Query 032998
Match_columns 129
No_of_seqs 102 out of 306
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 08:32:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032998.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032998hhsearch_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 9.6E-44 2.1E-48 298.7 7.4 104 25-129 183-302 (376)
2 PF08772 NOB1_Zn_bind: Nin one 100.0 9.2E-31 2E-35 179.2 2.9 67 62-129 1-69 (73)
3 COG1439 Predicted nucleic acid 99.9 2.2E-25 4.7E-30 174.2 4.8 69 32-102 100-169 (177)
4 PRK12496 hypothetical protein; 99.8 4.1E-21 8.9E-26 147.5 4.5 69 32-102 89-158 (164)
5 TIGR03875 RNA_lig_partner RNA 97.9 7.4E-06 1.6E-10 65.9 2.7 28 31-58 168-195 (206)
6 PRK04358 hypothetical protein; 97.8 1.6E-05 3.4E-10 64.5 2.5 28 31-58 172-199 (217)
7 PF09723 Zn-ribbon_8: Zinc rib 97.0 0.001 2.2E-08 40.6 3.3 32 68-100 3-40 (42)
8 smart00834 CxxC_CXXC_SSSS Puta 96.9 0.00075 1.6E-08 39.8 2.3 31 68-100 3-39 (41)
9 PF08745 UPF0278: UPF0278 fami 96.8 0.00057 1.2E-08 55.1 1.9 29 31-59 165-193 (205)
10 TIGR02605 CxxC_CxxC_SSSS putat 96.7 0.0015 3.2E-08 40.7 2.8 33 68-101 3-41 (52)
11 PF13248 zf-ribbon_3: zinc-rib 96.7 0.00063 1.4E-08 37.7 0.7 23 71-94 3-25 (26)
12 PF13240 zinc_ribbon_2: zinc-r 96.5 0.0009 1.9E-08 36.5 0.6 22 72-94 1-22 (23)
13 COG1545 Predicted nucleic-acid 95.8 0.017 3.6E-07 43.5 4.5 44 64-110 23-66 (140)
14 PF12172 DUF35_N: Rubredoxin-l 95.8 0.0071 1.5E-07 35.6 1.9 27 67-94 8-34 (37)
15 TIGR00100 hypA hydrogenase nic 95.7 0.0078 1.7E-07 43.8 2.4 28 67-94 67-95 (115)
16 PRK03681 hypA hydrogenase nick 95.7 0.0081 1.8E-07 43.7 2.3 28 67-94 67-96 (114)
17 PRK00564 hypA hydrogenase nick 95.6 0.01 2.2E-07 43.4 2.7 31 67-98 68-100 (117)
18 PRK00398 rpoP DNA-directed RNA 95.6 0.01 2.3E-07 36.4 2.4 25 70-94 3-30 (46)
19 PRK12380 hydrogenase nickel in 95.5 0.0099 2.2E-07 43.2 2.4 28 67-94 67-95 (113)
20 PF10571 UPF0547: Uncharacteri 95.5 0.0059 1.3E-07 34.2 0.9 22 72-94 2-23 (26)
21 cd00729 rubredoxin_SM Rubredox 95.5 0.013 2.8E-07 34.5 2.2 25 70-94 2-27 (34)
22 cd00350 rubredoxin_like Rubred 95.3 0.012 2.6E-07 34.1 1.8 25 70-94 1-26 (33)
23 smart00659 RPOLCX RNA polymera 95.1 0.023 5E-07 35.3 2.7 30 70-100 2-33 (44)
24 PRK03824 hypA hydrogenase nick 95.0 0.018 3.9E-07 43.1 2.4 26 69-94 69-116 (135)
25 PRK13130 H/ACA RNA-protein com 94.9 0.015 3.3E-07 38.1 1.6 29 70-102 5-33 (56)
26 PF09845 DUF2072: Zn-ribbon co 94.7 0.016 3.6E-07 43.9 1.5 30 71-101 2-34 (131)
27 PF01155 HypA: Hydrogenase exp 94.7 0.024 5.2E-07 41.0 2.2 30 65-94 65-95 (113)
28 PF10263 SprT-like: SprT-like 94.6 0.055 1.2E-06 39.8 4.1 58 41-100 85-156 (157)
29 COG1996 RPC10 DNA-directed RNA 94.6 0.027 5.8E-07 36.1 2.0 32 68-100 4-38 (49)
30 COG3364 Zn-ribbon containing p 94.5 0.019 4E-07 42.3 1.4 31 71-102 3-36 (112)
31 COG1592 Rubrerythrin [Energy p 94.3 0.031 6.7E-07 43.8 2.3 25 70-94 134-158 (166)
32 PF09538 FYDLN_acid: Protein o 94.2 0.022 4.7E-07 41.6 1.1 25 70-94 9-35 (108)
33 COG2093 DNA-directed RNA polym 94.0 0.026 5.7E-07 38.0 1.1 25 71-97 5-29 (64)
34 PF05191 ADK_lid: Adenylate ki 94.0 0.053 1.1E-06 32.4 2.3 28 71-99 2-34 (36)
35 PF04135 Nop10p: Nucleolar RNA 93.6 0.097 2.1E-06 34.0 3.2 26 69-98 4-29 (53)
36 COG2260 Predicted Zn-ribbon RN 93.2 0.048 1E-06 36.3 1.3 25 70-98 5-29 (59)
37 PRK06393 rpoE DNA-directed RNA 93.2 0.04 8.7E-07 37.1 1.0 24 70-97 5-28 (64)
38 PRK04351 hypothetical protein; 93.0 0.2 4.4E-06 38.2 4.7 55 41-100 85-145 (149)
39 PRK08351 DNA-directed RNA poly 92.9 0.051 1.1E-06 36.3 1.2 22 72-97 5-26 (61)
40 PF03604 DNA_RNApol_7kD: DNA d 92.9 0.09 2E-06 30.8 2.1 28 71-99 1-30 (32)
41 PRK07591 threonine synthase; V 92.5 0.1 2.2E-06 45.2 2.8 27 68-94 16-42 (421)
42 TIGR03844 cysteate_syn cysteat 92.0 0.11 2.4E-06 44.9 2.3 26 69-94 1-26 (398)
43 PRK00762 hypA hydrogenase nick 91.9 0.14 3.1E-06 37.7 2.6 30 67-98 67-104 (124)
44 TIGR02300 FYDLN_acid conserved 91.8 0.084 1.8E-06 40.0 1.3 25 70-94 9-35 (129)
45 PF15017 AF1Q: Drug resistance 91.8 0.093 2E-06 37.3 1.4 18 12-29 62-79 (87)
46 COG1645 Uncharacterized Zn-fin 91.7 0.084 1.8E-06 40.0 1.2 24 71-94 29-53 (131)
47 COG1579 Zn-ribbon protein, pos 91.6 0.11 2.4E-06 42.8 1.9 33 52-94 189-230 (239)
48 PF11023 DUF2614: Protein of u 91.5 0.12 2.6E-06 38.4 1.9 34 66-99 65-99 (114)
49 PRK06450 threonine synthase; V 91.3 0.13 2.8E-06 43.4 2.1 25 70-94 3-27 (338)
50 PF00301 Rubredoxin: Rubredoxi 91.1 0.21 4.6E-06 31.5 2.4 25 70-94 1-43 (47)
51 PRK00241 nudC NADH pyrophospha 91.0 0.26 5.6E-06 40.3 3.4 55 71-128 100-161 (256)
52 PF12773 DZR: Double zinc ribb 90.9 0.11 2.5E-06 31.7 1.0 21 73-94 1-21 (50)
53 COG2331 Uncharacterized protei 90.9 0.057 1.2E-06 37.9 -0.4 31 67-99 9-45 (82)
54 PF07295 DUF1451: Protein of u 90.8 0.18 4E-06 38.5 2.3 31 70-101 112-145 (146)
55 COG5257 GCD11 Translation init 90.7 0.37 8.1E-06 42.3 4.3 40 68-108 55-95 (415)
56 PF14803 Nudix_N_2: Nudix N-te 90.6 0.14 3E-06 30.4 1.1 15 86-101 1-15 (34)
57 COG1198 PriA Primosomal protei 90.5 0.22 4.7E-06 46.8 2.9 30 68-100 460-489 (730)
58 PF12773 DZR: Double zinc ribb 90.4 0.12 2.6E-06 31.6 0.8 20 72-92 31-50 (50)
59 PRK14714 DNA polymerase II lar 90.4 0.28 6.2E-06 48.6 3.7 29 63-94 660-688 (1337)
60 PRK06260 threonine synthase; V 90.1 0.21 4.6E-06 42.6 2.4 26 69-94 2-28 (397)
61 PF07191 zinc-ribbons_6: zinc- 90.1 0.29 6.2E-06 33.5 2.5 29 70-102 17-45 (70)
62 smart00731 SprT SprT homologue 89.9 0.42 9.1E-06 35.5 3.5 53 42-94 83-142 (146)
63 TIGR00595 priA primosomal prot 89.8 0.24 5.1E-06 44.0 2.4 28 70-100 240-267 (505)
64 PF14446 Prok-RING_1: Prokaryo 89.8 0.16 3.5E-06 33.2 1.1 25 70-94 5-30 (54)
65 TIGR02098 MJ0042_CXXC MJ0042 f 89.7 0.19 4E-06 29.3 1.2 25 70-94 2-34 (38)
66 PRK00420 hypothetical protein; 89.5 0.19 4.2E-06 37.0 1.4 24 71-94 24-49 (112)
67 PRK11032 hypothetical protein; 89.3 0.29 6.3E-06 38.1 2.3 31 70-101 124-157 (160)
68 cd00730 rubredoxin Rubredoxin; 89.2 0.21 4.5E-06 31.9 1.2 25 70-94 1-43 (50)
69 COG0375 HybF Zn finger protein 88.1 0.37 8E-06 35.8 2.1 33 65-98 65-98 (115)
70 PF07282 OrfB_Zn_ribbon: Putat 87.8 0.63 1.4E-05 30.1 2.8 46 43-94 7-55 (69)
71 PRK05978 hypothetical protein; 87.3 0.24 5.2E-06 38.1 0.7 32 68-101 31-66 (148)
72 PF09297 zf-NADH-PPase: NADH p 87.3 0.28 6.2E-06 27.9 0.8 10 85-94 3-12 (32)
73 TIGR00354 polC DNA polymerase, 87.1 0.46 1E-05 46.2 2.6 28 67-94 1009-1037(1095)
74 TIGR00354 polC DNA polymerase, 86.4 0.63 1.4E-05 45.3 3.1 30 65-98 620-649 (1095)
75 TIGR02827 RNR_anaer_Bdell anae 86.3 0.65 1.4E-05 42.6 3.0 51 42-102 509-562 (586)
76 cd01675 RNR_III Class III ribo 86.2 0.62 1.3E-05 42.0 2.8 30 71-102 519-548 (555)
77 PF13638 PIN_4: PIN domain; PD 86.1 0.9 1.9E-05 32.1 3.1 27 32-58 106-132 (133)
78 PRK14873 primosome assembly pr 85.9 0.53 1.1E-05 43.5 2.3 29 70-102 410-438 (665)
79 PF14205 Cys_rich_KTR: Cystein 85.6 0.9 2E-05 29.8 2.6 31 68-100 3-42 (55)
80 PF03119 DNA_ligase_ZBD: NAD-d 85.5 0.47 1E-05 26.8 1.1 11 87-99 1-11 (28)
81 PF14319 Zn_Tnp_IS91: Transpos 85.4 0.61 1.3E-05 33.8 2.0 27 68-94 40-69 (111)
82 PF14205 Cys_rich_KTR: Cystein 85.3 0.49 1.1E-05 31.1 1.3 15 86-101 5-19 (55)
83 PRK04023 DNA polymerase II lar 85.1 0.66 1.4E-05 45.3 2.6 28 67-94 1034-1062(1121)
84 PF14369 zf-RING_3: zinc-finge 84.9 0.74 1.6E-05 27.2 1.9 24 71-94 3-30 (35)
85 PRK14559 putative protein seri 84.7 0.43 9.4E-06 44.1 1.1 21 73-94 30-50 (645)
86 PRK14714 DNA polymerase II lar 84.6 0.71 1.5E-05 45.9 2.6 28 67-94 1250-1278(1337)
87 PF08792 A2L_zn_ribbon: A2L zi 84.5 0.66 1.4E-05 27.2 1.5 24 71-94 4-30 (33)
88 COG1933 Archaeal DNA polymeras 84.3 0.61 1.3E-05 38.8 1.7 30 65-94 162-192 (253)
89 PF02150 RNA_POL_M_15KD: RNA p 84.1 0.44 9.6E-06 28.1 0.6 9 86-94 2-10 (35)
90 PRK07111 anaerobic ribonucleos 84.0 0.65 1.4E-05 43.5 2.0 29 70-101 680-708 (735)
91 PF13597 NRDD: Anaerobic ribon 84.0 0.42 9.2E-06 43.0 0.8 29 70-101 491-519 (546)
92 PF14353 CpXC: CpXC protein 84.0 1.1 2.3E-05 32.4 2.7 28 85-112 38-65 (128)
93 PRK11788 tetratricopeptide rep 83.9 0.67 1.5E-05 37.4 1.8 28 71-99 355-382 (389)
94 smart00531 TFIIE Transcription 83.7 0.64 1.4E-05 34.8 1.5 27 68-94 97-132 (147)
95 PRK02935 hypothetical protein; 83.7 0.82 1.8E-05 33.8 2.0 32 67-98 67-99 (110)
96 PRK14890 putative Zn-ribbon RN 83.7 0.5 1.1E-05 31.4 0.8 21 70-93 36-56 (59)
97 PRK05580 primosome assembly pr 83.4 0.8 1.7E-05 42.1 2.3 27 70-99 408-434 (679)
98 PF13717 zinc_ribbon_4: zinc-r 83.2 0.84 1.8E-05 26.9 1.6 25 70-94 2-34 (36)
99 COG0267 RpmG Ribosomal protein 83.0 0.85 1.8E-05 29.4 1.6 31 68-99 5-47 (50)
100 PF06676 DUF1178: Protein of u 83.0 1.5 3.3E-05 33.7 3.3 33 67-101 2-47 (148)
101 COG0846 SIR2 NAD-dependent pro 82.8 1.1 2.5E-05 36.8 2.7 61 34-103 93-163 (250)
102 PLN02569 threonine synthase 82.7 1.3 2.7E-05 39.5 3.2 58 34-98 17-75 (484)
103 TIGR02487 NrdD anaerobic ribon 82.7 0.67 1.4E-05 42.1 1.5 49 42-100 501-552 (579)
104 COG3091 SprT Zn-dependent meta 82.3 0.81 1.8E-05 35.7 1.6 54 43-99 87-152 (156)
105 PRK14715 DNA polymerase II lar 82.2 1 2.2E-05 45.4 2.5 26 68-94 1540-1566(1627)
106 PRK14559 putative protein seri 82.1 0.63 1.4E-05 43.1 1.1 23 71-94 2-24 (645)
107 PRK11823 DNA repair protein Ra 82.0 1.1 2.3E-05 39.4 2.4 31 68-99 5-35 (446)
108 PRK05452 anaerobic nitric oxid 81.9 1 2.2E-05 39.8 2.2 25 70-94 425-467 (479)
109 PF13719 zinc_ribbon_5: zinc-r 81.9 1.1 2.3E-05 26.5 1.7 24 71-94 3-34 (37)
110 PRK05638 threonine synthase; V 81.5 0.94 2E-05 39.3 1.9 24 70-94 1-24 (442)
111 COG2888 Predicted Zn-ribbon RN 81.4 0.54 1.2E-05 31.5 0.3 8 86-93 51-58 (61)
112 PRK08270 anaerobic ribonucleos 81.4 1.1 2.3E-05 41.5 2.3 43 42-94 602-648 (656)
113 TIGR00686 phnA alkylphosphonat 81.4 1.2 2.6E-05 32.9 2.2 37 72-110 4-50 (109)
114 COG2888 Predicted Zn-ribbon RN 80.7 0.94 2E-05 30.3 1.3 31 70-101 9-42 (61)
115 PRK14890 putative Zn-ribbon RN 80.7 1.2 2.6E-05 29.6 1.7 30 70-100 7-39 (59)
116 cd01407 SIR2-fam SIR2 family o 80.5 1.5 3.2E-05 34.4 2.6 42 47-94 91-142 (218)
117 cd04476 RPA1_DBD_C RPA1_DBD_C: 80.3 3.2 6.9E-05 31.0 4.2 44 67-110 31-81 (166)
118 PRK10220 hypothetical protein; 80.1 1.4 3.1E-05 32.6 2.2 37 72-110 5-51 (111)
119 PF01907 Ribosomal_L37e: Ribos 80.1 1.1 2.4E-05 29.4 1.4 25 71-95 16-40 (55)
120 PF04606 Ogr_Delta: Ogr/Delta- 79.9 1.4 3.1E-05 27.1 1.8 24 87-111 1-24 (47)
121 cd01121 Sms Sms (bacterial rad 79.8 0.89 1.9E-05 39.1 1.2 28 71-99 1-28 (372)
122 PRK08579 anaerobic ribonucleos 78.8 1.1 2.4E-05 41.3 1.5 46 40-94 543-591 (625)
123 PRK06266 transcription initiat 78.8 1.5 3.1E-05 34.3 2.0 63 35-99 82-148 (178)
124 PF08271 TF_Zn_Ribbon: TFIIB z 78.6 0.91 2E-05 27.3 0.6 24 71-94 1-28 (43)
125 cd01408 SIRT1 SIRT1: Eukaryoti 78.4 1.7 3.6E-05 34.9 2.3 44 55-106 107-159 (235)
126 COG1110 Reverse gyrase [DNA re 78.1 0.83 1.8E-05 44.8 0.6 26 68-94 692-717 (1187)
127 PRK04023 DNA polymerase II lar 78.1 1.2 2.5E-05 43.7 1.5 21 71-94 627-647 (1121)
128 cd01413 SIR2_Af2 SIR2_Af2: Arc 78.0 1.5 3.4E-05 34.7 2.0 27 68-94 111-145 (222)
129 PRK08197 threonine synthase; V 77.9 1.7 3.7E-05 37.1 2.3 25 69-94 6-31 (394)
130 PRK08329 threonine synthase; V 77.8 1.5 3.3E-05 36.8 2.0 25 71-98 2-26 (347)
131 PF07754 DUF1610: Domain of un 77.7 1.4 3.1E-05 24.3 1.2 21 73-93 1-24 (24)
132 TIGR00416 sms DNA repair prote 77.4 1.6 3.4E-05 38.5 2.0 31 68-99 5-35 (454)
133 COG2126 RPL37A Ribosomal prote 77.3 1 2.3E-05 30.1 0.7 27 68-94 14-40 (61)
134 cd01410 SIRT7 SIRT7: Eukaryoti 77.2 1.8 3.8E-05 34.2 2.1 29 68-98 93-131 (206)
135 PRK00481 NAD-dependent deacety 77.2 1.9 4.2E-05 34.4 2.3 27 68-94 120-151 (242)
136 PRK08271 anaerobic ribonucleos 76.9 1.4 3E-05 40.7 1.6 44 42-94 543-589 (623)
137 PF06906 DUF1272: Protein of u 76.8 1 2.2E-05 29.8 0.5 29 66-94 22-50 (57)
138 TIGR00373 conserved hypothetic 76.7 1.7 3.7E-05 33.1 1.8 28 69-98 108-139 (158)
139 PF03833 PolC_DP2: DNA polymer 75.9 0.87 1.9E-05 43.7 0.0 22 70-94 655-676 (900)
140 PRK07218 replication factor A; 75.7 1.6 3.5E-05 38.5 1.6 68 42-112 267-339 (423)
141 PF05991 NYN_YacP: YacP-like N 75.6 3.3 7.1E-05 31.6 3.1 42 18-59 75-121 (166)
142 PF04216 FdhE: Protein involve 75.4 2.8 6.1E-05 34.4 2.9 41 69-110 196-236 (290)
143 PF14206 Cys_rich_CPCC: Cystei 75.4 1.4 3E-05 30.6 0.9 25 70-94 1-29 (78)
144 cd01411 SIR2H SIR2H: Uncharact 75.4 2 4.3E-05 34.2 1.9 27 68-94 116-145 (225)
145 PF02146 SIR2: Sir2 family; I 74.9 3.6 7.8E-05 31.1 3.2 27 68-94 103-138 (178)
146 PRK12366 replication factor A; 74.7 4.9 0.00011 37.0 4.5 48 63-110 525-576 (637)
147 PRK00432 30S ribosomal protein 74.4 2.5 5.3E-05 26.8 1.8 22 72-93 22-45 (50)
148 TIGR00155 pqiA_fam integral me 73.9 1.9 4E-05 37.6 1.5 28 70-99 215-242 (403)
149 COG2176 PolC DNA polymerase II 73.9 1.7 3.8E-05 43.4 1.5 27 71-99 915-951 (1444)
150 smart00661 RPOL9 RNA polymeras 73.8 2 4.4E-05 26.1 1.3 23 72-94 2-29 (52)
151 COG1458 Predicted DNA-binding 73.7 3 6.5E-05 34.1 2.6 28 31-58 172-199 (221)
152 PTZ00410 NAD-dependent SIR2; P 73.3 3.8 8.2E-05 35.5 3.2 27 68-94 145-180 (349)
153 PF03833 PolC_DP2: DNA polymer 73.2 1.1 2.4E-05 43.0 0.0 26 67-94 664-689 (900)
154 PRK14138 NAD-dependent deacety 73.0 3.1 6.6E-05 33.6 2.5 27 68-94 117-152 (244)
155 PRK04338 N(2),N(2)-dimethylgua 72.7 2.9 6.2E-05 36.1 2.4 27 68-94 242-270 (382)
156 PRK14704 anaerobic ribonucleos 72.7 2.1 4.6E-05 39.4 1.7 22 71-94 560-581 (618)
157 PRK15103 paraquat-inducible me 72.5 1.9 4E-05 37.9 1.2 27 71-99 11-42 (419)
158 PF02591 DUF164: Putative zinc 72.5 2 4.3E-05 27.2 1.0 22 72-93 24-54 (56)
159 TIGR03826 YvyF flagellar opero 72.5 0.99 2.1E-05 34.3 -0.4 23 72-94 5-27 (137)
160 COG1096 Predicted RNA-binding 72.1 2.5 5.5E-05 33.9 1.8 33 69-102 148-181 (188)
161 COG1867 TRM1 N2,N2-dimethylgua 72.0 2.6 5.5E-05 37.1 1.9 27 68-94 238-266 (380)
162 PF15499 Peptidase_C98: Ubiqui 72.0 2 4.4E-05 36.2 1.3 81 40-127 109-221 (275)
163 PF06221 zf-C2HC5: Putative zi 71.7 2.1 4.6E-05 28.1 1.1 32 63-94 11-44 (57)
164 TIGR00311 aIF-2beta translatio 71.7 4.5 9.7E-05 30.5 3.0 40 41-80 83-128 (133)
165 PRK03988 translation initiatio 71.7 3.7 8E-05 31.1 2.5 47 34-80 78-133 (138)
166 PRK04179 rpl37e 50S ribosomal 71.5 1.9 4.1E-05 28.9 0.8 25 70-94 17-42 (62)
167 COG4031 Predicted metal-bindin 71.4 3 6.5E-05 34.0 2.1 33 71-107 1-33 (227)
168 PF07975 C1_4: TFIIH C1-like d 71.2 2.1 4.6E-05 27.5 1.0 11 69-79 20-30 (51)
169 PTZ00408 NAD-dependent deacety 71.2 3 6.5E-05 33.8 2.1 25 68-92 115-144 (242)
170 PRK08402 replication factor A; 71.1 8 0.00017 33.4 4.8 43 68-110 210-258 (355)
171 PRK00415 rps27e 30S ribosomal 70.7 2.5 5.4E-05 28.1 1.2 29 69-99 10-42 (59)
172 COG1773 Rubredoxin [Energy pro 70.5 3.1 6.7E-05 27.3 1.6 13 70-82 3-15 (55)
173 COG1656 Uncharacterized conser 70.1 1.8 4E-05 34.0 0.6 23 33-56 47-69 (165)
174 PRK00504 rpmG 50S ribosomal pr 69.8 5.5 0.00012 25.4 2.6 31 68-99 5-47 (50)
175 cd01409 SIRT4 SIRT4: Eukaryoti 69.4 3.7 8.1E-05 33.5 2.3 14 68-81 116-129 (260)
176 PF01780 Ribosomal_L37ae: Ribo 69.2 2.6 5.5E-05 30.1 1.1 17 85-102 35-51 (90)
177 PHA02942 putative transposase; 69.2 6.7 0.00015 33.9 3.9 42 47-94 308-351 (383)
178 smart00653 eIF2B_5 domain pres 69.1 4.4 9.5E-05 29.5 2.4 45 34-78 56-109 (110)
179 COG3357 Predicted transcriptio 68.9 2.4 5.2E-05 30.7 0.9 27 71-98 59-88 (97)
180 PRK09263 anaerobic ribonucleos 68.6 4.5 9.8E-05 37.9 2.9 24 71-94 642-668 (711)
181 KOG2324 Prolyl-tRNA synthetase 68.5 17 0.00036 32.6 6.1 55 46-101 189-262 (457)
182 TIGR00155 pqiA_fam integral me 68.0 3.5 7.5E-05 36.0 1.9 28 70-99 13-45 (403)
183 PF01783 Ribosomal_L32p: Ribos 67.9 4.9 0.00011 25.7 2.1 21 71-93 27-47 (56)
184 cd00296 SIR2 SIR2 superfamily 67.7 4.9 0.00011 30.9 2.6 53 34-94 82-143 (222)
185 PRK14715 DNA polymerase II lar 67.5 4.6 0.0001 40.9 2.8 27 65-94 669-695 (1627)
186 PRK15103 paraquat-inducible me 67.2 3.1 6.7E-05 36.5 1.5 27 70-99 221-247 (419)
187 TIGR00308 TRM1 tRNA(guanine-26 67.0 4.8 0.0001 34.7 2.6 27 68-94 231-261 (374)
188 COG0675 Transposase and inacti 66.8 2.9 6.2E-05 32.9 1.1 22 71-94 310-331 (364)
189 cd01412 SIRT5_Af1_CobB SIRT5_A 66.3 4.1 8.9E-05 31.9 1.9 27 68-94 107-139 (224)
190 PRK00448 polC DNA polymerase I 66.3 2.7 5.9E-05 42.3 1.0 24 71-94 909-942 (1437)
191 TIGR00515 accD acetyl-CoA carb 66.1 3.1 6.8E-05 34.9 1.2 25 69-94 26-54 (285)
192 PTZ00073 60S ribosomal protein 65.8 2.9 6.4E-05 30.0 0.9 24 71-94 17-40 (91)
193 COG1997 RPL43A Ribosomal prote 65.5 3.8 8.3E-05 29.3 1.4 17 85-102 35-51 (89)
194 TIGR01023 rpmG_bact ribosomal 65.5 8.4 0.00018 24.8 2.9 32 67-99 8-51 (54)
195 PF09151 DUF1936: Domain of un 65.1 11 0.00025 22.4 3.1 25 86-114 2-26 (36)
196 PF01396 zf-C4_Topoisom: Topoi 64.8 4.1 9E-05 24.3 1.3 22 86-112 2-23 (39)
197 PHA00626 hypothetical protein 64.6 4.1 8.9E-05 27.1 1.3 12 87-99 2-13 (59)
198 PF04828 GFA: Glutathione-depe 64.4 2.3 5E-05 27.8 0.1 15 80-94 43-57 (92)
199 PRK00595 rpmG 50S ribosomal pr 64.2 8.7 0.00019 24.6 2.8 31 68-99 8-50 (53)
200 PF14690 zf-ISL3: zinc-finger 63.9 3.6 7.7E-05 24.5 0.9 12 86-98 3-14 (47)
201 PRK05654 acetyl-CoA carboxylas 63.8 4.2 9.1E-05 34.2 1.6 25 69-94 27-55 (292)
202 PF09332 Mcm10: Mcm10 replicat 63.7 5.5 0.00012 34.5 2.3 42 65-108 281-325 (344)
203 PRK12286 rpmF 50S ribosomal pr 63.5 4.8 0.0001 26.2 1.5 20 72-93 29-48 (57)
204 TIGR01031 rpmF_bact ribosomal 62.8 4.6 9.9E-05 26.0 1.3 21 71-93 27-47 (55)
205 TIGR01405 polC_Gram_pos DNA po 62.7 3.6 7.8E-05 40.8 1.1 27 71-99 684-720 (1213)
206 COG2995 PqiA Uncharacterized p 62.7 3.5 7.6E-05 36.7 0.9 24 71-94 221-244 (418)
207 CHL00174 accD acetyl-CoA carbo 62.5 4.1 8.9E-05 34.6 1.3 38 69-107 38-82 (296)
208 PRK04860 hypothetical protein; 62.5 18 0.0004 27.9 4.8 58 41-101 87-157 (160)
209 COG0384 Predicted epimerase, P 62.0 7.7 0.00017 32.7 2.8 49 40-98 32-80 (291)
210 CHL00104 rpl33 ribosomal prote 61.9 11 0.00024 25.4 3.0 31 68-99 10-62 (66)
211 PF10122 Mu-like_Com: Mu-like 61.6 5.3 0.00012 25.8 1.4 24 71-94 5-33 (51)
212 PF12677 DUF3797: Domain of un 61.6 3.8 8.2E-05 26.4 0.7 21 85-112 13-33 (49)
213 PRK07956 ligA NAD-dependent DN 61.4 11 0.00024 35.0 4.0 48 46-94 361-413 (665)
214 PRK00464 nrdR transcriptional 61.4 6.4 0.00014 30.3 2.1 23 87-110 2-24 (154)
215 PF09855 DUF2082: Nucleic-acid 61.3 7 0.00015 26.1 2.0 18 87-105 2-19 (64)
216 PF06677 Auto_anti-p27: Sjogre 60.5 7.8 0.00017 23.7 2.0 9 86-94 18-26 (41)
217 PF06827 zf-FPG_IleRS: Zinc fi 60.3 3.7 8E-05 22.8 0.4 14 87-102 3-16 (30)
218 COG1328 NrdD Oxygen-sensitive 60.2 5.1 0.00011 37.7 1.6 47 39-94 615-664 (700)
219 COG5270 PUA domain (predicted 59.7 7.8 0.00017 31.4 2.3 32 67-103 11-42 (202)
220 PRK12336 translation initiatio 59.6 11 0.00025 29.8 3.3 48 34-81 74-130 (201)
221 PTZ00255 60S ribosomal protein 59.4 9 0.00019 27.4 2.4 19 85-104 36-54 (90)
222 KOG3475 60S ribosomal protein 59.2 3.1 6.8E-05 29.7 0.0 23 72-94 18-40 (92)
223 PF14949 ARF7EP_C: ARF7 effect 58.9 5.4 0.00012 29.1 1.2 16 71-94 68-83 (103)
224 TIGR03831 YgiT_finger YgiT-typ 58.9 13 0.00027 21.6 2.7 22 88-110 1-24 (46)
225 TIGR00627 tfb4 transcription f 58.6 7.2 0.00016 32.7 2.1 26 68-94 253-278 (279)
226 PF02005 TRM: N2,N2-dimethylgu 58.4 7 0.00015 33.8 2.0 28 67-94 237-268 (377)
227 PRK12775 putative trifunctiona 58.3 5.3 0.00011 38.6 1.4 26 69-94 820-847 (1006)
228 PRK05333 NAD-dependent deacety 58.3 9 0.0002 31.5 2.6 13 68-80 126-138 (285)
229 KOG3084 NADH pyrophosphatase I 58.1 4.5 9.8E-05 35.1 0.8 12 85-97 150-161 (345)
230 TIGR00280 L37a ribosomal prote 58.0 10 0.00022 27.2 2.5 19 85-104 35-53 (91)
231 COG1998 RPS31 Ribosomal protei 57.9 6.6 0.00014 25.4 1.3 29 66-94 15-46 (51)
232 COG1379 PHP family phosphoeste 57.5 3.4 7.3E-05 36.3 -0.0 32 63-94 239-274 (403)
233 PRK09521 exosome complex RNA-b 57.3 6.5 0.00014 30.4 1.5 31 70-101 149-181 (189)
234 COG3791 Uncharacterized conser 57.1 7 0.00015 28.8 1.6 11 84-94 68-78 (133)
235 PRK06386 replication factor A; 56.9 7.2 0.00016 33.9 1.9 54 37-94 203-257 (358)
236 PF09082 DUF1922: Domain of un 56.6 6.1 0.00013 26.9 1.1 24 69-94 2-28 (68)
237 PF04216 FdhE: Protein involve 56.1 12 0.00027 30.6 3.1 10 85-94 172-181 (290)
238 TIGR00575 dnlj DNA ligase, NAD 56.1 15 0.00033 34.0 4.0 47 47-94 350-401 (652)
239 PRK03976 rpl37ae 50S ribosomal 55.9 12 0.00026 26.8 2.5 19 85-104 36-54 (90)
240 PF08646 Rep_fac-A_C: Replicat 55.6 19 0.00042 26.3 3.7 43 68-110 16-67 (146)
241 COG1066 Sms Predicted ATP-depe 55.6 9.2 0.0002 34.4 2.3 32 69-101 6-37 (456)
242 PF09862 DUF2089: Protein of u 54.1 16 0.00034 27.0 3.0 20 73-93 1-20 (113)
243 PTZ00409 Sir2 (Silent Informat 54.0 8.4 0.00018 31.8 1.7 26 68-94 135-173 (271)
244 PF13824 zf-Mss51: Zinc-finger 52.3 11 0.00023 24.7 1.7 22 73-94 2-23 (55)
245 PF14569 zf-UDP: Zinc-binding 52.3 2.9 6.3E-05 29.4 -1.0 28 71-100 37-64 (80)
246 PF10058 DUF2296: Predicted in 52.0 11 0.00025 24.1 1.8 27 67-93 19-52 (54)
247 PF08273 Prim_Zn_Ribbon: Zinc- 51.7 5.8 0.00013 24.2 0.3 20 86-108 4-23 (40)
248 COG3478 Predicted nucleic-acid 51.7 7.9 0.00017 26.4 1.0 14 88-102 7-20 (68)
249 PF14255 Cys_rich_CPXG: Cystei 51.6 19 0.00041 23.1 2.7 34 72-108 2-44 (52)
250 TIGR01384 TFS_arch transcripti 51.4 8.5 0.00018 26.7 1.2 23 72-94 2-25 (104)
251 TIGR01562 FdhE formate dehydro 51.0 18 0.00038 30.8 3.2 31 70-101 210-240 (305)
252 PF03854 zf-P11: P-11 zinc fin 50.9 3.6 7.7E-05 26.5 -0.7 23 71-94 22-44 (50)
253 PF13408 Zn_ribbon_recom: Reco 50.9 11 0.00023 22.9 1.5 10 85-94 5-14 (58)
254 PRK09678 DNA-binding transcrip 50.6 9.3 0.0002 26.1 1.2 20 86-106 2-21 (72)
255 PF12760 Zn_Tnp_IS1595: Transp 50.2 9.6 0.00021 23.1 1.2 10 85-94 18-27 (46)
256 PF15616 TerY-C: TerY-C metal 50.0 10 0.00022 28.7 1.5 22 72-94 91-114 (131)
257 TIGR00375 conserved hypothetic 50.0 11 0.00023 33.0 1.8 50 44-94 213-267 (374)
258 smart00440 ZnF_C2C2 C2C2 Zinc 49.9 26 0.00056 20.9 3.0 8 87-94 2-9 (40)
259 COG0498 ThrC Threonine synthas 49.9 9.8 0.00021 33.6 1.6 27 68-94 3-30 (411)
260 PF09334 tRNA-synt_1g: tRNA sy 49.9 20 0.00043 30.9 3.4 44 43-92 99-143 (391)
261 cd04511 Nudix_Hydrolase_4 Memb 49.8 38 0.00081 23.7 4.4 25 103-128 19-43 (130)
262 PF01747 ATP-sulfurylase: ATP- 49.4 24 0.00051 28.5 3.6 51 32-94 125-179 (215)
263 COG2816 NPY1 NTP pyrophosphohy 49.3 9.5 0.00021 32.2 1.4 28 71-99 112-142 (279)
264 TIGR01206 lysW lysine biosynth 48.7 16 0.00034 23.6 2.0 27 71-99 3-34 (54)
265 COG4640 Predicted membrane pro 48.5 8.9 0.00019 34.4 1.1 23 71-94 2-24 (465)
266 PF13453 zf-TFIIB: Transcripti 48.4 12 0.00027 22.1 1.4 13 88-102 2-14 (41)
267 COG1594 RPB9 DNA-directed RNA 48.4 7.7 0.00017 28.2 0.6 9 86-94 3-11 (113)
268 KOG1779 40s ribosomal protein 48.4 9.1 0.0002 27.0 0.9 24 71-94 35-62 (84)
269 COG4469 CoiA Competence protei 48.0 9 0.0002 33.3 1.1 10 85-94 25-34 (342)
270 COG2956 Predicted N-acetylgluc 47.9 4.8 0.0001 35.4 -0.6 36 60-98 346-381 (389)
271 PRK03564 formate dehydrogenase 47.7 23 0.00049 30.3 3.4 28 70-98 212-239 (309)
272 PF05876 Terminase_GpA: Phage 47.6 12 0.00026 33.9 1.8 29 66-94 196-238 (557)
273 COG4888 Uncharacterized Zn rib 47.4 15 0.00033 26.9 2.0 23 85-110 22-44 (104)
274 PRK14350 ligA NAD-dependent DN 47.3 20 0.00044 33.5 3.3 43 46-94 358-407 (669)
275 PRK04136 rpl40e 50S ribosomal 47.2 11 0.00024 24.1 1.1 27 70-98 14-40 (48)
276 PF08274 PhnA_Zn_Ribbon: PhnA 46.8 9.1 0.0002 22.0 0.6 21 73-93 5-27 (30)
277 KOG2906 RNA polymerase III sub 46.7 9.7 0.00021 28.0 0.9 9 86-94 2-10 (105)
278 PF10367 Vps39_2: Vacuolar sor 46.7 18 0.00039 24.3 2.2 31 75-110 71-101 (109)
279 PRK04011 peptide chain release 46.6 16 0.00035 31.9 2.4 27 68-94 326-359 (411)
280 cd03361 TOPRIM_TopoIA_RevGyr T 46.0 17 0.00037 27.8 2.2 26 68-94 75-100 (170)
281 COG2405 Predicted nucleic acid 45.7 17 0.00036 28.4 2.1 29 32-60 85-114 (157)
282 COG2816 NPY1 NTP pyrophosphohy 45.7 9.5 0.00021 32.3 0.8 10 85-94 111-120 (279)
283 PTZ00083 40S ribosomal protein 45.6 12 0.00026 26.6 1.2 25 70-94 35-63 (85)
284 TIGR01562 FdhE formate dehydro 45.6 11 0.00023 32.2 1.1 9 86-94 185-193 (305)
285 PF02132 RecR: RecR protein; 45.5 1.7 3.6E-05 26.2 -2.8 29 63-94 10-38 (41)
286 COG2995 PqiA Uncharacterized p 45.5 14 0.00029 33.0 1.8 32 67-100 15-51 (418)
287 TIGR03676 aRF1/eRF1 peptide ch 45.4 17 0.00036 31.8 2.3 27 68-94 318-351 (403)
288 COG1326 Uncharacterized archae 45.3 21 0.00046 28.9 2.7 23 86-108 31-60 (201)
289 COG4530 Uncharacterized protei 45.3 11 0.00024 28.4 1.0 24 71-94 10-35 (129)
290 COG1601 GCD7 Translation initi 45.1 5.9 0.00013 30.6 -0.4 41 41-81 91-137 (151)
291 PRK13764 ATPase; Provisional 45.1 21 0.00045 33.1 3.0 30 32-61 101-130 (602)
292 COG0777 AccD Acetyl-CoA carbox 45.1 10 0.00022 32.4 0.9 40 68-108 27-73 (294)
293 PF12674 Zn_ribbon_2: Putative 45.0 8.2 0.00018 26.6 0.3 23 86-110 1-24 (81)
294 COG0143 MetG Methionyl-tRNA sy 44.9 14 0.0003 33.9 1.8 30 63-92 119-149 (558)
295 PLN00209 ribosomal protein S27 44.8 12 0.00027 26.5 1.2 25 70-94 36-64 (86)
296 TIGR02820 formald_GSH S-(hydro 44.7 9.8 0.00021 30.1 0.7 16 83-99 87-102 (182)
297 PRK12267 methionyl-tRNA synthe 44.4 38 0.00083 30.8 4.5 32 63-94 118-152 (648)
298 PF04423 Rad50_zn_hook: Rad50 44.3 8.4 0.00018 24.0 0.3 8 87-94 22-29 (54)
299 PF02639 DUF188: Uncharacteriz 44.1 31 0.00067 25.7 3.3 32 33-64 51-82 (130)
300 PRK03564 formate dehydrogenase 44.1 18 0.00038 30.9 2.2 10 85-94 187-196 (309)
301 TIGR00340 zpr1_rel ZPR1-relate 44.0 12 0.00025 29.1 1.0 9 86-94 29-37 (163)
302 PRK05417 glutathione-dependent 44.0 9.3 0.0002 30.4 0.5 15 84-99 92-106 (191)
303 PF14447 Prok-RING_4: Prokaryo 43.9 16 0.00034 24.0 1.5 21 71-94 28-48 (55)
304 COG4260 Membrane protease subu 43.7 10 0.00023 32.7 0.8 10 85-94 334-343 (345)
305 PF01667 Ribosomal_S27e: Ribos 43.6 18 0.00039 23.6 1.7 28 70-99 7-38 (55)
306 PF11781 RRN7: RNA polymerase 43.5 11 0.00023 22.4 0.6 24 71-94 9-34 (36)
307 COG2401 ABC-type ATPase fused 43.0 17 0.00038 33.3 2.1 30 64-94 124-153 (593)
308 PF01873 eIF-5_eIF-2B: Domain 42.9 9.1 0.0002 28.4 0.3 36 43-78 81-122 (125)
309 PF14354 Lar_restr_allev: Rest 42.8 18 0.00039 22.6 1.6 12 86-98 4-15 (61)
310 COG3813 Uncharacterized protei 42.8 9.4 0.0002 26.8 0.3 35 66-102 22-56 (84)
311 PF13005 zf-IS66: zinc-finger 42.7 26 0.00057 20.8 2.3 17 61-77 31-47 (47)
312 PF00471 Ribosomal_L33: Riboso 42.5 12 0.00026 23.5 0.8 30 68-98 3-44 (48)
313 PF08996 zf-DNA_Pol: DNA Polym 42.3 17 0.00036 28.3 1.7 36 59-94 7-54 (188)
314 smart00532 LIGANc Ligase N fam 42.3 29 0.00063 30.8 3.3 47 46-94 356-408 (441)
315 COG2051 RPS27A Ribosomal prote 41.9 15 0.00031 25.1 1.1 26 69-94 18-47 (67)
316 PF06839 zf-GRF: GRF zinc fing 41.5 22 0.00047 21.5 1.8 23 87-111 2-25 (45)
317 COG0333 RpmF Ribosomal protein 41.5 17 0.00036 23.9 1.3 21 71-93 28-48 (57)
318 COG1412 Uncharacterized protei 41.3 33 0.00071 26.0 3.1 28 34-61 99-126 (136)
319 KOG2768 Translation initiation 41.3 15 0.00033 30.3 1.4 54 40-94 136-211 (231)
320 PF01096 TFIIS_C: Transcriptio 41.1 25 0.00054 20.8 2.0 8 87-94 2-9 (39)
321 PF01623 Carla_C4: Carlavirus 41.1 15 0.00033 26.3 1.2 24 69-94 52-75 (91)
322 PRK07217 replication factor A; 41.0 16 0.00035 31.3 1.6 39 64-105 182-224 (311)
323 COG1040 ComFC Predicted amidop 40.6 6.7 0.00014 31.4 -0.8 27 71-100 25-51 (225)
324 PF00628 PHD: PHD-finger; Int 40.4 23 0.00049 21.2 1.8 22 72-93 1-22 (51)
325 TIGR00622 ssl1 transcription f 40.2 17 0.00036 26.9 1.3 23 71-94 2-24 (112)
326 KOG4718 Non-SMC (structural ma 40.1 13 0.00029 30.7 0.8 29 64-93 188-224 (235)
