Query 028198
Match_columns 212
No_of_seqs 170 out of 303
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 07:48:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028198.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028198hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2463 Predicted RNA-binding 100.0 1.5E-61 3.3E-66 438.6 10.1 181 18-209 176-375 (376)
2 PF08772 NOB1_Zn_bind: Nin one 100.0 1.1E-33 2.3E-38 209.2 2.8 71 62-133 1-73 (73)
3 COG1439 Predicted nucleic acid 99.9 7.8E-24 1.7E-28 179.1 4.1 85 20-106 83-173 (177)
4 PRK12496 hypothetical protein; 99.7 5.5E-19 1.2E-23 147.3 2.9 80 20-101 76-157 (164)
5 TIGR03875 RNA_lig_partner RNA 97.7 1.2E-05 2.6E-10 70.2 1.0 28 31-58 168-195 (206)
6 PRK04358 hypothetical protein; 97.5 2.3E-05 4.9E-10 68.9 0.5 38 21-58 161-199 (217)
7 PF09723 Zn-ribbon_8: Zinc rib 96.4 0.0041 8.9E-08 41.2 3.3 32 68-100 3-40 (42)
8 smart00834 CxxC_CXXC_SSSS Puta 96.2 0.0041 8.8E-08 39.8 2.2 31 68-100 3-39 (41)
9 TIGR02605 CxxC_CxxC_SSSS putat 96.1 0.0059 1.3E-07 41.3 2.8 33 68-101 3-41 (52)
10 PF13248 zf-ribbon_3: zinc-rib 95.6 0.0035 7.5E-08 37.7 0.2 23 71-94 3-25 (26)
11 PF08745 UPF0278: UPF0278 fami 95.5 0.0069 1.5E-07 53.1 1.8 29 31-59 165-193 (205)
12 PF13240 zinc_ribbon_2: zinc-r 94.5 0.015 3.3E-07 34.3 0.7 22 72-94 1-22 (23)
13 COG1545 Predicted nucleic-acid 94.2 0.073 1.6E-06 43.6 4.5 44 65-111 24-67 (140)
14 PF12172 DUF35_N: Rubredoxin-l 94.1 0.035 7.6E-07 35.4 1.9 27 67-94 8-34 (37)
15 PRK03681 hypA hydrogenase nick 94.0 0.038 8.3E-07 43.8 2.3 30 65-94 65-96 (114)
16 PRK00564 hypA hydrogenase nick 94.0 0.046 9.9E-07 43.5 2.7 31 67-98 68-100 (117)
17 TIGR00100 hypA hydrogenase nic 93.9 0.046 1E-06 43.3 2.7 29 66-94 66-95 (115)
18 PRK12380 hydrogenase nickel in 93.8 0.044 9.6E-07 43.3 2.4 30 65-94 65-95 (113)
19 PRK13130 H/ACA RNA-protein com 93.5 0.044 9.6E-07 39.0 1.6 26 68-97 3-28 (56)
20 PF10571 UPF0547: Uncharacteri 93.4 0.04 8.6E-07 33.5 1.2 22 72-94 2-23 (26)
21 PRK00398 rpoP DNA-directed RNA 93.3 0.07 1.5E-06 35.5 2.3 25 70-94 3-30 (46)
22 PRK03824 hypA hydrogenase nick 93.0 0.073 1.6E-06 43.3 2.4 27 68-94 68-116 (135)
23 PF01155 HypA: Hydrogenase exp 92.9 0.078 1.7E-06 41.8 2.4 30 65-94 65-95 (113)
24 smart00659 RPOLCX RNA polymera 92.3 0.14 3.1E-06 34.5 2.7 30 70-100 2-33 (44)
25 COG3364 Zn-ribbon containing p 92.2 0.074 1.6E-06 42.5 1.4 30 71-101 3-35 (112)
26 PF09845 DUF2072: Zn-ribbon co 92.0 0.085 1.8E-06 43.5 1.6 30 71-101 2-34 (131)
27 cd00729 rubredoxin_SM Rubredox 91.7 0.15 3.3E-06 32.4 2.2 25 70-94 2-27 (34)
28 COG1579 Zn-ribbon protein, pos 91.5 0.11 2.3E-06 46.6 1.8 32 52-93 189-229 (239)
29 PF10263 SprT-like: SprT-like 91.3 0.3 6.5E-06 39.1 4.1 58 41-100 85-156 (157)
30 COG1996 RPC10 DNA-directed RNA 91.3 0.15 3.2E-06 35.5 2.0 32 68-100 4-38 (49)
31 cd00350 rubredoxin_like Rubred 91.2 0.15 3.3E-06 32.0 1.8 25 70-94 1-26 (33)
32 PF09538 FYDLN_acid: Protein o 90.8 0.11 2.4E-06 41.2 1.1 24 71-94 10-35 (108)
33 COG1592 Rubrerythrin [Energy p 90.8 0.17 3.7E-06 43.1 2.3 25 70-94 134-158 (166)
34 PF04135 Nop10p: Nucleolar RNA 90.7 0.34 7.4E-06 34.2 3.4 26 68-97 3-28 (53)
35 PRK04351 hypothetical protein; 89.6 0.55 1.2E-05 39.0 4.3 55 41-100 85-145 (149)
36 COG2093 DNA-directed RNA polym 89.5 0.17 3.8E-06 37.0 1.1 23 71-94 5-27 (64)
37 COG1645 Uncharacterized Zn-fin 89.2 0.29 6.3E-06 40.4 2.4 23 72-94 30-53 (131)
38 PRK00415 rps27e 30S ribosomal 88.9 0.31 6.8E-06 35.2 2.1 25 70-94 11-39 (59)
39 PRK06393 rpoE DNA-directed RNA 88.3 0.23 4.9E-06 36.4 1.0 24 70-97 5-28 (64)
40 PRK07591 threonine synthase; V 88.2 0.37 8E-06 45.5 2.7 27 68-94 16-42 (421)
41 TIGR03844 cysteate_syn cysteat 88.2 0.33 7.2E-06 45.8 2.4 26 69-94 1-26 (398)
42 PF03604 DNA_RNApol_7kD: DNA d 87.5 0.5 1.1E-05 30.0 2.2 28 71-99 1-30 (32)
43 COG2260 Predicted Zn-ribbon RN 87.5 0.25 5.5E-06 35.7 0.9 24 70-97 5-28 (59)
44 PRK08351 DNA-directed RNA poly 87.4 0.3 6.5E-06 35.4 1.2 22 72-97 5-26 (61)
45 PF11023 DUF2614: Protein of u 87.4 0.38 8.1E-06 38.9 1.9 33 65-97 64-97 (114)
46 COG1198 PriA Primosomal protei 87.3 0.46 9.9E-06 48.6 2.9 30 69-101 461-490 (730)
47 COG2331 Uncharacterized protei 86.9 0.45 9.7E-06 36.3 1.9 33 66-100 8-46 (82)
48 PRK00762 hypA hydrogenase nick 86.8 0.55 1.2E-05 37.7 2.6 32 65-98 65-104 (124)
49 TIGR02300 FYDLN_acid conserved 86.4 0.36 7.9E-06 39.7 1.3 25 70-94 9-35 (129)
50 PRK00241 nudC NADH pyrophospha 86.0 0.81 1.8E-05 40.8 3.5 55 71-128 100-161 (256)
51 TIGR00595 priA primosomal prot 85.8 0.55 1.2E-05 45.5 2.5 28 70-100 240-267 (505)
52 COG5257 GCD11 Translation init 85.8 1.1 2.4E-05 42.8 4.3 41 68-109 55-96 (415)
53 PRK06450 threonine synthase; V 85.6 0.51 1.1E-05 43.4 2.1 24 71-94 4-27 (338)
54 PRK14714 DNA polymerase II lar 85.6 0.66 1.4E-05 50.1 3.1 27 65-94 662-688 (1337)
55 PF07295 DUF1451: Protein of u 84.9 0.67 1.5E-05 38.6 2.3 31 70-101 112-145 (146)
56 PRK06260 threonine synthase; V 84.4 0.7 1.5E-05 43.1 2.4 26 69-94 2-28 (397)
57 PF05191 ADK_lid: Adenylate ki 84.2 0.96 2.1E-05 29.3 2.3 24 71-94 2-30 (36)
58 PF14803 Nudix_N_2: Nudix N-te 84.1 0.56 1.2E-05 30.2 1.1 15 86-101 1-15 (34)
59 PRK00420 hypothetical protein; 83.9 0.59 1.3E-05 37.5 1.5 24 71-94 24-49 (112)
60 COG0267 RpmG Ribosomal protein 83.4 0.75 1.6E-05 32.2 1.6 31 68-99 5-47 (50)
61 PRK11032 hypothetical protein; 83.2 0.88 1.9E-05 38.6 2.3 31 70-101 124-157 (160)
62 TIGR02098 MJ0042_CXXC MJ0042 f 83.1 0.97 2.1E-05 28.6 2.0 25 70-94 2-34 (38)
63 smart00731 SprT SprT homologue 82.9 1.6 3.4E-05 35.3 3.6 52 43-94 84-142 (146)
64 PRK14559 putative protein seri 82.6 0.53 1.2E-05 47.4 0.9 21 73-94 30-50 (645)
65 PF12773 DZR: Double zinc ribb 82.4 0.63 1.4E-05 30.9 0.9 22 72-93 14-37 (50)
66 PF12773 DZR: Double zinc ribb 82.4 0.68 1.5E-05 30.8 1.1 21 73-94 1-21 (50)
67 COG0375 HybF Zn finger protein 81.9 1 2.2E-05 36.4 2.1 33 65-98 65-98 (115)
68 PF14205 Cys_rich_KTR: Cystein 81.7 0.77 1.7E-05 32.8 1.2 15 86-101 5-19 (55)
69 PF02150 RNA_POL_M_15KD: RNA p 81.1 0.67 1.5E-05 29.7 0.6 9 86-94 2-10 (35)
70 PF09297 zf-NADH-PPase: NADH p 79.9 0.86 1.9E-05 28.2 0.9 9 86-94 4-12 (32)
71 PF14446 Prok-RING_1: Prokaryo 79.1 1 2.2E-05 32.0 1.1 25 70-94 5-30 (54)
72 PF14369 zf-RING_3: zinc-finge 79.1 1.5 3.4E-05 28.1 1.9 24 71-94 3-30 (35)
73 PRK14873 primosome assembly pr 79.0 1.5 3.3E-05 44.3 2.7 29 70-102 410-438 (665)
74 TIGR02827 RNR_anaer_Bdell anae 78.7 1.8 3.9E-05 43.4 3.0 49 42-100 509-560 (586)
75 PF06676 DUF1178: Protein of u 78.4 2.3 5E-05 35.6 3.2 33 67-101 2-47 (148)
76 TIGR00354 polC DNA polymerase, 78.1 1.9 4.1E-05 45.7 3.1 29 65-97 620-648 (1095)
77 cd01675 RNR_III Class III ribo 77.4 1.9 4.1E-05 42.5 2.8 30 70-101 518-547 (555)
78 PF07282 OrfB_Zn_ribbon: Putat 77.2 2.7 5.8E-05 29.6 2.8 45 44-94 8-55 (69)
79 PRK05580 primosome assembly pr 77.1 1.6 3.5E-05 43.8 2.3 28 70-100 408-435 (679)
80 PF14319 Zn_Tnp_IS91: Transpos 77.1 1.7 3.7E-05 34.3 2.0 27 68-94 40-69 (111)
81 COG3091 SprT Zn-dependent meta 76.6 1.5 3.3E-05 37.2 1.6 52 45-99 89-152 (156)
82 PF09151 DUF1936: Domain of un 76.4 4.2 9.1E-05 26.3 3.2 25 86-114 2-26 (36)
83 PRK07111 anaerobic ribonucleos 75.5 1.9 4.2E-05 44.1 2.4 26 70-98 680-705 (735)
84 PLN00209 ribosomal protein S27 75.5 1.7 3.8E-05 33.5 1.6 25 70-94 36-64 (86)
85 PF07191 zinc-ribbons_6: zinc- 75.5 2.4 5.2E-05 31.6 2.3 28 70-101 17-44 (70)
86 PF00301 Rubredoxin: Rubredoxi 75.4 2.7 5.9E-05 28.8 2.3 25 70-94 1-43 (47)
87 PTZ00083 40S ribosomal protein 74.9 1.8 4E-05 33.3 1.5 25 70-94 35-63 (85)
88 PF14205 Cys_rich_KTR: Cystein 74.8 3 6.6E-05 29.8 2.5 31 68-100 3-42 (55)
89 PRK04023 DNA polymerase II lar 74.4 2.5 5.4E-05 45.0 2.8 34 68-106 1035-1069(1121)
90 TIGR00354 polC DNA polymerase, 74.1 2.4 5.3E-05 44.9 2.7 27 68-94 1010-1037(1095)
91 COG1110 Reverse gyrase [DNA re 73.7 0.97 2.1E-05 48.1 -0.3 25 69-94 693-717 (1187)
92 PRK11788 tetratricopeptide rep 73.6 2.1 4.6E-05 37.8 1.9 27 71-98 355-381 (389)
93 PRK02935 hypothetical protein; 73.5 2.5 5.3E-05 34.0 2.0 30 67-96 67-97 (110)
94 smart00661 RPOL9 RNA polymeras 73.3 1.6 3.4E-05 29.0 0.7 9 86-94 1-9 (52)
95 PF15017 AF1Q: Drug resistance 73.3 1.9 4.1E-05 33.4 1.3 16 14-29 64-79 (87)
96 PRK05978 hypothetical protein; 73.1 1.1 2.5E-05 37.5 0.0 32 67-100 30-65 (148)
97 TIGR02487 NrdD anaerobic ribon 73.0 2 4.4E-05 42.5 1.8 44 42-94 501-547 (579)
98 PF08792 A2L_zn_ribbon: A2L zi 72.8 2.4 5.1E-05 27.0 1.4 23 71-93 4-29 (33)
99 COG0846 SIR2 NAD-dependent pro 72.7 3.5 7.5E-05 37.1 3.0 57 34-99 93-159 (250)
100 PRK14559 putative protein seri 72.7 1.8 3.8E-05 43.8 1.2 23 71-94 2-24 (645)
101 PRK14714 DNA polymerase II lar 72.6 2.8 6.2E-05 45.5 2.8 34 68-106 1251-1285(1337)
102 COG2888 Predicted Zn-ribbon RN 72.5 1.4 2.9E-05 32.1 0.3 8 86-93 51-58 (61)
103 PF13597 NRDD: Anaerobic ribon 72.5 1.9 4E-05 42.5 1.4 23 70-94 491-513 (546)
104 cd00730 rubredoxin Rubredoxin; 72.1 2.2 4.7E-05 29.6 1.2 25 70-94 1-43 (50)
105 PF03119 DNA_ligase_ZBD: NAD-d 72.0 2.2 4.7E-05 26.1 1.1 8 87-94 1-8 (28)
106 PRK14890 putative Zn-ribbon RN 71.6 1.8 4E-05 31.3 0.8 22 70-94 36-57 (59)
107 COG2888 Predicted Zn-ribbon RN 71.5 1.8 4E-05 31.5 0.8 31 70-101 9-42 (61)
108 PF14353 CpXC: CpXC protein 71.5 3.7 8.1E-05 32.3 2.6 9 86-94 39-47 (128)
109 PRK04023 DNA polymerase II lar 71.5 2.2 4.7E-05 45.5 1.6 10 139-148 773-782 (1121)
110 PRK11823 DNA repair protein Ra 71.4 3 6.5E-05 39.9 2.4 31 68-99 5-35 (446)
111 PRK07218 replication factor A; 71.4 5.8 0.00013 38.3 4.4 69 41-112 266-339 (423)
112 smart00531 TFIIE Transcription 71.0 3 6.5E-05 34.0 2.0 28 67-94 96-132 (147)
113 cd04476 RPA1_DBD_C RPA1_DBD_C: 70.5 6.3 0.00014 32.1 3.9 43 67-110 31-81 (166)
114 PRK14890 putative Zn-ribbon RN 70.5 2.7 5.8E-05 30.4 1.4 31 70-101 7-40 (59)
115 PF02591 DUF164: Putative zinc 70.3 2.3 4.9E-05 29.3 1.0 22 72-93 24-54 (56)
116 COG1933 Archaeal DNA polymeras 70.2 2.7 5.8E-05 38.1 1.7 27 68-94 165-192 (253)
117 PF13638 PIN_4: PIN domain; PD 69.4 5 0.00011 30.9 2.9 27 32-58 106-132 (133)
118 TIGR00686 phnA alkylphosphonat 69.1 3.7 8.1E-05 33.0 2.2 38 72-111 4-51 (109)
119 PRK08270 anaerobic ribonucleos 69.0 3.4 7.4E-05 41.8 2.4 43 42-94 602-648 (656)
120 COG4031 Predicted metal-bindin 68.6 3.6 7.7E-05 36.4 2.1 32 71-106 1-32 (227)
121 PRK14715 DNA polymerase II lar 68.2 3.8 8.2E-05 45.0 2.6 25 69-94 1541-1566(1627)
122 cd01121 Sms Sms (bacterial rad 68.0 2.6 5.6E-05 39.6 1.2 28 71-99 1-28 (372)
123 PF12677 DUF3797: Domain of un 67.8 5.5 0.00012 27.9 2.5 21 85-112 13-33 (49)
124 PRK08579 anaerobic ribonucleos 67.7 2.9 6.2E-05 42.2 1.5 46 40-94 543-591 (625)
125 PRK12366 replication factor A; 67.6 6.8 0.00015 39.3 4.2 48 63-110 525-576 (637)
126 PF04216 FdhE: Protein involve 67.6 5 0.00011 36.0 2.9 40 69-109 196-235 (290)
127 cd01407 SIR2-fam SIR2 family o 67.5 4.7 0.0001 34.5 2.6 41 48-94 92-142 (218)
128 PF01780 Ribosomal_L37ae: Ribo 67.5 2.2 4.9E-05 33.1 0.6 18 85-103 35-52 (90)
129 PRK00504 rpmG 50S ribosomal pr 66.7 6.4 0.00014 27.4 2.7 31 68-99 5-47 (50)
130 PRK08402 replication factor A; 66.7 9.8 0.00021 35.9 4.8 45 67-111 209-259 (355)
131 PF07754 DUF1610: Domain of un 66.7 3.5 7.7E-05 24.8 1.2 21 73-93 1-24 (24)
132 PRK10220 hypothetical protein; 66.7 4.6 9.9E-05 32.6 2.2 38 72-111 5-52 (111)
133 PRK03988 translation initiatio 66.5 5.3 0.00011 33.0 2.6 48 34-81 78-134 (138)
134 PF13717 zinc_ribbon_4: zinc-r 66.5 4.1 8.9E-05 26.1 1.6 24 70-93 2-33 (36)
135 PLN02569 threonine synthase 66.3 5.7 0.00012 38.7 3.2 57 35-98 18-75 (484)
136 PRK08329 threonine synthase; V 66.3 3.6 7.7E-05 37.8 1.7 25 71-98 2-26 (347)
137 PRK05638 threonine synthase; V 66.2 3.7 8.1E-05 38.9 1.9 24 70-94 1-24 (442)
138 PF13719 zinc_ribbon_5: zinc-r 65.8 5.1 0.00011 25.7 1.9 24 71-94 3-34 (37)
139 PF03833 PolC_DP2: DNA polymer 65.6 2 4.4E-05 44.9 0.0 10 139-148 802-811 (900)
140 COG1096 Predicted RNA-binding 65.3 4 8.7E-05 35.6 1.8 33 70-103 149-182 (188)
141 TIGR00311 aIF-2beta translatio 64.9 7 0.00015 32.1 3.0 39 42-80 84-128 (133)
142 TIGR01023 rpmG_bact ribosomal 64.8 8 0.00017 27.2 2.9 32 67-99 8-51 (54)
143 TIGR00416 sms DNA repair prote 64.6 4.4 9.4E-05 39.0 2.0 31 68-99 5-35 (454)
144 PRK08271 anaerobic ribonucleos 63.7 4 8.6E-05 41.2 1.6 44 42-94 543-589 (623)
145 COG1997 RPL43A Ribosomal prote 63.7 4.2 9E-05 31.7 1.4 17 85-102 35-51 (89)
146 PRK08197 threonine synthase; V 63.1 5.8 0.00013 37.0 2.5 25 69-94 6-31 (394)
147 cd01413 SIR2_Af2 SIR2_Af2: Arc 62.7 5.2 0.00011 34.6 2.0 27 68-94 111-145 (222)
148 cd01408 SIRT1 SIRT1: Eukaryoti 62.7 5.8 0.00013 34.7 2.3 34 55-94 107-149 (235)
149 COG0777 AccD Acetyl-CoA carbox 62.7 2.4 5.1E-05 39.2 -0.1 73 71-163 29-108 (294)
150 PF02146 SIR2: Sir2 family; I 62.4 8.4 0.00018 31.8 3.1 27 68-94 103-138 (178)
151 PRK00595 rpmG 50S ribosomal pr 62.4 8.8 0.00019 26.8 2.8 32 67-99 7-50 (53)
152 smart00653 eIF2B_5 domain pres 62.4 6.7 0.00015 31.1 2.4 45 34-78 56-109 (110)
153 PF08271 TF_Zn_Ribbon: TFIIB z 62.2 3.5 7.7E-05 26.9 0.7 23 71-93 1-27 (43)
154 PRK04338 N(2),N(2)-dimethylgua 61.9 6 0.00013 37.3 2.4 27 68-94 242-270 (382)
155 cd01410 SIRT7 SIRT7: Eukaryoti 61.0 6.1 0.00013 33.9 2.1 27 68-94 93-129 (206)
156 PRK00432 30S ribosomal protein 60.7 6.5 0.00014 27.1 1.8 8 86-93 21-28 (50)
157 PRK00481 NAD-dependent deacety 60.6 6.7 0.00015 34.2 2.4 27 68-94 120-151 (242)
158 PF07975 C1_4: TFIIH C1-like d 60.6 3.9 8.5E-05 28.6 0.7 10 73-82 2-11 (51)
159 PTZ00255 60S ribosomal protein 60.3 8.1 0.00018 30.0 2.5 20 84-104 35-54 (90)
160 PF03833 PolC_DP2: DNA polymer 60.3 2.9 6.2E-05 43.8 0.0 21 71-94 656-676 (900)
161 PF04606 Ogr_Delta: Ogr/Delta- 60.1 6.8 0.00015 26.3 1.8 23 87-110 1-23 (47)
162 CHL00104 rpl33 ribosomal prote 59.8 9 0.0002 28.1 2.5 32 67-99 9-62 (66)
163 PRK05452 anaerobic nitric oxid 59.7 6.3 0.00014 38.0 2.2 25 70-94 425-467 (479)
164 COG1867 TRM1 N2,N2-dimethylgua 59.3 6 0.00013 37.9 1.9 28 67-94 237-266 (380)
165 TIGR00280 L37a ribosomal prote 59.0 8.7 0.00019 29.9 2.5 19 85-104 35-53 (91)
166 TIGR00308 TRM1 tRNA(guanine-26 58.3 8 0.00017 36.5 2.6 27 68-94 231-261 (374)
167 cd01411 SIR2H SIR2H: Uncharact 58.1 6.9 0.00015 34.0 2.0 26 69-94 117-145 (225)
168 PRK14704 anaerobic ribonucleos 58.0 6 0.00013 39.8 1.8 23 70-94 559-581 (618)
169 COG0675 Transposase and inacti 58.0 5 0.00011 34.5 1.1 22 71-94 310-331 (364)
170 PF01907 Ribosomal_L37e: Ribos 57.8 6.5 0.00014 28.1 1.4 24 71-94 16-39 (55)
171 PTZ00408 NAD-dependent deacety 57.5 7.4 0.00016 34.5 2.1 26 68-93 115-145 (242)
172 PRK12336 translation initiatio 57.3 10 0.00023 32.7 2.9 47 35-81 75-130 (201)
173 TIGR00155 pqiA_fam integral me 57.2 6 0.00013 37.6 1.6 25 70-94 215-239 (403)
174 PRK06266 transcription initiat 57.1 7.4 0.00016 33.1 2.0 63 35-99 82-148 (178)
175 PTZ00410 NAD-dependent SIR2; P 56.6 11 0.00025 35.5 3.3 27 68-94 145-180 (349)
176 PHA00626 hypothetical protein 56.4 7.4 0.00016 28.1 1.6 14 87-101 2-15 (59)
177 PF06906 DUF1272: Protein of u 56.2 4.5 9.8E-05 29.1 0.4 29 66-94 22-50 (57)
178 PRK03976 rpl37ae 50S ribosomal 56.2 11 0.00023 29.4 2.5 19 85-104 36-54 (90)
179 COG1656 Uncharacterized conser 56.2 5.1 0.00011 34.3 0.8 23 33-56 47-69 (165)
180 PRK14138 NAD-dependent deacety 54.9 10 0.00022 33.4 2.5 26 69-94 118-152 (244)
181 PRK09263 anaerobic ribonucleos 54.8 10 0.00023 38.7 2.9 25 70-94 641-668 (711)
182 cd00296 SIR2 SIR2 superfamily 54.8 11 0.00023 31.7 2.6 53 34-94 82-143 (222)
183 PF05991 NYN_YacP: YacP-like N 54.6 13 0.00027 31.0 2.9 44 16-59 73-121 (166)
184 PRK15103 paraquat-inducible me 54.3 6.4 0.00014 37.7 1.2 24 71-94 11-39 (419)
185 COG2126 RPL37A Ribosomal prote 54.1 5.7 0.00012 28.9 0.7 27 68-94 14-40 (61)
186 PRK09521 exosome complex RNA-b 53.6 7.7 0.00017 32.7 1.5 31 70-101 149-181 (189)
187 PRK14289 chaperone protein Dna 53.4 51 0.0011 30.9 7.0 28 69-97 196-223 (386)
188 TIGR00373 conserved hypothetic 53.2 8.9 0.00019 31.9 1.8 27 68-94 107-137 (158)
189 COG2176 PolC DNA polymerase II 53.1 7.2 0.00016 42.6 1.5 24 71-94 915-948 (1444)
190 PRK05654 acetyl-CoA carboxylas 52.9 7.3 0.00016 35.7 1.3 25 70-94 27-55 (292)
191 PF01783 Ribosomal_L32p: Ribos 52.8 12 0.00026 26.1 2.2 21 71-93 27-47 (56)
192 TIGR00515 accD acetyl-CoA carb 52.5 7.6 0.00016 35.5 1.4 25 69-94 26-54 (285)
193 PF14206 Cys_rich_CPCC: Cystei 52.5 6.8 0.00015 29.6 0.9 23 71-93 2-28 (78)
194 CHL00174 accD acetyl-CoA carbo 52.4 7.4 0.00016 36.0 1.3 25 69-94 38-66 (296)
195 COG1379 PHP family phosphoeste 52.3 4.7 0.0001 38.4 -0.0 32 63-94 239-274 (403)
196 PRK04011 peptide chain release 52.2 16 0.00034 34.9 3.5 27 68-94 326-359 (411)
197 TIGR03826 YvyF flagellar opero 52.1 4.6 0.0001 33.4 -0.1 23 72-94 5-27 (137)
198 PRK14715 DNA polymerase II lar 51.8 12 0.00026 41.4 2.9 27 65-94 669-695 (1627)
199 PRK04860 hypothetical protein; 51.7 20 0.00043 30.2 3.7 58 41-101 87-157 (160)
200 COG3478 Predicted nucleic-acid 51.3 7.9 0.00017 28.7 1.0 7 88-94 7-13 (68)
201 cd01409 SIRT4 SIRT4: Eukaryoti 51.1 12 0.00025 33.4 2.3 14 68-81 116-129 (260)
202 PRK00448 polC DNA polymerase I 50.9 9.2 0.0002 42.2 1.9 24 71-94 909-942 (1437)
203 PF06221 zf-C2HC5: Putative zi 50.6 8.5 0.00018 27.5 1.1 32 63-94 11-44 (57)
204 TIGR00155 pqiA_fam integral me 50.4 10 0.00022 36.1 1.9 25 70-94 13-42 (403)
205 KOG3084 NADH pyrophosphatase I 50.1 7.1 0.00015 36.9 0.8 12 85-97 150-161 (345)
206 PF09082 DUF1922: Domain of un 50.1 9.3 0.0002 28.4 1.2 24 69-94 2-28 (68)
207 KOG1779 40s ribosomal protein 49.9 8 0.00017 29.7 0.9 24 71-94 35-62 (84)
208 cd01412 SIRT5_Af1_CobB SIRT5_A 49.6 11 0.00024 32.2 1.9 27 68-94 107-139 (224)
209 PF10122 Mu-like_Com: Mu-like 49.6 9.3 0.0002 26.9 1.1 24 70-93 4-32 (51)
210 COG1328 NrdD Oxygen-sensitive 49.3 9.5 0.00021 39.2 1.6 47 39-94 615-664 (700)
211 PF04828 GFA: Glutathione-depe 49.3 5.6 0.00012 28.3 -0.0 15 80-94 43-57 (92)
212 PF09855 DUF2082: Nucleic-acid 49.2 14 0.00029 26.9 2.0 19 87-106 2-20 (64)
213 PF06827 zf-FPG_IleRS: Zinc fi 48.9 7.3 0.00016 23.5 0.5 13 87-101 3-15 (30)
214 COG1631 RPL42A Ribosomal prote 48.8 12 0.00025 29.5 1.7 18 85-103 8-25 (94)
215 COG0498 ThrC Threonine synthas 48.6 10 0.00022 36.5 1.6 27 68-94 3-30 (411)
216 PHA02942 putative transposase; 47.9 24 0.00051 33.4 3.9 42 47-94 308-351 (383)
217 PRK15103 paraquat-inducible me 47.8 10 0.00022 36.3 1.5 24 70-94 221-244 (419)
218 TIGR01405 polC_Gram_pos DNA po 47.6 11 0.00025 40.8 2.0 24 71-94 684-717 (1213)
219 cd04511 Nudix_Hydrolase_4 Memb 47.4 36 0.00078 26.1 4.3 24 104-128 20-43 (130)
220 PF09332 Mcm10: Mcm10 replicat 46.7 15 0.00032 34.7 2.4 37 71-108 286-325 (344)
221 TIGR00340 zpr1_rel ZPR1-relate 46.4 15 0.00033 31.1 2.2 12 88-100 1-12 (163)
222 COG1458 Predicted DNA-binding 46.3 17 0.00036 32.5 2.4 28 31-58 172-199 (221)
223 PF01667 Ribosomal_S27e: Ribos 46.2 13 0.00028 26.5 1.4 25 70-94 7-35 (55)
224 PF14690 zf-ISL3: zinc-finger 45.8 10 0.00023 24.5 0.9 11 86-97 3-13 (47)
225 PF02005 TRM: N2,N2-dimethylgu 45.3 15 0.00033 34.6 2.2 28 67-94 237-268 (377)
226 PTZ00157 60S ribosomal protein 44.9 15 0.00033 28.3 1.7 19 85-104 9-27 (84)
227 TIGR01562 FdhE formate dehydro 44.7 23 0.0005 32.9 3.3 31 70-101 210-240 (305)
228 PRK00464 nrdR transcriptional 44.6 20 0.00043 30.1 2.6 8 86-93 29-36 (154)
229 KOG3799 Rab3 effector RIM1 and 44.5 11 0.00023 31.9 1.0 16 83-98 87-102 (169)
230 KOG2906 RNA polymerase III sub 43.9 10 0.00022 30.3 0.7 9 86-94 2-10 (105)
231 PRK12286 rpmF 50S ribosomal pr 43.9 16 0.00034 25.9 1.6 9 86-94 28-36 (57)
232 TIGR01031 rpmF_bact ribosomal 43.9 15 0.00032 25.8 1.4 19 72-92 28-46 (55)
233 COG3357 Predicted transcriptio 43.5 12 0.00025 29.6 1.0 26 71-97 59-87 (97)
234 COG3791 Uncharacterized conser 43.2 13 0.00027 30.0 1.2 12 83-94 67-78 (133)
235 PF00471 Ribosomal_L33: Riboso 42.4 12 0.00026 25.7 0.8 30 68-98 3-44 (48)
236 COG2051 RPS27A Ribosomal prote 42.1 15 0.00032 27.3 1.3 24 70-93 19-46 (67)
237 PF08646 Rep_fac-A_C: Replicat 41.9 39 0.00084 26.9 3.8 44 68-111 16-68 (146)
238 PF15616 TerY-C: TerY-C metal 41.7 16 0.00034 30.1 1.5 22 72-94 91-114 (131)
239 PRK12495 hypothetical protein; 41.5 16 0.00034 32.8 1.6 24 71-94 43-67 (226)
240 PRK03564 formate dehydrogenase 41.4 30 0.00064 32.3 3.4 29 69-98 211-239 (309)
241 PRK12775 putative trifunctiona 41.3 14 0.0003 39.1 1.4 25 70-94 821-847 (1006)
242 COG5270 PUA domain (predicted 41.3 22 0.00047 31.4 2.4 32 67-103 11-42 (202)
243 PRK05767 rpl44e 50S ribosomal 41.2 22 0.00048 27.8 2.2 19 85-104 8-26 (92)
244 PF01396 zf-C4_Topoisom: Topoi 41.0 17 0.00036 23.6 1.3 25 86-115 2-26 (39)
245 PF10058 DUF2296: Predicted in 40.8 21 0.00045 25.0 1.8 27 67-93 19-52 (54)
246 TIGR03831 YgiT_finger YgiT-typ 40.7 32 0.00068 21.7 2.6 21 74-94 21-41 (46)
247 PF09862 DUF2089: Protein of u 40.7 18 0.00038 29.2 1.6 19 73-92 1-19 (113)
248 COG2401 ABC-type ATPase fused 40.6 16 0.00034 36.5 1.5 50 36-94 104-153 (593)
249 PRK06386 replication factor A; 40.6 18 0.00039 34.3 1.9 68 39-112 205-278 (358)
250 PRK00241 nudC NADH pyrophospha 40.2 13 0.00027 33.2 0.8 10 85-94 99-108 (256)
251 COG1594 RPB9 DNA-directed RNA 40.1 12 0.00026 29.7 0.6 9 86-94 3-11 (113)
252 COG2816 NPY1 NTP pyrophosphohy 40.1 32 0.00069 31.8 3.4 28 71-99 112-142 (279)
253 PRK07956 ligA NAD-dependent DN 40.0 36 0.00077 34.6 4.0 47 46-94 361-413 (665)
254 PF01927 Mut7-C: Mut7-C RNAse 39.9 19 0.0004 29.3 1.7 13 87-101 93-105 (147)
255 PTZ00073 60S ribosomal protein 39.3 14 0.00031 28.8 0.9 24 71-94 17-40 (91)
256 KOG2324 Prolyl-tRNA synthetase 39.3 84 0.0018 30.7 6.1 55 46-101 189-262 (457)
257 PRK04179 rpl37e 50S ribosomal 39.0 14 0.0003 27.1 0.7 24 70-93 17-40 (62)
258 PF01623 Carla_C4: Carlavirus 39.0 17 0.00036 28.4 1.2 25 68-94 51-75 (91)
259 PRK05333 NAD-dependent deacety 38.8 26 0.00057 31.4 2.6 13 68-80 126-138 (285)
260 TIGR03676 aRF1/eRF1 peptide ch 38.5 23 0.00051 33.7 2.4 27 68-94 318-351 (403)
261 COG2995 PqiA Uncharacterized p 38.1 15 0.00032 35.6 1.0 24 71-94 221-244 (418)
262 TIGR00627 tfb4 transcription f 37.8 23 0.0005 32.4 2.1 24 70-94 255-278 (279)
263 COG2995 PqiA Uncharacterized p 37.4 19 0.00042 34.9 1.6 32 67-100 15-51 (418)
264 COG0384 Predicted epimerase, P 37.3 31 0.00066 31.7 2.8 50 39-98 31-80 (291)
265 COG1601 GCD7 Translation initi 37.1 9.6 0.00021 32.1 -0.4 42 40-81 90-137 (151)
266 COG2816 NPY1 NTP pyrophosphohy 36.7 16 0.00034 33.8 0.8 11 84-94 110-120 (279)
267 PF10609 ParA: ParA/MinD ATPas 36.6 15 0.00033 27.8 0.6 13 82-94 62-74 (81)
268 PF06677 Auto_anti-p27: Sjogre 36.5 30 0.00065 23.0 2.0 9 86-94 18-26 (41)
269 COG1066 Sms Predicted ATP-depe 36.1 27 0.00058 34.3 2.4 32 69-101 6-37 (456)
270 PF13408 Zn_ribbon_recom: Reco 36.0 19 0.0004 23.9 0.9 14 84-99 4-17 (58)
271 PF01873 eIF-5_eIF-2B: Domain 35.9 14 0.0003 29.9 0.4 37 43-79 81-123 (125)
272 PTZ00409 Sir2 (Silent Informat 35.9 23 0.0005 32.0 1.8 14 68-81 135-148 (271)
273 COG4888 Uncharacterized Zn rib 35.7 30 0.00066 27.6 2.2 22 85-109 22-43 (104)
274 PF05876 Terminase_GpA: Phage 35.0 24 0.00052 34.9 1.9 29 66-94 196-238 (557)
275 COG1773 Rubredoxin [Energy pro 34.9 27 0.00058 24.9 1.6 12 70-81 3-14 (55)
276 PF12760 Zn_Tnp_IS1595: Transp 34.6 23 0.00049 23.4 1.2 9 86-94 19-27 (46)
277 PF09862 DUF2089: Protein of u 34.5 18 0.0004 29.1 0.8 20 88-109 1-20 (113)
278 TIGR00575 dnlj DNA ligase, NAD 34.2 50 0.0011 33.5 4.0 48 46-94 349-401 (652)
279 PF14447 Prok-RING_4: Prokaryo 34.0 27 0.00058 25.0 1.5 21 71-94 28-48 (55)
280 COG4469 CoiA Competence protei 33.9 20 0.00044 33.9 1.1 10 85-94 25-34 (342)
281 KOG0402 60S ribosomal protein 33.5 13 0.00029 28.9 -0.1 20 84-104 35-54 (92)
282 KOG2768 Translation initiation 33.1 24 0.00052 31.7 1.4 54 40-94 136-211 (231)
283 PF14255 Cys_rich_CPXG: Cystei 32.8 31 0.00067 24.1 1.6 8 87-94 2-9 (52)
284 COG4640 Predicted membrane pro 32.5 18 0.0004 35.2 0.6 23 71-94 2-24 (465)
285 COG4260 Membrane protease subu 32.0 20 0.00044 33.7 0.8 9 86-94 335-343 (345)
286 smart00440 ZnF_C2C2 C2C2 Zinc 31.6 22 0.00049 23.1 0.7 8 87-94 2-9 (40)
287 KOG3475 60S ribosomal protein 31.6 16 0.00034 28.5 0.0 23 72-94 18-40 (92)
288 PF13453 zf-TFIIB: Transcripti 31.5 32 0.00069 22.2 1.5 13 88-102 2-14 (41)
289 PRK14350 ligA NAD-dependent DN 31.3 47 0.001 34.0 3.3 43 46-94 358-407 (669)
290 TIGR01384 TFS_arch transcripti 31.3 27 0.00057 26.5 1.2 23 72-94 2-25 (104)
291 KOG4718 Non-SMC (structural ma 31.3 16 0.00035 32.8 0.0 30 64-93 188-224 (235)
292 TIGR01562 FdhE formate dehydro 31.1 24 0.00052 32.7 1.1 10 85-94 184-193 (305)
293 TIGR02820 formald_GSH S-(hydro 31.1 21 0.00046 30.8 0.7 12 83-94 87-98 (182)
294 PF14569 zf-UDP: Zinc-binding 30.9 10 0.00022 29.0 -1.1 24 71-94 37-60 (80)
295 PRK05417 glutathione-dependent 30.8 20 0.00043 31.2 0.5 12 83-94 91-102 (191)
296 PF04216 FdhE: Protein involve 30.6 50 0.0011 29.6 3.0 23 85-110 172-196 (290)
297 COG4530 Uncharacterized protei 30.5 25 0.00055 28.7 1.0 24 71-94 10-35 (129)
298 PF15499 Peptidase_C98: Ubiqui 30.4 26 0.00057 32.3 1.2 83 40-129 109-223 (275)
299 COG3058 FdhE Uncharacterized p 30.3 36 0.00077 31.8 2.1 11 84-94 184-194 (308)
300 TIGR00375 conserved hypothetic 30.2 33 0.00071 32.7 1.9 50 44-94 213-267 (374)
301 PRK09678 DNA-binding transcrip 30.1 29 0.00064 25.8 1.2 21 86-107 2-22 (72)
302 PRK07225 DNA-directed RNA poly 29.7 36 0.00077 34.4 2.1 32 70-101 544-578 (605)
303 PF01747 ATP-sulfurylase: ATP- 29.6 76 0.0016 27.9 3.9 51 32-94 125-179 (215)
304 PRK07217 replication factor A; 29.6 31 0.00068 32.3 1.6 44 64-110 182-230 (311)
305 PF10083 DUF2321: Uncharacteri 29.5 4.9 0.00011 34.2 -3.3 15 85-100 28-42 (158)
306 PF06044 DRP: Dam-replacing fa 29.5 26 0.00057 32.0 1.0 14 86-100 32-45 (254)
307 PF13824 zf-Mss51: Zinc-finger 29.4 39 0.00084 24.1 1.7 22 73-94 2-23 (55)
308 TIGR00108 eRF peptide chain re 28.9 44 0.00095 31.9 2.5 27 68-94 322-355 (409)
309 TIGR00595 priA primosomal prot 28.9 26 0.00056 34.1 1.0 19 70-94 213-231 (505)
310 PRK14892 putative transcriptio 28.6 47 0.001 26.0 2.2 18 85-106 21-38 (99)
311 PF10601 zf-LITAF-like: LITAF- 28.6 52 0.0011 23.5 2.3 20 83-103 5-24 (73)
312 PRK14873 primosome assembly pr 28.5 33 0.00072 34.8 1.7 11 69-79 382-392 (665)
313 PF08273 Prim_Zn_Ribbon: Zinc- 28.5 23 0.0005 23.5 0.4 19 86-107 4-22 (40)
314 KOG0806 Carbon-nitrogen hydrol 28.0 1.3E+02 0.0029 28.0 5.3 94 41-150 83-177 (298)
315 PF15135 UPF0515: Uncharacteri 27.9 26 0.00057 32.2 0.8 25 70-94 132-164 (278)
316 PF01096 TFIIS_C: Transcriptio 27.8 28 0.00061 22.5 0.7 8 87-94 2-9 (39)
317 COG1571 Predicted DNA-binding 27.8 34 0.00073 33.3 1.5 33 62-94 339-376 (421)
318 PRK14287 chaperone protein Dna 27.7 1.3E+02 0.0028 28.2 5.3 24 70-94 181-204 (371)
319 cd03361 TOPRIM_TopoIA_RevGyr T 27.6 46 0.00099 27.8 2.1 26 68-94 75-100 (170)
320 PF14354 Lar_restr_allev: Rest 27.6 43 0.00092 22.8 1.6 9 86-94 4-12 (61)
321 PF08274 PhnA_Zn_Ribbon: PhnA 27.3 28 0.00061 21.8 0.6 21 73-93 5-27 (30)
322 COG2405 Predicted nucleic acid 27.3 45 0.00097 28.4 2.0 30 32-61 85-115 (157)
323 PF11781 RRN7: RNA polymerase 27.2 22 0.00048 22.9 0.1 25 70-94 8-34 (36)
324 PF10367 Vps39_2: Vacuolar sor 27.2 54 0.0012 24.0 2.2 23 86-110 79-101 (109)
325 COG5533 UBP5 Ubiquitin C-termi 27.1 76 0.0017 30.5 3.7 60 86-146 285-345 (415)
326 PF08996 zf-DNA_Pol: DNA Polym 27.1 39 0.00085 28.6 1.7 36 59-94 7-54 (188)
327 PRK03564 formate dehydrogenase 27.1 46 0.00099 31.0 2.2 12 84-95 186-197 (309)
328 PF14949 ARF7EP_C: ARF7 effect 27.1 35 0.00075 27.1 1.2 16 71-94 68-83 (103)
329 PF03243 MerB: Alkylmercury ly 27.0 58 0.0013 26.0 2.6 37 86-133 40-76 (127)
330 PRK14894 glycyl-tRNA synthetas 26.7 40 0.00087 33.8 1.9 36 63-99 81-117 (539)
331 PF02639 DUF188: Uncharacteriz 26.7 73 0.0016 25.9 3.1 30 34-63 52-81 (130)
332 smart00714 LITAF Possible memb 26.5 62 0.0013 22.8 2.4 18 85-103 3-20 (67)
333 TIGR02159 PA_CoA_Oxy4 phenylac 26.4 31 0.00068 28.5 0.9 11 86-96 106-116 (146)
334 PF05129 Elf1: Transcription e 26.3 42 0.00092 25.2 1.5 22 85-109 22-44 (81)
335 smart00532 LIGANc Ligase N fam 25.9 81 0.0017 30.6 3.7 46 46-94 356-408 (441)
336 PRK14301 chaperone protein Dna 25.7 2.6E+02 0.0056 26.2 7.0 9 86-94 198-206 (373)
337 KOG3022 Predicted ATPase, nucl 25.6 71 0.0015 29.9 3.1 46 34-94 184-231 (300)
338 PRK00566 DNA-directed RNA poly 25.4 33 0.00073 37.3 1.1 29 71-100 58-87 (1156)
339 PRK14283 chaperone protein Dna 25.2 2.7E+02 0.0058 26.1 7.0 27 69-96 188-214 (378)
340 PF00628 PHD: PHD-finger; Int 25.1 56 0.0012 21.2 1.8 22 72-93 1-22 (51)
341 COG1040 ComFC Predicted amidop 24.7 18 0.00039 31.6 -0.8 27 71-100 25-51 (225)
342 PF01363 FYVE: FYVE zinc finge 24.7 39 0.00085 23.5 1.0 22 72-93 11-33 (69)
343 PRK14296 chaperone protein Dna 24.6 1.9E+02 0.004 27.2 5.8 9 86-94 207-215 (372)
344 PF12674 Zn_ribbon_2: Putative 24.5 31 0.00067 26.0 0.5 23 86-110 1-24 (81)
345 COG2956 Predicted N-acetylgluc 24.4 23 0.00049 34.0 -0.3 36 60-98 346-381 (389)
346 PHA02325 hypothetical protein 24.3 35 0.00076 25.4 0.7 11 84-94 2-12 (72)
347 COG3880 Modulator of heat shoc 24.2 17 0.00037 31.5 -1.0 50 41-93 47-100 (176)
348 TIGR03670 rpoB_arch DNA-direct 24.2 54 0.0012 33.1 2.3 31 70-100 538-571 (599)
349 PRK14285 chaperone protein Dna 24.0 3.2E+02 0.007 25.5 7.2 9 86-94 200-208 (365)
350 COG0143 MetG Methionyl-tRNA sy 23.9 48 0.001 33.2 1.9 30 63-92 119-149 (558)
351 PF04032 Rpr2: RNAse P Rpr2/Rp 23.8 40 0.00086 24.2 1.0 13 82-94 43-55 (85)
352 PF04423 Rad50_zn_hook: Rad50 23.7 30 0.00065 23.5 0.3 8 87-94 22-29 (54)
353 PRK14284 chaperone protein Dna 23.7 2.7E+02 0.0058 26.2 6.7 11 140-150 260-270 (391)
354 COG5319 Uncharacterized protei 23.5 37 0.0008 28.4 0.8 32 67-99 2-45 (142)
355 PRK10546 pyrimidine (deoxy)nuc 23.4 1.4E+02 0.003 22.6 4.0 35 97-134 4-38 (135)
356 PF03854 zf-P11: P-11 zinc fin 23.3 19 0.00042 25.2 -0.7 23 71-94 22-44 (50)
357 PF06397 Desulfoferrod_N: Desu 23.2 72 0.0016 20.8 2.0 20 86-110 7-26 (36)
358 CHL00018 rpoC1 RNA polymerase 23.2 30 0.00064 35.5 0.2 32 66-100 64-99 (663)
359 COG1326 Uncharacterized archae 23.1 77 0.0017 28.1 2.8 12 97-108 49-60 (201)
360 PRK14293 chaperone protein Dna 23.0 2.8E+02 0.006 25.9 6.6 26 70-96 186-211 (374)
361 COG4311 SoxD Sarcosine oxidase 22.8 38 0.00083 26.8 0.7 11 84-94 2-12 (97)
362 PRK10445 endonuclease VIII; Pr 22.3 56 0.0012 29.1 1.8 16 85-102 235-250 (263)
363 PF02132 RecR: RecR protein; 22.3 7.2 0.00016 25.5 -2.9 29 63-94 10-38 (41)
364 PRK14810 formamidopyrimidine-D 22.2 57 0.0012 29.2 1.8 16 85-102 244-259 (272)
365 PF03367 zf-ZPR1: ZPR1 zinc-fi 22.1 76 0.0016 26.6 2.4 13 87-100 3-15 (161)
366 TIGR03830 CxxCG_CxxCG_HTH puta 22.1 67 0.0015 24.4 2.0 10 88-98 1-10 (127)
367 TIGR03655 anti_R_Lar restricti 22.0 42 0.00091 22.8 0.7 8 87-94 3-10 (53)
368 PRK02625 rpoC1 DNA-directed RN 22.0 46 0.001 34.0 1.3 26 66-94 66-92 (627)
369 PRK14351 ligA NAD-dependent DN 21.8 1.1E+02 0.0024 31.4 3.9 44 47-94 384-432 (689)
370 TIGR02387 rpoC1_cyan DNA-direc 21.6 35 0.00076 34.8 0.4 32 66-100 59-91 (619)
371 TIGR00201 comF comF family pro 21.6 46 0.001 27.8 1.0 21 73-94 1-21 (190)
372 COG2824 PhnA Uncharacterized Z 21.5 53 0.0012 26.6 1.3 26 69-94 2-29 (112)
373 TIGR01079 rplX_bact ribosomal 21.2 84 0.0018 24.7 2.4 23 85-110 71-93 (104)
374 PF09567 RE_MamI: MamI restric 21.2 43 0.00093 31.1 0.8 28 71-100 83-110 (314)
375 TIGR01206 lysW lysine biosynth 21.1 80 0.0017 22.2 2.0 27 71-99 3-34 (54)
376 PRK13764 ATPase; Provisional 21.0 79 0.0017 32.0 2.7 29 32-60 101-129 (602)
377 PF12387 Peptidase_C74: Pestiv 21.0 43 0.00093 29.4 0.8 45 42-96 142-186 (200)
378 PRK14278 chaperone protein Dna 21.0 3.4E+02 0.0073 25.5 6.8 26 70-96 182-207 (378)
379 TIGR03847 conserved hypothetic 21.0 55 0.0012 28.4 1.4 18 84-110 155-172 (177)
380 PRK14281 chaperone protein Dna 20.8 3E+02 0.0065 26.0 6.4 27 70-97 205-231 (397)
381 COG1885 Uncharacterized protei 20.7 82 0.0018 25.5 2.2 18 83-102 47-64 (115)
382 COG3809 Uncharacterized protei 20.7 42 0.00091 25.9 0.6 10 85-94 21-30 (88)
383 PLN02915 cellulose synthase A 20.6 43 0.00092 36.1 0.8 26 72-99 44-69 (1044)
384 PF06839 zf-GRF: GRF zinc fing 20.6 73 0.0016 20.9 1.7 14 87-102 2-15 (45)
385 COG0333 RpmF Ribosomal protein 20.3 61 0.0013 23.2 1.3 19 72-92 29-47 (57)
386 PLN02189 cellulose synthase 20.2 40 0.00088 36.3 0.5 28 72-101 63-90 (1040)
387 PRK13795 hypothetical protein; 20.2 87 0.0019 31.5 2.8 38 66-110 8-45 (636)
388 KOG1522 RNA polymerase II, sub 20.1 75 0.0016 29.3 2.1 20 32-51 17-36 (285)
No 1
>KOG2463 consensus Predicted RNA-binding protein Nob1p involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=1.5e-61 Score=438.64 Aligned_cols=181 Identities=41% Similarity=0.721 Sum_probs=156.0
Q ss_pred CcCCCCceeeec--------------CCCceeeEecchHHHHHHHHHhCceeecCCCCcceeeeeEEEEccCcccccccc
Q 028198 18 DECSEQSWMLRS--------------LSESTVACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEI 83 (212)
Q Consensus 18 d~~s~~~Wi~~~--------------l~~~~vac~TdDfAmQNVllqmGL~~~s~~g~~I~~~k~wvlrC~aC~k~~~~~ 83 (212)
||.++..||+++ ..++.|||+|+||||||||+||||+++++.|++|+++++|+|||||||+++++|
T Consensus 176 ed~DdDgwitp~ni~~~~~e~~al~~pe~~~Vac~TtDfamQNVlLqm~L~l~~~~G~~Ir~~r~~iLRCh~Cfsit~~m 255 (376)
T KOG2463|consen 176 EDADDDGWITPSNITEAIIELGALNRPENQLVACLTTDFAMQNVLLQMNLNLLAMSGMKIRSVRSYILRCHGCFSITSEM 255 (376)
T ss_pred cccccccccccchHHHHHHhhhcccccccceeeeecccHHHHHHHHHhcccccCccchhhhhhhhheeEeeeeeEecCcc
Confidence 333344499977 146789999999999999999999999999999999999999999999999999
Q ss_pred CccccCCCCCCCceeEEEEEeCCCceEEeec--CCccccccceeccCCCCCCCCCCCCCceecCCCCcccccchhhhcc-
Q 028198 84 GRIFCPKCGNGGTLRKVAVTVGENGIVLASR--RPRITLRGTKFSLPMPQGGRDAITKNLILREDQLPQKYLYPRNKKK- 160 (212)
Q Consensus 84 ~k~FCp~CG~~~TL~Rvsvsv~~~G~~~~~~--k~~~n~RG~~ySlPkpkgGk~~~~~~~IL~EDQ~~~~~~~~k~r~k- 160 (212)
++.|||+||++ ||+||+|||++||+++.|. +++||+||++||||+|||||+. +|+||+|||+++++..+++|+|
T Consensus 256 ~k~FCp~CG~~-TL~K~aVsv~~dG~~~~h~k~r~~~n~RG~~YSlp~PkGgk~~--kN~~LrEDQ~~~q~~~~q~rkk~ 332 (376)
T KOG2463|consen 256 PKDFCPSCGHK-TLTKCAVSVDEDGNGQTHFKKRFQWNNRGLQYSLPKPKGGKVA--KNPILREDQPEPQRRYVQTRKKV 332 (376)
T ss_pred chhcccccCCC-eeeEEEEEecCCCceeEEeecccccccCcceeecCCCCCCccc--cCccccccCchHHHHHHHHHHhh
Confidence 99999999999 9999999999999987665 5579999999999999999997 8999999998888888778887
Q ss_pred cCCCCCCccCCCCcccc--CCCccccCCchhhhhceeccccCCCCCCCCCC
Q 028198 161 VNKEGDNFVTSDDIFKH--HTDKRAPLQPPIRKALAVFSGRRNPNDNHYSH 209 (212)
Q Consensus 161 ~~~~d~dy~~~~~~f~~--~~~k~a~l~~~~~~~~~~~~grrNPN~~~~~~ 209 (212)
.+++++ | .||+. ..+++|.++ +|+.+.+|. |||||++|+++
T Consensus 333 ~~~~~~-y----gpf~~~d~~s~~a~~~--v~~~~~~~k-~rnpN~skr~~ 375 (376)
T KOG2463|consen 333 KKPLNE-Y----GPFSGHDVTSRSAILG--VRQHVRIGK-RRNPNESKRKS 375 (376)
T ss_pred hccccc-c----CCcccccccccccccc--hhhhhhhhc-cCCCchhcccc
Confidence 577776 7 38953 367777776 455565665 78999999875
No 2
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=99.98 E-value=1.1e-33 Score=209.23 Aligned_cols=71 Identities=48% Similarity=1.056 Sum_probs=24.5
Q ss_pred cceeeeeEEEEccCccccccccCccccCCCCCCCceeEEEEEeCCCceEEeec--CCccccccceeccCCCCCC
Q 028198 62 QIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGENGIVLASR--RPRITLRGTKFSLPMPQGG 133 (212)
Q Consensus 62 ~I~~~k~wvlrC~aC~k~~~~~~k~FCp~CG~~~TL~Rvsvsv~~~G~~~~~~--k~~~n~RG~~ySlPkpkgG 133 (212)
+|+++++|+|||||||+++.+|+++|||+|||+ ||.||+|+||+||++++|+ +++||+||++||||+|+||
T Consensus 1 rIk~~k~~vlrC~aCf~~t~~~~k~FCp~CGn~-TL~rvsvsv~~~G~~~~~~~~~~~~n~RG~~ySlPkPkgG 73 (73)
T PF08772_consen 1 RIKRVKTWVLRCHACFKITKDMTKQFCPKCGNA-TLKRVSVSVDEDGKIKLHLKKNFQWNLRGTKYSLPKPKGG 73 (73)
T ss_dssp -------EEEE-SSS--EES-SS--S-SSS--S---EEEE-B--SS---B------------------------
T ss_pred CcchhheeeEEccccccCcCCCCceeCcccCCC-cceEEEEEECCCCCEEEEecCCceeccCCCCccCCCCCCC
Confidence 589999999999999999999999999999998 9999999999999987665 4579999999999999998
No 3
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=99.88 E-value=7.8e-24 Score=179.06 Aligned_cols=85 Identities=34% Similarity=0.578 Sum_probs=68.7
Q ss_pred CCCCceeeecC-----CCceeeEecchHHHHHHHHHhCceeec-CCCCcceeeeeEEEEccCccccccccCccccCCCCC
Q 028198 20 CSEQSWMLRSL-----SESTVACITGDYAMQNVILQMGLRLLA-PGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGN 93 (212)
Q Consensus 20 ~s~~~Wi~~~l-----~~~~vac~TdDfAmQNVllqmGL~~~s-~~g~~I~~~k~wvlrC~aC~k~~~~~~k~FCp~CG~ 93 (212)
+|+++.-..+| .+.+|+++||||+|||||+||||+|.+ ..+..|+++++|++||+||+++|+ +..+|||.||+
T Consensus 83 LS~tDi~VlalAlel~~~~~v~l~TdDysvQNVa~~Lgi~~~~~~~~~~I~~v~~w~~rC~GC~~~f~-~~~~~Cp~CG~ 161 (177)
T COG1439 83 LSPTDIEVLALALELGEEVQVALATDDYSVQNVALQLGLNVRSISYKGKIKKVRKWRLRCHGCKRIFP-EPKDFCPICGS 161 (177)
T ss_pred cChhhHHHHHHHHhhccccceeEEecchHHHHHHHHhCceEEeeeccCccceEeeeeEEEecCceecC-CCCCcCCCCCC
Confidence 55555544443 235689999999999999999999998 456679999999999999999999 67899999999
Q ss_pred CCceeEEEEEeCC
Q 028198 94 GGTLRKVAVTVGE 106 (212)
Q Consensus 94 ~~TL~Rvsvsv~~ 106 (212)
+ ++++...+.+.
