Query 025946
Match_columns 245
No_of_seqs 93 out of 101
Neff 2.9
Searched_HMMs 46136
Date Fri Mar 29 11:20:48 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025946.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025946hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09538 FYDLN_acid: Protein o 98.9 7.7E-10 1.7E-14 88.8 1.8 31 161-195 9-39 (108)
2 TIGR02300 FYDLN_acid conserved 98.6 1.2E-08 2.7E-13 85.0 2.0 31 161-195 9-39 (129)
3 PF11023 DUF2614: Protein of u 98.4 5.9E-07 1.3E-11 73.8 7.0 60 134-198 39-101 (114)
4 PRK00420 hypothetical protein; 98.3 2.8E-07 6.1E-12 75.0 1.7 39 156-198 18-56 (112)
5 COG4530 Uncharacterized protei 98.2 4.4E-07 9.6E-12 75.4 0.7 30 161-194 9-38 (129)
6 PRK02935 hypothetical protein; 98.1 7.7E-06 1.7E-10 67.0 7.0 60 134-198 40-102 (110)
7 TIGR02098 MJ0042_CXXC MJ0042 f 98.1 2E-06 4.2E-11 56.1 2.5 35 160-194 1-37 (38)
8 PF13248 zf-ribbon_3: zinc-rib 97.9 2.7E-06 5.8E-11 52.7 0.8 26 160-192 1-26 (26)
9 PRK00398 rpoP DNA-directed RNA 97.8 2.4E-05 5.3E-10 53.3 3.1 35 160-197 2-36 (46)
10 smart00834 CxxC_CXXC_SSSS Puta 97.6 6E-05 1.3E-09 48.9 3.2 34 159-192 3-36 (41)
11 PF13719 zinc_ribbon_5: zinc-r 97.6 3.5E-05 7.6E-10 51.1 1.9 35 160-194 1-37 (37)
12 PF13240 zinc_ribbon_2: zinc-r 97.6 2.1E-05 4.6E-10 48.1 0.7 23 163-192 1-23 (23)
13 PF13717 zinc_ribbon_4: zinc-r 97.5 5.2E-05 1.1E-09 50.3 1.9 33 160-192 1-35 (36)
14 TIGR01206 lysW lysine biosynth 97.5 8.6E-05 1.9E-09 53.8 2.7 34 161-195 2-35 (54)
15 PF09723 Zn-ribbon_8: Zinc rib 97.3 0.00027 5.8E-09 47.9 3.3 34 159-192 3-37 (42)
16 smart00531 TFIIE Transcription 97.3 0.00013 2.9E-09 60.0 1.8 38 161-198 99-139 (147)
17 TIGR02605 CxxC_CxxC_SSSS putat 97.0 0.00072 1.6E-08 46.3 2.9 32 159-190 3-34 (52)
18 PF08271 TF_Zn_Ribbon: TFIIB z 96.9 0.00057 1.2E-08 46.0 1.9 30 163-194 2-31 (43)
19 PF14353 CpXC: CpXC protein 96.9 0.001 2.2E-08 52.8 3.6 44 161-204 1-60 (128)
20 PF10571 UPF0547: Uncharacteri 96.6 0.001 2.2E-08 42.0 1.2 24 163-193 2-25 (26)
21 PF09862 DUF2089: Protein of u 96.6 0.0011 2.4E-08 54.4 1.6 28 164-201 1-28 (113)
22 PF06677 Auto_anti-p27: Sjogre 96.5 0.0015 3.2E-08 45.1 1.8 31 155-189 11-41 (41)
23 PF14446 Prok-RING_1: Prokaryo 96.5 0.0013 2.8E-08 48.1 1.4 32 158-194 2-33 (54)
24 TIGR00373 conserved hypothetic 96.5 0.0014 3E-08 55.1 1.7 35 161-197 109-143 (158)
25 smart00659 RPOLCX RNA polymera 96.4 0.003 6.5E-08 43.8 3.0 32 161-196 2-33 (44)
26 PRK06266 transcription initiat 96.4 0.0015 3.3E-08 56.1 1.8 36 160-197 116-151 (178)
27 PF03604 DNA_RNApol_7kD: DNA d 96.1 0.0037 8E-08 41.2 1.9 27 163-193 2-28 (32)
28 COG1592 Rubrerythrin [Energy p 96.0 0.0036 7.9E-08 54.2 1.7 23 163-191 136-158 (166)
29 COG1645 Uncharacterized Zn-fin 95.9 0.004 8.7E-08 52.4 1.5 29 157-190 24-52 (131)
30 cd00729 rubredoxin_SM Rubredox 95.8 0.0069 1.5E-07 39.8 2.3 24 163-191 4-27 (34)
31 PRK13130 H/ACA RNA-protein com 95.5 0.0075 1.6E-07 44.2 1.6 33 162-209 6-38 (56)
32 cd00350 rubredoxin_like Rubred 95.5 0.011 2.3E-07 38.3 2.1 24 163-191 3-26 (33)
33 PRK03824 hypA hydrogenase nick 95.3 0.016 3.4E-07 47.9 3.2 40 162-201 71-128 (135)
34 PF03966 Trm112p: Trm112p-like 95.2 0.015 3.3E-07 42.4 2.3 20 178-197 49-68 (68)
35 PF09986 DUF2225: Uncharacteri 95.1 0.011 2.5E-07 51.6 1.9 34 161-195 5-61 (214)
36 PRK12380 hydrogenase nickel in 95.1 0.019 4.1E-07 46.1 2.8 34 162-200 71-106 (113)
37 PRK03681 hypA hydrogenase nick 95.0 0.019 4.2E-07 46.1 2.8 34 163-200 72-107 (114)
38 PF12773 DZR: Double zinc ribb 94.9 0.01 2.2E-07 40.3 0.8 26 163-192 14-39 (50)
39 PF01155 HypA: Hydrogenase exp 94.8 0.011 2.3E-07 47.2 0.7 34 163-201 72-107 (113)
40 COG1996 RPC10 DNA-directed RNA 94.6 0.027 5.8E-07 40.6 2.3 35 160-197 5-39 (49)
41 TIGR00100 hypA hydrogenase nic 94.5 0.033 7.3E-07 44.7 2.9 36 162-202 71-108 (115)
42 PF07282 OrfB_Zn_ribbon: Putat 94.4 0.025 5.5E-07 40.4 1.8 30 163-195 30-59 (69)
43 PRK00564 hypA hydrogenase nick 94.3 0.031 6.7E-07 45.1 2.3 37 163-203 73-111 (117)
44 smart00661 RPOL9 RNA polymeras 94.2 0.055 1.2E-06 36.6 3.1 34 163-197 2-35 (52)
45 PF14205 Cys_rich_KTR: Cystein 94.2 0.041 9E-07 40.7 2.6 38 163-200 6-46 (55)
46 PF12773 DZR: Double zinc ribb 94.0 0.027 5.9E-07 38.2 1.2 23 164-193 1-23 (50)
47 PF06044 DRP: Dam-replacing fa 93.9 0.02 4.3E-07 52.8 0.6 39 154-198 27-69 (254)
48 PRK12496 hypothetical protein; 93.6 0.035 7.6E-07 47.1 1.6 58 131-195 98-156 (164)
49 PRK00415 rps27e 30S ribosomal 93.6 0.047 1E-06 40.7 2.0 40 157-198 7-47 (59)
50 COG2051 RPS27A Ribosomal prote 93.6 0.047 1E-06 41.8 1.9 34 158-193 16-49 (67)
51 PF07191 zinc-ribbons_6: zinc- 93.2 0.038 8.3E-07 42.4 1.0 27 160-194 16-42 (70)
52 COG2888 Predicted Zn-ribbon RN 93.1 0.05 1.1E-06 41.0 1.5 31 159-189 25-57 (61)
53 COG0675 Transposase and inacti 92.8 0.042 9E-07 46.7 0.8 25 163-195 311-335 (364)
54 COG3877 Uncharacterized protei 92.8 0.062 1.3E-06 44.9 1.7 29 163-201 8-36 (122)
55 PRK00432 30S ribosomal protein 92.7 0.061 1.3E-06 38.2 1.4 26 163-192 22-47 (50)
56 PF05191 ADK_lid: Adenylate ki 92.6 0.099 2.1E-06 35.0 2.2 31 162-193 2-32 (36)
57 COG4888 Uncharacterized Zn rib 92.6 0.083 1.8E-06 43.3 2.2 45 163-208 24-71 (104)
58 PF07754 DUF1610: Domain of un 92.5 0.077 1.7E-06 33.4 1.4 23 164-190 1-24 (24)
59 TIGR00686 phnA alkylphosphonat 92.5 0.1 2.2E-06 43.1 2.6 30 163-196 4-33 (109)
60 PHA00626 hypothetical protein 92.1 0.14 3E-06 38.4 2.7 33 163-195 2-36 (59)
61 PRK14890 putative Zn-ribbon RN 92.0 0.1 2.2E-06 39.1 1.9 8 163-170 27-34 (59)
62 PRK00762 hypA hydrogenase nick 91.9 0.11 2.5E-06 42.2 2.2 42 161-203 70-115 (124)
63 COG1675 TFA1 Transcription ini 91.7 0.056 1.2E-06 47.3 0.2 32 163-196 115-146 (176)
64 PRK00423 tfb transcription ini 91.6 0.093 2E-06 48.0 1.6 30 162-193 12-41 (310)
65 PRK11827 hypothetical protein; 91.5 0.12 2.6E-06 38.5 1.8 33 163-198 10-42 (60)
66 COG1545 Predicted nucleic-acid 91.4 0.11 2.4E-06 43.1 1.7 29 158-193 26-54 (140)
67 PRK05978 hypothetical protein; 91.3 0.12 2.6E-06 44.1 1.9 35 162-198 34-68 (148)
68 PF01667 Ribosomal_S27e: Ribos 91.3 0.16 3.4E-06 37.3 2.2 39 158-198 4-43 (55)
69 PRK14892 putative transcriptio 91.1 0.14 3.1E-06 41.1 2.0 32 163-195 23-55 (99)
70 PF08274 PhnA_Zn_Ribbon: PhnA 91.1 0.085 1.9E-06 34.5 0.6 27 162-192 3-29 (30)
71 PF02150 RNA_POL_M_15KD: RNA p 91.1 0.14 3E-06 33.9 1.6 32 163-196 3-34 (35)
72 PF09845 DUF2072: Zn-ribbon co 91.0 0.12 2.6E-06 43.7 1.6 33 163-204 3-35 (131)
73 COG5216 Uncharacterized conser 91.0 0.14 3.1E-06 39.0 1.8 37 156-193 17-55 (67)
74 TIGR00515 accD acetyl-CoA carb 91.0 0.086 1.9E-06 48.7 0.8 39 163-203 28-76 (285)
75 PRK06260 threonine synthase; V 90.8 0.15 3.3E-06 47.6 2.1 32 160-196 2-33 (397)
76 PRK12286 rpmF 50S ribosomal pr 90.3 0.14 2.9E-06 37.5 1.1 20 163-190 29-48 (57)
77 PHA02942 putative transposase; 90.2 0.17 3.8E-06 47.9 2.0 27 163-193 327-353 (383)
78 PF09297 zf-NADH-PPase: NADH p 90.1 0.18 3.9E-06 32.2 1.5 28 162-192 4-31 (32)
79 PRK14559 putative protein seri 90.1 0.13 2.8E-06 52.3 1.2 22 163-191 29-50 (645)
80 PRK05654 acetyl-CoA carboxylas 90.1 0.11 2.5E-06 48.0 0.7 40 163-204 29-78 (292)
81 PF01783 Ribosomal_L32p: Ribos 89.9 0.17 3.8E-06 36.3 1.4 20 162-189 27-46 (56)
82 PRK12495 hypothetical protein; 89.6 0.17 3.7E-06 46.2 1.4 33 158-195 39-71 (226)
83 PF09889 DUF2116: Uncharacteri 89.4 0.045 9.7E-07 40.5 -2.0 25 162-193 4-29 (59)
84 PRK10220 hypothetical protein; 89.3 0.24 5.1E-06 41.1 1.9 30 163-196 5-34 (111)
85 COG2835 Uncharacterized conser 89.2 0.25 5.4E-06 37.1 1.8 38 158-198 4-42 (60)
86 PF14255 Cys_rich_CPXG: Cystei 89.2 0.23 4.9E-06 35.9 1.5 13 183-195 1-13 (52)
87 TIGR01384 TFS_arch transcripti 88.8 0.23 4.9E-06 38.3 1.4 28 163-195 2-29 (104)
88 PF13719 zinc_ribbon_5: zinc-r 88.8 0.12 2.7E-06 34.2 -0.0 21 183-203 3-23 (37)
89 PRK14559 putative protein seri 88.3 0.21 4.6E-06 50.8 1.2 16 183-198 28-43 (645)
90 COG3357 Predicted transcriptio 88.2 0.31 6.8E-06 39.6 1.9 36 163-202 60-95 (97)
91 PRK15103 paraquat-inducible me 88.0 0.52 1.1E-05 45.5 3.6 24 163-193 223-246 (419)
92 TIGR01031 rpmF_bact ribosomal 88.0 0.24 5.2E-06 35.8 1.0 19 163-189 28-46 (55)
93 KOG2923 Uncharacterized conser 87.9 0.34 7.3E-06 37.2 1.8 38 156-194 17-56 (67)
94 PRK08270 anaerobic ribonucleos 87.9 0.28 6.1E-06 49.9 1.7 28 158-193 623-650 (656)
95 PF09334 tRNA-synt_1g: tRNA sy 87.8 0.17 3.7E-06 47.8 0.2 12 182-193 149-160 (391)
96 PF05876 Terminase_GpA: Phage 87.8 0.3 6.5E-06 48.4 1.8 47 158-204 197-258 (557)
97 TIGR00155 pqiA_fam integral me 87.6 0.63 1.4E-05 44.6 3.9 25 163-193 217-241 (403)
98 TIGR03830 CxxCG_CxxCG_HTH puta 87.6 0.26 5.7E-06 38.0 1.1 18 178-195 27-44 (127)
99 PRK00481 NAD-dependent deacety 87.5 0.31 6.8E-06 42.7 1.6 31 162-193 123-153 (242)
100 PLN00209 ribosomal protein S27 87.3 0.4 8.6E-06 38.3 1.9 40 158-199 33-73 (86)
101 CHL00174 accD acetyl-CoA carbo 87.2 0.17 3.7E-06 47.4 -0.2 39 163-203 40-88 (296)
102 PRK00464 nrdR transcriptional 87.2 0.4 8.7E-06 41.0 2.1 31 163-193 2-39 (154)
103 COG4260 Membrane protease subu 87.1 0.25 5.4E-06 47.3 0.8 28 163-192 317-344 (345)
104 cd01412 SIRT5_Af1_CobB SIRT5_A 87.0 0.38 8.1E-06 41.5 1.8 31 163-193 111-141 (224)
105 PTZ00083 40S ribosomal protein 87.0 0.43 9.2E-06 38.0 2.0 47 158-206 32-80 (85)
106 PF08996 zf-DNA_Pol: DNA Polym 87.0 0.38 8.2E-06 41.3 1.8 33 160-193 17-56 (188)
107 PF12172 DUF35_N: Rubredoxin-l 86.9 0.37 8E-06 31.3 1.3 26 158-190 8-33 (37)
108 COG1405 SUA7 Transcription ini 86.9 0.31 6.8E-06 45.1 1.3 31 162-194 2-32 (285)
109 PRK07591 threonine synthase; V 86.9 0.43 9.3E-06 45.3 2.3 31 160-196 17-47 (421)
110 COG3364 Zn-ribbon containing p 86.8 0.25 5.5E-06 41.0 0.6 35 162-205 3-37 (112)
111 COG2331 Uncharacterized protei 86.8 0.15 3.3E-06 40.3 -0.6 44 159-206 10-54 (82)
112 PF11781 RRN7: RNA polymerase 86.8 0.37 7.9E-06 32.3 1.3 26 163-192 10-35 (36)
113 PF13395 HNH_4: HNH endonuclea 86.8 0.37 8E-06 33.8 1.4 25 185-209 1-33 (54)
114 PF08792 A2L_zn_ribbon: A2L zi 86.7 0.54 1.2E-05 31.1 2.0 29 162-193 4-32 (33)
115 TIGR02098 MJ0042_CXXC MJ0042 f 86.4 0.2 4.4E-06 32.4 -0.1 21 183-203 3-23 (38)
116 PRK14714 DNA polymerase II lar 86.2 0.36 7.8E-06 53.0 1.6 11 161-171 667-677 (1337)
117 PRK08579 anaerobic ribonucleos 86.2 0.38 8.2E-06 48.9 1.6 23 161-190 568-590 (625)
118 PF10005 DUF2248: Uncharacteri 86.1 0.46 9.9E-06 45.6 2.0 24 163-193 1-24 (343)
119 COG1655 Uncharacterized protei 86.0 0.24 5.3E-06 46.0 0.1 13 161-173 19-31 (267)
120 PF14803 Nudix_N_2: Nudix N-te 85.9 0.42 9.1E-06 31.8 1.2 27 163-191 2-31 (34)
121 KOG2593 Transcription initiati 85.7 0.25 5.5E-06 48.7 0.1 43 163-205 130-176 (436)
122 PF02146 SIR2: Sir2 family; I 85.4 0.62 1.3E-05 38.7 2.3 34 159-192 103-139 (178)
123 PF07295 DUF1451: Protein of u 85.3 0.91 2E-05 38.5 3.2 32 163-203 114-145 (146)
124 PF12677 DUF3797: Domain of un 85.3 0.94 2E-05 33.0 2.8 27 163-202 15-41 (49)
125 COG0777 AccD Acetyl-CoA carbox 84.8 0.36 7.8E-06 45.6 0.6 29 163-193 30-58 (294)
126 PRK09521 exosome complex RNA-b 84.5 0.73 1.6E-05 39.3 2.3 30 159-192 147-176 (189)
127 PRK07111 anaerobic ribonucleos 84.5 0.51 1.1E-05 48.6 1.6 25 158-190 677-701 (735)
128 COG4031 Predicted metal-bindin 84.3 0.54 1.2E-05 42.8 1.5 21 163-192 2-22 (227)
129 COG4640 Predicted membrane pro 84.2 0.46 9.9E-06 47.0 1.1 24 163-193 3-26 (465)
130 COG1096 Predicted RNA-binding 84.2 0.65 1.4E-05 41.5 1.9 27 160-191 148-174 (188)
131 PRK06450 threonine synthase; V 84.1 0.6 1.3E-05 43.3 1.8 31 161-197 3-33 (338)
132 PF10083 DUF2321: Uncharacteri 83.8 0.44 9.6E-06 41.6 0.8 34 163-196 41-82 (158)
133 PF11023 DUF2614: Protein of u 83.8 2 4.3E-05 35.9 4.5 73 108-198 11-85 (114)
134 COG2888 Predicted Zn-ribbon RN 83.8 0.62 1.3E-05 35.2 1.4 29 162-193 10-38 (61)
135 cd01407 SIR2-fam SIR2 family o 83.7 0.52 1.1E-05 40.6 1.1 31 162-192 110-143 (218)
136 TIGR03831 YgiT_finger YgiT-typ 83.6 0.98 2.1E-05 29.4 2.2 13 182-194 32-44 (46)
137 PF13717 zinc_ribbon_4: zinc-r 83.5 0.37 8.1E-06 31.9 0.1 21 183-203 3-23 (36)
138 PRK10445 endonuclease VIII; Pr 83.5 0.77 1.7E-05 41.3 2.2 27 162-189 236-262 (263)
139 COG1326 Uncharacterized archae 83.4 0.49 1.1E-05 42.7 0.9 32 160-192 5-40 (201)
140 COG4391 Uncharacterized protei 82.9 0.73 1.6E-05 34.9 1.5 17 178-194 44-60 (62)
141 PRK11032 hypothetical protein; 82.8 1.3 2.8E-05 38.4 3.2 31 163-203 126-157 (160)
142 PRK14714 DNA polymerase II lar 82.8 0.59 1.3E-05 51.4 1.4 9 163-171 681-689 (1337)
143 PF13597 NRDD: Anaerobic ribon 82.7 0.51 1.1E-05 46.8 0.8 25 159-191 489-513 (546)
144 PRK01103 formamidopyrimidine/5 82.5 0.88 1.9E-05 41.0 2.1 27 163-190 247-273 (274)
145 PF10263 SprT-like: SprT-like 82.4 1.1 2.4E-05 35.8 2.5 36 158-194 120-155 (157)
146 PRK08271 anaerobic ribonucleos 82.2 0.71 1.5E-05 47.0 1.6 26 158-190 563-588 (623)
147 TIGR03844 cysteate_syn cysteat 82.2 0.88 1.9E-05 43.3 2.1 31 161-197 2-32 (398)
148 PF03367 zf-ZPR1: ZPR1 zinc-fi 82.1 0.43 9.4E-06 40.6 0.0 31 161-192 1-40 (161)
149 COG1656 Uncharacterized conser 81.9 0.64 1.4E-05 40.7 1.0 34 161-199 97-146 (165)
150 PF14311 DUF4379: Domain of un 81.9 1 2.2E-05 31.5 1.8 26 163-188 30-55 (55)
151 PF07191 zinc-ribbons_6: zinc- 81.7 0.96 2.1E-05 34.8 1.8 27 161-192 1-27 (70)
152 cd01410 SIRT7 SIRT7: Eukaryoti 81.6 0.78 1.7E-05 39.8 1.4 29 163-192 97-130 (206)
153 PF13005 zf-IS66: zinc-finger 81.6 1.4 3.1E-05 29.4 2.4 26 181-206 1-26 (47)
154 KOG1088 Uncharacterized conser 81.2 0.73 1.6E-05 38.9 1.1 19 179-197 95-113 (124)
155 PRK09263 anaerobic ribonucleos 81.2 0.81 1.8E-05 47.1 1.6 33 156-191 636-668 (711)
156 PF14353 CpXC: CpXC protein 81.1 0.85 1.8E-05 36.2 1.4 18 156-173 33-50 (128)
157 COG2260 Predicted Zn-ribbon RN 81.1 1 2.3E-05 33.8 1.7 33 162-209 6-38 (59)
158 TIGR02827 RNR_anaer_Bdell anae 80.8 0.95 2.1E-05 45.9 1.9 26 158-190 529-554 (586)
159 TIGR00577 fpg formamidopyrimid 80.6 1.1 2.5E-05 40.4 2.2 25 163-188 247-271 (272)
160 COG0375 HybF Zn finger protein 80.4 1.2 2.6E-05 36.9 2.1 31 162-197 71-102 (115)
161 PF05180 zf-DNL: DNL zinc fing 80.0 0.71 1.5E-05 35.0 0.6 38 159-196 2-43 (66)
162 PF04135 Nop10p: Nucleolar RNA 79.8 1.7 3.8E-05 31.7 2.5 33 162-209 6-38 (53)
163 TIGR00354 polC DNA polymerase, 79.7 1 2.2E-05 48.7 1.7 23 161-192 625-647 (1095)
164 PF09855 DUF2082: Nucleic-acid 79.6 1.2 2.6E-05 33.4 1.7 13 163-175 2-14 (64)
165 cd01121 Sms Sms (bacterial rad 79.6 0.89 1.9E-05 43.1 1.2 27 163-196 2-28 (372)
166 PRK08402 replication factor A; 79.6 1.5 3.1E-05 41.9 2.6 32 156-190 207-238 (355)
167 PRK14704 anaerobic ribonucleos 79.6 0.92 2E-05 46.0 1.4 22 161-190 559-580 (618)
168 PRK04011 peptide chain release 79.6 1.2 2.7E-05 42.7 2.2 37 160-196 327-364 (411)
169 PRK12366 replication factor A; 79.5 1.9 4.1E-05 43.7 3.5 30 157-191 528-557 (637)
170 PRK14810 formamidopyrimidine-D 79.5 1.3 2.8E-05 40.1 2.1 26 163-189 246-271 (272)
171 PRK14890 putative Zn-ribbon RN 79.4 1.2 2.5E-05 33.5 1.5 27 162-192 8-35 (59)
172 TIGR02378 nirD_assim_sml nitri 79.3 1.6 3.5E-05 33.2 2.3 38 159-198 38-80 (105)
173 PF01927 Mut7-C: Mut7-C RNAse 79.1 1.4 3E-05 36.3 2.1 42 158-200 88-141 (147)
174 PRK13945 formamidopyrimidine-D 78.9 1.3 2.9E-05 40.1 2.1 26 163-189 256-281 (282)
175 PF09332 Mcm10: Mcm10 replicat 78.8 1.6 3.6E-05 41.8 2.7 32 163-204 287-319 (344)
176 PF06221 zf-C2HC5: Putative zi 78.7 1.2 2.5E-05 32.9 1.4 28 162-194 19-47 (57)
177 COG2093 DNA-directed RNA polym 78.7 0.9 2E-05 34.6 0.8 23 162-191 5-27 (64)
178 COG2824 PhnA Uncharacterized Z 78.5 1.9 4.2E-05 35.9 2.7 27 163-193 5-31 (112)
179 cd00730 rubredoxin Rubredoxin; 78.5 2 4.4E-05 30.7 2.5 29 163-191 3-43 (50)
180 TIGR00340 zpr1_rel ZPR1-relate 78.5 1.4 2.9E-05 38.1 1.9 28 164-191 1-37 (163)
181 PF01485 IBR: IBR domain; Int 78.5 1.7 3.6E-05 29.6 2.0 30 162-192 19-50 (64)
182 TIGR00155 pqiA_fam integral me 78.3 1.4 3E-05 42.3 2.1 31 163-194 15-45 (403)
183 PRK06386 replication factor A; 78.3 1.1 2.5E-05 42.9 1.5 20 162-190 237-256 (358)
184 COG0846 SIR2 NAD-dependent pro 78.1 1.3 2.7E-05 40.5 1.7 33 159-191 120-155 (250)
185 PRK14715 DNA polymerase II lar 77.9 1.1 2.4E-05 49.8 1.5 25 160-193 673-697 (1627)
186 PRK15103 paraquat-inducible me 77.9 1.6 3.5E-05 42.2 2.4 30 163-194 12-42 (419)
187 COG0333 RpmF Ribosomal protein 77.8 1.2 2.5E-05 33.1 1.1 21 162-190 28-48 (57)
188 PRK14811 formamidopyrimidine-D 77.6 1.6 3.4E-05 39.6 2.1 30 163-193 237-266 (269)
189 cd07973 Spt4 Transcription elo 77.5 1.5 3.2E-05 35.3 1.7 43 162-208 4-49 (98)
190 smart00350 MCM minichromosome 77.4 3.8 8.3E-05 39.9 4.8 74 163-243 39-116 (509)
191 PRK04023 DNA polymerase II lar 77.2 1.3 2.7E-05 48.2 1.6 20 163-191 628-647 (1121)
192 PF03884 DUF329: Domain of unk 77.1 1.4 3.1E-05 32.5 1.4 26 160-190 1-26 (57)
193 PF09581 Spore_III_AF: Stage I 77.1 3.9 8.4E-05 34.1 4.2 40 111-150 4-44 (188)
194 cd01413 SIR2_Af2 SIR2_Af2: Arc 77.0 1.3 2.8E-05 38.7 1.3 32 162-193 114-147 (222)
195 PRK11823 DNA repair protein Ra 76.9 1.2 2.6E-05 42.9 1.3 29 161-196 7-35 (446)
196 COG2176 PolC DNA polymerase II 76.7 1.9 4E-05 47.8 2.7 34 163-196 916-953 (1444)
197 PTZ00409 Sir2 (Silent Informat 76.5 1.4 3E-05 40.3 1.4 32 161-193 137-175 (271)
198 TIGR01405 polC_Gram_pos DNA po 76.4 1.5 3.2E-05 47.9 1.9 35 163-197 685-723 (1213)
199 cd03528 Rieske_RO_ferredoxin R 76.4 1.7 3.7E-05 32.2 1.7 39 160-200 37-75 (98)
200 TIGR00310 ZPR1_znf ZPR1 zinc f 76.2 1.2 2.7E-05 39.2 1.0 28 163-191 2-39 (192)
201 COG1594 RPB9 DNA-directed RNA 76.1 2.6 5.7E-05 34.2 2.8 34 163-197 4-37 (113)
202 TIGR00416 sms DNA repair prote 75.8 1.3 2.7E-05 43.0 1.1 29 161-196 7-35 (454)
203 TIGR00595 priA primosomal prot 75.7 1.4 3.1E-05 43.1 1.4 11 163-173 224-234 (505)
204 cd01675 RNR_III Class III ribo 75.6 1.5 3.3E-05 43.6 1.6 22 163-191 520-541 (555)
205 PRK01110 rpmF 50S ribosomal pr 75.6 1.5 3.3E-05 32.2 1.2 19 162-189 28-46 (60)
206 smart00709 Zpr1 Duplicated dom 75.4 1.7 3.7E-05 37.2 1.6 31 162-192 1-39 (160)
207 COG0143 MetG Methionyl-tRNA sy 75.1 1.2 2.7E-05 44.8 0.8 34 155-196 136-169 (558)
208 PRK04023 DNA polymerase II lar 75.0 1.5 3.3E-05 47.5 1.5 11 160-170 637-647 (1121)
209 PRK00448 polC DNA polymerase I 74.8 1.7 3.7E-05 48.2 1.9 35 163-197 910-948 (1437)
210 COG2816 NPY1 NTP pyrophosphohy 74.6 1.5 3.2E-05 41.1 1.2 35 155-192 105-139 (279)
211 PF06750 DiS_P_DiS: Bacterial 74.2 4.3 9.4E-05 31.7 3.5 34 161-194 33-70 (92)
212 KOG4517 Uncharacterized conser 74.1 3.7 8E-05 34.5 3.2 34 132-171 83-116 (117)
213 TIGR00201 comF comF family pro 73.8 1.6 3.5E-05 36.8 1.1 24 164-194 1-24 (190)
214 PF05605 zf-Di19: Drought indu 73.8 1.7 3.7E-05 30.2 1.1 28 162-190 3-39 (54)
215 PF03119 DNA_ligase_ZBD: NAD-d 73.7 2 4.4E-05 27.3 1.3 14 184-197 1-14 (28)
216 PF05129 Elf1: Transcription e 73.7 1.3 2.9E-05 34.1 0.5 33 163-195 24-59 (81)
217 PF02591 DUF164: Putative zinc 73.5 1.3 2.8E-05 31.1 0.4 32 160-191 21-55 (56)
218 PRK07218 replication factor A; 73.4 1.7 3.6E-05 42.5 1.2 20 163-191 299-318 (423)
219 PF10122 Mu-like_Com: Mu-like 73.4 1.1 2.3E-05 32.9 -0.1 39 160-199 3-41 (51)
220 PRK09710 lar restriction allev 73.2 2.2 4.7E-05 32.5 1.6 29 163-191 8-36 (64)
221 TIGR02487 NrdD anaerobic ribon 73.0 1.9 4.1E-05 43.2 1.6 27 158-191 521-547 (579)
222 PRK00241 nudC NADH pyrophospha 72.9 2.1 4.5E-05 38.6 1.7 34 156-192 94-127 (256)
223 PRK14138 NAD-dependent deacety 72.9 1.6 3.5E-05 38.8 0.9 29 163-192 121-153 (244)
224 cd04476 RPA1_DBD_C RPA1_DBD_C: 72.9 2.7 5.8E-05 34.6 2.2 31 158-192 31-61 (166)
225 PF15616 TerY-C: TerY-C metal 72.5 4.5 9.8E-05 34.2 3.5 31 163-197 79-120 (131)
226 PF03833 PolC_DP2: DNA polymer 72.5 1.2 2.6E-05 47.5 0.0 12 161-172 655-666 (900)
227 PF08646 Rep_fac-A_C: Replicat 72.4 1.9 4.2E-05 34.8 1.2 31 158-192 15-47 (146)
228 PF13824 zf-Mss51: Zinc-finger 72.3 2.5 5.3E-05 31.2 1.6 29 164-198 2-30 (55)
229 PF13453 zf-TFIIB: Transcripti 72.3 2 4.3E-05 28.6 1.0 28 163-192 1-29 (41)
230 COG1579 Zn-ribbon protein, pos 71.9 1.1 2.3E-05 41.1 -0.4 36 163-198 199-237 (239)
231 cd00296 SIR2 SIR2 superfamily 71.8 2 4.4E-05 36.2 1.3 39 161-200 113-152 (222)
232 COG1503 eRF1 Peptide chain rel 71.6 2.1 4.4E-05 42.2 1.4 37 160-196 326-362 (411)
233 COG1779 C4-type Zn-finger prot 71.5 2.4 5.1E-05 38.4 1.6 33 161-193 14-54 (201)
234 COG1066 Sms Predicted ATP-depe 71.4 2.1 4.6E-05 42.7 1.5 28 160-194 6-33 (456)
235 smart00647 IBR In Between Ring 71.0 4.4 9.5E-05 27.6 2.6 29 163-192 20-50 (64)
236 TIGR03826 YvyF flagellar opero 70.9 1.1 2.4E-05 37.8 -0.5 25 162-192 4-28 (137)
237 PHA02768 hypothetical protein; 70.9 2.1 4.6E-05 31.4 1.0 32 162-193 6-42 (55)
238 PF10080 DUF2318: Predicted me 70.9 1.9 4E-05 34.8 0.8 30 162-195 36-65 (102)
239 PRK08197 threonine synthase; V 70.7 2.5 5.5E-05 39.6 1.7 31 161-197 7-37 (394)
240 PF09889 DUF2116: Uncharacteri 70.7 1.7 3.7E-05 32.2 0.5 14 182-195 3-16 (59)
241 smart00064 FYVE Protein presen 70.6 2.8 6E-05 29.7 1.5 33 154-192 4-36 (68)
242 PRK08665 ribonucleotide-diphos 70.4 2.8 6E-05 43.5 2.1 23 163-190 726-748 (752)
243 TIGR02896 spore_III_AF stage I 70.2 12 0.00026 30.3 5.3 41 110-150 13-54 (106)
244 PF14354 Lar_restr_allev: Rest 70.1 2.9 6.3E-05 29.2 1.5 28 163-190 5-37 (61)
245 PF14369 zf-RING_3: zinc-finge 70.0 6.8 0.00015 26.0 3.2 26 164-191 5-30 (35)
246 TIGR03683 A-tRNA_syn_arch alan 69.9 3 6.6E-05 44.2 2.3 70 154-234 9-82 (902)
247 COG1040 ComFC Predicted amidop 69.8 1.1 2.3E-05 39.7 -0.9 36 153-195 15-51 (225)
248 PRK05580 primosome assembly pr 69.0 2.4 5.2E-05 42.9 1.3 11 163-173 392-402 (679)
249 PF10164 DUF2367: Uncharacteri 68.8 6 0.00013 32.3 3.3 12 160-171 87-98 (98)
250 PRK11788 tetratricopeptide rep 68.7 2.5 5.4E-05 37.1 1.2 22 163-191 356-377 (389)
251 PF10083 DUF2321: Uncharacteri 68.7 0.79 1.7E-05 40.0 -1.9 33 159-204 26-58 (158)
252 PRK08351 DNA-directed RNA poly 68.6 3 6.6E-05 31.2 1.4 21 163-192 5-25 (61)
253 COG4306 Uncharacterized protei 68.4 1.9 4.2E-05 37.3 0.4 36 163-198 41-84 (160)
254 cd03478 Rieske_AIFL_N AIFL (ap 68.3 3.7 8E-05 30.6 1.9 42 160-203 36-77 (95)
255 KOG2807 RNA polymerase II tran 68.2 3.1 6.7E-05 40.5 1.8 24 163-193 278-301 (378)
256 COG4311 SoxD Sarcosine oxidase 68.2 2.6 5.6E-05 34.4 1.1 37 182-221 3-43 (97)
257 PF04216 FdhE: Protein involve 68.2 2.6 5.6E-05 38.0 1.2 11 162-172 173-183 (290)
258 PF07503 zf-HYPF: HypF finger; 68.1 0.86 1.9E-05 30.5 -1.4 33 163-195 1-34 (35)
259 cd01411 SIR2H SIR2H: Uncharact 68.1 3 6.4E-05 36.6 1.5 29 162-193 119-147 (225)
260 TIGR00108 eRF peptide chain re 68.0 3.5 7.6E-05 39.7 2.1 38 160-197 323-361 (409)
261 COG3809 Uncharacterized protei 67.7 3.9 8.5E-05 32.8 2.0 35 163-199 3-37 (88)
262 COG1998 RPS31 Ribosomal protei 67.6 2.5 5.4E-05 31.1 0.8 26 163-192 21-47 (51)
263 cd01408 SIRT1 SIRT1: Eukaryoti 67.5 2.6 5.6E-05 37.2 1.1 32 161-193 116-151 (235)
264 PHA00732 hypothetical protein 67.5 1.6 3.4E-05 33.5 -0.3 37 163-199 3-44 (79)
265 PRK04338 N(2),N(2)-dimethylgua 67.5 4.9 0.00011 38.3 2.9 28 163-194 246-273 (382)
266 PF02397 Bac_transf: Bacterial 67.5 8.8 0.00019 33.6 4.3 45 129-173 3-52 (187)
267 TIGR00570 cdk7 CDK-activating 67.3 3.3 7.2E-05 39.3 1.8 34 163-196 5-57 (309)
268 PF10276 zf-CHCC: Zinc-finger 67.2 2.7 5.9E-05 29.0 0.9 15 178-192 23-39 (40)
269 KOG2324 Prolyl-tRNA synthetase 67.0 3.2 6.9E-05 41.2 1.6 27 163-190 229-255 (457)
270 PF04216 FdhE: Protein involve 67.0 2.5 5.5E-05 38.1 0.9 23 163-192 199-221 (290)
271 PF04475 DUF555: Protein of un 66.6 3.6 7.7E-05 33.9 1.6 16 178-193 43-58 (102)
272 PF09567 RE_MamI: MamI restric 66.5 3.1 6.7E-05 39.5 1.4 22 163-191 84-105 (314)
273 COG1198 PriA Primosomal protei 66.3 3 6.4E-05 43.5 1.3 10 182-191 475-484 (730)
274 PF06827 zf-FPG_IleRS: Zinc fi 66.3 2.8 6E-05 26.2 0.7 27 163-190 3-29 (30)
275 TIGR00627 tfb4 transcription f 65.9 3.3 7.1E-05 38.5 1.4 29 157-192 249-279 (279)
276 PTZ00408 NAD-dependent deacety 65.9 2.9 6.4E-05 37.4 1.1 27 162-189 118-144 (242)
277 cd03467 Rieske Rieske domain; 65.7 4.6 0.0001 29.9 2.0 43 160-204 38-80 (98)
278 PF01363 FYVE: FYVE zinc finge 65.6 3.4 7.4E-05 29.4 1.2 28 161-193 9-36 (69)
279 COG5525 Bacteriophage tail ass 65.6 3.7 8E-05 42.3 1.8 38 157-194 223-271 (611)
280 PRK10996 thioredoxin 2; Provis 65.3 4.7 0.0001 32.4 2.0 32 161-193 2-33 (139)
281 COG5257 GCD11 Translation init 65.2 4.6 0.0001 39.8 2.3 33 163-208 59-92 (415)
282 PF14255 Cys_rich_CPXG: Cystei 64.6 6.6 0.00014 28.4 2.5 32 163-194 2-36 (52)
283 PRK08332 ribonucleotide-diphos 64.5 4 8.7E-05 46.4 2.0 29 162-190 1705-1734(1740)
284 PF05207 zf-CSL: CSL zinc fing 64.4 2.9 6.3E-05 30.0 0.7 37 158-195 15-53 (55)
285 COG1439 Predicted nucleic acid 64.4 3.9 8.4E-05 36.3 1.5 25 163-194 141-165 (177)
286 PF14206 Cys_rich_CPCC: Cystei 64.2 5.2 0.00011 31.2 2.0 27 162-190 2-28 (78)
287 PF10058 DUF2296: Predicted in 64.2 4 8.7E-05 29.5 1.3 33 158-190 19-52 (54)
288 PF00301 Rubredoxin: Rubredoxi 64.1 4.9 0.00011 28.4 1.7 29 163-191 3-43 (47)
289 TIGR00622 ssl1 transcription f 64.1 4.4 9.6E-05 33.5 1.7 24 163-193 3-26 (112)
290 PF03833 PolC_DP2: DNA polymer 64.1 2.2 4.9E-05 45.5 0.0 27 159-193 665-691 (900)
291 TIGR00595 priA primosomal prot 63.9 4.6 0.0001 39.6 2.1 11 163-173 215-225 (505)
292 PRK00464 nrdR transcriptional 63.5 4.2 9E-05 34.9 1.5 23 158-180 23-47 (154)
293 smart00504 Ubox Modified RING 63.4 1.6 3.4E-05 29.9 -0.8 13 182-194 35-47 (63)
294 PF14319 Zn_Tnp_IS91: Transpos 62.5 6.9 0.00015 31.4 2.5 29 159-191 40-69 (111)
295 PRK13902 alaS alanyl-tRNA synt 62.4 5.7 0.00012 42.2 2.6 59 154-223 12-74 (900)
296 PF09788 Tmemb_55A: Transmembr 62.0 4.6 0.0001 37.7 1.6 34 159-194 155-189 (256)
297 TIGR02230 ATPase_gene1 F0F1-AT 61.7 12 0.00027 30.3 3.8 9 101-109 35-43 (100)
298 TIGR03829 YokU_near_AblA uncha 61.6 5.7 0.00012 31.7 1.9 14 181-194 34-47 (89)
299 KOG1247 Methionyl-tRNA synthet 61.4 2.4 5.2E-05 42.8 -0.3 31 154-192 145-175 (567)
300 PF05280 FlhC: Flagellar trans 61.3 6.8 0.00015 34.1 2.5 30 160-190 133-162 (175)
301 PRK03922 hypothetical protein; 61.0 3.9 8.4E-05 34.2 0.9 16 178-193 45-60 (113)
302 PLN02569 threonine synthase 60.7 5.4 0.00012 39.3 1.9 29 163-197 51-79 (484)
303 PF12660 zf-TFIIIC: Putative z 60.6 6.5 0.00014 31.0 2.0 31 162-192 56-98 (99)
304 COG1571 Predicted DNA-binding 60.5 4.7 0.0001 39.8 1.5 32 163-198 352-383 (421)
305 PRK12585 putative monovalent c 60.5 31 0.00068 31.3 6.5 48 105-152 43-90 (197)
306 TIGR01206 lysW lysine biosynth 60.4 5.3 0.00011 29.1 1.4 15 183-197 3-17 (54)
307 PRK14873 primosome assembly pr 60.3 4.6 0.0001 41.4 1.4 26 163-191 394-419 (665)
308 PTZ00410 NAD-dependent SIR2; P 60.1 4.6 0.0001 38.7 1.3 32 162-193 148-182 (349)
309 PRK08329 threonine synthase; V 60.0 5.9 0.00013 36.6 2.0 26 163-195 3-28 (347)
310 COG1241 MCM2 Predicted ATPase 59.9 17 0.00037 37.9 5.4 53 163-218 131-187 (682)
311 COG1867 TRM1 N2,N2-dimethylgua 59.8 5.9 0.00013 38.8 2.0 27 163-193 242-268 (380)
312 TIGR00308 TRM1 tRNA(guanine-26 59.7 7.2 0.00016 37.2 2.5 30 163-194 235-264 (374)
313 smart00714 LITAF Possible memb 59.6 16 0.00035 26.3 3.8 8 163-170 54-61 (67)
314 PF09082 DUF1922: Domain of un 59.6 5 0.00011 30.9 1.2 33 162-199 4-36 (68)
315 PRK08115 ribonucleotide-diphos 59.6 4.4 9.5E-05 43.1 1.2 28 162-193 828-855 (858)
316 KOG2879 Predicted E3 ubiquitin 59.2 3.5 7.7E-05 39.2 0.4 31 163-193 241-287 (298)
317 PF11672 DUF3268: Protein of u 59.0 5.5 0.00012 32.3 1.4 17 182-198 2-18 (102)
318 PRK05638 threonine synthase; V 58.2 6.2 0.00013 37.7 1.8 26 163-195 3-28 (442)
319 PF13913 zf-C2HC_2: zinc-finge 58.2 5.5 0.00012 24.5 1.0 11 163-173 4-14 (25)
320 PF04606 Ogr_Delta: Ogr/Delta- 57.8 6.5 0.00014 27.0 1.4 32 163-194 1-39 (47)
321 COG1997 RPL43A Ribosomal prote 57.8 7.1 0.00015 31.5 1.8 27 163-192 37-63 (89)
322 PF06676 DUF1178: Protein of u 57.7 5.2 0.00011 34.4 1.1 31 160-191 4-41 (148)
323 PF02318 FYVE_2: FYVE-type zin 57.6 5 0.00011 32.0 1.0 30 159-192 52-81 (118)
324 PHA00733 hypothetical protein 57.5 4.7 0.0001 33.0 0.8 32 162-193 74-110 (128)
325 PRK05580 primosome assembly pr 57.5 6.8 0.00015 39.8 2.0 11 163-173 383-393 (679)
326 PF03563 Bunya_G2: Bunyavirus 56.8 23 0.00051 33.6 5.3 27 163-197 236-265 (285)
327 PF10601 zf-LITAF-like: LITAF- 56.7 23 0.00049 25.9 4.2 11 182-192 58-68 (73)
328 TIGR03676 aRF1/eRF1 peptide ch 56.5 8.6 0.00019 37.1 2.5 37 160-196 319-356 (403)
329 COG0423 GRS1 Glycyl-tRNA synth 56.1 4.9 0.00011 41.1 0.8 37 163-200 90-146 (558)
330 COG0498 ThrC Threonine synthas 56.0 4.8 0.0001 39.2 0.7 38 158-200 2-39 (411)
331 KOG3507 DNA-directed RNA polym 55.6 6.7 0.00015 29.8 1.3 30 158-191 17-46 (62)
332 TIGR00375 conserved hypothetic 55.3 5.9 0.00013 38.2 1.2 33 158-193 237-269 (374)
333 PRK12586 putative monovalent c 55.2 30 0.00065 29.8 5.3 48 105-152 46-93 (145)
334 TIGR00398 metG methionyl-tRNA 55.2 3.9 8.4E-05 39.4 -0.1 6 163-168 122-127 (530)
335 cd01409 SIRT4 SIRT4: Eukaryoti 55.0 5.9 0.00013 35.7 1.1 11 162-172 119-129 (260)
336 PRK06393 rpoE DNA-directed RNA 55.0 5.8 0.00013 30.1 0.9 20 162-190 6-25 (64)
337 PRK04173 glycyl-tRNA synthetas 54.4 4.9 0.00011 39.0 0.5 29 163-191 88-134 (456)
338 cd03529 Rieske_NirD Assimilato 54.4 11 0.00024 28.7 2.3 42 159-201 37-82 (103)
339 PF14471 DUF4428: Domain of un 54.3 3.7 8.1E-05 29.2 -0.2 29 163-192 1-30 (51)
340 PF01096 TFIIS_C: Transcriptio 54.3 7.9 0.00017 25.9 1.3 30 163-192 2-38 (39)
341 KOG4080 Mitochondrial ribosoma 54.3 3.5 7.7E-05 36.6 -0.4 21 163-191 95-115 (176)
342 COG3478 Predicted nucleic-acid 53.7 6.3 0.00014 30.5 0.9 37 163-203 6-42 (68)
343 PF01780 Ribosomal_L37ae: Ribo 53.7 6 0.00013 31.7 0.8 27 163-192 37-63 (90)
344 COG0266 Nei Formamidopyrimidin 53.4 9.2 0.0002 35.7 2.1 25 163-189 247-272 (273)
345 PRK14894 glycyl-tRNA synthetas 53.2 7 0.00015 39.8 1.3 23 163-190 90-112 (539)
346 PF00096 zf-C2H2: Zinc finger, 53.1 5.6 0.00012 22.6 0.4 11 163-173 2-12 (23)
347 TIGR03655 anti_R_Lar restricti 52.9 10 0.00023 26.5 1.8 32 163-194 3-38 (53)
348 smart00547 ZnF_RBZ Zinc finger 52.1 7.9 0.00017 23.1 1.0 22 163-191 4-25 (26)
349 PRK06319 DNA topoisomerase I/S 52.1 11 0.00024 39.7 2.6 19 182-200 645-663 (860)
350 PRK11088 rrmA 23S rRNA methylt 52.0 8.1 0.00018 33.9 1.4 28 163-196 4-31 (272)
351 KOG2906 RNA polymerase III sub 51.9 12 0.00026 31.0 2.2 32 163-195 3-34 (105)
352 TIGR01562 FdhE formate dehydro 51.7 8.6 0.00019 36.2 1.6 9 163-171 186-194 (305)
353 PF15135 UPF0515: Uncharacteri 51.6 8.8 0.00019 36.2 1.6 34 158-193 152-185 (278)
354 PF14690 zf-ISL3: zinc-finger 51.6 14 0.0003 24.4 2.2 17 182-198 2-18 (47)
355 PF11241 DUF3043: Protein of u 51.4 48 0.001 29.2 6.0 21 105-125 74-94 (170)
356 TIGR02159 PA_CoA_Oxy4 phenylac 51.2 5.8 0.00013 33.5 0.4 33 161-193 105-141 (146)
357 cd00065 FYVE FYVE domain; Zinc 51.2 11 0.00023 25.7 1.6 26 162-192 3-28 (57)
358 PRK03564 formate dehydrogenase 51.0 9.2 0.0002 36.2 1.7 9 162-170 188-196 (309)
359 PRK01343 zinc-binding protein; 50.5 8 0.00017 28.8 1.0 11 182-192 9-19 (57)
360 PF14257 DUF4349: Domain of un 50.0 24 0.00053 31.1 4.1 22 136-157 240-261 (262)
361 COG2995 PqiA Uncharacterized p 49.8 13 0.00028 37.0 2.5 32 163-196 20-52 (418)
362 PF09986 DUF2225: Uncharacteri 49.6 10 0.00022 33.3 1.7 16 180-195 3-18 (214)
363 TIGR00630 uvra excinuclease AB 49.4 8 0.00017 41.2 1.1 38 163-200 252-295 (924)
364 COG1110 Reverse gyrase [DNA re 49.1 8 0.00017 42.5 1.1 23 163-192 696-718 (1187)
365 PF11290 DUF3090: Protein of u 49.1 6.8 0.00015 34.6 0.5 20 178-198 150-169 (171)
366 TIGR01374 soxD sarcosine oxida 49.0 7.4 0.00016 30.8 0.6 36 183-221 2-41 (84)
367 COG1198 PriA Primosomal protei 48.9 10 0.00023 39.7 1.8 27 163-192 446-472 (730)
368 PF01396 zf-C4_Topoisom: Topoi 48.8 11 0.00023 25.4 1.3 18 183-200 2-19 (39)
369 TIGR00847 ccoS cytochrome oxid 48.7 25 0.00055 25.5 3.3 31 132-162 3-33 (51)
370 PRK14873 primosome assembly pr 48.4 12 0.00026 38.5 2.1 20 163-194 385-404 (665)
371 PF12760 Zn_Tnp_IS1595: Transp 48.3 16 0.00035 24.8 2.1 25 162-190 19-45 (46)
372 PRK00133 metG methionyl-tRNA s 48.3 6.8 0.00015 39.5 0.4 12 159-170 137-148 (673)
373 cd03530 Rieske_NirD_small_Baci 48.1 15 0.00033 27.4 2.2 38 159-198 37-74 (98)
374 PRK09401 reverse gyrase; Revie 48.0 8.2 0.00018 42.1 1.0 23 163-192 680-702 (1176)
375 smart00532 LIGANc Ligase N fam 48.0 10 0.00023 37.1 1.6 13 182-194 399-411 (441)
376 PRK07217 replication factor A; 47.7 10 0.00022 36.2 1.4 20 163-191 190-211 (311)
377 smart00778 Prim_Zn_Ribbon Zinc 47.7 14 0.00031 25.1 1.8 29 161-190 3-33 (37)
378 smart00440 ZnF_C2C2 C2C2 Zinc 47.5 15 0.00032 24.8 1.9 30 163-192 2-38 (40)
379 PRK11088 rrmA 23S rRNA methylt 47.5 12 0.00026 32.8 1.8 21 183-203 3-23 (272)
380 PF02005 TRM: N2,N2-dimethylgu 47.4 7 0.00015 37.3 0.3 31 163-195 242-272 (377)
381 KOG1734 Predicted RING-contain 47.1 4.4 9.5E-05 38.8 -1.1 34 161-194 224-282 (328)
382 PF06397 Desulfoferrod_N: Desu 46.9 8.8 0.00019 26.1 0.7 25 163-193 8-34 (36)
383 KOG4272 Predicted GTP-binding 46.9 11 0.00025 33.2 1.5 32 108-139 120-151 (164)
384 PRK09965 3-phenylpropionate di 46.7 16 0.00034 28.1 2.1 39 160-200 38-77 (106)
385 TIGR02611 conserved hypothetic 46.6 36 0.00079 28.7 4.4 28 109-138 32-59 (121)
386 PRK14526 adenylate kinase; Pro 46.4 15 0.00033 31.9 2.2 31 162-193 123-153 (211)
387 COG4307 Uncharacterized protei 46.2 6.8 0.00015 37.7 0.0 28 163-197 5-32 (349)
388 KOG2462 C2H2-type Zn-finger pr 45.9 11 0.00024 35.7 1.4 10 163-172 189-198 (279)
389 COG4323 Predicted membrane pro 45.7 20 0.00043 29.5 2.6 48 107-167 33-80 (105)
390 PRK05452 anaerobic nitric oxid 45.5 13 0.00028 36.3 1.8 30 163-192 427-468 (479)
391 PRK14529 adenylate kinase; Pro 45.3 14 0.0003 33.0 1.8 29 162-193 127-159 (223)
392 PF04161 Arv1: Arv1-like famil 45.2 9.7 0.00021 33.2 0.9 38 163-203 2-42 (208)
393 TIGR03829 YokU_near_AblA uncha 45.2 8.4 0.00018 30.8 0.4 21 153-173 19-47 (89)
394 smart00132 LIM Zinc-binding do 45.1 14 0.0003 22.4 1.3 31 163-193 1-38 (39)
395 PRK05333 NAD-dependent deacety 45.0 12 0.00027 33.9 1.5 11 183-193 180-190 (285)
396 PF01307 Plant_vir_prot: Plant 44.8 23 0.0005 28.7 2.9 18 149-168 87-104 (104)
397 PF13894 zf-C2H2_4: C2H2-type 44.7 11 0.00025 20.6 0.8 11 163-173 2-12 (24)
398 COG3024 Uncharacterized protei 44.5 11 0.00023 29.0 0.9 16 158-173 4-19 (65)
399 KOG2462 C2H2-type Zn-finger pr 44.5 14 0.00031 34.9 1.9 30 163-192 132-171 (279)
400 PF00641 zf-RanBP: Zn-finger i 44.5 15 0.00033 22.8 1.4 22 163-191 6-27 (30)
401 COG1328 NrdD Oxygen-sensitive 44.5 11 0.00024 39.3 1.3 27 158-191 638-664 (700)
402 COG5151 SSL1 RNA polymerase II 44.5 9.3 0.0002 37.5 0.7 23 163-192 310-332 (421)
403 COG5349 Uncharacterized protei 44.1 9.4 0.0002 32.5 0.6 31 162-194 22-52 (126)
404 KOG3134 Predicted membrane pro 43.9 7 0.00015 36.0 -0.2 30 163-192 2-34 (225)
405 TIGR03847 conserved hypothetic 43.9 8.9 0.00019 34.2 0.4 11 182-192 156-166 (177)
406 PF05265 DUF723: Protein of un 43.8 16 0.00036 27.5 1.7 30 160-189 31-60 (60)
407 PF15616 TerY-C: TerY-C metal 43.7 15 0.00032 31.1 1.7 11 182-192 77-87 (131)
408 COG2995 PqiA Uncharacterized p 43.6 25 0.00055 35.0 3.5 30 161-196 220-249 (418)
409 COG1327 Predicted transcriptio 43.4 8.9 0.00019 33.6 0.3 16 162-177 29-44 (156)
410 TIGR01384 TFS_arch transcripti 43.4 14 0.0003 28.4 1.4 25 184-208 2-26 (104)
411 PLN02610 probable methionyl-tR 43.3 8 0.00017 40.5 0.0 22 23-44 16-37 (801)
412 PLN03086 PRLI-interacting fact 43.3 14 0.0003 37.8 1.7 27 163-192 435-463 (567)
413 PRK14973 DNA topoisomerase I; 42.8 21 0.00045 38.4 2.9 16 183-198 636-653 (936)
414 COG1885 Uncharacterized protei 42.7 12 0.00026 31.3 1.0 15 179-193 46-60 (115)
415 PF01921 tRNA-synt_1f: tRNA sy 42.7 15 0.00033 35.6 1.8 39 157-195 170-212 (360)
416 PF13829 DUF4191: Domain of un 42.5 42 0.00092 30.8 4.5 34 105-138 29-62 (224)
417 PF13465 zf-H2C2_2: Zinc-finge 42.4 10 0.00022 23.1 0.4 10 163-172 16-25 (26)
418 PRK01642 cls cardiolipin synth 42.3 45 0.00097 32.4 4.9 29 132-161 33-61 (483)
419 PF12666 PrgI: PrgI family pro 41.8 58 0.0013 24.5 4.5 44 104-147 18-61 (93)
420 PF00355 Rieske: Rieske [2Fe-2 41.6 20 0.00044 26.3 2.0 47 159-205 38-84 (97)
421 PF06906 DUF1272: Protein of u 41.6 12 0.00027 28.0 0.8 10 182-191 41-50 (57)
422 PF07787 DUF1625: Protein of u 41.5 62 0.0013 28.7 5.3 49 105-153 186-243 (248)
423 cd03469 Rieske_RO_Alpha_N Ries 41.5 34 0.00074 25.9 3.3 41 160-203 39-80 (118)
424 PRK01816 hypothetical protein; 41.1 38 0.00081 29.4 3.7 29 129-161 60-88 (143)
425 TIGR00244 transcriptional regu 40.8 21 0.00045 30.9 2.2 31 163-193 2-39 (147)
426 TIGR01300 CPA3_mnhG_phaG monov 40.5 83 0.0018 25.0 5.4 48 105-152 33-80 (97)
427 COG4068 Uncharacterized protei 40.4 10 0.00022 29.0 0.2 25 162-193 9-34 (64)
428 TIGR03022 WbaP_sugtrans Undeca 40.1 46 0.00099 31.5 4.5 30 126-155 258-287 (456)
429 PF04423 Rad50_zn_hook: Rad50 40.1 12 0.00025 26.1 0.4 18 178-195 16-33 (54)
430 PRK12587 putative monovalent c 40.1 73 0.0016 26.4 5.2 48 105-152 44-91 (118)
431 TIGR00244 transcriptional regu 39.8 15 0.00032 31.8 1.1 16 162-177 29-44 (147)
432 PRK03564 formate dehydrogenase 39.8 20 0.00043 34.0 2.1 22 163-191 214-235 (309)
433 PF04267 SoxD: Sarcosine oxida 39.8 7.4 0.00016 30.7 -0.6 35 183-220 2-40 (84)
434 TIGR01054 rgy reverse gyrase. 39.8 12 0.00027 40.7 0.8 22 163-191 680-701 (1171)
435 TIGR02642 phage_xxxx uncharact 39.6 51 0.0011 29.2 4.5 29 161-194 99-127 (186)
436 PF08882 Acetone_carb_G: Aceto 39.6 15 0.00034 30.6 1.2 15 182-196 74-88 (112)
437 PF12230 PRP21_like_P: Pre-mRN 39.5 9.8 0.00021 33.2 0.0 15 182-196 168-182 (229)
438 PF05502 Dynactin_p62: Dynacti 39.1 17 0.00036 36.1 1.5 39 161-199 26-69 (483)
439 PRK09678 DNA-binding transcrip 39.1 25 0.00054 27.0 2.1 33 163-195 3-42 (72)
440 PF10013 DUF2256: Uncharacteri 38.9 13 0.00029 26.3 0.6 15 158-172 5-19 (42)
441 PRK00349 uvrA excinuclease ABC 38.8 16 0.00034 39.2 1.4 39 163-201 254-298 (943)
442 PF06170 DUF983: Protein of un 38.8 13 0.00028 29.1 0.6 15 182-196 8-22 (86)
443 TIGR00389 glyS_dimeric glycyl- 38.8 10 0.00022 38.5 -0.0 52 140-191 63-133 (551)
444 COG3677 Transposase and inacti 38.8 31 0.00066 28.6 2.8 36 161-197 30-68 (129)
445 PF07975 C1_4: TFIIH C1-like d 38.6 15 0.00032 26.6 0.8 29 161-189 21-50 (51)
446 PRK00420 hypothetical protein; 38.6 21 0.00045 29.5 1.8 21 182-202 23-44 (112)
447 PHA02446 hypothetical protein 38.5 18 0.0004 31.3 1.5 33 163-195 64-101 (166)
448 PF11808 DUF3329: Domain of un 38.2 61 0.0013 24.9 4.2 20 117-136 13-32 (90)
449 TIGR01562 FdhE formate dehydro 38.1 19 0.00041 34.0 1.6 22 163-191 212-233 (305)
450 PF03904 DUF334: Domain of unk 38.0 94 0.002 28.9 6.0 46 108-153 154-219 (230)
451 smart00532 LIGANc Ligase N fam 37.6 19 0.00041 35.3 1.6 25 162-190 400-427 (441)
452 PRK14350 ligA NAD-dependent DN 37.2 18 0.00039 37.4 1.5 24 163-191 400-425 (669)
453 PF09862 DUF2089: Protein of u 37.2 20 0.00042 29.7 1.4 22 185-206 1-22 (113)
454 PF04641 Rtf2: Rtf2 RING-finge 37.0 13 0.00029 33.3 0.4 14 182-195 150-163 (260)
455 smart00531 TFIIE Transcription 36.8 13 0.00028 30.7 0.3 18 179-196 96-113 (147)
456 TIGR00280 L37a ribosomal prote 36.6 20 0.00044 28.8 1.4 27 163-192 37-63 (91)
457 PRK12267 methionyl-tRNA synthe 36.4 19 0.00042 36.0 1.5 36 163-201 127-164 (648)
458 PF12647 RNHCP: RNHCP domain; 36.2 23 0.0005 28.6 1.6 30 162-195 5-37 (92)
459 COG2191 Formylmethanofuran deh 36.2 18 0.00039 33.0 1.1 28 163-190 174-201 (206)
460 PF12273 RCR: Chitin synthesis 36.2 28 0.00062 28.0 2.2 32 142-173 10-41 (130)
461 PRK12775 putative trifunctiona 35.9 18 0.00039 38.6 1.2 31 163-193 798-849 (1006)
462 COG0551 TopA Zn-finger domain 35.8 34 0.00073 27.7 2.6 30 161-195 85-114 (140)
463 COG0068 HypF Hydrogenase matur 35.7 15 0.00033 38.8 0.7 14 163-176 125-138 (750)
464 COG1645 Uncharacterized Zn-fin 35.7 21 0.00046 30.4 1.4 20 182-201 28-47 (131)
465 TIGR02377 MocE_fam_FeS Rieske 35.7 30 0.00064 26.4 2.1 40 160-201 39-78 (101)
466 PRK04351 hypothetical protein; 35.6 36 0.00078 28.9 2.8 38 158-196 109-146 (149)
467 PRK12671 putative monovalent c 35.6 94 0.002 26.0 5.2 48 105-152 49-96 (120)
468 PF13806 Rieske_2: Rieske-like 35.5 12 0.00026 29.4 -0.0 38 160-198 39-80 (104)
469 TIGR01054 rgy reverse gyrase. 35.5 16 0.00035 39.8 0.9 29 159-190 5-33 (1171)
470 COG1379 PHP family phosphoeste 35.4 8.7 0.00019 37.7 -1.0 33 158-192 243-275 (403)
471 PF06093 Spt4: Spt4/RpoE2 zinc 35.3 6.9 0.00015 30.1 -1.4 29 162-195 2-30 (77)
472 PLN02294 cytochrome c oxidase 35.2 24 0.00052 31.5 1.7 15 181-195 140-154 (174)
473 COG2401 ABC-type ATPase fused 34.9 17 0.00038 37.2 0.9 27 163-196 132-158 (593)
474 TIGR03025 EPS_sugtrans exopoly 34.9 54 0.0012 30.9 4.1 31 126-156 257-287 (445)
475 PRK14351 ligA NAD-dependent DN 34.9 23 0.0005 36.7 1.8 10 163-172 425-434 (689)
476 PF04981 NMD3: NMD3 family ; 34.9 15 0.00031 32.5 0.3 40 160-202 12-53 (236)
477 PF04438 zf-HIT: HIT zinc fing 34.8 23 0.0005 22.8 1.2 21 162-192 3-23 (30)
478 PF14447 Prok-RING_4: Prokaryo 34.8 18 0.00039 26.9 0.7 16 181-196 38-53 (55)
479 PRK01345 heat shock protein Ht 34.8 58 0.0013 30.3 4.2 35 124-160 18-52 (317)
480 KOG3623 Homeobox transcription 34.7 12 0.00026 40.2 -0.3 31 163-194 283-321 (1007)
481 PF13397 DUF4109: Domain of un 34.5 41 0.00088 27.8 2.8 42 156-198 23-66 (105)
482 COG0068 HypF Hydrogenase matur 34.5 16 0.00035 38.7 0.6 33 163-195 153-186 (750)
483 smart00734 ZnF_Rad18 Rad18-lik 34.5 19 0.00041 22.4 0.7 10 162-171 2-11 (26)
484 PRK00241 nudC NADH pyrophospha 34.4 25 0.00054 31.8 1.7 26 178-203 95-120 (256)
485 PTZ00255 60S ribosomal protein 34.3 24 0.00052 28.4 1.4 27 163-192 38-64 (90)
486 PRK07956 ligA NAD-dependent DN 34.3 23 0.00051 36.4 1.7 23 163-188 406-431 (665)
487 TIGR03023 WcaJ_sugtrans Undeca 34.2 56 0.0012 30.8 4.1 50 126-175 260-313 (451)
488 PF13451 zf-trcl: Probable zin 34.1 19 0.00042 26.0 0.8 28 161-188 4-39 (49)
489 TIGR00143 hypF [NiFe] hydrogen 34.1 16 0.00035 37.9 0.5 33 163-195 120-153 (711)
490 PF08209 Sgf11: Sgf11 (transcr 34.0 20 0.00044 23.9 0.9 11 182-192 4-14 (33)
491 COG0272 Lig NAD-dependent DNA 33.9 19 0.00041 37.7 1.0 28 162-192 405-435 (667)
492 KOG1598 Transcription initiati 33.9 24 0.00051 36.0 1.6 29 163-193 2-30 (521)
493 PHA01886 TM2 domain-containing 33.8 30 0.00066 27.1 1.9 13 122-134 38-50 (78)
494 PLN02224 methionine-tRNA ligas 33.8 22 0.00047 36.3 1.4 28 163-193 192-219 (616)
495 PF12861 zf-Apc11: Anaphase-pr 33.7 30 0.00065 27.5 1.9 16 181-196 70-85 (85)
496 PRK03976 rpl37ae 50S ribosomal 33.6 25 0.00054 28.3 1.4 27 163-192 38-64 (90)
497 PF06127 DUF962: Protein of un 33.5 87 0.0019 24.3 4.4 47 107-166 25-71 (95)
498 COG1110 Reverse gyrase [DNA re 33.5 16 0.00034 40.4 0.4 27 159-188 6-32 (1187)
499 KOG3362 Predicted BBOX Zn-fing 33.3 14 0.0003 32.4 -0.0 20 163-192 120-139 (156)
500 PRK07219 DNA topoisomerase I; 33.3 38 0.00083 35.4 3.1 18 182-199 688-705 (822)
No 1
>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=98.87 E-value=7.7e-10 Score=88.82 Aligned_cols=31 Identities=35% Similarity=0.894 Sum_probs=29.4
Q ss_pred eccCCCCCceeeecccccCCCcccCCCCCCceeee
Q 025946 161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVV 195 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd 195 (245)
.++||+||++||+ ||++|++||+||+.++++
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 4699999999999 999999999999999888
No 2
>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=98.63 E-value=1.2e-08 Score=85.04 Aligned_cols=31 Identities=32% Similarity=0.636 Sum_probs=28.8
Q ss_pred eccCCCCCceeeecccccCCCcccCCCCCCceeee
Q 025946 161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVV 195 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd 195 (245)
.++||+||++||+ ||++|++||+||+.++.+
T Consensus 9 Kr~Cp~cg~kFYD----Lnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 9 KRICPNTGSKFYD----LNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred cccCCCcCccccc----cCCCCccCCCcCCccCcc
Confidence 4699999999999 999999999999998766
No 3
>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=98.44 E-value=5.9e-07 Score=73.83 Aligned_cols=60 Identities=27% Similarity=0.630 Sum_probs=41.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcC---cceeccCCCCCceeeecccccCCCcccCCCCCCceeeeCCe
Q 025946 134 VSIWLLAVIVPIVGFGAFLWWASR---DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDK 198 (245)
Q Consensus 134 ~~L~LlllllPIl~~~Gf~WWl~r---nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~ 198 (245)
.+++.++=++-+++..+.-.|++= +-+|.+||+|++..-. |.+. ..|++|++|+..|.+.