327 PF01927 Mut7-C: Mut7-C RNAse 40.1 14 0.00031 27.4 1.0 13 70-82 124-136 (147)
328 PF06044 DRP: Dam-replacing fa 40.1 14 0.00031 30.9 1.0 14 86-100 32-45 (254)
329 PTZ00157 60S ribosomal protein 39.3 26 0.00056 24.8 2.1 19 85-104 9-27 (84)
330 cd00817 ValRS_core catalytic c 39.3 54 0.0012 27.9 4.5 30 63-94 133-162 (382)
331 COG1885 Uncharacterized protei 39.2 14 0.0003 27.5 0.7 17 84-102 48-64 (115)
332 COG0272 Lig NAD-dependent DNA 39.1 43 0.00093 31.6 4.0 49 48-99 363-416 (667)
333 PF10601 zf-LITAF-like: LITAF- 39.0 31 0.00067 22.6 2.4 19 83-102 5-23 (73)
334 PF15135 UPF0515: Uncharacteri 38.9 14 0.00031 31.1 0.9 25 70-94 132-164 (278)
335 PRK00566 DNA-directed RNA poly 38.9 14 0.0003 36.8 0.9 31 71-102 58-89 (1156)
336 PF05129 Elf1: Transcription e 38.7 19 0.00041 24.8 1.3 20 85-107 22-41 (81)
337 PRK01343 zinc-binding protein; 38.6 16 0.00036 24.0 1.0 9 86-94 10-18 (57)
338 PRK14892 putative transcriptio 38.4 22 0.00048 25.6 1.7 10 85-94 42-51 (99)
339 PRK13794 hypothetical protein; 38.2 25 0.00055 31.3 2.4 32 67-103 7-38 (479)
340 PF12387 Peptidase_C74: Pestiv 37.9 16 0.00034 29.5 0.9 43 42-94 142-184 (200)
341 PRK05767 rpl44e 50S ribosomal 37.7 28 0.00061 25.0 2.1 19 85-104 8-26 (92)
342 TIGR00108 eRF peptide chain re 37.3 28 0.00061 30.4 2.5 27 68-94 322-355 (409)
343 PRK14529 adenylate kinase; Pro 37.3 16 0.00035 29.3 0.9 28 71-99 127-161 (223)
344 smart00547 ZnF_RBZ Zinc finger 37.2 20 0.00042 18.9 1.0 22 72-94 4-25 (26)
345 PRK10445 endonuclease VIII; Pr 37.1 23 0.00049 29.0 1.8 16 85-102 235-250 (263)
346 TIGR00201 comF comF family pro 37.1 17 0.00037 27.8 1.0 21 73-94 1-21 (190)
347 COG3058 FdhE Uncharacterized p 37.1 24 0.00053 30.3 2.0 11 84-94 184-194 (308)
348 TIGR00595 priA primosomal prot 36.9 17 0.00036 32.5 1.0 19 70-94 213-231 (505)
349 COG5349 Uncharacterized protei 36.8 13 0.00028 28.1 0.3 27 68-94 19-49 (126)
350 PRK07225 DNA-directed RNA poly 36.5 25 0.00054 32.5 2.1 33 69-101 543-578 (605)
351 PRK00133 metG methionyl-tRNA s 36.5 48 0.001 30.5 4.0 32 63-94 116-148 (673)
352 PF03884 DUF329: Domain of unk 36.4 24 0.00052 23.1 1.5 9 72-80 4-12 (57)
353 smart00714 LITAF Possible memb 36.2 37 0.0008 21.9 2.4 18 85-103 3-20 (67)
354 PRK14810 formamidopyrimidine-D 36.1 25 0.00054 28.9 1.8 16 85-102 244-259 (272)
355 PRK14873 primosome assembly pr 35.9 22 0.00049 33.0 1.7 21 68-94 381-401 (665)
356 KOG3362 Predicted BBOX Zn-fing 35.8 18 0.00038 28.3 0.9 20 75-94 108-127 (156)
357 PRK12495 hypothetical protein; 35.7 18 0.0004 29.8 1.0 24 71-94 43-67 (226)
358 PRK13795 hypothetical protein; 35.7 34 0.00073 31.5 2.8 33 66-103 8-40 (636)
359 PF09567 RE_MamI: MamI restric 35.6 16 0.00035 31.1 0.7 28 71-100 83-110 (314)
360 PRK14351 ligA NAD-dependent DN 35.6 49 0.0011 31.1 3.9 44 47-94 384-432 (689)
361 PF00641 zf-RanBP: Zn-finger i 35.1 27 0.00059 19.1 1.4 22 72-94 6-27 (30)
362 PRK00076 recR recombination pr 35.0 20 0.00042 28.8 1.1 29 63-94 46-74 (196)
363 PF03367 zf-ZPR1: ZPR1 zinc-fi 34.9 35 0.00076 26.2 2.4 23 87-110 3-26 (161)
364 PF00096 zf-C2H2: Zinc finger, 34.9 23 0.00049 17.7 1.0 12 71-82 1-12 (23)
365 PRK01110 rpmF 50S ribosomal pr 34.3 24 0.00051 23.1 1.2 20 71-93 28-47 (60)
366 PF01599 Ribosomal_S27: Riboso 34.2 26 0.00057 22.1 1.4 27 67-93 15-46 (47)
367 TIGR02387 rpoC1_cyan DNA-direc 34.1 21 0.00046 33.3 1.3 32 67-101 60-92 (619)
368 COG1675 TFA1 Transcription ini 34.1 17 0.00037 28.7 0.6 25 70-94 113-141 (176)
369 PRK12268 methionyl-tRNA synthe 33.8 57 0.0012 28.9 3.9 30 63-92 118-148 (556)
370 KOG0806 Carbon-nitrogen hydrol 33.7 85 0.0019 26.8 4.7 75 42-128 84-159 (298)
371 PF01363 FYVE: FYVE zinc finge 33.7 22 0.00048 22.6 1.0 10 69-78 24-33 (69)
372 CHL00018 rpoC1 RNA polymerase 33.7 20 0.00044 33.7 1.1 30 72-102 68-101 (663)
373 PRK14894 glycyl-tRNA synthetas 33.5 27 0.00059 32.1 1.8 34 64-98 82-116 (539)
374 PRK02625 rpoC1 DNA-directed RN 33.4 22 0.00048 33.3 1.3 23 71-94 69-92 (627)
375 PF11682 DUF3279: Protein of u 32.9 26 0.00057 26.4 1.4 22 71-94 98-119 (128)
376 PF09889 DUF2116: Uncharacteri 32.6 20 0.00044 23.6 0.7 10 85-94 3-12 (59)
377 PF04296 DUF448: Protein of un 32.3 55 0.0012 22.0 2.8 37 72-122 3-39 (78)
378 PLN02189 cellulose synthase 32.2 18 0.00039 35.7 0.5 27 72-100 63-89 (1040)
379 PRK10996 thioredoxin 2; Provis 32.0 35 0.00077 24.7 1.9 24 71-94 3-31 (139)
380 COG1571 Predicted DNA-binding 32.0 22 0.00049 31.7 1.0 32 63-94 340-376 (421)
381 TIGR03655 anti_R_Lar restricti 31.6 61 0.0013 20.1 2.8 9 86-94 2-10 (53)
382 PRK14526 adenylate kinase; Pro 31.5 25 0.00054 27.7 1.1 25 70-94 122-151 (211)
383 PF08458 PH_2: Plant pleckstri 31.5 70 0.0015 23.6 3.4 29 87-116 5-33 (110)
384 TIGR00339 sopT ATP sulphurylas 31.5 59 0.0013 28.3 3.5 45 37-93 300-348 (383)
385 PF07503 zf-HYPF: HypF finger; 31.4 13 0.00028 22.0 -0.4 22 73-94 2-30 (35)
386 PLN02915 cellulose synthase A 31.4 18 0.00038 35.8 0.3 26 72-99 44-69 (1044)
387 TIGR03670 rpoB_arch DNA-direct 31.1 37 0.0008 31.4 2.3 32 69-100 537-571 (599)
388 PRK08764 ferredoxin; Provision 31.0 42 0.00092 24.6 2.2 40 39-78 48-92 (135)
389 TIGR00577 fpg formamidopyrimid 31.0 33 0.00072 28.1 1.8 16 85-102 245-260 (272)
390 PF13920 zf-C3HC4_3: Zinc fing 30.7 20 0.00043 21.6 0.4 29 69-100 22-50 (50)
391 PRK00418 DNA gyrase inhibitor; 30.6 25 0.00055 23.5 0.9 9 71-79 7-15 (62)
392 smart00778 Prim_Zn_Ribbon Zinc 30.5 24 0.00053 21.1 0.7 9 86-94 4-12 (37)
393 PF10083 DUF2321: Uncharacteri 30.4 4.3 9.3E-05 31.8 -3.3 32 59-94 12-48 (158)
394 PHA02325 hypothetical protein 30.1 24 0.00053 24.1 0.7 14 84-98 2-15 (72)
395 PF07649 C1_3: C1-like domain; 30.0 25 0.00054 19.4 0.7 21 72-92 2-22 (30)
396 KOG0402 60S ribosomal protein 29.8 16 0.00036 26.1 -0.1 17 85-102 36-52 (92)
397 PF01485 IBR: IBR domain; Int 29.8 24 0.00052 21.5 0.6 23 72-94 20-49 (64)
398 KOG2264 Exostosin EXT1L [Signa 29.7 63 0.0014 30.8 3.5 34 40-79 820-853 (907)
399 PRK01103 formamidopyrimidine/5 29.7 36 0.00078 27.8 1.8 16 85-102 245-260 (274)
400 PF05495 zf-CHY: CHY zinc fing 29.7 33 0.0007 22.8 1.3 24 70-93 41-69 (71)
401 PRK14811 formamidopyrimidine-D 29.5 36 0.00078 27.9 1.8 22 78-102 229-250 (269)
402 PRK04149 sat sulfate adenylylt 29.4 65 0.0014 28.3 3.4 48 32-91 290-342 (391)
403 smart00064 FYVE Protein presen 29.3 33 0.00072 21.7 1.3 24 71-94 11-35 (68)
404 PF06170 DUF983: Protein of un 29.2 21 0.00046 24.9 0.4 15 85-101 8-22 (86)
405 cd00517 ATPS ATP-sulfurylase. 29.2 86 0.0019 27.1 4.1 41 37-89 270-314 (353)
406 KOG3940 Uncharacterized conser 29.0 29 0.00064 30.2 1.2 53 42-94 293-347 (351)
407 PF11706 zf-CGNR: CGNR zinc fi 29.0 14 0.0003 22.9 -0.6 24 71-94 3-34 (44)
408 PF15288 zf-CCHC_6: Zinc knuck 28.9 22 0.00049 21.8 0.4 22 71-92 2-23 (40)
409 PF06061 Baculo_ME53: Baculovi 28.8 23 0.0005 30.5 0.6 24 71-94 261-286 (327)
410 TIGR00244 transcriptional regu 28.6 55 0.0012 25.3 2.5 8 87-94 2-9 (147)
411 cd07973 Spt4 Transcription elo 28.5 31 0.00068 24.7 1.1 21 72-92 5-27 (98)
412 KOG3799 Rab3 effector RIM1 and 28.3 20 0.00043 28.0 0.1 14 85-98 89-102 (169)
413 PF04959 ARS2: Arsenite-resist 28.3 26 0.00057 28.4 0.8 22 61-82 68-89 (214)
414 PRK13945 formamidopyrimidine-D 28.2 39 0.00085 27.8 1.8 16 85-102 254-269 (282)
415 TIGR00398 metG methionyl-tRNA 28.2 81 0.0018 27.8 3.9 26 68-93 118-144 (530)
416 TIGR02159 PA_CoA_Oxy4 phenylac 28.2 34 0.00074 25.9 1.3 11 86-96 106-116 (146)
417 PF04032 Rpr2: RNAse P Rpr2/Rp 28.0 30 0.00066 22.7 0.9 11 84-94 45-55 (85)
418 smart00290 ZnF_UBP Ubiquitin C 27.9 29 0.00062 20.7 0.7 19 72-93 1-19 (50)
419 PF06397 Desulfoferrod_N: Desu 27.7 56 0.0012 19.5 1.9 20 86-110 7-26 (36)
420 PF10609 ParA: ParA/MinD ATPas 27.6 21 0.00046 24.8 0.1 14 81-94 61-74 (81)
421 COG0068 HypF Hydrogenase matur 27.5 21 0.00046 34.0 0.1 24 71-94 152-182 (750)
422 PRK00423 tfb transcription ini 27.5 27 0.00058 29.1 0.7 24 71-94 12-39 (310)
423 PRK13844 recombination protein 27.5 30 0.00066 27.9 1.0 29 63-94 50-78 (200)
424 cd00065 FYVE FYVE domain; Zinc 27.4 40 0.00086 20.5 1.3 7 73-79 5-11 (57)
425 PLN02436 cellulose synthase A 27.3 25 0.00055 34.9 0.6 27 72-100 65-91 (1094)
426 PF14149 YhfH: YhfH-like prote 27.3 14 0.0003 22.4 -0.8 15 80-94 8-22 (37)
427 PLN02638 cellulose synthase A 27.2 22 0.00047 35.3 0.2 23 72-94 46-68 (1079)
428 PF04161 Arv1: Arv1-like famil 27.2 27 0.00058 27.6 0.6 24 71-94 1-33 (208)
429 PRK00939 translation initiatio 27.1 32 0.00069 24.6 0.9 9 86-94 2-10 (99)
430 PF04438 zf-HIT: HIT zinc fing 26.7 36 0.00078 19.3 1.0 20 71-94 3-22 (30)
431 COG3809 Uncharacterized protei 26.5 32 0.00069 24.4 0.8 28 71-99 2-34 (88)
432 PF13913 zf-C2HC_2: zinc-finge 26.2 30 0.00064 18.6 0.5 9 86-94 3-11 (25)
433 COG5319 Uncharacterized protei 26.1 19 0.00042 27.6 -0.3 16 83-99 30-45 (142)
434 smart00647 IBR In Between Ring 26.0 55 0.0012 19.9 1.8 9 86-94 49-57 (64)
435 cd00279 YlxR Ylxr homologs; gr 25.6 86 0.0019 21.4 2.8 38 71-122 3-40 (79)
436 PLN02195 cellulose synthase A 25.6 31 0.00066 33.9 0.8 23 72-94 35-57 (977)
437 PF02348 CTP_transf_3: Cytidyl 25.5 1E+02 0.0022 23.0 3.6 25 33-57 41-65 (217)
438 PRK10246 exonuclease subunit S 25.5 29 0.00063 33.6 0.7 9 86-94 504-512 (1047)
439 PF05743 UEV: UEV domain; Int 25.5 47 0.001 24.2 1.6 31 99-129 18-52 (121)
440 TIGR00615 recR recombination p 25.4 19 0.00041 28.9 -0.5 29 63-94 46-74 (195)
441 PF03811 Zn_Tnp_IS1: InsA N-te 25.4 44 0.00096 19.8 1.2 13 86-99 6-19 (36)
442 KOG0856 Predicted pilin-like t 25.1 67 0.0014 24.9 2.4 47 47-94 32-78 (146)
443 COG4311 SoxD Sarcosine oxidase 24.9 34 0.00073 24.9 0.7 10 85-94 3-12 (97)
444 PRK09401 reverse gyrase; Revie 24.8 34 0.00074 34.0 1.0 27 67-94 675-701 (1176)
445 COG2824 PhnA Uncharacterized Z 24.6 35 0.00076 25.3 0.8 26 69-94 2-29 (112)
446 KOG2907 RNA polymerase I trans 24.6 33 0.00072 25.6 0.7 10 85-94 74-83 (116)
447 PRK00124 hypothetical protein; 24.6 1E+02 0.0022 23.8 3.3 43 20-63 55-97 (151)
448 KOG2593 Transcription initiati 24.6 33 0.00071 30.9 0.7 26 69-94 127-162 (436)
449 PRK07418 acetolactate synthase 24.5 35 0.00075 30.8 0.9 23 71-94 593-615 (616)
450 COG1671 Uncharacterized protei 24.3 92 0.002 24.2 3.1 47 15-62 49-95 (150)
451 smart00259 ZnF_A20 A20-like zi 24.3 30 0.00065 19.2 0.3 20 72-91 3-24 (26)
452 PF14952 zf-tcix: Putative tre 24.2 32 0.0007 21.6 0.5 9 86-94 12-20 (44)
453 COG4049 Uncharacterized protei 24.1 27 0.00059 23.4 0.1 14 69-82 16-29 (65)
454 PF11822 DUF3342: Domain of un 23.9 96 0.0021 26.8 3.4 48 68-120 178-235 (317)
455 TIGR00143 hypF [NiFe] hydrogen 23.9 27 0.00058 32.8 0.1 27 68-94 116-149 (711)
456 PF03243 MerB: Alkylmercury ly 23.8 78 0.0017 23.1 2.5 19 86-109 40-58 (127)
457 PF12225 MTHFR_C: Methylene-te 23.6 43 0.00092 24.1 1.1 28 63-90 13-40 (97)
458 PLN02400 cellulose synthase 23.6 38 0.00083 33.7 1.1 28 71-100 64-91 (1085)
459 TIGR01079 rplX_bact ribosomal 23.5 85 0.0018 22.6 2.6 23 85-110 71-93 (104)
460 COG1631 RPL42A Ribosomal prote 23.4 52 0.0011 23.8 1.5 18 85-103 8-25 (94)
461 PF03966 Trm112p: Trm112p-like 23.3 45 0.00097 21.6 1.0 42 40-82 18-65 (68)
462 COG0551 TopA Zn-finger domain 23.2 51 0.0011 24.1 1.4 17 82-99 14-30 (140)
463 PF14835 zf-RING_6: zf-RING of 23.1 25 0.00054 23.8 -0.2 12 87-98 42-53 (65)
464 KOG2807 RNA polymerase II tran 22.9 51 0.0011 29.0 1.6 27 67-94 273-299 (378)
465 PF11672 DUF3268: Protein of u 22.7 37 0.00081 24.6 0.6 13 86-98 3-15 (102)
466 PF05605 zf-Di19: Drought indu 22.7 49 0.0011 20.4 1.1 10 85-94 31-40 (54)
467 PF10005 DUF2248: Uncharacteri 22.7 48 0.001 28.9 1.4 21 72-94 1-22 (343)
468 PF06750 DiS_P_DiS: Bacterial 22.7 42 0.00092 23.4 0.9 10 85-94 33-42 (92)
469 TIGR00269 conserved hypothetic 22.6 37 0.00079 23.9 0.6 9 86-94 81-89 (104)
470 PRK03922 hypothetical protein; 22.5 67 0.0015 23.9 1.9 18 83-102 47-64 (113)
471 PF14311 DUF4379: Domain of un 22.5 73 0.0016 19.7 1.9 25 67-91 25-55 (55)
472 PRK14906 DNA-directed RNA poly 22.3 32 0.0007 35.2 0.3 31 71-102 60-91 (1460)
473 PRK06824 translation initiatio 22.1 47 0.001 24.6 1.1 16 79-94 10-25 (118)
474 COG1779 C4-type Zn-finger prot 22.0 64 0.0014 26.2 1.9 18 85-104 14-31 (201)
475 PRK05580 primosome assembly pr 21.8 44 0.00096 30.9 1.1 9 71-79 382-390 (679)
476 KOG1253 tRNA methyltransferase 21.8 66 0.0014 29.6 2.1 14 67-80 299-312 (525)
477 KOG4275 Predicted E3 ubiquitin 21.7 11 0.00024 32.6 -2.6 19 71-94 322-340 (350)
478 PF04475 DUF555: Protein of un 21.5 64 0.0014 23.6 1.6 17 84-102 46-62 (102)
479 PRK11595 DNA utilization prote 21.4 35 0.00075 27.0 0.3 8 87-94 36-43 (227)
480 PF00703 Glyco_hydro_2: Glycos 21.2 88 0.0019 20.3 2.2 21 92-113 82-102 (110)
481 PF13901 DUF4206: Domain of un 21.2 58 0.0013 25.6 1.5 24 70-93 172-197 (202)
482 PF05502 Dynactin_p62: Dynacti 20.6 63 0.0014 29.0 1.7 15 87-103 54-68 (483)
483 PF09986 DUF2225: Uncharacteri 20.5 66 0.0014 25.5 1.7 16 85-102 5-20 (214)
484 COG4416 Com Mu-like prophage p 20.4 33 0.00072 22.7 -0.0 24 71-94 5-33 (60)
485 PF06054 CoiA: Competence prot 20.3 57 0.0012 28.1 1.4 10 85-94 30-39 (375)
486 COG1138 CcmF Cytochrome c biog 20.1 48 0.001 31.2 0.9 18 35-52 59-76 (648)
487 smart00249 PHD PHD zinc finger 20.1 70 0.0015 17.7 1.3 22 73-94 2-23 (47)
488 smart00734 ZnF_Rad18 Rad18-lik 20.1 49 0.0011 18.0 0.6 9 86-94 2-10 (26)
489 PF14471 DUF4428: Domain of un 20.0 59 0.0013 20.5 1.1 7 88-94 2-8 (51)
490 TIGR00570 cdk7 CDK-activating 20.0 30 0.00065 29.7 -0.4 28 72-101 30-57 (309)
No 1
>KOG2463 consensus Predicted RNA-binding protein Nob1p involved in 26S proteasome assembly [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=9.6e-44 Score=298.70 Aligned_cols=104 Identities=46% Similarity=0.811 Sum_probs=97.7
Q ss_pred eeeec--------------CCCceeeEeechHHHHHHHHHhCceeecCCCCcceeeeeEEEEccCccccccccCccccCC
Q 032998 25 WMLRS--------------LSESTVACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPK 90 (129)
Q Consensus 25 wi~~~--------------~~~~~va~~TdDyamQNVl~~lGL~~~s~~g~~I~~~k~W~~rC~~C~k~~~~~~~~fCp~ 90 (129)
|||++ +.+..|+|+|+||||||||+||||+++++.|++|+++++|++||||||+++++|++.|||+
T Consensus 183 witp~ni~~~~~e~~al~~pe~~~Vac~TtDfamQNVlLqm~L~l~~~~G~~Ir~~r~~iLRCh~Cfsit~~m~k~FCp~ 262 (376)
T KOG2463|consen 183 WITPSNITEAIIELGALNRPENQLVACLTTDFAMQNVLLQMNLNLLAMSGMKIRSVRSYILRCHGCFSITSEMPKDFCPS 262 (376)
T ss_pred ccccchHHHHHHhhhcccccccceeeeecccHHHHHHHHHhcccccCccchhhhhhhhheeEeeeeeEecCccchhcccc
Confidence 99976 2567899999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCceeEEEEEeCCCceEEeec--CCccccCceeecCCC
Q 032998 91 CGNGGTLRKVAVTVGENGIVLASR--RPRITLRGTKVSISL 129 (129)
Q Consensus 91 CG~~~tL~rv~v~v~~~G~~~~~~--~~~~n~RG~~ySlP~ 129 (129)
||++ ||+|++|+|++||+++.|. |++||+||++||||+
T Consensus 263 CG~~-TL~K~aVsv~~dG~~~~h~k~r~~~n~RG~~YSlp~ 302 (376)
T KOG2463|consen 263 CGHK-TLTKCAVSVDEDGNGQTHFKKRFQWNNRGLQYSLPK 302 (376)
T ss_pred cCCC-eeeEEEEEecCCCceeEEeecccccccCcceeecCC
Confidence 9999 9999999999999987664 556999999999996
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=99.96 E-value=9.2e-31 Score=179.18 Aligned_cols=67 Identities=43% Similarity=0.933 Sum_probs=24.5
Q ss_pred cceeeeeEEEEccCccccccccCccccCCCCCCCceeEEEEEeCCCceEEeec--CCccccCceeecCCC
Q 032998 62 QIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGENGIVLASR--RPRITLRGTKVSISL 129 (129)
Q Consensus 62 ~I~~~k~W~~rC~~C~k~~~~~~~~fCp~CG~~~tL~rv~v~v~~~G~~~~~~--~~~~n~RG~~ySlP~ 129 (129)
+|+++++|+|||+|||+++.+|++.|||+|||+ ||+||+|+||+||++++|. ++++|+||++||||+
T Consensus 1 rIk~~k~~vlrC~aCf~~t~~~~k~FCp~CGn~-TL~rvsvsv~~~G~~~~~~~~~~~~n~RG~~ySlPk 69 (73)
T PF08772_consen 1 RIKRVKTWVLRCHACFKITKDMTKQFCPKCGNA-TLKRVSVSVDEDGKIKLHLKKNFQWNLRGTKYSLPK 69 (73)
T ss_dssp -------EEEE-SSS--EES-SS--S-SSS--S---EEEE-B--SS---B--------------------
T ss_pred CcchhheeeEEccccccCcCCCCceeCcccCCC-cceEEEEEECCCCCEEEEecCCceeccCCCCccCCC
Confidence 589999999999999999999999999999998 9999999999999987664 457999999999996
No 3
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=99.91 E-value=2.2e-25 Score=174.16 Aligned_cols=69 Identities=39% Similarity=0.703 Sum_probs=60.4
Q ss_pred CceeeEeechHHHHHHHHHhCceeec-CCCCcceeeeeEEEEccCccccccccCccccCCCCCCCceeEEEE
Q 032998 32 ESTVACITGDYAMQNVILQMGLRLLA-PGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAV 102 (129)
Q Consensus 32 ~~~va~~TdDyamQNVl~~lGL~~~s-~~g~~I~~~k~W~~rC~~C~k~~~~~~~~fCp~CG~~~tL~rv~v 102 (129)
+.+|+++||||+|||||++|||+|.+ ..+.+|+++++|++||+||+++|+ ++++|||.||++ ++++...
T Consensus 100 ~~~v~l~TdDysvQNVa~~Lgi~~~~~~~~~~I~~v~~w~~rC~GC~~~f~-~~~~~Cp~CG~~-~~~~~~~ 169 (177)
T COG1439 100 EVQVALATDDYSVQNVALQLGLNVRSISYKGKIKKVRKWRLRCHGCKRIFP-EPKDFCPICGSP-LKRKRVK 169 (177)
T ss_pred ccceeEEecchHHHHHHHHhCceEEeeeccCccceEeeeeEEEecCceecC-CCCCcCCCCCCc-eEEeeec
Confidence 36689999999999999999999997 445569999999999999999998 678999999999 6655443
No 4
>PRK12496 hypothetical protein; Provisional
Probab=99.83 E-value=4.1e-21 Score=147.52 Aligned_cols=69 Identities=23% Similarity=0.434 Sum_probs=62.1
Q ss_pred CceeeEeechHHHHHHHHHhCceeecCCCCcceeeeeEEEEccCcccccccc-CccccCCCCCCCceeEEEE
Q 032998 32 ESTVACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEI-GRIFCPKCGNGGTLRKVAV 102 (129)
Q Consensus 32 ~~~va~~TdDyamQNVl~~lGL~~~s~~g~~I~~~k~W~~rC~~C~k~~~~~-~~~fCp~CG~~~tL~rv~v 102 (129)
+.++.++||||++||||.+|||++.++.+++|+++++|+++|+||++.|+.. ..+|||+||++ |+|...
T Consensus 89 el~~~lvtDD~~~~~vA~~lgi~v~~~~~~~i~~~~~w~~~C~gC~~~~~~~~~~~~C~~CG~~--~~r~~~ 158 (164)
T PRK12496 89 ELNGTLYTDDYGIQNVAKKLNIKFENIKTKGIKKVIKWRKVCKGCKKKYPEDYPDDVCEICGSP--VKRKMV 158 (164)
T ss_pred HhCCcEECcHHHHHHHHHHcCCeEeccccccchhheeeeEECCCCCccccCCCCCCcCCCCCCh--hhhcch
Confidence 5678999999999999999999999999999999999999999999999753 46899999998 666543
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=97.90 E-value=7.4e-06 Score=65.88 Aligned_cols=28 Identities=21% Similarity=0.402 Sum_probs=25.7
Q ss_pred CCceeeEeechHHHHHHHHHhCceeecC
Q 032998 31 SESTVACITGDYAMQNVILQMGLRLLAP 58 (129)
Q Consensus 31 ~~~~va~~TdDyamQNVl~~lGL~~~s~ 58 (129)
.+++++++||||+|||+|.+|||++++.
T Consensus 168 ~ELda~lvTdD~giqn~A~~Lgi~~~~~ 195 (206)
T TIGR03875 168 KELDAAVVSADEGIRKWAERLGLRFVDA 195 (206)
T ss_pred HHcCcEEEeCcHHHHHHHHHcCCeeecH
Confidence 4789999999999999999999999873
No 6
>PRK04358 hypothetical protein; Provisional
Probab=97.75 E-value=1.6e-05 Score=64.45 Aligned_cols=28 Identities=21% Similarity=0.402 Sum_probs=25.7
Q ss_pred CCceeeEeechHHHHHHHHHhCceeecC
Q 032998 31 SESTVACITGDYAMQNVILQMGLRLLAP 58 (129)
Q Consensus 31 ~~~~va~~TdDyamQNVl~~lGL~~~s~ 58 (129)
.+.+++++||||+|||+|.+|||++++.
T Consensus 172 ~ELda~lvTdD~giqn~A~~LGI~~~~~ 199 (217)
T PRK04358 172 KELDAAVVSADEGIRKWAERLGLRFVDA 199 (217)
T ss_pred HHhCCEEEeCCHHHHHHHHHcCCeeecH
Confidence 4689999999999999999999999874
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=96.96 E-value=0.001 Score=40.61 Aligned_cols=32 Identities=25% Similarity=0.619 Sum_probs=24.5
Q ss_pred eEEEEccCccccccc------cCccccCCCCCCCceeEE
Q 032998 68 RWILKCHACYTITAE------IGRIFCPKCGNGGTLRKV 100 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~------~~~~fCp~CG~~~tL~rv 100 (129)
.|.|+|..|+..+.. .....||.||+. .++|+
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 478999999966642 235789999996 68875
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=96.90 E-value=0.00075 Score=39.79 Aligned_cols=31 Identities=23% Similarity=0.593 Sum_probs=23.2
Q ss_pred eEEEEccCccccccc------cCccccCCCCCCCceeEE
Q 032998 68 RWILKCHACYTITAE------IGRIFCPKCGNGGTLRKV 100 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~------~~~~fCp~CG~~~tL~rv 100 (129)
.|.++|..|++.+.. .....||.||.+ ++|+
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 478999999997642 224679999996 6664
No 9
>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=96.84 E-value=0.00057 Score=55.07 Aligned_cols=29 Identities=28% Similarity=0.481 Sum_probs=17.7
Q ss_pred CCceeeEeechHHHHHHHHHhCceeecCC
Q 032998 31 SESTVACITGDYAMQNVILQMGLRLLAPG 59 (129)
Q Consensus 31 ~~~~va~~TdDyamQNVl~~lGL~~~s~~ 59 (129)
.|.+++++|+||+|||+|.+|||+++...
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 47899999999999999999999998764
No 10
>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=96.75 E-value=0.0015 Score=40.74 Aligned_cols=33 Identities=27% Similarity=0.628 Sum_probs=24.1
Q ss_pred eEEEEccCcccccccc------CccccCCCCCCCceeEEE
Q 032998 68 RWILKCHACYTITAEI------GRIFCPKCGNGGTLRKVA 101 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~~------~~~fCp~CG~~~tL~rv~ 101 (129)
.|.|+|..|+..+... ....||.||+. .++|+-
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 4789999999866542 12469999996 576653
No 11
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=96.68 E-value=0.00063 Score=37.73 Aligned_cols=23 Identities=30% Similarity=0.761 Sum_probs=18.4
Q ss_pred EEccCccccccccCccccCCCCCC
Q 032998 71 LKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
..|+.|++.-. ..-.|||.||.+
T Consensus 3 ~~Cp~Cg~~~~-~~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAEID-PDAKFCPNCGAK 25 (26)
T ss_pred CCCcccCCcCC-cccccChhhCCC
Confidence 57999999543 356999999986
No 12
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=96.52 E-value=0.0009 Score=36.45 Aligned_cols=22 Identities=32% Similarity=0.860 Sum_probs=18.2
Q ss_pred EccCccccccccCccccCCCCCC
Q 032998 72 KCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 72 rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
+|+-|++...+ .-.|||.||.+
T Consensus 1 ~Cp~CG~~~~~-~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIED-DAKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCC-cCcchhhhCCc
Confidence 59999987765 35899999986
No 13
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=95.79 E-value=0.017 Score=43.51 Aligned_cols=44 Identities=30% Similarity=0.559 Sum_probs=33.0
Q ss_pred eeeeeEEEEccCccccccccCccccCCCCCCCceeEEEEEeCCCceE
Q 032998 64 RQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGENGIV 110 (129)
Q Consensus 64 ~~~k~W~~rC~~C~k~~~~~~~~fCp~CG~~~tL~rv~v~v~~~G~~ 110 (129)
++-+...-+|..||+++.. ++.+||.||+++.+.-|. +...|.+
T Consensus 23 ~~~kl~g~kC~~CG~v~~P-Pr~~Cp~C~~~~~~E~ve--ls~~G~V 66 (140)
T COG1545 23 KEGKLLGTKCKKCGRVYFP-PRAYCPKCGSETELEWVE--LSGEGKV 66 (140)
T ss_pred hhCcEEEEEcCCCCeEEcC-CcccCCCCCCCCceEEEE--eCCCeEE
Confidence 3345667899999999975 589999999984345444 4677876
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=95.77 E-value=0.0071 Score=35.56 Aligned_cols=27 Identities=26% Similarity=0.656 Sum_probs=16.4
Q ss_pred eeEEEEccCccccccccCccccCCCCCC
Q 032998 67 HRWILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 67 k~W~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
+-...+|..|++++.. ++.+||.||+.
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 4567899999998764 47999999986
No 15
>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=95.72 E-value=0.0078 Score=43.82 Aligned_cols=28 Identities=21% Similarity=0.333 Sum_probs=21.3
Q ss_pred eeEEEEccCccccccccC-ccccCCCCCC
Q 032998 67 HRWILKCHACYTITAEIG-RIFCPKCGNG 94 (129)
Q Consensus 67 k~W~~rC~~C~k~~~~~~-~~fCp~CG~~ 94 (129)
..-+.+|..|++.+.... ...||.||++
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (115)
T TIGR00100 67 EPVECECEDCSEEVSPEIDLYRCPKCHGI 95 (115)
T ss_pred eCcEEEcccCCCEEecCCcCccCcCCcCC
Confidence 344589999998886543 3449999998
No 16
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=95.67 E-value=0.0081 Score=43.75 Aligned_cols=28 Identities=21% Similarity=0.497 Sum_probs=21.0
Q ss_pred eeEEEEccCccccccccC-c-cccCCCCCC
Q 032998 67 HRWILKCHACYTITAEIG-R-IFCPKCGNG 94 (129)
Q Consensus 67 k~W~~rC~~C~k~~~~~~-~-~fCp~CG~~ 94 (129)
..-..+|..|+..++... . ..||.||+.
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~ 96 (114)
T PRK03681 67 QEAECWCETCQQYVTLLTQRVRRCPQCHGD 96 (114)
T ss_pred eCcEEEcccCCCeeecCCccCCcCcCcCCC
Confidence 345689999998876532 2 449999997
No 17
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=95.63 E-value=0.01 Score=43.44 Aligned_cols=31 Identities=19% Similarity=0.427 Sum_probs=22.3
Q ss_pred eeEEEEccCccccccccC-ccc-cCCCCCCCcee
Q 032998 67 HRWILKCHACYTITAEIG-RIF-CPKCGNGGTLR 98 (129)
Q Consensus 67 k~W~~rC~~C~k~~~~~~-~~f-Cp~CG~~~tL~ 98 (129)
..-..+|..|+..+.... ..+ ||.||++ .++
T Consensus 68 vp~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~-~~~ 100 (117)
T PRK00564 68 EKVELECKDCSHVFKPNALDYGVCEKCHSK-NVI 100 (117)
T ss_pred cCCEEEhhhCCCccccCCccCCcCcCCCCC-ceE
Confidence 345689999998776543 344 9999998 443
No 18
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=95.62 E-value=0.01 Score=36.42 Aligned_cols=25 Identities=28% Similarity=0.514 Sum_probs=19.2
Q ss_pred EEEccCcccccc---ccCccccCCCCCC
Q 032998 70 ILKCHACYTITA---EIGRIFCPKCGNG 94 (129)
Q Consensus 70 ~~rC~~C~k~~~---~~~~~fCp~CG~~ 94 (129)
.|+|..|+.... ......||.||++
T Consensus 3 ~y~C~~CG~~~~~~~~~~~~~Cp~CG~~ 30 (46)
T PRK00398 3 EYKCARCGREVELDEYGTGVRCPYCGYR 30 (46)
T ss_pred EEECCCCCCEEEECCCCCceECCCCCCe
Confidence 589999997652 2225789999998
No 19
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=95.53 E-value=0.0099 Score=43.21 Aligned_cols=28 Identities=18% Similarity=0.382 Sum_probs=21.3
Q ss_pred eeEEEEccCcccccccc-CccccCCCCCC
Q 032998 67 HRWILKCHACYTITAEI-GRIFCPKCGNG 94 (129)
Q Consensus 67 k~W~~rC~~C~k~~~~~-~~~fCp~CG~~ 94 (129)
..-+.+|..|+..+... ....||.||+.
T Consensus 67 vp~~~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (113)
T PRK12380 67 KPAQAWCWDCSQVVEIHQHDAQCPHCHGE 95 (113)
T ss_pred eCcEEEcccCCCEEecCCcCccCcCCCCC
Confidence 44568999999877653 24459999997
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=95.50 E-value=0.0059 Score=34.22 Aligned_cols=22 Identities=36% Similarity=0.890 Sum_probs=18.3
Q ss_pred EccCccccccccCccccCCCCCC
Q 032998 72 KCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 72 rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
.|+.|++.-+.. -.+||+||+.
T Consensus 2 ~CP~C~~~V~~~-~~~Cp~CG~~ 23 (26)
T PF10571_consen 2 TCPECGAEVPES-AKFCPHCGYD 23 (26)
T ss_pred cCCCCcCCchhh-cCcCCCCCCC
Confidence 699999887654 5889999985
No 21
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=95.46 E-value=0.013 Score=34.46 Aligned_cols=25 Identities=28% Similarity=0.584 Sum_probs=19.8
Q ss_pred EEEccCcccccccc-CccccCCCCCC
Q 032998 70 ILKCHACYTITAEI-GRIFCPKCGNG 94 (129)
Q Consensus 70 ~~rC~~C~k~~~~~-~~~fCp~CG~~ 94 (129)
.++|.-||.++... .-+.||.||.+
T Consensus 2 ~~~C~~CG~i~~g~~~p~~CP~Cg~~ 27 (34)
T cd00729 2 VWVCPVCGYIHEGEEAPEKCPICGAP 27 (34)
T ss_pred eEECCCCCCEeECCcCCCcCcCCCCc
Confidence 47999999886543 24789999986
No 22
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=95.33 E-value=0.012 Score=34.13 Aligned_cols=25 Identities=28% Similarity=0.562 Sum_probs=20.0
Q ss_pred EEEccCcccccccc-CccccCCCCCC
Q 032998 70 ILKCHACYTITAEI-GRIFCPKCGNG 94 (129)
Q Consensus 70 ~~rC~~C~k~~~~~-~~~fCp~CG~~ 94 (129)
+++|..|+.++... .-..||.||.+
T Consensus 1 ~~~C~~CGy~y~~~~~~~~CP~Cg~~ 26 (33)
T cd00350 1 KYVCPVCGYIYDGEEAPWVCPVCGAP 26 (33)
T ss_pred CEECCCCCCEECCCcCCCcCcCCCCc
Confidence 37899999987653 35789999986
No 23
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=95.10 E-value=0.023 Score=35.30 Aligned_cols=30 Identities=27% Similarity=0.455 Sum_probs=23.2
Q ss_pred EEEccCcccccccc--CccccCCCCCCCceeEE
Q 032998 70 ILKCHACYTITAEI--GRIFCPKCGNGGTLRKV 100 (129)
Q Consensus 70 ~~rC~~C~k~~~~~--~~~fCp~CG~~~tL~rv 100 (129)
.|+|..|+..+... ....||.||++ -|.|.