T Consensus 162 ~-~~~~~~~~~~~ 173 (177)
T COG1439 162 P-LKRKRVKSRSS 173 (177)
T ss_pred c-eEEeeechhhc
Confidence 9 76666554443
No 4
>PRK12496 hypothetical protein; Provisional
Probab=99.74 E-value=5.5e-19 Score=147.26 Aligned_cols=80 Identities=21% Similarity=0.365 Sum_probs=67.6
Q ss_pred CCCCceeeecC-CCceeeEecchHHHHHHHHHhCceeecCCCCcceeeeeEEEEccCcccccccc-CccccCCCCCCCce
Q 028198 20 CSEQSWMLRSL-SESTVACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEI-GRIFCPKCGNGGTL 97 (212)
Q Consensus 20 ~s~~~Wi~~~l-~~~~vac~TdDfAmQNVllqmGL~~~s~~g~~I~~~k~wvlrC~aC~k~~~~~-~k~FCp~CG~~~TL 97 (212)
+|+++--..+| .++++.++||||++|||+.+|||.+.++.+.+|++++.|+++|+||++.|+.. ..+|||.||++ |
T Consensus 76 Ls~~D~~~iaLA~el~~~lvtDD~~~~~vA~~lgi~v~~~~~~~i~~~~~w~~~C~gC~~~~~~~~~~~~C~~CG~~--~ 153 (164)
T PRK12496 76 LSNTDIEVLALALELNGTLYTDDYGIQNVAKKLNIKFENIKTKGIKKVIKWRKVCKGCKKKYPEDYPDDVCEICGSP--V 153 (164)
T ss_pred cchhhHHHHHHHHHhCCcEECcHHHHHHHHHHcCCeEeccccccchhheeeeEECCCCCccccCCCCCCcCCCCCCh--h
Confidence 55555544444 36678999999999999999999999999999999999999999999999753 46899999998 6
Q ss_pred eEEE
Q 028198 98 RKVA 101 (212)
Q Consensus 98 ~Rvs 101 (212)
+|..
T Consensus 154 ~r~~ 157 (164)
T PRK12496 154 KRKM 157 (164)
T ss_pred hhcc
Confidence 5544
No 5
>TIGR03875 RNA_lig_partner RNA ligase partner, MJ_0950 family. This uncharacterized protein family is found almost perfectly in the same set of genomes as the Pab1020 family described by model TIGR01209. These pairs are found mostly in Archaea, but also in a few bacteria (e.g. Alkalilimnicola ehrlichei MLHE-1, Aquifex aeolicus). While the partner protein has been described as homodimeric ligase that has RNA circularization activity, the function of this protein (also called UPF0278) is unknown.
Probab=97.70 E-value=1.2e-05 Score=70.18 Aligned_cols=28 Identities=21% Similarity=0.402 Sum_probs=25.6
Q ss_pred CCceeeEecchHHHHHHHHHhCceeecC
Q 028198 31 SESTVACITGDYAMQNVILQMGLRLLAP 58 (212)
Q Consensus 31 ~~~~vac~TdDfAmQNVllqmGL~~~s~ 58 (212)
.+++++++|+|||||||+.+|||.+++.
T Consensus 168 ~ELda~lvTdD~giqn~A~~Lgi~~~~~ 195 (206)
T TIGR03875 168 KELDAAVVSADEGIRKWAERLGLRFVDA 195 (206)
T ss_pred HHcCcEEEeCcHHHHHHHHHcCCeeecH
Confidence 4789999999999999999999999863
No 6
>PRK04358 hypothetical protein; Provisional
Probab=97.54 E-value=2.3e-05 Score=68.93 Aligned_cols=38 Identities=21% Similarity=0.316 Sum_probs=29.7
Q ss_pred CCCceeeecC-CCceeeEecchHHHHHHHHHhCceeecC
Q 028198 21 SEQSWMLRSL-SESTVACITGDYAMQNVILQMGLRLLAP 58 (212)
Q Consensus 21 s~~~Wi~~~l-~~~~vac~TdDfAmQNVllqmGL~~~s~ 58 (212)
|.+|....+| .+++++++|+||+|||++.+|||++++.
T Consensus 161 S~~DidvlaLA~ELda~lvTdD~giqn~A~~LGI~~~~~ 199 (217)
T PRK04358 161 SAEDLDVLLLAKELDAAVVSADEGIRKWAERLGLRFVDA 199 (217)
T ss_pred chhhHHHHHHHHHhCCEEEeCCHHHHHHHHHcCCeeecH
Confidence 3344433444 4789999999999999999999999864
No 7
>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=96.38 E-value=0.0041 Score=41.16 Aligned_cols=32 Identities=25% Similarity=0.619 Sum_probs=25.0
Q ss_pred eEEEEccCccccccc------cCccccCCCCCCCceeEE
Q 028198 68 RWILKCHACYTITAE------IGRIFCPKCGNGGTLRKV 100 (212)
Q Consensus 68 ~wvlrC~aC~k~~~~------~~k~FCp~CG~~~TL~Rv 100 (212)
.|.|+|..|+..+.. .....||.||+. .++||
T Consensus 3 ~Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~-~~~r~ 40 (42)
T PF09723_consen 3 IYEYRCEECGHEFEVLQSISEDDPVPCPECGST-EVRRV 40 (42)
T ss_pred CEEEEeCCCCCEEEEEEEcCCCCCCcCCCCCCC-ceEEe
Confidence 488999999976642 235789999995 68876
No 8
>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=96.15 E-value=0.0041 Score=39.76 Aligned_cols=31 Identities=23% Similarity=0.593 Sum_probs=23.4
Q ss_pred eEEEEccCccccccc------cCccccCCCCCCCceeEE
Q 028198 68 RWILKCHACYTITAE------IGRIFCPKCGNGGTLRKV 100 (212)
Q Consensus 68 ~wvlrC~aC~k~~~~------~~k~FCp~CG~~~TL~Rv 100 (212)
.|.++|..|++.+.. .....||.||.. ++|+
T Consensus 3 ~Y~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~--~~r~ 39 (41)
T smart00834 3 IYEYRCEDCGHTFEVLQKISDDPLATCPECGGD--VRRL 39 (41)
T ss_pred CEEEEcCCCCCEEEEEEecCCCCCCCCCCCCCc--ceec
Confidence 488999999997642 224679999985 6665
No 9
>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=96.06 E-value=0.0059 Score=41.26 Aligned_cols=33 Identities=27% Similarity=0.628 Sum_probs=24.5
Q ss_pred eEEEEccCcccccccc------CccccCCCCCCCceeEEE
Q 028198 68 RWILKCHACYTITAEI------GRIFCPKCGNGGTLRKVA 101 (212)
Q Consensus 68 ~wvlrC~aC~k~~~~~------~k~FCp~CG~~~TL~Rvs 101 (212)
.|.|+|..|+..+... ....||.||.. .++|+-
T Consensus 3 ~Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~-~~~r~~ 41 (52)
T TIGR02605 3 IYEYRCTACGHRFEVLQKMSDDPLATCPECGGE-KLRRLL 41 (52)
T ss_pred CEEEEeCCCCCEeEEEEecCCCCCCCCCCCCCC-ceeEEe
Confidence 4889999999976542 23469999995 676663
No 10
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=95.62 E-value=0.0035 Score=37.65 Aligned_cols=23 Identities=30% Similarity=0.791 Sum_probs=18.3
Q ss_pred EEccCccccccccCccccCCCCCC
Q 028198 71 LKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 71 lrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
..|+.|++.... .-.|||.||.+
T Consensus 3 ~~Cp~Cg~~~~~-~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEIDP-DAKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCCc-ccccChhhCCC
Confidence 579999996544 46899999985
No 11
>PF08745 UPF0278: UPF0278 family; InterPro: IPR022785 This entry contains proteins of the UPF0278 family and proteins containing PIN domains. Members of the UPF0278 family are uncharacterised and about 200 amino acids in length.; PDB: 2LCQ_A.
Probab=95.53 E-value=0.0069 Score=53.09 Aligned_cols=29 Identities=28% Similarity=0.481 Sum_probs=17.7
Q ss_pred CCceeeEecchHHHHHHHHHhCceeecCC
Q 028198 31 SESTVACITGDYAMQNVILQMGLRLLAPG 59 (212)
Q Consensus 31 ~~~~vac~TdDfAmQNVllqmGL~~~s~~ 59 (212)
.+++++++|+|++|||++.+|||+++...
T Consensus 165 ~El~a~lvt~D~gi~~~A~~lGi~~i~~~ 193 (205)
T PF08745_consen 165 LELDAVLVTDDYGIQNWAEKLGIRFIDAR 193 (205)
T ss_dssp HHHT--EE---HHHHHHHHHTT--EE---
T ss_pred HHcCCEEEeCCHhHHHHHHHCCCEEEecc
Confidence 37899999999999999999999998654
No 12
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=94.47 E-value=0.015 Score=34.27 Aligned_cols=22 Identities=32% Similarity=0.801 Sum_probs=17.9
Q ss_pred EccCccccccccCccccCCCCCC
Q 028198 72 KCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 72 rC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
+|+-|++...+. -.|||.||.+
T Consensus 1 ~Cp~CG~~~~~~-~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIEDD-AKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCCc-CcchhhhCCc
Confidence 489999887764 5799999985
No 13
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=94.24 E-value=0.073 Score=43.57 Aligned_cols=44 Identities=30% Similarity=0.517 Sum_probs=33.1
Q ss_pred eeeeEEEEccCccccccccCccccCCCCCCCceeEEEEEeCCCceEE
Q 028198 65 QLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGENGIVL 111 (212)
Q Consensus 65 ~~k~wvlrC~aC~k~~~~~~k~FCp~CG~~~TL~Rvsvsv~~~G~~~ 111 (212)
+-+-.-.+|..|++++-. ++.+||.||..+.+.-|. +...|.+.
T Consensus 24 ~~kl~g~kC~~CG~v~~P-Pr~~Cp~C~~~~~~E~ve--ls~~G~V~ 67 (140)
T COG1545 24 EGKLLGTKCKKCGRVYFP-PRAYCPKCGSETELEWVE--LSGEGKVE 67 (140)
T ss_pred hCcEEEEEcCCCCeEEcC-CcccCCCCCCCCceEEEE--eCCCeEEE
Confidence 345667899999999976 589999999984345554 56778764
No 14
>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=94.15 E-value=0.035 Score=35.38 Aligned_cols=27 Identities=26% Similarity=0.656 Sum_probs=16.5
Q ss_pred eeEEEEccCccccccccCccccCCCCCC
Q 028198 67 HRWILKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 67 k~wvlrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
+-.+.+|..|++++.. .+.+||.||+.
T Consensus 8 ~l~~~rC~~Cg~~~~p-Pr~~Cp~C~s~ 34 (37)
T PF12172_consen 8 RLLGQRCRDCGRVQFP-PRPVCPHCGSD 34 (37)
T ss_dssp -EEEEE-TTT--EEES---SEETTTT--
T ss_pred EEEEEEcCCCCCEecC-CCcCCCCcCcc
Confidence 4567899999999765 46899999985
No 15
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=94.02 E-value=0.038 Score=43.75 Aligned_cols=30 Identities=20% Similarity=0.452 Sum_probs=22.2
Q ss_pred eeeeEEEEccCccccccccC-c-cccCCCCCC
Q 028198 65 QLHRWILKCHACYTITAEIG-R-IFCPKCGNG 94 (212)
Q Consensus 65 ~~k~wvlrC~aC~k~~~~~~-k-~FCp~CG~~ 94 (212)
+...-..+|..|+..++... . ..||.||+.
T Consensus 65 ~~~p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~ 96 (114)
T PRK03681 65 EEQEAECWCETCQQYVTLLTQRVRRCPQCHGD 96 (114)
T ss_pred EeeCcEEEcccCCCeeecCCccCCcCcCcCCC
Confidence 33455689999998887642 2 349999987
No 16
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=93.99 E-value=0.046 Score=43.48 Aligned_cols=31 Identities=19% Similarity=0.427 Sum_probs=22.8
Q ss_pred eeEEEEccCccccccccC-ccc-cCCCCCCCcee
Q 028198 67 HRWILKCHACYTITAEIG-RIF-CPKCGNGGTLR 98 (212)
Q Consensus 67 k~wvlrC~aC~k~~~~~~-k~F-Cp~CG~~~TL~ 98 (212)
..-..+|..|+..++... ..+ ||.||+. .+.
T Consensus 68 vp~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~-~~~ 100 (117)
T PRK00564 68 EKVELECKDCSHVFKPNALDYGVCEKCHSK-NVI 100 (117)
T ss_pred cCCEEEhhhCCCccccCCccCCcCcCCCCC-ceE
Confidence 455689999998876643 344 9999997 443
No 17
>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=93.94 E-value=0.046 Score=43.28 Aligned_cols=29 Identities=21% Similarity=0.276 Sum_probs=22.0
Q ss_pred eeeEEEEccCccccccccC-ccccCCCCCC
Q 028198 66 LHRWILKCHACYTITAEIG-RIFCPKCGNG 94 (212)
Q Consensus 66 ~k~wvlrC~aC~k~~~~~~-k~FCp~CG~~ 94 (212)
...-..+|..|++.+.... ..-||.||+.
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (115)
T TIGR00100 66 DEPVECECEDCSEEVSPEIDLYRCPKCHGI 95 (115)
T ss_pred eeCcEEEcccCCCEEecCCcCccCcCCcCC
Confidence 3455689999998887643 3449999997
No 18
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=93.83 E-value=0.044 Score=43.33 Aligned_cols=30 Identities=17% Similarity=0.340 Sum_probs=22.6
Q ss_pred eeeeEEEEccCcccccccc-CccccCCCCCC
Q 028198 65 QLHRWILKCHACYTITAEI-GRIFCPKCGNG 94 (212)
Q Consensus 65 ~~k~wvlrC~aC~k~~~~~-~k~FCp~CG~~ 94 (212)
+...-..+|..|+..+... ....||.||+.
T Consensus 65 ~~vp~~~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (113)
T PRK12380 65 VYKPAQAWCWDCSQVVEIHQHDAQCPHCHGE 95 (113)
T ss_pred EeeCcEEEcccCCCEEecCCcCccCcCCCCC
Confidence 3445679999999887663 34459999987
No 19
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=93.45 E-value=0.044 Score=39.01 Aligned_cols=26 Identities=38% Similarity=0.713 Sum_probs=21.0
Q ss_pred eEEEEccCccccccccCccccCCCCCCCce
Q 028198 68 RWILKCHACYTITAEIGRIFCPKCGNGGTL 97 (212)
Q Consensus 68 ~wvlrC~aC~k~~~~~~k~FCp~CG~~~TL 97 (212)
.=+..|..|+..|- +..||.||.+ |.
T Consensus 3 s~mr~C~~CgvYTL---k~~CP~CG~~-t~ 28 (56)
T PRK13130 3 SKIRKCPKCGVYTL---KEICPVCGGK-TK 28 (56)
T ss_pred ccceECCCCCCEEc---cccCcCCCCC-CC
Confidence 34568999998876 6799999998 54
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=93.45 E-value=0.04 Score=33.49 Aligned_cols=22 Identities=36% Similarity=0.890 Sum_probs=18.4
Q ss_pred EccCccccccccCccccCCCCCC
Q 028198 72 KCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 72 rC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
.|+.|+++.+.. -.+||+||..
T Consensus 2 ~CP~C~~~V~~~-~~~Cp~CG~~ 23 (26)
T PF10571_consen 2 TCPECGAEVPES-AKFCPHCGYD 23 (26)
T ss_pred cCCCCcCCchhh-cCcCCCCCCC
Confidence 699999988764 4699999984
No 21
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=93.33 E-value=0.07 Score=35.54 Aligned_cols=25 Identities=28% Similarity=0.514 Sum_probs=19.4
Q ss_pred EEEccCcccccc---ccCccccCCCCCC
Q 028198 70 ILKCHACYTITA---EIGRIFCPKCGNG 94 (212)
Q Consensus 70 vlrC~aC~k~~~---~~~k~FCp~CG~~ 94 (212)
.++|..|+.... ......||.||++
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~ 30 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYR 30 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCe
Confidence 589999998753 2225789999997
No 22
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=92.97 E-value=0.073 Score=43.30 Aligned_cols=27 Identities=33% Similarity=0.667 Sum_probs=20.3
Q ss_pred eEEEEccCcccccccc----------------------CccccCCCCCC
Q 028198 68 RWILKCHACYTITAEI----------------------GRIFCPKCGNG 94 (212)
Q Consensus 68 ~wvlrC~aC~k~~~~~----------------------~k~FCp~CG~~ 94 (212)
.-.++|..|+.++... ....||.||+.
T Consensus 68 p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 68 EAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred ceEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCC
Confidence 3569999999887653 22349999987
No 23
>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=92.94 E-value=0.078 Score=41.76 Aligned_cols=30 Identities=20% Similarity=0.419 Sum_probs=20.0
Q ss_pred eeeeEEEEccCccccccccC-ccccCCCCCC
Q 028198 65 QLHRWILKCHACYTITAEIG-RIFCPKCGNG 94 (212)
Q Consensus 65 ~~k~wvlrC~aC~k~~~~~~-k~FCp~CG~~ 94 (212)
....-+.+|..|+..+.... ...||.||+.
T Consensus 65 e~~p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (113)
T PF01155_consen 65 EEVPARARCRDCGHEFEPDEFDFSCPRCGSP 95 (113)
T ss_dssp EEE--EEEETTTS-EEECHHCCHH-SSSSSS
T ss_pred EecCCcEECCCCCCEEecCCCCCCCcCCcCC
Confidence 44566799999999886433 4569999997
No 24
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=92.29 E-value=0.14 Score=34.51 Aligned_cols=30 Identities=27% Similarity=0.455 Sum_probs=22.8
Q ss_pred EEEccCcccccccc--CccccCCCCCCCceeEE
Q 028198 70 ILKCHACYTITAEI--GRIFCPKCGNGGTLRKV 100 (212)
Q Consensus 70 vlrC~aC~k~~~~~--~k~FCp~CG~~~TL~Rv 100 (212)
+|+|..|+..+... ....||.||++ -|-|.
T Consensus 2 ~Y~C~~Cg~~~~~~~~~~irC~~CG~r-IlyK~ 33 (44)
T smart00659 2 IYICGECGRENEIKSKDVVRCRECGYR-ILYKK 33 (44)
T ss_pred EEECCCCCCEeecCCCCceECCCCCce-EEEEe
Confidence 58999999876532 36889999998 66443
No 25
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=92.16 E-value=0.074 Score=42.52 Aligned_cols=30 Identities=27% Similarity=0.535 Sum_probs=24.4
Q ss_pred EEccCccccccccC---ccccCCCCCCCceeEEE
Q 028198 71 LKCHACYTITAEIG---RIFCPKCGNGGTLRKVA 101 (212)
Q Consensus 71 lrC~aC~k~~~~~~---k~FCp~CG~~~TL~Rvs 101 (212)
.+|+.|+++|++.. ..=||+||++ ....|+
T Consensus 3 H~CtrCG~vf~~g~~~il~GCp~CG~n-kF~yv~ 35 (112)
T COG3364 3 HQCTRCGEVFDDGSEEILSGCPKCGCN-KFLYVP 35 (112)
T ss_pred ceecccccccccccHHHHccCccccch-heEecc
Confidence 48999999998733 4569999997 777776
No 26
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=91.96 E-value=0.085 Score=43.49 Aligned_cols=30 Identities=23% Similarity=0.583 Sum_probs=23.0
Q ss_pred EEccCccccccccC---ccccCCCCCCCceeEEE
Q 028198 71 LKCHACYTITAEIG---RIFCPKCGNGGTLRKVA 101 (212)
Q Consensus 71 lrC~aC~k~~~~~~---k~FCp~CG~~~TL~Rvs 101 (212)
.+|+.|+++|.+-. ..=||.||++ ....|.
T Consensus 2 H~Ct~Cg~~f~dgs~eil~GCP~CGg~-kF~yv~ 34 (131)
T PF09845_consen 2 HQCTKCGRVFEDGSKEILSGCPECGGN-KFQYVP 34 (131)
T ss_pred cccCcCCCCcCCCcHHHHccCcccCCc-ceEEcC
Confidence 47999999998754 4679999997 554443
No 27
>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=91.72 E-value=0.15 Score=32.44 Aligned_cols=25 Identities=28% Similarity=0.584 Sum_probs=19.6
Q ss_pred EEEccCcccccccc-CccccCCCCCC
Q 028198 70 ILKCHACYTITAEI-GRIFCPKCGNG 94 (212)
Q Consensus 70 vlrC~aC~k~~~~~-~k~FCp~CG~~ 94 (212)
.++|.-|+.++... .-..||.||.+
T Consensus 2 ~~~C~~CG~i~~g~~~p~~CP~Cg~~ 27 (34)
T cd00729 2 VWVCPVCGYIHEGEEAPEKCPICGAP 27 (34)
T ss_pred eEECCCCCCEeECCcCCCcCcCCCCc
Confidence 47999999887542 34689999985
No 28
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=91.47 E-value=0.11 Score=46.60 Aligned_cols=32 Identities=28% Similarity=0.691 Sum_probs=22.4
Q ss_pred CceeecCCCCcceeeeeEEEEccCccccccc---------cCccccCCCCC
Q 028198 52 GLRLLAPGGMQIRQLHRWILKCHACYTITAE---------IGRIFCPKCGN 93 (212)
Q Consensus 52 GL~~~s~~g~~I~~~k~wvlrC~aC~k~~~~---------~~k~FCp~CG~ 93 (212)
|+-|+++.|. +|.||+-+-+. -...|||+||-
T Consensus 189 g~gvvpl~g~----------~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgR 229 (239)
T COG1579 189 GVGVVPLEGR----------VCGGCHMKLPSQTLSKVRKKDEIVFCPYCGR 229 (239)
T ss_pred CceEEeecCC----------cccCCeeeecHHHHHHHhcCCCCccCCccch
Confidence 5666666654 89999954331 23689999996
No 29
>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=91.34 E-value=0.3 Score=39.07 Aligned_cols=58 Identities=17% Similarity=0.380 Sum_probs=37.7
Q ss_pred hHHHHHHHHHhCceee------c-CCCCcce--eeeeEEEEccCccccccc-----cCccccCCCCCCCceeEE
Q 028198 41 DYAMQNVILQMGLRLL------A-PGGMQIR--QLHRWILKCHACYTITAE-----IGRIFCPKCGNGGTLRKV 100 (212)
Q Consensus 41 DfAmQNVllqmGL~~~------s-~~g~~I~--~~k~wvlrC~aC~k~~~~-----~~k~FCp~CG~~~TL~Rv 100 (212)
+-+=|.++..+|.... . .+...|. ...+|.++|..|+....- ..+..|+.||.+ |..|
T Consensus 85 g~~fk~~~~~ig~~~~~~~~~~~~~~~~~~~~~~~~~~~~~C~~C~~~~~r~~~~~~~~~~C~~C~~~--l~~~ 156 (157)
T PF10263_consen 85 GKEFKQWARRIGASPPRGRPNPTTCHSYEIEGKEYKKYVYRCPSCGREYKRHRRSKRKRYRCGRCGGP--LVQV 156 (157)
T ss_pred CHHHHHHHHHHCCcccccccccccccccccccccccceEEEcCCCCCEeeeecccchhhEECCCCCCE--EEEc
Confidence 3377889999998441 1 1222222 237899999999965532 224579999964 8765
No 30
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=91.32 E-value=0.15 Score=35.53 Aligned_cols=32 Identities=31% Similarity=0.476 Sum_probs=24.4
Q ss_pred eEEEEccCccccccc---cCccccCCCCCCCceeEE
Q 028198 68 RWILKCHACYTITAE---IGRIFCPKCGNGGTLRKV 100 (212)
Q Consensus 68 ~wvlrC~aC~k~~~~---~~k~FCp~CG~~~TL~Rv 100 (212)
.-+|+|.-|++.+.. ....-||.||++ -|-|.
T Consensus 4 ~~~Y~C~~Cg~~~~~~~~~~~irCp~Cg~r-Il~K~ 38 (49)
T COG1996 4 MMEYKCARCGREVELDQETRGIRCPYCGSR-ILVKE 38 (49)
T ss_pred eEEEEhhhcCCeeehhhccCceeCCCCCcE-EEEec
Confidence 457999999998862 235789999998 55443
No 31
>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=91.17 E-value=0.15 Score=32.00 Aligned_cols=25 Identities=28% Similarity=0.562 Sum_probs=19.8
Q ss_pred EEEccCcccccccc-CccccCCCCCC
Q 028198 70 ILKCHACYTITAEI-GRIFCPKCGNG 94 (212)
Q Consensus 70 vlrC~aC~k~~~~~-~k~FCp~CG~~ 94 (212)
+++|..|+-++... .-..||.||.+
T Consensus 1 ~~~C~~CGy~y~~~~~~~~CP~Cg~~ 26 (33)
T cd00350 1 KYVCPVCGYIYDGEEAPWVCPVCGAP 26 (33)
T ss_pred CEECCCCCCEECCCcCCCcCcCCCCc
Confidence 37899999997653 35689999985
No 32
>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=90.79 E-value=0.11 Score=41.20 Aligned_cols=24 Identities=33% Similarity=0.886 Sum_probs=19.6
Q ss_pred EEccCccccccccCc--cccCCCCCC
Q 028198 71 LKCHACYTITAEIGR--IFCPKCGNG 94 (212)
Q Consensus 71 lrC~aC~k~~~~~~k--~FCp~CG~~ 94 (212)
..|+.|++-|.++.| ..||+||..
T Consensus 10 R~Cp~CG~kFYDLnk~PivCP~CG~~ 35 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNKDPIVCPKCGTE 35 (108)
T ss_pred ccCCCCcchhccCCCCCccCCCCCCc
Confidence 479999988877664 679999975
No 33
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=90.76 E-value=0.17 Score=43.05 Aligned_cols=25 Identities=24% Similarity=0.569 Sum_probs=22.2
Q ss_pred EEEccCccccccccCccccCCCCCC
Q 028198 70 ILKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 70 vlrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
+++|.-|+.+....+-..||+||.+
T Consensus 134 ~~vC~vCGy~~~ge~P~~CPiCga~ 158 (166)
T COG1592 134 VWVCPVCGYTHEGEAPEVCPICGAP 158 (166)
T ss_pred EEEcCCCCCcccCCCCCcCCCCCCh
Confidence 8999999999887667899999975
No 34
>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=90.71 E-value=0.34 Score=34.21 Aligned_cols=26 Identities=38% Similarity=0.740 Sum_probs=20.1
Q ss_pred eEEEEccCccccccccCccccCCCCCCCce
Q 028198 68 RWILKCHACYTITAEIGRIFCPKCGNGGTL 97 (212)
Q Consensus 68 ~wvlrC~aC~k~~~~~~k~FCp~CG~~~TL 97 (212)
.++..|.+|...|-. +-||.||.. |+
T Consensus 3 ~~~r~c~~~~~YTLk---~~cp~cG~~-T~ 28 (53)
T PF04135_consen 3 YYIRKCPGCRVYTLK---DKCPPCGGP-TE 28 (53)
T ss_dssp EEEEECTTTCEEESS---SBBTTTSSB-SE
T ss_pred cccccCCCCCcEeCC---CccCCCCCC-Cc
Confidence 445599999976643 579999998 65
No 35
>PRK04351 hypothetical protein; Provisional
Probab=89.62 E-value=0.55 Score=39.05 Aligned_cols=55 Identities=22% Similarity=0.410 Sum_probs=36.5
Q ss_pred hHHHHHHHHHhCc-eeecCCCCcceeeeeEEEEccCcccccc-----ccCccccCCCCCCCceeEE
Q 028198 41 DYAMQNVILQMGL-RLLAPGGMQIRQLHRWILKCHACYTITA-----EIGRIFCPKCGNGGTLRKV 100 (212)
Q Consensus 41 DfAmQNVllqmGL-~~~s~~g~~I~~~k~wvlrC~aC~k~~~-----~~~k~FCp~CG~~~TL~Rv 100 (212)
|-.-|-+|.++|- ...+ +-.. .-+.|+|+|.+|+..+. +..+..|..||.. |.-+
T Consensus 85 g~~fk~~~~~v~~~r~~~-~~~~--~~~~y~Y~C~~Cg~~~~r~Rr~n~~~yrCg~C~g~--L~~~ 145 (149)
T PRK04351 85 DRDFKELLKQVGGPRYCP-PLPS--QKKNYLYECQSCGQQYLRKRRINTKRYRCGKCRGK--LKLI 145 (149)
T ss_pred CHHHHHHHHHhCCCcccC-CCCC--CCceEEEECCCCCCEeeeeeecCCCcEEeCCCCcE--eeec
Confidence 4455888888873 3222 1111 33679999999997663 3457899999985 6543
No 36
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=89.50 E-value=0.17 Score=37.00 Aligned_cols=23 Identities=35% Similarity=0.830 Sum_probs=18.9
Q ss_pred EEccCccccccccCccccCCCCCC
Q 028198 71 LKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 71 lrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
+.|+.|.+++++- ...||.||+.
T Consensus 5 kAC~~Ck~l~~~d-~e~CP~Cgs~ 27 (64)
T COG2093 5 KACKNCKRLTPED-TEICPVCGST 27 (64)
T ss_pred HHHhhccccCCCC-CccCCCCCCc
Confidence 4699999998763 4679999997
No 37
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=89.23 E-value=0.29 Score=40.36 Aligned_cols=23 Identities=39% Similarity=0.910 Sum_probs=17.7
Q ss_pred EccCcccc-ccccCccccCCCCCC
Q 028198 72 KCHACYTI-TAEIGRIFCPKCGNG 94 (212)
Q Consensus 72 rC~aC~k~-~~~~~k~FCp~CG~~ 94 (212)
-|+.|+.- |.-....|||+||..
T Consensus 30 hCp~Cg~PLF~KdG~v~CPvC~~~ 53 (131)
T COG1645 30 HCPKCGTPLFRKDGEVFCPVCGYR 53 (131)
T ss_pred hCcccCCcceeeCCeEECCCCCce
Confidence 49999954 444568999999974
No 38
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=88.88 E-value=0.31 Score=35.16 Aligned_cols=25 Identities=24% Similarity=0.517 Sum_probs=17.6
Q ss_pred EEEccCcccccc----ccCccccCCCCCC
Q 028198 70 ILKCHACYTITA----EIGRIFCPKCGNG 94 (212)
Q Consensus 70 vlrC~aC~k~~~----~~~k~FCp~CG~~ 94 (212)
..+|..|+.+.- ..+...|+.||..
T Consensus 11 ~VkCp~C~n~q~vFsha~t~V~C~~Cg~~ 39 (59)
T PRK00415 11 KVKCPDCGNEQVVFSHASTVVRCLVCGKT 39 (59)
T ss_pred EEECCCCCCeEEEEecCCcEEECcccCCC
Confidence 467999987762 1236789999974
No 39
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=88.27 E-value=0.23 Score=36.40 Aligned_cols=24 Identities=29% Similarity=0.631 Sum_probs=19.2
Q ss_pred EEEccCccccccccCccccCCCCCCCce
Q 028198 70 ILKCHACYTITAEIGRIFCPKCGNGGTL 97 (212)
Q Consensus 70 vlrC~aC~k~~~~~~k~FCp~CG~~~TL 97 (212)
.+.|.-|..++.+ ..||.||+. ++
T Consensus 5 ~~AC~~C~~i~~~---~~Cp~Cgs~-~~ 28 (64)
T PRK06393 5 YRACKKCKRLTPE---KTCPVHGDE-KT 28 (64)
T ss_pred hhhHhhCCcccCC---CcCCCCCCC-cC
Confidence 3579999999954 589999997 54
No 40
>PRK07591 threonine synthase; Validated
Probab=88.19 E-value=0.37 Score=45.50 Aligned_cols=27 Identities=22% Similarity=0.285 Sum_probs=22.1
Q ss_pred eEEEEccCccccccccCccccCCCCCC
Q 028198 68 RWILKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 68 ~wvlrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
.+.|+|..|++.++......||.||..
T Consensus 16 ~~~l~C~~Cg~~~~~~~~~~C~~cg~~ 42 (421)
T PRK07591 16 AVALKCRECGAEYPLGPIHVCEECFGP 42 (421)
T ss_pred eeEEEeCCCCCcCCCCCCccCCCCCCe
Confidence 457999999999975445779999974
No 41
>TIGR03844 cysteate_syn cysteate synthase. Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M.
Probab=88.18 E-value=0.33 Score=45.77 Aligned_cols=26 Identities=19% Similarity=0.446 Sum_probs=21.8
Q ss_pred EEEEccCccccccccCccccCCCCCC
Q 028198 69 WILKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 69 wvlrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
|.|+|..|++.+++.....||.||..
T Consensus 1 ~~l~C~~Cg~~~~~~~~~~C~~c~g~ 26 (398)
T TIGR03844 1 YTLRCPGCGEVLPDHYTLSCPLDCGL 26 (398)
T ss_pred CEEEeCCCCCccCCccccCCCCCCCc
Confidence 57999999999986556789999964
No 42
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=87.50 E-value=0.5 Score=30.01 Aligned_cols=28 Identities=32% Similarity=0.618 Sum_probs=19.4
Q ss_pred EEccCcccccccc--CccccCCCCCCCceeE
Q 028198 71 LKCHACYTITAEI--GRIFCPKCGNGGTLRK 99 (212)
Q Consensus 71 lrC~aC~k~~~~~--~k~FCp~CG~~~TL~R 99 (212)
|.|..|+...... ...-||.||++ .|-|
T Consensus 1 Y~C~~Cg~~~~~~~~~~irC~~CG~R-IlyK 30 (32)
T PF03604_consen 1 YICGECGAEVELKPGDPIRCPECGHR-ILYK 30 (32)
T ss_dssp EBESSSSSSE-BSTSSTSSBSSSS-S-EEBE
T ss_pred CCCCcCCCeeEcCCCCcEECCcCCCe-EEEe
Confidence 5789999877542 35789999998 6654
No 43
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=87.46 E-value=0.25 Score=35.65 Aligned_cols=24 Identities=42% Similarity=0.757 Sum_probs=18.9
Q ss_pred EEEccCccccccccCccccCCCCCCCce
Q 028198 70 ILKCHACYTITAEIGRIFCPKCGNGGTL 97 (212)
Q Consensus 70 vlrC~aC~k~~~~~~k~FCp~CG~~~TL 97 (212)
+.+|..|+..|-. +-||+||.. |.
T Consensus 5 ~rkC~~cg~YTLk---e~Cp~CG~~-t~ 28 (59)
T COG2260 5 IRKCPKCGRYTLK---EKCPVCGGD-TK 28 (59)
T ss_pred hhcCcCCCceeec---ccCCCCCCc-cc
Confidence 4579999987753 679999997 53
No 44
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=87.42 E-value=0.3 Score=35.41 Aligned_cols=22 Identities=45% Similarity=0.930 Sum_probs=18.0
Q ss_pred EccCccccccccCccccCCCCCCCce
Q 028198 72 KCHACYTITAEIGRIFCPKCGNGGTL 97 (212)
Q Consensus 72 rC~aC~k~~~~~~k~FCp~CG~~~TL 97 (212)
.|.-|..+... ..||.||+. +|
T Consensus 5 AC~~C~~i~~~---~~CP~Cgs~-~~ 26 (61)
T PRK08351 5 ACRHCHYITTE---DRCPVCGSR-DL 26 (61)
T ss_pred hhhhCCcccCC---CcCCCCcCC-cc
Confidence 79999999854 479999997 53
No 45
>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=87.38 E-value=0.38 Score=38.89 Aligned_cols=33 Identities=24% Similarity=0.366 Sum_probs=25.6
Q ss_pred eeeeEEEEccCccccccccC-ccccCCCCCCCce
Q 028198 65 QLHRWILKCHACYTITAEIG-RIFCPKCGNGGTL 97 (212)
Q Consensus 65 ~~k~wvlrC~aC~k~~~~~~-k~FCp~CG~~~TL 97 (212)
..+....+|+.|.|.|.... .+-|++|+.+-||
T Consensus 64 Stkav~V~CP~C~K~TKmLGr~D~CM~C~~pLTL 97 (114)
T PF11023_consen 64 STKAVQVECPNCGKQTKMLGRVDACMHCKEPLTL 97 (114)
T ss_pred cccceeeECCCCCChHhhhchhhccCcCCCcCcc
Confidence 34567788999999997655 4789999998443
No 46
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=87.33 E-value=0.46 Score=48.61 Aligned_cols=30 Identities=37% Similarity=0.671 Sum_probs=22.2
Q ss_pred EEEEccCccccccccCccccCCCCCCCceeEEE
Q 028198 69 WILKCHACYTITAEIGRIFCPKCGNGGTLRKVA 101 (212)
Q Consensus 69 wvlrC~aC~k~~~~~~k~FCp~CG~~~TL~Rvs 101 (212)
=.++||-|+...+.+ ..||.||+. +|+-+-
T Consensus 461 ~~L~CH~Cg~~~~~p--~~Cp~Cgs~-~L~~~G 490 (730)
T COG1198 461 GQLRCHYCGYQEPIP--QSCPECGSE-HLRAVG 490 (730)
T ss_pred CeeEeCCCCCCCCCC--CCCCCCCCC-eeEEec
Confidence 468899999874443 689999997 776443
No 47
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=86.86 E-value=0.45 Score=36.28 Aligned_cols=33 Identities=21% Similarity=0.529 Sum_probs=24.6
Q ss_pred eeeEEEEccCcccccc------ccCccccCCCCCCCceeEE
Q 028198 66 LHRWILKCHACYTITA------EIGRIFCPKCGNGGTLRKV 100 (212)
Q Consensus 66 ~k~wvlrC~aC~k~~~------~~~k~FCp~CG~~~TL~Rv 100 (212)
+=.|.|+|..|+..+. +-+...||.||.+ |+|+
T Consensus 8 MPtY~Y~c~~cg~~~dvvq~~~ddplt~ce~c~a~--~kk~ 46 (82)
T COG2331 8 MPTYSYECTECGNRFDVVQAMTDDPLTTCEECGAR--LKKL 46 (82)
T ss_pred ccceEEeecccchHHHHHHhcccCccccChhhChH--HHHh
Confidence 3479999999998774 3346789999975 5443
No 48
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=86.81 E-value=0.55 Score=37.66 Aligned_cols=32 Identities=25% Similarity=0.457 Sum_probs=20.9
Q ss_pred eeeeEEEEccCcccccccc--------CccccCCCCCCCcee
Q 028198 65 QLHRWILKCHACYTITAEI--------GRIFCPKCGNGGTLR 98 (212)
Q Consensus 65 ~~k~wvlrC~aC~k~~~~~--------~k~FCp~CG~~~TL~ 98 (212)
+...-..+| .|+..+... ...-||.||+. .+.
