=77.19 E-value=2 Score=41.35 Aligned_cols=17 Identities=18% Similarity=0.348 Sum_probs=13.2
Q ss_pred CeeecCCCCccccHHHH
Q 020131 16 QEYICPNCQRRYNALDA 32 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA 32 (330)
..+.|..|+..|...+.
T Consensus 127 ~~~~C~~C~~~~~~~~~ 143 (285)
T PRK05333 127 DGVRCMGCGARHPRAEI 143 (285)
T ss_pred CEEEECCCCCcCCHHHH
Confidence 35889999999985543
No 130
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=77.06 E-value=0.81 Score=34.84 Aligned_cols=32 Identities=22% Similarity=0.530 Sum_probs=23.0
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccc
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAES 56 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~ 56 (330)
=+|..||......+-. ..|.||+||..++...
T Consensus 10 ~~CtSCg~~i~p~e~~-------v~F~CPnCGe~~I~Rc 41 (61)
T COG2888 10 PVCTSCGREIAPGETA-------VKFPCPNCGEVEIYRC 41 (61)
T ss_pred ceeccCCCEeccCCce-------eEeeCCCCCceeeehh
Confidence 3799999887553322 3599999998776543
No 131
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=76.99 E-value=2.3 Score=31.10 Aligned_cols=35 Identities=20% Similarity=0.421 Sum_probs=28.9
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
.-.|--|+.+.+.-...++..- .....||+||-.|
T Consensus 22 ~~~C~gC~~~l~~~~~~~i~~~-~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 22 GGTCSGCHMELPPQELNEIRKG-DEIVFCPNCGRIL 56 (56)
T ss_pred CCccCCCCEEcCHHHHHHHHcC-CCeEECcCCCccC
Confidence 3489999999999988888554 4579999999765
No 132
>PF12773 DZR: Double zinc ribbon
Probab=76.84 E-value=1.3 Score=31.25 Aligned_cols=29 Identities=24% Similarity=0.581 Sum_probs=21.1
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
.-+||.||.... ......+.|+.||..+.
T Consensus 12 ~~fC~~CG~~l~--------~~~~~~~~C~~Cg~~~~ 40 (50)
T PF12773_consen 12 AKFCPHCGTPLP--------PPDQSKKICPNCGAENP 40 (50)
T ss_pred ccCChhhcCChh--------hccCCCCCCcCCcCCCc
Confidence 456999998877 22334688999999864
No 133
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=76.80 E-value=0.99 Score=35.36 Aligned_cols=27 Identities=30% Similarity=0.791 Sum_probs=17.3
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
..|.|+.|.+.|.. .-.||.|+.+|..
T Consensus 16 ~~~~C~~C~~~~~~------------~a~CPdC~~~Le~ 42 (70)
T PF07191_consen 16 GHYHCEACQKDYKK------------EAFCPDCGQPLEV 42 (70)
T ss_dssp TEEEETTT--EEEE------------EEE-TTT-SB-EE
T ss_pred CEEECcccccccee------------cccCCCcccHHHH
Confidence 47999999998865 5789999998853
No 134
>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=76.72 E-value=0.56 Score=32.19 Aligned_cols=31 Identities=16% Similarity=0.449 Sum_probs=15.9
Q ss_pred CCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 15 VQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 15 ~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
.++|+|..||.....+. .-.+.+.| ||.++.
T Consensus 4 ~~~YkC~~CGniVev~~------~g~g~lvC--CGe~M~ 34 (36)
T PF06397_consen 4 GEFYKCEHCGNIVEVVH------DGGGPLVC--CGEPME 34 (36)
T ss_dssp TEEEE-TTT--EEEEEE--------SS-EEE--TTEE-E
T ss_pred ccEEEccCCCCEEEEEE------CCCCCEEe--CCcccc
Confidence 35899999998875433 33346777 776653
No 135
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=76.68 E-value=1.6 Score=42.60 Aligned_cols=33 Identities=15% Similarity=0.245 Sum_probs=26.1
Q ss_pred CCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 15 VQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 15 ~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
.-..+||.|+..+-..+.... .+.||.||+-+.
T Consensus 25 ~~~~~c~~c~~~~~~~~l~~~------~~vc~~c~~h~r 57 (292)
T PRK05654 25 GLWTKCPSCGQVLYRKELEAN------LNVCPKCGHHMR 57 (292)
T ss_pred CCeeECCCccchhhHHHHHhc------CCCCCCCCCCee
Confidence 347899999998887765554 589999999774
No 136
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=76.27 E-value=1.4 Score=33.00 Aligned_cols=25 Identities=24% Similarity=0.514 Sum_probs=18.8
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
..+|+.||.- |. .-.||.||.++.-
T Consensus 5 mr~C~~CgvY-TL------------k~~CP~CG~~t~~ 29 (56)
T PRK13130 5 IRKCPKCGVY-TL------------KEICPVCGGKTKN 29 (56)
T ss_pred ceECCCCCCE-Ec------------cccCcCCCCCCCC
Confidence 4689999964 33 4689999998853
No 137
>COG1773 Rubredoxin [Energy production and conversion]
Probab=76.02 E-value=1.1 Score=33.48 Aligned_cols=34 Identities=18% Similarity=0.448 Sum_probs=23.4
Q ss_pred eeecCCCCccccHHHHHhh--cCC------CCCCeeccCCCc
Q 020131 17 EYICPNCQRRYNALDALRL--VSL------EDDSFHCENCNG 50 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~L--ld~------~~~~F~C~~Cg~ 50 (330)
-|+|..||-.|....-... +.+ ....+.||.||.
T Consensus 3 ~~~C~~CG~vYd~e~Gdp~~gi~pgT~fedlPd~w~CP~Cg~ 44 (55)
T COG1773 3 RWRCSVCGYVYDPEKGDPRCGIAPGTPFEDLPDDWVCPECGV 44 (55)
T ss_pred ceEecCCceEeccccCCccCCCCCCCchhhCCCccCCCCCCC
Confidence 5999999999986543321 222 234789999996
No 138
>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=75.96 E-value=1.7 Score=35.40 Aligned_cols=26 Identities=23% Similarity=0.667 Sum_probs=20.1
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
.||+||..+. +..+.|.|+.||....
T Consensus 2 fC~~Cg~~l~---------~~~~~~~C~~C~~~~~ 27 (104)
T TIGR01384 2 FCPKCGSLMT---------PKNGVYVCPSCGYEKE 27 (104)
T ss_pred CCcccCcccc---------cCCCeEECcCCCCccc
Confidence 6999998773 2335799999998753
No 139
>PRK11823 DNA repair protein RadA; Provisional
Probab=75.84 E-value=1.6 Score=44.66 Aligned_cols=25 Identities=20% Similarity=0.606 Sum_probs=20.5
Q ss_pred CCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCc
Q 020131 15 VQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNG 50 (330)
Q Consensus 15 ~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~ 50 (330)
+..|+|..||.++.. + ..+||.|+.
T Consensus 5 ~~~y~C~~Cg~~~~~-----~------~g~Cp~C~~ 29 (446)
T PRK11823 5 KTAYVCQECGAESPK-----W------LGRCPECGA 29 (446)
T ss_pred CCeEECCcCCCCCcc-----c------CeeCcCCCC
Confidence 457999999998865 3 689999984
No 140
>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=75.69 E-value=1.3 Score=27.24 Aligned_cols=17 Identities=35% Similarity=0.976 Sum_probs=15.0
Q ss_pred eecCCCCccccHHHHHh
Q 020131 18 YICPNCQRRYNALDALR 34 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~ 34 (330)
|.|..|++.|..+.++.
T Consensus 2 ~~C~~C~~~F~~~~~l~ 18 (27)
T PF13912_consen 2 FECDECGKTFSSLSALR 18 (27)
T ss_dssp EEETTTTEEESSHHHHH
T ss_pred CCCCccCCccCChhHHH
Confidence 89999999999888764
No 141
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=75.36 E-value=1.7 Score=32.39 Aligned_cols=29 Identities=24% Similarity=0.729 Sum_probs=22.6
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
...+|+.|+.+|+. .+....|+.||++--
T Consensus 4 ~~~~C~~Cg~~~~~---------~dDiVvCp~CgapyH 32 (54)
T PF14446_consen 4 EGCKCPVCGKKFKD---------GDDIVVCPECGAPYH 32 (54)
T ss_pred cCccChhhCCcccC---------CCCEEECCCCCCccc
Confidence 46789999999963 224689999999863
No 142
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=75.29 E-value=1.2 Score=33.86 Aligned_cols=33 Identities=27% Similarity=0.777 Sum_probs=20.9
Q ss_pred CCeeecCCCCcc--ccHHHHHhhcCCCCCCeeccCCCcc
Q 020131 15 VQEYICPNCQRR--YNALDALRLVSLEDDSFHCENCNGE 51 (330)
Q Consensus 15 ~~~Y~CP~C~~~--YT~lDA~~Lld~~~~~F~C~~Cg~e 51 (330)
-..|.||+||.. |--.---.+ + ..|+||.||.+
T Consensus 23 ~~~F~CPnCG~~~I~RC~~CRk~-~---~~Y~CP~CGF~ 57 (59)
T PRK14890 23 AVKFLCPNCGEVIIYRCEKCRKQ-S---NPYTCPKCGFE 57 (59)
T ss_pred cCEeeCCCCCCeeEeechhHHhc-C---CceECCCCCCc
Confidence 457999999975 222222222 2 26999999963
No 143
>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=73.99 E-value=1.7 Score=32.23 Aligned_cols=25 Identities=36% Similarity=0.918 Sum_probs=19.2
Q ss_pred eee--cCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 17 EYI--CPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 17 ~Y~--CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
+|+ |+.|+ .||. .-.|+.||++..-
T Consensus 3 ~~~r~c~~~~-~YTL------------k~~cp~cG~~T~~ 29 (53)
T PF04135_consen 3 YYIRKCPGCR-VYTL------------KDKCPPCGGPTES 29 (53)
T ss_dssp EEEEECTTTC-EEES------------SSBBTTTSSBSEE
T ss_pred cccccCCCCC-cEeC------------CCccCCCCCCCcC
Confidence 455 99998 6765 4689999998854
No 144
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=73.84 E-value=1.8 Score=42.24 Aligned_cols=31 Identities=26% Similarity=0.625 Sum_probs=24.2
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
+.||.|+.. .+ ..|+..|...|-.||..|.+
T Consensus 2 ~~CpeCg~~-~~-----~~d~~~ge~VC~~CG~Vi~~ 32 (285)
T COG1405 2 MSCPECGST-NI-----ITDYERGEIVCADCGLVLED 32 (285)
T ss_pred CCCCCCCCc-cc-----eeeccCCeEEeccCCEEecc
Confidence 579999998 11 33456789999999998865
No 145
>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=73.61 E-value=1.8 Score=35.83 Aligned_cols=16 Identities=25% Similarity=0.661 Sum_probs=12.5
Q ss_pred CCeeccCCCccccccc
Q 020131 41 DSFHCENCNGELVAES 56 (330)
Q Consensus 41 ~~F~C~~Cg~eL~~~~ 56 (330)
..|+|+.||..+...+
T Consensus 30 ~~~~C~~CGe~~~~~e 45 (127)
T TIGR03830 30 PGWYCPACGEELLDPE 45 (127)
T ss_pred eeeECCCCCCEEEcHH
Confidence 4789999999986543
No 146
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=73.28 E-value=2.3 Score=36.81 Aligned_cols=35 Identities=29% Similarity=0.722 Sum_probs=24.6
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
-.|.|..|+..|- =.....+ ...++|-.||+.|+.
T Consensus 111 ~~y~C~~C~~~~~--~~rr~~~--~~~y~C~~C~g~l~~ 145 (146)
T smart00731 111 YPYRCTGCGQRYL--RVRRSNN--VSRYRCGKCGGKLIL 145 (146)
T ss_pred EEEECCCCCCCCc--eEccccC--cceEEcCCCCCEEEe
Confidence 4799999999884 1112212 257999999999863
No 147
>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=72.76 E-value=2 Score=48.08 Aligned_cols=27 Identities=19% Similarity=0.508 Sum_probs=20.9
Q ss_pred CCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 13 NTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 13 ~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
.....++||.||.- |+ .++||.||+.-
T Consensus 621 vev~~RKCPkCG~y-Tl------------k~rCP~CG~~T 647 (1095)
T TIGR00354 621 VEIAIRKCPQCGKE-SF------------WLKCPVCGELT 647 (1095)
T ss_pred EEEEEEECCCCCcc-cc------------cccCCCCCCcc
Confidence 34457899999964 44 79999999774
No 148
>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=72.70 E-value=1.8 Score=45.71 Aligned_cols=49 Identities=18% Similarity=0.425 Sum_probs=30.5
Q ss_pred HHHHHHhhcCCCCee-ecCCCCccccHHHHHhhc------CCCCCCeeccCCCccccc
Q 020131 4 KLKDELECKNTVQEY-ICPNCQRRYNALDALRLV------SLEDDSFHCENCNGELVA 54 (330)
Q Consensus 4 ~Le~~l~~~~~~~~Y-~CP~C~~~YT~lDA~~Ll------d~~~~~F~C~~Cg~eL~~ 54 (330)
+|........-+.+| .||.||..+... ...| .+.+-.|.|+.||..+.+
T Consensus 186 ~I~~~~~~sdqr~~~vpCPhCg~~~~l~--~~~l~w~~~~~~~~a~y~C~~Cg~~i~e 241 (557)
T PF05876_consen 186 RIERLYEESDQRRYYVPCPHCGEEQVLE--WENLKWDKGEAPETARYVCPHCGCEIEE 241 (557)
T ss_pred HHHHHHHhCCceEEEccCCCCCCCcccc--ccceeecCCCCccceEEECCCCcCCCCH
Confidence 344444444333333 599999988743 1112 345567999999999865
No 149
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=72.60 E-value=2.3 Score=31.92 Aligned_cols=26 Identities=23% Similarity=0.430 Sum_probs=19.3
Q ss_pred CCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCc
Q 020131 13 NTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNG 50 (330)
Q Consensus 13 ~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~ 50 (330)
.......||.||.--- .-..|+.||.
T Consensus 23 ~~~~l~~C~~CG~~~~------------~H~vC~~CG~ 48 (57)
T PRK12286 23 KAPGLVECPNCGEPKL------------PHRVCPSCGY 48 (57)
T ss_pred cCCcceECCCCCCccC------------CeEECCCCCc
Confidence 4456788999997432 2689999995
No 150
>PHA02942 putative transposase; Provisional
Probab=72.34 E-value=2.4 Score=42.82 Aligned_cols=30 Identities=27% Similarity=0.661 Sum_probs=21.3
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
+=.||.||..... + ....|.|+.||..+-.
T Consensus 325 Sq~Cs~CG~~~~~-----l---~~r~f~C~~CG~~~dr 354 (383)
T PHA02942 325 SVSCPKCGHKMVE-----I---AHRYFHCPSCGYENDR 354 (383)
T ss_pred CccCCCCCCccCc-----C---CCCEEECCCCCCEeCc
Confidence 4469999986531 1 1236999999998844
No 151
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=72.21 E-value=1.7 Score=35.33 Aligned_cols=31 Identities=19% Similarity=0.582 Sum_probs=22.8
Q ss_pred CCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 15 VQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 15 ~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
+..|.|+.||+.----.|. |.+.|-.|...+
T Consensus 34 haky~CsfCGK~~vKR~Av-------GiW~C~~C~kv~ 64 (92)
T KOG0402|consen 34 HAKYTCSFCGKKTVKRKAV-------GIWKCGSCKKVV 64 (92)
T ss_pred hhhhhhhhcchhhhhhhce-------eEEecCCcccee
Confidence 3479999999875444443 459999998766
No 152
>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=72.16 E-value=2.3 Score=43.72 Aligned_cols=25 Identities=16% Similarity=0.608 Sum_probs=20.3
Q ss_pred CCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCc
Q 020131 15 VQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNG 50 (330)
Q Consensus 15 ~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~ 50 (330)
+..|+|..||.++.. + ..+||.|+.
T Consensus 5 ~~~y~C~~Cg~~~~~-----~------~g~Cp~C~~ 29 (454)
T TIGR00416 5 KSKFVCQHCGADSPK-----W------QGKCPACHA 29 (454)
T ss_pred CCeEECCcCCCCCcc-----c------cEECcCCCC
Confidence 457999999998864 2 689999983
No 153
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=71.89 E-value=3.1 Score=40.65 Aligned_cols=75 Identities=16% Similarity=0.203 Sum_probs=46.3
Q ss_pred CCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccchhhhhhcCCCCChhHHHHHHHHHHHHHHHHH--HhHH
Q 020131 14 TVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESDKLAAQEGGDGDDNARRRRREKLKDLLQKLE--VHLK 91 (330)
Q Consensus 14 ~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~~~~~~e~~~g~~na~r~~~e~~k~~l~r~n--~Qlk 91 (330)
..-.-+||.|+...-.-|.... .++|+.|++-.... |+ .++.-|- ..+.
T Consensus 25 e~lw~KCp~c~~~~y~~eL~~n------~~vcp~c~~h~ri~---------------A~--------~Ri~~llD~gsf~ 75 (294)
T COG0777 25 EGLWTKCPSCGEMLYRKELESN------LKVCPKCGHHMRIS---------------AR--------ERLEALLDEGSFE 75 (294)
T ss_pred CCceeECCCccceeeHHHHHhh------hhcccccCcccccC---------------HH--------HHHHHhhCCCcce
Confidence 4456799999987666566554 58999999987541 11 1112221 2245
Q ss_pred HHHHHHHhhcCcCCCCCCcHHHHHHH
Q 020131 92 PLMEQINRVKDLDVPEFGTLQAWEAR 117 (330)
Q Consensus 92 pI~~~Lk~id~i~iP~f~~~~aw~~~ 117 (330)
.|..-|.-.|-+.+|.-..+..|..+
T Consensus 76 el~~~l~~~dPL~F~d~k~Y~~rL~~ 101 (294)
T COG0777 76 ELDSPLEPKDPLKFPDSKKYKDRLEA 101 (294)
T ss_pred ecccCCCcCCcccCCcchhhHHHHHH
Confidence 55555666666667766566776654
No 154
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=71.87 E-value=2.3 Score=40.98 Aligned_cols=33 Identities=18% Similarity=0.709 Sum_probs=22.0
Q ss_pred CCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 15 VQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 15 ~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
..+|.||.|+..|+-.=.+..- =-|-.|+.++-
T Consensus 153 ~aef~C~~C~h~F~G~~qm~v~------sPCy~C~~~v~ 185 (278)
T PF15135_consen 153 IAEFHCPKCRHNFRGFAQMGVP------SPCYGCGNPVY 185 (278)
T ss_pred eeeeecccccccchhhhhcCCC------CCccCCCCccC
Confidence 3578888888888866333432 34777888773
No 155
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=71.78 E-value=1.1 Score=40.12 Aligned_cols=13 Identities=38% Similarity=0.743 Sum_probs=10.4
Q ss_pred CeeccCCCccccc
Q 020131 42 SFHCENCNGELVA 54 (330)
Q Consensus 42 ~F~C~~Cg~eL~~ 54 (330)
.|.|+.||..-.+
T Consensus 29 sf~C~~CGyk~~e 41 (160)
T smart00709 29 SFECEHCGYRNNE 41 (160)
T ss_pred EEECCCCCCccce
Confidence 6999999987544
No 156
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=71.77 E-value=3.1 Score=38.58 Aligned_cols=34 Identities=18% Similarity=0.393 Sum_probs=22.5
Q ss_pred CeeecCCCCccccHHHHHhh--cCCCCCCeeccCCCccc
Q 020131 16 QEYICPNCQRRYNALDALRL--VSLEDDSFHCENCNGEL 52 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~L--ld~~~~~F~C~~Cg~eL 52 (330)
.+|.||.|+..=+.-+++.- .++ ..+|..||+..
T Consensus 5 iy~~Cp~Cg~eev~hEVik~~g~~~---lvrC~eCG~V~ 40 (201)
T COG1326 5 IYIECPSCGSEEVSHEVIKERGREP---LVRCEECGTVH 40 (201)
T ss_pred EEEECCCCCcchhhHHHHHhcCCce---EEEccCCCcEe
Confidence 47899999933233344443 222 58999999877
No 157
>PRK02935 hypothetical protein; Provisional
Probab=71.69 E-value=1.8 Score=36.55 Aligned_cols=31 Identities=29% Similarity=0.655 Sum_probs=22.1
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccch
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESD 57 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~ 57 (330)
-.||+|++--.-| -- .-.|-+|+.||.-+.+
T Consensus 71 V~CP~C~K~TKmL---Gr------vD~CM~C~~PLTLd~~ 101 (110)
T PRK02935 71 VICPSCEKPTKML---GR------VDACMHCNQPLTLDRS 101 (110)
T ss_pred eECCCCCchhhhc---cc------eeecCcCCCcCCcCcc
Confidence 4799999854331 11 3479999999987654
No 158
>PTZ00410 NAD-dependent SIR2; Provisional
Probab=71.64 E-value=3.5 Score=41.38 Aligned_cols=39 Identities=21% Similarity=0.454 Sum_probs=26.2
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAE 55 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~ 55 (330)
....|..|+..|........+.. ...-+|+.||+.|..+
T Consensus 146 ~~~~C~~C~~~~~~~~~~~~~~~-~~vP~C~~CgG~lRPd 184 (349)
T PTZ00410 146 SAASCIECHTPYDIEQAYLEARS-GKVPHCSTCGGIVKPD 184 (349)
T ss_pred CeeEeCCCCCCcchhHHHHHhhc-CCCCCCCCCCCccCCc
Confidence 35789999999986544432221 1246799999988654
No 159
>PRK05978 hypothetical protein; Provisional
Probab=71.51 E-value=1.9 Score=38.34 Aligned_cols=33 Identities=18% Similarity=0.427 Sum_probs=22.2
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccc
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAES 56 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~ 56 (330)
-+||+||.-=-|- .++. -.=.|+.||..+....
T Consensus 34 grCP~CG~G~LF~---g~Lk---v~~~C~~CG~~~~~~~ 66 (148)
T PRK05978 34 GRCPACGEGKLFR---AFLK---PVDHCAACGEDFTHHR 66 (148)
T ss_pred CcCCCCCCCcccc---cccc---cCCCccccCCccccCC
Confidence 4799998754332 2222 2568999999997753
No 160
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=70.97 E-value=2.3 Score=46.48 Aligned_cols=8 Identities=50% Similarity=1.086 Sum_probs=6.2
Q ss_pred HHHHHHHH
Q 020131 232 EYIRAYYA 239 (330)
Q Consensus 232 e~l~aYyA 239 (330)
.-|+||||
T Consensus 569 sllkayya 576 (1007)
T KOG3623|consen 569 SLLKAYYA 576 (1007)
T ss_pred HHHHHHHH
Confidence 45888987
No 161
>PF10058 DUF2296: Predicted integral membrane metal-binding protein (DUF2296); InterPro: IPR019273 This domain, found mainly in the eukaryotic lunapark proteins, has no known function [].
Probab=70.96 E-value=2.7 Score=31.15 Aligned_cols=35 Identities=17% Similarity=0.460 Sum_probs=23.1
Q ss_pred CCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCc
Q 020131 13 NTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNG 50 (330)
Q Consensus 13 ~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~ 50 (330)
.++--.||++|...--.-= -.++..-.|+|++||.
T Consensus 18 ~~r~aLIC~~C~~hNGla~---~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 18 SNRYALICSKCFSHNGLAP---KEEFEEIQYRCPYCGA 52 (54)
T ss_pred cCceeEECcccchhhcccc---cccCCceEEEcCCCCC
Confidence 4566789999988655321 1122223799999996
No 162
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=70.78 E-value=2 Score=32.58 Aligned_cols=30 Identities=23% Similarity=0.558 Sum_probs=24.9
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
+||.|+..=+ .|+.......|..||..|..
T Consensus 13 kCp~C~n~q~------vFsha~t~V~C~~Cg~~L~~ 42 (59)
T PRK00415 13 KCPDCGNEQV------VFSHASTVVRCLVCGKTLAE 42 (59)
T ss_pred ECCCCCCeEE------EEecCCcEEECcccCCCccc
Confidence 6999998765 36777778999999999965
No 163
>PRK04023 DNA polymerase II large subunit; Validated
Probab=70.51 E-value=2.1 Score=48.11 Aligned_cols=12 Identities=25% Similarity=0.894 Sum_probs=7.7
Q ss_pred CCeeecCCCCcc
Q 020131 15 VQEYICPNCQRR 26 (330)
Q Consensus 15 ~~~Y~CP~C~~~ 26 (330)
...++||.||..
T Consensus 624 Vg~RfCpsCG~~ 635 (1121)
T PRK04023 624 IGRRKCPSCGKE 635 (1121)
T ss_pred ccCccCCCCCCc
Confidence 345677777766
No 164
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=69.86 E-value=2.2 Score=33.18 Aligned_cols=30 Identities=23% Similarity=0.542 Sum_probs=24.5
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
+||.|+..=+ .|+.....-.|..||..|..
T Consensus 21 kCpdC~N~q~------vFshast~V~C~~CG~~l~~ 50 (67)
T COG2051 21 KCPDCGNEQV------VFSHASTVVTCLICGTTLAE 50 (67)
T ss_pred ECCCCCCEEE------EeccCceEEEecccccEEEe
Confidence 6999998755 35666668999999999976
No 165
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=69.68 E-value=1.5 Score=33.75 Aligned_cols=34 Identities=26% Similarity=0.752 Sum_probs=18.7
Q ss_pred eecCCCCccccHHHHHh--------hcCCCCCCe---eccCCCcc
Q 020131 18 YICPNCQRRYNALDALR--------LVSLEDDSF---HCENCNGE 51 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~--------Lld~~~~~F---~C~~Cg~e 51 (330)
|+||.|+.+--..+-.+ +||..-..| .|++||..
T Consensus 1 y~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~CGYT 45 (64)
T PF09855_consen 1 YKCPKCGNEEYESGEVRATGGGLSKIFDVQNKKFTTVSCTNCGYT 45 (64)
T ss_pred CCCCCCCCcceecceEEccCCeeEEEEEecCcEEEEEECCCCCCE
Confidence 89999998532211111 122211222 79999976
No 166
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=69.66 E-value=1.9 Score=49.60 Aligned_cols=41 Identities=24% Similarity=0.524 Sum_probs=23.3
Q ss_pred CeeecCCCCccccHHH--HHhhcCCCCCCeeccCCCccccccchh
Q 020131 16 QEYICPNCQRRYNALD--ALRLVSLEDDSFHCENCNGELVAESDK 58 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lD--A~~Lld~~~~~F~C~~Cg~eL~~~~~~ 58 (330)
..|+||+|+..-=+.+ +..=+|.. .=.||.||++|.-+.-.
T Consensus 682 phy~c~~c~~~ef~~~~~~~sg~dlp--~k~cp~c~~~~~~dg~~ 724 (1213)
T TIGR01405 682 PHYLCPNCKYSEFITDGSVGSGFDLP--DKDCPKCGAPLKKDGQD 724 (1213)
T ss_pred ccccCcccccccccccccccccccCc--cccCccccccccccCCC
Confidence 4799999963211111 11112221 34899999998765543
No 167
>PHA00616 hypothetical protein
Probab=69.40 E-value=1.3 Score=31.70 Aligned_cols=15 Identities=20% Similarity=0.576 Sum_probs=11.9
Q ss_pred eecCCCCccccHHHH
Q 020131 18 YICPNCQRRYNALDA 32 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA 32 (330)
|.||+||..|...--
T Consensus 2 YqC~~CG~~F~~~s~ 16 (44)
T PHA00616 2 YQCLRCGGIFRKKKE 16 (44)
T ss_pred CccchhhHHHhhHHH
Confidence 889999999985443
No 168
>PTZ00408 NAD-dependent deacetylase; Provisional
Probab=69.39 E-value=3.5 Score=39.01 Aligned_cols=33 Identities=18% Similarity=0.433 Sum_probs=23.3
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCC--ccccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCN--GELVA 54 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg--~eL~~ 54 (330)
...|..|++.|...+... .....|+.|| +.|..
T Consensus 117 ~~~C~~C~~~~~~~~~~~-----~~~p~C~~Cg~~g~lrP 151 (242)
T PTZ00408 117 KVRCTATGHVFDWTEDVV-----HGSSRCKCCGCVGTLRP 151 (242)
T ss_pred eEEECCCCcccCchhhhh-----cCCCccccCCCCCCCCC
Confidence 578999999997644321 1247899998 66654
No 169
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=69.29 E-value=1.5 Score=33.31 Aligned_cols=36 Identities=19% Similarity=0.522 Sum_probs=23.0
Q ss_pred CeeecCCCCccc---cHHHHH------------------hhcCCCCCCeeccCCCcc
Q 020131 16 QEYICPNCQRRY---NALDAL------------------RLVSLEDDSFHCENCNGE 51 (330)
Q Consensus 16 ~~Y~CP~C~~~Y---T~lDA~------------------~Lld~~~~~F~C~~Cg~e 51 (330)
..-.||.|+... ...++. --++...|.++|+.||..
T Consensus 6 niL~Cp~ck~pL~~~~l~~~~~~~~~~lp~~~~~~~~~l~~~~i~eg~L~Cp~c~r~ 62 (68)
T PF03966_consen 6 NILACPVCKGPLDWEALVETAQLGLSELPKELPEDYHVLLEVEIVEGELICPECGRE 62 (68)
T ss_dssp GTBB-TTTSSBEHHHHHHHHHHCCCCHCHHCHHCHCEHHCTEETTTTEEEETTTTEE
T ss_pred hhhcCCCCCCcchHHHHHHHHHhCcccCCCCCccchhhhhcccccCCEEEcCCCCCE
Confidence 467899999944 111222 124667899999999964
No 170
>COG1503 eRF1 Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]
Probab=68.85 E-value=2 Score=43.89 Aligned_cols=38 Identities=21% Similarity=0.472 Sum_probs=25.2
Q ss_pred CCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 13 NTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 13 ~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
..+-.|.||.|+..+....-.. .. -.|+|+.||.++..
T Consensus 323 ~~r~~~~c~~~~~e~~~t~~~~--~~--~~~~~~~~~~e~~~ 360 (411)
T COG1503 323 KERVTYKCPTCGYENLKSKREF--EQ--KRFRCPECGSEMEE 360 (411)
T ss_pred ccceeecCCCcchhhhhccccc--cc--ccccCccccccccc
Confidence 3456899999999885421111 11 15799999997754
No 171
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=68.48 E-value=3 Score=25.87 Aligned_cols=18 Identities=17% Similarity=0.733 Sum_probs=14.7
Q ss_pred eecCCCCccccHHHHHhh
Q 020131 18 YICPNCQRRYNALDALRL 35 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~L 35 (330)
|.|+.|++.|+...++..
T Consensus 2 ~~C~~C~k~f~~~~~~~~ 19 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQ 19 (27)
T ss_dssp CBBTTTTBBBSSHHHHHC
T ss_pred CCcccCCCCcCCHHHHHH
Confidence 789999999998777653
No 172
>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=68.45 E-value=1.8 Score=37.98 Aligned_cols=28 Identities=25% Similarity=0.787 Sum_probs=20.8
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
++-||.|+++..... .+.|.|+.|+...
T Consensus 34 Y~aC~~C~kkv~~~~--------~~~~~C~~C~~~~ 61 (166)
T cd04476 34 YPACPGCNKKVVEEG--------NGTYRCEKCNKSV 61 (166)
T ss_pred EccccccCcccEeCC--------CCcEECCCCCCcC
Confidence 455999999876421 1579999999874
No 173
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=68.29 E-value=13 Score=37.79 Aligned_cols=26 Identities=23% Similarity=0.551 Sum_probs=17.4
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNG 50 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~ 50 (330)
.|.|+.|+..+. .+.+ ..=.|+.||+
T Consensus 240 ~~~c~~cg~~~~------~~~~--~~~~c~~Cg~ 265 (380)
T COG1867 240 IYHCSRCGEIVG------SFRE--VDEKCPHCGG 265 (380)
T ss_pred EEEcccccceec------cccc--ccccCCcccc
Confidence 599999993222 2222 3458999995
No 174
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=68.23 E-value=3.9 Score=39.14 Aligned_cols=37 Identities=22% Similarity=0.531 Sum_probs=25.9
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCc-ccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNG-ELV 53 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~-eL~ 53 (330)
..+.|..|+..|...++....... ..=+|+.||+ .|.