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 58999999866532 35889999999 77654
No 24
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=95.02 E-value=0.018 Score=43.07 Aligned_cols=26 Identities=35% Similarity=0.687 Sum_probs=19.8
Q ss_pred EEEEccCcccccccc----------------------CccccCCCCCC
Q 032998 69 WILKCHACYTITAEI----------------------GRIFCPKCGNG 94 (129)
Q Consensus 69 W~~rC~~C~k~~~~~----------------------~~~fCp~CG~~ 94 (129)
-.++|..|+..+... ....||.||+.
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCC
Confidence 568999999887643 12349999997
No 25
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=94.92 E-value=0.015 Score=38.12 Aligned_cols=29 Identities=34% Similarity=0.638 Sum_probs=22.4
Q ss_pred EEEccCccccccccCccccCCCCCCCceeEEEE
Q 032998 70 ILKCHACYTITAEIGRIFCPKCGNGGTLRKVAV 102 (129)
Q Consensus 70 ~~rC~~C~k~~~~~~~~fCp~CG~~~tL~rv~v 102 (129)
+.+|..|+.++- +..||.||.+ |..-++.
T Consensus 5 mr~C~~CgvYTL---k~~CP~CG~~-t~~~~P~ 33 (56)
T PRK13130 5 IRKCPKCGVYTL---KEICPVCGGK-TKNPHPP 33 (56)
T ss_pred ceECCCCCCEEc---cccCcCCCCC-CCCCCCC
Confidence 467999998775 5889999998 6554443
No 26
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=94.72 E-value=0.016 Score=43.88 Aligned_cols=30 Identities=23% Similarity=0.583 Sum_probs=23.7
Q ss_pred EEccCccccccccC---ccccCCCCCCCceeEEE
Q 032998 71 LKCHACYTITAEIG---RIFCPKCGNGGTLRKVA 101 (129)
Q Consensus 71 ~rC~~C~k~~~~~~---~~fCp~CG~~~tL~rv~ 101 (129)
.+|+.|+++|.+-. ..=||.||++ ....|+
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 4569999998 666554
No 27
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=94.65 E-value=0.024 Score=41.01 Aligned_cols=30 Identities=20% Similarity=0.419 Sum_probs=19.6
Q ss_pred eeeeEEEEccCccccccccC-ccccCCCCCC
Q 032998 65 QLHRWILKCHACYTITAEIG-RIFCPKCGNG 94 (129)
Q Consensus 65 ~~k~W~~rC~~C~k~~~~~~-~~fCp~CG~~ 94 (129)
+...-+.+|..|++.+.... ...||.||+.
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 33456799999999886433 4569999998
No 28
>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=94.61 E-value=0.055 Score=39.76 Aligned_cols=58 Identities=17% Similarity=0.375 Sum_probs=37.5
Q ss_pred hHHHHHHHHHhCceee----c---CCCCcce--eeeeEEEEccCccccccc-----cCccccCCCCCCCceeEE
Q 032998 41 DYAMQNVILQMGLRLL----A---PGGMQIR--QLHRWILKCHACYTITAE-----IGRIFCPKCGNGGTLRKV 100 (129)
Q Consensus 41 DyamQNVl~~lGL~~~----s---~~g~~I~--~~k~W~~rC~~C~k~~~~-----~~~~fCp~CG~~~tL~rv 100 (129)
+-+=|.++.++|..+. . .+...+. ...+|.++|..|+..+.- ..+..|+.||.+ |++|
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 3477889999998541 1 1122222 237899999999955432 123579999986 8765
No 29
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=94.55 E-value=0.027 Score=36.15 Aligned_cols=32 Identities=31% Similarity=0.476 Sum_probs=24.5
Q ss_pred eEEEEccCccccccc---cCccccCCCCCCCceeEE
Q 032998 68 RWILKCHACYTITAE---IGRIFCPKCGNGGTLRKV 100 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~---~~~~fCp~CG~~~tL~rv 100 (129)
.-.|+|..|++.+.. ....-||.||++ -|-|.
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 66553
No 30
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=94.51 E-value=0.019 Score=42.33 Aligned_cols=31 Identities=26% Similarity=0.498 Sum_probs=24.7
Q ss_pred EEccCccccccccC---ccccCCCCCCCceeEEEE
Q 032998 71 LKCHACYTITAEIG---RIFCPKCGNGGTLRKVAV 102 (129)
Q Consensus 71 ~rC~~C~k~~~~~~---~~fCp~CG~~~tL~rv~v 102 (129)
.+|+.|+++|++-. ..=||.||++ .+.+|+-
T Consensus 3 H~CtrCG~vf~~g~~~il~GCp~CG~n-kF~yv~~ 36 (112)
T COG3364 3 HQCTRCGEVFDDGSEEILSGCPKCGCN-KFLYVPE 36 (112)
T ss_pred ceecccccccccccHHHHccCccccch-heEeccc
Confidence 48999999998732 4569999998 7887764
No 31
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=94.31 E-value=0.031 Score=43.76 Aligned_cols=25 Identities=24% Similarity=0.569 Sum_probs=22.1
Q ss_pred EEEccCccccccccCccccCCCCCC
Q 032998 70 ILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 70 ~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
+++|.-||.+..+.+-..||+||.+
T Consensus 134 ~~vC~vCGy~~~ge~P~~CPiCga~ 158 (166)
T COG1592 134 VWVCPVCGYTHEGEAPEVCPICGAP 158 (166)
T ss_pred EEEcCCCCCcccCCCCCcCCCCCCh
Confidence 8899999988877667899999987
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=94.16 E-value=0.022 Score=41.59 Aligned_cols=25 Identities=32% Similarity=0.822 Sum_probs=20.1
Q ss_pred EEEccCccccccccCc--cccCCCCCC
Q 032998 70 ILKCHACYTITAEIGR--IFCPKCGNG 94 (129)
Q Consensus 70 ~~rC~~C~k~~~~~~~--~fCp~CG~~ 94 (129)
+..|+.|++.|.++.| ..||+||..
T Consensus 9 KR~Cp~CG~kFYDLnk~PivCP~CG~~ 35 (108)
T PF09538_consen 9 KRTCPSCGAKFYDLNKDPIVCPKCGTE 35 (108)
T ss_pred cccCCCCcchhccCCCCCccCCCCCCc
Confidence 3579999988877664 579999985
No 33
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=93.96 E-value=0.026 Score=38.02 Aligned_cols=25 Identities=36% Similarity=0.869 Sum_probs=19.9
Q ss_pred EEccCccccccccCccccCCCCCCCce
Q 032998 71 LKCHACYTITAEIGRIFCPKCGNGGTL 97 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG~~~tL 97 (129)
+.|..|.++.++ ....||.||++ .+
T Consensus 5 kAC~~Ck~l~~~-d~e~CP~Cgs~-~~ 29 (64)
T COG2093 5 KACKNCKRLTPE-DTEICPVCGST-DL 29 (64)
T ss_pred HHHhhccccCCC-CCccCCCCCCc-cc
Confidence 469999999876 34679999997 44
No 34
>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=93.95 E-value=0.053 Score=32.37 Aligned_cols=28 Identities=21% Similarity=0.402 Sum_probs=21.0
Q ss_pred EEccCccccccccC-----ccccCCCCCCCceeE
Q 032998 71 LKCHACYTITAEIG-----RIFCPKCGNGGTLRK 99 (129)
Q Consensus 71 ~rC~~C~k~~~~~~-----~~fCp~CG~~~tL~r 99 (129)
..|..|+++|.... ...|..||.+ ..+|
T Consensus 2 r~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~-L~qR 34 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNPPKVEGVCDNCGGE-LVQR 34 (36)
T ss_dssp EEETTTTEEEETTTB--SSTTBCTTTTEB-EBEE
T ss_pred cCcCCCCCccccccCCCCCCCccCCCCCe-eEeC
Confidence 57999999986422 4789999997 4443
No 35
>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=93.58 E-value=0.097 Score=34.01 Aligned_cols=26 Identities=38% Similarity=0.760 Sum_probs=19.8
Q ss_pred EEEEccCccccccccCccccCCCCCCCcee
Q 032998 69 WILKCHACYTITAEIGRIFCPKCGNGGTLR 98 (129)
Q Consensus 69 W~~rC~~C~k~~~~~~~~fCp~CG~~~tL~ 98 (129)
.+..|.+|+..+-. +-||.||.+ |..
T Consensus 4 ~~r~c~~~~~YTLk---~~cp~cG~~-T~~ 29 (53)
T PF04135_consen 4 YIRKCPGCRVYTLK---DKCPPCGGP-TES 29 (53)
T ss_dssp EEEECTTTCEEESS---SBBTTTSSB-SEE
T ss_pred ccccCCCCCcEeCC---CccCCCCCC-CcC
Confidence 34499999976643 679999998 654
No 36
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=93.21 E-value=0.048 Score=36.27 Aligned_cols=25 Identities=40% Similarity=0.700 Sum_probs=19.5
Q ss_pred EEEccCccccccccCccccCCCCCCCcee
Q 032998 70 ILKCHACYTITAEIGRIFCPKCGNGGTLR 98 (129)
Q Consensus 70 ~~rC~~C~k~~~~~~~~fCp~CG~~~tL~ 98 (129)
..+|..|+..|-. +-||+||.. |..
T Consensus 5 ~rkC~~cg~YTLk---e~Cp~CG~~-t~~ 29 (59)
T COG2260 5 IRKCPKCGRYTLK---EKCPVCGGD-TKV 29 (59)
T ss_pred hhcCcCCCceeec---ccCCCCCCc-ccc
Confidence 3579999987753 779999998 543
No 37
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=93.19 E-value=0.04 Score=37.11 Aligned_cols=24 Identities=29% Similarity=0.631 Sum_probs=19.4
Q ss_pred EEEccCccccccccCccccCCCCCCCce
Q 032998 70 ILKCHACYTITAEIGRIFCPKCGNGGTL 97 (129)
Q Consensus 70 ~~rC~~C~k~~~~~~~~fCp~CG~~~tL 97 (129)
.+.|..|.++..+ ..||.||+. ++
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 3579999999854 689999997 54
No 38
>PRK04351 hypothetical protein; Provisional
Probab=92.98 E-value=0.2 Score=38.23 Aligned_cols=55 Identities=22% Similarity=0.410 Sum_probs=36.9
Q ss_pred hHHHHHHHHHhCc-eeecCCCCcceeeeeEEEEccCcccccc-----ccCccccCCCCCCCceeEE
Q 032998 41 DYAMQNVILQMGL-RLLAPGGMQIRQLHRWILKCHACYTITA-----EIGRIFCPKCGNGGTLRKV 100 (129)
Q Consensus 41 DyamQNVl~~lGL-~~~s~~g~~I~~~k~W~~rC~~C~k~~~-----~~~~~fCp~CG~~~tL~rv 100 (129)
|-.=|-+|.++|- ..-+ +-.. ..++|.|+|.+|+..+. +..+..|..||.. |.-+
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 5556888888873 3322 1111 33679999999997653 3457899999997 6543
No 39
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=92.95 E-value=0.051 Score=36.26 Aligned_cols=22 Identities=45% Similarity=0.930 Sum_probs=18.2
Q ss_pred EccCccccccccCccccCCCCCCCce
Q 032998 72 KCHACYTITAEIGRIFCPKCGNGGTL 97 (129)
Q Consensus 72 rC~~C~k~~~~~~~~fCp~CG~~~tL 97 (129)
.|..|..+... +.||.||+. +|
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 79999998854 579999997 53
No 40
>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=92.92 E-value=0.09 Score=30.77 Aligned_cols=28 Identities=32% Similarity=0.618 Sum_probs=19.5
Q ss_pred EEccCcccccccc--CccccCCCCCCCceeE
Q 032998 71 LKCHACYTITAEI--GRIFCPKCGNGGTLRK 99 (129)
Q Consensus 71 ~rC~~C~k~~~~~--~~~fCp~CG~~~tL~r 99 (129)
|.|..|++..... ...-||.||++ .|.|
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 6799999876532 24689999998 6755
No 41
>PRK07591 threonine synthase; Validated
Probab=92.55 E-value=0.1 Score=45.16 Aligned_cols=27 Identities=22% Similarity=0.285 Sum_probs=22.2
Q ss_pred eEEEEccCccccccccCccccCCCCCC
Q 032998 68 RWILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
.+.++|..|++.|+......||.||+.
T Consensus 16 ~~~l~C~~Cg~~~~~~~~~~C~~cg~~ 42 (421)
T PRK07591 16 AVALKCRECGAEYPLGPIHVCEECFGP 42 (421)
T ss_pred eeEEEeCCCCCcCCCCCCccCCCCCCe
Confidence 457999999999975445779999986
No 42
>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=91.98 E-value=0.11 Score=44.93 Aligned_cols=26 Identities=19% Similarity=0.446 Sum_probs=21.8
Q ss_pred EEEEccCccccccccCccccCCCCCC
Q 032998 69 WILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 69 W~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
|.++|..|++.|++.....||.||.+
T Consensus 1 ~~l~C~~Cg~~~~~~~~~~C~~c~g~ 26 (398)
T TIGR03844 1 YTLRCPGCGEVLPDHYTLSCPLDCGL 26 (398)
T ss_pred CEEEeCCCCCccCCccccCCCCCCCc
Confidence 46899999999976556789999976
No 43
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=91.89 E-value=0.14 Score=37.70 Aligned_cols=30 Identities=27% Similarity=0.438 Sum_probs=19.8
Q ss_pred eeEEEEccCcccccccc--------CccccCCCCCCCcee
Q 032998 67 HRWILKCHACYTITAEI--------GRIFCPKCGNGGTLR 98 (129)
Q Consensus 67 k~W~~rC~~C~k~~~~~--------~~~fCp~CG~~~tL~ 98 (129)
-.-..+| .|+..+... ....||.||+. .++
T Consensus 67 vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~-~~~ 104 (124)
T PRK00762 67 IPVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNK-RAH 104 (124)
T ss_pred cCeeEEe-eCcCcccccccchhccccCCcCcCCCCC-CCE
Confidence 3456899 999875421 11349999987 443
No 44
>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=91.84 E-value=0.084 Score=39.99 Aligned_cols=25 Identities=12% Similarity=0.137 Sum_probs=20.2
Q ss_pred EEEccCccccccccC--ccccCCCCCC
Q 032998 70 ILKCHACYTITAEIG--RIFCPKCGNG 94 (129)
Q Consensus 70 ~~rC~~C~k~~~~~~--~~fCp~CG~~ 94 (129)
+..|+.|++.|.++. -..||+||..
T Consensus 9 Kr~Cp~cg~kFYDLnk~p~vcP~cg~~ 35 (129)
T TIGR02300 9 KRICPNTGSKFYDLNRRPAVSPYTGEQ 35 (129)
T ss_pred cccCCCcCccccccCCCCccCCCcCCc
Confidence 457999998887765 3789999975
No 45
>PF15017 AF1Q: Drug resistance and apoptosis regulator
Probab=91.80 E-value=0.093 Score=37.28 Aligned_cols=18 Identities=11% Similarity=0.318 Sum_probs=13.7
Q ss_pred eccccCCCCCCCceeeec
Q 032998 12 DVSYVDDECSEQSWMLRS 29 (129)
Q Consensus 12 ~~~~~~~~~~~~~wi~~~ 29 (129)
+.+++++|+++|+||||+
T Consensus 62 e~eee~~ddD~gGWITPs 79 (87)
T PF15017_consen 62 EEEEEEEDDDGGGWITPS 79 (87)
T ss_pred ccccccccCCCCccccch
Confidence 444556778889999988
No 46
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=91.72 E-value=0.084 Score=40.04 Aligned_cols=24 Identities=38% Similarity=0.843 Sum_probs=18.4
Q ss_pred EEccCcccc-ccccCccccCCCCCC
Q 032998 71 LKCHACYTI-TAEIGRIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~-~~~~~~~fCp~CG~~ 94 (129)
.-|+.|+.. |......|||+||..
T Consensus 29 ~hCp~Cg~PLF~KdG~v~CPvC~~~ 53 (131)
T COG1645 29 KHCPKCGTPLFRKDGEVFCPVCGYR 53 (131)
T ss_pred hhCcccCCcceeeCCeEECCCCCce
Confidence 359999954 444558999999984
No 47
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=91.58 E-value=0.11 Score=42.76 Aligned_cols=33 Identities=27% Similarity=0.657 Sum_probs=22.6
Q ss_pred CceeecCCCCcceeeeeEEEEccCcccc-cc--------ccCccccCCCCCC
Q 032998 52 GLRLLAPGGMQIRQLHRWILKCHACYTI-TA--------EIGRIFCPKCGNG 94 (129)
Q Consensus 52 GL~~~s~~g~~I~~~k~W~~rC~~C~k~-~~--------~~~~~fCp~CG~~ 94 (129)
|..++++.|. +|.||+=+ +. .....|||+||.=
T Consensus 189 g~gvvpl~g~----------~C~GC~m~l~~~~~~~V~~~d~iv~CP~CgRI 230 (239)
T COG1579 189 GVGVVPLEGR----------VCGGCHMKLPSQTLSKVRKKDEIVFCPYCGRI 230 (239)
T ss_pred CceEEeecCC----------cccCCeeeecHHHHHHHhcCCCCccCCccchH
Confidence 5666666654 89999943 32 2236899999974
No 48
>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=91.54 E-value=0.12 Score=38.38 Aligned_cols=34 Identities=24% Similarity=0.344 Sum_probs=25.8
Q ss_pred eeeEEEEccCccccccccC-ccccCCCCCCCceeE
Q 032998 66 LHRWILKCHACYTITAEIG-RIFCPKCGNGGTLRK 99 (129)
Q Consensus 66 ~k~W~~rC~~C~k~~~~~~-~~fCp~CG~~~tL~r 99 (129)
.+.-..+|+.|+|.+.-.. .+-|++|+.|-||.+
T Consensus 65 tkav~V~CP~C~K~TKmLGr~D~CM~C~~pLTLd~ 99 (114)
T PF11023_consen 65 TKAVQVECPNCGKQTKMLGRVDACMHCKEPLTLDP 99 (114)
T ss_pred ccceeeECCCCCChHhhhchhhccCcCCCcCccCc
Confidence 3456778999999986544 478999999955544
No 49
>PRK06450 threonine synthase; Validated
Probab=91.29 E-value=0.13 Score=43.36 Aligned_cols=25 Identities=32% Similarity=0.538 Sum_probs=20.7
Q ss_pred EEEccCccccccccCccccCCCCCC
Q 032998 70 ILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 70 ~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
.++|..|++.|.......||.||.+
T Consensus 3 ~~~C~~Cg~~~~~~~~~~C~~cg~~ 27 (338)
T PRK06450 3 KEVCMKCGKERESIYEIRCKKCGGP 27 (338)
T ss_pred eeEECCcCCcCCCcccccCCcCCCE
Confidence 3799999999876445679999986
No 50
>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=91.07 E-value=0.21 Score=31.50 Aligned_cols=25 Identities=24% Similarity=0.574 Sum_probs=17.9
Q ss_pred EEEccCccccccccCc------------------cccCCCCCC
Q 032998 70 ILKCHACYTITAEIGR------------------IFCPKCGNG 94 (129)
Q Consensus 70 ~~rC~~C~k~~~~~~~------------------~fCp~CG~~ 94 (129)
+++|..|+-+|..... -.||.||.+
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 5899999999865322 279999975
No 51
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=90.96 E-value=0.26 Score=40.27 Aligned_cols=55 Identities=22% Similarity=0.366 Sum_probs=34.0
Q ss_pred EEccCcccccc---ccCccccCCCCCCCcee----EEEEEeCCCceEEeecCCccccCceeecCC
Q 032998 71 LKCHACYTITA---EIGRIFCPKCGNGGTLR----KVAVTVGENGIVLASRRPRITLRGTKVSIS 128 (129)
Q Consensus 71 ~rC~~C~k~~~---~~~~~fCp~CG~~~tL~----rv~v~v~~~G~~~~~~~~~~n~RG~~ySlP 128 (129)
..|+.|+..+. .-.+..||.||.. -.- -|-+.+..++++++.+++++ ....|++|
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 47888987542 2235679999965 221 14455566677777665543 25578887
No 52
>PF12773 DZR: Double zinc ribbon
Probab=90.86 E-value=0.11 Score=31.74 Aligned_cols=21 Identities=38% Similarity=0.977 Sum_probs=14.1
Q ss_pred ccCccccccccCccccCCCCCC
Q 032998 73 CHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 73 C~~C~k~~~~~~~~fCp~CG~~ 94 (129)
|+.|++...+ ...|||.||.+
T Consensus 1 Cp~Cg~~~~~-~~~fC~~CG~~ 21 (50)
T PF12773_consen 1 CPHCGTPNPD-DAKFCPHCGTP 21 (50)
T ss_pred CCCcCCcCCc-cccCChhhcCC
Confidence 6677766543 35778888876
No 53
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=90.85 E-value=0.057 Score=37.89 Aligned_cols=31 Identities=23% Similarity=0.514 Sum_probs=23.8
Q ss_pred eeEEEEccCcccccc------ccCccccCCCCCCCceeE
Q 032998 67 HRWILKCHACYTITA------EIGRIFCPKCGNGGTLRK 99 (129)
Q Consensus 67 k~W~~rC~~C~k~~~------~~~~~fCp~CG~~~tL~r 99 (129)
=.|.|+|..|+..+. +-+.-.||.||.+ |+|
T Consensus 9 PtY~Y~c~~cg~~~dvvq~~~ddplt~ce~c~a~--~kk 45 (82)
T COG2331 9 PTYSYECTECGNRFDVVQAMTDDPLTTCEECGAR--LKK 45 (82)
T ss_pred cceEEeecccchHHHHHHhcccCccccChhhChH--HHH
Confidence 478999999997764 3346789999986 554
No 54
>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=90.82 E-value=0.18 Score=38.50 Aligned_cols=31 Identities=26% Similarity=0.524 Sum_probs=22.9
Q ss_pred EEEccCcccccc---ccCccccCCCCCCCceeEEE
Q 032998 70 ILKCHACYTITA---EIGRIFCPKCGNGGTLRKVA 101 (129)
Q Consensus 70 ~~rC~~C~k~~~---~~~~~fCp~CG~~~tL~rv~ 101 (129)
.|+|..|+.... .....-||.||+. ...|.+
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 599999996532 2226779999997 788764
No 55
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=90.67 E-value=0.37 Score=42.26 Aligned_cols=40 Identities=35% Similarity=0.679 Sum_probs=27.3
Q ss_pred eEEEEccCccccccccCccccCCCCCCCce-eEEEEEeCCCc
Q 032998 68 RWILKCHACYTITAEIGRIFCPKCGNGGTL-RKVAVTVGENG 108 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~~~~~fCp~CG~~~tL-~rv~v~v~~~G 108 (129)
.=.++|+.|++...-....-||.||.++.| ||||+ ||.-|
T Consensus 55 ~~i~kC~~c~~~~~y~~~~~C~~cg~~~~l~R~VSf-VDaPG 95 (415)
T COG5257 55 AKIYKCPECYRPECYTTEPKCPNCGAETELVRRVSF-VDAPG 95 (415)
T ss_pred CceEeCCCCCCCcccccCCCCCCCCCCccEEEEEEE-eeCCc
Confidence 346899999974333346789999987555 56665 66554
No 56
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=90.59 E-value=0.14 Score=30.35 Aligned_cols=15 Identities=40% Similarity=1.090 Sum_probs=6.0
Q ss_pred cccCCCCCCCceeEEE
Q 032998 86 IFCPKCGNGGTLRKVA 101 (129)
Q Consensus 86 ~fCp~CG~~~tL~rv~ 101 (129)
.|||.||++ +-.++.
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 499999998 434433
No 57
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=90.49 E-value=0.22 Score=46.75 Aligned_cols=30 Identities=37% Similarity=0.682 Sum_probs=22.4
Q ss_pred eEEEEccCccccccccCccccCCCCCCCceeEE
Q 032998 68 RWILKCHACYTITAEIGRIFCPKCGNGGTLRKV 100 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~~~~~fCp~CG~~~tL~rv 100 (129)
+=.++||-|++..+. -..||.||+. .|+-+
T Consensus 460 ~~~L~CH~Cg~~~~~--p~~Cp~Cgs~-~L~~~ 489 (730)
T COG1198 460 TGQLRCHYCGYQEPI--PQSCPECGSE-HLRAV 489 (730)
T ss_pred CCeeEeCCCCCCCCC--CCCCCCCCCC-eeEEe
Confidence 346899999986443 3789999998 77643
No 58
>PF12773 DZR: Double zinc ribbon
Probab=90.43 E-value=0.12 Score=31.61 Aligned_cols=20 Identities=35% Similarity=0.939 Sum_probs=8.8
Q ss_pred EccCccccccccCccccCCCC
Q 032998 72 KCHACYTITAEIGRIFCPKCG 92 (129)
Q Consensus 72 rC~~C~k~~~~~~~~fCp~CG 92 (129)
.|..|++.... .-.||+.||
T Consensus 31 ~C~~Cg~~~~~-~~~fC~~CG 50 (50)
T PF12773_consen 31 ICPNCGAENPP-NAKFCPNCG 50 (50)
T ss_pred CCcCCcCCCcC-CcCccCccc
Confidence 45555544322 234555554
No 59
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=90.41 E-value=0.28 Score=48.59 Aligned_cols=29 Identities=31% Similarity=0.577 Sum_probs=22.3
Q ss_pred ceeeeeEEEEccCccccccccCccccCCCCCC
Q 032998 63 IRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 63 I~~~k~W~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
+-++.....+|+.|+..... .|||.||.+
T Consensus 660 ~ieVEV~~rkCPkCG~~t~~---~fCP~CGs~ 688 (1337)
T PRK14714 660 VIEVEVGRRRCPSCGTETYE---NRCPDCGTH 688 (1337)
T ss_pred eEEEEEEEEECCCCCCcccc---ccCcccCCc
Confidence 44666778999999986543 589999987
No 60
>PRK06260 threonine synthase; Validated
Probab=90.12 E-value=0.21 Score=42.58 Aligned_cols=26 Identities=31% Similarity=0.584 Sum_probs=20.5
Q ss_pred EEEEccCccccccccC-ccccCCCCCC
Q 032998 69 WILKCHACYTITAEIG-RIFCPKCGNG 94 (129)
Q Consensus 69 W~~rC~~C~k~~~~~~-~~fCp~CG~~ 94 (129)
+.++|..|++.|+... ...||.||.+
T Consensus 2 ~~~~C~~cg~~~~~~~~~~~Cp~cg~~ 28 (397)
T PRK06260 2 YWLKCIECGKEYDPDEIIYTCPECGGL 28 (397)
T ss_pred CEEEECCCCCCCCCCCccccCCCCCCe
Confidence 3589999999987533 3569999986
No 61
>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=90.10 E-value=0.29 Score=33.53 Aligned_cols=29 Identities=31% Similarity=0.750 Sum_probs=19.1
Q ss_pred EEEccCccccccccCccccCCCCCCCceeEEEE
Q 032998 70 ILKCHACYTITAEIGRIFCPKCGNGGTLRKVAV 102 (129)
Q Consensus 70 ~~rC~~C~k~~~~~~~~fCp~CG~~~tL~rv~v 102 (129)
.+.|.+|.+-|.. .-+||.||.+ |.+...
T Consensus 17 ~~~C~~C~~~~~~--~a~CPdC~~~--Le~LkA 45 (70)
T PF07191_consen 17 HYHCEACQKDYKK--EAFCPDCGQP--LEVLKA 45 (70)
T ss_dssp EEEETTT--EEEE--EEE-TTT-SB---EEEEE
T ss_pred EEECcccccccee--cccCCCcccH--HHHHHH
Confidence 5899999997765 4889999998 776653
No 62
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=89.90 E-value=0.42 Score=35.50 Aligned_cols=53 Identities=17% Similarity=0.323 Sum_probs=33.1
Q ss_pred HHHHHHHHHhCceeec-CCCCcceeeeeEEEEccCcccccc------ccCccccCCCCCC
Q 032998 42 YAMQNVILQMGLRLLA-PGGMQIRQLHRWILKCHACYTITA------EIGRIFCPKCGNG 94 (129)
Q Consensus 42 yamQNVl~~lGL~~~s-~~g~~I~~~k~W~~rC~~C~k~~~------~~~~~fCp~CG~~ 94 (129)
-.=|..+.++|-..-. -....+..+++|.|+|..|+..+. +..+..|..||..
T Consensus 83 ~~f~~~~~~~~~~~~~~~h~~~~~~~~~~~y~C~~C~~~~~~~rr~~~~~~y~C~~C~g~ 142 (146)
T smart00731 83 DEWKRWMRQVNGLFPERCHTFLIESVKKYPYRCTGCGQRYLRVRRSNNVSRYRCGKCGGK 142 (146)
T ss_pred HHHHHHHHHHcCCCcceEcCCcccccceEEEECCCCCCCCceEccccCcceEEcCCCCCE
Confidence 4556666666544210 122334444689999999997653 2245789999996
No 63
>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=89.82 E-value=0.24 Score=44.04 Aligned_cols=28 Identities=32% Similarity=0.610 Sum_probs=20.7
Q ss_pred EEEccCccccccccCccccCCCCCCCceeEE
Q 032998 70 ILKCHACYTITAEIGRIFCPKCGNGGTLRKV 100 (129)
Q Consensus 70 ~~rC~~C~k~~~~~~~~fCp~CG~~~tL~rv 100 (129)
.++||-|+.....+ ..||.||++ .|+-+
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 57888888766543 679999997 66643
No 64
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=89.82 E-value=0.16 Score=33.15 Aligned_cols=25 Identities=28% Similarity=0.579 Sum_probs=20.3
Q ss_pred EEEccCcccccc-ccCccccCCCCCC
Q 032998 70 ILKCHACYTITA-EIGRIFCPKCGNG 94 (129)
Q Consensus 70 ~~rC~~C~k~~~-~~~~~fCp~CG~~ 94 (129)
..+|..|++.+. .....+||.||.+
T Consensus 5 ~~~C~~Cg~~~~~~dDiVvCp~Cgap 30 (54)
T PF14446_consen 5 GCKCPVCGKKFKDGDDIVVCPECGAP 30 (54)
T ss_pred CccChhhCCcccCCCCEEECCCCCCc
Confidence 358999998774 4458999999998
No 65
>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=89.71 E-value=0.19 Score=29.32 Aligned_cols=25 Identities=32% Similarity=0.683 Sum_probs=18.2
Q ss_pred EEEccCccccccc--------cCccccCCCCCC
Q 032998 70 ILKCHACYTITAE--------IGRIFCPKCGNG 94 (129)
Q Consensus 70 ~~rC~~C~k~~~~--------~~~~fCp~CG~~ 94 (129)
.+.|+.|++.+.- ..+..||+||+.
T Consensus 2 ~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 2 RIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHV 34 (38)
T ss_pred EEECCCCCCEEEeCHHHcCCCCCEEECCCCCCE
Confidence 3689999986542 124689999986
No 66
>PRK00420 hypothetical protein; Validated
Probab=89.48 E-value=0.19 Score=37.03 Aligned_cols=24 Identities=25% Similarity=0.512 Sum_probs=18.8
Q ss_pred EEccCcccccc--ccCccccCCCCCC
Q 032998 71 LKCHACYTITA--EIGRIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~~--~~~~~fCp~CG~~ 94 (129)
..|+.|+.... .....|||.||..
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~~ 49 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGKV 49 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCCe
Confidence 46999996544 3458999999997
No 67
>PRK11032 hypothetical protein; Provisional
Probab=89.30 E-value=0.29 Score=38.11 Aligned_cols=31 Identities=29% Similarity=0.600 Sum_probs=23.3
Q ss_pred EEEccCcccccc---ccCccccCCCCCCCceeEEE
Q 032998 70 ILKCHACYTITA---EIGRIFCPKCGNGGTLRKVA 101 (129)
Q Consensus 70 ~~rC~~C~k~~~---~~~~~fCp~CG~~~tL~rv~ 101 (129)
.++|..|+.... .....-||.||+. ..+|.+
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 489999996532 2236779999997 888865
No 68
>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=89.22 E-value=0.21 Score=31.85 Aligned_cols=25 Identities=32% Similarity=0.752 Sum_probs=18.8
Q ss_pred EEEccCcccccccc------------------CccccCCCCCC
Q 032998 70 ILKCHACYTITAEI------------------GRIFCPKCGNG 94 (129)
Q Consensus 70 ~~rC~~C~k~~~~~------------------~~~fCp~CG~~ 94 (129)
+++|..|+-+|... ..-.||.||.+
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 37899999999742 12279999976
No 69
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=88.08 E-value=0.37 Score=35.77 Aligned_cols=33 Identities=30% Similarity=0.400 Sum_probs=22.6
Q ss_pred eeeeEEEEccCcccccc-ccCccccCCCCCCCcee
Q 032998 65 QLHRWILKCHACYTITA-EIGRIFCPKCGNGGTLR 98 (129)
Q Consensus 65 ~~k~W~~rC~~C~k~~~-~~~~~fCp~CG~~~tL~ 98 (129)
+...=..+|.-|+..+. +.....||.||++ .++
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 33455689999976553 3335669999998 544
No 70
>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=87.75 E-value=0.63 Score=30.10 Aligned_cols=46 Identities=17% Similarity=0.407 Sum_probs=30.5
Q ss_pred HHHHHHHHhCceeecCCCCcceeeeeEEEEccCccccccc--cC-ccccCCCCCC
Q 032998 43 AMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAE--IG-RIFCPKCGNG 94 (129)
Q Consensus 43 amQNVl~~lGL~~~s~~g~~I~~~k~W~~rC~~C~k~~~~--~~-~~fCp~CG~~ 94 (129)
.|+-.+..-|+.++.++-... -..|+.|+..... .. .-.||.||..
T Consensus 7 ~L~yka~~~G~~v~~v~~~~T------Sq~C~~CG~~~~~~~~~r~~~C~~Cg~~ 55 (69)
T PF07282_consen 7 RLEYKAEEYGIQVVEVDEAYT------SQTCPRCGHRNKKRRSGRVFTCPNCGFE 55 (69)
T ss_pred HHHHHHHHhCCEEEEECCCCC------ccCccCcccccccccccceEEcCCCCCE
Confidence 356667778888876664332 2469999876554 12 4679999874
No 71
>PRK05978 hypothetical protein; Provisional
Probab=87.34 E-value=0.24 Score=38.10 Aligned_cols=32 Identities=19% Similarity=0.444 Sum_probs=22.5
Q ss_pred eEEEEccCccc--ccccc--CccccCCCCCCCceeEEE
Q 032998 68 RWILKCHACYT--ITAEI--GRIFCPKCGNGGTLRKVA 101 (129)
Q Consensus 68 ~W~~rC~~C~k--~~~~~--~~~fCp~CG~~~tL~rv~ 101 (129)
-+..||+.|++ ++... ..+.||+||.+ +.+..
T Consensus 31 Gl~grCP~CG~G~LF~g~Lkv~~~C~~CG~~--~~~~~ 66 (148)
T PRK05978 31 GFRGRCPACGEGKLFRAFLKPVDHCAACGED--FTHHR 66 (148)
T ss_pred HHcCcCCCCCCCcccccccccCCCccccCCc--cccCC
Confidence 56789999984 43321 25889999998 66543
No 72
>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=87.27 E-value=0.28 Score=27.92 Aligned_cols=10 Identities=40% Similarity=1.132 Sum_probs=6.0
Q ss_pred ccccCCCCCC
Q 032998 85 RIFCPKCGNG 94 (129)
Q Consensus 85 ~~fCp~CG~~ 94 (129)
-.|||.||++
T Consensus 3 ~rfC~~CG~~ 12 (32)
T PF09297_consen 3 HRFCGRCGAP 12 (32)
T ss_dssp TSB-TTT--B
T ss_pred CcccCcCCcc
Confidence 3799999999
No 73
>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=87.14 E-value=0.46 Score=46.17 Aligned_cols=28 Identities=36% Similarity=0.597 Sum_probs=23.9
Q ss_pred eeEEEEccCccccccccC-ccccCCCCCC
Q 032998 67 HRWILKCHACYTITAEIG-RIFCPKCGNG 94 (129)
Q Consensus 67 k~W~~rC~~C~k~~~~~~-~~fCp~CG~~ 94 (129)
.+=..||..|+..|..++ ..-||+||++
T Consensus 1009 srQ~fRC~kC~~kYRR~PL~G~C~kCGg~ 1037 (1095)
T TIGR00354 1009 SRQEVRCTKCNTKYRRIPLVGKCLKCGNN 1037 (1095)
T ss_pred hccceeecccCCccccCCCCCcccccCCe
Confidence 344689999999998877 6889999998
No 74
>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=86.37 E-value=0.63 Score=45.30 Aligned_cols=30 Identities=30% Similarity=0.537 Sum_probs=23.8
Q ss_pred eeeeEEEEccCccccccccCccccCCCCCCCcee
Q 032998 65 QLHRWILKCHACYTITAEIGRIFCPKCGNGGTLR 98 (129)
Q Consensus 65 ~~k~W~~rC~~C~k~~~~~~~~fCp~CG~~~tL~ 98 (129)
++-.-..+|+.|++.+. +..||.||.+ |..
T Consensus 620 ~vev~~RKCPkCG~yTl---k~rCP~CG~~-Te~ 649 (1095)
T TIGR00354 620 EVEIAIRKCPQCGKESF---WLKCPVCGEL-TEQ 649 (1095)
T ss_pred EEEEEEEECCCCCcccc---cccCCCCCCc-ccc
Confidence 55667799999999765 3779999998 643
No 75
>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=86.25 E-value=0.65 Score=42.57 Aligned_cols=51 Identities=18% Similarity=0.311 Sum_probs=31.0
Q ss_pred HHHHHHHHHh---CceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCCCceeEEEE
Q 032998 42 YAMQNVILQM---GLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAV 102 (129)
Q Consensus 42 yamQNVl~~l---GL~~~s~~g~~I~~~k~W~~rC~~C~k~~~~~~~~fCp~CG~~~tL~rv~v 102 (129)
-|+.++.+.+ ++...++.- =.-+|..|+.+.... ...||+||++ .+...+.
T Consensus 509 ea~~~lv~~~~~~~i~Y~tin~--------~~siC~~CGy~~g~~-~~~CP~CGs~-~~ev~sR 562 (586)
T TIGR02827 509 DGYRKLLRVAADTGCNYFCFNI--------KITICNDCHHIDKRT-LHRCPVCGSA-NIDYGTR 562 (586)
T ss_pred HHHHHHHHHHHhcCCceEEeCC--------CCeecCCCCCcCCCc-CCcCcCCCCc-cceEEEe
Confidence 4666665554 566555431 134799999854322 3789999986 5544443
No 76
>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=86.16 E-value=0.62 Score=42.02 Aligned_cols=30 Identities=27% Similarity=0.590 Sum_probs=21.0
Q ss_pred EEccCccccccccCccccCCCCCCCceeEEEE
Q 032998 71 LKCHACYTITAEIGRIFCPKCGNGGTLRKVAV 102 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG~~~tL~rv~v 102 (129)
.+|..|+..... ....||+||+. -+...+.
T Consensus 519 ~~C~~CG~~~~~-~~~~CP~CGs~-~~~~~~R 548 (555)
T cd01675 519 DICNDCGYIGEG-EGFKCPKCGSE-DVEVISR 548 (555)
T ss_pred ccCCCCCCCCcC-CCCCCcCCCCc-CceEEEe
Confidence 499999986532 24789999986 4544443
No 77
>PF13638 PIN_4: PIN domain; PDB: 2HWW_C 2HWX_A 2DOK_B 2HWY_B 2WP8_J.
Probab=86.10 E-value=0.9 Score=32.13 Aligned_cols=27 Identities=15% Similarity=0.137 Sum_probs=19.6
Q ss_pred CceeeEeechHHHHHHHHHhCceeecC
Q 032998 32 ESTVACITGDYAMQNVILQMGLRLLAP 58 (129)
Q Consensus 32 ~~~va~~TdDyamQNVl~~lGL~~~s~ 58 (129)
...|+++|+|..|++.|...||+..++
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 78
>PRK14873 primosome assembly protein PriA; Provisional
Probab=85.87 E-value=0.53 Score=43.54 Aligned_cols=29 Identities=34% Similarity=0.753 Sum_probs=20.5
Q ss_pred EEEccCccccccccCccccCCCCCCCceeEEEE
Q 032998 70 ILKCHACYTITAEIGRIFCPKCGNGGTLRKVAV 102 (129)
Q Consensus 70 ~~rC~~C~k~~~~~~~~fCp~CG~~~tL~rv~v 102 (129)
.++||-|+... . ...||.||+. .|+-+-+
T Consensus 410 ~l~Ch~CG~~~-~--p~~Cp~Cgs~-~l~~~g~ 438 (665)
T PRK14873 410 TPRCRWCGRAA-P--DWRCPRCGSD-RLRAVVV 438 (665)
T ss_pred eeECCCCcCCC-c--CccCCCCcCC-cceeeec
Confidence 58888888643 2 3679999997 6765443
No 79
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=85.65 E-value=0.9 Score=29.84 Aligned_cols=31 Identities=39% Similarity=0.819 Sum_probs=19.8
Q ss_pred eEEEEccCcccccc-----c----cCccccCCCCCCCceeEE
Q 032998 68 RWILKCHACYTITA-----E----IGRIFCPKCGNGGTLRKV 100 (129)
Q Consensus 68 ~W~~rC~~C~k~~~-----~----~~~~fCp~CG~~~tL~rv 100 (129)
.|+ .|+-|+..+. + ..-.|||+|-+. ||..|
T Consensus 3 ~Wi-~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~E-tlI~v 42 (55)
T PF14205_consen 3 EWI-LCPICGNKTRLKIREDTVLKNFPLYCPKCKQE-TLIDV 42 (55)
T ss_pred eEE-ECCCCCCccceeeecCceeccccccCCCCCce-EEEEe
Confidence 454 5899985442 1 123789999988 66544
No 80
>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=85.47 E-value=0.47 Score=26.75 Aligned_cols=11 Identities=45% Similarity=1.144 Sum_probs=5.9
Q ss_pred ccCCCCCCCceeE
Q 032998 87 FCPKCGNGGTLRK 99 (129)
Q Consensus 87 fCp~CG~~~tL~r 99 (129)
+||+||++ |.|
T Consensus 1 ~CP~C~s~--l~~ 11 (28)
T PF03119_consen 1 TCPVCGSK--LVR 11 (28)
T ss_dssp B-TTT--B--EEE
T ss_pred CcCCCCCE--eEc
Confidence 69999998 554
No 81
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=85.41 E-value=0.61 Score=33.77 Aligned_cols=27 Identities=19% Similarity=0.440 Sum_probs=19.4
Q ss_pred eEEEEccCccccccccC---ccccCCCCCC
Q 032998 68 RWILKCHACYTITAEIG---RIFCPKCGNG 94 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~~~---~~fCp~CG~~ 94 (129)
.-.++|..|+....-.. ..+||.||..