T Consensus 65 ~~vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~-~~~ 104 (124)
T PRK00762 65 EMIPVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNK-RAH 104 (124)
T ss_pred EecCeeEEe-eCcCcccccccchhccccCCcCcCCCCC-CCE
Confidence 334557899 999875421 11349999987 443
No 49
>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=86.37 E-value=0.36 Score=39.73 Aligned_cols=25 Identities=16% Similarity=0.211 Sum_probs=20.2
Q ss_pred EEEccCccccccccCc--cccCCCCCC
Q 028198 70 ILKCHACYTITAEIGR--IFCPKCGNG 94 (212)
Q Consensus 70 vlrC~aC~k~~~~~~k--~FCp~CG~~ 94 (212)
+..|+.|++-|.++.| ..||+||..
T Consensus 9 Kr~Cp~cg~kFYDLnk~p~vcP~cg~~ 35 (129)
T TIGR02300 9 KRICPNTGSKFYDLNRRPAVSPYTGEQ 35 (129)
T ss_pred cccCCCcCccccccCCCCccCCCcCCc
Confidence 3579999988877663 789999974
No 50
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=86.00 E-value=0.81 Score=40.76 Aligned_cols=55 Identities=22% Similarity=0.394 Sum_probs=35.2
Q ss_pred EEccCcccccc---ccCccccCCCCCCCcee----EEEEEeCCCceEEeecCCccccccceeccC
Q 028198 71 LKCHACYTITA---EIGRIFCPKCGNGGTLR----KVAVTVGENGIVLASRRPRITLRGTKFSLP 128 (212)
Q Consensus 71 lrC~aC~k~~~---~~~k~FCp~CG~~~TL~----Rvsvsv~~~G~~~~~~k~~~n~RG~~ySlP 128 (212)
..|..|+..+. ...+..|+.||.. -.- -|.|.|..++.+++.+++++ ....|++|
T Consensus 100 ~fC~~CG~~~~~~~~~~~~~C~~c~~~-~yp~~~paViv~V~~~~~iLL~rr~~~--~~g~wslP 161 (256)
T PRK00241 100 RFCGYCGHPMHPSKTEWAMLCPHCRER-YYPRIAPCIIVAVRRGDEILLARHPRH--RNGVYTVL 161 (256)
T ss_pred ccccccCCCCeecCCceeEECCCCCCE-ECCCCCCEEEEEEEeCCEEEEEEccCC--CCCcEeCc
Confidence 47999997643 2236789999964 221 25555666677777666544 25688876
No 51
>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=85.80 E-value=0.55 Score=45.54 Aligned_cols=28 Identities=32% Similarity=0.610 Sum_probs=20.5
Q ss_pred EEEccCccccccccCccccCCCCCCCceeEE
Q 028198 70 ILKCHACYTITAEIGRIFCPKCGNGGTLRKV 100 (212)
Q Consensus 70 vlrC~aC~k~~~~~~k~FCp~CG~~~TL~Rv 100 (212)
.++||-|+...... ..||.||+. .|+-+
T Consensus 240 ~l~Ch~Cg~~~~~~--~~Cp~C~s~-~l~~~ 267 (505)
T TIGR00595 240 KLRCHYCGYQEPIP--KTCPQCGSE-DLVYK 267 (505)
T ss_pred eEEcCCCcCcCCCC--CCCCCCCCC-eeEee
Confidence 57788888766544 589999997 66643
No 52
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=85.79 E-value=1.1 Score=42.77 Aligned_cols=41 Identities=34% Similarity=0.644 Sum_probs=29.1
Q ss_pred eEEEEccCccccccccCccccCCCCCCCce-eEEEEEeCCCce
Q 028198 68 RWILKCHACYTITAEIGRIFCPKCGNGGTL-RKVAVTVGENGI 109 (212)
Q Consensus 68 ~wvlrC~aC~k~~~~~~k~FCp~CG~~~TL-~Rvsvsv~~~G~ 109 (212)
.=+++|..|+.-..-....-||.||..+-| ++||+ ||.-|-
T Consensus 55 ~~i~kC~~c~~~~~y~~~~~C~~cg~~~~l~R~VSf-VDaPGH 96 (415)
T COG5257 55 AKIYKCPECYRPECYTTEPKCPNCGAETELVRRVSF-VDAPGH 96 (415)
T ss_pred CceEeCCCCCCCcccccCCCCCCCCCCccEEEEEEE-eeCCch
Confidence 457899999974333346789999987545 66665 777663
No 53
>PRK06450 threonine synthase; Validated
Probab=85.63 E-value=0.51 Score=43.42 Aligned_cols=24 Identities=33% Similarity=0.589 Sum_probs=20.2
Q ss_pred EEccCccccccccCccccCCCCCC
Q 028198 71 LKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 71 lrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
|+|..|++.+.......||.||.+
T Consensus 4 ~~C~~Cg~~~~~~~~~~C~~cg~~ 27 (338)
T PRK06450 4 EVCMKCGKERESIYEIRCKKCGGP 27 (338)
T ss_pred eEECCcCCcCCCcccccCCcCCCE
Confidence 899999999976446689999975
No 54
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=85.56 E-value=0.66 Score=50.07 Aligned_cols=27 Identities=33% Similarity=0.611 Sum_probs=18.8
Q ss_pred eeeeEEEEccCccccccccCccccCCCCCC
Q 028198 65 QLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 65 ~~k~wvlrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
++.....+|+.|+..+.. .|||.||.+
T Consensus 662 eVEV~~rkCPkCG~~t~~---~fCP~CGs~ 688 (1337)
T PRK14714 662 EVEVGRRRCPSCGTETYE---NRCPDCGTH 688 (1337)
T ss_pred EEEEEEEECCCCCCcccc---ccCcccCCc
Confidence 456677899999986543 377777765
No 55
>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=84.93 E-value=0.67 Score=38.56 Aligned_cols=31 Identities=26% Similarity=0.524 Sum_probs=23.1
Q ss_pred EEEccCcccccc---ccCccccCCCCCCCceeEEE
Q 028198 70 ILKCHACYTITA---EIGRIFCPKCGNGGTLRKVA 101 (212)
Q Consensus 70 vlrC~aC~k~~~---~~~k~FCp~CG~~~TL~Rvs 101 (212)
.|+|..|+.... .....-||+||+. ...|.+
T Consensus 112 ~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~-~F~R~~ 145 (146)
T PF07295_consen 112 TLVCENCGHEVELTHPERLPPCPKCGHT-EFTRQP 145 (146)
T ss_pred eEecccCCCEEEecCCCcCCCCCCCCCC-eeeeCC
Confidence 589999996542 2225679999997 888765
No 56
>PRK06260 threonine synthase; Validated
Probab=84.41 E-value=0.7 Score=43.09 Aligned_cols=26 Identities=31% Similarity=0.584 Sum_probs=20.5
Q ss_pred EEEEccCccccccccC-ccccCCCCCC
Q 028198 69 WILKCHACYTITAEIG-RIFCPKCGNG 94 (212)
Q Consensus 69 wvlrC~aC~k~~~~~~-k~FCp~CG~~ 94 (212)
+.|+|..|++.++... ...||.||..
T Consensus 2 ~~~~C~~cg~~~~~~~~~~~Cp~cg~~ 28 (397)
T PRK06260 2 YWLKCIECGKEYDPDEIIYTCPECGGL 28 (397)
T ss_pred CEEEECCCCCCCCCCCccccCCCCCCe
Confidence 4699999999997543 4569999974
No 57
>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=84.18 E-value=0.96 Score=29.28 Aligned_cols=24 Identities=25% Similarity=0.430 Sum_probs=18.9
Q ss_pred EEccCcccccccc-----CccccCCCCCC
Q 028198 71 LKCHACYTITAEI-----GRIFCPKCGNG 94 (212)
Q Consensus 71 lrC~aC~k~~~~~-----~k~FCp~CG~~ 94 (212)
..|..|+++|... ....|..||.+
T Consensus 2 r~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~ 30 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNPPKVEGVCDNCGGE 30 (36)
T ss_dssp EEETTTTEEEETTTB--SSTTBCTTTTEB
T ss_pred cCcCCCCCccccccCCCCCCCccCCCCCe
Confidence 5799999998642 24789999986
No 58
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=84.09 E-value=0.56 Score=30.17 Aligned_cols=15 Identities=40% Similarity=1.090 Sum_probs=5.9
Q ss_pred cccCCCCCCCceeEEE
Q 028198 86 IFCPKCGNGGTLRKVA 101 (212)
Q Consensus 86 ~FCp~CG~~~TL~Rvs 101 (212)
.|||.||.+ +-.++.
T Consensus 1 kfC~~CG~~-l~~~ip 15 (34)
T PF14803_consen 1 KFCPQCGGP-LERRIP 15 (34)
T ss_dssp -B-TTT--B--EEE--
T ss_pred CccccccCh-hhhhcC
Confidence 499999997 334443
No 59
>PRK00420 hypothetical protein; Validated
Probab=83.86 E-value=0.59 Score=37.50 Aligned_cols=24 Identities=25% Similarity=0.512 Sum_probs=18.4
Q ss_pred EEccCcccccc--ccCccccCCCCCC
Q 028198 71 LKCHACYTITA--EIGRIFCPKCGNG 94 (212)
Q Consensus 71 lrC~aC~k~~~--~~~k~FCp~CG~~ 94 (212)
..|+.|+.... ..+..|||.||..
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGKV 49 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCCe
Confidence 46999996544 3458999999986
No 60
>COG0267 RpmG Ribosomal protein L33 [Translation, ribosomal structure and biogenesis]
Probab=83.38 E-value=0.75 Score=32.19 Aligned_cols=31 Identities=32% Similarity=0.676 Sum_probs=22.4
Q ss_pred eEEEEccCcc-ccccc----------c-CccccCCCCCCCceeE
Q 028198 68 RWILKCHACY-TITAE----------I-GRIFCPKCGNGGTLRK 99 (212)
Q Consensus 68 ~wvlrC~aC~-k~~~~----------~-~k~FCp~CG~~~TL~R 99 (212)
.-.|.|.+|. +.|.. + -+.|||+|... ||-+
T Consensus 5 kI~L~ct~c~g~nY~t~kN~r~~~~rLelkKycp~~~kh-tlhk 47 (50)
T COG0267 5 KIKLACTACTSRNYTTTKNKRNKPERLELKKYCPVCRKH-TLHK 47 (50)
T ss_pred eEEEEEeccCCeeEEEeeccCCCcceEEEEecCcccccE-EEEe
Confidence 5679999999 54421 1 16899999997 7754
No 61
>PRK11032 hypothetical protein; Provisional
Probab=83.19 E-value=0.88 Score=38.56 Aligned_cols=31 Identities=29% Similarity=0.600 Sum_probs=23.6
Q ss_pred EEEccCcccccc---ccCccccCCCCCCCceeEEE
Q 028198 70 ILKCHACYTITA---EIGRIFCPKCGNGGTLRKVA 101 (212)
Q Consensus 70 vlrC~aC~k~~~---~~~k~FCp~CG~~~TL~Rvs 101 (212)
.|+|..|+.... .....-||+||+. ..+|++
T Consensus 124 ~LvC~~Cg~~~~~~~p~~i~pCp~C~~~-~F~R~~ 157 (160)
T PRK11032 124 NLVCEKCHHHLAFYTPEVLPLCPKCGHD-QFQRRP 157 (160)
T ss_pred eEEecCCCCEEEecCCCcCCCCCCCCCC-eeeeCC
Confidence 589999996543 2235779999997 888876
No 62
>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=83.11 E-value=0.97 Score=28.56 Aligned_cols=25 Identities=32% Similarity=0.683 Sum_probs=18.1
Q ss_pred EEEccCccccccc--------cCccccCCCCCC
Q 028198 70 ILKCHACYTITAE--------IGRIFCPKCGNG 94 (212)
Q Consensus 70 vlrC~aC~k~~~~--------~~k~FCp~CG~~ 94 (212)
.+.|+.|++.+.. ..+..||+||+.
T Consensus 2 ~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 2 RIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHV 34 (38)
T ss_pred EEECCCCCCEEEeCHHHcCCCCCEEECCCCCCE
Confidence 3689999985532 225799999985
No 63
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=82.94 E-value=1.6 Score=35.34 Aligned_cols=52 Identities=17% Similarity=0.344 Sum_probs=32.1
Q ss_pred HHHHHHHHhCceee-cCCCCcceeeeeEEEEccCcccccc------ccCccccCCCCCC
Q 028198 43 AMQNVILQMGLRLL-APGGMQIRQLHRWILKCHACYTITA------EIGRIFCPKCGNG 94 (212)
Q Consensus 43 AmQNVllqmGL~~~-s~~g~~I~~~k~wvlrC~aC~k~~~------~~~k~FCp~CG~~ 94 (212)
.=|.++.++|-..- -.....+..+++|.|+|..|+..+. +..+..|..||..
T Consensus 84 ~f~~~~~~~~~~~~~~~h~~~~~~~~~~~y~C~~C~~~~~~~rr~~~~~~y~C~~C~g~ 142 (146)
T smart00731 84 EWKRWMRQVNGLFPERCHTFLIESVKKYPYRCTGCGQRYLRVRRSNNVSRYRCGKCGGK 142 (146)
T ss_pred HHHHHHHHHcCCCcceEcCCcccccceEEEECCCCCCCCceEccccCcceEEcCCCCCE
Confidence 44555555554411 0122334444789999999997654 2245889999985
No 64
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=82.61 E-value=0.53 Score=47.44 Aligned_cols=21 Identities=33% Similarity=0.831 Sum_probs=9.5
Q ss_pred ccCccccccccCccccCCCCCC
Q 028198 73 CHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 73 C~aC~k~~~~~~k~FCp~CG~~ 94 (212)
|..|+...+. .-.|||.||.+
T Consensus 30 Cp~CG~~~~~-~~~fC~~CG~~ 50 (645)
T PRK14559 30 CPQCGTEVPV-DEAHCPNCGAE 50 (645)
T ss_pred CCCCCCCCCc-ccccccccCCc
Confidence 4444444332 22455555554
No 65
>PF12773 DZR: Double zinc ribbon
Probab=82.39 E-value=0.63 Score=30.92 Aligned_cols=22 Identities=32% Similarity=0.806 Sum_probs=9.2
Q ss_pred EccCcccccc--ccCccccCCCCC
Q 028198 72 KCHACYTITA--EIGRIFCPKCGN 93 (212)
Q Consensus 72 rC~aC~k~~~--~~~k~FCp~CG~ 93 (212)
.|..|+.... .....+||.||.
T Consensus 14 fC~~CG~~l~~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 14 FCPHCGTPLPPPDQSKKICPNCGA 37 (50)
T ss_pred CChhhcCChhhccCCCCCCcCCcC
Confidence 3444444333 222344555554
No 66
>PF12773 DZR: Double zinc ribbon
Probab=82.38 E-value=0.68 Score=30.77 Aligned_cols=21 Identities=38% Similarity=0.977 Sum_probs=17.2
Q ss_pred ccCccccccccCccccCCCCCC
Q 028198 73 CHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 73 C~aC~k~~~~~~k~FCp~CG~~ 94 (212)
|..|++...+ ...|||+||.+
T Consensus 1 Cp~Cg~~~~~-~~~fC~~CG~~ 21 (50)
T PF12773_consen 1 CPHCGTPNPD-DAKFCPHCGTP 21 (50)
T ss_pred CCCcCCcCCc-cccCChhhcCC
Confidence 7889987665 35899999997
No 67
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=81.89 E-value=1 Score=36.42 Aligned_cols=33 Identities=30% Similarity=0.400 Sum_probs=23.0
Q ss_pred eeeeEEEEccCcccccc-ccCccccCCCCCCCcee
Q 028198 65 QLHRWILKCHACYTITA-EIGRIFCPKCGNGGTLR 98 (212)
Q Consensus 65 ~~k~wvlrC~aC~k~~~-~~~k~FCp~CG~~~TL~ 98 (212)
+...-..+|.-|..... +.....||.||+. +++
T Consensus 65 e~~p~~~~C~~C~~~~~~e~~~~~CP~C~s~-~~~ 98 (115)
T COG0375 65 EEEPAECWCLDCGQEVELEELDYRCPKCGSI-NLR 98 (115)
T ss_pred EEeccEEEeccCCCeecchhheeECCCCCCC-ceE
Confidence 34455689999976554 4445669999998 554
No 68
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=81.72 E-value=0.77 Score=32.79 Aligned_cols=15 Identities=53% Similarity=1.057 Sum_probs=11.3
Q ss_pred cccCCCCCCCceeEEE
Q 028198 86 IFCPKCGNGGTLRKVA 101 (212)
Q Consensus 86 ~FCp~CG~~~TL~Rvs 101 (212)
..||.|||+ |..|+.
T Consensus 5 i~CP~CgnK-TR~kir 19 (55)
T PF14205_consen 5 ILCPICGNK-TRLKIR 19 (55)
T ss_pred EECCCCCCc-cceeee
Confidence 469999999 755554
No 69
>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=81.05 E-value=0.67 Score=29.71 Aligned_cols=9 Identities=67% Similarity=1.567 Sum_probs=7.2
Q ss_pred cccCCCCCC
Q 028198 86 IFCPKCGNG 94 (212)
Q Consensus 86 ~FCp~CG~~ 94 (212)
.|||.|||=
T Consensus 2 ~FCp~C~nl 10 (35)
T PF02150_consen 2 RFCPECGNL 10 (35)
T ss_dssp -BETTTTSB
T ss_pred eeCCCCCcc
Confidence 699999983
No 70
>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=79.94 E-value=0.86 Score=28.20 Aligned_cols=9 Identities=44% Similarity=1.235 Sum_probs=5.4
Q ss_pred cccCCCCCC
Q 028198 86 IFCPKCGNG 94 (212)
Q Consensus 86 ~FCp~CG~~ 94 (212)
.|||.||.+
T Consensus 4 rfC~~CG~~ 12 (32)
T PF09297_consen 4 RFCGRCGAP 12 (32)
T ss_dssp SB-TTT--B
T ss_pred cccCcCCcc
Confidence 699999998
No 71
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=79.13 E-value=1 Score=31.99 Aligned_cols=25 Identities=28% Similarity=0.579 Sum_probs=20.1
Q ss_pred EEEccCcccccc-ccCccccCCCCCC
Q 028198 70 ILKCHACYTITA-EIGRIFCPKCGNG 94 (212)
Q Consensus 70 vlrC~aC~k~~~-~~~k~FCp~CG~~ 94 (212)
.-+|..|++.+. .....+||.||.+
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~Cgap 30 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAP 30 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCc
Confidence 358999998875 4458999999976
No 72
>PF14369 zf-RING_3: zinc-finger
Probab=79.07 E-value=1.5 Score=28.10 Aligned_cols=24 Identities=29% Similarity=0.797 Sum_probs=17.2
Q ss_pred EEccCccccccc----cCccccCCCCCC
Q 028198 71 LKCHACYTITAE----IGRIFCPKCGNG 94 (212)
Q Consensus 71 lrC~aC~k~~~~----~~k~FCp~CG~~ 94 (212)
|.||.|.+.... ....+||.|++.
T Consensus 3 ywCh~C~~~V~~~~~~~~~~~CP~C~~g 30 (35)
T PF14369_consen 3 YWCHQCNRFVRIAPSPDSDVACPRCHGG 30 (35)
T ss_pred EeCccCCCEeEeCcCCCCCcCCcCCCCc
Confidence 689999976542 223469999985
No 73
>PRK14873 primosome assembly protein PriA; Provisional
Probab=78.95 E-value=1.5 Score=44.25 Aligned_cols=29 Identities=34% Similarity=0.762 Sum_probs=20.7
Q ss_pred EEEccCccccccccCccccCCCCCCCceeEEEE
Q 028198 70 ILKCHACYTITAEIGRIFCPKCGNGGTLRKVAV 102 (212)
Q Consensus 70 vlrC~aC~k~~~~~~k~FCp~CG~~~TL~Rvsv 102 (212)
.++||-|+.... -..||.||+. .|+-+-+
T Consensus 410 ~l~Ch~CG~~~~---p~~Cp~Cgs~-~l~~~g~ 438 (665)
T PRK14873 410 TPRCRWCGRAAP---DWRCPRCGSD-RLRAVVV 438 (665)
T ss_pred eeECCCCcCCCc---CccCCCCcCC-cceeeec
Confidence 588888886432 3589999997 6765544
No 74
>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=78.67 E-value=1.8 Score=43.36 Aligned_cols=49 Identities=18% Similarity=0.348 Sum_probs=30.1
Q ss_pred HHHHHHHHHh---CceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCCCceeEE
Q 028198 42 YAMQNVILQM---GLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKV 100 (212)
Q Consensus 42 fAmQNVllqm---GL~~~s~~g~~I~~~k~wvlrC~aC~k~~~~~~k~FCp~CG~~~TL~Rv 100 (212)
-|+.+++..+ +|...++. .=+-+|..|+.+.... ...||+||+. .+...
T Consensus 509 ea~~~lv~~~~~~~i~Y~tin--------~~~siC~~CGy~~g~~-~~~CP~CGs~-~~ev~ 560 (586)
T TIGR02827 509 DGYRKLLRVAADTGCNYFCFN--------IKITICNDCHHIDKRT-LHRCPVCGSA-NIDYG 560 (586)
T ss_pred HHHHHHHHHHHhcCCceEEeC--------CCCeecCCCCCcCCCc-CCcCcCCCCc-cceEE
Confidence 3666665554 55555544 2245799999854322 3689999986 54433
No 75
>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=78.37 E-value=2.3 Score=35.63 Aligned_cols=33 Identities=24% Similarity=0.446 Sum_probs=24.3
Q ss_pred eeEEEEccCccccccc-------------cCccccCCCCCCCceeEEE
Q 028198 67 HRWILKCHACYTITAE-------------IGRIFCPKCGNGGTLRKVA 101 (212)
Q Consensus 67 k~wvlrC~aC~k~~~~-------------~~k~FCp~CG~~~TL~Rvs 101 (212)
+.|-|+|. |+..|.- ....-||.||+. .+.|..
T Consensus 2 I~y~L~C~-~gH~FEgWF~ss~~fd~Q~~~glv~CP~Cgs~-~V~K~l 47 (148)
T PF06676_consen 2 IVYDLRCE-NGHEFEGWFRSSAAFDRQQARGLVSCPVCGST-EVSKAL 47 (148)
T ss_pred eeEEEecC-CCCccceecCCHHHHHHHHHcCCccCCCCCCC-eEeeec
Confidence 57899998 7777641 345789999997 666544
No 76
>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=78.05 E-value=1.9 Score=45.73 Aligned_cols=29 Identities=31% Similarity=0.508 Sum_probs=23.7
Q ss_pred eeeeEEEEccCccccccccCccccCCCCCCCce
Q 028198 65 QLHRWILKCHACYTITAEIGRIFCPKCGNGGTL 97 (212)
Q Consensus 65 ~~k~wvlrC~aC~k~~~~~~k~FCp~CG~~~TL 97 (212)
++-.-..+|+.|++.+.. ..||.||.+ |.
T Consensus 620 ~vev~~RKCPkCG~yTlk---~rCP~CG~~-Te 648 (1095)
T TIGR00354 620 EVEIAIRKCPQCGKESFW---LKCPVCGEL-TE 648 (1095)
T ss_pred EEEEEEEECCCCCccccc---ccCCCCCCc-cc
Confidence 566778999999998753 689999998 64
No 77
>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=77.40 E-value=1.9 Score=42.50 Aligned_cols=30 Identities=30% Similarity=0.657 Sum_probs=20.5
Q ss_pred EEEccCccccccccCccccCCCCCCCceeEEE
Q 028198 70 ILKCHACYTITAEIGRIFCPKCGNGGTLRKVA 101 (212)
Q Consensus 70 vlrC~aC~k~~~~~~k~FCp~CG~~~TL~Rvs 101 (212)
+.+|..|+.+... ....||+||+. -+..++
T Consensus 518 ~~~C~~CG~~~~~-~~~~CP~CGs~-~~~~~~ 547 (555)
T cd01675 518 IDICNDCGYIGEG-EGFKCPKCGSE-DVEVIS 547 (555)
T ss_pred CccCCCCCCCCcC-CCCCCcCCCCc-CceEEE
Confidence 3499999986632 24789999986 344333
No 78
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=77.24 E-value=2.7 Score=29.57 Aligned_cols=45 Identities=18% Similarity=0.420 Sum_probs=29.2
Q ss_pred HHHHHHHhCceeecCCCCcceeeeeEEEEccCccccccc--cC-ccccCCCCCC
Q 028198 44 MQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAE--IG-RIFCPKCGNG 94 (212)
Q Consensus 44 mQNVllqmGL~~~s~~g~~I~~~k~wvlrC~aC~k~~~~--~~-k~FCp~CG~~ 94 (212)
|+-.+..-|+.|+.++-... -..|+.|+..... .. ...||.||..
T Consensus 8 L~yka~~~G~~v~~v~~~~T------Sq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 8 LEYKAEEYGIQVVEVDEAYT------SQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred HHHHHHHhCCEEEEECCCCC------ccCccCcccccccccccceEEcCCCCCE
Confidence 55667777888876653322 2468888876654 22 4678888864
No 79
>PRK05580 primosome assembly protein PriA; Validated
Probab=77.14 E-value=1.6 Score=43.79 Aligned_cols=28 Identities=36% Similarity=0.693 Sum_probs=19.3
Q ss_pred EEEccCccccccccCccccCCCCCCCceeEE
Q 028198 70 ILKCHACYTITAEIGRIFCPKCGNGGTLRKV 100 (212)
Q Consensus 70 vlrC~aC~k~~~~~~k~FCp~CG~~~TL~Rv 100 (212)
.++||-|+...... ..||.||+. .|.-.
T Consensus 408 ~l~Ch~Cg~~~~~~--~~Cp~Cg~~-~l~~~ 435 (679)
T PRK05580 408 RLRCHHCGYQEPIP--KACPECGST-DLVPV 435 (679)
T ss_pred eEECCCCcCCCCCC--CCCCCCcCC-eeEEe
Confidence 46788888665543 579999996 55543
No 80
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=77.13 E-value=1.7 Score=34.27 Aligned_cols=27 Identities=19% Similarity=0.443 Sum_probs=19.5
Q ss_pred eEEEEccCcccccc---ccCccccCCCCCC
Q 028198 68 RWILKCHACYTITA---EIGRIFCPKCGNG 94 (212)
Q Consensus 68 ~wvlrC~aC~k~~~---~~~k~FCp~CG~~ 94 (212)
.-+++|..|+...- ...-.|||.||..
T Consensus 40 ~~~~~C~~Cg~~~~~~~SCk~R~CP~C~~~ 69 (111)
T PF14319_consen 40 FHRYRCEDCGHEKIVYNSCKNRHCPSCQAK 69 (111)
T ss_pred cceeecCCCCceEEecCcccCcCCCCCCCh
Confidence 34689999997653 2234599999987
No 81
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=76.61 E-value=1.5 Score=37.18 Aligned_cols=52 Identities=23% Similarity=0.489 Sum_probs=32.3
Q ss_pred HHHHHHh-CceeecCCCCcceee--eeEEEEccCcccccc-----ccCc----cccCCCCCCCceeE
Q 028198 45 QNVILQM-GLRLLAPGGMQIRQL--HRWILKCHACYTITA-----EIGR----IFCPKCGNGGTLRK 99 (212)
Q Consensus 45 QNVllqm-GL~~~s~~g~~I~~~--k~wvlrC~aC~k~~~-----~~~k----~FCp~CG~~~TL~R 99 (212)
|=+|.+. ||........-++++ .+|.|+|. |+..+- +..+ ..|.+||.+ |..
T Consensus 89 k~lm~qV~~l~~~~~h~~~~~~v~~~~~~Y~C~-C~q~~l~~RRhn~~~~g~~YrC~~C~gk--L~~ 152 (156)
T COG3091 89 KLLMQQVLGLRFCRTHQFEVQSVRRTTYPYRCQ-CQQHYLRIRRHNTVRRGEVYRCGKCGGK--LVF 152 (156)
T ss_pred HHHHHHhCCCCCCccchHHHhhccccceeEEee-cCCccchhhhcccccccceEEeccCCce--EEe
Confidence 3344443 355544444444443 48999999 998763 2234 789999986 654
No 82
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=76.36 E-value=4.2 Score=26.31 Aligned_cols=25 Identities=40% Similarity=0.818 Sum_probs=14.9
Q ss_pred cccCCCCCCCceeEEEEEeCCCceEEeec
Q 028198 86 IFCPKCGNGGTLRKVAVTVGENGIVLASR 114 (212)
Q Consensus 86 ~FCp~CG~~~TL~Rvsvsv~~~G~~~~~~ 114 (212)
..||+||-. .|. +| .++.|++.+.+
T Consensus 2 hlcpkcgvg-vl~--pv-y~~kgeikvfr 26 (36)
T PF09151_consen 2 HLCPKCGVG-VLE--PV-YNQKGEIKVFR 26 (36)
T ss_dssp -B-TTTSSS-BEE--EE-E-TTS-EEEEE
T ss_pred ccCCccCce-EEE--Ee-ecCCCcEEEEE
Confidence 479999986 664 33 38889886654
No 83
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=75.54 E-value=1.9 Score=44.06 Aligned_cols=26 Identities=27% Similarity=0.709 Sum_probs=18.6
Q ss_pred EEEccCccccccccCccccCCCCCCCcee
Q 028198 70 ILKCHACYTITAEIGRIFCPKCGNGGTLR 98 (212)
Q Consensus 70 vlrC~aC~k~~~~~~k~FCp~CG~~~TL~ 98 (212)
+-+|..|+.+... ...||.||+. .+.
T Consensus 680 ~~~C~~CG~~~~~--~~~CP~CG~~-~~~ 705 (735)
T PRK07111 680 VDRCPVCGYLGVI--EDKCPKCGST-NIQ 705 (735)
T ss_pred CeecCCCCCCCCc--CccCcCCCCc-cce
Confidence 4589999954433 3789999985 443
No 84
>PLN00209 ribosomal protein S27; Provisional
Probab=75.53 E-value=1.7 Score=33.53 Aligned_cols=25 Identities=28% Similarity=0.701 Sum_probs=17.5
Q ss_pred EEEccCccccccc----cCccccCCCCCC
Q 028198 70 ILKCHACYTITAE----IGRIFCPKCGNG 94 (212)
Q Consensus 70 vlrC~aC~k~~~~----~~k~FCp~CG~~ 94 (212)
..+|.+|+.+... .+...|..||..
T Consensus 36 ~VkCp~C~n~q~VFShA~t~V~C~~Cg~~ 64 (86)
T PLN00209 36 DVKCQGCFNITTVFSHSQTVVVCGSCQTV 64 (86)
T ss_pred EEECCCCCCeeEEEecCceEEEccccCCE
Confidence 3679999877532 236789999874
No 85
>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=75.50 E-value=2.4 Score=31.58 Aligned_cols=28 Identities=32% Similarity=0.776 Sum_probs=18.2
Q ss_pred EEEccCccccccccCccccCCCCCCCceeEEE
Q 028198 70 ILKCHACYTITAEIGRIFCPKCGNGGTLRKVA 101 (212)
Q Consensus 70 vlrC~aC~k~~~~~~k~FCp~CG~~~TL~Rvs 101 (212)
.+.|.+|.+-+.. .-+||.||.+ |.++.
T Consensus 17 ~~~C~~C~~~~~~--~a~CPdC~~~--Le~Lk 44 (70)
T PF07191_consen 17 HYHCEACQKDYKK--EAFCPDCGQP--LEVLK 44 (70)
T ss_dssp EEEETTT--EEEE--EEE-TTT-SB---EEEE
T ss_pred EEECcccccccee--cccCCCcccH--HHHHH
Confidence 5899999998765 4799999998 77654
No 86
>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=75.38 E-value=2.7 Score=28.77 Aligned_cols=25 Identities=24% Similarity=0.574 Sum_probs=17.2
Q ss_pred EEEccCccccccccCc------------------cccCCCCCC
Q 028198 70 ILKCHACYTITAEIGR------------------IFCPKCGNG 94 (212)
Q Consensus 70 vlrC~aC~k~~~~~~k------------------~FCp~CG~~ 94 (212)
+++|..|+-+|....- --||.||..
T Consensus 1 ky~C~~CgyvYd~~~Gd~~~~i~pGt~F~~Lp~~w~CP~C~a~ 43 (47)
T PF00301_consen 1 KYQCPVCGYVYDPEKGDPENGIPPGTPFEDLPDDWVCPVCGAP 43 (47)
T ss_dssp EEEETTTSBEEETTTBBGGGTB-TT--GGGS-TT-B-TTTSSB
T ss_pred CcCCCCCCEEEcCCcCCcccCcCCCCCHHHCCCCCcCcCCCCc
Confidence 4789999998864321 269999964
No 87
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=74.90 E-value=1.8 Score=33.35 Aligned_cols=25 Identities=28% Similarity=0.635 Sum_probs=17.7
Q ss_pred EEEccCccccccc----cCccccCCCCCC
Q 028198 70 ILKCHACYTITAE----IGRIFCPKCGNG 94 (212)
Q Consensus 70 vlrC~aC~k~~~~----~~k~FCp~CG~~ 94 (212)
..+|.+|+.+... .+...|..||..
T Consensus 35 ~VkCp~C~n~q~VFShA~t~V~C~~Cg~~ 63 (85)
T PTZ00083 35 DVKCPGCSQITTVFSHAQTVVLCGGCSSQ 63 (85)
T ss_pred EEECCCCCCeeEEEecCceEEEccccCCE
Confidence 3679999977632 236789999873
No 88
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=74.84 E-value=3 Score=29.78 Aligned_cols=31 Identities=35% Similarity=0.830 Sum_probs=21.3
Q ss_pred eEEEEccCcccccc-----cc----CccccCCCCCCCceeEE
Q 028198 68 RWILKCHACYTITA-----EI----GRIFCPKCGNGGTLRKV 100 (212)
Q Consensus 68 ~wvlrC~aC~k~~~-----~~----~k~FCp~CG~~~TL~Rv 100 (212)
.| +.|+-|+..+. |+ .-.|||+|-.. ||..|
T Consensus 3 ~W-i~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~E-tlI~v 42 (55)
T PF14205_consen 3 EW-ILCPICGNKTRLKIREDTVLKNFPLYCPKCKQE-TLIDV 42 (55)
T ss_pred eE-EECCCCCCccceeeecCceeccccccCCCCCce-EEEEe
Confidence 35 46999995552 21 24799999998 87544
No 89
>PRK04023 DNA polymerase II large subunit; Validated
Probab=74.36 E-value=2.5 Score=45.05 Aligned_cols=34 Identities=29% Similarity=0.552 Sum_probs=26.3
Q ss_pred eEEEEccCccccccccC-ccccCCCCCCCceeEEEEEeCC
Q 028198 68 RWILKCHACYTITAEIG-RIFCPKCGNGGTLRKVAVTVGE 106 (212)
Q Consensus 68 ~wvlrC~aC~k~~~~~~-k~FCp~CG~~~TL~Rvsvsv~~ 106 (212)
+=..||..|+..|.-++ ..-||+||++ |-.||.+
T Consensus 1035 rQ~fRC~kC~~kYRR~PL~G~C~kCGg~-----lilTVh~ 1069 (1121)
T PRK04023 1035 RQEFRCTKCGAKYRRPPLSGKCPKCGGN-----LILTVHK 1069 (1121)
T ss_pred ccceeecccCcccccCCCCCcCccCCCe-----EEEEEec
Confidence 33589999999998777 6789999997 4445544
No 90
>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=74.09 E-value=2.4 Score=44.94 Aligned_cols=27 Identities=37% Similarity=0.621 Sum_probs=23.0
Q ss_pred eEEEEccCccccccccC-ccccCCCCCC
Q 028198 68 RWILKCHACYTITAEIG-RIFCPKCGNG 94 (212)
Q Consensus 68 ~wvlrC~aC~k~~~~~~-k~FCp~CG~~ 94 (212)
+=..||..|+..|.-++ ..-||+||++
T Consensus 1010 rQ~fRC~kC~~kYRR~PL~G~C~kCGg~ 1037 (1095)
T TIGR00354 1010 RQEVRCTKCNTKYRRIPLVGKCLKCGNN 1037 (1095)
T ss_pred ccceeecccCCccccCCCCCcccccCCe
Confidence 33589999999998777 6789999997
No 91
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=73.74 E-value=0.97 Score=48.14 Aligned_cols=25 Identities=28% Similarity=0.671 Sum_probs=21.3
Q ss_pred EEEEccCccccccccCccccCCCCCC
Q 028198 69 WILKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 69 wvlrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
-+.||..|+..+.+. ..+||.||+.
T Consensus 693 tIKrC~dcg~q~~~~-~~~cP~Cgs~ 717 (1187)
T COG1110 693 TIKRCRDCGEQFVDS-EDKCPRCGSR 717 (1187)
T ss_pred HHHHHhhcCceeccc-cccCCCCCCc
Confidence 348999999998876 6699999995
No 92
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=73.64 E-value=2.1 Score=37.77 Aligned_cols=27 Identities=22% Similarity=0.626 Sum_probs=22.0
Q ss_pred EEccCccccccccCccccCCCCCCCcee
Q 028198 71 LKCHACYTITAEIGRIFCPKCGNGGTLR 98 (212)
Q Consensus 71 lrC~aC~k~~~~~~k~FCp~CG~~~TL~ 98 (212)
++|.-|+.+.... -..||.||.-+||+
T Consensus 355 ~~c~~cg~~~~~~-~~~c~~c~~~~~~~ 381 (389)
T PRK11788 355 YRCRNCGFTARTL-YWHCPSCKAWETIK 381 (389)
T ss_pred EECCCCCCCCccc-eeECcCCCCccCcC
Confidence 4599999988764 57899999887775
No 93
>PRK02935 hypothetical protein; Provisional
Probab=73.53 E-value=2.5 Score=34.01 Aligned_cols=30 Identities=23% Similarity=0.370 Sum_probs=24.2
Q ss_pred eeEEEEccCccccccccC-ccccCCCCCCCc
Q 028198 67 HRWILKCHACYTITAEIG-RIFCPKCGNGGT 96 (212)
Q Consensus 67 k~wvlrC~aC~k~~~~~~-k~FCp~CG~~~T 96 (212)
+.-...|+.|.|.|+... -+-|.+|+.+=|
T Consensus 67 kavqV~CP~C~K~TKmLGrvD~CM~C~~PLT 97 (110)
T PRK02935 67 KAVQVICPSCEKPTKMLGRVDACMHCNQPLT 97 (110)
T ss_pred cceeeECCCCCchhhhccceeecCcCCCcCC
Confidence 355569999999998766 478999999833
No 94
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=73.34 E-value=1.6 Score=29.03 Aligned_cols=9 Identities=78% Similarity=1.685 Sum_probs=7.7
Q ss_pred cccCCCCCC
Q 028198 86 IFCPKCGNG 94 (212)
Q Consensus 86 ~FCp~CG~~ 94 (212)
.|||.||+-
T Consensus 1 ~FCp~Cg~~ 9 (52)
T smart00661 1 KFCPKCGNM 9 (52)
T ss_pred CCCCCCCCc
Confidence 499999985
No 95
>PF15017 AF1Q: Drug resistance and apoptosis regulator
Probab=73.28 E-value=1.9 Score=33.36 Aligned_cols=16 Identities=13% Similarity=0.341 Sum_probs=12.1
Q ss_pred ccCCCcCCCCceeeec
Q 028198 14 SYVDDECSEQSWMLRS 29 (212)
Q Consensus 14 ~~~~d~~s~~~Wi~~~ 29 (212)
++.++++++++|||++
T Consensus 64 eee~~ddD~gGWITPs 79 (87)
T PF15017_consen 64 EEEEEDDDGGGWITPS 79 (87)
T ss_pred ccccccCCCCccccch
Confidence 4455667789999988
No 96
>PRK05978 hypothetical protein; Provisional
Probab=73.09 E-value=1.1 Score=37.46 Aligned_cols=32 Identities=19% Similarity=0.456 Sum_probs=22.0
Q ss_pred eeEEEEccCccc--ccccc--CccccCCCCCCCceeEE
Q 028198 67 HRWILKCHACYT--ITAEI--GRIFCPKCGNGGTLRKV 100 (212)
Q Consensus 67 k~wvlrC~aC~k--~~~~~--~k~FCp~CG~~~TL~Rv 100 (212)
+.+..||+.|++ ++... ..+.||+||.+ +...
T Consensus 30 rGl~grCP~CG~G~LF~g~Lkv~~~C~~CG~~--~~~~ 65 (148)
T PRK05978 30 RGFRGRCPACGEGKLFRAFLKPVDHCAACGED--FTHH 65 (148)
T ss_pred HHHcCcCCCCCCCcccccccccCCCccccCCc--cccC
Confidence 356789999984 43321 25789999987 5543
No 97
>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=73.03 E-value=2 Score=42.54 Aligned_cols=44 Identities=20% Similarity=0.376 Sum_probs=26.4
Q ss_pred HHHHHHHHH---hCceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCC
Q 028198 42 YAMQNVILQ---MGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 42 fAmQNVllq---mGL~~~s~~g~~I~~~k~wvlrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
=|+..|... .|+...++. .=+-+|..|+..... ....||+||+.
T Consensus 501 eal~~lv~~a~~~~i~Y~~~n--------~~~~~C~~CG~~g~~-~~~~CP~Cgs~ 547 (579)
T TIGR02487 501 EALKDITKKAMKNGIGYFGIN--------PPVDVCEDCGYTGEG-LNDKCPKCGSH 547 (579)
T ss_pred HHHHHHHHHHHhcCCceEEec--------cCCccCCCCCCCCCC-CCCcCcCCCCc
Confidence 456655544 344544443 223579999974332 23589999986
No 98
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=72.83 E-value=2.4 Score=27.02 Aligned_cols=23 Identities=30% Similarity=0.512 Sum_probs=16.3
Q ss_pred EEccCcccc--c-cccCccccCCCCC
Q 028198 71 LKCHACYTI--T-AEIGRIFCPKCGN 93 (212)
Q Consensus 71 lrC~aC~k~--~-~~~~k~FCp~CG~ 93 (212)
.+|..|+.- . ++-...||+.||.
T Consensus 4 ~~C~~C~~~~i~~~~~~~~~C~~Cg~ 29 (33)
T PF08792_consen 4 KKCSKCGGNGIVNKEDDYEVCIFCGS 29 (33)
T ss_pred eEcCCCCCCeEEEecCCeEEcccCCc
Confidence 468888743 3 4455789999996
No 99
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=72.75 E-value=3.5 Score=37.08 Aligned_cols=57 Identities=25% Similarity=0.376 Sum_probs=35.3
Q ss_pred eeeEecchHHHHHHHHHhCc-eeecCCCCcceeeeeEEEEccCcccccc-cc----Ccc----ccCCCCCCCceeE
Q 028198 34 TVACITGDYAMQNVILQMGL-RLLAPGGMQIRQLHRWILKCHACYTITA-EI----GRI----FCPKCGNGGTLRK 99 (212)
Q Consensus 34 ~vac~TdDfAmQNVllqmGL-~~~s~~g~~I~~~k~wvlrC~aC~k~~~-~~----~k~----FCp~CG~~~TL~R 99 (212)
.+.++|.- +.|.-.+.|. +|+.++|. -+..+|..|+..+. +. ... -||.||.+ -|+.
T Consensus 93 ~~~iiTQN--iD~Lhe~AGs~~Vi~lHGs------l~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~-~lrP 159 (250)
T COG0846 93 LLRIITQN--IDGLHERAGSKNVIELHGS------LKRVRCSKCGNQYYDEDVIKFIEDGLIPRCPKCGGP-VLRP 159 (250)
T ss_pred ceEEEecc--cchHHHHcCCCcEEEeccc------eeeeEeCCCcCccchhhhhhhcccCCCCcCccCCCc-cccC
Confidence 45677742 3455666664 44566665 67789999986664 11 122 39999995 3443
No 100
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=72.67 E-value=1.8 Score=43.82 Aligned_cols=23 Identities=35% Similarity=0.788 Sum_probs=16.5
Q ss_pred EEccCccccccccCccccCCCCCC
Q 028198 71 LKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 71 lrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
.+|+.|+...++.. .||+.||.+
T Consensus 2 ~~Cp~Cg~~n~~~a-kFC~~CG~~ 24 (645)
T PRK14559 2 LICPQCQFENPNNN-RFCQKCGTS 24 (645)
T ss_pred CcCCCCCCcCCCCC-ccccccCCC
Confidence 47888887766543 588888876
No 101
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=72.59 E-value=2.8 Score=45.49 Aligned_cols=34 Identities=32% Similarity=0.540 Sum_probs=26.4
Q ss_pred eEEEEccCccccccccC-ccccCCCCCCCceeEEEEEeCC
Q 028198 68 RWILKCHACYTITAEIG-RIFCPKCGNGGTLRKVAVTVGE 106 (212)
Q Consensus 68 ~wvlrC~aC~k~~~~~~-k~FCp~CG~~~TL~Rvsvsv~~ 106 (212)
+=..||..|+..|.-|+ ..-||+||++ +-.||.+
T Consensus 1251 rQ~~RC~kC~~kyRR~PL~G~C~kCGg~-----iilTv~~ 1285 (1337)
T PRK14714 1251 RQEFRCLKCGTKYRRMPLAGKCRKCGGR-----IILTVHE 1285 (1337)
T ss_pred ccceeecccCcccccCCCCCcccccCCe-----EEEEEec
Confidence 33589999999998877 6789999996 4445544
No 102
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=72.52 E-value=1.4 Score=32.14 Aligned_cols=8 Identities=63% Similarity=1.389 Sum_probs=5.7
Q ss_pred cccCCCCC
Q 028198 86 IFCPKCGN 93 (212)
Q Consensus 86 ~FCp~CG~ 93 (212)
..||+||-
T Consensus 51 Y~Cp~CGF 58 (61)
T COG2888 51 YRCPKCGF 58 (61)
T ss_pred eECCCcCc
Confidence 46888874
No 103
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=72.50 E-value=1.9 Score=42.51 Aligned_cols=23 Identities=43% Similarity=0.768 Sum_probs=11.8
Q ss_pred EEEccCccccccccCccccCCCCCC
Q 028198 70 ILKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 70 vlrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
+-+|..|+.+... ...||+||++
T Consensus 491 ~~~C~~CG~~~~~--~~~CP~CGs~ 513 (546)
T PF13597_consen 491 IDICPDCGYIGGE--GDKCPKCGSE 513 (546)
T ss_dssp EEEETTT---S----EEE-CCC---
T ss_pred cccccCCCcCCCC--CCCCCCCCCc
Confidence 5689999987765 5789999997
No 104
>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=72.05 E-value=2.2 Score=29.60 Aligned_cols=25 Identities=32% Similarity=0.752 Sum_probs=18.4
Q ss_pred EEEccCcccccccc------------------CccccCCCCCC
Q 028198 70 ILKCHACYTITAEI------------------GRIFCPKCGNG 94 (212)
Q Consensus 70 vlrC~aC~k~~~~~------------------~k~FCp~CG~~ 94 (212)
+++|..|+-+|... .---||.||..