T Consensus 121 ~~~~C~~C~~~~~~~~~~~~~~~~-~~p~C~~Cg~~~lr 158 (250)
T COG0846 121 KRVRCSKCGNQYYDEDVIKFIEDG-LIPRCPKCGGPVLR 158 (250)
T ss_pred eeeEeCCCcCccchhhhhhhcccC-CCCcCccCCCcccc
Confidence 457899999999987754433221 2358999999 553
No 175
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=67.52 E-value=1.9 Score=32.67 Aligned_cols=13 Identities=23% Similarity=0.692 Sum_probs=10.0
Q ss_pred CeeecCCCCcccc
Q 020131 16 QEYICPNCQRRYN 28 (330)
Q Consensus 16 ~~Y~CP~C~~~YT 28 (330)
.++.||+|+..|-
T Consensus 16 ~~lrCPRC~~~FR 28 (65)
T COG4049 16 EFLRCPRCGMVFR 28 (65)
T ss_pred eeeeCCchhHHHH
Confidence 4788888888775
No 176
>PRK08402 replication factor A; Reviewed
Probab=67.51 E-value=2.8 Score=42.08 Aligned_cols=28 Identities=21% Similarity=0.566 Sum_probs=21.4
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNG 50 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~ 50 (330)
-+.-||.|+++.+. +..++.++|+.||.
T Consensus 211 ~y~aCp~CnKkv~~-------~~~~~~~~Ce~~~~ 238 (355)
T PRK08402 211 VYDACPECRRKVDY-------DPATDTWICPEHGE 238 (355)
T ss_pred eEecCCCCCeEEEE-------ecCCCCEeCCCCCC
Confidence 45689999998863 23456899999983
No 177
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=67.45 E-value=2.2 Score=49.85 Aligned_cols=40 Identities=25% Similarity=0.692 Sum_probs=23.9
Q ss_pred CeeecCCCCccccHH-H---HHhhcCCCCCCeeccCCCccccccchhh
Q 020131 16 QEYICPNCQRRYNAL-D---ALRLVSLEDDSFHCENCNGELVAESDKL 59 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~l-D---A~~Lld~~~~~F~C~~Cg~eL~~~~~~~ 59 (330)
..|+||+|+ |+.. + +..=+|.. .=.||.||++|.-+.-.+
T Consensus 907 phy~C~~C~--~~ef~~~~~~~sG~Dlp--dk~Cp~Cg~~~~kdg~~l 950 (1437)
T PRK00448 907 PHYVCPNCK--YSEFFTDGSVGSGFDLP--DKDCPKCGTKLKKDGHDI 950 (1437)
T ss_pred ccccCcccc--cccccccccccccccCc--cccCccccccccccCCCc
Confidence 479999996 4321 1 11112221 248999999997655543
No 178
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=67.24 E-value=2.8 Score=34.81 Aligned_cols=37 Identities=19% Similarity=0.408 Sum_probs=23.2
Q ss_pred CCeeecCCCCccccH-HHHHhhcCCCCCCeeccCCCccccccc
Q 020131 15 VQEYICPNCQRRYNA-LDALRLVSLEDDSFHCENCNGELVAES 56 (330)
Q Consensus 15 ~~~Y~CP~C~~~YT~-lDA~~Lld~~~~~F~C~~Cg~eL~~~~ 56 (330)
...|.||+|+. ++. ....+ ....-.|+.||.--....
T Consensus 19 pt~f~CP~Cge-~~v~v~~~k----~~~h~~C~~CG~y~~~~V 56 (99)
T PRK14892 19 PKIFECPRCGK-VSISVKIKK----NIAIITCGNCGLYTEFEV 56 (99)
T ss_pred CcEeECCCCCC-eEeeeecCC----CcceEECCCCCCccCEEC
Confidence 46899999994 321 11111 235689999998764433
No 179
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=67.10 E-value=2.7 Score=48.28 Aligned_cols=11 Identities=36% Similarity=0.909 Sum_probs=5.6
Q ss_pred eccCCCccccc
Q 020131 44 HCENCNGELVA 54 (330)
Q Consensus 44 ~C~~Cg~eL~~ 54 (330)
.||+||.+++.
T Consensus 711 ~CP~CGtplv~ 721 (1337)
T PRK14714 711 ECPRCDVELTP 721 (1337)
T ss_pred cCCCCCCcccc
Confidence 45555555543
No 180
>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=66.90 E-value=1.3 Score=44.32 Aligned_cols=31 Identities=32% Similarity=0.707 Sum_probs=15.2
Q ss_pred CCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 15 VQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 15 ~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
.-||.|+.|+.+.+.++ .| | .-.|+.||...
T Consensus 283 KRFFkC~~C~~Rt~sl~--r~--P---~~~C~~Cg~~~ 313 (344)
T PF09332_consen 283 KRFFKCKDCGNRTISLE--RL--P---KKHCSNCGSSK 313 (344)
T ss_dssp -EEEE-T-TS-EEEESS--SS-------S--TTT-S--
T ss_pred eeeEECCCCCCeeeecc--cC--C---CCCCCcCCcCc
Confidence 45899999999988763 23 3 35899999764
No 181
>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=66.57 E-value=1.5 Score=39.39 Aligned_cols=32 Identities=25% Similarity=0.553 Sum_probs=18.6
Q ss_pred cCCCCcc-ccHHHHHhhcCC------CCCCeeccCCCcccc
Q 020131 20 CPNCQRR-YNALDALRLVSL------EDDSFHCENCNGELV 53 (330)
Q Consensus 20 CP~C~~~-YT~lDA~~Lld~------~~~~F~C~~Cg~eL~ 53 (330)
||.||.. .+.. +.+.+. .-..|.|+.||..-.
T Consensus 1 CP~Cg~~~~~~~--~~~~~IP~F~evii~sf~C~~CGyr~~ 39 (163)
T TIGR00340 1 CPVCGSRTLKAV--TYDYDIPYFGKIMLSTYICEKCGYRST 39 (163)
T ss_pred CCCCCCcceEee--eEeccCCCcceEEEEEEECCCCCCchh
Confidence 9999975 2221 112221 113699999998754
No 182
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=66.41 E-value=6.2 Score=35.33 Aligned_cols=22 Identities=23% Similarity=0.569 Sum_probs=17.9
Q ss_pred eeecCCCCccccHHHHHhhcCC
Q 020131 17 EYICPNCQRRYNALDALRLVSL 38 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~ 38 (330)
--.|+.|+.+||.+|-..|.-+
T Consensus 28 RReC~~C~~RFTTfE~~El~~~ 49 (156)
T COG1327 28 RRECLECGERFTTFERAELRPL 49 (156)
T ss_pred hhcccccccccchhheeeeccc
Confidence 4569999999999998888654
No 183
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=65.77 E-value=3.1 Score=44.77 Aligned_cols=29 Identities=24% Similarity=0.494 Sum_probs=21.4
Q ss_pred cCCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcc
Q 020131 12 KNTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGE 51 (330)
Q Consensus 12 ~~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~e 51 (330)
..+...=+|+.||..|.- ..|.||.||..
T Consensus 563 ~inp~~~~C~~CG~~~~g-----------~~~~CP~CGs~ 591 (625)
T PRK08579 563 SYTPAITVCNKCGRSTTG-----------LYTRCPRCGSE 591 (625)
T ss_pred EeCCCCccCCCCCCccCC-----------CCCcCcCCCCc
Confidence 345567789999996621 26999999973
No 184
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=65.55 E-value=1.8 Score=34.78 Aligned_cols=32 Identities=19% Similarity=0.428 Sum_probs=22.2
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
..||+|+...-.-+.... ..=.||.|++.+..
T Consensus 2 llCP~C~v~l~~~~rs~v-----EiD~CPrCrGVWLD 33 (88)
T COG3809 2 LLCPICGVELVMSVRSGV-----EIDYCPRCRGVWLD 33 (88)
T ss_pred cccCcCCceeeeeeecCc-----eeeeCCccccEeec
Confidence 479999987655444433 12369999999964
No 185
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=65.43 E-value=1.8 Score=38.54 Aligned_cols=15 Identities=13% Similarity=0.344 Sum_probs=11.0
Q ss_pred eeccCCCccccccch
Q 020131 43 FHCENCNGELVAESD 57 (330)
Q Consensus 43 F~C~~Cg~eL~~~~~ 57 (330)
..|+.||......+.
T Consensus 29 ~~c~~c~~~f~~~e~ 43 (154)
T PRK00464 29 RECLACGKRFTTFER 43 (154)
T ss_pred eeccccCCcceEeEe
Confidence 589999987655443
No 186
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=65.42 E-value=3.3 Score=47.95 Aligned_cols=27 Identities=19% Similarity=0.583 Sum_probs=21.1
Q ss_pred CCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 14 TVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 14 ~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
....++||.||+. ++ .++||.||+...
T Consensus 671 ei~~~~Cp~Cg~~-~~------------~~~Cp~CG~~~~ 697 (1627)
T PRK14715 671 EIAFFKCPKCGKV-GL------------YHVCPFCGTRVE 697 (1627)
T ss_pred EEEeeeCCCCCCc-cc------------cccCcccCCccc
Confidence 3458999999975 22 689999998854
No 187
>PRK12366 replication factor A; Reviewed
Probab=65.21 E-value=3.4 Score=44.44 Aligned_cols=26 Identities=38% Similarity=1.000 Sum_probs=20.4
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCcc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGE 51 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~e 51 (330)
+.-||.|+++-+. ..+.|+|+.||..
T Consensus 532 y~aCp~CnkKv~~---------~~g~~~C~~c~~~ 557 (637)
T PRK12366 532 LYLCPNCRKRVEE---------VDGEYICEFCGEV 557 (637)
T ss_pred EecccccCeEeEc---------CCCcEECCCCCCC
Confidence 5679999998752 2378999999975
No 188
>KOG3078 consensus Adenylate kinase [Nucleotide transport and metabolism]
Probab=64.49 E-value=10 Score=36.16 Aligned_cols=64 Identities=19% Similarity=0.210 Sum_probs=46.7
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccchhhhhhcCCCCChhHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESDKLAAQEGGDGDDNARRRRREKLKDLLQKLEVHLKPLMEQ 96 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~~~~~~e~~~g~~na~r~~~e~~k~~l~r~n~QlkpI~~~ 96 (330)
.++||.||+.|.. -+.|.....+=..-|.+|+...++.+ +.++.+|..++.|.+|++++
T Consensus 138 r~ihp~sG~~Yh~-----~~~pPk~~~~dDitgepL~qr~dD~~----------------e~v~~rL~~y~~~~~pv~ey 196 (235)
T KOG3078|consen 138 RRIHPASGRVYHL-----EFNPPKVPGKDDITGEPLIQREDDKP----------------EVVKKRLKAYKEQTKPVLEY 196 (235)
T ss_pred ccccCcccceecc-----cccCCccccccccccChhhcCccccH----------------HHHHHHHHHHhhcchHHHHH
Confidence 4889999999983 23333333445556677887776533 45678899999999999999
Q ss_pred HHhhc
Q 020131 97 INRVK 101 (330)
Q Consensus 97 Lk~id 101 (330)
.++--
T Consensus 197 Y~k~~ 201 (235)
T KOG3078|consen 197 YKKKG 201 (235)
T ss_pred HHhcC
Confidence 99874
No 189
>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=64.43 E-value=3.1 Score=46.71 Aligned_cols=37 Identities=24% Similarity=0.446 Sum_probs=28.4
Q ss_pred CCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccchh
Q 020131 13 NTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESDK 58 (330)
Q Consensus 13 ~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~~ 58 (330)
-.+|.|.|..|+.+|-- -|. .=.|+.||+.|+.-..+
T Consensus 1008 FsrQ~fRC~kC~~kYRR-------~PL--~G~C~kCGg~lilTV~~ 1044 (1095)
T TIGR00354 1008 FSRQEVRCTKCNTKYRR-------IPL--VGKCLKCGNNLTLTVSK 1044 (1095)
T ss_pred hhccceeecccCCcccc-------CCC--CCcccccCCeEEEEEec
Confidence 35789999999999964 122 46899999999875553
No 190
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=64.33 E-value=3.5 Score=41.46 Aligned_cols=22 Identities=23% Similarity=0.649 Sum_probs=18.4
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCCc
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCNG 50 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~ 50 (330)
|+|.+||..+.- . ..+||.|+.
T Consensus 1 ~~c~~cg~~~~~-----~------~g~cp~c~~ 22 (372)
T cd01121 1 YVCSECGYVSPK-----W------LGKCPECGE 22 (372)
T ss_pred CCCCCCCCCCCC-----c------cEECcCCCC
Confidence 899999998864 2 579999984
No 191
>PRK04023 DNA polymerase II large subunit; Validated
Probab=64.25 E-value=3.8 Score=46.23 Aligned_cols=11 Identities=27% Similarity=0.528 Sum_probs=7.7
Q ss_pred CeeecCCCCcc
Q 020131 16 QEYICPNCQRR 26 (330)
Q Consensus 16 ~~Y~CP~C~~~ 26 (330)
..+.||.||..
T Consensus 637 ~~frCP~CG~~ 647 (1121)
T PRK04023 637 FYRRCPFCGTH 647 (1121)
T ss_pred CcccCCCCCCC
Confidence 35678888776
No 192
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=64.13 E-value=2.8 Score=42.61 Aligned_cols=32 Identities=19% Similarity=0.525 Sum_probs=22.4
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
-.||.|+.-+..- .+ . ....-+|++||+.|..
T Consensus 14 ~~C~~Cd~l~~~~---~l-~-~g~~a~CpRCg~~L~~ 45 (403)
T TIGR00155 14 ILCSQCDMLVALP---RI-E-SGQKAACPRCGTTLTV 45 (403)
T ss_pred eeCCCCCCccccc---CC-C-CCCeeECCCCCCCCcC
Confidence 3599999987641 11 1 2246899999999954
No 193
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=63.85 E-value=5.6 Score=33.97 Aligned_cols=40 Identities=23% Similarity=0.558 Sum_probs=26.4
Q ss_pred CCCeeecCCCCccccHHHHHhhcCCCCC---CeeccCCCcccc
Q 020131 14 TVQEYICPNCQRRYNALDALRLVSLEDD---SFHCENCNGELV 53 (330)
Q Consensus 14 ~~~~Y~CP~C~~~YT~lDA~~Lld~~~~---~F~C~~Cg~eL~ 53 (330)
-...-+||.||..=-..-.++|=|.+.| -|.|++|+..-.
T Consensus 71 a~I~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k~~ 113 (116)
T KOG2907|consen 71 AVIKHKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYKFT 113 (116)
T ss_pred cchhccCcccCCchhhhhhhhcccccCCceEEEEcCccceeee
Confidence 3446789999985444444566555433 489999997654
No 194
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=63.81 E-value=1.6 Score=35.51 Aligned_cols=36 Identities=19% Similarity=0.399 Sum_probs=30.7
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
=.||.|+++-...|-.=+++.---.-+|.+|+.++-
T Consensus 34 S~C~~C~~~L~~~~lIPi~S~l~lrGrCr~C~~~I~ 69 (92)
T PF06750_consen 34 SHCPHCGHPLSWWDLIPILSYLLLRGRCRYCGAPIP 69 (92)
T ss_pred CcCcCCCCcCcccccchHHHHHHhCCCCcccCCCCC
Confidence 469999999999998888887656779999999884
No 195
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=63.66 E-value=4.9 Score=29.22 Aligned_cols=32 Identities=25% Similarity=0.495 Sum_probs=21.5
Q ss_pred CCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCC
Q 020131 13 NTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENC 48 (330)
Q Consensus 13 ~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~C 48 (330)
.....++|+.||..|..-=..+. ...-.||+|
T Consensus 24 ~~~v~W~C~~Cgh~w~~~v~~R~----~~~~~CP~C 55 (55)
T PF14311_consen 24 NKKVWWKCPKCGHEWKASVNDRT----RRGKGCPYC 55 (55)
T ss_pred CCEEEEECCCCCCeeEccHhhhc----cCCCCCCCC
Confidence 34456889999998886433333 245678888
No 196
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=63.53 E-value=2.2 Score=28.81 Aligned_cols=29 Identities=21% Similarity=0.589 Sum_probs=12.6
Q ss_pred ecCCCCccccHHHHHhhcC-CCCCCeeccCCCcc
Q 020131 19 ICPNCQRRYNALDALRLVS-LEDDSFHCENCNGE 51 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld-~~~~~F~C~~Cg~e 51 (330)
.||.||..-.. .+++ -....+.|+.||..
T Consensus 2 fC~~CG~~l~~----~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 2 FCPQCGGPLER----RIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp B-TTT--B-EE----E--TT-SS-EEEETTTTEE
T ss_pred ccccccChhhh----hcCCCCCccceECCCCCCE
Confidence 48888877432 1111 12246788888853
No 197
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=63.25 E-value=4.5 Score=41.16 Aligned_cols=27 Identities=19% Similarity=0.475 Sum_probs=20.4
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCcccccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAE 55 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~ 55 (330)
.||.|+..+. ....-+||+||+.|...
T Consensus 217 ~C~~Cd~~~~----------~~~~a~CpRC~~~L~~~ 243 (403)
T TIGR00155 217 SCSACHTTIL----------PAQEPVCPRCSTPLYVR 243 (403)
T ss_pred cCCCCCCccC----------CCCCcCCcCCCCcccCC
Confidence 4999999552 23467899999999553
No 198
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=63.21 E-value=3.7 Score=44.92 Aligned_cols=37 Identities=27% Similarity=0.707 Sum_probs=22.8
Q ss_pred eeecCCCCccccHH----HHHhhcCCCCCCeeccCCCccccc
Q 020131 17 EYICPNCQRRYNAL----DALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 17 ~Y~CP~C~~~YT~l----DA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
-|+|+.|++-|-|- |=+++.+-.. .|.|++|+....+
T Consensus 281 KFKCtECgKAFKfKHHLKEHlRIHSGEK-PfeCpnCkKRFSH 321 (1007)
T KOG3623|consen 281 KFKCTECGKAFKFKHHLKEHLRIHSGEK-PFECPNCKKRFSH 321 (1007)
T ss_pred cccccccchhhhhHHHHHhhheeecCCC-CcCCccccccccc
Confidence 47788888877754 3334433332 5788888766654
No 199
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=63.16 E-value=5.8 Score=33.33 Aligned_cols=30 Identities=20% Similarity=0.546 Sum_probs=18.9
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
....|.+|++.|.+ |++. +-.|..|+..+=
T Consensus 53 ~~~~C~~C~~~fg~-----l~~~---~~~C~~C~~~VC 82 (118)
T PF02318_consen 53 GERHCARCGKPFGF-----LFNR---GRVCVDCKHRVC 82 (118)
T ss_dssp CCSB-TTTS-BCSC-----TSTT---CEEETTTTEEEE
T ss_pred CCcchhhhCCcccc-----cCCC---CCcCCcCCcccc
Confidence 56799999999986 3332 467777766553
No 200
>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=63.16 E-value=1.8 Score=38.24 Aligned_cols=36 Identities=14% Similarity=0.448 Sum_probs=26.3
Q ss_pred eecCCCCccccHHHHHhhcCCC--CCCeeccCCCcccccc
Q 020131 18 YICPNCQRRYNALDALRLVSLE--DDSFHCENCNGELVAE 55 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~--~~~F~C~~Cg~eL~~~ 55 (330)
-.||+||+..|.+. ..|.++ ...|+|..|..+..++
T Consensus 106 ~~cp~c~s~~t~~~--s~fg~t~cka~~~c~~c~epf~~f 143 (146)
T TIGR02159 106 VQCPRCGSADTTIT--SIFGPTACKALYRCRACKEPFEYF 143 (146)
T ss_pred CcCCCCCCCCcEee--cCCCChhhHHHhhhhhhCCcHhhc
Confidence 57999999999743 344443 4568999999887553
No 201
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=62.49 E-value=2.8 Score=42.83 Aligned_cols=33 Identities=18% Similarity=0.467 Sum_probs=22.6
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCCcccccc
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAE 55 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~ 55 (330)
-.||.|+.-+..-.. +....-+|++||++|...
T Consensus 11 ~~C~~Cd~l~~~~~l-----~~g~~a~CpRCg~~L~~~ 43 (419)
T PRK15103 11 ILCPQCDMLVALPRL-----EHGQKAACPRCGTTLTVR 43 (419)
T ss_pred ccCCCCCceeecCCC-----CCCCeeECCCCCCCCcCC
Confidence 569999988753111 122358999999999543
No 202
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=62.31 E-value=2.3 Score=39.22 Aligned_cols=13 Identities=31% Similarity=0.457 Sum_probs=10.4
Q ss_pred CeeccCCCccccc
Q 020131 42 SFHCENCNGELVA 54 (330)
Q Consensus 42 ~F~C~~Cg~eL~~ 54 (330)
.|.|+.||..-.+
T Consensus 30 sf~C~~CGyr~~e 42 (192)
T TIGR00310 30 STICEHCGYRSND 42 (192)
T ss_pred EEECCCCCCccce
Confidence 6999999987543
No 203
>PRK12495 hypothetical protein; Provisional
Probab=61.63 E-value=8 Score=36.60 Aligned_cols=46 Identities=17% Similarity=0.382 Sum_probs=32.0
Q ss_pred hHHHHHHhhcCCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccch
Q 020131 3 KKLKDELECKNTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESD 57 (330)
Q Consensus 3 k~Le~~l~~~~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~ 57 (330)
|+|-.-|......-.|.|+.||.-.- .+ .|.-+|+.|+..+....+
T Consensus 28 ~~ma~lL~~gatmsa~hC~~CG~PIp-----a~----pG~~~Cp~CQ~~~~~~~~ 73 (226)
T PRK12495 28 ERMSELLLQGATMTNAHCDECGDPIF-----RH----DGQEFCPTCQQPVTEDGA 73 (226)
T ss_pred HHHHHHHHhhcccchhhcccccCccc-----CC----CCeeECCCCCCccccccc
Confidence 34445555666667899999997432 12 478899999999876544
No 204
>COG5189 SFP1 Putative transcriptional repressor regulating G2/M transition [Transcription / Cell division and chromosome partitioning]
Probab=61.48 E-value=3.1 Score=41.52 Aligned_cols=38 Identities=29% Similarity=0.846 Sum_probs=24.5
Q ss_pred CCeeecC--CCCccccHHHHH----------------------hhcCCCCCCeeccCCCccc
Q 020131 15 VQEYICP--NCQRRYNALDAL----------------------RLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 15 ~~~Y~CP--~C~~~YT~lDA~----------------------~Lld~~~~~F~C~~Cg~eL 52 (330)
.+.|+|| .|.++|.----+ +.|+..+-.|+|++|+..-
T Consensus 347 ~KpykCpV~gC~K~YknqnGLKYH~lhGH~~~~~~~~p~p~~~~~F~~~~KPYrCevC~KRY 408 (423)
T COG5189 347 GKPYKCPVEGCNKKYKNQNGLKYHMLHGHQNQKLHENPSPEKMNIFSAKDKPYRCEVCDKRY 408 (423)
T ss_pred CceecCCCCCchhhhccccchhhhhhccccCcccCCCCCccccccccccCCceeccccchhh
Confidence 3689997 599998742222 2232233457999999765
No 205
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=61.47 E-value=3.8 Score=35.80 Aligned_cols=33 Identities=21% Similarity=0.508 Sum_probs=23.9
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccch
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESD 57 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~ 57 (330)
.+|.+||+.|..-... +++ =||.||+-...+..
T Consensus 2 H~Ct~Cg~~f~dgs~e-il~------GCP~CGg~kF~yv~ 34 (131)
T PF09845_consen 2 HQCTKCGRVFEDGSKE-ILS------GCPECGGNKFQYVP 34 (131)
T ss_pred cccCcCCCCcCCCcHH-HHc------cCcccCCcceEEcC
Confidence 4799999999854332 332 39999998876654
No 206
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=60.87 E-value=5.4 Score=30.38 Aligned_cols=34 Identities=21% Similarity=0.573 Sum_probs=26.1
Q ss_pred CCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 13 NTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 13 ~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
+....|+|-.|+.+-+. .. ...|.|..||..+..
T Consensus 16 ~~~miYiCgdC~~en~l-------k~-~D~irCReCG~RIly 49 (62)
T KOG3507|consen 16 TATMIYICGDCGQENTL-------KR-GDVIRCRECGYRILY 49 (62)
T ss_pred cccEEEEeccccccccc-------cC-CCcEehhhcchHHHH
Confidence 45678999999988653 22 347999999998854
No 207
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=60.74 E-value=3.8 Score=39.42 Aligned_cols=11 Identities=36% Similarity=0.860 Sum_probs=4.0
Q ss_pred eeccCCCcccc
Q 020131 43 FHCENCNGELV 53 (330)
Q Consensus 43 F~C~~Cg~eL~ 53 (330)
++|..|++.+.
T Consensus 198 L~Cs~C~t~W~ 208 (290)
T PF04216_consen 198 LHCSLCGTEWR 208 (290)
T ss_dssp EEETTT--EEE
T ss_pred EEcCCCCCeee
Confidence 34444444443
No 208
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=60.73 E-value=5.6 Score=38.72 Aligned_cols=35 Identities=17% Similarity=0.543 Sum_probs=18.6
Q ss_pred CeeecCCCCcccc---HHHHHhhcCCCCC--CeeccCCCccc
Q 020131 16 QEYICPNCQRRYN---ALDALRLVSLEDD--SFHCENCNGEL 52 (330)
Q Consensus 16 ~~Y~CP~C~~~YT---~lDA~~Lld~~~~--~F~C~~Cg~eL 52 (330)
..++|+.||+.|+ .|.. .|-.-|| .|.|+.|+.-.
T Consensus 186 l~c~C~iCGKaFSRPWLLQG--HiRTHTGEKPF~C~hC~kAF 225 (279)
T KOG2462|consen 186 LPCECGICGKAFSRPWLLQG--HIRTHTGEKPFSCPHCGKAF 225 (279)
T ss_pred CCcccccccccccchHHhhc--ccccccCCCCccCCcccchh
Confidence 4667777777777 3322 1222222 37777776555
No 209
>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=60.72 E-value=2.9 Score=34.04 Aligned_cols=39 Identities=21% Similarity=0.397 Sum_probs=24.7
Q ss_pred CeeecCCCCccc---cHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 16 QEYICPNCQRRY---NALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 16 ~~Y~CP~C~~~Y---T~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
....||.||..= ..+..-.-=.+++--|+|..||..+.+
T Consensus 61 ~~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~~ 102 (104)
T TIGR01384 61 TRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWRE 102 (104)
T ss_pred ccCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeEe
Confidence 368999999754 322211111244557999999998865
No 210
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=60.65 E-value=5.7 Score=24.72 Aligned_cols=17 Identities=29% Similarity=0.669 Sum_probs=12.8
Q ss_pred eecCCCCccccHHHHHh
Q 020131 18 YICPNCQRRYNALDALR 34 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~ 34 (330)
..||.||++|...-...
T Consensus 3 ~~C~~CgR~F~~~~l~~ 19 (25)
T PF13913_consen 3 VPCPICGRKFNPDRLEK 19 (25)
T ss_pred CcCCCCCCEECHHHHHH
Confidence 47999999997654443
No 211
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=60.32 E-value=4.9 Score=29.84 Aligned_cols=25 Identities=24% Similarity=0.497 Sum_probs=18.3
Q ss_pred CCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCc
Q 020131 14 TVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNG 50 (330)
Q Consensus 14 ~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~ 50 (330)
....-.||.||.--- .-+.|+.||.
T Consensus 23 ~p~l~~C~~cG~~~~------------~H~vc~~cG~ 47 (55)
T TIGR01031 23 APTLVVCPNCGEFKL------------PHRVCPSCGY 47 (55)
T ss_pred CCcceECCCCCCccc------------CeeECCccCe
Confidence 355678999997332 2699999994
No 212
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=59.97 E-value=3.8 Score=34.80 Aligned_cols=28 Identities=25% Similarity=0.670 Sum_probs=21.3
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAE 55 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~ 55 (330)
.-.||.||+.--. ..++|++|++.+.-.
T Consensus 6 ~~~cPvcg~~~iV-----------TeL~c~~~etTVrg~ 33 (122)
T COG3877 6 INRCPVCGRKLIV-----------TELKCSNCETTVRGN 33 (122)
T ss_pred CCCCCccccccee-----------EEEecCCCCceEecc
Confidence 3579999987532 379999999998543
No 213
>cd00817 ValRS_core catalytic core domain of valyl-tRNA synthetases. Valine amino-acyl tRNA synthetase (ValRS) catalytic core domain. This enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. ValRS has an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids.
Probab=59.53 E-value=4.4 Score=40.51 Aligned_cols=33 Identities=9% Similarity=0.287 Sum_probs=25.9
Q ss_pred cCCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccc
Q 020131 12 KNTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAES 56 (330)
Q Consensus 12 ~~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~ 56 (330)
......|.||.|++-++.-|+ |.+||++++...
T Consensus 135 ~~~~~~~yc~~~~t~l~~~ev------------c~~cg~~~~~~~ 167 (382)
T cd00817 135 RDNRLVNWCPKLRTAISDIEV------------CSRSGDVIEPLL 167 (382)
T ss_pred eeeeEEeecCCcCCCCCcchh------------cccCCCeEEEEe
Confidence 334567889999998887554 999999997643
No 214
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=59.48 E-value=7 Score=30.25 Aligned_cols=40 Identities=28% Similarity=0.590 Sum_probs=27.2
Q ss_pred hhcCCCCeeecC-CCCcccc-HHHHHhhcCCCCCCeeccCCCccc
Q 020131 10 ECKNTVQEYICP-NCQRRYN-ALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 10 ~~~~~~~~Y~CP-~C~~~YT-~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
+.....+.|.|| .||-+|. .+|-+.+ -...-.||.|.-.+
T Consensus 13 e~~~e~~~y~yPCpCGDrf~It~edL~~---ge~Va~CpsCSL~I 54 (67)
T KOG2923|consen 13 EFDEENQTYYYPCPCGDRFQITLEDLEN---GEDVARCPSCSLII 54 (67)
T ss_pred eeccCCCeEEcCCCCCCeeeecHHHHhC---CCeeecCCCceEEE
Confidence 344556677777 5999998 5666655 12357899998655
No 215
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=59.43 E-value=2.8 Score=35.11 Aligned_cols=38 Identities=18% Similarity=0.417 Sum_probs=26.0
Q ss_pred CeeecCCCCccccH---HHHHhhcCCCCCCeeccCCCccccccch
Q 020131 16 QEYICPNCQRRYNA---LDALRLVSLEDDSFHCENCNGELVAESD 57 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~---lDA~~Lld~~~~~F~C~~Cg~eL~~~~~ 57 (330)
..|-||+|++.-.. ++.... .+...|-+||-.-..+..
T Consensus 21 k~FtCp~Cghe~vs~ctvkk~~~----~g~~~Cg~CGls~e~ev~ 61 (104)
T COG4888 21 KTFTCPRCGHEKVSSCTVKKTVN----IGTAVCGNCGLSFECEVP 61 (104)
T ss_pred ceEecCccCCeeeeEEEEEecCc----eeEEEcccCcceEEEecc
Confidence 47999999987654 444333 356899999977655433
No 216
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=59.15 E-value=4.7 Score=33.95 Aligned_cols=33 Identities=12% Similarity=0.331 Sum_probs=22.6
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAES 56 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~ 56 (330)
...|.+||..|..-+-. ++ ==||.||.-.....