T Consensus 39 m~ifmllG~L~~l~S~~VYfwIGmlStkav~V~CP~C~K~TKm----LGr~-D~CM~C~~pLTLd~~l 101 (114)
T PF11023_consen 39 MVIFMLLGLLAILASTAVYFWIGMLSTKAVQVECPNCGKQTKM----LGRV-DACMHCKEPLTLDPSL 101 (114)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhcccceeeECCCCCChHhh----hchh-hccCcCCCcCccCchh
Confidence 333333334444455666667764 6788899999988765 4444 4999999999987653
No 4
>PRK00420 hypothetical protein; Validated
Probab=98.28 E-value=2.8e-07 Score=74.97 Aligned_cols=39 Identities=26% Similarity=0.577 Sum_probs=35.0
Q ss_pred cCcceeccCCCCCceeeecccccCCCcccCCCCCCceeeeCCe
Q 025946 156 SRDIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDK 198 (245)
Q Consensus 156 ~rnLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~ 198 (245)
++..+..+||+||.+++- +++++.+||+||+++.+++++
T Consensus 18 Ga~ml~~~CP~Cg~pLf~----lk~g~~~Cp~Cg~~~~v~~~e 56 (112)
T PRK00420 18 GAKMLSKHCPVCGLPLFE----LKDGEVVCPVHGKVYIVKSDE 56 (112)
T ss_pred HHHHccCCCCCCCCccee----cCCCceECCCCCCeeeeccHH
Confidence 556678899999999999 799999999999999998866
No 5
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=98.18 E-value=4.4e-07 Score=75.36 Aligned_cols=30 Identities=23% Similarity=0.470 Sum_probs=27.3
Q ss_pred eccCCCCCceeeecccccCCCcccCCCCCCceee
Q 025946 161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSV 194 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~V 194 (245)
.++||+||++||+ ||++|++|||||+.++.
T Consensus 9 KridPetg~KFYD----LNrdPiVsPytG~s~P~ 38 (129)
T COG4530 9 KRIDPETGKKFYD----LNRDPIVSPYTGKSYPR 38 (129)
T ss_pred cccCccccchhhc----cCCCccccCcccccchH
Confidence 3589999999999 99999999999998853
No 6
>PRK02935 hypothetical protein; Provisional
Probab=98.14 E-value=7.7e-06 Score=66.96 Aligned_cols=60 Identities=22% Similarity=0.592 Sum_probs=42.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhc---CcceeccCCCCCceeeecccccCCCcccCCCCCCceeeeCCe
Q 025946 134 VSIWLLAVIVPIVGFGAFLWWAS---RDIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDK 198 (245)
Q Consensus 134 ~~L~LlllllPIl~~~Gf~WWl~---rnLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~ 198 (245)
..+++++=++-+++..+.-+|++ -+-+|.+||+|++.--. |. ..-.|++|+|||..|.++
T Consensus 40 m~ifm~~G~l~~l~S~vvYFwiGmlStkavqV~CP~C~K~TKm----LG-rvD~CM~C~~PLTLd~~l 102 (110)
T PRK02935 40 MTIFMLLGFLAVIASTVVYFWIGMLSTKAVQVICPSCEKPTKM----LG-RVDACMHCNQPLTLDRSL 102 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhcccceeeECCCCCchhhh----cc-ceeecCcCCCcCCcCccc
Confidence 33444444445555566677876 58899999999987665 33 345899999999988765
No 7
>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=98.11 E-value=2e-06 Score=56.06 Aligned_cols=35 Identities=26% Similarity=0.651 Sum_probs=29.3
Q ss_pred eeccCCCCCceeeecccccCCC--cccCCCCCCceee
Q 025946 160 VQDSCPNCGNDFQIFKSTLNDE--LQLCPYCSQPFSV 194 (245)
Q Consensus 160 IE~tCPnCG~eF~~~ed~Ln~d--~iqCPnCGE~L~V 194 (245)
+..+||+|++.|+..++.+.+. .++||+||+++.+
T Consensus 1 M~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~~ 37 (38)
T TIGR02098 1 MRIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWYA 37 (38)
T ss_pred CEEECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEEe
Confidence 3568999999999988877654 6999999999864
No 8
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=97.95 E-value=2.7e-06 Score=52.71 Aligned_cols=26 Identities=31% Similarity=0.974 Sum_probs=21.7
Q ss_pred eeccCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
++..||+||++... +...||+||++|
T Consensus 1 m~~~Cp~Cg~~~~~-------~~~fC~~CG~~L 26 (26)
T PF13248_consen 1 MEMFCPNCGAEIDP-------DAKFCPNCGAKL 26 (26)
T ss_pred CcCCCcccCCcCCc-------ccccChhhCCCC
Confidence 57799999986444 899999999975
No 9
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=97.76 E-value=2.4e-05 Score=53.27 Aligned_cols=35 Identities=20% Similarity=0.556 Sum_probs=27.6
Q ss_pred eeccCCCCCceeeecccccCCCcccCCCCCCceeeeCC
Q 025946 160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDD 197 (245)
Q Consensus 160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~ 197 (245)
++..||+||.++..++.. +...||+||.++..+++
T Consensus 2 ~~y~C~~CG~~~~~~~~~---~~~~Cp~CG~~~~~~~~ 36 (46)
T PRK00398 2 AEYKCARCGREVELDEYG---TGVRCPYCGYRILFKER 36 (46)
T ss_pred CEEECCCCCCEEEECCCC---CceECCCCCCeEEEccC
Confidence 466899999999884333 38999999999886654
No 10
>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=97.62 E-value=6e-05 Score=48.93 Aligned_cols=34 Identities=29% Similarity=0.808 Sum_probs=27.1
Q ss_pred ceeccCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 159 IVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 159 LIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
+|+-.||.||++|......-......||.||..+
T Consensus 3 ~Y~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~ 36 (41)
T smart00834 3 IYEYRCEDCGHTFEVLQKISDDPLATCPECGGDV 36 (41)
T ss_pred CEEEEcCCCCCEEEEEEecCCCCCCCCCCCCCcc
Confidence 5778999999999875544346789999999854
No 11
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=97.59 E-value=3.5e-05 Score=51.14 Aligned_cols=35 Identities=31% Similarity=0.722 Sum_probs=28.8
Q ss_pred eeccCCCCCceeeecccccCC--CcccCCCCCCceee
Q 025946 160 VQDSCPNCGNDFQIFKSTLND--ELQLCPYCSQPFSV 194 (245)
Q Consensus 160 IE~tCPnCG~eF~~~ed~Ln~--d~iqCPnCGE~L~V 194 (245)
+..+||+|+..|.+.++-|.. ..+.||+|++.+.+
T Consensus 1 M~i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~v 37 (37)
T PF13719_consen 1 MIITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFRV 37 (37)
T ss_pred CEEECCCCCceEEcCHHHcccCCcEEECCCCCcEeeC
Confidence 356899999999998776544 58999999998754
No 12
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=97.58 E-value=2.1e-05 Score=48.06 Aligned_cols=23 Identities=39% Similarity=1.224 Sum_probs=19.8
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
-||+||++..+ +...||+||.+|
T Consensus 1 ~Cp~CG~~~~~-------~~~fC~~CG~~l 23 (23)
T PF13240_consen 1 YCPNCGAEIED-------DAKFCPNCGTPL 23 (23)
T ss_pred CCcccCCCCCC-------cCcchhhhCCcC
Confidence 39999999665 899999999875
No 13
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=97.51 E-value=5.2e-05 Score=50.30 Aligned_cols=33 Identities=24% Similarity=0.635 Sum_probs=27.7
Q ss_pred eeccCCCCCceeeecccccCCC--cccCCCCCCce
Q 025946 160 VQDSCPNCGNDFQIFKSTLNDE--LQLCPYCSQPF 192 (245)
Q Consensus 160 IE~tCPnCG~eF~~~ed~Ln~d--~iqCPnCGE~L 192 (245)
+..+||+|+++|.+.|+.+-.. .++||+||+.+
T Consensus 1 M~i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 1 MIITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred CEEECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 4578999999999987776653 79999999876
No 14
>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=97.48 E-value=8.6e-05 Score=53.81 Aligned_cols=34 Identities=35% Similarity=0.825 Sum_probs=29.2
Q ss_pred eccCCCCCceeeecccccCCCcccCCCCCCceeee
Q 025946 161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVV 195 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd 195 (245)
+.+||.||.++...++.+ ...+.||.||..|++.
T Consensus 2 ~~~CP~CG~~iev~~~~~-GeiV~Cp~CGaeleVv 35 (54)
T TIGR01206 2 QFECPDCGAEIELENPEL-GELVICDECGAELEVV 35 (54)
T ss_pred ccCCCCCCCEEecCCCcc-CCEEeCCCCCCEEEEE
Confidence 458999999999866666 6789999999999975
No 15
>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=97.30 E-value=0.00027 Score=47.90 Aligned_cols=34 Identities=29% Similarity=0.790 Sum_probs=28.1
Q ss_pred ceeccCCCCCceeeecccccCCCcccCCCCCC-ce
Q 025946 159 IVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQ-PF 192 (245)
Q Consensus 159 LIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE-~L 192 (245)
+|+-.|+.||.+|-..-..-.+++..||.||+ .+
T Consensus 3 ~Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~~ 37 (42)
T PF09723_consen 3 IYEYRCEECGHEFEVLQSISEDDPVPCPECGSTEV 37 (42)
T ss_pred CEEEEeCCCCCEEEEEEEcCCCCCCcCCCCCCCce
Confidence 68889999999999865554568999999998 44
No 16
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=97.26 E-value=0.00013 Score=59.97 Aligned_cols=38 Identities=24% Similarity=0.616 Sum_probs=29.5
Q ss_pred eccCCCCCceeeecccccC-C--CcccCCCCCCceeeeCCe
Q 025946 161 QDSCPNCGNDFQIFKSTLN-D--ELQLCPYCSQPFSVVDDK 198 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~Ln-~--d~iqCPnCGE~L~Vd~~~ 198 (245)
.-.||+||.+|..+|.... + +...||+||+++..+++.
T Consensus 99 ~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~~dn~ 139 (147)
T smart00531 99 YYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEEDDNS 139 (147)
T ss_pred EEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEEEcCch
Confidence 3489999999998665532 2 248999999999988774
No 17
>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=96.97 E-value=0.00072 Score=46.34 Aligned_cols=32 Identities=31% Similarity=0.841 Sum_probs=24.4
Q ss_pred ceeccCCCCCceeeecccccCCCcccCCCCCC
Q 025946 159 IVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQ 190 (245)
Q Consensus 159 LIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE 190 (245)
+|+-.|+.||.+|-.....=.++.+.||.||.
T Consensus 3 ~Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 3 IYEYRCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred CEEEEeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 57889999999888843221236788999998
No 18
>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=96.90 E-value=0.00057 Score=46.03 Aligned_cols=30 Identities=30% Similarity=0.763 Sum_probs=22.0
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceee
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSV 194 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~V 194 (245)
.||+||.+...+ | -.+++.+||+||.+++-
T Consensus 2 ~Cp~Cg~~~~~~-D-~~~g~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 2 KCPNCGSKEIVF-D-PERGELVCPNCGLVLEE 31 (43)
T ss_dssp SBTTTSSSEEEE-E-TTTTEEEETTT-BBEE-
T ss_pred CCcCCcCCceEE-c-CCCCeEECCCCCCEeec
Confidence 699999987432 2 45689999999999863
No 19
>PF14353 CpXC: CpXC protein
Probab=96.90 E-value=0.001 Score=52.83 Aligned_cols=44 Identities=23% Similarity=0.663 Sum_probs=30.6
Q ss_pred eccCCCCCceeee-cccccCC--C-------------cccCCCCCCceeeeCCeeEEecc
Q 025946 161 QDSCPNCGNDFQI-FKSTLND--E-------------LQLCPYCSQPFSVVDDKFVRESV 204 (245)
Q Consensus 161 E~tCPnCG~eF~~-~ed~Ln~--d-------------~iqCPnCGE~L~Vd~~~F~R~~~ 204 (245)
|.+||+||++|.. ..+.+|- + ..+||+||+.+.++-.=-..|+.
T Consensus 1 ~itCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~~~~~p~lY~D~~ 60 (128)
T PF14353_consen 1 EITCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKFRLEYPLLYHDPE 60 (128)
T ss_pred CcCCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCceecCCCEEEEcCC
Confidence 5699999999876 2222332 1 57899999998887665555544
No 20
>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=96.59 E-value=0.001 Score=41.97 Aligned_cols=24 Identities=33% Similarity=1.045 Sum_probs=20.7
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
+||.|+.+... +...||+||-.|.
T Consensus 2 ~CP~C~~~V~~-------~~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAEVPE-------SAKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCCchh-------hcCcCCCCCCCCc
Confidence 79999999766 8999999998763
No 21
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=96.56 E-value=0.0011 Score=54.36 Aligned_cols=28 Identities=29% Similarity=0.859 Sum_probs=25.5
Q ss_pred CCCCCceeeecccccCCCcccCCCCCCceeeeCCeeEE
Q 025946 164 CPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVR 201 (245)
Q Consensus 164 CPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R 201 (245)
||+||.++.+ +...||+|++.+ +|+|.-
T Consensus 1 CPvCg~~l~v-------t~l~C~~C~t~i---~G~F~l 28 (113)
T PF09862_consen 1 CPVCGGELVV-------TRLKCPSCGTEI---EGEFEL 28 (113)
T ss_pred CCCCCCceEE-------EEEEcCCCCCEE---Eeeecc
Confidence 9999999999 899999999998 677864
No 22
>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=96.51 E-value=0.0015 Score=45.07 Aligned_cols=31 Identities=23% Similarity=0.651 Sum_probs=27.5
Q ss_pred hcCcceeccCCCCCceeeecccccCCCcccCCCCC
Q 025946 155 ASRDIVQDSCPNCGNDFQIFKSTLNDELQLCPYCS 189 (245)
Q Consensus 155 l~rnLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCG 189 (245)
.+|.++..+||.||.+..- ..++.+.||.|+
T Consensus 11 ~G~~ML~~~Cp~C~~PL~~----~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 11 QGWTMLDEHCPDCGTPLMR----DKDGKIYCVSCG 41 (41)
T ss_pred HhHhHhcCccCCCCCeeEE----ecCCCEECCCCC
Confidence 5788999999999999887 577899999996
No 23
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=96.47 E-value=0.0013 Score=48.08 Aligned_cols=32 Identities=31% Similarity=0.895 Sum_probs=26.6
Q ss_pred cceeccCCCCCceeeecccccCCCcccCCCCCCceee
Q 025946 158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSV 194 (245)
Q Consensus 158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~V 194 (245)
|+....||.||.+|.. .+|-++||.||+|+..
T Consensus 2 ~~~~~~C~~Cg~~~~~-----~dDiVvCp~CgapyHR 33 (54)
T PF14446_consen 2 NYEGCKCPVCGKKFKD-----GDDIVVCPECGAPYHR 33 (54)
T ss_pred CccCccChhhCCcccC-----CCCEEECCCCCCcccH
Confidence 4567799999999975 5588999999999853
No 24
>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=96.46 E-value=0.0014 Score=55.10 Aligned_cols=35 Identities=23% Similarity=0.467 Sum_probs=27.4
Q ss_pred eccCCCCCceeeecccccCCCcccCCCCCCceeeeCC
Q 025946 161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDD 197 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~ 197 (245)
.-.||+|+.+++. +++++ ..-.||.||++|.-.|+
T Consensus 109 ~Y~Cp~c~~r~tf-~eA~~-~~F~Cp~Cg~~L~~~dn 143 (158)
T TIGR00373 109 FFICPNMCVRFTF-NEAME-LNFTCPRCGAMLDYLDN 143 (158)
T ss_pred eEECCCCCcEeeH-HHHHH-cCCcCCCCCCEeeeccC
Confidence 3489999988776 55555 46999999999986664
No 25
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=96.44 E-value=0.003 Score=43.85 Aligned_cols=32 Identities=19% Similarity=0.438 Sum_probs=25.9
Q ss_pred eccCCCCCceeeecccccCCCcccCCCCCCceeeeC
Q 025946 161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVD 196 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~ 196 (245)
.-.|..||.++.. -..+++.||+||..+-...
T Consensus 2 ~Y~C~~Cg~~~~~----~~~~~irC~~CG~rIlyK~ 33 (44)
T smart00659 2 IYICGECGRENEI----KSKDVVRCRECGYRILYKK 33 (44)
T ss_pred EEECCCCCCEeec----CCCCceECCCCCceEEEEe
Confidence 4579999999987 2468999999999876554
No 26
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=96.43 E-value=0.0015 Score=56.05 Aligned_cols=36 Identities=25% Similarity=0.486 Sum_probs=27.5
Q ss_pred eeccCCCCCceeeecccccCCCcccCCCCCCceeeeCC
Q 025946 160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDD 197 (245)
Q Consensus 160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~ 197 (245)
..-.||+|+.+++.+ ++++ ..-.||.||++|.-.|+
T Consensus 116 ~~Y~Cp~C~~rytf~-eA~~-~~F~Cp~Cg~~L~~~dn 151 (178)
T PRK06266 116 MFFFCPNCHIRFTFD-EAME-YGFRCPQCGEMLEEYDN 151 (178)
T ss_pred CEEECCCCCcEEeHH-HHhh-cCCcCCCCCCCCeeccc
Confidence 334899999888874 4554 47999999999986543
No 27
>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=96.11 E-value=0.0037 Score=41.18 Aligned_cols=27 Identities=22% Similarity=0.679 Sum_probs=20.7
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
.|..||.++.. -..++++||+||-.+-
T Consensus 2 ~C~~Cg~~~~~----~~~~~irC~~CG~RIl 28 (32)
T PF03604_consen 2 ICGECGAEVEL----KPGDPIRCPECGHRIL 28 (32)
T ss_dssp BESSSSSSE-B----STSSTSSBSSSS-SEE
T ss_pred CCCcCCCeeEc----CCCCcEECCcCCCeEE
Confidence 59999999986 4568999999997653
No 28
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=95.96 E-value=0.0036 Score=54.18 Aligned_cols=23 Identities=35% Similarity=1.032 Sum_probs=20.3
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCc
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQP 191 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~ 191 (245)
.||+||+...+ ..|-+||.||.+
T Consensus 136 vC~vCGy~~~g------e~P~~CPiCga~ 158 (166)
T COG1592 136 VCPVCGYTHEG------EAPEVCPICGAP 158 (166)
T ss_pred EcCCCCCcccC------CCCCcCCCCCCh
Confidence 79999998876 369999999976
No 29
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=95.86 E-value=0.004 Score=52.42 Aligned_cols=29 Identities=28% Similarity=0.801 Sum_probs=24.4
Q ss_pred CcceeccCCCCCceeeecccccCCCcccCCCCCC
Q 025946 157 RDIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQ 190 (245)
Q Consensus 157 rnLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE 190 (245)
-.++.-+||.||.+++- +++.+.||.||.
T Consensus 24 AkML~~hCp~Cg~PLF~-----KdG~v~CPvC~~ 52 (131)
T COG1645 24 AKMLAKHCPKCGTPLFR-----KDGEVFCPVCGY 52 (131)
T ss_pred hHHHHhhCcccCCccee-----eCCeEECCCCCc
Confidence 34566799999999886 779999999994
No 30
>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=95.84 E-value=0.0069 Score=39.80 Aligned_cols=24 Identities=33% Similarity=0.895 Sum_probs=19.6
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCc
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQP 191 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~ 191 (245)
.|++||+.... ++.|..||.||.+
T Consensus 4 ~C~~CG~i~~g-----~~~p~~CP~Cg~~ 27 (34)
T cd00729 4 VCPVCGYIHEG-----EEAPEKCPICGAP 27 (34)
T ss_pred ECCCCCCEeEC-----CcCCCcCcCCCCc
Confidence 79999988766 3357899999985
No 31
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=95.48 E-value=0.0075 Score=44.22 Aligned_cols=33 Identities=36% Similarity=0.792 Sum_probs=24.2
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCCCceeeeCCeeEEeccccccc
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESVRFSNE 209 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R~~~~f~~~ 209 (245)
..||+||. |. | ..+||.||++.. ...+++||-.
T Consensus 6 r~C~~Cgv--YT----L---k~~CP~CG~~t~------~~~P~rfSp~ 38 (56)
T PRK13130 6 RKCPKCGV--YT----L---KEICPVCGGKTK------NPHPPRFSPE 38 (56)
T ss_pred eECCCCCC--EE----c---cccCcCCCCCCC------CCCCCCCCCC
Confidence 38999993 33 2 678999999864 3467888763
No 32
>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=95.46 E-value=0.011 Score=38.29 Aligned_cols=24 Identities=33% Similarity=0.944 Sum_probs=19.5
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCc
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQP 191 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~ 191 (245)
.|++||+.... ...+-.||.||.+
T Consensus 3 ~C~~CGy~y~~-----~~~~~~CP~Cg~~ 26 (33)
T cd00350 3 VCPVCGYIYDG-----EEAPWVCPVCGAP 26 (33)
T ss_pred ECCCCCCEECC-----CcCCCcCcCCCCc
Confidence 69999988765 3378899999984
No 33
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=95.33 E-value=0.016 Score=47.85 Aligned_cols=40 Identities=28% Similarity=0.644 Sum_probs=24.5
Q ss_pred ccCCCCCceeeecc---c-------------ccCCCcccCCCCCCc-eeee-CCeeEE
Q 025946 162 DSCPNCGNDFQIFK---S-------------TLNDELQLCPYCSQP-FSVV-DDKFVR 201 (245)
Q Consensus 162 ~tCPnCG~eF~~~e---d-------------~Ln~d~iqCPnCGE~-L~Vd-~~~F~R 201 (245)
..|++||+.+...+ + .+.+....||+||.. +.+. ++.+.=
T Consensus 71 ~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G~el~i 128 (135)
T PRK03824 71 LKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIVKGRGVYI 128 (135)
T ss_pred EECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCCCcEEecCceEEE
Confidence 38999998887631 0 001234679999985 6644 444443
No 34
>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=95.16 E-value=0.015 Score=42.39 Aligned_cols=20 Identities=20% Similarity=0.694 Sum_probs=18.2
Q ss_pred cCCCcccCCCCCCceeeeCC
Q 025946 178 LNDELQLCPYCSQPFSVVDD 197 (245)
Q Consensus 178 Ln~d~iqCPnCGE~L~Vd~~ 197 (245)
.-++..+||+||..|+++||
T Consensus 49 i~eg~L~Cp~c~r~YPI~dG 68 (68)
T PF03966_consen 49 IVEGELICPECGREYPIRDG 68 (68)
T ss_dssp TTTTEEEETTTTEEEEEETT
T ss_pred ccCCEEEcCCCCCEEeCCCC
Confidence 67789999999999999986
No 35
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=95.14 E-value=0.011 Score=51.63 Aligned_cols=34 Identities=29% Similarity=0.689 Sum_probs=22.9
Q ss_pred eccCCCCCceeeecccc--------------------cCC---CcccCCCCCCceeee
Q 025946 161 QDSCPNCGNDFQIFKST--------------------LND---ELQLCPYCSQPFSVV 195 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~--------------------Ln~---d~iqCPnCGE~L~Vd 195 (245)
+.+||+|+++|... .+ +|. +..+||+||-....+
T Consensus 5 ~~~CPvC~~~F~~~-~vrs~~~r~~~~d~D~~~~Y~~vnP~~Y~V~vCP~CgyA~~~~ 61 (214)
T PF09986_consen 5 KITCPVCGKEFKTK-KVRSGKIRVIRRDSDFCPRYKGVNPLFYEVWVCPHCGYAAFEE 61 (214)
T ss_pred ceECCCCCCeeeee-EEEcCCceEeeecCCCccccCCCCCeeeeEEECCCCCCccccc
Confidence 45899999999862 11 111 257899999776433
No 36
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=95.07 E-value=0.019 Score=46.07 Aligned_cols=34 Identities=24% Similarity=0.553 Sum_probs=22.8
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCCCc-eeee-CCeeE
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQP-FSVV-DDKFV 200 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~-L~Vd-~~~F~ 200 (245)
..|+.||++|.. .+....||.||.. +.+. +.++.
T Consensus 71 ~~C~~Cg~~~~~-----~~~~~~CP~Cgs~~~~i~~G~El~ 106 (113)
T PRK12380 71 AWCWDCSQVVEI-----HQHDAQCPHCHGERLRVDTGDSLI 106 (113)
T ss_pred EEcccCCCEEec-----CCcCccCcCCCCCCcEEccCCeEE
Confidence 389999988887 2234459999974 4544 44443
No 37
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=95.02 E-value=0.019 Score=46.08 Aligned_cols=34 Identities=24% Similarity=0.659 Sum_probs=22.5
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCc-eee-eCCeeE
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQP-FSV-VDDKFV 200 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~-L~V-d~~~F~ 200 (245)
.|+.||+.|.. .......||.||.. +.+ .+++|.
T Consensus 72 ~C~~Cg~~~~~----~~~~~~~CP~Cgs~~~~i~~G~El~ 107 (114)
T PRK03681 72 WCETCQQYVTL----LTQRVRRCPQCHGDMLRIVADDGLQ 107 (114)
T ss_pred EcccCCCeeec----CCccCCcCcCcCCCCcEEccCCeEE
Confidence 89999988776 22223679999975 444 444443
No 38
>PF12773 DZR: Double zinc ribbon
Probab=94.95 E-value=0.01 Score=40.28 Aligned_cols=26 Identities=27% Similarity=0.815 Sum_probs=13.0
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
.||.||..+.. -.....+||+||+++
T Consensus 14 fC~~CG~~l~~----~~~~~~~C~~Cg~~~ 39 (50)
T PF12773_consen 14 FCPHCGTPLPP----PDQSKKICPNCGAEN 39 (50)
T ss_pred CChhhcCChhh----ccCCCCCCcCCcCCC
Confidence 55566655541 122345566666554
No 39
>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=94.80 E-value=0.011 Score=47.23 Aligned_cols=34 Identities=24% Similarity=0.586 Sum_probs=21.5
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCce-e-eeCCeeEE
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPF-S-VVDDKFVR 201 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L-~-Vd~~~F~R 201 (245)
.|+.||++|... +....||+||..- . ++++.+.=
T Consensus 72 ~C~~Cg~~~~~~-----~~~~~CP~Cgs~~~~i~~G~el~i 107 (113)
T PF01155_consen 72 RCRDCGHEFEPD-----EFDFSCPRCGSPDVEIISGRELRI 107 (113)
T ss_dssp EETTTS-EEECH-----HCCHH-SSSSSS-EEEEESS-EEE
T ss_pred ECCCCCCEEecC-----CCCCCCcCCcCCCcEEccCCeEEE
Confidence 899999999872 2336799999973 4 45555543
No 40
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=94.60 E-value=0.027 Score=40.58 Aligned_cols=35 Identities=23% Similarity=0.674 Sum_probs=26.8
Q ss_pred eeccCCCCCceeeecccccCCCcccCCCCCCceeeeCC
Q 025946 160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDD 197 (245)
Q Consensus 160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~ 197 (245)
++-.|-.||+++.. .-+.+.+.||+||..+-+...
T Consensus 5 ~~Y~C~~Cg~~~~~---~~~~~~irCp~Cg~rIl~K~R 39 (49)
T COG1996 5 MEYKCARCGREVEL---DQETRGIRCPYCGSRILVKER 39 (49)
T ss_pred EEEEhhhcCCeeeh---hhccCceeCCCCCcEEEEecc
Confidence 45589999999943 245589999999998766543
No 41
>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=94.49 E-value=0.033 Score=44.69 Aligned_cols=36 Identities=17% Similarity=0.450 Sum_probs=24.5
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCCCce-e-eeCCeeEEe
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPF-S-VVDDKFVRE 202 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L-~-Vd~~~F~R~ 202 (245)
..|++||++|.. .+....||.||..- . +.++++.=+
T Consensus 71 ~~C~~Cg~~~~~-----~~~~~~CP~Cgs~~~~i~~G~El~I~ 108 (115)
T TIGR00100 71 CECEDCSEEVSP-----EIDLYRCPKCHGIMLQVRAGKELNLK 108 (115)
T ss_pred EEcccCCCEEec-----CCcCccCcCCcCCCcEEecCCeEEEE
Confidence 399999988876 22357799999853 4 445555443
No 42
>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=94.38 E-value=0.025 Score=40.44 Aligned_cols=30 Identities=23% Similarity=0.632 Sum_probs=23.4
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceeee
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVV 195 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd 195 (245)
+||.||...-. .+++....||+||....-|
T Consensus 30 ~C~~CG~~~~~---~~~~r~~~C~~Cg~~~~rD 59 (69)
T PF07282_consen 30 TCPRCGHRNKK---RRSGRVFTCPNCGFEMDRD 59 (69)
T ss_pred CccCccccccc---ccccceEEcCCCCCEECcH
Confidence 89999987665 4666799999999876433
No 43
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=94.27 E-value=0.031 Score=45.09 Aligned_cols=37 Identities=16% Similarity=0.383 Sum_probs=24.7
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCc-ee-eeCCeeEEec
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQP-FS-VVDDKFVRES 203 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~-L~-Vd~~~F~R~~ 203 (245)
.|+.||+.|... ......||.||.+ +. +.+++|.=++
T Consensus 73 ~C~~Cg~~~~~~----~~~~~~CP~Cgs~~~~i~~G~El~I~~ 111 (117)
T PRK00564 73 ECKDCSHVFKPN----ALDYGVCEKCHSKNVIITQGNEMRLLS 111 (117)
T ss_pred EhhhCCCccccC----CccCCcCcCCCCCceEEecCCEEEEEE
Confidence 899999888761 1233459999985 45 4555665443
No 44
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=94.22 E-value=0.055 Score=36.61 Aligned_cols=34 Identities=21% Similarity=0.472 Sum_probs=23.7
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceeeeCC
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDD 197 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~ 197 (245)
-||.||...+..++. ++...+||.||-...++..
T Consensus 2 FCp~Cg~~l~~~~~~-~~~~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 2 FCPKCGNMLIPKEGK-EKRRFVCRKCGYEEPIEQK 35 (52)
T ss_pred CCCCCCCccccccCC-CCCEEECCcCCCeEECCCc
Confidence 599999988773211 1237899999987666554
No 45
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=94.20 E-value=0.041 Score=40.67 Aligned_cols=38 Identities=29% Similarity=0.568 Sum_probs=27.8
Q ss_pred cCCCCCceee--ecc-cccCCCcccCCCCCCceeeeCCeeE
Q 025946 163 SCPNCGNDFQ--IFK-STLNDELQLCPYCSQPFSVVDDKFV 200 (245)
Q Consensus 163 tCPnCG~eF~--~~e-d~Ln~d~iqCPnCGE~L~Vd~~~F~ 200 (245)
-||.||.+-. .-+ .+|.+=|..||.|-+.--++=.+|+
T Consensus 6 ~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~EtlI~v~~~~ 46 (55)
T PF14205_consen 6 LCPICGNKTRLKIREDTVLKNFPLYCPKCKQETLIDVKQLK 46 (55)
T ss_pred ECCCCCCccceeeecCceeccccccCCCCCceEEEEeeccE
Confidence 7999996543 333 4488889999999987766655554
No 46
>PF12773 DZR: Double zinc ribbon
Probab=93.99 E-value=0.027 Score=38.16 Aligned_cols=23 Identities=35% Similarity=1.084 Sum_probs=19.3
Q ss_pred CCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 164 CPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 164 CPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
||.||+.... +...||+||+++.
T Consensus 1 Cp~Cg~~~~~-------~~~fC~~CG~~l~ 23 (50)
T PF12773_consen 1 CPHCGTPNPD-------DAKFCPHCGTPLP 23 (50)
T ss_pred CCCcCCcCCc-------cccCChhhcCChh
Confidence 8999988444 7889999999998
No 47
>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=93.89 E-value=0.02 Score=52.85 Aligned_cols=39 Identities=31% Similarity=0.905 Sum_probs=19.1
Q ss_pred HhcCcceeccCCCCCce-eeecccccCCC---cccCCCCCCceeeeCCe
Q 025946 154 WASRDIVQDSCPNCGND-FQIFKSTLNDE---LQLCPYCSQPFSVVDDK 198 (245)
Q Consensus 154 Wl~rnLIE~tCPnCG~e-F~~~ed~Ln~d---~iqCPnCGE~L~Vd~~~ 198 (245)
|+.+|. -||+||.+ ..-+ -|+. .-.||+|+|.+++...+
T Consensus 27 Wv~~n~---yCP~Cg~~~L~~f---~NN~PVaDF~C~~C~eeyELKSk~ 69 (254)
T PF06044_consen 27 WVAENM---YCPNCGSKPLSKF---ENNRPVADFYCPNCNEEYELKSKK 69 (254)
T ss_dssp HHHHH------TTT--SS-EE-----------EEE-TTT--EEEEEEEE
T ss_pred HHHHCC---cCCCCCChhHhhc---cCCCccceeECCCCchHHhhhhhc
Confidence 555544 69999988 5542 2333 56899999999988766
No 48
>PRK12496 hypothetical protein; Provisional
Probab=93.65 E-value=0.035 Score=47.11 Aligned_cols=58 Identities=12% Similarity=0.213 Sum_probs=33.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCcc-eeccCCCCCceeeecccccCCCcccCCCCCCceeee
Q 025946 131 DAIVSIWLLAVIVPIVGFGAFLWWASRDI-VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVV 195 (245)
Q Consensus 131 d~~~~L~LlllllPIl~~~Gf~WWl~rnL-IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd 195 (245)
|..+--++-.+=++++.+-.-+ ++..+ -.-.||.||++|-. +.....||.||.++...
T Consensus 98 D~~~~~vA~~lgi~v~~~~~~~--i~~~~~w~~~C~gC~~~~~~-----~~~~~~C~~CG~~~~r~ 156 (164)
T PRK12496 98 DYGIQNVAKKLNIKFENIKTKG--IKKVIKWRKVCKGCKKKYPE-----DYPDDVCEICGSPVKRK 156 (164)
T ss_pred HHHHHHHHHHcCCeEecccccc--chhheeeeEECCCCCccccC-----CCCCCcCCCCCChhhhc
Confidence 5555555555555665532111 11111 12379999987753 23456899999998543
No 49
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=93.60 E-value=0.047 Score=40.68 Aligned_cols=40 Identities=23% Similarity=0.630 Sum_probs=30.0
Q ss_pred CcceeccCCCCCceeeecccccCCCcccCCCCCCcee-eeCCe
Q 025946 157 RDIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS-VVDDK 198 (245)
Q Consensus 157 rnLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~-Vd~~~ 198 (245)
-.++...||.|+++-.++. =.++.+.|+.||..|. ..+|+
T Consensus 7 S~F~~VkCp~C~n~q~vFs--ha~t~V~C~~Cg~~L~~PtGGK 47 (59)
T PRK00415 7 SRFLKVKCPDCGNEQVVFS--HASTVVRCLVCGKTLAEPTGGK 47 (59)
T ss_pred CeEEEEECCCCCCeEEEEe--cCCcEEECcccCCCcccCCCcc
Confidence 3578889999999987731 2346999999999985 44444
No 50
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=93.55 E-value=0.047 Score=41.76 Aligned_cols=34 Identities=24% Similarity=0.726 Sum_probs=26.5
Q ss_pred cceeccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
.++.+.||.||++-..+. =....+.|+.||..|-
T Consensus 16 ~Fl~VkCpdC~N~q~vFs--hast~V~C~~CG~~l~ 49 (67)
T COG2051 16 RFLRVKCPDCGNEQVVFS--HASTVVTCLICGTTLA 49 (67)
T ss_pred eEEEEECCCCCCEEEEec--cCceEEEecccccEEE
Confidence 467789999999988731 1236899999999885
No 51
>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=93.18 E-value=0.038 Score=42.36 Aligned_cols=27 Identities=33% Similarity=0.854 Sum_probs=14.6
Q ss_pred eeccCCCCCceeeecccccCCCcccCCCCCCceee
Q 025946 160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSV 194 (245)
Q Consensus 160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~V 194 (245)
-+..|+.|...|.. ...||.|+++|++
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 34456666665555 7788888888875
No 52
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=93.12 E-value=0.05 Score=40.97 Aligned_cols=31 Identities=29% Similarity=0.533 Sum_probs=14.2
Q ss_pred ceeccCCCCCceeee-cccc-cCCCcccCCCCC
Q 025946 159 IVQDSCPNCGNDFQI-FKST-LNDELQLCPYCS 189 (245)
Q Consensus 159 LIE~tCPnCG~eF~~-~ed~-Ln~d~iqCPnCG 189 (245)
.+.-.|||||++... -+.- -...+.+||+||
T Consensus 25 ~v~F~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CG 57 (61)
T COG2888 25 AVKFPCPNCGEVEIYRCAKCRKLGNPYRCPKCG 57 (61)
T ss_pred eeEeeCCCCCceeeehhhhHHHcCCceECCCcC
Confidence 344467777733222 1111 112366677776
No 53
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=92.84 E-value=0.042 Score=46.74 Aligned_cols=25 Identities=36% Similarity=0.841 Sum_probs=19.2
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceeee
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVV 195 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd 195 (245)
+||.||. +......||+||....-|
T Consensus 311 ~C~~cg~--------~~~r~~~C~~cg~~~~rD 335 (364)
T COG0675 311 TCPCCGH--------LSGRLFKCPRCGFVHDRD 335 (364)
T ss_pred cccccCC--------ccceeEECCCCCCeehhh
Confidence 8999998 344788999998765443
No 54
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=92.77 E-value=0.062 Score=44.90 Aligned_cols=29 Identities=24% Similarity=0.676 Sum_probs=24.6
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceeeeCCeeEE
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVR 201 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R 201 (245)
.||+||.+..+ ++..||+|+..+ .|.|.-
T Consensus 8 ~cPvcg~~~iV-------TeL~c~~~etTV---rg~F~~ 36 (122)
T COG3877 8 RCPVCGRKLIV-------TELKCSNCETTV---RGNFKM 36 (122)
T ss_pred CCCccccccee-------EEEecCCCCceE---ecceec
Confidence 79999999998 899999999987 455543
No 55
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=92.73 E-value=0.061 Score=38.20 Aligned_cols=26 Identities=27% Similarity=0.582 Sum_probs=20.2
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
.||.||.+|.. ..++...|+.||-..
T Consensus 22 fCP~Cg~~~m~----~~~~r~~C~~Cgyt~ 47 (50)
T PRK00432 22 FCPRCGSGFMA----EHLDRWHCGKCGYTE 47 (50)
T ss_pred cCcCCCcchhe----ccCCcEECCCcCCEE
Confidence 89999987555 455788999998654
No 56
>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=92.64 E-value=0.099 Score=35.00 Aligned_cols=31 Identities=23% Similarity=0.546 Sum_probs=21.5
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
++||+||..+-.. ..--+.+-.|.+||++|.
T Consensus 2 r~C~~Cg~~Yh~~-~~pP~~~~~Cd~cg~~L~ 32 (36)
T PF05191_consen 2 RICPKCGRIYHIE-FNPPKVEGVCDNCGGELV 32 (36)
T ss_dssp EEETTTTEEEETT-TB--SSTTBCTTTTEBEB
T ss_pred cCcCCCCCccccc-cCCCCCCCccCCCCCeeE
Confidence 4899999776651 111224789999999874
No 57
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=92.57 E-value=0.083 Score=43.33 Aligned_cols=45 Identities=27% Similarity=0.540 Sum_probs=35.3
Q ss_pred cCCCCCceeee---cccccCCCcccCCCCCCceeeeCCeeEEecccccc
Q 025946 163 SCPNCGNDFQI---FKSTLNDELQLCPYCSQPFSVVDDKFVRESVRFSN 208 (245)
Q Consensus 163 tCPnCG~eF~~---~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R~~~~f~~ 208 (245)
+||.||.+... .|-..+...+.|-+||..++.+-.+-. +++..||
T Consensus 24 tCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~ev~~l~-~~vDvYs 71 (104)
T COG4888 24 TCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFECEVPELS-EPVDVYS 71 (104)
T ss_pred ecCccCCeeeeEEEEEecCceeEEEcccCcceEEEeccccc-cchhHHH
Confidence 99999998877 666778889999999999998877654 3344443
No 58
>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=92.48 E-value=0.077 Score=33.35 Aligned_cols=23 Identities=26% Similarity=0.648 Sum_probs=16.0
Q ss_pred CCCCCceeeecccccC-CCcccCCCCCC
Q 025946 164 CPNCGNDFQIFKSTLN-DELQLCPYCSQ 190 (245)
Q Consensus 164 CPnCG~eF~~~ed~Ln-~d~iqCPnCGE 190 (245)
|..||..+.. .+ -.+-.|||||+
T Consensus 1 C~sC~~~i~~----r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAP----REQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccC----cccCceEeCCCCCC
Confidence 6678777666 33 24788999985
No 59
>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=92.47 E-value=0.1 Score=43.09 Aligned_cols=30 Identities=20% Similarity=0.751 Sum_probs=24.3
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceeeeC
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVD 196 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~ 196 (245)
.||.|+.+++- -..+...||.|+-.+..++
T Consensus 4 ~CP~C~seytY----~dg~~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 4 PCPKCNSEYTY----HDGTQLICPSCLYEWNENE 33 (109)
T ss_pred cCCcCCCcceE----ecCCeeECccccccccccc
Confidence 79999988876 3446899999999987554
No 60
>PHA00626 hypothetical protein
Probab=92.10 E-value=0.14 Score=38.39 Aligned_cols=33 Identities=27% Similarity=0.464 Sum_probs=21.7
Q ss_pred cCCCCCceeeecccccCC--CcccCCCCCCceeee
Q 025946 163 SCPNCGNDFQIFKSTLND--ELQLCPYCSQPFSVV 195 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~--d~iqCPnCGE~L~Vd 195 (245)
.||+||..-..--...++ ....||.||-.+.-|
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSKD 36 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeechh
Confidence 599999853332222333 688999998766543
No 61
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=92.02 E-value=0.1 Score=39.06 Aligned_cols=8 Identities=63% Similarity=1.535 Sum_probs=3.8
Q ss_pred cCCCCCce
Q 025946 163 SCPNCGND 170 (245)
Q Consensus 163 tCPnCG~e 170 (245)
.||+||++
T Consensus 27 ~CPnCG~~ 34 (59)
T PRK14890 27 LCPNCGEV 34 (59)
T ss_pred eCCCCCCe
Confidence 45555544
No 62
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=91.88 E-value=0.11 Score=42.24 Aligned_cols=42 Identities=14% Similarity=0.374 Sum_probs=24.5
Q ss_pred eccCCCCCceeeecccccCCC--cccCCCCCC-cee-eeCCeeEEec
Q 025946 161 QDSCPNCGNDFQIFKSTLNDE--LQLCPYCSQ-PFS-VVDDKFVRES 203 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~Ln~d--~iqCPnCGE-~L~-Vd~~~F~R~~ 203 (245)
+..| .||++|...++.+..- ...||.||. .+. +.++++.=++
T Consensus 70 ~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G~El~i~~ 115 (124)
T PRK00762 70 EIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHILGGRECNVKN 115 (124)
T ss_pred eEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEecCCeEEEEE
Confidence 3389 9998877632111111 257999994 444 5555665544
No 63
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=91.70 E-value=0.056 Score=47.29 Aligned_cols=32 Identities=25% Similarity=0.558 Sum_probs=25.4
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceeeeC
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVD 196 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~ 196 (245)
.||+|..++.-+|.... +..||.||+.|.-.+
T Consensus 115 ~C~~~~~r~sfdeA~~~--~F~Cp~Cg~~L~~~d 146 (176)
T COG1675 115 VCPNCHVKYSFDEAMEL--GFTCPKCGEDLEEYD 146 (176)
T ss_pred eCCCCCCcccHHHHHHh--CCCCCCCCchhhhcc
Confidence 89999999887655543 489999999997544
No 64
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=91.59 E-value=0.093 Score=48.01 Aligned_cols=30 Identities=27% Similarity=0.576 Sum_probs=22.5
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
..||.||.+-.+ +| ...++++|.+||.+++
T Consensus 12 ~~Cp~Cg~~~iv-~d-~~~Ge~vC~~CG~Vl~ 41 (310)
T PRK00423 12 LVCPECGSDKLI-YD-YERGEIVCADCGLVIE 41 (310)
T ss_pred CcCcCCCCCCee-EE-CCCCeEeecccCCccc
Confidence 379999974332 22 3679999999999885
No 65
>PRK11827 hypothetical protein; Provisional
Probab=91.53 E-value=0.12 Score=38.46 Aligned_cols=33 Identities=18% Similarity=0.471 Sum_probs=27.2
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceeeeCCe
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDK 198 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~ 198 (245)
.||.|..++.-++ ...+..|+.|+-.|++.||-
T Consensus 10 aCP~ckg~L~~~~---~~~~Lic~~~~laYPI~dgI 42 (60)
T PRK11827 10 ACPVCNGKLWYNQ---EKQELICKLDNLAFPLRDGI 42 (60)
T ss_pred ECCCCCCcCeEcC---CCCeEECCccCeeccccCCc
Confidence 8999999988632 23689999999999999873
No 66
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=91.41 E-value=0.11 Score=43.12 Aligned_cols=29 Identities=21% Similarity=0.632 Sum_probs=25.1
Q ss_pred cceeccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
+++-..|++||+.++= ....||+||.+-.