T Consensus 1 ~y~C~~CgyiYd~~~Gd~~~~i~pGt~f~~Lp~~w~CP~C~a~ 43 (50)
T cd00730 1 KYECRICGYIYDPAEGDPDEGIPPGTPFEDLPDDWVCPVCGAG 43 (50)
T ss_pred CcCCCCCCeEECCCCCCcccCcCCCCCHhHCCCCCCCCCCCCc
Confidence 37899999998741 12279999975
No 105
>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=72.04 E-value=2.2 Score=26.13 Aligned_cols=8 Identities=50% Similarity=1.377 Sum_probs=4.4
Q ss_pred ccCCCCCC
Q 028198 87 FCPKCGNG 94 (212)
Q Consensus 87 FCp~CG~~ 94 (212)
+||.||++
T Consensus 1 ~CP~C~s~ 8 (28)
T PF03119_consen 1 TCPVCGSK 8 (28)
T ss_dssp B-TTT--B
T ss_pred CcCCCCCE
Confidence 69999997
No 106
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=71.60 E-value=1.8 Score=31.26 Aligned_cols=22 Identities=36% Similarity=0.914 Sum_probs=13.4
Q ss_pred EEEccCccccccccCccccCCCCCC
Q 028198 70 ILKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 70 vlrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
+.||..|.+.... ..||+||-.
T Consensus 36 I~RC~~CRk~~~~---Y~CP~CGF~ 57 (59)
T PRK14890 36 IYRCEKCRKQSNP---YTCPKCGFE 57 (59)
T ss_pred EeechhHHhcCCc---eECCCCCCc
Confidence 4555555554433 469999853
No 107
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=71.49 E-value=1.8 Score=31.46 Aligned_cols=31 Identities=26% Similarity=0.524 Sum_probs=22.4
Q ss_pred EEEccCcccccc-c--cCccccCCCCCCCceeEEE
Q 028198 70 ILKCHACYTITA-E--IGRIFCPKCGNGGTLRKVA 101 (212)
Q Consensus 70 vlrC~aC~k~~~-~--~~k~FCp~CG~~~TL~Rvs 101 (212)
.-+|++|+..-. . ..+--||.||+. ++.|.+
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~-~I~Rc~ 42 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGEV-EIYRCA 42 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCce-eeehhh
Confidence 568999998762 2 225669999987 776654
No 108
>PF14353 CpXC: CpXC protein
Probab=71.49 E-value=3.7 Score=32.26 Aligned_cols=9 Identities=44% Similarity=1.339 Sum_probs=5.9
Q ss_pred cccCCCCCC
Q 028198 86 IFCPKCGNG 94 (212)
Q Consensus 86 ~FCp~CG~~ 94 (212)
..||.||..
T Consensus 39 ~~CP~Cg~~ 47 (128)
T PF14353_consen 39 FTCPSCGHK 47 (128)
T ss_pred EECCCCCCc
Confidence 457777765
No 109
>PRK04023 DNA polymerase II large subunit; Validated
Probab=71.47 E-value=2.2 Score=45.49 Aligned_cols=10 Identities=40% Similarity=0.468 Sum_probs=7.4
Q ss_pred CCceecCCCC
Q 028198 139 KNLILREDQL 148 (212)
Q Consensus 139 ~~~IL~EDQ~ 148 (212)
.+|+-.|||+
T Consensus 773 G~pL~~~dQi 782 (1121)
T PRK04023 773 GNPLESEDQI 782 (1121)
T ss_pred CCCCCCccce
Confidence 3788888883
No 110
>PRK11823 DNA repair protein RadA; Provisional
Probab=71.42 E-value=3 Score=39.91 Aligned_cols=31 Identities=26% Similarity=0.475 Sum_probs=25.4
Q ss_pred eEEEEccCccccccccCccccCCCCCCCceeE
Q 028198 68 RWILKCHACYTITAEIGRIFCPKCGNGGTLRK 99 (212)
Q Consensus 68 ~wvlrC~aC~k~~~~~~k~FCp~CG~~~TL~R 99 (212)
+-.|+|..|+..+.. ..-.||.||.-+|+..
T Consensus 5 ~~~y~C~~Cg~~~~~-~~g~Cp~C~~w~t~~e 35 (446)
T PRK11823 5 KTAYVCQECGAESPK-WLGRCPECGAWNTLVE 35 (446)
T ss_pred CCeEECCcCCCCCcc-cCeeCcCCCCccceee
Confidence 457999999987765 3567999999889976
No 111
>PRK07218 replication factor A; Provisional
Probab=71.40 E-value=5.8 Score=38.26 Aligned_cols=69 Identities=14% Similarity=0.235 Sum_probs=42.1
Q ss_pred hHHHHHHHHHhCceeecCCCC--cceeeeeEEEEccCccccccccCccccCCCCCC--CceeEEEEEeCCC-ceEEe
Q 028198 41 DYAMQNVILQMGLRLLAPGGM--QIRQLHRWILKCHACYTITAEIGRIFCPKCGNG--GTLRKVAVTVGEN-GIVLA 112 (212)
Q Consensus 41 DfAmQNVllqmGL~~~s~~g~--~I~~~k~wvlrC~aC~k~~~~~~k~FCp~CG~~--~TL~Rvsvsv~~~-G~~~~ 112 (212)
...+.+++-.-|.--+.+.|. .|+.-...+.||+.|.++-.. -.||.||.. --..|+...+|+. |.+..
T Consensus 266 ~~~I~e~~~~~g~~~Vev~G~Iv~i~~gsgli~rCP~C~r~v~~---~~C~~hG~ve~~~dlrik~vLDDGtg~~~~ 339 (423)
T PRK07218 266 RLKIREAVERGGIFDVELVGNIISVRDGSGLIERCPECGRVIQK---GQCRSHGAVEGEDDLRIKAILDDGTGSVTV 339 (423)
T ss_pred ccchhhhhccCCcceEEEEEEEEEeccCCcceecCcCccccccC---CcCCCCCCcCCeeeeEEEEEEECCCCeEEE
Confidence 345555444433321333443 345667889999999997743 689999954 1246777777654 65544
No 112
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=71.05 E-value=3 Score=34.02 Aligned_cols=28 Identities=25% Similarity=0.663 Sum_probs=20.5
Q ss_pred eeEEEEccCccccccc--------cC-ccccCCCCCC
Q 028198 67 HRWILKCHACYTITAE--------IG-RIFCPKCGNG 94 (212)
Q Consensus 67 k~wvlrC~aC~k~~~~--------~~-k~FCp~CG~~ 94 (212)
-.-.|.|+.|+..+.. ++ .-.||.||..
T Consensus 96 ~~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~ 132 (147)
T smart00531 96 NNAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEE 132 (147)
T ss_pred CCcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCE
Confidence 3558999999977742 11 2579999986
No 113
>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=70.53 E-value=6.3 Score=32.11 Aligned_cols=43 Identities=23% Similarity=0.529 Sum_probs=28.4
Q ss_pred eeEEEEccCcccccccc--CccccCCCCCCCc-----eeEEEEEeC-CCceE
Q 028198 67 HRWILKCHACYTITAEI--GRIFCPKCGNGGT-----LRKVAVTVG-ENGIV 110 (212)
Q Consensus 67 k~wvlrC~aC~k~~~~~--~k~FCp~CG~~~T-----L~Rvsvsv~-~~G~~ 110 (212)
.-|-..|+.|.+..... ...+|++|+.. . .-++.+.+. ..|.+
T Consensus 31 ~~~Y~aC~~C~kkv~~~~~~~~~C~~C~~~-~~~~~~ry~l~~~i~D~Tg~~ 81 (166)
T cd04476 31 NWWYPACPGCNKKVVEEGNGTYRCEKCNKS-VPNPEYRYILSLNVADHTGEA 81 (166)
T ss_pred CeEEccccccCcccEeCCCCcEECCCCCCc-CCCccEEEEEEEEEEeCCCCE
Confidence 35566799999765443 46899999984 2 345555554 44665
No 114
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=70.45 E-value=2.7 Score=30.44 Aligned_cols=31 Identities=26% Similarity=0.607 Sum_probs=22.3
Q ss_pred EEEccCccccccc---cCccccCCCCCCCceeEEE
Q 028198 70 ILKCHACYTITAE---IGRIFCPKCGNGGTLRKVA 101 (212)
Q Consensus 70 vlrC~aC~k~~~~---~~k~FCp~CG~~~TL~Rvs 101 (212)
...|..|+..-.. ..+-.||.||.. +|.|.+
T Consensus 7 ~~~CtSCg~~i~~~~~~~~F~CPnCG~~-~I~RC~ 40 (59)
T PRK14890 7 PPKCTSCGIEIAPREKAVKFLCPNCGEV-IIYRCE 40 (59)
T ss_pred CccccCCCCcccCCCccCEeeCCCCCCe-eEeech
Confidence 3479999976553 236689999986 677754
No 115
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=70.28 E-value=2.3 Score=29.29 Aligned_cols=22 Identities=32% Similarity=0.875 Sum_probs=16.2
Q ss_pred EccCccccccc---------cCccccCCCCC
Q 028198 72 KCHACYTITAE---------IGRIFCPKCGN 93 (212)
Q Consensus 72 rC~aC~k~~~~---------~~k~FCp~CG~ 93 (212)
.|.||+-.-+. ....|||.||-
T Consensus 24 ~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgR 54 (56)
T PF02591_consen 24 TCSGCHMELPPQELNEIRKGDEIVFCPNCGR 54 (56)
T ss_pred ccCCCCEEcCHHHHHHHHcCCCeEECcCCCc
Confidence 89999955432 23589999994
No 116
>COG1933 Archaeal DNA polymerase II, large subunit [DNA replication, recombination, and repair]
Probab=70.16 E-value=2.7 Score=38.15 Aligned_cols=27 Identities=30% Similarity=0.535 Sum_probs=21.6
Q ss_pred eEEEEccCccccccccC-ccccCCCCCC
Q 028198 68 RWILKCHACYTITAEIG-RIFCPKCGNG 94 (212)
Q Consensus 68 ~wvlrC~aC~k~~~~~~-k~FCp~CG~~ 94 (212)
+-..||.+|.+.+.-++ ..-||+||+.
T Consensus 165 rq~~rc~~c~~k~rr~pl~g~c~kcg~~ 192 (253)
T COG1933 165 RQEFRCVKCNTKFRRPPLDGKCPICGGK 192 (253)
T ss_pred hheeehHhhhhhhcCCCccccccccCCe
Confidence 34589999999886544 5789999994
No 117
>PF13638 PIN_4: PIN domain; PDB: 2HWW_C 2HWX_A 2DOK_B 2HWY_B 2WP8_J.
Probab=69.37 E-value=5 Score=30.86 Aligned_cols=27 Identities=15% Similarity=0.137 Sum_probs=19.6
Q ss_pred CceeeEecchHHHHHHHHHhCceeecC
Q 028198 32 ESTVACITGDYAMQNVILQMGLRLLAP 58 (212)
Q Consensus 32 ~~~vac~TdDfAmQNVllqmGL~~~s~ 58 (212)
...|+++|.|..|.+.|...||..+++
T Consensus 106 ~~~vvLvT~D~~l~~~A~~~gi~~~~~ 132 (133)
T PF13638_consen 106 GRKVVLVTNDKNLRLKARAEGIPAVSY 132 (133)
T ss_dssp CEEEEEEE--HHHHHHHHHTT--EE--
T ss_pred CCeEEEEeCCHHHHHHHhhcccccccC
Confidence 568999999999999999999998765
No 118
>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=69.14 E-value=3.7 Score=32.99 Aligned_cols=38 Identities=21% Similarity=0.452 Sum_probs=25.2
Q ss_pred EccCcccc--ccccCccccCCCCCCCceeEE--------EEEeCCCceEE
Q 028198 72 KCHACYTI--TAEIGRIFCPKCGNGGTLRKV--------AVTVGENGIVL 111 (212)
Q Consensus 72 rC~aC~k~--~~~~~k~FCp~CG~~~TL~Rv--------svsv~~~G~~~ 111 (212)
.|+.|.-. |.+.....||.||+. -... .+..|+||+++
T Consensus 4 ~CP~C~seytY~dg~~~iCpeC~~E--W~~~~~~~~~~~~~~kDsnG~~L 51 (109)
T TIGR00686 4 PCPKCNSEYTYHDGTQLICPSCLYE--WNENEVNDDDDELIVKDCNGNLL 51 (109)
T ss_pred cCCcCCCcceEecCCeeECcccccc--ccccccccccCCceEEcCCCCCc
Confidence 58999854 445557889999986 2211 24568888753
No 119
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=69.04 E-value=3.4 Score=41.77 Aligned_cols=43 Identities=23% Similarity=0.431 Sum_probs=29.2
Q ss_pred HHHHHHHHHh----CceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCC
Q 028198 42 YAMQNVILQM----GLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 42 fAmQNVllqm----GL~~~s~~g~~I~~~k~wvlrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
=|+.++...+ ++...+++ .=+-+|..|+.+... ...||+||+.
T Consensus 602 ~a~~~lv~~~~~~~~i~Y~~in--------~~~~~C~~CG~~~g~--~~~CP~CG~~ 648 (656)
T PRK08270 602 EACKKLVKKALENYRLPYITIT--------PTFSICPKHGYLSGE--HEFCPKCGEE 648 (656)
T ss_pred HHHHHHHHHHHHhCCCceEEeC--------CCCcccCCCCCcCCC--CCCCcCCcCc
Confidence 5777777754 46665554 223479999975433 4789999975
No 120
>COG4031 Predicted metal-binding protein [General function prediction only]
Probab=68.55 E-value=3.6 Score=36.43 Aligned_cols=32 Identities=31% Similarity=0.563 Sum_probs=21.3
Q ss_pred EEccCccccccccCccccCCCCCCCceeEEEEEeCC
Q 028198 71 LKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGE 106 (212)
Q Consensus 71 lrC~aC~k~~~~~~k~FCp~CG~~~TL~Rvsvsv~~ 106 (212)
++| .|+..-+.+ .||+.||.+ ----+-|++++
T Consensus 1 ~~C-rCG~~l~~p--~~Cl~Cg~~-~av~~~vy~~~ 32 (227)
T COG4031 1 LIC-RCGAELSSP--AFCLNCGRR-HAVGCGVYVSE 32 (227)
T ss_pred Ccc-ccCCccccc--chhcccCCc-ceeEeeeeccc
Confidence 468 899766554 899999987 33334444443
No 121
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=68.16 E-value=3.8 Score=45.00 Aligned_cols=25 Identities=28% Similarity=0.679 Sum_probs=21.5
Q ss_pred EEEEccCccccccccC-ccccCCCCCC
Q 028198 69 WILKCHACYTITAEIG-RIFCPKCGNG 94 (212)
Q Consensus 69 wvlrC~aC~k~~~~~~-k~FCp~CG~~ 94 (212)
=..|| .|+..|.-++ ..-||+||++
T Consensus 1541 Q~~RC-kC~~kyRR~PL~G~C~kCGg~ 1566 (1627)
T PRK14715 1541 QEFRC-KCGAKYRRVPLKGKCPKCGSK 1566 (1627)
T ss_pred cceee-cCCCccccCCCCCcCcccCCe
Confidence 35899 9999998776 6789999997
No 122
>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=68.04 E-value=2.6 Score=39.58 Aligned_cols=28 Identities=29% Similarity=0.580 Sum_probs=23.1
Q ss_pred EEccCccccccccCccccCCCCCCCceeE
Q 028198 71 LKCHACYTITAEIGRIFCPKCGNGGTLRK 99 (212)
Q Consensus 71 lrC~aC~k~~~~~~k~FCp~CG~~~TL~R 99 (212)
|+|..|+..+.. ..-.||.||.=+||..
T Consensus 1 ~~c~~cg~~~~~-~~g~cp~c~~w~~~~e 28 (372)
T cd01121 1 YVCSECGYVSPK-WLGKCPECGEWNTLVE 28 (372)
T ss_pred CCCCCCCCCCCC-ccEECcCCCCceeeee
Confidence 589999987765 4567999998889876
No 123
>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=67.78 E-value=5.5 Score=27.88 Aligned_cols=21 Identities=43% Similarity=0.835 Sum_probs=13.8
Q ss_pred ccccCCCCCCCceeEEEEEeCCCceEEe
Q 028198 85 RIFCPKCGNGGTLRKVAVTVGENGIVLA 112 (212)
Q Consensus 85 k~FCp~CG~~~TL~Rvsvsv~~~G~~~~ 112 (212)
..+||.|||. +| .+..|++++
T Consensus 13 Y~~Cp~CGN~----~v---GngEG~liV 33 (49)
T PF12677_consen 13 YCKCPKCGND----KV---GNGEGTLIV 33 (49)
T ss_pred hccCcccCCc----Ee---ecCcceEEE
Confidence 4689999997 22 255566543
No 124
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=67.69 E-value=2.9 Score=42.15 Aligned_cols=46 Identities=22% Similarity=0.411 Sum_probs=28.9
Q ss_pred chHHHHHHHHHh---CceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCC
Q 028198 40 GDYAMQNVILQM---GLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 40 dDfAmQNVllqm---GL~~~s~~g~~I~~~k~wvlrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
+=-|+..+...+ ++...++. .=+-+|..|+..+... ...||+||+.
T Consensus 543 n~~al~~lv~~~~~~~i~Y~~in--------p~~~~C~~CG~~~~g~-~~~CP~CGs~ 591 (625)
T PRK08579 543 DPEALAKLTKRIMNTKLVYWSYT--------PAITVCNKCGRSTTGL-YTRCPRCGSE 591 (625)
T ss_pred CHHHHHHHHHHHHhcCCceEEeC--------CCCccCCCCCCccCCC-CCcCcCCCCc
Confidence 446777777775 23333332 2245799999854332 5789999985
No 125
>PRK12366 replication factor A; Reviewed
Probab=67.64 E-value=6.8 Score=39.34 Aligned_cols=48 Identities=25% Similarity=0.497 Sum_probs=30.0
Q ss_pred ceeeeeEEEEccCccccccc-cCccccCCCCCCC--ceeEEEEEeCCC-ceE
Q 028198 63 IRQLHRWILKCHACYTITAE-IGRIFCPKCGNGG--TLRKVAVTVGEN-GIV 110 (212)
Q Consensus 63 I~~~k~wvlrC~aC~k~~~~-~~k~FCp~CG~~~--TL~Rvsvsv~~~-G~~ 110 (212)
|+.-..|..+|+.|.|.-.. ...-.||.||... -+-++++.+++. |.+
T Consensus 525 i~~~~~~y~aCp~CnkKv~~~~g~~~C~~c~~~~p~~~~~l~~~i~D~TG~~ 576 (637)
T PRK12366 525 IRKQKIILYLCPNCRKRVEEVDGEYICEFCGEVEPNELLMLNFTLDDGTGTI 576 (637)
T ss_pred EeCCCEEEecccccCeEeEcCCCcEECCCCCCCCCcEEEEEEEEEEcCCCCE
Confidence 34445688999999976543 2345799999731 223455666544 665
No 126
>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=67.60 E-value=5 Score=35.98 Aligned_cols=40 Identities=33% Similarity=0.401 Sum_probs=16.3
Q ss_pred EEEEccCccccccccCccccCCCCCCCceeEEEEEeCCCce
Q 028198 69 WILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGENGI 109 (212)
Q Consensus 69 wvlrC~aC~k~~~~~~k~FCp~CG~~~TL~Rvsvsv~~~G~ 109 (212)
-.+.|.-|+....- .+.-||.|||..-.+-..+++++++.
T Consensus 196 R~L~Cs~C~t~W~~-~R~~Cp~Cg~~~~~~l~~~~~e~~~~ 235 (290)
T PF04216_consen 196 RYLHCSLCGTEWRF-VRIKCPYCGNTDHEKLEYFTVEGEPA 235 (290)
T ss_dssp EEEEETTT--EEE---TTS-TTT---SS-EEE--------S
T ss_pred EEEEcCCCCCeeee-cCCCCcCCCCCCCcceeeEecCCCCc
Confidence 35889999987754 47889999997433333333444443
No 127
>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=67.50 E-value=4.7 Score=34.54 Aligned_cols=41 Identities=22% Similarity=0.397 Sum_probs=24.7
Q ss_pred HHHhCce-eecCCCCcceeeeeEEEEccCcccccccc---------CccccCCCCCC
Q 028198 48 ILQMGLR-LLAPGGMQIRQLHRWILKCHACYTITAEI---------GRIFCPKCGNG 94 (212)
Q Consensus 48 llqmGL~-~~s~~g~~I~~~k~wvlrC~aC~k~~~~~---------~k~FCp~CG~~ 94 (212)
..+.|.+ |+.++|. ...++|..|.+.+... ...-||.||..
T Consensus 92 ~~~aG~~~v~elHG~------~~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~ 142 (218)
T cd01407 92 HQRAGSPKVIELHGS------LFRVRCTKCGKEYPRDELQADIDREEVPRCPKCGGL 142 (218)
T ss_pred HHHcCCCCEEECcCC------cCcceeCCCcCCCcHHHHhHhhccCCCCcCCCCCCc
Confidence 4444543 5555554 4457899998765421 12469999874
No 128
>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=67.50 E-value=2.2 Score=33.12 Aligned_cols=18 Identities=33% Similarity=0.866 Sum_probs=14.8
Q ss_pred ccccCCCCCCCceeEEEEE
Q 028198 85 RIFCPKCGNGGTLRKVAVT 103 (212)
Q Consensus 85 k~FCp~CG~~~TL~Rvsvs 103 (212)
+.+||.||.. +++|+++-
T Consensus 35 ky~Cp~Cgk~-~vkR~a~G 52 (90)
T PF01780_consen 35 KYTCPFCGKT-SVKRVATG 52 (90)
T ss_dssp -BEESSSSSS-EEEEEETT
T ss_pred CCcCCCCCCc-eeEEeeeE
Confidence 6789999998 89999863
No 129
>PRK00504 rpmG 50S ribosomal protein L33; Validated
Probab=66.73 E-value=6.4 Score=27.38 Aligned_cols=31 Identities=32% Similarity=0.747 Sum_probs=21.5
Q ss_pred eEEEEccCccccc-c---c--------cCccccCCCCCCCceeE
Q 028198 68 RWILKCHACYTIT-A---E--------IGRIFCPKCGNGGTLRK 99 (212)
Q Consensus 68 ~wvlrC~aC~k~~-~---~--------~~k~FCp~CG~~~TL~R 99 (212)
.-.|.|..|.... . . .-+.|||.|... ||-+
T Consensus 5 ~i~L~C~~c~~rnY~t~KNk~~~~~rLelkKycp~c~kh-tlhk 47 (50)
T PRK00504 5 KITLACTECKSRNYTTTKNKKNTPERLELKKFCPRCNKH-TLHK 47 (50)
T ss_pred EEEEEEcCCCCccEeEcCCCCCCCceEEEECcCCCCCCe-Eeee
Confidence 5678999998432 1 0 126899999997 8753
No 130
>PRK08402 replication factor A; Reviewed
Probab=66.72 E-value=9.8 Score=35.85 Aligned_cols=45 Identities=13% Similarity=0.299 Sum_probs=30.3
Q ss_pred eeEEEEccCcccccc-c--cCccccCCCC--CCCceeEEEEEeCCC-ceEE
Q 028198 67 HRWILKCHACYTITA-E--IGRIFCPKCG--NGGTLRKVAVTVGEN-GIVL 111 (212)
Q Consensus 67 k~wvlrC~aC~k~~~-~--~~k~FCp~CG--~~~TL~Rvsvsv~~~-G~~~ 111 (212)
..|..+|+.|.|... + ...-.|+.|| .+.-.-.+++.+++. |.+-
T Consensus 209 ~~~y~aCp~CnKkv~~~~~~~~~~Ce~~~~v~p~~ryil~~~l~D~TG~~~ 259 (355)
T PRK08402 209 VLVYDACPECRRKVDYDPATDTWICPEHGEVEPIKITILDFGLDDGTGYIR 259 (355)
T ss_pred CeeEecCCCCCeEEEEecCCCCEeCCCCCCcCcceeEEEEEEEEcCCCcEE
Confidence 348899999998764 2 2356899999 552334566666544 7663
No 131
>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=66.68 E-value=3.5 Score=24.77 Aligned_cols=21 Identities=33% Similarity=0.695 Sum_probs=12.5
Q ss_pred ccCcccccccc---CccccCCCCC
Q 028198 73 CHACYTITAEI---GRIFCPKCGN 93 (212)
Q Consensus 73 C~aC~k~~~~~---~k~FCp~CG~ 93 (212)
|..|+..-... ..--||.||.
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCcccCceEeCCCCCC
Confidence 67775443321 2456999983
No 132
>PRK10220 hypothetical protein; Provisional
Probab=66.65 E-value=4.6 Score=32.58 Aligned_cols=38 Identities=24% Similarity=0.608 Sum_probs=24.8
Q ss_pred EccCcccc--ccccCccccCCCCCCCceeEE--------EEEeCCCceEE
Q 028198 72 KCHACYTI--TAEIGRIFCPKCGNGGTLRKV--------AVTVGENGIVL 111 (212)
Q Consensus 72 rC~aC~k~--~~~~~k~FCp~CG~~~TL~Rv--------svsv~~~G~~~ 111 (212)
.|+.|.-. |.+.....||-||+. -..- .+..|++|+++
T Consensus 5 ~CP~C~seytY~d~~~~vCpeC~hE--W~~~~~~~~~~~~~vkDsnG~~L 52 (111)
T PRK10220 5 HCPKCNSEYTYEDNGMYICPECAHE--WNDAEPAQESDELIVKDANGNLL 52 (111)
T ss_pred cCCCCCCcceEcCCCeEECCcccCc--CCccccccccCCceEEcCCCCCc
Confidence 58888844 455567899999975 2111 14568888753
No 133
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=66.55 E-value=5.3 Score=32.98 Aligned_cols=48 Identities=23% Similarity=0.446 Sum_probs=30.2
Q ss_pred eeeEecchH---HHHHHHHHhCceee------cCCCCcceeeeeEEEEccCcccccc
Q 028198 34 TVACITGDY---AMQNVILQMGLRLL------APGGMQIRQLHRWILKCHACYTITA 81 (212)
Q Consensus 34 ~vac~TdDf---AmQNVllqmGL~~~------s~~g~~I~~~k~wvlrC~aC~k~~~ 81 (212)
...+++..| -||++|...=-.+| +++...|++-+.|.++|.||+...+
T Consensus 78 ~~lii~G~~~~~~i~~~L~~yI~~yVlC~~C~spdT~l~k~~r~~~l~C~ACGa~~~ 134 (138)
T PRK03988 78 GRLILQGKFSPRVINEKIDRYVKEYVICPECGSPDTKLIKEGRIWVLKCEACGAETP 134 (138)
T ss_pred CEEEEEEeeCHHHHHHHHHHHHHhcEECCCCCCCCcEEEEcCCeEEEEcccCCCCCc
Confidence 344555444 46777666433332 6777777777788888888886543
No 134
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=66.47 E-value=4.1 Score=26.11 Aligned_cols=24 Identities=29% Similarity=0.725 Sum_probs=17.4
Q ss_pred EEEccCccccccc--------cCccccCCCCC
Q 028198 70 ILKCHACYTITAE--------IGRIFCPKCGN 93 (212)
Q Consensus 70 vlrC~aC~k~~~~--------~~k~FCp~CG~ 93 (212)
+..|..|.+.|.. ..+.-|++||+
T Consensus 2 ~i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~ 33 (36)
T PF13717_consen 2 IITCPNCQAKYEIDDEKIPPKGRKVRCSKCGH 33 (36)
T ss_pred EEECCCCCCEEeCCHHHCCCCCcEEECCCCCC
Confidence 3579999887752 22578999997
No 135
>PLN02569 threonine synthase
Probab=66.28 E-value=5.7 Score=38.68 Aligned_cols=57 Identities=16% Similarity=0.057 Sum_probs=36.5
Q ss_pred eeEecchHHHHHHHHHhCceeecCCCCcceeeeeEEEEccCccccccccC-ccccCCCCCCCcee
Q 028198 35 VACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIG-RIFCPKCGNGGTLR 98 (212)
Q Consensus 35 vac~TdDfAmQNVllqmGL~~~s~~g~~I~~~k~wvlrC~aC~k~~~~~~-k~FCp~CG~~~TL~ 98 (212)
..-.|.|-++|-++.+ +... +.+. +.-...+-|+|..|++.|+... ...| .||.. |.
T Consensus 18 ~~~~~~~~~~~~~~~~-~~~~-~~~~--~~~~~~~~l~C~~Cg~~y~~~~~~~~C-~cgg~--l~ 75 (484)
T PLN02569 18 ATKFTADENIRDEARR-GPPA-PPDE--FSAKYVPFLECPLTGEKYSLDEVVYRS-KSGGL--LD 75 (484)
T ss_pred ccccCcchhhhhhhhh-cCCC-CCcc--cccccccccEeCCCCCcCCCccccccC-CCCCe--EE
Confidence 3457889999999988 2221 1122 2112233599999999997543 4679 69975 64
No 136
>PRK08329 threonine synthase; Validated
Probab=66.26 E-value=3.6 Score=37.78 Aligned_cols=25 Identities=32% Similarity=0.695 Sum_probs=19.8
Q ss_pred EEccCccccccccCccccCCCCCCCcee
Q 028198 71 LKCHACYTITAEIGRIFCPKCGNGGTLR 98 (212)
Q Consensus 71 lrC~aC~k~~~~~~k~FCp~CG~~~TL~ 98 (212)
|+|..|++.++......| .||.. |.
T Consensus 2 l~C~~Cg~~~~~~~~~~C-~c~~~--l~ 26 (347)
T PRK08329 2 LRCTKCGRTYEEKFKLRC-DCGGT--LL 26 (347)
T ss_pred cCcCCCCCCcCCCCceec-CCCCc--EE
Confidence 799999999976445679 69975 64
No 137
>PRK05638 threonine synthase; Validated
Probab=66.21 E-value=3.7 Score=38.88 Aligned_cols=24 Identities=29% Similarity=0.539 Sum_probs=19.2
Q ss_pred EEEccCccccccccCccccCCCCCC
Q 028198 70 ILKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 70 vlrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
+|+|..|++.++......| .||..
T Consensus 1 ~l~C~~Cg~~~~~~~~~~C-~c~~~ 24 (442)
T PRK05638 1 KMKCPKCGREYNSYIPPFC-ICGEL 24 (442)
T ss_pred CeEeCCCCCCCCCCCceec-CCCCc
Confidence 4799999999975445679 89975
No 138
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=65.78 E-value=5.1 Score=25.67 Aligned_cols=24 Identities=33% Similarity=0.744 Sum_probs=17.0
Q ss_pred EEccCccccccc--------cCccccCCCCCC
Q 028198 71 LKCHACYTITAE--------IGRIFCPKCGNG 94 (212)
Q Consensus 71 lrC~aC~k~~~~--------~~k~FCp~CG~~ 94 (212)
.+|+.|...|.. ..+.-||+||+.
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~ 34 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHV 34 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCcE
Confidence 578899877742 225779999873
No 139
>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=65.55 E-value=2 Score=44.86 Aligned_cols=10 Identities=20% Similarity=0.338 Sum_probs=0.0
Q ss_pred CCceecCCCC
Q 028198 139 KNLILREDQL 148 (212)
Q Consensus 139 ~~~IL~EDQ~ 148 (212)
.+|+-.+||+
T Consensus 802 G~pL~~~dQi 811 (900)
T PF03833_consen 802 GKPLESDDQI 811 (900)
T ss_dssp ----------
T ss_pred CCccCCccce
Confidence 3788899993
No 140
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=65.27 E-value=4 Score=35.59 Aligned_cols=33 Identities=30% Similarity=0.633 Sum_probs=23.4
Q ss_pred EEEccCccccc-cccCccccCCCCCCCceeEEEEE
Q 028198 70 ILKCHACYTIT-AEIGRIFCPKCGNGGTLRKVAVT 103 (212)
Q Consensus 70 vlrC~aC~k~~-~~~~k~FCp~CG~~~TL~Rvsvs 103 (212)
.-+|.-|...- ..-...-||.||+. -.+|+|.-
T Consensus 149 ~A~CsrC~~~L~~~~~~l~Cp~Cg~t-EkRKia~~ 182 (188)
T COG1096 149 YARCSRCRAPLVKKGNMLKCPNCGNT-EKRKIAKD 182 (188)
T ss_pred EEEccCCCcceEEcCcEEECCCCCCE-Eeeeeccc
Confidence 35899998543 22235789999996 78888854
No 141
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=64.88 E-value=7 Score=32.06 Aligned_cols=39 Identities=21% Similarity=0.341 Sum_probs=24.9
Q ss_pred HHHHHHHHHhCceee------cCCCCcceeeeeEEEEccCccccc
Q 028198 42 YAMQNVILQMGLRLL------APGGMQIRQLHRWILKCHACYTIT 80 (212)
Q Consensus 42 fAmQNVllqmGL~~~------s~~g~~I~~~k~wvlrC~aC~k~~ 80 (212)
-.+|++|...=-.+| +++...+++-+.|.++|.||+...
T Consensus 84 ~~i~~~L~~yI~~yVlC~~C~sPdT~l~k~~r~~~l~C~ACGa~~ 128 (133)
T TIGR00311 84 FLLNERIEDYVRKYVICRECNRPDTRIIKEGRVSLLKCEACGAKA 128 (133)
T ss_pred HHHHHHHHHHHhheEECCCCCCCCcEEEEeCCeEEEecccCCCCC
Confidence 346777766433332 566677776777777777777644
No 142
>TIGR01023 rpmG_bact ribosomal protein L33, bacterial type. This model describes bacterial ribosomal protein L33 and its chloroplast and mitochondrial equivalents.
Probab=64.81 E-value=8 Score=27.19 Aligned_cols=32 Identities=34% Similarity=0.654 Sum_probs=22.0
Q ss_pred eeEEEEccCcccccc----c-------c-CccccCCCCCCCceeE
Q 028198 67 HRWILKCHACYTITA----E-------I-GRIFCPKCGNGGTLRK 99 (212)
Q Consensus 67 k~wvlrC~aC~k~~~----~-------~-~k~FCp~CG~~~TL~R 99 (212)
....|.|.+|...+. . + -+.|||.|+.. ||-+
T Consensus 8 ~~i~L~ct~c~~~nY~t~Kn~~~~~~kL~lkKycp~~~kh-tlhk 51 (54)
T TIGR01023 8 ELIRLVCTACTGINYTTTKNRRNKPEKLELRKYCPVCRKH-VLHK 51 (54)
T ss_pred eEEEEEecCCCCCCEEEcCCCCCCCCceEEECcCCCCCCe-EeEE
Confidence 467899999963321 1 1 16899999997 7753
No 143
>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=64.59 E-value=4.4 Score=38.99 Aligned_cols=31 Identities=19% Similarity=0.406 Sum_probs=24.9
Q ss_pred eEEEEccCccccccccCccccCCCCCCCceeE
Q 028198 68 RWILKCHACYTITAEIGRIFCPKCGNGGTLRK 99 (212)
Q Consensus 68 ~wvlrC~aC~k~~~~~~k~FCp~CG~~~TL~R 99 (212)
+-.|+|..|+..+.. ..-.||.||.=+|+.-
T Consensus 5 ~~~y~C~~Cg~~~~~-~~g~Cp~C~~w~t~~~ 35 (454)
T TIGR00416 5 KSKFVCQHCGADSPK-WQGKCPACHAWNTITE 35 (454)
T ss_pred CCeEECCcCCCCCcc-ccEECcCCCCccccch
Confidence 347999999987765 3567999999888875
No 144
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=63.68 E-value=4 Score=41.21 Aligned_cols=44 Identities=23% Similarity=0.408 Sum_probs=27.0
Q ss_pred HHHHHHHHH---hCceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCC
Q 028198 42 YAMQNVILQ---MGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 42 fAmQNVllq---mGL~~~s~~g~~I~~~k~wvlrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
=|+.+++.. .|+...++. .=+-+|..|+.+... ....||+||+.
T Consensus 543 eal~~lv~~~~~~~i~Yf~in--------~~~~iC~~CG~~~~g-~~~~CP~CGs~ 589 (623)
T PRK08271 543 EGYRKLLNIAAKTGCNYFAFN--------VKITICNDCHHIDKR-TGKRCPICGSE 589 (623)
T ss_pred HHHHHHHHHHHHcCCceEEeC--------CCCccCCCCCCcCCC-CCcCCcCCCCc
Confidence 345554443 355555544 123479999976332 35789999986
No 145
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=63.65 E-value=4.2 Score=31.66 Aligned_cols=17 Identities=35% Similarity=0.958 Sum_probs=13.6
Q ss_pred ccccCCCCCCCceeEEEE
Q 028198 85 RIFCPKCGNGGTLRKVAV 102 (212)
Q Consensus 85 k~FCp~CG~~~TL~Rvsv 102 (212)
+..||.||.+ +++|++.
T Consensus 35 ~~~Cp~C~~~-~VkR~a~ 51 (89)
T COG1997 35 KHVCPFCGRT-TVKRIAT 51 (89)
T ss_pred CCcCCCCCCc-ceeeecc
Confidence 5678888887 8888875
No 146
>PRK08197 threonine synthase; Validated
Probab=63.11 E-value=5.8 Score=36.99 Aligned_cols=25 Identities=28% Similarity=0.563 Sum_probs=19.6
Q ss_pred EEEEccCccccccccC-ccccCCCCCC
Q 028198 69 WILKCHACYTITAEIG-RIFCPKCGNG 94 (212)
Q Consensus 69 wvlrC~aC~k~~~~~~-k~FCp~CG~~ 94 (212)
+.|+|..|++.++... ...| .||..
T Consensus 6 ~~~~C~~Cg~~~~~~~~~~~C-~cg~~ 31 (394)
T PRK08197 6 SHLECSKCGETYDADQVHNLC-KCGKP 31 (394)
T ss_pred eEEEECCCCCCCCCCCcceec-CCCCe
Confidence 3599999999997543 3569 89976
No 147
>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=62.74 E-value=5.2 Score=34.61 Aligned_cols=27 Identities=26% Similarity=0.338 Sum_probs=17.0
Q ss_pred eEEEEccCcccccccc--------CccccCCCCCC
Q 028198 68 RWILKCHACYTITAEI--------GRIFCPKCGNG 94 (212)
Q Consensus 68 ~wvlrC~aC~k~~~~~--------~k~FCp~CG~~ 94 (212)
.+.++|..|.+.+... ....||.||..
T Consensus 111 l~~~~C~~C~~~~~~~~~~~~~~~~~p~C~~Cgg~ 145 (222)
T cd01413 111 LQTAYCVNCGSKYDLEEVKYAKKHEVPRCPKCGGI 145 (222)
T ss_pred cCcceECCCCCCcchhHHHHhccCCCCcCCCCCCc
Confidence 3457788888766421 12458888864
No 148
>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=62.68 E-value=5.8 Score=34.69 Aligned_cols=34 Identities=21% Similarity=0.380 Sum_probs=21.9
Q ss_pred eecCCCCcceeeeeEEEEccCcccccccc---------CccccCCCCCC
Q 028198 55 LLAPGGMQIRQLHRWILKCHACYTITAEI---------GRIFCPKCGNG 94 (212)
Q Consensus 55 ~~s~~g~~I~~~k~wvlrC~aC~k~~~~~---------~k~FCp~CG~~ 94 (212)
|+.++|. .+.++|..|.+.+... ...-||.||+.
T Consensus 107 V~elHG~------l~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cgg~ 149 (235)
T cd01408 107 IIEAHGS------FATAHCIKCKHKYPGDWMREDIFNQEVPKCPRCGGL 149 (235)
T ss_pred EEEeCcC------CCccccccCCCcCCHHHHHHHHhCCCCccCCCCCCC
Confidence 4555554 4557899999876421 12359999975
No 149
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=62.65 E-value=2.4 Score=39.25 Aligned_cols=73 Identities=23% Similarity=0.352 Sum_probs=44.9
Q ss_pred EEccCcccccc--c--cCccccCCCCCCCce---eEEEEEeCCCceEEeecCCccccccceeccCCCCCCCCCCCCCcee
Q 028198 71 LKCHACYTITA--E--IGRIFCPKCGNGGTL---RKVAVTVGENGIVLASRRPRITLRGTKFSLPMPQGGRDAITKNLIL 143 (212)
Q Consensus 71 lrC~aC~k~~~--~--~~k~FCp~CG~~~TL---~Rvsvsv~~~G~~~~~~k~~~n~RG~~ySlPkpkgGk~~~~~~~IL 143 (212)
..|++|+.+.. + .....||+||+...+ .|+.. +--.|.-..+..|. .. .||+-
T Consensus 29 ~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ri~A~~Ri~~---------------llD~gsf~el~~~l---~~--~dPL~ 88 (294)
T COG0777 29 TKCPSCGEMLYRKELESNLKVCPKCGHHMRISARERLEA---------------LLDEGSFEELDSPL---EP--KDPLK 88 (294)
T ss_pred eECCCccceeeHHHHHhhhhcccccCcccccCHHHHHHH---------------hhCCCcceecccCC---Cc--CCccc
Confidence 57999998753 2 235789999997111 11122 22244444444442 22 48888
Q ss_pred cCCCCcccccchhhhcccCC
Q 028198 144 REDQLPQKYLYPRNKKKVNK 163 (212)
Q Consensus 144 ~EDQ~~~~~~~~k~r~k~~~ 163 (212)
..|.+.|.-+.+++++++..
T Consensus 89 F~d~k~Y~~rL~~a~~~tg~ 108 (294)
T COG0777 89 FPDSKKYKDRLEAARKKTGL 108 (294)
T ss_pred CCcchhhHHHHHHHHhhcCC
Confidence 99988887777788877543
No 150
>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=62.43 E-value=8.4 Score=31.76 Aligned_cols=27 Identities=30% Similarity=0.567 Sum_probs=20.0
Q ss_pred eEEEEccCccccccc---------cCccccCCCCCC
Q 028198 68 RWILKCHACYTITAE---------IGRIFCPKCGNG 94 (212)
Q Consensus 68 ~wvlrC~aC~k~~~~---------~~k~FCp~CG~~ 94 (212)
.+..+|..|.+.+.. ....-||.||..
T Consensus 103 l~~~~C~~C~~~~~~~~~~~~~~~~~~~~C~~C~~~ 138 (178)
T PF02146_consen 103 LFRLRCSKCGKEYDREDIVDSIDEEEPPRCPKCGGL 138 (178)
T ss_dssp EEEEEETTTSBEEEGHHHHHHHHTTSSCBCTTTSCB
T ss_pred hceeeecCCCccccchhhcccccccccccccccCcc
Confidence 677899999997742 123469999984
No 151
>PRK00595 rpmG 50S ribosomal protein L33; Validated
Probab=62.39 E-value=8.8 Score=26.81 Aligned_cols=32 Identities=13% Similarity=0.017 Sum_probs=21.9
Q ss_pred eeEEEEccCccccccc-----------c-CccccCCCCCCCceeE
Q 028198 67 HRWILKCHACYTITAE-----------I-GRIFCPKCGNGGTLRK 99 (212)
Q Consensus 67 k~wvlrC~aC~k~~~~-----------~-~k~FCp~CG~~~TL~R 99 (212)
....|.|.+|...... + -+.|||.|+.. ||-+
T Consensus 7 ~~i~L~ct~c~~~nY~t~Kn~k~~~~rL~lkKycp~~~kh-tlhk 50 (53)
T PRK00595 7 VKIKLESTEGTGRFYTTTKNKRNTPEKLELKKYDPVLRKH-VLHK 50 (53)
T ss_pred eEEEEEecCCCCEEEEEccCCCCCCCceEEECcCCCCCCE-EeEE
Confidence 3567999999843210 1 16899999997 7754
No 152
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=62.38 E-value=6.7 Score=31.14 Aligned_cols=45 Identities=20% Similarity=0.433 Sum_probs=28.5
Q ss_pred eeeEecchH---HHHHHHHHhCceee------cCCCCcceeeeeEEEEccCccc
Q 028198 34 TVACITGDY---AMQNVILQMGLRLL------APGGMQIRQLHRWILKCHACYT 78 (212)
Q Consensus 34 ~vac~TdDf---AmQNVllqmGL~~~------s~~g~~I~~~k~wvlrC~aC~k 78 (212)
..++++..| .||++|...=-.+| +++...+++-+.|.++|.||+.
T Consensus 56 ~rlii~G~~~~~~i~~~l~~yI~~yVlC~~C~spdT~l~k~~r~~~l~C~aCGa 109 (110)
T smart00653 56 GRLIVNGRFTPKKLQDLLRRYIKEYVLCPECGSPDTELIKENRLFFLKCEACGA 109 (110)
T ss_pred CeEEEEEeeCHHHHHHHHHHHHHhcEECCCCCCCCcEEEEeCCeEEEEccccCC
Confidence 445555554 46676665433322 6677777777788888888874
No 153
>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=62.20 E-value=3.5 Score=26.93 Aligned_cols=23 Identities=35% Similarity=0.953 Sum_probs=11.5
Q ss_pred EEccCccccc--cc--cCccccCCCCC
Q 028198 71 LKCHACYTIT--AE--IGRIFCPKCGN 93 (212)
Q Consensus 71 lrC~aC~k~~--~~--~~k~FCp~CG~ 93 (212)
++|+.|+... .+ ....+|+.||.
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~ 27 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGL 27 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-B
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCC
Confidence 4566676532 11 22456777765
No 154
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=61.94 E-value=6 Score=37.27 Aligned_cols=27 Identities=22% Similarity=0.523 Sum_probs=19.6
Q ss_pred eEEEEccCcccccccc--CccccCCCCCC
Q 028198 68 RWILKCHACYTITAEI--GRIFCPKCGNG 94 (212)
Q Consensus 68 ~wvlrC~aC~k~~~~~--~k~FCp~CG~~ 94 (212)
.|++.|+.|....... ....||.||.+
T Consensus 242 g~~~~C~~c~~~~~~~~~~~~~C~~c~~~ 270 (382)
T PRK04338 242 GYVYYCPKCLYREEVEGLPPEECPVCGGK 270 (382)
T ss_pred eeEEECCCCCcEEEecCCCCCCCCCCCCc
Confidence 6789999999754321 24579999986
No 155
>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=61.00 E-value=6.1 Score=33.93 Aligned_cols=27 Identities=22% Similarity=0.379 Sum_probs=17.4
Q ss_pred eEEEEccCcccccccc----------CccccCCCCCC
Q 028198 68 RWILKCHACYTITAEI----------GRIFCPKCGNG 94 (212)
Q Consensus 68 ~wvlrC~aC~k~~~~~----------~k~FCp~CG~~ 94 (212)
-+.++|..|.+.+... ....||.||+.
T Consensus 93 ~~~~~C~~C~~~~~~~~~~~~~~~~~~~p~C~~Cgg~ 129 (206)
T cd01410 93 MFIEVCKSCGPEYVRDDVVETRGDKETGRRCHACGGI 129 (206)
T ss_pred cCcccCCCCCCccchHHHHHHhhcCCCCCcCCCCcCc
Confidence 4567899999776421 12348999864
No 156
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=60.67 E-value=6.5 Score=27.09 Aligned_cols=8 Identities=63% Similarity=1.900 Sum_probs=3.8
Q ss_pred cccCCCCC
Q 028198 86 IFCPKCGN 93 (212)
Q Consensus 86 ~FCp~CG~ 93 (212)
.|||.||+
T Consensus 21 ~fCP~Cg~ 28 (50)
T PRK00432 21 KFCPRCGS 28 (50)
T ss_pred CcCcCCCc
Confidence 34444444
No 157
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=60.62 E-value=6.7 Score=34.16 Aligned_cols=27 Identities=26% Similarity=0.420 Sum_probs=17.9
Q ss_pred eEEEEccCcccccccc-----CccccCCCCCC
Q 028198 68 RWILKCHACYTITAEI-----GRIFCPKCGNG 94 (212)
Q Consensus 68 ~wvlrC~aC~k~~~~~-----~k~FCp~CG~~ 94 (212)
...++|..|.+.+... ...-||.||..