T Consensus 40 ~~~~~C~~Cg~~~~~~~SCk~R~CP~C~~~ 69 (111)
T PF14319_consen 40 FHRYRCEDCGHEKIVYNSCKNRHCPSCQAK 69 (111)
T ss_pred cceeecCCCCceEEecCcccCcCCCCCCCh
Confidence 34689999997643211 3599999987
No 82
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=85.33 E-value=0.49 Score=31.08 Aligned_cols=15 Identities=53% Similarity=1.057 Sum_probs=10.8
Q ss_pred cccCCCCCCCceeEEE
Q 032998 86 IFCPKCGNGGTLRKVA 101 (129)
Q Consensus 86 ~fCp~CG~~~tL~rv~ 101 (129)
..||+||++ |-.|+.
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 544443
No 83
>PRK04023 DNA polymerase II large subunit; Validated
Probab=85.09 E-value=0.66 Score=45.32 Aligned_cols=28 Identities=29% Similarity=0.566 Sum_probs=23.9
Q ss_pred eeEEEEccCccccccccC-ccccCCCCCC
Q 032998 67 HRWILKCHACYTITAEIG-RIFCPKCGNG 94 (129)
Q Consensus 67 k~W~~rC~~C~k~~~~~~-~~fCp~CG~~ 94 (129)
.+=..||..|+..|..++ ..-||+||++
T Consensus 1034 srQ~fRC~kC~~kYRR~PL~G~C~kCGg~ 1062 (1121)
T PRK04023 1034 SRQEFRCTKCGAKYRRPPLSGKCPKCGGN 1062 (1121)
T ss_pred cccceeecccCcccccCCCCCcCccCCCe
Confidence 344689999999998877 6889999998
No 84
>PF14369 zf-RING_3: zinc-finger
Probab=84.95 E-value=0.74 Score=27.18 Aligned_cols=24 Identities=29% Similarity=0.797 Sum_probs=17.0
Q ss_pred EEccCccccccc----cCccccCCCCCC
Q 032998 71 LKCHACYTITAE----IGRIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~~~----~~~~fCp~CG~~ 94 (129)
|.||.|.+.-.. ....+||.|++.
T Consensus 3 ywCh~C~~~V~~~~~~~~~~~CP~C~~g 30 (35)
T PF14369_consen 3 YWCHQCNRFVRIAPSPDSDVACPRCHGG 30 (35)
T ss_pred EeCccCCCEeEeCcCCCCCcCCcCCCCc
Confidence 789999965432 223469999985
No 85
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=84.73 E-value=0.43 Score=44.13 Aligned_cols=21 Identities=33% Similarity=0.831 Sum_probs=9.6
Q ss_pred ccCccccccccCccccCCCCCC
Q 032998 73 CHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 73 C~~C~k~~~~~~~~fCp~CG~~ 94 (129)
|+.|+...+. .-.|||.||.+
T Consensus 30 Cp~CG~~~~~-~~~fC~~CG~~ 50 (645)
T PRK14559 30 CPQCGTEVPV-DEAHCPNCGAE 50 (645)
T ss_pred CCCCCCCCCc-ccccccccCCc
Confidence 4444443322 23456666654
No 86
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=84.61 E-value=0.71 Score=45.94 Aligned_cols=28 Identities=29% Similarity=0.508 Sum_probs=24.0
Q ss_pred eeEEEEccCccccccccC-ccccCCCCCC
Q 032998 67 HRWILKCHACYTITAEIG-RIFCPKCGNG 94 (129)
Q Consensus 67 k~W~~rC~~C~k~~~~~~-~~fCp~CG~~ 94 (129)
.+=..||..|+..|..++ ..-||+||++
T Consensus 1250 srQ~~RC~kC~~kyRR~PL~G~C~kCGg~ 1278 (1337)
T PRK14714 1250 SRQEFRCLKCGTKYRRMPLAGKCRKCGGR 1278 (1337)
T ss_pred hccceeecccCcccccCCCCCcccccCCe
Confidence 344689999999998877 6889999997
No 87
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=84.54 E-value=0.66 Score=27.17 Aligned_cols=24 Identities=33% Similarity=0.591 Sum_probs=16.5
Q ss_pred EEccCccc--cc-cccCccccCCCCCC
Q 032998 71 LKCHACYT--IT-AEIGRIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k--~~-~~~~~~fCp~CG~~ 94 (129)
.+|..|+. ++ .+....||+.||.-
T Consensus 4 ~~C~~C~~~~i~~~~~~~~~C~~Cg~~ 30 (33)
T PF08792_consen 4 KKCSKCGGNGIVNKEDDYEVCIFCGSS 30 (33)
T ss_pred eEcCCCCCCeEEEecCCeEEcccCCcE
Confidence 46888874 23 44457899999873
No 88
>COG1933 Archaeal DNA polymerase II, large subunit [DNA replication, recombination, and repair]
Probab=84.26 E-value=0.61 Score=38.83 Aligned_cols=30 Identities=27% Similarity=0.503 Sum_probs=23.6
Q ss_pred eeeeEEEEccCccccccccC-ccccCCCCCC
Q 032998 65 QLHRWILKCHACYTITAEIG-RIFCPKCGNG 94 (129)
Q Consensus 65 ~~k~W~~rC~~C~k~~~~~~-~~fCp~CG~~ 94 (129)
...+-..||..|.+.|..++ ..-||+||+.
T Consensus 162 ~f~rq~~rc~~c~~k~rr~pl~g~c~kcg~~ 192 (253)
T COG1933 162 SFTRQEFRCVKCNTKFRRPPLDGKCPICGGK 192 (253)
T ss_pred hhhhheeehHhhhhhhcCCCccccccccCCe
Confidence 33445689999999887655 6889999995
No 89
>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=84.08 E-value=0.44 Score=28.07 Aligned_cols=9 Identities=67% Similarity=1.567 Sum_probs=7.4
Q ss_pred cccCCCCCC
Q 032998 86 IFCPKCGNG 94 (129)
Q Consensus 86 ~fCp~CG~~ 94 (129)
.|||.|||-
T Consensus 2 ~FCp~C~nl 10 (35)
T PF02150_consen 2 RFCPECGNL 10 (35)
T ss_dssp -BETTTTSB
T ss_pred eeCCCCCcc
Confidence 699999995
No 90
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=84.04 E-value=0.65 Score=43.47 Aligned_cols=29 Identities=24% Similarity=0.696 Sum_probs=19.8
Q ss_pred EEEccCccccccccCccccCCCCCCCceeEEE
Q 032998 70 ILKCHACYTITAEIGRIFCPKCGNGGTLRKVA 101 (129)
Q Consensus 70 ~~rC~~C~k~~~~~~~~fCp~CG~~~tL~rv~ 101 (129)
.-+|..|+..... ...||.||+. .+.+.+
T Consensus 680 ~~~C~~CG~~~~~--~~~CP~CG~~-~~~~~~ 708 (735)
T PRK07111 680 VDRCPVCGYLGVI--EDKCPKCGST-NIQRIR 708 (735)
T ss_pred CeecCCCCCCCCc--CccCcCCCCc-cceeee
Confidence 3579999954432 4789999985 444433
No 91
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=84.02 E-value=0.42 Score=43.03 Aligned_cols=29 Identities=34% Similarity=0.633 Sum_probs=13.9
Q ss_pred EEEccCccccccccCccccCCCCCCCceeEEE
Q 032998 70 ILKCHACYTITAEIGRIFCPKCGNGGTLRKVA 101 (129)
Q Consensus 70 ~~rC~~C~k~~~~~~~~fCp~CG~~~tL~rv~ 101 (129)
.-+|..|+..... ...||+||++ -+...+
T Consensus 491 ~~~C~~CG~~~~~--~~~CP~CGs~-~~~~~~ 519 (546)
T PF13597_consen 491 IDICPDCGYIGGE--GDKCPKCGSE-NIEVYS 519 (546)
T ss_dssp EEEETTT---S----EEE-CCC-----EEEEB
T ss_pred cccccCCCcCCCC--CCCCCCCCCc-ccceEE
Confidence 4589999987765 5789999998 444433
No 92
>PF14353 CpXC: CpXC protein
Probab=84.01 E-value=1.1 Score=32.45 Aligned_cols=28 Identities=18% Similarity=0.325 Sum_probs=15.8
Q ss_pred ccccCCCCCCCceeEEEEEeCCCceEEe
Q 032998 85 RIFCPKCGNGGTLRKVAVTVGENGIVLA 112 (129)
Q Consensus 85 ~~fCp~CG~~~tL~rv~v~v~~~G~~~~ 112 (129)
.-.||.||....+.---++.|...++.+
T Consensus 38 ~~~CP~Cg~~~~~~~p~lY~D~~~~~~i 65 (128)
T PF14353_consen 38 SFTCPSCGHKFRLEYPLLYHDPEKKFMI 65 (128)
T ss_pred EEECCCCCCceecCCCEEEEcCCCCEEE
Confidence 3569999987444333344455555433
No 93
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=83.90 E-value=0.67 Score=37.45 Aligned_cols=28 Identities=21% Similarity=0.511 Sum_probs=22.5
Q ss_pred EEccCccccccccCccccCCCCCCCceeE
Q 032998 71 LKCHACYTITAEIGRIFCPKCGNGGTLRK 99 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG~~~tL~r 99 (129)
++|.-|+.+... .-..||.||+-.||.-
T Consensus 355 ~~c~~cg~~~~~-~~~~c~~c~~~~~~~~ 382 (389)
T PRK11788 355 YRCRNCGFTART-LYWHCPSCKAWETIKP 382 (389)
T ss_pred EECCCCCCCCcc-ceeECcCCCCccCcCC
Confidence 459999987765 4588999999877763
No 94
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=83.70 E-value=0.64 Score=34.82 Aligned_cols=27 Identities=26% Similarity=0.673 Sum_probs=20.1
Q ss_pred eEEEEccCccccccc--------cC-ccccCCCCCC
Q 032998 68 RWILKCHACYTITAE--------IG-RIFCPKCGNG 94 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~--------~~-~~fCp~CG~~ 94 (129)
.-.|.|+.|++.|.- ++ .-.||.||.+
T Consensus 97 ~~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~ 132 (147)
T smart00531 97 NAYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEE 132 (147)
T ss_pred CcEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCE
Confidence 457999999977642 11 2579999997
No 95
>PRK02935 hypothetical protein; Provisional
Probab=83.68 E-value=0.82 Score=33.80 Aligned_cols=32 Identities=25% Similarity=0.386 Sum_probs=24.7
Q ss_pred eeEEEEccCccccccccC-ccccCCCCCCCcee
Q 032998 67 HRWILKCHACYTITAEIG-RIFCPKCGNGGTLR 98 (129)
Q Consensus 67 k~W~~rC~~C~k~~~~~~-~~fCp~CG~~~tL~ 98 (129)
|.-...|+.|.|.++-.. -+-|.+|+.|=||.
T Consensus 67 kavqV~CP~C~K~TKmLGrvD~CM~C~~PLTLd 99 (110)
T PRK02935 67 KAVQVICPSCEKPTKMLGRVDACMHCNQPLTLD 99 (110)
T ss_pred cceeeECCCCCchhhhccceeecCcCCCcCCcC
Confidence 355569999999998665 47899999994443
No 96
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=83.68 E-value=0.5 Score=31.44 Aligned_cols=21 Identities=38% Similarity=0.964 Sum_probs=12.4
Q ss_pred EEEccCccccccccCccccCCCCC
Q 032998 70 ILKCHACYTITAEIGRIFCPKCGN 93 (129)
Q Consensus 70 ~~rC~~C~k~~~~~~~~fCp~CG~ 93 (129)
++||..|.+... ...||+||-
T Consensus 36 I~RC~~CRk~~~---~Y~CP~CGF 56 (59)
T PRK14890 36 IYRCEKCRKQSN---PYTCPKCGF 56 (59)
T ss_pred EeechhHHhcCC---ceECCCCCC
Confidence 344555555443 256999985
No 97
>PRK05580 primosome assembly protein PriA; Validated
Probab=83.40 E-value=0.8 Score=42.10 Aligned_cols=27 Identities=33% Similarity=0.677 Sum_probs=19.0
Q ss_pred EEEccCccccccccCccccCCCCCCCceeE
Q 032998 70 ILKCHACYTITAEIGRIFCPKCGNGGTLRK 99 (129)
Q Consensus 70 ~~rC~~C~k~~~~~~~~fCp~CG~~~tL~r 99 (129)
.++||-|+.....+ ..||.||+. .|+-
T Consensus 408 ~l~Ch~Cg~~~~~~--~~Cp~Cg~~-~l~~ 434 (679)
T PRK05580 408 RLRCHHCGYQEPIP--KACPECGST-DLVP 434 (679)
T ss_pred eEECCCCcCCCCCC--CCCCCCcCC-eeEE
Confidence 46788888655433 679999997 5554
No 98
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=83.20 E-value=0.84 Score=26.94 Aligned_cols=25 Identities=28% Similarity=0.662 Sum_probs=17.6
Q ss_pred EEEccCcccccccc--------CccccCCCCCC
Q 032998 70 ILKCHACYTITAEI--------GRIFCPKCGNG 94 (129)
Q Consensus 70 ~~rC~~C~k~~~~~--------~~~fCp~CG~~ 94 (129)
...|+.|++.|... .+.-|++||+.
T Consensus 2 ~i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~ 34 (36)
T PF13717_consen 2 IITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHV 34 (36)
T ss_pred EEECCCCCCEEeCCHHHCCCCCcEEECCCCCCE
Confidence 35799999887531 24679999873
No 99
>COG0267 RpmG Ribosomal protein L33 [Translation, ribosomal structure and biogenesis]
Probab=82.99 E-value=0.85 Score=29.35 Aligned_cols=31 Identities=32% Similarity=0.715 Sum_probs=22.1
Q ss_pred eEEEEccCcc-ccccc----------cC-ccccCCCCCCCceeE
Q 032998 68 RWILKCHACY-TITAE----------IG-RIFCPKCGNGGTLRK 99 (129)
Q Consensus 68 ~W~~rC~~C~-k~~~~----------~~-~~fCp~CG~~~tL~r 99 (129)
.-.|.|.+|. +.|.. +. +.|||+|... ||-|
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 4578999999 54421 11 5899999997 7754
No 100
>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=82.95 E-value=1.5 Score=33.75 Aligned_cols=33 Identities=24% Similarity=0.446 Sum_probs=24.4
Q ss_pred eeEEEEccCccccccc-------------cCccccCCCCCCCceeEEE
Q 032998 67 HRWILKCHACYTITAE-------------IGRIFCPKCGNGGTLRKVA 101 (129)
Q Consensus 67 k~W~~rC~~C~k~~~~-------------~~~~fCp~CG~~~tL~rv~ 101 (129)
+.|-|+|. |+..|.. .....||.||+. .+.|..
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 57889998 7776642 345789999997 777754
No 101
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=82.78 E-value=1.1 Score=36.85 Aligned_cols=61 Identities=25% Similarity=0.342 Sum_probs=37.0
Q ss_pred eeeEeechHHHHHHHHHhCce-eecCCCCcceeeeeEEEEccCcccccc-cc----Cc----cccCCCCCCCceeEEEEE
Q 032998 34 TVACITGDYAMQNVILQMGLR-LLAPGGMQIRQLHRWILKCHACYTITA-EI----GR----IFCPKCGNGGTLRKVAVT 103 (129)
Q Consensus 34 ~va~~TdDyamQNVl~~lGL~-~~s~~g~~I~~~k~W~~rC~~C~k~~~-~~----~~----~fCp~CG~~~tL~rv~v~ 103 (129)
...++|. -+.|.-.+.|.. |+.++|. -+..+|..|+..+. +. .. .-||.||.+ -||.--|.
T Consensus 93 ~~~iiTQ--NiD~Lhe~AGs~~Vi~lHGs------l~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~-~lrP~VV~ 163 (250)
T COG0846 93 LLRIITQ--NIDGLHERAGSKNVIELHGS------LKRVRCSKCGNQYYDEDVIKFIEDGLIPRCPKCGGP-VLRPDVVW 163 (250)
T ss_pred ceEEEec--ccchHHHHcCCCcEEEeccc------eeeeEeCCCcCccchhhhhhhcccCCCCcCccCCCc-cccCCEEE
Confidence 4566664 234556666644 4556664 67789999986664 11 11 239999995 36543333
No 102
>PLN02569 threonine synthase
Probab=82.72 E-value=1.3 Score=39.55 Aligned_cols=58 Identities=16% Similarity=0.050 Sum_probs=37.8
Q ss_pred eeeEeechHHHHHHHHHhCceeecCCCCcceeeeeEEEEccCccccccccC-ccccCCCCCCCcee
Q 032998 34 TVACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIG-RIFCPKCGNGGTLR 98 (129)
Q Consensus 34 ~va~~TdDyamQNVl~~lGL~~~s~~g~~I~~~k~W~~rC~~C~k~~~~~~-~~fCp~CG~~~tL~ 98 (129)
...-.+.|-++|-++++ +.... .+. +.-...+.++|..|++.|+... ...| .||.+ |.
T Consensus 17 ~~~~~~~~~~~~~~~~~-~~~~~-~~~--~~~~~~~~l~C~~Cg~~y~~~~~~~~C-~cgg~--l~ 75 (484)
T PLN02569 17 SATKFTADENIRDEARR-GPPAP-PDE--FSAKYVPFLECPLTGEKYSLDEVVYRS-KSGGL--LD 75 (484)
T ss_pred cccccCcchhhhhhhhh-cCCCC-Ccc--cccccccccEeCCCCCcCCCccccccC-CCCCe--EE
Confidence 34567889999999998 22211 121 2222344699999999986433 4669 69986 54
No 103
>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=82.66 E-value=0.67 Score=42.07 Aligned_cols=49 Identities=18% Similarity=0.369 Sum_probs=28.3
Q ss_pred HHHHHHHHH---hCceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCCCceeEE
Q 032998 42 YAMQNVILQ---MGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKV 100 (129)
Q Consensus 42 yamQNVl~~---lGL~~~s~~g~~I~~~k~W~~rC~~C~k~~~~~~~~fCp~CG~~~tL~rv 100 (129)
-|+..+... .|+...++. .=.-+|..|+..... ....||+||+. -+.+.
T Consensus 501 eal~~lv~~a~~~~i~Y~~~n--------~~~~~C~~CG~~g~~-~~~~CP~Cgs~-~~~~~ 552 (579)
T TIGR02487 501 EALKDITKKAMKNGIGYFGIN--------PPVDVCEDCGYTGEG-LNDKCPKCGSH-DIEVI 552 (579)
T ss_pred HHHHHHHHHHHhcCCceEEec--------cCCccCCCCCCCCCC-CCCcCcCCCCc-cceeh
Confidence 566666544 344444443 113479999974332 23689999986 34333
No 104
>COG3091 SprT Zn-dependent metalloprotease, SprT family [General function prediction only]
Probab=82.28 E-value=0.81 Score=35.70 Aligned_cols=54 Identities=22% Similarity=0.465 Sum_probs=33.0
Q ss_pred HHHHHHHHh-CceeecCCCCcceee--eeEEEEccCcccccc-----ccCc----cccCCCCCCCceeE
Q 032998 43 AMQNVILQM-GLRLLAPGGMQIRQL--HRWILKCHACYTITA-----EIGR----IFCPKCGNGGTLRK 99 (129)
Q Consensus 43 amQNVl~~l-GL~~~s~~g~~I~~~--k~W~~rC~~C~k~~~-----~~~~----~fCp~CG~~~tL~r 99 (129)
.-|=++.+. |+.+......-++++ .++.|+|. |+..+. +..+ ..|.+||.+ |..
T Consensus 87 ewk~lm~qV~~l~~~~~h~~~~~~v~~~~~~Y~C~-C~q~~l~~RRhn~~~~g~~YrC~~C~gk--L~~ 152 (156)
T COG3091 87 EWKLLMQQVLGLRFCRTHQFEVQSVRRTTYPYRCQ-CQQHYLRIRRHNTVRRGEVYRCGKCGGK--LVF 152 (156)
T ss_pred hHHHHHHHhCCCCCCccchHHHhhccccceeEEee-cCCccchhhhcccccccceEEeccCCce--EEe
Confidence 334444443 466554433434433 48999999 998763 2224 789999997 554
No 105
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=82.24 E-value=1 Score=45.38 Aligned_cols=26 Identities=31% Similarity=0.713 Sum_probs=22.5
Q ss_pred eEEEEccCccccccccC-ccccCCCCCC
Q 032998 68 RWILKCHACYTITAEIG-RIFCPKCGNG 94 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~~~-~~fCp~CG~~ 94 (129)
+=..|| .|+..|..++ ..-||+||++
T Consensus 1540 rQ~~RC-kC~~kyRR~PL~G~C~kCGg~ 1566 (1627)
T PRK14715 1540 RQEFRC-KCGAKYRRVPLKGKCPKCGSK 1566 (1627)
T ss_pred ccceee-cCCCccccCCCCCcCcccCCe
Confidence 446899 9999998877 6889999998
No 106
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=82.13 E-value=0.63 Score=43.09 Aligned_cols=23 Identities=35% Similarity=0.787 Sum_probs=16.5
Q ss_pred EEccCccccccccCccccCCCCCC
Q 032998 71 LKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
.+|+.|+...++. -.||+.||.+
T Consensus 2 ~~Cp~Cg~~n~~~-akFC~~CG~~ 24 (645)
T PRK14559 2 LICPQCQFENPNN-NRFCQKCGTS 24 (645)
T ss_pred CcCCCCCCcCCCC-CccccccCCC
Confidence 4688888765543 4688888876
No 107
>PRK11823 DNA repair protein RadA; Provisional
Probab=82.03 E-value=1.1 Score=39.36 Aligned_cols=31 Identities=26% Similarity=0.475 Sum_probs=25.3
Q ss_pred eEEEEccCccccccccCccccCCCCCCCceeE
Q 032998 68 RWILKCHACYTITAEIGRIFCPKCGNGGTLRK 99 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~~~~~fCp~CG~~~tL~r 99 (129)
+-.|+|..|+..+.. ..-.||.||.-+|+..
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 457999999987764 4578999999888876
No 108
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=81.86 E-value=1 Score=39.83 Aligned_cols=25 Identities=28% Similarity=0.775 Sum_probs=19.2
Q ss_pred EEEccCccccccccC------------------ccccCCCCCC
Q 032998 70 ILKCHACYTITAEIG------------------RIFCPKCGNG 94 (129)
Q Consensus 70 ~~rC~~C~k~~~~~~------------------~~fCp~CG~~ 94 (129)
+++|..|+.+|.+.. .--||.||.+
T Consensus 425 ~~~c~~c~~~yd~~~g~~~~~~~~gt~~~~lp~~~~cp~c~~~ 467 (479)
T PRK05452 425 RMQCSVCQWIYDPAKGEPMQDVAPGTPWSEVPDNFLCPECSLG 467 (479)
T ss_pred eEEECCCCeEECCCCCCcccCCCCCCChhhCCCCCcCcCCCCc
Confidence 479999999997531 1269999976
No 109
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=81.86 E-value=1.1 Score=26.54 Aligned_cols=24 Identities=33% Similarity=0.771 Sum_probs=16.9
Q ss_pred EEccCcccccccc--------CccccCCCCCC
Q 032998 71 LKCHACYTITAEI--------GRIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~~~~--------~~~fCp~CG~~ 94 (129)
.+|+.|...|... .+.-||+||+.
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 5789998777532 25679999874
No 110
>PRK05638 threonine synthase; Validated
Probab=81.49 E-value=0.94 Score=39.28 Aligned_cols=24 Identities=29% Similarity=0.539 Sum_probs=19.4
Q ss_pred EEEccCccccccccCccccCCCCCC
Q 032998 70 ILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 70 ~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
+++|..|++.|+......| .||.+
T Consensus 1 ~l~C~~Cg~~~~~~~~~~C-~c~~~ 24 (442)
T PRK05638 1 KMKCPKCGREYNSYIPPFC-ICGEL 24 (442)
T ss_pred CeEeCCCCCCCCCCCceec-CCCCc
Confidence 4799999999875445679 89987
No 111
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=81.45 E-value=0.54 Score=31.49 Aligned_cols=8 Identities=63% Similarity=1.389 Sum_probs=5.7
Q ss_pred cccCCCCC
Q 032998 86 IFCPKCGN 93 (129)
Q Consensus 86 ~fCp~CG~ 93 (129)
..||+||-
T Consensus 51 Y~Cp~CGF 58 (61)
T COG2888 51 YRCPKCGF 58 (61)
T ss_pred eECCCcCc
Confidence 55888884
No 112
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=81.42 E-value=1.1 Score=41.53 Aligned_cols=43 Identities=23% Similarity=0.448 Sum_probs=29.2
Q ss_pred HHHHHHHHHh----CceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCC
Q 032998 42 YAMQNVILQM----GLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 42 yamQNVl~~l----GL~~~s~~g~~I~~~k~W~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
-|+.++...+ ++...++.-. .-+|..|+..... ...||+||++
T Consensus 602 ~a~~~lv~~~~~~~~i~Y~~in~~--------~~~C~~CG~~~g~--~~~CP~CG~~ 648 (656)
T PRK08270 602 EACKKLVKKALENYRLPYITITPT--------FSICPKHGYLSGE--HEFCPKCGEE 648 (656)
T ss_pred HHHHHHHHHHHHhCCCceEEeCCC--------CcccCCCCCcCCC--CCCCcCCcCc
Confidence 6777777654 4666555421 3479999975433 4789999986
No 113
>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=81.41 E-value=1.2 Score=32.90 Aligned_cols=37 Identities=19% Similarity=0.428 Sum_probs=24.6
Q ss_pred EccCcccc--ccccCccccCCCCCCCceeEE--------EEEeCCCceE
Q 032998 72 KCHACYTI--TAEIGRIFCPKCGNGGTLRKV--------AVTVGENGIV 110 (129)
Q Consensus 72 rC~~C~k~--~~~~~~~fCp~CG~~~tL~rv--------~v~v~~~G~~ 110 (129)
.|+.|.-. |.+-....||.||+. -... .+..|++|++
T Consensus 4 ~CP~C~seytY~dg~~~iCpeC~~E--W~~~~~~~~~~~~~~kDsnG~~ 50 (109)
T TIGR00686 4 PCPKCNSEYTYHDGTQLICPSCLYE--WNENEVNDDDDELIVKDCNGNL 50 (109)
T ss_pred cCCcCCCcceEecCCeeECcccccc--ccccccccccCCceEEcCCCCC
Confidence 58889843 455557889999986 2211 2456888875
No 114
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=80.73 E-value=0.94 Score=30.32 Aligned_cols=31 Identities=26% Similarity=0.524 Sum_probs=21.7
Q ss_pred EEEccCcccccc-c--cCccccCCCCCCCceeEEE
Q 032998 70 ILKCHACYTITA-E--IGRIFCPKCGNGGTLRKVA 101 (129)
Q Consensus 70 ~~rC~~C~k~~~-~--~~~~fCp~CG~~~tL~rv~ 101 (129)
.-+|++|+..-. . ..+--||.||+. .+.|-+
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 568999997652 2 225569999987 776643
No 115
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=80.72 E-value=1.2 Score=29.64 Aligned_cols=30 Identities=27% Similarity=0.609 Sum_probs=21.3
Q ss_pred EEEccCcccccccc---CccccCCCCCCCceeEE
Q 032998 70 ILKCHACYTITAEI---GRIFCPKCGNGGTLRKV 100 (129)
Q Consensus 70 ~~rC~~C~k~~~~~---~~~fCp~CG~~~tL~rv 100 (129)
...|+.|+..-... .+-.||.||.. .|.|-
T Consensus 7 ~~~CtSCg~~i~~~~~~~~F~CPnCG~~-~I~RC 39 (59)
T PRK14890 7 PPKCTSCGIEIAPREKAVKFLCPNCGEV-IIYRC 39 (59)
T ss_pred CccccCCCCcccCCCccCEeeCCCCCCe-eEeec
Confidence 35799999765422 25679999996 67764
No 116
>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=80.48 E-value=1.5 Score=34.43 Aligned_cols=42 Identities=21% Similarity=0.411 Sum_probs=26.6
Q ss_pred HHHHhCce-eecCCCCcceeeeeEEEEccCccccccc---------cCccccCCCCCC
Q 032998 47 VILQMGLR-LLAPGGMQIRQLHRWILKCHACYTITAE---------IGRIFCPKCGNG 94 (129)
Q Consensus 47 Vl~~lGL~-~~s~~g~~I~~~k~W~~rC~~C~k~~~~---------~~~~fCp~CG~~ 94 (129)
.-.+.|.+ ++.++|. ...++|..|++.+.. .....||.||..
T Consensus 91 L~~~aG~~~v~elHG~------~~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~ 142 (218)
T cd01407 91 LHQRAGSPKVIELHGS------LFRVRCTKCGKEYPRDELQADIDREEVPRCPKCGGL 142 (218)
T ss_pred hHHHcCCCCEEECcCC------cCcceeCCCcCCCcHHHHhHhhccCCCCcCCCCCCc
Confidence 34444553 5556654 445789999986642 113569999987
No 117
>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=80.33 E-value=3.2 Score=31.02 Aligned_cols=44 Identities=23% Similarity=0.490 Sum_probs=27.9
Q ss_pred eeEEEEccCcccccccc--CccccCCCCCCC--c--eeEEEEEe-CCCceE
Q 032998 67 HRWILKCHACYTITAEI--GRIFCPKCGNGG--T--LRKVAVTV-GENGIV 110 (129)
Q Consensus 67 k~W~~rC~~C~k~~~~~--~~~fCp~CG~~~--t--L~rv~v~v-~~~G~~ 110 (129)
.-|-..|+.|.|.-... ...+|+.|+... . .-++.+.+ |..|.+
T Consensus 31 ~~~Y~aC~~C~kkv~~~~~~~~~C~~C~~~~~~~~~ry~l~~~i~D~Tg~~ 81 (166)
T cd04476 31 NWWYPACPGCNKKVVEEGNGTYRCEKCNKSVPNPEYRYILSLNVADHTGEA 81 (166)
T ss_pred CeEEccccccCcccEeCCCCcEECCCCCCcCCCccEEEEEEEEEEeCCCCE
Confidence 35566799999765433 368999999851 1 24455555 455665
No 118
>PRK10220 hypothetical protein; Provisional
Probab=80.09 E-value=1.4 Score=32.60 Aligned_cols=37 Identities=22% Similarity=0.608 Sum_probs=24.2
Q ss_pred EccCccc--cccccCccccCCCCCCCceeEE--------EEEeCCCceE
Q 032998 72 KCHACYT--ITAEIGRIFCPKCGNGGTLRKV--------AVTVGENGIV 110 (129)
Q Consensus 72 rC~~C~k--~~~~~~~~fCp~CG~~~tL~rv--------~v~v~~~G~~ 110 (129)
.|+.|.- +|.+.....||.||+. -..- .+..|++|++
T Consensus 5 ~CP~C~seytY~d~~~~vCpeC~hE--W~~~~~~~~~~~~~vkDsnG~~ 51 (111)
T PRK10220 5 HCPKCNSEYTYEDNGMYICPECAHE--WNDAEPAQESDELIVKDANGNL 51 (111)
T ss_pred cCCCCCCcceEcCCCeEECCcccCc--CCccccccccCCceEEcCCCCC
Confidence 5888884 3555557889999986 2211 1345788875
No 119
>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=80.07 E-value=1.1 Score=29.41 Aligned_cols=25 Identities=24% Similarity=0.555 Sum_probs=20.8
Q ss_pred EEccCccccccccCccccCCCCCCC
Q 032998 71 LKCHACYTITAEIGRIFCPKCGNGG 95 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG~~~ 95 (129)
-.|..|++.....-+..|..||.|+
T Consensus 16 ~~CrRCG~~syH~qK~~CasCGyp~ 40 (55)
T PF01907_consen 16 TLCRRCGRRSYHIQKKTCASCGYPA 40 (55)
T ss_dssp EE-TTTSSEEEETTTTEETTTBTTT
T ss_pred eeecccCCeeeecCCCcccccCCCc
Confidence 4799999888777899999999983
No 120
>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=79.88 E-value=1.4 Score=27.15 Aligned_cols=24 Identities=21% Similarity=0.411 Sum_probs=15.9
Q ss_pred ccCCCCCCCceeEEEEEeCCCceEE
Q 032998 87 FCPKCGNGGTLRKVAVTVGENGIVL 111 (129)
Q Consensus 87 fCp~CG~~~tL~rv~v~v~~~G~~~ 111 (129)
.||.||++ ...|.+..+......+
T Consensus 1 ~CP~Cg~~-a~ir~S~~~s~~~~~~ 24 (47)
T PF04606_consen 1 RCPHCGSK-ARIRTSRQLSPLTREL 24 (47)
T ss_pred CcCCCCCe-eEEEEchhhCcceEEE
Confidence 39999999 5555566555554443
No 121
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=79.83 E-value=0.89 Score=39.09 Aligned_cols=28 Identities=29% Similarity=0.580 Sum_probs=23.0
Q ss_pred EEccCccccccccCccccCCCCCCCceeE
Q 032998 71 LKCHACYTITAEIGRIFCPKCGNGGTLRK 99 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG~~~tL~r 99 (129)
|+|..|+..+.. ..-.||.||.-+|+..
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 689999987765 4678999998878876
No 122
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=78.76 E-value=1.1 Score=41.34 Aligned_cols=46 Identities=22% Similarity=0.411 Sum_probs=29.1
Q ss_pred chHHHHHHHHHh---CceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCC
Q 032998 40 GDYAMQNVILQM---GLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 40 dDyamQNVl~~l---GL~~~s~~g~~I~~~k~W~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
+=-|+..+...+ ++...++. .=.-+|..|+..+... ...||+||++
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 446777777764 23333332 1235799999854332 5789999986
No 123
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=78.75 E-value=1.5 Score=34.28 Aligned_cols=63 Identities=13% Similarity=0.054 Sum_probs=34.2
Q ss_pred eeEeechHHHHHHHHHhCceeecCCCCcceeeeeEEEEccCccccccc----cCccccCCCCCCCceeE
Q 032998 35 VACITGDYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAE----IGRIFCPKCGNGGTLRK 99 (129)
Q Consensus 35 va~~TdDyamQNVl~~lGL~~~s~~g~~I~~~k~W~~rC~~C~k~~~~----~~~~fCp~CG~~~tL~r 99 (129)
.-.+|.+.+.+-+..++---+..+....-.+.-.=-|.|+.|++.|.- ...-.||.||+. |..
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 345677777776666653111111111111112345899999976631 123559999997 654
No 124
>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=78.64 E-value=0.91 Score=27.32 Aligned_cols=24 Identities=33% Similarity=0.868 Sum_probs=12.6
Q ss_pred EEccCccccc--cc--cCccccCCCCCC
Q 032998 71 LKCHACYTIT--AE--IGRIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~--~~--~~~~fCp~CG~~ 94 (129)
++|+.|+... .+ .....|+.||.-
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~V 28 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGLV 28 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-BB
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCCE
Confidence 4577777532 12 224577777764
No 125
>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=78.42 E-value=1.7 Score=34.89 Aligned_cols=44 Identities=23% Similarity=0.382 Sum_probs=26.9
Q ss_pred eecCCCCcceeeeeEEEEccCcccccccc---------CccccCCCCCCCceeEEEEEeCC
Q 032998 55 LLAPGGMQIRQLHRWILKCHACYTITAEI---------GRIFCPKCGNGGTLRKVAVTVGE 106 (129)
Q Consensus 55 ~~s~~g~~I~~~k~W~~rC~~C~k~~~~~---------~~~fCp~CG~~~tL~rv~v~v~~ 106 (129)
++.++|. ...++|..|++.++.. ...-||.||+. |+=--|..+|
T Consensus 107 V~elHG~------l~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cgg~--lrP~Vv~FGE 159 (235)
T cd01408 107 IIEAHGS------FATAHCIKCKHKYPGDWMREDIFNQEVPKCPRCGGL--VKPDIVFFGE 159 (235)
T ss_pred EEEeCcC------CCccccccCCCcCCHHHHHHHHhCCCCccCCCCCCC--ccCcEEECCC
Confidence 4555554 4557899999876421 12459999986 6543333333
No 126
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=78.14 E-value=0.83 Score=44.83 Aligned_cols=26 Identities=27% Similarity=0.641 Sum_probs=21.5
Q ss_pred eEEEEccCccccccccCccccCCCCCC
Q 032998 68 RWILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
.-+.||..|+..+.+. .++||.||++
T Consensus 692 ~tIKrC~dcg~q~~~~-~~~cP~Cgs~ 717 (1187)
T COG1110 692 DTIKRCRDCGEQFVDS-EDKCPRCGSR 717 (1187)
T ss_pred HHHHHHhhcCceeccc-cccCCCCCCc
Confidence 3348999999988775 5799999995
No 127
>PRK04023 DNA polymerase II large subunit; Validated
Probab=78.09 E-value=1.2 Score=43.68 Aligned_cols=21 Identities=38% Similarity=0.686 Sum_probs=11.2
Q ss_pred EEccCccccccccCccccCCCCCC
Q 032998 71 LKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
.+|+.|++.+. ..+||.||..
T Consensus 627 RfCpsCG~~t~---~frCP~CG~~ 647 (1121)
T PRK04023 627 RKCPSCGKETF---YRRCPFCGTH 647 (1121)
T ss_pred ccCCCCCCcCC---cccCCCCCCC
Confidence 45666665532 2456666553
No 128
>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=78.00 E-value=1.5 Score=34.69 Aligned_cols=27 Identities=26% Similarity=0.338 Sum_probs=19.6
Q ss_pred eEEEEccCcccccccc--------CccccCCCCCC
Q 032998 68 RWILKCHACYTITAEI--------GRIFCPKCGNG 94 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~~--------~~~fCp~CG~~ 94 (129)
...++|..|++.+... ....||.||..
T Consensus 111 l~~~~C~~C~~~~~~~~~~~~~~~~~p~C~~Cgg~ 145 (222)
T cd01413 111 LQTAYCVNCGSKYDLEEVKYAKKHEVPRCPKCGGI 145 (222)
T ss_pred cCcceECCCCCCcchhHHHHhccCCCCcCCCCCCc
Confidence 4558899999876421 13569999986
No 129
>PRK08197 threonine synthase; Validated
Probab=77.89 E-value=1.7 Score=37.10 Aligned_cols=25 Identities=28% Similarity=0.563 Sum_probs=19.6
Q ss_pred EEEEccCccccccccC-ccccCCCCCC
Q 032998 69 WILKCHACYTITAEIG-RIFCPKCGNG 94 (129)
Q Consensus 69 W~~rC~~C~k~~~~~~-~~fCp~CG~~ 94 (129)
+.++|..|++.|+... ...| .||.+
T Consensus 6 ~~~~C~~Cg~~~~~~~~~~~C-~cg~~ 31 (394)
T PRK08197 6 SHLECSKCGETYDADQVHNLC-KCGKP 31 (394)
T ss_pred eEEEECCCCCCCCCCCcceec-CCCCe
Confidence 3699999999987543 3569 89987
No 130
>PRK08329 threonine synthase; Validated
Probab=77.83 E-value=1.5 Score=36.79 Aligned_cols=25 Identities=32% Similarity=0.695 Sum_probs=19.8
Q ss_pred EEccCccccccccCccccCCCCCCCcee
Q 032998 71 LKCHACYTITAEIGRIFCPKCGNGGTLR 98 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG~~~tL~ 98 (129)
++|..|++.|+......| .||.+ |.
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 789999999975445679 69987 55
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=77.66 E-value=1.4 Score=24.34 Aligned_cols=21 Identities=33% Similarity=0.695 Sum_probs=11.9
Q ss_pred ccCcccccccc---CccccCCCCC
Q 032998 73 CHACYTITAEI---GRIFCPKCGN 93 (129)
Q Consensus 73 C~~C~k~~~~~---~~~fCp~CG~ 93 (129)
|..|+..-... ..--||.||.
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCcccCceEeCCCCCC
Confidence 67775443221 1346999983
No 132
>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=77.41 E-value=1.6 Score=38.48 Aligned_cols=31 Identities=19% Similarity=0.406 Sum_probs=24.9
Q ss_pred eEEEEccCccccccccCccccCCCCCCCceeE
Q 032998 68 RWILKCHACYTITAEIGRIFCPKCGNGGTLRK 99 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~~~~~fCp~CG~~~tL~r 99 (129)
+-.|+|..|+..+.. ..-.||.||+=+|+..
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 347999999987654 4577999998888875
No 133
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=77.32 E-value=1 Score=30.07 Aligned_cols=27 Identities=22% Similarity=0.733 Sum_probs=22.9
Q ss_pred eEEEEccCccccccccCccccCCCCCC
Q 032998 68 RWILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
+--.+|..|++.....-+..|..||-+
T Consensus 14 ~tH~~CRRCGr~syhv~k~~CaaCGfg 40 (61)
T COG2126 14 KTHIRCRRCGRRSYHVRKKYCAACGFG 40 (61)
T ss_pred cceehhhhccchheeeccceecccCCC
Confidence 445689999998777778999999987
No 134
>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=77.21 E-value=1.8 Score=34.16 Aligned_cols=29 Identities=24% Similarity=0.430 Sum_probs=20.1
Q ss_pred eEEEEccCcccccccc----------CccccCCCCCCCcee
Q 032998 68 RWILKCHACYTITAEI----------GRIFCPKCGNGGTLR 98 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~~----------~~~fCp~CG~~~tL~ 98 (129)
-+..+|..|++.+... ....||.||+. |+
T Consensus 93 ~~~~~C~~C~~~~~~~~~~~~~~~~~~~p~C~~Cgg~--lr 131 (206)
T cd01410 93 MFIEVCKSCGPEYVRDDVVETRGDKETGRRCHACGGI--LK 131 (206)
T ss_pred cCcccCCCCCCccchHHHHHHhhcCCCCCcCCCCcCc--cC
Confidence 4567899999876421 12459999986 55
No 135
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=77.17 E-value=1.9 Score=34.39 Aligned_cols=27 Identities=26% Similarity=0.420 Sum_probs=18.9
Q ss_pred eEEEEccCcccccccc-----CccccCCCCCC
Q 032998 68 RWILKCHACYTITAEI-----GRIFCPKCGNG 94 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~~-----~~~fCp~CG~~ 94 (129)
...++|..|++.+... ...-||.||+.