T Consensus 26 kl~g~kC~~CG~v~~P-------Pr~~Cp~C~~~~~ 54 (140)
T COG1545 26 KLLGTKCKKCGRVYFP-------PRAYCPKCGSETE 54 (140)
T ss_pred cEEEEEcCCCCeEEcC-------CcccCCCCCCCCc
Confidence 6777799999999887 7899999998853
No 67
>PRK05978 hypothetical protein; Provisional
Probab=91.32 E-value=0.12 Score=44.12 Aligned_cols=35 Identities=23% Similarity=0.666 Sum_probs=24.4
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCCCceeeeCCe
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDK 198 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~ 198 (245)
..||+||+-=. ++ .+.+-...||+||+.++.++.-
T Consensus 34 grCP~CG~G~L-F~-g~Lkv~~~C~~CG~~~~~~~a~ 68 (148)
T PRK05978 34 GRCPACGEGKL-FR-AFLKPVDHCAACGEDFTHHRAD 68 (148)
T ss_pred CcCCCCCCCcc-cc-cccccCCCccccCCccccCCcc
Confidence 48999996422 11 1445678999999999877543
No 68
>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=91.28 E-value=0.16 Score=37.31 Aligned_cols=39 Identities=21% Similarity=0.463 Sum_probs=24.3
Q ss_pred cceeccCCCCCceeeecccccCCCcccCCCCCCcee-eeCCe
Q 025946 158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS-VVDDK 198 (245)
Q Consensus 158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~-Vd~~~ 198 (245)
.++.+.||.|+++-.++ .=.+..+.|..||+.|. ..+|+
T Consensus 4 ~Fm~VkCp~C~~~q~vF--Sha~t~V~C~~Cg~~L~~PtGGK 43 (55)
T PF01667_consen 4 YFMDVKCPGCYNIQTVF--SHAQTVVKCVVCGTVLAQPTGGK 43 (55)
T ss_dssp -EEEEE-TTT-SEEEEE--TT-SS-EE-SSSTSEEEEE-SSS
T ss_pred cEEEEECCCCCCeeEEE--ecCCeEEEcccCCCEecCCCCcC
Confidence 46788999999998883 12346999999999985 44444
No 69
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=91.14 E-value=0.14 Score=41.10 Aligned_cols=32 Identities=22% Similarity=0.398 Sum_probs=20.4
Q ss_pred cCCCCCceee-ecccccCCCcccCCCCCCceeee
Q 025946 163 SCPNCGNDFQ-IFKSTLNDELQLCPYCSQPFSVV 195 (245)
Q Consensus 163 tCPnCG~eF~-~~ed~Ln~d~iqCPnCGE~L~Vd 195 (245)
+||+||.... ..-+ =+...+.||+||.-...+
T Consensus 23 ~CP~Cge~~v~v~~~-k~~~h~~C~~CG~y~~~~ 55 (99)
T PRK14892 23 ECPRCGKVSISVKIK-KNIAIITCGNCGLYTEFE 55 (99)
T ss_pred ECCCCCCeEeeeecC-CCcceEECCCCCCccCEE
Confidence 8999994322 1101 144699999999876443
No 70
>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=91.12 E-value=0.085 Score=34.45 Aligned_cols=27 Identities=33% Similarity=1.005 Sum_probs=14.6
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
..||.|+.++.- ..+...+||.|+..+
T Consensus 3 p~Cp~C~se~~y----~D~~~~vCp~C~~ew 29 (30)
T PF08274_consen 3 PKCPLCGSEYTY----EDGELLVCPECGHEW 29 (30)
T ss_dssp ---TTT-----E----E-SSSEEETTTTEEE
T ss_pred CCCCCCCCccee----ccCCEEeCCcccccC
Confidence 479999988776 445789999998654
No 71
>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=91.08 E-value=0.14 Score=33.94 Aligned_cols=32 Identities=22% Similarity=0.457 Sum_probs=22.0
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceeeeC
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVD 196 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~ 196 (245)
-||.||+-.+..++....- .|+.||-..++++
T Consensus 3 FCp~C~nlL~p~~~~~~~~--~C~~C~Y~~~~~~ 34 (35)
T PF02150_consen 3 FCPECGNLLYPKEDKEKRV--ACRTCGYEEPISQ 34 (35)
T ss_dssp BETTTTSBEEEEEETTTTE--EESSSS-EEE-SS
T ss_pred eCCCCCccceEcCCCccCc--CCCCCCCccCCCC
Confidence 5999999999854443322 7999998877653
No 72
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=91.02 E-value=0.12 Score=43.74 Aligned_cols=33 Identities=27% Similarity=0.582 Sum_probs=22.3
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceeeeCCeeEEecc
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESV 204 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R~~~ 204 (245)
.|-+||+.|-+-...+. .=||+|| +++|+-.+.
T Consensus 3 ~Ct~Cg~~f~dgs~eil---~GCP~CG------g~kF~yv~~ 35 (131)
T PF09845_consen 3 QCTKCGRVFEDGSKEIL---SGCPECG------GNKFQYVPE 35 (131)
T ss_pred ccCcCCCCcCCCcHHHH---ccCcccC------CcceEEcCC
Confidence 69999999988332222 3499999 456665543
No 73
>COG5216 Uncharacterized conserved protein [Function unknown]
Probab=91.01 E-value=0.14 Score=39.00 Aligned_cols=37 Identities=30% Similarity=0.707 Sum_probs=26.7
Q ss_pred cCcceeccCCCCCceeee-cccccCC-CcccCCCCCCcee
Q 025946 156 SRDIVQDSCPNCGNDFQI-FKSTLND-ELQLCPYCSQPFS 193 (245)
Q Consensus 156 ~rnLIE~tCPnCG~eF~~-~ed~Ln~-d~iqCPnCGE~L~ 193 (245)
..+.+.-.|| ||.+|.+ +||+.|. ...+||.|.-.+-
T Consensus 17 e~~~ftyPCP-CGDRFeIsLeDl~~GE~VArCPSCSLiv~ 55 (67)
T COG5216 17 EEKTFTYPCP-CGDRFEISLEDLRNGEVVARCPSCSLIVC 55 (67)
T ss_pred CCceEEecCC-CCCEeEEEHHHhhCCceEEEcCCceEEEE
Confidence 3467778999 9999998 4555433 4789999975443
No 74
>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=91.00 E-value=0.086 Score=48.67 Aligned_cols=39 Identities=26% Similarity=0.711 Sum_probs=29.8
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceee----------eCCeeEEec
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSV----------VDDKFVRES 203 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~V----------d~~~F~R~~ 203 (245)
.||.|++.+|. ..|.+...+||+||--+.. |++.|+.-+
T Consensus 28 ~c~~c~~~~~~--~~l~~~~~vc~~c~~h~rl~areRi~~L~D~gsF~E~~ 76 (285)
T TIGR00515 28 KCPKCGQVLYT--KELERNLEVCPKCDHHMRMDARERIESLLDEGSFEEFN 76 (285)
T ss_pred ECCCCcchhhH--HHHHhhCCCCCCCCCcCcCCHHHHHHHceeCCeeEEeC
Confidence 79999999887 2356667899999986654 677776553
No 75
>PRK06260 threonine synthase; Validated
Probab=90.76 E-value=0.15 Score=47.64 Aligned_cols=32 Identities=22% Similarity=0.625 Sum_probs=24.6
Q ss_pred eeccCCCCCceeeecccccCCCcccCCCCCCceeeeC
Q 025946 160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVD 196 (245)
Q Consensus 160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~ 196 (245)
+.-.|+.||+++-. +.-...||.||.+|.++=
T Consensus 2 ~~~~C~~cg~~~~~-----~~~~~~Cp~cg~~l~~~y 33 (397)
T PRK06260 2 YWLKCIECGKEYDP-----DEIIYTCPECGGLLEVIY 33 (397)
T ss_pred CEEEECCCCCCCCC-----CCccccCCCCCCeEEEEe
Confidence 45689999998654 233578999999988773
No 76
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=90.26 E-value=0.14 Score=37.46 Aligned_cols=20 Identities=40% Similarity=1.079 Sum_probs=16.1
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCC
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQ 190 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE 190 (245)
.||+||..-. ....||+||.
T Consensus 29 ~C~~CG~~~~--------~H~vC~~CG~ 48 (57)
T PRK12286 29 ECPNCGEPKL--------PHRVCPSCGY 48 (57)
T ss_pred ECCCCCCccC--------CeEECCCCCc
Confidence 7999996433 5899999993
No 77
>PHA02942 putative transposase; Provisional
Probab=90.17 E-value=0.17 Score=47.92 Aligned_cols=27 Identities=30% Similarity=0.770 Sum_probs=19.9
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
+||.||..-.. +.+-.-.||+||....
T Consensus 327 ~Cs~CG~~~~~----l~~r~f~C~~CG~~~d 353 (383)
T PHA02942 327 SCPKCGHKMVE----IAHRYFHCPSCGYEND 353 (383)
T ss_pred cCCCCCCccCc----CCCCEEECCCCCCEeC
Confidence 79999976432 4455789999988653
No 78
>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=90.15 E-value=0.18 Score=32.15 Aligned_cols=28 Identities=21% Similarity=0.481 Sum_probs=15.0
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
.-||.||.+.... -..-..+||.||...
T Consensus 4 rfC~~CG~~t~~~---~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 4 RFCGRCGAPTKPA---PGGWARRCPSCGHEH 31 (32)
T ss_dssp SB-TTT--BEEE----SSSS-EEESSSS-EE
T ss_pred cccCcCCccccCC---CCcCEeECCCCcCEe
Confidence 3589999887772 222478899998653
No 79
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=90.13 E-value=0.13 Score=52.31 Aligned_cols=22 Identities=32% Similarity=1.078 Sum_probs=11.4
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCc
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQP 191 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~ 191 (245)
.||.||++... +.-.||+||++
T Consensus 29 ~Cp~CG~~~~~-------~~~fC~~CG~~ 50 (645)
T PRK14559 29 PCPQCGTEVPV-------DEAHCPNCGAE 50 (645)
T ss_pred cCCCCCCCCCc-------ccccccccCCc
Confidence 45555554333 55566666654
No 80
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=90.12 E-value=0.11 Score=47.99 Aligned_cols=40 Identities=30% Similarity=0.759 Sum_probs=30.2
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceee----------eCCeeEEecc
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSV----------VDDKFVRESV 204 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~V----------d~~~F~R~~~ 204 (245)
.||.|+..+|. + .|.+...+||.||--+.+ |++.|+--..
T Consensus 29 ~c~~c~~~~~~-~-~l~~~~~vc~~c~~h~rl~areRi~~L~D~gsF~E~~~ 78 (292)
T PRK05654 29 KCPSCGQVLYR-K-ELEANLNVCPKCGHHMRISARERLDLLLDEGSFVELDA 78 (292)
T ss_pred ECCCccchhhH-H-HHHhcCCCCCCCCCCeeCCHHHHHHHHccCCccEEecC
Confidence 89999999887 2 355567899999987765 5777765543
No 81
>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=89.93 E-value=0.17 Score=36.26 Aligned_cols=20 Identities=40% Similarity=1.158 Sum_probs=16.2
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCC
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCS 189 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCG 189 (245)
..||+||. +.. ..-.||+||
T Consensus 27 ~~c~~cg~-~~~-------~H~vc~~cG 46 (56)
T PF01783_consen 27 VKCPNCGE-PKL-------PHRVCPSCG 46 (56)
T ss_dssp EESSSSSS-EES-------TTSBCTTTB
T ss_pred eeeccCCC-Eec-------ccEeeCCCC
Confidence 58999994 333 689999998
No 82
>PRK12495 hypothetical protein; Provisional
Probab=89.61 E-value=0.17 Score=46.22 Aligned_cols=33 Identities=27% Similarity=0.708 Sum_probs=26.8
Q ss_pred cceeccCCCCCceeeecccccCCCcccCCCCCCceeee
Q 025946 158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVV 195 (245)
Q Consensus 158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd 195 (245)
......||+||..+.- + .+.+.||.|++.+.-+
T Consensus 39 tmsa~hC~~CG~PIpa----~-pG~~~Cp~CQ~~~~~~ 71 (226)
T PRK12495 39 TMTNAHCDECGDPIFR----H-DGQEFCPTCQQPVTED 71 (226)
T ss_pred ccchhhcccccCcccC----C-CCeeECCCCCCccccc
Confidence 4455699999999985 4 7899999999887643
No 83
>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=89.39 E-value=0.045 Score=40.53 Aligned_cols=25 Identities=28% Similarity=0.934 Sum_probs=18.5
Q ss_pred ccCCCCCceeeecccccCCCcccC-CCCCCcee
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLC-PYCSQPFS 193 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqC-PnCGE~L~ 193 (245)
..||+||++.-. ++..| |.|++.+.
T Consensus 4 kHC~~CG~~Ip~-------~~~fCS~~C~~~~~ 29 (59)
T PF09889_consen 4 KHCPVCGKPIPP-------DESFCSPKCREEYR 29 (59)
T ss_pred CcCCcCCCcCCc-------chhhhCHHHHHHHH
Confidence 368888877554 78888 68877664
No 84
>PRK10220 hypothetical protein; Provisional
Probab=89.25 E-value=0.24 Score=41.12 Aligned_cols=30 Identities=20% Similarity=0.871 Sum_probs=24.3
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceeeeC
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVD 196 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~ 196 (245)
.||.|+.+++- -..+...||.|+-.++.++
T Consensus 5 ~CP~C~seytY----~d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 5 HCPKCNSEYTY----EDNGMYICPECAHEWNDAE 34 (111)
T ss_pred cCCCCCCcceE----cCCCeEECCcccCcCCccc
Confidence 79999988876 2336899999999887665
No 85
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=89.19 E-value=0.25 Score=37.10 Aligned_cols=38 Identities=18% Similarity=0.566 Sum_probs=29.9
Q ss_pred cceec-cCCCCCceeeecccccCCCcccCCCCCCceeeeCCe
Q 025946 158 DIVQD-SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDK 198 (245)
Q Consensus 158 nLIE~-tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~ 198 (245)
++++. .||.|.-.++.+++ +....||.|+..++++||-
T Consensus 4 ~LLeiLaCP~~kg~L~~~~~---~~~L~c~~~~~aYpI~dGI 42 (60)
T COG2835 4 RLLEILACPVCKGPLVYDEE---KQELICPRCKLAYPIRDGI 42 (60)
T ss_pred hhheeeeccCcCCcceEecc---CCEEEecccCceeecccCc
Confidence 44554 89999999887422 2699999999999999873
No 86
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=89.15 E-value=0.23 Score=35.92 Aligned_cols=13 Identities=38% Similarity=1.298 Sum_probs=10.6
Q ss_pred ccCCCCCCceeee
Q 025946 183 QLCPYCSQPFSVV 195 (245)
Q Consensus 183 iqCPnCGE~L~Vd 195 (245)
++|||||+++.+.
T Consensus 1 i~CPyCge~~~~~ 13 (52)
T PF14255_consen 1 IQCPYCGEPIEIL 13 (52)
T ss_pred CCCCCCCCeeEEE
Confidence 5799999988764
No 87
>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=88.83 E-value=0.23 Score=38.28 Aligned_cols=28 Identities=25% Similarity=0.662 Sum_probs=22.6
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceeee
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVV 195 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd 195 (245)
.||.||..++. ..+...||+||...+.+
T Consensus 2 fC~~Cg~~l~~-----~~~~~~C~~C~~~~~~~ 29 (104)
T TIGR01384 2 FCPKCGSLMTP-----KNGVYVCPSCGYEKEKK 29 (104)
T ss_pred CCcccCccccc-----CCCeEECcCCCCccccc
Confidence 69999998875 34689999999887653
No 88
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=88.82 E-value=0.12 Score=34.18 Aligned_cols=21 Identities=38% Similarity=0.722 Sum_probs=17.5
Q ss_pred ccCCCCCCceeeeCCeeEEec
Q 025946 183 QLCPYCSQPFSVVDDKFVRES 203 (245)
Q Consensus 183 iqCPnCGE~L~Vd~~~F~R~~ 203 (245)
++||+|++.+.+++.+....+
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~ 23 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGG 23 (37)
T ss_pred EECCCCCceEEcCHHHcccCC
Confidence 689999999999998865443
No 89
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=88.29 E-value=0.21 Score=50.82 Aligned_cols=16 Identities=25% Similarity=0.667 Sum_probs=9.6
Q ss_pred ccCCCCCCceeeeCCe
Q 025946 183 QLCPYCSQPFSVVDDK 198 (245)
Q Consensus 183 iqCPnCGE~L~Vd~~~ 198 (245)
..||+||+.++.+...
T Consensus 28 ~~Cp~CG~~~~~~~~f 43 (645)
T PRK14559 28 KPCPQCGTEVPVDEAH 43 (645)
T ss_pred CcCCCCCCCCCccccc
Confidence 3577777776655443
No 90
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=88.18 E-value=0.31 Score=39.61 Aligned_cols=36 Identities=28% Similarity=0.732 Sum_probs=26.1
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceeeeCCeeEEe
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRE 202 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R~ 202 (245)
.|-+||++|.++ -+ +-|..||.|-... +++-+|.-+
T Consensus 60 ~CkkCGfef~~~--~i-k~pSRCP~CKSE~-Ie~prF~ie 95 (97)
T COG3357 60 RCKKCGFEFRDD--KI-KKPSRCPKCKSEW-IEEPRFVIE 95 (97)
T ss_pred hhcccCcccccc--cc-CCcccCCcchhhc-ccCCceeec
Confidence 899999999882 11 2489999998776 555555544
No 91
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=88.04 E-value=0.52 Score=45.49 Aligned_cols=24 Identities=25% Similarity=0.607 Sum_probs=18.5
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
.||.|+.-.. .+...||.||..+.
T Consensus 223 ~C~~Cd~l~~-------~~~a~CpRC~~~L~ 246 (419)
T PRK15103 223 SCSCCTAILP-------ADQPVCPRCHTKGY 246 (419)
T ss_pred cCCCCCCCCC-------CCCCCCCCCCCcCc
Confidence 4999997532 25668999999984
No 92
>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=87.97 E-value=0.24 Score=35.81 Aligned_cols=19 Identities=42% Similarity=1.078 Sum_probs=15.3
Q ss_pred cCCCCCceeeecccccCCCcccCCCCC
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCS 189 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCG 189 (245)
.||+||+.-. ..-+||+||
T Consensus 28 ~C~~cG~~~~--------~H~vc~~cG 46 (55)
T TIGR01031 28 VCPNCGEFKL--------PHRVCPSCG 46 (55)
T ss_pred ECCCCCCccc--------CeeECCccC
Confidence 7999995332 689999998
No 93
>KOG2923 consensus Uncharacterized conserved protein [Function unknown]
Probab=87.87 E-value=0.34 Score=37.17 Aligned_cols=38 Identities=34% Similarity=0.740 Sum_probs=29.0
Q ss_pred cCcceeccCCCCCceeeecccccCC--CcccCCCCCCceee
Q 025946 156 SRDIVQDSCPNCGNDFQIFKSTLND--ELQLCPYCSQPFSV 194 (245)
Q Consensus 156 ~rnLIE~tCPnCG~eF~~~ed~Ln~--d~iqCPnCGE~L~V 194 (245)
..+.+.-.|| ||..|.+.++.|.+ +-.+||.|.=.+.|
T Consensus 17 e~~~y~yPCp-CGDrf~It~edL~~ge~Va~CpsCSL~I~V 56 (67)
T KOG2923|consen 17 ENQTYYYPCP-CGDRFQITLEDLENGEDVARCPSCSLIIRV 56 (67)
T ss_pred CCCeEEcCCC-CCCeeeecHHHHhCCCeeecCCCceEEEEE
Confidence 3456667898 99999997777655 57899999766554
No 94
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=87.87 E-value=0.28 Score=49.90 Aligned_cols=28 Identities=25% Similarity=0.507 Sum_probs=19.9
Q ss_pred cceeccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
|.--+.|++||+. .. ..-.||+||.+++
T Consensus 623 n~~~~~C~~CG~~-~g-------~~~~CP~CG~~~~ 650 (656)
T PRK08270 623 TPTFSICPKHGYL-SG-------EHEFCPKCGEETE 650 (656)
T ss_pred CCCCcccCCCCCc-CC-------CCCCCcCCcCccc
Confidence 3444599999973 33 3688999998754
No 95
>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=87.82 E-value=0.17 Score=47.83 Aligned_cols=12 Identities=25% Similarity=0.769 Sum_probs=8.9
Q ss_pred cccCCCCCCcee
Q 025946 182 LQLCPYCSQPFS 193 (245)
Q Consensus 182 ~iqCPnCGE~L~ 193 (245)
.-+|+.||.+++
T Consensus 149 g~~Ce~cG~~~~ 160 (391)
T PF09334_consen 149 GDQCENCGRPLE 160 (391)
T ss_dssp TTEETTTSSBEE
T ss_pred CCcccCCCCCcc
Confidence 456778888877
No 96
>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=87.77 E-value=0.3 Score=48.36 Aligned_cols=47 Identities=17% Similarity=0.408 Sum_probs=33.3
Q ss_pred cceeccCCCCCceeeec-cccc-------CCCcccCCCCCCceee-------eCCeeEEecc
Q 025946 158 DIVQDSCPNCGNDFQIF-KSTL-------NDELQLCPYCSQPFSV-------VDDKFVRESV 204 (245)
Q Consensus 158 nLIE~tCPnCG~eF~~~-ed~L-------n~d~iqCPnCGE~L~V-------d~~~F~R~~~ 204 (245)
..+...||.||..+... +++. ..--.+||.||..++- ..|+++.+.+
T Consensus 197 r~~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e~~k~~m~~~G~Wv~~~~ 258 (557)
T PF05876_consen 197 RRYYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEEHDKRRMVRRGRWVATNP 258 (557)
T ss_pred eEEEccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCHHHHhhccCCeEEEeccc
Confidence 35667999999888763 2221 1126799999998874 4688888777
No 97
>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=87.60 E-value=0.63 Score=44.62 Aligned_cols=25 Identities=32% Similarity=0.801 Sum_probs=19.3
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
.||.|+..... ..+..||.||.++.
T Consensus 217 ~C~~Cd~~~~~------~~~a~CpRC~~~L~ 241 (403)
T TIGR00155 217 SCSACHTTILP------AQEPVCPRCSTPLY 241 (403)
T ss_pred cCCCCCCccCC------CCCcCCcCCCCccc
Confidence 49999985432 35788999999993
No 98
>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=87.55 E-value=0.26 Score=38.04 Aligned_cols=18 Identities=17% Similarity=0.333 Sum_probs=12.5
Q ss_pred cCCCcccCCCCCCceeee
Q 025946 178 LNDELQLCPYCSQPFSVV 195 (245)
Q Consensus 178 Ln~d~iqCPnCGE~L~Vd 195 (245)
++-.-..||.||+.+...
T Consensus 27 v~~~~~~C~~CGe~~~~~ 44 (127)
T TIGR03830 27 IGVPGWYCPACGEELLDP 44 (127)
T ss_pred EeeeeeECCCCCCEEEcH
Confidence 333567899999977543
No 99
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=87.48 E-value=0.31 Score=42.70 Aligned_cols=31 Identities=26% Similarity=0.677 Sum_probs=21.3
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
..|..|++.+ ..++.+..+...||.||.++.
T Consensus 123 ~~C~~C~~~~-~~~~~~~~~~p~C~~Cgg~lr 153 (242)
T PRK00481 123 ARCTKCGQTY-DLDEYLKPEPPRCPKCGGILR 153 (242)
T ss_pred eeeCCCCCCc-ChhhhccCCCCCCCCCCCccC
Confidence 3999998764 445555555556999987653
No 100
>PLN00209 ribosomal protein S27; Provisional
Probab=87.30 E-value=0.4 Score=38.26 Aligned_cols=40 Identities=18% Similarity=0.363 Sum_probs=29.5
Q ss_pred cceeccCCCCCceeeecccccCCCcccCCCCCCcee-eeCCee
Q 025946 158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS-VVDDKF 199 (245)
Q Consensus 158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~-Vd~~~F 199 (245)
.++.+.||.|+++-.++. =....+.|..||+.|. ..+|+.
T Consensus 33 ~Fm~VkCp~C~n~q~VFS--hA~t~V~C~~Cg~~L~~PTGGKa 73 (86)
T PLN00209 33 FFMDVKCQGCFNITTVFS--HSQTVVVCGSCQTVLCQPTGGKA 73 (86)
T ss_pred EEEEEECCCCCCeeEEEe--cCceEEEccccCCEeeccCCCCe
Confidence 456779999999888731 2346999999999984 445543
No 101
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=87.25 E-value=0.17 Score=47.43 Aligned_cols=39 Identities=15% Similarity=0.359 Sum_probs=30.0
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCcee----------eeCCeeEEec
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFS----------VVDDKFVRES 203 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~----------Vd~~~F~R~~ 203 (245)
.||+|++.+|. ..|.+...+||+||--+. +|++.|+.-.
T Consensus 40 kc~~C~~~~~~--~~l~~~~~vcp~c~~h~rltAreRI~~L~D~gSF~E~~ 88 (296)
T CHL00174 40 QCENCYGLNYK--KFLKSKMNICEQCGYHLKMSSSDRIELLIDPGTWNPMD 88 (296)
T ss_pred ECCCccchhhH--HHHHHcCCCCCCCCCCcCCCHHHHHHHHccCCccEEcC
Confidence 89999999987 336777899999998554 5667776554
No 102
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=87.22 E-value=0.4 Score=40.96 Aligned_cols=31 Identities=29% Similarity=0.711 Sum_probs=19.1
Q ss_pred cCCCCCcee-eecccc-cCCC-----cccCCCCCCcee
Q 025946 163 SCPNCGNDF-QIFKST-LNDE-----LQLCPYCSQPFS 193 (245)
Q Consensus 163 tCPnCG~eF-~~~ed~-Ln~d-----~iqCPnCGE~L~ 193 (245)
.||-||.+. ..-++. +.++ --+||+||-.+.
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~ 39 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFT 39 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcce
Confidence 599999866 332222 2221 268999988765
No 103
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=87.09 E-value=0.25 Score=47.26 Aligned_cols=28 Identities=36% Similarity=0.675 Sum_probs=19.7
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
.||+||..++.+ .-|...-.||+||+++
T Consensus 317 fc~ncG~~~t~~--~~ng~a~fcp~cgq~~ 344 (345)
T COG4260 317 FCLNCGCGTTAD--FDNGKAKFCPECGQGF 344 (345)
T ss_pred cccccCcccccC--CccchhhhChhhcCCC
Confidence 788888666652 1233588999999875
No 104
>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=87.01 E-value=0.38 Score=41.46 Aligned_cols=31 Identities=26% Similarity=0.557 Sum_probs=21.9
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
.|+.|+++.+..+.......-.||.||.++.
T Consensus 111 ~C~~C~~~~~~~~~~~~~~~p~C~~Cgg~lr 141 (224)
T cd01412 111 RCSSCGYVGENNEEIPEEELPRCPKCGGLLR 141 (224)
T ss_pred ccCCCCCCCCcchhhhccCCCCCCCCCCccC
Confidence 9999999877632222334578999998653
No 105
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=86.99 E-value=0.43 Score=38.02 Aligned_cols=47 Identities=23% Similarity=0.476 Sum_probs=32.1
Q ss_pred cceeccCCCCCceeeecccccCCCcccCCCCCCcee-eeCCeeE-Eecccc
Q 025946 158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS-VVDDKFV-RESVRF 206 (245)
Q Consensus 158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~-Vd~~~F~-R~~~~f 206 (245)
.++.+.||.|+++-.++. =.++.+.|..||+.|. ..+|+.. .|+..|
T Consensus 32 ~Fm~VkCp~C~n~q~VFS--hA~t~V~C~~Cg~~L~~PTGGKa~l~~gc~f 80 (85)
T PTZ00083 32 YFMDVKCPGCSQITTVFS--HAQTVVLCGGCSSQLCQPTGGKAKLTEGCSF 80 (85)
T ss_pred eEEEEECCCCCCeeEEEe--cCceEEEccccCCEeeccCCCCeEecCCceE
Confidence 456779999999888731 2346999999999994 4444432 334444
No 106
>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=86.98 E-value=0.38 Score=41.28 Aligned_cols=33 Identities=33% Similarity=0.904 Sum_probs=17.5
Q ss_pred eeccCCCCCceeeecccccC-------CCcccCCCCCCcee
Q 025946 160 VQDSCPNCGNDFQIFKSTLN-------DELQLCPYCSQPFS 193 (245)
Q Consensus 160 IE~tCPnCG~eF~~~ed~Ln-------~d~iqCPnCGE~L~ 193 (245)
++.+||.|++++.. +.+.. ..-..||+|+..++
T Consensus 17 l~~~C~~C~~~~~f-~g~~~~~~~~~~~~~~~C~~C~~~~~ 56 (188)
T PF08996_consen 17 LKLTCPSCGTEFEF-PGVFEEDGDDVSPSGLQCPNCSTPLS 56 (188)
T ss_dssp EEEE-TTT--EEEE--SSS--SSEEEETTEEEETTT--B--
T ss_pred eEeECCCCCCCccc-cccccCCccccccCcCcCCCCCCcCC
Confidence 45699999999876 33333 34789999998543
No 107
>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=86.90 E-value=0.37 Score=31.34 Aligned_cols=26 Identities=23% Similarity=0.672 Sum_probs=15.9
Q ss_pred cceeccCCCCCceeeecccccCCCcccCCCCCC
Q 025946 158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQ 190 (245)
Q Consensus 158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE 190 (245)
.++-..|+.||...+- ....||+||.
T Consensus 8 ~l~~~rC~~Cg~~~~p-------Pr~~Cp~C~s 33 (37)
T PF12172_consen 8 RLLGQRCRDCGRVQFP-------PRPVCPHCGS 33 (37)
T ss_dssp -EEEEE-TTT--EEES---------SEETTTT-
T ss_pred EEEEEEcCCCCCEecC-------CCcCCCCcCc
Confidence 4556689999988776 6789999985
No 108
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=86.88 E-value=0.31 Score=45.10 Aligned_cols=31 Identities=23% Similarity=0.499 Sum_probs=23.2
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCCCceee
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSV 194 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~V 194 (245)
..||+||.+-. .....+++.+|-.||..++-
T Consensus 2 ~~CpeCg~~~~--~~d~~~ge~VC~~CG~Vi~~ 32 (285)
T COG1405 2 MSCPECGSTNI--ITDYERGEIVCADCGLVLED 32 (285)
T ss_pred CCCCCCCCccc--eeeccCCeEEeccCCEEecc
Confidence 47999998822 22245799999999998853
No 109
>PRK07591 threonine synthase; Validated
Probab=86.87 E-value=0.43 Score=45.32 Aligned_cols=31 Identities=26% Similarity=0.765 Sum_probs=24.3
Q ss_pred eeccCCCCCceeeecccccCCCcccCCCCCCceeeeC
Q 025946 160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVD 196 (245)
Q Consensus 160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~ 196 (245)
..-.|+.||+++-. . ....||.||.+|.++=
T Consensus 17 ~~l~C~~Cg~~~~~-----~-~~~~C~~cg~~l~~~y 47 (421)
T PRK07591 17 VALKCRECGAEYPL-----G-PIHVCEECFGPLEVAY 47 (421)
T ss_pred eEEEeCCCCCcCCC-----C-CCccCCCCCCeEEEEe
Confidence 34589999998754 2 2378999999999884
No 110
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=86.85 E-value=0.25 Score=40.95 Aligned_cols=35 Identities=29% Similarity=0.631 Sum_probs=23.2
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCCCceeeeCCeeEEeccc
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESVR 205 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R~~~~ 205 (245)
-.|..||+.|-+-+..+ -.=||+||- ++|...+..
T Consensus 3 H~CtrCG~vf~~g~~~i---l~GCp~CG~------nkF~yv~~e 37 (112)
T COG3364 3 HQCTRCGEVFDDGSEEI---LSGCPKCGC------NKFLYVPEE 37 (112)
T ss_pred ceecccccccccccHHH---HccCccccc------hheEecccc
Confidence 47999998887722222 335999994 567666543
No 111
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=86.82 E-value=0.15 Score=40.26 Aligned_cols=44 Identities=23% Similarity=0.615 Sum_probs=30.6
Q ss_pred ceeccCCCCCceeeecccccCCC-cccCCCCCCceeeeCCeeEEecccc
Q 025946 159 IVQDSCPNCGNDFQIFKSTLNDE-LQLCPYCSQPFSVVDDKFVRESVRF 206 (245)
Q Consensus 159 LIE~tCPnCG~eF~~~ed~Ln~d-~iqCPnCGE~L~Vd~~~F~R~~~~f 206 (245)
+|-..|-+||+.+... +.++++ ...||.||.++ ...|.|.+.-|
T Consensus 10 tY~Y~c~~cg~~~dvv-q~~~ddplt~ce~c~a~~---kk~l~~vgi~f 54 (82)
T COG2331 10 TYSYECTECGNRFDVV-QAMTDDPLTTCEECGARL---KKLLNAVGIVF 54 (82)
T ss_pred ceEEeecccchHHHHH-HhcccCccccChhhChHH---HHhhccceEEE
Confidence 3455899999988763 335554 67899999977 45555555544
No 112
>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=86.81 E-value=0.37 Score=32.28 Aligned_cols=26 Identities=27% Similarity=0.765 Sum_probs=22.2
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
.||+||..++. .+++...|-.||...
T Consensus 10 ~C~~C~~~~~~----~~dG~~yC~~cG~~~ 35 (36)
T PF11781_consen 10 PCPVCGSRWFY----SDDGFYYCDRCGHQS 35 (36)
T ss_pred cCCCCCCeEeE----ccCCEEEhhhCceEc
Confidence 59999999877 788899999998764
No 113
>PF13395 HNH_4: HNH endonuclease
Probab=86.77 E-value=0.37 Score=33.82 Aligned_cols=25 Identities=32% Similarity=0.804 Sum_probs=18.3
Q ss_pred CCCCCCceeeeC--------CeeEEeccccccc
Q 025946 185 CPYCSQPFSVVD--------DKFVRESVRFSNE 209 (245)
Q Consensus 185 CPnCGE~L~Vd~--------~~F~R~~~~f~~~ 209 (245)
|||||+++..++ +||.--+..+.+.
T Consensus 1 C~Y~g~~i~~~~l~~~~~~iDHiiP~s~~~~~s 33 (54)
T PF13395_consen 1 CPYCGKPISIENLFKNKYEIDHIIPRSRGGDDS 33 (54)
T ss_pred CCCCCCCCChhhcccCCceeEEEecccccCCCC
Confidence 999999999888 6666555554443
No 114
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=86.66 E-value=0.54 Score=31.05 Aligned_cols=29 Identities=24% Similarity=0.810 Sum_probs=22.4
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
..|+.|+...... -+++..+||.||..++
T Consensus 4 ~~C~~C~~~~i~~---~~~~~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 4 KKCSKCGGNGIVN---KEDDYEVCIFCGSSFP 32 (33)
T ss_pred eEcCCCCCCeEEE---ecCCeEEcccCCcEee
Confidence 4799999876541 3557999999998765
No 115
>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=86.39 E-value=0.2 Score=32.39 Aligned_cols=21 Identities=33% Similarity=0.729 Sum_probs=16.9
Q ss_pred ccCCCCCCceeeeCCeeEEec
Q 025946 183 QLCPYCSQPFSVVDDKFVRES 203 (245)
Q Consensus 183 iqCPnCGE~L~Vd~~~F~R~~ 203 (245)
+.||+|++.+.+++.+...++
T Consensus 3 ~~CP~C~~~~~v~~~~~~~~~ 23 (38)
T TIGR02098 3 IQCPNCKTSFRVVDSQLGANG 23 (38)
T ss_pred EECCCCCCEEEeCHHHcCCCC
Confidence 689999999999987765443
No 116
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=86.25 E-value=0.36 Score=52.97 Aligned_cols=11 Identities=36% Similarity=1.213 Sum_probs=7.1
Q ss_pred eccCCCCCcee
Q 025946 161 QDSCPNCGNDF 171 (245)
Q Consensus 161 E~tCPnCG~eF 171 (245)
.+.||.||.+.
T Consensus 667 ~rkCPkCG~~t 677 (1337)
T PRK14714 667 RRRCPSCGTET 677 (1337)
T ss_pred EEECCCCCCcc
Confidence 34777777653
No 117
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=86.15 E-value=0.38 Score=48.88 Aligned_cols=23 Identities=26% Similarity=0.654 Sum_probs=18.2
Q ss_pred eccCCCCCceeeecccccCCCcccCCCCCC
Q 025946 161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQ 190 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE 190 (245)
-+.||+||+++.. ..-.||.||+
T Consensus 568 ~~~C~~CG~~~~g-------~~~~CP~CGs 590 (625)
T PRK08579 568 ITVCNKCGRSTTG-------LYTRCPRCGS 590 (625)
T ss_pred CccCCCCCCccCC-------CCCcCcCCCC
Confidence 3499999997654 3679999997
No 118
>PF10005 DUF2248: Uncharacterized protein conserved in bacteria (DUF2248); InterPro: IPR011201 This is a family of uncharacterised bacterial proteins.
Probab=86.05 E-value=0.46 Score=45.64 Aligned_cols=24 Identities=38% Similarity=0.863 Sum_probs=21.5
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
+||+||..++- +..+|-+||..|-
T Consensus 1 ~C~~Cg~~v~F-------eNt~C~~Cg~~LG 24 (343)
T PF10005_consen 1 SCPNCGQPVFF-------ENTRCLSCGSALG 24 (343)
T ss_pred CCCCCCCccee-------CCCccccCCcccc
Confidence 69999999998 7889999999774
No 119
>COG1655 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=85.96 E-value=0.24 Score=46.02 Aligned_cols=13 Identities=31% Similarity=0.835 Sum_probs=10.8
Q ss_pred eccCCCCCceeee
Q 025946 161 QDSCPNCGNDFQI 173 (245)
Q Consensus 161 E~tCPnCG~eF~~ 173 (245)
+.+||+|+++|.-
T Consensus 19 ~ieCPvC~tkFkk 31 (267)
T COG1655 19 TIECPVCNTKFKK 31 (267)
T ss_pred eeccCcccchhhh
Confidence 3599999999875
No 120
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=85.88 E-value=0.42 Score=31.84 Aligned_cols=27 Identities=30% Similarity=0.742 Sum_probs=13.9
Q ss_pred cCCCCCceeeeccccc---CCCcccCCCCCCc
Q 025946 163 SCPNCGNDFQIFKSTL---NDELQLCPYCSQP 191 (245)
Q Consensus 163 tCPnCG~eF~~~ed~L---n~d~iqCPnCGE~ 191 (245)
-||+||.+... .+. +..-.+||.||..
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 49999988654 122 3346789999864
No 121
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=85.74 E-value=0.25 Score=48.71 Aligned_cols=43 Identities=21% Similarity=0.541 Sum_probs=33.9
Q ss_pred cCCCCCceeeecccc--cCC--CcccCCCCCCceeeeCCeeEEeccc
Q 025946 163 SCPNCGNDFQIFKST--LND--ELQLCPYCSQPFSVVDDKFVRESVR 205 (245)
Q Consensus 163 tCPnCG~eF~~~ed~--Ln~--d~iqCPnCGE~L~Vd~~~F~R~~~~ 205 (245)
.||+|.++|..+|-. +.. +...|-+|+..|..|+..-..+.++
T Consensus 130 ~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelveDe~~~~~~e~~ 176 (436)
T KOG2593|consen 130 VCPNCQKKYTSLEALQLLDNETGEFHCENCGGELVEDENKLPSKESR 176 (436)
T ss_pred cCCccccchhhhHHHHhhcccCceEEEecCCCchhcccccCchHHHH
Confidence 899999999987665 443 6999999999999888766554443
No 122
>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=85.40 E-value=0.62 Score=38.67 Aligned_cols=34 Identities=21% Similarity=0.573 Sum_probs=23.3
Q ss_pred ceeccCCCCCceeeeccc---ccCCCcccCCCCCCce
Q 025946 159 IVQDSCPNCGNDFQIFKS---TLNDELQLCPYCSQPF 192 (245)
Q Consensus 159 LIE~tCPnCG~eF~~~ed---~Ln~d~iqCPnCGE~L 192 (245)
+.+..|+.|++++...+. .-++..-.||.||..+
T Consensus 103 l~~~~C~~C~~~~~~~~~~~~~~~~~~~~C~~C~~~l 139 (178)
T PF02146_consen 103 LFRLRCSKCGKEYDREDIVDSIDEEEPPRCPKCGGLL 139 (178)
T ss_dssp EEEEEETTTSBEEEGHHHHHHHHTTSSCBCTTTSCBE
T ss_pred hceeeecCCCccccchhhcccccccccccccccCccC
Confidence 444599999998865321 1234566999999855
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=85.28 E-value=0.91 Score=38.53 Aligned_cols=32 Identities=31% Similarity=0.904 Sum_probs=23.5
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceeeeCCeeEEec
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRES 203 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R~~ 203 (245)
.|-+||.+..... -.--..||.|| +..|+|.+
T Consensus 114 ~C~~Cg~~~~~~~---~~~l~~Cp~C~------~~~F~R~~ 145 (146)
T PF07295_consen 114 VCENCGHEVELTH---PERLPPCPKCG------HTEFTRQP 145 (146)
T ss_pred ecccCCCEEEecC---CCcCCCCCCCC------CCeeeeCC
Confidence 8999999988721 11356799998 55677765
No 124
>PF12677 DUF3797: Domain of unknown function (DUF3797); InterPro: IPR024256 This presumed domain is functionally uncharacterised. This domain family is found in bacteria and viruses, and is approximately 50 amino acids in length. There is a conserved CGN sequence motif.
Probab=85.25 E-value=0.94 Score=32.97 Aligned_cols=27 Identities=41% Similarity=0.710 Sum_probs=20.5
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceeeeCCeeEEe
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRE 202 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R~ 202 (245)
.||+||+.... | =+-.|.|+|+-|.|.
T Consensus 15 ~Cp~CGN~~vG-----n--------gEG~liV~edtfkRt 41 (49)
T PF12677_consen 15 KCPKCGNDKVG-----N--------GEGTLIVEEDTFKRT 41 (49)
T ss_pred cCcccCCcEee-----c--------CcceEEEeccceeee
Confidence 79999988877 2 123568999999885
No 125
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=84.76 E-value=0.36 Score=45.60 Aligned_cols=29 Identities=31% Similarity=0.896 Sum_probs=23.8
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
.||.|+...|. ..|.....+||+|+--+.
T Consensus 30 KCp~c~~~~y~--~eL~~n~~vcp~c~~h~r 58 (294)
T COG0777 30 KCPSCGEMLYR--KELESNLKVCPKCGHHMR 58 (294)
T ss_pred ECCCccceeeH--HHHHhhhhcccccCcccc
Confidence 79999999997 346778999999987543
No 126
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=84.45 E-value=0.73 Score=39.25 Aligned_cols=30 Identities=17% Similarity=0.478 Sum_probs=23.0
Q ss_pred ceeccCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 159 IVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 159 LIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
.+...||.||....- ..-++..||+||..-
T Consensus 147 vv~a~~~~~g~~~~~----~~~~~~~c~~~~~~e 176 (189)
T PRK09521 147 VIYAMCSRCRTPLVK----KGENELKCPNCGNIE 176 (189)
T ss_pred EEEEEccccCCceEE----CCCCEEECCCCCCEE
Confidence 345589999998876 455789999998643
No 127
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=84.45 E-value=0.51 Score=48.64 Aligned_cols=25 Identities=36% Similarity=0.709 Sum_probs=17.3
Q ss_pred cceeccCCCCCceeeecccccCCCcccCCCCCC
Q 025946 158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQ 190 (245)
Q Consensus 158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE 190 (245)
+.--+.||+||+..-. .-.||.||.
T Consensus 677 n~~~~~C~~CG~~~~~--------~~~CP~CG~ 701 (735)
T PRK07111 677 NHPVDRCPVCGYLGVI--------EDKCPKCGS 701 (735)
T ss_pred CCCCeecCCCCCCCCc--------CccCcCCCC
Confidence 3334499999954322 479999996
No 128
>COG4031 Predicted metal-binding protein [General function prediction only]
Probab=84.26 E-value=0.54 Score=42.81 Aligned_cols=21 Identities=24% Similarity=0.803 Sum_probs=18.0
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
.| -||+++.. |..||+||++=
T Consensus 2 ~C-rCG~~l~~--------p~~Cl~Cg~~~ 22 (227)
T COG4031 2 IC-RCGAELSS--------PAFCLNCGRRH 22 (227)
T ss_pred cc-ccCCcccc--------cchhcccCCcc
Confidence 58 99999775 79999999983
No 129
>COG4640 Predicted membrane protein [Function unknown]
Probab=84.24 E-value=0.46 Score=47.04 Aligned_cols=24 Identities=29% Similarity=0.886 Sum_probs=18.3
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
-||.||.. =++|..+||-||.++.
T Consensus 3 fC~kcG~q-------k~Ed~~qC~qCG~~~t 26 (465)
T COG4640 3 FCPKCGSQ-------KAEDDVQCTQCGHKFT 26 (465)
T ss_pred cccccccc-------cccccccccccCCcCC
Confidence 69999943 1346788999999874
No 130
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=84.18 E-value=0.65 Score=41.46 Aligned_cols=27 Identities=19% Similarity=0.646 Sum_probs=21.5
Q ss_pred eeccCCCCCceeeecccccCCCcccCCCCCCc
Q 025946 160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQP 191 (245)
Q Consensus 160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~ 191 (245)
+-..|++|+....- ......||+||..
T Consensus 148 I~A~CsrC~~~L~~-----~~~~l~Cp~Cg~t 174 (188)
T COG1096 148 IYARCSRCRAPLVK-----KGNMLKCPNCGNT 174 (188)
T ss_pred EEEEccCCCcceEE-----cCcEEECCCCCCE
Confidence 44599999988775 4568999999974
No 131
>PRK06450 threonine synthase; Validated
Probab=84.14 E-value=0.6 Score=43.30 Aligned_cols=31 Identities=26% Similarity=0.627 Sum_probs=23.2
Q ss_pred eccCCCCCceeeecccccCCCcccCCCCCCceeeeCC
Q 025946 161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDD 197 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~ 197 (245)
.-.|+.||+++.. .....||.||.+|.++-+
T Consensus 3 ~~~C~~Cg~~~~~------~~~~~C~~cg~~l~~~~d 33 (338)
T PRK06450 3 KEVCMKCGKERES------IYEIRCKKCGGPFEILID 33 (338)
T ss_pred eeEECCcCCcCCC------cccccCCcCCCEeEEeec
Confidence 3489999998532 235789999999988743
No 132
>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=83.83 E-value=0.44 Score=41.57 Aligned_cols=34 Identities=26% Similarity=0.661 Sum_probs=20.9
Q ss_pred cCCCCCceeeecc---cc--c---CCCcccCCCCCCceeeeC
Q 025946 163 SCPNCGNDFQIFK---ST--L---NDELQLCPYCSQPFSVVD 196 (245)
Q Consensus 163 tCPnCG~eF~~~e---d~--L---n~d~iqCPnCGE~L~Vd~ 196 (245)
.||+|++...+.. ++ | ..-|..|-+||.+++-.+
T Consensus 41 ~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpyPWt~ 82 (158)
T PF10083_consen 41 SCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPYPWTE 82 (158)
T ss_pred HCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCCchHH
Confidence 6888887765532 11 1 113777888888877544
No 133
>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=83.82 E-value=2 Score=35.90 Aligned_cols=73 Identities=12% Similarity=0.200 Sum_probs=40.1
Q ss_pred hHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcceeccCCCCCceeeecccc--cCCCcccC
Q 025946 108 LGNLALAIGLTYFSMTGQLGWVLDAIVSIWLLAVIVPIVGFGAFLWWASRDIVQDSCPNCGNDFQIFKST--LNDELQLC 185 (245)
Q Consensus 108 lgn~l~~l~l~~LL~T~gLgWLvd~~~~L~LlllllPIl~~~Gf~WWl~rnLIE~tCPnCG~eF~~~ed~--Ln~d~iqC 185 (245)
+++|+..+.++-..+-. +|.++...-++..+.+++++|...+.. -.|..=.. .+--+++|
T Consensus 11 ~R~~al~lif~g~~vmy-~gi~f~~~~~im~ifmllG~L~~l~S~-----------------~VYfwIGmlStkav~V~C 72 (114)
T PF11023_consen 11 IRTFALSLIFIGMIVMY-IGIFFKASPIIMVIFMLLGLLAILAST-----------------AVYFWIGMLSTKAVQVEC 72 (114)
T ss_pred HHHHHHHHHHHHHHHHh-hhhhhcccHHHHHHHHHHHHHHHHHHH-----------------HHHHHhhhhcccceeeEC
Confidence 34555444333332222 245556667778888888877755544 12211011 12248889
Q ss_pred CCCCCceeeeCCe
Q 025946 186 PYCSQPFSVVDDK 198 (245)
Q Consensus 186 PnCGE~L~Vd~~~ 198 (245)
|+|+.+-..-++.
T Consensus 73 P~C~K~TKmLGr~ 85 (114)
T PF11023_consen 73 PNCGKQTKMLGRV 85 (114)
T ss_pred CCCCChHhhhchh
Confidence 9999887655544
No 134
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=83.77 E-value=0.62 Score=35.22 Aligned_cols=29 Identities=21% Similarity=0.474 Sum_probs=20.9
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
-.|-.||..+...| .-..-.||||||..-
T Consensus 10 ~~CtSCg~~i~p~e---~~v~F~CPnCGe~~I 38 (61)
T COG2888 10 PVCTSCGREIAPGE---TAVKFPCPNCGEVEI 38 (61)
T ss_pred ceeccCCCEeccCC---ceeEeeCCCCCceee
Confidence 38999999985421 225788999997653
No 135
>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=83.75 E-value=0.52 Score=40.65 Aligned_cols=31 Identities=23% Similarity=0.613 Sum_probs=21.3
Q ss_pred ccCCCCCceeeeccc---ccCCCcccCCCCCCce
Q 025946 162 DSCPNCGNDFQIFKS---TLNDELQLCPYCSQPF 192 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed---~Ln~d~iqCPnCGE~L 192 (245)
..|+.|++++...+. ..+.....||.||.++
T Consensus 110 ~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~l 143 (218)
T cd01407 110 VRCTKCGKEYPRDELQADIDREEVPRCPKCGGLL 143 (218)
T ss_pred ceeCCCcCCCcHHHHhHhhccCCCCcCCCCCCcc
Confidence 389999998765321 1233467899999774
No 136
>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=83.63 E-value=0.98 Score=29.37 Aligned_cols=13 Identities=23% Similarity=0.759 Sum_probs=9.8
Q ss_pred cccCCCCCCceee
Q 025946 182 LQLCPYCSQPFSV 194 (245)
Q Consensus 182 ~iqCPnCGE~L~V 194 (245)
-.+||.|||.+..
T Consensus 32 ~~~C~~CGE~~~~ 44 (46)
T TIGR03831 32 ALVCPQCGEEYLD 44 (46)
T ss_pred ccccccCCCEeeC
Confidence 3479999998753
No 137
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=83.48 E-value=0.37 Score=31.93 Aligned_cols=21 Identities=24% Similarity=0.657 Sum_probs=17.3
Q ss_pred ccCCCCCCceeeeCCeeEEec
Q 025946 183 QLCPYCSQPFSVVDDKFVRES 203 (245)
Q Consensus 183 iqCPnCGE~L~Vd~~~F~R~~ 203 (245)
++||+|+..+.++|.+.-..+
T Consensus 3 i~Cp~C~~~y~i~d~~ip~~g 23 (36)
T PF13717_consen 3 ITCPNCQAKYEIDDEKIPPKG 23 (36)
T ss_pred EECCCCCCEEeCCHHHCCCCC
Confidence 689999999999998755443
No 138
>PRK10445 endonuclease VIII; Provisional
Probab=83.47 E-value=0.77 Score=41.32 Aligned_cols=27 Identities=22% Similarity=0.680 Sum_probs=21.0
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCC
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCS 189 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCG 189 (245)
..||+||.+... ..+-..+...||+|-
T Consensus 236 ~~Cp~Cg~~I~~-~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 236 EACERCGGIIEK-TTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCCCCEeEE-EEECCCCcEECCCCc
Confidence 489999988875 344566899999994
No 139
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=83.40 E-value=0.49 Score=42.69 Aligned_cols=32 Identities=22% Similarity=0.599 Sum_probs=20.6
Q ss_pred eeccCCCCCceeeecccccCC----CcccCCCCCCce
Q 025946 160 VQDSCPNCGNDFQIFKSTLND----ELQLCPYCSQPF 192 (245)
Q Consensus 160 IE~tCPnCG~eF~~~ed~Ln~----d~iqCPnCGE~L 192 (245)
+...||+||.+=+. -.+++. -...|++||+..
T Consensus 5 iy~~Cp~Cg~eev~-hEVik~~g~~~lvrC~eCG~V~ 40 (201)
T COG1326 5 IYIECPSCGSEEVS-HEVIKERGREPLVRCEECGTVH 40 (201)
T ss_pred EEEECCCCCcchhh-HHHHHhcCCceEEEccCCCcEe
Confidence 44589999933221 122333 268999999987
No 140
>COG4391 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=82.85 E-value=0.73 Score=34.93 Aligned_cols=17 Identities=29% Similarity=0.854 Sum_probs=13.7
Q ss_pred cCCCcccCCCCCCceee
Q 025946 178 LNDELQLCPYCSQPFSV 194 (245)
Q Consensus 178 Ln~d~iqCPnCGE~L~V 194 (245)
=+++++.||||++.+..
T Consensus 44 g~~gev~CPYC~t~y~l 60 (62)
T COG4391 44 GDEGEVVCPYCSTRYRL 60 (62)
T ss_pred CCCCcEecCccccEEEe
Confidence 34579999999998764
No 141
>PRK11032 hypothetical protein; Provisional
Probab=82.83 E-value=1.3 Score=38.42 Aligned_cols=31 Identities=35% Similarity=0.892 Sum_probs=23.5
Q ss_pred cCCCCCceeeecccccCCC-cccCCCCCCceeeeCCeeEEec
Q 025946 163 SCPNCGNDFQIFKSTLNDE-LQLCPYCSQPFSVVDDKFVRES 203 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d-~iqCPnCGE~L~Vd~~~F~R~~ 203 (245)
.|-+||.+... -..+ -..||.|| +.+|+|.+
T Consensus 126 vC~~Cg~~~~~----~~p~~i~pCp~C~------~~~F~R~~ 157 (160)
T PRK11032 126 VCEKCHHHLAF----YTPEVLPLCPKCG------HDQFQRRP 157 (160)
T ss_pred EecCCCCEEEe----cCCCcCCCCCCCC------CCeeeeCC
Confidence 89999999876 2223 56799998 56788875
No 142
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=82.79 E-value=0.59 Score=51.38 Aligned_cols=9 Identities=44% Similarity=1.401 Sum_probs=5.4
Q ss_pred cCCCCCcee
Q 025946 163 SCPNCGNDF 171 (245)
Q Consensus 163 tCPnCG~eF 171 (245)
.||.||...
T Consensus 681 fCP~CGs~t 689 (1337)
T PRK14714 681 RCPDCGTHT 689 (1337)
T ss_pred cCcccCCcC
Confidence 566666553
No 143
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=82.71 E-value=0.51 Score=46.82 Aligned_cols=25 Identities=36% Similarity=0.683 Sum_probs=11.4
Q ss_pred ceeccCCCCCceeeecccccCCCcccCCCCCCc
Q 025946 159 IVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQP 191 (245)
Q Consensus 159 LIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~ 191 (245)
.--+.|++||+.-- ..-.||.||++
T Consensus 489 ~~~~~C~~CG~~~~--------~~~~CP~CGs~ 513 (546)
T PF13597_consen 489 PPIDICPDCGYIGG--------EGDKCPKCGSE 513 (546)
T ss_dssp --EEEETTT---S----------EEE-CCC---
T ss_pred cCcccccCCCcCCC--------CCCCCCCCCCc
Confidence 33459999997422 26789999998
No 144
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=82.47 E-value=0.88 Score=40.97 Aligned_cols=27 Identities=22% Similarity=0.646 Sum_probs=20.3
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCC
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQ 190 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE 190 (245)
.||+||.++.- ..+-..+...||.|-.
T Consensus 247 pC~~Cg~~I~~-~~~~gR~t~~CP~CQ~ 273 (274)
T PRK01103 247 PCRRCGTPIEK-IKQGGRSTFFCPRCQK 273 (274)
T ss_pred CCCCCCCeeEE-EEECCCCcEECcCCCC
Confidence 79999988765 3333458999999953
No 145
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=82.44 E-value=1.1 Score=35.84 Aligned_cols=36 Identities=19% Similarity=0.590 Sum_probs=25.8
Q ss_pred cceeccCCCCCceeeecccccCCCcccCCCCCCceee
Q 025946 158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSV 194 (245)
Q Consensus 158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~V 194 (245)
..+...|+.|+.++.-...+ +.....||.|+.+|..
T Consensus 120 ~~~~~~C~~C~~~~~r~~~~-~~~~~~C~~C~~~l~~ 155 (157)
T PF10263_consen 120 KKYVYRCPSCGREYKRHRRS-KRKRYRCGRCGGPLVQ 155 (157)
T ss_pred cceEEEcCCCCCEeeeeccc-chhhEECCCCCCEEEE
Confidence 34555999999998773333 4456789999988753
No 146
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=82.18 E-value=0.71 Score=47.04 Aligned_cols=26 Identities=19% Similarity=0.515 Sum_probs=18.8
Q ss_pred cceeccCCCCCceeeecccccCCCcccCCCCCC
Q 025946 158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQ 190 (245)
Q Consensus 158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE 190 (245)
|.--+.||+||+.... ..-.||.||.