T Consensus 120 ~~~~~C~~C~~~~~~~~~~~~~~p~C~~Cgg~ 151 (242)
T PRK00481 120 LLRARCTKCGQTYDLDEYLKPEPPRCPKCGGI 151 (242)
T ss_pred cCceeeCCCCCCcChhhhccCCCCCCCCCCCc
Confidence 4457899998877421 12239999975
No 158
>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=60.62 E-value=3.9 Score=28.59 Aligned_cols=10 Identities=20% Similarity=0.667 Sum_probs=4.4
Q ss_pred ccCccccccc
Q 028198 73 CHACYTITAE 82 (212)
Q Consensus 73 C~aC~k~~~~ 82 (212)
|+||.+.++.
T Consensus 2 CfgC~~~~~~ 11 (51)
T PF07975_consen 2 CFGCQKPFPD 11 (51)
T ss_dssp ETTTTEE-TT
T ss_pred CccCCCCCCC
Confidence 4555544444
No 159
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=60.34 E-value=8.1 Score=30.04 Aligned_cols=20 Identities=35% Similarity=0.948 Sum_probs=16.2
Q ss_pred CccccCCCCCCCceeEEEEEe
Q 028198 84 GRIFCPKCGNGGTLRKVAVTV 104 (212)
Q Consensus 84 ~k~FCp~CG~~~TL~Rvsvsv 104 (212)
.+.+||.||.. .++|+++-+
T Consensus 35 a~y~CpfCgk~-~vkR~a~GI 54 (90)
T PTZ00255 35 AKYFCPFCGKH-AVKRQAVGI 54 (90)
T ss_pred CCccCCCCCCC-ceeeeeeEE
Confidence 36789999987 899999743
No 160
>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=60.30 E-value=2.9 Score=43.78 Aligned_cols=21 Identities=33% Similarity=0.711 Sum_probs=0.0
Q ss_pred EEccCccccccccCccccCCCCCC
Q 028198 71 LKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 71 lrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
.+|+.|++.+.. ..||.||..
T Consensus 656 r~Cp~Cg~~t~~---~~Cp~CG~~ 676 (900)
T PF03833_consen 656 RRCPKCGKETFY---NRCPECGSH 676 (900)
T ss_dssp ------------------------
T ss_pred ccCcccCCcchh---hcCcccCCc
Confidence 456666654432 345555554
No 161
>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=60.14 E-value=6.8 Score=26.26 Aligned_cols=23 Identities=17% Similarity=0.371 Sum_probs=15.2
Q ss_pred ccCCCCCCCceeEEEEEeCCCceE
Q 028198 87 FCPKCGNGGTLRKVAVTVGENGIV 110 (212)
Q Consensus 87 FCp~CG~~~TL~Rvsvsv~~~G~~ 110 (212)
.||.||.+ ...|.+..+......
T Consensus 1 ~CP~Cg~~-a~ir~S~~~s~~~~~ 23 (47)
T PF04606_consen 1 RCPHCGSK-ARIRTSRQLSPLTRE 23 (47)
T ss_pred CcCCCCCe-eEEEEchhhCcceEE
Confidence 39999998 566666555554443
No 162
>CHL00104 rpl33 ribosomal protein L33
Probab=59.76 E-value=9 Score=28.13 Aligned_cols=32 Identities=31% Similarity=0.594 Sum_probs=21.8
Q ss_pred eeEEEEccCccccc--------------cc--------cCccccCCCCCCCceeE
Q 028198 67 HRWILKCHACYTIT--------------AE--------IGRIFCPKCGNGGTLRK 99 (212)
Q Consensus 67 k~wvlrC~aC~k~~--------------~~--------~~k~FCp~CG~~~TL~R 99 (212)
....|.|..|..-. .. .-+.|||.|... ||-+
T Consensus 9 ~~I~L~Ct~c~~~n~~~~~~g~~rY~T~KNkkn~p~rLelkKycp~c~kH-tlhk 62 (66)
T CHL00104 9 VTVILECTSCVRNGVNKESTGISRYITQKNRHNTPNRLELKKFCPYCYKH-TIHK 62 (66)
T ss_pred EEEEEEecCCcCCCccccCcccceEEECCCCCCCCceeEEECcCCCCCCE-eeEe
Confidence 35679999995332 11 125799999997 8754
No 163
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=59.75 E-value=6.3 Score=38.05 Aligned_cols=25 Identities=28% Similarity=0.775 Sum_probs=18.9
Q ss_pred EEEccCccccccccC------------------ccccCCCCCC
Q 028198 70 ILKCHACYTITAEIG------------------RIFCPKCGNG 94 (212)
Q Consensus 70 vlrC~aC~k~~~~~~------------------k~FCp~CG~~ 94 (212)
.++|..|+.+|.+.. ---||.||..
T Consensus 425 ~~~c~~c~~~yd~~~g~~~~~~~~gt~~~~lp~~~~cp~c~~~ 467 (479)
T PRK05452 425 RMQCSVCQWIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSLG 467 (479)
T ss_pred eEEECCCCeEECCCCCCcccCCCCCCChhhCCCCCcCcCCCCc
Confidence 479999999997521 1269999965
No 164
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=59.33 E-value=6 Score=37.88 Aligned_cols=28 Identities=29% Similarity=0.636 Sum_probs=20.2
Q ss_pred eeEEEEccCccccccc--cCccccCCCCCC
Q 028198 67 HRWILKCHACYTITAE--IGRIFCPKCGNG 94 (212)
Q Consensus 67 k~wvlrC~aC~k~~~~--~~k~FCp~CG~~ 94 (212)
..|++.|..|+++... ..+.-||+||..
T Consensus 237 ~g~~~~c~~cg~~~~~~~~~~~~c~~Cg~~ 266 (380)
T COG1867 237 LGYIYHCSRCGEIVGSFREVDEKCPHCGGK 266 (380)
T ss_pred cCcEEEcccccceecccccccccCCccccc
Confidence 3577999999855432 236789999975
No 165
>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=59.00 E-value=8.7 Score=29.94 Aligned_cols=19 Identities=26% Similarity=0.793 Sum_probs=15.9
Q ss_pred ccccCCCCCCCceeEEEEEe
Q 028198 85 RIFCPKCGNGGTLRKVAVTV 104 (212)
Q Consensus 85 k~FCp~CG~~~TL~Rvsvsv 104 (212)
+..||.||.. .++|+++-+
T Consensus 35 ~y~CpfCgk~-~vkR~a~GI 53 (91)
T TIGR00280 35 KYVCPFCGKK-TVKRGSTGI 53 (91)
T ss_pred CccCCCCCCC-ceEEEeeEE
Confidence 6789999987 899999754
No 166
>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=58.30 E-value=8 Score=36.46 Aligned_cols=27 Identities=19% Similarity=0.527 Sum_probs=19.3
Q ss_pred eEEEEccCccccccc----cCccccCCCCCC
Q 028198 68 RWILKCHACYTITAE----IGRIFCPKCGNG 94 (212)
Q Consensus 68 ~wvlrC~aC~k~~~~----~~k~FCp~CG~~ 94 (212)
.|++.|+.|+..... .....||.||.+
T Consensus 231 g~v~~C~~c~~~~~~~~~~~~~~~C~~c~~~ 261 (374)
T TIGR00308 231 GYTYHCSRCLHNKPVNGISQRKGRCKECGGE 261 (374)
T ss_pred eeEEECCCcccccccccccCCCCCCCCCCCc
Confidence 678999999865321 224579999986
No 167
>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=58.12 E-value=6.9 Score=33.97 Aligned_cols=26 Identities=19% Similarity=0.411 Sum_probs=17.5
Q ss_pred EEEEccCcccccccc---CccccCCCCCC
Q 028198 69 WILKCHACYTITAEI---GRIFCPKCGNG 94 (212)
Q Consensus 69 wvlrC~aC~k~~~~~---~k~FCp~CG~~ 94 (212)
..++|..|.+.+... ....||.||..
T Consensus 117 ~~~~C~~C~~~~~~~~~~~~p~C~~Cgg~ 145 (225)
T cd01411 117 YRIYCTVCGKTVDWEEYLKSPYHAKCGGV 145 (225)
T ss_pred CeeEeCCCCCccchhhcCCCCCCCCCCCE
Confidence 447899998776421 12469999964
No 168
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=58.03 E-value=6 Score=39.85 Aligned_cols=23 Identities=30% Similarity=0.652 Sum_probs=16.5
Q ss_pred EEEccCccccccccCccccCCCCCC
Q 028198 70 ILKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 70 vlrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
+-+|..|+... . -...||+||+.
T Consensus 559 ~~~C~~CGy~g-~-~~~~CP~CG~~ 581 (618)
T PRK14704 559 VDRCKCCSYHG-V-IGNECPSCGNE 581 (618)
T ss_pred CeecCCCCCCC-C-cCccCcCCCCC
Confidence 45799999632 2 13579999986
No 169
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=58.02 E-value=5 Score=34.53 Aligned_cols=22 Identities=27% Similarity=0.585 Sum_probs=16.4
Q ss_pred EEccCccccccccCccccCCCCCC
Q 028198 71 LKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 71 lrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
..|+.|+. ......+||.||..
T Consensus 310 ~~C~~cg~--~~~r~~~C~~cg~~ 331 (364)
T COG0675 310 KTCPCCGH--LSGRLFKCPRCGFV 331 (364)
T ss_pred ccccccCC--ccceeEECCCCCCe
Confidence 67999998 22234689999985
No 170
>PF01907 Ribosomal_L37e: Ribosomal protein L37e; InterPro: IPR001569 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 consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A19_A 4A1D_A 4A18_A 4A1B_A 1S1I_Y 3O5H_d 3IZS_l 3O58_d 2ZKR_2 3IZR_l ....
Probab=57.77 E-value=6.5 Score=28.10 Aligned_cols=24 Identities=25% Similarity=0.571 Sum_probs=20.1
Q ss_pred EEccCccccccccCccccCCCCCC
Q 028198 71 LKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 71 lrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
-.|.-|++.....-+..|..||.+
T Consensus 16 ~~CrRCG~~syH~qK~~CasCGyp 39 (55)
T PF01907_consen 16 TLCRRCGRRSYHIQKKTCASCGYP 39 (55)
T ss_dssp EE-TTTSSEEEETTTTEETTTBTT
T ss_pred eeecccCCeeeecCCCcccccCCC
Confidence 479999988877778999999988
No 171
>PTZ00408 NAD-dependent deacetylase; Provisional
Probab=57.52 E-value=7.4 Score=34.46 Aligned_cols=26 Identities=23% Similarity=0.383 Sum_probs=16.7
Q ss_pred eEEEEccCcccccccc-----CccccCCCCC
Q 028198 68 RWILKCHACYTITAEI-----GRIFCPKCGN 93 (212)
Q Consensus 68 ~wvlrC~aC~k~~~~~-----~k~FCp~CG~ 93 (212)
-+.++|..|.+.+.-. ....||.||.
T Consensus 115 ~~~~~C~~C~~~~~~~~~~~~~~p~C~~Cg~ 145 (242)
T PTZ00408 115 LLKVRCTATGHVFDWTEDVVHGSSRCKCCGC 145 (242)
T ss_pred cceEEECCCCcccCchhhhhcCCCccccCCC
Confidence 3447899999776421 1145999983
No 172
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=57.34 E-value=10 Score=32.74 Aligned_cols=47 Identities=19% Similarity=0.330 Sum_probs=28.2
Q ss_pred eeEecchH---HHHHHHHHhCceee------cCCCCcceeeeeEEEEccCcccccc
Q 028198 35 VACITGDY---AMQNVILQMGLRLL------APGGMQIRQLHRWILKCHACYTITA 81 (212)
Q Consensus 35 vac~TdDf---AmQNVllqmGL~~~------s~~g~~I~~~k~wvlrC~aC~k~~~ 81 (212)
..+++..| -+|++|...=-.++ +++...+++-+.|.++|.||+...+
T Consensus 75 ~~ii~G~~~~~~i~~~l~~yi~~yV~C~~C~~pdT~l~k~~~~~~l~C~aCGa~~~ 130 (201)
T PRK12336 75 RAVFNGKFTEEDIQAAIDAYVDEYVICSECGLPDTRLVKEDRVLMLRCDACGAHRP 130 (201)
T ss_pred EEEEEeeeCHHHHHHHHHHHHHheEECCCCCCCCcEEEEcCCeEEEEcccCCCCcc
Confidence 34555544 46666655322222 5666667666777788888776554
No 173
>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=57.15 E-value=6 Score=37.64 Aligned_cols=25 Identities=28% Similarity=0.693 Sum_probs=19.6
Q ss_pred EEEccCccccccccCccccCCCCCC
Q 028198 70 ILKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 70 vlrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
...|+.|........+-.||.||..
T Consensus 215 ~~~C~~Cd~~~~~~~~a~CpRC~~~ 239 (403)
T TIGR00155 215 LRSCSACHTTILPAQEPVCPRCSTP 239 (403)
T ss_pred CCcCCCCCCccCCCCCcCCcCCCCc
Confidence 4469999986655556789999985
No 174
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=57.13 E-value=7.4 Score=33.07 Aligned_cols=63 Identities=13% Similarity=0.081 Sum_probs=35.1
Q ss_pred eeEecchHHHHHHHHHhCceeecCCCCcceeeeeEEEEccCccccccc---c-CccccCCCCCCCceeE
Q 028198 35 VACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAE---I-GRIFCPKCGNGGTLRK 99 (212)
Q Consensus 35 vac~TdDfAmQNVllqmGL~~~s~~g~~I~~~k~wvlrC~aC~k~~~~---~-~k~FCp~CG~~~TL~R 99 (212)
.-.+|.+-+.+-+...+---+..+....-...-.=-|.|+.|+..++- + .---||.||.. |.-
T Consensus 82 ~w~l~~~~i~d~ik~~~~~~~~klk~~l~~e~~~~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~--L~~ 148 (178)
T PRK06266 82 TWKPELEKLPEIIKKKKMEELKKLKEQLEEEENNMFFFCPNCHIRFTFDEAMEYGFRCPQCGEM--LEE 148 (178)
T ss_pred EEEeCHHHHHHHHHHHHHHHHHHHHHHhhhccCCCEEECCCCCcEEeHHHHhhcCCcCCCCCCC--Cee
Confidence 345777777777776653211111111111222346899999976641 1 23459999986 653
No 175
>PTZ00410 NAD-dependent SIR2; Provisional
Probab=56.59 E-value=11 Score=35.47 Aligned_cols=27 Identities=22% Similarity=0.282 Sum_probs=18.6
Q ss_pred eEEEEccCcccccccc---------CccccCCCCCC
Q 028198 68 RWILKCHACYTITAEI---------GRIFCPKCGNG 94 (212)
Q Consensus 68 ~wvlrC~aC~k~~~~~---------~k~FCp~CG~~ 94 (212)
-+..+|..|.+.+... ....||.||..
T Consensus 145 l~~~~C~~C~~~~~~~~~~~~~~~~~vP~C~~CgG~ 180 (349)
T PTZ00410 145 FSAASCIECHTPYDIEQAYLEARSGKVPHCSTCGGI 180 (349)
T ss_pred CCeeEeCCCCCCcchhHHHHHhhcCCCCCCCCCCCc
Confidence 4557899999876521 12369999974
No 176
>PHA00626 hypothetical protein
Probab=56.37 E-value=7.4 Score=28.12 Aligned_cols=14 Identities=50% Similarity=1.158 Sum_probs=10.2
Q ss_pred ccCCCCCCCceeEEE
Q 028198 87 FCPKCGNGGTLRKVA 101 (212)
Q Consensus 87 FCp~CG~~~TL~Rvs 101 (212)
.||.||+. ++.|..
T Consensus 2 ~CP~CGS~-~Ivrcg 15 (59)
T PHA00626 2 SCPKCGSG-NIAKEK 15 (59)
T ss_pred CCCCCCCc-eeeeec
Confidence 69999986 666544
No 177
>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=56.23 E-value=4.5 Score=29.09 Aligned_cols=29 Identities=21% Similarity=0.504 Sum_probs=22.5
Q ss_pred eeeEEEEccCccccccccCccccCCCCCC
Q 028198 66 LHRWILKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 66 ~k~wvlrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
.+.-.+.|+-|..-...+-...||.||..
T Consensus 22 A~ICSfECTFC~~C~e~~l~~~CPNCgGe 50 (57)
T PF06906_consen 22 AYICSFECTFCADCAETMLNGVCPNCGGE 50 (57)
T ss_pred ceEEeEeCcccHHHHHHHhcCcCcCCCCc
Confidence 34555889999887766656889999986
No 178
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=56.20 E-value=11 Score=29.39 Aligned_cols=19 Identities=26% Similarity=0.842 Sum_probs=15.9
Q ss_pred ccccCCCCCCCceeEEEEEe
Q 028198 85 RIFCPKCGNGGTLRKVAVTV 104 (212)
Q Consensus 85 k~FCp~CG~~~TL~Rvsvsv 104 (212)
+..||.||.. .++|+++-+
T Consensus 36 ~y~CpfCgk~-~vkR~a~GI 54 (90)
T PRK03976 36 KHVCPVCGRP-KVKRVGTGI 54 (90)
T ss_pred CccCCCCCCC-ceEEEEEEE
Confidence 6789999987 899999754
No 179
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=56.17 E-value=5.1 Score=34.32 Aligned_cols=23 Identities=13% Similarity=0.278 Sum_probs=14.6
Q ss_pred ceeeEecchHHHHHHHHHhCceee
Q 028198 33 STVACITGDYAMQNVILQMGLRLL 56 (212)
Q Consensus 33 ~~vac~TdDfAmQNVllqmGL~~~ 56 (212)
.+-+++|.|+.|=-=+ .+|++.+
T Consensus 47 e~rIllTRDr~L~~r~-k~g~~~i 69 (165)
T COG1656 47 EGRILLTRDRELYKRA-KLGIKAI 69 (165)
T ss_pred CCeEEEeccHHHHHHh-hccCceE
Confidence 4567788888775544 5665543
No 180
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=54.89 E-value=10 Score=33.42 Aligned_cols=26 Identities=15% Similarity=0.138 Sum_probs=16.4
Q ss_pred EEEEccCcccccccc---------CccccCCCCCC
Q 028198 69 WILKCHACYTITAEI---------GRIFCPKCGNG 94 (212)
Q Consensus 69 wvlrC~aC~k~~~~~---------~k~FCp~CG~~ 94 (212)
..++|..|.+.+... ...-||.||..
T Consensus 118 ~~~~C~~C~~~~~~~~~~~~~~~~~~p~Cp~Cgg~ 152 (244)
T PRK14138 118 EEYYCVRCGKRYTVEDVIEKLEKSDVPRCDDCSGL 152 (244)
T ss_pred CeeEECCCCCcccHHHHHHHHhcCCCCCCCCCCCe
Confidence 447788888776420 12348888864
No 181
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=54.84 E-value=10 Score=38.71 Aligned_cols=25 Identities=36% Similarity=0.627 Sum_probs=16.5
Q ss_pred EEEccCccccccc---cCccccCCCCCC
Q 028198 70 ILKCHACYTITAE---IGRIFCPKCGNG 94 (212)
Q Consensus 70 vlrC~aC~k~~~~---~~k~FCp~CG~~ 94 (212)
+-+|..|+..... .....||.||+.
T Consensus 641 ~~~C~~CG~~Ge~~~~~~~~~CP~CG~~ 668 (711)
T PRK09263 641 IDECYECGFTGEFECTEKGFTCPKCGNH 668 (711)
T ss_pred CcccCCCCCCccccCCCCCCcCcCCCCC
Confidence 3589999973211 112579999985
No 182
>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=54.83 E-value=11 Score=31.73 Aligned_cols=53 Identities=23% Similarity=0.343 Sum_probs=34.0
Q ss_pred eeeEecchHHHHHHHHHhCce---eecCCCCcceeeeeEEEEccCcccccccc------CccccCCCCCC
Q 028198 34 TVACITGDYAMQNVILQMGLR---LLAPGGMQIRQLHRWILKCHACYTITAEI------GRIFCPKCGNG 94 (212)
Q Consensus 34 ~vac~TdDfAmQNVllqmGL~---~~s~~g~~I~~~k~wvlrC~aC~k~~~~~------~k~FCp~CG~~ 94 (212)
.+.++|.- +.+...+.|.. |+-++|. ....+|..|.+.+... ....||.||..
T Consensus 82 ~~~iiTqN--iD~L~~~ag~~~~~v~~lHG~------~~~~~C~~C~~~~~~~~~~~~~~~p~C~~C~~~ 143 (222)
T cd00296 82 LKRIITQN--VDGLHERAGSRRNRVIELHGS------LDRVRCTSCGKEYPRDEVLEREKPPRCPKCGGL 143 (222)
T ss_pred CceEEecC--hHHHHHHhCCCcCcEEEecCC------CCccEECCCCCCcchhhhhhccCCCCCCCCCCc
Confidence 34677764 35666777765 6667775 3446799998765321 13469999975
No 183
>PF05991 NYN_YacP: YacP-like NYN domain; InterPro: IPR010298 This family consists of several hypothetical bacterial proteins as well as some uncharacterised sequences from Arabidopsis thaliana. The function of this family is unknown.
Probab=54.62 E-value=13 Score=31.00 Aligned_cols=44 Identities=14% Similarity=0.245 Sum_probs=32.8
Q ss_pred CCCcCCCCceeeecC---C--CceeeEecchHHHHHHHHHhCceeecCC
Q 028198 16 VDDECSEQSWMLRSL---S--ESTVACITGDYAMQNVILQMGLRLLAPG 59 (212)
Q Consensus 16 ~~d~~s~~~Wi~~~l---~--~~~vac~TdDfAmQNVllqmGL~~~s~~ 59 (212)
+.+..+-.+||..-+ . ...|.++|+|.++|..+...|...++..
T Consensus 73 t~~~~tAD~~Ie~~v~~~~~~~~~v~VVTSD~~iq~~~~~~GA~~iss~ 121 (166)
T PF05991_consen 73 TKEGETADDYIERLVRELKNRPRQVTVVTSDREIQRAARGRGAKRISSE 121 (166)
T ss_pred CCCCCCHHHHHHHHHHHhccCCCeEEEEeCCHHHHHHHhhCCCEEEcHH
Confidence 334455566776432 2 4789999999999999999999988654
No 184
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=54.33 E-value=6.4 Score=37.70 Aligned_cols=24 Identities=29% Similarity=0.787 Sum_probs=18.7
Q ss_pred EEccCcccccccc-----CccccCCCCCC
Q 028198 71 LKCHACYTITAEI-----GRIFCPKCGNG 94 (212)
Q Consensus 71 lrC~aC~k~~~~~-----~k~FCp~CG~~ 94 (212)
..|+.|..+.... .+-.||.||+.
T Consensus 11 ~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~ 39 (419)
T PRK15103 11 ILCPQCDMLVALPRLEHGQKAACPRCGTT 39 (419)
T ss_pred ccCCCCCceeecCCCCCCCeeECCCCCCC
Confidence 5599999887532 25679999986
No 185
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=54.15 E-value=5.7 Score=28.87 Aligned_cols=27 Identities=22% Similarity=0.733 Sum_probs=23.0
Q ss_pred eEEEEccCccccccccCccccCCCCCC
Q 028198 68 RWILKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 68 ~wvlrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
.---+|..|++.....-+..|..||-+
T Consensus 14 ~tH~~CRRCGr~syhv~k~~CaaCGfg 40 (61)
T COG2126 14 KTHIRCRRCGRRSYHVRKKYCAACGFG 40 (61)
T ss_pred cceehhhhccchheeeccceecccCCC
Confidence 455689999998877778999999986
No 186
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=53.58 E-value=7.7 Score=32.73 Aligned_cols=31 Identities=32% Similarity=0.635 Sum_probs=22.2
Q ss_pred EEEccCccccc-ccc-CccccCCCCCCCceeEEE
Q 028198 70 ILKCHACYTIT-AEI-GRIFCPKCGNGGTLRKVA 101 (212)
Q Consensus 70 vlrC~aC~k~~-~~~-~k~FCp~CG~~~TL~Rvs 101 (212)
.-+|..|+... +-. ....||.||+. -.+|||
T Consensus 149 ~a~~~~~g~~~~~~~~~~~~c~~~~~~-e~rkva 181 (189)
T PRK09521 149 YAMCSRCRTPLVKKGENELKCPNCGNI-ETRKLS 181 (189)
T ss_pred EEEccccCCceEECCCCEEECCCCCCE-Eeeccc
Confidence 34788899743 322 35789999987 678887
No 187
>PRK14289 chaperone protein DnaJ; Provisional
Probab=53.38 E-value=51 Score=30.86 Aligned_cols=28 Identities=25% Similarity=0.455 Sum_probs=18.5
Q ss_pred EEEEccCccccccccCccccCCCCCCCce
Q 028198 69 WILKCHACYTITAEIGRIFCPKCGNGGTL 97 (212)
Q Consensus 69 wvlrC~aC~k~~~~~~k~FCp~CG~~~TL 97 (212)
....|..|.-.... .+.+|+.|++.+++
T Consensus 196 ~~~~C~~C~G~G~~-~~~~C~~C~G~g~v 223 (386)
T PRK14289 196 TQSTCPTCNGEGKI-IKKKCKKCGGEGIV 223 (386)
T ss_pred EEEecCCCCccccc-cCcCCCCCCCCcEE
Confidence 35678888755433 25689999987444
No 188
>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=53.21 E-value=8.9 Score=31.85 Aligned_cols=27 Identities=19% Similarity=0.424 Sum_probs=18.6
Q ss_pred eEEEEccCccccccc---c-CccccCCCCCC
Q 028198 68 RWILKCHACYTITAE---I-GRIFCPKCGNG 94 (212)
Q Consensus 68 ~wvlrC~aC~k~~~~---~-~k~FCp~CG~~ 94 (212)
.=-|.|+.|+..++- + .---||.||..
T Consensus 107 ~~~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 107 NMFFICPNMCVRFTFNEAMELNFTCPRCGAM 137 (158)
T ss_pred CCeEECCCCCcEeeHHHHHHcCCcCCCCCCE
Confidence 345899999966641 1 12459999985
No 189
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=53.10 E-value=7.2 Score=42.56 Aligned_cols=24 Identities=29% Similarity=0.686 Sum_probs=18.4
Q ss_pred EEccCcccc--cc--------ccCccccCCCCCC
Q 028198 71 LKCHACYTI--TA--------EIGRIFCPKCGNG 94 (212)
Q Consensus 71 lrC~aC~k~--~~--------~~~k~FCp~CG~~ 94 (212)
|+|+-|... .. |++-.-||+||.+
T Consensus 915 Y~Cp~Cky~Ef~~d~svgsGfDLpdK~CPkCg~p 948 (1444)
T COG2176 915 YLCPECKYSEFIDDGSVGSGFDLPDKDCPKCGTP 948 (1444)
T ss_pred ccCCCCceeeeecCCCcCCCCCCCCCCCCcCCCc
Confidence 899999843 22 3556789999998
No 190
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=52.95 E-value=7.3 Score=35.71 Aligned_cols=25 Identities=32% Similarity=0.768 Sum_probs=18.5
Q ss_pred EEEccCccccccc--c--CccccCCCCCC
Q 028198 70 ILKCHACYTITAE--I--GRIFCPKCGNG 94 (212)
Q Consensus 70 vlrC~aC~k~~~~--~--~k~FCp~CG~~ 94 (212)
-.+|..|+++... . ....||+||+.
T Consensus 27 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h 55 (292)
T PRK05654 27 WTKCPSCGQVLYRKELEANLNVCPKCGHH 55 (292)
T ss_pred eeECCCccchhhHHHHHhcCCCCCCCCCC
Confidence 3589999987532 1 24689999997
No 191
>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=52.80 E-value=12 Score=26.07 Aligned_cols=21 Identities=33% Similarity=0.816 Sum_probs=15.4
Q ss_pred EEccCccccccccCccccCCCCC
Q 028198 71 LKCHACYTITAEIGRIFCPKCGN 93 (212)
Q Consensus 71 lrC~aC~k~~~~~~k~FCp~CG~ 93 (212)
-.|..|+.+.. ....||.||.
T Consensus 27 ~~c~~cg~~~~--~H~vc~~cG~ 47 (56)
T PF01783_consen 27 VKCPNCGEPKL--PHRVCPSCGY 47 (56)
T ss_dssp EESSSSSSEES--TTSBCTTTBB
T ss_pred eeeccCCCEec--ccEeeCCCCe
Confidence 57888986553 4578999984
No 192
>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=52.53 E-value=7.6 Score=35.52 Aligned_cols=25 Identities=32% Similarity=0.878 Sum_probs=18.6
Q ss_pred EEEEccCccccccc--c--CccccCCCCCC
Q 028198 69 WILKCHACYTITAE--I--GRIFCPKCGNG 94 (212)
Q Consensus 69 wvlrC~aC~k~~~~--~--~k~FCp~CG~~ 94 (212)
|. +|..|+++... . ....||+||++
T Consensus 26 ~~-~c~~c~~~~~~~~l~~~~~vc~~c~~h 54 (285)
T TIGR00515 26 WT-KCPKCGQVLYTKELERNLEVCPKCDHH 54 (285)
T ss_pred ee-ECCCCcchhhHHHHHhhCCCCCCCCCc
Confidence 54 69999987532 1 34789999997
No 193
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=52.46 E-value=6.8 Score=29.60 Aligned_cols=23 Identities=30% Similarity=0.462 Sum_probs=12.1
Q ss_pred EEccCcccccccc----CccccCCCCC
Q 028198 71 LKCHACYTITAEI----GRIFCPKCGN 93 (212)
Q Consensus 71 lrC~aC~k~~~~~----~k~FCp~CG~ 93 (212)
+.|+-|+..|-+. +.+.||+|+=
T Consensus 2 ~~CPCCg~~Tl~~~~~~~ydIC~VC~W 28 (78)
T PF14206_consen 2 YPCPCCGYYTLEERGEGTYDICPVCFW 28 (78)
T ss_pred ccCCCCCcEEeccCCCcCceECCCCCc
Confidence 4566666554321 1346666664
No 194
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=52.42 E-value=7.4 Score=36.00 Aligned_cols=25 Identities=28% Similarity=0.963 Sum_probs=18.4
Q ss_pred EEEEccCccccccc----cCccccCCCCCC
Q 028198 69 WILKCHACYTITAE----IGRIFCPKCGNG 94 (212)
Q Consensus 69 wvlrC~aC~k~~~~----~~k~FCp~CG~~ 94 (212)
|. +|..|+++... -....||+||+.
T Consensus 38 w~-kc~~C~~~~~~~~l~~~~~vcp~c~~h 66 (296)
T CHL00174 38 WV-QCENCYGLNYKKFLKSKMNICEQCGYH 66 (296)
T ss_pred ee-ECCCccchhhHHHHHHcCCCCCCCCCC
Confidence 54 69999987532 224689999997
No 195
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=52.33 E-value=4.7 Score=38.45 Aligned_cols=32 Identities=34% Similarity=0.563 Sum_probs=23.0
Q ss_pred ceeeeeEEEEccCcccccccc----CccccCCCCCC
Q 028198 63 IRQLHRWILKCHACYTITAEI----GRIFCPKCGNG 94 (212)
Q Consensus 63 I~~~k~wvlrC~aC~k~~~~~----~k~FCp~CG~~ 94 (212)
.+--|-+.-.|..|++.|+-. .+--||+||..
T Consensus 239 P~LGKY~~TAC~rC~t~y~le~A~~~~wrCpkCGg~ 274 (403)
T COG1379 239 PRLGKYHLTACSRCYTRYSLEEAKSLRWRCPKCGGK 274 (403)
T ss_pred ccccchhHHHHHHhhhccCcchhhhhcccCcccccc
Confidence 444456777899999887632 24679999985
No 196
>PRK04011 peptide chain release factor 1; Provisional
Probab=52.21 E-value=16 Score=34.93 Aligned_cols=27 Identities=37% Similarity=0.728 Sum_probs=20.1
Q ss_pred eEEEEccCcccccc-------ccCccccCCCCCC
Q 028198 68 RWILKCHACYTITA-------EIGRIFCPKCGNG 94 (212)
Q Consensus 68 ~wvlrC~aC~k~~~-------~~~k~FCp~CG~~ 94 (212)
.+.++|..|+.... ......||.||..
T Consensus 326 r~~~~c~~c~~~~~~~~~~~~~~~~~~c~~~~~~ 359 (411)
T PRK04011 326 RVTYKCPNCGYEEEKTVKRREELPEKTCPKCGSE 359 (411)
T ss_pred eEEEEcCCCCcceeeecccccccccccCcccCcc
Confidence 57899999986532 1234689999986
No 197
>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=52.11 E-value=4.6 Score=33.39 Aligned_cols=23 Identities=30% Similarity=0.780 Sum_probs=19.9
Q ss_pred EccCccccccccCccccCCCCCC
Q 028198 72 KCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 72 rC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
-|.-|+++|.......||.|...
T Consensus 5 nC~~CgklF~~~~~~iCp~C~~~ 27 (137)
T TIGR03826 5 NCPKCGRLFVKTGRDVCPSCYEE 27 (137)
T ss_pred cccccchhhhhcCCccCHHHhHH
Confidence 69999999987678899999963
No 198
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=51.78 E-value=12 Score=41.36 Aligned_cols=27 Identities=26% Similarity=0.634 Sum_probs=22.6
Q ss_pred eeeeEEEEccCccccccccCccccCCCCCC
Q 028198 65 QLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 65 ~~k~wvlrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
.+-.-..+|+.|++++.. ..||.||.+
T Consensus 669 ~vei~~~~Cp~Cg~~~~~---~~Cp~CG~~ 695 (1627)
T PRK14715 669 DIEIAFFKCPKCGKVGLY---HVCPFCGTR 695 (1627)
T ss_pred eEEEEeeeCCCCCCcccc---ccCcccCCc
Confidence 667778999999998764 579999976
No 199
>PRK04860 hypothetical protein; Provisional
Probab=51.74 E-value=20 Score=30.16 Aligned_cols=58 Identities=14% Similarity=0.275 Sum_probs=34.5
Q ss_pred hHHHHHHHHH-hCceeecCCCCccee--eeeEEEEccCcccccc----------ccCccccCCCCCCCceeEEE
Q 028198 41 DYAMQNVILQ-MGLRLLAPGGMQIRQ--LHRWILKCHACYTITA----------EIGRIFCPKCGNGGTLRKVA 101 (212)
Q Consensus 41 DfAmQNVllq-mGL~~~s~~g~~I~~--~k~wvlrC~aC~k~~~----------~~~k~FCp~CG~~~TL~Rvs 101 (212)
|-.-|-+|.+ +|+..-......|.. .+.|.|+|. |.+... ...+..|..|+.. |..+.
T Consensus 87 g~ewk~lm~~v~g~~~r~~h~~~~~~~~~~~~~Y~C~-C~~~~~~~rrH~ri~~g~~~YrC~~C~~~--l~~~~ 157 (160)
T PRK04860 87 GKEWQWMMESVLGVPARRTHQFEVQSVRGKTFPYRCK-CQEHQLTVRRHNRVVRGEAVYRCRRCGET--LVFKG 157 (160)
T ss_pred CHHHHHHHHHhcCCCCcccCCCcCCccccCEEEEEcC-CCCeeCHHHHHHHHhcCCccEECCCCCce--eEEec
Confidence 5666777776 466332222122222 467999997 965332 1234789999985 76554
No 200
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=51.26 E-value=7.9 Score=28.72 Aligned_cols=7 Identities=86% Similarity=2.048 Sum_probs=6.6
Q ss_pred cCCCCCC
Q 028198 88 CPKCGNG 94 (212)
Q Consensus 88 Cp~CG~~ 94 (212)
||+||+.
T Consensus 7 CpKCgn~ 13 (68)
T COG3478 7 CPKCGNT 13 (68)
T ss_pred CCCcCCc
Confidence 9999996
No 201
>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=51.12 E-value=12 Score=33.40 Aligned_cols=14 Identities=21% Similarity=0.266 Sum_probs=9.7
Q ss_pred eEEEEccCcccccc
Q 028198 68 RWILKCHACYTITA 81 (212)
Q Consensus 68 ~wvlrC~aC~k~~~ 81 (212)
.+.++|..|.+.+.
T Consensus 116 ~~~~~C~~C~~~~~ 129 (260)
T cd01409 116 LHRVVCLSCGFRTP 129 (260)
T ss_pred cCEEEeCCCcCccC
Confidence 45577888887653
No 202
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=50.93 E-value=9.2 Score=42.19 Aligned_cols=24 Identities=29% Similarity=0.674 Sum_probs=18.4
Q ss_pred EEccCcccccc----------ccCccccCCCCCC
Q 028198 71 LKCHACYTITA----------EIGRIFCPKCGNG 94 (212)
Q Consensus 71 lrC~aC~k~~~----------~~~k~FCp~CG~~ 94 (212)
|+|+-|...-. |++..-||+||.+
T Consensus 909 y~C~~C~~~ef~~~~~~~sG~Dlpdk~Cp~Cg~~ 942 (1437)
T PRK00448 909 YVCPNCKYSEFFTDGSVGSGFDLPDKDCPKCGTK 942 (1437)
T ss_pred ccCcccccccccccccccccccCccccCcccccc
Confidence 89999985432 4556789999987
No 203
>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=50.63 E-value=8.5 Score=27.50 Aligned_cols=32 Identities=31% Similarity=0.557 Sum_probs=24.3
Q ss_pred ceeeeeEEEEccCccccccc-cC-ccccCCCCCC
Q 028198 63 IRQLHRWILKCHACYTITAE-IG-RIFCPKCGNG 94 (212)
Q Consensus 63 I~~~k~wvlrC~aC~k~~~~-~~-k~FCp~CG~~ 94 (212)
.+.+..|+--|..|+++.=. .. ..-|+.||++
T Consensus 11 ~H~L~~~~~NCl~CGkIiC~~Eg~~~pC~fCg~~ 44 (57)
T PF06221_consen 11 RHPLFPYAPNCLNCGKIICEQEGPLGPCPFCGTP 44 (57)
T ss_pred cCCCccccccccccChhhcccccCcCcCCCCCCc
Confidence 45566778899999999633 23 5789999987
No 204
>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=50.40 E-value=10 Score=36.10 Aligned_cols=25 Identities=28% Similarity=0.713 Sum_probs=18.9
Q ss_pred EEEccCccccccc-----cCccccCCCCCC
Q 028198 70 ILKCHACYTITAE-----IGRIFCPKCGNG 94 (212)
Q Consensus 70 vlrC~aC~k~~~~-----~~k~FCp~CG~~ 94 (212)
...|+.|..+... ..+-.||.||..
T Consensus 13 ~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~ 42 (403)
T TIGR00155 13 HILCSQCDMLVALPRIESGQKAACPRCGTT 42 (403)
T ss_pred eeeCCCCCCcccccCCCCCCeeECCCCCCC
Confidence 4579999988743 235679999986
No 205
>KOG3084 consensus NADH pyrophosphatase I of the Nudix family of hydrolases [Replication, recombination and repair]
Probab=50.14 E-value=7.1 Score=36.87 Aligned_cols=12 Identities=50% Similarity=1.079 Sum_probs=10.1
Q ss_pred ccccCCCCCCCce
Q 028198 85 RIFCPKCGNGGTL 97 (212)
Q Consensus 85 k~FCp~CG~~~TL 97 (212)
..|||.||++ |.
T Consensus 150 ykFCp~CG~~-tk 161 (345)
T KOG3084|consen 150 YKFCPGCGSP-TK 161 (345)
T ss_pred hccCcccCCC-cc
Confidence 4799999998 65
No 206
>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=50.06 E-value=9.3 Score=28.38 Aligned_cols=24 Identities=29% Similarity=0.661 Sum_probs=14.9
Q ss_pred EEEEccCcccc-ccc--cCccccCCCCCC
Q 028198 69 WILKCHACYTI-TAE--IGRIFCPKCGNG 94 (212)
Q Consensus 69 wvlrC~aC~k~-~~~--~~k~FCp~CG~~ 94 (212)
.+.|| .|++. +.+ ....-| .||..
T Consensus 2 lifrC-~Cgr~lya~e~~kTkkC-~CG~~ 28 (68)
T PF09082_consen 2 LIFRC-DCGRYLYAKEGAKTKKC-VCGKT 28 (68)
T ss_dssp EEEEE-TTS--EEEETT-SEEEE-TTTEE
T ss_pred EEEEe-cCCCEEEecCCcceeEe-cCCCe
Confidence 47899 89975 332 224679 99984
No 207
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=49.92 E-value=8 Score=29.70 Aligned_cols=24 Identities=29% Similarity=0.747 Sum_probs=18.4
Q ss_pred EEccCccccccc----cCccccCCCCCC
Q 028198 71 LKCHACYTITAE----IGRIFCPKCGNG 94 (212)
Q Consensus 71 lrC~aC~k~~~~----~~k~FCp~CG~~ 94 (212)
.+|.+|++++.- .+-..|+.|+.-
T Consensus 35 VkC~gc~~iT~vfSHaqtvVvc~~c~~i 62 (84)
T KOG1779|consen 35 VKCPGCFKITTVFSHAQTVVVCEGCSTI 62 (84)
T ss_pred EEcCCceEEEEEeecCceEEEcCCCceE
Confidence 689999999853 235789999863
No 208
>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=49.64 E-value=11 Score=32.22 Aligned_cols=27 Identities=26% Similarity=0.608 Sum_probs=18.6
Q ss_pred eEEEEccCcccccccc------CccccCCCCCC
Q 028198 68 RWILKCHACYTITAEI------GRIFCPKCGNG 94 (212)
Q Consensus 68 ~wvlrC~aC~k~~~~~------~k~FCp~CG~~ 94 (212)
...++|..|.+.+... ....||.||..
T Consensus 107 ~~~~~C~~C~~~~~~~~~~~~~~~p~C~~Cgg~ 139 (224)
T cd01412 107 LFRVRCSSCGYVGENNEEIPEEELPRCPKCGGL 139 (224)
T ss_pred cCccccCCCCCCCCcchhhhccCCCCCCCCCCc
Confidence 4457899999876531 12469999974
No 209
>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=49.56 E-value=9.3 Score=26.94 Aligned_cols=24 Identities=29% Similarity=0.778 Sum_probs=17.1
Q ss_pred EEEccCcccccccc-----CccccCCCCC
Q 028198 70 ILKCHACYTITAEI-----GRIFCPKCGN 93 (212)
Q Consensus 70 vlrC~aC~k~~~~~-----~k~FCp~CG~ 93 (212)
..||..|.++-... -..-||.||.
T Consensus 4 eiRC~~CnklLa~~g~~~~leIKCpRC~t 32 (51)
T PF10122_consen 4 EIRCGHCNKLLAKAGEVIELEIKCPRCKT 32 (51)
T ss_pred ceeccchhHHHhhhcCccEEEEECCCCCc
Confidence 36999999875432 1356999995
No 210
>COG1328 NrdD Oxygen-sensitive ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]
Probab=49.28 E-value=9.5 Score=39.18 Aligned_cols=47 Identities=19% Similarity=0.356 Sum_probs=29.0
Q ss_pred cchHHHHHHHHH---hCceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCC
Q 028198 39 TGDYAMQNVILQ---MGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 39 TdDfAmQNVllq---mGL~~~s~~g~~I~~~k~wvlrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
.+-=|+.++... .++..++.. .. +-.|..|+....-.... ||+||+.
T Consensus 615 ~~~eal~~l~k~~~~~ri~Y~~~n-~~-------i~~C~~cg~~~~~~~~~-Cp~CG~~ 664 (700)
T COG1328 615 ADPEALMDLTKYIYKTRIGYWGYT-TP-------ISVCNRCGYSGEGLRTR-CPKCGSE 664 (700)
T ss_pred CCHHHHHHHHHHHHhcCcceEecC-CC-------ceeeccCCccccccccc-CCCCCCc
Confidence 345677777663 355555554 22 34699999865422212 9999997
No 211
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=49.26 E-value=5.6 Score=28.28 Aligned_cols=15 Identities=40% Similarity=1.057 Sum_probs=9.9
Q ss_pred ccccCccccCCCCCC
Q 028198 80 TAEIGRIFCPKCGNG 94 (212)
Q Consensus 80 ~~~~~k~FCp~CG~~ 94 (212)
.....+.||+.||..
T Consensus 43 ~~~~~r~FC~~CGs~ 57 (92)
T PF04828_consen 43 GKGVERYFCPTCGSP 57 (92)
T ss_dssp TSSCEEEEETTT--E
T ss_pred CCcCcCcccCCCCCe
Confidence 444568999999986
No 212
>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=49.24 E-value=14 Score=26.94 Aligned_cols=19 Identities=37% Similarity=0.677 Sum_probs=12.7
Q ss_pred ccCCCCCCCceeEEEEEeCC
Q 028198 87 FCPKCGNGGTLRKVAVTVGE 106 (212)
Q Consensus 87 FCp~CG~~~TL~Rvsvsv~~ 106 (212)
-||+||+. ...-=.|..+.
T Consensus 2 ~C~KCg~~-~~e~~~v~~tg 20 (64)
T PF09855_consen 2 KCPKCGNE-EYESGEVRATG 20 (64)
T ss_pred CCCCCCCc-ceecceEEccC
Confidence 49999997 66555544433
No 213
>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=48.86 E-value=7.3 Score=23.51 Aligned_cols=13 Identities=31% Similarity=0.848 Sum_probs=5.5
Q ss_pred ccCCCCCCCceeEEE
Q 028198 87 FCPKCGNGGTLRKVA 101 (212)
Q Consensus 87 FCp~CG~~~TL~Rvs 101 (212)
-||.||+. +.++.
T Consensus 3 ~C~rC~~~--~~~~~ 15 (30)
T PF06827_consen 3 KCPRCWNY--IEDIG 15 (30)
T ss_dssp B-TTT--B--BEEEE
T ss_pred cCccCCCc--ceEeE
Confidence 37777764 55444
No 214
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=48.78 E-value=12 Score=29.48 Aligned_cols=18 Identities=39% Similarity=0.861 Sum_probs=14.7
Q ss_pred ccccCCCCCCCceeEEEEE
Q 028198 85 RIFCPKCGNGGTLRKVAVT 103 (212)
Q Consensus 85 k~FCp~CG~~~TL~Rvsvs 103 (212)
+.|||.|... |+..|+-.
T Consensus 8 ~tyCp~Ckkh-T~H~V~~~ 25 (94)
T COG1631 8 RTYCPYCKKH-TIHKVERV 25 (94)
T ss_pred eecCcccccc-eeeeeeeh
Confidence 5699999997 98888743
No 215
>COG0498 ThrC Threonine synthase [Amino acid transport and metabolism]
Probab=48.60 E-value=10 Score=36.49 Aligned_cols=27 Identities=26% Similarity=0.472 Sum_probs=21.9
Q ss_pred eEEEEccCcccccccc-CccccCCCCCC
Q 028198 68 RWILKCHACYTITAEI-GRIFCPKCGNG 94 (212)
Q Consensus 68 ~wvlrC~aC~k~~~~~-~k~FCp~CG~~ 94 (212)
-..+||..|++.+.+- -...||.||..