T Consensus 2 pH~CtrCG~vf~~g~~~-il------~GCp~CG~nkF~yv 34 (112)
T COG3364 2 PHQCTRCGEVFDDGSEE-IL------SGCPKCGCNKFLYV 34 (112)
T ss_pred CceecccccccccccHH-HH------ccCccccchheEec
Confidence 35799999999974222 22 24999998775443
No 217
>PRK11893 methionyl-tRNA synthetase; Reviewed
Probab=58.95 E-value=4.5 Score=41.43 Aligned_cols=41 Identities=12% Similarity=0.384 Sum_probs=30.4
Q ss_pred hcCCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccch
Q 020131 11 CKNTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESD 57 (330)
Q Consensus 11 ~~~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~ 57 (330)
++.....|.|+.|++-++..+ |+++ ..+|..||.+|+....
T Consensus 116 Y~~~~~~~~~~~~~~~l~~~~---l~~~---~p~~~~~~~~~~~~~~ 156 (511)
T PRK11893 116 YLGKYEGWYCVRCEEFYTESE---LIED---GYRCPPTGAPVEWVEE 156 (511)
T ss_pred EEeeeeeeccccccccCCHHH---hcCC---CCCCCCCCCcceEEec
Confidence 345567899999998888766 3343 2689999999976543
No 218
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=58.76 E-value=5.3 Score=37.72 Aligned_cols=49 Identities=12% Similarity=0.379 Sum_probs=27.7
Q ss_pred HHHHHHhhcCCCCeeecCCCCccccHHHHHhh-cCC--CCCCeeccCCCccc
Q 020131 4 KLKDELECKNTVQEYICPNCQRRYNALDALRL-VSL--EDDSFHCENCNGEL 52 (330)
Q Consensus 4 ~Le~~l~~~~~~~~Y~CP~C~~~YT~lDA~~L-ld~--~~~~F~C~~Cg~eL 52 (330)
+++.-+....+...|.|-.|++.|+.--.+.- +-. .--.++|..||.-.
T Consensus 104 s~k~t~gsssd~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgf 155 (267)
T KOG3576|consen 104 SPKSTIGSSSDQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGF 155 (267)
T ss_pred CCcccccCCCCCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcc
Confidence 34444555566677888888888876544431 111 01235677777655
No 219
>TIGR00320 dfx_rbo desulfoferrodoxin. This protein is described in some articles as rubredoxin oxidoreductase (rbo), and its gene shares an operon with the rubredoxin gene in Desulfovibrio vulgaris Hildenborough.
Probab=58.18 E-value=5.9 Score=34.07 Aligned_cols=32 Identities=25% Similarity=0.521 Sum_probs=20.8
Q ss_pred CCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 15 VQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 15 ~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
..+|+|+.||..+-.+ ....+...| ||.+|..
T Consensus 5 ~~fYkC~~CGniv~v~------~~g~~~l~C--Cge~m~~ 36 (125)
T TIGR00320 5 LQVYKCEVCGNIVEVL------NAGIGQLVC--CNQPMKL 36 (125)
T ss_pred CcEEECCCCCcEEEEE------ECCCcceee--CCcccee
Confidence 3599999999988432 222345666 6876643
No 220
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=58.14 E-value=6 Score=35.44 Aligned_cols=39 Identities=31% Similarity=0.695 Sum_probs=27.9
Q ss_pred CCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 14 TVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 14 ~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
.+-.|.|. |+..|-.--..+.+-- ...++|-.|++.|+.
T Consensus 114 ~~~~Y~C~-C~q~~l~~RRhn~~~~-g~~YrC~~C~gkL~~ 152 (156)
T COG3091 114 TTYPYRCQ-CQQHYLRIRRHNTVRR-GEVYRCGKCGGKLVF 152 (156)
T ss_pred cceeEEee-cCCccchhhhcccccc-cceEEeccCCceEEe
Confidence 55689999 9999865444444221 125999999999976
No 221
>PF14353 CpXC: CpXC protein
Probab=57.77 E-value=9.3 Score=32.13 Aligned_cols=35 Identities=20% Similarity=0.469 Sum_probs=22.3
Q ss_pred HHHHHHhhcCCCCeeecCCCCccccHHHHHhhcCCC
Q 020131 4 KLKDELECKNTVQEYICPNCQRRYNALDALRLVSLE 39 (330)
Q Consensus 4 ~Le~~l~~~~~~~~Y~CP~C~~~YT~lDA~~Lld~~ 39 (330)
.|+.++-+ ..--.|.||.||..|...=-.-+.|+.
T Consensus 26 ~l~e~il~-g~l~~~~CP~Cg~~~~~~~p~lY~D~~ 60 (128)
T PF14353_consen 26 ELKEKILD-GSLFSFTCPSCGHKFRLEYPLLYHDPE 60 (128)
T ss_pred HHHHHHHc-CCcCEEECCCCCCceecCCCEEEEcCC
Confidence 45556653 344579999999999763333445553
No 222
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=57.70 E-value=4.5 Score=34.94 Aligned_cols=37 Identities=16% Similarity=0.562 Sum_probs=24.1
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccc
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAES 56 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~ 56 (330)
-.||.|+..+ .....-. .--...|+|+.|+.......
T Consensus 31 ~~cP~C~s~~-~~k~g~~-~~~~qRyrC~~C~~tf~~~~ 67 (129)
T COG3677 31 VNCPRCKSSN-VVKIGGI-RRGHQRYKCKSCGSTFTVET 67 (129)
T ss_pred CcCCCCCccc-eeeECCc-cccccccccCCcCcceeeec
Confidence 4699999988 3222222 11135799999998886543
No 223
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=57.64 E-value=3.9 Score=30.01 Aligned_cols=33 Identities=15% Similarity=0.281 Sum_probs=20.9
Q ss_pred eecCCCCccccHHHHHhhcCCCC-CCeeccCCCc
Q 020131 18 YICPNCQRRYNALDALRLVSLED-DSFHCENCNG 50 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~-~~F~C~~Cg~ 50 (330)
.-||.||..-........++... ....|..||.
T Consensus 4 kPCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 4 KPCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred cCCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 45999997766555544433211 2356999998
No 224
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=57.58 E-value=5.2 Score=23.95 Aligned_cols=17 Identities=24% Similarity=0.850 Sum_probs=12.7
Q ss_pred eecCCCCccccHHHHHh
Q 020131 18 YICPNCQRRYNALDALR 34 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~ 34 (330)
|.|..|++.|+....++
T Consensus 1 ~~C~~C~~~f~s~~~~~ 17 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLR 17 (25)
T ss_dssp EEETTTTEEESSHHHHH
T ss_pred CCCCCCCCCcCCHHHHH
Confidence 67888888888665553
No 225
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=57.40 E-value=6.1 Score=43.13 Aligned_cols=32 Identities=16% Similarity=0.412 Sum_probs=20.0
Q ss_pred cCCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCc
Q 020131 12 KNTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNG 50 (330)
Q Consensus 12 ~~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~ 50 (330)
..+...=+|+.||. +- -+.+....|.||.||.
T Consensus 636 ~in~~~~~C~~CG~--~G-----e~~~~~~~~~CP~CG~ 667 (711)
T PRK09263 636 GTNTPIDECYECGF--TG-----EFECTEKGFTCPKCGN 667 (711)
T ss_pred EeCCCCcccCCCCC--Cc-----cccCCCCCCcCcCCCC
Confidence 34556668999995 21 1111223599999995
No 226
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=57.39 E-value=4.7 Score=46.76 Aligned_cols=36 Identities=25% Similarity=0.565 Sum_probs=27.9
Q ss_pred CCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccchh
Q 020131 13 NTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESDK 58 (330)
Q Consensus 13 ~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~~ 58 (330)
-.+|.|.| .|+.+|-- -|. .=.|+.||+.|+.-.++
T Consensus 1538 FsrQ~~RC-kC~~kyRR-------~PL--~G~C~kCGg~~ilTV~k 1573 (1627)
T PRK14715 1538 FSRQEFRC-KCGAKYRR-------VPL--KGKCPKCGSKLILTVSK 1573 (1627)
T ss_pred hhccceee-cCCCcccc-------CCC--CCcCcccCCeEEEEEec
Confidence 45789999 99999964 122 46899999999876654
No 227
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=57.35 E-value=6.4 Score=40.27 Aligned_cols=25 Identities=20% Similarity=0.446 Sum_probs=19.1
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
.||.|+.-+. .+.-+|++||+.|..
T Consensus 223 ~C~~Cd~l~~-----------~~~a~CpRC~~~L~~ 247 (419)
T PRK15103 223 SCSCCTAILP-----------ADQPVCPRCHTKGYV 247 (419)
T ss_pred cCCCCCCCCC-----------CCCCCCCCCCCcCcC
Confidence 4999998641 234689999999954
No 228
>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=56.88 E-value=4.1 Score=29.57 Aligned_cols=35 Identities=17% Similarity=0.364 Sum_probs=20.6
Q ss_pred ecCCCCcccc-HHHHHhhcCCCCCCeeccCCCccccc
Q 020131 19 ICPNCQRRYN-ALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 19 ~CP~C~~~YT-~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
-||.||.+=- +-......+ ..+.|.|..||.....
T Consensus 3 PCPfCGg~~~~~~~~~~~~~-~~~~~~C~~Cga~~~~ 38 (53)
T TIGR03655 3 PCPFCGGADVYLRRGFDPLD-LSHYFECSTCGASGPV 38 (53)
T ss_pred CCCCCCCcceeeEeccCCCC-CEEEEECCCCCCCccc
Confidence 4999997543 111111111 2346799999998865
No 229
>cd03361 TOPRIM_TopoIA_RevGyr TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to the ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=56.87 E-value=7.2 Score=34.87 Aligned_cols=45 Identities=24% Similarity=0.481 Sum_probs=30.3
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccchhhhhhcCCCCChhHHHHHHHHHHHHHHHHHHhHHHHHHHHH
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESDKLAAQEGGDGDDNARRRRREKLKDLLQKLEVHLKPLMEQIN 98 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~~~~~~e~~~g~~na~r~~~e~~k~~l~r~n~QlkpI~~~Lk 98 (330)
.|+.|+..|.+ ..|.|+.|+.++.... ..|++-|..+++
T Consensus 79 ~c~pc~~lF~~-----------~~~~cp~c~~~~~~~~------------------------------~~~~~~l~~l~~ 117 (170)
T cd03361 79 RCRDCGYQFTE-----------DSDKCPRCGSENIDDK------------------------------LETLEALRELAL 117 (170)
T ss_pred ccCCccccccc-----------ccccCCcCCCcCCcch------------------------------HHHHHHHHHHHh
Confidence 67777777741 2468999998884310 146777778888
Q ss_pred hhcCcC
Q 020131 99 RVKDLD 104 (330)
Q Consensus 99 ~id~i~ 104 (330)
+++.+.
T Consensus 118 ~~~~ii 123 (170)
T cd03361 118 EVDEVL 123 (170)
T ss_pred hCCEEE
Confidence 887654
No 230
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=56.67 E-value=3.6 Score=45.05 Aligned_cols=12 Identities=33% Similarity=0.794 Sum_probs=7.9
Q ss_pred eecCCCCccccH
Q 020131 18 YICPNCQRRYNA 29 (330)
Q Consensus 18 Y~CP~C~~~YT~ 29 (330)
+.||+|...+|+
T Consensus 445 ~~Cp~Cd~~lt~ 456 (730)
T COG1198 445 AECPNCDSPLTL 456 (730)
T ss_pred ccCCCCCcceEE
Confidence 347777777665
No 231
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=56.58 E-value=4.8 Score=25.90 Aligned_cols=14 Identities=36% Similarity=0.778 Sum_probs=7.8
Q ss_pred eccCCCccccccch
Q 020131 44 HCENCNGELVAESD 57 (330)
Q Consensus 44 ~C~~Cg~eL~~~~~ 57 (330)
.||.||++|+..++
T Consensus 1 ~CP~C~s~l~~~~~ 14 (28)
T PF03119_consen 1 TCPVCGSKLVREEG 14 (28)
T ss_dssp B-TTT--BEEE-CC
T ss_pred CcCCCCCEeEcCCC
Confidence 59999999986543
No 232
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=56.48 E-value=5.3 Score=34.80 Aligned_cols=26 Identities=27% Similarity=0.551 Sum_probs=20.6
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
.+=+|++||+.|-. | .-.|+.|+.+.
T Consensus 28 ~g~kC~~CG~v~~P--------P---r~~Cp~C~~~~ 53 (140)
T COG1545 28 LGTKCKKCGRVYFP--------P---RAYCPKCGSET 53 (140)
T ss_pred EEEEcCCCCeEEcC--------C---cccCCCCCCCC
Confidence 45689999999854 2 57899999885
No 233
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=56.31 E-value=4.9 Score=42.42 Aligned_cols=28 Identities=25% Similarity=0.539 Sum_probs=13.8
Q ss_pred cCCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcc
Q 020131 12 KNTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGE 51 (330)
Q Consensus 12 ~~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~e 51 (330)
..+...=+|+.||.... +.+.||.||.+
T Consensus 486 ~in~~~~~C~~CG~~~~------------~~~~CP~CGs~ 513 (546)
T PF13597_consen 486 TINPPIDICPDCGYIGG------------EGDKCPKCGSE 513 (546)
T ss_dssp EEE--EEEETTT---S--------------EEE-CCC---
T ss_pred EEecCcccccCCCcCCC------------CCCCCCCCCCc
Confidence 44566778999997542 26999999998
No 234
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 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 HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=56.17 E-value=5 Score=26.25 Aligned_cols=16 Identities=44% Similarity=1.034 Sum_probs=9.5
Q ss_pred CCeeecCCCCccccHH
Q 020131 15 VQEYICPNCQRRYNAL 30 (330)
Q Consensus 15 ~~~Y~CP~C~~~YT~l 30 (330)
...|.||+|+..|=.|
T Consensus 11 ~~kY~Cp~C~~~~CSl 26 (30)
T PF04438_consen 11 PAKYRCPRCGARYCSL 26 (30)
T ss_dssp EESEE-TTT--EESSH
T ss_pred CCEEECCCcCCceeCc
Confidence 3469999999988544
No 235
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=55.50 E-value=9.9 Score=41.74 Aligned_cols=10 Identities=30% Similarity=0.846 Sum_probs=5.4
Q ss_pred CeeccCCCcc
Q 020131 42 SFHCENCNGE 51 (330)
Q Consensus 42 ~F~C~~Cg~e 51 (330)
.+.||.||++
T Consensus 475 p~~Cp~Cgs~ 484 (730)
T COG1198 475 PQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCC
Confidence 3555555555
No 236
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=55.47 E-value=7.5 Score=41.89 Aligned_cols=28 Identities=21% Similarity=0.488 Sum_probs=20.2
Q ss_pred cCCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCc
Q 020131 12 KNTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNG 50 (330)
Q Consensus 12 ~~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~ 50 (330)
..+...=+|+.||...+ ...+.||.||.
T Consensus 561 ~in~~~~iC~~CG~~~~-----------g~~~~CP~CGs 588 (623)
T PRK08271 561 AFNVKITICNDCHHIDK-----------RTGKRCPICGS 588 (623)
T ss_pred EeCCCCccCCCCCCcCC-----------CCCcCCcCCCC
Confidence 34566668999997521 13699999997
No 237
>smart00355 ZnF_C2H2 zinc finger.
Probab=55.27 E-value=6.3 Score=22.67 Aligned_cols=15 Identities=33% Similarity=0.986 Sum_probs=10.2
Q ss_pred eecCCCCccccHHHH
Q 020131 18 YICPNCQRRYNALDA 32 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA 32 (330)
|.|+.|++.|.....
T Consensus 1 ~~C~~C~~~f~~~~~ 15 (26)
T smart00355 1 YRCPECGKVFKSKSA 15 (26)
T ss_pred CCCCCCcchhCCHHH
Confidence 578888877765433
No 238
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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 ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=55.22 E-value=1.5 Score=30.58 Aligned_cols=29 Identities=28% Similarity=0.658 Sum_probs=18.3
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCC
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENC 48 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~C 48 (330)
-+|..||+..+ ++..|+.-..+.|+|..|
T Consensus 2 ~~CSFCgr~~~--~v~~li~g~~~~~IC~~C 30 (41)
T PF06689_consen 2 KRCSFCGRPES--EVGRLISGPNGAYICDEC 30 (41)
T ss_dssp -B-TTT--BTT--TSSSEEEES-SEEEEHHH
T ss_pred CCccCCCCCHH--HHhceecCCCCcEECHHH
Confidence 36999999887 456677655568999888
No 239
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=55.19 E-value=7.5 Score=28.76 Aligned_cols=23 Identities=30% Similarity=0.658 Sum_probs=16.8
Q ss_pred CCeeecCCCCccccHHHHHhhcCCCCCCeeccCCC
Q 020131 15 VQEYICPNCQRRYNALDALRLVSLEDDSFHCENCN 49 (330)
Q Consensus 15 ~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg 49 (330)
...-.||.||.-- + ..++|+.||
T Consensus 24 ~~l~~c~~cg~~~-------~-----~H~vc~~cG 46 (56)
T PF01783_consen 24 PNLVKCPNCGEPK-------L-----PHRVCPSCG 46 (56)
T ss_dssp TSEEESSSSSSEE-------S-----TTSBCTTTB
T ss_pred cceeeeccCCCEe-------c-----ccEeeCCCC
Confidence 3567899999522 1 369999997
No 240
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=55.16 E-value=7.1 Score=42.00 Aligned_cols=28 Identities=18% Similarity=0.318 Sum_probs=20.0
Q ss_pred cCCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcc
Q 020131 12 KNTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGE 51 (330)
Q Consensus 12 ~~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~e 51 (330)
..+...=+|+.||..-.. .|.||.||..
T Consensus 554 sin~~~~~C~~CGy~g~~------------~~~CP~CG~~ 581 (618)
T PRK14704 554 SINHPVDRCKCCSYHGVI------------GNECPSCGNE 581 (618)
T ss_pred EeCCCCeecCCCCCCCCc------------CccCcCCCCC
Confidence 346677789999953221 3899999973
No 241
>TIGR00630 uvra excinuclease ABC, A subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=54.93 E-value=6.3 Score=44.31 Aligned_cols=34 Identities=26% Similarity=0.607 Sum_probs=26.1
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNG 50 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~ 50 (330)
..+.||.|+..|..++.. +||+..-.=.|+.|++
T Consensus 249 ~~~~c~~~g~~~~~~~~~-~FSfNsp~G~Cp~C~G 282 (924)
T TIGR00630 249 KHAACPECGFSLPELEPR-LFSFNSPYGACPECSG 282 (924)
T ss_pred hcccCcccCcccCcCChh-hcCCCCCcCCCCCCcc
Confidence 458899999999977654 6677655568999953
No 242
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=54.88 E-value=6 Score=33.81 Aligned_cols=33 Identities=15% Similarity=0.466 Sum_probs=22.6
Q ss_pred cCCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 12 KNTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 12 ~~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
+..+....|..|+..|+.. ...|.||.||+.-.
T Consensus 65 e~~p~~~~C~~C~~~~~~e---------~~~~~CP~C~s~~~ 97 (115)
T COG0375 65 EEEPAECWCLDCGQEVELE---------ELDYRCPKCGSINL 97 (115)
T ss_pred EEeccEEEeccCCCeecch---------hheeECCCCCCCce
Confidence 3445678999997766542 23567999996543
No 243
>PTZ00409 Sir2 (Silent Information Regulator) protein; Provisional
Probab=54.84 E-value=8.8 Score=37.02 Aligned_cols=38 Identities=16% Similarity=0.306 Sum_probs=22.9
Q ss_pred CeeecCCCCccccHHHHHhhcCC---CCCCeeccCCCccccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSL---EDDSFHCENCNGELVA 54 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~---~~~~F~C~~Cg~eL~~ 54 (330)
..+.|..|+.+|...+.+-...+ ....-+|+ ||+.|..
T Consensus 136 ~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~P~C~-Cgg~lrP 176 (271)
T PTZ00409 136 FEARCCTCRKTIQLNKIMLQKTSHFMHQLPPECP-CGGIFKP 176 (271)
T ss_pred CcceeCCCCCCcccCHHHHhhhhhhccCCCCCCC-CCCcccC
Confidence 35789999999875433211000 01124799 9998865
No 244
>PRK07218 replication factor A; Provisional
Probab=53.89 E-value=6.1 Score=40.64 Aligned_cols=22 Identities=23% Similarity=0.486 Sum_probs=18.0
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCcc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGE 51 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~e 51 (330)
.+.||.|++.-. .+.|+.||..
T Consensus 297 i~rCP~C~r~v~-------------~~~C~~hG~v 318 (423)
T PRK07218 297 IERCPECGRVIQ-------------KGQCRSHGAV 318 (423)
T ss_pred eecCcCcccccc-------------CCcCCCCCCc
Confidence 588999999872 3899999954
No 245
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=53.56 E-value=4.5 Score=38.99 Aligned_cols=35 Identities=23% Similarity=0.743 Sum_probs=24.8
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
-.|-.|.++|...=....+.. +.|+|+.|+....-
T Consensus 133 SRCr~C~~rYDPVP~dkmwG~--aef~C~~C~h~F~G 167 (278)
T PF15135_consen 133 SRCRKCRKRYDPVPCDKMWGI--AEFHCPKCRHNFRG 167 (278)
T ss_pred ccccccccccCCCccccccce--eeeecccccccchh
Confidence 457788999986444444333 58999999998853
No 246
>COG4640 Predicted membrane protein [Function unknown]
Probab=53.25 E-value=11 Score=38.55 Aligned_cols=25 Identities=28% Similarity=0.840 Sum_probs=17.4
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
.||.||+.=.. +..| |+.||++.-.
T Consensus 3 fC~kcG~qk~E----------d~~q-C~qCG~~~t~ 27 (465)
T COG4640 3 FCPKCGSQKAE----------DDVQ-CTQCGHKFTS 27 (465)
T ss_pred ccccccccccc----------cccc-ccccCCcCCc
Confidence 59999964321 2235 9999999843
No 247
>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=52.83 E-value=7 Score=29.26 Aligned_cols=31 Identities=23% Similarity=0.493 Sum_probs=20.7
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
-+||.|++.=+ .||.....-.|..||..|..
T Consensus 8 VkCp~C~~~q~------vFSha~t~V~C~~Cg~~L~~ 38 (55)
T PF01667_consen 8 VKCPGCYNIQT------VFSHAQTVVKCVVCGTVLAQ 38 (55)
T ss_dssp EE-TTT-SEEE------EETT-SS-EE-SSSTSEEEE
T ss_pred EECCCCCCeeE------EEecCCeEEEcccCCCEecC
Confidence 37999998755 36777778999999999965
No 248
>PRK11827 hypothetical protein; Provisional
Probab=52.73 E-value=10 Score=28.84 Aligned_cols=26 Identities=23% Similarity=0.405 Sum_probs=18.1
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCC
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCN 49 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg 49 (330)
...||.|+...... .....+.|..|+
T Consensus 8 ILaCP~ckg~L~~~-------~~~~~Lic~~~~ 33 (60)
T PRK11827 8 IIACPVCNGKLWYN-------QEKQELICKLDN 33 (60)
T ss_pred heECCCCCCcCeEc-------CCCCeEECCccC
Confidence 46799998876542 223468999998
No 249
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=52.71 E-value=7.9 Score=38.59 Aligned_cols=13 Identities=46% Similarity=1.155 Sum_probs=7.9
Q ss_pred eeecCCCCccccH
Q 020131 17 EYICPNCQRRYNA 29 (330)
Q Consensus 17 ~Y~CP~C~~~YT~ 29 (330)
.|.||+|+..|-.
T Consensus 19 ~YtCPRCn~~YCs 31 (383)
T KOG4317|consen 19 EYTCPRCNLLYCS 31 (383)
T ss_pred cccCCCCCcccee
Confidence 3666666666644
No 250
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=52.37 E-value=7.7 Score=42.52 Aligned_cols=27 Identities=19% Similarity=0.314 Sum_probs=19.3
Q ss_pred cCCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCc
Q 020131 12 KNTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNG 50 (330)
Q Consensus 12 ~~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~ 50 (330)
..+..+=+|+.||..-.. .|.||.||.
T Consensus 675 sin~~~~~C~~CG~~~~~------------~~~CP~CG~ 701 (735)
T PRK07111 675 SINHPVDRCPVCGYLGVI------------EDKCPKCGS 701 (735)
T ss_pred EeCCCCeecCCCCCCCCc------------CccCcCCCC
Confidence 455666699999943221 489999996
No 251
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=51.90 E-value=6.7 Score=42.39 Aligned_cols=12 Identities=17% Similarity=0.634 Sum_probs=8.5
Q ss_pred eeecCCCCcccc
Q 020131 17 EYICPNCQRRYN 28 (330)
Q Consensus 17 ~Y~CP~C~~~YT 28 (330)
.-+||.||...+
T Consensus 15 akFC~~CG~~l~ 26 (645)
T PRK14559 15 NRFCQKCGTSLT 26 (645)
T ss_pred CccccccCCCCC
Confidence 345888888774
No 252
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=51.72 E-value=5.5 Score=29.98 Aligned_cols=37 Identities=19% Similarity=0.493 Sum_probs=30.1
Q ss_pred eecCCCCcccc----HHHHHhhcCCCCCCeeccCCCccccc
Q 020131 18 YICPNCQRRYN----ALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 18 Y~CP~C~~~YT----~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
-+|-.|++.++ .++|-+|-+-.-..|.|+.|...+..
T Consensus 3 vkC~lCdk~~~Id~~~~~aKrLrnrPi~tYmC~eC~~RI~~ 43 (56)
T PF09963_consen 3 VKCILCDKKEEIDEDTPEAKRLRNRPIHTYMCDECKERIRE 43 (56)
T ss_pred eEEEecCCEEEeccCCHHHHHhhcCCCcceeChhHHHHHhH
Confidence 47999999998 45677887766678999999998855
No 253
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=51.66 E-value=7 Score=42.27 Aligned_cols=25 Identities=36% Similarity=0.818 Sum_probs=17.2
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
.||.||+.... +.-.|+.||+.+..
T Consensus 29 ~Cp~CG~~~~~-----------~~~fC~~CG~~~~~ 53 (645)
T PRK14559 29 PCPQCGTEVPV-----------DEAHCPNCGAETGT 53 (645)
T ss_pred cCCCCCCCCCc-----------ccccccccCCcccc
Confidence 58888887322 45678888887753
No 254
>PRK12267 methionyl-tRNA synthetase; Reviewed
Probab=51.49 E-value=8.2 Score=41.27 Aligned_cols=39 Identities=15% Similarity=0.477 Sum_probs=28.5
Q ss_pred cCCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccch
Q 020131 12 KNTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESD 57 (330)
Q Consensus 12 ~~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~ 57 (330)
......+.||.|++-|+.-++. + .-+|+.||++++....
T Consensus 120 ~~~~~~~yc~~~~~~l~~~~l~---~----~~~c~~cg~~~e~~~~ 158 (648)
T PRK12267 120 KGEYEGWYCVSCETFFTESQLV---D----GGKCPDCGREVELVKE 158 (648)
T ss_pred EeeEEEeecCCCCccCChHHhc---c----CCcCCCCCCcCeEEec
Confidence 3445678899999999986632 2 1469999999876554
No 255
>TIGR00108 eRF peptide chain release factor eRF/aRF, subunit 1. Alternative names include eRF1, SUP45, omnipotent suppressor protein 1.
Probab=51.23 E-value=6.9 Score=39.89 Aligned_cols=37 Identities=19% Similarity=0.367 Sum_probs=21.6
Q ss_pred CCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 15 VQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 15 ~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
+..|+||+|+.. ..+-..+. .....|.|+.||.++..
T Consensus 322 r~~~r~~~~~~~-~~~~~~~~--~~~~~~~c~~~~~~~~~ 358 (409)
T TIGR00108 322 RVTYKCAECGEV-IEKTVREL--KDKKFAICPACGQEMDV 358 (409)
T ss_pred eEEEEcCCCCce-eecccccc--cccccccCcccCccccc
Confidence 346999999852 11101111 01235899999999843
No 256
>PRK12722 transcriptional activator FlhC; Provisional
Probab=51.03 E-value=9.6 Score=35.16 Aligned_cols=31 Identities=19% Similarity=0.341 Sum_probs=21.1
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
---|..|+..|-. ...++ ...|.|+.|+.+=
T Consensus 134 l~~C~~Cgg~fv~----~~~e~-~~~f~CplC~~ps 164 (187)
T PRK12722 134 LSSCNCCGGHFVT----HAHDP-VGSFVCGLCQPPS 164 (187)
T ss_pred eccCCCCCCCeec----ccccc-CCCCcCCCCCCcc
Confidence 3459999999962 11122 3589999999843
No 257
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=50.99 E-value=4.7 Score=33.29 Aligned_cols=31 Identities=19% Similarity=0.494 Sum_probs=22.6
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCCcccccc
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAE 55 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~ 55 (330)
=.|-.||..|..+.+ .. .=+||.|.++++++
T Consensus 59 a~CkkCGfef~~~~i----k~---pSRCP~CKSE~Ie~ 89 (97)
T COG3357 59 ARCKKCGFEFRDDKI----KK---PSRCPKCKSEWIEE 89 (97)
T ss_pred hhhcccCcccccccc----CC---cccCCcchhhcccC
Confidence 369999988876222 21 46899999999764
No 258
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=50.65 E-value=9.1 Score=24.14 Aligned_cols=19 Identities=21% Similarity=0.289 Sum_probs=15.7
Q ss_pred ecCCCCccccHHHHHhhcC
Q 020131 19 ICPNCQRRYNALDALRLVS 37 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld 37 (330)
.||.|++.++.......+|
T Consensus 3 ~CPiC~~~v~~~~in~HLD 21 (26)
T smart00734 3 QCPVCFREVPENLINSHLD 21 (26)
T ss_pred cCCCCcCcccHHHHHHHHH
Confidence 5999999998877777766
No 259
>KOG2817 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=50.47 E-value=12 Score=38.26 Aligned_cols=40 Identities=28% Similarity=0.471 Sum_probs=26.4
Q ss_pred CCCeeecCC---------------CCccccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 14 TVQEYICPN---------------CQRRYNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 14 ~~~~Y~CP~---------------C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
-+..|+||. ||..-+-.=..+|...-.-.|+||+|-.+-.
T Consensus 331 fHSvF~CPVlKeqtsdeNPPm~L~CGHVISkdAlnrLS~ng~~sfKCPYCP~e~~ 385 (394)
T KOG2817|consen 331 FHSVFICPVLKEQTSDENPPMMLICGHVISKDALNRLSKNGSQSFKCPYCPVEQL 385 (394)
T ss_pred ccceeecccchhhccCCCCCeeeeccceecHHHHHHHhhCCCeeeeCCCCCcccC
Confidence 345789994 9998886444455333222499999976653
No 260
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=50.41 E-value=4.6 Score=34.10 Aligned_cols=38 Identities=21% Similarity=0.394 Sum_probs=24.4
Q ss_pred eeecCCCCccccHHHHHhhcC---CCCCCeeccCCCccccc
Q 020131 17 EYICPNCQRRYNALDALRLVS---LEDDSFHCENCNGELVA 54 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld---~~~~~F~C~~Cg~eL~~ 54 (330)
...||.||..=-..--+++-+ |++--|+|..||..+.+
T Consensus 72 ~~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~wre 112 (113)
T COG1594 72 KEKCPKCGNKEAYYWQLQTRSADEPETRFYKCTRCGYRWRE 112 (113)
T ss_pred cccCCCCCCceeEEEeeehhccCCCceEEEEecccCCEeec
Confidence 478999987533333333322 45556899999988753
No 261
>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=50.29 E-value=5.3 Score=44.34 Aligned_cols=39 Identities=18% Similarity=0.373 Sum_probs=0.0
Q ss_pred CCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 15 VQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 15 ~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
...++||.||..--..--...=.++.-.|.|+.|+..+.
T Consensus 653 i~~r~Cp~Cg~~t~~~~Cp~CG~~T~~~~~Cp~C~~~~~ 691 (900)
T PF03833_consen 653 IGRRRCPKCGKETFYNRCPECGSHTEPVYVCPDCGIEVE 691 (900)
T ss_dssp ---------------------------------------
T ss_pred eecccCcccCCcchhhcCcccCCccccceeccccccccC
Confidence 345667777654221111111112223456666666553
No 262
>TIGR00613 reco DNA repair protein RecO. All proteins in this family for which functions are known are DNA binding proteins that are involved in the initiation of recombination or recombinational repair.