T Consensus 120 ~~~~~C~~C~~~~~~~~~~~~~~p~C~~Cgg~ 151 (242)
T PRK00481 120 LLRARCTKCGQTYDLDEYLKPEPPRCPKCGGI 151 (242)
T ss_pred cCceeeCCCCCCcChhhhccCCCCCCCCCCCc
Confidence 4458899999877521 12349999987
No 136
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=76.86 E-value=1.4 Score=40.71 Aligned_cols=44 Identities=23% Similarity=0.436 Sum_probs=27.0
Q ss_pred HHHHHHHHH---hCceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCC
Q 032998 42 YAMQNVILQ---MGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 42 yamQNVl~~---lGL~~~s~~g~~I~~~k~W~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
-|+.++... .|+...++.- . .-+|..|+..... ....||+||++
T Consensus 543 eal~~lv~~~~~~~i~Yf~in~-~-------~~iC~~CG~~~~g-~~~~CP~CGs~ 589 (623)
T PRK08271 543 EGYRKLLNIAAKTGCNYFAFNV-K-------ITICNDCHHIDKR-TGKRCPICGSE 589 (623)
T ss_pred HHHHHHHHHHHHcCCceEEeCC-C-------CccCCCCCCcCCC-CCcCCcCCCCc
Confidence 455554443 3555555431 1 3479999976332 35789999986
No 137
>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=76.77 E-value=1 Score=29.81 Aligned_cols=29 Identities=21% Similarity=0.504 Sum_probs=22.7
Q ss_pred eeeEEEEccCccccccccCccccCCCCCC
Q 032998 66 LHRWILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 66 ~k~W~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
.+.-.+.|+-|..-...+-...||.||..
T Consensus 22 A~ICSfECTFC~~C~e~~l~~~CPNCgGe 50 (57)
T PF06906_consen 22 AYICSFECTFCADCAETMLNGVCPNCGGE 50 (57)
T ss_pred ceEEeEeCcccHHHHHHHhcCcCcCCCCc
Confidence 44556899999977666546889999997
No 138
>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=76.71 E-value=1.7 Score=33.14 Aligned_cols=28 Identities=21% Similarity=0.388 Sum_probs=19.4
Q ss_pred EEEEccCccccccc----cCccccCCCCCCCcee
Q 032998 69 WILKCHACYTITAE----IGRIFCPKCGNGGTLR 98 (129)
Q Consensus 69 W~~rC~~C~k~~~~----~~~~fCp~CG~~~tL~ 98 (129)
=-|.|+.|+..+.- ...-.||.||+. |.
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~--L~ 139 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAMELNFTCPRCGAM--LD 139 (158)
T ss_pred CeEECCCCCcEeeHHHHHHcCCcCCCCCCE--ee
Confidence 45899999966531 113459999997 54
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=75.86 E-value=0.87 Score=43.71 Aligned_cols=22 Identities=32% Similarity=0.656 Sum_probs=0.0
Q ss_pred EEEccCccccccccCccccCCCCCC
Q 032998 70 ILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 70 ~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
..+|+.|++.+. ...||.||.+
T Consensus 655 ~r~Cp~Cg~~t~---~~~Cp~CG~~ 676 (900)
T PF03833_consen 655 RRRCPKCGKETF---YNRCPECGSH 676 (900)
T ss_dssp -------------------------
T ss_pred cccCcccCCcch---hhcCcccCCc
Confidence 356666665443 2446666655
No 140
>PRK07218 replication factor A; Provisional
Probab=75.66 E-value=1.6 Score=38.51 Aligned_cols=68 Identities=15% Similarity=0.248 Sum_probs=39.5
Q ss_pred HHHHHHHHHhCceeecCCCC--cceeeeeEEEEccCccccccccCccccCCCCCCC--ceeEEEEEeCC-CceEEe
Q 032998 42 YAMQNVILQMGLRLLAPGGM--QIRQLHRWILKCHACYTITAEIGRIFCPKCGNGG--TLRKVAVTVGE-NGIVLA 112 (129)
Q Consensus 42 yamQNVl~~lGL~~~s~~g~--~I~~~k~W~~rC~~C~k~~~~~~~~fCp~CG~~~--tL~rv~v~v~~-~G~~~~ 112 (129)
..+.++...-|..-+.+.|. .|++-.....||+.|.|+-. +..||.||... -..|+...+|. .|.+.+
T Consensus 267 ~~I~e~~~~~g~~~Vev~G~Iv~i~~gsgli~rCP~C~r~v~---~~~C~~hG~ve~~~dlrik~vLDDGtg~~~~ 339 (423)
T PRK07218 267 LKIREAVERGGIFDVELVGNIISVRDGSGLIERCPECGRVIQ---KGQCRSHGAVEGEDDLRIKAILDDGTGSVTV 339 (423)
T ss_pred cchhhhhccCCcceEEEEEEEEEeccCCcceecCcCcccccc---CCcCCCCCCcCCeeeeEEEEEEECCCCeEEE
Confidence 35555444333221233332 24555678899999999764 37899999541 24556666653 365543
No 141
>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=75.57 E-value=3.3 Score=31.62 Aligned_cols=42 Identities=14% Similarity=0.259 Sum_probs=32.0
Q ss_pred CCCCCCceeeecC----C-CceeeEeechHHHHHHHHHhCceeecCC
Q 032998 18 DECSEQSWMLRSL----S-ESTVACITGDYAMQNVILQMGLRLLAPG 59 (129)
Q Consensus 18 ~~~~~~~wi~~~~----~-~~~va~~TdDyamQNVl~~lGL~~~s~~ 59 (129)
+..+..+||..-. . ...+.++|+|.++|..+...|...++..
T Consensus 75 ~~~tAD~~Ie~~v~~~~~~~~~v~VVTSD~~iq~~~~~~GA~~iss~ 121 (166)
T PF05991_consen 75 EGETADDYIERLVRELKNRPRQVTVVTSDREIQRAARGRGAKRISSE 121 (166)
T ss_pred CCCCHHHHHHHHHHHhccCCCeEEEEeCCHHHHHHHhhCCCEEEcHH
Confidence 3345566777331 2 4789999999999999999999988653
No 142
>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=75.43 E-value=2.8 Score=34.40 Aligned_cols=41 Identities=32% Similarity=0.422 Sum_probs=16.2
Q ss_pred EEEEccCccccccccCccccCCCCCCCceeEEEEEeCCCceE
Q 032998 69 WILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGENGIV 110 (129)
Q Consensus 69 W~~rC~~C~k~~~~~~~~fCp~CG~~~tL~rv~v~v~~~G~~ 110 (129)
=.+.|.-|+.... ..+.-||.||+....+-..+++++++..
T Consensus 196 R~L~Cs~C~t~W~-~~R~~Cp~Cg~~~~~~l~~~~~e~~~~~ 236 (290)
T PF04216_consen 196 RYLHCSLCGTEWR-FVRIKCPYCGNTDHEKLEYFTVEGEPAY 236 (290)
T ss_dssp EEEEETTT--EEE---TTS-TTT---SS-EEE--------SE
T ss_pred EEEEcCCCCCeee-ecCCCCcCCCCCCCcceeeEecCCCCcE
Confidence 3478999998764 3578899999973333333334444433
No 143
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=75.43 E-value=1.4 Score=30.64 Aligned_cols=25 Identities=28% Similarity=0.388 Sum_probs=17.6
Q ss_pred EEEccCccccccccC----ccccCCCCCC
Q 032998 70 ILKCHACYTITAEIG----RIFCPKCGNG 94 (129)
Q Consensus 70 ~~rC~~C~k~~~~~~----~~fCp~CG~~ 94 (129)
++.|+-|+..+.+.. .+.||+|+=.
T Consensus 1 K~~CPCCg~~Tl~~~~~~~ydIC~VC~WE 29 (78)
T PF14206_consen 1 KYPCPCCGYYTLEERGEGTYDICPVCFWE 29 (78)
T ss_pred CccCCCCCcEEeccCCCcCceECCCCCcc
Confidence 367999997765321 5689999843
No 144
>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=75.39 E-value=2 Score=34.19 Aligned_cols=27 Identities=19% Similarity=0.373 Sum_probs=19.0
Q ss_pred eEEEEccCccccccccC---ccccCCCCCC
Q 032998 68 RWILKCHACYTITAEIG---RIFCPKCGNG 94 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~~~---~~fCp~CG~~ 94 (129)
-...+|..|.+.+.... ...||.||+.
T Consensus 116 ~~~~~C~~C~~~~~~~~~~~~p~C~~Cgg~ 145 (225)
T cd01411 116 LYRIYCTVCGKTVDWEEYLKSPYHAKCGGV 145 (225)
T ss_pred cCeeEeCCCCCccchhhcCCCCCCCCCCCE
Confidence 34478999998774211 2569999986
No 145
>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=74.89 E-value=3.6 Score=31.09 Aligned_cols=27 Identities=30% Similarity=0.567 Sum_probs=20.3
Q ss_pred eEEEEccCccccccc---------cCccccCCCCCC
Q 032998 68 RWILKCHACYTITAE---------IGRIFCPKCGNG 94 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~---------~~~~fCp~CG~~ 94 (129)
.+..+|..|++.+.. .....||.||..
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 667899999997742 113469999996
No 146
>PRK12366 replication factor A; Reviewed
Probab=74.75 E-value=4.9 Score=36.96 Aligned_cols=48 Identities=23% Similarity=0.426 Sum_probs=28.9
Q ss_pred ceeeeeEEEEccCccccccc-cCccccCCCCCCCce--eEEEEEeC-CCceE
Q 032998 63 IRQLHRWILKCHACYTITAE-IGRIFCPKCGNGGTL--RKVAVTVG-ENGIV 110 (129)
Q Consensus 63 I~~~k~W~~rC~~C~k~~~~-~~~~fCp~CG~~~tL--~rv~v~v~-~~G~~ 110 (129)
|+.-.-|-.+|+.|.|.-.. ...-.||.||...-. .++++.++ ..|.+
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 34445678999999976432 223579999973122 33445554 44655
No 147
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=74.44 E-value=2.5 Score=26.79 Aligned_cols=22 Identities=32% Similarity=0.785 Sum_probs=11.4
Q ss_pred EccCccc-cc-cccCccccCCCCC
Q 032998 72 KCHACYT-IT-AEIGRIFCPKCGN 93 (129)
Q Consensus 72 rC~~C~k-~~-~~~~~~fCp~CG~ 93 (129)
.|+.|+. +. ....+..|+.||.
T Consensus 22 fCP~Cg~~~m~~~~~r~~C~~Cgy 45 (50)
T PRK00432 22 FCPRCGSGFMAEHLDRWHCGKCGY 45 (50)
T ss_pred cCcCCCcchheccCCcEECCCcCC
Confidence 5666665 22 2223556666665
No 148
>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=73.94 E-value=1.9 Score=37.64 Aligned_cols=28 Identities=29% Similarity=0.625 Sum_probs=20.8
Q ss_pred EEEccCccccccccCccccCCCCCCCceeE
Q 032998 70 ILKCHACYTITAEIGRIFCPKCGNGGTLRK 99 (129)
Q Consensus 70 ~~rC~~C~k~~~~~~~~fCp~CG~~~tL~r 99 (129)
...|+.|........+-.||.||+. |.|
T Consensus 215 ~~~C~~Cd~~~~~~~~a~CpRC~~~--L~~ 242 (403)
T TIGR00155 215 LRSCSACHTTILPAQEPVCPRCSTP--LYV 242 (403)
T ss_pred CCcCCCCCCccCCCCCcCCcCCCCc--ccC
Confidence 4469999986554446789999997 643
No 149
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=73.87 E-value=1.7 Score=43.35 Aligned_cols=27 Identities=33% Similarity=0.738 Sum_probs=19.9
Q ss_pred EEccCccccc--c--------ccCccccCCCCCCCceeE
Q 032998 71 LKCHACYTIT--A--------EIGRIFCPKCGNGGTLRK 99 (129)
Q Consensus 71 ~rC~~C~k~~--~--------~~~~~fCp~CG~~~tL~r 99 (129)
|+|+.|+... . +++..-||+||.| |++
T Consensus 915 Y~Cp~Cky~Ef~~d~svgsGfDLpdK~CPkCg~p--l~k 951 (1444)
T COG2176 915 YLCPECKYSEFIDDGSVGSGFDLPDKDCPKCGTP--LKK 951 (1444)
T ss_pred ccCCCCceeeeecCCCcCCCCCCCCCCCCcCCCc--ccc
Confidence 8999998432 2 3556789999998 553
No 150
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=73.80 E-value=2 Score=26.07 Aligned_cols=23 Identities=30% Similarity=0.681 Sum_probs=13.4
Q ss_pred EccCcccccccc-----CccccCCCCCC
Q 032998 72 KCHACYTITAEI-----GRIFCPKCGNG 94 (129)
Q Consensus 72 rC~~C~k~~~~~-----~~~fCp~CG~~ 94 (129)
.|+.|+.+-... .+..||.||..
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~ 29 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYE 29 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCe
Confidence 477777653221 14568888864
No 151
>COG1458 Predicted DNA-binding protein containing PIN domain [General function prediction only]
Probab=73.68 E-value=3 Score=34.09 Aligned_cols=28 Identities=21% Similarity=0.398 Sum_probs=26.0
Q ss_pred CCceeeEeechHHHHHHHHHhCceeecC
Q 032998 31 SESTVACITGDYAMQNVILQMGLRLLAP 58 (129)
Q Consensus 31 ~~~~va~~TdDyamQNVl~~lGL~~~s~ 58 (129)
.|+++++++.|.++.--|.+|||.|++.
T Consensus 172 kELdaavVssD~Gir~WAe~LGlrfv~a 199 (221)
T COG1458 172 KELDAAVVSSDEGIRTWAEKLGLRFVDA 199 (221)
T ss_pred HHhCceEEecchhHHHHHHHhCCeeeCH
Confidence 4789999999999999999999999865
No 152
>PTZ00410 NAD-dependent SIR2; Provisional
Probab=73.30 E-value=3.8 Score=35.47 Aligned_cols=27 Identities=22% Similarity=0.282 Sum_probs=18.9
Q ss_pred eEEEEccCcccccccc---------CccccCCCCCC
Q 032998 68 RWILKCHACYTITAEI---------GRIFCPKCGNG 94 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~~---------~~~fCp~CG~~ 94 (129)
....+|..|++.+... ....||.||..
T Consensus 145 l~~~~C~~C~~~~~~~~~~~~~~~~~vP~C~~CgG~ 180 (349)
T PTZ00410 145 FSAASCIECHTPYDIEQAYLEARSGKVPHCSTCGGI 180 (349)
T ss_pred CCeeEeCCCCCCcchhHHHHHhhcCCCCCCCCCCCc
Confidence 4557899999876421 12469999986
No 153
>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=73.21 E-value=1.1 Score=43.02 Aligned_cols=26 Identities=27% Similarity=0.686 Sum_probs=0.0
Q ss_pred eeEEEEccCccccccccCccccCCCCCC
Q 032998 67 HRWILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 67 k~W~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
.++..+|+-|+..+.. ..+||.||..
T Consensus 664 ~t~~~~Cp~CG~~T~~--~~~Cp~C~~~ 689 (900)
T PF03833_consen 664 ETFYNRCPECGSHTEP--VYVCPDCGIE 689 (900)
T ss_dssp ----------------------------
T ss_pred cchhhcCcccCCcccc--ceeccccccc
Confidence 4677788888876543 2445555544
No 154
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=72.99 E-value=3.1 Score=33.62 Aligned_cols=27 Identities=15% Similarity=0.108 Sum_probs=18.8
Q ss_pred eEEEEccCcccccccc---------CccccCCCCCC
Q 032998 68 RWILKCHACYTITAEI---------GRIFCPKCGNG 94 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~~---------~~~fCp~CG~~ 94 (129)
....+|..|++.+... ...-||.||.+
T Consensus 117 ~~~~~C~~C~~~~~~~~~~~~~~~~~~p~Cp~Cgg~ 152 (244)
T PRK14138 117 VEEYYCVRCGKRYTVEDVIEKLEKSDVPRCDDCSGL 152 (244)
T ss_pred cCeeEECCCCCcccHHHHHHHHhcCCCCCCCCCCCe
Confidence 3457899999877521 12459999986
No 155
>PRK04338 N(2),N(2)-dimethylguanosine tRNA methyltransferase; Provisional
Probab=72.71 E-value=2.9 Score=36.08 Aligned_cols=27 Identities=22% Similarity=0.523 Sum_probs=20.0
Q ss_pred eEEEEccCcccccccc--CccccCCCCCC
Q 032998 68 RWILKCHACYTITAEI--GRIFCPKCGNG 94 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~~--~~~fCp~CG~~ 94 (129)
.|++.|+.|+...... ....||.||.+
T Consensus 242 g~~~~C~~c~~~~~~~~~~~~~C~~c~~~ 270 (382)
T PRK04338 242 GYVYYCPKCLYREEVEGLPPEECPVCGGK 270 (382)
T ss_pred eeEEECCCCCcEEEecCCCCCCCCCCCCc
Confidence 6789999999754321 24579999986
No 156
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=72.69 E-value=2.1 Score=39.43 Aligned_cols=22 Identities=32% Similarity=0.635 Sum_probs=16.1
Q ss_pred EEccCccccccccCccccCCCCCC
Q 032998 71 LKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
-+|..|+... . -...||+||++
T Consensus 560 ~~C~~CGy~g-~-~~~~CP~CG~~ 581 (618)
T PRK14704 560 DRCKCCSYHG-V-IGNECPSCGNE 581 (618)
T ss_pred eecCCCCCCC-C-cCccCcCCCCC
Confidence 5799999632 2 23679999986
No 157
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=72.53 E-value=1.9 Score=37.86 Aligned_cols=27 Identities=30% Similarity=0.726 Sum_probs=20.3
Q ss_pred EEccCcccccccc-----CccccCCCCCCCceeE
Q 032998 71 LKCHACYTITAEI-----GRIFCPKCGNGGTLRK 99 (129)
Q Consensus 71 ~rC~~C~k~~~~~-----~~~fCp~CG~~~tL~r 99 (129)
..|+.|+.+...+ .+-.||.||++ |.|
T Consensus 11 ~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~--L~~ 42 (419)
T PRK15103 11 ILCPQCDMLVALPRLEHGQKAACPRCGTT--LTV 42 (419)
T ss_pred ccCCCCCceeecCCCCCCCeeECCCCCCC--CcC
Confidence 5599999887533 24679999998 654
No 158
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=72.51 E-value=2 Score=27.15 Aligned_cols=22 Identities=32% Similarity=0.871 Sum_probs=15.7
Q ss_pred EccCcccccc---------ccCccccCCCCC
Q 032998 72 KCHACYTITA---------EIGRIFCPKCGN 93 (129)
Q Consensus 72 rC~~C~k~~~---------~~~~~fCp~CG~ 93 (129)
.|.||+-.-+ .....+||.||-
T Consensus 24 ~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgR 54 (56)
T PF02591_consen 24 TCSGCHMELPPQELNEIRKGDEIVFCPNCGR 54 (56)
T ss_pred ccCCCCEEcCHHHHHHHHcCCCeEECcCCCc
Confidence 8999995432 123589999995
No 159
>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=72.45 E-value=0.99 Score=34.26 Aligned_cols=23 Identities=30% Similarity=0.780 Sum_probs=19.7
Q ss_pred EccCccccccccCccccCCCCCC
Q 032998 72 KCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 72 rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
-|+.|+++|.......||.|...
T Consensus 5 nC~~CgklF~~~~~~iCp~C~~~ 27 (137)
T TIGR03826 5 NCPKCGRLFVKTGRDVCPSCYEE 27 (137)
T ss_pred cccccchhhhhcCCccCHHHhHH
Confidence 69999999987668899999963
No 160
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=72.12 E-value=2.5 Score=33.86 Aligned_cols=33 Identities=30% Similarity=0.615 Sum_probs=23.1
Q ss_pred EEEEccCccccc-cccCccccCCCCCCCceeEEEE
Q 032998 69 WILKCHACYTIT-AEIGRIFCPKCGNGGTLRKVAV 102 (129)
Q Consensus 69 W~~rC~~C~k~~-~~~~~~fCp~CG~~~tL~rv~v 102 (129)
-.-+|..|+..- ..-....||+||+. -.||++.
T Consensus 148 I~A~CsrC~~~L~~~~~~l~Cp~Cg~t-EkRKia~ 181 (188)
T COG1096 148 IYARCSRCRAPLVKKGNMLKCPNCGNT-EKRKIAK 181 (188)
T ss_pred EEEEccCCCcceEEcCcEEECCCCCCE-Eeeeecc
Confidence 346899998542 22224779999996 6788775
No 161
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=71.98 E-value=2.6 Score=37.09 Aligned_cols=27 Identities=30% Similarity=0.683 Sum_probs=19.8
Q ss_pred eEEEEccCccccccc--cCccccCCCCCC
Q 032998 68 RWILKCHACYTITAE--IGRIFCPKCGNG 94 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~--~~~~fCp~CG~~ 94 (129)
.+++.|..|+++... ..+..||+||..
T Consensus 238 g~~~~c~~cg~~~~~~~~~~~~c~~Cg~~ 266 (380)
T COG1867 238 GYIYHCSRCGEIVGSFREVDEKCPHCGGK 266 (380)
T ss_pred CcEEEcccccceecccccccccCCccccc
Confidence 466999999855432 236789999985
No 162
>PF15499 Peptidase_C98: Ubiquitin-specific peptidase-like, SUMO isopeptidase
Probab=71.96 E-value=2 Score=36.21 Aligned_cols=81 Identities=12% Similarity=0.225 Sum_probs=49.2
Q ss_pred chHHHHHHHHHhCceeecCCCCcceeeeeEEEEccCccccccc---------------------cCccccCCCCCCCcee
Q 032998 40 GDYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAE---------------------IGRIFCPKCGNGGTLR 98 (129)
Q Consensus 40 dDyamQNVl~~lGL~~~s~~g~~I~~~k~W~~rC~~C~k~~~~---------------------~~~~fCp~CG~~~tL~ 98 (129)
.=||+...| +|+--.. +.-....+|...|..||..|.+ ....-|+.|+++ .-+
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 348888865 4443322 3345677999999999976542 113459999998 556
Q ss_pred EEEEEeCCCceE---E-----eec---CCccccCceeecC
Q 032998 99 KVAVTVGENGIV---L-----ASR---RPRITLRGTKVSI 127 (129)
Q Consensus 99 rv~v~v~~~G~~---~-----~~~---~~~~n~RG~~ySl 127 (129)
|.+| +++--.+ + .++ ..-+...|..|+|
T Consensus 183 rkMv-lekv~~vfmLHFVeGLP~ndl~~ysF~feg~~Y~V 221 (275)
T PF15499_consen 183 RKMV-LEKVPPVFMLHFVEGLPHNDLQHYSFHFEGCLYQV 221 (275)
T ss_pred Hhhh-hhcCchhhhhhhhccCCccCCCccceeecCeeEEE
Confidence 5554 3331111 1 111 2237788988886
No 163
>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=71.73 E-value=2.1 Score=28.07 Aligned_cols=32 Identities=28% Similarity=0.488 Sum_probs=24.1
Q ss_pred ceeeeeEEEEccCccccccccC--ccccCCCCCC
Q 032998 63 IRQLHRWILKCHACYTITAEIG--RIFCPKCGNG 94 (129)
Q Consensus 63 I~~~k~W~~rC~~C~k~~~~~~--~~fCp~CG~~ 94 (129)
.+.+..+.--|..|||+.=... ..-|+.||++
T Consensus 11 ~H~L~~~~~NCl~CGkIiC~~Eg~~~pC~fCg~~ 44 (57)
T PF06221_consen 11 RHPLFPYAPNCLNCGKIICEQEGPLGPCPFCGTP 44 (57)
T ss_pred cCCCccccccccccChhhcccccCcCcCCCCCCc
Confidence 4555667889999999963322 4789999987
No 164
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=71.68 E-value=4.5 Score=30.45 Aligned_cols=40 Identities=20% Similarity=0.336 Sum_probs=24.3
Q ss_pred hHHHHHHHHHhCceee------cCCCCcceeeeeEEEEccCccccc
Q 032998 41 DYAMQNVILQMGLRLL------APGGMQIRQLHRWILKCHACYTIT 80 (129)
Q Consensus 41 DyamQNVl~~lGL~~~------s~~g~~I~~~k~W~~rC~~C~k~~ 80 (129)
...+|+++...=-++| +++...+++-+.|.++|.|||...
T Consensus 83 ~~~i~~~L~~yI~~yVlC~~C~sPdT~l~k~~r~~~l~C~ACGa~~ 128 (133)
T TIGR00311 83 HFLLNERIEDYVRKYVICRECNRPDTRIIKEGRVSLLKCEACGAKA 128 (133)
T ss_pred HHHHHHHHHHHHhheEECCCCCCCCcEEEEeCCeEEEecccCCCCC
Confidence 3456777766433332 566666666667777777777543
No 165
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=71.67 E-value=3.7 Score=31.08 Aligned_cols=47 Identities=23% Similarity=0.453 Sum_probs=28.7
Q ss_pred eeeEeechH---HHHHHHHHhCceee------cCCCCcceeeeeEEEEccCccccc
Q 032998 34 TVACITGDY---AMQNVILQMGLRLL------APGGMQIRQLHRWILKCHACYTIT 80 (129)
Q Consensus 34 ~va~~TdDy---amQNVl~~lGL~~~------s~~g~~I~~~k~W~~rC~~C~k~~ 80 (129)
+..+++..| .+|+++.+.=-+++ +++...+++-+.|.++|.|||...
T Consensus 78 ~~lii~G~~~~~~i~~~L~~yI~~yVlC~~C~spdT~l~k~~r~~~l~C~ACGa~~ 133 (138)
T PRK03988 78 GRLILQGKFSPRVINEKIDRYVKEYVICPECGSPDTKLIKEGRIWVLKCEACGAET 133 (138)
T ss_pred CEEEEEEeeCHHHHHHHHHHHHHhcEECCCCCCCCcEEEEcCCeEEEEcccCCCCC
Confidence 445555444 56666665433332 667676777777788888887644
No 166
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=71.46 E-value=1.9 Score=28.94 Aligned_cols=25 Identities=20% Similarity=0.711 Sum_probs=21.5
Q ss_pred EEEccCccccccccCccccCCCCC-C
Q 032998 70 ILKCHACYTITAEIGRIFCPKCGN-G 94 (129)
Q Consensus 70 ~~rC~~C~k~~~~~~~~fCp~CG~-~ 94 (129)
--.|..|++......+..|..||. |
T Consensus 17 Ht~CrRCG~~syh~qK~~CasCGygp 42 (62)
T PRK04179 17 HIRCRRCGRHSYNVRKKYCAACGFGR 42 (62)
T ss_pred cchhcccCcccccccccchhhcCCCc
Confidence 357999999877777899999999 6
No 167
>COG4031 Predicted metal-binding protein [General function prediction only]
Probab=71.39 E-value=3 Score=34.00 Aligned_cols=33 Identities=30% Similarity=0.555 Sum_probs=21.5
Q ss_pred EEccCccccccccCccccCCCCCCCceeEEEEEeCCC
Q 032998 71 LKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGEN 107 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG~~~tL~rv~v~v~~~ 107 (129)
++| .|+..-..+ .||+.||.+ ----..|++++.
T Consensus 1 ~~C-rCG~~l~~p--~~Cl~Cg~~-~av~~~vy~~~~ 33 (227)
T COG4031 1 LIC-RCGAELSSP--AFCLNCGRR-HAVGCGVYVSES 33 (227)
T ss_pred Ccc-ccCCccccc--chhcccCCc-ceeEeeeecccc
Confidence 468 899755443 899999998 333344444443
No 168
>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=71.21 E-value=2.1 Score=27.48 Aligned_cols=11 Identities=18% Similarity=0.446 Sum_probs=3.6
Q ss_pred EEEEccCcccc
Q 032998 69 WILKCHACYTI 79 (129)
Q Consensus 69 W~~rC~~C~k~ 79 (129)
-+|+|+.|+..
T Consensus 20 ~~y~C~~C~~~ 30 (51)
T PF07975_consen 20 SRYRCPKCKNH 30 (51)
T ss_dssp EEE--TTTT--
T ss_pred CeEECCCCCCc
Confidence 44555555543
No 169
>PTZ00408 NAD-dependent deacetylase; Provisional
Probab=71.18 E-value=3 Score=33.84 Aligned_cols=25 Identities=24% Similarity=0.422 Sum_probs=17.2
Q ss_pred eEEEEccCcccccccc-----CccccCCCC
Q 032998 68 RWILKCHACYTITAEI-----GRIFCPKCG 92 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~~-----~~~fCp~CG 92 (129)
.+.++|..|++.+.-. ....||.||
T Consensus 115 ~~~~~C~~C~~~~~~~~~~~~~~p~C~~Cg 144 (242)
T PTZ00408 115 LLKVRCTATGHVFDWTEDVVHGSSRCKCCG 144 (242)
T ss_pred cceEEECCCCcccCchhhhhcCCCccccCC
Confidence 3458899999876421 114599999
No 170
>PRK08402 replication factor A; Reviewed
Probab=71.13 E-value=8 Score=33.39 Aligned_cols=43 Identities=14% Similarity=0.319 Sum_probs=28.1
Q ss_pred eEEEEccCcccccc-c--cCccccCCCC--CCCceeEEEEEeC-CCceE
Q 032998 68 RWILKCHACYTITA-E--IGRIFCPKCG--NGGTLRKVAVTVG-ENGIV 110 (129)
Q Consensus 68 ~W~~rC~~C~k~~~-~--~~~~fCp~CG--~~~tL~rv~v~v~-~~G~~ 110 (129)
.|..+|+.|.|.-. + ...-.|+.|| .|.-..++++.++ ..|.+
T Consensus 210 ~~y~aCp~CnKkv~~~~~~~~~~Ce~~~~v~p~~ryil~~~l~D~TG~~ 258 (355)
T PRK08402 210 LVYDACPECRRKVDYDPATDTWICPEHGEVEPIKITILDFGLDDGTGYI 258 (355)
T ss_pred eeEecCCCCCeEEEEecCCCCEeCCCCCCcCcceeEEEEEEEEcCCCcE
Confidence 48899999998764 2 2356799999 5523344555554 44665
No 171
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=70.68 E-value=2.5 Score=28.08 Aligned_cols=29 Identities=24% Similarity=0.507 Sum_probs=20.5
Q ss_pred EEEEccCccccc---cc-cCccccCCCCCCCceeE
Q 032998 69 WILKCHACYTIT---AE-IGRIFCPKCGNGGTLRK 99 (129)
Q Consensus 69 W~~rC~~C~k~~---~~-~~~~fCp~CG~~~tL~r 99 (129)
..-+|+.|+.+. .. .+...|+.||.. |-+
T Consensus 10 ~~VkCp~C~n~q~vFsha~t~V~C~~Cg~~--L~~ 42 (59)
T PRK00415 10 LKVKCPDCGNEQVVFSHASTVVRCLVCGKT--LAE 42 (59)
T ss_pred EEEECCCCCCeEEEEecCCcEEECcccCCC--ccc
Confidence 346899999775 21 236889999995 643
No 172
>COG1773 Rubredoxin [Energy production and conversion]
Probab=70.51 E-value=3.1 Score=27.26 Aligned_cols=13 Identities=15% Similarity=0.437 Sum_probs=10.5
Q ss_pred EEEccCccccccc
Q 032998 70 ILKCHACYTITAE 82 (129)
Q Consensus 70 ~~rC~~C~k~~~~ 82 (129)
+++|..|+-+|..
T Consensus 3 ~~~C~~CG~vYd~ 15 (55)
T COG1773 3 RWRCSVCGYVYDP 15 (55)
T ss_pred ceEecCCceEecc
Confidence 5789999988863
No 173
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=70.12 E-value=1.8 Score=33.98 Aligned_cols=23 Identities=13% Similarity=0.278 Sum_probs=16.5
Q ss_pred ceeeEeechHHHHHHHHHhCceee
Q 032998 33 STVACITGDYAMQNVILQMGLRLL 56 (129)
Q Consensus 33 ~~va~~TdDyamQNVl~~lGL~~~ 56 (129)
.+-+++|.|+.|=-=+ .+|++.+
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 5678889998886655 5776653
No 174
>PRK00504 rpmG 50S ribosomal protein L33; Validated
Probab=69.80 E-value=5.5 Score=25.43 Aligned_cols=31 Identities=32% Similarity=0.765 Sum_probs=21.3
Q ss_pred eEEEEccCccccccc-----------c-CccccCCCCCCCceeE
Q 032998 68 RWILKCHACYTITAE-----------I-GRIFCPKCGNGGTLRK 99 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~-----------~-~~~fCp~CG~~~tL~r 99 (129)
.-.|.|..|+..... . -+.|||.|... ||-+
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 457899999843210 1 15899999997 7754
No 175
>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=69.40 E-value=3.7 Score=33.47 Aligned_cols=14 Identities=21% Similarity=0.266 Sum_probs=11.1
Q ss_pred eEEEEccCcccccc
Q 032998 68 RWILKCHACYTITA 81 (129)
Q Consensus 68 ~W~~rC~~C~k~~~ 81 (129)
.+..+|..|++.+.
T Consensus 116 ~~~~~C~~C~~~~~ 129 (260)
T cd01409 116 LHRVVCLSCGFRTP 129 (260)
T ss_pred cCEEEeCCCcCccC
Confidence 45689999998764
No 176
>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=69.23 E-value=2.6 Score=30.15 Aligned_cols=17 Identities=35% Similarity=0.938 Sum_probs=14.2
Q ss_pred ccccCCCCCCCceeEEEE
Q 032998 85 RIFCPKCGNGGTLRKVAV 102 (129)
Q Consensus 85 ~~fCp~CG~~~tL~rv~v 102 (129)
+.+||.||.. .++|+++
T Consensus 35 ky~Cp~Cgk~-~vkR~a~ 51 (90)
T PF01780_consen 35 KYTCPFCGKT-SVKRVAT 51 (90)
T ss_dssp -BEESSSSSS-EEEEEET
T ss_pred CCcCCCCCCc-eeEEeee
Confidence 5789999998 8999886
No 177
>PHA02942 putative transposase; Provisional
Probab=69.21 E-value=6.7 Score=33.89 Aligned_cols=42 Identities=21% Similarity=0.399 Sum_probs=26.1
Q ss_pred HHHHhCceeecCCCCcceeeeeEEEEccCccccccccC--ccccCCCCCC
Q 032998 47 VILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIG--RIFCPKCGNG 94 (129)
Q Consensus 47 Vl~~lGL~~~s~~g~~I~~~k~W~~rC~~C~k~~~~~~--~~fCp~CG~~ 94 (129)
-+...|+.|+-++-.. + -..|+.|+....... .-.||.||..
T Consensus 308 KA~~~G~~Vv~V~p~y-T-----Sq~Cs~CG~~~~~l~~r~f~C~~CG~~ 351 (383)
T PHA02942 308 QAKKHGMIVEFVNPSY-S-----SVSCPKCGHKMVEIAHRYFHCPSCGYE 351 (383)
T ss_pred HHHHhCCEEEEECCCC-C-----CccCCCCCCccCcCCCCEEECCCCCCE
Confidence 5556677776655321 1 267999997654322 2469999985
No 178
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=69.13 E-value=4.4 Score=29.52 Aligned_cols=45 Identities=20% Similarity=0.433 Sum_probs=27.7
Q ss_pred eeeEeechH---HHHHHHHHhCceee------cCCCCcceeeeeEEEEccCccc
Q 032998 34 TVACITGDY---AMQNVILQMGLRLL------APGGMQIRQLHRWILKCHACYT 78 (129)
Q Consensus 34 ~va~~TdDy---amQNVl~~lGL~~~------s~~g~~I~~~k~W~~rC~~C~k 78 (129)
+..+++..| .+|+++...=-++| +++...+++-+.|.++|.|||.
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 455555544 46666655432322 5677767777778888888874
No 179
>COG3357 Predicted transcriptional regulator containing an HTH domain fused to a Zn-ribbon [Transcription]
Probab=68.89 E-value=2.4 Score=30.70 Aligned_cols=27 Identities=22% Similarity=0.463 Sum_probs=19.6
Q ss_pred EEccCcccccccc--C-ccccCCCCCCCcee
Q 032998 71 LKCHACYTITAEI--G-RIFCPKCGNGGTLR 98 (129)
Q Consensus 71 ~rC~~C~k~~~~~--~-~~fCp~CG~~~tL~ 98 (129)
-+|..||..+.+. . -.-||.|-+. -+.
T Consensus 59 a~CkkCGfef~~~~ik~pSRCP~CKSE-~Ie 88 (97)
T COG3357 59 ARCKKCGFEFRDDKIKKPSRCPKCKSE-WIE 88 (97)
T ss_pred hhhcccCccccccccCCcccCCcchhh-ccc
Confidence 4799999888761 1 2469999987 543
No 180
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=68.64 E-value=4.5 Score=37.87 Aligned_cols=24 Identities=33% Similarity=0.598 Sum_probs=16.0
Q ss_pred EEccCccccccc---cCccccCCCCCC
Q 032998 71 LKCHACYTITAE---IGRIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~~~---~~~~fCp~CG~~ 94 (129)
-+|..|+..... .....||.||+.
T Consensus 642 ~~C~~CG~~Ge~~~~~~~~~CP~CG~~ 668 (711)
T PRK09263 642 DECYECGFTGEFECTEKGFTCPKCGNH 668 (711)
T ss_pred cccCCCCCCccccCCCCCCcCcCCCCC
Confidence 579999963211 112579999985
No 181
>KOG2324 consensus Prolyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=68.50 E-value=17 Score=32.58 Aligned_cols=55 Identities=24% Similarity=0.544 Sum_probs=33.6
Q ss_pred HHHHHhCceeecCC------CCcceeeee--------EEEEccCccccccc----cCc-cccCCCCCCCceeEEE
Q 032998 46 NVILQMGLRLLAPG------GMQIRQLHR--------WILKCHACYTITAE----IGR-IFCPKCGNGGTLRKVA 101 (129)
Q Consensus 46 NVl~~lGL~~~s~~------g~~I~~~k~--------W~~rC~~C~k~~~~----~~~-~fCp~CG~~~tL~rv~ 101 (129)
-+-++||++|+.+. |--+.+..- .++.|+.|+.-.+. .++ .-||+|-.. +|+++.
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 45689999997432 222333222 35899999743321 122 679999985 687654
No 182
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=67.97 E-value=3.5 Score=35.97 Aligned_cols=28 Identities=29% Similarity=0.685 Sum_probs=20.4
Q ss_pred EEEccCcccccccc-----CccccCCCCCCCceeE
Q 032998 70 ILKCHACYTITAEI-----GRIFCPKCGNGGTLRK 99 (129)
Q Consensus 70 ~~rC~~C~k~~~~~-----~~~fCp~CG~~~tL~r 99 (129)
...|+.|..+...+ .+-.||.||+. |.|
T Consensus 13 ~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~--L~~ 45 (403)
T TIGR00155 13 HILCSQCDMLVALPRIESGQKAACPRCGTT--LTV 45 (403)
T ss_pred eeeCCCCCCcccccCCCCCCeeECCCCCCC--CcC
Confidence 45799999877432 24579999997 654
No 183
>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=67.87 E-value=4.9 Score=25.74 Aligned_cols=21 Identities=33% Similarity=0.879 Sum_probs=15.7
Q ss_pred EEccCccccccccCccccCCCCC
Q 032998 71 LKCHACYTITAEIGRIFCPKCGN 93 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG~ 93 (129)
-.|+.|+.+. +..-.||.||.
T Consensus 27 ~~c~~cg~~~--~~H~vc~~cG~ 47 (56)
T PF01783_consen 27 VKCPNCGEPK--LPHRVCPSCGY 47 (56)
T ss_dssp EESSSSSSEE--STTSBCTTTBB
T ss_pred eeeccCCCEe--cccEeeCCCCe
Confidence 5799999754 34678999984
No 184
>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=67.69 E-value=4.9 Score=30.92 Aligned_cols=53 Identities=23% Similarity=0.343 Sum_probs=34.7
Q ss_pred eeeEeechHHHHHHHHHhCce---eecCCCCcceeeeeEEEEccCcccccccc------CccccCCCCCC
Q 032998 34 TVACITGDYAMQNVILQMGLR---LLAPGGMQIRQLHRWILKCHACYTITAEI------GRIFCPKCGNG 94 (129)
Q Consensus 34 ~va~~TdDyamQNVl~~lGL~---~~s~~g~~I~~~k~W~~rC~~C~k~~~~~------~~~fCp~CG~~ 94 (129)
...++|.- +.+...+.|.. ++-++|. ....+|..|.+.+... ....||.||..