T Consensus 3 ~~~~rc~~cg~~f~~a~~~~~c~~cGl~ 30 (411)
T COG0498 3 YVSLRCLKCGREFSQALLQGLCPDCGLF 30 (411)
T ss_pred eeEeecCCCCcchhhHHhhCcCCcCCcc
Confidence 4679999999888743 35899999985
No 216
>PHA02942 putative transposase; Provisional
Probab=47.92 E-value=24 Score=33.37 Aligned_cols=42 Identities=24% Similarity=0.426 Sum_probs=25.1
Q ss_pred HHHHhCceeecCCCCcceeeeeEEEEccCccccccccC-c-cccCCCCCC
Q 028198 47 VILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIG-R-IFCPKCGNG 94 (212)
Q Consensus 47 VllqmGL~~~s~~g~~I~~~k~wvlrC~aC~k~~~~~~-k-~FCp~CG~~ 94 (212)
.+...|+.|+-++-.- =-..|+.|+....... + -.||.||..
T Consensus 308 KA~~~G~~Vv~V~p~y------TSq~Cs~CG~~~~~l~~r~f~C~~CG~~ 351 (383)
T PHA02942 308 QAKKHGMIVEFVNPSY------SSVSCPKCGHKMVEIAHRYFHCPSCGYE 351 (383)
T ss_pred HHHHhCCEEEEECCCC------CCccCCCCCCccCcCCCCEEECCCCCCE
Confidence 4555677776554221 1267888987654322 2 458889875
No 217
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=47.77 E-value=10 Score=36.30 Aligned_cols=24 Identities=25% Similarity=0.779 Sum_probs=18.8
Q ss_pred EEEccCccccccccCccccCCCCCC
Q 028198 70 ILKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 70 vlrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
...|+.|..+.+. .+..||.||..
T Consensus 221 l~~C~~Cd~l~~~-~~a~CpRC~~~ 244 (419)
T PRK15103 221 LRSCSCCTAILPA-DQPVCPRCHTK 244 (419)
T ss_pred CCcCCCCCCCCCC-CCCCCCCCCCc
Confidence 4469999998754 45689999985
No 218
>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=47.57 E-value=11 Score=40.78 Aligned_cols=24 Identities=29% Similarity=0.650 Sum_probs=18.2
Q ss_pred EEccCccccc----------cccCccccCCCCCC
Q 028198 71 LKCHACYTIT----------AEIGRIFCPKCGNG 94 (212)
Q Consensus 71 lrC~aC~k~~----------~~~~k~FCp~CG~~ 94 (212)
|+|+-|.... .|++..-||+||.+
T Consensus 684 y~c~~c~~~ef~~~~~~~sg~dlp~k~cp~c~~~ 717 (1213)
T TIGR01405 684 YLCPNCKYSEFITDGSVGSGFDLPDKDCPKCGAP 717 (1213)
T ss_pred ccCcccccccccccccccccccCccccCcccccc
Confidence 8999998532 24556789999986
No 219
>cd04511 Nudix_Hydrolase_4 Members of the Nudix hydrolase superfamily catalyze the hydrolysis of NUcleoside DIphosphates linked to other moieties, X. Enzymes belonging to this superfamily require a divalent cation, such as Mg2+ or Mn2+, for their activity and contain a highly conserved 23-residue nudix motif (GX5EX7REUXEEXGU, U=I, L or V), which functions as a metal binding and catalytic site. Substrates of nudix hydrolases include intact and oxidatively damaged nucleoside triphosphates, dinucleoside polyphosphates, nucleotide-sugars and dinucleotide enzymes. These substrates are metabolites or cell signaling molecules that require regulation during different stages of the cell cycle or during periods of stress. In general, the role of the nudix hydrolase is to sanitize the nucleotide pools and to maintain cell viability, thereby serving as surveillance & "house-cleaning" enzymes. Substrate specificity is used to define families within the superfamily. Differences in substrate specifici
Probab=47.43 E-value=36 Score=26.07 Aligned_cols=24 Identities=33% Similarity=0.350 Sum_probs=13.5
Q ss_pred eCCCceEEeecCCccccccceeccC
Q 028198 104 VGENGIVLASRRPRITLRGTKFSLP 128 (212)
Q Consensus 104 v~~~G~~~~~~k~~~n~RG~~ySlP 128 (212)
+-.+|.+++.++.... +...|+||
T Consensus 20 i~~~~~vLL~kr~~~~-~~g~w~lP 43 (130)
T cd04511 20 PEWEGKVLLCRRAIEP-RHGFWTLP 43 (130)
T ss_pred EecCCEEEEEEecCCC-CCCeEECC
Confidence 3445777666554322 33468877
No 220
>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=46.66 E-value=15 Score=34.72 Aligned_cols=37 Identities=22% Similarity=0.619 Sum_probs=14.3
Q ss_pred EEccCccccc---cccCccccCCCCCCCceeEEEEEeCCCc
Q 028198 71 LKCHACYTIT---AEIGRIFCPKCGNGGTLRKVAVTVGENG 108 (212)
Q Consensus 71 lrC~aC~k~~---~~~~k~FCp~CG~~~TL~Rvsvsv~~~G 108 (212)
.+|..|+.-+ ..++..-|++||+. -..|+++.-...|
T Consensus 286 FkC~~C~~Rt~sl~r~P~~~C~~Cg~~-~wer~~M~~ek~~ 325 (344)
T PF09332_consen 286 FKCKDCGNRTISLERLPKKHCSNCGSS-KWERTGMLKEKKG 325 (344)
T ss_dssp EE-T-TS-EEEESSSS--S--TTT-S----EEE---SSS--
T ss_pred EECCCCCCeeeecccCCCCCCCcCCcC-ceeehhhhhhhcc
Confidence 6899998532 23456789999986 7899887543334
No 221
>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=46.44 E-value=15 Score=31.06 Aligned_cols=12 Identities=58% Similarity=1.320 Sum_probs=7.7
Q ss_pred cCCCCCCCceeEE
Q 028198 88 CPKCGNGGTLRKV 100 (212)
Q Consensus 88 Cp~CG~~~TL~Rv 100 (212)
||.||++ +++.+
T Consensus 1 CP~Cg~~-~~~~~ 12 (163)
T TIGR00340 1 CPVCGSR-TLKAV 12 (163)
T ss_pred CCCCCCc-ceEee
Confidence 7777765 56554
No 222
>COG1458 Predicted DNA-binding protein containing PIN domain [General function prediction only]
Probab=46.30 E-value=17 Score=32.45 Aligned_cols=28 Identities=21% Similarity=0.398 Sum_probs=25.8
Q ss_pred CCceeeEecchHHHHHHHHHhCceeecC
Q 028198 31 SESTVACITGDYAMQNVILQMGLRLLAP 58 (212)
Q Consensus 31 ~~~~vac~TdDfAmQNVllqmGL~~~s~ 58 (212)
.++++++++.|.++.--+.+|||.++..
T Consensus 172 kELdaavVssD~Gir~WAe~LGlrfv~a 199 (221)
T COG1458 172 KELDAAVVSSDEGIRTWAEKLGLRFVDA 199 (221)
T ss_pred HHhCceEEecchhHHHHHHHhCCeeeCH
Confidence 4789999999999999999999999865
No 223
>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=46.22 E-value=13 Score=26.45 Aligned_cols=25 Identities=32% Similarity=0.703 Sum_probs=14.2
Q ss_pred EEEccCccccccc----cCccccCCCCCC
Q 028198 70 ILKCHACYTITAE----IGRIFCPKCGNG 94 (212)
Q Consensus 70 vlrC~aC~k~~~~----~~k~FCp~CG~~ 94 (212)
..+|.+|+++.-. .+...|..||..
T Consensus 7 ~VkCp~C~~~q~vFSha~t~V~C~~Cg~~ 35 (55)
T PF01667_consen 7 DVKCPGCYNIQTVFSHAQTVVKCVVCGTV 35 (55)
T ss_dssp EEE-TTT-SEEEEETT-SS-EE-SSSTSE
T ss_pred EEECCCCCCeeEEEecCCeEEEcccCCCE
Confidence 4679999976532 236789999973
No 224
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=45.76 E-value=10 Score=24.49 Aligned_cols=11 Identities=36% Similarity=1.047 Sum_probs=8.8
Q ss_pred cccCCCCCCCce
Q 028198 86 IFCPKCGNGGTL 97 (212)
Q Consensus 86 ~FCp~CG~~~TL 97 (212)
..||.||+. ++
T Consensus 3 ~~Cp~Cg~~-~~ 13 (47)
T PF14690_consen 3 PRCPHCGSP-SV 13 (47)
T ss_pred ccCCCcCCC-ce
Confidence 479999998 54
No 225
>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=45.34 E-value=15 Score=34.63 Aligned_cols=28 Identities=21% Similarity=0.635 Sum_probs=16.9
Q ss_pred eeEEEEccCcccc--ccccC--ccccCCCCCC
Q 028198 67 HRWILKCHACYTI--TAEIG--RIFCPKCGNG 94 (212)
Q Consensus 67 k~wvlrC~aC~k~--~~~~~--k~FCp~CG~~ 94 (212)
..|++.|+.|... ..... +..||.||.+
T Consensus 237 ~G~v~~C~~C~~~~~~~~~~~~~~~c~~cg~~ 268 (377)
T PF02005_consen 237 LGYVYYCPSCGYREEVKGLQKLKSKCPECGSK 268 (377)
T ss_dssp EEEEEEETTT--EECCT-GCC--CEETTT-SC
T ss_pred eeEEEECCCccccccccCccccCCcCCCCCCc
Confidence 5799999999742 11111 3679999997
No 226
>PTZ00157 60S ribosomal protein L36a; Provisional
Probab=44.88 E-value=15 Score=28.30 Aligned_cols=19 Identities=37% Similarity=0.744 Sum_probs=16.1
Q ss_pred ccccCCCCCCCceeEEEEEe
Q 028198 85 RIFCPKCGNGGTLRKVAVTV 104 (212)
Q Consensus 85 k~FCp~CG~~~TL~Rvsvsv 104 (212)
+-|||.|+.. |+.+|+-.-
T Consensus 9 ~tyC~~C~kH-t~HkV~qyK 27 (84)
T PTZ00157 9 KTYCKKCGKH-TSHKVSQYK 27 (84)
T ss_pred cccCcCCCCC-ccEEEEEec
Confidence 5799999998 999998653
No 227
>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=44.75 E-value=23 Score=32.85 Aligned_cols=31 Identities=26% Similarity=0.475 Sum_probs=21.7
Q ss_pred EEEccCccccccccCccccCCCCCCCceeEEE
Q 028198 70 ILKCHACYTITAEIGRIFCPKCGNGGTLRKVA 101 (212)
Q Consensus 70 vlrC~aC~k~~~~~~k~FCp~CG~~~TL~Rvs 101 (212)
.+.|.-|.....- .+.-||.||+...|...+
T Consensus 210 yL~CslC~teW~~-~R~~C~~Cg~~~~l~y~~ 240 (305)
T TIGR01562 210 YLSCSLCATEWHY-VRVKCSHCEESKHLAYLS 240 (305)
T ss_pred EEEcCCCCCcccc-cCccCCCCCCCCceeeEe
Confidence 5788888876653 478899999864444443
No 228
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=44.57 E-value=20 Score=30.10 Aligned_cols=8 Identities=38% Similarity=0.891 Sum_probs=4.3
Q ss_pred cccCCCCC
Q 028198 86 IFCPKCGN 93 (212)
Q Consensus 86 ~FCp~CG~ 93 (212)
.-||.||.
T Consensus 29 ~~c~~c~~ 36 (154)
T PRK00464 29 RECLACGK 36 (154)
T ss_pred eeccccCC
Confidence 34666653
No 229
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=44.53 E-value=11 Score=31.93 Aligned_cols=16 Identities=38% Similarity=0.858 Sum_probs=11.6
Q ss_pred cCccccCCCCCCCcee
Q 028198 83 IGRIFCPKCGNGGTLR 98 (212)
Q Consensus 83 ~~k~FCp~CG~~~TL~ 98 (212)
....||..||.+.+|+
T Consensus 87 Cq~r~CARCGGrv~lr 102 (169)
T KOG3799|consen 87 CQTRFCARCGGRVSLR 102 (169)
T ss_pred hhhhHHHhcCCeeeec
Confidence 3457999999984443
No 230
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=43.94 E-value=10 Score=30.27 Aligned_cols=9 Identities=67% Similarity=1.752 Sum_probs=8.0
Q ss_pred cccCCCCCC
Q 028198 86 IFCPKCGNG 94 (212)
Q Consensus 86 ~FCp~CG~~ 94 (212)
.|||.|||-
T Consensus 2 ~FCP~Cgn~ 10 (105)
T KOG2906|consen 2 LFCPTCGNM 10 (105)
T ss_pred cccCCCCCE
Confidence 599999995
No 231
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=43.93 E-value=16 Score=25.93 Aligned_cols=9 Identities=44% Similarity=1.350 Sum_probs=4.3
Q ss_pred cccCCCCCC
Q 028198 86 IFCPKCGNG 94 (212)
Q Consensus 86 ~FCp~CG~~ 94 (212)
..||.||+.
T Consensus 28 ~~C~~CG~~ 36 (57)
T PRK12286 28 VECPNCGEP 36 (57)
T ss_pred eECCCCCCc
Confidence 345555544
No 232
>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=43.85 E-value=15 Score=25.81 Aligned_cols=19 Identities=32% Similarity=0.871 Sum_probs=9.9
Q ss_pred EccCccccccccCccccCCCC
Q 028198 72 KCHACYTITAEIGRIFCPKCG 92 (212)
Q Consensus 72 rC~aC~k~~~~~~k~FCp~CG 92 (212)
.|..|+.... .-..||.||
T Consensus 28 ~C~~cG~~~~--~H~vc~~cG 46 (55)
T TIGR01031 28 VCPNCGEFKL--PHRVCPSCG 46 (55)
T ss_pred ECCCCCCccc--CeeECCccC
Confidence 4666665432 234566666
No 233
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=43.50 E-value=12 Score=29.57 Aligned_cols=26 Identities=23% Similarity=0.475 Sum_probs=18.9
Q ss_pred EEccCcccccccc--C-ccccCCCCCCCce
Q 028198 71 LKCHACYTITAEI--G-RIFCPKCGNGGTL 97 (212)
Q Consensus 71 lrC~aC~k~~~~~--~-k~FCp~CG~~~TL 97 (212)
-+|..|+.++.+. . ---||.|-+. -+
T Consensus 59 a~CkkCGfef~~~~ik~pSRCP~CKSE-~I 87 (97)
T COG3357 59 ARCKKCGFEFRDDKIKKPSRCPKCKSE-WI 87 (97)
T ss_pred hhhcccCccccccccCCcccCCcchhh-cc
Confidence 4799999888761 1 2469999986 44
No 234
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=43.22 E-value=13 Score=29.96 Aligned_cols=12 Identities=58% Similarity=1.375 Sum_probs=9.9
Q ss_pred cCccccCCCCCC
Q 028198 83 IGRIFCPKCGNG 94 (212)
Q Consensus 83 ~~k~FCp~CG~~ 94 (212)
..+.||+.||.+
T Consensus 67 ~~r~FC~~CGs~ 78 (133)
T COG3791 67 AGRGFCPTCGSP 78 (133)
T ss_pred CCCeecccCCCc
Confidence 346799999997
No 235
>PF00471 Ribosomal_L33: Ribosomal protein L33; InterPro: IPR001705 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 L33 is one of the proteins from the large ribosomal subunit. In Escherichia coli, L33 has been shown to be on the surface of 50S subunit. L33 belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, , ], groups: Eubacterial L33. Algal and plant chloroplast L33. Cyanelle L33. L33 is a small protein of 49 to 66 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3PIO_1 3PIP_1 3PYT_3 3MS1_3 3F1F_6 3F1H_6 3MRZ_3 3PYO_3 3D5B_6 3D5D_6 ....
Probab=42.37 E-value=12 Score=25.69 Aligned_cols=30 Identities=27% Similarity=0.644 Sum_probs=20.6
Q ss_pred eEEEEccCcccccc-----------cc-CccccCCCCCCCcee
Q 028198 68 RWILKCHACYTITA-----------EI-GRIFCPKCGNGGTLR 98 (212)
Q Consensus 68 ~wvlrC~aC~k~~~-----------~~-~k~FCp~CG~~~TL~ 98 (212)
.-.|.|.+|....- -+ -+.|||.|+.. ||-
T Consensus 3 ~i~L~c~~c~~~nY~t~kn~~~~~~rL~lkKycp~~~kh-tlh 44 (48)
T PF00471_consen 3 KIKLVCTECGGRNYTTTKNKKNTPERLELKKYCPRCRKH-TLH 44 (48)
T ss_dssp CEEEEEEESSSSEEEEEEETTTSSSSSEEEEEETSSSSE-EEE
T ss_pred EEEEEEcCCCCeeEEEecCCCCCCceeeEeccCCCCCCE-ecE
Confidence 34688999975431 11 16899999997 774
No 236
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=42.11 E-value=15 Score=27.30 Aligned_cols=24 Identities=25% Similarity=0.573 Sum_probs=16.0
Q ss_pred EEEccCccccc---cc-cCccccCCCCC
Q 028198 70 ILKCHACYTIT---AE-IGRIFCPKCGN 93 (212)
Q Consensus 70 vlrC~aC~k~~---~~-~~k~FCp~CG~ 93 (212)
.-+|..|+... +. .+..-|..||.
T Consensus 19 ~VkCpdC~N~q~vFshast~V~C~~CG~ 46 (67)
T COG2051 19 RVKCPDCGNEQVVFSHASTVVTCLICGT 46 (67)
T ss_pred EEECCCCCCEEEEeccCceEEEeccccc
Confidence 45788888653 22 33677888886
No 237
>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=41.92 E-value=39 Score=26.94 Aligned_cols=44 Identities=18% Similarity=0.450 Sum_probs=25.0
Q ss_pred eEEEEcc--Ccccc-ccc-cCccccCCCCCC--Ccee--EEEEEe-CCCceEE
Q 028198 68 RWILKCH--ACYTI-TAE-IGRIFCPKCGNG--GTLR--KVAVTV-GENGIVL 111 (212)
Q Consensus 68 ~wvlrC~--aC~k~-~~~-~~k~FCp~CG~~--~TL~--Rvsvsv-~~~G~~~ 111 (212)
-|=.-|+ .|.+. ... .+..+|++||.. .... ++.+.| |..|++.
T Consensus 16 ~~Y~aC~~~~C~kKv~~~~~~~y~C~~C~~~~~~~~~ry~l~~~i~D~tg~~~ 68 (146)
T PF08646_consen 16 WYYPACPNEKCNKKVTENGDGSYRCEKCNKTVENPKYRYRLSLKISDGTGSIW 68 (146)
T ss_dssp TEEEE-TSTTTS-B-EEETTTEEEETTTTEEESS-EEEEEEEEEEEETTEEEE
T ss_pred cEECCCCCccCCCEeecCCCcEEECCCCCCcCCCeeEEEEEEEEEEeCCCeEE
Confidence 4677899 99974 433 235699999964 1223 344444 4557653
No 238
>PF15616 TerY-C: TerY-C metal binding domain
Probab=41.72 E-value=16 Score=30.15 Aligned_cols=22 Identities=36% Similarity=0.898 Sum_probs=16.4
Q ss_pred EccCccccc--cccCccccCCCCCC
Q 028198 72 KCHACYTIT--AEIGRIFCPKCGNG 94 (212)
Q Consensus 72 rC~aC~k~~--~~~~k~FCp~CG~~ 94 (212)
.| +|++++ .......||.||+.
T Consensus 91 ~C-~CGkl~Ci~g~~~~~CPwCg~~ 114 (131)
T PF15616_consen 91 VC-GCGKLFCIDGEGEVTCPWCGNE 114 (131)
T ss_pred Ee-cCCCEEEeCCCCCEECCCCCCe
Confidence 45 899886 33446889999986
No 239
>PRK12495 hypothetical protein; Provisional
Probab=41.55 E-value=16 Score=32.82 Aligned_cols=24 Identities=29% Similarity=0.733 Sum_probs=17.2
Q ss_pred EEccCccccc-cccCccccCCCCCC
Q 028198 71 LKCHACYTIT-AEIGRIFCPKCGNG 94 (212)
Q Consensus 71 lrC~aC~k~~-~~~~k~FCp~CG~~ 94 (212)
+.|..|+.-. ......|||.|+..
T Consensus 43 ~hC~~CG~PIpa~pG~~~Cp~CQ~~ 67 (226)
T PRK12495 43 AHCDECGDPIFRHDGQEFCPTCQQP 67 (226)
T ss_pred hhcccccCcccCCCCeeECCCCCCc
Confidence 4588888543 33457899999975
No 240
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=41.37 E-value=30 Score=32.25 Aligned_cols=29 Identities=28% Similarity=0.601 Sum_probs=20.6
Q ss_pred EEEEccCccccccccCccccCCCCCCCcee
Q 028198 69 WILKCHACYTITAEIGRIFCPKCGNGGTLR 98 (212)
Q Consensus 69 wvlrC~aC~k~~~~~~k~FCp~CG~~~TL~ 98 (212)
=.+.|.-|.....- .+.-||.||+...|.
T Consensus 211 RyL~CslC~teW~~-~R~~C~~Cg~~~~l~ 239 (309)
T PRK03564 211 RYLHCNLCESEWHV-VRVKCSNCEQSGKLH 239 (309)
T ss_pred eEEEcCCCCCcccc-cCccCCCCCCCCcee
Confidence 34788888876653 478899999864443
No 241
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=41.29 E-value=14 Score=39.11 Aligned_cols=25 Identities=24% Similarity=0.719 Sum_probs=19.8
Q ss_pred EEEccCccccccc--cCccccCCCCCC
Q 028198 70 ILKCHACYTITAE--IGRIFCPKCGNG 94 (212)
Q Consensus 70 vlrC~aC~k~~~~--~~k~FCp~CG~~ 94 (212)
-+||.-|++++.- -+..-||.||.+
T Consensus 821 ~~~~~~~~~~~~~~~~~~~~~~~~~~~ 847 (1006)
T PRK12775 821 QWRCDDCGKVSEGFAFPYGMCPACGGK 847 (1006)
T ss_pred eeehhhhccccccccCCcCcCcccccc
Confidence 4899999999753 335779999986
No 242
>COG5270 PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis]
Probab=41.29 E-value=22 Score=31.40 Aligned_cols=32 Identities=22% Similarity=0.402 Sum_probs=23.1
Q ss_pred eeEEEEccCccccccccCccccCCCCCCCceeEEEEE
Q 028198 67 HRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVT 103 (212)
Q Consensus 67 k~wvlrC~aC~k~~~~~~k~FCp~CG~~~TL~Rvsvs 103 (212)
+-|+|.|.-|.=... -..|+.||.. ...+.+|
T Consensus 11 k~~iyWCe~cNlPl~---~~~c~~cg~~--~~~l~LT 42 (202)
T COG5270 11 KFPIYWCEKCNLPLL---GRRCSVCGSK--VEELRLT 42 (202)
T ss_pred ccceeehhhCCCccc---cccccccCCc--ceEEEeC
Confidence 579999999985443 3579999976 4445444
No 243
>PRK05767 rpl44e 50S ribosomal protein L44e; Validated
Probab=41.17 E-value=22 Score=27.78 Aligned_cols=19 Identities=32% Similarity=0.653 Sum_probs=16.1
Q ss_pred ccccCCCCCCCceeEEEEEe
Q 028198 85 RIFCPKCGNGGTLRKVAVTV 104 (212)
Q Consensus 85 k~FCp~CG~~~TL~Rvsvsv 104 (212)
+-|||.|+.. |+.+|+-+-
T Consensus 8 ~tyCp~CkkH-t~HkV~qyK 26 (92)
T PRK05767 8 RTYCPYCKTH-TEHEVEKVK 26 (92)
T ss_pred cccCcCCCCc-ccEEEEEEe
Confidence 5799999998 999998654
No 244
>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=40.97 E-value=17 Score=23.63 Aligned_cols=25 Identities=32% Similarity=0.668 Sum_probs=15.0
Q ss_pred cccCCCCCCCceeEEEEEeCCCceEEeecC
Q 028198 86 IFCPKCGNGGTLRKVAVTVGENGIVLASRR 115 (212)
Q Consensus 86 ~FCp~CG~~~TL~Rvsvsv~~~G~~~~~~k 115 (212)
..||.||+. .+.|- ...|.++.-.+
T Consensus 2 ~~CP~Cg~~-lv~r~----~k~g~F~~Cs~ 26 (39)
T PF01396_consen 2 EKCPKCGGP-LVLRR----GKKGKFLGCSN 26 (39)
T ss_pred cCCCCCCce-eEEEE----CCCCCEEECCC
Confidence 469999976 33332 46676554444
No 245
>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=40.78 E-value=21 Score=25.01 Aligned_cols=27 Identities=33% Similarity=0.835 Sum_probs=19.0
Q ss_pred eeEEEEccCcccccc-------ccCccccCCCCC
Q 028198 67 HRWILKCHACYTITA-------EIGRIFCPKCGN 93 (212)
Q Consensus 67 k~wvlrC~aC~k~~~-------~~~k~FCp~CG~ 93 (212)
.++.+.|.-|+...- +...-.||.||.
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 478999999986431 122567999996
No 246
>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=40.65 E-value=32 Score=21.74 Aligned_cols=21 Identities=19% Similarity=0.659 Sum_probs=10.7
Q ss_pred cCccccccccCccccCCCCCC
Q 028198 74 HACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 74 ~aC~k~~~~~~k~FCp~CG~~ 94 (212)
-+...+..+.+-.+|+.||..
T Consensus 21 ~~~~~~i~~vp~~~C~~CGE~ 41 (46)
T TIGR03831 21 GGELIVIENVPALVCPQCGEE 41 (46)
T ss_pred CCEEEEEeCCCccccccCCCE
Confidence 444444444444556666653
No 247
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=40.65 E-value=18 Score=29.19 Aligned_cols=19 Identities=37% Similarity=0.903 Sum_probs=7.8
Q ss_pred ccCccccccccCccccCCCC
Q 028198 73 CHACYTITAEIGRIFCPKCG 92 (212)
Q Consensus 73 C~aC~k~~~~~~k~FCp~CG 92 (212)
|+.|+.-... ++..|+.||
T Consensus 1 CPvCg~~l~v-t~l~C~~C~ 19 (113)
T PF09862_consen 1 CPVCGGELVV-TRLKCPSCG 19 (113)
T ss_pred CCCCCCceEE-EEEEcCCCC
Confidence 4444433222 234455554
No 248
>COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]
Probab=40.64 E-value=16 Score=36.45 Aligned_cols=50 Identities=22% Similarity=0.375 Sum_probs=33.0
Q ss_pred eEecchHHHHHHHHHhCceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCC
Q 028198 36 ACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 36 ac~TdDfAmQNVllqmGL~~~s~~g~~I~~~k~wvlrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
|..-.||--=-=|.|.- ..-++-+-=+.+|.-|+.+..-..+..| .||.+
T Consensus 104 a~ye~dfe~i~~leqyh--------yas~k~~va~w~c~~cg~~iean~kp~c-~cg~~ 153 (593)
T COG2401 104 ATYEEDFEFIAELEQYH--------YASQKEKVALWRCEKCGTIIEANTKPEC-KCGSH 153 (593)
T ss_pred hhHHHHHHHHHHHHHhh--------hccccceEEEEecchhchhhhhcCCccc-CCCCc
Confidence 56667776443344421 1122334556799999998877778899 99986
No 249
>PRK06386 replication factor A; Reviewed
Probab=40.60 E-value=18 Score=34.33 Aligned_cols=68 Identities=18% Similarity=0.324 Sum_probs=38.3
Q ss_pred cchHHHHHHHHHhC-ceeecCCCC--cceeeeeEEEEccCccccccccCccccCCCCCCC--ceeEEEEEeCC-CceEEe
Q 028198 39 TGDYAMQNVILQMG-LRLLAPGGM--QIRQLHRWILKCHACYTITAEIGRIFCPKCGNGG--TLRKVAVTVGE-NGIVLA 112 (212)
Q Consensus 39 TdDfAmQNVllqmG-L~~~s~~g~--~I~~~k~wvlrC~aC~k~~~~~~k~FCp~CG~~~--TL~Rvsvsv~~-~G~~~~ 112 (212)
+..+.+..+.--+| +.+. |. .|++-..-+.||+.|.++-.. -+||.||... -..|+-..+|+ .|.+..
T Consensus 205 ~~~~~I~di~~~~g~v~i~---G~iv~i~~gsgli~rCP~C~R~l~~---g~C~~HG~v~~~~dlr~k~vLDDGtg~~~~ 278 (358)
T PRK06386 205 SRNIFIFEIKSPVGGITIM---GFIVSVGQGSRIFTKCSVCNKIIED---GVCKDHPDAPVYLDIFGYFTISDGTGFVTC 278 (358)
T ss_pred ccccchhhhhccCCeEEEE---EEEEEEcCCcEeEecCcCCCeEccC---CcCCCCCCCCCeeEEEEEEEEECCCCeEEE
Confidence 34445555554443 3332 32 133345678999999998764 5899999541 12455444543 355543
No 250
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=40.18 E-value=13 Score=33.22 Aligned_cols=10 Identities=40% Similarity=1.022 Sum_probs=9.0
Q ss_pred ccccCCCCCC
Q 028198 85 RIFCPKCGNG 94 (212)
Q Consensus 85 k~FCp~CG~~ 94 (212)
..|||.||.+
T Consensus 99 ~~fC~~CG~~ 108 (256)
T PRK00241 99 HRFCGYCGHP 108 (256)
T ss_pred CccccccCCC
Confidence 5799999998
No 251
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=40.14 E-value=12 Score=29.68 Aligned_cols=9 Identities=67% Similarity=1.534 Sum_probs=8.0
Q ss_pred cccCCCCCC
Q 028198 86 IFCPKCGNG 94 (212)
Q Consensus 86 ~FCp~CG~~ 94 (212)
.|||.||+-
T Consensus 3 ~FCp~Cgsl 11 (113)
T COG1594 3 RFCPKCGSL 11 (113)
T ss_pred cccCCccCe
Confidence 699999984
No 252
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=40.07 E-value=32 Score=31.76 Aligned_cols=28 Identities=32% Similarity=0.531 Sum_probs=18.1
Q ss_pred EEccCccccccc---cCccccCCCCCCCceeE
Q 028198 71 LKCHACYTITAE---IGRIFCPKCGNGGTLRK 99 (212)
Q Consensus 71 lrC~aC~k~~~~---~~k~FCp~CG~~~TL~R 99 (212)
--|..|+..+.. -.+.-||+||+. ..=|
T Consensus 112 RFCg~CG~~~~~~~~g~~~~C~~cg~~-~fPR 142 (279)
T COG2816 112 RFCGRCGTKTYPREGGWARVCPKCGHE-HFPR 142 (279)
T ss_pred cCCCCCCCcCccccCceeeeCCCCCCc-cCCC
Confidence 458888865532 236789999986 5443
No 253
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=40.01 E-value=36 Score=34.65 Aligned_cols=47 Identities=19% Similarity=0.329 Sum_probs=30.2
Q ss_pred HHHHHhCcee-----ecCCCCcceeeeeEEEEccCccc-cccccCccccCCCCCC
Q 028198 46 NVILQMGLRL-----LAPGGMQIRQLHRWILKCHACYT-ITAEIGRIFCPKCGNG 94 (212)
Q Consensus 46 NVllqmGL~~-----~s~~g~~I~~~k~wvlrC~aC~k-~~~~~~k~FCp~CG~~ 94 (212)
+-+.++||.+ +.-.|..|-++-.-+.....=.. .+.. -.+||.||++
T Consensus 361 ~~i~~~~i~iGD~V~V~raGdVIP~i~~vv~~~r~~~~~~~~~--P~~CP~Cgs~ 413 (665)
T PRK07956 361 DEIERKDIRIGDTVVVRRAGDVIPEVVGVVLEKRPGDEREIVM--PTHCPVCGSE 413 (665)
T ss_pred HHHHHcCCCCCCEEEEEECCCccceeeeeecccCCCCCccCcC--CCCCCCCCCE
Confidence 4467777776 44568999998887765443211 1222 2589999997
No 254
>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=39.91 E-value=19 Score=29.29 Aligned_cols=13 Identities=54% Similarity=1.086 Sum_probs=7.9
Q ss_pred ccCCCCCCCceeEEE
Q 028198 87 FCPKCGNGGTLRKVA 101 (212)
Q Consensus 87 FCp~CG~~~TL~Rvs 101 (212)
-|+.|+.. |..|+
T Consensus 93 RC~~CN~~--L~~v~ 105 (147)
T PF01927_consen 93 RCPKCNGP--LRPVS 105 (147)
T ss_pred ccCCCCcE--eeech
Confidence 47777764 65554
No 255
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=39.30 E-value=14 Score=28.82 Aligned_cols=24 Identities=21% Similarity=0.548 Sum_probs=20.8
Q ss_pred EEccCccccccccCccccCCCCCC
Q 028198 71 LKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 71 lrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
-.|..|++.....-+..|..||.+
T Consensus 17 tlCrRCG~~syH~qK~~CasCGyp 40 (91)
T PTZ00073 17 TLCRRCGKRSFHVQKKRCASCGYP 40 (91)
T ss_pred chhcccCccccccccccchhcCCc
Confidence 469999988777778899999997
No 256
>KOG2324 consensus Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=39.29 E-value=84 Score=30.69 Aligned_cols=55 Identities=24% Similarity=0.550 Sum_probs=33.8
Q ss_pred HHHHHhCceeecC------CCCcceeee--------eEEEEccCcccccc----ccCc-cccCCCCCCCceeEEE
Q 028198 46 NVILQMGLRLLAP------GGMQIRQLH--------RWILKCHACYTITA----EIGR-IFCPKCGNGGTLRKVA 101 (212)
Q Consensus 46 NVllqmGL~~~s~------~g~~I~~~k--------~wvlrC~aC~k~~~----~~~k-~FCp~CG~~~TL~Rvs 101 (212)
-+.++|||.|+.+ .|--+.+-. -.++-|..|+--.. +.++ .-||+|-.. +|+++.
T Consensus 189 ~iFkqL~~pfVkv~AdsG~iGG~vShEfhl~~~vgED~l~~C~~C~~s~n~e~~~~sk~~~Cp~C~~~-~L~~~~ 262 (457)
T KOG2324|consen 189 RIFKQLGLPFVKVWADSGDIGGEVSHEFHLIHPVGEDTLMSCPSCGYSKNSEDLDLSKIASCPKCNEG-RLTKTK 262 (457)
T ss_pred HHHHHcCCCeEEEeecccccCceeeeeEeccCccCccceeecCcCCccCchhhhcCCccccCCcccCC-Cccccc
Confidence 4568999999743 222233222 24589999963322 1222 689999985 787765
No 257
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=38.97 E-value=14 Score=27.08 Aligned_cols=24 Identities=21% Similarity=0.754 Sum_probs=20.4
Q ss_pred EEEccCccccccccCccccCCCCC
Q 028198 70 ILKCHACYTITAEIGRIFCPKCGN 93 (212)
Q Consensus 70 vlrC~aC~k~~~~~~k~FCp~CG~ 93 (212)
--.|.-|++.....-+..|..||.
T Consensus 17 Ht~CrRCG~~syh~qK~~CasCGy 40 (62)
T PRK04179 17 HIRCRRCGRHSYNVRKKYCAACGF 40 (62)
T ss_pred cchhcccCcccccccccchhhcCC
Confidence 357999998877777899999998
No 258
>PF01623 Carla_C4: Carlavirus putative nucleic acid binding protein; InterPro: IPR002568 This family of carlavirus nucleic acid binding proteins includes a motif for a potential C-4 type zinc finger this has four highly conserved cysteine residues and is a conserved feature of the carlaviruses 3' terminal ORF []. These proteins may function as viral transcriptional regulators. The carlavirus family includes Garlic latent virus and Potato virus S and Potato virus M, these viruses are positive strand, ssRNA with no DNA stage.; GO: 0003676 nucleic acid binding, 0006355 regulation of transcription, DNA-dependent
Probab=38.96 E-value=17 Score=28.45 Aligned_cols=25 Identities=32% Similarity=0.825 Sum_probs=19.2
Q ss_pred eEEEEccCccccccccCccccCCCCCC
Q 028198 68 RWILKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 68 ~wvlrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
+-+-|||-||++++.. .|=.+|-|+
T Consensus 51 ~sigRC~RCyRv~Ppf--~~t~rCDnk 75 (91)
T PF01623_consen 51 KSIGRCHRCYRVYPPF--YFTKRCDNK 75 (91)
T ss_pred HHhCCCCCCeeecCCc--eeCccCCCC
Confidence 3467999999999863 455678887
No 259
>PRK05333 NAD-dependent deacetylase; Provisional
Probab=38.78 E-value=26 Score=31.44 Aligned_cols=13 Identities=15% Similarity=0.225 Sum_probs=9.6
Q ss_pred eEEEEccCccccc
Q 028198 68 RWILKCHACYTIT 80 (212)
Q Consensus 68 ~wvlrC~aC~k~~ 80 (212)
...++|..|.+.+
T Consensus 126 ~~~~~C~~C~~~~ 138 (285)
T PRK05333 126 LDGVRCMGCGARH 138 (285)
T ss_pred cCEEEECCCCCcC
Confidence 4458899999654
No 260
>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=38.46 E-value=23 Score=33.73 Aligned_cols=27 Identities=33% Similarity=0.632 Sum_probs=19.5
Q ss_pred eEEEEccCccccccc-------cCccccCCCCCC
Q 028198 68 RWILKCHACYTITAE-------IGRIFCPKCGNG 94 (212)
Q Consensus 68 ~wvlrC~aC~k~~~~-------~~k~FCp~CG~~ 94 (212)
++.+||..|+..... ....|||.||..
T Consensus 318 r~~~rc~~c~~~~~~~~~~~~~~~~~~~~~~~~~ 351 (403)
T TIGR03676 318 RVTFKCPNCGYEEEKTVKPEEGDKSEACPKCGSE 351 (403)
T ss_pred eEEEEcCCCCcceeeecccccccccccCcccCcc
Confidence 578999999865321 112689999986
No 261
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=38.06 E-value=15 Score=35.63 Aligned_cols=24 Identities=29% Similarity=0.692 Sum_probs=19.4
Q ss_pred EEccCccccccccCccccCCCCCC
Q 028198 71 LKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 71 lrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
--|++|..+...-.+.-||.||.+
T Consensus 221 ~~C~~C~~~~~~~~~~~CpRC~~~ 244 (418)
T COG2995 221 RSCLCCHYILPHDAEPRCPRCGSK 244 (418)
T ss_pred eecccccccCCHhhCCCCCCCCCh
Confidence 469999987765457889999997
No 262
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=37.81 E-value=23 Score=32.38 Aligned_cols=24 Identities=17% Similarity=0.600 Sum_probs=18.7
Q ss_pred EEEccCccccccccCccccCCCCCC
Q 028198 70 ILKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 70 vlrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
-|.|.-|.-++-+.+ ..||.||.+
T Consensus 255 GyvCs~Clsi~C~~p-~~C~~Cgt~ 278 (279)
T TIGR00627 255 GFVCSVCLSVLCQYT-PICKTCKTA 278 (279)
T ss_pred eEECCCccCCcCCCC-CCCCCCCCC
Confidence 489999998886654 489999964
No 263
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=37.43 E-value=19 Score=34.89 Aligned_cols=32 Identities=25% Similarity=0.703 Sum_probs=23.0
Q ss_pred eeEEEEccCcccccccc-----CccccCCCCCCCceeEE
Q 028198 67 HRWILKCHACYTITAEI-----GRIFCPKCGNGGTLRKV 100 (212)
Q Consensus 67 k~wvlrC~aC~k~~~~~-----~k~FCp~CG~~~TL~Rv 100 (212)
..-..+|..|.-..+-+ ..-+||.||+ ||++.
T Consensus 15 ~~~~~~C~eCd~~~~~P~l~~~q~A~CPRC~~--~l~~~ 51 (418)
T COG2995 15 PGHLILCPECDMLVSLPRLDSGQSAYCPRCGH--TLTRG 51 (418)
T ss_pred ccceecCCCCCceeccccCCCCCcccCCCCCC--ccccC
Confidence 45678999999776532 2579999997 47643
No 264
>COG0384 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]
Probab=37.27 E-value=31 Score=31.75 Aligned_cols=50 Identities=22% Similarity=0.142 Sum_probs=28.5
Q ss_pred cchHHHHHHHHHhCceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCCCcee
Q 028198 39 TGDYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLR 98 (212)
Q Consensus 39 TdDfAmQNVllqmGL~~~s~~g~~I~~~k~wvlrC~aC~k~~~~~~k~FCp~CG~~~TL~ 98 (212)
=+|-.||+++.++|+.--..- .....-..|.+|= .|+. ..=|-||++ ||=
T Consensus 31 Lsd~~MQ~IA~e~n~SET~Fv-~~~~~~~~~rlR~-----FTP~---~Evpf~GHa-Tlg 80 (291)
T COG0384 31 LSDEQMQAIAREFNLSETAFV-LPPDDPADARLRI-----FTPT---TEVPFAGHA-TLG 80 (291)
T ss_pred CCHHHHHHHHHHhCCceeEEE-cCCCCcCceEEEE-----eCCC---cccccCCCH-HHH
Confidence 378999999999998753211 0011112455551 1222 234559998 874
No 265
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=37.07 E-value=9.6 Score=32.07 Aligned_cols=42 Identities=26% Similarity=0.376 Sum_probs=28.2
Q ss_pred chHHHHHHHHHhCceee------cCCCCcceeeeeEEEEccCcccccc
Q 028198 40 GDYAMQNVILQMGLRLL------APGGMQIRQLHRWILKCHACYTITA 81 (212)
Q Consensus 40 dDfAmQNVllqmGL~~~------s~~g~~I~~~k~wvlrC~aC~k~~~ 81 (212)
.|.-++|++....-.++ +++...++.-|.|.+.|-+|+...+
T Consensus 90 ~~~~i~~~i~~yi~~yv~C~~c~s~dt~l~~~~R~~~l~c~acGa~~p 137 (151)
T COG1601 90 SDSEIVNEIERYIAEYVKCKECGSPDTELIKEERLLFLKCEACGAIRP 137 (151)
T ss_pred cHHHHHHHHHHHHHheeEeccCCCCchhhhhhhhhHhhHHHHhCCccc
Confidence 45567777766554443 5666667777888888888887655
No 266
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=36.72 E-value=16 Score=33.75 Aligned_cols=11 Identities=36% Similarity=1.081 Sum_probs=9.5
Q ss_pred CccccCCCCCC
Q 028198 84 GRIFCPKCGNG 94 (212)
Q Consensus 84 ~k~FCp~CG~~ 94 (212)
+-.||+.||.+
T Consensus 110 ~~RFCg~CG~~ 120 (279)
T COG2816 110 SHRFCGRCGTK 120 (279)
T ss_pred hCcCCCCCCCc
Confidence 35799999998
No 267
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=36.61 E-value=15 Score=27.82 Aligned_cols=13 Identities=31% Similarity=1.045 Sum_probs=6.2
Q ss_pred ccCccccCCCCCC
Q 028198 82 EIGRIFCPKCGNG 94 (212)
Q Consensus 82 ~~~k~FCp~CG~~ 94 (212)
.|+...||+||+.
T Consensus 62 NMs~~~Cp~Cg~~ 74 (81)
T PF10609_consen 62 NMSYFVCPHCGER 74 (81)
T ss_dssp CT-EEE-TTT--E
T ss_pred CCCccCCCCCCCe
Confidence 4666678888864
No 268
>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=36.52 E-value=30 Score=23.05 Aligned_cols=9 Identities=44% Similarity=1.250 Sum_probs=5.9
Q ss_pred cccCCCCCC
Q 028198 86 IFCPKCGNG 94 (212)
Q Consensus 86 ~FCp~CG~~ 94 (212)
..||.||.+
T Consensus 18 ~~Cp~C~~P 26 (41)
T PF06677_consen 18 EHCPDCGTP 26 (41)
T ss_pred CccCCCCCe
Confidence 457777665
No 269
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=36.13 E-value=27 Score=34.30 Aligned_cols=32 Identities=25% Similarity=0.451 Sum_probs=24.5
Q ss_pred EEEEccCccccccccCccccCCCCCCCceeEEE
Q 028198 69 WILKCHACYTITAEIGRIFCPKCGNGGTLRKVA 101 (212)
Q Consensus 69 wvlrC~aC~k~~~~~~k~FCp~CG~~~TL~Rvs 101 (212)
=.|.|..|+...+. +---||.||.=+||.-+.
T Consensus 6 t~f~C~~CG~~s~K-W~GkCp~Cg~Wns~vE~~ 37 (456)
T COG1066 6 TAFVCQECGYVSPK-WLGKCPACGAWNTLVEEV 37 (456)
T ss_pred cEEEcccCCCCCcc-ccccCCCCCCccceEEee
Confidence 56899999987765 456799999776775444
No 270
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=35.96 E-value=19 Score=23.88 Aligned_cols=14 Identities=29% Similarity=0.897 Sum_probs=10.7
Q ss_pred CccccCCCCCCCceeE
Q 028198 84 GRIFCPKCGNGGTLRK 99 (212)
Q Consensus 84 ~k~FCp~CG~~~TL~R 99 (212)
...+|+.||.+ |..
T Consensus 4 g~l~C~~CG~~--m~~ 17 (58)
T PF13408_consen 4 GLLRCGHCGSK--MTR 17 (58)
T ss_pred CcEEcccCCcE--eEE
Confidence 35799999986 544
No 271
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=35.93 E-value=14 Score=29.91 Aligned_cols=37 Identities=22% Similarity=0.363 Sum_probs=24.2
Q ss_pred HHHHHHHHhCceee------cCCCCcceeeeeEEEEccCcccc
Q 028198 43 AMQNVILQMGLRLL------APGGMQIRQLHRWILKCHACYTI 79 (212)
Q Consensus 43 AmQNVllqmGL~~~------s~~g~~I~~~k~wvlrC~aC~k~ 79 (212)
.||++|...=-.+| +++...+++-+.|.++|.||+..
T Consensus 81 ~i~~~L~~fI~~yVlC~~C~spdT~l~k~~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 81 QIQDLLDKFIKEYVLCPECGSPDTELIKEGRLIFLKCKACGAS 123 (125)
T ss_dssp HHHHHHHHHHCHHSSCTSTSSSSEEEEEETTCCEEEETTTSCE
T ss_pred HHHHHHHHHHHHEEEcCCCCCCccEEEEcCCEEEEEecccCCc
Confidence 57777766422222 56666677778888888888753
No 272
>PTZ00409 Sir2 (Silent Information Regulator) protein; Provisional
Probab=35.92 E-value=23 Score=31.98 Aligned_cols=14 Identities=14% Similarity=0.468 Sum_probs=9.8
Q ss_pred eEEEEccCcccccc
Q 028198 68 RWILKCHACYTITA 81 (212)
Q Consensus 68 ~wvlrC~aC~k~~~ 81 (212)
.+.++|..|.+.+.
T Consensus 135 l~~~~C~~C~~~~~ 148 (271)
T PTZ00409 135 VFEARCCTCRKTIQ 148 (271)
T ss_pred cCcceeCCCCCCcc
Confidence 45578888886654
No 273
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=35.66 E-value=30 Score=27.64 Aligned_cols=22 Identities=27% Similarity=0.573 Sum_probs=15.1
Q ss_pred ccccCCCCCCCceeEEEEEeCCCce
Q 028198 85 RIFCPKCGNGGTLRKVAVTVGENGI 109 (212)
Q Consensus 85 k~FCp~CG~~~TL~Rvsvsv~~~G~ 109 (212)
.-.||.||+. + -++++|+..+.
T Consensus 22 ~FtCp~Cghe-~--vs~ctvkk~~~ 43 (104)
T COG4888 22 TFTCPRCGHE-K--VSSCTVKKTVN 43 (104)
T ss_pred eEecCccCCe-e--eeEEEEEecCc
Confidence 3469999986 4 46677776544
No 274
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=34.96 E-value=24 Score=34.91 Aligned_cols=29 Identities=28% Similarity=0.679 Sum_probs=22.2
Q ss_pred eeeEEEEccCccccccc--------------cCccccCCCCCC
Q 028198 66 LHRWILKCHACYTITAE--------------IGRIFCPKCGNG 94 (212)
Q Consensus 66 ~k~wvlrC~aC~k~~~~--------------~~k~FCp~CG~~ 94 (212)
.+.|-..|+.|+..... ..+..||+||..