Probab=50.21 E-value=5.4 Score=36.71 Aligned_cols=31 Identities=19% Similarity=0.456 Sum_probs=24.0
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCcc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGE 51 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~e 51 (330)
.-.|..||.. +....+++..|+|.|+.|...
T Consensus 147 l~~C~~cg~~----~~~~~fs~~~gg~~C~~c~~~ 177 (241)
T TIGR00613 147 LDKCAVCGSK----EDLIYFSMTYGGALCRQCGEK 177 (241)
T ss_pred cCccCCCCCc----CCCceEchhcCeEEChhhCcc
Confidence 3479999972 234578888999999999864
No 263
>PLN00209 ribosomal protein S27; Provisional
Probab=50.06 E-value=8.1 Score=31.45 Aligned_cols=30 Identities=20% Similarity=0.445 Sum_probs=24.7
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
+||.|+..=+ .|+.....-.|..||..|..
T Consensus 38 kCp~C~n~q~------VFShA~t~V~C~~Cg~~L~~ 67 (86)
T PLN00209 38 KCQGCFNITT------VFSHSQTVVVCGSCQTVLCQ 67 (86)
T ss_pred ECCCCCCeeE------EEecCceEEEccccCCEeec
Confidence 6999998755 46777778899999999965
No 264
>PRK12860 transcriptional activator FlhC; Provisional
Probab=49.77 E-value=10 Score=34.99 Aligned_cols=30 Identities=17% Similarity=0.372 Sum_probs=20.5
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCcc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGE 51 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~e 51 (330)
--.|..|+..|-.- ..+ ....|.|+.|..+
T Consensus 134 l~~C~~Cgg~fv~~----~~e-~~~~f~CplC~~p 163 (189)
T PRK12860 134 LARCCRCGGKFVTH----AHD-LRHNFVCGLCQPP 163 (189)
T ss_pred eccCCCCCCCeecc----ccc-cCCCCcCCCCCCc
Confidence 45699999999631 112 2347999999944
No 265
>PLN03086 PRLI-interacting factor K; Provisional
Probab=49.72 E-value=21 Score=38.10 Aligned_cols=37 Identities=14% Similarity=0.319 Sum_probs=20.5
Q ss_pred CeeecCCCCccccHHHHHhhcC--CCCCCeeccCCCcccc
Q 020131 16 QEYICPNCQRRYNALDALRLVS--LEDDSFHCENCNGELV 53 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld--~~~~~F~C~~Cg~eL~ 53 (330)
..|.|| |+..+.-.+....+. -..-.+.|++|+..+.
T Consensus 477 kpv~Cp-Cg~~~~R~~L~~H~~thCp~Kpi~C~fC~~~v~ 515 (567)
T PLN03086 477 EPLQCP-CGVVLEKEQMVQHQASTCPLRLITCRFCGDMVQ 515 (567)
T ss_pred CCccCC-CCCCcchhHHHhhhhccCCCCceeCCCCCCccc
Confidence 557777 776665544333321 1123567777776663
No 266
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=49.61 E-value=4 Score=26.22 Aligned_cols=35 Identities=23% Similarity=0.542 Sum_probs=20.7
Q ss_pred ecCCCCccccHH-HHHhhcC--CCCCCeeccCCCcccc
Q 020131 19 ICPNCQRRYNAL-DALRLVS--LEDDSFHCENCNGELV 53 (330)
Q Consensus 19 ~CP~C~~~YT~l-DA~~Lld--~~~~~F~C~~Cg~eL~ 53 (330)
+|+.|+...... .+....+ ....=|.|..|+.+|.
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 478888766543 2222211 1123599999999884
No 267
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=49.55 E-value=7.3 Score=33.63 Aligned_cols=15 Identities=27% Similarity=0.764 Sum_probs=13.9
Q ss_pred CCeeecCCCCccccH
Q 020131 15 VQEYICPNCQRRYNA 29 (330)
Q Consensus 15 ~~~Y~CP~C~~~YT~ 29 (330)
.+.|+|+.|++.|+.
T Consensus 51 ~qRyrC~~C~~tf~~ 65 (129)
T COG3677 51 HQRYKCKSCGSTFTV 65 (129)
T ss_pred ccccccCCcCcceee
Confidence 678999999999987
No 268
>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=49.33 E-value=6.6 Score=26.95 Aligned_cols=17 Identities=29% Similarity=0.735 Sum_probs=11.5
Q ss_pred cCCCCeeecCCCCcccc
Q 020131 12 KNTVQEYICPNCQRRYN 28 (330)
Q Consensus 12 ~~~~~~Y~CP~C~~~YT 28 (330)
+....+|+|..|+.+|.
T Consensus 23 E~~T~fy~C~~C~~~wr 39 (39)
T PF01096_consen 23 EPMTLFYVCCNCGHRWR 39 (39)
T ss_dssp SSSEEEEEESSSTEEEE
T ss_pred CCCeEEEEeCCCCCeeC
Confidence 33445788888887773
No 269
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=49.17 E-value=7.2 Score=29.23 Aligned_cols=35 Identities=20% Similarity=0.535 Sum_probs=21.8
Q ss_pred eeecCCCCccc----cHHHHHhhcCCCCCCeeccCCCccccccc
Q 020131 17 EYICPNCQRRY----NALDALRLVSLEDDSFHCENCNGELVAES 56 (330)
Q Consensus 17 ~Y~CP~C~~~Y----T~lDA~~Lld~~~~~F~C~~Cg~eL~~~~ 56 (330)
-+.||.||.+- -..-++.. + .+.||.|..+-.-+.
T Consensus 4 Wi~CP~CgnKTR~kir~DT~LkN--f---PlyCpKCK~EtlI~v 42 (55)
T PF14205_consen 4 WILCPICGNKTRLKIREDTVLKN--F---PLYCPKCKQETLIDV 42 (55)
T ss_pred EEECCCCCCccceeeecCceecc--c---cccCCCCCceEEEEe
Confidence 57899999432 22223322 2 578999997765443
No 270
>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=49.06 E-value=4 Score=26.59 Aligned_cols=26 Identities=19% Similarity=0.480 Sum_probs=12.7
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCcc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGE 51 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~e 51 (330)
.||+||..-....+ .-..+|+.||.+
T Consensus 5 fC~~CG~~t~~~~~-------g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 5 FCGRCGAPTKPAPG-------GWARRCPSCGHE 30 (32)
T ss_dssp B-TTT--BEEE-SS-------SS-EEESSSS-E
T ss_pred ccCcCCccccCCCC-------cCEeECCCCcCE
Confidence 58888876544222 235788888865
No 271
>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=48.79 E-value=5.6 Score=32.31 Aligned_cols=31 Identities=16% Similarity=0.454 Sum_probs=17.2
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNG 50 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~ 50 (330)
-.+.||.|+-+=. .-.+++..+.|+|-.||.
T Consensus 32 ~~~~CPfH~d~~p----S~~i~~~k~~~~Cf~Cg~ 62 (97)
T PF01807_consen 32 YRCLCPFHDDKTP----SFSINPDKNRFKCFGCGK 62 (97)
T ss_dssp EEE--SSS--SS------EEEETTTTEEEETTT--
T ss_pred EEEECcCCCCCCC----ceEEECCCCeEEECCCCC
Confidence 3467899884311 125677788999999984
No 272
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=48.22 E-value=9.9 Score=39.44 Aligned_cols=37 Identities=19% Similarity=0.583 Sum_probs=28.1
Q ss_pred CCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccchhh
Q 020131 14 TVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESDKL 59 (330)
Q Consensus 14 ~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~~~ 59 (330)
+...-.||.|+.+|+..- -.-+|..||..+-.+.++.
T Consensus 177 Ds~V~~CP~Ca~~F~l~r---------RrHHCRLCG~VmC~~C~k~ 213 (505)
T KOG1842|consen 177 DSSVQFCPECANSFGLTR---------RRHHCRLCGRVMCRDCSKF 213 (505)
T ss_pred CCcccccccccchhhhHH---------HhhhhhhcchHHHHHHHHh
Confidence 344678999999998732 2578999999888777754
No 273
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.12 E-value=7.8 Score=33.53 Aligned_cols=33 Identities=21% Similarity=0.347 Sum_probs=22.2
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccc
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAES 56 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~ 56 (330)
-.||+||.-+-|.=-+.. .=.|..||.++-+.+
T Consensus 22 grCP~CGeGrLF~gFLK~------~p~C~aCG~dyg~~~ 54 (126)
T COG5349 22 GRCPRCGEGRLFRGFLKV------VPACEACGLDYGFAD 54 (126)
T ss_pred CCCCCCCCchhhhhhccc------CchhhhccccccCCc
Confidence 369999988755222222 347999999996543
No 274
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=48.12 E-value=7 Score=38.94 Aligned_cols=30 Identities=27% Similarity=0.663 Sum_probs=23.5
Q ss_pred CCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 14 TVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 14 ~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
...+|.||+|+.+.-. | .-.||.|...|+-
T Consensus 305 ~~gGy~CP~CktkVCs-----L------Pi~CP~Csl~Lil 334 (421)
T COG5151 305 KGGGYECPVCKTKVCS-----L------PISCPICSLQLIL 334 (421)
T ss_pred ccCceeCCcccceeec-----C------CccCcchhHHHHH
Confidence 3458999999988654 3 5789999999864
No 275
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=47.94 E-value=11 Score=36.96 Aligned_cols=13 Identities=31% Similarity=0.746 Sum_probs=11.3
Q ss_pred CeeccCCCccccc
Q 020131 42 SFHCENCNGELVA 54 (330)
Q Consensus 42 ~F~C~~Cg~eL~~ 54 (330)
.|.||.||+.++.
T Consensus 276 sf~Cp~Cg~~~~~ 288 (298)
T KOG2879|consen 276 SFTCPLCGENVEP 288 (298)
T ss_pred hcccCccCCCCcc
Confidence 6999999999863
No 276
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=47.75 E-value=5.8 Score=43.27 Aligned_cols=18 Identities=33% Similarity=0.706 Sum_probs=14.6
Q ss_pred eeecCCCCccccHHHHHh
Q 020131 17 EYICPNCQRRYNALDALR 34 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~ 34 (330)
|-.|.+||-|||..+++-
T Consensus 123 F~~CT~CGPRfTIi~alP 140 (750)
T COG0068 123 FINCTNCGPRFTIIEALP 140 (750)
T ss_pred ccccCCCCcceeeeccCC
Confidence 336999999999988874
No 277
>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=47.67 E-value=11 Score=25.39 Aligned_cols=12 Identities=25% Similarity=0.714 Sum_probs=6.1
Q ss_pred CeeccCCCcccc
Q 020131 42 SFHCENCNGELV 53 (330)
Q Consensus 42 ~F~C~~Cg~eL~ 53 (330)
.|.|++|+-++.
T Consensus 4 ~~~C~nC~R~v~ 15 (33)
T PF08209_consen 4 YVECPNCGRPVA 15 (33)
T ss_dssp EEE-TTTSSEEE
T ss_pred eEECCCCcCCcc
Confidence 356666665553
No 278
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=47.34 E-value=11 Score=25.28 Aligned_cols=15 Identities=13% Similarity=0.350 Sum_probs=10.1
Q ss_pred CCCeeecCCCCcccc
Q 020131 14 TVQEYICPNCQRRYN 28 (330)
Q Consensus 14 ~~~~Y~CP~C~~~YT 28 (330)
+...|+|+.|+..|.
T Consensus 18 ~~~~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 18 EDDYEVCIFCGSSFP 32 (33)
T ss_pred cCCeEEcccCCcEee
Confidence 445677888877664
No 279
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=47.05 E-value=8 Score=28.52 Aligned_cols=29 Identities=24% Similarity=0.653 Sum_probs=19.5
Q ss_pred CeeecCCCCc-cccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 16 QEYICPNCQR-RYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 16 ~~Y~CP~C~~-~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
..-.||+||. .|-+ +. ...+.|-.||...
T Consensus 18 k~~~CPrCG~gvfmA-------~H-~dR~~CGkCgyTe 47 (51)
T COG1998 18 KNRFCPRCGPGVFMA-------DH-KDRWACGKCGYTE 47 (51)
T ss_pred ccccCCCCCCcchhh-------hc-CceeEeccccceE
Confidence 3457999997 5533 11 1378999999754
No 280
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=47.02 E-value=11 Score=28.91 Aligned_cols=32 Identities=31% Similarity=0.741 Sum_probs=22.4
Q ss_pred eeecCCCCcccc-HHHHHhhcCCCCCCeeccCCCccc
Q 020131 17 EYICPNCQRRYN-ALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 17 ~Y~CP~C~~~YT-~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
.|-|| ||-||. .||-+++= .-.-+||.|.-.+
T Consensus 22 tyPCP-CGDRFeIsLeDl~~G---E~VArCPSCSLiv 54 (67)
T COG5216 22 TYPCP-CGDRFEISLEDLRNG---EVVARCPSCSLIV 54 (67)
T ss_pred EecCC-CCCEeEEEHHHhhCC---ceEEEcCCceEEE
Confidence 56777 999998 56666651 1136899998665
No 281
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=46.80 E-value=9.9 Score=30.89 Aligned_cols=30 Identities=23% Similarity=0.628 Sum_probs=24.6
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
+||.|...=+ .||.....-.|..||..|..
T Consensus 37 kCp~C~n~q~------VFShA~t~V~C~~Cg~~L~~ 66 (85)
T PTZ00083 37 KCPGCSQITT------VFSHAQTVVLCGGCSSQLCQ 66 (85)
T ss_pred ECCCCCCeeE------EEecCceEEEccccCCEeec
Confidence 6999998755 46777778899999999965
No 282
>PHA02998 RNA polymerase subunit; Provisional
Probab=46.63 E-value=4.9 Score=36.95 Aligned_cols=38 Identities=16% Similarity=0.407 Sum_probs=24.6
Q ss_pred eeecCCCCcccc---HHHHHhhcCCCCCCeeccCCCccccc
Q 020131 17 EYICPNCQRRYN---ALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 17 ~Y~CP~C~~~YT---~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
.-.||.|+..=. .+..-.-=-|++.-|.|..||..+..
T Consensus 143 ~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkp 183 (195)
T PHA02998 143 NTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKP 183 (195)
T ss_pred CCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCC
Confidence 357999987544 33332222356667899999988754
No 283
>PRK05580 primosome assembly protein PriA; Validated
Probab=46.56 E-value=16 Score=39.47 Aligned_cols=27 Identities=19% Similarity=0.560 Sum_probs=14.8
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
.||+|+...++-. ..+.++|++||..-
T Consensus 392 ~C~~C~~~l~~h~-------~~~~l~Ch~Cg~~~ 418 (679)
T PRK05580 392 ECPHCDASLTLHR-------FQRRLRCHHCGYQE 418 (679)
T ss_pred CCCCCCCceeEEC-------CCCeEECCCCcCCC
Confidence 4777776554321 12356676666553
No 284
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 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 FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=46.21 E-value=7 Score=29.22 Aligned_cols=31 Identities=19% Similarity=0.616 Sum_probs=15.7
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAES 56 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~ 56 (330)
.-.|..|++.|+++ .-..+|..||..+=..-
T Consensus 9 ~~~C~~C~~~F~~~---------~rrhhCr~CG~~vC~~C 39 (69)
T PF01363_consen 9 ASNCMICGKKFSLF---------RRRHHCRNCGRVVCSSC 39 (69)
T ss_dssp -SB-TTT--B-BSS---------S-EEE-TTT--EEECCC
T ss_pred CCcCcCcCCcCCCc---------eeeEccCCCCCEECCch
Confidence 45799999999862 23789999998765443
No 285
>PRK12495 hypothetical protein; Provisional
Probab=46.18 E-value=9.6 Score=36.10 Aligned_cols=15 Identities=20% Similarity=0.689 Sum_probs=12.8
Q ss_pred CCCCeeccCCCcccc
Q 020131 39 EDDSFHCENCNGELV 53 (330)
Q Consensus 39 ~~~~F~C~~Cg~eL~ 53 (330)
....|+|+.||.+|.
T Consensus 39 tmsa~hC~~CG~PIp 53 (226)
T PRK12495 39 TMTNAHCDECGDPIF 53 (226)
T ss_pred ccchhhcccccCccc
Confidence 446899999999996
No 286
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=46.13 E-value=8.7 Score=28.99 Aligned_cols=13 Identities=54% Similarity=0.958 Sum_probs=11.2
Q ss_pred CeeccCCCccccc
Q 020131 42 SFHCENCNGELVA 54 (330)
Q Consensus 42 ~F~C~~Cg~eL~~ 54 (330)
.-+||+||++|+.
T Consensus 41 ~~~CPNCgGelv~ 53 (57)
T PF06906_consen 41 NGVCPNCGGELVR 53 (57)
T ss_pred cCcCcCCCCcccc
Confidence 4689999999975
No 287
>PLN03086 PRLI-interacting factor K; Provisional
Probab=45.70 E-value=13 Score=39.69 Aligned_cols=35 Identities=14% Similarity=0.472 Sum_probs=20.2
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
.+.|+.|+..|..-+.......-...+.|+ ||..+
T Consensus 453 H~~C~~Cgk~f~~s~LekH~~~~Hkpv~Cp-Cg~~~ 487 (567)
T PLN03086 453 HVHCEKCGQAFQQGEMEKHMKVFHEPLQCP-CGVVL 487 (567)
T ss_pred CccCCCCCCccchHHHHHHHHhcCCCccCC-CCCCc
Confidence 468888888887433322211112467888 88543
No 288
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=45.47 E-value=6.1 Score=35.16 Aligned_cols=22 Identities=18% Similarity=0.564 Sum_probs=18.4
Q ss_pred eeecCCCCccccHHHHHhhcCC
Q 020131 17 EYICPNCQRRYNALDALRLVSL 38 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~ 38 (330)
--.|+.|+++||..|-..+..+
T Consensus 28 RReC~~C~~RFTTyErve~~~l 49 (147)
T TIGR00244 28 RRECLECHERFTTFERAELLPP 49 (147)
T ss_pred cccCCccCCccceeeecccccc
Confidence 4579999999999998887554
No 289
>PRK14873 primosome assembly protein PriA; Provisional
Probab=45.41 E-value=7.1 Score=42.30 Aligned_cols=28 Identities=14% Similarity=0.375 Sum_probs=15.5
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCcc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGE 51 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~e 51 (330)
...||+|+...++-. ..+.++|++||..
T Consensus 392 ~~~C~~C~~~L~~h~-------~~~~l~Ch~CG~~ 419 (665)
T PRK14873 392 PARCRHCTGPLGLPS-------AGGTPRCRWCGRA 419 (665)
T ss_pred eeECCCCCCceeEec-------CCCeeECCCCcCC
Confidence 346777776665411 1234666666654
No 290
>KOG2846 consensus Predicted membrane protein [Function unknown]
Probab=45.17 E-value=8.4 Score=38.36 Aligned_cols=34 Identities=24% Similarity=0.583 Sum_probs=22.0
Q ss_pred CCCCeeecCCCCcc---ccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 13 NTVQEYICPNCQRR---YNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 13 ~~~~~Y~CP~C~~~---YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
+++--.||+.|+.. +.. +...+ -.|+|++|+.--
T Consensus 216 ~~ryALIC~~C~~HNGla~~-ee~~y-----i~F~C~~Cn~LN 252 (328)
T KOG2846|consen 216 NNRYALICSQCHHHNGLARK-EEYEY-----ITFRCPHCNALN 252 (328)
T ss_pred cchhhhcchhhccccCcCCh-hhcCc-----eEEECccccccC
Confidence 44556799999763 222 22222 379999999755
No 291
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=45.06 E-value=13 Score=36.68 Aligned_cols=9 Identities=33% Similarity=1.032 Sum_probs=5.9
Q ss_pred ecCCCCccc
Q 020131 19 ICPNCQRRY 27 (330)
Q Consensus 19 ~CP~C~~~Y 27 (330)
.||.||..=
T Consensus 186 ~CPvCGs~P 194 (305)
T TIGR01562 186 LCPACGSPP 194 (305)
T ss_pred cCCCCCChh
Confidence 577777654
No 292
>PRK00635 excinuclease ABC subunit A; Provisional
Probab=44.98 E-value=12 Score=44.89 Aligned_cols=34 Identities=26% Similarity=0.479 Sum_probs=25.7
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNG 50 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~ 50 (330)
..|.||.|+..|..++.. +||+..-.-.||.|.+
T Consensus 243 ~~~~cp~~~~~~~~~~p~-~FSfNsp~GaCp~C~G 276 (1809)
T PRK00635 243 TQATIPETQQTYTPLTPQ-LFSPHSLEDRCPQCQG 276 (1809)
T ss_pred ccccCCccCcccCcCChh-hcCCCCccccCCCCCC
Confidence 468999999998876544 6676555668999953
No 293
>PRK00349 uvrA excinuclease ABC subunit A; Reviewed
Probab=44.94 E-value=11 Score=42.37 Aligned_cols=34 Identities=26% Similarity=0.660 Sum_probs=25.9
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNG 50 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~ 50 (330)
..+.||.|+..|..+... +||+..-.=.|+.|++
T Consensus 251 ~~~~c~~~g~~~~~~~p~-~FSfN~p~G~Cp~C~G 284 (943)
T PRK00349 251 EKFACPVCGFSIPELEPR-LFSFNSPYGACPTCDG 284 (943)
T ss_pred ccccCcccCCCcCcCChh-hcCCCCccCCCCcCCC
Confidence 468899999999976654 5676555568999964
No 294
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=44.91 E-value=12 Score=35.18 Aligned_cols=25 Identities=28% Similarity=0.760 Sum_probs=18.0
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNG 50 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~ 50 (330)
.|.||.|+..++. ....++|++++.
T Consensus 2 ~~~CP~C~~~l~~---------~~~~~~C~~~h~ 26 (272)
T PRK11088 2 SYQCPLCHQPLTL---------EENSWICPQNHQ 26 (272)
T ss_pred cccCCCCCcchhc---------CCCEEEcCCCCC
Confidence 4899999987643 124699998664
No 295
>COG0423 GRS1 Glycyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=44.85 E-value=14 Score=39.15 Aligned_cols=36 Identities=31% Similarity=0.640 Sum_probs=24.4
Q ss_pred eecCCCCcccc----HHHHHhh-----cCC-------CCCCeeccCCCcccc
Q 020131 18 YICPNCQRRYN----ALDALRL-----VSL-------EDDSFHCENCNGELV 53 (330)
Q Consensus 18 Y~CP~C~~~YT----~lDA~~L-----ld~-------~~~~F~C~~Cg~eL~ 53 (330)
-.|+.|+.+|- ..+++.- +++ ....-+||.||++|.
T Consensus 89 v~c~~c~~~yRADHLiEe~l~~~~~~~~~~~e~~~ii~~~~ir~p~~g~~l~ 140 (558)
T COG0423 89 VECKKCGERYRADHLIEEYLGKDGHGNMSPEELTEIIREYDIRCPECGGELN 140 (558)
T ss_pred eeccccchhhhhhHHHHHHhhhcccccCCHHHHHHHHHHcCCcCCCcCCccC
Confidence 46999999998 3444432 111 124679999999996
No 296
>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=44.42 E-value=7.1 Score=40.72 Aligned_cols=27 Identities=22% Similarity=0.653 Sum_probs=15.4
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
.||+|+...|+-. ..+.++|++||...
T Consensus 224 ~C~~C~~~l~~h~-------~~~~l~Ch~Cg~~~ 250 (505)
T TIGR00595 224 CCPNCDVSLTYHK-------KEGKLRCHYCGYQE 250 (505)
T ss_pred CCCCCCCceEEec-------CCCeEEcCCCcCcC
Confidence 3777776555421 12456777777654
No 297
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=44.26 E-value=11 Score=38.03 Aligned_cols=29 Identities=28% Similarity=0.608 Sum_probs=20.8
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
.|.|+.|+.+...-. .....|+.||..+.
T Consensus 244 ~~~C~~c~~~~~~~~--------~~~~~C~~c~~~~~ 272 (382)
T PRK04338 244 VYYCPKCLYREEVEG--------LPPEECPVCGGKFG 272 (382)
T ss_pred EEECCCCCcEEEecC--------CCCCCCCCCCCcce
Confidence 567999999877421 12458999998764
No 298
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=44.06 E-value=9.8 Score=35.14 Aligned_cols=29 Identities=21% Similarity=0.419 Sum_probs=23.7
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCC
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCN 49 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg 49 (330)
.-.|-.||+.-. ...+++..|+|.|..|+
T Consensus 149 l~~C~~Cg~~~~----~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 149 LDHCAVCGAPGD----HRYFSPKEGGAVCSECG 177 (247)
T ss_pred hhhHhcCCCCCC----ceEEecccCCccccccc
Confidence 347999998754 45688899999999997
No 299
>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=44.03 E-value=2.9 Score=42.12 Aligned_cols=37 Identities=22% Similarity=0.442 Sum_probs=17.4
Q ss_pred eecCCCCccccHHHHHhhcC--CCCCCeeccCCCccccccc
Q 020131 18 YICPNCQRRYNALDALRLVS--LEDDSFHCENCNGELVAES 56 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld--~~~~~F~C~~Cg~eL~~~~ 56 (330)
=+|++||+..|. .+.. +| -.+-.|.|+.||..-....
T Consensus 175 piC~~cGri~tt-~v~~-~d~~~~~v~Y~c~~cG~~g~~~i 213 (360)
T PF01921_consen 175 PICEKCGRIDTT-EVTE-YDPEGGTVTYRCEECGHEGEVDI 213 (360)
T ss_dssp EEETTTEE--EE-EEEE-E--SSSEEEEE--TTS---EEET
T ss_pred eeccccCCcccc-eeeE-eecCCCEEEEEecCCCCEEEEec
Confidence 379999995442 1111 12 2233699999998886544
No 300
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=44.02 E-value=21 Score=27.35 Aligned_cols=37 Identities=16% Similarity=0.239 Sum_probs=22.6
Q ss_pred CeeecCC------------CCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 16 QEYICPN------------CQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 16 ~~Y~CP~------------C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
..|.||. ||.+|.-.-..+.+.- ....||.|+.+|..
T Consensus 3 ~~f~CpIt~~lM~dPVi~~~G~tyer~~I~~~l~~--~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 3 DEFLCPITGELMRDPVILPSGHTYERSAIERWLEQ--NGGTDPFTRQPLSE 51 (73)
T ss_dssp GGGB-TTTSSB-SSEEEETTSEEEEHHHHHHHHCT--TSSB-TTT-SB-SG
T ss_pred cccCCcCcCcHhhCceeCCcCCEEcHHHHHHHHHc--CCCCCCCCCCcCCc
Confidence 4678885 5677775555555443 57999999999865
No 301
>PHA02540 61 DNA primase; Provisional
Probab=43.36 E-value=13 Score=37.23 Aligned_cols=34 Identities=26% Similarity=0.586 Sum_probs=21.7
Q ss_pred eeecCCCCccccH-HHHHhhcCCCCC--CeeccCCCc
Q 020131 17 EYICPNCQRRYNA-LDALRLVSLEDD--SFHCENCNG 50 (330)
Q Consensus 17 ~Y~CP~C~~~YT~-lDA~~Lld~~~~--~F~C~~Cg~ 50 (330)
...||.|+-+=.. --+.=.++|..+ .|+|-.||.
T Consensus 27 ~~~CPf~~ds~~~~~kpsF~V~p~k~~~~yhCFgCGa 63 (337)
T PHA02540 27 NFRCPICGDSQKDKNKARGWIYEKKDGGVFKCHNCGY 63 (337)
T ss_pred EecCCCCCCccccCcCCcEEEeccCCceEEEecCCCC
Confidence 4679999873100 000115777777 899999994
No 302
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=43.31 E-value=15 Score=26.48 Aligned_cols=28 Identities=7% Similarity=-0.083 Sum_probs=17.8
Q ss_pred CCccccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 23 CQRRYNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 23 C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
||..|.-.=...++.. ...||.|+.+|.
T Consensus 19 ~G~v~~~~~i~~~~~~---~~~cP~~~~~~~ 46 (63)
T smart00504 19 SGQTYERRAIEKWLLS---HGTDPVTGQPLT 46 (63)
T ss_pred CCCEEeHHHHHHHHHH---CCCCCCCcCCCC
Confidence 5566664444444432 468999999884
No 303
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=43.25 E-value=9.6 Score=37.36 Aligned_cols=43 Identities=21% Similarity=0.544 Sum_probs=31.0
Q ss_pred hhHHHHHHhhcCCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 2 RKKLKDELECKNTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 2 rk~Le~~l~~~~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
+++|++-|+...| -+|--|++.+--==.+.| |.|+|-+|-+.=
T Consensus 13 ~~~l~~Ll~~~~N---~~CADC~a~~P~WaSwnl-----GvFiC~~C~giH 55 (287)
T KOG0703|consen 13 KRRLRELLREPDN---KVCADCGAKGPRWASWNL-----GVFICLRCAGIH 55 (287)
T ss_pred HHHHHHHHcCccc---CcccccCCCCCCeEEeec-----CeEEEeeccccc
Confidence 5678887877664 569999998654223344 899999998653
No 304
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=43.05 E-value=15 Score=36.45 Aligned_cols=9 Identities=33% Similarity=0.866 Sum_probs=5.4
Q ss_pred ecCCCCccc
Q 020131 19 ICPNCQRRY 27 (330)
Q Consensus 19 ~CP~C~~~Y 27 (330)
.||.||..=
T Consensus 189 ~CPvCGs~P 197 (309)
T PRK03564 189 FCPVCGSMP 197 (309)
T ss_pred CCCCCCCcc
Confidence 466666653
No 305
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=42.85 E-value=11 Score=30.17 Aligned_cols=13 Identities=31% Similarity=1.012 Sum_probs=5.7
Q ss_pred CeeecCCCCcccc
Q 020131 16 QEYICPNCQRRYN 28 (330)
Q Consensus 16 ~~Y~CP~C~~~YT 28 (330)
.+|.||.|+.++.
T Consensus 64 s~~~Cp~Cg~~~~ 76 (81)
T PF10609_consen 64 SYFVCPHCGERIY 76 (81)
T ss_dssp -EEE-TTT--EEE
T ss_pred CccCCCCCCCeec
Confidence 4667777776653
No 306
>PLN02224 methionine-tRNA ligase
Probab=42.75 E-value=14 Score=39.67 Aligned_cols=39 Identities=15% Similarity=0.280 Sum_probs=28.7
Q ss_pred cCCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccch
Q 020131 12 KNTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESD 57 (330)
Q Consensus 12 ~~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~ 57 (330)
......|.||.|++-|+..++ +++ ..|+.||.+++....
T Consensus 185 ~~~~~~~yc~~ce~f~~~~~l---~~~----~~~~~~~~~~~~~~e 223 (616)
T PLN02224 185 RADYEGLYCVNCEEYKDEKEL---LEN----NCCPVHQMPCVARKE 223 (616)
T ss_pred EeeeeeeecCCCCCCCCHHHH---cCC----CCCCCCCCcceEEec
Confidence 345668999999998887664 332 479999999865443
No 307
>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=42.60 E-value=5.4 Score=26.88 Aligned_cols=28 Identities=21% Similarity=0.570 Sum_probs=14.8
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
.||.|+.-.-..+... ....|..|+..-
T Consensus 3 FCp~C~nlL~p~~~~~------~~~~C~~C~Y~~ 30 (35)
T PF02150_consen 3 FCPECGNLLYPKEDKE------KRVACRTCGYEE 30 (35)
T ss_dssp BETTTTSBEEEEEETT------TTEEESSSS-EE
T ss_pred eCCCCCccceEcCCCc------cCcCCCCCCCcc
Confidence 4888887543222111 123688888754
No 308
>PF04641 Rtf2: Rtf2 RING-finger
Probab=42.54 E-value=23 Score=33.72 Aligned_cols=37 Identities=24% Similarity=0.605 Sum_probs=24.9
Q ss_pred CCCeeecCC----------------CCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 14 TVQEYICPN----------------CQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 14 ~~~~Y~CP~----------------C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
....|+||. ||..|+. .|+..+. ....|+.||.+...