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 35677753 35666677765 6667765 3447799999765321 13569999997
No 185
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=67.47 E-value=4.6 Score=40.92 Aligned_cols=27 Identities=26% Similarity=0.634 Sum_probs=22.4
Q ss_pred eeeeEEEEccCccccccccCccccCCCCCC
Q 032998 65 QLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 65 ~~k~W~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
++-.-..+|+.|++++.. ..||.||.+
T Consensus 669 ~vei~~~~Cp~Cg~~~~~---~~Cp~CG~~ 695 (1627)
T PRK14715 669 DIEIAFFKCPKCGKVGLY---HVCPFCGTR 695 (1627)
T ss_pred eEEEEeeeCCCCCCcccc---ccCcccCCc
Confidence 566778999999998754 679999986
No 186
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=67.24 E-value=3.1 Score=36.48 Aligned_cols=27 Identities=22% Similarity=0.595 Sum_probs=20.4
Q ss_pred EEEccCccccccccCccccCCCCCCCceeE
Q 032998 70 ILKCHACYTITAEIGRIFCPKCGNGGTLRK 99 (129)
Q Consensus 70 ~~rC~~C~k~~~~~~~~fCp~CG~~~tL~r 99 (129)
...|+.|+.+.+. .+..||.||+. |.|
T Consensus 221 l~~C~~Cd~l~~~-~~a~CpRC~~~--L~~ 247 (419)
T PRK15103 221 LRSCSCCTAILPA-DQPVCPRCHTK--GYV 247 (419)
T ss_pred CCcCCCCCCCCCC-CCCCCCCCCCc--CcC
Confidence 4569999998754 35679999997 643
No 187
>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=66.98 E-value=4.8 Score=34.75 Aligned_cols=27 Identities=19% Similarity=0.527 Sum_probs=19.7
Q ss_pred eEEEEccCccccccc----cCccccCCCCCC
Q 032998 68 RWILKCHACYTITAE----IGRIFCPKCGNG 94 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~----~~~~fCp~CG~~ 94 (129)
.|++.|+.|+..... .....||.||.+
T Consensus 231 g~v~~C~~c~~~~~~~~~~~~~~~C~~c~~~ 261 (374)
T TIGR00308 231 GYTYHCSRCLHNKPVNGISQRKGRCKECGGE 261 (374)
T ss_pred eeEEECCCcccccccccccCCCCCCCCCCCc
Confidence 678999999864321 224689999986
No 188
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=66.82 E-value=2.9 Score=32.94 Aligned_cols=22 Identities=27% Similarity=0.585 Sum_probs=16.3
Q ss_pred EEccCccccccccCccccCCCCCC
Q 032998 71 LKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
..|+.||. ...-..+||.||..
T Consensus 310 ~~C~~cg~--~~~r~~~C~~cg~~ 331 (364)
T COG0675 310 KTCPCCGH--LSGRLFKCPRCGFV 331 (364)
T ss_pred ccccccCC--ccceeEECCCCCCe
Confidence 67999998 22224789999985
No 189
>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=66.35 E-value=4.1 Score=31.94 Aligned_cols=27 Identities=26% Similarity=0.608 Sum_probs=19.4
Q ss_pred eEEEEccCcccccccc------CccccCCCCCC
Q 032998 68 RWILKCHACYTITAEI------GRIFCPKCGNG 94 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~~------~~~fCp~CG~~ 94 (129)
...++|..|.+.+... ....||.||+.
T Consensus 107 ~~~~~C~~C~~~~~~~~~~~~~~~p~C~~Cgg~ 139 (224)
T cd01412 107 LFRVRCSSCGYVGENNEEIPEEELPRCPKCGGL 139 (224)
T ss_pred cCccccCCCCCCCCcchhhhccCCCCCCCCCCc
Confidence 4458899999876531 12569999986
No 190
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=66.31 E-value=2.7 Score=42.32 Aligned_cols=24 Identities=29% Similarity=0.674 Sum_probs=18.5
Q ss_pred EEccCcccccc----------ccCccccCCCCCC
Q 032998 71 LKCHACYTITA----------EIGRIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~~----------~~~~~fCp~CG~~ 94 (129)
|+|+.|+.... |++..-||+||.+
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 3456789999997
No 191
>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=66.05 E-value=3.1 Score=34.86 Aligned_cols=25 Identities=32% Similarity=0.809 Sum_probs=18.6
Q ss_pred EEEEccCccccccc----cCccccCCCCCC
Q 032998 69 WILKCHACYTITAE----IGRIFCPKCGNG 94 (129)
Q Consensus 69 W~~rC~~C~k~~~~----~~~~fCp~CG~~ 94 (129)
|. +|+.|+++... .....||.||+.
T Consensus 26 ~~-~c~~c~~~~~~~~l~~~~~vc~~c~~h 54 (285)
T TIGR00515 26 WT-KCPKCGQVLYTKELERNLEVCPKCDHH 54 (285)
T ss_pred ee-ECCCCcchhhHHHHHhhCCCCCCCCCc
Confidence 65 69999987532 124789999997
No 192
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=65.81 E-value=2.9 Score=29.98 Aligned_cols=24 Identities=21% Similarity=0.548 Sum_probs=21.3
Q ss_pred EEccCccccccccCccccCCCCCC
Q 032998 71 LKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
-.|..|++......+..|..||.|
T Consensus 17 tlCrRCG~~syH~qK~~CasCGyp 40 (91)
T PTZ00073 17 TLCRRCGKRSFHVQKKRCASCGYP 40 (91)
T ss_pred chhcccCccccccccccchhcCCc
Confidence 579999998777778999999998
No 193
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=65.52 E-value=3.8 Score=29.29 Aligned_cols=17 Identities=35% Similarity=0.958 Sum_probs=10.9
Q ss_pred ccccCCCCCCCceeEEEE
Q 032998 85 RIFCPKCGNGGTLRKVAV 102 (129)
Q Consensus 85 ~~fCp~CG~~~tL~rv~v 102 (129)
+..||.||.+ +++|++.
T Consensus 35 ~~~Cp~C~~~-~VkR~a~ 51 (89)
T COG1997 35 KHVCPFCGRT-TVKRIAT 51 (89)
T ss_pred CCcCCCCCCc-ceeeecc
Confidence 3557777776 6666654
No 194
>TIGR01023 rpmG_bact ribosomal protein L33, bacterial type. This model describes bacterial ribosomal protein L33 and its chloroplast and mitochondrial equivalents.
Probab=65.47 E-value=8.4 Score=24.84 Aligned_cols=32 Identities=34% Similarity=0.681 Sum_probs=21.8
Q ss_pred eeEEEEccCccccccc-----------cC-ccccCCCCCCCceeE
Q 032998 67 HRWILKCHACYTITAE-----------IG-RIFCPKCGNGGTLRK 99 (129)
Q Consensus 67 k~W~~rC~~C~k~~~~-----------~~-~~fCp~CG~~~tL~r 99 (129)
..-.|.|.+|...+.. .. +.|||.|+.. +|-+
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 3568999999643211 11 5899999997 7653
No 195
>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=65.06 E-value=11 Score=22.36 Aligned_cols=25 Identities=40% Similarity=0.818 Sum_probs=14.7
Q ss_pred cccCCCCCCCceeEEEEEeCCCceEEeec
Q 032998 86 IFCPKCGNGGTLRKVAVTVGENGIVLASR 114 (129)
Q Consensus 86 ~fCp~CG~~~tL~rv~v~v~~~G~~~~~~ 114 (129)
..||+||-- -|. +| .++.|++.+.+
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 369999987 554 55 37889886643
No 196
>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=64.83 E-value=4.1 Score=24.30 Aligned_cols=22 Identities=36% Similarity=0.756 Sum_probs=13.8
Q ss_pred cccCCCCCCCceeEEEEEeCCCceEEe
Q 032998 86 IFCPKCGNGGTLRKVAVTVGENGIVLA 112 (129)
Q Consensus 86 ~fCp~CG~~~tL~rv~v~v~~~G~~~~ 112 (129)
..||.||++ .+.|. ...|.++.
T Consensus 2 ~~CP~Cg~~-lv~r~----~k~g~F~~ 23 (39)
T PF01396_consen 2 EKCPKCGGP-LVLRR----GKKGKFLG 23 (39)
T ss_pred cCCCCCCce-eEEEE----CCCCCEEE
Confidence 469999987 44432 35665544
No 197
>PHA00626 hypothetical protein
Probab=64.56 E-value=4.1 Score=27.09 Aligned_cols=12 Identities=58% Similarity=1.414 Sum_probs=8.1
Q ss_pred ccCCCCCCCceeE
Q 032998 87 FCPKCGNGGTLRK 99 (129)
Q Consensus 87 fCp~CG~~~tL~r 99 (129)
.||.||+. .+.|
T Consensus 2 ~CP~CGS~-~Ivr 13 (59)
T PHA00626 2 SCPKCGSG-NIAK 13 (59)
T ss_pred CCCCCCCc-eeee
Confidence 58888885 5555
No 198
>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=64.43 E-value=2.3 Score=27.77 Aligned_cols=15 Identities=40% Similarity=1.057 Sum_probs=10.0
Q ss_pred ccccCccccCCCCCC
Q 032998 80 TAEIGRIFCPKCGNG 94 (129)
Q Consensus 80 ~~~~~~~fCp~CG~~ 94 (129)
.....+.||+.||.+
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 344558999999998
No 199
>PRK00595 rpmG 50S ribosomal protein L33; Validated
Probab=64.16 E-value=8.7 Score=24.61 Aligned_cols=31 Identities=13% Similarity=0.077 Sum_probs=21.4
Q ss_pred eEEEEccCccccccc-----------cC-ccccCCCCCCCceeE
Q 032998 68 RWILKCHACYTITAE-----------IG-RIFCPKCGNGGTLRK 99 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~-----------~~-~~fCp~CG~~~tL~r 99 (129)
.-.|.|.+|...+.. .. +.|||.|+.. +|-+
T Consensus 8 ~i~L~ct~c~~~nY~t~Kn~k~~~~rL~lkKycp~~~kh-tlhk 50 (53)
T PRK00595 8 KIKLESTEGTGRFYTTTKNKRNTPEKLELKKYDPVLRKH-VLHK 50 (53)
T ss_pred EEEEEecCCCCEEEEEccCCCCCCCceEEECcCCCCCCE-EeEE
Confidence 567999999843211 11 5799999987 7754
No 200
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=63.92 E-value=3.6 Score=24.50 Aligned_cols=12 Identities=33% Similarity=0.977 Sum_probs=9.2
Q ss_pred cccCCCCCCCcee
Q 032998 86 IFCPKCGNGGTLR 98 (129)
Q Consensus 86 ~fCp~CG~~~tL~ 98 (129)
..||.||++ ++.
T Consensus 3 ~~Cp~Cg~~-~~~ 14 (47)
T PF14690_consen 3 PRCPHCGSP-SVH 14 (47)
T ss_pred ccCCCcCCC-ceE
Confidence 569999998 543
No 201
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=63.85 E-value=4.2 Score=34.16 Aligned_cols=25 Identities=36% Similarity=0.933 Sum_probs=18.5
Q ss_pred EEEEccCccccccc----cCccccCCCCCC
Q 032998 69 WILKCHACYTITAE----IGRIFCPKCGNG 94 (129)
Q Consensus 69 W~~rC~~C~k~~~~----~~~~fCp~CG~~ 94 (129)
| .+|+.|+++... .....||+||+.
T Consensus 27 ~-~~c~~c~~~~~~~~l~~~~~vc~~c~~h 55 (292)
T PRK05654 27 W-TKCPSCGQVLYRKELEANLNVCPKCGHH 55 (292)
T ss_pred e-eECCCccchhhHHHHHhcCCCCCCCCCC
Confidence 5 579999987532 124689999997
No 202
>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=63.75 E-value=5.5 Score=34.48 Aligned_cols=42 Identities=21% Similarity=0.629 Sum_probs=16.6
Q ss_pred eeeeEEEEccCccccc---cccCccccCCCCCCCceeEEEEEeCCCc
Q 032998 65 QLHRWILKCHACYTIT---AEIGRIFCPKCGNGGTLRKVAVTVGENG 108 (129)
Q Consensus 65 ~~k~W~~rC~~C~k~~---~~~~~~fCp~CG~~~tL~rv~v~v~~~G 108 (129)
-+++| ++|..|+.-+ ..++..-|++||+. -..|++..-...|
T Consensus 281 a~KRF-FkC~~C~~Rt~sl~r~P~~~C~~Cg~~-~wer~~M~~ek~~ 325 (344)
T PF09332_consen 281 AVKRF-FKCKDCGNRTISLERLPKKHCSNCGSS-KWERTGMLKEKKG 325 (344)
T ss_dssp EE-EE-EE-T-TS-EEEESSSS--S--TTT-S----EEE---SSS--
T ss_pred eeeee-EECCCCCCeeeecccCCCCCCCcCCcC-ceeehhhhhhhcc
Confidence 33444 7899999632 33456889999997 7899888544444
No 203
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=63.51 E-value=4.8 Score=26.18 Aligned_cols=20 Identities=30% Similarity=0.793 Sum_probs=9.0
Q ss_pred EccCccccccccCccccCCCCC
Q 032998 72 KCHACYTITAEIGRIFCPKCGN 93 (129)
Q Consensus 72 rC~~C~k~~~~~~~~fCp~CG~ 93 (129)
.|+.|+.... ..-.||.||.
T Consensus 29 ~C~~CG~~~~--~H~vC~~CG~ 48 (57)
T PRK12286 29 ECPNCGEPKL--PHRVCPSCGY 48 (57)
T ss_pred ECCCCCCccC--CeEECCCCCc
Confidence 4555554322 2344555553
No 204
>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=62.75 E-value=4.6 Score=26.03 Aligned_cols=21 Identities=29% Similarity=0.858 Sum_probs=11.5
Q ss_pred EEccCccccccccCccccCCCCC
Q 032998 71 LKCHACYTITAEIGRIFCPKCGN 93 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG~ 93 (129)
-.|..|+... +..-.||.||.
T Consensus 27 ~~C~~cG~~~--~~H~vc~~cG~ 47 (55)
T TIGR01031 27 VVCPNCGEFK--LPHRVCPSCGY 47 (55)
T ss_pred eECCCCCCcc--cCeeECCccCe
Confidence 3466666533 23455666664
No 205
>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=62.72 E-value=3.6 Score=40.80 Aligned_cols=27 Identities=33% Similarity=0.700 Sum_probs=19.7
Q ss_pred EEccCccccc----------cccCccccCCCCCCCceeE
Q 032998 71 LKCHACYTIT----------AEIGRIFCPKCGNGGTLRK 99 (129)
Q Consensus 71 ~rC~~C~k~~----------~~~~~~fCp~CG~~~tL~r 99 (129)
|+|+-|+... .+++..-||+||.+ |.|
T Consensus 684 y~c~~c~~~ef~~~~~~~sg~dlp~k~cp~c~~~--~~~ 720 (1213)
T TIGR01405 684 YLCPNCKYSEFITDGSVGSGFDLPDKDCPKCGAP--LKK 720 (1213)
T ss_pred ccCcccccccccccccccccccCccccCcccccc--ccc
Confidence 8999998532 23456789999997 553
No 206
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=62.71 E-value=3.5 Score=36.65 Aligned_cols=24 Identities=29% Similarity=0.692 Sum_probs=19.5
Q ss_pred EEccCccccccccCccccCCCCCC
Q 032998 71 LKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
-.|++|......-.+..||.||.+
T Consensus 221 ~~C~~C~~~~~~~~~~~CpRC~~~ 244 (418)
T COG2995 221 RSCLCCHYILPHDAEPRCPRCGSK 244 (418)
T ss_pred eecccccccCCHhhCCCCCCCCCh
Confidence 469999987655357889999998
No 207
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=62.54 E-value=4.1 Score=34.57 Aligned_cols=38 Identities=18% Similarity=0.701 Sum_probs=23.7
Q ss_pred EEEEccCccccccc----cCccccCCCCCCCce---eEEEEEeCCC
Q 032998 69 WILKCHACYTITAE----IGRIFCPKCGNGGTL---RKVAVTVGEN 107 (129)
Q Consensus 69 W~~rC~~C~k~~~~----~~~~fCp~CG~~~tL---~rv~v~v~~~ 107 (129)
|. +|+.|+++... .....||+||+...| .|+..-+|++
T Consensus 38 w~-kc~~C~~~~~~~~l~~~~~vcp~c~~h~rltAreRI~~L~D~g 82 (296)
T CHL00174 38 WV-QCENCYGLNYKKFLKSKMNICEQCGYHLKMSSSDRIELLIDPG 82 (296)
T ss_pred ee-ECCCccchhhHHHHHHcCCCCCCCCCCcCCCHHHHHHHHccCC
Confidence 64 69999987432 124789999997222 2444444544
No 208
>PRK04860 hypothetical protein; Provisional
Probab=62.50 E-value=18 Score=27.86 Aligned_cols=58 Identities=14% Similarity=0.279 Sum_probs=34.7
Q ss_pred hHHHHHHHHH-hCceeecCCCCccee--eeeEEEEccCccccccc----------cCccccCCCCCCCceeEEE
Q 032998 41 DYAMQNVILQ-MGLRLLAPGGMQIRQ--LHRWILKCHACYTITAE----------IGRIFCPKCGNGGTLRKVA 101 (129)
Q Consensus 41 DyamQNVl~~-lGL~~~s~~g~~I~~--~k~W~~rC~~C~k~~~~----------~~~~fCp~CG~~~tL~rv~ 101 (129)
|-.=|-++.+ +|++..--....+.. .+.|.|+|. |++.... ..+..|..||.+ |..+.
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 6667778876 577332111112222 457999997 9653321 234789999997 66543
No 209
>COG0384 Predicted epimerase, PhzC/PhzF homolog [General function prediction only]
Probab=61.95 E-value=7.7 Score=32.65 Aligned_cols=49 Identities=22% Similarity=0.148 Sum_probs=28.3
Q ss_pred chHHHHHHHHHhCceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCCCcee
Q 032998 40 GDYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLR 98 (129)
Q Consensus 40 dDyamQNVl~~lGL~~~s~~g~~I~~~k~W~~rC~~C~k~~~~~~~~fCp~CG~~~tL~ 98 (129)
+|-.||+++.++|+.--.+- .+...-..|++| +|.. ..+=|-||++ ||=
T Consensus 32 sd~~MQ~IA~e~n~SET~Fv-~~~~~~~~~rlR------~FTP--~~Evpf~GHa-Tlg 80 (291)
T COG0384 32 SDEQMQAIAREFNLSETAFV-LPPDDPADARLR------IFTP--TTEVPFAGHA-TLG 80 (291)
T ss_pred CHHHHHHHHHHhCCceeEEE-cCCCCcCceEEE------EeCC--CcccccCCCH-HHH
Confidence 78899999999998752211 001111345555 3322 1334559998 875
No 210
>CHL00104 rpl33 ribosomal protein L33
Probab=61.85 E-value=11 Score=25.41 Aligned_cols=31 Identities=32% Similarity=0.694 Sum_probs=21.1
Q ss_pred eEEEEccCccccc--------------cc-------c-CccccCCCCCCCceeE
Q 032998 68 RWILKCHACYTIT--------------AE-------I-GRIFCPKCGNGGTLRK 99 (129)
Q Consensus 68 ~W~~rC~~C~k~~--------------~~-------~-~~~fCp~CG~~~tL~r 99 (129)
.-.|.|..|..-. .+ . -+.|||.|... ||-+
T Consensus 10 ~I~L~Ct~c~~~n~~~~~~g~~rY~T~KNkkn~p~rLelkKycp~c~kH-tlhk 62 (66)
T CHL00104 10 TVILECTSCVRNGVNKESTGISRYITQKNRHNTPNRLELKKFCPYCYKH-TIHK 62 (66)
T ss_pred EEEEEecCCcCCCccccCcccceEEECCCCCCCCceeEEECcCCCCCCE-eeEe
Confidence 5679999996432 10 1 15799999987 7754
No 211
>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=61.56 E-value=5.3 Score=25.85 Aligned_cols=24 Identities=29% Similarity=0.751 Sum_probs=17.1
Q ss_pred EEccCcccccccc---C--ccccCCCCCC
Q 032998 71 LKCHACYTITAEI---G--RIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~~~~---~--~~fCp~CG~~ 94 (129)
.||..|.+.-... . ..-||.||.-
T Consensus 5 iRC~~CnklLa~~g~~~~leIKCpRC~ti 33 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVIELEIKCPRCKTI 33 (51)
T ss_pred eeccchhHHHhhhcCccEEEEECCCCCcc
Confidence 6899999864431 1 3569999975
No 212
>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=61.55 E-value=3.8 Score=26.35 Aligned_cols=21 Identities=38% Similarity=0.786 Sum_probs=13.8
Q ss_pred ccccCCCCCCCceeEEEEEeCCCceEEe
Q 032998 85 RIFCPKCGNGGTLRKVAVTVGENGIVLA 112 (129)
Q Consensus 85 ~~fCp~CG~~~tL~rv~v~v~~~G~~~~ 112 (129)
...||.|||. - | .+..|++.+
T Consensus 13 Y~~Cp~CGN~-~---v---GngEG~liV 33 (49)
T PF12677_consen 13 YCKCPKCGND-K---V---GNGEGTLIV 33 (49)
T ss_pred hccCcccCCc-E---e---ecCcceEEE
Confidence 4789999997 2 2 245566644
No 213
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=61.42 E-value=11 Score=35.02 Aligned_cols=48 Identities=19% Similarity=0.335 Sum_probs=29.5
Q ss_pred HHHHHhCcee-----ecCCCCcceeeeeEEEEccCccccccccCccccCCCCCC
Q 032998 46 NVILQMGLRL-----LAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 46 NVl~~lGL~~-----~s~~g~~I~~~k~W~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
+-+.++||.+ +.-.|..|-++-.-+.....=......++ ..||.||++
T Consensus 361 ~~i~~~~i~iGD~V~V~raGdVIP~i~~vv~~~r~~~~~~~~~P-~~CP~Cgs~ 413 (665)
T PRK07956 361 DEIERKDIRIGDTVVVRRAGDVIPEVVGVVLEKRPGDEREIVMP-THCPVCGSE 413 (665)
T ss_pred HHHHHcCCCCCCEEEEEECCCccceeeeeecccCCCCCccCcCC-CCCCCCCCE
Confidence 3356777765 44558888888776655433221111222 589999998
No 214
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=61.40 E-value=6.4 Score=30.31 Aligned_cols=23 Identities=30% Similarity=0.481 Sum_probs=13.0
Q ss_pred ccCCCCCCCceeEEEEEeCCCceE
Q 032998 87 FCPKCGNGGTLRKVAVTVGENGIV 110 (129)
Q Consensus 87 fCp~CG~~~tL~rv~v~v~~~G~~ 110 (129)
-||.||++.|--+-+.. .++|+.
T Consensus 2 ~cp~c~~~~~~~~~s~~-~~~~~~ 24 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRP-AEDGNA 24 (154)
T ss_pred cCCCCCCCCCEeEeccc-cCCCCc
Confidence 39999998433333332 344654
No 215
>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=61.29 E-value=7 Score=26.09 Aligned_cols=18 Identities=39% Similarity=0.730 Sum_probs=12.4
Q ss_pred ccCCCCCCCceeEEEEEeC
Q 032998 87 FCPKCGNGGTLRKVAVTVG 105 (129)
Q Consensus 87 fCp~CG~~~tL~rv~v~v~ 105 (129)
-||+||+. ...--++...
T Consensus 2 ~C~KCg~~-~~e~~~v~~t 19 (64)
T PF09855_consen 2 KCPKCGNE-EYESGEVRAT 19 (64)
T ss_pred CCCCCCCc-ceecceEEcc
Confidence 39999998 6665555443
No 216
>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=60.46 E-value=7.8 Score=23.71 Aligned_cols=9 Identities=44% Similarity=1.250 Sum_probs=6.6
Q ss_pred cccCCCCCC
Q 032998 86 IFCPKCGNG 94 (129)
Q Consensus 86 ~fCp~CG~~ 94 (129)
..||.||.|
T Consensus 18 ~~Cp~C~~P 26 (41)
T PF06677_consen 18 EHCPDCGTP 26 (41)
T ss_pred CccCCCCCe
Confidence 567777777
No 217
>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=60.34 E-value=3.7 Score=22.78 Aligned_cols=14 Identities=29% Similarity=0.861 Sum_probs=6.3
Q ss_pred ccCCCCCCCceeEEEE
Q 032998 87 FCPKCGNGGTLRKVAV 102 (129)
Q Consensus 87 fCp~CG~~~tL~rv~v 102 (129)
-||.||+. +.++.+
T Consensus 3 ~C~rC~~~--~~~~~~ 16 (30)
T PF06827_consen 3 KCPRCWNY--IEDIGI 16 (30)
T ss_dssp B-TTT--B--BEEEEE
T ss_pred cCccCCCc--ceEeEe
Confidence 47777775 555443
No 218
>COG1328 NrdD Oxygen-sensitive ribonucleoside-triphosphate reductase [Nucleotide transport and metabolism]
Probab=60.21 E-value=5.1 Score=37.73 Aligned_cols=47 Identities=19% Similarity=0.356 Sum_probs=29.3
Q ss_pred echHHHHHHHHH---hCceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCC
Q 032998 39 TGDYAMQNVILQ---MGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 39 TdDyamQNVl~~---lGL~~~s~~g~~I~~~k~W~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
.+--|++++.+. .++.+.+.. ..| -.|..|+....-.... ||+||+.
T Consensus 615 ~~~eal~~l~k~~~~~ri~Y~~~n-~~i-------~~C~~cg~~~~~~~~~-Cp~CG~~ 664 (700)
T COG1328 615 ADPEALMDLTKYIYKTRIGYWGYT-TPI-------SVCNRCGYSGEGLRTR-CPKCGSE 664 (700)
T ss_pred CCHHHHHHHHHHHHhcCcceEecC-CCc-------eeeccCCccccccccc-CCCCCCc
Confidence 356688887763 245555443 223 4699999865432222 9999987
No 219
>COG5270 PUA domain (predicted RNA-binding domain) [Translation, ribosomal structure and biogenesis]
Probab=59.70 E-value=7.8 Score=31.40 Aligned_cols=32 Identities=22% Similarity=0.402 Sum_probs=23.3
Q ss_pred eeEEEEccCccccccccCccccCCCCCCCceeEEEEE
Q 032998 67 HRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVT 103 (129)
Q Consensus 67 k~W~~rC~~C~k~~~~~~~~fCp~CG~~~tL~rv~v~ 103 (129)
+-|+|.|.-|.=... ...|+.||+. ...+.+|
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 579999999985333 4779999986 4445543
No 220
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=59.62 E-value=11 Score=29.77 Aligned_cols=48 Identities=19% Similarity=0.315 Sum_probs=31.9
Q ss_pred eeeEeechH---HHHHHHHHhCceee------cCCCCcceeeeeEEEEccCcccccc
Q 032998 34 TVACITGDY---AMQNVILQMGLRLL------APGGMQIRQLHRWILKCHACYTITA 81 (129)
Q Consensus 34 ~va~~TdDy---amQNVl~~lGL~~~------s~~g~~I~~~k~W~~rC~~C~k~~~ 81 (129)
+..+++..| .+|++|.+.=-+++ +++...+++-+.|.++|.+||...+
T Consensus 74 ~~~ii~G~~~~~~i~~~l~~yi~~yV~C~~C~~pdT~l~k~~~~~~l~C~aCGa~~~ 130 (201)
T PRK12336 74 GRAVFNGKFTEEDIQAAIDAYVDEYVICSECGLPDTRLVKEDRVLMLRCDACGAHRP 130 (201)
T ss_pred CEEEEEeeeCHHHHHHHHHHHHHheEECCCCCCCCcEEEEcCCeEEEEcccCCCCcc
Confidence 345555544 56777765433332 6777778777889999999997654
No 221
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=59.38 E-value=9 Score=27.36 Aligned_cols=19 Identities=37% Similarity=0.988 Sum_probs=14.8
Q ss_pred ccccCCCCCCCceeEEEEEe
Q 032998 85 RIFCPKCGNGGTLRKVAVTV 104 (129)
Q Consensus 85 ~~fCp~CG~~~tL~rv~v~v 104 (129)
+..||.||.. .++|+++-+
T Consensus 36 ~y~CpfCgk~-~vkR~a~GI 54 (90)
T PTZ00255 36 KYFCPFCGKH-AVKRQAVGI 54 (90)
T ss_pred CccCCCCCCC-ceeeeeeEE
Confidence 5779999987 888888743
No 222
>KOG3475 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=59.22 E-value=3.1 Score=29.74 Aligned_cols=23 Identities=26% Similarity=0.621 Sum_probs=19.9
Q ss_pred EccCccccccccCccccCCCCCC
Q 032998 72 KCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 72 rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
.|..|++-....-+..|..||.|
T Consensus 18 lC~RCG~~syH~QKstC~~CGYp 40 (92)
T KOG3475|consen 18 LCRRCGRRSYHIQKSTCSSCGYP 40 (92)
T ss_pred HHHHhCchhhhhhcccccccCCc
Confidence 58999987767678999999999
No 223
>PF14949 ARF7EP_C: ARF7 effector protein C-terminus
Probab=58.90 E-value=5.4 Score=29.07 Aligned_cols=16 Identities=44% Similarity=1.161 Sum_probs=12.1
Q ss_pred EEccCccccccccCccccCCCCCC
Q 032998 71 LKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
.-|.||+- + ||.||+.
T Consensus 68 ~~C~GC~~---P-----C~~C~S~ 83 (103)
T PF14949_consen 68 EDCPGCHY---P-----CPKCGSR 83 (103)
T ss_pred CCCCCccc---c-----CCCCCCC
Confidence 45899983 2 9999985
No 224
>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=58.90 E-value=13 Score=21.63 Aligned_cols=22 Identities=32% Similarity=0.590 Sum_probs=13.1
Q ss_pred cCCCCCCCceeEEE--EEeCCCceE
Q 032998 88 CPKCGNGGTLRKVA--VTVGENGIV 110 (129)
Q Consensus 88 Cp~CG~~~tL~rv~--v~v~~~G~~ 110 (129)
||.||+. ++.+.. .++.-+|..
T Consensus 1 C~~C~~~-~~~~~~~~~~~~~~~~~ 24 (46)
T TIGR03831 1 CPICGGE-ELEGKTTTETYEYGGEL 24 (46)
T ss_pred CCCCCCc-eecceEEEEEEEeCCEE
Confidence 8999876 665443 333444544
No 225
>TIGR00627 tfb4 transcription factor tfb4. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=58.64 E-value=7.2 Score=32.69 Aligned_cols=26 Identities=15% Similarity=0.529 Sum_probs=20.1
Q ss_pred eEEEEccCccccccccCccccCCCCCC
Q 032998 68 RWILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
.-.|.|+-|.-++-+.+ ..||.||.+
T Consensus 253 ~~GyvCs~Clsi~C~~p-~~C~~Cgt~ 278 (279)
T TIGR00627 253 SIGFVCSVCLSVLCQYT-PICKTCKTA 278 (279)
T ss_pred cceEECCCccCCcCCCC-CCCCCCCCC
Confidence 33489999998886654 589999975
No 226
>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=58.40 E-value=7 Score=33.78 Aligned_cols=28 Identities=21% Similarity=0.634 Sum_probs=17.2
Q ss_pred eeEEEEccCccccc--cccC--ccccCCCCCC
Q 032998 67 HRWILKCHACYTIT--AEIG--RIFCPKCGNG 94 (129)
Q Consensus 67 k~W~~rC~~C~k~~--~~~~--~~fCp~CG~~ 94 (129)
..|++.|+.|+... .... +..||.||++
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 57999999998421 1111 3679999998
No 227
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=58.33 E-value=5.3 Score=38.60 Aligned_cols=26 Identities=23% Similarity=0.682 Sum_probs=20.2
Q ss_pred EEEEccCccccccc--cCccccCCCCCC
Q 032998 69 WILKCHACYTITAE--IGRIFCPKCGNG 94 (129)
Q Consensus 69 W~~rC~~C~k~~~~--~~~~fCp~CG~~ 94 (129)
..+||.-|++++.. -+..-||.||.+
T Consensus 820 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 847 (1006)
T PRK12775 820 LQWRCDDCGKVSEGFAFPYGMCPACGGK 847 (1006)
T ss_pred eeeehhhhccccccccCCcCcCcccccc
Confidence 34899999998754 235789999986
No 228
>PRK05333 NAD-dependent deacetylase; Provisional
Probab=58.32 E-value=9 Score=31.51 Aligned_cols=13 Identities=15% Similarity=0.225 Sum_probs=9.8
Q ss_pred eEEEEccCccccc
Q 032998 68 RWILKCHACYTIT 80 (129)
Q Consensus 68 ~W~~rC~~C~k~~ 80 (129)
...++|..|.+.+
T Consensus 126 ~~~~~C~~C~~~~ 138 (285)
T PRK05333 126 LDGVRCMGCGARH 138 (285)
T ss_pred cCEEEECCCCCcC
Confidence 4558999999654
No 229
>KOG3084 consensus NADH pyrophosphatase I of the Nudix family of hydrolases [Replication, recombination and repair]
Probab=58.07 E-value=4.5 Score=35.12 Aligned_cols=12 Identities=50% Similarity=1.079 Sum_probs=10.0
Q ss_pred ccccCCCCCCCce
Q 032998 85 RIFCPKCGNGGTL 97 (129)
Q Consensus 85 ~~fCp~CG~~~tL 97 (129)
..|||.||++ |.
T Consensus 150 ykFCp~CG~~-tk 161 (345)
T KOG3084|consen 150 YKFCPGCGSP-TK 161 (345)
T ss_pred hccCcccCCC-cc
Confidence 4899999998 54
No 230
>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=58.00 E-value=10 Score=27.17 Aligned_cols=19 Identities=26% Similarity=0.793 Sum_probs=14.5
Q ss_pred ccccCCCCCCCceeEEEEEe
Q 032998 85 RIFCPKCGNGGTLRKVAVTV 104 (129)
Q Consensus 85 ~~fCp~CG~~~tL~rv~v~v 104 (129)
+..||.||.. .++|+++-+
T Consensus 35 ~y~CpfCgk~-~vkR~a~GI 53 (91)
T TIGR00280 35 KYVCPFCGKK-TVKRGSTGI 53 (91)
T ss_pred CccCCCCCCC-ceEEEeeEE
Confidence 5678888887 788888744
No 231
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=57.88 E-value=6.6 Score=25.44 Aligned_cols=29 Identities=28% Similarity=0.497 Sum_probs=19.0
Q ss_pred eeeEEEEccCccc---cccccCccccCCCCCC
Q 032998 66 LHRWILKCHACYT---ITAEIGRIFCPKCGNG 94 (129)
Q Consensus 66 ~k~W~~rC~~C~k---~~~~~~~~fCp~CG~~ 94 (129)
+++-...|+.|+- +.....+.-|.+||.-
T Consensus 15 v~rk~~~CPrCG~gvfmA~H~dR~~CGkCgyT 46 (51)
T COG1998 15 VKRKNRFCPRCGPGVFMADHKDRWACGKCGYT 46 (51)
T ss_pred EEEccccCCCCCCcchhhhcCceeEeccccce
Confidence 4445567888882 2334557889999873
No 232
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=57.47 E-value=3.4 Score=36.29 Aligned_cols=32 Identities=34% Similarity=0.600 Sum_probs=22.6
Q ss_pred ceeeeeEEEEccCccccccccC----ccccCCCCCC
Q 032998 63 IRQLHRWILKCHACYTITAEIG----RIFCPKCGNG 94 (129)
Q Consensus 63 I~~~k~W~~rC~~C~k~~~~~~----~~fCp~CG~~ 94 (129)
++--|.+.-.|..|++.|.-.. +--||.||..
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 3334566778999998775322 3579999996
No 233
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=57.26 E-value=6.5 Score=30.39 Aligned_cols=31 Identities=32% Similarity=0.635 Sum_probs=21.6
Q ss_pred EEEccCccccc-ccc-CccccCCCCCCCceeEEE
Q 032998 70 ILKCHACYTIT-AEI-GRIFCPKCGNGGTLRKVA 101 (129)
Q Consensus 70 ~~rC~~C~k~~-~~~-~~~fCp~CG~~~tL~rv~ 101 (129)
.-+|..|+... +-. ....||.||+. -.|||+
T Consensus 149 ~a~~~~~g~~~~~~~~~~~~c~~~~~~-e~rkva 181 (189)
T PRK09521 149 YAMCSRCRTPLVKKGENELKCPNCGNI-ETRKLS 181 (189)
T ss_pred EEEccccCCceEECCCCEEECCCCCCE-Eeeccc
Confidence 45799999743 222 35789999987 567776
No 234
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=57.13 E-value=7 Score=28.81 Aligned_cols=11 Identities=64% Similarity=1.524 Sum_probs=9.5
Q ss_pred CccccCCCCCC
Q 032998 84 GRIFCPKCGNG 94 (129)
Q Consensus 84 ~~~fCp~CG~~ 94 (129)
.+.|||.||.+
T Consensus 68 ~r~FC~~CGs~ 78 (133)
T COG3791 68 GRGFCPTCGSP 78 (133)
T ss_pred CCeecccCCCc
Confidence 36799999998
No 235
>PRK06386 replication factor A; Reviewed
Probab=56.95 E-value=7.2 Score=33.88 Aligned_cols=54 Identities=15% Similarity=0.285 Sum_probs=31.5
Q ss_pred EeechHHHHHHHHHhC-ceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCC
Q 032998 37 CITGDYAMQNVILQMG-LRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 37 ~~TdDyamQNVl~~lG-L~~~s~~g~~I~~~k~W~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
+-+..+.+..+..-.| +++.+.- -.|++-..-..||+.|.|+-.. -+||.||..
T Consensus 203 v~~~~~~I~di~~~~g~v~i~G~i-v~i~~gsgli~rCP~C~R~l~~---g~C~~HG~v 257 (358)
T PRK06386 203 LESRNIFIFEIKSPVGGITIMGFI-VSVGQGSRIFTKCSVCNKIIED---GVCKDHPDA 257 (358)
T ss_pred cCccccchhhhhccCCeEEEEEEE-EEEcCCcEeEecCcCCCeEccC---CcCCCCCCC
Confidence 3344555555554442 3333210 1123334677999999997653 689999964
No 236
>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=56.64 E-value=6.1 Score=26.94 Aligned_cols=24 Identities=33% Similarity=0.742 Sum_probs=15.2
Q ss_pred EEEEccCcccc-ccccC--ccccCCCCCC
Q 032998 69 WILKCHACYTI-TAEIG--RIFCPKCGNG 94 (129)
Q Consensus 69 W~~rC~~C~k~-~~~~~--~~fCp~CG~~ 94 (129)
.++|| .|++. |.+.+ ..-| .||..
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 46899 89975 33322 4669 99986
No 237
>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=56.12 E-value=12 Score=30.61 Aligned_cols=10 Identities=50% Similarity=1.334 Sum_probs=4.3
Q ss_pred ccccCCCCCC
Q 032998 85 RIFCPKCGNG 94 (129)
Q Consensus 85 ~~fCp~CG~~ 94 (129)
+..||+||++
T Consensus 172 ~g~CPvCGs~ 181 (290)
T PF04216_consen 172 RGYCPVCGSP 181 (290)
T ss_dssp -SS-TTT---
T ss_pred CCcCCCCCCc
Confidence 4689999987
No 238
>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=56.06 E-value=15 Score=33.99 Aligned_cols=47 Identities=21% Similarity=0.424 Sum_probs=27.4
Q ss_pred HHHHhCcee-----ecCCCCcceeeeeEEEEccCccccccccCccccCCCCCC
Q 032998 47 VILQMGLRL-----LAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 47 Vl~~lGL~~-----~s~~g~~I~~~k~W~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
-+.++||.+ +.-.|..|-++-.-+..-..=......+ -..||.||++
T Consensus 350 ~i~~~~i~iGD~V~V~raGdVIP~i~~vv~~~r~~~~~~~~~-P~~CP~C~s~ 401 (652)
T TIGR00575 350 EIEELDIRIGDTVVVRKAGDVIPKVVRVLLEKRTGSERPIRF-PTHCPSCGSP 401 (652)
T ss_pred HHHHcCCCCCCEEEEEecCCcCceeeeeccccCCCCCCCCCC-CCCCCCCCCE
Confidence 356777765 4455888888876554322111111112 2589999998
No 239
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=55.87 E-value=12 Score=26.75 Aligned_cols=19 Identities=26% Similarity=0.842 Sum_probs=14.5
Q ss_pred ccccCCCCCCCceeEEEEEe
Q 032998 85 RIFCPKCGNGGTLRKVAVTV 104 (129)
Q Consensus 85 ~~fCp~CG~~~tL~rv~v~v 104 (129)
+..||.||.. .++|+++-+
T Consensus 36 ~y~CpfCgk~-~vkR~a~GI 54 (90)
T PRK03976 36 KHVCPVCGRP-KVKRVGTGI 54 (90)
T ss_pred CccCCCCCCC-ceEEEEEEE
Confidence 5678888887 788888743
No 240
>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=55.59 E-value=19 Score=26.26 Aligned_cols=43 Identities=19% Similarity=0.466 Sum_probs=24.2
Q ss_pred eEEEEcc--Ccccc-ccc-cCccccCCCCCC--CceeE--EEEEe-CCCceE
Q 032998 68 RWILKCH--ACYTI-TAE-IGRIFCPKCGNG--GTLRK--VAVTV-GENGIV 110 (129)
Q Consensus 68 ~W~~rC~--~C~k~-~~~-~~~~fCp~CG~~--~tL~r--v~v~v-~~~G~~ 110 (129)
-|=..|+ .|++. ... ....+|+.||.. ....| +.+.+ |..|++
T Consensus 16 ~~Y~aC~~~~C~kKv~~~~~~~y~C~~C~~~~~~~~~ry~l~~~i~D~tg~~ 67 (146)
T PF08646_consen 16 WYYPACPNEKCNKKVTENGDGSYRCEKCNKTVENPKYRYRLSLKISDGTGSI 67 (146)
T ss_dssp TEEEE-TSTTTS-B-EEETTTEEEETTTTEEESS-EEEEEEEEEEEETTEEE
T ss_pred cEECCCCCccCCCEeecCCCcEEECCCCCCcCCCeeEEEEEEEEEEeCCCeE
Confidence 4778899 99975 333 224699999965 12233 33333 455765
No 241
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=55.56 E-value=9.2 Score=34.43 Aligned_cols=32 Identities=25% Similarity=0.451 Sum_probs=24.6
Q ss_pred EEEEccCccccccccCccccCCCCCCCceeEEE
Q 032998 69 WILKCHACYTITAEIGRIFCPKCGNGGTLRKVA 101 (129)
Q Consensus 69 W~~rC~~C~k~~~~~~~~fCp~CG~~~tL~rv~ 101 (129)
=.|.|..|+...+. +..-||.||.=+||.-..
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 56899999987764 557799999766776544
No 242
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=54.09 E-value=16 Score=27.04 Aligned_cols=20 Identities=35% Similarity=0.949 Sum_probs=9.3
Q ss_pred ccCccccccccCccccCCCCC
Q 032998 73 CHACYTITAEIGRIFCPKCGN 93 (129)
Q Consensus 73 C~~C~k~~~~~~~~fCp~CG~ 93 (129)
|+.|+.-.. .++..||.||.