T Consensus 196 qr~~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~ 238 (557)
T PF05876_consen 196 QRRYYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCE 238 (557)
T ss_pred ceEEEccCCCCCCCccccccceeecCCCCccceEEECCCCcCC
Confidence 35899999999976531 246789999986
No 275
>COG1773 Rubredoxin [Energy production and conversion]
Probab=34.86 E-value=27 Score=24.93 Aligned_cols=12 Identities=17% Similarity=0.487 Sum_probs=9.9
Q ss_pred EEEccCcccccc
Q 028198 70 ILKCHACYTITA 81 (212)
Q Consensus 70 vlrC~aC~k~~~ 81 (212)
.++|..|+-+|.
T Consensus 3 ~~~C~~CG~vYd 14 (55)
T COG1773 3 RWRCSVCGYVYD 14 (55)
T ss_pred ceEecCCceEec
Confidence 478999998885
No 276
>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=34.65 E-value=23 Score=23.43 Aligned_cols=9 Identities=44% Similarity=1.431 Sum_probs=7.4
Q ss_pred cccCCCCCC
Q 028198 86 IFCPKCGNG 94 (212)
Q Consensus 86 ~FCp~CG~~ 94 (212)
..||+||+.
T Consensus 19 ~~CP~Cg~~ 27 (46)
T PF12760_consen 19 FVCPHCGST 27 (46)
T ss_pred CCCCCCCCe
Confidence 469999984
No 277
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=34.54 E-value=18 Score=29.08 Aligned_cols=20 Identities=25% Similarity=0.654 Sum_probs=12.4
Q ss_pred cCCCCCCCceeEEEEEeCCCce
Q 028198 88 CPKCGNGGTLRKVAVTVGENGI 109 (212)
Q Consensus 88 Cp~CG~~~TL~Rvsvsv~~~G~ 109 (212)
||+||++-.++++.| ..-|+
T Consensus 1 CPvCg~~l~vt~l~C--~~C~t 20 (113)
T PF09862_consen 1 CPVCGGELVVTRLKC--PSCGT 20 (113)
T ss_pred CCCCCCceEEEEEEc--CCCCC
Confidence 999999833355554 34444
No 278
>TIGR00575 dnlj DNA ligase, NAD-dependent. The member of this family from Treponema pallidum differs in having three rather than just one copy of the BRCT (BRCA1 C Terminus) domain (pfam00533) at the C-terminus. It is included in the seed.
Probab=34.20 E-value=50 Score=33.52 Aligned_cols=48 Identities=21% Similarity=0.430 Sum_probs=28.3
Q ss_pred HHHHHhCcee-----ecCCCCcceeeeeEEEEccCccccccccCccccCCCCCC
Q 028198 46 NVILQMGLRL-----LAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 46 NVllqmGL~~-----~s~~g~~I~~~k~wvlrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
+-+.++||.+ +.-.|..|-++..-+..-..=......+ -..||.||++
T Consensus 349 ~~i~~~~i~iGD~V~V~raGdVIP~i~~vv~~~r~~~~~~~~~-P~~CP~C~s~ 401 (652)
T TIGR00575 349 DEIEELDIRIGDTVVVRKAGDVIPKVVRVLLEKRTGSERPIRF-PTHCPSCGSP 401 (652)
T ss_pred HHHHHcCCCCCCEEEEEecCCcCceeeeeccccCCCCCCCCCC-CCCCCCCCCE
Confidence 3467788776 4456888888877554322111111112 2589999997
No 279
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=33.98 E-value=27 Score=24.97 Aligned_cols=21 Identities=33% Similarity=0.747 Sum_probs=15.3
Q ss_pred EEccCccccccccCccccCCCCCC
Q 028198 71 LKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 71 lrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
+.|.+||-...- -=||.||.+
T Consensus 28 ~I~~~~f~~~rY---ngCPfC~~~ 48 (55)
T PF14447_consen 28 LICDNCFPGERY---NGCPFCGTP 48 (55)
T ss_pred eeeccccChhhc---cCCCCCCCc
Confidence 678888865432 359999987
No 280
>COG4469 CoiA Competence protein CoiA-like family, contains a predicted nuclease domain [General function prediction only]
Probab=33.94 E-value=20 Score=33.95 Aligned_cols=10 Identities=60% Similarity=1.643 Sum_probs=8.7
Q ss_pred ccccCCCCCC
Q 028198 85 RIFCPKCGNG 94 (212)
Q Consensus 85 k~FCp~CG~~ 94 (212)
+-|||.||++
T Consensus 25 ~ffCPaC~~~ 34 (342)
T COG4469 25 RFFCPACGSQ 34 (342)
T ss_pred ccccCCCCCe
Confidence 4699999998
No 281
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=33.51 E-value=13 Score=28.91 Aligned_cols=20 Identities=30% Similarity=0.708 Sum_probs=15.4
Q ss_pred CccccCCCCCCCceeEEEEEe
Q 028198 84 GRIFCPKCGNGGTLRKVAVTV 104 (212)
Q Consensus 84 ~k~FCp~CG~~~TL~Rvsvsv 104 (212)
.+.+|+-||.. |++|-+|-+
T Consensus 35 aky~CsfCGK~-~vKR~AvGi 54 (92)
T KOG0402|consen 35 AKYTCSFCGKK-TVKRKAVGI 54 (92)
T ss_pred hhhhhhhcchh-hhhhhceeE
Confidence 46788888887 888887754
No 282
>KOG2768 consensus Translation initiation factor 2, beta subunit (eIF-2beta) [Translation, ribosomal structure and biogenesis]
Probab=33.06 E-value=24 Score=31.74 Aligned_cols=54 Identities=30% Similarity=0.607 Sum_probs=34.5
Q ss_pred chHHHHHHHHHhCceeecCCCCc------------ce-eeeeEE---EEccCcccccccc---Cc---cccCCCCCC
Q 028198 40 GDYAMQNVILQMGLRLLAPGGMQ------------IR-QLHRWI---LKCHACYTITAEI---GR---IFCPKCGNG 94 (212)
Q Consensus 40 dDfAmQNVllqmGL~~~s~~g~~------------I~-~~k~wv---lrC~aC~k~~~~~---~k---~FCp~CG~~ 94 (212)
.|--||=.+.+||-.- |++|.. |. -+|+|+ ..|+.|.-.-... ++ .-|..||+.
T Consensus 136 pdHv~~FLlAELgTsG-Sidg~~rLviKGrfq~kq~e~VLRrYI~eyV~C~~CkSpdt~L~kenRLfFL~C~~cgs~ 211 (231)
T KOG2768|consen 136 PDHVMQFLLAELGTSG-SIDGQQRLVIKGRFQQKQFENVLRRYIKEYVTCKTCKSPDTILQKENRLFFLRCEKCGSR 211 (231)
T ss_pred hHHHHHHHHHHhcccc-ccCCCceEEEeccccHHHHHHHHHHHHHHheEeeecCChhHHhhhhcceEEEEecCCCCe
Confidence 6777999999999764 444432 11 123444 5799998654321 22 459999985
No 283
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=32.84 E-value=31 Score=24.13 Aligned_cols=8 Identities=50% Similarity=1.323 Sum_probs=6.8
Q ss_pred ccCCCCCC
Q 028198 87 FCPKCGNG 94 (212)
Q Consensus 87 FCp~CG~~ 94 (212)
.||.||..
T Consensus 2 ~CPyCge~ 9 (52)
T PF14255_consen 2 QCPYCGEP 9 (52)
T ss_pred CCCCCCCe
Confidence 59999986
No 284
>COG4640 Predicted membrane protein [Function unknown]
Probab=32.46 E-value=18 Score=35.22 Aligned_cols=23 Identities=30% Similarity=0.660 Sum_probs=15.9
Q ss_pred EEccCccccccccCccccCCCCCC
Q 028198 71 LKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 71 lrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
+-|+-|+.--.+- -.||+.||++
T Consensus 2 ~fC~kcG~qk~Ed-~~qC~qCG~~ 24 (465)
T COG4640 2 KFCPKCGSQKAED-DVQCTQCGHK 24 (465)
T ss_pred Ccccccccccccc-cccccccCCc
Confidence 4699999443332 2469999997
No 285
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=32.04 E-value=20 Score=33.66 Aligned_cols=9 Identities=67% Similarity=1.870 Sum_probs=5.8
Q ss_pred cccCCCCCC
Q 028198 86 IFCPKCGNG 94 (212)
Q Consensus 86 ~FCp~CG~~ 94 (212)
.|||.||.+
T Consensus 335 ~fcp~cgq~ 343 (345)
T COG4260 335 KFCPECGQG 343 (345)
T ss_pred hhChhhcCC
Confidence 577777654
No 286
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=31.59 E-value=22 Score=23.14 Aligned_cols=8 Identities=75% Similarity=1.639 Sum_probs=7.0
Q ss_pred ccCCCCCC
Q 028198 87 FCPKCGNG 94 (212)
Q Consensus 87 FCp~CG~~ 94 (212)
-||+||+.
T Consensus 2 ~Cp~C~~~ 9 (40)
T smart00440 2 PCPKCGNR 9 (40)
T ss_pred cCCCCCCC
Confidence 49999987
No 287
>KOG3475 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=31.58 E-value=16 Score=28.48 Aligned_cols=23 Identities=26% Similarity=0.621 Sum_probs=19.2
Q ss_pred EccCccccccccCccccCCCCCC
Q 028198 72 KCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 72 rC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
.|..|++-....-+..|..||.+
T Consensus 18 lC~RCG~~syH~QKstC~~CGYp 40 (92)
T KOG3475|consen 18 LCRRCGRRSYHIQKSTCSSCGYP 40 (92)
T ss_pred HHHHhCchhhhhhcccccccCCc
Confidence 48899987666668899999998
No 288
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=31.47 E-value=32 Score=22.15 Aligned_cols=13 Identities=46% Similarity=1.229 Sum_probs=10.3
Q ss_pred cCCCCCCCceeEEEE
Q 028198 88 CPKCGNGGTLRKVAV 102 (212)
Q Consensus 88 Cp~CG~~~TL~Rvsv 102 (212)
||+|+.. |..+.+
T Consensus 2 CP~C~~~--l~~~~~ 14 (41)
T PF13453_consen 2 CPRCGTE--LEPVRL 14 (41)
T ss_pred cCCCCcc--cceEEE
Confidence 9999985 776665
No 289
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=31.33 E-value=47 Score=33.96 Aligned_cols=43 Identities=21% Similarity=0.268 Sum_probs=28.1
Q ss_pred HHHHHhCcee-----ecCCCCcceeeeeEEE--EccCccccccccCccccCCCCCC
Q 028198 46 NVILQMGLRL-----LAPGGMQIRQLHRWIL--KCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 46 NVllqmGL~~-----~s~~g~~I~~~k~wvl--rC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
+-+.++||.+ +.-.|..|-++-.-+. |... +..+ ..||.||++
T Consensus 358 ~~I~~~di~iGD~V~V~raGdVIP~I~~v~~~~r~~~----~~~P--~~CP~C~s~ 407 (669)
T PRK14350 358 DYIDSIGLNVGDVVKISRRGDVIPAVELVIEKLSVGF----FKIP--DNCPSCKTA 407 (669)
T ss_pred HHHHHcCCCCCCEEEEEecCCCCCceeeecccccCCC----CCCC--CCCCCCCCE
Confidence 4567788776 4456888988866444 4333 2222 479999987
No 290
>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=31.32 E-value=27 Score=26.46 Aligned_cols=23 Identities=30% Similarity=0.787 Sum_probs=14.3
Q ss_pred EccCccccccc-cCccccCCCCCC
Q 028198 72 KCHACYTITAE-IGRIFCPKCGNG 94 (212)
Q Consensus 72 rC~aC~k~~~~-~~k~FCp~CG~~ 94 (212)
.|+-|+.+... .....|+.||+.
T Consensus 2 fC~~Cg~~l~~~~~~~~C~~C~~~ 25 (104)
T TIGR01384 2 FCPKCGSLMTPKNGVYVCPSCGYE 25 (104)
T ss_pred CCcccCcccccCCCeEECcCCCCc
Confidence 37777766533 235678888864
No 291
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=31.32 E-value=16 Score=32.85 Aligned_cols=30 Identities=27% Similarity=0.538 Sum_probs=19.4
Q ss_pred eeeeeEEEEccCcccccc-------ccCccccCCCCC
Q 028198 64 RQLHRWILKCHACYTITA-------EIGRIFCPKCGN 93 (212)
Q Consensus 64 ~~~k~wvlrC~aC~k~~~-------~~~k~FCp~CG~ 93 (212)
+.+-.|..||-.|.--+. -..+..||+||.
T Consensus 188 h~LvIqg~rCg~c~i~~h~~c~qty~q~~~~cphc~d 224 (235)
T KOG4718|consen 188 HCLVIQGIRCGSCNIQYHRGCIQTYLQRRDICPHCGD 224 (235)
T ss_pred HHHhheeeccCcccchhhhHHHHHHhcccCcCCchhc
Confidence 455678899999932111 012678999985
No 292
>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=31.12 E-value=24 Score=32.74 Aligned_cols=10 Identities=50% Similarity=1.404 Sum_probs=8.4
Q ss_pred ccccCCCCCC
Q 028198 85 RIFCPKCGNG 94 (212)
Q Consensus 85 k~FCp~CG~~ 94 (212)
+.+||+||+.
T Consensus 184 ~~~CPvCGs~ 193 (305)
T TIGR01562 184 RTLCPACGSP 193 (305)
T ss_pred CCcCCCCCCh
Confidence 5689999987
No 293
>TIGR02820 formald_GSH S-(hydroxymethyl)glutathione synthase. The formation of S-(hydroxymethyl)glutathione synthase from glutathione and formaldehyde occurs naturally, but this enzyme speeds its formation in some species as part of a pathway of formaldehyde detoxification.
Probab=31.11 E-value=21 Score=30.80 Aligned_cols=12 Identities=42% Similarity=0.838 Sum_probs=10.0
Q ss_pred cCccccCCCCCC
Q 028198 83 IGRIFCPKCGNG 94 (212)
Q Consensus 83 ~~k~FCp~CG~~ 94 (212)
..+.||+.||..
T Consensus 87 ~~R~FC~~CGS~ 98 (182)
T TIGR02820 87 IQRHACKGCGTH 98 (182)
T ss_pred EEeecCCCCCCc
Confidence 347899999997
No 294
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=30.91 E-value=10 Score=29.00 Aligned_cols=24 Identities=29% Similarity=0.837 Sum_probs=14.4
Q ss_pred EEccCccccccccCccccCCCCCC
Q 028198 71 LKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 71 lrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
..|..|+..-.....+-||.|+.+
T Consensus 37 PvCr~CyEYErkeg~q~CpqCkt~ 60 (80)
T PF14569_consen 37 PVCRPCYEYERKEGNQVCPQCKTR 60 (80)
T ss_dssp ---HHHHHHHHHTS-SB-TTT--B
T ss_pred ccchhHHHHHhhcCcccccccCCC
Confidence 568888887777778999999976
No 295
>PRK05417 glutathione-dependent formaldehyde-activating enzyme; Provisional
Probab=30.81 E-value=20 Score=31.16 Aligned_cols=12 Identities=42% Similarity=0.827 Sum_probs=10.0
Q ss_pred cCccccCCCCCC
Q 028198 83 IGRIFCPKCGNG 94 (212)
Q Consensus 83 ~~k~FCp~CG~~ 94 (212)
..+.|||.||..
T Consensus 91 i~R~FC~~CGS~ 102 (191)
T PRK05417 91 IQRHACKECGVH 102 (191)
T ss_pred eEeeeCCCCCCc
Confidence 347899999997
No 296
>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=30.55 E-value=50 Score=29.57 Aligned_cols=23 Identities=35% Similarity=0.710 Sum_probs=8.5
Q ss_pred ccccCCCCCCCceeEEEEEeCCC--ceE
Q 028198 85 RIFCPKCGNGGTLRKVAVTVGEN--GIV 110 (212)
Q Consensus 85 k~FCp~CG~~~TL~Rvsvsv~~~--G~~ 110 (212)
+.+||+||+.. .+++-.... |.-
T Consensus 172 ~g~CPvCGs~P---~~s~l~~~~~~G~R 196 (290)
T PF04216_consen 172 RGYCPVCGSPP---VLSVLRGGEREGKR 196 (290)
T ss_dssp -SS-TTT---E---EEEEEE------EE
T ss_pred CCcCCCCCCcC---ceEEEecCCCCccE
Confidence 46899999873 344444444 753
No 297
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.46 E-value=25 Score=28.75 Aligned_cols=24 Identities=17% Similarity=0.115 Sum_probs=17.1
Q ss_pred EEccCccccccccCc--cccCCCCCC
Q 028198 71 LKCHACYTITAEIGR--IFCPKCGNG 94 (212)
Q Consensus 71 lrC~aC~k~~~~~~k--~FCp~CG~~ 94 (212)
..|+-|++.|.+..| ..||.||..
T Consensus 10 ridPetg~KFYDLNrdPiVsPytG~s 35 (129)
T COG4530 10 RIDPETGKKFYDLNRDPIVSPYTGKS 35 (129)
T ss_pred ccCccccchhhccCCCccccCccccc
Confidence 458888877766553 678888863
No 298
>PF15499 Peptidase_C98: Ubiquitin-specific peptidase-like, SUMO isopeptidase
Probab=30.44 E-value=26 Score=32.25 Aligned_cols=83 Identities=12% Similarity=0.271 Sum_probs=47.7
Q ss_pred chHHHHHHHHHhCceeecCCCCcceeeeeEEEEccCccccccc---------------------cCccccCCCCCCCcee
Q 028198 40 GDYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAE---------------------IGRIFCPKCGNGGTLR 98 (212)
Q Consensus 40 dDfAmQNVllqmGL~~~s~~g~~I~~~k~wvlrC~aC~k~~~~---------------------~~k~FCp~CG~~~TL~ 98 (212)
.=||+..+| +|+-.+. .......+|...|..|+..+.+ ....-|+.|+++ .-+
T Consensus 109 PVFAlPLLL-k~d~~~E----~lF~~sf~WeFeC~~Cg~~~~~R~~K~L~TFtnv~pdwhPLnA~h~~pCn~C~~k-sQ~ 182 (275)
T PF15499_consen 109 PVFALPLLL-KLDPWIE----KLFLYSFSWEFECSQCGHKYQNRCTKTLVTFTNVIPDWHPLNAVHFGPCNSCNSK-SQR 182 (275)
T ss_pred cHHHhHHHH-hcchHHH----hHhheeeEEEEEccccCChhhhhheeeecccCCCCCCCCcccccccCCCcccCCh-HHh
Confidence 348988755 5543332 3345667999999999965532 113459999998 444
Q ss_pred EEEEEeCC----------CceEEeec-CCccccccceeccCC
Q 028198 99 KVAVTVGE----------NGIVLASR-RPRITLRGTKFSLPM 129 (212)
Q Consensus 99 Rvsvsv~~----------~G~~~~~~-k~~~n~RG~~ySlPk 129 (212)
|-.| ++. .|--+..+ .+-++..|..|+|-.
T Consensus 183 rkMv-lekv~~vfmLHFVeGLP~ndl~~ysF~feg~~Y~Vt~ 223 (275)
T PF15499_consen 183 RKMV-LEKVPPVFMLHFVEGLPHNDLQHYSFHFEGCLYQVTS 223 (275)
T ss_pred Hhhh-hhcCchhhhhhhhccCCccCCCccceeecCeeEEEEE
Confidence 4333 222 22222222 234667777777654
No 299
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=30.32 E-value=36 Score=31.83 Aligned_cols=11 Identities=45% Similarity=1.247 Sum_probs=9.7
Q ss_pred CccccCCCCCC
Q 028198 84 GRIFCPKCGNG 94 (212)
Q Consensus 84 ~k~FCp~CG~~ 94 (212)
.+.+||.||+.
T Consensus 184 ~~~~CPvCGS~ 194 (308)
T COG3058 184 SRQYCPVCGSM 194 (308)
T ss_pred ccccCCCcCCC
Confidence 57899999997
No 300
>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=30.16 E-value=33 Score=32.70 Aligned_cols=50 Identities=20% Similarity=0.336 Sum_probs=30.1
Q ss_pred HHHHHHHhCce-eecCCCCcceeeeeEEEEccCcccccccc-Cc---cccCCCCCC
Q 028198 44 MQNVILQMGLR-LLAPGGMQIRQLHRWILKCHACYTITAEI-GR---IFCPKCGNG 94 (212)
Q Consensus 44 mQNVllqmGL~-~~s~~g~~I~~~k~wvlrC~aC~k~~~~~-~k---~FCp~CG~~ 94 (212)
+..++..+.-. +...-|.-.+.=|-+.-.|..|+...... +. .-|| ||.+
T Consensus 213 ~~~~l~ai~~~~i~~~~g~~P~~GKYh~~~c~~C~~~~~~~~~~~~~~~Cp-CG~~ 267 (374)
T TIGR00375 213 FALALKAIDDRKIIANYGLDPLLGKYHQTACEACGEPAVSEDAETACANCP-CGGR 267 (374)
T ss_pred HHHHHHHhhCCceEeeeeECcCCCccchhhhcccCCcCCchhhhhcCCCCC-CCCc
Confidence 56666654422 22223444555566677899998766532 12 5699 9986
No 301
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=30.07 E-value=29 Score=25.78 Aligned_cols=21 Identities=14% Similarity=0.529 Sum_probs=13.7
Q ss_pred cccCCCCCCCceeEEEEEeCCC
Q 028198 86 IFCPKCGNGGTLRKVAVTVGEN 107 (212)
Q Consensus 86 ~FCp~CG~~~TL~Rvsvsv~~~ 107 (212)
..||.||++ ...|-+-.+++.
T Consensus 2 m~CP~Cg~~-a~irtSr~~s~~ 22 (72)
T PRK09678 2 FHCPLCQHA-AHARTSRYITDT 22 (72)
T ss_pred ccCCCCCCc-cEEEEChhcChh
Confidence 479999998 455555555443
No 302
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated
Probab=29.69 E-value=36 Score=34.42 Aligned_cols=32 Identities=31% Similarity=0.669 Sum_probs=20.0
Q ss_pred EEEccCccccccc---cCccccCCCCCCCceeEEE
Q 028198 70 ILKCHACYTITAE---IGRIFCPKCGNGGTLRKVA 101 (212)
Q Consensus 70 vlrC~aC~k~~~~---~~k~FCp~CG~~~TL~Rvs 101 (212)
++.|..|+.+... ....+|+.|++...+.+|.
T Consensus 544 ~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~i~~v~ 578 (605)
T PRK07225 544 IYVCAKCGMIAIYDKKRNRKYCPICGEETDIYPVE 578 (605)
T ss_pred EEeecCcCcceehhcccCceeecccCCCCceeecc
Confidence 4669999887632 1245699998653455554
No 303
>PF01747 ATP-sulfurylase: ATP-sulfurylase; InterPro: IPR002650 This entry consists of sulphate adenylyltransferase or ATP-sulfurylase (2.7.7.4 from EC) some of which are part of a bifunctional polypeptide chain associated with adenosyl phosphosulphate (APS) kinase, IPR002891 from INTERPRO. Both enzymes are required for PAPS (phosphoadenosine-phosphosulphate) synthesis from inorganic sulphate []. ATP sulfurylase catalyses the synthesis of adenosine-phosphosulphate APS from ATP and inorganic sulphate [].; GO: 0004781 sulfate adenylyltransferase (ATP) activity, 0000103 sulfate assimilation; PDB: 3CR8_B 1M8P_C 1I2D_B 1JHD_A 1V47_B 1X6V_B 1XNJ_A 1XJQ_B 2QJF_A 2GKS_B ....
Probab=29.60 E-value=76 Score=27.91 Aligned_cols=51 Identities=16% Similarity=0.313 Sum_probs=35.6
Q ss_pred CceeeEecchHHHHHHHHH----hCceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCC
Q 028198 32 ESTVACITGDYAMQNVILQ----MGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 32 ~~~vac~TdDfAmQNVllq----mGL~~~s~~g~~I~~~k~wvlrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
+..+..+=++|+.|.++.. +||.++.+ .+...|..|..+.+. ..||+.-..
T Consensus 125 hAg~g~~Y~~~~a~~i~~~~~~el~I~~v~~---------~~~~Yc~~~~~~~~~---~~cp~~~~~ 179 (215)
T PF01747_consen 125 HAGVGDFYDPYEAQEIFDEYAGELGIEPVPF---------PEMVYCPKCGQYVSA---KTCPHGKHH 179 (215)
T ss_dssp TT-SCBSS-TTHHHHHHHHHHHHCTSEEEE------------EEEETTTTEEEEC---GGSSTTTGG
T ss_pred CCCccccCCccHHHHHHHcCcccCCceEEec---------ceEEEEcCCCeEeec---cccCCCCCc
Confidence 4556678889999999877 67776655 355669999998764 579988775
No 304
>PRK07217 replication factor A; Reviewed
Probab=29.56 E-value=31 Score=32.25 Aligned_cols=44 Identities=11% Similarity=0.223 Sum_probs=29.3
Q ss_pred eeeeeEEEEccC--ccccccccCccccCCCCCCC--ceeEEEEEeCCC-ceE
Q 028198 64 RQLHRWILKCHA--CYTITAEIGRIFCPKCGNGG--TLRKVAVTVGEN-GIV 110 (212)
Q Consensus 64 ~~~k~wvlrC~a--C~k~~~~~~k~FCp~CG~~~--TL~Rvsvsv~~~-G~~ 110 (212)
+.--..+.||+. |.++-.. -.||.||... -..|+-..+|+. |.+
T Consensus 182 ~~GsglI~rCP~~~C~Rvl~~---g~C~~HG~ve~~~DLrik~vlDDGt~~~ 230 (311)
T PRK07217 182 QSGSGLIKRCPEEDCTRVLQN---GRCSEHGKVEGEFDLRIKGVLDDGEEVQ 230 (311)
T ss_pred eCCCCCeecCCccccCccccC---CCCCCCCCcCCceeeEEEEEEECCCCeE
Confidence 344567899999 9998743 5899999531 135666666543 443
No 305
>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=29.50 E-value=4.9 Score=34.21 Aligned_cols=15 Identities=40% Similarity=0.939 Sum_probs=8.4
Q ss_pred ccccCCCCCCCceeEE
Q 028198 85 RIFCPKCGNGGTLRKV 100 (212)
Q Consensus 85 k~FCp~CG~~~TL~Rv 100 (212)
..||.+||.+ |+..+
T Consensus 28 ~~fC~kCG~~-tI~~C 42 (158)
T PF10083_consen 28 EKFCSKCGAK-TITSC 42 (158)
T ss_pred HHHHHHhhHH-HHHHC
Confidence 4566666665 55544
No 306
>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=29.47 E-value=26 Score=31.96 Aligned_cols=14 Identities=43% Similarity=1.251 Sum_probs=5.8
Q ss_pred cccCCCCCCCceeEE
Q 028198 86 IFCPKCGNGGTLRKV 100 (212)
Q Consensus 86 ~FCp~CG~~~TL~Rv 100 (212)
.+||.||+. -|.+.
T Consensus 32 ~yCP~Cg~~-~L~~f 45 (254)
T PF06044_consen 32 MYCPNCGSK-PLSKF 45 (254)
T ss_dssp ---TTT--S-S-EE-
T ss_pred CcCCCCCCh-hHhhc
Confidence 589999997 78765
No 307
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=29.36 E-value=39 Score=24.09 Aligned_cols=22 Identities=27% Similarity=0.613 Sum_probs=13.0
Q ss_pred ccCccccccccCccccCCCCCC
Q 028198 73 CHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 73 C~aC~k~~~~~~k~FCp~CG~~ 94 (212)
|+-|..-..-.....||.||-+
T Consensus 2 Cpv~~~~~~~~v~~~Cp~cGip 23 (55)
T PF13824_consen 2 CPVCKKDLPAHVNFECPDCGIP 23 (55)
T ss_pred CCCCccccccccCCcCCCCCCc
Confidence 5555543322234579999987
No 308
>TIGR00108 eRF peptide chain release factor eRF/aRF, subunit 1. Alternative names include eRF1, SUP45, omnipotent suppressor protein 1.
Probab=28.91 E-value=44 Score=31.90 Aligned_cols=27 Identities=30% Similarity=0.722 Sum_probs=18.5
Q ss_pred eEEEEccCcccccc-------ccCccccCCCCCC
Q 028198 68 RWILKCHACYTITA-------EIGRIFCPKCGNG 94 (212)
Q Consensus 68 ~wvlrC~aC~k~~~-------~~~k~FCp~CG~~ 94 (212)
++.+||..|+.+-. +.....||.||..
T Consensus 322 r~~~r~~~~~~~~~~~~~~~~~~~~~~c~~~~~~ 355 (409)
T TIGR00108 322 RVTYKCAECGEVIEKTVRELKDKKFAICPACGQE 355 (409)
T ss_pred eEEEEcCCCCceeecccccccccccccCcccCcc
Confidence 57899999985310 1112479999986
No 309
>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=28.91 E-value=26 Score=34.13 Aligned_cols=19 Identities=37% Similarity=0.868 Sum_probs=12.2
Q ss_pred EEEccCccccccccCccccCCCCCC
Q 028198 70 ILKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 70 vlrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
.+.|..|+.+. -||+|+..
T Consensus 213 ~~~C~~Cg~~~------~C~~C~~~ 231 (505)
T TIGR00595 213 NLLCRSCGYIL------CCPNCDVS 231 (505)
T ss_pred eeEhhhCcCcc------CCCCCCCc
Confidence 46888888643 36666654
No 310
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=28.62 E-value=47 Score=26.05 Aligned_cols=18 Identities=28% Similarity=0.798 Sum_probs=10.8
Q ss_pred ccccCCCCCCCceeEEEEEeCC
Q 028198 85 RIFCPKCGNGGTLRKVAVTVGE 106 (212)
Q Consensus 85 k~FCp~CG~~~TL~Rvsvsv~~ 106 (212)
...||.||+. .|+|.++.
T Consensus 21 ~f~CP~Cge~----~v~v~~~k 38 (99)
T PRK14892 21 IFECPRCGKV----SISVKIKK 38 (99)
T ss_pred EeECCCCCCe----EeeeecCC
Confidence 4557777753 45555555
No 311
>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=28.55 E-value=52 Score=23.50 Aligned_cols=20 Identities=30% Similarity=0.640 Sum_probs=14.9
Q ss_pred cCccccCCCCCCCceeEEEEE
Q 028198 83 IGRIFCPKCGNGGTLRKVAVT 103 (212)
Q Consensus 83 ~~k~FCp~CG~~~TL~Rvsvs 103 (212)
+....||.||+. ...+|...
T Consensus 5 p~~~~CP~C~~~-~~T~v~~~ 24 (73)
T PF10601_consen 5 PVRIYCPYCQQQ-VQTRVEYK 24 (73)
T ss_pred ceeeECCCCCCE-EEEEEEEE
Confidence 346799999997 77777643
No 312
>PRK14873 primosome assembly protein PriA; Provisional
Probab=28.51 E-value=33 Score=34.85 Aligned_cols=11 Identities=36% Similarity=0.501 Sum_probs=6.6
Q ss_pred EEEEccCcccc
Q 028198 69 WILKCHACYTI 79 (212)
Q Consensus 69 wvlrC~aC~k~ 79 (212)
-.+.|..|+.+
T Consensus 382 p~l~C~~Cg~~ 392 (665)
T PRK14873 382 PSLACARCRTP 392 (665)
T ss_pred CeeEhhhCcCe
Confidence 35666666654
No 313
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=28.50 E-value=23 Score=23.50 Aligned_cols=19 Identities=21% Similarity=0.518 Sum_probs=8.5
Q ss_pred cccCCCCCCCceeEEEEEeCCC
Q 028198 86 IFCPKCGNGGTLRKVAVTVGEN 107 (212)
Q Consensus 86 ~FCp~CG~~~TL~Rvsvsv~~~ 107 (212)
.-||.||.. .|-.|..|.+
T Consensus 4 ~pCP~CGG~---DrFri~~d~~ 22 (40)
T PF08273_consen 4 GPCPICGGK---DRFRIFDDKD 22 (40)
T ss_dssp E--TTTT-T---TTEEEETT--
T ss_pred CCCCCCcCc---cccccCcCcc
Confidence 359999987 3444444433
No 314
>KOG0806 consensus Carbon-nitrogen hydrolase [Amino acid transport and metabolism]
Probab=27.97 E-value=1.3e+02 Score=28.03 Aligned_cols=94 Identities=14% Similarity=0.128 Sum_probs=59.4
Q ss_pred hHHHHHHHHHhCceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCCCceeEEEEEeCCCceEEeecCCccc-
Q 028198 41 DYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGENGIVLASRRPRIT- 119 (212)
Q Consensus 41 DfAmQNVllqmGL~~~s~~g~~I~~~k~wvlrC~aC~k~~~~~~k~FCp~CG~~~TL~Rvsvsv~~~G~~~~~~k~~~n- 119 (212)
=+.||||+.++.+.++ .|. |.+.. .|-+.+-....--||.=|-. .-|-.+-.|.||......++...
T Consensus 83 ~~~ls~va~~~~~~~i--~g~-i~~~~-------~~~k~yns~~~~~~~g~l~~--~yrk~hlFD~d~~~~~ry~e~~~~ 150 (298)
T KOG0806|consen 83 RQGLSEVAERLSCYII--GGS-IEEEA-------LGDKLYNSCADSSCPGDGLA--KYRKNHLFDTDGPGVIRYRESHLL 150 (298)
T ss_pred HHHhHHHHhhceEEEe--cCc-chhhc-------ccccccCcccccCCCcchhh--eeeeeEEeccCCccceeeeeeecc
Confidence 3679999999987765 333 33221 24444433334457766654 44555667888876554444333
Q ss_pred cccceeccCCCCCCCCCCCCCceecCCCCcc
Q 028198 120 LRGTKFSLPMPQGGRDAITKNLILREDQLPQ 150 (212)
Q Consensus 120 ~RG~~ySlPkpkgGk~~~~~~~IL~EDQ~~~ 150 (212)
..|..|.+|.+..||-| .-.|=|++.+
T Consensus 151 ~~g~~f~~~~~~~gkfG----i~IC~Di~F~ 177 (298)
T KOG0806|consen 151 SPGDQFTVVDTSYGKFG----IFICFDIRFY 177 (298)
T ss_pred CCCcCCCcccCCCCceE----EEEEeccccc
Confidence 35999999999999875 5667777543
No 315
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=27.85 E-value=26 Score=32.17 Aligned_cols=25 Identities=24% Similarity=0.764 Sum_probs=14.1
Q ss_pred EEEccCccccccccC--------ccccCCCCCC
Q 028198 70 ILKCHACYTITAEIG--------RIFCPKCGNG 94 (212)
Q Consensus 70 vlrC~aC~k~~~~~~--------k~FCp~CG~~ 94 (212)
+-||+.|.+-|...+ .--||.||+.
T Consensus 132 VSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~ 164 (278)
T PF15135_consen 132 VSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHN 164 (278)
T ss_pred cccccccccccCCCccccccceeeeeccccccc
Confidence 456777776664311 2347777763
No 316
>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=27.85 E-value=28 Score=22.51 Aligned_cols=8 Identities=63% Similarity=1.609 Sum_probs=4.7
Q ss_pred ccCCCCCC
Q 028198 87 FCPKCGNG 94 (212)
Q Consensus 87 FCp~CG~~ 94 (212)
.||.||++
T Consensus 2 ~Cp~Cg~~ 9 (39)
T PF01096_consen 2 KCPKCGHN 9 (39)
T ss_dssp --SSS-SS
T ss_pred CCcCCCCC
Confidence 59999997
No 317
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=27.83 E-value=34 Score=33.32 Aligned_cols=33 Identities=33% Similarity=0.642 Sum_probs=22.0
Q ss_pred cceeeeeEEE---EccCccccccccCc--cccCCCCCC
Q 028198 62 QIRQLHRWIL---KCHACYTITAEIGR--IFCPKCGNG 94 (212)
Q Consensus 62 ~I~~~k~wvl---rC~aC~k~~~~~~k--~FCp~CG~~ 94 (212)
+|.++-.|.. +|+-|+.......+ --||+||..
T Consensus 339 ~v~~l~~~~~~~p~Cp~Cg~~m~S~G~~g~rC~kCg~~ 376 (421)
T COG1571 339 QVLKLARYERVNPVCPRCGGRMKSAGRNGFRCKKCGTR 376 (421)
T ss_pred EEEEeeeeEEcCCCCCccCCchhhcCCCCccccccccc
Confidence 4555545654 79999987765443 459999975
No 318
>PRK14287 chaperone protein DnaJ; Provisional
Probab=27.68 E-value=1.3e+02 Score=28.15 Aligned_cols=24 Identities=25% Similarity=0.495 Sum_probs=14.9
Q ss_pred EEEccCccccccccCccccCCCCCC
Q 028198 70 ILKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 70 vlrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
...|..|.-.... .+.-|+.|+..
T Consensus 181 ~~~C~~C~G~G~~-~~~~C~~C~G~ 204 (371)
T PRK14287 181 RRVCHHCEGTGKI-IKQKCATCGGK 204 (371)
T ss_pred EEeCCCCCCCCcc-ccccCCCCCCe
Confidence 3467777654433 24558888875
No 319
>cd03361 TOPRIM_TopoIA_RevGyr TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to the ATP-dependent reverse gyrase found in archaea and thermophilic bacteria. Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=27.61 E-value=46 Score=27.81 Aligned_cols=26 Identities=31% Similarity=0.658 Sum_probs=19.5
Q ss_pred eEEEEccCccccccccCccccCCCCCC
Q 028198 68 RWILKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 68 ~wvlrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
.+..+|.+|++.+.. ....||.||.+
T Consensus 75 ~~~~~c~pc~~lF~~-~~~~cp~c~~~ 100 (170)
T cd03361 75 DSIKRCRDCGYQFTE-DSDKCPRCGSE 100 (170)
T ss_pred eEeeccCCccccccc-ccccCCcCCCc
Confidence 345689999988853 34579999975
No 320
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=27.57 E-value=43 Score=22.82 Aligned_cols=9 Identities=44% Similarity=1.087 Sum_probs=7.5
Q ss_pred cccCCCCCC
Q 028198 86 IFCPKCGNG 94 (212)
Q Consensus 86 ~FCp~CG~~ 94 (212)
.=||-||.+
T Consensus 4 kPCPFCG~~ 12 (61)
T PF14354_consen 4 KPCPFCGSA 12 (61)
T ss_pred cCCCCCCCc
Confidence 459999987
No 321
>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=27.34 E-value=28 Score=21.79 Aligned_cols=21 Identities=29% Similarity=0.814 Sum_probs=8.2
Q ss_pred ccCccccc--cccCccccCCCCC
Q 028198 73 CHACYTIT--AEIGRIFCPKCGN 93 (212)
Q Consensus 73 C~aC~k~~--~~~~k~FCp~CG~ 93 (212)
|.-|.-.+ .+.....||.||+
T Consensus 5 Cp~C~se~~y~D~~~~vCp~C~~ 27 (30)
T PF08274_consen 5 CPLCGSEYTYEDGELLVCPECGH 27 (30)
T ss_dssp -TTT-----EE-SSSEEETTTTE
T ss_pred CCCCCCcceeccCCEEeCCcccc
Confidence 55555332 3334456666665
No 322
>COG2405 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=27.31 E-value=45 Score=28.39 Aligned_cols=30 Identities=23% Similarity=0.337 Sum_probs=25.8
Q ss_pred Ccee-eEecchHHHHHHHHHhCceeecCCCC
Q 028198 32 ESTV-ACITGDYAMQNVILQMGLRLLAPGGM 61 (212)
Q Consensus 32 ~~~v-ac~TdDfAmQNVllqmGL~~~s~~g~ 61 (212)
+.++ -+++||+.=.|++..|||.+.++-|-
T Consensus 85 e~~ad~Ll~Ddr~aR~~A~~lgL~V~GtlGv 115 (157)
T COG2405 85 ELKADLLLMDDRDARNVAKSLGLKVTGTLGV 115 (157)
T ss_pred HcCCCeeeeccHHHHHHHHHcCCeeeehhHH
Confidence 4566 78999999999999999999877654
No 323
>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=27.22 E-value=22 Score=22.88 Aligned_cols=25 Identities=24% Similarity=0.582 Sum_probs=14.4
Q ss_pred EEEccCcccccc--ccCccccCCCCCC
Q 028198 70 ILKCHACYTITA--EIGRIFCPKCGNG 94 (212)
Q Consensus 70 vlrC~aC~k~~~--~~~k~FCp~CG~~ 94 (212)
..+|.-|..... +-.+.+|-.||+.
T Consensus 8 ~~~C~~C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 8 NEPCPVCGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CCcCCCCCCeEeEccCCEEEhhhCceE
Confidence 345777775432 2346677777763
No 324
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=27.16 E-value=54 Score=24.01 Aligned_cols=23 Identities=30% Similarity=0.440 Sum_probs=16.1
Q ss_pred cccCCCCCCCceeEEEEEeCCCceE
Q 028198 86 IFCPKCGNGGTLRKVAVTVGENGIV 110 (212)
Q Consensus 86 ~FCp~CG~~~TL~Rvsvsv~~~G~~ 110 (212)
..|+.||.+ |.--.+.+-.+|.+
T Consensus 79 ~~C~vC~k~--l~~~~f~~~p~~~v 101 (109)
T PF10367_consen 79 TKCSVCGKP--LGNSVFVVFPCGHV 101 (109)
T ss_pred CCccCcCCc--CCCceEEEeCCCeE
Confidence 469999997 54455566777743
No 325
>COG5533 UBP5 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=27.09 E-value=76 Score=30.45 Aligned_cols=60 Identities=20% Similarity=0.401 Sum_probs=34.8
Q ss_pred cccCCCCCCC-ceeEEEEEeCCCceEEeecCCccccccceeccCCCCCCCCCCCCCceecCC
Q 028198 86 IFCPKCGNGG-TLRKVAVTVGENGIVLASRRPRITLRGTKFSLPMPQGGRDAITKNLILRED 146 (212)
Q Consensus 86 ~FCp~CG~~~-TL~Rvsvsv~~~G~~~~~~k~~~n~RG~~ySlPkpkgGk~~~~~~~IL~ED 146 (212)
--||+||-+- .-+++.+++-.+--++.-.|+.+..-| +|+|-.|.|=+.-.....+..||
T Consensus 285 W~CpkC~~k~ss~K~~~I~~lP~~LII~i~RF~i~V~~-~~kiD~p~gw~~~~~~e~~v~~~ 345 (415)
T COG5533 285 WRCPKCGRKESSRKRMEILVLPDVLIIHISRFHISVMG-RKKIDTPQGWKNTASVEVNVTLL 345 (415)
T ss_pred ccCchhcccccchheEEEEecCceEEEEeeeeeEEeec-ccccCCCcchhccCCceeccccc
Confidence 3599999542 336677777776544444455544444 46777887765432233344444
No 326
>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=27.08 E-value=39 Score=28.62 Aligned_cols=36 Identities=19% Similarity=0.400 Sum_probs=19.6
Q ss_pred CCCcceeeeeEEEEccCccccccc------------cCccccCCCCCC
Q 028198 59 GGMQIRQLHRWILKCHACYTITAE------------IGRIFCPKCGNG 94 (212)
Q Consensus 59 ~g~~I~~~k~wvlrC~aC~k~~~~------------~~k~FCp~CG~~ 94 (212)
+..+-+....+.++|+.|.+.+.- .....||+|+..
T Consensus 7 d~erf~~c~~l~~~C~~C~~~~~f~g~~~~~~~~~~~~~~~C~~C~~~ 54 (188)
T PF08996_consen 7 DEERFKDCEPLKLTCPSCGTEFEFPGVFEEDGDDVSPSGLQCPNCSTP 54 (188)
T ss_dssp -TTTTTT---EEEE-TTT--EEEE-SSS--SSEEEETTEEEETTT--B
T ss_pred HHHHhcCCCceEeECCCCCCCccccccccCCccccccCcCcCCCCCCc
Confidence 445677888999999999987631 224679999975
No 327
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=27.07 E-value=46 Score=31.03 Aligned_cols=12 Identities=50% Similarity=1.112 Sum_probs=9.6
Q ss_pred CccccCCCCCCC
Q 028198 84 GRIFCPKCGNGG 95 (212)
Q Consensus 84 ~k~FCp~CG~~~ 95 (212)
.+.+||+||+..
T Consensus 186 ~~~~CPvCGs~P 197 (309)
T PRK03564 186 QRQFCPVCGSMP 197 (309)
T ss_pred CCCCCCCCCCcc
Confidence 368999999873
No 328
>PF14949 ARF7EP_C: ARF7 effector protein C-terminus
Probab=27.06 E-value=35 Score=27.11 Aligned_cols=16 Identities=44% Similarity=1.092 Sum_probs=12.3
Q ss_pred EEccCccccccccCccccCCCCCC
Q 028198 71 LKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 71 lrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
.-|.|||- -||+||+.
T Consensus 68 ~~C~GC~~--------PC~~C~S~ 83 (103)
T PF14949_consen 68 EDCPGCHY--------PCPKCGSR 83 (103)
T ss_pred CCCCCccc--------cCCCCCCC
Confidence 45899983 39999985
No 329
>PF03243 MerB: Alkylmercury lyase; InterPro: IPR004927 Mercury is a highly toxic metal. Toxicity can result from three different mercurial forms: elemental, inorganic ion and organomercurial compounds. The ability of bacteria to detoxify mercurial compounds by reduction and volatilisation is conferred by the Mer genes, which are usually plasmid encoded (although chromosome resistance determinants have also occasionally been identified) []. Organomercurial lyase (MerB), also known as alkylmercury lyase, mediates the first of the two steps in the microbial detoxification of organomercurial salts (the other catalysed by mercuric reductase). Organomercurial lyase catalyses the protonolysis of the C-Hg bond in a wide range of organomercurial salts (primary, secondary, tertiary, alkyl, vinyl, allyl and aryl) to Hg(II) and the respective organic compound []: RHg(+) + H(+) = RH + Hg(2+) Hg(II) is subsequently detoxified by mercuric reductase. The enzyme has been purified to homogeneity in Escherichia coli and has been found to be a 22.4kDa monomer with no detectable cofactors or metal ions.; GO: 0018836 alkylmercury lyase activity, 0046413 organomercury catabolic process; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=26.99 E-value=58 Score=25.98 Aligned_cols=37 Identities=27% Similarity=0.442 Sum_probs=18.2
Q ss_pred cccCCCCCCCceeEEEEEeCCCceEEeecCCccccccceeccCCCCCC
Q 028198 86 IFCPKCGNGGTLRKVAVTVGENGIVLASRRPRITLRGTKFSLPMPQGG 133 (212)
Q Consensus 86 ~FCp~CG~~~TL~Rvsvsv~~~G~~~~~~k~~~n~RG~~ySlPkpkgG 133 (212)
-.||.||.+ |.++|+.+|... ++..+...|++.|..+
T Consensus 40 S~cp~tg~p-----I~l~v~~~~i~~------~~P~~~vV~~~~~~~~ 76 (127)
T PF03243_consen 40 SRCPATGEP-----IRLTVDPGGITD------VEPATAVVSFVDPDAG 76 (127)
T ss_dssp EE-TTT--E-----EEEEE-SSSEEE------EESTT-EEEE----TT
T ss_pred EcCCCCCCe-----EEEEEeCCceee------cCCCCEEEEecCcccc
Confidence 369999987 778888877432 3445666677766555
No 330
>PRK14894 glycyl-tRNA synthetase; Provisional
Probab=26.75 E-value=40 Score=33.81 Aligned_cols=36 Identities=19% Similarity=0.446 Sum_probs=24.4
Q ss_pred ceeeeeEEEEccCccccccc-cCccccCCCCCCCceeE
Q 028198 63 IRQLHRWILKCHACYTITAE-IGRIFCPKCGNGGTLRK 99 (212)
Q Consensus 63 I~~~k~wvlrC~aC~k~~~~-~~k~FCp~CG~~~TL~R 99 (212)
+....-|+..|.-|++.+.- --...||.||+. .|..