T Consensus 110 ~~~~~~CPvt~~~~~~~~~fv~l~~cG~V~s~-~alke~k---~~~~Cp~c~~~f~~ 162 (260)
T PF04641_consen 110 SEGRFICPVTGKEFNGKHKFVYLRPCGCVFSE-KALKELK---KSKKCPVCGKPFTE 162 (260)
T ss_pred CCceeECCCCCcccCCceeEEEEcCCCCEeeH-HHHHhhc---ccccccccCCcccc
Confidence 456899996 5555554 4555443 24669999999863
No 309
>COG0498 ThrC Threonine synthase [Amino acid transport and metabolism]
Probab=42.46 E-value=15 Score=37.66 Aligned_cols=31 Identities=26% Similarity=0.420 Sum_probs=23.4
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAES 56 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~ 56 (330)
..+|..|++.|+.... ..+|+.||..|...-
T Consensus 5 ~~rc~~cg~~f~~a~~---------~~~c~~cGl~lp~~~ 35 (411)
T COG0498 5 SLRCLKCGREFSQALL---------QGLCPDCGLFLPAEY 35 (411)
T ss_pred EeecCCCCcchhhHHh---------hCcCCcCCccccccc
Confidence 5689999988875322 378999999886643
No 310
>TIGR00467 lysS_arch lysyl-tRNA synthetase, archaeal and spirochete. This model represents the lysyl-tRNA synthetases that are class I amino-acyl tRNA synthetases. It includes archaeal and spirochete examples of the enzyme. All other known examples are class IIc amino-acyl tRNA synthetases and seem to form a separate orthologous set.
Probab=42.28 E-value=8.7 Score=40.43 Aligned_cols=34 Identities=24% Similarity=0.611 Sum_probs=22.5
Q ss_pred ecCCCCccccHHHHHhhcCCC-CCCeeccCCCccccccc
Q 020131 19 ICPNCQRRYNALDALRLVSLE-DDSFHCENCNGELVAES 56 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~-~~~F~C~~Cg~eL~~~~ 56 (330)
+||+||+-.|... . ++.. +-.|.|. ||..-+...
T Consensus 170 ic~~cGrv~~~~~--~-~~~~~~v~Y~c~-cG~~g~~~~ 204 (515)
T TIGR00467 170 FCENCGRDTTTVN--N-YDNEYSIEYSCE-CGNQESVDI 204 (515)
T ss_pred ecCCcCccCceEE--E-ecCCceEEEEcC-CCCEEEEee
Confidence 7999999977322 2 2322 3579996 998876543
No 311
>PRK14873 primosome assembly protein PriA; Provisional
Probab=41.85 E-value=23 Score=38.54 Aligned_cols=23 Identities=22% Similarity=0.640 Sum_probs=16.3
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGE 51 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~e 51 (330)
...+|..||... . .+.|+.||+.
T Consensus 409 ~~l~Ch~CG~~~-~------------p~~Cp~Cgs~ 431 (665)
T PRK14873 409 GTPRCRWCGRAA-P------------DWRCPRCGSD 431 (665)
T ss_pred CeeECCCCcCCC-c------------CccCCCCcCC
Confidence 357788888643 1 4788888876
No 312
>COG5109 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=41.82 E-value=17 Score=36.39 Aligned_cols=38 Identities=29% Similarity=0.519 Sum_probs=25.0
Q ss_pred CCeeecCC---------------CCccccHHHHHhhcCC-CCCCeeccCCCcccc
Q 020131 15 VQEYICPN---------------CQRRYNALDALRLVSL-EDDSFHCENCNGELV 53 (330)
Q Consensus 15 ~~~Y~CP~---------------C~~~YT~lDA~~Lld~-~~~~F~C~~Cg~eL~ 53 (330)
+..|+||. ||..-+- +|++-++- -.-.|+||+|-..-+
T Consensus 334 Hs~FiCPVlKe~~t~ENpP~ml~CgHVIsk-eal~~LS~nG~~~FKCPYCP~~~~ 387 (396)
T COG5109 334 HSLFICPVLKELCTDENPPVMLECGHVISK-EALSVLSQNGVLSFKCPYCPEMSK 387 (396)
T ss_pred cceeeccccHhhhcccCCCeeeeccceeeH-HHHHHHhhcCcEEeeCCCCCcchh
Confidence 34688984 8877764 45544443 234799999976543
No 313
>PRK05580 primosome assembly protein PriA; Validated
Probab=41.81 E-value=7.9 Score=41.83 Aligned_cols=23 Identities=17% Similarity=0.520 Sum_probs=14.4
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCcc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGE 51 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~e 51 (330)
..+|..||.++.. ...||.||+.
T Consensus 408 ~l~Ch~Cg~~~~~------------~~~Cp~Cg~~ 430 (679)
T PRK05580 408 RLRCHHCGYQEPI------------PKACPECGST 430 (679)
T ss_pred eEECCCCcCCCCC------------CCCCCCCcCC
Confidence 4567777766544 4567777665
No 314
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=41.76 E-value=6.4 Score=41.21 Aligned_cols=35 Identities=26% Similarity=0.526 Sum_probs=22.8
Q ss_pred ecCCCCccccHHHHHhhcCCCC--CCeeccCCCccccccc
Q 020131 19 ICPNCQRRYNALDALRLVSLED--DSFHCENCNGELVAES 56 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~--~~F~C~~Cg~eL~~~~ 56 (330)
+||+||+-.+.--. -+|... -.|.|. ||+.-+...
T Consensus 177 ic~~cg~~~~~~~~--~~d~~~~~v~y~~~-cG~~~~~~~ 213 (510)
T PRK00750 177 ICPKCGKVLTTPVI--SYDAEAGTVTYDCE-CGHEGEVPV 213 (510)
T ss_pred eCCCCCccceEEEE--EEeCCCCEEEEEcC-CCCEEEEec
Confidence 79999999874221 234432 368886 998776543
No 315
>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=41.75 E-value=15 Score=38.35 Aligned_cols=25 Identities=20% Similarity=0.441 Sum_probs=20.5
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
...+|..||.++.. ...||.||+.-
T Consensus 239 ~~l~Ch~Cg~~~~~------------~~~Cp~C~s~~ 263 (505)
T TIGR00595 239 GKLRCHYCGYQEPI------------PKTCPQCGSED 263 (505)
T ss_pred CeEEcCCCcCcCCC------------CCCCCCCCCCe
Confidence 46789999988865 57999999863
No 316
>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.
Probab=41.47 E-value=12 Score=39.96 Aligned_cols=29 Identities=21% Similarity=0.464 Sum_probs=19.5
Q ss_pred cCCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcc
Q 020131 12 KNTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGE 51 (330)
Q Consensus 12 ~~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~e 51 (330)
..+..+=+|+.||... -.+ .|.||.||..
T Consensus 527 tin~~~siC~~CGy~~-----g~~------~~~CP~CGs~ 555 (586)
T TIGR02827 527 CFNIKITICNDCHHID-----KRT------LHRCPVCGSA 555 (586)
T ss_pred EeCCCCeecCCCCCcC-----CCc------CCcCcCCCCc
Confidence 3456677899999610 001 4899999953
No 317
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=40.84 E-value=9.7 Score=28.68 Aligned_cols=29 Identities=21% Similarity=0.362 Sum_probs=22.7
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
-.|.+||+.+-..+.. ..-|++||++|..
T Consensus 19 ~NCl~CGkIiC~~Eg~--------~~pC~fCg~~l~~ 47 (57)
T PF06221_consen 19 PNCLNCGKIICEQEGP--------LGPCPFCGTPLLS 47 (57)
T ss_pred ccccccChhhcccccC--------cCcCCCCCCcccC
Confidence 4699999998876543 3679999999965
No 318
>PLN02842 nucleotide kinase
Probab=40.78 E-value=35 Score=36.06 Aligned_cols=58 Identities=17% Similarity=0.236 Sum_probs=38.1
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccchhhhhhcCCCCChhHHHHHHHHHHHHHHHHHHhHHHHHHH
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESDKLAAQEGGDGDDNARRRRREKLKDLLQKLEVHLKPLMEQ 96 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~~~~~~e~~~g~~na~r~~~e~~k~~l~r~n~QlkpI~~~ 96 (330)
...||.||..|... +.|. .++.|+..|+...++ ..+.++.+|..|...+.||+..
T Consensus 121 R~~dp~tG~iYh~~-----~~pP----~~~~~~~rL~~R~DD----------------~eE~IkkRL~~Y~~~t~pIl~~ 175 (505)
T PLN02842 121 RRLDPVTGKIYHIK-----NFPP----ESEEIKARLITRPDD----------------TEEKVKARLQIYKKNAEAILST 175 (505)
T ss_pred cccccccCCccccc-----cCCC----CccccccccccCCCC----------------CHHHHHHHHHHHHHHhhhHHHh
Confidence 46799999999762 3332 123344556544332 1246788899999999999988
Q ss_pred HHh
Q 020131 97 INR 99 (330)
Q Consensus 97 Lk~ 99 (330)
...
T Consensus 176 Y~~ 178 (505)
T PLN02842 176 YSD 178 (505)
T ss_pred cCc
Confidence 865
No 319
>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=39.99 E-value=10 Score=26.49 Aligned_cols=28 Identities=29% Similarity=0.822 Sum_probs=14.0
Q ss_pred ecCCCCccccHHHHHhhcCC--CCCCeeccCCCc
Q 020131 19 ICPNCQRRYNALDALRLVSL--EDDSFHCENCNG 50 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~--~~~~F~C~~Cg~ 50 (330)
-||.|+-+ |..++++- ..+.|.|-.|+.
T Consensus 5 pCP~CGG~----DrFri~~d~~~~G~~~C~~C~~ 34 (40)
T PF08273_consen 5 PCPICGGK----DRFRIFDDKDGRGTWICRQCGG 34 (40)
T ss_dssp --TTTT-T----TTEEEETT----S-EEETTTTB
T ss_pred CCCCCcCc----cccccCcCcccCCCEECCCCCC
Confidence 49999873 22232222 248899999965
No 320
>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=39.96 E-value=13 Score=31.94 Aligned_cols=29 Identities=31% Similarity=0.796 Sum_probs=19.0
Q ss_pred CeeecC--CCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 16 QEYICP--NCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 16 ~~Y~CP--~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
-+.-|| .|+++.+.. .++.|.|+.|+..+
T Consensus 17 ~Y~aC~~~~C~kKv~~~--------~~~~y~C~~C~~~~ 47 (146)
T PF08646_consen 17 YYPACPNEKCNKKVTEN--------GDGSYRCEKCNKTV 47 (146)
T ss_dssp EEEE-TSTTTS-B-EEE--------TTTEEEETTTTEEE
T ss_pred EECCCCCccCCCEeecC--------CCcEEECCCCCCcC
Confidence 355799 999986541 23579999999885
No 321
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=39.87 E-value=10 Score=36.20 Aligned_cols=31 Identities=13% Similarity=0.393 Sum_probs=21.5
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
.-.||.||...... ...-...|+.||...-.
T Consensus 99 ~~fC~~CG~~~~~~-------~~~~~~~C~~c~~~~yp 129 (256)
T PRK00241 99 HRFCGYCGHPMHPS-------KTEWAMLCPHCRERYYP 129 (256)
T ss_pred CccccccCCCCeec-------CCceeEECCCCCCEECC
Confidence 44699999986542 12236899999976644
No 322
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=39.69 E-value=9.4 Score=32.41 Aligned_cols=30 Identities=33% Similarity=0.710 Sum_probs=21.0
Q ss_pred eecCCCCccc---------cHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 18 YICPNCQRRY---------NALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 18 Y~CP~C~~~Y---------T~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
-.||+||.+= -..++|.| -|+|-.||..+.
T Consensus 74 ~~C~~C~~~eavffQ~~~~r~d~~m~l------~yvC~~C~h~wt 112 (113)
T KOG2691|consen 74 KHCPKCGHREAVFFQAQTRRADEAMRL------FYVCCSCGHRWT 112 (113)
T ss_pred ccCCccCCcceEEEecccccccceEEE------EEEecccccccc
Confidence 4599998752 23456666 689999998763
No 323
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.68 E-value=12 Score=35.84 Aligned_cols=18 Identities=17% Similarity=0.611 Sum_probs=14.2
Q ss_pred CeeecCCCCccccHHHHH
Q 020131 16 QEYICPNCQRRYNALDAL 33 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~ 33 (330)
...-||.|+.+|--.++.
T Consensus 18 k~ieCPvC~tkFkkeev~ 35 (267)
T COG1655 18 KTIECPVCNTKFKKEEVK 35 (267)
T ss_pred ceeccCcccchhhhhhee
Confidence 357799999999876654
No 324
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=39.58 E-value=15 Score=33.25 Aligned_cols=37 Identities=16% Similarity=0.434 Sum_probs=22.5
Q ss_pred CeeecCCCCcccc---HHHHHhhcCC-----CCCCeeccCCCccc
Q 020131 16 QEYICPNCQRRYN---ALDALRLVSL-----EDDSFHCENCNGEL 52 (330)
Q Consensus 16 ~~Y~CP~C~~~YT---~lDA~~Lld~-----~~~~F~C~~Cg~eL 52 (330)
.+=.||.|+..-. -.+|..-+-+ ...-++|+.||..-
T Consensus 96 e~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiY 140 (165)
T COG1656 96 EFSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIY 140 (165)
T ss_pred ccccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccc
Confidence 3668999998654 4444422221 22235699999775
No 325
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=38.74 E-value=8.3 Score=33.83 Aligned_cols=26 Identities=27% Similarity=0.591 Sum_probs=19.6
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
.||.||+-|.. + +..+||.|....+.
T Consensus 5 nC~~CgklF~~--~--------~~~iCp~C~~~~e~ 30 (137)
T TIGR03826 5 NCPKCGRLFVK--T--------GRDVCPSCYEEEER 30 (137)
T ss_pred cccccchhhhh--c--------CCccCHHHhHHHHH
Confidence 59999998875 1 25679999876643
No 326
>COG4307 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.42 E-value=9.6 Score=37.31 Aligned_cols=26 Identities=31% Similarity=0.822 Sum_probs=20.4
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
-|.||+||.+.-| .+-.|..||.-|-
T Consensus 3 ~FhC~~CgQ~v~F-----------eN~~C~~Cg~~Lg 28 (349)
T COG4307 3 DFHCPNCGQRVAF-----------ENSACLSCGSALG 28 (349)
T ss_pred cccCCCCCCeeee-----------cchHHHhhhhHhh
Confidence 5889999987765 2567999998875
No 327
>PF10005 DUF2248: Uncharacterized protein conserved in bacteria (DUF2248); InterPro: IPR011201 This is a family of uncharacterised bacterial proteins.
Probab=38.14 E-value=16 Score=36.78 Aligned_cols=27 Identities=30% Similarity=0.711 Sum_probs=18.4
Q ss_pred cCCCCccccHHHHHhhcCCCCCCeeccCCCccccccch
Q 020131 20 CPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESD 57 (330)
Q Consensus 20 CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~ 57 (330)
|++|+....| .+-.|..||..|-...+
T Consensus 2 C~~Cg~~v~F-----------eNt~C~~Cg~~LGf~p~ 28 (343)
T PF10005_consen 2 CPNCGQPVFF-----------ENTRCLSCGSALGFDPD 28 (343)
T ss_pred CCCCCCccee-----------CCCccccCCccccCCCC
Confidence 8888877554 35678888877755444
No 328
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=37.89 E-value=15 Score=25.28 Aligned_cols=11 Identities=27% Similarity=1.123 Sum_probs=7.8
Q ss_pred ecCCCCccccH
Q 020131 19 ICPNCQRRYNA 29 (330)
Q Consensus 19 ~CP~C~~~YT~ 29 (330)
.||+|++.|.-
T Consensus 4 ~CprC~kg~Hw 14 (36)
T PF14787_consen 4 LCPRCGKGFHW 14 (36)
T ss_dssp C-TTTSSSCS-
T ss_pred cCcccCCCcch
Confidence 59999998863
No 329
>PF07818 HCNGP: HCNGP-like protein; InterPro: IPR012479 This family comprises sequences bearing significant similarity to the mouse transcriptional regulator protein HCNGP (Q02614 from SWISSPROT). This protein is localised to the nucleus and is thought to be involved in the regulation of beta-2-microglobulin genes.
Probab=37.82 E-value=35 Score=28.08 Aligned_cols=19 Identities=37% Similarity=0.483 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHHHHHHHh
Q 020131 236 AYYAALLKKQQELDEAAKN 254 (330)
Q Consensus 236 aYyAal~k~q~~~~~~~~~ 254 (330)
+||.+|++.|....+++.+
T Consensus 76 ~y~e~L~k~Qk~~~~k~ek 94 (96)
T PF07818_consen 76 DYYEELAKAQKEEMEKREK 94 (96)
T ss_pred HHHHHHHHHHHHHHHHHHh
Confidence 6999999999988777654
No 330
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=37.69 E-value=6.2 Score=36.75 Aligned_cols=35 Identities=23% Similarity=0.418 Sum_probs=21.0
Q ss_pred eeecCCCCccccHHHHHhhcCCC------CCCeeccCCCcccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLE------DDSFHCENCNGELV 53 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~------~~~F~C~~Cg~eL~ 53 (330)
.--||.||..+.. .+.+++-. -....|.+||....
T Consensus 14 ~~~CPvCg~~l~~--~~~~~~IPyFG~V~i~t~~C~~CgYR~~ 54 (201)
T COG1779 14 RIDCPVCGGTLKA--HMYLYDIPYFGEVLISTGVCERCGYRST 54 (201)
T ss_pred eecCCcccceeeE--EEeeecCCccceEEEEEEEccccCCccc
Confidence 4579999994332 22223321 12459999998764
No 331
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=37.56 E-value=12 Score=38.31 Aligned_cols=36 Identities=19% Similarity=0.425 Sum_probs=24.9
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAES 56 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~ 56 (330)
..-.||.|+..++.- .++.. ..=.||+||+.|..-.
T Consensus 17 ~~~~C~eCd~~~~~P----~l~~~-q~A~CPRC~~~l~~~~ 52 (418)
T COG2995 17 HLILCPECDMLVSLP----RLDSG-QSAYCPRCGHTLTRGG 52 (418)
T ss_pred ceecCCCCCceeccc----cCCCC-CcccCCCCCCccccCC
Confidence 456799999999853 22221 3468999999996533
No 332
>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=37.47 E-value=7.8 Score=38.86 Aligned_cols=33 Identities=18% Similarity=0.489 Sum_probs=20.2
Q ss_pred ecCCCCccccHHHHHhhcCC--CCCCeeccCCCcccccc
Q 020131 19 ICPNCQRRYNALDALRLVSL--EDDSFHCENCNGELVAE 55 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~--~~~~F~C~~Cg~eL~~~ 55 (330)
+||+|| +.+ -.+.. +|. .+-.|.|. ||.+-...
T Consensus 171 ~c~~cg-~~~-~~v~~-~d~~~~~v~y~c~-cG~~g~~~ 205 (353)
T cd00674 171 YCEKCG-KDT-TTVEA-YDAKAGTVTYKCE-CGHEETVD 205 (353)
T ss_pred ecCCcC-cce-eEEEE-EeCCCCeEEEEcC-CCCEEEEe
Confidence 799999 443 22222 233 23469995 99887653
No 333
>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....
Probab=37.10 E-value=17 Score=36.66 Aligned_cols=38 Identities=24% Similarity=0.454 Sum_probs=20.2
Q ss_pred CCeeecCCCCccccHHHHHhhc-----CCCCCCeeccCCCcccc
Q 020131 15 VQEYICPNCQRRYNALDALRLV-----SLEDDSFHCENCNGELV 53 (330)
Q Consensus 15 ~~~Y~CP~C~~~YT~lDA~~Ll-----d~~~~~F~C~~Cg~eL~ 53 (330)
...+.|+.|+.=++.-.+...- +. ..+..|+.||.++.
T Consensus 118 ~~~~Yc~~~e~fl~e~~v~g~CP~C~~~~-a~g~~Ce~cG~~~~ 160 (391)
T PF09334_consen 118 YEGWYCPSCERFLPESFVEGTCPYCGSDK-ARGDQCENCGRPLE 160 (391)
T ss_dssp EEEEEETTTTEEE-GGGETCEETTT--SS-CTTTEETTTSSBEE
T ss_pred cceeEecCcCcccccceeeccccCcCccc-cCCCcccCCCCCcc
Confidence 3466677777766554442211 11 12466777777665
No 334
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=37.05 E-value=26 Score=24.62 Aligned_cols=12 Identities=33% Similarity=0.850 Sum_probs=6.6
Q ss_pred eeccCCCccccc
Q 020131 43 FHCENCNGELVA 54 (330)
Q Consensus 43 F~C~~Cg~eL~~ 54 (330)
-.|+.||.+|..
T Consensus 18 ~~Cp~C~~PL~~ 29 (41)
T PF06677_consen 18 EHCPDCGTPLMR 29 (41)
T ss_pred CccCCCCCeeEE
Confidence 455556555544
No 335
>PF13397 DUF4109: Domain of unknown function (DUF4109)
Probab=36.93 E-value=20 Score=30.25 Aligned_cols=39 Identities=18% Similarity=0.322 Sum_probs=22.7
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccch
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESD 57 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~ 57 (330)
..|.||+ |..|..-=|.+-- ....+.|+.||.+-..+..
T Consensus 27 v~Y~C~~-Gh~~~v~Fa~eAe--vP~~WeC~~cG~~A~~~~~ 65 (105)
T PF13397_consen 27 VSYWCPN-GHETEVPFAAEAE--VPATWECPRCGLPAGRDDG 65 (105)
T ss_pred EEEECCC-CCEEeccccccCC--CCCceeCCCCCCcccccCC
Confidence 4799999 4444421111111 1247999999988544433
No 336
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=36.71 E-value=15 Score=30.79 Aligned_cols=15 Identities=33% Similarity=0.795 Sum_probs=12.6
Q ss_pred CCCeeccCCCccccc
Q 020131 40 DDSFHCENCNGELVA 54 (330)
Q Consensus 40 ~~~F~C~~Cg~eL~~ 54 (330)
.-.|.||+||++.+-
T Consensus 20 ~k~FtCp~Cghe~vs 34 (104)
T COG4888 20 PKTFTCPRCGHEKVS 34 (104)
T ss_pred CceEecCccCCeeee
Confidence 347999999999875
No 337
>KOG2893 consensus Zn finger protein [General function prediction only]
Probab=36.67 E-value=15 Score=35.47 Aligned_cols=34 Identities=24% Similarity=0.535 Sum_probs=24.7
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
-|=.|++.|....++--.--. -.|+|+.|+..|.
T Consensus 12 wcwycnrefddekiliqhqka-khfkchichkkl~ 45 (341)
T KOG2893|consen 12 WCWYCNREFDDEKILIQHQKA-KHFKCHICHKKLF 45 (341)
T ss_pred eeeecccccchhhhhhhhhhh-ccceeeeehhhhc
Confidence 488899999987776332212 3699999998884
No 338
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=36.30 E-value=42 Score=24.92 Aligned_cols=29 Identities=14% Similarity=0.387 Sum_probs=18.3
Q ss_pred cCCCCccccHHHHHhhcCCCCCCeeccCCC
Q 020131 20 CPNCQRRYNALDALRLVSLEDDSFHCENCN 49 (330)
Q Consensus 20 CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg 49 (330)
...|+..|.-.=++++|. ..+.+.||.-|
T Consensus 27 s~~C~H~fek~aI~~~i~-~~~~~~CPv~G 55 (57)
T PF11789_consen 27 SKKCGHTFEKEAILQYIQ-RNGSKRCPVAG 55 (57)
T ss_dssp ESSS--EEEHHHHHHHCT-TTS-EE-SCCC
T ss_pred cCCCCCeecHHHHHHHHH-hcCCCCCCCCC
Confidence 336999999888888883 34689999833
No 339
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=36.26 E-value=1.1e+02 Score=23.55 Aligned_cols=18 Identities=6% Similarity=0.152 Sum_probs=9.7
Q ss_pred HHHHHHHHHhHHHHHHHH
Q 020131 80 KDLLQKLEVHLKPLMEQI 97 (330)
Q Consensus 80 k~~l~r~n~QlkpI~~~L 97 (330)
+.+..+|+-|+--|..+|
T Consensus 37 r~R~r~~~~~~~li~aLi 54 (64)
T COG4068 37 RKRQRNFMILMFLILALI 54 (64)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 344456666665555543
No 340
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=35.98 E-value=16 Score=28.21 Aligned_cols=22 Identities=32% Similarity=0.700 Sum_probs=14.2
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCcc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGE 51 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~e 51 (330)
-|-+|++-- .. ..=.||+||.+
T Consensus 6 AC~~Ck~l~---------~~--d~e~CP~Cgs~ 27 (64)
T COG2093 6 ACKNCKRLT---------PE--DTEICPVCGST 27 (64)
T ss_pred HHhhccccC---------CC--CCccCCCCCCc
Confidence 477777532 22 34679999987
No 341
>PRK09401 reverse gyrase; Reviewed
Probab=35.55 E-value=21 Score=41.34 Aligned_cols=25 Identities=20% Similarity=0.600 Sum_probs=18.3
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
.|+.||..|+.. .-.||.|+..+..
T Consensus 680 ~c~~~g~~f~~~-----------~~~~~~c~~~~~~ 704 (1176)
T PRK09401 680 RCRDCGYQFTDE-----------SDKCPRCGSTNIE 704 (1176)
T ss_pred cccccccccccc-----------cccccccccccCC
Confidence 488898888872 1289999987753
No 342
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=35.47 E-value=9.7 Score=29.41 Aligned_cols=33 Identities=18% Similarity=0.316 Sum_probs=22.6
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCcccccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAE 55 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~ 55 (330)
-||.||..--...+... -..|.|.-|+...-..
T Consensus 8 PCPFCG~~~~~v~~~~g----~~~v~C~~CgA~~~~~ 40 (64)
T PRK09710 8 PCPFCGCPSVTVKAISG----YYRAKCNGCESRTGYG 40 (64)
T ss_pred CCCCCCCceeEEEecCc----eEEEEcCCCCcCcccc
Confidence 49999987655554432 1358999999976543
No 343
>PRK04011 peptide chain release factor 1; Provisional
Probab=35.40 E-value=20 Score=36.57 Aligned_cols=37 Identities=27% Similarity=0.519 Sum_probs=21.6
Q ss_pred CCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 15 VQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 15 ~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
+..|+||.|+..... .+.-.. ....-.|+.||.+|..
T Consensus 326 r~~~~c~~c~~~~~~--~~~~~~-~~~~~~c~~~~~~~~~ 362 (411)
T PRK04011 326 RVTYKCPNCGYEEEK--TVKRRE-ELPEKTCPKCGSELEI 362 (411)
T ss_pred eEEEEcCCCCcceee--eccccc-ccccccCcccCccccc
Confidence 357999999865432 000000 1123589999999854
No 344
>COG0178 UvrA Excinuclease ATPase subunit [DNA replication, recombination, and repair]
Probab=35.09 E-value=17 Score=40.54 Aligned_cols=34 Identities=29% Similarity=0.716 Sum_probs=26.9
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNG 50 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~ 50 (330)
..|-||.|+-+|..++- +|||+..-.=.||.|.+
T Consensus 244 ~~~acp~~g~~~~elep-rlFSFNsP~GaCp~C~G 277 (935)
T COG0178 244 ENFACPVCGFSIPELEP-RLFSFNSPFGACPTCDG 277 (935)
T ss_pred cccCCCccCcccCCCCc-ccccCCCCCCCCCcCCC
Confidence 46899999999998763 56777655568999985
No 345
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=34.64 E-value=13 Score=29.62 Aligned_cols=28 Identities=29% Similarity=0.424 Sum_probs=16.7
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCCcc
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCNGE 51 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~e 51 (330)
|.||-||.. |+.+-. .....+|++|+=+
T Consensus 2 ~~CPCCg~~-Tl~~~~-----~~~ydIC~VC~WE 29 (78)
T PF14206_consen 2 YPCPCCGYY-TLEERG-----EGTYDICPVCFWE 29 (78)
T ss_pred ccCCCCCcE-EeccCC-----CcCceECCCCCcc
Confidence 789999864 221111 1114699999844
No 346
>COG5415 Predicted integral membrane metal-binding protein [General function prediction only]
Probab=34.52 E-value=17 Score=34.33 Aligned_cols=35 Identities=29% Similarity=0.620 Sum_probs=22.3
Q ss_pred cCCCCeeecCCCCccccHHHHHhhcCC---CCCCeeccCCCccc
Q 020131 12 KNTVQEYICPNCQRRYNALDALRLVSL---EDDSFHCENCNGEL 52 (330)
Q Consensus 12 ~~~~~~Y~CP~C~~~YT~lDA~~Lld~---~~~~F~C~~Cg~eL 52 (330)
..+..-.|||.|...=. |+.+ .-..|.|++|++--
T Consensus 187 ~~~~~alIC~~C~hhng------l~~~~ek~~~efiC~~Cn~~n 224 (251)
T COG5415 187 LSPFKALICPQCHHHNG------LYRLAEKPIIEFICPHCNHKN 224 (251)
T ss_pred cCchhhhcccccccccc------ccccccccchheecccchhhc
Confidence 35556689999976422 2222 22369999999654
No 347
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=34.38 E-value=22 Score=36.90 Aligned_cols=24 Identities=17% Similarity=0.551 Sum_probs=18.7
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNG 50 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~ 50 (330)
..|+|..||..+.- . .=+|+.||.
T Consensus 6 t~f~C~~CG~~s~K-----W------~GkCp~Cg~ 29 (456)
T COG1066 6 TAFVCQECGYVSPK-----W------LGKCPACGA 29 (456)
T ss_pred cEEEcccCCCCCcc-----c------cccCCCCCC
Confidence 57999999987753 1 358999993
No 348
>PF14369 zf-RING_3: zinc-finger
Probab=34.21 E-value=16 Score=24.69 Aligned_cols=32 Identities=28% Similarity=0.695 Sum_probs=21.4
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
.|-|=.|.+..+.... . +..-.||+|++-.++
T Consensus 2 ~ywCh~C~~~V~~~~~-----~-~~~~~CP~C~~gFvE 33 (35)
T PF14369_consen 2 RYWCHQCNRFVRIAPS-----P-DSDVACPRCHGGFVE 33 (35)
T ss_pred CEeCccCCCEeEeCcC-----C-CCCcCCcCCCCcEeE
Confidence 5889999998875221 1 112359999987655
No 349
>PRK06386 replication factor A; Reviewed
Probab=34.08 E-value=19 Score=36.35 Aligned_cols=22 Identities=14% Similarity=0.273 Sum_probs=18.0
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNG 50 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~ 50 (330)
-.+.||.|++.-+. -.|+.||.
T Consensus 235 li~rCP~C~R~l~~-------------g~C~~HG~ 256 (358)
T PRK06386 235 IFTKCSVCNKIIED-------------GVCKDHPD 256 (358)
T ss_pred eEecCcCCCeEccC-------------CcCCCCCC
Confidence 46899999998762 38999996
No 350
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=33.96 E-value=33 Score=25.88 Aligned_cols=24 Identities=0% Similarity=-0.316 Sum_probs=16.7
Q ss_pred CCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCc
Q 020131 14 TVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNG 50 (330)
Q Consensus 14 ~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~ 50 (330)
....-+||+||.-.-. ...|+ ||.
T Consensus 24 ~~~~~~c~~cg~~~~p------------H~vc~-cG~ 47 (60)
T PRK01110 24 APTLSVDKTTGEYHLP------------HHVSP-KGY 47 (60)
T ss_pred CCceeEcCCCCceecc------------ceecC-Ccc
Confidence 3446689999975432 57899 983
No 351
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=33.83 E-value=16 Score=41.67 Aligned_cols=26 Identities=19% Similarity=0.599 Sum_probs=20.6
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCcccccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAE 55 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~ 55 (330)
+|-.||..|+.. .-.||+||+..+++
T Consensus 696 rC~dcg~q~~~~-----------~~~cP~Cgs~~v~d 721 (1187)
T COG1110 696 RCRDCGEQFVDS-----------EDKCPRCGSRNVED 721 (1187)
T ss_pred HHhhcCceeccc-----------cccCCCCCCccccc
Confidence 599999999872 23899999977654
No 352
>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=33.69 E-value=26 Score=37.60 Aligned_cols=29 Identities=28% Similarity=0.801 Sum_probs=21.2
Q ss_pred CeeecCC--CCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 16 QEYICPN--CQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 16 ~~Y~CP~--C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
-++-||. |+++-+. ..++.|+|+.|+...