T Consensus 563 n~~~~iC~~CG~~~~g-------~~~~CP~CGs 588 (623)
T PRK08271 563 NVKITICNDCHHIDKR-------TGKRCPICGS 588 (623)
T ss_pred CCCCccCCCCCCcCCC-------CCcCCcCCCC
Confidence 3444599999976333 4689999996
No 147
>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=82.15 E-value=0.88 Score=43.33 Aligned_cols=31 Identities=19% Similarity=0.336 Sum_probs=23.5
Q ss_pred eccCCCCCceeeecccccCCCcccCCCCCCceeeeCC
Q 025946 161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDD 197 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~ 197 (245)
.-.|+.||+++-+ + ....||.|+.+|.++-+
T Consensus 2 ~l~C~~Cg~~~~~--~----~~~~C~~c~g~l~~~y~ 32 (398)
T TIGR03844 2 TLRCPGCGEVLPD--H----YTLSCPLDCGLLRAEYA 32 (398)
T ss_pred EEEeCCCCCccCC--c----cccCCCCCCCceEEeec
Confidence 4579999999742 1 25789999999888744
No 148
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=82.13 E-value=0.43 Score=40.60 Aligned_cols=31 Identities=29% Similarity=0.507 Sum_probs=14.8
Q ss_pred eccCCCCCceeeecccccCC---------CcccCCCCCCce
Q 025946 161 QDSCPNCGNDFQIFKSTLND---------ELQLCPYCSQPF 192 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~Ln~---------d~iqCPnCGE~L 192 (245)
|+.||+||..-..- -.+-+ ....||+||-..
T Consensus 1 ~s~Cp~C~~~~~~~-~~~~~IP~F~evii~sf~C~~CGyk~ 40 (161)
T PF03367_consen 1 ESLCPNCGENGTTR-ILLTDIPYFKEVIIMSFECEHCGYKN 40 (161)
T ss_dssp -EE-TTTSSCCEEE-EEEEEETTTEEEEEEEEE-TTT--EE
T ss_pred CCcCCCCCCCcEEE-EEEEcCCCCceEEEEEeECCCCCCEe
Confidence 56899999875430 01111 145899998643
No 149
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=81.91 E-value=0.64 Score=40.73 Aligned_cols=34 Identities=21% Similarity=0.704 Sum_probs=22.9
Q ss_pred eccCCCCCceeeecccccCCC----------------cccCCCCCCceeeeCCee
Q 025946 161 QDSCPNCGNDFQIFKSTLNDE----------------LQLCPYCSQPFSVVDDKF 199 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~Ln~d----------------~iqCPnCGE~L~Vd~~~F 199 (245)
-..||.|+.++.. +..+ -..||+||..+ -.+.||
T Consensus 97 ~~RCp~CN~~L~~----vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiY-W~GsHw 146 (165)
T COG1656 97 FSRCPECNGELEK----VSREEVKEKVPEKVYRNYEEFYRCPKCGKIY-WKGSHW 146 (165)
T ss_pred cccCcccCCEecc----CcHHHHhhccchhhhhcccceeECCCCcccc-cCchHH
Confidence 3489999998876 2222 33499999876 334444
No 150
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=81.90 E-value=1 Score=31.51 Aligned_cols=26 Identities=31% Similarity=0.925 Sum_probs=18.3
Q ss_pred cCCCCCceeeecccccCCCcccCCCC
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYC 188 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnC 188 (245)
.||.||.++...=+.--.....||+|
T Consensus 30 ~C~~Cgh~w~~~v~~R~~~~~~CP~C 55 (55)
T PF14311_consen 30 KCPKCGHEWKASVNDRTRRGKGCPYC 55 (55)
T ss_pred ECCCCCCeeEccHhhhccCCCCCCCC
Confidence 79999999887211111358899998
No 151
>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=81.67 E-value=0.96 Score=34.80 Aligned_cols=27 Identities=19% Similarity=0.765 Sum_probs=13.8
Q ss_pred eccCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
|..||.|..++.- ..+...|+.|.+.+
T Consensus 1 e~~CP~C~~~L~~-----~~~~~~C~~C~~~~ 27 (70)
T PF07191_consen 1 ENTCPKCQQELEW-----QGGHYHCEACQKDY 27 (70)
T ss_dssp --B-SSS-SBEEE-----ETTEEEETTT--EE
T ss_pred CCcCCCCCCccEE-----eCCEEECccccccc
Confidence 3467777777554 33677777775543
No 152
>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=81.62 E-value=0.78 Score=39.83 Aligned_cols=29 Identities=17% Similarity=0.592 Sum_probs=19.5
Q ss_pred cCCCCCceeeeccccc-----CCCcccCCCCCCce
Q 025946 163 SCPNCGNDFQIFKSTL-----NDELQLCPYCSQPF 192 (245)
Q Consensus 163 tCPnCG~eF~~~ed~L-----n~d~iqCPnCGE~L 192 (245)
.|+.|+..+.. ++.. .+....||.||.++
T Consensus 97 ~C~~C~~~~~~-~~~~~~~~~~~~~p~C~~Cgg~l 130 (206)
T cd01410 97 VCKSCGPEYVR-DDVVETRGDKETGRRCHACGGIL 130 (206)
T ss_pred cCCCCCCccch-HHHHHHhhcCCCCCcCCCCcCcc
Confidence 89999977543 3322 12346799998764
No 153
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=81.59 E-value=1.4 Score=29.38 Aligned_cols=26 Identities=23% Similarity=0.572 Sum_probs=18.0
Q ss_pred CcccCCCCCCceeeeCCeeEEecccc
Q 025946 181 ELQLCPYCSQPFSVVDDKFVRESVRF 206 (245)
Q Consensus 181 d~iqCPnCGE~L~Vd~~~F~R~~~~f 206 (245)
++..||.||..|..-+..++|+-..+
T Consensus 1 e~~~C~~Cg~~l~~ig~~~~~q~l~~ 26 (47)
T PF13005_consen 1 EPRACPDCGGELKEIGEEKVRQVLDL 26 (47)
T ss_pred CCCcCCCCCceeeECCceeeEEEEee
Confidence 35678888888887777766654443
No 154
>KOG1088 consensus Uncharacterized conserved protein [Function unknown]
Probab=81.23 E-value=0.73 Score=38.92 Aligned_cols=19 Identities=21% Similarity=0.471 Sum_probs=12.8
Q ss_pred CCCcccCCCCCCceeeeCC
Q 025946 179 NDELQLCPYCSQPFSVVDD 197 (245)
Q Consensus 179 n~d~iqCPnCGE~L~Vd~~ 197 (245)
-+++.+||+||..+++.+|
T Consensus 95 ~EG~l~CpetG~vfpI~~G 113 (124)
T KOG1088|consen 95 IEGELVCPETGRVFPISDG 113 (124)
T ss_pred ccceEecCCCCcEeecccC
Confidence 4456777777777776665
No 155
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=81.19 E-value=0.81 Score=47.07 Aligned_cols=33 Identities=21% Similarity=0.448 Sum_probs=19.3
Q ss_pred cCcceeccCCCCCceeeecccccCCCcccCCCCCCc
Q 025946 156 SRDIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQP 191 (245)
Q Consensus 156 ~rnLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~ 191 (245)
.-|.--+.||+||++ + |-......-.||+||..
T Consensus 636 ~in~~~~~C~~CG~~--G-e~~~~~~~~~CP~CG~~ 668 (711)
T PRK09263 636 GTNTPIDECYECGFT--G-EFECTEKGFTCPKCGNH 668 (711)
T ss_pred EeCCCCcccCCCCCC--c-cccCCCCCCcCcCCCCC
Confidence 334444699999973 2 00011123689999964
No 156
>PF14353 CpXC: CpXC protein
Probab=81.11 E-value=0.85 Score=36.22 Aligned_cols=18 Identities=28% Similarity=0.947 Sum_probs=15.8
Q ss_pred cCcceeccCCCCCceeee
Q 025946 156 SRDIVQDSCPNCGNDFQI 173 (245)
Q Consensus 156 ~rnLIE~tCPnCG~eF~~ 173 (245)
...+...+||+||++++.
T Consensus 33 ~g~l~~~~CP~Cg~~~~~ 50 (128)
T PF14353_consen 33 DGSLFSFTCPSCGHKFRL 50 (128)
T ss_pred cCCcCEEECCCCCCceec
Confidence 567778899999999988
No 157
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=81.11 E-value=1 Score=33.81 Aligned_cols=33 Identities=36% Similarity=0.879 Sum_probs=23.5
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCCCceeeeCCeeEEeccccccc
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESVRFSNE 209 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R~~~~f~~~ 209 (245)
+.||+|| ..+. .-.||.||+...+ -.+++||-.
T Consensus 6 rkC~~cg-~YTL--------ke~Cp~CG~~t~~------~~PprFSPe 38 (59)
T COG2260 6 RKCPKCG-RYTL--------KEKCPVCGGDTKV------PHPPRFSPE 38 (59)
T ss_pred hcCcCCC-ceee--------cccCCCCCCcccc------CCCCCCCcc
Confidence 4799999 3333 3679999987654 457888763
No 158
>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=80.82 E-value=0.95 Score=45.87 Aligned_cols=26 Identities=27% Similarity=0.736 Sum_probs=17.2
Q ss_pred cceeccCCCCCceeeecccccCCCcccCCCCCC
Q 025946 158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQ 190 (245)
Q Consensus 158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE 190 (245)
+.--+.||+||+ +.. .-.-.||.||+
T Consensus 529 n~~~siC~~CGy-~~g------~~~~~CP~CGs 554 (586)
T TIGR02827 529 NIKITICNDCHH-IDK------RTLHRCPVCGS 554 (586)
T ss_pred CCCCeecCCCCC-cCC------CcCCcCcCCCC
Confidence 333459999997 211 11369999996
No 159
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=80.64 E-value=1.1 Score=40.36 Aligned_cols=25 Identities=24% Similarity=0.713 Sum_probs=19.7
Q ss_pred cCCCCCceeeecccccCCCcccCCCC
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYC 188 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnC 188 (245)
.||.||.++.- ..+-..+...||.|
T Consensus 247 pC~~Cg~~I~~-~~~~gR~t~~CP~C 271 (272)
T TIGR00577 247 PCRRCGTPIEK-IKVGGRGTHFCPQC 271 (272)
T ss_pred CCCCCCCeeEE-EEECCCCCEECCCC
Confidence 89999998876 23345689999999
No 160
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=80.38 E-value=1.2 Score=36.89 Aligned_cols=31 Identities=19% Similarity=0.626 Sum_probs=21.3
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCC-CceeeeCC
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCS-QPFSVVDD 197 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCG-E~L~Vd~~ 197 (245)
-.|+.|+.++.. ..-...||.|| -.+.+.+|
T Consensus 71 ~~C~~C~~~~~~-----e~~~~~CP~C~s~~~~i~~G 102 (115)
T COG0375 71 CWCLDCGQEVEL-----EELDYRCPKCGSINLRIIGG 102 (115)
T ss_pred EEeccCCCeecc-----hhheeECCCCCCCceEEecC
Confidence 389999988776 23334499999 45665554
No 161
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=80.04 E-value=0.71 Score=34.99 Aligned_cols=38 Identities=21% Similarity=0.488 Sum_probs=23.2
Q ss_pred ceeccCCCCCceeee--cccccCCC--cccCCCCCCceeeeC
Q 025946 159 IVQDSCPNCGNDFQI--FKSTLNDE--LQLCPYCSQPFSVVD 196 (245)
Q Consensus 159 LIE~tCPnCG~eF~~--~ed~Ln~d--~iqCPnCGE~L~Vd~ 196 (245)
+++-||..|+.+..- .+...+++ -++||.|...--+.|
T Consensus 2 ~l~FTC~~C~~Rs~~~~sk~aY~~GvViv~C~gC~~~HlIaD 43 (66)
T PF05180_consen 2 QLTFTCNKCGTRSAKMFSKQAYHKGVVIVQCPGCKNRHLIAD 43 (66)
T ss_dssp EEEEEETTTTEEEEEEEEHHHHHTSEEEEE-TTS--EEES--
T ss_pred eEEEEcCCCCCccceeeCHHHHhCCeEEEECCCCcceeeehh
Confidence 356799999988764 34445555 789999987655443
No 162
>PF04135 Nop10p: Nucleolar RNA-binding protein, Nop10p family; InterPro: IPR007264 H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs. More than 100 mammalian H/ACA RNAs form an equal number of ribonucleoproteins (RNPs) by associating with the same four core proteins: Cbf5, Gar1, Nhp2 and Nop10. The function of these H/ACA RNPs is essential for biogenesis of the ribosome, splicing of precursor mRNAs (pre-mRNAs), maintenance of telomeres and probably for additional cellular processes []. Recent crystal structures of archaeal H/ACA protein complexes show how the same four proteins accommodate >100 distinct but related H/ACA RNAs []. The complex contains a stable core composed of Cbf5 and Nop10, to which Gar1 and Nhp2 subsequently bind, the complex interacts with snoRNAs []. In eukaryotes Nop10 is a nucleolar protein that is specifically associated with H/ACA snoRNAs. It is essential for normal 18S rRNA production and rRNA pseudouridylation by the ribonucleoprotein particles containing H/ACA snoRNAs (H/ACA snoRNPs). Nop10 is probably necessary for the stability of these RNPs [].; PDB: 2RFK_B 3LWR_B 2HVY_C 3HAX_C 3MQK_B 3LWO_B 3LWV_B 3HAY_C 3HJY_B 2EY4_E ....
Probab=79.77 E-value=1.7 Score=31.69 Aligned_cols=33 Identities=33% Similarity=0.795 Sum_probs=23.2
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCCCceeeeCCeeEEeccccccc
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESVRFSNE 209 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R~~~~f~~~ 209 (245)
..|+.|+ .|. |+ -.||.||++.. +.-+++||-.
T Consensus 6 r~c~~~~--~YT----Lk---~~cp~cG~~T~------~ahPaRFSPd 38 (53)
T PF04135_consen 6 RKCPGCR--VYT----LK---DKCPPCGGPTE------SAHPARFSPD 38 (53)
T ss_dssp EECTTTC--EEE----SS---SBBTTTSSBSE------ESSSSSS-TT
T ss_pred ccCCCCC--cEe----CC---CccCCCCCCCc------CCcCCCCCCC
Confidence 4799998 565 44 48999999774 3457777753
No 163
>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=79.68 E-value=1 Score=48.72 Aligned_cols=23 Identities=30% Similarity=0.820 Sum_probs=18.3
Q ss_pred eccCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
.+.||+||+.-+ ...||.||+.-
T Consensus 625 ~RKCPkCG~yTl---------k~rCP~CG~~T 647 (1095)
T TIGR00354 625 IRKCPQCGKESF---------WLKCPVCGELT 647 (1095)
T ss_pred EEECCCCCcccc---------cccCCCCCCcc
Confidence 349999996633 57999999984
No 164
>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=79.63 E-value=1.2 Score=33.37 Aligned_cols=13 Identities=38% Similarity=0.830 Sum_probs=9.9
Q ss_pred cCCCCCceeeecc
Q 025946 163 SCPNCGNDFQIFK 175 (245)
Q Consensus 163 tCPnCG~eF~~~e 175 (245)
.||.||.+-+..+
T Consensus 2 ~C~KCg~~~~e~~ 14 (64)
T PF09855_consen 2 KCPKCGNEEYESG 14 (64)
T ss_pred CCCCCCCcceecc
Confidence 5999998877643
No 165
>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=79.62 E-value=0.89 Score=43.07 Aligned_cols=27 Identities=30% Similarity=0.598 Sum_probs=22.0
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceeeeC
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVD 196 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~ 196 (245)
.|.+||++..- =.-+||.||+-=.+++
T Consensus 2 ~c~~cg~~~~~-------~~g~cp~c~~w~~~~e 28 (372)
T cd01121 2 VCSECGYVSPK-------WLGKCPECGEWNTLVE 28 (372)
T ss_pred CCCCCCCCCCC-------ccEECcCCCCceeeee
Confidence 69999998776 5789999998666555
No 166
>PRK08402 replication factor A; Reviewed
Probab=79.62 E-value=1.5 Score=41.90 Aligned_cols=32 Identities=25% Similarity=0.557 Sum_probs=23.4
Q ss_pred cCcceeccCCCCCceeeecccccCCCcccCCCCCC
Q 025946 156 SRDIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQ 190 (245)
Q Consensus 156 ~rnLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE 190 (245)
+++.+-..||+|.+++... -.++.-+|+.||+
T Consensus 207 ~~~~~y~aCp~CnKkv~~~---~~~~~~~Ce~~~~ 238 (355)
T PRK08402 207 YRVLVYDACPECRRKVDYD---PATDTWICPEHGE 238 (355)
T ss_pred ecCeeEecCCCCCeEEEEe---cCCCCEeCCCCCC
Confidence 3455666999999998731 2235789999996
No 167
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=79.60 E-value=0.92 Score=46.05 Aligned_cols=22 Identities=32% Similarity=0.661 Sum_probs=15.9
Q ss_pred eccCCCCCceeeecccccCCCcccCCCCCC
Q 025946 161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQ 190 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE 190 (245)
=+.|++||++... .-.||.||.
T Consensus 559 ~~~C~~CGy~g~~--------~~~CP~CG~ 580 (618)
T PRK14704 559 VDRCKCCSYHGVI--------GNECPSCGN 580 (618)
T ss_pred CeecCCCCCCCCc--------CccCcCCCC
Confidence 3489999973211 268999997
No 168
>PRK04011 peptide chain release factor 1; Provisional
Probab=79.58 E-value=1.2 Score=42.70 Aligned_cols=37 Identities=30% Similarity=0.634 Sum_probs=24.2
Q ss_pred eeccCCCCCceeeec-ccccCCCcccCCCCCCceeeeC
Q 025946 160 VQDSCPNCGNDFQIF-KSTLNDELQLCPYCSQPFSVVD 196 (245)
Q Consensus 160 IE~tCPnCG~eF~~~-ed~Ln~d~iqCPnCGE~L~Vd~ 196 (245)
+...||+||++.... +..-..+...||+||..+++.+
T Consensus 327 ~~~~c~~c~~~~~~~~~~~~~~~~~~c~~~~~~~~~~~ 364 (411)
T PRK04011 327 VTYKCPNCGYEEEKTVKRREELPEKTCPKCGSELEIVE 364 (411)
T ss_pred EEEEcCCCCcceeeecccccccccccCcccCcccccch
Confidence 344799999876441 1111234679999999987754
No 169
>PRK12366 replication factor A; Reviewed
Probab=79.52 E-value=1.9 Score=43.65 Aligned_cols=30 Identities=27% Similarity=0.706 Sum_probs=23.7
Q ss_pred CcceeccCCCCCceeeecccccCCCcccCCCCCCc
Q 025946 157 RDIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQP 191 (245)
Q Consensus 157 rnLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~ 191 (245)
.+.+--.||.|.++... .++.-.||.||+.
T Consensus 528 ~~~~y~aCp~CnkKv~~-----~~g~~~C~~c~~~ 557 (637)
T PRK12366 528 QKIILYLCPNCRKRVEE-----VDGEYICEFCGEV 557 (637)
T ss_pred CCEEEecccccCeEeEc-----CCCcEECCCCCCC
Confidence 35566699999998763 3578899999987
No 170
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=79.46 E-value=1.3 Score=40.12 Aligned_cols=26 Identities=23% Similarity=0.613 Sum_probs=19.8
Q ss_pred cCCCCCceeeecccccCCCcccCCCCC
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCS 189 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCG 189 (245)
.||.||.++.- ..+-..+...||.|-
T Consensus 246 pCprCG~~I~~-~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 246 PCLNCKTPIRR-VVVAGRSSHYCPHCQ 271 (272)
T ss_pred cCCCCCCeeEE-EEECCCccEECcCCc
Confidence 89999988865 233355799999995
No 171
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=79.38 E-value=1.2 Score=33.48 Aligned_cols=27 Identities=26% Similarity=0.672 Sum_probs=21.2
Q ss_pred ccCCCCCceeeecccccC-CCcccCCCCCCce
Q 025946 162 DSCPNCGNDFQIFKSTLN-DELQLCPYCSQPF 192 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln-~d~iqCPnCGE~L 192 (245)
..|-.||..+.. .+ ...-.|||||+.+
T Consensus 8 ~~CtSCg~~i~~----~~~~~~F~CPnCG~~~ 35 (59)
T PRK14890 8 PKCTSCGIEIAP----REKAVKFLCPNCGEVI 35 (59)
T ss_pred ccccCCCCcccC----CCccCEeeCCCCCCee
Confidence 379999999876 33 3578999999973
No 172
>TIGR02378 nirD_assim_sml nitrite reductase [NAD(P)H], small subunit. This model describes NirD, the small subunit of nitrite reductase [NAD(P)H] (the assimilatory nitrite reductase), which associates with NirB, the large subunit (TIGR02374). In a few bacteria such as Klebsiella pneumoniae and in Fungi, the two regions are fused.
Probab=79.33 E-value=1.6 Score=33.17 Aligned_cols=38 Identities=21% Similarity=0.463 Sum_probs=26.7
Q ss_pred ceeccCCCC-CceeeecccccCCCc----ccCCCCCCceeeeCCe
Q 025946 159 IVQDSCPNC-GNDFQIFKSTLNDEL----QLCPYCSQPFSVVDDK 198 (245)
Q Consensus 159 LIE~tCPnC-G~eF~~~ed~Ln~d~----iqCPnCGE~L~Vd~~~ 198 (245)
-++..||.. +..+.. ..+.++. ++||..|..|.++.|+
T Consensus 38 a~~~~CpH~g~~~L~~--g~~~~~~~~~~i~Cp~Hg~~Fdl~tG~ 80 (105)
T TIGR02378 38 AIQNMCPHKRAFVLSR--GIVGDAQGELWVACPLHKRNFRLEDGR 80 (105)
T ss_pred EEeCcCCCCCCccccc--eEEccCCCcEEEECCcCCCEEEcCCcc
Confidence 466799999 544432 2233444 9999999999988765
No 173
>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=79.08 E-value=1.4 Score=36.30 Aligned_cols=42 Identities=24% Similarity=0.586 Sum_probs=26.5
Q ss_pred cceeccCCCCCceeeec-cccc-----------CCCcccCCCCCCceeeeCCeeE
Q 025946 158 DIVQDSCPNCGNDFQIF-KSTL-----------NDELQLCPYCSQPFSVVDDKFV 200 (245)
Q Consensus 158 nLIE~tCPnCG~eF~~~-ed~L-----------n~d~iqCPnCGE~L~Vd~~~F~ 200 (245)
+-.-+.||.|+.++..- ++.. .+.--+||.||+.+ =++.|+.
T Consensus 88 ~~~~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiy-W~GsH~~ 141 (147)
T PF01927_consen 88 DPIFSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIY-WEGSHWR 141 (147)
T ss_pred CCCCCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEe-cccccHH
Confidence 33456999999988662 2211 12356899999876 4455543
No 174
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=78.89 E-value=1.3 Score=40.12 Aligned_cols=26 Identities=23% Similarity=0.698 Sum_probs=20.4
Q ss_pred cCCCCCceeeecccccCCCcccCCCCC
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCS 189 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCG 189 (245)
.||.||.++.- +.+-..+...||.|-
T Consensus 256 pC~~Cg~~I~~-~~~~gR~t~~CP~CQ 281 (282)
T PRK13945 256 PCRKCGTPIER-IKLAGRSTHWCPNCQ 281 (282)
T ss_pred CCCcCCCeeEE-EEECCCccEECCCCc
Confidence 89999988775 344456899999994
No 175
>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=78.75 E-value=1.6 Score=41.76 Aligned_cols=32 Identities=25% Similarity=0.658 Sum_probs=15.2
Q ss_pred cCCCCCceeeecccccCC-CcccCCCCCCceeeeCCeeEEecc
Q 025946 163 SCPNCGNDFQIFKSTLND-ELQLCPYCSQPFSVVDDKFVRESV 204 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~-d~iqCPnCGE~L~Vd~~~F~R~~~ 204 (245)
.|++|+++...+ .. ....|++||. .+|.|++.
T Consensus 287 kC~~C~~Rt~sl----~r~P~~~C~~Cg~------~~wer~~M 319 (344)
T PF09332_consen 287 KCKDCGNRTISL----ERLPKKHCSNCGS------SKWERTGM 319 (344)
T ss_dssp E-T-TS-EEEES----SSS--S--TTT-S---------EEE--
T ss_pred ECCCCCCeeeec----ccCCCCCCCcCCc------Cceeehhh
Confidence 899999998884 33 4489999995 46888875
No 176
>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=78.73 E-value=1.2 Score=32.93 Aligned_cols=28 Identities=32% Similarity=0.834 Sum_probs=22.4
Q ss_pred ccCCCCCceeeecccccCCC-cccCCCCCCceee
Q 025946 162 DSCPNCGNDFQIFKSTLNDE-LQLCPYCSQPFSV 194 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d-~iqCPnCGE~L~V 194 (245)
..|.+||+-+.. .++ ...||.||+++-.
T Consensus 19 ~NCl~CGkIiC~-----~Eg~~~pC~fCg~~l~~ 47 (57)
T PF06221_consen 19 PNCLNCGKIICE-----QEGPLGPCPFCGTPLLS 47 (57)
T ss_pred ccccccChhhcc-----cccCcCcCCCCCCcccC
Confidence 489999977766 455 6899999998754
No 177
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=78.69 E-value=0.9 Score=34.63 Aligned_cols=23 Identities=26% Similarity=0.863 Sum_probs=17.5
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCCCc
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQP 191 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~ 191 (245)
..|-+|.+- .+++.-+||+||.+
T Consensus 5 kAC~~Ck~l-------~~~d~e~CP~Cgs~ 27 (64)
T COG2093 5 KACKNCKRL-------TPEDTEICPVCGST 27 (64)
T ss_pred HHHhhcccc-------CCCCCccCCCCCCc
Confidence 468889854 44578899999976
No 178
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=78.51 E-value=1.9 Score=35.91 Aligned_cols=27 Identities=22% Similarity=0.883 Sum_probs=21.8
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
.||.|+.+++-. ......||.|+-++.
T Consensus 5 ~cp~c~sEytYe----d~~~~~cpec~~ew~ 31 (112)
T COG2824 5 PCPKCNSEYTYE----DGGQLICPECAHEWN 31 (112)
T ss_pred CCCccCCceEEe----cCceEeCchhccccc
Confidence 799999888762 225899999998886
No 179
>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=78.49 E-value=2 Score=30.65 Aligned_cols=29 Identities=21% Similarity=0.550 Sum_probs=18.3
Q ss_pred cCCCCCceeeecccc----------c--CCCcccCCCCCCc
Q 025946 163 SCPNCGNDFQIFKST----------L--NDELQLCPYCSQP 191 (245)
Q Consensus 163 tCPnCG~eF~~~ed~----------L--n~d~iqCPnCGE~ 191 (245)
.|+.||+.+.-.+.. + ..+.-.||.||.+
T Consensus 3 ~C~~CgyiYd~~~Gd~~~~i~pGt~f~~Lp~~w~CP~C~a~ 43 (50)
T cd00730 3 ECRICGYIYDPAEGDPDEGIPPGTPFEDLPDDWVCPVCGAG 43 (50)
T ss_pred CCCCCCeEECCCCCCcccCcCCCCCHhHCCCCCCCCCCCCc
Confidence 699999766532111 1 1235599999975
No 180
>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=78.45 E-value=1.4 Score=38.05 Aligned_cols=28 Identities=21% Similarity=0.708 Sum_probs=15.7
Q ss_pred CCCCCce-eeecc---cc--cCC---CcccCCCCCCc
Q 025946 164 CPNCGND-FQIFK---ST--LND---ELQLCPYCSQP 191 (245)
Q Consensus 164 CPnCG~e-F~~~e---d~--Ln~---d~iqCPnCGE~ 191 (245)
||+||.+ +.... +. +.+ ....||+||-.
T Consensus 1 CP~Cg~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr 37 (163)
T TIGR00340 1 CPVCGSRTLKAVTYDYDIPYFGKIMLSTYICEKCGYR 37 (163)
T ss_pred CCCCCCcceEeeeEeccCCCcceEEEEEEECCCCCCc
Confidence 9999975 33210 00 111 25689999864
No 181
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=78.45 E-value=1.7 Score=29.59 Aligned_cols=30 Identities=30% Similarity=0.647 Sum_probs=14.4
Q ss_pred ccCCC--CCceeeecccccCCCcccCCCCCCce
Q 025946 162 DSCPN--CGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 162 ~tCPn--CG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
..||+ |+.-+...+ ..+...++||.|+..+
T Consensus 19 ~~Cp~~~C~~~~~~~~-~~~~~~~~C~~C~~~f 50 (64)
T PF01485_consen 19 RWCPNPDCEYIIEKDD-GCNSPIVTCPSCGTEF 50 (64)
T ss_dssp C--TTSST---ECS-S-STTS--CCTTSCCSEE
T ss_pred cCCCCCCCcccEEecC-CCCCCeeECCCCCCcC
Confidence 38988 998877721 1111238999998754
No 182
>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=78.32 E-value=1.4 Score=42.35 Aligned_cols=31 Identities=19% Similarity=0.536 Sum_probs=21.5
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceee
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSV 194 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~V 194 (245)
.||.|+.-... ...-.++...||.||.++..
T Consensus 15 ~C~~Cd~l~~~-~~l~~g~~a~CpRCg~~L~~ 45 (403)
T TIGR00155 15 LCSQCDMLVAL-PRIESGQKAACPRCGTTLTV 45 (403)
T ss_pred eCCCCCCcccc-cCCCCCCeeECCCCCCCCcC
Confidence 59999966543 22223357889999999953
No 183
>PRK06386 replication factor A; Reviewed
Probab=78.30 E-value=1.1 Score=42.88 Aligned_cols=20 Identities=15% Similarity=0.443 Sum_probs=16.9
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCCC
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQ 190 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE 190 (245)
..||.|+...+. -+||.||+
T Consensus 237 ~rCP~C~R~l~~---------g~C~~HG~ 256 (358)
T PRK06386 237 TKCSVCNKIIED---------GVCKDHPD 256 (358)
T ss_pred ecCcCCCeEccC---------CcCCCCCC
Confidence 489999988764 39999998
No 184
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=78.09 E-value=1.3 Score=40.49 Aligned_cols=33 Identities=27% Similarity=0.718 Sum_probs=22.4
Q ss_pred ceeccCCCCCceeeecccc--cCC-CcccCCCCCCc
Q 025946 159 IVQDSCPNCGNDFQIFKST--LND-ELQLCPYCSQP 191 (245)
Q Consensus 159 LIE~tCPnCG~eF~~~ed~--Ln~-d~iqCPnCGE~ 191 (245)
+....|..||..++..+-. ..+ .+..||.||.+
T Consensus 120 l~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~ 155 (250)
T COG0846 120 LKRVRCSKCGNQYYDEDVIKFIEDGLIPRCPKCGGP 155 (250)
T ss_pred eeeeEeCCCcCccchhhhhhhcccCCCCcCccCCCc
Confidence 3444999999999864311 111 36789999995
No 185
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=77.91 E-value=1.1 Score=49.85 Aligned_cols=25 Identities=28% Similarity=0.809 Sum_probs=19.5
Q ss_pred eeccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
..+.||+||+.-+ ..+||.||+..+
T Consensus 673 ~~~~Cp~Cg~~~~---------~~~Cp~CG~~~~ 697 (1627)
T PRK14715 673 AFFKCPKCGKVGL---------YHVCPFCGTRVE 697 (1627)
T ss_pred EeeeCCCCCCccc---------cccCcccCCccc
Confidence 3449999997744 579999999843
No 186
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=77.88 E-value=1.6 Score=42.19 Aligned_cols=30 Identities=27% Similarity=0.730 Sum_probs=21.1
Q ss_pred cCCCCCceeeecccccCC-CcccCCCCCCceee
Q 025946 163 SCPNCGNDFQIFKSTLND-ELQLCPYCSQPFSV 194 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~-d~iqCPnCGE~L~V 194 (245)
.||.|+.-... ..++. ....||.||.++..
T Consensus 12 ~C~~Cd~l~~~--~~l~~g~~a~CpRCg~~L~~ 42 (419)
T PRK15103 12 LCPQCDMLVAL--PRLEHGQKAACPRCGTTLTV 42 (419)
T ss_pred cCCCCCceeec--CCCCCCCeeECCCCCCCCcC
Confidence 59999976543 12333 46789999999953
No 187
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=77.76 E-value=1.2 Score=33.09 Aligned_cols=21 Identities=33% Similarity=0.823 Sum_probs=16.3
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCCC
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQ 190 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE 190 (245)
..||+||.... ..-+||+||.
T Consensus 28 ~~c~~cG~~~l--------~Hrvc~~cg~ 48 (57)
T COG0333 28 SVCPNCGEYKL--------PHRVCLKCGY 48 (57)
T ss_pred eeccCCCCccc--------CceEcCCCCC
Confidence 38999995544 5889999993
No 188
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=77.57 E-value=1.6 Score=39.58 Aligned_cols=30 Identities=23% Similarity=0.620 Sum_probs=22.7
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
.||.||.++.- ..+-..+...||.|-...+
T Consensus 237 pC~~Cg~~I~~-~~~~gR~ty~Cp~CQ~~~~ 266 (269)
T PRK14811 237 PCPRCGTPIEK-IVVGGRGTHFCPQCQPLRP 266 (269)
T ss_pred CCCcCCCeeEE-EEECCCCcEECCCCcCCCC
Confidence 89999998876 3334568999999976543
No 189
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=77.45 E-value=1.5 Score=35.32 Aligned_cols=43 Identities=19% Similarity=0.269 Sum_probs=27.6
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCCCceeeeCCe---eEEecccccc
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDK---FVRESVRFSN 208 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~---F~R~~~~f~~ 208 (245)
+.|-.|+.-.... .-....||||+..+..++++ ...-++.|+.
T Consensus 4 rAC~~C~~I~~~~----qf~~~gCpnC~~~l~~~g~~~~v~~~tT~~f~G 49 (98)
T cd07973 4 RACLLCSLIKTED----QFERDGCPNCEGYLDMKGNHERVYDCTSPNFEG 49 (98)
T ss_pred chhccCCcccccc----cccCCCCCCCcchhccCCCccccccccCCCcce
Confidence 3799999655431 01246899999988888765 2233555655
No 190
>smart00350 MCM minichromosome maintenance proteins.
Probab=77.45 E-value=3.8 Score=39.90 Aligned_cols=74 Identities=18% Similarity=0.407 Sum_probs=42.1
Q ss_pred cCCCCCceeeecccc-cCCCcccCCC--CCCceeeeCCeeEEecccccc-ccccccccccccCCCCCCCCCCCceeEEee
Q 025946 163 SCPNCGNDFQIFKST-LNDELQLCPY--CSQPFSVVDDKFVRESVRFSN-ESTTFGQAFSDFFPGSRKGRESSTSVVDVE 238 (245)
Q Consensus 163 tCPnCG~eF~~~ed~-Ln~d~iqCPn--CGE~L~Vd~~~F~R~~~~f~~-~~~~~~~af~~~~~~~~~~~~~~~~vvdve 238 (245)
.|+.||.+++...+. -...|..||+ |+..-++ .+..+...|.+ |.-.-++..++. ..|.-|....|-+|
T Consensus 39 ~C~~C~~~~~~~~~~~~~~~p~~C~~~~C~~~~~f---~l~~~~s~~~D~Q~I~iQE~~e~~----p~G~~Prsi~v~l~ 111 (509)
T smart00350 39 TCEKCGATLGPEIQSGRETEPTVCPPRECQSPTPF---SLNHERSTFIDFQKIKLQESPEEV----PAGQLPRSVDVILD 111 (509)
T ss_pred EecCCCCEEeEEecCCcccCCCcCCCCcCCCCCce---EeccCCCeEEEEEEEEEEcCcccC----CCCCCCcEEEEEEc
Confidence 899999988774322 2235889999 9874211 12334466776 555555543332 23444555555555
Q ss_pred eeeec
Q 025946 239 AEIKD 243 (245)
Q Consensus 239 aev~d 243 (245)
-+..|
T Consensus 112 ~dLvd 116 (509)
T smart00350 112 GDLVD 116 (509)
T ss_pred ccccC
Confidence 44443
No 191
>PRK04023 DNA polymerase II large subunit; Validated
Probab=77.16 E-value=1.3 Score=48.17 Aligned_cols=20 Identities=35% Similarity=1.163 Sum_probs=12.9
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCc
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQP 191 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~ 191 (245)
.||.||... ....||+||+.
T Consensus 628 fCpsCG~~t---------~~frCP~CG~~ 647 (1121)
T PRK04023 628 KCPSCGKET---------FYRRCPFCGTH 647 (1121)
T ss_pred cCCCCCCcC---------CcccCCCCCCC
Confidence 788888763 23566666654
No 192
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=77.13 E-value=1.4 Score=32.52 Aligned_cols=26 Identities=31% Similarity=0.792 Sum_probs=11.7
Q ss_pred eeccCCCCCceeeecccccCCCcccCCCCCC
Q 025946 160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQ 190 (245)
Q Consensus 160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE 190 (245)
|++.||.||+.+.- ..+...-|.|.+
T Consensus 1 m~v~CP~C~k~~~~-----~~~n~~rPFCS~ 26 (57)
T PF03884_consen 1 MTVKCPICGKPVEW-----SPENPFRPFCSE 26 (57)
T ss_dssp -EEE-TTT--EEE------SSSSS--SSSSH
T ss_pred CcccCCCCCCeecc-----cCCCCcCCcccH
Confidence 45678888877665 334455666654
No 193
>PF09581 Spore_III_AF: Stage III sporulation protein AF (Spore_III_AF); InterPro: IPR014245 This family represents the stage III sporulation protein AF (SpoIIIAF) of the bacterial endospore formation program, which exists in some but not all members of the Firmicutes (formerly called low-GC Gram-positives). The C-terminal region of these proteins is poorly conserved.
Probab=77.07 E-value=3.9 Score=34.09 Aligned_cols=40 Identities=18% Similarity=0.258 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHhcccchhHHHHHHHHHH-HHHHHHHHHHHH
Q 025946 111 LALAIGLTYFSMTGQLGWVLDAIVSIWL-LAVIVPIVGFGA 150 (245)
Q Consensus 111 ~l~~l~l~~LL~T~gLgWLvd~~~~L~L-lllllPIl~~~G 150 (245)
++++.++-+|||....+=.+..+.||++ ++++.||+.+++
T Consensus 4 ~ll~~~ie~LlP~~~~kkYvr~v~GLili~~il~Pil~l~~ 44 (188)
T PF09581_consen 4 ILLATFIEMLLPNSKYKKYVRFVLGLILILAILSPILSLFG 44 (188)
T ss_pred eHHHHHHHHhCCchhHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3556667889999999999999998887 456779998654
No 194
>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=77.00 E-value=1.3 Score=38.68 Aligned_cols=32 Identities=25% Similarity=0.674 Sum_probs=20.4
Q ss_pred ccCCCCCceeeeccc--ccCCCcccCCCCCCcee
Q 025946 162 DSCPNCGNDFQIFKS--TLNDELQLCPYCSQPFS 193 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed--~Ln~d~iqCPnCGE~L~ 193 (245)
..|++|++.+...+. ......-.||.||.++.
T Consensus 114 ~~C~~C~~~~~~~~~~~~~~~~~p~C~~Cgg~lr 147 (222)
T cd01413 114 AYCVNCGSKYDLEEVKYAKKHEVPRCPKCGGIIR 147 (222)
T ss_pred ceECCCCCCcchhHHHHhccCCCCcCCCCCCccC
Confidence 389999987654211 11223467999998764
No 195
>PRK11823 DNA repair protein RadA; Provisional
Probab=76.91 E-value=1.2 Score=42.88 Aligned_cols=29 Identities=28% Similarity=0.570 Sum_probs=22.9
Q ss_pred eccCCCCCceeeecccccCCCcccCCCCCCceeeeC
Q 025946 161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVD 196 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~ 196 (245)
...|.+||++..- =.-+||.|++-=.+++
T Consensus 7 ~y~C~~Cg~~~~~-------~~g~Cp~C~~w~t~~e 35 (446)
T PRK11823 7 AYVCQECGAESPK-------WLGRCPECGAWNTLVE 35 (446)
T ss_pred eEECCcCCCCCcc-------cCeeCcCCCCccceee
Confidence 3479999998776 5789999998665555
No 196
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=76.75 E-value=1.9 Score=47.81 Aligned_cols=34 Identities=24% Similarity=0.516 Sum_probs=23.7
Q ss_pred cCCCCCceeeecccccCC----CcccCCCCCCceeeeC
Q 025946 163 SCPNCGNDFQIFKSTLND----ELQLCPYCSQPFSVVD 196 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~----d~iqCPnCGE~L~Vd~ 196 (245)
.||+|.+.=..++..... ..-.||.||++|.-|+
T Consensus 916 ~Cp~Cky~Ef~~d~svgsGfDLpdK~CPkCg~pl~kDG 953 (1444)
T COG2176 916 LCPECKYSEFIDDGSVGSGFDLPDKDCPKCGTPLKKDG 953 (1444)
T ss_pred cCCCCceeeeecCCCcCCCCCCCCCCCCcCCCccccCC
Confidence 799999765553333333 3778999999975544
No 197
>PTZ00409 Sir2 (Silent Information Regulator) protein; Provisional
Probab=76.48 E-value=1.4 Score=40.27 Aligned_cols=32 Identities=28% Similarity=0.600 Sum_probs=20.4
Q ss_pred eccCCCCCceeeecccccC-------CCcccCCCCCCcee
Q 025946 161 QDSCPNCGNDFQIFKSTLN-------DELQLCPYCSQPFS 193 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~Ln-------~d~iqCPnCGE~L~ 193 (245)
+..|+.|++++...+.... +.+-.|| ||.++.
T Consensus 137 ~~~C~~C~~~~~~~~~~~~~~~~~~~~~~P~C~-Cgg~lr 175 (271)
T PTZ00409 137 EARCCTCRKTIQLNKIMLQKTSHFMHQLPPECP-CGGIFK 175 (271)
T ss_pred cceeCCCCCCcccCHHHHhhhhhhccCCCCCCC-CCCccc
Confidence 3499999998875433321 1235799 987653
No 198
>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=76.42 E-value=1.5 Score=47.89 Aligned_cols=35 Identities=26% Similarity=0.558 Sum_probs=23.6
Q ss_pred cCCCCCceeeecccccCC----CcccCCCCCCceeeeCC
Q 025946 163 SCPNCGNDFQIFKSTLND----ELQLCPYCSQPFSVVDD 197 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~----d~iqCPnCGE~L~Vd~~ 197 (245)
.||+|.+.-...+..... ..-.||+||+++.-|+-
T Consensus 685 ~c~~c~~~ef~~~~~~~sg~dlp~k~cp~c~~~~~~dg~ 723 (1213)
T TIGR01405 685 LCPNCKYSEFITDGSVGSGFDLPDKDCPKCGAPLKKDGQ 723 (1213)
T ss_pred cCcccccccccccccccccccCccccCccccccccccCC
Confidence 699999855543322222 36789999999866554
No 199
>cd03528 Rieske_RO_ferredoxin Rieske non-heme iron oxygenase (RO) family, Rieske ferredoxin component; composed of the Rieske ferredoxin component of some three-component RO systems including biphenyl dioxygenase (BPDO) and carbazole 1,9a-dioxygenase (CARDO). The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable microorganisms to tolerate and even exclusively utilize aromatic compounds for growth. ROs consist of two or three components: reductase, oxygenase, and ferredoxin (in some cases) components. The ferredoxin component contains either a plant-type or Rieske-type [2Fe-2S] cluster. The Rieske ferredoxin component in this family carries an electron from the RO reductase component to the terminal RO oxygenase component. BPDO degrades biphenyls and polychlorinated biphenyls. BPDO ferredoxin (BphF) has structural features consistent with a minimal and perhaps archetypical Rieske protein in that the in
Probab=76.36 E-value=1.7 Score=32.16 Aligned_cols=39 Identities=15% Similarity=0.327 Sum_probs=30.1
Q ss_pred eeccCCCCCceeeecccccCCCcccCCCCCCceeeeCCeeE
Q 025946 160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFV 200 (245)
Q Consensus 160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~ 200 (245)
++..||..|..+.. ....++.+.||+.|..|.+++|+-.
T Consensus 37 ~~~~CpH~g~~L~~--g~~~~~~i~Cp~Hg~~fd~~~G~~~ 75 (98)
T cd03528 37 TDDLCTHGDASLSE--GYVEGGVIECPLHGGRFDLRTGKAL 75 (98)
T ss_pred ECCcCCCCCCCCCC--CeEeCCEEEeCCcCCEEECCCCccc
Confidence 55699999988754 2245678999999999999777654
No 200
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=76.19 E-value=1.2 Score=39.17 Aligned_cols=28 Identities=21% Similarity=0.693 Sum_probs=16.8
Q ss_pred cCCCCCceeeecccccCC----------CcccCCCCCCc
Q 025946 163 SCPNCGNDFQIFKSTLND----------ELQLCPYCSQP 191 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~----------d~iqCPnCGE~ 191 (245)
.||+||++.... -.+-+ ....||+||-.
T Consensus 2 ~Cp~C~~~~~~~-~~~~~~IP~F~evii~sf~C~~CGyr 39 (192)
T TIGR00310 2 DCPSCGGECETV-MKTVNDIPYFGEVLETSTICEHCGYR 39 (192)
T ss_pred cCCCCCCCCEEE-EEEEcCCCCcceEEEEEEECCCCCCc
Confidence 699998664431 11111 25679999864
No 201
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=76.05 E-value=2.6 Score=34.15 Aligned_cols=34 Identities=21% Similarity=0.407 Sum_probs=26.4
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceeeeCC
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDD 197 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~ 197 (245)
-||.||.-.+.-++..+ .-.+|+.||-..++++.
T Consensus 4 FCp~Cgsll~p~~~~~~-~~l~C~kCgye~~~~~~ 37 (113)
T COG1594 4 FCPKCGSLLYPKKDDEG-GKLVCRKCGYEEEASNK 37 (113)
T ss_pred ccCCccCeeEEeEcCCC-cEEECCCCCcchhcccc
Confidence 59999988888544433 38999999998888764
No 202
>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=75.82 E-value=1.3 Score=42.99 Aligned_cols=29 Identities=24% Similarity=0.508 Sum_probs=22.8
Q ss_pred eccCCCCCceeeecccccCCCcccCCCCCCceeeeC
Q 025946 161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVD 196 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~ 196 (245)
...|.+||++..- =.-+||.|++==.+++
T Consensus 7 ~y~C~~Cg~~~~~-------~~g~Cp~C~~w~t~~~ 35 (454)
T TIGR00416 7 KFVCQHCGADSPK-------WQGKCPACHAWNTITE 35 (454)
T ss_pred eEECCcCCCCCcc-------ccEECcCCCCccccch
Confidence 4589999998776 4789999998555544
No 203
>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=75.73 E-value=1.4 Score=43.08 Aligned_cols=11 Identities=36% Similarity=1.035 Sum_probs=7.2
Q ss_pred cCCCCCceeee
Q 025946 163 SCPNCGNDFQI 173 (245)
Q Consensus 163 tCPnCG~eF~~ 173 (245)
.||+|+...+.
T Consensus 224 ~C~~C~~~l~~ 234 (505)
T TIGR00595 224 CCPNCDVSLTY 234 (505)
T ss_pred CCCCCCCceEE
Confidence 57777766554
No 204
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=75.64 E-value=1.5 Score=43.57 Aligned_cols=22 Identities=32% Similarity=0.591 Sum_probs=17.3
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCc
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQP 191 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~ 191 (245)
.|++||+.... ..-.||.||+.
T Consensus 520 ~C~~CG~~~~~-------~~~~CP~CGs~ 541 (555)
T cd01675 520 ICNDCGYIGEG-------EGFKCPKCGSE 541 (555)
T ss_pred cCCCCCCCCcC-------CCCCCcCCCCc
Confidence 89999975433 46799999964
No 205
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=75.61 E-value=1.5 Score=32.25 Aligned_cols=19 Identities=11% Similarity=0.083 Sum_probs=15.3
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCC
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCS 189 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCG 189 (245)
..||+||+... ..-.|| ||
T Consensus 28 ~~c~~cg~~~~--------pH~vc~-cG 46 (60)
T PRK01110 28 SVDKTTGEYHL--------PHHVSP-KG 46 (60)
T ss_pred eEcCCCCceec--------cceecC-Cc
Confidence 48999996554 488899 99
No 206
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=75.38 E-value=1.7 Score=37.19 Aligned_cols=31 Identities=23% Similarity=0.484 Sum_probs=16.9
Q ss_pred ccCCCCCceeeec---ccc--cCC---CcccCCCCCCce
Q 025946 162 DSCPNCGNDFQIF---KST--LND---ELQLCPYCSQPF 192 (245)
Q Consensus 162 ~tCPnCG~eF~~~---ed~--Ln~---d~iqCPnCGE~L 192 (245)
+.||+||.....- .+. +.+ ....||+||-.-
T Consensus 1 s~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~ 39 (160)
T smart00709 1 SDCPSCGGNGTTRMLLTSIPYFREVIIMSFECEHCGYRN 39 (160)
T ss_pred CcCCCCCCCCEEEEEEecCCCcceEEEEEEECCCCCCcc
Confidence 3699998664420 000 111 156799998643
No 207
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=75.07 E-value=1.2 Score=44.83 Aligned_cols=34 Identities=21% Similarity=0.589 Sum_probs=22.5
Q ss_pred hcCcceeccCCCCCceeeecccccCCCcccCCCCCCceeeeC
Q 025946 155 ASRDIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVD 196 (245)
Q Consensus 155 l~rnLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~ 196 (245)
+-..+++.+||.||.+-.. --||-+||..+...+
T Consensus 136 l~dr~v~g~cp~cg~~~ar--------GD~Ce~Cg~~~~P~~ 169 (558)
T COG0143 136 LPDRYVEGTCPKCGGEDAR--------GDQCENCGRTLDPTE 169 (558)
T ss_pred ccchheeccCCCcCccccC--------cchhhhccCcCCchh
Confidence 4456677788888855332 457778887777644
No 208
>PRK04023 DNA polymerase II large subunit; Validated
Probab=74.99 E-value=1.5 Score=47.52 Aligned_cols=11 Identities=36% Similarity=0.996 Sum_probs=9.0
Q ss_pred eeccCCCCCce
Q 025946 160 VQDSCPNCGND 170 (245)
Q Consensus 160 IE~tCPnCG~e 170 (245)
.+..||+||..
T Consensus 637 ~~frCP~CG~~ 647 (1121)
T PRK04023 637 FYRRCPFCGTH 647 (1121)
T ss_pred CcccCCCCCCC
Confidence 55699999976
No 209
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=74.80 E-value=1.7 Score=48.23 Aligned_cols=35 Identities=20% Similarity=0.459 Sum_probs=24.0
Q ss_pred cCCCCCceeeecccccCC----CcccCCCCCCceeeeCC
Q 025946 163 SCPNCGNDFQIFKSTLND----ELQLCPYCSQPFSVVDD 197 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~----d~iqCPnCGE~L~Vd~~ 197 (245)
.||+|.+.=...+..... ..-.||+||+++.-|+-
T Consensus 910 ~C~~C~~~ef~~~~~~~sG~Dlpdk~Cp~Cg~~~~kdg~ 948 (1437)
T PRK00448 910 VCPNCKYSEFFTDGSVGSGFDLPDKDCPKCGTKLKKDGH 948 (1437)
T ss_pred cCcccccccccccccccccccCccccCccccccccccCC
Confidence 699998766553332222 26789999999866554
No 210
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=74.60 E-value=1.5 Score=41.13 Aligned_cols=35 Identities=17% Similarity=0.324 Sum_probs=25.2
Q ss_pred hcCcceeccCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 155 ASRDIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 155 l~rnLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
+.|.-.-+-||.||.+.+.- -...-.+||+||...
T Consensus 105 ~~w~~~~RFCg~CG~~~~~~---~~g~~~~C~~cg~~~ 139 (279)
T COG2816 105 LEWYRSHRFCGRCGTKTYPR---EGGWARVCPKCGHEH 139 (279)
T ss_pred HHHHhhCcCCCCCCCcCccc---cCceeeeCCCCCCcc
Confidence 34555567899999998872 122488999999853
No 211
>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=74.22 E-value=4.3 Score=31.71 Aligned_cols=34 Identities=26% Similarity=0.673 Sum_probs=22.6
Q ss_pred eccCCCCCceeeecccc--c--CCCcccCCCCCCceee
Q 025946 161 QDSCPNCGNDFQIFKST--L--NDELQLCPYCSQPFSV 194 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~--L--n~d~iqCPnCGE~L~V 194 (245)
.+.||+|++++.-.|-. + ---.-.|.+|+++++.
T Consensus 33 rS~C~~C~~~L~~~~lIPi~S~l~lrGrCr~C~~~I~~ 70 (92)
T PF06750_consen 33 RSHCPHCGHPLSWWDLIPILSYLLLRGRCRYCGAPIPP 70 (92)
T ss_pred CCcCcCCCCcCcccccchHHHHHHhCCCCcccCCCCCh
Confidence 36999999998873221 0 0013479999998864
No 212
>KOG4517 consensus Uncharacterized conserved protein [Function unknown]
Probab=74.15 E-value=3.7 Score=34.48 Aligned_cols=34 Identities=29% Similarity=0.714 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCcceeccCCCCCcee
Q 025946 132 AIVSIWLLAVIVPIVGFGAFLWWASRDIVQDSCPNCGNDF 171 (245)
Q Consensus 132 ~~~~L~LlllllPIl~~~Gf~WWl~rnLIE~tCPnCG~eF 171 (245)
.++++++.+++-|.-.+--| ++-+++|||||..|
T Consensus 83 talgi~~ai~~fP~g~ic~~------alr~rrc~ncg~~f 116 (117)
T KOG4517|consen 83 TALGIFLAIILFPFGFICCF------ALRKRRCPNCGPTF 116 (117)
T ss_pred HHhhHHHHHHHhhhHHHhhH------hhhhccCCCccccc
Confidence 34677777888886553333 24477999999765
No 213
>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=73.85 E-value=1.6 Score=36.76 Aligned_cols=24 Identities=29% Similarity=0.624 Sum_probs=18.7
Q ss_pred CCCCCceeeecccccCCCcccCCCCCCceee
Q 025946 164 CPNCGNDFQIFKSTLNDELQLCPYCSQPFSV 194 (245)
Q Consensus 164 CPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~V 194 (245)
||.||..+.. ....|+.|.+.+..
T Consensus 1 C~~C~~~~~~-------~~~~C~~C~~~~~~ 24 (190)
T TIGR00201 1 CSLCGRPYQS-------VHALCRQCGSWRTR 24 (190)
T ss_pred CCcccccccc-------ccCCchhhCCcccc
Confidence 9999976543 45789999998763
No 214
>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=73.81 E-value=1.7 Score=30.22 Aligned_cols=28 Identities=36% Similarity=0.825 Sum_probs=18.0
Q ss_pred ccCCCCCceeeecccc---------cCCCcccCCCCCC
Q 025946 162 DSCPNCGNDFQIFKST---------LNDELQLCPYCSQ 190 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~---------Ln~d~iqCPnCGE 190 (245)
-+||-||+.+.. +++ .......||-|.+
T Consensus 3 f~CP~C~~~~~~-~~L~~H~~~~H~~~~~~v~CPiC~~ 39 (54)
T PF05605_consen 3 FTCPYCGKGFSE-SSLVEHCEDEHRSESKNVVCPICSS 39 (54)
T ss_pred cCCCCCCCccCH-HHHHHHHHhHCcCCCCCccCCCchh
Confidence 489999995432 221 1124789999975
No 215
>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=73.69 E-value=2 Score=27.26 Aligned_cols=14 Identities=21% Similarity=0.669 Sum_probs=6.0
Q ss_pred cCCCCCCceeeeCC
Q 025946 184 LCPYCSQPFSVVDD 197 (245)
Q Consensus 184 qCPnCGE~L~Vd~~ 197 (245)
.||.||+++.-+++
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 47777777764443
No 216
>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=73.66 E-value=1.3 Score=34.08 Aligned_cols=33 Identities=18% Similarity=0.557 Sum_probs=16.6
Q ss_pred cCCCCCceeee---cccccCCCcccCCCCCCceeee
Q 025946 163 SCPNCGNDFQI---FKSTLNDELQLCPYCSQPFSVV 195 (245)
Q Consensus 163 tCPnCG~eF~~---~ed~Ln~d~iqCPnCGE~L~Vd 195 (245)
+||.|+.+-.. .+...+...+.|-+||+.++.+
T Consensus 24 ~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~ 59 (81)
T PF05129_consen 24 DCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTK 59 (81)
T ss_dssp --TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE
T ss_pred cCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEc
Confidence 89999944222 1111233699999999988765
No 217
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=73.52 E-value=1.3 Score=31.13 Aligned_cols=32 Identities=19% Similarity=0.597 Sum_probs=21.9
Q ss_pred eeccCCCCCceeee--cccccCC-CcccCCCCCCc
Q 025946 160 VQDSCPNCGNDFQI--FKSTLND-ELQLCPYCSQP 191 (245)
Q Consensus 160 IE~tCPnCG~eF~~--~ed~Ln~-d~iqCPnCGE~ 191 (245)
...+|-.|+-++.. ..++.+. .-+.||+||--
T Consensus 21 ~~~~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgRi 55 (56)
T PF02591_consen 21 EGGTCSGCHMELPPQELNEIRKGDEIVFCPNCGRI 55 (56)
T ss_pred eCCccCCCCEEcCHHHHHHHHcCCCeEECcCCCcc
Confidence 34599999988776 2222233 57999999853
No 218
>PRK07218 replication factor A; Provisional
Probab=73.44 E-value=1.7 Score=42.51 Aligned_cols=20 Identities=30% Similarity=0.669 Sum_probs=16.8
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCc
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQP 191 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~ 191 (245)
.||.|+...+. -+||.||++
T Consensus 299 rCP~C~r~v~~---------~~C~~hG~v 318 (423)
T PRK07218 299 RCPECGRVIQK---------GQCRSHGAV 318 (423)
T ss_pred cCcCccccccC---------CcCCCCCCc
Confidence 89999988642 699999986
No 219
>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=73.43 E-value=1.1 Score=32.88 Aligned_cols=39 Identities=15% Similarity=0.214 Sum_probs=26.5
Q ss_pred eeccCCCCCceeeecccccCCCcccCCCCCCceeeeCCee
Q 025946 160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKF 199 (245)
Q Consensus 160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F 199 (245)
-+..|++|++-+..-++ ...-++-||-|++...+..-..