T Consensus 1 CPvCg~~l~-vt~l~C~~C~t 20 (113)
T PF09862_consen 1 CPVCGGELV-VTRLKCPSCGT 20 (113)
T ss_pred CCCCCCceE-EEEEEcCCCCC
Confidence 555554322 23455555554
No 243
>PTZ00409 Sir2 (Silent Information Regulator) protein; Provisional
Probab=53.99 E-value=8.4 Score=31.84 Aligned_cols=26 Identities=23% Similarity=0.492 Sum_probs=17.4
Q ss_pred eEEEEccCcccccccc-----------C--ccccCCCCCC
Q 032998 68 RWILKCHACYTITAEI-----------G--RIFCPKCGNG 94 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~~-----------~--~~fCp~CG~~ 94 (129)
.+..+|..|++.+... . ...|| ||+.
T Consensus 135 l~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~P~C~-Cgg~ 173 (271)
T PTZ00409 135 VFEARCCTCRKTIQLNKIMLQKTSHFMHQLPPECP-CGGI 173 (271)
T ss_pred cCcceeCCCCCCcccCHHHHhhhhhhccCCCCCCC-CCCc
Confidence 4568999998765410 0 13599 9986
No 244
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=52.30 E-value=11 Score=24.73 Aligned_cols=22 Identities=27% Similarity=0.613 Sum_probs=13.8
Q ss_pred ccCccccccccCccccCCCCCC
Q 032998 73 CHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 73 C~~C~k~~~~~~~~fCp~CG~~ 94 (129)
|+-|.+.........||.||-+
T Consensus 2 Cpv~~~~~~~~v~~~Cp~cGip 23 (55)
T PF13824_consen 2 CPVCKKDLPAHVNFECPDCGIP 23 (55)
T ss_pred CCCCccccccccCCcCCCCCCc
Confidence 5566653332334679999987
No 245
>PF14569 zf-UDP: Zinc-binding RING-finger; PDB: 1WEO_A.
Probab=52.25 E-value=2.9 Score=29.35 Aligned_cols=28 Identities=25% Similarity=0.758 Sum_probs=14.4
Q ss_pred EEccCccccccccCccccCCCCCCCceeEE
Q 032998 71 LKCHACYTITAEIGRIFCPKCGNGGTLRKV 100 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG~~~tL~rv 100 (129)
..|..|+.+......+-||.|+.+ -+|+
T Consensus 37 PvCr~CyEYErkeg~q~CpqCkt~--ykr~ 64 (80)
T PF14569_consen 37 PVCRPCYEYERKEGNQVCPQCKTR--YKRH 64 (80)
T ss_dssp ---HHHHHHHHHTS-SB-TTT--B------
T ss_pred ccchhHHHHHhhcCcccccccCCC--cccc
Confidence 468889987777778999999987 4443
No 246
>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=52.03 E-value=11 Score=24.12 Aligned_cols=27 Identities=33% Similarity=0.835 Sum_probs=18.3
Q ss_pred eeEEEEccCcccccc-------ccCccccCCCCC
Q 032998 67 HRWILKCHACYTITA-------EIGRIFCPKCGN 93 (129)
Q Consensus 67 k~W~~rC~~C~k~~~-------~~~~~fCp~CG~ 93 (129)
.++.+.|.-|+...- ....-.||.||.
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 378899999986431 112456999986
No 247
>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=51.75 E-value=5.8 Score=24.20 Aligned_cols=20 Identities=25% Similarity=0.602 Sum_probs=9.1
Q ss_pred cccCCCCCCCceeEEEEEeCCCc
Q 032998 86 IFCPKCGNGGTLRKVAVTVGENG 108 (129)
Q Consensus 86 ~fCp~CG~~~tL~rv~v~v~~~G 108 (129)
.-||.||.. .|-++..+.+|
T Consensus 4 ~pCP~CGG~---DrFri~~d~~~ 23 (40)
T PF08273_consen 4 GPCPICGGK---DRFRIFDDKDG 23 (40)
T ss_dssp E--TTTT-T---TTEEEETT---
T ss_pred CCCCCCcCc---cccccCcCccc
Confidence 459999997 44555445443
No 248
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=51.66 E-value=7.9 Score=26.39 Aligned_cols=14 Identities=43% Similarity=1.108 Sum_probs=9.6
Q ss_pred cCCCCCCCceeEEEE
Q 032998 88 CPKCGNGGTLRKVAV 102 (129)
Q Consensus 88 Cp~CG~~~tL~rv~v 102 (129)
||+||+. ....-++
T Consensus 7 CpKCgn~-~~~ekei 20 (68)
T COG3478 7 CPKCGNT-NYEEKEI 20 (68)
T ss_pred CCCcCCc-chhhcee
Confidence 9999997 4443344
No 249
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=51.64 E-value=19 Score=23.09 Aligned_cols=34 Identities=26% Similarity=0.330 Sum_probs=21.6
Q ss_pred EccCcccccc---------ccCccccCCCCCCCceeEEEEEeCCCc
Q 032998 72 KCHACYTITA---------EIGRIFCPKCGNGGTLRKVAVTVGENG 108 (129)
Q Consensus 72 rC~~C~k~~~---------~~~~~fCp~CG~~~tL~rv~v~v~~~G 108 (129)
.|+-||.... -.+.+-|++|-+| ..+.+++++++
T Consensus 2 ~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~P---I~~~v~~d~~~ 44 (52)
T PF14255_consen 2 QCPYCGEPIEILIDPSAGDQEYIEDCQVCCRP---IEVQVTVDEDE 44 (52)
T ss_pred CCCCCCCeeEEEEecCCCCeeEEeehhhcCCc---cEEEEEECCCC
Confidence 4777776442 1234679999998 34566677764
No 250
>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=51.43 E-value=8.5 Score=26.74 Aligned_cols=23 Identities=30% Similarity=0.787 Sum_probs=16.5
Q ss_pred EccCccccccc-cCccccCCCCCC
Q 032998 72 KCHACYTITAE-IGRIFCPKCGNG 94 (129)
Q Consensus 72 rC~~C~k~~~~-~~~~fCp~CG~~ 94 (129)
.|+.|+.+... .....||.||+.
T Consensus 2 fC~~Cg~~l~~~~~~~~C~~C~~~ 25 (104)
T TIGR01384 2 FCPKCGSLMTPKNGVYVCPSCGYE 25 (104)
T ss_pred CCcccCcccccCCCeEECcCCCCc
Confidence 48888877543 236789999965
No 251
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=51.02 E-value=18 Score=30.82 Aligned_cols=31 Identities=26% Similarity=0.497 Sum_probs=22.1
Q ss_pred EEEccCccccccccCccccCCCCCCCceeEEE
Q 032998 70 ILKCHACYTITAEIGRIFCPKCGNGGTLRKVA 101 (129)
Q Consensus 70 ~~rC~~C~k~~~~~~~~fCp~CG~~~tL~rv~ 101 (129)
.+.|.-|..... ..+.-||.||+...|...+
T Consensus 210 yL~CslC~teW~-~~R~~C~~Cg~~~~l~y~~ 240 (305)
T TIGR01562 210 YLSCSLCATEWH-YVRVKCSHCEESKHLAYLS 240 (305)
T ss_pred EEEcCCCCCccc-ccCccCCCCCCCCceeeEe
Confidence 478888887664 4588899999974444433
No 252
>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=50.91 E-value=3.6 Score=26.54 Aligned_cols=23 Identities=30% Similarity=0.683 Sum_probs=16.3
Q ss_pred EEccCccccccccCccccCCCCCC
Q 032998 71 LKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
|-|..|-...-.. .++||.||.+
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 6677777655433 4899999987
No 253
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=50.85 E-value=11 Score=22.94 Aligned_cols=10 Identities=30% Similarity=0.859 Sum_probs=9.0
Q ss_pred ccccCCCCCC
Q 032998 85 RIFCPKCGNG 94 (129)
Q Consensus 85 ~~fCp~CG~~ 94 (129)
..+|+.||++
T Consensus 5 ~l~C~~CG~~ 14 (58)
T PF13408_consen 5 LLRCGHCGSK 14 (58)
T ss_pred cEEcccCCcE
Confidence 5899999997
No 254
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=50.61 E-value=9.3 Score=26.09 Aligned_cols=20 Identities=15% Similarity=0.547 Sum_probs=12.9
Q ss_pred cccCCCCCCCceeEEEEEeCC
Q 032998 86 IFCPKCGNGGTLRKVAVTVGE 106 (129)
Q Consensus 86 ~fCp~CG~~~tL~rv~v~v~~ 106 (129)
..||.||++ ...|-+..+++
T Consensus 2 m~CP~Cg~~-a~irtSr~~s~ 21 (72)
T PRK09678 2 FHCPLCQHA-AHARTSRYITD 21 (72)
T ss_pred ccCCCCCCc-cEEEEChhcCh
Confidence 369999998 45555554443
No 255
>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=50.25 E-value=9.6 Score=23.12 Aligned_cols=10 Identities=40% Similarity=1.255 Sum_probs=8.0
Q ss_pred ccccCCCCCC
Q 032998 85 RIFCPKCGNG 94 (129)
Q Consensus 85 ~~fCp~CG~~ 94 (129)
...||+||+.
T Consensus 18 g~~CP~Cg~~ 27 (46)
T PF12760_consen 18 GFVCPHCGST 27 (46)
T ss_pred CCCCCCCCCe
Confidence 3569999995
No 256
>PF15616 TerY-C: TerY-C metal binding domain
Probab=50.03 E-value=10 Score=28.68 Aligned_cols=22 Identities=36% Similarity=0.898 Sum_probs=16.6
Q ss_pred EccCccccc--cccCccccCCCCCC
Q 032998 72 KCHACYTIT--AEIGRIFCPKCGNG 94 (129)
Q Consensus 72 rC~~C~k~~--~~~~~~fCp~CG~~ 94 (129)
.| +|++++ .......||.||+.
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 899885 34446889999997
No 257
>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=50.02 E-value=11 Score=32.98 Aligned_cols=50 Identities=20% Similarity=0.333 Sum_probs=30.4
Q ss_pred HHHHHHHhCce-eecCCCCcceeeeeEEEEccCccccccccC-c---cccCCCCCC
Q 032998 44 MQNVILQMGLR-LLAPGGMQIRQLHRWILKCHACYTITAEIG-R---IFCPKCGNG 94 (129)
Q Consensus 44 mQNVl~~lGL~-~~s~~g~~I~~~k~W~~rC~~C~k~~~~~~-~---~fCp~CG~~ 94 (129)
++.++..+.-. +..--|.-++.-|.+.-.|..|+..+.... . .-|| ||++
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 56666554322 222224445666677789999997665321 2 5699 9997
No 258
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=49.91 E-value=26 Score=20.91 Aligned_cols=8 Identities=75% Similarity=1.639 Sum_probs=6.9
Q ss_pred ccCCCCCC
Q 032998 87 FCPKCGNG 94 (129)
Q Consensus 87 fCp~CG~~ 94 (129)
-||+||++
T Consensus 2 ~Cp~C~~~ 9 (40)
T smart00440 2 PCPKCGNR 9 (40)
T ss_pred cCCCCCCC
Confidence 49999987
No 259
>COG0498 ThrC Threonine synthase [Amino acid transport and metabolism]
Probab=49.88 E-value=9.8 Score=33.57 Aligned_cols=27 Identities=26% Similarity=0.472 Sum_probs=21.7
Q ss_pred eEEEEccCccccccccC-ccccCCCCCC
Q 032998 68 RWILKCHACYTITAEIG-RIFCPKCGNG 94 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~~~-~~fCp~CG~~ 94 (129)
-..+||..|++.|.+-. ...||.||..
T Consensus 3 ~~~~rc~~cg~~f~~a~~~~~c~~cGl~ 30 (411)
T COG0498 3 YVSLRCLKCGREFSQALLQGLCPDCGLF 30 (411)
T ss_pred eeEeecCCCCcchhhHHhhCcCCcCCcc
Confidence 46789999998886333 5889999996
No 260
>PF09334 tRNA-synt_1g: tRNA synthetases class I (M); InterPro: IPR015413 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This domain is found in methionyl and leucyl tRNA synthetases. ; GO: 0000166 nucleotide binding, 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding, 0006418 tRNA aminoacylation for protein translation, 0005737 cytoplasm; PDB: 2D5B_A 1A8H_A 1WOY_A 2D54_A 4DLP_A 2CT8_B 2CSX_A 1MED_A 1PFU_A 1PFW_A ....
Probab=49.88 E-value=20 Score=30.92 Aligned_cols=44 Identities=23% Similarity=0.320 Sum_probs=24.7
Q ss_pred HHHHHHHHhCceeecCCCCcceeeeeEEEEccCccccccccC-ccccCCCC
Q 032998 43 AMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIG-RIFCPKCG 92 (129)
Q Consensus 43 amQNVl~~lGL~~~s~~g~~I~~~k~W~~rC~~C~k~~~~~~-~~fCp~CG 92 (129)
..|.+..+|-- .|. |.+...=.+.|..|.+...+.. ...||.||
T Consensus 99 ~v~~i~~~L~~-----~G~-I~~~~~~~~Yc~~~e~fl~e~~v~g~CP~C~ 143 (391)
T PF09334_consen 99 FVQEIFKRLYD-----NGY-IYKREYEGWYCPSCERFLPESFVEGTCPYCG 143 (391)
T ss_dssp HHHHHHHHHHH-----TTS-EEEEEEEEEEETTTTEEE-GGGETCEETTT-
T ss_pred HHHHHHHHHHh-----cCc-eeecccceeEecCcCcccccceeeccccCcC
Confidence 34666655411 233 5555556688999998776644 35566544
No 261
>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=49.78 E-value=38 Score=23.73 Aligned_cols=25 Identities=24% Similarity=0.142 Sum_probs=13.2
Q ss_pred EeCCCceEEeecCCccccCceeecCC
Q 032998 103 TVGENGIVLASRRPRITLRGTKVSIS 128 (129)
Q Consensus 103 ~v~~~G~~~~~~~~~~n~RG~~ySlP 128 (129)
.+..+|.+++.++.... +...|++|
T Consensus 19 ii~~~~~vLL~kr~~~~-~~g~w~lP 43 (130)
T cd04511 19 VPEWEGKVLLCRRAIEP-RHGFWTLP 43 (130)
T ss_pred EEecCCEEEEEEecCCC-CCCeEECC
Confidence 33455777665554322 33357777
No 262
>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=49.37 E-value=24 Score=28.45 Aligned_cols=51 Identities=16% Similarity=0.313 Sum_probs=35.8
Q ss_pred CceeeEeechHHHHHHHHH----hCceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCC
Q 032998 32 ESTVACITGDYAMQNVILQ----MGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 32 ~~~va~~TdDyamQNVl~~----lGL~~~s~~g~~I~~~k~W~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
+.++..+=++|+-|.++.. +||+++.+ .+..+|..|+++.+. ..||.....
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 4556677889999999876 67877766 455669999997654 779988775
No 263
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=49.27 E-value=9.5 Score=32.24 Aligned_cols=28 Identities=32% Similarity=0.531 Sum_probs=18.7
Q ss_pred EEccCccccccc---cCccccCCCCCCCceeE
Q 032998 71 LKCHACYTITAE---IGRIFCPKCGNGGTLRK 99 (129)
Q Consensus 71 ~rC~~C~k~~~~---~~~~fCp~CG~~~tL~r 99 (129)
..|..||..+.. -.+..||+||+. ..=|
T Consensus 112 RFCg~CG~~~~~~~~g~~~~C~~cg~~-~fPR 142 (279)
T COG2816 112 RFCGRCGTKTYPREGGWARVCPKCGHE-HFPR 142 (279)
T ss_pred cCCCCCCCcCccccCceeeeCCCCCCc-cCCC
Confidence 468888865532 226789999986 4433
No 264
>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=48.67 E-value=16 Score=23.65 Aligned_cols=27 Identities=22% Similarity=0.561 Sum_probs=18.2
Q ss_pred EEccCcccccccc-----CccccCCCCCCCceeE
Q 032998 71 LKCHACYTITAEI-----GRIFCPKCGNGGTLRK 99 (129)
Q Consensus 71 ~rC~~C~k~~~~~-----~~~fCp~CG~~~tL~r 99 (129)
..|+-|+....-. ....||.||.. |.=
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 4799998654311 24689999996 653
No 265
>COG4640 Predicted membrane protein [Function unknown]
Probab=48.54 E-value=8.9 Score=34.37 Aligned_cols=23 Identities=30% Similarity=0.716 Sum_probs=16.3
Q ss_pred EEccCccccccccCccccCCCCCC
Q 032998 71 LKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
+-|+-||.--.+ .-.+||.||++
T Consensus 2 ~fC~kcG~qk~E-d~~qC~qCG~~ 24 (465)
T COG4640 2 KFCPKCGSQKAE-DDVQCTQCGHK 24 (465)
T ss_pred Cccccccccccc-ccccccccCCc
Confidence 469999944333 23569999998
No 266
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=48.44 E-value=12 Score=22.06 Aligned_cols=13 Identities=46% Similarity=1.229 Sum_probs=10.2
Q ss_pred cCCCCCCCceeEEEE
Q 032998 88 CPKCGNGGTLRKVAV 102 (129)
Q Consensus 88 Cp~CG~~~tL~rv~v 102 (129)
||+|+.. |..+.+
T Consensus 2 CP~C~~~--l~~~~~ 14 (41)
T PF13453_consen 2 CPRCGTE--LEPVRL 14 (41)
T ss_pred cCCCCcc--cceEEE
Confidence 9999996 776665
No 267
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=48.42 E-value=7.7 Score=28.25 Aligned_cols=9 Identities=67% Similarity=1.534 Sum_probs=8.1
Q ss_pred cccCCCCCC
Q 032998 86 IFCPKCGNG 94 (129)
Q Consensus 86 ~fCp~CG~~ 94 (129)
.|||.||+-
T Consensus 3 ~FCp~Cgsl 11 (113)
T COG1594 3 RFCPKCGSL 11 (113)
T ss_pred cccCCccCe
Confidence 799999995
No 268
>KOG1779 consensus 40s ribosomal protein S27 [Translation, ribosomal structure and biogenesis]
Probab=48.41 E-value=9.1 Score=27.05 Aligned_cols=24 Identities=29% Similarity=0.747 Sum_probs=18.2
Q ss_pred EEccCccccccc----cCccccCCCCCC
Q 032998 71 LKCHACYTITAE----IGRIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~~~----~~~~fCp~CG~~ 94 (129)
-+|.||++++.- .+-..|+.|+.-
T Consensus 35 VkC~gc~~iT~vfSHaqtvVvc~~c~~i 62 (84)
T KOG1779|consen 35 VKCPGCFKITTVFSHAQTVVVCEGCSTI 62 (84)
T ss_pred EEcCCceEEEEEeecCceEEEcCCCceE
Confidence 589999998742 235789999875
No 269
>COG4469 CoiA Competence protein CoiA-like family, contains a predicted nuclease domain [General function prediction only]
Probab=47.98 E-value=9 Score=33.32 Aligned_cols=10 Identities=60% Similarity=1.643 Sum_probs=8.8
Q ss_pred ccccCCCCCC
Q 032998 85 RIFCPKCGNG 94 (129)
Q Consensus 85 ~~fCp~CG~~ 94 (129)
+-|||+||++
T Consensus 25 ~ffCPaC~~~ 34 (342)
T COG4469 25 RFFCPACGSQ 34 (342)
T ss_pred ccccCCCCCe
Confidence 3699999998
No 270
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=47.94 E-value=4.8 Score=35.40 Aligned_cols=36 Identities=25% Similarity=0.516 Sum_probs=25.2
Q ss_pred CCcceeeeeEEEEccCccccccccCccccCCCCCCCcee
Q 032998 60 GMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLR 98 (129)
Q Consensus 60 g~~I~~~k~W~~rC~~C~k~~~~~~~~fCp~CG~~~tL~ 98 (129)
|.++++ +-.|||+.|+..... -.--||.|-.=.|++
T Consensus 346 ge~l~~--~~~YRC~~CGF~a~~-l~W~CPsC~~W~Tik 381 (389)
T COG2956 346 GEQLRR--KPRYRCQNCGFTAHT-LYWHCPSCRAWETIK 381 (389)
T ss_pred HHHHhh--cCCceecccCCccee-eeeeCCCcccccccC
Confidence 455555 778999999965543 246699998765554
No 271
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=47.66 E-value=23 Score=30.26 Aligned_cols=28 Identities=29% Similarity=0.700 Sum_probs=20.8
Q ss_pred EEEccCccccccccCccccCCCCCCCcee
Q 032998 70 ILKCHACYTITAEIGRIFCPKCGNGGTLR 98 (129)
Q Consensus 70 ~~rC~~C~k~~~~~~~~fCp~CG~~~tL~ 98 (129)
-+.|.-|+.... ..+.-||.||+...|.
T Consensus 212 yL~CslC~teW~-~~R~~C~~Cg~~~~l~ 239 (309)
T PRK03564 212 YLHCNLCESEWH-VVRVKCSNCEQSGKLH 239 (309)
T ss_pred EEEcCCCCCccc-ccCccCCCCCCCCcee
Confidence 478999997664 4588899999863343
No 272
>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=47.65 E-value=12 Score=33.86 Aligned_cols=29 Identities=28% Similarity=0.679 Sum_probs=22.0
Q ss_pred eeeEEEEccCccccccc--------------cCccccCCCCCC
Q 032998 66 LHRWILKCHACYTITAE--------------IGRIFCPKCGNG 94 (129)
Q Consensus 66 ~k~W~~rC~~C~k~~~~--------------~~~~fCp~CG~~ 94 (129)
.+.|-..|+.|+....- .....||+||..
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 35899999999975431 235679999986
No 273
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=47.39 E-value=15 Score=26.92 Aligned_cols=23 Identities=26% Similarity=0.593 Sum_probs=15.3
Q ss_pred ccccCCCCCCCceeEEEEEeCCCceE
Q 032998 85 RIFCPKCGNGGTLRKVAVTVGENGIV 110 (129)
Q Consensus 85 ~~fCp~CG~~~tL~rv~v~v~~~G~~ 110 (129)
.-.||.||+. + -++++|+..+++
T Consensus 22 ~FtCp~Cghe-~--vs~ctvkk~~~~ 44 (104)
T COG4888 22 TFTCPRCGHE-K--VSSCTVKKTVNI 44 (104)
T ss_pred eEecCccCCe-e--eeEEEEEecCce
Confidence 3569999997 3 356667655443
No 274
>PRK14350 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=47.28 E-value=20 Score=33.49 Aligned_cols=43 Identities=21% Similarity=0.273 Sum_probs=27.5
Q ss_pred HHHHHhCcee-----ecCCCCcceeeeeE--EEEccCccccccccCccccCCCCCC
Q 032998 46 NVILQMGLRL-----LAPGGMQIRQLHRW--ILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 46 NVl~~lGL~~-----~s~~g~~I~~~k~W--~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
+-..++||.+ +.-.|+.|-++-.- ..|... +..+ ..||.||++
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 4456777776 44558888888664 344332 2222 579999998
No 275
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=47.15 E-value=11 Score=24.13 Aligned_cols=27 Identities=30% Similarity=0.509 Sum_probs=19.6
Q ss_pred EEEccCccccccccCccccCCCCCCCcee
Q 032998 70 ILKCHACYTITAEIGRIFCPKCGNGGTLR 98 (129)
Q Consensus 70 ~~rC~~C~k~~~~~~~~fCp~CG~~~tL~ 98 (129)
++.|.-|+.--+. .-.-|-+||+. .|+
T Consensus 14 k~ICrkC~ARnp~-~A~~CRKCg~~-~LR 40 (48)
T PRK04136 14 KKICMRCNARNPW-RATKCRKCGYK-NLR 40 (48)
T ss_pred ccchhcccCCCCc-cccccccCCCC-CcC
Confidence 5789999964443 24679999996 675
No 276
>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=46.80 E-value=9.1 Score=22.02 Aligned_cols=21 Identities=29% Similarity=0.814 Sum_probs=8.6
Q ss_pred ccCcccc--ccccCccccCCCCC
Q 032998 73 CHACYTI--TAEIGRIFCPKCGN 93 (129)
Q Consensus 73 C~~C~k~--~~~~~~~fCp~CG~ 93 (129)
|+-|+-. +.+.....||.||+
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 5555532 23333456666665
No 277
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=46.74 E-value=9.7 Score=27.95 Aligned_cols=9 Identities=67% Similarity=1.752 Sum_probs=8.1
Q ss_pred cccCCCCCC
Q 032998 86 IFCPKCGNG 94 (129)
Q Consensus 86 ~fCp~CG~~ 94 (129)
.|||.|||-
T Consensus 2 ~FCP~Cgn~ 10 (105)
T KOG2906|consen 2 LFCPTCGNM 10 (105)
T ss_pred cccCCCCCE
Confidence 699999995
No 278
>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=46.66 E-value=18 Score=24.30 Aligned_cols=31 Identities=29% Similarity=0.382 Sum_probs=20.4
Q ss_pred CccccccccCccccCCCCCCCceeEEEEEeCCCceE
Q 032998 75 ACYTITAEIGRIFCPKCGNGGTLRKVAVTVGENGIV 110 (129)
Q Consensus 75 ~C~k~~~~~~~~fCp~CG~~~tL~rv~v~v~~~G~~ 110 (129)
.+..++.+ ..|++||.+ |.--.+.+-.+|.+
T Consensus 71 ~~v~i~~~---~~C~vC~k~--l~~~~f~~~p~~~v 101 (109)
T PF10367_consen 71 RSVVITES---TKCSVCGKP--LGNSVFVVFPCGHV 101 (109)
T ss_pred ceEEECCC---CCccCcCCc--CCCceEEEeCCCeE
Confidence 33444543 569999998 54456667788854
No 279
>PRK04011 peptide chain release factor 1; Provisional
Probab=46.62 E-value=16 Score=31.89 Aligned_cols=27 Identities=37% Similarity=0.728 Sum_probs=20.1
Q ss_pred eEEEEccCcccccc-------ccCccccCCCCCC
Q 032998 68 RWILKCHACYTITA-------EIGRIFCPKCGNG 94 (129)
Q Consensus 68 ~W~~rC~~C~k~~~-------~~~~~fCp~CG~~ 94 (129)
++.++|+.|+.... ......||.||.+
T Consensus 326 r~~~~c~~c~~~~~~~~~~~~~~~~~~c~~~~~~ 359 (411)
T PRK04011 326 RVTYKCPNCGYEEEKTVKRREELPEKTCPKCGSE 359 (411)
T ss_pred eEEEEcCCCCcceeeecccccccccccCcccCcc
Confidence 57899999996431 1234789999987
No 280
>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=46.03 E-value=17 Score=27.80 Aligned_cols=26 Identities=31% Similarity=0.658 Sum_probs=19.5
Q ss_pred eEEEEccCccccccccCccccCCCCCC
Q 032998 68 RWILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
.+..+|.+|++.+.. ....||.||++
T Consensus 75 ~~~~~c~pc~~lF~~-~~~~cp~c~~~ 100 (170)
T cd03361 75 DSIKRCRDCGYQFTE-DSDKCPRCGSE 100 (170)
T ss_pred eEeeccCCccccccc-ccccCCcCCCc
Confidence 445689999988853 34679999964
No 281
>COG2405 Predicted nucleic acid-binding protein, contains PIN domain [General function prediction only]
Probab=45.74 E-value=17 Score=28.45 Aligned_cols=29 Identities=24% Similarity=0.330 Sum_probs=24.9
Q ss_pred Ccee-eEeechHHHHHHHHHhCceeecCCC
Q 032998 32 ESTV-ACITGDYAMQNVILQMGLRLLAPGG 60 (129)
Q Consensus 32 ~~~v-a~~TdDyamQNVl~~lGL~~~s~~g 60 (129)
+.++ -+++||+.=.|+|..|||++.+.-|
T Consensus 85 e~~ad~Ll~Ddr~aR~~A~~lgL~V~GtlG 114 (157)
T COG2405 85 ELKADLLLMDDRDARNVAKSLGLKVTGTLG 114 (157)
T ss_pred HcCCCeeeeccHHHHHHHHHcCCeeeehhH
Confidence 4556 8999999999999999999987654
No 282
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=45.67 E-value=9.5 Score=32.26 Aligned_cols=10 Identities=40% Similarity=1.175 Sum_probs=9.3
Q ss_pred ccccCCCCCC
Q 032998 85 RIFCPKCGNG 94 (129)
Q Consensus 85 ~~fCp~CG~~ 94 (129)
..||+.||++
T Consensus 111 ~RFCg~CG~~ 120 (279)
T COG2816 111 HRFCGRCGTK 120 (279)
T ss_pred CcCCCCCCCc
Confidence 5899999999
No 283
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=45.63 E-value=12 Score=26.57 Aligned_cols=25 Identities=28% Similarity=0.666 Sum_probs=18.6
Q ss_pred EEEccCcccccc---c-cCccccCCCCCC
Q 032998 70 ILKCHACYTITA---E-IGRIFCPKCGNG 94 (129)
Q Consensus 70 ~~rC~~C~k~~~---~-~~~~fCp~CG~~ 94 (129)
.-+|++|+.+.- . .+...|..||..
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 468999997653 2 236889999985
No 284
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=45.61 E-value=11 Score=32.15 Aligned_cols=9 Identities=44% Similarity=1.387 Sum_probs=4.4
Q ss_pred cccCCCCCC
Q 032998 86 IFCPKCGNG 94 (129)
Q Consensus 86 ~fCp~CG~~ 94 (129)
.+||+||+.
T Consensus 185 ~~CPvCGs~ 193 (305)
T TIGR01562 185 TLCPACGSP 193 (305)
T ss_pred CcCCCCCCh
Confidence 345555544
No 285
>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=45.53 E-value=1.7 Score=26.20 Aligned_cols=29 Identities=21% Similarity=0.486 Sum_probs=16.6
Q ss_pred ceeeeeEEEEccCccccccccCccccCCCCCC
Q 032998 63 IRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 63 I~~~k~W~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
|.+++.-+..|.-|+.++.. ..|+.|-++
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 34455567789999988765 679999876
No 286
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=45.52 E-value=14 Score=33.04 Aligned_cols=32 Identities=22% Similarity=0.666 Sum_probs=23.0
Q ss_pred eeEEEEccCcccccccc-----CccccCCCCCCCceeEE
Q 032998 67 HRWILKCHACYTITAEI-----GRIFCPKCGNGGTLRKV 100 (129)
Q Consensus 67 k~W~~rC~~C~k~~~~~-----~~~fCp~CG~~~tL~rv 100 (129)
.....+|+.|.-..+-+ ..-+||.||+. |++.
T Consensus 15 ~~~~~~C~eCd~~~~~P~l~~~q~A~CPRC~~~--l~~~ 51 (418)
T COG2995 15 PGHLILCPECDMLVSLPRLDSGQSAYCPRCGHT--LTRG 51 (418)
T ss_pred ccceecCCCCCceeccccCCCCCcccCCCCCCc--cccC
Confidence 45678999999766422 25789999995 7653
No 287
>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=45.40 E-value=17 Score=31.78 Aligned_cols=27 Identities=33% Similarity=0.632 Sum_probs=19.4
Q ss_pred eEEEEccCccccccc-------cCccccCCCCCC
Q 032998 68 RWILKCHACYTITAE-------IGRIFCPKCGNG 94 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~-------~~~~fCp~CG~~ 94 (129)
++.+||..|+..... ....+||.||..
T Consensus 318 r~~~rc~~c~~~~~~~~~~~~~~~~~~~~~~~~~ 351 (403)
T TIGR03676 318 RVTFKCPNCGYEEEKTVKPEEGDKSEACPKCGSE 351 (403)
T ss_pred eEEEEcCCCCcceeeecccccccccccCcccCcc
Confidence 578999999964321 112679999997
No 288
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=45.30 E-value=21 Score=28.94 Aligned_cols=23 Identities=26% Similarity=0.504 Sum_probs=13.1
Q ss_pred cccCCCCCCC-------ceeEEEEEeCCCc
Q 032998 86 IFCPKCGNGG-------TLRKVAVTVGENG 108 (129)
Q Consensus 86 ~fCp~CG~~~-------tL~rv~v~v~~~G 108 (129)
..|+.||.-+ -+.+|.+.|+..+
T Consensus 31 vrC~eCG~V~~~~i~~~k~~~v~viVS~~~ 60 (201)
T COG1326 31 VRCEECGTVHPAIIKTPKPVRVRVIVSRHE 60 (201)
T ss_pred EEccCCCcEeeceeeccccceEEEEEecCC
Confidence 4566666531 2456777766554
No 289
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=45.26 E-value=11 Score=28.39 Aligned_cols=24 Identities=17% Similarity=0.115 Sum_probs=18.8
Q ss_pred EEccCccccccccCc--cccCCCCCC
Q 032998 71 LKCHACYTITAEIGR--IFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~--~fCp~CG~~ 94 (129)
..|+-|++.|.+..+ ..||.||..
T Consensus 10 ridPetg~KFYDLNrdPiVsPytG~s 35 (129)
T COG4530 10 RIDPETGKKFYDLNRDPIVSPYTGKS 35 (129)
T ss_pred ccCccccchhhccCCCccccCccccc
Confidence 469999988876553 689999963
No 290
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=45.14 E-value=5.9 Score=30.59 Aligned_cols=41 Identities=27% Similarity=0.382 Sum_probs=24.1
Q ss_pred hHHHHHHHHHhCceee------cCCCCcceeeeeEEEEccCcccccc
Q 032998 41 DYAMQNVILQMGLRLL------APGGMQIRQLHRWILKCHACYTITA 81 (129)
Q Consensus 41 DyamQNVl~~lGL~~~------s~~g~~I~~~k~W~~rC~~C~k~~~ 81 (129)
|.-+||++....-.++ +++...++..|.|.+.|-+|+...+
T Consensus 91 ~~~i~~~i~~yi~~yv~C~~c~s~dt~l~~~~R~~~l~c~acGa~~p 137 (151)
T COG1601 91 DSEIVNEIERYIAEYVKCKECGSPDTELIKEERLLFLKCEACGAIRP 137 (151)
T ss_pred HHHHHHHHHHHHHheeEeccCCCCchhhhhhhhhHhhHHHHhCCccc
Confidence 4556776665443332 4555556666667777777775443
No 291
>PRK13764 ATPase; Provisional
Probab=45.09 E-value=21 Score=33.07 Aligned_cols=30 Identities=17% Similarity=0.131 Sum_probs=26.4
Q ss_pred CceeeEeechHHHHHHHHHhCceeecCCCC
Q 032998 32 ESTVACITGDYAMQNVILQMGLRLLAPGGM 61 (129)
Q Consensus 32 ~~~va~~TdDyamQNVl~~lGL~~~s~~g~ 61 (129)
+.++.++|.|+.+..+|..+||+++.+...
T Consensus 101 ~~~~~lvT~D~~l~~~A~~~GI~V~~l~~~ 130 (602)
T PRK13764 101 ELGATLVTSDRVQAEVARAKGIDVIYLKPE 130 (602)
T ss_pred HcCCEEEeCCHHHHHHHHHcCCEEEEeCCC
Confidence 568999999999999999999999876543
No 292
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=45.09 E-value=10 Score=32.41 Aligned_cols=40 Identities=25% Similarity=0.633 Sum_probs=24.6
Q ss_pred eEEEEccCccccccc----cCccccCCCCCCCce---eEEEEEeCCCc
Q 032998 68 RWILKCHACYTITAE----IGRIFCPKCGNGGTL---RKVAVTVGENG 108 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~----~~~~fCp~CG~~~tL---~rv~v~v~~~G 108 (129)
-| ..|++|+.+... .....||+||+..-+ .|+...+|++.
T Consensus 27 lw-~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ri~A~~Ri~~llD~gs 73 (294)
T COG0777 27 LW-TKCPSCGEMLYRKELESNLKVCPKCGHHMRISARERLEALLDEGS 73 (294)
T ss_pred ce-eECCCccceeeHHHHHhhhhcccccCcccccCHHHHHHHhhCCCc
Confidence 45 479999987432 225789999997222 34444445544
No 293
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=45.03 E-value=8.2 Score=26.64 Aligned_cols=23 Identities=30% Similarity=0.554 Sum_probs=15.2
Q ss_pred cccCCCCCCCceeEEE-EEeCCCceE
Q 032998 86 IFCPKCGNGGTLRKVA-VTVGENGIV 110 (129)
Q Consensus 86 ~fCp~CG~~~tL~rv~-v~v~~~G~~ 110 (129)
+||..||-| |..-. .-.++||..
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 65544 334566653
No 294
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=44.86 E-value=14 Score=33.88 Aligned_cols=30 Identities=30% Similarity=0.442 Sum_probs=23.4
Q ss_pred ceeeeeEEEEccCccccccccC-ccccCCCC
Q 032998 63 IRQLHRWILKCHACYTITAEIG-RIFCPKCG 92 (129)
Q Consensus 63 I~~~k~W~~rC~~C~k~~~~~~-~~fCp~CG 92 (129)
|.....=.++|..|.+..++.. ...||.||
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 4444445689999999988766 78899999
No 295
>PLN00209 ribosomal protein S27; Provisional
Probab=44.77 E-value=12 Score=26.53 Aligned_cols=25 Identities=28% Similarity=0.732 Sum_probs=18.5
Q ss_pred EEEccCcccccc---c-cCccccCCCCCC
Q 032998 70 ILKCHACYTITA---E-IGRIFCPKCGNG 94 (129)
Q Consensus 70 ~~rC~~C~k~~~---~-~~~~fCp~CG~~ 94 (129)
.-+|++|+++.- . .+...|..||..
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 468999997653 2 236889999985
No 296
>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=44.72 E-value=9.8 Score=30.15 Aligned_cols=16 Identities=31% Similarity=0.652 Sum_probs=11.6
Q ss_pred cCccccCCCCCCCceeE
Q 032998 83 IGRIFCPKCGNGGTLRK 99 (129)
Q Consensus 83 ~~~~fCp~CG~~~tL~r 99 (129)
..+.||+.||++ ...+
T Consensus 87 ~~R~FC~~CGS~-L~~~ 102 (182)
T TIGR02820 87 IQRHACKGCGTH-MYGR 102 (182)
T ss_pred EEeecCCCCCCc-cccc
Confidence 346899999998 4443
No 297
>PRK12267 methionyl-tRNA synthetase; Reviewed
Probab=44.38 E-value=38 Score=30.85 Aligned_cols=32 Identities=28% Similarity=0.385 Sum_probs=23.3
Q ss_pred ceeeeeEEEEccCccccccccC---ccccCCCCCC
Q 032998 63 IRQLHRWILKCHACYTITAEIG---RIFCPKCGNG 94 (129)
Q Consensus 63 I~~~k~W~~rC~~C~k~~~~~~---~~fCp~CG~~ 94 (129)
|-....=.+.|..|.+...+.. ...||.||++
T Consensus 118 IY~~~~~~~yc~~~~~~l~~~~l~~~~~c~~cg~~ 152 (648)
T PRK12267 118 IYKGEYEGWYCVSCETFFTESQLVDGGKCPDCGRE 152 (648)
T ss_pred EEEeeEEEeecCCCCccCChHHhccCCcCCCCCCc
Confidence 4443444578999999887743 2579999998
No 298
>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=44.34 E-value=8.4 Score=24.01 Aligned_cols=8 Identities=50% Similarity=1.373 Sum_probs=4.3
Q ss_pred ccCCCCCC
Q 032998 87 FCPKCGNG 94 (129)
Q Consensus 87 fCp~CG~~ 94 (129)
-||.||.+
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 79999987
No 299
>PF02639 DUF188: Uncharacterized BCR, YaiI/YqxD family COG1671; InterPro: IPR003791 This entry describes proteins of unknown function.
Probab=44.12 E-value=31 Score=25.69 Aligned_cols=32 Identities=25% Similarity=0.395 Sum_probs=27.4
Q ss_pred ceeeEeechHHHHHHHHHhCceeecCCCCcce
Q 032998 33 STVACITGDYAMQNVILQMGLRLLAPGGMQIR 64 (129)
Q Consensus 33 ~~va~~TdDyamQNVl~~lGL~~~s~~g~~I~ 64 (129)
..-.++|.||.|-..++.-|..+++..|...+
T Consensus 51 ~gDiVITqDigLA~~~l~Kga~vl~~rG~~yt 82 (130)
T PF02639_consen 51 PGDIVITQDIGLASLLLAKGAYVLNPRGKEYT 82 (130)
T ss_pred CCCEEEECCHHHHHHHHHCCCEEECCCCCCCC
Confidence 44479999999999999999999999987543
No 300
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=44.07 E-value=18 Score=30.94 Aligned_cols=10 Identities=60% Similarity=1.421 Sum_probs=6.6
Q ss_pred ccccCCCCCC
Q 032998 85 RIFCPKCGNG 94 (129)
Q Consensus 85 ~~fCp~CG~~ 94 (129)
+.+||+||+.