T Consensus 473 ~Y~ACp~~~CnKKV~~--------~~~g~~~CekC~~~~ 503 (608)
T TIGR00617 473 LYRACPSEDCNKKVVD--------QGDGTYRCEKCNKNF 503 (608)
T ss_pred EeccCChhhCCCcccc--------CCCCCEECCCCCCCC
Confidence 3567987 9998643 224689999999754
No 353
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated
Probab=33.68 E-value=34 Score=36.83 Aligned_cols=39 Identities=23% Similarity=0.396 Sum_probs=25.5
Q ss_pred HHHHHhhcC-CCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCc
Q 020131 5 LKDELECKN-TVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNG 50 (330)
Q Consensus 5 Le~~l~~~~-~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~ 50 (330)
|.++|-... ....|+|..||..-... .....+.|..|+.
T Consensus 531 L~Erl~~~SD~~~~~vC~~CG~~~~~~-------~~~~~~~C~~C~~ 570 (605)
T PRK07225 531 LKERLLDESDKVEIYVCAKCGMIAIYD-------KKRNRKYCPICGE 570 (605)
T ss_pred HHHHHhccCcceeEEeecCcCcceehh-------cccCceeecccCC
Confidence 556664433 34569999999965421 2224789999985
No 354
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=33.57 E-value=19 Score=38.08 Aligned_cols=31 Identities=19% Similarity=0.430 Sum_probs=24.0
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCcccccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAE 55 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~ 55 (330)
.|++|+..==. .|+.+|...|.-||..|+.+
T Consensus 2 ~C~~C~~s~fe------~d~a~g~~~C~~CG~v~E~~ 32 (521)
T KOG1598|consen 2 VCKNCGGSNFE------RDEATGNLYCTACGTVLEYN 32 (521)
T ss_pred cCCCCCCCCcc------cccccCCceeccccceeecc
Confidence 69999876433 35567899999999999654
No 355
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=33.53 E-value=18 Score=35.87 Aligned_cols=27 Identities=19% Similarity=0.604 Sum_probs=22.2
Q ss_pred CCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCc
Q 020131 13 NTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNG 50 (330)
Q Consensus 13 ~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~ 50 (330)
....+..|..|+..|.+ -...|++||.
T Consensus 208 ~G~RyL~CslC~teW~~-----------~R~~C~~Cg~ 234 (309)
T PRK03564 208 QGLRYLHCNLCESEWHV-----------VRVKCSNCEQ 234 (309)
T ss_pred CCceEEEcCCCCCcccc-----------cCccCCCCCC
Confidence 34568899999999987 3679999995
No 356
>PRK14894 glycyl-tRNA synthetase; Provisional
Probab=33.39 E-value=19 Score=38.26 Aligned_cols=27 Identities=30% Similarity=0.700 Sum_probs=19.9
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCCc-ccc
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCNG-ELV 53 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~-eL~ 53 (330)
-.|+.|+++|-..- | ..+||.||+ .|.
T Consensus 89 V~CkkCk~ryRaD~---L------iikCP~CGs~dLT 116 (539)
T PRK14894 89 VDCRDCKMRWRADH---I------QGVCPNCGSRDLT 116 (539)
T ss_pred eECCCCCccccCcc---c------eeeCCCCCCcCCC
Confidence 47999999997532 2 268999995 654
No 357
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=32.79 E-value=39 Score=21.68 Aligned_cols=34 Identities=9% Similarity=0.179 Sum_probs=22.4
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
.+..+.|+..|-..=...++.. +.+.||.|+..|
T Consensus 12 ~~~~~~C~H~~c~~C~~~~~~~--~~~~Cp~C~~~~ 45 (45)
T cd00162 12 PVVLLPCGHVFCRSCIDKWLKS--GKNTCPLCRTPI 45 (45)
T ss_pred ceEecCCCChhcHHHHHHHHHh--CcCCCCCCCCcC
Confidence 4556678888865555444432 467899998764
No 358
>KOG4317 consensus Predicted Zn-finger protein [Function unknown]
Probab=32.66 E-value=18 Score=36.08 Aligned_cols=14 Identities=29% Similarity=0.607 Sum_probs=10.5
Q ss_pred CCeeecCCCC---cccc
Q 020131 15 VQEYICPNCQ---RRYN 28 (330)
Q Consensus 15 ~~~Y~CP~C~---~~YT 28 (330)
..+-+|+.|+ ++||
T Consensus 5 s~~~~C~ic~vq~~~Yt 21 (383)
T KOG4317|consen 5 SSFLACGICGVQKREYT 21 (383)
T ss_pred Cceeecccccccccccc
Confidence 4577899997 4786
No 359
>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=32.52 E-value=24 Score=30.62 Aligned_cols=39 Identities=18% Similarity=0.371 Sum_probs=23.0
Q ss_pred CCCeeecCCCCccccHHHHHh---hcCC-----CCCCeeccCCCccc
Q 020131 14 TVQEYICPNCQRRYNALDALR---LVSL-----EDDSFHCENCNGEL 52 (330)
Q Consensus 14 ~~~~Y~CP~C~~~YT~lDA~~---Lld~-----~~~~F~C~~Cg~eL 52 (330)
+..+-.|+.|+..+...+... .+-+ ...-+.|+.||..-
T Consensus 88 ~~~~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiy 134 (147)
T PF01927_consen 88 DPIFSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIY 134 (147)
T ss_pred CCCCCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEe
Confidence 334668899988775443332 2211 23356899998765
No 360
>PRK03918 chromosome segregation protein; Provisional
Probab=32.51 E-value=68 Score=35.11 Aligned_cols=12 Identities=42% Similarity=0.875 Sum_probs=10.1
Q ss_pred eccCCCcccccc
Q 020131 44 HCENCNGELVAE 55 (330)
Q Consensus 44 ~C~~Cg~eL~~~ 55 (330)
.||.|+.+|...
T Consensus 437 ~Cp~c~~~L~~~ 448 (880)
T PRK03918 437 KCPVCGRELTEE 448 (880)
T ss_pred CCCCCCCcCCch
Confidence 788899999764
No 361
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=32.32 E-value=14 Score=30.92 Aligned_cols=15 Identities=33% Similarity=0.545 Sum_probs=11.2
Q ss_pred CCCCeeccCCCcccc
Q 020131 39 EDDSFHCENCNGELV 53 (330)
Q Consensus 39 ~~~~F~C~~Cg~eL~ 53 (330)
.-|...||.||.+|.
T Consensus 44 evG~~~cP~Cge~~~ 58 (102)
T PF04475_consen 44 EVGDTICPKCGEELD 58 (102)
T ss_pred ecCcccCCCCCCccC
Confidence 446678999998874
No 362
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=32.31 E-value=53 Score=22.97 Aligned_cols=34 Identities=24% Similarity=0.479 Sum_probs=20.4
Q ss_pred CCCeeecCC--CCccccHHHHHhhcCCCCCCeeccCC
Q 020131 14 TVQEYICPN--CQRRYNALDALRLVSLEDDSFHCENC 48 (330)
Q Consensus 14 ~~~~Y~CP~--C~~~YT~lDA~~Lld~~~~~F~C~~C 48 (330)
-.+++.|++ |..+|...=+..++...... .||.|
T Consensus 8 v~~G~~C~~~~C~~r~H~~C~~~y~r~~~~~-~CP~C 43 (43)
T PF08746_consen 8 VTQGQRCSNRDCNVRLHDDCFKKYFRHRSNP-KCPNC 43 (43)
T ss_dssp -SSSEE-SS--S--EE-HHHHHHHTTT-SS--B-TTT
T ss_pred HeeeccCCCCccCchHHHHHHHHHHhcCCCC-CCcCC
Confidence 356889994 99999988888887776544 89887
No 363
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=31.93 E-value=26 Score=37.41 Aligned_cols=29 Identities=14% Similarity=0.342 Sum_probs=19.1
Q ss_pred cCCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcc
Q 020131 12 KNTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGE 51 (330)
Q Consensus 12 ~~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~e 51 (330)
..+...=+|+.||..=.. ..|.||.||..
T Consensus 519 ~~n~~~~~C~~CG~~g~~-----------~~~~CP~Cgs~ 547 (579)
T TIGR02487 519 GINPPVDVCEDCGYTGEG-----------LNDKCPKCGSH 547 (579)
T ss_pred EeccCCccCCCCCCCCCC-----------CCCcCcCCCCc
Confidence 345566689999952111 13899999964
No 364
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=31.90 E-value=18 Score=35.38 Aligned_cols=35 Identities=17% Similarity=0.358 Sum_probs=24.4
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccchh
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESDK 58 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~~ 58 (330)
.-+|++||.+-..-+ ..-...|+.||...-...+.
T Consensus 111 ~RFCg~CG~~~~~~~-------~g~~~~C~~cg~~~fPR~dP 145 (279)
T COG2816 111 HRFCGRCGTKTYPRE-------GGWARVCPKCGHEHFPRIDP 145 (279)
T ss_pred CcCCCCCCCcCcccc-------CceeeeCCCCCCccCCCCCC
Confidence 457999998865422 22357999999988666554
No 365
>TIGR00398 metG methionyl-tRNA synthetase. The methionyl-tRNA synthetase (metG) is a class I amino acyl-tRNA ligase. This model appears to recognize the methionyl-tRNA synthetase of every species, including eukaryotic cytosolic and mitochondrial forms. The UPGMA difference tree calculated after search and alignment according to this model shows an unusual deep split between two families of MetG. One family contains forms from the Archaea, yeast cytosol, spirochetes, and E. coli, among others. The other family includes forms from yeast mitochondrion, Synechocystis sp., Bacillus subtilis, the Mycoplasmas, Aquifex aeolicus, and Helicobacter pylori. The E. coli enzyme is homodimeric, although monomeric forms can be prepared that are fully active. Activity of this enzyme in bacteria includes aminoacylation of fMet-tRNA with Met; subsequent formylation of the Met to fMet is catalyzed by a separate enzyme. Note that the protein from Aquifex aeolicus is split into an alpha (large) and beta (sma
Probab=31.86 E-value=22 Score=36.84 Aligned_cols=19 Identities=16% Similarity=0.499 Sum_probs=12.4
Q ss_pred CCCCeeecCCCCccccHHH
Q 020131 13 NTVQEYICPNCQRRYNALD 31 (330)
Q Consensus 13 ~~~~~Y~CP~C~~~YT~lD 31 (330)
.+...|.||.|++-++.-.
T Consensus 116 ~~~~v~~~~~~~~~l~~~~ 134 (530)
T TIGR00398 116 KEIKQLYCPECEMFLPDRY 134 (530)
T ss_pred eeeEEEecCCCCcCCchhh
Confidence 3445677887777776543
No 366
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the COG4031 Predicted metal-binding protein [General function prediction only]
Probab=31.17 E-value=22 Score=33.14 Aligned_cols=9 Identities=33% Similarity=0.792 Sum_probs=5.2
Q ss_pred eeccCCCcc
Q 020131 43 FHCENCNGE 51 (330)
Q Consensus 43 F~C~~Cg~e 51 (330)
..|++||.+
T Consensus 13 ~~Cl~Cg~~ 21 (227)
T COG4031 13 AFCLNCGRR 21 (227)
T ss_pred chhcccCCc
Confidence 456666654
No 368
>KOG3454 consensus U1 snRNP-specific protein C [RNA processing and modification]
Probab=30.84 E-value=92 Score=28.31 Aligned_cols=54 Identities=20% Similarity=0.363 Sum_probs=33.8
Q ss_pred CeeccCCCccccccchhhh-hhcCCCCChhHHHHHHHHHHHHHHHHH-HhHHHHHHHHHhhcC
Q 020131 42 SFHCENCNGELVAESDKLA-AQEGGDGDDNARRRRREKLKDLLQKLE-VHLKPLMEQINRVKD 102 (330)
Q Consensus 42 ~F~C~~Cg~eL~~~~~~~~-~~e~~~g~~na~r~~~e~~k~~l~r~n-~QlkpI~~~Lk~id~ 102 (330)
.|.|++|++-|.++.-..- .+- +| ++. .+..++-+++++ +|-+.+|+.+.....
T Consensus 3 RYyCDYCdt~LthDslsvRK~H~---~G---rkH-~~nvk~YY~k~~eeqAq~liD~~~~~~~ 58 (165)
T KOG3454|consen 3 RYYCDYCDTYLTHDSLSVRKTHC---GG---RKH-KDNVKDYYQKWMEEQAQKLIDETILRFI 58 (165)
T ss_pred cchhhhhhhhhhcccHHHHHhhh---hh---HHH-HHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 5889999999988654321 110 01 111 234477788887 777788888776644
No 369
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=30.69 E-value=18 Score=25.13 Aligned_cols=15 Identities=27% Similarity=0.647 Sum_probs=11.7
Q ss_pred eecCCCCccccHHHH
Q 020131 18 YICPNCQRRYNALDA 32 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA 32 (330)
-.||.||-.|+....
T Consensus 14 ~~C~~CgM~Y~~~~~ 28 (41)
T PF13878_consen 14 TTCPTCGMLYSPGSP 28 (41)
T ss_pred cCCCCCCCEECCCCH
Confidence 489999999986443
No 370
>TIGR03670 rpoB_arch DNA-directed RNA polymerase subunit B. This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
Probab=30.40 E-value=41 Score=36.18 Aligned_cols=40 Identities=23% Similarity=0.387 Sum_probs=26.2
Q ss_pred HHHHHhhcC-CCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcc
Q 020131 5 LKDELECKN-TVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGE 51 (330)
Q Consensus 5 Le~~l~~~~-~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~e 51 (330)
|+++|-... ....|+|..||...... .....|.|..|+..
T Consensus 525 L~ErL~~~SD~~~~~vC~~CG~~~~~~-------~~~~~~~C~~c~~~ 565 (599)
T TIGR03670 525 LKERLLDESDKYVVYVCENCGHIAWED-------KRKGTAYCPVCGET 565 (599)
T ss_pred HHHHHhccCcceeEEeecccCceeehh-------cccCceeccccCCC
Confidence 556664433 33569999999987531 11236899999873
No 371
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=30.08 E-value=32 Score=26.29 Aligned_cols=26 Identities=23% Similarity=0.660 Sum_probs=16.2
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCC
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCN 49 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg 49 (330)
-..||.|+-.. .++...+.+.|+.|+
T Consensus 8 iLaCP~~kg~L-------~~~~~~~~L~c~~~~ 33 (60)
T COG2835 8 ILACPVCKGPL-------VYDEEKQELICPRCK 33 (60)
T ss_pred eeeccCcCCcc-------eEeccCCEEEecccC
Confidence 35678777662 234445567888877
No 372
>PRK10220 hypothetical protein; Provisional
Probab=30.05 E-value=24 Score=29.98 Aligned_cols=18 Identities=33% Similarity=0.888 Sum_probs=15.1
Q ss_pred CCCeeecCCCCccccHHH
Q 020131 14 TVQEYICPNCQRRYNALD 31 (330)
Q Consensus 14 ~~~~Y~CP~C~~~YT~lD 31 (330)
+..-|+||.|+..|+..+
T Consensus 17 d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 17 DNGMYICPECAHEWNDAE 34 (111)
T ss_pred CCCeEECCcccCcCCccc
Confidence 345799999999999876
No 373
>PF12647 RNHCP: RNHCP domain; InterPro: IPR024439 This domain is found in uncharacterised bacterial proteins. It is typically between 94 and 143 amino acids in length and has a conserved RNHCP sequence motif.
Probab=29.72 E-value=18 Score=29.88 Aligned_cols=34 Identities=24% Similarity=0.511 Sum_probs=23.2
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
..|.|..||...+.+-+-.- ..=+||.|=..|--
T Consensus 3 ~~F~C~~CG~~V~p~~~g~~-----~RNHCP~CL~S~Hv 36 (92)
T PF12647_consen 3 ESFTCVHCGLTVSPLAAGSA-----HRNHCPSCLSSLHV 36 (92)
T ss_pred cccCccccCCCcccCCCCCC-----ccCcCccccccccc
Confidence 46999999998776433321 24589999877743
No 374
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.68 E-value=22 Score=28.33 Aligned_cols=14 Identities=57% Similarity=0.947 Sum_probs=11.6
Q ss_pred CeeccCCCcccccc
Q 020131 42 SFHCENCNGELVAE 55 (330)
Q Consensus 42 ~F~C~~Cg~eL~~~ 55 (330)
.-.||+||++|+..
T Consensus 41 ~g~CPnCGGelv~R 54 (84)
T COG3813 41 HGLCPNCGGELVAR 54 (84)
T ss_pred cCcCCCCCchhhcC
Confidence 45899999999864
No 375
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.54 E-value=28 Score=26.77 Aligned_cols=14 Identities=43% Similarity=1.080 Sum_probs=10.4
Q ss_pred CeeecCCCCccccH
Q 020131 16 QEYICPNCQRRYNA 29 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~ 29 (330)
.+-+||-|+++|..
T Consensus 47 gev~CPYC~t~y~l 60 (62)
T COG4391 47 GEVVCPYCSTRYRL 60 (62)
T ss_pred CcEecCccccEEEe
Confidence 35678888888863
No 376
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=29.53 E-value=30 Score=24.61 Aligned_cols=30 Identities=20% Similarity=0.621 Sum_probs=22.5
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccc
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAES 56 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~ 56 (330)
..|+.|++.|++ + ....+|..||..+-..-
T Consensus 3 ~~C~~C~~~F~~------~---~rk~~Cr~Cg~~~C~~C 32 (57)
T cd00065 3 SSCMGCGKPFTL------T---RRRHHCRNCGRIFCSKC 32 (57)
T ss_pred CcCcccCccccC------C---ccccccCcCcCCcChHH
Confidence 469999999997 1 23689999998875433
No 377
>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]
Probab=29.51 E-value=16 Score=39.95 Aligned_cols=33 Identities=27% Similarity=0.520 Sum_probs=20.8
Q ss_pred CCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCC
Q 020131 13 NTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENC 48 (330)
Q Consensus 13 ~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~C 48 (330)
..+..|+|+.||..+....-..-+.+ .-.|+.|
T Consensus 125 ~~~~~~~C~~Cg~~~~~~~~~~~~~~---~~~C~~~ 157 (682)
T COG1241 125 LKKAVFECPKCGREVEVEQSEFRVEP---PRECENC 157 (682)
T ss_pred eEEEEEEcCCCCCEEEEEeccccccC---CccCCCc
Confidence 34568999999998764222211222 3469999
No 378
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=29.41 E-value=34 Score=24.83 Aligned_cols=35 Identities=20% Similarity=0.357 Sum_probs=24.1
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
..+.|.+|+.+.|.+ ++. .+....++|-.||--..
T Consensus 2 ~~~~C~~C~~~~T~~--WR~-g~~g~~~LCnaCgl~~~ 36 (52)
T smart00401 2 SGRSCSNCGTTETPL--WRR-GPSGNKTLCNACGLYYK 36 (52)
T ss_pred CCCCcCCCCCCCCCc--ccc-CCCCCCcEeecccHHHH
Confidence 357899999999852 222 23333599999997664
No 379
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=29.26 E-value=11 Score=27.45 Aligned_cols=30 Identities=20% Similarity=0.749 Sum_probs=22.2
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
+|+.||..-..+-...+ .+ +|+|..|-..|
T Consensus 1 ~C~iCg~kigl~~~~k~---~D-G~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKI---KD-GYICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceec---cC-ccchHHHHHHh
Confidence 59999998876544333 33 49999999887
No 380
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=29.14 E-value=53 Score=32.42 Aligned_cols=27 Identities=19% Similarity=0.429 Sum_probs=17.8
Q ss_pred eeecCCCCcccc--HHHHH-hhcCCCCCCeec
Q 020131 17 EYICPNCQRRYN--ALDAL-RLVSLEDDSFHC 45 (330)
Q Consensus 17 ~Y~CP~C~~~YT--~lDA~-~Lld~~~~~F~C 45 (330)
.|+||.|+.-|. .-+-. .|+|+ +.|.-
T Consensus 57 ~~vcp~c~~h~rltAreRI~~L~D~--gSF~E 86 (296)
T CHL00174 57 MNICEQCGYHLKMSSSDRIELLIDP--GTWNP 86 (296)
T ss_pred CCCCCCCCCCcCCCHHHHHHHHccC--CccEE
Confidence 699999998664 44444 46776 34653
No 381
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=29.08 E-value=26 Score=29.38 Aligned_cols=35 Identities=20% Similarity=0.518 Sum_probs=24.1
Q ss_pred eecCCCCccccHHHHHhhcCCC----CCCeeccCCCccc
Q 020131 18 YICPNCQRRYNALDALRLVSLE----DDSFHCENCNGEL 52 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~----~~~F~C~~Cg~eL 52 (330)
=+||-||..-..-....++... .-.|+|+.|++=+
T Consensus 3 ~~CpYCg~~~~l~~~~~iYg~~~~~~~~~y~C~~C~AyV 41 (102)
T PF11672_consen 3 IICPYCGGPAELVDGSEIYGHRYDDGPYLYVCTPCDAYV 41 (102)
T ss_pred cccCCCCCeeEEcccchhcCccCCCCceeEECCCCCcee
Confidence 3799999877765555554422 1138999999877
No 382
>smart00507 HNHc HNH nucleases.
Probab=29.02 E-value=18 Score=24.18 Aligned_cols=11 Identities=18% Similarity=0.622 Sum_probs=9.5
Q ss_pred eecCCCCcccc
Q 020131 18 YICPNCQRRYN 28 (330)
Q Consensus 18 Y~CP~C~~~YT 28 (330)
|.|+.|+..++
T Consensus 11 ~~C~~C~~~~~ 21 (52)
T smart00507 11 GVCAYCGKPAS 21 (52)
T ss_pred CCCcCCcCCCC
Confidence 78999998876
No 383
>PF12660 zf-TFIIIC: Putative zinc-finger of transcription factor IIIC complex; InterPro: IPR024764 This zinc-finger domain is at the very C terminus of a number of different TFIIIC subunit proteins. This domain might be involved in protein-DNA and/or protein-protein interactions [].; PDB: 2J04_C.
Probab=28.79 E-value=30 Score=28.44 Aligned_cols=17 Identities=29% Similarity=0.561 Sum_probs=6.9
Q ss_pred eeecCCCCccccHHHHH
Q 020131 17 EYICPNCQRRYNALDAL 33 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~ 33 (330)
..+|+.|+.+|-..+..
T Consensus 55 ~r~C~~C~~~~l~~~~~ 71 (99)
T PF12660_consen 55 VRVCPVCGRRALDPEPE 71 (99)
T ss_dssp EEE-TTT--EEE-GGG-
T ss_pred eeEcCCCCCEEecCccc
Confidence 35666666666554443
No 384
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=28.75 E-value=28 Score=29.72 Aligned_cols=10 Identities=50% Similarity=1.398 Sum_probs=6.0
Q ss_pred eeecCCCCcc
Q 020131 17 EYICPNCQRR 26 (330)
Q Consensus 17 ~Y~CP~C~~~ 26 (330)
+|.||.||..
T Consensus 74 EyyCP~Cgt~ 83 (112)
T PF08882_consen 74 EYYCPGCGTQ 83 (112)
T ss_pred EEECCCCcce
Confidence 4666666653
No 385
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=28.74 E-value=32 Score=22.88 Aligned_cols=25 Identities=20% Similarity=0.453 Sum_probs=13.3
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGE 51 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~e 51 (330)
....|+.|+..+-. | .-.|+.|++.
T Consensus 10 ~~~rC~~Cg~~~~p--------P---r~~Cp~C~s~ 34 (37)
T PF12172_consen 10 LGQRCRDCGRVQFP--------P---RPVCPHCGSD 34 (37)
T ss_dssp EEEE-TTT--EEES-------------SEETTTT--
T ss_pred EEEEcCCCCCEecC--------C---CcCCCCcCcc
Confidence 35689999987432 2 4789999853
No 386
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=28.56 E-value=85 Score=28.75 Aligned_cols=35 Identities=17% Similarity=0.413 Sum_probs=24.4
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccchh
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESDK 58 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~~ 58 (330)
.-.||+|+.+|..+=-. +.|=|..|-.......+.
T Consensus 74 ~l~C~~C~~Tfk~f~~~-------g~fGCaeCY~tf~~~i~p 108 (176)
T COG3880 74 LLGCHNCGMTFKEFIQS-------GLFGCAECYKTFESQISP 108 (176)
T ss_pred HhcCccccccHHHHHHh-------cccchHHHHHHHHHHhhH
Confidence 46899999999864333 458899997665544443
No 387
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=28.52 E-value=38 Score=33.50 Aligned_cols=28 Identities=14% Similarity=0.525 Sum_probs=22.7
Q ss_pred CCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcc
Q 020131 13 NTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGE 51 (330)
Q Consensus 13 ~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~e 51 (330)
....+..|..|+..|.+ -...|++||..
T Consensus 206 ~G~RyL~CslC~teW~~-----------~R~~C~~Cg~~ 233 (305)
T TIGR01562 206 TGLRYLSCSLCATEWHY-----------VRVKCSHCEES 233 (305)
T ss_pred CCceEEEcCCCCCcccc-----------cCccCCCCCCC
Confidence 34468899999999987 36899999964
No 388
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=28.45 E-value=25 Score=25.91 Aligned_cols=33 Identities=18% Similarity=0.580 Sum_probs=23.0
Q ss_pred eecCCCCccccHHHHHhhcCCCCC--Ce--eccCCCcccccc
Q 020131 18 YICPNCQRRYNALDALRLVSLEDD--SF--HCENCNGELVAE 55 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~--~F--~C~~Cg~eL~~~ 55 (330)
+.||.||..++. ++|+..+ .| -|+.|-.|+...
T Consensus 1 i~CPyCge~~~~-----~iD~s~~~Q~yiEDC~vCC~PI~~~ 37 (52)
T PF14255_consen 1 IQCPYCGEPIEI-----LIDPSAGDQEYIEDCQVCCRPIEVQ 37 (52)
T ss_pred CCCCCCCCeeEE-----EEecCCCCeeEEeehhhcCCccEEE
Confidence 579999999886 4555332 23 599999887543
No 389
>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=28.37 E-value=28 Score=23.52 Aligned_cols=14 Identities=36% Similarity=1.087 Sum_probs=8.1
Q ss_pred CCCeeecCCCCccc
Q 020131 14 TVQEYICPNCQRRY 27 (330)
Q Consensus 14 ~~~~Y~CP~C~~~Y 27 (330)
+...++|+.||-.|
T Consensus 29 ~vp~~~C~~CGE~~ 42 (46)
T TIGR03831 29 NVPALVCPQCGEEY 42 (46)
T ss_pred CCCccccccCCCEe
Confidence 33456666666554
No 390
>COG1040 ComFC Predicted amidophosphoribosyltransferases [General function prediction only]
Probab=28.37 E-value=18 Score=33.75 Aligned_cols=27 Identities=22% Similarity=0.525 Sum_probs=20.8
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCCcccccc
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAE 55 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~ 55 (330)
=.|+.|++.+..... .|+.|+.+|...
T Consensus 25 ~~C~~C~~~~~~~~~-----------~C~~C~~~l~~~ 51 (225)
T COG1040 25 GLCSGCQADLPLIGN-----------LCPLCGLPLSSH 51 (225)
T ss_pred CcChhhhhchhHHHh-----------hhHhhhChhccc
Confidence 479999998876432 688898888775
No 391
>COG1651 DsbG Protein-disulfide isomerase [Posttranslational modification, protein turnover, chaperones]
Probab=28.21 E-value=19 Score=32.90 Aligned_cols=22 Identities=23% Similarity=0.733 Sum_probs=17.1
Q ss_pred CeeecCCCCccccHHHHHhhcCC
Q 020131 16 QEYICPNCQRRYNALDALRLVSL 38 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~ 38 (330)
..|.||.|...|..+.. .++++
T Consensus 92 ~d~~Cp~C~~~~~~l~~-~~i~~ 113 (244)
T COG1651 92 FDYTCPYCKEAFPELKK-KYIDD 113 (244)
T ss_pred ecCcCccHHHHHHHHHH-Hhhhc
Confidence 36899999999998888 55444
No 392
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 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. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=28.21 E-value=16 Score=24.86 Aligned_cols=15 Identities=40% Similarity=0.815 Sum_probs=9.6
Q ss_pred CeeecCCCCccccHH
Q 020131 16 QEYICPNCQRRYNAL 30 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~l 30 (330)
++--|+.||-+|+.+
T Consensus 20 ~~isC~~CGPr~~i~ 34 (35)
T PF07503_consen 20 QFISCTNCGPRYSII 34 (35)
T ss_dssp TT--BTTCC-SCCCE
T ss_pred cCccCCCCCCCEEEe
Confidence 345699999999864
No 393
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=28.09 E-value=32 Score=22.58 Aligned_cols=15 Identities=27% Similarity=0.452 Sum_probs=11.9
Q ss_pred CCeeecCCCCccccH
Q 020131 15 VQEYICPNCQRRYNA 29 (330)
Q Consensus 15 ~~~Y~CP~C~~~YT~ 29 (330)
..+|+|..|+..+..
T Consensus 5 ~~~ykC~~Cgniv~v 19 (34)
T TIGR00319 5 GQVYKCEVCGNIVEV 19 (34)
T ss_pred CcEEEcCCCCcEEEE
Confidence 458999999988854
No 394
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=27.88 E-value=27 Score=25.72 Aligned_cols=31 Identities=26% Similarity=0.712 Sum_probs=13.7
Q ss_pred CCeeecCCCCccccHH-HHHhhcCCCCCCeeccCCC
Q 020131 15 VQEYICPNCQRRYNAL-DALRLVSLEDDSFHCENCN 49 (330)
Q Consensus 15 ~~~Y~CP~C~~~YT~l-DA~~Lld~~~~~F~C~~Cg 49 (330)
...|.||+|+..|=.. |+.-. + .-..||-|.
T Consensus 19 ~~~y~C~~C~~~FC~dCD~fiH---E-~LH~CPGC~ 50 (51)
T PF07975_consen 19 SSRYRCPKCKNHFCIDCDVFIH---E-TLHNCPGCE 50 (51)
T ss_dssp -EEE--TTTT--B-HHHHHTTT---T-TS-SSSTT-
T ss_pred CCeEECCCCCCccccCcChhhh---c-cccCCcCCC
Confidence 4689999999999742 33211 1 245677774
No 395
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=27.66 E-value=42 Score=22.79 Aligned_cols=25 Identities=20% Similarity=0.491 Sum_probs=11.9
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCC
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCN 49 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg 49 (330)
=+|-.|++.|.. |+....|-|++|.
T Consensus 4 ~~C~eC~~~f~d-------SyL~~~F~~~VCD 28 (34)
T PF01286_consen 4 PKCDECGKPFMD-------SYLLNNFDLPVCD 28 (34)
T ss_dssp EE-TTT--EES--------SSCCCCTS-S--T
T ss_pred chHhHhCCHHHH-------HHHHHhCCccccc
Confidence 479999999975 3333467777665
No 396
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=27.64 E-value=16 Score=29.47 Aligned_cols=13 Identities=38% Similarity=0.950 Sum_probs=6.3
Q ss_pred cCCCCccccHHHH
Q 020131 20 CPNCQRRYNALDA 32 (330)
Q Consensus 20 CP~C~~~YT~lDA 32 (330)
|+.||..|+..++
T Consensus 11 C~~CG~d~~~~~a 23 (86)
T PF06170_consen 11 CPHCGLDYSHARA 23 (86)
T ss_pred ccccCCccccCCc
Confidence 5555555544443
No 397
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=27.62 E-value=32 Score=29.25 Aligned_cols=18 Identities=28% Similarity=0.713 Sum_probs=14.7
Q ss_pred CCCeeecCCCCccccHHH
Q 020131 14 TVQEYICPNCQRRYNALD 31 (330)
Q Consensus 14 ~~~~Y~CP~C~~~YT~lD 31 (330)
+..-|+||.|+..|+..+
T Consensus 16 dg~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 16 DGTQLICPSCLYEWNENE 33 (109)
T ss_pred cCCeeECccccccccccc
Confidence 345799999999999765
No 398
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.56 E-value=46 Score=32.39 Aligned_cols=37 Identities=22% Similarity=0.556 Sum_probs=25.6
Q ss_pred CCCCeeecCC----------------CCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 13 NTVQEYICPN----------------CQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 13 ~~~~~Y~CP~----------------C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
+++..|+||. ||-.|+.- |+.-| ..=.|+.||.....