T Consensus 3 ~eiRC~~CnklLa~~g~-~~~leIKCpRC~tiN~~~a~~~ 41 (51)
T PF10122_consen 3 KEIRCGHCNKLLAKAGE-VIELEIKCPRCKTINHVRATSP 41 (51)
T ss_pred cceeccchhHHHhhhcC-ccEEEEECCCCCccceEeccCC
Confidence 35689999976654111 2234999999999877765443
No 220
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=73.24 E-value=2.2 Score=32.50 Aligned_cols=29 Identities=24% Similarity=0.424 Sum_probs=22.3
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCc
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQP 191 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~ 191 (245)
.||.||.+....+...+--...|+.||+.
T Consensus 8 PCPFCG~~~~~v~~~~g~~~v~C~~CgA~ 36 (64)
T PRK09710 8 PCPFCGCPSVTVKAISGYYRAKCNGCESR 36 (64)
T ss_pred CCCCCCCceeEEEecCceEEEEcCCCCcC
Confidence 79999998887665533346899999985
No 221
>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=73.02 E-value=1.9 Score=43.15 Aligned_cols=27 Identities=26% Similarity=0.586 Sum_probs=17.4
Q ss_pred cceeccCCCCCceeeecccccCCCcccCCCCCCc
Q 025946 158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQP 191 (245)
Q Consensus 158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~ 191 (245)
|.--+.|++||+. + ....-.||.||..
T Consensus 521 n~~~~~C~~CG~~--g-----~~~~~~CP~Cgs~ 547 (579)
T TIGR02487 521 NPPVDVCEDCGYT--G-----EGLNDKCPKCGSH 547 (579)
T ss_pred ccCCccCCCCCCC--C-----CCCCCcCcCCCCc
Confidence 4444599999962 2 0112589999963
No 222
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=72.94 E-value=2.1 Score=38.59 Aligned_cols=34 Identities=24% Similarity=0.505 Sum_probs=23.7
Q ss_pred cCcceeccCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 156 SRDIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 156 ~rnLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
.|.--..-||.||.+....+ ..-...||.||...
T Consensus 94 ~w~~~~~fC~~CG~~~~~~~---~~~~~~C~~c~~~~ 127 (256)
T PRK00241 94 EFYRSHRFCGYCGHPMHPSK---TEWAMLCPHCRERY 127 (256)
T ss_pred HHhhcCccccccCCCCeecC---CceeEECCCCCCEE
Confidence 34444678999999877632 22467899999744
No 223
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=72.91 E-value=1.6 Score=38.85 Aligned_cols=29 Identities=21% Similarity=0.715 Sum_probs=19.4
Q ss_pred cCCCCCceeeeccccc----CCCcccCCCCCCce
Q 025946 163 SCPNCGNDFQIFKSTL----NDELQLCPYCSQPF 192 (245)
Q Consensus 163 tCPnCG~eF~~~ed~L----n~d~iqCPnCGE~L 192 (245)
.|+.|++++.. ++.. ..+.-.||.||.++
T Consensus 121 ~C~~C~~~~~~-~~~~~~~~~~~~p~Cp~Cgg~l 153 (244)
T PRK14138 121 YCVRCGKRYTV-EDVIEKLEKSDVPRCDDCSGLI 153 (244)
T ss_pred EECCCCCcccH-HHHHHHHhcCCCCCCCCCCCeE
Confidence 89999987654 3222 12346799998764
No 224
>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=72.88 E-value=2.7 Score=34.56 Aligned_cols=31 Identities=16% Similarity=0.455 Sum_probs=24.0
Q ss_pred cceeccCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
+.+-.-||.|.++... -+++...|+.|++..
T Consensus 31 ~~~Y~aC~~C~kkv~~----~~~~~~~C~~C~~~~ 61 (166)
T cd04476 31 NWWYPACPGCNKKVVE----EGNGTYRCEKCNKSV 61 (166)
T ss_pred CeEEccccccCcccEe----CCCCcEECCCCCCcC
Confidence 3556689999999876 222689999999875
No 225
>PF15616 TerY-C: TerY-C metal binding domain
Probab=72.54 E-value=4.5 Score=34.17 Aligned_cols=31 Identities=35% Similarity=0.787 Sum_probs=21.5
Q ss_pred cCCCCCce-----------eeecccccCCCcccCCCCCCceeeeCC
Q 025946 163 SCPNCGND-----------FQIFKSTLNDELQLCPYCSQPFSVVDD 197 (245)
Q Consensus 163 tCPnCG~e-----------F~~~ed~Ln~d~iqCPnCGE~L~Vd~~ 197 (245)
.||-||+. +... ..+...||.||+...+...
T Consensus 79 gCP~CGn~~~fa~C~CGkl~Ci~----g~~~~~CPwCg~~g~~~~~ 120 (131)
T PF15616_consen 79 GCPHCGNQYAFAVCGCGKLFCID----GEGEVTCPWCGNEGSFGAG 120 (131)
T ss_pred CCCCCcChhcEEEecCCCEEEeC----CCCCEECCCCCCeeeeccc
Confidence 67777766 3431 2358999999998876554
No 226
>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=72.49 E-value=1.2 Score=47.48 Aligned_cols=12 Identities=33% Similarity=1.046 Sum_probs=0.0
Q ss_pred eccCCCCCceee
Q 025946 161 QDSCPNCGNDFQ 172 (245)
Q Consensus 161 E~tCPnCG~eF~ 172 (245)
.+.||.||...+
T Consensus 655 ~r~Cp~Cg~~t~ 666 (900)
T PF03833_consen 655 RRRCPKCGKETF 666 (900)
T ss_dssp ------------
T ss_pred cccCcccCCcch
Confidence 347777776544
No 227
>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=72.36 E-value=1.9 Score=34.78 Aligned_cols=31 Identities=19% Similarity=0.504 Sum_probs=21.3
Q ss_pred cceeccCC--CCCceeeecccccCCCcccCCCCCCce
Q 025946 158 DIVQDSCP--NCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 158 nLIE~tCP--nCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
+.+-.-|| .|+++... -.++...|+.|++..
T Consensus 15 ~~~Y~aC~~~~C~kKv~~----~~~~~y~C~~C~~~~ 47 (146)
T PF08646_consen 15 NWYYPACPNEKCNKKVTE----NGDGSYRCEKCNKTV 47 (146)
T ss_dssp TTEEEE-TSTTTS-B-EE----ETTTEEEETTTTEEE
T ss_pred CcEECCCCCccCCCEeec----CCCcEEECCCCCCcC
Confidence 44556899 99998776 234678999999876
No 228
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=72.34 E-value=2.5 Score=31.24 Aligned_cols=29 Identities=28% Similarity=0.700 Sum_probs=20.3
Q ss_pred CCCCCceeeecccccCCCcccCCCCCCceeeeCCe
Q 025946 164 CPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDK 198 (245)
Q Consensus 164 CPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~ 198 (245)
||+|+.... +.....||.||-|..-+..+
T Consensus 2 Cpv~~~~~~------~~v~~~Cp~cGipthcS~eh 30 (55)
T PF13824_consen 2 CPVCKKDLP------AHVNFECPDCGIPTHCSEEH 30 (55)
T ss_pred CCCCccccc------cccCCcCCCCCCcCccCHHH
Confidence 899987642 23578899999887654433
No 229
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=72.32 E-value=2 Score=28.64 Aligned_cols=28 Identities=36% Similarity=1.060 Sum_probs=18.1
Q ss_pred cCCCCCceeeecccccCC-CcccCCCCCCce
Q 025946 163 SCPNCGNDFQIFKSTLND-ELQLCPYCSQPF 192 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~-d~iqCPnCGE~L 192 (245)
.||.|+...... .+.+ .--.||.||-.+
T Consensus 1 ~CP~C~~~l~~~--~~~~~~id~C~~C~G~W 29 (41)
T PF13453_consen 1 KCPRCGTELEPV--RLGDVEIDVCPSCGGIW 29 (41)
T ss_pred CcCCCCcccceE--EECCEEEEECCCCCeEE
Confidence 599999865541 1223 244699998665
No 230
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=71.88 E-value=1.1 Score=41.05 Aligned_cols=36 Identities=19% Similarity=0.594 Sum_probs=26.0
Q ss_pred cCCCCCceeee--cccccCC-CcccCCCCCCceeeeCCe
Q 025946 163 SCPNCGNDFQI--FKSTLND-ELQLCPYCSQPFSVVDDK 198 (245)
Q Consensus 163 tCPnCG~eF~~--~ed~Ln~-d~iqCPnCGE~L~Vd~~~ 198 (245)
.|-.|.-.++. ..++.++ +.++||+||.-|..++.+
T Consensus 199 ~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgRILy~~e~~ 237 (239)
T COG1579 199 VCGGCHMKLPSQTLSKVRKKDEIVFCPYCGRILYYDESE 237 (239)
T ss_pred cccCCeeeecHHHHHHHhcCCCCccCCccchHHHhhhcc
Confidence 89999988776 2233444 689999999877666554
No 231
>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=71.79 E-value=2 Score=36.19 Aligned_cols=39 Identities=21% Similarity=0.521 Sum_probs=24.7
Q ss_pred eccCCCCCceeeecccccC-CCcccCCCCCCceeeeCCeeE
Q 025946 161 QDSCPNCGNDFQIFKSTLN-DELQLCPYCSQPFSVVDDKFV 200 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~Ln-~d~iqCPnCGE~L~Vd~~~F~ 200 (245)
+..|..|+..+.. ++... +....||.||.++..+=-.|.
T Consensus 113 ~~~C~~C~~~~~~-~~~~~~~~~p~C~~C~~~l~p~v~~fg 152 (222)
T cd00296 113 RVRCTSCGKEYPR-DEVLEREKPPRCPKCGGLLRPDVVDFG 152 (222)
T ss_pred ccEECCCCCCcch-hhhhhccCCCCCCCCCCcccCceEECC
Confidence 3489999976444 33332 356789999987654443333
No 232
>COG1503 eRF1 Peptide chain release factor 1 (eRF1) [Translation, ribosomal structure and biogenesis]
Probab=71.63 E-value=2.1 Score=42.17 Aligned_cols=37 Identities=27% Similarity=0.586 Sum_probs=24.0
Q ss_pred eeccCCCCCceeeecccccCCCcccCCCCCCceeeeC
Q 025946 160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVD 196 (245)
Q Consensus 160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~ 196 (245)
+.-.||+||+++.-.+.-......+||.||.+..+..
T Consensus 326 ~~~~c~~~~~e~~~t~~~~~~~~~~~~~~~~e~~~v~ 362 (411)
T COG1503 326 VTYKCPTCGYENLKSKREFEQKRFRCPECGSEMEEVE 362 (411)
T ss_pred eeecCCCcchhhhhcccccccccccCccccccccchh
Confidence 3458999999985532222222339999999876543
No 233
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=71.50 E-value=2.4 Score=38.37 Aligned_cols=33 Identities=18% Similarity=0.475 Sum_probs=21.4
Q ss_pred eccCCCCCceeeecccccCC--------CcccCCCCCCcee
Q 025946 161 QDSCPNCGNDFQIFKSTLND--------ELQLCPYCSQPFS 193 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~Ln~--------d~iqCPnCGE~L~ 193 (245)
..+||+||.+++......+- ...+|-+||-...
T Consensus 14 ~~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~ 54 (201)
T COG1779 14 RIDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGYRST 54 (201)
T ss_pred eecCCcccceeeEEEeeecCCccceEEEEEEEccccCCccc
Confidence 34999999988763222221 2578999986543
No 234
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=71.43 E-value=2.1 Score=42.66 Aligned_cols=28 Identities=25% Similarity=0.425 Sum_probs=21.7
Q ss_pred eeccCCCCCceeeecccccCCCcccCCCCCCceee
Q 025946 160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSV 194 (245)
Q Consensus 160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~V 194 (245)
-+-.|.+||++..- =.-+||+||+==++
T Consensus 6 t~f~C~~CG~~s~K-------W~GkCp~Cg~Wns~ 33 (456)
T COG1066 6 TAFVCQECGYVSPK-------WLGKCPACGAWNTL 33 (456)
T ss_pred cEEEcccCCCCCcc-------ccccCCCCCCccce
Confidence 34589999998766 68899999975443
No 235
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=70.96 E-value=4.4 Score=27.59 Aligned_cols=29 Identities=24% Similarity=0.626 Sum_probs=20.5
Q ss_pred cCC--CCCceeeecccccCCCcccCCCCCCce
Q 025946 163 SCP--NCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 163 tCP--nCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
-|| .|+.-....+ ......+.||.||..+
T Consensus 20 ~CP~~~C~~~~~~~~-~~~~~~v~C~~C~~~f 50 (64)
T smart00647 20 WCPAPDCSAAIIVTE-EEGCNRVTCPKCGFSF 50 (64)
T ss_pred CCCCCCCcceEEecC-CCCCCeeECCCCCCeE
Confidence 699 9987766632 2244689999998654
No 236
>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=70.93 E-value=1.1 Score=37.80 Aligned_cols=25 Identities=32% Similarity=0.828 Sum_probs=19.0
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
.+||.||+-|.- ..+..||.|.+..
T Consensus 4 ~nC~~CgklF~~------~~~~iCp~C~~~~ 28 (137)
T TIGR03826 4 ANCPKCGRLFVK------TGRDVCPSCYEEE 28 (137)
T ss_pred ccccccchhhhh------cCCccCHHHhHHH
Confidence 389999987764 2667899997643
No 237
>PHA02768 hypothetical protein; Provisional
Probab=70.90 E-value=2.1 Score=31.45 Aligned_cols=32 Identities=22% Similarity=0.356 Sum_probs=22.3
Q ss_pred ccCCCCCceeeeccccc-----CCCcccCCCCCCcee
Q 025946 162 DSCPNCGNDFQIFKSTL-----NDELQLCPYCSQPFS 193 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~L-----n~d~iqCPnCGE~L~ 193 (245)
-.||.||+.|....... ...+-.|.+|+..+.
T Consensus 6 y~C~~CGK~Fs~~~~L~~H~r~H~k~~kc~~C~k~f~ 42 (55)
T PHA02768 6 YECPICGEIYIKRKSMITHLRKHNTNLKLSNCKRISL 42 (55)
T ss_pred cCcchhCCeeccHHHHHHHHHhcCCcccCCcccceec
Confidence 37999999998743331 113779999987654
No 238
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=70.87 E-value=1.9 Score=34.84 Aligned_cols=30 Identities=23% Similarity=0.575 Sum_probs=25.2
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCCCceeee
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVV 195 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd 195 (245)
+.|-.||.+-|. ...+.++|-+||..+..+
T Consensus 36 daCeiC~~~GY~----q~g~~lvC~~C~~~~~~~ 65 (102)
T PF10080_consen 36 DACEICGPKGYY----QEGDQLVCKNCGVRFNLP 65 (102)
T ss_pred EeccccCCCceE----EECCEEEEecCCCEEehh
Confidence 489999999888 677999999998877543
No 239
>PRK08197 threonine synthase; Validated
Probab=70.71 E-value=2.5 Score=39.57 Aligned_cols=31 Identities=29% Similarity=0.773 Sum_probs=23.1
Q ss_pred eccCCCCCceeeecccccCCCcccCCCCCCceeeeCC
Q 025946 161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDD 197 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~ 197 (245)
.-.|+.||+++-. ..-...| .||.+|.+.-+
T Consensus 7 ~~~C~~Cg~~~~~-----~~~~~~C-~cg~~l~~~~d 37 (394)
T PRK08197 7 HLECSKCGETYDA-----DQVHNLC-KCGKPLLVRYD 37 (394)
T ss_pred EEEECCCCCCCCC-----CCcceec-CCCCeeEEEec
Confidence 3589999998765 2235679 79999988744
No 240
>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=70.71 E-value=1.7 Score=32.22 Aligned_cols=14 Identities=29% Similarity=0.795 Sum_probs=11.6
Q ss_pred cccCCCCCCceeee
Q 025946 182 LQLCPYCSQPFSVV 195 (245)
Q Consensus 182 ~iqCPnCGE~L~Vd 195 (245)
.-.||+||++++.+
T Consensus 3 HkHC~~CG~~Ip~~ 16 (59)
T PF09889_consen 3 HKHCPVCGKPIPPD 16 (59)
T ss_pred CCcCCcCCCcCCcc
Confidence 35799999999865
No 241
>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 PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=70.41 E-value=2.8 Score=43.50 Aligned_cols=23 Identities=26% Similarity=0.846 Sum_probs=15.8
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCC
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQ 190 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE 190 (245)
.||.||.++. ..++=..|++||=
T Consensus 726 ~Cp~Cg~~l~-----~~~GC~~C~~CG~ 748 (752)
T PRK08665 726 ACPECGSILE-----HEEGCVVCHSCGY 748 (752)
T ss_pred CCCCCCcccE-----ECCCCCcCCCCCC
Confidence 5888885543 3456778888873
No 243
>TIGR02896 spore_III_AF stage III sporulation protein AF. This family represents the stage III sporulation protein AF of the bacterial endospore formation program, which exists in some but not all members of the Firmicutes (formerly called low-GC Gram-positives). The C-terminal region of this protein is poorly conserved, so only the N-terminal region, which includes two predicted transmembrane domains, is included in the seed alignment.
Probab=70.16 E-value=12 Score=30.31 Aligned_cols=41 Identities=20% Similarity=0.252 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHHhcccchhHHHHHHHHHHH-HHHHHHHHHHH
Q 025946 110 NLALAIGLTYFSMTGQLGWVLDAIVSIWLL-AVIVPIVGFGA 150 (245)
Q Consensus 110 n~l~~l~l~~LL~T~gLgWLvd~~~~L~Ll-llllPIl~~~G 150 (245)
..+++.++-.|+|.....=-+..+.||+|+ +++.||+.+.+
T Consensus 13 ~~il~t~~~~llP~~~~kkYvr~v~Gl~Li~~il~Pi~~l~~ 54 (106)
T TIGR02896 13 LILLATILEMLLPNSSLKKYVKFVVGLILMVVILNPIIKLLT 54 (106)
T ss_pred HHHHHHHHHHHCCCccHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 344555667788999999999998888774 56779988554
No 244
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=70.08 E-value=2.9 Score=29.21 Aligned_cols=28 Identities=21% Similarity=0.506 Sum_probs=19.3
Q ss_pred cCCCCCceeeecccccCC-----CcccCCCCCC
Q 025946 163 SCPNCGNDFQIFKSTLND-----ELQLCPYCSQ 190 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~-----d~iqCPnCGE 190 (245)
.||-||..-...++.... --+.|.+||.
T Consensus 5 PCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 5 PCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 699999776664433222 2477999998
No 245
>PF14369 zf-RING_3: zinc-finger
Probab=69.98 E-value=6.8 Score=25.99 Aligned_cols=26 Identities=27% Similarity=0.548 Sum_probs=16.8
Q ss_pred CCCCCceeeecccccCCCcccCCCCCCc
Q 025946 164 CPNCGNDFQIFKSTLNDELQLCPYCSQP 191 (245)
Q Consensus 164 CPnCG~eF~~~ed~Ln~d~iqCPnCGE~ 191 (245)
|=.|...+.... ..++.+.||+|+.-
T Consensus 5 Ch~C~~~V~~~~--~~~~~~~CP~C~~g 30 (35)
T PF14369_consen 5 CHQCNRFVRIAP--SPDSDVACPRCHGG 30 (35)
T ss_pred CccCCCEeEeCc--CCCCCcCCcCCCCc
Confidence 778887777621 13345569999543
No 246
>TIGR03683 A-tRNA_syn_arch alanyl-tRNA synthetase. This family of alanyl-tRNA synthetases is limited to the archaea, and is a subset of those sequences identified by the model pfam07973 covering the second additional domain (SAD) of alanyl and threonyl tRNA synthetases.
Probab=69.94 E-value=3 Score=44.16 Aligned_cols=70 Identities=27% Similarity=0.529 Sum_probs=40.3
Q ss_pred HhcCcceeccCCCCCceeeecccccCCCcccCC--CCCCceeeeCCeeEEecccccccccc--ccccccccCCCCCCCCC
Q 025946 154 WASRDIVQDSCPNCGNDFQIFKSTLNDELQLCP--YCSQPFSVVDDKFVRESVRFSNESTT--FGQAFSDFFPGSRKGRE 229 (245)
Q Consensus 154 Wl~rnLIE~tCPnCG~eF~~~ed~Ln~d~iqCP--nCGE~L~Vd~~~F~R~~~~f~~~~~~--~~~af~~~~~~~~~~~~ 229 (245)
+-...+...+||.||..|-. +..+...|+ .|. ++++-++ + .++..-+. .-++|-+||.+..-.--
T Consensus 9 f~~~g~~r~~c~~c~~~fwt----~~~~r~~cgd~~c~-~y~fi~~-----~-~~~~~~~~~eiR~~fl~FF~~~gH~~v 77 (902)
T TIGR03683 9 FKENGFVRKQCQVCGSYFWT----LDPERETCGDAPCD-EYSFIGN-----P-IFSKKYTLDEMREAFLSFFEKHGHTRI 77 (902)
T ss_pred HHhCCceEeECcccCCcccc----CCCCcCCCCCCCCc-cceecCC-----C-CcCCCCCHHHHHHHHHHHHHhCCCEEe
Confidence 44556667799999999998 666666674 475 4433332 2 33333222 33788888865333223
Q ss_pred CCcee
Q 025946 230 SSTSV 234 (245)
Q Consensus 230 ~~~~v 234 (245)
||..|
T Consensus 78 ~s~pv 82 (902)
T TIGR03683 78 KRYPV 82 (902)
T ss_pred CCcCc
Confidence 44443
No 247
>COG1040 ComFC Predicted amidophosphoribosyltransferases [General function prediction only]
Probab=69.78 E-value=1.1 Score=39.73 Aligned_cols=36 Identities=28% Similarity=0.707 Sum_probs=27.5
Q ss_pred HHhcCcceec-cCCCCCceeeecccccCCCcccCCCCCCceeee
Q 025946 153 WWASRDIVQD-SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVV 195 (245)
Q Consensus 153 WWl~rnLIE~-tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd 195 (245)
|+-...+... .|+.|+..+.- + ...||.||.++..+
T Consensus 15 ~~~~~~l~~~~~C~~C~~~~~~----~---~~~C~~C~~~l~~~ 51 (225)
T COG1040 15 WLCLLLLFFPGLCSGCQADLPL----I---GNLCPLCGLPLSSH 51 (225)
T ss_pred HHHhhhccCCCcChhhhhchhH----H---HhhhHhhhChhccc
Confidence 5555566666 99999998877 2 22999999999876
No 248
>PRK05580 primosome assembly protein PriA; Validated
Probab=69.03 E-value=2.4 Score=42.91 Aligned_cols=11 Identities=27% Similarity=1.123 Sum_probs=7.3
Q ss_pred cCCCCCceeee
Q 025946 163 SCPNCGNDFQI 173 (245)
Q Consensus 163 tCPnCG~eF~~ 173 (245)
.||+|+..+.-
T Consensus 392 ~C~~C~~~l~~ 402 (679)
T PRK05580 392 ECPHCDASLTL 402 (679)
T ss_pred CCCCCCCceeE
Confidence 67777766554
No 249
>PF10164 DUF2367: Uncharacterized conserved protein (DUF2367); InterPro: IPR019317 This is a highly conserved set of proteins which contains three pairs of cysteine residues within a length of 42 amino acids and is rich in proline residues towards the N terminus. It includes a membrane protein that has been found to be highly expressed in the mouse brain and consequently, several members have been assigned as brain protein i3 (Bri3). Their function is unknown.
Probab=68.83 E-value=6 Score=32.34 Aligned_cols=12 Identities=42% Similarity=1.102 Sum_probs=9.7
Q ss_pred eeccCCCCCcee
Q 025946 160 VQDSCPNCGNDF 171 (245)
Q Consensus 160 IE~tCPnCG~eF 171 (245)
-|..|++||..|
T Consensus 87 r~~rC~nCG~~f 98 (98)
T PF10164_consen 87 RERRCSNCGATF 98 (98)
T ss_pred CccccCCCCccC
Confidence 467999999875
No 250
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=68.72 E-value=2.5 Score=37.10 Aligned_cols=22 Identities=32% Similarity=0.667 Sum_probs=17.7
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCc
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQP 191 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~ 191 (245)
.|..||..-.. =.-.||+||+-
T Consensus 356 ~c~~cg~~~~~-------~~~~c~~c~~~ 377 (389)
T PRK11788 356 RCRNCGFTART-------LYWHCPSCKAW 377 (389)
T ss_pred ECCCCCCCCcc-------ceeECcCCCCc
Confidence 79999977554 47899999873
No 251
>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=68.71 E-value=0.79 Score=40.04 Aligned_cols=33 Identities=30% Similarity=0.745 Sum_probs=23.7
Q ss_pred ceeccCCCCCceeeecccccCCCcccCCCCCCceeeeCCeeEEecc
Q 025946 159 IVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESV 204 (245)
Q Consensus 159 LIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R~~~ 204 (245)
..|.-|..||.+.. ..||+|+.+. .|+++-|++
T Consensus 26 ~~~~fC~kCG~~tI----------~~Cp~C~~~I---rG~y~v~gv 58 (158)
T PF10083_consen 26 LREKFCSKCGAKTI----------TSCPNCSTPI---RGDYHVEGV 58 (158)
T ss_pred HHHHHHHHhhHHHH----------HHCcCCCCCC---CCceecCCe
Confidence 45668999997754 4899999988 455555444
No 252
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=68.64 E-value=3 Score=31.23 Aligned_cols=21 Identities=24% Similarity=0.574 Sum_probs=14.9
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
.|-+|.+-. +..+||+||..-
T Consensus 5 AC~~C~~i~---------~~~~CP~Cgs~~ 25 (61)
T PRK08351 5 ACRHCHYIT---------TEDRCPVCGSRD 25 (61)
T ss_pred hhhhCCccc---------CCCcCCCCcCCc
Confidence 799998543 233799999843
No 253
>COG4306 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=68.43 E-value=1.9 Score=37.34 Aligned_cols=36 Identities=22% Similarity=0.564 Sum_probs=25.8
Q ss_pred cCCCCCceeeec---ccccC-----CCcccCCCCCCceeeeCCe
Q 025946 163 SCPNCGNDFQIF---KSTLN-----DELQLCPYCSQPFSVVDDK 198 (245)
Q Consensus 163 tCPnCG~eF~~~---ed~Ln-----~d~iqCPnCGE~L~Vd~~~ 198 (245)
+||.|...+.++ |.+|. +.|..|-|||.+++-.+.+
T Consensus 41 qcp~csasirgd~~vegvlglg~dye~psfchncgs~fpwterk 84 (160)
T COG4306 41 QCPICSASIRGDYYVEGVLGLGGDYEPPSFCHNCGSRFPWTERK 84 (160)
T ss_pred cCCccCCcccccceeeeeeccCCCCCCcchhhcCCCCCCcHHHH
Confidence 799999887663 23332 2388999999998876654
No 254
>cd03478 Rieske_AIFL_N AIFL (apoptosis-inducing factor like) family, N-terminal Rieske domain; members of this family show similarity to human AIFL, containing an N-terminal Rieske domain and a C-terminal pyridine nucleotide-disulfide oxidoreductase domain (Pyr_redox). The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. AIFL shares 35% homology with human AIF (apoptosis-inducing factor), mainly in the Pyr_redox domain. AIFL is predominantly localized to the mitochondria. AIFL induces apoptosis in a caspase-dependent manner.
Probab=68.30 E-value=3.7 Score=30.57 Aligned_cols=42 Identities=19% Similarity=0.445 Sum_probs=32.0
Q ss_pred eeccCCCCCceeeecccccCCCcccCCCCCCceeeeCCeeEEec
Q 025946 160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRES 203 (245)
Q Consensus 160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R~~ 203 (245)
++..||.-|..+.. ..+.++.+.||+-|..|.+++|+-...+
T Consensus 36 ~~~~CpH~g~~L~~--g~~~~~~i~CP~Hg~~Fdl~tG~~~~~p 77 (95)
T cd03478 36 IGAKCPHYGAPLAK--GVLTDGRIRCPWHGACFNLRTGDIEDAP 77 (95)
T ss_pred EcCcCcCCCCccCC--CeEeCCEEEcCCCCCEEECCCCcCcCCC
Confidence 55699999987653 3455679999999999999888765433
No 255
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=68.24 E-value=3.1 Score=40.53 Aligned_cols=24 Identities=29% Similarity=0.629 Sum_probs=21.5
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
.||+|+.+... =|+.||-|+-.|-
T Consensus 278 ~CP~CkakvCs-------LP~eCpiC~ltLV 301 (378)
T KOG2807|consen 278 FCPQCKAKVCS-------LPIECPICSLTLV 301 (378)
T ss_pred eCCcccCeeec-------CCccCCccceeEe
Confidence 59999999998 4999999998874
No 256
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=68.19 E-value=2.6 Score=34.41 Aligned_cols=37 Identities=19% Similarity=0.594 Sum_probs=23.1
Q ss_pred cccCCCCCCceeeeCCeeEEec-cccccc---cccccccccccC
Q 025946 182 LQLCPYCSQPFSVVDDKFVRES-VRFSNE---STTFGQAFSDFF 221 (245)
Q Consensus 182 ~iqCPnCGE~L~Vd~~~F~R~~-~~f~~~---~~~~~~af~~~~ 221 (245)
-+.||+||+ .++.+|.--+ +.-..+ ++....+|.+|+
T Consensus 3 LI~CP~Cg~---R~e~EFt~~G~A~i~RP~d~a~~sde~w~dY~ 43 (97)
T COG4311 3 LIPCPYCGE---RPEEEFTYAGDAHIARPADPADASDEEWGDYV 43 (97)
T ss_pred eecCCCCCC---CchhheeecccccccCCCCcccCCHHHHhhhe
Confidence 478999998 5677787766 444443 333335666654
No 257
>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=68.17 E-value=2.6 Score=38.05 Aligned_cols=11 Identities=36% Similarity=0.851 Sum_probs=5.2
Q ss_pred ccCCCCCceee
Q 025946 162 DSCPNCGNDFQ 172 (245)
Q Consensus 162 ~tCPnCG~eF~ 172 (245)
..||+||..=.
T Consensus 173 g~CPvCGs~P~ 183 (290)
T PF04216_consen 173 GYCPVCGSPPV 183 (290)
T ss_dssp SS-TTT---EE
T ss_pred CcCCCCCCcCc
Confidence 59999997633
No 258
>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=68.11 E-value=0.86 Score=30.54 Aligned_cols=33 Identities=15% Similarity=0.524 Sum_probs=18.4
Q ss_pred cCCCCCceeeecccc-cCCCcccCCCCCCceeee
Q 025946 163 SCPNCGNDFQIFKST-LNDELQLCPYCSQPFSVV 195 (245)
Q Consensus 163 tCPnCG~eF~~~ed~-Ln~d~iqCPnCGE~L~Vd 195 (245)
.||.|-+++.+-.+- ..-.++-|++||-.+.+-
T Consensus 1 lC~~C~~Ey~~p~~RR~~~~~isC~~CGPr~~i~ 34 (35)
T PF07503_consen 1 LCDDCLKEYFDPSNRRFHYQFISCTNCGPRYSII 34 (35)
T ss_dssp --HHHHHHHCSTTSTTTT-TT--BTTCC-SCCCE
T ss_pred CCHHHHHHHcCCCCCcccCcCccCCCCCCCEEEe
Confidence 378888887663332 333689999999877653
No 259
>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=68.08 E-value=3 Score=36.58 Aligned_cols=29 Identities=17% Similarity=0.358 Sum_probs=19.0
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
..|..|+.++.. ++.. ..-.||.||.++.
T Consensus 119 ~~C~~C~~~~~~-~~~~--~~p~C~~Cgg~lr 147 (225)
T cd01411 119 IYCTVCGKTVDW-EEYL--KSPYHAKCGGVIR 147 (225)
T ss_pred eEeCCCCCccch-hhcC--CCCCCCCCCCEeC
Confidence 399999876543 2222 2467999987653
No 260
>TIGR00108 eRF peptide chain release factor eRF/aRF, subunit 1. Alternative names include eRF1, SUP45, omnipotent suppressor protein 1.
Probab=68.03 E-value=3.5 Score=39.68 Aligned_cols=38 Identities=29% Similarity=0.734 Sum_probs=23.4
Q ss_pred eeccCCCCCceeeeccccc-CCCcccCCCCCCceeeeCC
Q 025946 160 VQDSCPNCGNDFQIFKSTL-NDELQLCPYCSQPFSVVDD 197 (245)
Q Consensus 160 IE~tCPnCG~eF~~~ed~L-n~d~iqCPnCGE~L~Vd~~ 197 (245)
+...||+||++.+...... +.+...||+||..+.+.+.
T Consensus 323 ~~~r~~~~~~~~~~~~~~~~~~~~~~c~~~~~~~~~~~~ 361 (409)
T TIGR00108 323 VTYKCAECGEVIEKTVRELKDKKFAICPACGQEMDVVEE 361 (409)
T ss_pred EEEEcCCCCceeecccccccccccccCcccCccccchhh
Confidence 3468999998633311111 1134689999999876543
No 261
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=67.67 E-value=3.9 Score=32.78 Aligned_cols=35 Identities=23% Similarity=0.627 Sum_probs=23.1
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceeeeCCee
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKF 199 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F 199 (245)
-||+|+.+..-. +.-+-.--.||-|+-++ +|.|+.
T Consensus 3 lCP~C~v~l~~~-~rs~vEiD~CPrCrGVW-LDrGEL 37 (88)
T COG3809 3 LCPICGVELVMS-VRSGVEIDYCPRCRGVW-LDRGEL 37 (88)
T ss_pred ccCcCCceeeee-eecCceeeeCCccccEe-ecchhH
Confidence 599999998862 11122355899998876 455544
No 262
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=67.55 E-value=2.5 Score=31.05 Aligned_cols=26 Identities=27% Similarity=0.572 Sum_probs=19.2
Q ss_pred cCCCCCc-eeeecccccCCCcccCCCCCCce
Q 025946 163 SCPNCGN-DFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 163 tCPnCG~-eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
.||.||. .|.. -..+-..|-.||-..
T Consensus 21 ~CPrCG~gvfmA----~H~dR~~CGkCgyTe 47 (51)
T COG1998 21 FCPRCGPGVFMA----DHKDRWACGKCGYTE 47 (51)
T ss_pred cCCCCCCcchhh----hcCceeEeccccceE
Confidence 7999997 5555 355788898888654
No 263
>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=67.55 E-value=2.6 Score=37.25 Aligned_cols=32 Identities=22% Similarity=0.573 Sum_probs=19.8
Q ss_pred eccCCCCCceeeecccc---c-CCCcccCCCCCCcee
Q 025946 161 QDSCPNCGNDFQIFKST---L-NDELQLCPYCSQPFS 193 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~---L-n~d~iqCPnCGE~L~ 193 (245)
...|..|+..+.. +.. + +.+.-.||.||..+.
T Consensus 116 ~~~C~~C~~~~~~-~~~~~~~~~~~~p~C~~Cgg~lr 151 (235)
T cd01408 116 TAHCIKCKHKYPG-DWMREDIFNQEVPKCPRCGGLVK 151 (235)
T ss_pred ccccccCCCcCCH-HHHHHHHhCCCCccCCCCCCCcc
Confidence 3389999986532 211 1 223467999986653
No 264
>PHA00732 hypothetical protein
Probab=67.54 E-value=1.6 Score=33.46 Aligned_cols=37 Identities=24% Similarity=0.672 Sum_probs=25.0
Q ss_pred cCCCCCceeeecccc---cC--CCcccCCCCCCceeeeCCee
Q 025946 163 SCPNCGNDFQIFKST---LN--DELQLCPYCSQPFSVVDDKF 199 (245)
Q Consensus 163 tCPnCG~eF~~~ed~---Ln--~d~iqCPnCGE~L~Vd~~~F 199 (245)
.|+.||+.|....+. +. ..+..|+.||+.+.--..|+
T Consensus 3 ~C~~Cgk~F~s~s~Lk~H~r~~H~~~~C~~CgKsF~~l~~H~ 44 (79)
T PHA00732 3 KCPICGFTTVTLFALKQHARRNHTLTKCPVCNKSYRRLNQHF 44 (79)
T ss_pred cCCCCCCccCCHHHHHHHhhcccCCCccCCCCCEeCChhhhh
Confidence 599999999873322 11 23458999999887544444
No 265
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=67.49 E-value=4.9 Score=38.26 Aligned_cols=28 Identities=25% Similarity=0.561 Sum_probs=19.9
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceee
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSV 194 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~V 194 (245)
.|+.||..-.... ..+..||+||.++.+
T Consensus 246 ~C~~c~~~~~~~~----~~~~~C~~c~~~~~~ 273 (382)
T PRK04338 246 YCPKCLYREEVEG----LPPEECPVCGGKFGT 273 (382)
T ss_pred ECCCCCcEEEecC----CCCCCCCCCCCccee
Confidence 6999998765521 346689999886543
No 266
>PF02397 Bac_transf: Bacterial sugar transferase; InterPro: IPR003362 This entry represents a conserved region from a number of different bacterial sugar transferases, involved in diverse biosynthesis pathways. Examples include galactosyl-P-P-undecaprenol synthetase (2.7.8.6 from EC), which transfers galatose-1-phosphate to the lipid precursor undecaprenol phosphate in the first steps of O-polysaccharide biosynthesis; UDP-galactose-lipid carrier transferase, which is involved in the biosynthesis of amylovoran; and galactosyl transferase CpsD, which is essential for assembly of the group B Streptococci (GBS) type III capsular polysaccharide.
Probab=67.45 E-value=8.8 Score=33.59 Aligned_cols=45 Identities=22% Similarity=0.376 Sum_probs=33.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcC---cc--eeccCCCCCceeee
Q 025946 129 VLDAIVSIWLLAVIVPIVGFGAFLWWASR---DI--VQDSCPNCGNDFQI 173 (245)
Q Consensus 129 Lvd~~~~L~LlllllPIl~~~Gf~WWl~r---nL--IE~tCPnCG~eF~~ 173 (245)
++|.+++++++++++|++++.++.=|+.. .+ .|..--.-|+.|..
T Consensus 3 ~~Di~~a~~~li~~~Pl~l~iai~i~l~~~~gpvff~q~RvG~~gk~F~~ 52 (187)
T PF02397_consen 3 AFDIVLALLLLILLSPLFLIIAILIKLESSPGPVFFRQERVGKNGKPFRI 52 (187)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCceeEcccceeccccccc
Confidence 68999999999999999999998888832 22 23344445666655
No 267
>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=67.35 E-value=3.3 Score=39.34 Aligned_cols=34 Identities=24% Similarity=0.492 Sum_probs=23.2
Q ss_pred cCCCCCceeeeccc-------------------ccCCCcccCCCCCCceeeeC
Q 025946 163 SCPNCGNDFQIFKS-------------------TLNDELQLCPYCSQPFSVVD 196 (245)
Q Consensus 163 tCPnCG~eF~~~ed-------------------~Ln~d~iqCPnCGE~L~Vd~ 196 (245)
.||.|...-|...+ .+..++..||.|++++...+
T Consensus 5 ~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~~~~~~CP~C~~~lrk~~ 57 (309)
T TIGR00570 5 GCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFVRGSGSCPECDTPLRKNN 57 (309)
T ss_pred CCCcCCCCCccCcccccccCCCCCcccHHHHHHHhcCCCCCCCCCCCccchhh
Confidence 67777765554333 23467789999999886554
No 268
>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=67.20 E-value=2.7 Score=28.99 Aligned_cols=15 Identities=40% Similarity=1.134 Sum_probs=10.5
Q ss_pred cCC--CcccCCCCCCce
Q 025946 178 LND--ELQLCPYCSQPF 192 (245)
Q Consensus 178 Ln~--d~iqCPnCGE~L 192 (245)
|++ ++..|||||..+
T Consensus 23 l~~~~~~~~CpYCg~~y 39 (40)
T PF10276_consen 23 LDDEPGPVVCPYCGTRY 39 (40)
T ss_dssp -TTTTCEEEETTTTEEE
T ss_pred cCCCCCeEECCCCCCEE
Confidence 455 358999998765
No 269
>KOG2324 consensus Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=67.01 E-value=3.2 Score=41.19 Aligned_cols=27 Identities=30% Similarity=0.762 Sum_probs=18.4
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCC
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQ 190 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE 190 (245)
+||+||++-.. |+.--..+.-||+|.+
T Consensus 229 ~C~~C~~s~n~-e~~~~sk~~~Cp~C~~ 255 (457)
T KOG2324|consen 229 SCPSCGYSKNS-EDLDLSKIASCPKCNE 255 (457)
T ss_pred ecCcCCccCch-hhhcCCccccCCcccC
Confidence 89999965443 2222223589999998
No 270
>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=66.98 E-value=2.5 Score=38.11 Aligned_cols=23 Identities=30% Similarity=0.914 Sum_probs=12.3
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
.|+-||++-.. .-+.||+||+.=
T Consensus 199 ~Cs~C~t~W~~-------~R~~Cp~Cg~~~ 221 (290)
T PF04216_consen 199 HCSLCGTEWRF-------VRIKCPYCGNTD 221 (290)
T ss_dssp EETTT--EEE---------TTS-TTT---S
T ss_pred EcCCCCCeeee-------cCCCCcCCCCCC
Confidence 79999988776 678899998753
No 271
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=66.59 E-value=3.6 Score=33.89 Aligned_cols=16 Identities=19% Similarity=0.654 Sum_probs=12.4
Q ss_pred cCCCcccCCCCCCcee
Q 025946 178 LNDELQLCPYCSQPFS 193 (245)
Q Consensus 178 Ln~d~iqCPnCGE~L~ 193 (245)
+.-+...||.||++++
T Consensus 43 IevG~~~cP~Cge~~~ 58 (102)
T PF04475_consen 43 IEVGDTICPKCGEELD 58 (102)
T ss_pred EecCcccCCCCCCccC
Confidence 5557888999998873
No 272
>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=66.48 E-value=3.1 Score=39.48 Aligned_cols=22 Identities=32% Similarity=0.853 Sum_probs=19.0
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCc
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQP 191 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~ 191 (245)
.|-+||..... =+..||+||..
T Consensus 84 ~C~~CGa~V~~-------~e~~Cp~C~St 105 (314)
T PF09567_consen 84 KCNNCGANVSR-------LEESCPNCGST 105 (314)
T ss_pred hhccccceeee-------hhhcCCCCCcc
Confidence 89999999887 47889999974
No 273
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=66.28 E-value=3 Score=43.52 Aligned_cols=10 Identities=40% Similarity=0.876 Sum_probs=8.0
Q ss_pred cccCCCCCCc
Q 025946 182 LQLCPYCSQP 191 (245)
Q Consensus 182 ~iqCPnCGE~ 191 (245)
|..||+||+.
T Consensus 475 p~~Cp~Cgs~ 484 (730)
T COG1198 475 PQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCC
Confidence 7788888876
No 274
>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=66.27 E-value=2.8 Score=26.17 Aligned_cols=27 Identities=30% Similarity=0.659 Sum_probs=15.4
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCC
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQ 190 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE 190 (245)
.||.|+..+.. ...-.+....||.|-+
T Consensus 3 ~C~rC~~~~~~-~~~~~r~~~~C~rCq~ 29 (30)
T PF06827_consen 3 KCPRCWNYIED-IGINGRSTYLCPRCQK 29 (30)
T ss_dssp B-TTT--BBEE-EEETTEEEEE-TTTCC
T ss_pred cCccCCCcceE-eEecCCCCeECcCCcC
Confidence 69999988665 2223446899999953
No 275
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=65.94 E-value=3.3 Score=38.46 Aligned_cols=29 Identities=21% Similarity=0.485 Sum_probs=22.2
Q ss_pred Ccceec--cCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 157 RDIVQD--SCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 157 rnLIE~--tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
.+++.. .||+|-..|.. -+..||-||+.|
T Consensus 249 ~k~v~~GyvCs~Clsi~C~-------~p~~C~~Cgt~f 279 (279)
T TIGR00627 249 HQLVSIGFVCSVCLSVLCQ-------YTPICKTCKTAF 279 (279)
T ss_pred CccccceEECCCccCCcCC-------CCCCCCCCCCCC
Confidence 344443 89999988877 478999999864
No 276
>PTZ00408 NAD-dependent deacetylase; Provisional
Probab=65.88 E-value=2.9 Score=37.42 Aligned_cols=27 Identities=19% Similarity=0.440 Sum_probs=18.6
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCC
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCS 189 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCG 189 (245)
..|+.|++.+...++ +....-.||.||
T Consensus 118 ~~C~~C~~~~~~~~~-~~~~~p~C~~Cg 144 (242)
T PTZ00408 118 VRCTATGHVFDWTED-VVHGSSRCKCCG 144 (242)
T ss_pred EEECCCCcccCchhh-hhcCCCccccCC
Confidence 399999987654322 333456799998
No 277
>cd03467 Rieske Rieske domain; a [2Fe-2S] cluster binding domain commonly found in Rieske non-heme iron oxygenase (RO) systems such as naphthalene and biphenyl dioxygenases, as well as in plant/cyanobacterial chloroplast b6f and mitochondrial cytochrome bc(1) complexes. The Rieske domain can be divided into two subdomains, with an incomplete six-stranded, antiparallel beta-barrel at one end, and an iron-sulfur cluster binding subdomain at the other. The Rieske iron-sulfur center contains a [2Fe-2S] cluster, which is involved in electron transfer, and is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs. In RO systems, the N-terminal Rieske domain of the alpha subunit acts as an electron shuttle that accepts electrons from a reductase or ferredoxin component and transfers them to the mononuclear iron in the alpha subunit C-terminal domain to be used for catalysis.
Probab=65.72 E-value=4.6 Score=29.93 Aligned_cols=43 Identities=16% Similarity=0.356 Sum_probs=33.2
Q ss_pred eeccCCCCCceeeecccccCCCcccCCCCCCceeeeCCeeEEecc
Q 025946 160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESV 204 (245)
Q Consensus 160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R~~~ 204 (245)
++..||.-|..+.. ...++..++||.-|..|.+++|+-...+.
T Consensus 38 ~~~~CpH~g~~l~~--~~~~~~~i~Cp~H~~~f~~~~G~~~~~p~ 80 (98)
T cd03467 38 LSNRCTHQGCPLSE--GEGEDGCIVCPCHGSRFDLRTGEVVSGPA 80 (98)
T ss_pred EcCcCCCCCccCCc--CccCCCEEEeCCCCCEEeCCCccCcCCCC
Confidence 45599998876644 23567899999999999999998765443
No 278
>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=65.62 E-value=3.4 Score=29.35 Aligned_cols=28 Identities=21% Similarity=0.619 Sum_probs=14.0
Q ss_pred eccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
...|+.|+++|.. -.-.-.|..||+.+=
T Consensus 9 ~~~C~~C~~~F~~-----~~rrhhCr~CG~~vC 36 (69)
T PF01363_consen 9 ASNCMICGKKFSL-----FRRRHHCRNCGRVVC 36 (69)
T ss_dssp -SB-TTT--B-BS-----SS-EEE-TTT--EEE
T ss_pred CCcCcCcCCcCCC-----ceeeEccCCCCCEEC
Confidence 4589999999954 466778888888654
No 279
>COG5525 Bacteriophage tail assembly protein [General function prediction only]
Probab=65.58 E-value=3.7 Score=42.31 Aligned_cols=38 Identities=24% Similarity=0.498 Sum_probs=26.1
Q ss_pred CcceeccCCCCCceeeecc-cc-----cCCC-----cccCCCCCCceee
Q 025946 157 RDIVQDSCPNCGNDFQIFK-ST-----LNDE-----LQLCPYCSQPFSV 194 (245)
Q Consensus 157 rnLIE~tCPnCG~eF~~~e-d~-----Ln~d-----~iqCPnCGE~L~V 194 (245)
+.-+...||.||++++-.- +. +... -++||.|+..+.-
T Consensus 223 ~rr~yvpCPHCGe~q~l~~~e~~~~~g~~~~~~~~~~~~c~h~~~~i~~ 271 (611)
T COG5525 223 QRRFYVPCPHCGEEQQLKFGEKSGPRGLKDTPAEAAFIQCEHCGCVIRP 271 (611)
T ss_pred ceeEEeeCCCCCchhhccccccCCCcCcccchhhhhhhhccccCceeee
Confidence 3456679999999988721 11 1222 3599999998876
No 280
>PRK10996 thioredoxin 2; Provisional
Probab=65.32 E-value=4.7 Score=32.37 Aligned_cols=32 Identities=13% Similarity=0.378 Sum_probs=23.9
Q ss_pred eccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
...||.|..+... -+.+..+..+||.|++.+.
T Consensus 2 ~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~ 33 (139)
T PRK10996 2 NTVCTSCQAINRL-PDERIEDAAKCGRCGHDLF 33 (139)
T ss_pred eEECCCCCCcCCC-CCccccCCCcCCCCCCccC
Confidence 4579999866554 3445667999999998775
No 281
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=65.16 E-value=4.6 Score=39.76 Aligned_cols=33 Identities=30% Similarity=0.694 Sum_probs=23.3
Q ss_pred cCCCCCce-eeecccccCCCcccCCCCCCceeeeCCeeEEecccccc
Q 025946 163 SCPNCGND-FQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESVRFSN 208 (245)
Q Consensus 163 tCPnCG~e-F~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R~~~~f~~ 208 (245)
.||.|... -|. +...||+||.+- +|.|. ++|..
T Consensus 59 kC~~c~~~~~y~-------~~~~C~~cg~~~-----~l~R~-VSfVD 92 (415)
T COG5257 59 KCPECYRPECYT-------TEPKCPNCGAET-----ELVRR-VSFVD 92 (415)
T ss_pred eCCCCCCCcccc-------cCCCCCCCCCCc-----cEEEE-EEEee
Confidence 89999974 222 588999999876 66664 44544
No 282
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=64.56 E-value=6.6 Score=28.41 Aligned_cols=32 Identities=28% Similarity=0.831 Sum_probs=23.6
Q ss_pred cCCCCCceeeecccccCCC---cccCCCCCCceee
Q 025946 163 SCPNCGNDFQIFKSTLNDE---LQLCPYCSQPFSV 194 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d---~iqCPnCGE~L~V 194 (245)
+||-||..+...-|.-..+ ---|+.|-.|+.+
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~PI~~ 36 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCCRPIEV 36 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhcCCccEE
Confidence 7999999998854443333 3459999998865
No 283
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=64.48 E-value=4 Score=46.37 Aligned_cols=29 Identities=21% Similarity=0.489 Sum_probs=18.4
Q ss_pred ccCCCCCceeeec-ccccCCCcccCCCCCC
Q 025946 162 DSCPNCGNDFQIF-KSTLNDELQLCPYCSQ 190 (245)
Q Consensus 162 ~tCPnCG~eF~~~-ed~Ln~d~iqCPnCGE 190 (245)
..||+||.+--.+ |=....+=..||+||=
T Consensus 1705 ~~cp~c~~~~~~~~~~~~~~gc~~c~~cg~ 1734 (1740)
T PRK08332 1705 VYCPVCYEKEGKLVELRMESGCATCPVCGW 1734 (1740)
T ss_pred CCCCCCCCCCCcceeeEecCCceeCCCCCC
Confidence 3499999871000 0014557889999984
No 284
>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=64.44 E-value=2.9 Score=29.98 Aligned_cols=37 Identities=27% Similarity=0.609 Sum_probs=28.9
Q ss_pred cceeccCCCCCceeeecccccCC--CcccCCCCCCceeee
Q 025946 158 DIVQDSCPNCGNDFQIFKSTLND--ELQLCPYCSQPFSVV 195 (245)
Q Consensus 158 nLIE~tCPnCG~eF~~~ed~Ln~--d~iqCPnCGE~L~Vd 195 (245)
..+...| -||-.|...++.|.+ .-++|+.|.-.+.|.
T Consensus 15 ~~~~y~C-RCG~~f~i~e~~l~~~~~iv~C~sCSL~I~V~ 53 (55)
T PF05207_consen 15 GVYSYPC-RCGGEFEISEEDLEEGEVIVQCDSCSLWIRVN 53 (55)
T ss_dssp TEEEEEE-TTSSEEEEEHHHHHCT--EEEETTTTEEEEEE
T ss_pred CEEEEcC-CCCCEEEEcchhccCcCEEEECCCCccEEEEE
Confidence 3566799 899999998888765 478999998776653
No 285
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=64.43 E-value=3.9 Score=36.28 Aligned_cols=25 Identities=28% Similarity=0.801 Sum_probs=21.2
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceee
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSV 194 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~V 194 (245)
.|-.|++.|.- +.-.||.||.++..
T Consensus 141 rC~GC~~~f~~-------~~~~Cp~CG~~~~~ 165 (177)
T COG1439 141 RCHGCKRIFPE-------PKDFCPICGSPLKR 165 (177)
T ss_pred EEecCceecCC-------CCCcCCCCCCceEE
Confidence 89999999874 67799999998653
No 286
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=64.24 E-value=5.2 Score=31.15 Aligned_cols=27 Identities=26% Similarity=0.524 Sum_probs=17.2
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCCC
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQ 190 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE 190 (245)
..||.||+..... .-..+--.||.|+=
T Consensus 2 ~~CPCCg~~Tl~~--~~~~~ydIC~VC~W 28 (78)
T PF14206_consen 2 YPCPCCGYYTLEE--RGEGTYDICPVCFW 28 (78)
T ss_pred ccCCCCCcEEecc--CCCcCceECCCCCc
Confidence 3799999765541 11112569999963
No 287
>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=64.16 E-value=4 Score=29.47 Aligned_cols=33 Identities=21% Similarity=0.493 Sum_probs=21.5
Q ss_pred cceeccCCCCCceeeec-ccccCCCcccCCCCCC
Q 025946 158 DIVQDSCPNCGNDFQIF-KSTLNDELQLCPYCSQ 190 (245)
Q Consensus 158 nLIE~tCPnCG~eF~~~-ed~Ln~d~iqCPnCGE 190 (245)
+.+-..|++|....=.- +.....-.-.||+||+
T Consensus 19 ~r~aLIC~~C~~hNGla~~~~~~~i~y~C~~Cg~ 52 (54)
T PF10058_consen 19 NRYALICSKCFSHNGLAPKEEFEEIQYRCPYCGA 52 (54)
T ss_pred CceeEECcccchhhcccccccCCceEEEcCCCCC
Confidence 34555899998654332 3334445889999986
No 288
>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=64.14 E-value=4.9 Score=28.44 Aligned_cols=29 Identities=31% Similarity=0.819 Sum_probs=16.1
Q ss_pred cCCCCCceeeecccc----------cC--CCcccCCCCCCc
Q 025946 163 SCPNCGNDFQIFKST----------LN--DELQLCPYCSQP 191 (245)
Q Consensus 163 tCPnCG~eF~~~ed~----------Ln--~d~iqCPnCGE~ 191 (245)
.|++||+.+--.+.. ++ .+.-.||.|+.+
T Consensus 3 ~C~~CgyvYd~~~Gd~~~~i~pGt~F~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 3 QCPVCGYVYDPEKGDPENGIPPGTPFEDLPDDWVCPVCGAP 43 (47)
T ss_dssp EETTTSBEEETTTBBGGGTB-TT--GGGS-TT-B-TTTSSB
T ss_pred CCCCCCEEEcCCcCCcccCcCCCCCHHHCCCCCcCcCCCCc
Confidence 699999655432211 11 235689999875
No 289
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=64.12 E-value=4.4 Score=33.53 Aligned_cols=24 Identities=25% Similarity=0.588 Sum_probs=20.7
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
.||.|+.+... =|+.||-||-.|-
T Consensus 3 ~CPrC~skvC~-------LP~~CpiCgLtLV 26 (112)
T TIGR00622 3 FCPQCRAKVCE-------LPVECPICGLTLI 26 (112)
T ss_pred cCCCCCCCccC-------CCCcCCcCCCEEe
Confidence 69999998887 4999999998773
No 290
>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=64.08 E-value=2.2 Score=45.48 Aligned_cols=27 Identities=26% Similarity=0.791 Sum_probs=0.0
Q ss_pred ceeccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 159 IVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 159 LIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
-++..||.||..-.- ...||.||..+.
T Consensus 665 t~~~~Cp~CG~~T~~--------~~~Cp~C~~~~~ 691 (900)
T PF03833_consen 665 TFYNRCPECGSHTEP--------VYVCPDCGIEVE 691 (900)
T ss_dssp -----------------------------------
T ss_pred chhhcCcccCCcccc--------ceeccccccccC
Confidence 445589989866332 456666666554
No 291
>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=63.93 E-value=4.6 Score=39.59 Aligned_cols=11 Identities=27% Similarity=0.631 Sum_probs=6.8
Q ss_pred cCCCCCceeee
Q 025946 163 SCPNCGNDFQI 173 (245)
Q Consensus 163 tCPnCG~eF~~ 173 (245)
.|+.||.....