T Consensus 81 ~~~F~DpmV~CkkCk~ryRaD~LiikCP~CGs~-dLTe 117 (539)
T PRK14894 81 EETFNDPLVDCRDCKMRWRADHIQGVCPNCGSR-DLTE 117 (539)
T ss_pred CCCCCCceeECCCCCccccCccceeeCCCCCCc-CCCc
Confidence 44555678999999988752 113469999974 4543
No 331
>PF02639 DUF188: Uncharacterized BCR, YaiI/YqxD family COG1671; InterPro: IPR003791 This entry describes proteins of unknown function.
Probab=26.71 E-value=73 Score=25.86 Aligned_cols=30 Identities=27% Similarity=0.419 Sum_probs=26.3
Q ss_pred eeeEecchHHHHHHHHHhCceeecCCCCcc
Q 028198 34 TVACITGDYAMQNVILQMGLRLLAPGGMQI 63 (212)
Q Consensus 34 ~vac~TdDfAmQNVllqmGL~~~s~~g~~I 63 (212)
.=.++|.||.|-..++.-|..+++..|...
T Consensus 52 gDiVITqDigLA~~~l~Kga~vl~~rG~~y 81 (130)
T PF02639_consen 52 GDIVITQDIGLASLLLAKGAYVLNPRGKEY 81 (130)
T ss_pred CCEEEECCHHHHHHHHHCCCEEECCCCCCC
Confidence 346899999999999999999999998743
No 332
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=26.48 E-value=62 Score=22.75 Aligned_cols=18 Identities=33% Similarity=0.968 Sum_probs=14.3
Q ss_pred ccccCCCCCCCceeEEEEE
Q 028198 85 RIFCPKCGNGGTLRKVAVT 103 (212)
Q Consensus 85 k~FCp~CG~~~TL~Rvsvs 103 (212)
..+||.|++. ..++|...
T Consensus 3 ~i~Cp~C~~~-~~T~v~~~ 20 (67)
T smart00714 3 QLFCPRCQNN-VTTRVETE 20 (67)
T ss_pred ceECCCCCCE-EEEEEEEE
Confidence 4689999997 77777754
No 333
>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=26.39 E-value=31 Score=28.54 Aligned_cols=11 Identities=45% Similarity=1.343 Sum_probs=9.0
Q ss_pred cccCCCCCCCc
Q 028198 86 IFCPKCGNGGT 96 (212)
Q Consensus 86 ~FCp~CG~~~T 96 (212)
.-||.||+..|
T Consensus 106 ~~cp~c~s~~t 116 (146)
T TIGR02159 106 VQCPRCGSADT 116 (146)
T ss_pred CcCCCCCCCCc
Confidence 68999999744
No 334
>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=26.28 E-value=42 Score=25.16 Aligned_cols=22 Identities=32% Similarity=0.745 Sum_probs=10.3
Q ss_pred ccccCCCCCCCceeEEEEEeCCC-ce
Q 028198 85 RIFCPKCGNGGTLRKVAVTVGEN-GI 109 (212)
Q Consensus 85 k~FCp~CG~~~TL~Rvsvsv~~~-G~ 109 (212)
.--||.||+. .-|.|.++.. |.
T Consensus 22 ~F~CPfC~~~---~sV~v~idkk~~~ 44 (81)
T PF05129_consen 22 VFDCPFCNHE---KSVSVKIDKKEGI 44 (81)
T ss_dssp ----TTT--S---S-EEEEEETTTTE
T ss_pred eEcCCcCCCC---CeEEEEEEccCCE
Confidence 3459999976 2477777754 44
No 335
>smart00532 LIGANc Ligase N family.
Probab=25.92 E-value=81 Score=30.61 Aligned_cols=46 Identities=17% Similarity=0.307 Sum_probs=27.7
Q ss_pred HHHHHhCcee-----ecCCCCcceeeeeEEEEccCccc--cccccCccccCCCCCC
Q 028198 46 NVILQMGLRL-----LAPGGMQIRQLHRWILKCHACYT--ITAEIGRIFCPKCGNG 94 (212)
Q Consensus 46 NVllqmGL~~-----~s~~g~~I~~~k~wvlrC~aC~k--~~~~~~k~FCp~CG~~ 94 (212)
+-+.++||.+ +.-.|..|-++-.-+. ...... .+. + -.+||.||++
T Consensus 356 ~~i~~~~i~iGd~V~V~raGdVIP~I~~vv~-~~r~~~~~~~~-~-P~~CP~C~s~ 408 (441)
T smart00532 356 DEIEEKDIRIGDTVVVRKAGDVIPKVVGVVK-EKRPGDEREIE-M-PTHCPSCGSE 408 (441)
T ss_pred HHHHHcCCCCCCEEEEEECCCcCcceeeccc-ccCCCCCccCc-C-CCCCCCCCCE
Confidence 4467788876 4456888888766443 111111 111 1 2689999997
No 336
>PRK14301 chaperone protein DnaJ; Provisional
Probab=25.72 E-value=2.6e+02 Score=26.18 Aligned_cols=9 Identities=44% Similarity=1.018 Sum_probs=5.2
Q ss_pred cccCCCCCC
Q 028198 86 IFCPKCGNG 94 (212)
Q Consensus 86 ~FCp~CG~~ 94 (212)
..|+.|.+.
T Consensus 198 ~~C~~C~G~ 206 (373)
T PRK14301 198 HPCPKCKGS 206 (373)
T ss_pred CCCCCCCCC
Confidence 346666654
No 337
>KOG3022 consensus Predicted ATPase, nucleotide-binding [Cell cycle control, cell division, chromosome partitioning]
Probab=25.57 E-value=71 Score=29.87 Aligned_cols=46 Identities=24% Similarity=0.527 Sum_probs=28.5
Q ss_pred eeeEecc--hHHHHHHHHHhCceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCC
Q 028198 34 TVACITG--DYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 34 ~vac~Td--DfAmQNVllqmGL~~~s~~g~~I~~~k~wvlrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
.++++|| ++|+|-|.+.+++=- =.+ | .+..+-.+|..-.||+||+.
T Consensus 184 gAviVTTPQ~vAl~Dv~K~i~fc~--K~~--I-----------~ilGvVENMs~f~Cp~C~~~ 231 (300)
T KOG3022|consen 184 GAVIVTTPQEVALQDVRKEIDFCR--KAG--I-----------PILGVVENMSGFVCPKCGHS 231 (300)
T ss_pred ceEEEeCchhhhhHHHHhhhhhhh--hcC--C-----------ceEEEEeccccccCCCCCCc
Confidence 3567776 789999888765210 000 0 11223456778889999997
No 338
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=25.42 E-value=33 Score=37.27 Aligned_cols=29 Identities=31% Similarity=0.527 Sum_probs=17.7
Q ss_pred EEccCccccccccC-ccccCCCCCCCceeEE
Q 028198 71 LKCHACYTITAEIG-RIFCPKCGNGGTLRKV 100 (212)
Q Consensus 71 lrC~aC~k~~~~~~-k~FCp~CG~~~TL~Rv 100 (212)
+.| +|+|...... -.+|+.||-.-|..+|
T Consensus 58 ~eC-~Cgkyk~~~~~~~~C~~cgve~~~~~v 87 (1156)
T PRK00566 58 YEC-LCGKYKRVRYKGIICERCGVEVTRSKV 87 (1156)
T ss_pred cEE-eCccccccCcCCcCCCCCCceeeechh
Confidence 467 7887443211 3799999987333333
No 339
>PRK14283 chaperone protein DnaJ; Provisional
Probab=25.23 E-value=2.7e+02 Score=26.07 Aligned_cols=27 Identities=19% Similarity=0.373 Sum_probs=16.8
Q ss_pred EEEEccCccccccccCccccCCCCCCCc
Q 028198 69 WILKCHACYTITAEIGRIFCPKCGNGGT 96 (212)
Q Consensus 69 wvlrC~aC~k~~~~~~k~FCp~CG~~~T 96 (212)
....|..|.-.... .+..|..|.+.++
T Consensus 188 ~~~~C~~C~G~G~~-~~~~C~~C~G~g~ 214 (378)
T PRK14283 188 NVTTCPDCQGEGKI-VEKPCSNCHGKGV 214 (378)
T ss_pred EEEECCCCCcccee-cCCCCCCCCCcee
Confidence 34577777654433 2456999988633
No 340
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=25.12 E-value=56 Score=21.21 Aligned_cols=22 Identities=23% Similarity=0.530 Sum_probs=14.5
Q ss_pred EccCccccccccCccccCCCCC
Q 028198 72 KCHACYTITAEIGRIFCPKCGN 93 (212)
Q Consensus 72 rC~aC~k~~~~~~k~FCp~CG~ 93 (212)
+|.-|++...+....+|..|+.
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~ 22 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNR 22 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSC
T ss_pred eCcCCCCcCCCCCeEEcCCCCh
Confidence 4777777554445677877775
No 341
>COG1040 ComFC Predicted amidophosphoribosyltransferases [General function prediction only]
Probab=24.74 E-value=18 Score=31.61 Aligned_cols=27 Identities=33% Similarity=0.659 Sum_probs=20.7
Q ss_pred EEccCccccccccCccccCCCCCCCceeEE
Q 028198 71 LKCHACYTITAEIGRIFCPKCGNGGTLRKV 100 (212)
Q Consensus 71 lrC~aC~k~~~~~~k~FCp~CG~~~TL~Rv 100 (212)
..|.+|++-...... +|+.||.+ |...
T Consensus 25 ~~C~~C~~~~~~~~~-~C~~C~~~--l~~~ 51 (225)
T COG1040 25 GLCSGCQADLPLIGN-LCPLCGLP--LSSH 51 (225)
T ss_pred CcChhhhhchhHHHh-hhHhhhCh--hccc
Confidence 579999987765433 89999997 5544
No 342
>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=24.67 E-value=39 Score=23.48 Aligned_cols=22 Identities=27% Similarity=0.667 Sum_probs=7.1
Q ss_pred EccCccccccccC-ccccCCCCC
Q 028198 72 KCHACYTITAEIG-RIFCPKCGN 93 (212)
Q Consensus 72 rC~aC~k~~~~~~-k~FCp~CG~ 93 (212)
.|..|.+.+.-.. +..|..||.
T Consensus 11 ~C~~C~~~F~~~~rrhhCr~CG~ 33 (69)
T PF01363_consen 11 NCMICGKKFSLFRRRHHCRNCGR 33 (69)
T ss_dssp B-TTT--B-BSSS-EEE-TTT--
T ss_pred cCcCcCCcCCCceeeEccCCCCC
Confidence 4555655554322 455555554
No 343
>PRK14296 chaperone protein DnaJ; Provisional
Probab=24.60 E-value=1.9e+02 Score=27.17 Aligned_cols=9 Identities=22% Similarity=0.567 Sum_probs=5.8
Q ss_pred cccCCCCCC
Q 028198 86 IFCPKCGNG 94 (212)
Q Consensus 86 ~FCp~CG~~ 94 (212)
..|+.|.+.
T Consensus 207 ~~C~~C~G~ 215 (372)
T PRK14296 207 NKCKNCKGK 215 (372)
T ss_pred ccccCCCCc
Confidence 447777765
No 344
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=24.48 E-value=31 Score=25.95 Aligned_cols=23 Identities=30% Similarity=0.554 Sum_probs=14.8
Q ss_pred cccCCCCCCCceeEEE-EEeCCCceE
Q 028198 86 IFCPKCGNGGTLRKVA-VTVGENGIV 110 (212)
Q Consensus 86 ~FCp~CG~~~TL~Rvs-vsv~~~G~~ 110 (212)
+||-+||-+ |..-. ...++||..
T Consensus 1 k~CQSCGMP--l~~~~~~Gte~dGs~ 24 (81)
T PF12674_consen 1 KFCQSCGMP--LSKDEDFGTEADGSK 24 (81)
T ss_pred CcCCcCcCc--cCCccccccccCCCC
Confidence 489999998 65444 334455643
No 345
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=24.40 E-value=23 Score=33.99 Aligned_cols=36 Identities=25% Similarity=0.582 Sum_probs=25.6
Q ss_pred CCcceeeeeEEEEccCccccccccCccccCCCCCCCcee
Q 028198 60 GMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLR 98 (212)
Q Consensus 60 g~~I~~~k~wvlrC~aC~k~~~~~~k~FCp~CG~~~TL~ 98 (212)
|.+|++ +-.|||+-|+...... .--||.|-.=.|++
T Consensus 346 ge~l~~--~~~YRC~~CGF~a~~l-~W~CPsC~~W~Tik 381 (389)
T COG2956 346 GEQLRR--KPRYRCQNCGFTAHTL-YWHCPSCRAWETIK 381 (389)
T ss_pred HHHHhh--cCCceecccCCcceee-eeeCCCcccccccC
Confidence 455555 7889999999665443 35699998765654
No 346
>PHA02325 hypothetical protein
Probab=24.34 E-value=35 Score=25.42 Aligned_cols=11 Identities=45% Similarity=1.147 Sum_probs=8.7
Q ss_pred CccccCCCCCC
Q 028198 84 GRIFCPKCGNG 94 (212)
Q Consensus 84 ~k~FCp~CG~~ 94 (212)
....||+||..
T Consensus 2 ~~k~CPkC~A~ 12 (72)
T PHA02325 2 DTKICPKCGAR 12 (72)
T ss_pred CccccCccCCE
Confidence 45689999975
No 347
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction mechanisms]
Probab=24.22 E-value=17 Score=31.45 Aligned_cols=50 Identities=24% Similarity=0.417 Sum_probs=29.5
Q ss_pred hHHHHHHHHHhCceeecC-CCCcceeeeeEEEEccCccccccc---cCccccCCCCC
Q 028198 41 DYAMQNVILQMGLRLLAP-GGMQIRQLHRWILKCHACYTITAE---IGRIFCPKCGN 93 (212)
Q Consensus 41 DfAmQNVllqmGL~~~s~-~g~~I~~~k~wvlrC~aC~k~~~~---~~k~FCp~CG~ 93 (212)
=|+|+|||..+ |..+.. .+...... . .++|+-|+.+|.+ ..+.=|..|=.
T Consensus 47 ~fs~~~~ls~~-l~~~~t~~~~~~~~~-e-~l~C~~C~~Tfk~f~~~g~fGCaeCY~ 100 (176)
T COG3880 47 VFSIHNVLSGE-LDNLKTKWQIEQEDE-E-LLGCHNCGMTFKEFIQSGLFGCAECYK 100 (176)
T ss_pred chhHHHHHHHH-HhccccccchhhhHH-H-HhcCccccccHHHHHHhcccchHHHHH
Confidence 48999998765 333322 12111221 2 7899999988875 22333888864
No 348
>TIGR03670 rpoB_arch DNA-directed RNA polymerase subunit B. This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
Probab=24.21 E-value=54 Score=33.09 Aligned_cols=31 Identities=35% Similarity=0.867 Sum_probs=18.7
Q ss_pred EEEccCccccccc---cCccccCCCCCCCceeEE
Q 028198 70 ILKCHACYTITAE---IGRIFCPKCGNGGTLRKV 100 (212)
Q Consensus 70 vlrC~aC~k~~~~---~~k~FCp~CG~~~TL~Rv 100 (212)
++.|..|+.+... ....+|..|++.+.+.+|
T Consensus 538 ~~vC~~CG~~~~~~~~~~~~~C~~c~~~~~i~~v 571 (599)
T TIGR03670 538 VYVCENCGHIAWEDKRKGTAYCPVCGETGDISPV 571 (599)
T ss_pred EEeecccCceeehhcccCceeccccCCCCceeee
Confidence 3568888877532 124568888875334444
No 349
>PRK14285 chaperone protein DnaJ; Provisional
Probab=23.97 E-value=3.2e+02 Score=25.49 Aligned_cols=9 Identities=22% Similarity=0.523 Sum_probs=5.1
Q ss_pred cccCCCCCC
Q 028198 86 IFCPKCGNG 94 (212)
Q Consensus 86 ~FCp~CG~~ 94 (212)
..|+.|.+.
T Consensus 200 ~~C~~C~G~ 208 (365)
T PRK14285 200 NPCKSCKGK 208 (365)
T ss_pred CCCCCCCCC
Confidence 346666655
No 350
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=23.92 E-value=48 Score=33.22 Aligned_cols=30 Identities=30% Similarity=0.442 Sum_probs=23.5
Q ss_pred ceeeeeEEEEccCccccccccC-ccccCCCC
Q 028198 63 IRQLHRWILKCHACYTITAEIG-RIFCPKCG 92 (212)
Q Consensus 63 I~~~k~wvlrC~aC~k~~~~~~-k~FCp~CG 92 (212)
|..-..=.+.|..|.+..++.. ...||.||
T Consensus 119 I~~~~~~~~Yc~~~e~fl~dr~v~g~cp~cg 149 (558)
T COG0143 119 IYLREYEGLYCVSCERFLPDRYVEGTCPKCG 149 (558)
T ss_pred EeccceeeeEcccccccccchheeccCCCcC
Confidence 5444455689999999988755 78899999
No 351
>PF04032 Rpr2: RNAse P Rpr2/Rpp21/SNM1 subunit domain; InterPro: IPR007175 This family contains a ribonuclease P subunit of human and yeast. Other members of the family include the probable archaeal homologues. This subunit possibly binds the precursor tRNA [].; PDB: 2K3R_A 2KI7_B 2ZAE_B 1X0T_A.
Probab=23.78 E-value=40 Score=24.23 Aligned_cols=13 Identities=54% Similarity=1.032 Sum_probs=6.9
Q ss_pred ccCccccCCCCCC
Q 028198 82 EIGRIFCPKCGNG 94 (212)
Q Consensus 82 ~~~k~FCp~CG~~ 94 (212)
+..+.||..||..
T Consensus 43 ~~kr~~Ck~C~~~ 55 (85)
T PF04032_consen 43 EIKRTICKKCGSL 55 (85)
T ss_dssp TCCCTB-TTT--B
T ss_pred HHhcccccCCCCE
Confidence 3456799999974
No 352
>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=23.68 E-value=30 Score=23.46 Aligned_cols=8 Identities=50% Similarity=1.373 Sum_probs=4.3
Q ss_pred ccCCCCCC
Q 028198 87 FCPKCGNG 94 (212)
Q Consensus 87 FCp~CG~~ 94 (212)
-||.||.+
T Consensus 22 ~CPlC~r~ 29 (54)
T PF04423_consen 22 CCPLCGRP 29 (54)
T ss_dssp E-TTT--E
T ss_pred cCCCCCCC
Confidence 79999986
No 353
>PRK14284 chaperone protein DnaJ; Provisional
Probab=23.66 E-value=2.7e+02 Score=26.21 Aligned_cols=11 Identities=27% Similarity=0.323 Sum_probs=5.3
Q ss_pred CceecCCCCcc
Q 028198 140 NLILREDQLPQ 150 (212)
Q Consensus 140 ~~IL~EDQ~~~ 150 (212)
++|+.=.+.++
T Consensus 260 DL~v~i~v~~h 270 (391)
T PRK14284 260 DLYVFIDVEPH 270 (391)
T ss_pred CEEEEEEEecC
Confidence 55554444443
No 354
>COG5319 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.52 E-value=37 Score=28.38 Aligned_cols=32 Identities=31% Similarity=0.693 Sum_probs=19.6
Q ss_pred eeEEEEccCccccc------------cccCccccCCCCCCCceeE
Q 028198 67 HRWILKCHACYTIT------------AEIGRIFCPKCGNGGTLRK 99 (212)
Q Consensus 67 k~wvlrC~aC~k~~------------~~~~k~FCp~CG~~~TL~R 99 (212)
+.|-|+|---.++. ..+....||.||+. ++.|
T Consensus 2 i~y~L~Cd~~HeFEGWF~ssaDfd~Q~~rgLv~CPvCgs~-~VsK 45 (142)
T COG5319 2 IRYALRCDKGHEFEGWFGSSADFDRQRERGLVTCPVCGST-EVSK 45 (142)
T ss_pred ceeeeeccCCCcccccccCchhHHHHHHcCceeCCCCCcH-HHHH
Confidence 45677775443321 12456789999996 5543
No 355
>PRK10546 pyrimidine (deoxy)nucleoside triphosphate pyrophosphohydrolase; Provisional
Probab=23.43 E-value=1.4e+02 Score=22.58 Aligned_cols=35 Identities=23% Similarity=0.494 Sum_probs=23.6
Q ss_pred eeEEEEEeCCCceEEeecCCccccccceeccCCCCCCC
Q 028198 97 LRKVAVTVGENGIVLASRRPRITLRGTKFSLPMPQGGR 134 (212)
Q Consensus 97 L~Rvsvsv~~~G~~~~~~k~~~n~RG~~ySlPkpkgGk 134 (212)
+..|++-+..+|.+++.+|+.-..-+..|++| ||+
T Consensus 4 ~~~~~~ii~~~~~vLL~~R~~~~~~~g~w~~P---gG~ 38 (135)
T PRK10546 4 IDVVAAIIERDGKILLAQRPAHSDQAGLWEFA---GGK 38 (135)
T ss_pred EEEEEEEEecCCEEEEEEccCCCCCCCcEECC---ccc
Confidence 55666667778888777665333456788888 554
No 356
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 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 RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=23.31 E-value=19 Score=25.24 Aligned_cols=23 Identities=30% Similarity=0.683 Sum_probs=15.2
Q ss_pred EEccCccccccccCccccCCCCCC
Q 028198 71 LKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 71 lrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
|-|..|-.+--.. -++||.||.+
T Consensus 22 YLCl~CLt~ml~~-s~~C~iC~~~ 44 (50)
T PF03854_consen 22 YLCLNCLTLMLSR-SDRCPICGKP 44 (50)
T ss_dssp EEEHHHHHHT-SS-SSEETTTTEE
T ss_pred hHHHHHHHHHhcc-ccCCCcccCc
Confidence 5667776554332 4799999986
No 357
>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=23.18 E-value=72 Score=20.83 Aligned_cols=20 Identities=35% Similarity=0.589 Sum_probs=8.6
Q ss_pred cccCCCCCCCceeEEEEEeCCCceE
Q 028198 86 IFCPKCGNGGTLRKVAVTVGENGIV 110 (212)
Q Consensus 86 ~FCp~CG~~~TL~Rvsvsv~~~G~~ 110 (212)
..|.+|||- |.|..+..|.+
T Consensus 7 YkC~~CGni-----Vev~~~g~g~l 26 (36)
T PF06397_consen 7 YKCEHCGNI-----VEVVHDGGGPL 26 (36)
T ss_dssp EE-TTT--E-----EEEEE--SS-E
T ss_pred EEccCCCCE-----EEEEECCCCCE
Confidence 458899984 55555555544
No 358
>CHL00018 rpoC1 RNA polymerase beta' subunit
Probab=23.16 E-value=30 Score=35.53 Aligned_cols=32 Identities=28% Similarity=0.456 Sum_probs=17.8
Q ss_pred eeeEEEEccCccccccc----cCccccCCCCCCCceeEE
Q 028198 66 LHRWILKCHACYTITAE----IGRIFCPKCGNGGTLRKV 100 (212)
Q Consensus 66 ~k~wvlrC~aC~k~~~~----~~k~FCp~CG~~~TL~Rv 100 (212)
++.| .| +|++.-.. ....||+.||-.=|..||
T Consensus 64 ~k~~--~C-~CGkyk~~~~~~~~~~~C~~CgVE~t~s~v 99 (663)
T CHL00018 64 IKSG--IC-ACGNYRVIGDEKEDPKFCEQCGVEFTDSRV 99 (663)
T ss_pred CcCC--EE-eCCCccccCccccCCCccCCcCCEechhhh
Confidence 3444 45 66653321 124699999976344443
No 359
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=23.12 E-value=77 Score=28.06 Aligned_cols=12 Identities=25% Similarity=0.241 Sum_probs=8.0
Q ss_pred eeEEEEEeCCCc
Q 028198 97 LRKVAVTVGENG 108 (212)
Q Consensus 97 L~Rvsvsv~~~G 108 (212)
+.+|.|.|+..+
T Consensus 49 ~~~v~viVS~~~ 60 (201)
T COG1326 49 PVRVRVIVSRHE 60 (201)
T ss_pred cceEEEEEecCC
Confidence 466777777665
No 360
>PRK14293 chaperone protein DnaJ; Provisional
Probab=22.99 E-value=2.8e+02 Score=25.91 Aligned_cols=26 Identities=23% Similarity=0.529 Sum_probs=16.9
Q ss_pred EEEccCccccccccCccccCCCCCCCc
Q 028198 70 ILKCHACYTITAEIGRIFCPKCGNGGT 96 (212)
Q Consensus 70 vlrC~aC~k~~~~~~k~FCp~CG~~~T 96 (212)
...|..|.=.... .+..|+.|.+.++
T Consensus 186 ~~~C~~C~G~G~~-~~~~C~~C~G~g~ 211 (374)
T PRK14293 186 VSECPTCNGTGQV-IEDPCDACGGQGV 211 (374)
T ss_pred EeeCCCCCcceeE-eccCCCCCCCCcc
Confidence 4678888654443 2456999988633
No 361
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=22.81 E-value=38 Score=26.76 Aligned_cols=11 Identities=45% Similarity=0.866 Sum_probs=9.0
Q ss_pred CccccCCCCCC
Q 028198 84 GRIFCPKCGNG 94 (212)
Q Consensus 84 ~k~FCp~CG~~ 94 (212)
...+||.||-+
T Consensus 2 lLI~CP~Cg~R 12 (97)
T COG4311 2 LLIPCPYCGER 12 (97)
T ss_pred ceecCCCCCCC
Confidence 35789999986
No 362
>PRK10445 endonuclease VIII; Provisional
Probab=22.27 E-value=56 Score=29.15 Aligned_cols=16 Identities=25% Similarity=0.636 Sum_probs=12.5
Q ss_pred ccccCCCCCCCceeEEEE
Q 028198 85 RIFCPKCGNGGTLRKVAV 102 (212)
Q Consensus 85 k~FCp~CG~~~TL~Rvsv 102 (212)
..-||.||.+ |.++.+
T Consensus 235 g~~Cp~Cg~~--I~~~~~ 250 (263)
T PRK10445 235 GEACERCGGI--IEKTTL 250 (263)
T ss_pred CCCCCCCCCE--eEEEEE
Confidence 4679999985 887775
No 363
>PF02132 RecR: RecR protein; InterPro: IPR023628 The bacterial protein RecR seems to play a role in a recombinational process of DNA repair []. It may act with RecF and RecO. RecR's structure consists of a N-terminal helix-hairpin-helix (HhH) motif, followed by a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif []. This entry represents the C4-type zinc finger.; PDB: 1VDD_D 2V1C_B.
Probab=22.25 E-value=7.2 Score=25.49 Aligned_cols=29 Identities=21% Similarity=0.486 Sum_probs=16.6
Q ss_pred ceeeeeEEEEccCccccccccCccccCCCCCC
Q 028198 63 IRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 63 I~~~k~wvlrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
|..++.-+..|.-|+.++.. ..|+.|-++
T Consensus 10 l~~~~~~i~~C~~C~nlse~---~~C~IC~d~ 38 (41)
T PF02132_consen 10 LKEAKENIKFCSICGNLSEE---DPCEICSDP 38 (41)
T ss_dssp HHHHHHH-EE-SSS--EESS---SS-HHHH-T
T ss_pred HHHHHHcCCccCCCCCcCCC---CcCcCCCCC
Confidence 44556667889999988875 579998764
No 364
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=22.24 E-value=57 Score=29.23 Aligned_cols=16 Identities=31% Similarity=0.603 Sum_probs=12.2
Q ss_pred ccccCCCCCCCceeEEEE
Q 028198 85 RIFCPKCGNGGTLRKVAV 102 (212)
Q Consensus 85 k~FCp~CG~~~TL~Rvsv 102 (212)
..-||.||.+ |.++.+
T Consensus 244 g~pCprCG~~--I~~~~~ 259 (272)
T PRK14810 244 GEPCLNCKTP--IRRVVV 259 (272)
T ss_pred CCcCCCCCCe--eEEEEE
Confidence 3579999975 877764
No 365
>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=22.06 E-value=76 Score=26.58 Aligned_cols=13 Identities=31% Similarity=1.140 Sum_probs=8.5
Q ss_pred ccCCCCCCCceeEE
Q 028198 87 FCPKCGNGGTLRKV 100 (212)
Q Consensus 87 FCp~CG~~~TL~Rv 100 (212)
-||.||.+ ...|+
T Consensus 3 ~Cp~C~~~-~~~~~ 15 (161)
T PF03367_consen 3 LCPNCGEN-GTTRI 15 (161)
T ss_dssp E-TTTSSC-CEEEE
T ss_pred cCCCCCCC-cEEEE
Confidence 59999988 45555
No 366
>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=22.06 E-value=67 Score=24.44 Aligned_cols=10 Identities=60% Similarity=1.481 Sum_probs=7.6
Q ss_pred cCCCCCCCcee
Q 028198 88 CPKCGNGGTLR 98 (212)
Q Consensus 88 Cp~CG~~~TL~ 98 (212)
||.||.. ++.
T Consensus 1 C~~C~~~-~~~ 10 (127)
T TIGR03830 1 CPICGSG-ELV 10 (127)
T ss_pred CCCCCCc-cce
Confidence 9999975 453
No 367
>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=22.00 E-value=42 Score=22.80 Aligned_cols=8 Identities=50% Similarity=1.290 Sum_probs=7.1
Q ss_pred ccCCCCCC
Q 028198 87 FCPKCGNG 94 (212)
Q Consensus 87 FCp~CG~~ 94 (212)
-||.||..
T Consensus 3 PCPfCGg~ 10 (53)
T TIGR03655 3 PCPFCGGA 10 (53)
T ss_pred CCCCCCCc
Confidence 59999997
No 368
>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional
Probab=22.00 E-value=46 Score=33.98 Aligned_cols=26 Identities=27% Similarity=0.687 Sum_probs=14.9
Q ss_pred eeeEEEEccCccccccc-cCccccCCCCCC
Q 028198 66 LHRWILKCHACYTITAE-IGRIFCPKCGNG 94 (212)
Q Consensus 66 ~k~wvlrC~aC~k~~~~-~~k~FCp~CG~~ 94 (212)
++.|. | +|+|.-.. ....||+.||-.
T Consensus 66 ~k~~e--C-~CGkyk~~~~~~~~C~~CgvE 92 (627)
T PRK02625 66 SKDWE--C-HCGKYKRVRHRGIVCERCGVE 92 (627)
T ss_pred ccCcE--E-eCCCccccCcCCcCCCCCCcE
Confidence 34444 5 56653321 124799999965
No 369
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=21.78 E-value=1.1e+02 Score=31.45 Aligned_cols=44 Identities=20% Similarity=0.311 Sum_probs=27.2
Q ss_pred HHHHhCcee-----ecCCCCcceeeeeEEEEccCccccccccCccccCCCCCC
Q 028198 47 VILQMGLRL-----LAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 47 VllqmGL~~-----~s~~g~~I~~~k~wvlrC~aC~k~~~~~~k~FCp~CG~~ 94 (212)
-+.++||.+ +.-.|..|-++-.-+.+ ..... +. ++ ..||.||++
T Consensus 384 ~i~~~di~iGD~V~V~raGdVIPkI~~vv~~-~~~~~-~~-~P-~~CP~C~~~ 432 (689)
T PRK14351 384 EIEELGVNVGDRVRVKRAGDVIPYVEEVVEK-DSEGT-FE-FP-DTCPVCDSA 432 (689)
T ss_pred HHHHcCCCCCCEEEEEecCCccceeeeeecc-cCCCC-Cc-CC-CCCCCCCCE
Confidence 456777765 45568889888775542 22222 11 22 489999997
No 370
>TIGR02387 rpoC1_cyan DNA-directed RNA polymerase, gamma subunit. The RNA polymerase gamma subunit, encoded by the rpoC1 gene, is found in cyanobacteria and corresponds to the N-terminal region the beta' subunit, encoded by rpoC, in other bacteria. The equivalent subunit in plastids and chloroplasts is designated beta', while the product of the rpoC2 gene is designated beta''.
Probab=21.61 E-value=35 Score=34.76 Aligned_cols=32 Identities=28% Similarity=0.583 Sum_probs=17.4
Q ss_pred eeeEEEEccCccccccc-cCccccCCCCCCCceeEE
Q 028198 66 LHRWILKCHACYTITAE-IGRIFCPKCGNGGTLRKV 100 (212)
Q Consensus 66 ~k~wvlrC~aC~k~~~~-~~k~FCp~CG~~~TL~Rv 100 (212)
++.|. | +|+|.-.. ....||+.||-.-|..||
T Consensus 59 ~k~~e--C-~CGkyk~~~~~~~~C~~CgvE~t~s~v 91 (619)
T TIGR02387 59 SKDWE--C-HCGKYKRVRHRGIVCERCGVEVTESRV 91 (619)
T ss_pred CcCcE--E-eCCCccccCcCCcCCCCCCCEEchhhh
Confidence 34554 4 56653321 124799999976333333
No 371
>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=21.57 E-value=46 Score=27.76 Aligned_cols=21 Identities=24% Similarity=0.713 Sum_probs=15.5
Q ss_pred ccCccccccccCccccCCCCCC
Q 028198 73 CHACYTITAEIGRIFCPKCGNG 94 (212)
Q Consensus 73 C~aC~k~~~~~~k~FCp~CG~~ 94 (212)
|..|++..... ..+|+.|+..
T Consensus 1 C~~C~~~~~~~-~~~C~~C~~~ 21 (190)
T TIGR00201 1 CSLCGRPYQSV-HALCRQCGSW 21 (190)
T ss_pred CCccccccccc-cCCchhhCCc
Confidence 88999864332 3689999875
No 372
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=21.52 E-value=53 Score=26.58 Aligned_cols=26 Identities=23% Similarity=0.723 Sum_probs=18.2
Q ss_pred EEEEccCcccc--ccccCccccCCCCCC
Q 028198 69 WILKCHACYTI--TAEIGRIFCPKCGNG 94 (212)
Q Consensus 69 wvlrC~aC~k~--~~~~~k~FCp~CG~~ 94 (212)
|.--|+-|... |.+.....||.|+++
T Consensus 2 ~lp~cp~c~sEytYed~~~~~cpec~~e 29 (112)
T COG2824 2 SLPPCPKCNSEYTYEDGGQLICPECAHE 29 (112)
T ss_pred CCCCCCccCCceEEecCceEeCchhccc
Confidence 44568888644 345556789999987
No 373
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=21.22 E-value=84 Score=24.65 Aligned_cols=23 Identities=35% Similarity=0.624 Sum_probs=19.2
Q ss_pred ccccCCCCCCCceeEEEEEeCCCceE
Q 028198 85 RIFCPKCGNGGTLRKVAVTVGENGIV 110 (212)
Q Consensus 85 k~FCp~CG~~~TL~Rvsvsv~~~G~~ 110 (212)
..+||.|+.+ | ||..-+++||+-
T Consensus 71 ~lv~p~~~k~-~--rv~~~~~~~g~k 93 (104)
T TIGR01079 71 MLFDPKTGKA-T--RVGIRFEEDGKK 93 (104)
T ss_pred EEEcCcCCCC-e--EEEEEEccCCcE
Confidence 5799999987 4 899988888864
No 374
>PF09567 RE_MamI: MamI restriction endonuclease; InterPro: IPR019067 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the MamI restriction endonuclease which recognises and cleaves GATNN^NNATC. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=21.18 E-value=43 Score=31.06 Aligned_cols=28 Identities=25% Similarity=0.720 Sum_probs=20.3
Q ss_pred EEccCccccccccCccccCCCCCCCceeEE
Q 028198 71 LKCHACYTITAEIGRIFCPKCGNGGTLRKV 100 (212)
Q Consensus 71 lrC~aC~k~~~~~~k~FCp~CG~~~TL~Rv 100 (212)
-.|--|+...... ...||.||+. .+.|.
T Consensus 83 ~~C~~CGa~V~~~-e~~Cp~C~St-nI~r~ 110 (314)
T PF09567_consen 83 GKCNNCGANVSRL-EESCPNCGST-NIKRK 110 (314)
T ss_pred hhhccccceeeeh-hhcCCCCCcc-ccccc
Confidence 4688898766543 4689999996 66654
No 375
>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=21.07 E-value=80 Score=22.21 Aligned_cols=27 Identities=22% Similarity=0.539 Sum_probs=17.0
Q ss_pred EEccCccccccc-----cCccccCCCCCCCceeE
Q 028198 71 LKCHACYTITAE-----IGRIFCPKCGNGGTLRK 99 (212)
Q Consensus 71 lrC~aC~k~~~~-----~~k~FCp~CG~~~TL~R 99 (212)
..|+-|+....- -...-||.||.. |.=
T Consensus 3 ~~CP~CG~~iev~~~~~GeiV~Cp~CGae--leV 34 (54)
T TIGR01206 3 FECPDCGAEIELENPELGELVICDECGAE--LEV 34 (54)
T ss_pred cCCCCCCCEEecCCCccCCEEeCCCCCCE--EEE
Confidence 368888865431 125679999974 553
No 376
>PRK13764 ATPase; Provisional
Probab=21.04 E-value=79 Score=32.00 Aligned_cols=29 Identities=17% Similarity=0.158 Sum_probs=26.1
Q ss_pred CceeeEecchHHHHHHHHHhCceeecCCC
Q 028198 32 ESTVACITGDYAMQNVILQMGLRLLAPGG 60 (212)
Q Consensus 32 ~~~vac~TdDfAmQNVllqmGL~~~s~~g 60 (212)
+..+.++|.|+.+..+|..+||.++.+..
T Consensus 101 ~~~~~lvT~D~~l~~~A~~~GI~V~~l~~ 129 (602)
T PRK13764 101 ELGATLVTSDRVQAEVARAKGIDVIYLKP 129 (602)
T ss_pred HcCCEEEeCCHHHHHHHHHcCCEEEEeCC
Confidence 56899999999999999999999987654
No 377
>PF12387 Peptidase_C74: Pestivirus NS2 peptidase; InterPro: IPR022120 The pestivirus NS2 peptidase is responsible for single cleavage between NS2 and NS3 of the Bovine viral diarrhea virus 1 polyprotein, a cleavage that is correlated with cytopathogenicity []. The peptidase is activated by its interaction with 'J-domain protein interacting with viral protein' - Jiv. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0004252 serine-type endopeptidase activity, 0016817 hydrolase activity, acting on acid anhydrides, 0017111 nucleoside-triphosphatase activity, 0070008 serine-type exopeptidase activity
Probab=21.04 E-value=43 Score=29.37 Aligned_cols=45 Identities=27% Similarity=0.540 Sum_probs=25.7
Q ss_pred HHHHHHHHHhCceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCCCc
Q 028198 42 YAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGT 96 (212)
Q Consensus 42 fAmQNVllqmGL~~~s~~g~~I~~~k~wvlrC~aC~k~~~~~~k~FCp~CG~~~T 96 (212)
|+|+-|+.-+-..-++-. +.-..|+-|-.-- -....||+||..++
T Consensus 142 yGmpKi~~iika~tLsk~--------~hcilCtvCe~r~--w~g~~CPKCGr~G~ 186 (200)
T PF12387_consen 142 YGMPKIITIIKAATLSKS--------KHCILCTVCEGRE--WKGGNCPKCGRHGK 186 (200)
T ss_pred cCcchhhhhhhHHhccCC--------CceEEEeeeecCc--cCCCCCCcccCCCC
Confidence 666666655443333222 3446788886432 23467999997643
No 378
>PRK14278 chaperone protein DnaJ; Provisional
Probab=21.00 E-value=3.4e+02 Score=25.48 Aligned_cols=26 Identities=23% Similarity=0.528 Sum_probs=14.4
Q ss_pred EEEccCccccccccCccccCCCCCCCc
Q 028198 70 ILKCHACYTITAEIGRIFCPKCGNGGT 96 (212)
Q Consensus 70 vlrC~aC~k~~~~~~k~FCp~CG~~~T 96 (212)
...|..|.=.-... +.-|+.|...++
T Consensus 182 ~~~C~~C~G~G~~~-~~~C~~C~G~g~ 207 (378)
T PRK14278 182 SRPCPTCRGVGEVI-PDPCHECAGDGR 207 (378)
T ss_pred EEECCCCCccceee-CCCCCCCCCcee
Confidence 34676665433222 345888887633
No 379
>TIGR03847 conserved hypothetical protein. The conserved hypothetical protein described here occurs as part of the trio of uncharacterized proteins common in the Actinobacteria.
Probab=20.99 E-value=55 Score=28.45 Aligned_cols=18 Identities=39% Similarity=0.946 Sum_probs=13.9
Q ss_pred CccccCCCCCCCceeEEEEEeCCCceE
Q 028198 84 GRIFCPKCGNGGTLRKVAVTVGENGIV 110 (212)
Q Consensus 84 ~k~FCp~CG~~~TL~Rvsvsv~~~G~~ 110 (212)
.+..||-||.+ +|.+|-+
T Consensus 155 GRP~CPlCg~P---------ldP~GH~ 172 (177)
T TIGR03847 155 GRPPCPLCGRP---------IDPDGHI 172 (177)
T ss_pred CCCCCCCCCCC---------CCCCCcc
Confidence 47789999998 5777754
No 380
>PRK14281 chaperone protein DnaJ; Provisional
Probab=20.79 E-value=3e+02 Score=25.99 Aligned_cols=27 Identities=26% Similarity=0.518 Sum_probs=16.9
Q ss_pred EEEccCccccccccCccccCCCCCCCce
Q 028198 70 ILKCHACYTITAEIGRIFCPKCGNGGTL 97 (212)
Q Consensus 70 vlrC~aC~k~~~~~~k~FCp~CG~~~TL 97 (212)
...|..|.=.-... +.-|+.|.+.+++
T Consensus 205 ~~~C~~C~G~G~~~-~~~C~~C~G~g~v 231 (397)
T PRK14281 205 ITACPTCGGEGRVV-KDRCPACYGEGIK 231 (397)
T ss_pred EEecCCCcceeeee-CCCCCCCCCCccE
Confidence 44677776544332 4569999887444
No 381
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.71 E-value=82 Score=25.52 Aligned_cols=18 Identities=39% Similarity=0.916 Sum_probs=12.0
Q ss_pred cCccccCCCCCCCceeEEEE
Q 028198 83 IGRIFCPKCGNGGTLRKVAV 102 (212)
Q Consensus 83 ~~k~FCp~CG~~~TL~Rvsv 102 (212)
+...-||+||.+ +.-+-+
T Consensus 47 ~G~t~CP~Cg~~--~e~~fv 64 (115)
T COG1885 47 VGSTSCPKCGEP--FESAFV 64 (115)
T ss_pred cccccCCCCCCc--cceeEE
Confidence 344579999997 554443
No 382
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.68 E-value=42 Score=25.95 Aligned_cols=10 Identities=30% Similarity=0.943 Sum_probs=6.5
Q ss_pred ccccCCCCCC
Q 028198 85 RIFCPKCGNG 94 (212)
Q Consensus 85 k~FCp~CG~~ 94 (212)
.+.||.|+.-
T Consensus 21 iD~CPrCrGV 30 (88)
T COG3809 21 IDYCPRCRGV 30 (88)
T ss_pred eeeCCccccE
Confidence 4567777763
No 383
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=20.64 E-value=43 Score=36.13 Aligned_cols=26 Identities=27% Similarity=0.866 Sum_probs=20.2
Q ss_pred EccCccccccccCccccCCCCCCCceeE
Q 028198 72 KCHACYTITAEIGRIFCPKCGNGGTLRK 99 (212)
Q Consensus 72 rC~aC~k~~~~~~k~FCp~CG~~~TL~R 99 (212)
.|..|+........+-||.|+.+ -+|
T Consensus 44 vCr~cyeye~~~g~~~cp~c~t~--y~~ 69 (1044)
T PLN02915 44 VCKPCYEYERSEGNQCCPQCNTR--YKR 69 (1044)
T ss_pred cccchhhhhhhcCCccCCccCCc--hhh
Confidence 57888877666678899999986 554
No 384
>PF06839 zf-GRF: GRF zinc finger; InterPro: IPR010666 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 presumed zinc-binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to IPR000380 from INTERPRO. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=20.61 E-value=73 Score=20.90 Aligned_cols=14 Identities=36% Similarity=1.009 Sum_probs=10.8
Q ss_pred ccCCCCCCCceeEEEE
Q 028198 87 FCPKCGNGGTLRKVAV 102 (212)
Q Consensus 87 FCp~CG~~~TL~Rvsv 102 (212)
.|+ ||.+ .+.+++.
T Consensus 2 ~C~-Cg~~-~~~~~s~ 15 (45)
T PF06839_consen 2 KCP-CGEP-AVRRTSK 15 (45)
T ss_pred CCC-CCCE-eEEEEEe
Confidence 599 9987 6777775
No 385
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=20.28 E-value=61 Score=23.21 Aligned_cols=19 Identities=32% Similarity=0.723 Sum_probs=8.0
Q ss_pred EccCccccccccCccccCCCC
Q 028198 72 KCHACYTITAEIGRIFCPKCG 92 (212)
Q Consensus 72 rC~aC~k~~~~~~k~FCp~CG 92 (212)
.|..|++..- .-..|+.||
T Consensus 29 ~c~~cG~~~l--~Hrvc~~cg 47 (57)
T COG0333 29 VCPNCGEYKL--PHRVCLKCG 47 (57)
T ss_pred eccCCCCccc--CceEcCCCC
Confidence 4445554322 123455555
No 386
>PLN02189 cellulose synthase
Probab=20.24 E-value=40 Score=36.28 Aligned_cols=28 Identities=25% Similarity=0.772 Sum_probs=20.4
Q ss_pred EccCccccccccCccccCCCCCCCceeEEE
Q 028198 72 KCHACYTITAEIGRIFCPKCGNGGTLRKVA 101 (212)
Q Consensus 72 rC~aC~k~~~~~~k~FCp~CG~~~TL~Rvs 101 (212)
.|..|+........+-||.|+.+ -+|+-
T Consensus 63 vCr~Cyeyer~eg~q~CpqCkt~--Y~r~k 90 (1040)
T PLN02189 63 VCRPCYEYERREGTQNCPQCKTR--YKRLK 90 (1040)
T ss_pred cccchhhhhhhcCCccCcccCCc--hhhcc
Confidence 56777876666667899999975 55443
No 387
>PRK13795 hypothetical protein; Provisional
Probab=20.23 E-value=87 Score=31.55 Aligned_cols=38 Identities=26% Similarity=0.342 Sum_probs=25.8
Q ss_pred eeeEEEEccCccccccccCccccCCCCCCCceeEEEEEeCCCceE
Q 028198 66 LHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGENGIV 110 (212)
Q Consensus 66 ~k~wvlrC~aC~k~~~~~~k~FCp~CG~~~TL~Rvsvsv~~~G~~ 110 (212)
-+.|++.|..|.--.- ..-|..||+. | .+|.+ ..-|-+
T Consensus 8 ~~~~~~wc~~cn~p~~---~~~c~~c~~~-~-~~~~~--t~p~d~ 45 (636)
T PRK13795 8 GKDHIYWCEKCNVPLL---GKKCGICGKE-G-FKVRL--TPPGDV 45 (636)
T ss_pred cceeEEEcccCCCeec---cccccccCCC-c-eEeec--CCCCCC
Confidence 3579999999984322 2359999998 6 56665 444443
No 388
>KOG1522 consensus RNA polymerase II, subunit POLR2C/RPB3 [Transcription]
Probab=20.13 E-value=75 Score=29.31 Aligned_cols=20 Identities=10% Similarity=0.169 Sum_probs=12.1
Q ss_pred CceeeEecchHHHHHHHHHh
Q 028198 32 ESTVACITGDYAMQNVILQM 51 (212)
Q Consensus 32 ~~~vac~TdDfAmQNVllqm 51 (212)
.++.++--+|.||-|.|.+.
T Consensus 17 ~vkF~L~nTdlsvANsLRRV 36 (285)
T KOG1522|consen 17 NVKFVLSNTDLSVANSLRRV 36 (285)
T ss_pred ceEEEEecChHHHHHHHHHH
Confidence 34556666666666666553
Done!