T Consensus 107 ~~~a~fiCPvtgleMng~~~F~~l~~CGcV~Ser-AlKei----kas~C~~C~a~y~~ 159 (293)
T KOG3113|consen 107 TQRARFICPVTGLEMNGKYRFCALRCCGCVFSER-ALKEI----KASVCHVCGAAYQE 159 (293)
T ss_pred cccceeecccccceecceEEEEEEeccceeccHH-HHHHh----hhccccccCCcccc
Confidence 4577899995 78877753 33332 24589999998854
No 399
>KOG2324 consensus Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=27.54 E-value=35 Score=34.94 Aligned_cols=32 Identities=31% Similarity=0.634 Sum_probs=20.3
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCc-ccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNG-ELV 53 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~-eL~ 53 (330)
-|.||+|+..-. .+..++ ...-.|+.|+. .|.
T Consensus 227 l~~C~~C~~s~n-~e~~~~----sk~~~Cp~C~~~~L~ 259 (457)
T KOG2324|consen 227 LMSCPSCGYSKN-SEDLDL----SKIASCPKCNEGRLT 259 (457)
T ss_pred eeecCcCCccCc-hhhhcC----CccccCCcccCCCcc
Confidence 589999993332 233333 12378999998 654
No 400
>KOG2703 consensus C4-type Zn-finger protein [General function prediction only]
Probab=27.43 E-value=18 Score=37.19 Aligned_cols=52 Identities=17% Similarity=0.167 Sum_probs=28.7
Q ss_pred HhhcCCCCeeecCCCCcccc-HHHHHhhcCC---CCCCeeccCCCccccccchhhh
Q 020131 9 LECKNTVQEYICPNCQRRYN-ALDALRLVSL---EDDSFHCENCNGELVAESDKLA 60 (330)
Q Consensus 9 l~~~~~~~~Y~CP~C~~~YT-~lDA~~Lld~---~~~~F~C~~Cg~eL~~~~~~~~ 60 (330)
+.+......-.|++|+..=+ -|-...+-.+ .-..|.|+.||..-.+.-++..
T Consensus 31 ~~~~~~EvES~Cm~Cg~nG~TRlllT~IP~fREvVimSF~CpHCG~kN~eiQ~a~~ 86 (460)
T KOG2703|consen 31 EGNPVQEVESLCMNCGENGTTRLLLTSIPYFREVVIMSFECPHCGHKNNEIQSAEE 86 (460)
T ss_pred hcCchHHHHHhhhhcccCCceeEEEeecchhheeeeEEeecCccCCccccccchhc
Confidence 33333345678999988632 1111111111 1136999999988776665543
No 401
>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=27.29 E-value=34 Score=22.48 Aligned_cols=14 Identities=21% Similarity=0.524 Sum_probs=11.4
Q ss_pred CeeecCCCCccccH
Q 020131 16 QEYICPNCQRRYNA 29 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~ 29 (330)
++|+|..||..+..
T Consensus 3 ~~ykC~~CGniv~v 16 (34)
T cd00974 3 EVYKCEICGNIVEV 16 (34)
T ss_pred cEEEcCCCCcEEEE
Confidence 58999999988854
No 402
>KOG3993 consensus Transcription factor (contains Zn finger) [Transcription]
Probab=27.18 E-value=25 Score=36.46 Aligned_cols=14 Identities=36% Similarity=1.061 Sum_probs=12.3
Q ss_pred CCeeecCCCCcccc
Q 020131 15 VQEYICPNCQRRYN 28 (330)
Q Consensus 15 ~~~Y~CP~C~~~YT 28 (330)
+.+|+||.|.+.|+
T Consensus 293 ~vEYrCPEC~KVFs 306 (500)
T KOG3993|consen 293 HVEYRCPECDKVFS 306 (500)
T ss_pred EeeecCCccccccc
Confidence 45899999999997
No 403
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=27.00 E-value=20 Score=30.30 Aligned_cols=14 Identities=21% Similarity=0.465 Sum_probs=9.2
Q ss_pred CCCeeccCCCcccc
Q 020131 40 DDSFHCENCNGELV 53 (330)
Q Consensus 40 ~~~F~C~~Cg~eL~ 53 (330)
-|...||.||.++.
T Consensus 47 ~G~t~CP~Cg~~~e 60 (115)
T COG1885 47 VGSTSCPKCGEPFE 60 (115)
T ss_pred cccccCCCCCCccc
Confidence 45567777777663
No 404
>KOG3854 consensus SPRT-like metalloprotease [Function unknown]
Probab=26.98 E-value=23 Score=37.10 Aligned_cols=38 Identities=21% Similarity=0.624 Sum_probs=27.4
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccchh
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESDK 58 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~~ 58 (330)
.|.|..|++.+-..- +.|++ ..|+|-+|.++++...-.
T Consensus 408 ~Y~C~~C~~~~~~~s--kSl~t--~~~~C~~Ckg~i~l~~~~ 445 (505)
T KOG3854|consen 408 KYTCTKCNKLSGGHS--KSLDT--SRLRCRYCKGEISLKPVK 445 (505)
T ss_pred EEEecccCccccccc--ccccH--hHHHHHhcccceEEEeee
Confidence 699999999876421 11333 579999999999876543
No 405
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=26.94 E-value=48 Score=34.12 Aligned_cols=28 Identities=18% Similarity=0.338 Sum_probs=21.2
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
--.|..|....... ..=+|++||.+|-.
T Consensus 220 ~~~C~~C~~~~~~~----------~~~~CpRC~~~Ly~ 247 (418)
T COG2995 220 LRSCLCCHYILPHD----------AEPRCPRCGSKLYV 247 (418)
T ss_pred ceecccccccCCHh----------hCCCCCCCCChhhc
Confidence 34689998776653 35799999999954
No 406
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=26.93 E-value=58 Score=31.90 Aligned_cols=22 Identities=23% Similarity=0.449 Sum_probs=15.0
Q ss_pred eeecCCCCcccc--HHH-HHhhcCC
Q 020131 17 EYICPNCQRRYN--ALD-ALRLVSL 38 (330)
Q Consensus 17 ~Y~CP~C~~~YT--~lD-A~~Lld~ 38 (330)
.|+||.|+.-|- .-+ ...|+|+
T Consensus 46 ~~vc~~c~~h~rl~areRi~~L~D~ 70 (292)
T PRK05654 46 LNVCPKCGHHMRISARERLDLLLDE 70 (292)
T ss_pred CCCCCCCCCCeeCCHHHHHHHHccC
Confidence 589999999875 223 3345676
No 407
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=26.74 E-value=28 Score=26.40 Aligned_cols=12 Identities=25% Similarity=0.808 Sum_probs=10.2
Q ss_pred eccCCCcccccc
Q 020131 44 HCENCNGELVAE 55 (330)
Q Consensus 44 ~C~~Cg~eL~~~ 55 (330)
+|++||.++..+
T Consensus 5 HC~~CG~~Ip~~ 16 (59)
T PF09889_consen 5 HCPVCGKPIPPD 16 (59)
T ss_pred cCCcCCCcCCcc
Confidence 799999999754
No 408
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=26.71 E-value=53 Score=31.96 Aligned_cols=48 Identities=23% Similarity=0.364 Sum_probs=30.4
Q ss_pred CeeecCCC----------------CccccHHHHHhhcCCCCCCeeccCCCccccccchhhhhhcCCCC
Q 020131 16 QEYICPNC----------------QRRYNALDALRLVSLEDDSFHCENCNGELVAESDKLAAQEGGDG 67 (330)
Q Consensus 16 ~~Y~CP~C----------------~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~~~~~~e~~~g 67 (330)
..|+||.| |..++..=|-.|| ....+|+.|+.+|.+. +-+..+-+|-|
T Consensus 220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEkli---r~D~v~pv~d~plkdr-diI~LqrGGTG 283 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLI---RKDMVDPVTDKPLKDR-DIIGLQRGGTG 283 (303)
T ss_pred cceecccchhhhcCccceEEeccCCcEeeHHHHHHhc---cccccccCCCCcCccc-ceEeeeccccc
Confidence 68999975 4555555555553 3578999999999654 33333433333
No 409
>PF02005 TRM: N2,N2-dimethylguanosine tRNA methyltransferase; InterPro: IPR002905 This enzyme 2.1.1.32 from EC uses S-adenosyl-L-methionine to methylate tRNA: S-AdoMet + tRNA = S-adenosyl-L-homocysteine + tRNA containing N2-methylguanine The TRM1 gene of Saccharomyces cerevisiae is necessary for the N2,N2-dimethylguanosine modification of both mitochondrial and cytoplasmic tRNAs []. The enzyme is found in both eukaryotes and archaea [].; GO: 0003723 RNA binding, 0004809 tRNA (guanine-N2-)-methyltransferase activity, 0008033 tRNA processing; PDB: 2YTZ_B 2DUL_A 2EJU_A 2EJT_A 3AXT_A 3AXS_A.
Probab=26.68 E-value=21 Score=36.07 Aligned_cols=33 Identities=27% Similarity=0.608 Sum_probs=17.2
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
-.|.|+.|+.+-... +.......|+.||..+..
T Consensus 239 ~v~~C~~C~~~~~~~------~~~~~~~~c~~cg~~~~~ 271 (377)
T PF02005_consen 239 YVYYCPSCGYREEVK------GLQKLKSKCPECGSKLHI 271 (377)
T ss_dssp EEEEETTT--EECCT-------GCC--CEETTT-SCCCE
T ss_pred EEEECCCcccccccc------CccccCCcCCCCCCccce
Confidence 368899996432111 111113789999988753
No 410
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=26.60 E-value=29 Score=24.68 Aligned_cols=21 Identities=24% Similarity=0.540 Sum_probs=14.9
Q ss_pred CCCeeecCCCCccccHHHHHh
Q 020131 14 TVQEYICPNCQRRYNALDALR 34 (330)
Q Consensus 14 ~~~~Y~CP~C~~~YT~lDA~~ 34 (330)
+...=+||.|++-||---.+.
T Consensus 5 ~lp~K~C~~C~rpf~WRKKW~ 25 (42)
T PF10013_consen 5 NLPSKICPVCGRPFTWRKKWA 25 (42)
T ss_pred cCCCCcCcccCCcchHHHHHH
Confidence 344568999999998654443
No 411
>TIGR00396 leuS_bact leucyl-tRNA synthetase, eubacterial and mitochondrial family. The leucyl-tRNA synthetases belong to two families so broadly different that they are represented by separate models. This model includes both eubacterial and mitochondrial leucyl-tRNA synthetases. It generates higher scores for some valyl-tRNA synthetases than for any archaeal or eukaryotic cytosolic leucyl-tRNA synthetase. Note that the enzyme from Aquifex aeolicus is split into alpha and beta chains; neither chain is long enough to score above the trusted cutoff, but the alpha chain scores well above the noise cutoff. The beta chain must be found by a model and search designed for partial length matches.
Probab=26.50 E-value=43 Score=37.33 Aligned_cols=38 Identities=8% Similarity=-0.062 Sum_probs=29.0
Q ss_pred hhcCCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 10 ECKNTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 10 ~~~~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
=+......+.||.|++-.+..++.. .-.|.+||.+++.
T Consensus 145 iy~~~~~v~wcp~~~t~La~~ev~~-------~g~~~~~g~~v~~ 182 (842)
T TIGR00396 145 AYVKEADVNWCPNDGTVLANEQVDS-------DGRSWRGGTPVEK 182 (842)
T ss_pred eEeeccceEEeCCCCCCccHHHHhh-------cCccccCCCcceE
Confidence 3455667899999999999988821 1389999998743
No 412
>smart00350 MCM minichromosome maintenance proteins.
Probab=26.38 E-value=26 Score=36.53 Aligned_cols=34 Identities=12% Similarity=0.334 Sum_probs=21.6
Q ss_pred CCCeeecCCCCccccHHHHHhhcCCCCCCeeccC--CCc
Q 020131 14 TVQEYICPNCQRRYNALDALRLVSLEDDSFHCEN--CNG 50 (330)
Q Consensus 14 ~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~--Cg~ 50 (330)
....|.|..|+..+...--...+. ..+.|+. |+.
T Consensus 34 ~~~~f~C~~C~~~~~~~~~~~~~~---~p~~C~~~~C~~ 69 (509)
T smart00350 34 KRASFTCEKCGATLGPEIQSGRET---EPTVCPPRECQS 69 (509)
T ss_pred EEEEEEecCCCCEEeEEecCCccc---CCCcCCCCcCCC
Confidence 345899999998775431111122 2468998 985
No 413
>TIGR00201 comF comF family protein. This protein is found in species that do (Bacillus subtilis, Haemophilus influenzae) or do not (E. coli, Borrelia burgdorferi) have described systems for natural transformation with exogenous DNA. It is involved in competence for transformation in Bacillus subtilis.
Probab=25.80 E-value=31 Score=30.94 Aligned_cols=23 Identities=26% Similarity=0.637 Sum_probs=14.0
Q ss_pred cCCCCccccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 20 CPNCQRRYNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 20 CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
|+.|++-+.. ....|+.|...|.
T Consensus 1 C~~C~~~~~~-----------~~~~C~~C~~~~~ 23 (190)
T TIGR00201 1 CSLCGRPYQS-----------VHALCRQCGSWRT 23 (190)
T ss_pred CCcccccccc-----------ccCCchhhCCccc
Confidence 7777764321 1357777777664
No 414
>TIGR00382 clpX endopeptidase Clp ATP-binding regulatory subunit (clpX). A member of the ATP-dependent proteases, ClpX has ATP-dependent chaperone activity and is required for specific ATP-dependent proteolytic activities expressed by ClpPX. The gene is also found to be involved in stress tolerance in Bacillus subtilis and is essential for the efficient acquisition of genes specifying type IA and IB restriction.
Probab=25.58 E-value=34 Score=35.08 Aligned_cols=29 Identities=17% Similarity=0.590 Sum_probs=21.7
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCC
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCN 49 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg 49 (330)
..|..||+.-.. +..|+.-. +.|+|..|=
T Consensus 8 ~~c~fc~~~~~~--~~~~~~~~-~~~ic~~c~ 36 (413)
T TIGR00382 8 LYCSFCGKSQDE--VRKLIAGP-GVYICDECI 36 (413)
T ss_pred eecCCCCCChhh--cccccCCC-CCcCCCchH
Confidence 479999997654 66666543 469999995
No 415
>TIGR01054 rgy reverse gyrase. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.
Probab=25.58 E-value=35 Score=39.47 Aligned_cols=25 Identities=20% Similarity=0.610 Sum_probs=16.1
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
.|+.||..|+.. .=.||+|+.....
T Consensus 680 ~~~~~~~~f~~~-----------~~~~p~~~~~~~~ 704 (1171)
T TIGR01054 680 RCRDCGYQFTED-----------RESCPKCGSENIE 704 (1171)
T ss_pred cCCchhhhcccc-----------ccccccccccccc
Confidence 377777777651 1278999866543
No 416
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=25.42 E-value=41 Score=25.38 Aligned_cols=23 Identities=26% Similarity=0.545 Sum_probs=15.8
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNG 50 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~ 50 (330)
..=+||+||..--. .-+|..||.
T Consensus 26 ~~~~c~~cG~~~l~------------Hrvc~~cg~ 48 (57)
T COG0333 26 TLSVCPNCGEYKLP------------HRVCLKCGY 48 (57)
T ss_pred cceeccCCCCcccC------------ceEcCCCCC
Confidence 35689999875322 568888884
No 417
>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=25.41 E-value=30 Score=34.87 Aligned_cols=31 Identities=26% Similarity=0.582 Sum_probs=18.7
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
.|.|+.|+.+... ..+.+ ..-.|+.||+.+.
T Consensus 233 v~~C~~c~~~~~~----~~~~~--~~~~C~~c~~~~~ 263 (374)
T TIGR00308 233 TYHCSRCLHNKPV----NGISQ--RKGRCKECGGEYH 263 (374)
T ss_pred EEECCCccccccc----ccccC--CCCCCCCCCCcce
Confidence 4569999765431 11111 2347999998764
No 418
>PF05741 zf-nanos: Nanos RNA binding domain; InterPro: IPR024161 Nanos is a highly conserved RNA-binding protein in higher eukaryotes and functions as a key regulatory protein in translational control using a 3' untranslated region during the development and maintenance of germ cells. Nanos comprises a non-conserved amino-terminus and highly conserved carboxy- terminal regions. The C-terminal region has two conserved Cys-Cys-His-Cys (CCHC)-type zinc-finger motifs that are indispensable for nanos function [, , ]. The structure of the nanos-type zinc finger is composed of two independent zinc-finger (ZF) lobes, the N-terminal ZF1 and the C-terminal ZF2, which are connected by a linker helix []. These lobes create a large cleft. Zinc ions in ZF1 and ZF2 are bound to the CCHC motif by tetrahedral coordination.; PDB: 3ALR_B.
Probab=25.37 E-value=28 Score=26.10 Aligned_cols=10 Identities=40% Similarity=1.268 Sum_probs=3.4
Q ss_pred eeecCCCCcc
Q 020131 17 EYICPNCQRR 26 (330)
Q Consensus 17 ~Y~CP~C~~~ 26 (330)
.|+||.||++
T Consensus 33 ~y~Cp~CgAt 42 (55)
T PF05741_consen 33 KYVCPICGAT 42 (55)
T ss_dssp G---TTT---
T ss_pred cCcCCCCcCc
Confidence 5899999985
No 419
>KOG4021 consensus Mitochondrial ribosomal protein S18b [Translation, ribosomal structure and biogenesis]
Probab=25.35 E-value=35 Score=32.02 Aligned_cols=75 Identities=15% Similarity=0.264 Sum_probs=43.3
Q ss_pred eeecCCCCccccHHHHH--hhcCCCCCCeeccCCCccccccchhhhhhcCCCCChhHHHHHHHHHHHHHHHHHHhHHHHH
Q 020131 17 EYICPNCQRRYNALDAL--RLVSLEDDSFHCENCNGELVAESDKLAAQEGGDGDDNARRRRREKLKDLLQKLEVHLKPLM 94 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~--~Lld~~~~~F~C~~Cg~eL~~~~~~~~~~e~~~g~~na~r~~~e~~k~~l~r~n~QlkpI~ 94 (330)
+--||.|--.|-.+|-- .|| ..|+|+.-|.++..-... -.+.+-.||+.+|..-.
T Consensus 108 gnpCPICRDeyL~~DyRN~~Ll----EQF~~~htg~~i~y~ktG-------------------lC~kqh~rL~~a~qkAr 164 (239)
T KOG4021|consen 108 GNPCPICRDEYLYFDYRNPGLL----EQFLADHTGQPIDYLKTG-------------------LCRKQHTRLRAALQKAR 164 (239)
T ss_pred CCCCCccccceEEEeccCHHHH----HHHhccCCCCchhhhhcc-------------------hHHHHHHHHHHHHHHhh
Confidence 45699999988765543 233 379999999888553221 11334466666665444
Q ss_pred HHHHhhcCcCCCCCCcHHHHH
Q 020131 95 EQINRVKDLDVPEFGTLQAWE 115 (330)
Q Consensus 95 ~~Lk~id~i~iP~f~~~~aw~ 115 (330)
+.=--+=+|++-.|+ +..|-
T Consensus 165 dhG~lty~VpfR~~D-ys~~y 184 (239)
T KOG4021|consen 165 DHGTLTYGVPFRNFD-YSQWY 184 (239)
T ss_pred hcCeEEecCCcccCc-hHHhc
Confidence 433333334444577 35554
No 420
>COG1933 Archaeal DNA polymerase II, large subunit [DNA replication, recombination, and repair]
Probab=25.07 E-value=27 Score=33.59 Aligned_cols=35 Identities=26% Similarity=0.589 Sum_probs=24.7
Q ss_pred CCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccch
Q 020131 14 TVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESD 57 (330)
Q Consensus 14 ~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~ 57 (330)
.++.|.|..|+++|-- -| -.-.|+.||+.|.--..
T Consensus 164 ~rq~~rc~~c~~k~rr-------~p--l~g~c~kcg~~~~ltv~ 198 (253)
T COG1933 164 TRQEFRCVKCNTKFRR-------PP--LDGKCPICGGKIVLTVS 198 (253)
T ss_pred hhheeehHhhhhhhcC-------CC--ccccccccCCeEEEEEe
Confidence 3567888889988864 12 24689999998865444
No 421
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=25.02 E-value=38 Score=28.51 Aligned_cols=16 Identities=19% Similarity=0.696 Sum_probs=12.3
Q ss_pred CCeeecCCCCccccHH
Q 020131 15 VQEYICPNCQRRYNAL 30 (330)
Q Consensus 15 ~~~Y~CP~C~~~YT~l 30 (330)
+..-+||.||..|...
T Consensus 24 k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 24 KDPIVCPKCGTEFPPE 39 (108)
T ss_pred CCCccCCCCCCccCcc
Confidence 3445799999999875
No 422
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=24.86 E-value=37 Score=26.69 Aligned_cols=39 Identities=21% Similarity=0.576 Sum_probs=19.4
Q ss_pred eecCCCCccccHHHHHhhcC-CCCCCeecc--CCCccccccc
Q 020131 18 YICPNCQRRYNALDALRLVS-LEDDSFHCE--NCNGELVAES 56 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld-~~~~~F~C~--~Cg~eL~~~~ 56 (330)
+.||.||..-..-+...+-+ ...-.+.|. .||...+-..
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF~t~e 43 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDTTKERYHQCQNVNCSATFITYE 43 (72)
T ss_pred ccCCCCCCccEEEEChhcChhhheeeeecCCCCCCCEEEEEE
Confidence 56888877552211111100 111257787 7887665443
No 423
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=24.58 E-value=43 Score=28.06 Aligned_cols=32 Identities=22% Similarity=0.555 Sum_probs=21.1
Q ss_pred CCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 14 TVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 14 ~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
....|.|+.||...-. ..|- ..-.||.||..-
T Consensus 39 G~~~~~C~~Cg~~~~~-----~~SC--k~R~CP~C~~~~ 70 (111)
T PF14319_consen 39 GFHRYRCEDCGHEKIV-----YNSC--KNRHCPSCQAKA 70 (111)
T ss_pred CcceeecCCCCceEEe-----cCcc--cCcCCCCCCChH
Confidence 3457899999987633 2232 245888888765
No 424
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=24.58 E-value=46 Score=30.61 Aligned_cols=31 Identities=16% Similarity=0.657 Sum_probs=20.6
Q ss_pred CeeecCCCCccccHHHHHhhcCCCC-CCeeccCCCccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLED-DSFHCENCNGEL 52 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~-~~F~C~~Cg~eL 52 (330)
.+|+|..|+.. .. ++-+.. ..+.|+.|++.-
T Consensus 151 kGfiCe~C~~~-~~-----IfPF~~~~~~~C~~C~~v~ 182 (202)
T PF13901_consen 151 KGFICEICNSD-DI-----IFPFQIDTTVRCPKCKSVF 182 (202)
T ss_pred CCCCCccCCCC-CC-----CCCCCCCCeeeCCcCcccc
Confidence 47889999764 32 333333 678999998754
No 425
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=24.55 E-value=44 Score=27.41 Aligned_cols=23 Identities=13% Similarity=0.426 Sum_probs=15.3
Q ss_pred CCCeeecCCCCccccHHHHHhhc
Q 020131 14 TVQEYICPNCQRRYNALDALRLV 36 (330)
Q Consensus 14 ~~~~Y~CP~C~~~YT~lDA~~Ll 36 (330)
+..-++|+.||-.|-..++..-+
T Consensus 32 nVPa~~C~~CGe~y~~dev~~eI 54 (89)
T TIGR03829 32 ETPSISCSHCGMEYQDDTTVKEI 54 (89)
T ss_pred cCCcccccCCCcEeecHHHHHHH
Confidence 44567777777777766666543
No 426
>PHA02325 hypothetical protein
Probab=24.53 E-value=31 Score=26.85 Aligned_cols=11 Identities=45% Similarity=1.135 Sum_probs=9.1
Q ss_pred eecCCCCcccc
Q 020131 18 YICPNCQRRYN 28 (330)
Q Consensus 18 Y~CP~C~~~YT 28 (330)
-+||.|+++|-
T Consensus 4 k~CPkC~A~Wl 14 (72)
T PHA02325 4 KICPKCGARWL 14 (72)
T ss_pred cccCccCCEeE
Confidence 47999999884
No 427
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=24.46 E-value=62 Score=29.18 Aligned_cols=40 Identities=23% Similarity=0.468 Sum_probs=23.4
Q ss_pred ecCCCCcc----ccHHHHHhhcCCCCCCeeccCCCccccccchh
Q 020131 19 ICPNCQRR----YNALDALRLVSLEDDSFHCENCNGELVAESDK 58 (330)
Q Consensus 19 ~CP~C~~~----YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~~ 58 (330)
.||+|+.- |-...+..+-.+..-.--|.+||.+.-=-.+.
T Consensus 41 ~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpyPWt~~~ 84 (158)
T PF10083_consen 41 SCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPYPWTENA 84 (158)
T ss_pred HCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCCchHHHH
Confidence 58999874 44444444422222345799999876443333
No 428
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=24.32 E-value=42 Score=21.38 Aligned_cols=11 Identities=18% Similarity=0.845 Sum_probs=6.9
Q ss_pred eecCCCCcccc
Q 020131 18 YICPNCQRRYN 28 (330)
Q Consensus 18 Y~CP~C~~~YT 28 (330)
|.|..|++.|+
T Consensus 4 ~~C~~C~~~~~ 14 (35)
T smart00451 4 FYCKLCNVTFT 14 (35)
T ss_pred eEccccCCccC
Confidence 55666666666
No 429
>TIGR00618 sbcc exonuclease SbcC. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=24.28 E-value=61 Score=36.75 Aligned_cols=37 Identities=16% Similarity=0.067 Sum_probs=25.5
Q ss_pred CeeecCCCCccccHHHHH-hhcCCCCCCeeccCCCcccccc
Q 020131 16 QEYICPNCQRRYNALDAL-RLVSLEDDSFHCENCNGELVAE 55 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~-~Lld~~~~~F~C~~Cg~eL~~~ 55 (330)
.+=-||.||+.-.+.... .++.| .=.|+.|...+...
T Consensus 500 ~~~~cplcgs~~hp~~~~~~~~~~---~~~~~~~~~~~~~~ 537 (1042)
T TIGR00618 500 QEEPCPLCGSCIHPNPARQDIDNP---GPLTRRMQRGEQTY 537 (1042)
T ss_pred CCCCCCCCCCCCCCChhhccCCCC---CHHHHHHHHHHHHH
Confidence 356799999988874443 34443 35899999888553
No 430
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=24.15 E-value=31 Score=32.45 Aligned_cols=13 Identities=31% Similarity=0.782 Sum_probs=11.3
Q ss_pred CeeccCCCccccc
Q 020131 42 SFHCENCNGELVA 54 (330)
Q Consensus 42 ~F~C~~Cg~eL~~ 54 (330)
.|.||.|+.+|..
T Consensus 2 ~~~CP~C~~~l~~ 14 (272)
T PRK11088 2 SYQCPLCHQPLTL 14 (272)
T ss_pred cccCCCCCcchhc
Confidence 4999999999963
No 431
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=24.12 E-value=41 Score=34.17 Aligned_cols=29 Identities=28% Similarity=0.547 Sum_probs=21.0
Q ss_pred eeecCCCCccc-cHHHHHhhcCCCCCCeeccCCCc
Q 020131 17 EYICPNCQRRY-NALDALRLVSLEDDSFHCENCNG 50 (330)
Q Consensus 17 ~Y~CP~C~~~Y-T~lDA~~Lld~~~~~F~C~~Cg~ 50 (330)
.+.||.|+-+- |+ .+++..+.|+|-.||.
T Consensus 34 ~~~CPfh~ek~pSf-----~v~~~k~~~~Cf~Cg~ 63 (415)
T TIGR01391 34 VGLCPFHHEKTPSF-----SVSPEKQFYHCFGCGA 63 (415)
T ss_pred EeeCCCCCCCCCeE-----EEEcCCCcEEECCCCC
Confidence 45799997652 22 4567788899999984
No 432
>PF11494 Ta0938: Ta0938; InterPro: IPR021585 Ta0938 is a protein of unknown function however the structure has been determined. The protein has a novel fold and a putative Zn-binding motif. The structure has two different parts, one region contains a beta sheet flanked by two alpha helices and the other contains a bundle of loops which contain all cysteines in the protein. ; PDB: 2FQH_A.
Probab=24.09 E-value=25 Score=29.37 Aligned_cols=36 Identities=28% Similarity=0.516 Sum_probs=15.7
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
+.--|..||++|. +..+-++-..--|-|..|-.+..
T Consensus 13 ke~~CalCG~tWg--~~y~Ev~G~rLfFCCd~ca~EF~ 48 (105)
T PF11494_consen 13 KEMGCALCGATWG--DYYEEVDGERLFFCCDDCAKEFK 48 (105)
T ss_dssp GGGS-SS---S-----SS-B-TT--BSSS--SSSS-TT
T ss_pred ccccccccCCcHH--HHHHhhcCCEEEEEcHHHHHHHH
Confidence 4567999999998 45555555555799999986664
No 433
>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=24.08 E-value=30 Score=27.56 Aligned_cols=11 Identities=45% Similarity=0.978 Sum_probs=3.8
Q ss_pred CCeeccCCCcc
Q 020131 41 DSFHCENCNGE 51 (330)
Q Consensus 41 ~~F~C~~Cg~e 51 (330)
..|.||+||+.
T Consensus 21 ~~F~CPfC~~~ 31 (81)
T PF05129_consen 21 KVFDCPFCNHE 31 (81)
T ss_dssp S----TTT--S
T ss_pred ceEcCCcCCCC
Confidence 47999999954
No 434
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=23.77 E-value=38 Score=31.28 Aligned_cols=23 Identities=26% Similarity=0.442 Sum_probs=17.0
Q ss_pred CeeecCCCCccccHHHHHhhcCC
Q 020131 16 QEYICPNCQRRYNALDALRLVSL 38 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~ 38 (330)
..|.|+.||.+++......-+.|
T Consensus 29 ~sf~C~~CGyr~~ev~~~g~~~p 51 (192)
T TIGR00310 29 TSTICEHCGYRSNDVKTLGAKEP 51 (192)
T ss_pred EEEECCCCCCccceeEECCCCCC
Confidence 57999999999987654444444
No 435
>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional
Probab=23.37 E-value=37 Score=36.76 Aligned_cols=19 Identities=16% Similarity=0.385 Sum_probs=13.0
Q ss_pred CCCCCCchhhhcccccccc
Q 020131 176 PQKVLPPWMIKQGMNLTKE 194 (330)
Q Consensus 176 ~qnaLP~Wm~~Stv~l~~e 194 (330)
.-+..|.||.=+.+.+-.-
T Consensus 237 ~~~~~PewmiL~~lPV~Pp 255 (627)
T PRK02625 237 ATGSRPEWMVLDVIPVIPP 255 (627)
T ss_pred hcCCCccEEEEEeeecCCC
Confidence 5567888888776655443
No 436
>PRK05342 clpX ATP-dependent protease ATP-binding subunit ClpX; Provisional
Probab=23.26 E-value=43 Score=34.24 Aligned_cols=32 Identities=16% Similarity=0.538 Sum_probs=23.4
Q ss_pred CCCeeecCCCCccccHHHHHhhcCCCCCCeeccCC
Q 020131 14 TVQEYICPNCQRRYNALDALRLVSLEDDSFHCENC 48 (330)
Q Consensus 14 ~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~C 48 (330)
+....+|..||+.-.. +..|+.-. +.|+|..|
T Consensus 6 ~~~~~~CSFCGr~~~e--v~~li~g~-~~~IC~~C 37 (412)
T PRK05342 6 SKKLLYCSFCGKSQHE--VRKLIAGP-GVYICDEC 37 (412)
T ss_pred CCCccccCCCCCChhh--ccccccCC-CCcccchH
Confidence 3445689999998544 66666653 57999999
No 437
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=23.20 E-value=24 Score=29.51 Aligned_cols=32 Identities=25% Similarity=0.535 Sum_probs=20.2
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
-+|-.|+..... .++..-|.|+|..|.+.-..