T Consensus 215 ~C~~Cg~~~~C 225 (505)
T TIGR00595 215 LCRSCGYILCC 225 (505)
T ss_pred EhhhCcCccCC
Confidence 57777765554
No 292
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=63.47 E-value=4.2 Score=34.87 Aligned_cols=23 Identities=22% Similarity=0.567 Sum_probs=17.9
Q ss_pred ccee--ccCCCCCceeeecccccCC
Q 025946 158 DIVQ--DSCPNCGNDFQIFKSTLND 180 (245)
Q Consensus 158 nLIE--~tCPnCG~eF~~~ed~Ln~ 180 (245)
|.+. ..||+||.+|...|.+.+.
T Consensus 23 ~~~~~~~~c~~c~~~f~~~e~~~~~ 47 (154)
T PRK00464 23 NAIRRRRECLACGKRFTTFERVELV 47 (154)
T ss_pred CceeeeeeccccCCcceEeEeccCc
Confidence 3555 6999999999998777444
No 293
>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=63.42 E-value=1.6 Score=29.90 Aligned_cols=13 Identities=23% Similarity=0.278 Sum_probs=9.2
Q ss_pred cccCCCCCCceee
Q 025946 182 LQLCPYCSQPFSV 194 (245)
Q Consensus 182 ~iqCPnCGE~L~V 194 (245)
...||.|++++..
T Consensus 35 ~~~cP~~~~~~~~ 47 (63)
T smart00504 35 HGTDPVTGQPLTH 47 (63)
T ss_pred CCCCCCCcCCCCh
Confidence 4568888887744
No 294
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=62.45 E-value=6.9 Score=31.41 Aligned_cols=29 Identities=24% Similarity=0.699 Sum_probs=21.1
Q ss_pred ceeccCCCCCceeeecccccCC-CcccCCCCCCc
Q 025946 159 IVQDSCPNCGNDFQIFKSTLND-ELQLCPYCSQP 191 (245)
Q Consensus 159 LIE~tCPnCG~eF~~~ed~Ln~-d~iqCPnCGE~ 191 (245)
..+..|++||.+.+. -+- ..-.||.||..
T Consensus 40 ~~~~~C~~Cg~~~~~----~~SCk~R~CP~C~~~ 69 (111)
T PF14319_consen 40 FHRYRCEDCGHEKIV----YNSCKNRHCPSCQAK 69 (111)
T ss_pred cceeecCCCCceEEe----cCcccCcCCCCCCCh
Confidence 345699999998876 222 35599999874
No 295
>PRK13902 alaS alanyl-tRNA synthetase; Provisional
Probab=62.40 E-value=5.7 Score=42.17 Aligned_cols=59 Identities=25% Similarity=0.582 Sum_probs=36.3
Q ss_pred HhcCcceeccCCCCCceeeecccccCCCcccCCC--CCCceeeeCCeeEEecccccccccccc--ccccccCCC
Q 025946 154 WASRDIVQDSCPNCGNDFQIFKSTLNDELQLCPY--CSQPFSVVDDKFVRESVRFSNESTTFG--QAFSDFFPG 223 (245)
Q Consensus 154 Wl~rnLIE~tCPnCG~eF~~~ed~Ln~d~iqCPn--CGE~L~Vd~~~F~R~~~~f~~~~~~~~--~af~~~~~~ 223 (245)
+-...+...+||.||..|-. ++.+...|+- |. +++ |.-.+ .++.+-+..+ +.|=+||.+
T Consensus 12 f~~~g~~r~~c~~cg~~fwt----~~~~r~~cgd~pc~-~y~-----fi~~~-~~~~~~~~~eiR~~Fl~FF~~ 74 (900)
T PRK13902 12 FEENGFERKQCKKCGSYFWT----LDPDRETCGDAPCD-EYS-----FIGNP-IFSKKYTLKEMREKFLSFFEK 74 (900)
T ss_pred HHhCCceEeECCccCCceec----CCCCcCCCCCCCCc-cce-----ecCCC-CcCCCCCHHHHHHHHHHHHHh
Confidence 44556667799999999998 6666667744 65 343 33333 3333323333 777777764
No 296
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=62.00 E-value=4.6 Score=37.68 Aligned_cols=34 Identities=35% Similarity=0.652 Sum_probs=25.5
Q ss_pred ceeccCCCCCceeeecccccC-CCcccCCCCCCceee
Q 025946 159 IVQDSCPNCGNDFQIFKSTLN-DELQLCPYCSQPFSV 194 (245)
Q Consensus 159 LIE~tCPnCG~eF~~~ed~Ln-~d~iqCPnCGE~L~V 194 (245)
....+|+.|.++|.-. .++ ++...||.|.+.=+|
T Consensus 155 ~~rv~CghC~~~Fl~~--~~~~~tlARCPHCrKvSSV 189 (256)
T PF09788_consen 155 SCRVICGHCSNTFLFN--TLTSNTLARCPHCRKVSSV 189 (256)
T ss_pred ceeEECCCCCCcEecc--CCCCCccccCCCCceeccc
Confidence 3556999999999873 556 578899999744333
No 297
>TIGR02230 ATPase_gene1 F0F1-ATPase subunit, putative. This model represents a protein found encoded in F1F0-ATPase operons in several genomes, including Methanosarcina barkeri (archaeal) and Chlorobium tepidum (bacterial). It is a small protein (about 100 amino acids) with long hydrophic stretches and is presumed to be a subunit of the enzyme.
Probab=61.71 E-value=12 Score=30.26 Aligned_cols=9 Identities=22% Similarity=0.050 Sum_probs=4.1
Q ss_pred CCCCcchhH
Q 025946 101 NSNNARILG 109 (245)
Q Consensus 101 ~~~~~r~lg 109 (245)
++...|-++
T Consensus 35 ~~~~~~~l~ 43 (100)
T TIGR02230 35 TRSIWEGLG 43 (100)
T ss_pred CCcHHHHHH
Confidence 344455444
No 298
>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=61.60 E-value=5.7 Score=31.75 Aligned_cols=14 Identities=14% Similarity=0.380 Sum_probs=9.6
Q ss_pred CcccCCCCCCceee
Q 025946 181 ELQLCPYCSQPFSV 194 (245)
Q Consensus 181 d~iqCPnCGE~L~V 194 (245)
..+.||+||+.+.-
T Consensus 34 Pa~~C~~CGe~y~~ 47 (89)
T TIGR03829 34 PSISCSHCGMEYQD 47 (89)
T ss_pred CcccccCCCcEeec
Confidence 35678888887643
No 299
>KOG1247 consensus Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=61.39 E-value=2.4 Score=42.81 Aligned_cols=31 Identities=26% Similarity=0.614 Sum_probs=22.7
Q ss_pred HhcCcceeccCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 154 WASRDIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 154 Wl~rnLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
+|-|+++|.+||-||+.=- ---||-+||..+
T Consensus 145 fladr~veg~cp~C~yd~A--------RGDqcd~cG~l~ 175 (567)
T KOG1247|consen 145 FLADRFVEGKCPFCGYDDA--------RGDQCDKCGKLV 175 (567)
T ss_pred cccchhhhccCCCCCCccc--------cchhhhhhhhhc
Confidence 4678899999999986522 245788888755
No 300
>PF05280 FlhC: Flagellar transcriptional activator (FlhC); InterPro: IPR007944 This family consists of several bacterial flagellar transcriptional activator (FlhC) proteins. FlhC combines with FlhD to form a regulatory complex in Escherichia coli, this complex has been shown to be a global regulator involved in many cellular processes as well as a flagellar transcriptional activator [].; GO: 0003677 DNA binding, 0030092 regulation of flagellum assembly, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2AVU_E.
Probab=61.30 E-value=6.8 Score=34.11 Aligned_cols=30 Identities=23% Similarity=0.685 Sum_probs=12.3
Q ss_pred eeccCCCCCceeeecccccCCCcccCCCCCC
Q 025946 160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQ 190 (245)
Q Consensus 160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE 190 (245)
.-.+|+.||.+|......+ .....||.|..
T Consensus 133 ~l~~C~~C~~~fv~~~~~~-~~~~~Cp~C~~ 162 (175)
T PF05280_consen 133 QLAPCRRCGGHFVTHAHDP-RHSFVCPFCQP 162 (175)
T ss_dssp EEEE-TTT--EEEEESS---SS----TT---
T ss_pred cccCCCCCCCCeECcCCCC-CcCcCCCCCCC
Confidence 3349999999999832222 23689999974
No 301
>PRK03922 hypothetical protein; Provisional
Probab=60.98 E-value=3.9 Score=34.21 Aligned_cols=16 Identities=38% Similarity=1.072 Sum_probs=12.3
Q ss_pred cCCCcccCCCCCCcee
Q 025946 178 LNDELQLCPYCSQPFS 193 (245)
Q Consensus 178 Ln~d~iqCPnCGE~L~ 193 (245)
+.-+..+||.||++++
T Consensus 45 ievG~~~cP~cge~~~ 60 (113)
T PRK03922 45 VEVGLTICPKCGEPFD 60 (113)
T ss_pred EecCcccCCCCCCcCC
Confidence 4447889999999873
No 302
>PLN02569 threonine synthase
Probab=60.75 E-value=5.4 Score=39.29 Aligned_cols=29 Identities=17% Similarity=0.426 Sum_probs=22.6
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceeeeCC
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDD 197 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~ 197 (245)
.|+.||+++-. ..-...| .||.+|.+.-+
T Consensus 51 ~C~~Cg~~y~~-----~~~~~~C-~cgg~l~~~~d 79 (484)
T PLN02569 51 ECPLTGEKYSL-----DEVVYRS-KSGGLLDVRHD 79 (484)
T ss_pred EeCCCCCcCCC-----ccccccC-CCCCeEEEecc
Confidence 89999988654 3446789 69999998854
No 303
>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=60.62 E-value=6.5 Score=31.04 Aligned_cols=31 Identities=29% Similarity=0.681 Sum_probs=13.8
Q ss_pred ccCCCCCceeeecccccCCC------------cccCCCCCCce
Q 025946 162 DSCPNCGNDFQIFKSTLNDE------------LQLCPYCSQPF 192 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d------------~iqCPnCGE~L 192 (245)
..||.|+..+-..+..-.++ ...|.|||.++
T Consensus 56 r~C~~C~~~~l~~~~~~~~~~~~~~~~~Ll~~~d~CiyCGgkf 98 (99)
T PF12660_consen 56 RVCPVCGRRALDPEPEDPNEYGWLTVTILLESFDVCIYCGGKF 98 (99)
T ss_dssp EE-TTT--EEE-GGG-SSS---HHHHHHHHHTSSB-TTT--B-
T ss_pred eEcCCCCCEEecCcccccccccchhHHHHHhCCCEEeCCCCCc
Confidence 58999998887744432222 24899998765
No 304
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=60.53 E-value=4.7 Score=39.84 Aligned_cols=32 Identities=22% Similarity=0.411 Sum_probs=24.2
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceeeeCCe
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDK 198 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~ 198 (245)
.||.||.+.-. .-++-..||.||....-..-+
T Consensus 352 ~Cp~Cg~~m~S----~G~~g~rC~kCg~~~~~~~~~ 383 (421)
T COG1571 352 VCPRCGGRMKS----AGRNGFRCKKCGTRARETLIK 383 (421)
T ss_pred CCCccCCchhh----cCCCCcccccccccCCccccc
Confidence 79999988665 344478999999987655443
No 305
>PRK12585 putative monovalent cation/H+ antiporter subunit G; Reviewed
Probab=60.48 E-value=31 Score=31.29 Aligned_cols=48 Identities=8% Similarity=0.155 Sum_probs=35.2
Q ss_pred cchhHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHHHHHHHHH
Q 025946 105 ARILGNLALAIGLTYFSMTGQLGWVLDAIVSIWLLAVIVPIVGFGAFL 152 (245)
Q Consensus 105 ~r~lgn~l~~l~l~~LL~T~gLgWLvd~~~~L~LlllllPIl~~~Gf~ 152 (245)
+-.+|-++++++++.........+.+.++++++++++..|+..-..-+
T Consensus 43 a~TLGv~LILlgv~l~~~~~~~~~slklLLiIvFllLTaPVaSHaIAR 90 (197)
T PRK12585 43 SNTFGVSLLLFATVGYFFHSGEGFNARVLLAVLFIFLTTPVASHLINR 90 (197)
T ss_pred chhhhHHHHHHHHHHHHHhccchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 556777777776655444445568889999999999999998755544
No 306
>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=60.43 E-value=5.3 Score=29.10 Aligned_cols=15 Identities=20% Similarity=0.550 Sum_probs=13.0
Q ss_pred ccCCCCCCceeeeCC
Q 025946 183 QLCPYCSQPFSVVDD 197 (245)
Q Consensus 183 iqCPnCGE~L~Vd~~ 197 (245)
..||.||+.+.+.+.
T Consensus 3 ~~CP~CG~~iev~~~ 17 (54)
T TIGR01206 3 FECPDCGAEIELENP 17 (54)
T ss_pred cCCCCCCCEEecCCC
Confidence 479999999998775
No 307
>PRK14873 primosome assembly protein PriA; Provisional
Probab=60.35 E-value=4.6 Score=41.37 Aligned_cols=26 Identities=15% Similarity=0.584 Sum_probs=15.3
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCc
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQP 191 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~ 191 (245)
.||+|+..+..-+ +.....|.+||..
T Consensus 394 ~C~~C~~~L~~h~---~~~~l~Ch~CG~~ 419 (665)
T PRK14873 394 RCRHCTGPLGLPS---AGGTPRCRWCGRA 419 (665)
T ss_pred ECCCCCCceeEec---CCCeeECCCCcCC
Confidence 6777776665421 2245667777764
No 308
>PTZ00410 NAD-dependent SIR2; Provisional
Probab=60.07 E-value=4.6 Score=38.70 Aligned_cols=32 Identities=19% Similarity=0.486 Sum_probs=19.6
Q ss_pred ccCCCCCceeeecccc---cCCCcccCCCCCCcee
Q 025946 162 DSCPNCGNDFQIFKST---LNDELQLCPYCSQPFS 193 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~---Ln~d~iqCPnCGE~L~ 193 (245)
..|..|+.++...+.. .....-.||.||..+.
T Consensus 148 ~~C~~C~~~~~~~~~~~~~~~~~vP~C~~CgG~lR 182 (349)
T PTZ00410 148 ASCIECHTPYDIEQAYLEARSGKVPHCSTCGGIVK 182 (349)
T ss_pred eEeCCCCCCcchhHHHHHhhcCCCCCCCCCCCccC
Confidence 4999999765432111 1223457999987553
No 309
>PRK08329 threonine synthase; Validated
Probab=59.96 E-value=5.9 Score=36.60 Aligned_cols=26 Identities=23% Similarity=0.597 Sum_probs=20.3
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceeee
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVV 195 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd 195 (245)
.|+.||+++-. +....| .||.+|.+.
T Consensus 3 ~C~~Cg~~~~~------~~~~~C-~c~~~l~~~ 28 (347)
T PRK08329 3 RCTKCGRTYEE------KFKLRC-DCGGTLLVE 28 (347)
T ss_pred CcCCCCCCcCC------CCceec-CCCCcEEEE
Confidence 79999998853 123689 599999887
No 310
>COG1241 MCM2 Predicted ATPase involved in replication control, Cdc46/Mcm family [DNA replication, recombination, and repair]
Probab=59.92 E-value=17 Score=37.90 Aligned_cols=53 Identities=17% Similarity=0.417 Sum_probs=30.7
Q ss_pred cCCCCCceeeecccccCC-CcccCCCCCCceeeeCCeeEEe--cccccc-cccccccccc
Q 025946 163 SCPNCGNDFQIFKSTLND-ELQLCPYCSQPFSVVDDKFVRE--SVRFSN-ESTTFGQAFS 218 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~-d~iqCPnCGE~L~Vd~~~F~R~--~~~f~~-~~~~~~~af~ 218 (245)
.||.||.++....+.... .+..||+| ... ..+.|.++ .+.|.+ |.-..++.-+
T Consensus 131 ~C~~Cg~~~~~~~~~~~~~~~~~C~~~-~~~--~~~~~~~~~~~s~f~d~Q~vkiQE~pe 187 (682)
T COG1241 131 ECPKCGREVEVEQSEFRVEPPRECENC-GKF--GKGPLKLVPRKSEFIDFQKVKIQELPE 187 (682)
T ss_pred EcCCCCCEEEEEeccccccCCccCCCc-ccc--CCCceEEecCcceeeeceEEEEecCcc
Confidence 799999999885444333 56779999 222 44445443 333444 4434444333
No 311
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=59.82 E-value=5.9 Score=38.81 Aligned_cols=27 Identities=22% Similarity=0.621 Sum_probs=19.7
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
.|+.||+.... +.+....||.||..+.
T Consensus 242 ~c~~cg~~~~~----~~~~~~~c~~Cg~~~~ 268 (380)
T COG1867 242 HCSRCGEIVGS----FREVDEKCPHCGGKVH 268 (380)
T ss_pred Ecccccceecc----cccccccCCcccccce
Confidence 79999944444 5566889999986443
No 312
>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=59.71 E-value=7.2 Score=37.23 Aligned_cols=30 Identities=13% Similarity=0.522 Sum_probs=19.5
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceee
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSV 194 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~V 194 (245)
.||.|+..-.. ..+...+..||+||.++.+
T Consensus 235 ~C~~c~~~~~~--~~~~~~~~~C~~c~~~~~~ 264 (374)
T TIGR00308 235 HCSRCLHNKPV--NGISQRKGRCKECGGEYHL 264 (374)
T ss_pred ECCCccccccc--ccccCCCCCCCCCCCccee
Confidence 69999875432 1123456689999987643
No 313
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=59.62 E-value=16 Score=26.31 Aligned_cols=8 Identities=63% Similarity=1.427 Sum_probs=3.8
Q ss_pred cCCCCCce
Q 025946 163 SCPNCGND 170 (245)
Q Consensus 163 tCPnCG~e 170 (245)
.||+||..
T Consensus 54 ~Cp~C~~~ 61 (67)
T smart00714 54 YCPNCGAF 61 (67)
T ss_pred ECCCCCCE
Confidence 45555543
No 314
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=59.62 E-value=5 Score=30.85 Aligned_cols=33 Identities=18% Similarity=0.567 Sum_probs=21.6
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCCCceeeeCCee
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKF 199 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F 199 (245)
-.| .||...|..|+. ..-.| +||..+.++.-.+
T Consensus 4 frC-~Cgr~lya~e~~---kTkkC-~CG~~l~vk~~rI 36 (68)
T PF09082_consen 4 FRC-DCGRYLYAKEGA---KTKKC-VCGKTLKVKERRI 36 (68)
T ss_dssp EEE-TTS--EEEETT----SEEEE-TTTEEEE--SSS-
T ss_pred EEe-cCCCEEEecCCc---ceeEe-cCCCeeeeeeEEE
Confidence 368 799999995443 57889 9999999987654
No 315
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=59.60 E-value=4.4 Score=43.14 Aligned_cols=28 Identities=18% Similarity=0.490 Sum_probs=20.1
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
.+||.|+..-.- --.+=..|++||..|.
T Consensus 828 ~~cp~c~~~~~~----~~~~c~~c~~c~~~~~ 855 (858)
T PRK08115 828 NTCPVCREGTVE----EIGGCNTCTNCGAQLK 855 (858)
T ss_pred CCCCccCCCcee----ecCCCccccchhhhhc
Confidence 399999965443 1235779999998764
No 316
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=59.21 E-value=3.5 Score=39.17 Aligned_cols=31 Identities=35% Similarity=0.786 Sum_probs=0.0
Q ss_pred cCCCCCce----------------eeecccccCCCcccCCCCCCcee
Q 025946 163 SCPNCGND----------------FQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 163 tCPnCG~e----------------F~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
+||.||.. +..-.+.+-+-...||.|||+.+
T Consensus 241 ~C~~Cg~~PtiP~~~~~C~HiyCY~Ci~ts~~~~asf~Cp~Cg~~~~ 287 (298)
T KOG2879|consen 241 ECPVCGEPPTIPHVIGKCGHIYCYYCIATSRLWDASFTCPLCGENVE 287 (298)
T ss_pred eeeccCCCCCCCeeeccccceeehhhhhhhhcchhhcccCccCCCCc
No 317
>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=59.00 E-value=5.5 Score=32.34 Aligned_cols=17 Identities=41% Similarity=1.019 Sum_probs=14.0
Q ss_pred cccCCCCCCceeeeCCe
Q 025946 182 LQLCPYCSQPFSVVDDK 198 (245)
Q Consensus 182 ~iqCPnCGE~L~Vd~~~ 198 (245)
|+.|||||.+..+..+.
T Consensus 2 p~~CpYCg~~~~l~~~~ 18 (102)
T PF11672_consen 2 PIICPYCGGPAELVDGS 18 (102)
T ss_pred CcccCCCCCeeEEcccc
Confidence 68999999998876653
No 318
>PRK05638 threonine synthase; Validated
Probab=58.24 E-value=6.2 Score=37.66 Aligned_cols=26 Identities=23% Similarity=0.892 Sum_probs=20.4
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceeee
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVV 195 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd 195 (245)
.|+.||+++-. +....| .||.+|.++
T Consensus 3 ~C~~Cg~~~~~------~~~~~C-~c~~~l~~~ 28 (442)
T PRK05638 3 KCPKCGREYNS------YIPPFC-ICGELLEII 28 (442)
T ss_pred EeCCCCCCCCC------CCceec-CCCCcEEEE
Confidence 79999998643 134789 899999887
No 319
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=58.19 E-value=5.5 Score=24.46 Aligned_cols=11 Identities=45% Similarity=1.232 Sum_probs=8.4
Q ss_pred cCCCCCceeee
Q 025946 163 SCPNCGNDFQI 173 (245)
Q Consensus 163 tCPnCG~eF~~ 173 (245)
.||.||.+|..
T Consensus 4 ~C~~CgR~F~~ 14 (25)
T PF13913_consen 4 PCPICGRKFNP 14 (25)
T ss_pred cCCCCCCEECH
Confidence 68888888843
No 320
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=57.82 E-value=6.5 Score=27.05 Aligned_cols=32 Identities=28% Similarity=0.689 Sum_probs=20.6
Q ss_pred cCCCCCceeeecccc-----cCCCcccCCC--CCCceee
Q 025946 163 SCPNCGNDFQIFKST-----LNDELQLCPY--CSQPFSV 194 (245)
Q Consensus 163 tCPnCG~eF~~~ed~-----Ln~d~iqCPn--CGE~L~V 194 (245)
.||.||..-.+-.+. +.+--.||.| ||-.+..
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg~tfv~ 39 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSPLTRELYCQCTNPECGHTFVA 39 (47)
T ss_pred CcCCCCCeeEEEEchhhCcceEEEEEEECCCcCCCEEEE
Confidence 599999877763222 2223567887 9887643
No 321
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=57.76 E-value=7.1 Score=31.48 Aligned_cols=27 Identities=26% Similarity=0.663 Sum_probs=19.7
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
.||.||.+-.- -+..+--+|..||..+
T Consensus 37 ~Cp~C~~~~Vk---R~a~GIW~C~kCg~~f 63 (89)
T COG1997 37 VCPFCGRTTVK---RIATGIWKCRKCGAKF 63 (89)
T ss_pred cCCCCCCccee---eeccCeEEcCCCCCee
Confidence 89999988332 1333677999998766
No 322
>PF06676 DUF1178: Protein of unknown function (DUF1178); InterPro: IPR009562 This family consists of several hypothetical bacterial proteins of around 150 residues in length. The function of this family is unknown.
Probab=57.74 E-value=5.2 Score=34.38 Aligned_cols=31 Identities=26% Similarity=0.585 Sum_probs=21.5
Q ss_pred eeccCCCCCceeee-------cccccCCCcccCCCCCCc
Q 025946 160 VQDSCPNCGNDFQI-------FKSTLNDELQLCPYCSQP 191 (245)
Q Consensus 160 IE~tCPnCG~eF~~-------~ed~Ln~d~iqCPnCGE~ 191 (245)
|.-.|. ||.+|-. +|+-..++.+.||.||..
T Consensus 4 y~L~C~-~gH~FEgWF~ss~~fd~Q~~~glv~CP~Cgs~ 41 (148)
T PF06676_consen 4 YDLRCE-NGHEFEGWFRSSAAFDRQQARGLVSCPVCGST 41 (148)
T ss_pred EEEecC-CCCccceecCCHHHHHHHHHcCCccCCCCCCC
Confidence 455787 8888755 223344578999999875
No 323
>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=57.64 E-value=5 Score=32.05 Aligned_cols=30 Identities=23% Similarity=0.620 Sum_probs=22.0
Q ss_pred ceeccCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 159 IVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 159 LIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
+-+.+|..|+.+|.. |.+...+|++|...+
T Consensus 52 ~~~~~C~~C~~~fg~----l~~~~~~C~~C~~~V 81 (118)
T PF02318_consen 52 YGERHCARCGKPFGF----LFNRGRVCVDCKHRV 81 (118)
T ss_dssp HCCSB-TTTS-BCSC----TSTTCEEETTTTEEE
T ss_pred cCCcchhhhCCcccc----cCCCCCcCCcCCccc
Confidence 456799999999876 666779999997654
No 324
>PHA00733 hypothetical protein
Probab=57.52 E-value=4.7 Score=33.03 Aligned_cols=32 Identities=28% Similarity=0.661 Sum_probs=21.8
Q ss_pred ccCCCCCceeeecccc---cC--CCcccCCCCCCcee
Q 025946 162 DSCPNCGNDFQIFKST---LN--DELQLCPYCSQPFS 193 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~---Ln--~d~iqCPnCGE~L~ 193 (245)
..|+.||+.|...... .. ..+..|+.|++.+.
T Consensus 74 y~C~~Cgk~Fss~s~L~~H~r~h~~~~~C~~CgK~F~ 110 (128)
T PHA00733 74 YVCPLCLMPFSSSVSLKQHIRYTEHSKVCPVCGKEFR 110 (128)
T ss_pred ccCCCCCCcCCCHHHHHHHHhcCCcCccCCCCCCccC
Confidence 4899999988762221 11 24679999988764
No 325
>PRK05580 primosome assembly protein PriA; Validated
Probab=57.45 E-value=6.8 Score=39.79 Aligned_cols=11 Identities=27% Similarity=0.625 Sum_probs=6.8
Q ss_pred cCCCCCceeee
Q 025946 163 SCPNCGNDFQI 173 (245)
Q Consensus 163 tCPnCG~eF~~ 173 (245)
.|..||+....
T Consensus 383 ~C~~Cg~~~~C 393 (679)
T PRK05580 383 LCRDCGWVAEC 393 (679)
T ss_pred EhhhCcCccCC
Confidence 67777765543
No 326
>PF03563 Bunya_G2: Bunyavirus glycoprotein G2; InterPro: IPR005168 Bunyavirus has three genomic segments: small (S), middle-sized (M), and large (L). The S segment encodes the nucleocapsid and a non-structural protein. The M segment codes for two glycoproteins, G1 and G2, and another non-structural protein (NSm). The L segment codes for an RNA polymerase. This entry represents the polyprotein region forming the G2 glycoprotein, which interacts with the IPR005167 from INTERPRO G1 glycoprotein [].
Probab=56.82 E-value=23 Score=33.64 Aligned_cols=27 Identities=30% Similarity=0.765 Sum_probs=17.8
Q ss_pred cCCCCCceeeecccccCCCcccCC---CCCCceeeeCC
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCP---YCSQPFSVVDD 197 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCP---nCGE~L~Vd~~ 197 (245)
.||+||-..-- -.-|| .||..++-.|.
T Consensus 236 ~C~nC~La~HP--------FtnC~s~CvCG~~f~~sd~ 265 (285)
T PF03563_consen 236 KCKNCGLAYHP--------FTNCGSHCVCGMKFETSDR 265 (285)
T ss_pred hCcccCeeccC--------CCCCCCeeeccccccchHH
Confidence 89999965443 34455 38888875543
No 327
>PF10601 zf-LITAF-like: LITAF-like zinc ribbon domain; InterPro: IPR006629 Members of this family display a conserved zinc ribbon structure [] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [].
Probab=56.74 E-value=23 Score=25.90 Aligned_cols=11 Identities=27% Similarity=0.872 Sum_probs=5.0
Q ss_pred cccCCCCCCce
Q 025946 182 LQLCPYCSQPF 192 (245)
Q Consensus 182 ~iqCPnCGE~L 192 (245)
.-.||+|+..+
T Consensus 58 ~H~Cp~C~~~l 68 (73)
T PF10601_consen 58 YHYCPNCGAFL 68 (73)
T ss_pred eEECCCCCCEe
Confidence 44444444443
No 328
>TIGR03676 aRF1/eRF1 peptide chain release factor 1, archaeal and eukaryotic forms. Directs the termination of nascent peptide synthesis (translation) in response to the termination codons UAA, UAG and UGA. This model identifies both archaeal (aRF1) and eukaryotic (eRF1) of the protein. Also known as translation termination factor 1.
Probab=56.52 E-value=8.6 Score=37.10 Aligned_cols=37 Identities=32% Similarity=0.723 Sum_probs=22.6
Q ss_pred eeccCCCCCceeeec-ccccCCCcccCCCCCCceeeeC
Q 025946 160 VQDSCPNCGNDFQIF-KSTLNDELQLCPYCSQPFSVVD 196 (245)
Q Consensus 160 IE~tCPnCG~eF~~~-ed~Ln~d~iqCPnCGE~L~Vd~ 196 (245)
+...||+||.+.... +..-...+..||+||..+.+.+
T Consensus 319 ~~~rc~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 356 (403)
T TIGR03676 319 VTFKCPNCGYEEEKTVKPEEGDKSEACPKCGSELEIVE 356 (403)
T ss_pred EEEEcCCCCcceeeecccccccccccCcccCcccccch
Confidence 346899999876531 0000112246999999988543
No 329
>COG0423 GRS1 Glycyl-tRNA synthetase (class II) [Translation, ribosomal structure and biogenesis]
Probab=56.06 E-value=4.9 Score=41.07 Aligned_cols=37 Identities=22% Similarity=0.574 Sum_probs=26.3
Q ss_pred cCCCCCceeee---ccccc-----------------CCCcccCCCCCCceeeeCCeeE
Q 025946 163 SCPNCGNDFQI---FKSTL-----------------NDELQLCPYCSQPFSVVDDKFV 200 (245)
Q Consensus 163 tCPnCG~eF~~---~ed~L-----------------n~d~iqCPnCGE~L~Vd~~~F~ 200 (245)
.|++||..|.. .|+.+ .+..+.||.||.++. +=.+|.
T Consensus 90 ~c~~c~~~yRADHLiEe~l~~~~~~~~~~~e~~~ii~~~~ir~p~~g~~l~-~v~~FN 146 (558)
T COG0423 90 ECKKCGERYRADHLIEEYLGKDGHGNMSPEELTEIIREYDIRCPECGGELN-EVREFN 146 (558)
T ss_pred eccccchhhhhhHHHHHHhhhcccccCCHHHHHHHHHHcCCcCCCcCCccC-Ccceee
Confidence 89999999983 23333 235789999999987 555553
No 330
>COG0498 ThrC Threonine synthase [Amino acid transport and metabolism]
Probab=55.98 E-value=4.8 Score=39.24 Aligned_cols=38 Identities=26% Similarity=0.472 Sum_probs=28.6
Q ss_pred cceeccCCCCCceeeecccccCCCcccCCCCCCceeeeCCeeE
Q 025946 158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFV 200 (245)
Q Consensus 158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~ 200 (245)
+++.-.|.+||.+|.. ..-+..||.||-.++++=..+.
T Consensus 2 ~~~~~rc~~cg~~f~~-----a~~~~~c~~cGl~lp~~~~~~~ 39 (411)
T COG0498 2 KYVSLRCLKCGREFSQ-----ALLQGLCPDCGLFLPAEYPYFS 39 (411)
T ss_pred ceeEeecCCCCcchhh-----HHhhCcCCcCCcccccccCccc
Confidence 3566789999988764 1127899999999988666654
No 331
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=55.58 E-value=6.7 Score=29.83 Aligned_cols=30 Identities=17% Similarity=0.483 Sum_probs=23.2
Q ss_pred cceeccCCCCCceeeecccccCCCcccCCCCCCc
Q 025946 158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQP 191 (245)
Q Consensus 158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~ 191 (245)
..+-..|-.||.+... =..|.++|-.||--
T Consensus 17 ~~miYiCgdC~~en~l----k~~D~irCReCG~R 46 (62)
T KOG3507|consen 17 ATMIYICGDCGQENTL----KRGDVIRCRECGYR 46 (62)
T ss_pred ccEEEEeccccccccc----cCCCcEehhhcchH
Confidence 4556689999988776 34489999999953
No 332
>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=55.33 E-value=5.9 Score=38.24 Aligned_cols=33 Identities=21% Similarity=0.508 Sum_probs=22.5
Q ss_pred cceeccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
+|...-|-.|+..+.- ++.... ...|| ||.++.
T Consensus 237 KYh~~~c~~C~~~~~~-~~~~~~-~~~Cp-CG~~i~ 269 (374)
T TIGR00375 237 KYHQTACEACGEPAVS-EDAETA-CANCP-CGGRIK 269 (374)
T ss_pred ccchhhhcccCCcCCc-hhhhhc-CCCCC-CCCcce
Confidence 7778899999977664 111111 36799 999843
No 333
>PRK12586 putative monovalent cation/H+ antiporter subunit G; Reviewed
Probab=55.18 E-value=30 Score=29.76 Aligned_cols=48 Identities=13% Similarity=0.124 Sum_probs=38.6
Q ss_pred cchhHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHHHHHHHHH
Q 025946 105 ARILGNLALAIGLTYFSMTGQLGWVLDAIVSIWLLAVIVPIVGFGAFL 152 (245)
Q Consensus 105 ~r~lgn~l~~l~l~~LL~T~gLgWLvd~~~~L~LlllllPIl~~~Gf~ 152 (245)
+-.+|-+++++++++..+.....+.+..+++++++++..|+-.-..-+
T Consensus 46 a~TlG~~liLlg~~l~~~~~~~~~~~k~lLii~fl~lTaPVaah~iaR 93 (145)
T PRK12586 46 SSTLSVLLTLIGVLIYFIVNTGFFSVRLLLSLVFINLTSPVGMHLIAR 93 (145)
T ss_pred chhhHHHHHHHHHHHHHhcccchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 567888888888887776666667889999999999999998755544
No 334
>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=55.18 E-value=3.9 Score=39.45 Aligned_cols=6 Identities=50% Similarity=1.597 Sum_probs=3.0
Q ss_pred cCCCCC
Q 025946 163 SCPNCG 168 (245)
Q Consensus 163 tCPnCG 168 (245)
-||.|+
T Consensus 122 ~~~~~~ 127 (530)
T TIGR00398 122 YCPECE 127 (530)
T ss_pred ecCCCC
Confidence 355555
No 335
>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=55.02 E-value=5.9 Score=35.67 Aligned_cols=11 Identities=27% Similarity=0.561 Sum_probs=9.1
Q ss_pred ccCCCCCceee
Q 025946 162 DSCPNCGNDFQ 172 (245)
Q Consensus 162 ~tCPnCG~eF~ 172 (245)
..|+.|++++.
T Consensus 119 ~~C~~C~~~~~ 129 (260)
T cd01409 119 VVCLSCGFRTP 129 (260)
T ss_pred EEeCCCcCccC
Confidence 39999999864
No 336
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=54.96 E-value=5.8 Score=30.10 Aligned_cols=20 Identities=20% Similarity=0.532 Sum_probs=14.5
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCCC
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQ 190 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE 190 (245)
..|.+|.+-. +..+||+||.
T Consensus 6 ~AC~~C~~i~---------~~~~Cp~Cgs 25 (64)
T PRK06393 6 RACKKCKRLT---------PEKTCPVHGD 25 (64)
T ss_pred hhHhhCCccc---------CCCcCCCCCC
Confidence 3789998543 2349999997
No 337
>PRK04173 glycyl-tRNA synthetase; Provisional
Probab=54.41 E-value=4.9 Score=39.04 Aligned_cols=29 Identities=17% Similarity=0.565 Sum_probs=20.7
Q ss_pred cCCCCCceeeecc---c---------------ccCCCcccCCCCCCc
Q 025946 163 SCPNCGNDFQIFK---S---------------TLNDELQLCPYCSQP 191 (245)
Q Consensus 163 tCPnCG~eF~~~e---d---------------~Ln~d~iqCPnCGE~ 191 (245)
.|+.|+..+..++ + .+..-++.||+|+..
T Consensus 88 ~~~~~~~~~r~d~~~~~~~~~~~~~~~~~~~~~~~~~~m~cp~~~~~ 134 (456)
T PRK04173 88 ECKKCKKRYRADHLIEELGIDAEGLSNEELKELIRENDIKCPECGGE 134 (456)
T ss_pred EeCCCCCEeechhhhHHHhhhhccccHHHHHHHHHHhCCCCCCCCCC
Confidence 7899999887643 1 133348999999843
No 338
>cd03529 Rieske_NirD Assimilatory nitrite reductase (NirD) family, Rieske domain; Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium. Members include bacterial and fungal proteins. The bacterial NirD contains a single Rieske domain while fungal proteins have a C-terminal Rieske domain in addition to several other domains. The fungal NirD is involved in nutrient acquisition, functioning at the soil/fungus interface to control nutrient exchange between the fungus and the host plant. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. The Rieske [2Fe-2S] cluster is liganded to two histidine and two cysteine residues present in conserved sequences called Rieske motifs. In this family, only a few members contain these residues. Other members may have lost the ability to bind the Rieske [2Fe-2S] cluster.
Probab=54.37 E-value=11 Score=28.66 Aligned_cols=42 Identities=17% Similarity=0.302 Sum_probs=28.7
Q ss_pred ceeccCCCCCceeeeccccc----CCCcccCCCCCCceeeeCCeeEE
Q 025946 159 IVQDSCPNCGNDFQIFKSTL----NDELQLCPYCSQPFSVVDDKFVR 201 (245)
Q Consensus 159 LIE~tCPnCG~eF~~~ed~L----n~d~iqCPnCGE~L~Vd~~~F~R 201 (245)
-++..||.-|..... +..+ +++.++||.-|..|.++.|+=..
T Consensus 37 A~~~~CpH~g~~ll~-~G~~~~~~~~~~i~Cp~Hg~~Fdl~tG~~~~ 82 (103)
T cd03529 37 AVQNMDPHSRANVLS-RGIVGDIGGEPVVASPLYKQHFSLKTGRCLE 82 (103)
T ss_pred EEeCcCCCCCCcccC-CceEcccCCCeEEECCCCCCEEEcCCCCccC
Confidence 466799999976321 1222 22479999999999988776443
No 339
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=54.29 E-value=3.7 Score=29.20 Aligned_cols=29 Identities=28% Similarity=0.782 Sum_probs=22.3
Q ss_pred cCCCCCceeeecccc-cCCCcccCCCCCCce
Q 025946 163 SCPNCGNDFQIFKST-LNDELQLCPYCSQPF 192 (245)
Q Consensus 163 tCPnCG~eF~~~ed~-Ln~d~iqCPnCGE~L 192 (245)
+|+.||++.-.+... +.++ ..|..|-+.+
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHh
Confidence 599999998885533 5555 8999997666
No 340
>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=54.26 E-value=7.9 Score=25.93 Aligned_cols=30 Identities=23% Similarity=0.775 Sum_probs=14.8
Q ss_pred cCCCCCceeeecccc--cCCC-----cccCCCCCCce
Q 025946 163 SCPNCGNDFQIFKST--LNDE-----LQLCPYCSQPF 192 (245)
Q Consensus 163 tCPnCG~eF~~~ed~--Ln~d-----~iqCPnCGE~L 192 (245)
+||+||.+-..+-+. -..| -..|.+||..+
T Consensus 2 ~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~w 38 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRW 38 (39)
T ss_dssp --SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEE
T ss_pred CCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCee
Confidence 699999775553221 1112 34688887654
No 341
>KOG4080 consensus Mitochondrial ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=54.25 E-value=3.5 Score=36.64 Aligned_cols=21 Identities=38% Similarity=1.141 Sum_probs=16.4
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCc
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQP 191 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~ 191 (245)
+||.||. ++.....|++|=+.
T Consensus 95 ~CP~CGh--------~k~a~~LC~~Cy~k 115 (176)
T KOG4080|consen 95 TCPACGH--------IKPAHTLCDYCYAK 115 (176)
T ss_pred cCcccCc--------cccccccHHHHHHH
Confidence 8999995 45568999999443
No 342
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=53.67 E-value=6.3 Score=30.45 Aligned_cols=37 Identities=30% Similarity=0.416 Sum_probs=20.6
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceeeeCCeeEEec
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRES 203 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R~~ 203 (245)
.||.||.+-|..+++..-+. .=...+.|++++|.-..
T Consensus 6 kCpKCgn~~~~ekei~~tg~----~lskifdvq~n~f~~it 42 (68)
T COG3478 6 KCPKCGNTNYEEKEIAATGG----GLSKIFDVQNNKFIVIT 42 (68)
T ss_pred cCCCcCCcchhhceeeccCC----CcceeEEecccEEEEEE
Confidence 39999998887433322111 11234566666666543
No 343
>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=53.65 E-value=6 Score=31.72 Aligned_cols=27 Identities=26% Similarity=0.625 Sum_probs=19.6
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
+||.||++-..-. .-+--+|..||..+
T Consensus 37 ~Cp~Cgk~~vkR~---a~GIW~C~~C~~~~ 63 (90)
T PF01780_consen 37 TCPFCGKTSVKRV---ATGIWKCKKCGKKF 63 (90)
T ss_dssp EESSSSSSEEEEE---ETTEEEETTTTEEE
T ss_pred cCCCCCCceeEEe---eeEEeecCCCCCEE
Confidence 8999998875521 12567999998665
No 344
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=53.41 E-value=9.2 Score=35.75 Aligned_cols=25 Identities=28% Similarity=0.776 Sum_probs=17.9
Q ss_pred cCCCCCceeeeccccc-CCCcccCCCCC
Q 025946 163 SCPNCGNDFQIFKSTL-NDELQLCPYCS 189 (245)
Q Consensus 163 tCPnCG~eF~~~ed~L-n~d~iqCPnCG 189 (245)
.|+.||....- ..+ .++.-.||+|-
T Consensus 247 pC~~CGt~I~k--~~~~gR~t~~CP~CQ 272 (273)
T COG0266 247 PCRRCGTPIEK--IKLGGRSTFYCPVCQ 272 (273)
T ss_pred CCCccCCEeEE--EEEcCCcCEeCCCCC
Confidence 79999987665 233 34788899984
No 345
>PRK14894 glycyl-tRNA synthetase; Provisional
Probab=53.18 E-value=7 Score=39.84 Aligned_cols=23 Identities=22% Similarity=0.707 Sum_probs=18.3
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCC
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQ 190 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE 190 (245)
.|++|++.+..+.. .+.||+||+
T Consensus 90 ~CkkCk~ryRaD~L-----iikCP~CGs 112 (539)
T PRK14894 90 DCRDCKMRWRADHI-----QGVCPNCGS 112 (539)
T ss_pred ECCCCCccccCccc-----eeeCCCCCC
Confidence 89999999887432 357999995
No 346
>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=53.05 E-value=5.6 Score=22.61 Aligned_cols=11 Identities=45% Similarity=1.247 Sum_probs=7.7
Q ss_pred cCCCCCceeee
Q 025946 163 SCPNCGNDFQI 173 (245)
Q Consensus 163 tCPnCG~eF~~ 173 (245)
+||.|++.|..
T Consensus 2 ~C~~C~~~f~~ 12 (23)
T PF00096_consen 2 KCPICGKSFSS 12 (23)
T ss_dssp EETTTTEEESS
T ss_pred CCCCCCCccCC
Confidence 57777777765
No 347
>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=52.86 E-value=10 Score=26.47 Aligned_cols=32 Identities=25% Similarity=0.531 Sum_probs=19.1
Q ss_pred cCCCCCceeeecc---cccCCC-cccCCCCCCceee
Q 025946 163 SCPNCGNDFQIFK---STLNDE-LQLCPYCSQPFSV 194 (245)
Q Consensus 163 tCPnCG~eF~~~e---d~Ln~d-~iqCPnCGE~L~V 194 (245)
.||-||.+-..+. +..... -..|+.||...++
T Consensus 3 PCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~~ 38 (53)
T TIGR03655 3 PCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGPV 38 (53)
T ss_pred CCCCCCCcceeeEeccCCCCCEEEEECCCCCCCccc
Confidence 6999997655221 111111 3369999988765
No 348
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=52.09 E-value=7.9 Score=23.07 Aligned_cols=22 Identities=27% Similarity=0.557 Sum_probs=17.5
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCc
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQP 191 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~ 191 (245)
+||.|+..-+. ....|-.|+++
T Consensus 4 ~C~~C~~~N~~-------~~~~C~~C~~p 25 (26)
T smart00547 4 ECPACTFLNFA-------SRSKCFACGAP 25 (26)
T ss_pred cCCCCCCcChh-------hhccccccCCc
Confidence 79999976555 67889999875
No 349
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=52.05 E-value=11 Score=39.67 Aligned_cols=19 Identities=26% Similarity=0.586 Sum_probs=14.8
Q ss_pred cccCCCCCCceeeeCCeeE
Q 025946 182 LQLCPYCSQPFSVVDDKFV 200 (245)
Q Consensus 182 ~iqCPnCGE~L~Vd~~~F~ 200 (245)
...||.||..+....++|-
T Consensus 645 ~~~CP~Cg~~m~lK~gr~G 663 (860)
T PRK06319 645 DSPCPLCGGEMKVRHGRFG 663 (860)
T ss_pred CCcCccCCCeeEEecCCCC
Confidence 3479999998888777654
No 350
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=52.04 E-value=8.1 Score=33.94 Aligned_cols=28 Identities=21% Similarity=0.727 Sum_probs=20.2
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceeeeC
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVD 196 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~ 196 (245)
.||.|+..+.. .+....|++ |-.+.+..
T Consensus 4 ~CP~C~~~l~~-----~~~~~~C~~-~h~fd~a~ 31 (272)
T PRK11088 4 QCPLCHQPLTL-----EENSWICPQ-NHQFDCAK 31 (272)
T ss_pred cCCCCCcchhc-----CCCEEEcCC-CCCCcccc
Confidence 69999988854 456789998 55565443
No 351
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=51.86 E-value=12 Score=31.05 Aligned_cols=32 Identities=25% Similarity=0.529 Sum_probs=24.4
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceeee
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVV 195 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd 195 (245)
-||.||+.+.+.++.. -....|+-|+-.++++
T Consensus 3 FCP~Cgn~Live~g~~-~~rf~C~tCpY~~~I~ 34 (105)
T KOG2906|consen 3 FCPTCGNMLIVESGES-CNRFSCRTCPYVFPIS 34 (105)
T ss_pred ccCCCCCEEEEecCCe-EeeEEcCCCCceeeEe
Confidence 4999999998844332 3467899999888887
No 352
>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=51.70 E-value=8.6 Score=36.24 Aligned_cols=9 Identities=44% Similarity=1.154 Sum_probs=7.8
Q ss_pred cCCCCCcee
Q 025946 163 SCPNCGNDF 171 (245)
Q Consensus 163 tCPnCG~eF 171 (245)
.||+||..=
T Consensus 186 ~CPvCGs~P 194 (305)
T TIGR01562 186 LCPACGSPP 194 (305)
T ss_pred cCCCCCChh
Confidence 999999764
No 353
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=51.60 E-value=8.8 Score=36.25 Aligned_cols=34 Identities=26% Similarity=0.583 Sum_probs=24.9
Q ss_pred cceeccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
-+-|-.||+|+.+|.+. ..-..+.-|=.||.++.
T Consensus 152 G~aef~C~~C~h~F~G~--~qm~v~sPCy~C~~~v~ 185 (278)
T PF15135_consen 152 GIAEFHCPKCRHNFRGF--AQMGVPSPCYGCGNPVY 185 (278)
T ss_pred ceeeeecccccccchhh--hhcCCCCCccCCCCccC
Confidence 45566999999999984 22235788999998764
No 354
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=51.59 E-value=14 Score=24.37 Aligned_cols=17 Identities=24% Similarity=0.442 Sum_probs=10.8
Q ss_pred cccCCCCCCceeeeCCe
Q 025946 182 LQLCPYCSQPFSVVDDK 198 (245)
Q Consensus 182 ~iqCPnCGE~L~Vd~~~ 198 (245)
+..||+||..-....|.
T Consensus 2 ~~~Cp~Cg~~~~~~~g~ 18 (47)
T PF14690_consen 2 PPRCPHCGSPSVHRHGY 18 (47)
T ss_pred CccCCCcCCCceECCce
Confidence 56799998766443333
No 355
>PF11241 DUF3043: Protein of unknown function (DUF3043); InterPro: IPR021403 Some members in this family of proteins with unknown function are annotated as membrane proteins. This cannot be confirmed.
Probab=51.41 E-value=48 Score=29.25 Aligned_cols=21 Identities=14% Similarity=0.328 Sum_probs=12.5
Q ss_pred cchhHHHHHHHHHHHHHhccc
Q 025946 105 ARILGNLALAIGLTYFSMTGQ 125 (245)
Q Consensus 105 ~r~lgn~l~~l~l~~LL~T~g 125 (245)
-|.+|.|+.-+++++|+.+..
T Consensus 74 R~~i~e~fmP~alv~lv~~~v 94 (170)
T PF11241_consen 74 RRNIGEFFMPVALVLLVLSFV 94 (170)
T ss_pred ccchHHHHHHHHHHHHHHHHH
Confidence 356777776666666555433
No 356
>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=51.24 E-value=5.8 Score=33.49 Aligned_cols=33 Identities=30% Similarity=0.721 Sum_probs=22.8
Q ss_pred eccCCCCCceeeecccccCCC----cccCCCCCCcee
Q 025946 161 QDSCPNCGNDFQIFKSTLNDE----LQLCPYCSQPFS 193 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~Ln~d----~iqCPnCGE~L~ 193 (245)
...||.||..-+-..+.+-.+ ..+|-.|.|+|+
T Consensus 105 ~~~cp~c~s~~t~~~s~fg~t~cka~~~c~~c~epf~ 141 (146)
T TIGR02159 105 SVQCPRCGSADTTITSIFGPTACKALYRCRACKEPFE 141 (146)
T ss_pred CCcCCCCCCCCcEeecCCCChhhHHHhhhhhhCCcHh
Confidence 368999998777644443333 567888988874
No 357
>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=51.23 E-value=11 Score=25.66 Aligned_cols=26 Identities=31% Similarity=0.832 Sum_probs=19.1
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
..|+.|+++|.. ......|..||..+
T Consensus 3 ~~C~~C~~~F~~-----~~rk~~Cr~Cg~~~ 28 (57)
T cd00065 3 SSCMGCGKPFTL-----TRRRHHCRNCGRIF 28 (57)
T ss_pred CcCcccCccccC-----CccccccCcCcCCc
Confidence 479999988886 34567777777764
No 358
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=50.95 E-value=9.2 Score=36.23 Aligned_cols=9 Identities=44% Similarity=1.147 Sum_probs=7.9
Q ss_pred ccCCCCCce
Q 025946 162 DSCPNCGND 170 (245)
Q Consensus 162 ~tCPnCG~e 170 (245)
..||+||..
T Consensus 188 ~~CPvCGs~ 196 (309)
T PRK03564 188 QFCPVCGSM 196 (309)
T ss_pred CCCCCCCCc
Confidence 599999977
No 359
>PRK01343 zinc-binding protein; Provisional
Probab=50.52 E-value=8 Score=28.76 Aligned_cols=11 Identities=36% Similarity=0.984 Sum_probs=5.2
Q ss_pred cccCCCCCCce
Q 025946 182 LQLCPYCSQPF 192 (245)
Q Consensus 182 ~iqCPnCGE~L 192 (245)
...||.||+++
T Consensus 9 ~~~CP~C~k~~ 19 (57)
T PRK01343 9 TRPCPECGKPS 19 (57)
T ss_pred CCcCCCCCCcC
Confidence 34455555543
No 360
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=50.05 E-value=24 Score=31.10 Aligned_cols=22 Identities=18% Similarity=0.095 Sum_probs=11.4
Q ss_pred HHHHHHHHHHHHHHHHHHHhcC
Q 025946 136 IWLLAVIVPIVGFGAFLWWASR 157 (245)
Q Consensus 136 L~LlllllPIl~~~Gf~WWl~r 157 (245)
++.++.++|+++++++.||+-|
T Consensus 240 l~~l~p~~~~~~~~~~~~~~~~ 261 (262)
T PF14257_consen 240 LVGLLPWLPLILIIGLLVRFVR 261 (262)
T ss_pred HHHHHHHHHHHHHHHHHHheEe
Confidence 3344455555555555555543
No 361
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=49.78 E-value=13 Score=36.98 Aligned_cols=32 Identities=22% Similarity=0.597 Sum_probs=24.1
Q ss_pred cCCCCCceeeecccccCC-CcccCCCCCCceeeeC
Q 025946 163 SCPNCGNDFQIFKSTLND-ELQLCPYCSQPFSVVD 196 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~-d~iqCPnCGE~L~Vd~ 196 (245)
-||.|+..+..- .|.. ...+||-||..+..-.
T Consensus 20 ~C~eCd~~~~~P--~l~~~q~A~CPRC~~~l~~~~ 52 (418)
T COG2995 20 LCPECDMLVSLP--RLDSGQSAYCPRCGHTLTRGG 52 (418)
T ss_pred cCCCCCceeccc--cCCCCCcccCCCCCCccccCC
Confidence 799999887762 3444 5789999999986443
No 362
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=49.65 E-value=10 Score=33.35 Aligned_cols=16 Identities=31% Similarity=0.769 Sum_probs=12.9
Q ss_pred CCcccCCCCCCceeee
Q 025946 180 DELQLCPYCSQPFSVV 195 (245)
Q Consensus 180 ~d~iqCPnCGE~L~Vd 195 (245)
+..++||.|++.+..+
T Consensus 3 ~k~~~CPvC~~~F~~~ 18 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTK 18 (214)
T ss_pred CCceECCCCCCeeeee
Confidence 4689999999887654
No 363
>TIGR00630 uvra excinuclease ABC, A subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=49.38 E-value=8 Score=41.23 Aligned_cols=38 Identities=24% Similarity=0.595 Sum_probs=28.9
Q ss_pred cCCCCCceeeecc---cccCCCcccCCCC---CCceeeeCCeeE
Q 025946 163 SCPNCGNDFQIFK---STLNDELQLCPYC---SQPFSVVDDKFV 200 (245)
Q Consensus 163 tCPnCG~eF~~~e---d~Ln~d~iqCPnC---GE~L~Vd~~~F~ 200 (245)
.||.||.+|...+ ..+|...--||.| |....+|.+...
T Consensus 252 ~c~~~g~~~~~~~~~~FSfNsp~G~Cp~C~G~G~~~~~d~~~li 295 (924)
T TIGR00630 252 ACPECGFSLPELEPRLFSFNSPYGACPECSGLGIKQEFDPDLII 295 (924)
T ss_pred cCcccCcccCcCChhhcCCCCCcCCCCCCccceeeeecCHHHcC
Confidence 8999999988422 2367778899999 888877766555
No 364
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=49.12 E-value=8 Score=42.54 Aligned_cols=23 Identities=30% Similarity=0.809 Sum_probs=19.2
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
.|-.||+.|.+ ++-.||+||..-
T Consensus 696 rC~dcg~q~~~-------~~~~cP~Cgs~~ 718 (1187)
T COG1110 696 RCRDCGEQFVD-------SEDKCPRCGSRN 718 (1187)
T ss_pred HHhhcCceecc-------ccccCCCCCCcc
Confidence 79999999998 444899999843
No 365
>PF11290 DUF3090: Protein of unknown function (DUF3090); InterPro: IPR021441 This family of proteins with unknown function appears to be restricted to Actinobacteria.
Probab=49.09 E-value=6.8 Score=34.64 Aligned_cols=20 Identities=20% Similarity=0.592 Sum_probs=12.4
Q ss_pred cCCCcccCCCCCCceeeeCCe
Q 025946 178 LNDELQLCPYCSQPFSVVDDK 198 (245)
Q Consensus 178 Ln~d~iqCPnCGE~L~Vd~~~ 198 (245)
.+.+--.||.||+|+..+ ||
T Consensus 150 VaAGRP~CPlCg~PlDP~-GH 169 (171)
T PF11290_consen 150 VAAGRPPCPLCGEPLDPE-GH 169 (171)
T ss_pred HhCCCCCCCCCCCCCCCC-CC
Confidence 344566777777776554 44
No 366
>TIGR01374 soxD sarcosine oxidase, delta subunit family, heterotetrameric form. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate. The enzyme is known in monomeric and heterotetrameric (alpha,beta,gamma,delta) form
Probab=49.01 E-value=7.4 Score=30.84 Aligned_cols=36 Identities=17% Similarity=0.517 Sum_probs=21.6
Q ss_pred ccCCCCCCceeeeCCeeEEeccccc----cccccccccccccC
Q 025946 183 QLCPYCSQPFSVVDDKFVRESVRFS----NESTTFGQAFSDFF 221 (245)
Q Consensus 183 iqCPnCGE~L~Vd~~~F~R~~~~f~----~~~~~~~~af~~~~ 221 (245)
|.||+|| +-++.+|.--+.--- ..+....++|.+|.
T Consensus 2 I~CP~CG---~R~~~EF~y~G~A~~~rP~~~~~~sd~~W~~Yl 41 (84)
T TIGR01374 2 IPCPYCG---PRPEEEFTYGGDAHIVRPADPAAASDEEWEDYL 41 (84)
T ss_pred ccCCCCC---CccHhhEeccceecccCCCCCCcCCHHHHHHhc
Confidence 6899999 477888855543222 22333346777753
No 367
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=48.94 E-value=10 Score=39.66 Aligned_cols=27 Identities=30% Similarity=0.748 Sum_probs=16.1
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
.||+|...++--+ ......|.+||-.-
T Consensus 446 ~Cp~Cd~~lt~H~---~~~~L~CH~Cg~~~ 472 (730)
T COG1198 446 ECPNCDSPLTLHK---ATGQLRCHYCGYQE 472 (730)
T ss_pred cCCCCCcceEEec---CCCeeEeCCCCCCC
Confidence 5666665554411 11588888888763
No 368
>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=48.75 E-value=11 Score=25.35 Aligned_cols=18 Identities=28% Similarity=0.599 Sum_probs=12.2
Q ss_pred ccCCCCCCceeeeCCeeE
Q 025946 183 QLCPYCSQPFSVVDDKFV 200 (245)
Q Consensus 183 iqCPnCGE~L~Vd~~~F~ 200 (245)
..||.||..+....+++-
T Consensus 2 ~~CP~Cg~~lv~r~~k~g 19 (39)
T PF01396_consen 2 EKCPKCGGPLVLRRGKKG 19 (39)
T ss_pred cCCCCCCceeEEEECCCC
Confidence 468888877776666554
No 369
>TIGR00847 ccoS cytochrome oxidase maturation protein, cbb3-type. CcoS from Rhodobacter capsulatus has been shown essential for incorporation of redox-active prosthetic groups (heme, Cu) into cytochrome cbb(3) oxidase. FixS of Bradyrhizobium japonicum appears to have the same function. Members of this family are found so far in organisms with a cbb3-type cytochrome oxidase, including Neisseria meningitidis, Helicobacter pylori, Campylobacter jejuni, Caulobacter crescentus, Bradyrhizobium japonicum, and Rhodobacter capsulatus.
Probab=48.70 E-value=25 Score=25.48 Aligned_cols=31 Identities=23% Similarity=0.404 Sum_probs=18.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCcceec
Q 025946 132 AIVSIWLLAVIVPIVGFGAFLWWASRDIVQD 162 (245)
Q Consensus 132 ~~~~L~LlllllPIl~~~Gf~WWl~rnLIE~ 162 (245)
++..++.+-+++=++++++|.|=++..-+++
T Consensus 3 il~~LIpiSl~l~~~~l~~f~Wavk~GQfDD 33 (51)
T TIGR00847 3 ILTILIPISLLLGGVGLVAFLWSLKSGQYDD 33 (51)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHccCCCCC
Confidence 4455566666666677667775555554444
No 370
>PRK14873 primosome assembly protein PriA; Provisional
Probab=48.36 E-value=12 Score=38.48 Aligned_cols=20 Identities=25% Similarity=0.861 Sum_probs=13.9
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceee
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSV 194 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~V 194 (245)
.|..||+ ...||+|+-+|.+
T Consensus 385 ~C~~Cg~------------~~~C~~C~~~L~~ 404 (665)
T PRK14873 385 ACARCRT------------PARCRHCTGPLGL 404 (665)
T ss_pred EhhhCcC------------eeECCCCCCceeE
Confidence 6777773 4567777777766
No 371
>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=48.33 E-value=16 Score=24.81 Aligned_cols=25 Identities=28% Similarity=0.653 Sum_probs=16.2
Q ss_pred ccCCCCCce-eeecccccCC-CcccCCCCCC
Q 025946 162 DSCPNCGND-FQIFKSTLND-ELQLCPYCSQ 190 (245)
Q Consensus 162 ~tCPnCG~e-F~~~ed~Ln~-d~iqCPnCGE 190 (245)
..||.||.+ .+- ++. ..-.|-.|+.
T Consensus 19 ~~CP~Cg~~~~~~----~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGSTKHYR----LKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCeeeEE----eCCCCeEECCCCCC
Confidence 468888874 333 344 6777877764
No 372
>PRK00133 metG methionyl-tRNA synthetase; Reviewed
Probab=48.32 E-value=6.8 Score=39.55 Aligned_cols=12 Identities=42% Similarity=1.329 Sum_probs=6.8
Q ss_pred ceeccCCCCCce
Q 025946 159 IVQDSCPNCGND 170 (245)
Q Consensus 159 LIE~tCPnCG~e 170 (245)
+++.+||.|+.+
T Consensus 137 ~v~g~cp~C~~~ 148 (673)
T PRK00133 137 FVKGTCPKCGAE 148 (673)
T ss_pred heecccCCCCCc
Confidence 344466666655
No 373
>cd03530 Rieske_NirD_small_Bacillus Small subunit of nitrite reductase (NirD) family, Rieske domain; composed of proteins similar to the Bacillus subtilis small subunit of assimilatory nitrite reductase containing a Rieske domain. The Rieske domain is a [2Fe-2S] cluster binding domain involved in electron transfer. Assimilatory nitrate and nitrite reductases convert nitrate through nitrite to ammonium.
Probab=48.09 E-value=15 Score=27.35 Aligned_cols=38 Identities=16% Similarity=0.427 Sum_probs=29.1
Q ss_pred ceeccCCCCCceeeecccccCCCcccCCCCCCceeeeCCe
Q 025946 159 IVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDK 198 (245)
Q Consensus 159 LIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~ 198 (245)
-++..||.-|..+.. ..+.++.++||+=|..|.+++|+
T Consensus 37 A~~~~CpH~g~~L~~--g~~~~~~i~Cp~Hg~~Fdl~~G~ 74 (98)
T cd03530 37 ALENRCPHKGGPLSE--GIVHGEYVTCPLHNWVIDLETGE 74 (98)
T ss_pred EEcCcCCCCCCCccC--CEEcCCEEECCCCCCEEECCCCC
Confidence 355699999987653 23456789999999999988775
No 374
>PRK09401 reverse gyrase; Reviewed
Probab=48.03 E-value=8.2 Score=42.08 Aligned_cols=23 Identities=35% Similarity=0.871 Sum_probs=18.7
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
.|+.||+.|.+ ..-.||.||...
T Consensus 680 ~c~~~g~~f~~-------~~~~~~~c~~~~ 702 (1176)
T PRK09401 680 RCRDCGYQFTD-------ESDKCPRCGSTN 702 (1176)
T ss_pred ccccccccccc-------cccccccccccc
Confidence 69999999988 334999999654
No 375
>smart00532 LIGANc Ligase N family.
Probab=47.97 E-value=10 Score=37.10 Aligned_cols=13 Identities=23% Similarity=0.605 Sum_probs=7.0
Q ss_pred cccCCCCCCceee
Q 025946 182 LQLCPYCSQPFSV 194 (245)
Q Consensus 182 ~iqCPnCGE~L~V 194 (245)
|..||.||+++..
T Consensus 399 P~~CP~C~s~l~~ 411 (441)
T smart00532 399 PTHCPSCGSELVR 411 (441)
T ss_pred CCCCCCCCCEeEe
Confidence 4555555555543
No 376
>PRK07217 replication factor A; Reviewed
Probab=47.73 E-value=10 Score=36.25 Aligned_cols=20 Identities=25% Similarity=0.572 Sum_probs=16.5
Q ss_pred cCCC--CCceeeecccccCCCcccCCCCCCc
Q 025946 163 SCPN--CGNDFQIFKSTLNDELQLCPYCSQP 191 (245)
Q Consensus 163 tCPn--CG~eF~~~ed~Ln~d~iqCPnCGE~ 191 (245)
.||. |+...+. -+||.||++
T Consensus 190 rCP~~~C~Rvl~~---------g~C~~HG~v 211 (311)
T PRK07217 190 RCPEEDCTRVLQN---------GRCSEHGKV 211 (311)
T ss_pred cCCccccCccccC---------CCCCCCCCc
Confidence 7999 9988643 599999974
No 377
>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=47.68 E-value=14 Score=25.08 Aligned_cols=29 Identities=31% Similarity=0.864 Sum_probs=17.6
Q ss_pred eccCCCCCc--eeeecccccCCCcccCCCCCC
Q 025946 161 QDSCPNCGN--DFQIFKSTLNDELQLCPYCSQ 190 (245)
Q Consensus 161 E~tCPnCG~--eF~~~ed~Ln~d~iqCPnCGE 190 (245)
...||+||- .|. +++.-..+...|-.||.
T Consensus 3 ~~pCP~CGG~DrFr-~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 3 HGPCPNCGGSDRFR-FDDKDGRGTWFCSVCGA 33 (37)
T ss_pred ccCCCCCCCccccc-cccCCCCcCEEeCCCCC
Confidence 357999986 444 33322236778888863
No 378
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=47.51 E-value=15 Score=24.76 Aligned_cols=30 Identities=33% Similarity=0.827 Sum_probs=17.6
Q ss_pred cCCCCCceeeecccc-cC--CC----cccCCCCCCce
Q 025946 163 SCPNCGNDFQIFKST-LN--DE----LQLCPYCSQPF 192 (245)
Q Consensus 163 tCPnCG~eF~~~ed~-Ln--~d----~iqCPnCGE~L 192 (245)
.||+||..-..+-.+ .. ++ -.+|.+||..+
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w 38 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRW 38 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEe
Confidence 699999765543221 11 11 45788998654
No 379
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=47.49 E-value=12 Score=32.84 Aligned_cols=21 Identities=24% Similarity=0.793 Sum_probs=16.8
Q ss_pred ccCCCCCCceeeeCCeeEEec
Q 025946 183 QLCPYCSQPFSVVDDKFVRES 203 (245)
Q Consensus 183 iqCPnCGE~L~Vd~~~F~R~~ 203 (245)
.+||.|+++|.++++.+..+.
T Consensus 3 ~~CP~C~~~l~~~~~~~~C~~ 23 (272)
T PRK11088 3 YQCPLCHQPLTLEENSWICPQ 23 (272)
T ss_pred ccCCCCCcchhcCCCEEEcCC
Confidence 589999999988877666554
No 380
>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=47.41 E-value=7 Score=37.33 Aligned_cols=31 Identities=26% Similarity=0.695 Sum_probs=16.8
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceeee
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVV 195 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd 195 (245)
.|+.|+..-.. ..+...+..||+||+.+.+.
T Consensus 242 ~C~~C~~~~~~--~~~~~~~~~c~~cg~~~~~~ 272 (377)
T PF02005_consen 242 YCPSCGYREEV--KGLQKLKSKCPECGSKLHIS 272 (377)
T ss_dssp EETTT--EECC--T-GCC--CEETTT-SCCCEE
T ss_pred ECCCccccccc--cCccccCCcCCCCCCcccee
Confidence 89999864222 11222348999999887653
No 381
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=47.11 E-value=4.4 Score=38.81 Aligned_cols=34 Identities=24% Similarity=0.774 Sum_probs=23.4
Q ss_pred eccCCCCCceeeecccc---cCC----------------------CcccCCCCCCceee
Q 025946 161 QDSCPNCGNDFQIFKST---LND----------------------ELQLCPYCSQPFSV 194 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~---Ln~----------------------d~iqCPnCGE~L~V 194 (245)
++.|-+||+.+..++|. +++ ..+.||||.|.++.
T Consensus 224 d~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivGKkqtCPYCKekVdl 282 (328)
T KOG1734|consen 224 DSVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVGKKQTCPYCKEKVDL 282 (328)
T ss_pred cchhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeecCCCCCchHHHHhhH
Confidence 44899999998875421 211 24689999988754
No 382
>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=46.94 E-value=8.8 Score=26.12 Aligned_cols=25 Identities=32% Similarity=0.994 Sum_probs=13.8
Q ss_pred cCCCCCceeeecccccCC--CcccCCCCCCcee
Q 025946 163 SCPNCGNDFQIFKSTLND--ELQLCPYCSQPFS 193 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~--d~iqCPnCGE~L~ 193 (245)
.|..||+..-. +++ ++..| |||+.+
T Consensus 8 kC~~CGniVev----~~~g~g~lvC--CGe~M~ 34 (36)
T PF06397_consen 8 KCEHCGNIVEV----VHDGGGPLVC--CGEPME 34 (36)
T ss_dssp E-TTT--EEEE----EE--SS-EEE--TTEE-E
T ss_pred EccCCCCEEEE----EECCCCCEEe--CCcccc
Confidence 79999988776 454 46777 787764
No 383
>KOG4272 consensus Predicted GTP-binding protein [General function prediction only]
Probab=46.88 E-value=11 Score=33.23 Aligned_cols=32 Identities=25% Similarity=0.312 Sum_probs=25.8
Q ss_pred hHHHHHHHHHHHHHhcccchhHHHHHHHHHHH
Q 025946 108 LGNLALAIGLTYFSMTGQLGWVLDAIVSIWLL 139 (245)
Q Consensus 108 lgn~l~~l~l~~LL~T~gLgWLvd~~~~L~Ll 139 (245)
||-|++.++=++-|+-.+..||||.+++.+..
T Consensus 120 LGy~~~glgKl~tlGGlgIw~lVDiiLI~lg~ 151 (164)
T KOG4272|consen 120 LGYWALGLGKLFTLGGLGIWWLVDIILISLGY 151 (164)
T ss_pred eCchHHhHhhhhccccchhHHHHHHHHHHhcc
Confidence 67788888888888888899999998776543
No 384
>PRK09965 3-phenylpropionate dioxygenase ferredoxin subunit; Provisional
Probab=46.72 E-value=16 Score=28.14 Aligned_cols=39 Identities=21% Similarity=0.437 Sum_probs=29.5
Q ss_pred eeccCCCCCceeeecccccCC-CcccCCCCCCceeeeCCeeE
Q 025946 160 VQDSCPNCGNDFQIFKSTLND-ELQLCPYCSQPFSVVDDKFV 200 (245)
Q Consensus 160 IE~tCPnCG~eF~~~ed~Ln~-d~iqCPnCGE~L~Vd~~~F~ 200 (245)
++..||.=|..+.. ..+.+ +.++||.-|..|.+++|+=.
T Consensus 38 ~~~~CpH~g~~L~~--G~~~~~~~i~Cp~Hg~~Fd~~tG~~~ 77 (106)
T PRK09965 38 IDDRCSHGNASLSE--GYLEDDATVECPLHAASFCLRTGKAL 77 (106)
T ss_pred EeCcCCCCCCCCCc--eEECCCCEEEcCCCCCEEEcCCCCee
Confidence 45699999987742 33455 57999999999998877754
No 385
>TIGR02611 conserved hypothetical protein TIGR02611. Members of this family are Actinobacterial putative proteins of about 150 amino acids in length with three apparent transmembrane helix and an unusual motif with consensus sequence PGPGW.
Probab=46.60 E-value=36 Score=28.74 Aligned_cols=28 Identities=18% Similarity=0.409 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHhcccchhHHHHHHHHHH
Q 025946 109 GNLALAIGLTYFSMTGQLGWVLDAIVSIWL 138 (245)
Q Consensus 109 gn~l~~l~l~~LL~T~gLgWLvd~~~~L~L 138 (245)
|-.++++++ .+++.+|.||++ .+++|.+
T Consensus 32 G~~~~~~Gi-~ml~lPGpG~l~-i~iGl~i 59 (121)
T TIGR02611 32 GWVVLIVGI-ITIPLPGPGWLT-IFIGLAI 59 (121)
T ss_pred HHHHHHHHH-HHhccCCchHHH-HHHHHHH
Confidence 334444444 445888999997 4444443
No 386
>PRK14526 adenylate kinase; Provisional
Probab=46.40 E-value=15 Score=31.93 Aligned_cols=31 Identities=26% Similarity=0.649 Sum_probs=20.9
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
..||.||..+-.. ..=-+.+..|+.||+.+.
T Consensus 123 ~~~~~~g~~y~~~-~~pp~~~~~~~~~~~~l~ 153 (211)
T PRK14526 123 RICKSCNNIFNIY-TLPTKEKGICDVCKGDLY 153 (211)
T ss_pred CcccccCCccccc-cCCCCccCcCCCCCCeee
Confidence 4899999777651 111123678999998765
No 387
>COG4307 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.16 E-value=6.8 Score=37.67 Aligned_cols=28 Identities=29% Similarity=0.702 Sum_probs=22.9
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceeeeCC
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDD 197 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~ 197 (245)
.||+||....- +...|-.||..|-+..|
T Consensus 5 hC~~CgQ~v~F-------eN~~C~~Cg~~Lg~~~G 32 (349)
T COG4307 5 HCPNCGQRVAF-------ENSACLSCGSALGFSLG 32 (349)
T ss_pred cCCCCCCeeee-------cchHHHhhhhHhhhccc
Confidence 79999998877 68899999998865544
No 388
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=45.89 E-value=11 Score=35.66 Aligned_cols=10 Identities=40% Similarity=1.102 Sum_probs=5.1
Q ss_pred cCCCCCceee
Q 025946 163 SCPNCGNDFQ 172 (245)
Q Consensus 163 tCPnCG~eF~ 172 (245)
.|+.||+.|.
T Consensus 189 ~C~iCGKaFS 198 (279)
T KOG2462|consen 189 ECGICGKAFS 198 (279)
T ss_pred cccccccccc
Confidence 4555555544
No 389
>COG4323 Predicted membrane protein [Function unknown]
Probab=45.67 E-value=20 Score=29.51 Aligned_cols=48 Identities=19% Similarity=0.517 Sum_probs=33.5
Q ss_pred hhHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcceeccCCCC
Q 025946 107 ILGNLALAIGLTYFSMTGQLGWVLDAIVSIWLLAVIVPIVGFGAFLWWASRDIVQDSCPNC 167 (245)
Q Consensus 107 ~lgn~l~~l~l~~LL~T~gLgWLvd~~~~L~LlllllPIl~~~Gf~WWl~rnLIE~tCPnC 167 (245)
++|..|.+..+..+..++...| +|.+|+++ -||. |++-=..|-+=|..
T Consensus 33 ~vGs~LvlvcL~~~Vf~~~w~w-----------llAapv~G-YgFA-WvGHFvFEKNRPAT 80 (105)
T COG4323 33 VVGSSLVLVCLVLGVFRGDWRW-----------LLAAPVIG-YGFA-WVGHFVFEKNRPAT 80 (105)
T ss_pred hhhhHHHHHHHHHHHHhcchHH-----------HHHhhhhc-ccce-eeeeeeeecCCCcc
Confidence 3556665555555555555554 56789999 8999 99988888877765
No 390
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=45.55 E-value=13 Score=36.32 Aligned_cols=30 Identities=27% Similarity=0.408 Sum_probs=18.2
Q ss_pred cCCCCCceeeecccc------------cCCCcccCCCCCCce
Q 025946 163 SCPNCGNDFQIFKST------------LNDELQLCPYCSQPF 192 (245)
Q Consensus 163 tCPnCG~eF~~~ed~------------Ln~d~iqCPnCGE~L 192 (245)
.|+.||+.+--.+.. =..+.-.||.||.+-
T Consensus 427 ~c~~c~~~yd~~~g~~~~~~~~gt~~~~lp~~~~cp~c~~~k 468 (479)
T PRK05452 427 QCSVCQWIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSLGK 468 (479)
T ss_pred EECCCCeEECCCCCCcccCCCCCCChhhCCCCCcCcCCCCcH
Confidence 799999654432110 011356999999763
No 391
>PRK14529 adenylate kinase; Provisional
Probab=45.35 E-value=14 Score=32.96 Aligned_cols=29 Identities=24% Similarity=0.405 Sum_probs=20.7
Q ss_pred ccCCCCCceeeecccccCCC----cccCCCCCCcee
Q 025946 162 DSCPNCGNDFQIFKSTLNDE----LQLCPYCSQPFS 193 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d----~iqCPnCGE~L~ 193 (245)
+.||.||..++.. ..+. ...|..||++|.
T Consensus 127 ~~c~~~~~~~~~~---~~~~p~~~~~~cd~~~~~l~ 159 (223)
T PRK14529 127 RLCKNDNNHPNNI---FIDAIKPDGDVCRVCGGELS 159 (223)
T ss_pred ccccccCCccccc---ccCCCcccCCcCcCcCCccc
Confidence 4899999888772 2221 237999999875
No 392
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=45.23 E-value=9.7 Score=33.21 Aligned_cols=38 Identities=21% Similarity=0.513 Sum_probs=22.2
Q ss_pred cCCCCCceeeecccccCCC---cccCCCCCCceeeeCCeeEEec
Q 025946 163 SCPNCGNDFQIFKSTLNDE---LQLCPYCSQPFSVVDDKFVRES 203 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d---~iqCPnCGE~L~Vd~~~F~R~~ 203 (245)
.|=+||.+....=....++ -.+||+||+.. |.-.+-|.
T Consensus 2 iCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~va---DkYiE~d~ 42 (208)
T PF04161_consen 2 ICIECGHPVKSLYRQYSPGNIRLTKCPNCGKVA---DKYIEYDN 42 (208)
T ss_pred EeccCCCcchhhhhccCCCcEEEeeccccCCcc---cceecccc
Confidence 5889999853211112222 57999999765 44444443
No 393
>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=45.16 E-value=8.4 Score=30.82 Aligned_cols=21 Identities=29% Similarity=0.754 Sum_probs=15.1
Q ss_pred HHh--cCcceec------cCCCCCceeee
Q 025946 153 WWA--SRDIVQD------SCPNCGNDFQI 173 (245)
Q Consensus 153 WWl--~rnLIE~------tCPnCG~eF~~ 173 (245)
|++ +..++.. .||+||..++.
T Consensus 19 ~el~~G~~~IvIknVPa~~C~~CGe~y~~ 47 (89)
T TIGR03829 19 WELPDGTKAIEIKETPSISCSHCGMEYQD 47 (89)
T ss_pred EEecCCceEEEEecCCcccccCCCcEeec
Confidence 566 3355554 89999988877
No 394
>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=45.12 E-value=14 Score=22.36 Aligned_cols=31 Identities=23% Similarity=0.566 Sum_probs=18.0
Q ss_pred cCCCCCceeeecccccCC-C------cccCCCCCCcee
Q 025946 163 SCPNCGNDFQIFKSTLND-E------LQLCPYCSQPFS 193 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~-d------~iqCPnCGE~L~ 193 (245)
.|+.|++.++..+..+.. + =..|..|+++|+
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L~ 38 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPLG 38 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcCc
Confidence 478888877664222221 2 256777777763
No 395
>PRK05333 NAD-dependent deacetylase; Provisional
Probab=45.00 E-value=12 Score=33.87 Aligned_cols=11 Identities=27% Similarity=0.785 Sum_probs=8.7
Q ss_pred ccCCCCCCcee
Q 025946 183 QLCPYCSQPFS 193 (245)
Q Consensus 183 iqCPnCGE~L~ 193 (245)
-.||.||.++.
T Consensus 180 P~C~~Cgg~lr 190 (285)
T PRK05333 180 PACPACGGILK 190 (285)
T ss_pred CCCCCCCCccc
Confidence 46999998764
No 396
>PF01307 Plant_vir_prot: Plant viral movement protein; InterPro: IPR001896 This family of membrane/coat proteins are found in a number of different ssRNA plant virus families that include Potexvirus, Hordeivirus and Carlavirus.
Probab=44.80 E-value=23 Score=28.65 Aligned_cols=18 Identities=28% Similarity=0.577 Sum_probs=11.0
Q ss_pred HHHHHHhcCcceeccCCCCC
Q 025946 149 GAFLWWASRDIVQDSCPNCG 168 (245)
Q Consensus 149 ~Gf~WWl~rnLIE~tCPnCG 168 (245)
....+|-.+ ....|+.|+
T Consensus 87 ~~~~~~~~~--~~~~C~~C~ 104 (104)
T PF01307_consen 87 YLSSRFSSR--RRRRCPHCS 104 (104)
T ss_pred HHhhcccCC--CCCcCCCCC
Confidence 445545444 566888885
No 397
>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=44.70 E-value=11 Score=20.55 Aligned_cols=11 Identities=45% Similarity=1.289 Sum_probs=6.0
Q ss_pred cCCCCCceeee
Q 025946 163 SCPNCGNDFQI 173 (245)
Q Consensus 163 tCPnCG~eF~~ 173 (245)
.||.|+++|..
T Consensus 2 ~C~~C~~~~~~ 12 (24)
T PF13894_consen 2 QCPICGKSFRS 12 (24)
T ss_dssp E-SSTS-EESS
T ss_pred CCcCCCCcCCc
Confidence 47777777654
No 398
>COG3024 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.53 E-value=11 Score=29.00 Aligned_cols=16 Identities=25% Similarity=0.600 Sum_probs=11.8
Q ss_pred cceeccCCCCCceeee
Q 025946 158 DIVQDSCPNCGNDFQI 173 (245)
Q Consensus 158 nLIE~tCPnCG~eF~~ 173 (245)
+.+++.||.||+...-
T Consensus 4 ~~~~v~CP~Cgkpv~w 19 (65)
T COG3024 4 LRITVPCPTCGKPVVW 19 (65)
T ss_pred ccccccCCCCCCcccc
Confidence 4567788888887655
No 399
>KOG2462 consensus C2H2-type Zn-finger protein [Transcription]
Probab=44.53 E-value=14 Score=34.91 Aligned_cols=30 Identities=23% Similarity=0.769 Sum_probs=18.2
Q ss_pred cCCCCCceeeeccc----------ccCCCcccCCCCCCce
Q 025946 163 SCPNCGNDFQIFKS----------TLNDELQLCPYCSQPF 192 (245)
Q Consensus 163 tCPnCG~eF~~~ed----------~Ln~d~iqCPnCGE~L 192 (245)
.||.||+.+..... .-.+-.-.||+||..+
T Consensus 132 ~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~Y 171 (279)
T KOG2462|consen 132 KCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVY 171 (279)
T ss_pred eccccccccccccccchhhcccccccccccccCCCCCcee
Confidence 78888877665321 1113456788886654
No 400
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=44.51 E-value=15 Score=22.82 Aligned_cols=22 Identities=27% Similarity=0.655 Sum_probs=15.7
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCc
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQP 191 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~ 191 (245)
+||.|...-.. ....|-.||.+
T Consensus 6 ~C~~C~~~N~~-------~~~~C~~C~~~ 27 (30)
T PF00641_consen 6 KCPSCTFMNPA-------SRSKCVACGAP 27 (30)
T ss_dssp EETTTTEEEES-------SSSB-TTT--B
T ss_pred cCCCCcCCchH-------HhhhhhCcCCC
Confidence 79999977666 78889999875
No 401
>COG1328 NrdD Oxygen-sensitive ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]
Probab=44.51 E-value=11 Score=39.33 Aligned_cols=27 Identities=22% Similarity=0.454 Sum_probs=18.2
Q ss_pred cceeccCCCCCceeeecccccCCCcccCCCCCCc
Q 025946 158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQP 191 (245)
Q Consensus 158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~ 191 (245)
+.--+.|+.||+..-. ....||.||..
T Consensus 638 n~~i~~C~~cg~~~~~-------~~~~Cp~CG~~ 664 (700)
T COG1328 638 TTPISVCNRCGYSGEG-------LRTRCPKCGSE 664 (700)
T ss_pred CCCceeeccCCccccc-------ccccCCCCCCc
Confidence 3444689999976443 22339999965
No 402
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=44.46 E-value=9.3 Score=37.45 Aligned_cols=23 Identities=30% Similarity=0.690 Sum_probs=20.4
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
.||+|..+... =|+.||-|...|
T Consensus 310 ~CP~CktkVCs-------LPi~CP~Csl~L 332 (421)
T COG5151 310 ECPVCKTKVCS-------LPISCPICSLQL 332 (421)
T ss_pred eCCcccceeec-------CCccCcchhHHH
Confidence 79999999998 499999998755
No 403
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.12 E-value=9.4 Score=32.49 Aligned_cols=31 Identities=23% Similarity=0.788 Sum_probs=20.9
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCCCceee
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSV 194 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~V 194 (245)
..||+||.- +.++ -+-+..-.|-.||+.+..
T Consensus 22 grCP~CGeG-rLF~-gFLK~~p~C~aCG~dyg~ 52 (126)
T COG5349 22 GRCPRCGEG-RLFR-GFLKVVPACEACGLDYGF 52 (126)
T ss_pred CCCCCCCCc-hhhh-hhcccCchhhhccccccC
Confidence 389999842 2221 245566789999998854
No 404
>KOG3134 consensus Predicted membrane protein [Function unknown]
Probab=43.94 E-value=7 Score=35.99 Aligned_cols=30 Identities=23% Similarity=0.711 Sum_probs=19.4
Q ss_pred cCCCCCceeeecccccCCC---cccCCCCCCce
Q 025946 163 SCPNCGNDFQIFKSTLNDE---LQLCPYCSQPF 192 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d---~iqCPnCGE~L 192 (245)
.|-+||.+...+--..+++ -.+||||+|+.
T Consensus 2 ~CVeCg~~vksLy~~Ys~g~irlt~C~nC~e~v 34 (225)
T KOG3134|consen 2 RCVECGSEVKSLYTQYSPGNIRLTKCPNCQEVV 34 (225)
T ss_pred cccccCchHHHHHHhcCCCcEEEeeCCchhhHH
Confidence 5889997754421112333 56899999976
No 405
>TIGR03847 conserved hypothetical protein. The conserved hypothetical protein described here occurs as part of the trio of uncharacterized proteins common in the Actinobacteria.
Probab=43.92 E-value=8.9 Score=34.19 Aligned_cols=11 Identities=36% Similarity=1.102 Sum_probs=5.0
Q ss_pred cccCCCCCCce
Q 025946 182 LQLCPYCSQPF 192 (245)
Q Consensus 182 ~iqCPnCGE~L 192 (245)
--.||.||+|+
T Consensus 156 RP~CPlCg~Pl 166 (177)
T TIGR03847 156 RPPCPLCGRPI 166 (177)
T ss_pred CCCCCCCCCCC
Confidence 33444444444
No 406
>PF05265 DUF723: Protein of unknown function (DUF723); InterPro: IPR007929 This family contains several uncharacterised proteins from Neisseria meningitidis. These proteins may have a role in DNA binding.
Probab=43.82 E-value=16 Score=27.48 Aligned_cols=30 Identities=27% Similarity=0.416 Sum_probs=23.6
Q ss_pred eeccCCCCCceeeecccccCCCcccCCCCC
Q 025946 160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCS 189 (245)
Q Consensus 160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCG 189 (245)
+...||.=|...+...+.+.++..=||.||
T Consensus 31 vtI~CP~HG~~~~s~~~~~~~sk~GCP~Cg 60 (60)
T PF05265_consen 31 VTIRCPKHGNFTCSTFNSFIKSKHGCPECG 60 (60)
T ss_pred eEEECCCCCcEEeccHHhhhhhccCCCCCC
Confidence 445899999888886666666777899997
No 407
>PF15616 TerY-C: TerY-C metal binding domain
Probab=43.67 E-value=15 Score=31.12 Aligned_cols=11 Identities=27% Similarity=0.866 Sum_probs=8.6
Q ss_pred cccCCCCCCce
Q 025946 182 LQLCPYCSQPF 192 (245)
Q Consensus 182 ~iqCPnCGE~L 192 (245)
.--||+||..+
T Consensus 77 ~PgCP~CGn~~ 87 (131)
T PF15616_consen 77 APGCPHCGNQY 87 (131)
T ss_pred CCCCCCCcChh
Confidence 36799999874
No 408
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=43.57 E-value=25 Score=34.99 Aligned_cols=30 Identities=27% Similarity=0.464 Sum_probs=23.5
Q ss_pred eccCCCCCceeeecccccCCCcccCCCCCCceeeeC
Q 025946 161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVD 196 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~ 196 (245)
.+.|..|.+...- +++..||-||.++.+..
T Consensus 220 ~~~C~~C~~~~~~------~~~~~CpRC~~~Ly~rr 249 (418)
T COG2995 220 LRSCLCCHYILPH------DAEPRCPRCGSKLYVRR 249 (418)
T ss_pred ceecccccccCCH------hhCCCCCCCCChhhccC
Confidence 3489999977665 27899999999996543
No 409
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=43.41 E-value=8.9 Score=33.63 Aligned_cols=16 Identities=31% Similarity=0.910 Sum_probs=13.6
Q ss_pred ccCCCCCceeeecccc
Q 025946 162 DSCPNCGNDFQIFKST 177 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~ 177 (245)
+.||+||..|+.+|-+
T Consensus 29 ReC~~C~~RFTTfE~~ 44 (156)
T COG1327 29 RECLECGERFTTFERA 44 (156)
T ss_pred hcccccccccchhhee
Confidence 3899999999997665
No 410
>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=43.41 E-value=14 Score=28.39 Aligned_cols=25 Identities=20% Similarity=0.562 Sum_probs=20.3
Q ss_pred cCCCCCCceeeeCCeeEEecccccc
Q 025946 184 LCPYCSQPFSVVDDKFVRESVRFSN 208 (245)
Q Consensus 184 qCPnCGE~L~Vd~~~F~R~~~~f~~ 208 (245)
.||+||..|...++.+.-..=.+..
T Consensus 2 fC~~Cg~~l~~~~~~~~C~~C~~~~ 26 (104)
T TIGR01384 2 FCPKCGSLMTPKNGVYVCPSCGYEK 26 (104)
T ss_pred CCcccCcccccCCCeEECcCCCCcc
Confidence 6999999999988888876666554
No 411
>PLN02610 probable methionyl-tRNA synthetase
Probab=43.29 E-value=8 Score=40.49 Aligned_cols=22 Identities=9% Similarity=-0.271 Sum_probs=12.3
Q ss_pred CccceeeccCCCCccccccCce
Q 025946 23 KNRTSCYSLTRPKIGSFQGNSC 44 (245)
Q Consensus 23 k~~~~~~~~~~~~~~~~~~~~~ 44 (245)
+++..+-++.-.-+|..|-+..
T Consensus 16 ~~~~~ITt~~pY~Ng~~HlGH~ 37 (801)
T PLN02610 16 KRNILITSALPYVNNVPHLGNI 37 (801)
T ss_pred CCCEEEeCCCCCCCCCcccchh
Confidence 4455555555555666665543
No 412
>PLN03086 PRLI-interacting factor K; Provisional
Probab=43.25 E-value=14 Score=37.85 Aligned_cols=27 Identities=30% Similarity=0.719 Sum_probs=13.4
Q ss_pred cCCC--CCceeeecccccCCCcccCCCCCCce
Q 025946 163 SCPN--CGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 163 tCPn--CG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
.||+ ||..|..- --+....||+||+.+
T Consensus 435 ~Cp~~~Cg~v~~r~---el~~H~~C~~Cgk~f 463 (567)
T PLN03086 435 VCPHDGCGIVLRVE---EAKNHVHCEKCGQAF 463 (567)
T ss_pred eCCcccccceeecc---ccccCccCCCCCCcc
Confidence 4664 66555431 112345666666655
No 413
>PRK14973 DNA topoisomerase I; Provisional
Probab=42.75 E-value=21 Score=38.35 Aligned_cols=16 Identities=13% Similarity=0.291 Sum_probs=11.0
Q ss_pred ccCCCCCCc--eeeeCCe
Q 025946 183 QLCPYCSQP--FSVVDDK 198 (245)
Q Consensus 183 iqCPnCGE~--L~Vd~~~ 198 (245)
..||.||.+ +.+..|+
T Consensus 636 ~~Cp~CG~p~~~~~r~Gr 653 (936)
T PRK14973 636 EVCPIHHLNHVRLIRKGA 653 (936)
T ss_pred CCCCCCCCCceEEeecCC
Confidence 469999984 4445565
No 414
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=42.74 E-value=12 Score=31.33 Aligned_cols=15 Identities=33% Similarity=0.853 Sum_probs=11.6
Q ss_pred CCCcccCCCCCCcee
Q 025946 179 NDELQLCPYCSQPFS 193 (245)
Q Consensus 179 n~d~iqCPnCGE~L~ 193 (245)
.-+...||.||++++
T Consensus 46 e~G~t~CP~Cg~~~e 60 (115)
T COG1885 46 EVGSTSCPKCGEPFE 60 (115)
T ss_pred ecccccCCCCCCccc
Confidence 336788999999873
No 415
>PF01921 tRNA-synt_1f: tRNA synthetases class I (K); InterPro: IPR002904 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and in a number of bacterial groups that include the alphaproteobacteria and spirochaetes[]. A refined crystal structures shows that the active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [].; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IRX_A.
Probab=42.69 E-value=15 Score=35.57 Aligned_cols=39 Identities=15% Similarity=0.167 Sum_probs=18.2
Q ss_pred CcceeccCCCCCceeee-ccccc-CCC--cccCCCCCCceeee
Q 025946 157 RDIVQDSCPNCGNDFQI-FKSTL-NDE--LQLCPYCSQPFSVV 195 (245)
Q Consensus 157 rnLIE~tCPnCG~eF~~-~ed~L-n~d--~iqCPnCGE~L~Vd 195 (245)
|--++..||+||+-.+. -.+.- ..+ .-+|+.||..-+++
T Consensus 170 y~Pf~piC~~cGri~tt~v~~~d~~~~~v~Y~c~~cG~~g~~~ 212 (360)
T PF01921_consen 170 YSPFLPICEKCGRIDTTEVTEYDPEGGTVTYRCEECGHEGEVD 212 (360)
T ss_dssp --SEEEEETTTEE--EEEEEEE--SSSEEEEE--TTS---EEE
T ss_pred eeeeeeeccccCCcccceeeEeecCCCEEEEEecCCCCEEEEe
Confidence 33566799999983332 11111 122 67899999976654
No 416
>PF13829 DUF4191: Domain of unknown function (DUF4191)
Probab=42.47 E-value=42 Score=30.77 Aligned_cols=34 Identities=21% Similarity=0.111 Sum_probs=15.9
Q ss_pred cchhHHHHHHHHHHHHHhcccchhHHHHHHHHHH
Q 025946 105 ARILGNLALAIGLTYFSMTGQLGWVLDAIVSIWL 138 (245)
Q Consensus 105 ~r~lgn~l~~l~l~~LL~T~gLgWLvd~~~~L~L 138 (245)
+-+++-++..+++.++++..-..|++-++++|.+
T Consensus 29 ~~ml~a~l~~~~v~v~ig~l~~~~~~~~i~gi~~ 62 (224)
T PF13829_consen 29 WLMLGAFLGPIAVFVLIGLLFGSWWYWLIIGILL 62 (224)
T ss_pred HHHHHHHHHHHHHHHHHHHHHccHHHHHHHHHHH
Confidence 3444444444444444444444555544444443
No 417
>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=42.44 E-value=10 Score=23.07 Aligned_cols=10 Identities=50% Similarity=1.477 Sum_probs=8.0
Q ss_pred cCCCCCceee
Q 025946 163 SCPNCGNDFQ 172 (245)
Q Consensus 163 tCPnCG~eF~ 172 (245)
.||.|++.|.
T Consensus 16 ~C~~C~k~F~ 25 (26)
T PF13465_consen 16 KCPYCGKSFS 25 (26)
T ss_dssp EESSSSEEES
T ss_pred CCCCCcCeeC
Confidence 7888888774
No 418
>PRK01642 cls cardiolipin synthetase; Reviewed
Probab=42.34 E-value=45 Score=32.44 Aligned_cols=29 Identities=21% Similarity=0.298 Sum_probs=20.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCccee
Q 025946 132 AIVSIWLLAVIVPIVGFGAFLWWASRDIVQ 161 (245)
Q Consensus 132 ~~~~L~LlllllPIl~~~Gf~WWl~rnLIE 161 (245)
+.++=+++++++|++++..+ |.++++...
T Consensus 33 ~~~aWl~~i~~~P~~G~~lY-~~fG~~~~~ 61 (483)
T PRK01642 33 GAIAWLLILYILPYVGIIAY-LLFGELYLG 61 (483)
T ss_pred HHHHHHHHHHHHHHHHHHHH-HhcCCChHh
Confidence 55666778999999995444 477876543
No 419
>PF12666 PrgI: PrgI family protein; InterPro: IPR024414 This family of bacterial proteins is functionally uncharacterised. Proteins in this family are typically between 116 and 146 amino acids in length. PrgI is found encoded on plasmids of Enterococcus faecalis, its function is not known.
Probab=41.76 E-value=58 Score=24.45 Aligned_cols=44 Identities=16% Similarity=0.006 Sum_probs=20.5
Q ss_pred CcchhHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHHHH
Q 025946 104 NARILGNLALAIGLTYFSMTGQLGWVLDAIVSIWLLAVIVPIVG 147 (245)
Q Consensus 104 ~~r~lgn~l~~l~l~~LL~T~gLgWLvd~~~~L~LlllllPIl~ 147 (245)
|.|=+.+++..+++++.+...--.++=..+..++.+++++|+.+
T Consensus 18 T~RQl~~l~~~~~~~~~~~~~~~~~l~~~~~~~~~i~~~~p~~~ 61 (93)
T PF12666_consen 18 TLRQLICLAIGALVGVGVYLLLWFFLGPDIASWIMIPIALPFAF 61 (93)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHHHH
Confidence 56766666666555544332111111133344445555566444
No 420
>PF00355 Rieske: Rieske [2Fe-2S] domain; InterPro: IPR017941 There are multiple types of iron-sulphur clusters which are grouped into three main categories based on their atomic content: [2Fe-2S], [3Fe-4S], [4Fe-4S] (see PDOC00176 from PROSITEDOC), and other hybrid or mixed metal types. Two general types of [2Fe-2S] clusters are known and they differ in their coordinating residues. The ferredoxin-type [2Fe-2S] clusters are coordinated to the protein by four cysteine residues (see PDOC00175 from PROSITEDOC). The Rieske-type [2Fe-2S] cluster is coordinated to its protein by two cysteine residues and two histidine residues [, ]. The structure of several Rieske domains has been solved []. It contains three layers of antiparallel beta sheets forming two beta sandwiches. Both beta sandwiches share the central sheet 2. The metal-binding site is at the top of the beta sandwich formed by the sheets 2 and 3. The Fe1 iron of the Rieske cluster is coordinated by two cysteines while the other iron Fe2 is coordinated by two histidines. Two inorganic sulphide ions bridge the two iron ions forming a flat, rhombic cluster. Rieske-type iron-sulphur clusters are common to electron transfer chains of mitochondria and chloroplast and to non-haem iron oxygenase systems: The Rieske protein of the Ubiquinol-cytochrome c reductase (1.10.2.2 from EC) (also known as the bc1 complex or complex III), a complex of the electron transport chains of mitochondria and of some aerobic prokaryotes; it catalyses the oxidoreduction of ubiquinol and cytochrome c. The Rieske protein of chloroplastic plastoquinone-plastocyanin reductase (1.10.99.1 from EC) (also known as the b6f complex). It is functionally similar to the bc1 complex and catalyses the oxidoreduction of plastoquinol and cytochrome f. Bacterial naphthalene 1,2-dioxygenase subunit alpha, a component of the naphthalene dioxygenase (NDO) multicomponent enzyme system which catalyses the incorporation of both atoms of molecular oxygen into naphthalene to form cis-naphthalene dihydrodiol. Bacterial 3-phenylpropionate dioxygenase ferredoxin subunit. Bacterial toluene monoxygenase. Bacterial biphenyl dioxygenase. ; GO: 0016491 oxidoreductase activity, 0051537 2 iron, 2 sulfur cluster binding, 0055114 oxidation-reduction process; PDB: 2XRX_A 2XR8_O 2XSH_G 2XSO_I 2YFI_C 2YFL_A 2YFJ_K 1G8J_D 1G8K_D 1NYK_B ....
Probab=41.64 E-value=20 Score=26.26 Aligned_cols=47 Identities=15% Similarity=0.275 Sum_probs=34.0
Q ss_pred ceeccCCCCCceeeecccccCCCcccCCCCCCceeeeCCeeEEeccc
Q 025946 159 IVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVRESVR 205 (245)
Q Consensus 159 LIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R~~~~ 205 (245)
-++..||.=|..+..-....+.+.++||.=|-.|.++.|+...-++.
T Consensus 38 A~~~~CpH~g~~l~~~~~~~~~~~i~Cp~Hg~~Fd~~tG~~~~~p~~ 84 (97)
T PF00355_consen 38 AFSNRCPHQGCPLSEGPFSEDGGVIVCPCHGWRFDLDTGECVGGPAP 84 (97)
T ss_dssp EEESB-TTTSBBGGCSSEETTTTEEEETTTTEEEETTTSBEEESTTC
T ss_pred EEEccCCccceeEcceecccccCEEEeCCcCCEEeCCCceEecCCCC
Confidence 35669999998876632123456899999999999998888776654
No 421
>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=41.59 E-value=12 Score=28.02 Aligned_cols=10 Identities=30% Similarity=0.863 Sum_probs=7.1
Q ss_pred cccCCCCCCc
Q 025946 182 LQLCPYCSQP 191 (245)
Q Consensus 182 ~iqCPnCGE~ 191 (245)
.-+|||||-.
T Consensus 41 ~~~CPNCgGe 50 (57)
T PF06906_consen 41 NGVCPNCGGE 50 (57)
T ss_pred cCcCcCCCCc
Confidence 4689999543
No 422
>PF07787 DUF1625: Protein of unknown function (DUF1625); InterPro: IPR012430 Sequences making up this family are derived from hypothetical proteins expressed by both prokaryotic and eukaryotic species. The region in question is approximately 250 residues long.
Probab=41.50 E-value=62 Score=28.70 Aligned_cols=49 Identities=18% Similarity=0.246 Sum_probs=31.0
Q ss_pred cchhHHHHHHHHHHHHHhc--------ccchhHHHHHHHHHHHHHHHHHHHH-HHHHH
Q 025946 105 ARILGNLALAIGLTYFSMT--------GQLGWVLDAIVSIWLLAVIVPIVGF-GAFLW 153 (245)
Q Consensus 105 ~r~lgn~l~~l~l~~LL~T--------~gLgWLvd~~~~L~LlllllPIl~~-~Gf~W 153 (245)
.|++|-+|..+++.+++.. +-+|.|+.....++.+++.+|+-++ .|+.|
T Consensus 186 lR~~G~llmf~G~~~~~~~l~~l~~~~P~lg~l~~~~~~~~~~~~s~~lsl~~Ia~aW 243 (248)
T PF07787_consen 186 LRFIGWLLMFIGFFLLFSPLYTLVDWIPLLGNLVGFGLFLVAFIISFSLSLLTIALAW 243 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhceeechhhhHHHHHHHHHHHHHHHHHHHHhh
Confidence 6888888888877666542 1234455555666667777766544 45664
No 423
>cd03469 Rieske_RO_Alpha_N Rieske non-heme iron oxygenase (RO) family, N-terminal Rieske domain of the oxygenase alpha subunit; The RO family comprise a large class of aromatic ring-hydroxylating dioxygenases found predominantly in microorganisms. These enzymes enable microorganisms to tolerate and even exclusively utilize aromatic compounds for growth. ROs consist of two or three components: reductase, oxygenase, and ferredoxin (in some cases) components. The oxygenase component may contain alpha and beta subunits, with the beta subunit having a purely structural function. Some oxygenase components contain only an alpha subunit. The oxygenase alpha subunit has two domains, an N-terminal Rieske domain with an [2Fe-2S] cluster and a C-terminal catalytic domain with a mononuclear Fe(II) binding site. The Rieske [2Fe-2S] cluster accepts electrons from the reductase or ferredoxin component and transfers them to the mononuclear iron for catalysis. Reduced pyridine nucleotide is used as the i
Probab=41.46 E-value=34 Score=25.95 Aligned_cols=41 Identities=22% Similarity=0.441 Sum_probs=31.7
Q ss_pred eeccCCCCCceeeeccccc-CCCcccCCCCCCceeeeCCeeEEec
Q 025946 160 VQDSCPNCGNDFQIFKSTL-NDELQLCPYCSQPFSVVDDKFVRES 203 (245)
Q Consensus 160 IE~tCPnCG~eF~~~ed~L-n~d~iqCPnCGE~L~Vd~~~F~R~~ 203 (245)
++..||.=|..+.. ... .++.++||+-|..|..+ |+-...+
T Consensus 39 ~~n~CpH~g~~L~~--g~~~~~~~i~Cp~Hg~~Fd~~-G~~~~~P 80 (118)
T cd03469 39 FHNVCPHRGARLCE--GRGGNAGRLVCPYHGWTYDLD-GKLVGVP 80 (118)
T ss_pred EEEeCCCCCCEeee--ccCCCCCEEECCCCCCEECCC-CcEEeCC
Confidence 56699999988775 223 45789999999999998 7766543
No 424
>PRK01816 hypothetical protein; Provisional
Probab=41.09 E-value=38 Score=29.40 Aligned_cols=29 Identities=34% Similarity=0.732 Sum_probs=22.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcCccee
Q 025946 129 VLDAIVSIWLLAVIVPIVGFGAFLWWASRDIVQ 161 (245)
Q Consensus 129 Lvd~~~~L~LlllllPIl~~~Gf~WWl~rnLIE 161 (245)
-+--.+...||++.+|+=+ .|||++.-.+
T Consensus 60 ~L~~ai~~aLFalSLPlQG----L~WLGkRa~t 88 (143)
T PRK01816 60 QLGPAVATALFALSLPLQG----LWWLGKRSVT 88 (143)
T ss_pred ccHHHHHHHHHHHHhHHHH----HHHhccccCC
Confidence 4555777889999999998 6899985433
No 425
>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=40.76 E-value=21 Score=30.94 Aligned_cols=31 Identities=26% Similarity=0.680 Sum_probs=17.0
Q ss_pred cCCCCCceee-ecccccCCC------cccCCCCCCcee
Q 025946 163 SCPNCGNDFQ-IFKSTLNDE------LQLCPYCSQPFS 193 (245)
Q Consensus 163 tCPnCG~eF~-~~ed~Ln~d------~iqCPnCGE~L~ 193 (245)
.||-||+.=+ ..|+=..++ -=.|++||.-|.
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFT 39 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFT 39 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccc
Confidence 4888887322 223322222 236888887553
No 426
>TIGR01300 CPA3_mnhG_phaG monovalent cation/proton antiporter, MnhG/PhaG subunit. This model represents a subfamily of small, transmembrane proteins believed to be components of Na+/H+ and K+/H+ antiporters. Members, including proteins designated MnhG from Staphylococcus aureus and PhaG from Rhizobium meliloti, show some similarity to chain L of the NADH dehydrogenase I, which also translocates protons.
Probab=40.51 E-value=83 Score=25.02 Aligned_cols=48 Identities=10% Similarity=0.223 Sum_probs=37.3
Q ss_pred cchhHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHHHHHHHHH
Q 025946 105 ARILGNLALAIGLTYFSMTGQLGWVLDAIVSIWLLAVIVPIVGFGAFL 152 (245)
Q Consensus 105 ~r~lgn~l~~l~l~~LL~T~gLgWLvd~~~~L~LlllllPIl~~~Gf~ 152 (245)
+-.+|.+++++++..........+.+..++.++++++..|+-.-..-+
T Consensus 33 ~~tlG~~lil~g~~l~~~~~~~~~~~~~lli~~f~~lT~Pvaah~iar 80 (97)
T TIGR01300 33 GTTLGTILILLGVALIALVLDLAVSIKLLLIALFILLTNPVGAHLLAR 80 (97)
T ss_pred hHHHHHHHHHHHHHHHHhccchhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 556888888888777666445668889999999999999998755444
No 427
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=40.38 E-value=10 Score=28.95 Aligned_cols=25 Identities=24% Similarity=0.684 Sum_probs=16.4
Q ss_pred ccCCCCCceeeecccccCCCcccCC-CCCCcee
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCP-YCSQPFS 193 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCP-nCGE~L~ 193 (245)
+.||+||+..-- |+.+|. .|||-++
T Consensus 9 ~HC~VCg~aIp~-------de~~CSe~C~eil~ 34 (64)
T COG4068 9 RHCVVCGKAIPP-------DEQVCSEECGEILN 34 (64)
T ss_pred ccccccCCcCCC-------ccchHHHHHHHHHH
Confidence 478888877544 677775 4666553
No 428
>TIGR03022 WbaP_sugtrans Undecaprenyl-phosphate galactose phosphotransferase, WbaP. This model includes the enterobacterial enzymes, where the function is presumed to be identical to the S. typhimurium enzyme as well as a somewhat broader group which are likely to catalyze the same or highly similar reactions based on a phylogenetic tree-building analysis of the broader sugar transferase family. Most of these genes are found within large operons dedicated to the production of complex exopolysaccharides such as the enterobacterial O-antigen. The most likely heterogeneity would be in the precise nature of the sugar molecule transferred.
Probab=40.14 E-value=46 Score=31.46 Aligned_cols=30 Identities=23% Similarity=0.374 Sum_probs=26.0
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025946 126 LGWVLDAIVSIWLLAVIVPIVGFGAFLWWA 155 (245)
Q Consensus 126 LgWLvd~~~~L~LlllllPIl~~~Gf~WWl 155 (245)
+..++|.++++++++++.|++++.++.=++
T Consensus 258 ~Kr~~D~~~~~~~l~~~~p~~~~~a~~ikl 287 (456)
T TIGR03022 258 IKRTLDLVLSLLALPLLLPLLLVIALLIRL 287 (456)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 578899999999999999999988876455
No 429
>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=40.10 E-value=12 Score=26.14 Aligned_cols=18 Identities=28% Similarity=0.772 Sum_probs=7.7
Q ss_pred cCCCcccCCCCCCceeee
Q 025946 178 LNDELQLCPYCSQPFSVV 195 (245)
Q Consensus 178 Ln~d~iqCPnCGE~L~Vd 195 (245)
|++....||-|+.+|.-+
T Consensus 16 l~~~~~~CPlC~r~l~~e 33 (54)
T PF04423_consen 16 LKEAKGCCPLCGRPLDEE 33 (54)
T ss_dssp HTT-SEE-TTT--EE-HH
T ss_pred HhcCCCcCCCCCCCCCHH
Confidence 344444788888777543
No 430
>PRK12587 putative monovalent cation/H+ antiporter subunit G; Reviewed
Probab=40.06 E-value=73 Score=26.38 Aligned_cols=48 Identities=21% Similarity=0.250 Sum_probs=36.2
Q ss_pred cchhHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHHHHHHHHH
Q 025946 105 ARILGNLALAIGLTYFSMTGQLGWVLDAIVSIWLLAVIVPIVGFGAFL 152 (245)
Q Consensus 105 ~r~lgn~l~~l~l~~LL~T~gLgWLvd~~~~L~LlllllPIl~~~Gf~ 152 (245)
+-.+|.+++++++++..+....-..+..+++++++++..|+-.-..-|
T Consensus 44 ~~TlG~~lil~g~~l~~~~~~~~~~~k~ll~~~f~~lT~Pvaah~iaR 91 (118)
T PRK12587 44 ASTLGAMSLLFGTFLYFIATQGYVNMQLIVGIIFVLITGPLSSHMIMK 91 (118)
T ss_pred hhHhhHHHHHHHHHHHHhcchhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 556888888888777666544445678899999999999998755544
No 431
>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=39.78 E-value=15 Score=31.82 Aligned_cols=16 Identities=25% Similarity=0.744 Sum_probs=13.6
Q ss_pred ccCCCCCceeeecccc
Q 025946 162 DSCPNCGNDFQIFKST 177 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~ 177 (245)
+.|++||+.|+..|-+
T Consensus 29 ReC~~C~~RFTTyErv 44 (147)
T TIGR00244 29 RECLECHERFTTFERA 44 (147)
T ss_pred ccCCccCCccceeeec
Confidence 3899999999996655
No 432
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=39.78 E-value=20 Score=34.01 Aligned_cols=22 Identities=23% Similarity=0.715 Sum_probs=18.3
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCc
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQP 191 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~ 191 (245)
.|+-|+.+-.. .-+.||+||+.
T Consensus 214 ~CslC~teW~~-------~R~~C~~Cg~~ 235 (309)
T PRK03564 214 HCNLCESEWHV-------VRVKCSNCEQS 235 (309)
T ss_pred EcCCCCCcccc-------cCccCCCCCCC
Confidence 89999988766 68899999973
No 433
>PF04267 SoxD: Sarcosine oxidase, delta subunit family ; InterPro: IPR006279 These sequences represent the delta subunit of a family of known and putative heterotetrameric sarcosine oxidases. Five operons of such oxidases are found in Rhizobium loti (Mesorhizobium loti) and three in Agrobacterium tumefaciens, a high enough copy number to suggest that not all members share the same function. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate []. Bacterial sarcosine oxidases have been isolated from over a dozen different organisms and fall into two major classes (1) monomeric form that contains only covalent flavin and (2) heterotetrameric (alpha, beta, gamma, delta) form that contain a covalent and noncovalent flavin, this entry represents the heterotetrameric form.; GO: 0008115 sarcosine oxidase activity, 0046653 tetrahydrofolate metabolic process; PDB: 3AD7_D 1X31_D 1VRQ_D 3AD8_D 3ADA_D 3AD9_D 2GAG_D 2GAH_D.