T Consensus 14 ~~CaDCg~~~p~-----w~s~~~GiflC~~Cag~HR~ 45 (116)
T PF01412_consen 14 KVCADCGAPNPT-----WASLNYGIFLCLECAGIHRS 45 (116)
T ss_dssp TB-TTT-SBS-------EEETTTTEEE-HHHHHHHHH
T ss_pred CcCCCCCCCCCC-----EEEeecChhhhHHHHHHHHH
Confidence 579999988773 55555689999999866533
No 438
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.17 E-value=25 Score=25.90 Aligned_cols=16 Identities=38% Similarity=0.833 Sum_probs=12.1
Q ss_pred CeeecCCCCccccHHH
Q 020131 16 QEYICPNCQRRYNALD 31 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lD 31 (330)
.--|||.|++-|+---
T Consensus 11 p~KICpvCqRPFsWRk 26 (54)
T COG4338 11 PDKICPVCQRPFSWRK 26 (54)
T ss_pred chhhhhhhcCchHHHH
Confidence 3458999999998543
No 439
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=23.17 E-value=39 Score=31.65 Aligned_cols=14 Identities=14% Similarity=0.446 Sum_probs=11.1
Q ss_pred CCeeccCCCccccc
Q 020131 41 DSFHCENCNGELVA 54 (330)
Q Consensus 41 ~~F~C~~Cg~eL~~ 54 (330)
....|+.||.-+..
T Consensus 34 ~v~~C~~Cg~~~~~ 47 (236)
T PF04981_consen 34 EVTICPKCGRYRIG 47 (236)
T ss_pred CceECCCCCCEECC
Confidence 46799999987754
No 440
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=23.10 E-value=46 Score=32.51 Aligned_cols=27 Identities=26% Similarity=0.572 Sum_probs=17.1
Q ss_pred eeecCCCCcccc--HHHHH-hhcCCCCCCeec
Q 020131 17 EYICPNCQRRYN--ALDAL-RLVSLEDDSFHC 45 (330)
Q Consensus 17 ~Y~CP~C~~~YT--~lDA~-~Lld~~~~~F~C 45 (330)
.|+||.|+..|- .-+-. .|+|+ +.|.-
T Consensus 45 ~~vc~~c~~h~rl~areRi~~L~D~--gsF~E 74 (285)
T TIGR00515 45 LEVCPKCDHHMRMDARERIESLLDE--GSFEE 74 (285)
T ss_pred CCCCCCCCCcCcCCHHHHHHHceeC--CeeEE
Confidence 699999998764 33333 35665 34543
No 441
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=23.04 E-value=37 Score=35.03 Aligned_cols=13 Identities=23% Similarity=0.685 Sum_probs=12.0
Q ss_pred eeecCCCCccccH
Q 020131 17 EYICPNCQRRYNA 29 (330)
Q Consensus 17 ~Y~CP~C~~~YT~ 29 (330)
+|+||.||++|..
T Consensus 367 g~rC~kCg~~~~~ 379 (421)
T COG1571 367 GFRCKKCGTRARE 379 (421)
T ss_pred CcccccccccCCc
Confidence 9999999999975
No 442
>PRK07219 DNA topoisomerase I; Validated
Probab=22.89 E-value=34 Score=37.98 Aligned_cols=32 Identities=28% Similarity=0.592 Sum_probs=18.4
Q ss_pred eeecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 17 EYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
++.||.|...-.... +......||.||+.|..
T Consensus 669 ~~~CP~C~~~~~~~~------~~~~~~~CP~Cg~~l~~ 700 (822)
T PRK07219 669 VVGCPDCEAEKEEED------PDEVIGPCPKCGGELAI 700 (822)
T ss_pred cccCCCCCCCccccc------cccccccCCCCCCeeEE
Confidence 344777764432211 11125789999988765
No 443
>PRK03922 hypothetical protein; Provisional
Probab=22.82 E-value=28 Score=29.69 Aligned_cols=14 Identities=14% Similarity=0.292 Sum_probs=10.3
Q ss_pred CCCeeccCCCcccc
Q 020131 40 DDSFHCENCNGELV 53 (330)
Q Consensus 40 ~~~F~C~~Cg~eL~ 53 (330)
.|.-.||.||.++.
T Consensus 47 vG~~~cP~cge~~~ 60 (113)
T PRK03922 47 VGLTICPKCGEPFD 60 (113)
T ss_pred cCcccCCCCCCcCC
Confidence 45568888888774
No 444
>PRK00133 metG methionyl-tRNA synthetase; Reviewed
Probab=22.79 E-value=33 Score=37.02 Aligned_cols=16 Identities=13% Similarity=0.079 Sum_probs=9.6
Q ss_pred CCCeeecCCCCccccH
Q 020131 14 TVQEYICPNCQRRYNA 29 (330)
Q Consensus 14 ~~~~Y~CP~C~~~YT~ 29 (330)
....|.||.|++-++.
T Consensus 120 ~~~~~y~~~~~~~l~~ 135 (673)
T PRK00133 120 TIEQLYDPEKGMFLPD 135 (673)
T ss_pred eeEEEEeCCCCCCccc
Confidence 3446666666665554
No 445
>PF10276 zf-CHCC: Zinc-finger domain; InterPro: IPR019401 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 short conserved zinc-finger domain. It contains the sequence motif Cx8Hx14Cx2C. ; PDB: 2JVM_A 2JRR_A 2JZ8_A.
Probab=22.74 E-value=34 Score=23.93 Aligned_cols=11 Identities=45% Similarity=1.271 Sum_probs=9.5
Q ss_pred eeecCCCCccc
Q 020131 17 EYICPNCQRRY 27 (330)
Q Consensus 17 ~Y~CP~C~~~Y 27 (330)
.-.||-|+++|
T Consensus 29 ~~~CpYCg~~y 39 (40)
T PF10276_consen 29 PVVCPYCGTRY 39 (40)
T ss_dssp EEEETTTTEEE
T ss_pred eEECCCCCCEE
Confidence 57899999988
No 446
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=22.73 E-value=41 Score=30.11 Aligned_cols=33 Identities=12% Similarity=0.241 Sum_probs=21.4
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCC
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENC 48 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~C 48 (330)
+.|.||.||.+++......-+.|..-.+.+...
T Consensus 28 ~sf~C~~CGyk~~ev~~~~~~~p~G~r~~l~V~ 60 (160)
T smart00709 28 MSFECEHCGYRNNEVKSGGAIEPKGTRITLKVE 60 (160)
T ss_pred EEEECCCCCCccceEEECcccCCCceEEEEEEC
Confidence 579999999999876555555554223444433
No 447
>PRK00390 leuS leucyl-tRNA synthetase; Validated
Probab=22.48 E-value=53 Score=36.38 Aligned_cols=39 Identities=13% Similarity=0.230 Sum_probs=29.9
Q ss_pred HhhcCCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcccccc
Q 020131 9 LECKNTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAE 55 (330)
Q Consensus 9 l~~~~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~ 55 (330)
+=+......|.||.|++-.+..|+.. -.|++||.+++..
T Consensus 147 liy~~~~~v~wcp~~~t~La~~ev~~--------~~~~~~~~~~~~~ 185 (805)
T PRK00390 147 LAYRKESPVNWCPVDGTVLANEQVID--------GRCWRCGAPVEKK 185 (805)
T ss_pred CEEEecCEEEecCCcCCCCCHHHhhC--------CeecccCCeeEEE
Confidence 33445667889999999999988751 2599999988654
No 448
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=22.41 E-value=43 Score=25.65 Aligned_cols=19 Identities=26% Similarity=0.831 Sum_probs=14.8
Q ss_pred eeecCCCCccccHHHHHhh
Q 020131 17 EYICPNCQRRYNALDALRL 35 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~L 35 (330)
.|.|+.|++.|....++..
T Consensus 50 ~~~C~~C~~~f~s~~~l~~ 68 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQE 68 (100)
T ss_dssp SEEBSSSS-EESSHHHHHH
T ss_pred CCCCCccCCCCcCHHHHHH
Confidence 5999999999987777764
No 449
>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=22.08 E-value=42 Score=30.22 Aligned_cols=22 Identities=27% Similarity=0.520 Sum_probs=15.7
Q ss_pred CeeecCCCCccccHHHHHhhcC
Q 020131 16 QEYICPNCQRRYNALDALRLVS 37 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld 37 (330)
+.|.|+.||.+++......-+.
T Consensus 27 ~sf~C~~CGyr~~ev~~~~~~~ 48 (163)
T TIGR00340 27 STYICEKCGYRSTDVYQLEEKE 48 (163)
T ss_pred EEEECCCCCCchhheeEcCCcC
Confidence 5799999999998654433333
No 450
>PHA02565 49 recombination endonuclease VII; Provisional
Probab=22.05 E-value=29 Score=31.26 Aligned_cols=42 Identities=21% Similarity=0.378 Sum_probs=25.1
Q ss_pred CCCeeecCCCCccccHH-HHHhhcCC-------CCC---CeeccCCCccccccc
Q 020131 14 TVQEYICPNCQRRYNAL-DALRLVSL-------EDD---SFHCENCNGELVAES 56 (330)
Q Consensus 14 ~~~~Y~CP~C~~~YT~l-DA~~Lld~-------~~~---~F~C~~Cg~eL~~~~ 56 (330)
..+.-.||.|+..+... ... .+|. .+| +.+|..|+.-|-...
T Consensus 17 e~Q~G~CaiC~~~l~~~~~~~-~vDHDH~l~g~~TG~VRGLLC~~CN~~lG~~~ 69 (157)
T PHA02565 17 EAQNGICPLCKRELDGDVSKN-HLDHDHELNGPNAGRVRGLLCNLCNALEGQMK 69 (157)
T ss_pred HHhCCcCCCCCCccCCCcccc-ccCCCCCCCCcccccccccCchhhhhhhhhhh
Confidence 34678999999886521 111 2333 222 368999998664443
No 451
>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=22.02 E-value=38 Score=23.20 Aligned_cols=14 Identities=36% Similarity=0.878 Sum_probs=10.8
Q ss_pred eccCCCccccccch
Q 020131 44 HCENCNGELVAESD 57 (330)
Q Consensus 44 ~C~~Cg~eL~~~~~ 57 (330)
.||.||+.|+....
T Consensus 3 ~CP~Cg~~lv~r~~ 16 (39)
T PF01396_consen 3 KCPKCGGPLVLRRG 16 (39)
T ss_pred CCCCCCceeEEEEC
Confidence 59999999876543
No 452
>PHA02562 46 endonuclease subunit; Provisional
Probab=22.00 E-value=1.3e+02 Score=31.00 Aligned_cols=14 Identities=14% Similarity=0.439 Sum_probs=9.5
Q ss_pred CeeccCCCcccccc
Q 020131 42 SFHCENCNGELVAE 55 (330)
Q Consensus 42 ~F~C~~Cg~eL~~~ 55 (330)
.-.||.|+..+...
T Consensus 284 ~~~Cp~C~~~~~~~ 297 (562)
T PHA02562 284 GGVCPTCTQQISEG 297 (562)
T ss_pred CCCCCCCCCcCCCc
Confidence 34788888777543
No 453
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=21.89 E-value=38 Score=23.23 Aligned_cols=30 Identities=17% Similarity=0.468 Sum_probs=13.2
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCcc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGE 51 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~e 51 (330)
.|.+|+.-... .-.|+.....|+|..|+..
T Consensus 4 rC~~C~aylNp---~~~~~~~~~~w~C~~C~~~ 33 (40)
T PF04810_consen 4 RCRRCRAYLNP---FCQFDDGGKTWICNFCGTK 33 (40)
T ss_dssp B-TTT--BS-T---TSEEETTTTEEEETTT--E
T ss_pred ccCCCCCEECC---cceEcCCCCEEECcCCCCc
Confidence 46666654332 1123334457999999874
No 454
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=21.71 E-value=46 Score=24.52 Aligned_cols=34 Identities=15% Similarity=0.383 Sum_probs=20.9
Q ss_pred CeeecCCCCccccHHHHHhhcCCCCCCeeccCCCccc
Q 020131 16 QEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGEL 52 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL 52 (330)
=+|-| |||-.|...+..-- .. ....-|+.|.--+
T Consensus 17 ~~y~C-RCG~~f~i~e~~l~-~~-~~iv~C~sCSL~I 50 (55)
T PF05207_consen 17 YSYPC-RCGGEFEISEEDLE-EG-EVIVQCDSCSLWI 50 (55)
T ss_dssp EEEEE-TTSSEEEEEHHHHH-CT---EEEETTTTEEE
T ss_pred EEEcC-CCCCEEEEcchhcc-Cc-CEEEECCCCccEE
Confidence 47889 99999984333321 00 1258899997544
No 455
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=21.62 E-value=21 Score=29.94 Aligned_cols=37 Identities=19% Similarity=0.454 Sum_probs=23.0
Q ss_pred eeecCCCCcc---ccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 17 EYICPNCQRR---YNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 17 ~Y~CP~C~~~---YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
.=.||.||.. |-+|..-.-=.|++.-++|-+|+..+.
T Consensus 65 ~~~Cp~Cgh~rayF~qlQtRSADEPmT~FYkC~~C~~~Wr 104 (105)
T KOG2906|consen 65 EATCPTCGHERAYFMQLQTRSADEPMTTFYKCCKCKHRWR 104 (105)
T ss_pred cCcCCCCCCCceEEEEeeeccCCCcHhHhhhhhccccccc
Confidence 4568888763 334443333335666678999988763
No 456
>PF10186 Atg14: UV radiation resistance protein and autophagy-related subunit 14; InterPro: IPR018791 Class III phosphatidylinositol 3-kinase (PI3-kinase) regulates multiple membrane trafficking. In yeast, two distinct PI3-kinase complexes are known: complex I (Vps34, Vps15, Vps30/Atg6, and Atg14) is involved in autophagy, and complex II (Vps34, Vps15, Vps30/Atg6, and Vps38) functions in the vacuolar protein sorting pathway. In mammals, the counterparts of Vps34, Vps15, and Vps30/Atg6 are Vps34, p150, and Beclin 1, respectively. Mammalian UV irradiation resistance-associated gene (UVRAG) has been identified as identical to yeast Vps38 []. The Atg14 (autophagy-related protein 14) proteins are hydrophilic proteins and have a coiled-coil motif at the N terminus region. Yeast cells with mutant Atg14 are defective not only in autophagy but also in sorting of carboxypeptidase Y (CPY), a vacuolar-soluble hydrolase, to the vacuole []. This entry represents Atg14 and UVRAG, which bind Beclin 1 to forms two distinct PI3-kinase complexes. This entry also includes Bakor (beclin-1-associated autophagy-related key regulator), also known as autophagy-related protein 14-like protein, which share sequence similarity to the yeast Atg14 protein []. Barkor positively regulates autophagy through its interaction with Beclin-1, with decreased levels of autophagosome formation observed when Barkor expression is eliminated []. Autophagy mediates the cellular response to nutrient deprivation, protein aggregation, and pathogen invasion in humans, and malfunction of autophagy has been implicated in multiple human diseases including cancer. ; GO: 0010508 positive regulation of autophagy
Probab=21.58 E-value=30 Score=32.32 Aligned_cols=18 Identities=39% Similarity=1.004 Sum_probs=13.1
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCC
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCN 49 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg 49 (330)
.||.|+... ..|.|..|=
T Consensus 1 ~C~iC~~~~-------------~~~~C~~C~ 18 (302)
T PF10186_consen 1 QCPICHNSR-------------RRFYCANCV 18 (302)
T ss_pred CCCCCCCCC-------------CCeECHHHH
Confidence 499998332 369999995
No 457
>PRK00893 aspartate carbamoyltransferase regulatory subunit; Reviewed
Probab=21.50 E-value=32 Score=30.82 Aligned_cols=38 Identities=26% Similarity=0.571 Sum_probs=22.8
Q ss_pred eeecC--CCCcccc-HHHHH-hhcCCCCCCeeccCCCccccc
Q 020131 17 EYICP--NCQRRYN-ALDAL-RLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 17 ~Y~CP--~C~~~YT-~lDA~-~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
.++|| +|=+... ..+.. .+.+.....++|.||+..+..
T Consensus 105 i~kC~Np~CITn~~E~v~~~F~v~~~~~~~~rC~YCe~~~~~ 146 (152)
T PRK00893 105 VLKCPNPNCITNTNEPVESRFYVVDKEPIKLRCKYCEKEFSE 146 (152)
T ss_pred eEECCCCCCcCCCCcCcCcEEEEEeCCCCEEEeeCCCCEech
Confidence 57895 5766532 11111 123345568999999998854
No 458
>PF06054 CoiA: Competence protein CoiA-like family; InterPro: IPR010330 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. Many of the members of this family are described as transcription factors. CoiA falls within a competence-specific operon in Streptococcus. CoiA is an uncharacterised protein.
Probab=21.47 E-value=46 Score=33.53 Aligned_cols=18 Identities=11% Similarity=0.608 Sum_probs=14.3
Q ss_pred CCCeeccCCCccccccch
Q 020131 40 DDSFHCENCNGELVAESD 57 (330)
Q Consensus 40 ~~~F~C~~Cg~eL~~~~~ 57 (330)
.+.|.||.|+++|+....
T Consensus 28 ~~~~~CP~C~~~v~lk~G 45 (375)
T PF06054_consen 28 KGKYFCPGCGEPVILKKG 45 (375)
T ss_pred CCcEECCCCCCeeEEEEc
Confidence 468999999999986544
No 459
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=21.42 E-value=31 Score=30.06 Aligned_cols=44 Identities=20% Similarity=0.354 Sum_probs=27.7
Q ss_pred hHHHHHHhhcCCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcc
Q 020131 3 KKLKDELECKNTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGE 51 (330)
Q Consensus 3 k~Le~~l~~~~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~e 51 (330)
+.|+.-|+.-.. .+=.||.|++-=|.|.-..- ....+|.-||+.
T Consensus 84 ~~i~~~L~~yI~-~yVlC~~C~sPdT~l~k~~r----~~~l~C~ACGa~ 127 (133)
T TIGR00311 84 FLLNERIEDYVR-KYVICRECNRPDTRIIKEGR----VSLLKCEACGAK 127 (133)
T ss_pred HHHHHHHHHHHh-heEECCCCCCCCcEEEEeCC----eEEEecccCCCC
Confidence 445566655432 46679999997776553221 113599999964
No 460
>PF09567 RE_MamI: MamI restriction endonuclease; InterPro: IPR019067 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the MamI restriction endonuclease which recognises and cleaves GATNN^NNATC. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=21.30 E-value=38 Score=32.99 Aligned_cols=29 Identities=28% Similarity=0.572 Sum_probs=21.4
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccch
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESD 57 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~ 57 (330)
-+|.+||+.-+. + .-.||+||..-+...+
T Consensus 83 ~~C~~CGa~V~~-----~------e~~Cp~C~StnI~r~D 111 (314)
T PF09567_consen 83 GKCNNCGANVSR-----L------EESCPNCGSTNIKRKD 111 (314)
T ss_pred hhhccccceeee-----h------hhcCCCCCcccccccC
Confidence 479999998765 3 5689999977654443
No 461
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=20.98 E-value=33 Score=28.47 Aligned_cols=30 Identities=23% Similarity=0.464 Sum_probs=21.8
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCcccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGELV 53 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~ 53 (330)
+|-.|+..... .++..-|.|+|..|.+.-.
T Consensus 5 ~CaDC~~~~p~-----w~s~~~GifvC~~CsgiHR 34 (112)
T smart00105 5 KCFDCGAPNPT-----WASVNLGVFLCIECSGIHR 34 (112)
T ss_pred cccCCCCCCCC-----cEEeccceeEhHHhHHHHH
Confidence 69999986532 4455558999999987653
No 462
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=20.96 E-value=53 Score=32.80 Aligned_cols=25 Identities=24% Similarity=0.741 Sum_probs=16.4
Q ss_pred CCCccccHHHHHh--hcCCCCCCeeccCCCc
Q 020131 22 NCQRRYNALDALR--LVSLEDDSFHCENCNG 50 (330)
Q Consensus 22 ~C~~~YT~lDA~~--Lld~~~~~F~C~~Cg~ 50 (330)
-|+..|.. ++.. ||+. .|.|++|..
T Consensus 292 cC~~~fc~-eci~~al~ds---Df~CpnC~r 318 (427)
T COG5222 292 CCGHTFCD-ECIGTALLDS---DFKCPNCSR 318 (427)
T ss_pred cccchHHH-HHHhhhhhhc---cccCCCccc
Confidence 35666664 3333 5554 799999997
No 463
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=20.83 E-value=69 Score=35.17 Aligned_cols=38 Identities=21% Similarity=0.431 Sum_probs=24.1
Q ss_pred eeecCCCCccccHHHHHhhcCC----------CCCCeeccCCCccccc
Q 020131 17 EYICPNCQRRYNALDALRLVSL----------EDDSFHCENCNGELVA 54 (330)
Q Consensus 17 ~Y~CP~C~~~YT~lDA~~Lld~----------~~~~F~C~~Cg~eL~~ 54 (330)
-.+||.|..+|-..=....+-- .+-.=+||.||...-.
T Consensus 643 ~LkCs~Cn~R~Kd~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFga 690 (698)
T KOG0978|consen 643 LLKCSVCNTRWKDAVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGA 690 (698)
T ss_pred ceeCCCccCchhhHHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCc
Confidence 5789999999876554443210 1122389999987643
No 464
>PRK10996 thioredoxin 2; Provisional
Probab=20.82 E-value=39 Score=28.67 Aligned_cols=31 Identities=19% Similarity=0.525 Sum_probs=22.7
Q ss_pred eecCCCCcccc-HHHHHhhcCCCCCCeeccCCCccccc
Q 020131 18 YICPNCQRRYN-ALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 18 Y~CP~C~~~YT-~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
-+||.|...|. .+.+..+ .=.|+.|+..+..
T Consensus 3 ~~~~~~~~~~~~~~~~~~~------~~~~~~~~~~~~~ 34 (139)
T PRK10996 3 TVCTSCQAINRLPDERIED------AAKCGRCGHDLFD 34 (139)
T ss_pred EECCCCCCcCCCCCccccC------CCcCCCCCCccCC
Confidence 47999999986 3333333 5689999998863
No 465
>TIGR02387 rpoC1_cyan DNA-directed RNA polymerase, gamma subunit. The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''.
Probab=20.81 E-value=45 Score=36.07 Aligned_cols=20 Identities=15% Similarity=0.376 Sum_probs=14.0
Q ss_pred CCCCCCCchhhhcccccccc
Q 020131 175 TPQKVLPPWMIKQGMNLTKE 194 (330)
Q Consensus 175 ~~qnaLP~Wm~~Stv~l~~e 194 (330)
...+..|.||.=+.+.+-.-
T Consensus 229 ~~~~~~PewmiL~~lPV~Pp 248 (619)
T TIGR02387 229 IATSSRPEWMVLDVIPVIPP 248 (619)
T ss_pred HhcCCCcceEEEEecccCCc
Confidence 45678899998877765443
No 466
>KOG1088 consensus Uncharacterized conserved protein [Function unknown]
Probab=20.73 E-value=47 Score=28.71 Aligned_cols=15 Identities=27% Similarity=0.627 Sum_probs=11.9
Q ss_pred CeeecCCCCccccHH
Q 020131 16 QEYICPNCQRRYNAL 30 (330)
Q Consensus 16 ~~Y~CP~C~~~YT~l 30 (330)
-..+||.||+.|..-
T Consensus 97 G~l~CpetG~vfpI~ 111 (124)
T KOG1088|consen 97 GELVCPETGRVFPIS 111 (124)
T ss_pred ceEecCCCCcEeecc
Confidence 457899999999753
No 467
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=20.71 E-value=40 Score=25.30 Aligned_cols=11 Identities=27% Similarity=0.745 Sum_probs=8.8
Q ss_pred ecCCCCccccH
Q 020131 19 ICPNCQRRYNA 29 (330)
Q Consensus 19 ~CP~C~~~YT~ 29 (330)
-||.|+++|.+
T Consensus 41 gCPfC~~~~~~ 51 (55)
T PF14447_consen 41 GCPFCGTPFEF 51 (55)
T ss_pred CCCCCCCcccC
Confidence 48999988865
No 468
>PF11238 DUF3039: Protein of unknown function (DUF3039); InterPro: IPR021400 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=20.65 E-value=21 Score=27.05 Aligned_cols=14 Identities=36% Similarity=0.973 Sum_probs=11.5
Q ss_pred eeecCCCCccccHH
Q 020131 17 EYICPNCQRRYNAL 30 (330)
Q Consensus 17 ~Y~CP~C~~~YT~l 30 (330)
+=+||.|+..|..|
T Consensus 44 ~PVCP~Ck~iye~l 57 (58)
T PF11238_consen 44 FPVCPECKEIYESL 57 (58)
T ss_pred CCCCcCHHHHHHhc
Confidence 66899999988754
No 469
>PF02197 RIIa: Regulatory subunit of type II PKA R-subunit; InterPro: IPR003117 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. In the absence of cAMP, Protein Kinase A (PKA) exists as an equimolar tetramer of regulatory (R) and catalytic (C) subunits []. In addition to its role as an inhibitor of the C subunit, the R subunit anchors the holoenzyme to specific intracellular locations and prevents the C subunit from entering the nucleus. All R subunits have a conserved domain structure consisting of the N-terminal dimerization domain, inhibitory region, cAMP-binding domain A and cAMP-binding domain B. R subunits interact with C subunits primarily through the inhibitory site. The cAMP-binding domains show extensive sequence similarity and bind cAMP cooperatively. Two types of regulatory (R) subunits exist - types I and I - which differ in molecular weight, sequence, autophosphorylation cabaility, cellular location and tissue distribution. Types I and II were further sub-divided into alpha and beta subtypes, based mainly on sequence similarity. This entry represents types I-alpha, I-beta, II-alpha and II-beta regulatory subunits of PKA proteins. These subunits contain the dimerisation interface and binding site for A-kinase-anchoring proteins (AKAPs).; GO: 0008603 cAMP-dependent protein kinase regulator activity, 0007165 signal transduction; PDB: 2IZY_E 1R2A_A 1L6E_A 2IZX_B 2KYG_A 2EZW_B 3IM4_B 3IM3_A 4F9K_C 2HWN_B ....
Probab=20.25 E-value=79 Score=21.57 Aligned_cols=14 Identities=21% Similarity=0.596 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHHHH
Q 020131 232 EYIRAYYAALLKKQ 245 (330)
Q Consensus 232 e~l~aYyAal~k~q 245 (330)
.+.+.||..|++++
T Consensus 24 ~F~a~yF~~L~~~R 37 (38)
T PF02197_consen 24 QFAADYFEKLEKQR 37 (38)
T ss_dssp HHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhh
Confidence 57889999988876
No 470
>KOG4602 consensus Nanos and related proteins [General function prediction only]
Probab=20.24 E-value=41 Score=32.82 Aligned_cols=11 Identities=36% Similarity=1.002 Sum_probs=9.3
Q ss_pred eeecCCCCccc
Q 020131 17 EYICPNCQRRY 27 (330)
Q Consensus 17 ~Y~CP~C~~~Y 27 (330)
.|+||.||.+=
T Consensus 268 ~YVCPiCGATg 278 (318)
T KOG4602|consen 268 SYVCPICGATG 278 (318)
T ss_pred hhcCccccccC
Confidence 59999999864
No 471
>COG1328 NrdD Oxygen-sensitive ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]
Probab=20.23 E-value=44 Score=36.69 Aligned_cols=28 Identities=25% Similarity=0.548 Sum_probs=19.4
Q ss_pred CCCCeeecCCCCccccHHHHHhhcCCCCCCeeccCCCcc
Q 020131 13 NTVQEYICPNCQRRYNALDALRLVSLEDDSFHCENCNGE 51 (330)
Q Consensus 13 ~~~~~Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~e 51 (330)
.+...=+|+.||..+.++- =.||.||..
T Consensus 637 ~n~~i~~C~~cg~~~~~~~-----------~~Cp~CG~~ 664 (700)
T COG1328 637 YTTPISVCNRCGYSGEGLR-----------TRCPKCGSE 664 (700)
T ss_pred cCCCceeeccCCccccccc-----------ccCCCCCCc
Confidence 4455668999999876521 129999944
No 472
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=20.07 E-value=51 Score=36.98 Aligned_cols=36 Identities=28% Similarity=0.614 Sum_probs=25.0
Q ss_pred eecCCCCccccHHHHHhhcCCCCCCeeccCCCccccccch
Q 020131 18 YICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVAESD 57 (330)
Q Consensus 18 Y~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~~~~ 57 (330)
-.|..|++.|+.+- .++. .-..+|..||..+-..++
T Consensus 461 dtC~~C~kkFfSls--K~L~--~RKHHCRkCGrVFC~~CS 496 (1374)
T PTZ00303 461 DSCPSCGRAFISLS--RPLG--TRAHHCRSCGIRLCVFCI 496 (1374)
T ss_pred CcccCcCCcccccc--cccc--cccccccCCccccCcccc
Confidence 45999999998751 1111 125789999998866655
No 473
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=20.06 E-value=40 Score=27.22 Aligned_cols=30 Identities=27% Similarity=0.593 Sum_probs=24.0
Q ss_pred ecCCCCccccHHHHHhhcCCCCCCeeccCCCccccc
Q 020131 19 ICPNCQRRYNALDALRLVSLEDDSFHCENCNGELVA 54 (330)
Q Consensus 19 ~CP~C~~~YT~lDA~~Lld~~~~~F~C~~Cg~eL~~ 54 (330)
+||.|.+.-+ .||.....-.|+.|+..|..
T Consensus 36 kC~gc~~iT~------vfSHaqtvVvc~~c~~il~~ 65 (84)
T KOG1779|consen 36 KCPGCFKITT------VFSHAQTVVVCEGCSTILCQ 65 (84)
T ss_pred EcCCceEEEE------EeecCceEEEcCCCceEEEE
Confidence 6999987655 36777778999999999865
No 474
>KOG2683 consensus Sirtuin 4 and related class II sirtuins (SIR2 family) [Chromatin structure and dynamics; Transcription]
Probab=20.05 E-value=75 Score=30.90 Aligned_cols=39 Identities=26% Similarity=0.558 Sum_probs=27.3
Q ss_pred eecCCCCcccc---HHHHHhhcCCC-----------------------CCCe---eccCCCccccccc
Q 020131 18 YICPNCQRRYN---ALDALRLVSLE-----------------------DDSF---HCENCNGELVAES 56 (330)
Q Consensus 18 Y~CP~C~~~YT---~lDA~~Lld~~-----------------------~~~F---~C~~Cg~eL~~~~ 56 (330)
-+|-.|+..++ +-|-+..++|. ..+| .|..||+.|..+.
T Consensus 158 VkCl~C~y~~~R~~~Qdrl~~~NP~fke~~~~~~~~~pDgDv~lpl~~e~gF~IPeC~~CgG~lKpdV 225 (305)
T KOG2683|consen 158 VKCLSCGYIEPRQTFQDRLKYLNPGFKEAIVSPGHQRPDGDVELPLEFEEGFQIPECEKCGGLLKPDV 225 (305)
T ss_pred EEecccCcccchHHHHHHHHhcCcchhhhccCccccCCCCCeecchhhhhcccCCcccccCCccCCce
Confidence 47999998876 66666767662 1123 6999999886543
Done!