Probab=39.76 E-value=7.4 Score=30.74 Aligned_cols=35 Identities=14% Similarity=0.378 Sum_probs=20.7
Q ss_pred ccCCCCCCceeeeCCeeEEecccccc-c---ccccccccccc
Q 025946 183 QLCPYCSQPFSVVDDKFVRESVRFSN-E---STTFGQAFSDF 220 (245)
Q Consensus 183 iqCPnCGE~L~Vd~~~F~R~~~~f~~-~---~~~~~~af~~~ 220 (245)
+.||+||+ -+..+|.--+.-.-. + ++...++|.+|
T Consensus 2 I~CP~CG~---R~~~EF~y~G~a~i~rP~~~~~~sd~~w~~y 40 (84)
T PF04267_consen 2 IPCPHCGP---RDESEFTYGGEAHIARPADPASVSDEEWADY 40 (84)
T ss_dssp EEETTTEE---EEGGGSEEEEESS----S-GGGS-HHHHHHH
T ss_pred ccCCCCCc---cchhheecCcEeccccCCCCCcCCHHHHHHH
Confidence 57999998 677778776655422 2 22234666664
No 434
>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=39.76 E-value=12 Score=40.74 Aligned_cols=22 Identities=32% Similarity=0.957 Sum_probs=18.3
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCc
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQP 191 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~ 191 (245)
.|+.||+.|.+ +.-.||+||+.
T Consensus 680 ~~~~~~~~f~~-------~~~~~p~~~~~ 701 (1171)
T TIGR01054 680 RCRDCGYQFTE-------DRESCPKCGSE 701 (1171)
T ss_pred cCCchhhhccc-------ccccccccccc
Confidence 69999999887 44599999854
No 435
>TIGR02642 phage_xxxx uncharacterized phage protein. This uncharacterized protein is found in prophage regions of Shewanella oneidensis MR-1, Vibrio vulnificus YJ016, Yersinia pseudotuberculosis IP 32953, and Aeromonas hydrophila ATCC7966. It appears to have regions of sequence similarity to phage lambda antitermination protein Q.
Probab=39.61 E-value=51 Score=29.24 Aligned_cols=29 Identities=21% Similarity=0.409 Sum_probs=19.9
Q ss_pred eccCCCCCceeeecccccCCCcccCCCCCCceee
Q 025946 161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSV 194 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~V 194 (245)
+.+||.|+=+-.. + .++-.||.|+-.=.+
T Consensus 99 ~~~C~~C~G~G~~----i-~~~~~C~~C~G~G~v 127 (186)
T TIGR02642 99 SCKCPRCRGTGLI----Q-RRQRECDTCAGTGRF 127 (186)
T ss_pred CCcCCCCCCeeEE----e-cCCCCCCCCCCccEE
Confidence 6799999877555 1 233789999764333
No 436
>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=39.61 E-value=15 Score=30.63 Aligned_cols=15 Identities=27% Similarity=0.572 Sum_probs=12.3
Q ss_pred cccCCCCCCceeeeC
Q 025946 182 LQLCPYCSQPFSVVD 196 (245)
Q Consensus 182 ~iqCPnCGE~L~Vd~ 196 (245)
+-.||.||+.+++|-
T Consensus 74 EyyCP~Cgt~levE~ 88 (112)
T PF08882_consen 74 EYYCPGCGTQLEVEA 88 (112)
T ss_pred EEECCCCcceeEEcc
Confidence 456999999998873
No 437
>PF12230 PRP21_like_P: Pre-mRNA splicing factor PRP21 like protein; InterPro: IPR022030 This domain family is found in eukaryotes, and is typically between 212 and 238 amino acids in length. The family is found in association with PF01805 from PFAM. There are two completely conserved residues (W and H) that may be functionally important. PRP21 is required for assembly of the prespliceosome and it interacts with U2 snRNP and/or pre-mRNA in the prespliceosome. This family also contains proteins similar to PRP21, such as the mammalian SF3a. SF3a also interacts with U2 snRNP from the prespliceosome, converting it to its active form. ; PDB: 4DGW_B.
Probab=39.52 E-value=9.8 Score=33.24 Aligned_cols=15 Identities=13% Similarity=0.503 Sum_probs=0.0
Q ss_pred cccCCCCCCceeeeC
Q 025946 182 LQLCPYCSQPFSVVD 196 (245)
Q Consensus 182 ~iqCPnCGE~L~Vd~ 196 (245)
-+.||.||+.+++++
T Consensus 168 ~~~cPitGe~IP~~e 182 (229)
T PF12230_consen 168 MIICPITGEMIPADE 182 (229)
T ss_dssp ---------------
T ss_pred ccccccccccccccc
Confidence 589999999988764
No 438
>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=39.15 E-value=17 Score=36.06 Aligned_cols=39 Identities=26% Similarity=0.459 Sum_probs=23.9
Q ss_pred eccCCCCCceeeecccccCCC-----cccCCCCCCceeeeCCee
Q 025946 161 QDSCPNCGNDFQIFKSTLNDE-----LQLCPYCSQPFSVVDDKF 199 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~Ln~d-----~iqCPnCGE~L~Vd~~~F 199 (245)
-.-||+|-.++...|--.+.. =-+||.|..+|.+.--.-
T Consensus 26 ~~yCp~CL~~~p~~e~~~~~nrC~r~Cf~CP~C~~~L~~~~~~~ 69 (483)
T PF05502_consen 26 SYYCPNCLFEVPSSEARSEKNRCSRNCFDCPICFSPLSVRASDT 69 (483)
T ss_pred eeECccccccCChhhheeccceeccccccCCCCCCcceeEeccc
Confidence 336888877766533222222 256888888888764443
No 439
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=39.08 E-value=25 Score=26.98 Aligned_cols=33 Identities=24% Similarity=0.547 Sum_probs=22.2
Q ss_pred cCCCCCceeeecccc-----cCCCcccCC--CCCCceeee
Q 025946 163 SCPNCGNDFQIFKST-----LNDELQLCP--YCSQPFSVV 195 (245)
Q Consensus 163 tCPnCG~eF~~~ed~-----Ln~d~iqCP--nCGE~L~Vd 195 (245)
.||.||..-.+-++- +.+--.+|. +||..|..-
T Consensus 3 ~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF~t~ 42 (72)
T PRK09678 3 HCPLCQHAAHARTSRYITDTTKERYHQCQNVNCSATFITY 42 (72)
T ss_pred cCCCCCCccEEEEChhcChhhheeeeecCCCCCCCEEEEE
Confidence 699999887553322 333467888 999887543
No 440
>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=38.87 E-value=13 Score=26.28 Aligned_cols=15 Identities=33% Similarity=0.970 Sum_probs=10.6
Q ss_pred cceeccCCCCCceee
Q 025946 158 DIVQDSCPNCGNDFQ 172 (245)
Q Consensus 158 nLIE~tCPnCG~eF~ 172 (245)
++-+-+||+||.+|.
T Consensus 5 ~lp~K~C~~C~rpf~ 19 (42)
T PF10013_consen 5 NLPSKICPVCGRPFT 19 (42)
T ss_pred cCCCCcCcccCCcch
Confidence 455667888887775
No 441
>PRK00349 uvrA excinuclease ABC subunit A; Reviewed
Probab=38.84 E-value=16 Score=39.21 Aligned_cols=39 Identities=26% Similarity=0.554 Sum_probs=28.7
Q ss_pred cCCCCCceeeec---ccccCCCcccCCCC---CCceeeeCCeeEE
Q 025946 163 SCPNCGNDFQIF---KSTLNDELQLCPYC---SQPFSVVDDKFVR 201 (245)
Q Consensus 163 tCPnCG~eF~~~---ed~Ln~d~iqCPnC---GE~L~Vd~~~F~R 201 (245)
.||.||..|... ...+|...--||.| |....++.++..-
T Consensus 254 ~c~~~g~~~~~~~p~~FSfN~p~G~Cp~C~G~G~~~~~d~~~~i~ 298 (943)
T PRK00349 254 ACPVCGFSIPELEPRLFSFNSPYGACPTCDGLGVKLEFDPDLVVP 298 (943)
T ss_pred cCcccCCCcCcCChhhcCCCCccCCCCcCCCceeEeecCHhhcCC
Confidence 899999887732 23367778899999 7777777765553
No 442
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=38.82 E-value=13 Score=29.06 Aligned_cols=15 Identities=27% Similarity=0.623 Sum_probs=10.5
Q ss_pred cccCCCCCCceeeeC
Q 025946 182 LQLCPYCSQPFSVVD 196 (245)
Q Consensus 182 ~iqCPnCGE~L~Vd~ 196 (245)
.-.||+||+.++..+
T Consensus 8 ~~~C~~CG~d~~~~~ 22 (86)
T PF06170_consen 8 APRCPHCGLDYSHAR 22 (86)
T ss_pred CCcccccCCccccCC
Confidence 457888888776544
No 443
>TIGR00389 glyS_dimeric glycyl-tRNA synthetase, dimeric type. This model describes a glycyl-tRNA synthetase distinct from the two alpha and two beta chains of the tetrameric E. coli glycyl-tRNA synthetase. This enzyme is a homodimeric class II tRNA synthetase and is recognized by pfam model tRNA-synt_2b, which recognizes His, Ser, Pro, and this set of glycyl-tRNA synthetases.
Probab=38.82 E-value=10 Score=38.49 Aligned_cols=52 Identities=19% Similarity=0.231 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHHHHHhcCcceeccCCCCCceeeecc---cccC----------------CCcccCCCCCCc
Q 025946 140 AVIVPIVGFGAFLWWASRDIVQDSCPNCGNDFQIFK---STLN----------------DELQLCPYCSQP 191 (245)
Q Consensus 140 llllPIl~~~Gf~WWl~rnLIE~tCPnCG~eF~~~e---d~Ln----------------~d~iqCPnCGE~ 191 (245)
.+++|=..|-+-+=|-+=.=.-..|++||..|..++ +.+. +-.+.||+||..
T Consensus 63 ~~i~~~~v~~aSGh~~~F~D~mv~~~~~~~~~RaD~l~e~~~~~~~~~~~~~~~~~~i~~~~i~~p~~g~~ 133 (551)
T TIGR00389 63 PIITPEEVLKASGHVDNFTDWMVDCKSCKERFRADHLIEEKLGKRLWGFSGPELNEVMEKYDINCPNCGGE 133 (551)
T ss_pred cccCCHHHHHhcCCccccCCceeecCCCCCEecchHHHHHHhhhhcccCCHHHHHHHHHHcCCCCCCCCCC
Confidence 345565565666644444445559999999988742 1111 224789999986
No 444
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=38.80 E-value=31 Score=28.60 Aligned_cols=36 Identities=22% Similarity=0.525 Sum_probs=23.2
Q ss_pred eccCCCCCceeeecccc--cC-CCcccCCCCCCceeeeCC
Q 025946 161 QDSCPNCGNDFQIFKST--LN-DELQLCPYCSQPFSVVDD 197 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~--Ln-~d~iqCPnCGE~L~Vd~~ 197 (245)
...||-|+..- ..+-- .. ..--.||.|+..+.++.+
T Consensus 30 ~~~cP~C~s~~-~~k~g~~~~~~qRyrC~~C~~tf~~~~~ 68 (129)
T COG3677 30 KVNCPRCKSSN-VVKIGGIRRGHQRYKCKSCGSTFTVETG 68 (129)
T ss_pred cCcCCCCCccc-eeeECCccccccccccCCcCcceeeecc
Confidence 35899999776 31111 12 236689999888876554
No 445
>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=38.61 E-value=15 Score=26.64 Aligned_cols=29 Identities=34% Similarity=0.809 Sum_probs=17.3
Q ss_pred eccCCCCCceeeecccc-cCCCcccCCCCC
Q 025946 161 QDSCPNCGNDFQIFKST-LNDELQLCPYCS 189 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~-Ln~d~iqCPnCG 189 (245)
-..||.|+..|-.+=|+ +.+.--.||-|.
T Consensus 21 ~y~C~~C~~~FC~dCD~fiHE~LH~CPGC~ 50 (51)
T PF07975_consen 21 RYRCPKCKNHFCIDCDVFIHETLHNCPGCE 50 (51)
T ss_dssp EE--TTTT--B-HHHHHTTTTTS-SSSTT-
T ss_pred eEECCCCCCccccCcChhhhccccCCcCCC
Confidence 34899999999987777 466788899884
No 446
>PRK00420 hypothetical protein; Validated
Probab=38.59 E-value=21 Score=29.49 Aligned_cols=21 Identities=29% Similarity=0.569 Sum_probs=15.8
Q ss_pred cccCCCCCCceee-eCCeeEEe
Q 025946 182 LQLCPYCSQPFSV-VDDKFVRE 202 (245)
Q Consensus 182 ~iqCPnCGE~L~V-d~~~F~R~ 202 (245)
...||.||.|+.- .+++-+..
T Consensus 23 ~~~CP~Cg~pLf~lk~g~~~Cp 44 (112)
T PRK00420 23 SKHCPVCGLPLFELKDGEVVCP 44 (112)
T ss_pred cCCCCCCCCcceecCCCceECC
Confidence 4789999999975 66665543
No 447
>PHA02446 hypothetical protein
Probab=38.46 E-value=18 Score=31.29 Aligned_cols=33 Identities=30% Similarity=0.716 Sum_probs=17.0
Q ss_pred cCCCCCceeeeccccc-CC--C--cccCCCCCCceeee
Q 025946 163 SCPNCGNDFQIFKSTL-ND--E--LQLCPYCSQPFSVV 195 (245)
Q Consensus 163 tCPnCG~eF~~~ed~L-n~--d--~iqCPnCGE~L~Vd 195 (245)
.||.||..-....+-. .. + -+.||-.|+.+..|
T Consensus 64 ~cp~cg~dawv~~~g~~eahpd~l~qecplsgqsv~td 101 (166)
T PHA02446 64 QCPLCGQDAWVIHTGIVEAHPDKLLQECPLSGQSVATD 101 (166)
T ss_pred cCCCcccceeEeecCccccCcHHHHHhCCCCCCccccc
Confidence 6777776655422111 11 1 35677777666443
No 448
>PF11808 DUF3329: Domain of unknown function (DUF3329); InterPro: IPR021766 This family of proteins are functionally uncharacterised. This family is only found in bacteria. ; GO: 0004673 protein histidine kinase activity
Probab=38.19 E-value=61 Score=24.93 Aligned_cols=20 Identities=15% Similarity=0.388 Sum_probs=13.0
Q ss_pred HHHHHhcccchhHHHHHHHH
Q 025946 117 LTYFSMTGQLGWVLDAIVSI 136 (245)
Q Consensus 117 l~~LL~T~gLgWLvd~~~~L 136 (245)
+++++++..+||+++.+...
T Consensus 13 ~~~~l~~~lvG~~~g~~~~~ 32 (90)
T PF11808_consen 13 LLLLLAAALVGWLFGHLWWA 32 (90)
T ss_pred HHHHHHHHHHHHHHhHHHHH
Confidence 44455555678998887544
No 449
>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=38.12 E-value=19 Score=34.04 Aligned_cols=22 Identities=23% Similarity=0.700 Sum_probs=18.3
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCc
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQP 191 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~ 191 (245)
.|+-|+.+-.. .-+.||+||+.
T Consensus 212 ~CslC~teW~~-------~R~~C~~Cg~~ 233 (305)
T TIGR01562 212 SCSLCATEWHY-------VRVKCSHCEES 233 (305)
T ss_pred EcCCCCCcccc-------cCccCCCCCCC
Confidence 89999988666 68899999984
No 450
>PF03904 DUF334: Domain of unknown function (DUF334); InterPro: IPR005602 This is a family of proteins found in Staphylococcus aureus plasmid with no characterised function.
Probab=37.97 E-value=94 Score=28.89 Aligned_cols=46 Identities=26% Similarity=0.530 Sum_probs=29.3
Q ss_pred hHHHHHHHHHHHHHhcccch---hH-----HHHH-----------HHHHHHHHHHHHHH-HHHHHH
Q 025946 108 LGNLALAIGLTYFSMTGQLG---WV-----LDAI-----------VSIWLLAVIVPIVG-FGAFLW 153 (245)
Q Consensus 108 lgn~l~~l~l~~LL~T~gLg---WL-----vd~~-----------~~L~LlllllPIl~-~~Gf~W 153 (245)
++..+.++++..|++|++.. |+ -+.+ ..||.++-++|-++ +++|.|
T Consensus 154 i~aml~Vf~LF~lvmt~g~d~m~fl~v~~ly~~ia~~ik~se~~~~~lwyi~Y~vPY~~~ig~~i~ 219 (230)
T PF03904_consen 154 IGAMLFVFMLFALVMTIGSDFMDFLHVDHLYKAIASKIKASESFWTYLWYIAYLVPYIFAIGLFIY 219 (230)
T ss_pred HHHHHHHHHHHHHHHHhcccchhhhhHHHHHHHHHHHHhhhHhHHHHHHHHHHhhHHHHHHHHHHH
Confidence 45666677777777766554 22 1222 45888888888777 666764
No 451
>smart00532 LIGANc Ligase N family.
Probab=37.58 E-value=19 Score=35.35 Aligned_cols=25 Identities=32% Similarity=1.016 Sum_probs=16.5
Q ss_pred ccCCCCCceeeecccccCCCccc-CCC--CCC
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQL-CPY--CSQ 190 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iq-CPn--CGE 190 (245)
..||+||.++.. ..++... ||| |-+
T Consensus 400 ~~CP~C~s~l~~----~~~~~~~~C~n~~C~a 427 (441)
T smart00532 400 THCPSCGSELVR----EEGEVDIRCPNPLCPA 427 (441)
T ss_pred CCCCCCCCEeEe----cCCceEEEeCCCCCHH
Confidence 499999999875 1223433 886 743
No 452
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=37.17 E-value=18 Score=37.40 Aligned_cols=24 Identities=21% Similarity=0.661 Sum_probs=14.6
Q ss_pred cCCCCCceeeecccccCCCcccCCC--CCCc
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPY--CSQP 191 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPn--CGE~ 191 (245)
.||+||.+... +.....||| |-+.
T Consensus 400 ~CP~C~s~l~~-----~~~~~~C~n~~C~aq 425 (669)
T PRK14350 400 NCPSCKTALIK-----EGAHLFCVNNHCPSV 425 (669)
T ss_pred CCCCCCCEeee-----CCEEEEECCCCCHHH
Confidence 78888877654 223566764 6443
No 453
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=37.16 E-value=20 Score=29.74 Aligned_cols=22 Identities=23% Similarity=0.421 Sum_probs=15.7
Q ss_pred CCCCCCceeeeCCeeEEecccc
Q 025946 185 CPYCSQPFSVVDDKFVRESVRF 206 (245)
Q Consensus 185 CPnCGE~L~Vd~~~F~R~~~~f 206 (245)
||.||.++.+..=+-..-....
T Consensus 1 CPvCg~~l~vt~l~C~~C~t~i 22 (113)
T PF09862_consen 1 CPVCGGELVVTRLKCPSCGTEI 22 (113)
T ss_pred CCCCCCceEEEEEEcCCCCCEE
Confidence 9999999998865554444333
No 454
>PF04641 Rtf2: Rtf2 RING-finger
Probab=37.02 E-value=13 Score=33.33 Aligned_cols=14 Identities=36% Similarity=0.975 Sum_probs=11.0
Q ss_pred cccCCCCCCceeee
Q 025946 182 LQLCPYCSQPFSVV 195 (245)
Q Consensus 182 ~iqCPnCGE~L~Vd 195 (245)
...||.||++|..+
T Consensus 150 ~~~Cp~c~~~f~~~ 163 (260)
T PF04641_consen 150 SKKCPVCGKPFTEE 163 (260)
T ss_pred cccccccCCccccC
Confidence 45799999998743
No 455
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=36.75 E-value=13 Score=30.70 Aligned_cols=18 Identities=22% Similarity=0.785 Sum_probs=13.4
Q ss_pred CCCcccCCCCCCceeeeC
Q 025946 179 NDELQLCPYCSQPFSVVD 196 (245)
Q Consensus 179 n~d~iqCPnCGE~L~Vd~ 196 (245)
++....||+||..++.++
T Consensus 96 ~~~~Y~Cp~C~~~y~~~e 113 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLE 113 (147)
T ss_pred CCcEEECcCCCCEeeHHH
Confidence 334667999999888654
No 456
>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=36.63 E-value=20 Score=28.82 Aligned_cols=27 Identities=26% Similarity=0.575 Sum_probs=18.7
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
+||-||+.-.-- ..-+--.|..||..+
T Consensus 37 ~CpfCgk~~vkR---~a~GIW~C~~C~~~~ 63 (91)
T TIGR00280 37 VCPFCGKKTVKR---GSTGIWTCRKCGAKF 63 (91)
T ss_pred cCCCCCCCceEE---EeeEEEEcCCCCCEE
Confidence 899999654331 112568999998876
No 457
>PRK12267 methionyl-tRNA synthetase; Reviewed
Probab=36.42 E-value=19 Score=36.00 Aligned_cols=36 Identities=22% Similarity=0.534 Sum_probs=22.0
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceee--eCCeeEE
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSV--VDDKFVR 201 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~V--d~~~F~R 201 (245)
-||.|+. |+.+.++.+ .-.||.||++++. ++.-|-+
T Consensus 127 yc~~~~~-~l~~~~l~~--~~~c~~cg~~~e~~~~~~~f~~ 164 (648)
T PRK12267 127 YCVSCET-FFTESQLVD--GGKCPDCGREVELVKEESYFFR 164 (648)
T ss_pred ecCCCCc-cCChHHhcc--CCcCCCCCCcCeEEecceEEEE
Confidence 7999994 444222221 1479999998763 3344444
No 458
>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=36.20 E-value=23 Score=28.64 Aligned_cols=30 Identities=27% Similarity=0.549 Sum_probs=23.5
Q ss_pred ccCCCCCceeeecccccCCC---cccCCCCCCceeee
Q 025946 162 DSCPNCGNDFQIFKSTLNDE---LQLCPYCSQPFSVV 195 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d---~iqCPnCGE~L~Vd 195 (245)
-+|++||.+... +..+ --.||+|=..+.+|
T Consensus 5 F~C~~CG~~V~p----~~~g~~~RNHCP~CL~S~Hvd 37 (92)
T PF12647_consen 5 FTCVHCGLTVSP----LAAGSAHRNHCPSCLSSLHVD 37 (92)
T ss_pred cCccccCCCccc----CCCCCCccCcCcccccccccC
Confidence 389999998866 3333 46899999988887
No 459
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=36.17 E-value=18 Score=32.97 Aligned_cols=28 Identities=21% Similarity=0.626 Sum_probs=25.2
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCC
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQ 190 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE 190 (245)
.|-.||..|+-.+..+.++..+|+-|-+
T Consensus 174 ~C~kCGE~~~e~~~~~~ng~~vC~~C~~ 201 (206)
T COG2191 174 RCSKCGELFMEPRAVVLNGKPVCKPCAE 201 (206)
T ss_pred eccccCcccccchhhhcCCceecccccc
Confidence 8999999999988888899999999955
No 460
>PF12273 RCR: Chitin synthesis regulation, resistance to Congo red; InterPro: IPR020999 RCR proteins are ER membrane proteins that regulate chitin deposition in fungal cell walls. Although chitin, a linear polymer of beta-1,4-linked N-acetylglucosamine, constitutes only 2% of the cell wall it plays a vital role in the overall protection of the cell wall against stress, noxious chemicals and osmotic pressure changes. Congo red is a cell wall-disrupting benzidine-type dye extensively used in many cell wall mutant studies that specifically targets chitin in yeast cells and inhibits growth. RCR proteins render the yeasts resistant to Congo red by diminishing the content of chitin in the cell wall []. RCR proteins are probably regulating chitin synthase III interact directly with ubiquitin ligase Rsp5, and the VPEY motif is necessary for this, via interaction with the WW domains of Rsp5 [].
Probab=36.17 E-value=28 Score=28.00 Aligned_cols=32 Identities=13% Similarity=0.109 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHHhcCcceeccCCCCCceeee
Q 025946 142 IVPIVGFGAFLWWASRDIVQDSCPNCGNDFQI 173 (245)
Q Consensus 142 llPIl~~~Gf~WWl~rnLIE~tCPnCG~eF~~ 173 (245)
++-+|+|+++.|..+|+.-...=|.=|+....
T Consensus 10 ~~i~l~~~~~~~~~rRR~r~G~~P~~gt~w~~ 41 (130)
T PF12273_consen 10 VAILLFLFLFYCHNRRRRRRGLQPIYGTRWMA 41 (130)
T ss_pred HHHHHHHHHHHHHHHHHhhcCCCCcCCceecC
Confidence 33333444555455665555555555554443
No 461
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=35.90 E-value=18 Score=38.64 Aligned_cols=31 Identities=19% Similarity=0.541 Sum_probs=19.9
Q ss_pred cCCCCCceeeecccccC--C------------------Cc-ccCCCCCCcee
Q 025946 163 SCPNCGNDFQIFKSTLN--D------------------EL-QLCPYCSQPFS 193 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln--~------------------d~-iqCPnCGE~L~ 193 (245)
+||.|..+.-++|..+- . -| -.||+||-.++
T Consensus 798 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 849 (1006)
T PRK12775 798 TCPKCHRPLEGDEEYVCCATSELQWRCDDCGKVSEGFAFPYGMCPACGGKLQ 849 (1006)
T ss_pred cCcccCCCCCCCceeEEecCcceeeehhhhccccccccCCcCcCcccccchh
Confidence 88888777665544321 0 12 57999998876
No 462
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=35.77 E-value=34 Score=27.69 Aligned_cols=30 Identities=20% Similarity=0.351 Sum_probs=20.2
Q ss_pred eccCCCCCceeeecccccCCCcccCCCCCCceeee
Q 025946 161 QDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVV 195 (245)
Q Consensus 161 E~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd 195 (245)
-.+||.|...-.. ......||.||...-++
T Consensus 85 ~~~~Pkc~~~~~~-----~~~~~~cp~c~~~~~~~ 114 (140)
T COG0551 85 CSNYPKCRFTEKP-----KPKEKKCPKCGSRKLVE 114 (140)
T ss_pred ecCCCcCceeecC-----CcccccCCcCCCceeEE
Confidence 4588888876654 33455699999844443
No 463
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=35.74 E-value=15 Score=38.78 Aligned_cols=14 Identities=43% Similarity=1.130 Sum_probs=8.8
Q ss_pred cCCCCCceeeeccc
Q 025946 163 SCPNCGNDFQIFKS 176 (245)
Q Consensus 163 tCPnCG~eF~~~ed 176 (245)
.|.+||-+|++.|.
T Consensus 125 ~CT~CGPRfTIi~a 138 (750)
T COG0068 125 NCTNCGPRFTIIEA 138 (750)
T ss_pred ccCCCCcceeeecc
Confidence 67777766666443
No 464
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=35.70 E-value=21 Score=30.37 Aligned_cols=20 Identities=25% Similarity=0.574 Sum_probs=15.6
Q ss_pred cccCCCCCCceeeeCCeeEE
Q 025946 182 LQLCPYCSQPFSVVDDKFVR 201 (245)
Q Consensus 182 ~iqCPnCGE~L~Vd~~~F~R 201 (245)
...||.||.||.-.+|.-..
T Consensus 28 ~~hCp~Cg~PLF~KdG~v~C 47 (131)
T COG1645 28 AKHCPKCGTPLFRKDGEVFC 47 (131)
T ss_pred HhhCcccCCcceeeCCeEEC
Confidence 56899999999777766543
No 465
>TIGR02377 MocE_fam_FeS Rieske [2Fe-2S] domain protein, MocE subfamily. This model describes a subfamily of the Rieske-like [2Fe-2S] family of ferredoxins that includes MocE, part of the rhizopine (3-O-methyl-scyllo-inosamine) catabolic cluster in Rhizobium. Members of this family are related to, yet distinct from, the small subunit of nitrite reductase [NAD(P)H].
Probab=35.68 E-value=30 Score=26.45 Aligned_cols=40 Identities=13% Similarity=0.194 Sum_probs=29.6
Q ss_pred eeccCCCCCceeeecccccCCCcccCCCCCCceeeeCCeeEE
Q 025946 160 VQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVDDKFVR 201 (245)
Q Consensus 160 IE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~~~F~R 201 (245)
++..||.=|..+. +..+.++.+.||.-|..|.+++|+=..
T Consensus 39 ~~~~CpH~g~~L~--~G~~~~~~i~CP~Hg~~Fdl~tG~~~~ 78 (101)
T TIGR02377 39 TDGLCTHEYAHLA--DGLVMDTTVECPKHAGCFDYRTGEALN 78 (101)
T ss_pred EcCcCCCCCCCCC--CCEEcCCEEECCccCCEEECCCCcccC
Confidence 4458999776654 234667889999999999988876543
No 466
>PRK04351 hypothetical protein; Provisional
Probab=35.65 E-value=36 Score=28.88 Aligned_cols=38 Identities=16% Similarity=0.440 Sum_probs=28.6
Q ss_pred cceeccCCCCCceeeecccccCCCcccCCCCCCceeeeC
Q 025946 158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVD 196 (245)
Q Consensus 158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~ 196 (245)
.-+.-.|..||..+.-- --+|.....|-.|+..|...+
T Consensus 109 ~~y~Y~C~~Cg~~~~r~-Rr~n~~~yrCg~C~g~L~~~~ 146 (149)
T PRK04351 109 KNYLYECQSCGQQYLRK-RRINTKRYRCGKCRGKLKLIN 146 (149)
T ss_pred ceEEEECCCCCCEeeee-eecCCCcEEeCCCCcEeeecc
Confidence 44677999999876653 235777899999999987653
No 467
>PRK12671 putative monovalent cation/H+ antiporter subunit G; Reviewed
Probab=35.64 E-value=94 Score=26.04 Aligned_cols=48 Identities=15% Similarity=0.020 Sum_probs=35.5
Q ss_pred cchhHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHHHHHHHHH
Q 025946 105 ARILGNLALAIGLTYFSMTGQLGWVLDAIVSIWLLAVIVPIVGFGAFL 152 (245)
Q Consensus 105 ~r~lgn~l~~l~l~~LL~T~gLgWLvd~~~~L~LlllllPIl~~~Gf~ 152 (245)
.-.+|-.++++++++..........+..+++++++++..|+-.-..-+
T Consensus 49 a~TlG~~liL~g~~l~~~~~~~~~~~k~lli~~Fl~lTaPvaaH~iaR 96 (120)
T PRK12671 49 GTSWGAGGILIASILYFSVLQSRPVLHEVLIGVFVVVTTPVTLMLLSR 96 (120)
T ss_pred hhhhhHHHHHHHHHHHhhcccchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 556788888877766555444456778899999999999998755555
No 468
>PF13806 Rieske_2: Rieske-like [2Fe-2S] domain; PDB: 2JO6_A 3C0D_A 3D89_A 2JZA_A.
Probab=35.54 E-value=12 Score=29.35 Aligned_cols=38 Identities=16% Similarity=0.382 Sum_probs=25.3
Q ss_pred eeccCCCCCceeeecccccCCC----cccCCCCCCceeeeCCe
Q 025946 160 VQDSCPNCGNDFQIFKSTLNDE----LQLCPYCSQPFSVVDDK 198 (245)
Q Consensus 160 IE~tCPnCG~eF~~~ed~Ln~d----~iqCPnCGE~L~Vd~~~ 198 (245)
++..||.|..-... +-.+.+. .+.||-.+..+.++.|+
T Consensus 39 i~n~Cph~~~~~Ls-~G~i~~~~g~~~V~CPlH~~~f~L~tG~ 80 (104)
T PF13806_consen 39 IDNRCPHSQAGPLS-DGLIGDGNGEPCVACPLHKWRFDLRTGE 80 (104)
T ss_dssp EESBETTTTSSCGC-GSEEEECTTEEEEEETTTTEEEETTTTE
T ss_pred EeccCCccCCcccc-eeEEccCCCCEEEECCCCCCeEECCCcC
Confidence 45689998432222 2223333 79999999999998875
No 469
>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=35.51 E-value=16 Score=39.82 Aligned_cols=29 Identities=24% Similarity=0.572 Sum_probs=20.3
Q ss_pred ceeccCCCCCceeeecccccCCCcccCCCCCC
Q 025946 159 IVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQ 190 (245)
Q Consensus 159 LIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE 190 (245)
++...|||||-..++. -.. ....|+.|-.
T Consensus 5 ~y~~~CPnCgg~i~~~-rl~--~~~~c~~Clp 33 (1171)
T TIGR01054 5 VYSNLCPNCGGEISSE-RLE--KGLPCARCLP 33 (1171)
T ss_pred hhcCCCCCCCCccchh-Hhh--cCCCccccCc
Confidence 4566899999999982 111 3567888854
No 470
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=35.43 E-value=8.7 Score=37.74 Aligned_cols=33 Identities=15% Similarity=0.476 Sum_probs=24.0
Q ss_pred cceeccCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 158 DIVQDSCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 158 nLIE~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
+|.+..|-.|.+.|.. ++. ....-.||+||..+
T Consensus 243 KY~~TAC~rC~t~y~l-e~A-~~~~wrCpkCGg~i 275 (403)
T COG1379 243 KYHLTACSRCYTRYSL-EEA-KSLRWRCPKCGGKI 275 (403)
T ss_pred chhHHHHHHhhhccCc-chh-hhhcccCcccccch
Confidence 6788899999977765 222 22468999999843
No 471
>PF06093 Spt4: Spt4/RpoE2 zinc finger; InterPro: IPR022800 This entry consists of several eukaryotic transcription elongation Spt4 proteins as well as archaebacterial RpoE2 []. Three transcription-elongation factors Spt4, Spt5, and Spt6 are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. Spt4 and Spt5 are tightly associated in a complex, while the physical association of the Spt4-Spt5 complex with Spt6 is considerably weaker. It has been demonstrated that Spt4, Spt5, and Spt6 play roles in transcription elongation in both yeast and humans including a role in activation by Tat. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles []. RpoE2 is one of 13 subunits in the archaeal RNA polymerase. These proteins contain a C4-type zinc finger, and the structure has been solved in []. The structure reveals that Spt4-Spt5 binding is governed by an acid-dipole interaction between Spt5 and Spt4, and the complex binds to and travels along the elongating RNA polymerase. The Spt4-Spt5 complex is likely to be an ancient, core component of the transcription elongation machinery. ; PDB: 2EXU_A 3H7H_A 3LPE_F 3P8B_A 1RYQ_A 3QQC_E.
Probab=35.31 E-value=6.9 Score=30.15 Aligned_cols=29 Identities=17% Similarity=0.306 Sum_probs=13.7
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCCCceeee
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVV 195 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd 195 (245)
+-|-.|+.-.... .+ ....|||| +.|...
T Consensus 2 rAC~~C~~i~t~~--qF--~~~gCpnC-~~l~~~ 30 (77)
T PF06093_consen 2 RACLRCRLIKTED--QF--RDEGCPNC-PFLQMK 30 (77)
T ss_dssp EEETTT-BEECCC--HH--HHH--TTT-HHHH-T
T ss_pred cccccCCcccCHh--Hc--cCCCCCCC-cccccc
Confidence 4688998544431 00 12579999 555444
No 472
>PLN02294 cytochrome c oxidase subunit Vb
Probab=35.17 E-value=24 Score=31.47 Aligned_cols=15 Identities=33% Similarity=0.698 Sum_probs=11.0
Q ss_pred CcccCCCCCCceeee
Q 025946 181 ELQLCPYCSQPFSVV 195 (245)
Q Consensus 181 d~iqCPnCGE~L~Vd 195 (245)
.+.+||.||+.|..+
T Consensus 140 kp~RCpeCG~~fkL~ 154 (174)
T PLN02294 140 KSFECPVCTQYFELE 154 (174)
T ss_pred CceeCCCCCCEEEEE
Confidence 477788888877665
No 473
>COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]
Probab=34.95 E-value=17 Score=37.17 Aligned_cols=27 Identities=19% Similarity=0.657 Sum_probs=20.2
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCceeeeC
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFSVVD 196 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~Vd~ 196 (245)
.|+.||.-+-. +..-.| .||..+.+.+
T Consensus 132 ~c~~cg~~iea------n~kp~c-~cg~~~~~~e 158 (593)
T COG2401 132 RCEKCGTIIEA------NTKPEC-KCGSHVHILE 158 (593)
T ss_pred ecchhchhhhh------cCCccc-CCCCceEEEE
Confidence 89999976554 234499 9999877654
No 474
>TIGR03025 EPS_sugtrans exopolysaccharide biosynthesis polyprenyl glycosylphosphotransferase. Certain closely related transferase enzymes such as Sinorhizobium ExoY and Lactococcus EpsD lack the N-terminal domain and are not found by this model.
Probab=34.92 E-value=54 Score=30.87 Aligned_cols=31 Identities=19% Similarity=0.232 Sum_probs=26.1
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 025946 126 LGWVLDAIVSIWLLAVIVPIVGFGAFLWWAS 156 (245)
Q Consensus 126 LgWLvd~~~~L~LlllllPIl~~~Gf~WWl~ 156 (245)
+..++|.++++++++++.|++++.++.=++.
T Consensus 257 ~Kr~~d~~~~~~~~~~~~p~~~~~~~~~~~~ 287 (445)
T TIGR03025 257 LKRLFDIVLSLLALLLLSPLMLAIALAIKLD 287 (445)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 4789999999999999999999777654443
No 475
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=34.90 E-value=23 Score=36.72 Aligned_cols=10 Identities=30% Similarity=1.079 Sum_probs=5.8
Q ss_pred cCCCCCceee
Q 025946 163 SCPNCGNDFQ 172 (245)
Q Consensus 163 tCPnCG~eF~ 172 (245)
.||+||.+..
T Consensus 425 ~CP~C~~~l~ 434 (689)
T PRK14351 425 TCPVCDSAVE 434 (689)
T ss_pred CCCCCCCEee
Confidence 5666665554
No 476
>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=34.87 E-value=15 Score=32.54 Aligned_cols=40 Identities=23% Similarity=0.506 Sum_probs=24.0
Q ss_pred eeccCCCCCceeeecccccCC--CcccCCCCCCceeeeCCeeEEe
Q 025946 160 VQDSCPNCGNDFQIFKSTLND--ELQLCPYCSQPFSVVDDKFVRE 202 (245)
Q Consensus 160 IE~tCPnCG~eF~~~ed~Ln~--d~iqCPnCGE~L~Vd~~~F~R~ 202 (245)
+...||.|=.+-...-+ +.+ .-.+||.||.-+.- ++.++.
T Consensus 12 ~~~lC~~C~~~~~~i~e-i~~~i~v~~C~~Cg~~~~~--~~W~~~ 53 (236)
T PF04981_consen 12 IDGLCPDCYLKRFDIIE-IPDRIEVTICPKCGRYRIG--GRWVDP 53 (236)
T ss_pred ccccChHHhcccCCeee-cCCccCceECCCCCCEECC--CEeeec
Confidence 44566666555444222 222 57899999987754 666655
No 477
>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=34.81 E-value=23 Score=22.82 Aligned_cols=21 Identities=33% Similarity=0.904 Sum_probs=12.4
Q ss_pred ccCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
..|-+||. . ....||.|+.++
T Consensus 3 ~~C~vC~~--~--------~kY~Cp~C~~~~ 23 (30)
T PF04438_consen 3 KLCSVCGN--P--------AKYRCPRCGARY 23 (30)
T ss_dssp EEETSSSS--E--------ESEE-TTT--EE
T ss_pred CCCccCcC--C--------CEEECCCcCCce
Confidence 36788886 2 367899888764
No 478
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=34.80 E-value=18 Score=26.87 Aligned_cols=16 Identities=38% Similarity=1.030 Sum_probs=12.1
Q ss_pred CcccCCCCCCceeeeC
Q 025946 181 ELQLCPYCSQPFSVVD 196 (245)
Q Consensus 181 d~iqCPnCGE~L~Vd~ 196 (245)
+-.-||.||.+++.++
T Consensus 38 rYngCPfC~~~~~~~~ 53 (55)
T PF14447_consen 38 RYNGCPFCGTPFEFDD 53 (55)
T ss_pred hccCCCCCCCcccCCC
Confidence 3556999999987654
No 479
>PRK01345 heat shock protein HtpX; Provisional
Probab=34.79 E-value=58 Score=30.35 Aligned_cols=35 Identities=20% Similarity=0.478 Sum_probs=18.2
Q ss_pred ccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcce
Q 025946 124 GQLGWVLDAIVSIWLLAVIVPIVGFGAFLWWASRDIV 160 (245)
Q Consensus 124 ~gLgWLvd~~~~L~LlllllPIl~~~Gf~WWl~rnLI 160 (245)
..+||++....+++..++ -.+++.-+.||....++
T Consensus 18 ~~~g~l~~~~~~~~~~~~--~~~~~~~~~~~~~~~~~ 52 (317)
T PRK01345 18 MGVGYLIGGAGGMMIALV--IAAGMNLFSYWNSDKMV 52 (317)
T ss_pred HHHHHHHhhhhhHHHHHH--HHHHHHHHHHHHhHHHH
Confidence 367888877654333222 23333455666654443
No 480
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=34.75 E-value=12 Score=40.23 Aligned_cols=31 Identities=35% Similarity=0.876 Sum_probs=22.0
Q ss_pred cCCCCCceeeecccccCC--------CcccCCCCCCceee
Q 025946 163 SCPNCGNDFQIFKSTLND--------ELQLCPYCSQPFSV 194 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~--------d~iqCPnCGE~L~V 194 (245)
.|+.||+-|-- |--|++ -|..||||++-|+-
T Consensus 283 KCtECgKAFKf-KHHLKEHlRIHSGEKPfeCpnCkKRFSH 321 (1007)
T KOG3623|consen 283 KCTECGKAFKF-KHHLKEHLRIHSGEKPFECPNCKKRFSH 321 (1007)
T ss_pred cccccchhhhh-HHHHHhhheeecCCCCcCCccccccccc
Confidence 79999998864 222222 38999999876654
No 481
>PF13397 DUF4109: Domain of unknown function (DUF4109)
Probab=34.54 E-value=41 Score=27.81 Aligned_cols=42 Identities=26% Similarity=0.465 Sum_probs=28.1
Q ss_pred cCcceeccCCCCCceeeecccccCC--CcccCCCCCCceeeeCCe
Q 025946 156 SRDIVQDSCPNCGNDFQIFKSTLND--ELQLCPYCSQPFSVVDDK 198 (245)
Q Consensus 156 ~rnLIE~tCPnCG~eF~~~ed~Ln~--d~iqCPnCGE~L~Vd~~~ 198 (245)
-|..++..||+ |.+|...-..-.+ ..-.||.||.+=..+++.
T Consensus 23 pR~~v~Y~C~~-Gh~~~v~Fa~eAevP~~WeC~~cG~~A~~~~~~ 66 (105)
T PF13397_consen 23 PRQRVSYWCPN-GHETEVPFAAEAEVPATWECPRCGLPAGRDDGN 66 (105)
T ss_pred CceEEEEECCC-CCEEeccccccCCCCCceeCCCCCCcccccCCC
Confidence 46677889999 8887773222112 367899999986555443
No 482
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=34.53 E-value=16 Score=38.66 Aligned_cols=33 Identities=21% Similarity=0.584 Sum_probs=24.3
Q ss_pred cCCCCCceeeecccc-cCCCcccCCCCCCceeee
Q 025946 163 SCPNCGNDFQIFKST-LNDELQLCPYCSQPFSVV 195 (245)
Q Consensus 163 tCPnCG~eF~~~ed~-Ln~d~iqCPnCGE~L~Vd 195 (245)
-||.|-+++.+-.|- +.-.++-||.||-.+...
T Consensus 153 lC~~C~~EY~dP~nRRfHAQp~aCp~CGP~~~l~ 186 (750)
T COG0068 153 LCPFCDKEYKDPLNRRFHAQPIACPKCGPHLFLV 186 (750)
T ss_pred CCHHHHHHhcCccccccccccccCcccCCCeEEE
Confidence 699999887773222 333689999999988766
No 483
>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=34.48 E-value=19 Score=22.42 Aligned_cols=10 Identities=30% Similarity=0.786 Sum_probs=6.6
Q ss_pred ccCCCCCcee
Q 025946 162 DSCPNCGNDF 171 (245)
Q Consensus 162 ~tCPnCG~eF 171 (245)
+.||.|++.+
T Consensus 2 v~CPiC~~~v 11 (26)
T smart00734 2 VQCPVCFREV 11 (26)
T ss_pred CcCCCCcCcc
Confidence 3677777665
No 484
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=34.36 E-value=25 Score=31.76 Aligned_cols=26 Identities=15% Similarity=0.515 Sum_probs=20.2
Q ss_pred cCCCcccCCCCCCceeeeCCeeEEec
Q 025946 178 LNDELQLCPYCSQPFSVVDDKFVRES 203 (245)
Q Consensus 178 Ln~d~iqCPnCGE~L~Vd~~~F~R~~ 203 (245)
-.+....||+||+++...++...+.-
T Consensus 95 w~~~~~fC~~CG~~~~~~~~~~~~~C 120 (256)
T PRK00241 95 FYRSHRFCGYCGHPMHPSKTEWAMLC 120 (256)
T ss_pred HhhcCccccccCCCCeecCCceeEEC
Confidence 45578999999999988776666543
No 485
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=34.34 E-value=24 Score=28.37 Aligned_cols=27 Identities=22% Similarity=0.444 Sum_probs=18.4
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
+||-||++-.-- ..-+--.|-.||..+
T Consensus 38 ~CpfCgk~~vkR---~a~GIW~C~~C~~~~ 64 (90)
T PTZ00255 38 FCPFCGKHAVKR---QAVGIWRCKGCKKTV 64 (90)
T ss_pred cCCCCCCCceee---eeeEEEEcCCCCCEE
Confidence 899998654331 112568899998876
No 486
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=34.34 E-value=23 Score=36.41 Aligned_cols=23 Identities=26% Similarity=0.837 Sum_probs=0.0
Q ss_pred cCCCCCceeeecccccCCCcccCCC---C
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPY---C 188 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPn---C 188 (245)
.||+||.++.-.++. ....||| |
T Consensus 406 ~CP~Cgs~l~~~~~~---~~~~C~n~~~C 431 (665)
T PRK07956 406 HCPVCGSELVRVEGE---AVLRCTNGLSC 431 (665)
T ss_pred CCCCCCCEeEecCCC---eEEECCCCCCC
No 487
>TIGR03023 WcaJ_sugtrans Undecaprenyl-phosphate glucose phosphotransferase. Colanic acid biosynthesis utilizes a glucose-undecaprenyl carrier, knockout of EpsB abolishes incorporation of UDP-glucose into the lipid phase and the C-terminal portion of GumD has been shown to be responsible for the glucosyl-1-transferase activity.
Probab=34.19 E-value=56 Score=30.81 Aligned_cols=50 Identities=16% Similarity=0.292 Sum_probs=35.4
Q ss_pred chhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCc----ceeccCCCCCceeeecc
Q 025946 126 LGWVLDAIVSIWLLAVIVPIVGFGAFLWWASRD----IVQDSCPNCGNDFQIFK 175 (245)
Q Consensus 126 LgWLvd~~~~L~LlllllPIl~~~Gf~WWl~rn----LIE~tCPnCG~eF~~~e 175 (245)
+..++|.++++++++++.|++++.+..=.+... +-|..--.-|++|...|
T Consensus 260 ~Kr~~d~~~~~~~~~~~~p~~~~~~~~~~~~~~g~~~~~~~r~g~~~~~f~~~k 313 (451)
T TIGR03023 260 IKRAFDIVLALLVLLLLSPLLLLIAIAIKLTSPGPVLFRQERYGLDGRPFMVYK 313 (451)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCceEEeeccCCCCeEEEEEE
Confidence 468899999999999999999988776455431 22334445666776643
No 488
>PF13451 zf-trcl: Probable zinc-binding domain
Probab=34.09 E-value=19 Score=25.96 Aligned_cols=28 Identities=29% Similarity=0.829 Sum_probs=17.8
Q ss_pred eccCCCCCceeeecc--------cccCCCcccCCCC
Q 025946 161 QDSCPNCGNDFQIFK--------STLNDELQLCPYC 188 (245)
Q Consensus 161 E~tCPnCG~eF~~~e--------d~Ln~d~iqCPnC 188 (245)
+.+|-.||.+|.-.. --+.+.|..||.|
T Consensus 4 ~l~C~dCg~~FvfTa~EQ~fy~eKgf~n~p~RC~~C 39 (49)
T PF13451_consen 4 TLTCKDCGAEFVFTAGEQKFYAEKGFDNEPKRCPSC 39 (49)
T ss_pred eEEcccCCCeEEEehhHHHHHHhcCCcCCCccCHHH
Confidence 347888888876521 1144567788877
No 489
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=34.08 E-value=16 Score=37.87 Aligned_cols=33 Identities=21% Similarity=0.670 Sum_probs=19.4
Q ss_pred cCCCCCceeeecccc-cCCCcccCCCCCCceeee
Q 025946 163 SCPNCGNDFQIFKST-LNDELQLCPYCSQPFSVV 195 (245)
Q Consensus 163 tCPnCG~eF~~~ed~-Ln~d~iqCPnCGE~L~Vd 195 (245)
.||.|-+++.+-.+- ..-.++-||+||=.+...
T Consensus 120 ~C~~C~~ey~~p~~rr~h~~~~~C~~Cgp~l~l~ 153 (711)
T TIGR00143 120 LCPDCAKEYKDPLDRRFHAQPIACPRCGPQLNFV 153 (711)
T ss_pred CCHHHHHHhcCCccccCCCCCccCCCCCcEEEEE
Confidence 577777665442111 223477788888877653
No 490
>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=34.00 E-value=20 Score=23.85 Aligned_cols=11 Identities=36% Similarity=1.044 Sum_probs=6.1
Q ss_pred cccCCCCCCce
Q 025946 182 LQLCPYCSQPF 192 (245)
Q Consensus 182 ~iqCPnCGE~L 192 (245)
...||||+.++
T Consensus 4 ~~~C~nC~R~v 14 (33)
T PF08209_consen 4 YVECPNCGRPV 14 (33)
T ss_dssp EEE-TTTSSEE
T ss_pred eEECCCCcCCc
Confidence 45677776654
No 491
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=33.87 E-value=19 Score=37.66 Aligned_cols=28 Identities=21% Similarity=0.672 Sum_probs=18.0
Q ss_pred ccCCCCCceeeecccccCCCcccCCC---CCCce
Q 025946 162 DSCPNCGNDFQIFKSTLNDELQLCPY---CSQPF 192 (245)
Q Consensus 162 ~tCPnCG~eF~~~ed~Ln~d~iqCPn---CGE~L 192 (245)
..||+||.++.-.| .+-.+.||| |-...
T Consensus 405 ~~CP~C~s~l~r~~---~e~~~rC~n~~~C~aq~ 435 (667)
T COG0272 405 THCPVCGSELVREE---GEVVIRCTNGLNCPAQL 435 (667)
T ss_pred CCCCCCCCeeEecc---CceeEecCCCCCChHHH
Confidence 36888888877621 124778887 75544
No 492
>KOG1598 consensus Transcription initiation factor TFIIIB, Brf1 subunit [Transcription]
Probab=33.86 E-value=24 Score=36.04 Aligned_cols=29 Identities=21% Similarity=0.430 Sum_probs=23.1
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
.|++||.+-.. ....++...|--||..++
T Consensus 2 ~C~~C~~s~fe--~d~a~g~~~C~~CG~v~E 30 (521)
T KOG1598|consen 2 VCKNCGGSNFE--RDEATGNLYCTACGTVLE 30 (521)
T ss_pred cCCCCCCCCcc--cccccCCceeccccceee
Confidence 69999977655 234678999999999875
No 493
>PHA01886 TM2 domain-containing protein
Probab=33.82 E-value=30 Score=27.12 Aligned_cols=13 Identities=23% Similarity=0.560 Sum_probs=7.7
Q ss_pred hcccchhHHHHHH
Q 025946 122 MTGQLGWVLDAIV 134 (245)
Q Consensus 122 ~T~gLgWLvd~~~ 134 (245)
+-.+++||+|.+.
T Consensus 38 G~~gig~liD~fl 50 (78)
T PHA01886 38 GLFGIGWFIDLFL 50 (78)
T ss_pred HHHHHHHHHHHHH
Confidence 3336667777664
No 494
>PLN02224 methionine-tRNA ligase
Probab=33.82 E-value=22 Score=36.30 Aligned_cols=28 Identities=29% Similarity=0.643 Sum_probs=20.5
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCcee
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPFS 193 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L~ 193 (245)
-||.|+ +|+...+++++ ..||.||.+++
T Consensus 192 yc~~ce-~f~~~~~l~~~--~~~~~~~~~~~ 219 (616)
T PLN02224 192 YCVNCE-EYKDEKELLEN--NCCPVHQMPCV 219 (616)
T ss_pred ecCCCC-CCCCHHHHcCC--CCCCCCCCcce
Confidence 799999 46665555543 36999999865
No 495
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=33.70 E-value=30 Score=27.52 Aligned_cols=16 Identities=31% Similarity=0.850 Sum_probs=12.1
Q ss_pred CcccCCCCCCceeeeC
Q 025946 181 ELQLCPYCSQPFSVVD 196 (245)
Q Consensus 181 d~iqCPnCGE~L~Vd~ 196 (245)
++.+||.|=+++++.+
T Consensus 70 ~~~~CPmCR~~w~~k~ 85 (85)
T PF12861_consen 70 SKGQCPMCRQPWKFKE 85 (85)
T ss_pred CCCCCCCcCCeeeeCC
Confidence 4678999988887653
No 496
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=33.63 E-value=25 Score=28.27 Aligned_cols=27 Identities=26% Similarity=0.603 Sum_probs=18.5
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
+||.||+.-.-- ..-+--.|..||..+
T Consensus 38 ~CpfCgk~~vkR---~a~GIW~C~~C~~~~ 64 (90)
T PRK03976 38 VCPVCGRPKVKR---VGTGIWECRKCGAKF 64 (90)
T ss_pred cCCCCCCCceEE---EEEEEEEcCCCCCEE
Confidence 899998654431 111567899998876
No 497
>PF06127 DUF962: Protein of unknown function (DUF962); InterPro: IPR009305 This family consists of several eukaryotic and prokaryotic proteins of unknown function. The yeast protein P25338 from SWISSPROT has been found to be non-essential for cell growth.
Probab=33.48 E-value=87 Score=24.30 Aligned_cols=47 Identities=19% Similarity=0.311 Sum_probs=29.9
Q ss_pred hhHHHHHHHHHHHHHhcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcceeccCCC
Q 025946 107 ILGNLALAIGLTYFSMTGQLGWVLDAIVSIWLLAVIVPIVGFGAFLWWASRDIVQDSCPN 166 (245)
Q Consensus 107 ~lgn~l~~l~l~~LL~T~gLgWLvd~~~~L~LlllllPIl~~~Gf~WWl~rnLIE~tCPn 166 (245)
.+|-.++++.++.++.+.. +-+++.+++++ .+++ |++--++|..=|.
T Consensus 25 ~igvp~~~~~~~~~~~~~~-----------~~~~l~~~~~g-~~~q-~~GH~~~E~~~Pa 71 (95)
T PF06127_consen 25 FIGVPLIIFSLLLLLARIP-----------WWLALAVFVVG-WGLQ-FIGHFFFEKNKPA 71 (95)
T ss_pred HHHHHHHHHHHHHHHHHcc-----------HHHHHHHHHHH-HHHH-HHhHHHHHcCCCc
Confidence 3455555555555544433 55566678888 7888 7888888876664
No 498
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=33.46 E-value=16 Score=40.37 Aligned_cols=27 Identities=41% Similarity=0.894 Sum_probs=18.0
Q ss_pred ceeccCCCCCceeeecccccCCCcccCCCC
Q 025946 159 IVQDSCPNCGNDFQIFKSTLNDELQLCPYC 188 (245)
Q Consensus 159 LIE~tCPnCG~eF~~~ed~Ln~d~iqCPnC 188 (245)
+|..-|||||=.... |- |.++ ..|+.|
T Consensus 6 iY~~~CpNCGG~iss-eR-L~~g-lpCe~C 32 (1187)
T COG1110 6 IYGSSCPNCGGDISS-ER-LEKG-LPCERC 32 (1187)
T ss_pred hhhccCCCCCCcCcH-HH-HhcC-CCchhc
Confidence 456789999988776 22 3332 239999
No 499
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=33.30 E-value=14 Score=32.44 Aligned_cols=20 Identities=25% Similarity=0.640 Sum_probs=16.8
Q ss_pred cCCCCCceeeecccccCCCcccCCCCCCce
Q 025946 163 SCPNCGNDFQIFKSTLNDELQLCPYCSQPF 192 (245)
Q Consensus 163 tCPnCG~eF~~~ed~Ln~d~iqCPnCGE~L 192 (245)
.|-+|| |+ +...|-+||+.+
T Consensus 120 fCaVCG---~~-------S~ysC~~CG~ky 139 (156)
T KOG3362|consen 120 FCAVCG---YD-------SKYSCVNCGTKY 139 (156)
T ss_pred hhhhcC---CC-------chhHHHhcCCce
Confidence 899999 44 688999999876
No 500
>PRK07219 DNA topoisomerase I; Validated
Probab=33.29 E-value=38 Score=35.42 Aligned_cols=18 Identities=22% Similarity=0.678 Sum_probs=13.1
Q ss_pred cccCCCCCCceeeeCCee
Q 025946 182 LQLCPYCSQPFSVVDDKF 199 (245)
Q Consensus 182 ~iqCPnCGE~L~Vd~~~F 199 (245)
...||.||..+....++|
T Consensus 688 ~~~CP~Cg~~l~~k~gr~ 705 (822)
T PRK07219 688 IGPCPKCGGELAIKQLKY 705 (822)
T ss_pred cccCCCCCCeeEEEcCCC
Confidence 467999988777665554
Done!