T Consensus 187 ~~~CPvCGs~ 196 (309)
T PRK03564 187 RQFCPVCGSM 196 (309)
T ss_pred CCCCCCCCCc
Confidence 4667777765
No 301
>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=43.98 E-value=12 Score=29.13 Aligned_cols=9 Identities=44% Similarity=1.117 Sum_probs=6.2
Q ss_pred cccCCCCCC
Q 032998 86 IFCPKCGNG 94 (129)
Q Consensus 86 ~fCp~CG~~ 94 (129)
-+|++||.+
T Consensus 29 f~C~~CGyr 37 (163)
T TIGR00340 29 YICEKCGYR 37 (163)
T ss_pred EECCCCCCc
Confidence 457777776
No 302
>PRK05417 glutathione-dependent formaldehyde-activating enzyme; Provisional
Probab=43.96 E-value=9.3 Score=30.44 Aligned_cols=15 Identities=27% Similarity=0.598 Sum_probs=11.4
Q ss_pred CccccCCCCCCCceeE
Q 032998 84 GRIFCPKCGNGGTLRK 99 (129)
Q Consensus 84 ~~~fCp~CG~~~tL~r 99 (129)
.+.|||.||.+ ...+
T Consensus 92 ~R~FC~~CGS~-L~~~ 106 (191)
T PRK05417 92 QRHACKECGVH-MYGR 106 (191)
T ss_pred EeeeCCCCCCc-cccc
Confidence 46899999997 4444
No 303
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=43.93 E-value=16 Score=23.99 Aligned_cols=21 Identities=33% Similarity=0.762 Sum_probs=15.0
Q ss_pred EEccCccccccccCccccCCCCCC
Q 032998 71 LKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
+.|.+||-..+ .-=||.||.+
T Consensus 28 ~I~~~~f~~~r---YngCPfC~~~ 48 (55)
T PF14447_consen 28 LICDNCFPGER---YNGCPFCGTP 48 (55)
T ss_pred eeeccccChhh---ccCCCCCCCc
Confidence 67888885432 2459999987
No 304
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=43.66 E-value=10 Score=32.71 Aligned_cols=10 Identities=60% Similarity=1.663 Sum_probs=7.0
Q ss_pred ccccCCCCCC
Q 032998 85 RIFCPKCGNG 94 (129)
Q Consensus 85 ~~fCp~CG~~ 94 (129)
-.|||.||.+
T Consensus 334 a~fcp~cgq~ 343 (345)
T COG4260 334 AKFCPECGQG 343 (345)
T ss_pred hhhChhhcCC
Confidence 3677777765
No 305
>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=43.56 E-value=18 Score=23.56 Aligned_cols=28 Identities=32% Similarity=0.713 Sum_probs=16.3
Q ss_pred EEEccCcccccc---c-cCccccCCCCCCCceeE
Q 032998 70 ILKCHACYTITA---E-IGRIFCPKCGNGGTLRK 99 (129)
Q Consensus 70 ~~rC~~C~k~~~---~-~~~~fCp~CG~~~tL~r 99 (129)
.-+|++|+++.- . .+...|..||.. |-+
T Consensus 7 ~VkCp~C~~~q~vFSha~t~V~C~~Cg~~--L~~ 38 (55)
T PF01667_consen 7 DVKCPGCYNIQTVFSHAQTVVKCVVCGTV--LAQ 38 (55)
T ss_dssp EEE-TTT-SEEEEETT-SS-EE-SSSTSE--EEE
T ss_pred EEECCCCCCeeEEEecCCeEEEcccCCCE--ecC
Confidence 468999997642 2 236889999985 643
No 306
>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=43.47 E-value=11 Score=22.36 Aligned_cols=24 Identities=25% Similarity=0.645 Sum_probs=13.4
Q ss_pred EEccCcccccc--ccCccccCCCCCC
Q 032998 71 LKCHACYTITA--EIGRIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~~--~~~~~fCp~CG~~ 94 (129)
.+|.-|+.... +-...+|..||+.
T Consensus 9 ~~C~~C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 9 EPCPVCGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CcCCCCCCeEeEccCCEEEhhhCceE
Confidence 44777764422 2235677777763
No 307
>COG2401 ABC-type ATPase fused to a predicted acetyltransferase domain [General function prediction only]
Probab=42.99 E-value=17 Score=33.31 Aligned_cols=30 Identities=27% Similarity=0.551 Sum_probs=23.9
Q ss_pred eeeeeEEEEccCccccccccCccccCCCCCC
Q 032998 64 RQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 64 ~~~k~W~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
++-+.=+.+|.-||.+-.-..+..| .||++
T Consensus 124 ~k~~va~w~c~~cg~~iean~kp~c-~cg~~ 153 (593)
T COG2401 124 QKEKVALWRCEKCGTIIEANTKPEC-KCGSH 153 (593)
T ss_pred ccceEEEEecchhchhhhhcCCccc-CCCCc
Confidence 3344556799999998877778899 99997
No 308
>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=42.92 E-value=9.1 Score=28.44 Aligned_cols=36 Identities=22% Similarity=0.333 Sum_probs=23.4
Q ss_pred HHHHHHHHhCcee------ecCCCCcceeeeeEEEEccCccc
Q 032998 43 AMQNVILQMGLRL------LAPGGMQIRQLHRWILKCHACYT 78 (129)
Q Consensus 43 amQNVl~~lGL~~------~s~~g~~I~~~k~W~~rC~~C~k 78 (129)
.||++|...=-++ -+++...+++-+.|.++|.+||.
T Consensus 81 ~i~~~L~~fI~~yVlC~~C~spdT~l~k~~r~~~l~C~aCGa 122 (125)
T PF01873_consen 81 QIQDLLDKFIKEYVLCPECGSPDTELIKEGRLIFLKCKACGA 122 (125)
T ss_dssp HHHHHHHHHHCHHSSCTSTSSSSEEEEEETTCCEEEETTTSC
T ss_pred HHHHHHHHHHHHEEEcCCCCCCccEEEEcCCEEEEEecccCC
Confidence 5777776542222 25666666677778888888875
No 309
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=42.81 E-value=18 Score=22.60 Aligned_cols=12 Identities=33% Similarity=0.805 Sum_probs=8.9
Q ss_pred cccCCCCCCCcee
Q 032998 86 IFCPKCGNGGTLR 98 (129)
Q Consensus 86 ~fCp~CG~~~tL~ 98 (129)
.-||-||.+ .+.
T Consensus 4 kPCPFCG~~-~~~ 15 (61)
T PF14354_consen 4 KPCPFCGSA-DVL 15 (61)
T ss_pred cCCCCCCCc-ceE
Confidence 559999988 443
No 310
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=42.77 E-value=9.4 Score=26.77 Aligned_cols=35 Identities=20% Similarity=0.468 Sum_probs=21.7
Q ss_pred eeeEEEEccCccccccccCccccCCCCCCCceeEEEE
Q 032998 66 LHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAV 102 (129)
Q Consensus 66 ~k~W~~rC~~C~k~~~~~~~~fCp~CG~~~tL~rv~v 102 (129)
.+.-.+.|+-|---..+.-...||.||.. |.+.++
T Consensus 22 A~ICtfEcTFCadCae~~l~g~CPnCGGe--lv~RP~ 56 (84)
T COG3813 22 ARICTFECTFCADCAENRLHGLCPNCGGE--LVARPI 56 (84)
T ss_pred eeEEEEeeehhHhHHHHhhcCcCCCCCch--hhcCcC
Confidence 34455677777644333335789999998 444454
No 311
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=42.72 E-value=26 Score=20.79 Aligned_cols=17 Identities=18% Similarity=0.389 Sum_probs=13.4
Q ss_pred CcceeeeeEEEEccCcc
Q 032998 61 MQIRQLHRWILKCHACY 77 (129)
Q Consensus 61 ~~I~~~k~W~~rC~~C~ 77 (129)
..+.+....+|+|+.|+
T Consensus 31 ~~V~e~~~~~y~C~~C~ 47 (47)
T PF13005_consen 31 PEVTEHVRHKYACPCCG 47 (47)
T ss_pred eEEEEEEeceEECCCCC
Confidence 45677788889999885
No 312
>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=42.47 E-value=12 Score=23.52 Aligned_cols=30 Identities=27% Similarity=0.683 Sum_probs=20.4
Q ss_pred eEEEEccCcccccc-----------ccC-ccccCCCCCCCcee
Q 032998 68 RWILKCHACYTITA-----------EIG-RIFCPKCGNGGTLR 98 (129)
Q Consensus 68 ~W~~rC~~C~k~~~-----------~~~-~~fCp~CG~~~tL~ 98 (129)
.-.|.|.+|+.... .+. +.|||.|+.. ||-
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 34688999985431 111 5899999997 764
No 313
>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=42.32 E-value=17 Score=28.29 Aligned_cols=36 Identities=19% Similarity=0.400 Sum_probs=19.2
Q ss_pred CCCcceeeeeEEEEccCccccccc------------cCccccCCCCCC
Q 032998 59 GGMQIRQLHRWILKCHACYTITAE------------IGRIFCPKCGNG 94 (129)
Q Consensus 59 ~g~~I~~~k~W~~rC~~C~k~~~~------------~~~~fCp~CG~~ 94 (129)
+..+-+..-.+.++|+.|++.+.- .....||.|+..
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 445677788999999999976631 224679999885
No 314
>smart00532 LIGANc Ligase N family.
Probab=42.28 E-value=29 Score=30.81 Aligned_cols=47 Identities=19% Similarity=0.323 Sum_probs=27.2
Q ss_pred HHHHHhCcee-----ecCCCCcceeeeeEEEEccCcccc-ccccCccccCCCCCC
Q 032998 46 NVILQMGLRL-----LAPGGMQIRQLHRWILKCHACYTI-TAEIGRIFCPKCGNG 94 (129)
Q Consensus 46 NVl~~lGL~~-----~s~~g~~I~~~k~W~~rC~~C~k~-~~~~~~~fCp~CG~~ 94 (129)
+-+.++||.+ +.-.|..|-++-.-+. ....... ...+ -.+||.||++
T Consensus 356 ~~i~~~~i~iGd~V~V~raGdVIP~I~~vv~-~~r~~~~~~~~~-P~~CP~C~s~ 408 (441)
T smart00532 356 DEIEEKDIRIGDTVVVRKAGDVIPKVVGVVK-EKRPGDEREIEM-PTHCPSCGSE 408 (441)
T ss_pred HHHHHcCCCCCCEEEEEECCCcCcceeeccc-ccCCCCCccCcC-CCCCCCCCCE
Confidence 4466788775 4455888888766443 1111111 1112 2789999998
No 315
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=41.91 E-value=15 Score=25.09 Aligned_cols=26 Identities=23% Similarity=0.478 Sum_probs=18.1
Q ss_pred EEEEccCcccc---ccc-cCccccCCCCCC
Q 032998 69 WILKCHACYTI---TAE-IGRIFCPKCGNG 94 (129)
Q Consensus 69 W~~rC~~C~k~---~~~-~~~~fCp~CG~~ 94 (129)
..-+|+.|+.. |.. .+..-|+.||.-
T Consensus 18 l~VkCpdC~N~q~vFshast~V~C~~CG~~ 47 (67)
T COG2051 18 LRVKCPDCGNEQVVFSHASTVVTCLICGTT 47 (67)
T ss_pred EEEECCCCCCEEEEeccCceEEEecccccE
Confidence 34689999964 333 236789999983
No 316
>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=41.53 E-value=22 Score=21.48 Aligned_cols=23 Identities=30% Similarity=0.641 Sum_probs=14.6
Q ss_pred ccCCCCCCCceeEEEE-EeCCCceEE
Q 032998 87 FCPKCGNGGTLRKVAV-TVGENGIVL 111 (129)
Q Consensus 87 fCp~CG~~~tL~rv~v-~v~~~G~~~ 111 (129)
.|+ ||.+ .+++++. +-..-|...
T Consensus 2 ~C~-Cg~~-~~~~~s~k~~~N~GR~F 25 (45)
T PF06839_consen 2 KCP-CGEP-AVRRTSKKTGPNPGRRF 25 (45)
T ss_pred CCC-CCCE-eEEEEEeCCCCCCCCcc
Confidence 599 9987 6777666 433335543
No 317
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=41.45 E-value=17 Score=23.93 Aligned_cols=21 Identities=29% Similarity=0.662 Sum_probs=10.9
Q ss_pred EEccCccccccccCccccCCCCC
Q 032998 71 LKCHACYTITAEIGRIFCPKCGN 93 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG~ 93 (129)
-.|..||+.- ...-.|+.||.
T Consensus 28 ~~c~~cG~~~--l~Hrvc~~cg~ 48 (57)
T COG0333 28 SVCPNCGEYK--LPHRVCLKCGY 48 (57)
T ss_pred eeccCCCCcc--cCceEcCCCCC
Confidence 4566666532 22355666664
No 318
>COG1412 Uncharacterized proteins of PilT N-term./Vapc superfamily [General function prediction only]
Probab=41.27 E-value=33 Score=25.99 Aligned_cols=28 Identities=11% Similarity=0.157 Sum_probs=25.8
Q ss_pred eeeEeechHHHHHHHHHhCceeecCCCC
Q 032998 34 TVACITGDYAMQNVILQMGLRLLAPGGM 61 (129)
Q Consensus 34 ~va~~TdDyamQNVl~~lGL~~~s~~g~ 61 (129)
.++++|.|-++..-|+.-|++++.+.|.
T Consensus 99 ~~iVaTnD~eLk~rlr~~GIPvi~lr~r 126 (136)
T COG1412 99 RYIVATNDKELKRRLRENGIPVITLRQR 126 (136)
T ss_pred CEEEEeCCHHHHHHHHHcCCCEEEEeCC
Confidence 5999999999999999999999998754
No 319
>KOG2768 consensus Translation initiation factor 2, beta subunit (eIF-2beta) [Translation, ribosomal structure and biogenesis]
Probab=41.26 E-value=15 Score=30.29 Aligned_cols=54 Identities=28% Similarity=0.537 Sum_probs=33.6
Q ss_pred chHHHHHHHHHhCceeecCCCCc------------cee-eeeEE---EEccCccccccc------cCccccCCCCCC
Q 032998 40 GDYAMQNVILQMGLRLLAPGGMQ------------IRQ-LHRWI---LKCHACYTITAE------IGRIFCPKCGNG 94 (129)
Q Consensus 40 dDyamQNVl~~lGL~~~s~~g~~------------I~~-~k~W~---~rC~~C~k~~~~------~~~~fCp~CG~~ 94 (129)
+|--||=.+.+||-.- |++|.+ |.. +|+|+ -.|+.|.-.-.. ....-|..||+.
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 6777999999999775 455433 110 12222 469999854321 112459999996
No 320
>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=41.15 E-value=25 Score=20.84 Aligned_cols=8 Identities=63% Similarity=1.609 Sum_probs=4.7
Q ss_pred ccCCCCCC
Q 032998 87 FCPKCGNG 94 (129)
Q Consensus 87 fCp~CG~~ 94 (129)
.||.||++
T Consensus 2 ~Cp~Cg~~ 9 (39)
T PF01096_consen 2 KCPKCGHN 9 (39)
T ss_dssp --SSS-SS
T ss_pred CCcCCCCC
Confidence 49999998
No 321
>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=41.07 E-value=15 Score=26.30 Aligned_cols=24 Identities=33% Similarity=0.822 Sum_probs=18.1
Q ss_pred EEEEccCccccccccCccccCCCCCC
Q 032998 69 WILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 69 W~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
-+-|||.|+++++.. .|=.+|-++
T Consensus 52 sigRC~RCyRv~Ppf--~~t~rCDnk 75 (91)
T PF01623_consen 52 SIGRCHRCYRVYPPF--YFTKRCDNK 75 (91)
T ss_pred HhCCCCCCeeecCCc--eeCccCCCC
Confidence 357999999999762 455677776
No 322
>PRK07217 replication factor A; Reviewed
Probab=41.00 E-value=16 Score=31.31 Aligned_cols=39 Identities=13% Similarity=0.213 Sum_probs=26.0
Q ss_pred eeeeeEEEEccC--ccccccccCccccCCCCCCC--ceeEEEEEeC
Q 032998 64 RQLHRWILKCHA--CYTITAEIGRIFCPKCGNGG--TLRKVAVTVG 105 (129)
Q Consensus 64 ~~~k~W~~rC~~--C~k~~~~~~~~fCp~CG~~~--tL~rv~v~v~ 105 (129)
+.--.-++||+. |.|+-. +..||.||... -.-|+-..+|
T Consensus 182 ~~GsglI~rCP~~~C~Rvl~---~g~C~~HG~ve~~~DLrik~vlD 224 (311)
T PRK07217 182 QSGSGLIKRCPEEDCTRVLQ---NGRCSEHGKVEGEFDLRIKGVLD 224 (311)
T ss_pred eCCCCCeecCCccccCcccc---CCCCCCCCCcCCceeeEEEEEEE
Confidence 333467799999 999764 36899999531 1245555554
No 323
>COG1040 ComFC Predicted amidophosphoribosyltransferases [General function prediction only]
Probab=40.60 E-value=6.7 Score=31.44 Aligned_cols=27 Identities=33% Similarity=0.621 Sum_probs=20.3
Q ss_pred EEccCccccccccCccccCCCCCCCceeEE
Q 032998 71 LKCHACYTITAEIGRIFCPKCGNGGTLRKV 100 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG~~~tL~rv 100 (129)
..|.+|++-..... .+||.||.+ +...
T Consensus 25 ~~C~~C~~~~~~~~-~~C~~C~~~--l~~~ 51 (225)
T COG1040 25 GLCSGCQADLPLIG-NLCPLCGLP--LSSH 51 (225)
T ss_pred CcChhhhhchhHHH-hhhHhhhCh--hccc
Confidence 57999998766543 389999998 5544
No 324
>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=40.43 E-value=23 Score=21.16 Aligned_cols=22 Identities=23% Similarity=0.530 Sum_probs=14.6
Q ss_pred EccCccccccccCccccCCCCC
Q 032998 72 KCHACYTITAEIGRIFCPKCGN 93 (129)
Q Consensus 72 rC~~C~k~~~~~~~~fCp~CG~ 93 (129)
+|.-|++...+....+|..|+.
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 4777777554444677888875
No 325
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=40.22 E-value=17 Score=26.93 Aligned_cols=23 Identities=30% Similarity=0.733 Sum_probs=17.3
Q ss_pred EEccCccccccccCccccCCCCCC
Q 032998 71 LKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
|.|+.|+..+-+.+ ..||.||-.
T Consensus 2 Y~CPrC~skvC~LP-~~CpiCgLt 24 (112)
T TIGR00622 2 YFCPQCRAKVCELP-VECPICGLT 24 (112)
T ss_pred ccCCCCCCCccCCC-CcCCcCCCE
Confidence 67999996554444 679999973
No 326
>KOG4718 consensus Non-SMC (structural maintenance of chromosomes) element 1 protein (NSE1) [Chromatin structure and dynamics]
Probab=40.11 E-value=13 Score=30.71 Aligned_cols=29 Identities=28% Similarity=0.626 Sum_probs=19.0
Q ss_pred eeeeeEEEEccCcccc--------ccccCccccCCCCC
Q 032998 64 RQLHRWILKCHACYTI--------TAEIGRIFCPKCGN 93 (129)
Q Consensus 64 ~~~k~W~~rC~~C~k~--------~~~~~~~fCp~CG~ 93 (129)
+.+-.|..||..|+-- |.. .+..||+||.
T Consensus 188 h~LvIqg~rCg~c~i~~h~~c~qty~q-~~~~cphc~d 224 (235)
T KOG4718|consen 188 HCLVIQGIRCGSCNIQYHRGCIQTYLQ-RRDICPHCGD 224 (235)
T ss_pred HHHhheeeccCcccchhhhHHHHHHhc-ccCcCCchhc
Confidence 3455788899999311 111 2688999985
No 327
>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=40.10 E-value=14 Score=27.43 Aligned_cols=13 Identities=31% Similarity=0.606 Sum_probs=10.7
Q ss_pred EEEccCccccccc
Q 032998 70 ILKCHACYTITAE 82 (129)
Q Consensus 70 ~~rC~~C~k~~~~ 82 (129)
-++|++|+++|=.
T Consensus 124 f~~C~~C~kiyW~ 136 (147)
T PF01927_consen 124 FWRCPGCGKIYWE 136 (147)
T ss_pred EEECCCCCCEecc
Confidence 5899999999843
No 328
>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=40.05 E-value=14 Score=30.91 Aligned_cols=14 Identities=43% Similarity=1.251 Sum_probs=5.7
Q ss_pred cccCCCCCCCceeEE
Q 032998 86 IFCPKCGNGGTLRKV 100 (129)
Q Consensus 86 ~fCp~CG~~~tL~rv 100 (129)
.+||.||+. .|.+.
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 679999997 67764
No 329
>PTZ00157 60S ribosomal protein L36a; Provisional
Probab=39.31 E-value=26 Score=24.79 Aligned_cols=19 Identities=37% Similarity=0.744 Sum_probs=15.7
Q ss_pred ccccCCCCCCCceeEEEEEe
Q 032998 85 RIFCPKCGNGGTLRKVAVTV 104 (129)
Q Consensus 85 ~~fCp~CG~~~tL~rv~v~v 104 (129)
+-|||.|+.. |.-+|+-+-
T Consensus 9 ~tyC~~C~kH-t~HkV~qyK 27 (84)
T PTZ00157 9 KTYCKKCGKH-TSHKVSQYK 27 (84)
T ss_pred cccCcCCCCC-ccEEEEEec
Confidence 5799999997 888888753
No 330
>cd00817 ValRS_core catalytic core domain of valyl-tRNA synthetases. Valine amino-acyl tRNA synthetase (ValRS) catalytic core domain. This enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. ValRS has an insertion in the core domain, which is subject to both deletions and rearrangements. This editing region hydrolyzes mischarged cognate tRNAs and thus prevents the incorporation of chemically similar amino acids.
Probab=39.26 E-value=54 Score=27.94 Aligned_cols=30 Identities=23% Similarity=0.387 Sum_probs=24.6
Q ss_pred ceeeeeEEEEccCccccccccCccccCCCCCC
Q 032998 63 IRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 63 I~~~k~W~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
|-+...-++.|+.|.+...+. +.|..||.+
T Consensus 133 iy~~~~~~~yc~~~~t~l~~~--evc~~cg~~ 162 (382)
T cd00817 133 IYRDNRLVNWCPKLRTAISDI--EVCSRSGDV 162 (382)
T ss_pred EEeeeeEEeecCCcCCCCCcc--hhcccCCCe
Confidence 556667789999999887764 669999997
No 331
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=39.24 E-value=14 Score=27.50 Aligned_cols=17 Identities=41% Similarity=0.909 Sum_probs=11.7
Q ss_pred CccccCCCCCCCceeEEEE
Q 032998 84 GRIFCPKCGNGGTLRKVAV 102 (129)
Q Consensus 84 ~~~fCp~CG~~~tL~rv~v 102 (129)
...-||+||.+ +.-+-+
T Consensus 48 G~t~CP~Cg~~--~e~~fv 64 (115)
T COG1885 48 GSTSCPKCGEP--FESAFV 64 (115)
T ss_pred ccccCCCCCCc--cceeEE
Confidence 34569999998 564444
No 332
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=39.06 E-value=43 Score=31.65 Aligned_cols=49 Identities=22% Similarity=0.388 Sum_probs=28.7
Q ss_pred HHHhCcee-----ecCCCCcceeeeeEEEEccCccccccccCccccCCCCCCCceeE
Q 032998 48 ILQMGLRL-----LAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRK 99 (129)
Q Consensus 48 l~~lGL~~-----~s~~g~~I~~~k~W~~rC~~C~k~~~~~~~~fCp~CG~~~tL~r 99 (129)
..+++|.+ +.-.|+.|-++-.-+..=..=......+ -.+||.||++ |.|
T Consensus 363 I~rkdIrIGDtV~V~kAGdVIP~V~~Vv~e~R~~~~~~~~~-P~~CP~C~s~--l~r 416 (667)
T COG0272 363 IKRKDIRIGDTVVVRKAGDVIPQVVGVVLEKRPGNEKPIPF-PTHCPVCGSE--LVR 416 (667)
T ss_pred HHhcCCCCCCEEEEEecCCCCcceeeeecccCCCCCCCCCC-CCCCCCCCCe--eEe
Confidence 33677665 4455888888766554422222222123 3789999998 665
No 333
>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=38.97 E-value=31 Score=22.56 Aligned_cols=19 Identities=32% Similarity=0.672 Sum_probs=14.4
Q ss_pred cCccccCCCCCCCceeEEEE
Q 032998 83 IGRIFCPKCGNGGTLRKVAV 102 (129)
Q Consensus 83 ~~~~fCp~CG~~~tL~rv~v 102 (129)
+....||.||+. ...+|..
T Consensus 5 p~~~~CP~C~~~-~~T~v~~ 23 (73)
T PF10601_consen 5 PVRIYCPYCQQQ-VQTRVEY 23 (73)
T ss_pred ceeeECCCCCCE-EEEEEEE
Confidence 346889999997 6677665
No 334
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=38.87 E-value=14 Score=31.15 Aligned_cols=25 Identities=24% Similarity=0.764 Sum_probs=18.1
Q ss_pred EEEccCccccccccC--------ccccCCCCCC
Q 032998 70 ILKCHACYTITAEIG--------RIFCPKCGNG 94 (129)
Q Consensus 70 ~~rC~~C~k~~~~~~--------~~fCp~CG~~ 94 (129)
+-||+.|.+.|+..+ .--||.||+.
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 468999998876422 3459999985
No 335
>PRK00566 DNA-directed RNA polymerase subunit beta'; Provisional
Probab=38.86 E-value=14 Score=36.79 Aligned_cols=31 Identities=29% Similarity=0.465 Sum_probs=19.4
Q ss_pred EEccCccccccccC-ccccCCCCCCCceeEEEE
Q 032998 71 LKCHACYTITAEIG-RIFCPKCGNGGTLRKVAV 102 (129)
Q Consensus 71 ~rC~~C~k~~~~~~-~~fCp~CG~~~tL~rv~v 102 (129)
+.| +|+|...... ..+|+.||-.-|..+|..
T Consensus 58 ~eC-~Cgkyk~~~~~~~~C~~cgve~~~~~vrr 89 (1156)
T PRK00566 58 YEC-LCGKYKRVRYKGIICERCGVEVTRSKVRR 89 (1156)
T ss_pred cEE-eCccccccCcCCcCCCCCCceeeechhhh
Confidence 467 8887443222 479999998744444443
No 336
>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=38.75 E-value=19 Score=24.79 Aligned_cols=20 Identities=25% Similarity=0.644 Sum_probs=8.9
Q ss_pred ccccCCCCCCCceeEEEEEeCCC
Q 032998 85 RIFCPKCGNGGTLRKVAVTVGEN 107 (129)
Q Consensus 85 ~~fCp~CG~~~tL~rv~v~v~~~ 107 (129)
.-.||.||+. .-|.|.++..
T Consensus 22 ~F~CPfC~~~---~sV~v~idkk 41 (81)
T PF05129_consen 22 VFDCPFCNHE---KSVSVKIDKK 41 (81)
T ss_dssp ----TTT--S---S-EEEEEETT
T ss_pred eEcCCcCCCC---CeEEEEEEcc
Confidence 3459999987 3366666643
No 337
>PRK01343 zinc-binding protein; Provisional
Probab=38.56 E-value=16 Score=23.99 Aligned_cols=9 Identities=44% Similarity=1.161 Sum_probs=5.4
Q ss_pred cccCCCCCC
Q 032998 86 IFCPKCGNG 94 (129)
Q Consensus 86 ~fCp~CG~~ 94 (129)
..||.||.+
T Consensus 10 ~~CP~C~k~ 18 (57)
T PRK01343 10 RPCPECGKP 18 (57)
T ss_pred CcCCCCCCc
Confidence 456666665
No 338
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=38.41 E-value=22 Score=25.59 Aligned_cols=10 Identities=40% Similarity=0.707 Sum_probs=6.0
Q ss_pred ccccCCCCCC
Q 032998 85 RIFCPKCGNG 94 (129)
Q Consensus 85 ~~fCp~CG~~ 94 (129)
...||+||.-
T Consensus 42 h~~C~~CG~y 51 (99)
T PRK14892 42 IITCGNCGLY 51 (99)
T ss_pred eEECCCCCCc
Confidence 4556666654
No 339
>PRK13794 hypothetical protein; Provisional
Probab=38.23 E-value=25 Score=31.27 Aligned_cols=32 Identities=28% Similarity=0.537 Sum_probs=23.4
Q ss_pred eeEEEEccCccccccccCccccCCCCCCCceeEEEEE
Q 032998 67 HRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVT 103 (129)
Q Consensus 67 k~W~~rC~~C~k~~~~~~~~fCp~CG~~~tL~rv~v~ 103 (129)
+.+++.|..|.--- . ..-|..||++ -++|.+|
T Consensus 7 ~~~~~wc~~cn~p~--~-~~~c~~cg~~--~~~~~~~ 38 (479)
T PRK13794 7 KIHLKWCDNCNVPV--L-GKKCAICGSE--TREVKVT 38 (479)
T ss_pred ceEEEEcCCCCCee--c-CCchhHhCCC--eeEEecC
Confidence 46899999999522 2 2459999997 4667764
No 340
>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=37.93 E-value=16 Score=29.49 Aligned_cols=43 Identities=28% Similarity=0.537 Sum_probs=25.2
Q ss_pred HHHHHHHHHhCceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCC
Q 032998 42 YAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 42 yamQNVl~~lGL~~~s~~g~~I~~~k~W~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
|+|+-++......-++- .+.-..|+-|-.. +-....||+||..
T Consensus 142 yGmpKi~~iika~tLsk--------~~hcilCtvCe~r--~w~g~~CPKCGr~ 184 (200)
T PF12387_consen 142 YGMPKIITIIKAATLSK--------SKHCILCTVCEGR--EWKGGNCPKCGRH 184 (200)
T ss_pred cCcchhhhhhhHHhccC--------CCceEEEeeeecC--ccCCCCCCcccCC
Confidence 56666654433332222 2456789999753 2235779999975
No 341
>PRK05767 rpl44e 50S ribosomal protein L44e; Validated
Probab=37.69 E-value=28 Score=24.97 Aligned_cols=19 Identities=32% Similarity=0.653 Sum_probs=15.7
Q ss_pred ccccCCCCCCCceeEEEEEe
Q 032998 85 RIFCPKCGNGGTLRKVAVTV 104 (129)
Q Consensus 85 ~~fCp~CG~~~tL~rv~v~v 104 (129)
+-|||.|+.. |..+|+-+-
T Consensus 8 ~tyCp~CkkH-t~HkV~qyK 26 (92)
T PRK05767 8 RTYCPYCKTH-TEHEVEKVK 26 (92)
T ss_pred cccCcCCCCc-ccEEEEEEe
Confidence 5799999997 898888753
No 342
>TIGR00108 eRF peptide chain release factor eRF/aRF, subunit 1. Alternative names include eRF1, SUP45, omnipotent suppressor protein 1.
Probab=37.31 E-value=28 Score=30.41 Aligned_cols=27 Identities=30% Similarity=0.722 Sum_probs=18.5
Q ss_pred eEEEEccCcccccc-------ccCccccCCCCCC
Q 032998 68 RWILKCHACYTITA-------EIGRIFCPKCGNG 94 (129)
Q Consensus 68 ~W~~rC~~C~k~~~-------~~~~~fCp~CG~~ 94 (129)
++.+||..|+..-. +.....||.||..
T Consensus 322 r~~~r~~~~~~~~~~~~~~~~~~~~~~c~~~~~~ 355 (409)
T TIGR00108 322 RVTYKCAECGEVIEKTVRELKDKKFAICPACGQE 355 (409)
T ss_pred eEEEEcCCCCceeecccccccccccccCcccCcc
Confidence 57899999995310 1112469999987
No 343
>PRK14529 adenylate kinase; Provisional
Probab=37.28 E-value=16 Score=29.31 Aligned_cols=28 Identities=18% Similarity=0.260 Sum_probs=17.9
Q ss_pred EEccCccccccccC-------ccccCCCCCCCceeE
Q 032998 71 LKCHACYTITAEIG-------RIFCPKCGNGGTLRK 99 (129)
Q Consensus 71 ~rC~~C~k~~~~~~-------~~fCp~CG~~~tL~r 99 (129)
..|.+|+..+.... ...|..||.+ ..+|
T Consensus 127 ~~c~~~~~~~~~~~~~~p~~~~~~cd~~~~~-l~~R 161 (223)
T PRK14529 127 RLCKNDNNHPNNIFIDAIKPDGDVCRVCGGE-LSTR 161 (223)
T ss_pred ccccccCCcccccccCCCcccCCcCcCcCCc-cccC
Confidence 45999886553322 1279999997 4443
No 344
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=37.18 E-value=20 Score=18.88 Aligned_cols=22 Identities=32% Similarity=0.683 Sum_probs=15.6
Q ss_pred EccCccccccccCccccCCCCCC
Q 032998 72 KCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 72 rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
.|.+|...-. .....|..||.+
T Consensus 4 ~C~~C~~~N~-~~~~~C~~C~~p 25 (26)
T smart00547 4 ECPACTFLNF-ASRSKCFACGAP 25 (26)
T ss_pred cCCCCCCcCh-hhhccccccCCc
Confidence 5888985433 346789999875
No 345
>PRK10445 endonuclease VIII; Provisional
Probab=37.11 E-value=23 Score=28.95 Aligned_cols=16 Identities=25% Similarity=0.636 Sum_probs=13.1
Q ss_pred ccccCCCCCCCceeEEEE
Q 032998 85 RIFCPKCGNGGTLRKVAV 102 (129)
Q Consensus 85 ~~fCp~CG~~~tL~rv~v 102 (129)
.+-||.||.+ |.++.+
T Consensus 235 g~~Cp~Cg~~--I~~~~~ 250 (263)
T PRK10445 235 GEACERCGGI--IEKTTL 250 (263)
T ss_pred CCCCCCCCCE--eEEEEE
Confidence 4679999997 887776
No 346
>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=37.11 E-value=17 Score=27.76 Aligned_cols=21 Identities=24% Similarity=0.713 Sum_probs=15.9
Q ss_pred ccCccccccccCccccCCCCCC
Q 032998 73 CHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 73 C~~C~k~~~~~~~~fCp~CG~~ 94 (129)
|..|++..... ..+|+.|+.+
T Consensus 1 C~~C~~~~~~~-~~~C~~C~~~ 21 (190)
T TIGR00201 1 CSLCGRPYQSV-HALCRQCGSW 21 (190)
T ss_pred CCccccccccc-cCCchhhCCc
Confidence 89999864332 4789999986
No 347
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=37.09 E-value=24 Score=30.26 Aligned_cols=11 Identities=45% Similarity=1.247 Sum_probs=9.5
Q ss_pred CccccCCCCCC
Q 032998 84 GRIFCPKCGNG 94 (129)
Q Consensus 84 ~~~fCp~CG~~ 94 (129)
.+.+||+||++
T Consensus 184 ~~~~CPvCGS~ 194 (308)
T COG3058 184 SRQYCPVCGSM 194 (308)
T ss_pred ccccCCCcCCC
Confidence 47899999997
No 348
>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=36.85 E-value=17 Score=32.46 Aligned_cols=19 Identities=37% Similarity=0.868 Sum_probs=11.7
Q ss_pred EEEccCccccccccCccccCCCCCC
Q 032998 70 ILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 70 ~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
.+.|..|+.+. -||+|+.+
T Consensus 213 ~~~C~~Cg~~~------~C~~C~~~ 231 (505)
T TIGR00595 213 NLLCRSCGYIL------CCPNCDVS 231 (505)
T ss_pred eeEhhhCcCcc------CCCCCCCc
Confidence 36788888643 26666654
No 349
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.82 E-value=13 Score=28.15 Aligned_cols=27 Identities=19% Similarity=0.298 Sum_probs=18.9
Q ss_pred eEEEEccCcc--ccccc--cCccccCCCCCC
Q 032998 68 RWILKCHACY--TITAE--IGRIFCPKCGNG 94 (129)
Q Consensus 68 ~W~~rC~~C~--k~~~~--~~~~fCp~CG~~ 94 (129)
--.-||+.|+ |.|+- ....-|..||..
T Consensus 19 Gl~grCP~CGeGrLF~gFLK~~p~C~aCG~d 49 (126)
T COG5349 19 GLRGRCPRCGEGRLFRGFLKVVPACEACGLD 49 (126)
T ss_pred HhcCCCCCCCCchhhhhhcccCchhhhcccc
Confidence 3456899998 45532 225779999987
No 350
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated
Probab=36.53 E-value=25 Score=32.55 Aligned_cols=33 Identities=30% Similarity=0.605 Sum_probs=21.6
Q ss_pred EEEEccCccccccc---cCccccCCCCCCCceeEEE
Q 032998 69 WILKCHACYTITAE---IGRIFCPKCGNGGTLRKVA 101 (129)
Q Consensus 69 W~~rC~~C~k~~~~---~~~~fCp~CG~~~tL~rv~ 101 (129)
=.+.|..|+.+... ....+|+.|++.+.+.++.
T Consensus 543 ~~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~i~~v~ 578 (605)
T PRK07225 543 EIYVCAKCGMIAIYDKKRNRKYCPICGEETDIYPVE 578 (605)
T ss_pred eEEeecCcCcceehhcccCceeecccCCCCceeecc
Confidence 34779999987531 1246799998753455554
No 351
>PRK00133 metG methionyl-tRNA synthetase; Reviewed
Probab=36.51 E-value=48 Score=30.48 Aligned_cols=32 Identities=22% Similarity=0.143 Sum_probs=20.2
Q ss_pred ceeeeeEEEEccCccccccccC-ccccCCCCCC
Q 032998 63 IRQLHRWILKCHACYTITAEIG-RIFCPKCGNG 94 (129)
Q Consensus 63 I~~~k~W~~rC~~C~k~~~~~~-~~fCp~CG~~ 94 (129)
|-+...=++.|..|.+...+.. ...||.||..
T Consensus 116 iy~~~~~~~y~~~~~~~l~~~~v~g~cp~C~~~ 148 (673)
T PRK00133 116 IYEKTIEQLYDPEKGMFLPDRFVKGTCPKCGAE 148 (673)
T ss_pred EEEeeeEEEEeCCCCCCccchheecccCCCCCc
Confidence 3333445788999988776544 3457777754
No 352
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=36.39 E-value=24 Score=23.12 Aligned_cols=9 Identities=33% Similarity=0.660 Sum_probs=2.7
Q ss_pred EccCccccc
Q 032998 72 KCHACYTIT 80 (129)
Q Consensus 72 rC~~C~k~~ 80 (129)
.|+.|++..
T Consensus 4 ~CP~C~k~~ 12 (57)
T PF03884_consen 4 KCPICGKPV 12 (57)
T ss_dssp E-TTT--EE
T ss_pred cCCCCCCee
Confidence 444554443
No 353
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=36.24 E-value=37 Score=21.88 Aligned_cols=18 Identities=33% Similarity=0.968 Sum_probs=14.0
Q ss_pred ccccCCCCCCCceeEEEEE
Q 032998 85 RIFCPKCGNGGTLRKVAVT 103 (129)
Q Consensus 85 ~~fCp~CG~~~tL~rv~v~ 103 (129)
..+||.|++. ...+|...
T Consensus 3 ~i~Cp~C~~~-~~T~v~~~ 20 (67)
T smart00714 3 QLFCPRCQNN-VTTRVETE 20 (67)
T ss_pred ceECCCCCCE-EEEEEEEE
Confidence 4689999998 77777754
No 354
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=36.07 E-value=25 Score=28.88 Aligned_cols=16 Identities=31% Similarity=0.603 Sum_probs=12.8
Q ss_pred ccccCCCCCCCceeEEEE
Q 032998 85 RIFCPKCGNGGTLRKVAV 102 (129)
Q Consensus 85 ~~fCp~CG~~~tL~rv~v 102 (129)
..-||.||.+ |+++.+
T Consensus 244 g~pCprCG~~--I~~~~~ 259 (272)
T PRK14810 244 GEPCLNCKTP--IRRVVV 259 (272)
T ss_pred CCcCCCCCCe--eEEEEE
Confidence 4679999987 887665
No 355
>PRK14873 primosome assembly protein PriA; Provisional
Probab=35.90 E-value=22 Score=33.05 Aligned_cols=21 Identities=29% Similarity=0.513 Sum_probs=13.5
Q ss_pred eEEEEccCccccccccCccccCCCCCC
Q 032998 68 RWILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
.-.+.|..|+... -||+|+.+
T Consensus 381 ap~l~C~~Cg~~~------~C~~C~~~ 401 (665)
T PRK14873 381 VPSLACARCRTPA------RCRHCTGP 401 (665)
T ss_pred CCeeEhhhCcCee------ECCCCCCc
Confidence 3457788887633 27777765
No 356
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=35.80 E-value=18 Score=28.30 Aligned_cols=20 Identities=30% Similarity=0.453 Sum_probs=12.2
Q ss_pred CccccccccCccccCCCCCC
Q 032998 75 ACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 75 ~C~k~~~~~~~~fCp~CG~~ 94 (129)
+|-+-+..+.+.||.+||..
T Consensus 108 ~~a~p~~KP~r~fCaVCG~~ 127 (156)
T KOG3362|consen 108 AYAKPSFKPLRKFCAVCGYD 127 (156)
T ss_pred cccCCCCCCcchhhhhcCCC
Confidence 44444444557788888876
No 357
>PRK12495 hypothetical protein; Provisional
Probab=35.69 E-value=18 Score=29.79 Aligned_cols=24 Identities=29% Similarity=0.733 Sum_probs=17.4
Q ss_pred EEccCccccc-cccCccccCCCCCC
Q 032998 71 LKCHACYTIT-AEIGRIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~-~~~~~~fCp~CG~~ 94 (129)
+.|..|+.-- ......|||.|+..
T Consensus 43 ~hC~~CG~PIpa~pG~~~Cp~CQ~~ 67 (226)
T PRK12495 43 AHCDECGDPIFRHDGQEFCPTCQQP 67 (226)
T ss_pred hhcccccCcccCCCCeeECCCCCCc
Confidence 5699998643 33447899999976
No 358
>PRK13795 hypothetical protein; Provisional
Probab=35.68 E-value=34 Score=31.52 Aligned_cols=33 Identities=27% Similarity=0.421 Sum_probs=24.2
Q ss_pred eeeEEEEccCccccccccCccccCCCCCCCceeEEEEE
Q 032998 66 LHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVT 103 (129)
Q Consensus 66 ~k~W~~rC~~C~k~~~~~~~~fCp~CG~~~tL~rv~v~ 103 (129)
-+.|++.|..|.--- . ..-|..||++ + .+|.+|
T Consensus 8 ~~~~~~wc~~cn~p~--~-~~~c~~c~~~-~-~~~~~t 40 (636)
T PRK13795 8 GKDHIYWCEKCNVPL--L-GKKCGICGKE-G-FKVRLT 40 (636)
T ss_pred cceeEEEcccCCCee--c-cccccccCCC-c-eEeecC
Confidence 357999999999522 2 2559999998 5 667664
No 359
>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=35.64 E-value=16 Score=31.10 Aligned_cols=28 Identities=25% Similarity=0.635 Sum_probs=20.3
Q ss_pred EEccCccccccccCccccCCCCCCCceeEE
Q 032998 71 LKCHACYTITAEIGRIFCPKCGNGGTLRKV 100 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG~~~tL~rv 100 (129)
-.|-.|+..-.. ....||.||+. .+.|.
T Consensus 83 ~~C~~CGa~V~~-~e~~Cp~C~St-nI~r~ 110 (314)
T PF09567_consen 83 GKCNNCGANVSR-LEESCPNCGST-NIKRK 110 (314)
T ss_pred hhhccccceeee-hhhcCCCCCcc-ccccc
Confidence 468899965543 35789999997 67654
No 360
>PRK14351 ligA NAD-dependent DNA ligase LigA; Provisional
Probab=35.63 E-value=49 Score=31.09 Aligned_cols=44 Identities=20% Similarity=0.311 Sum_probs=26.4
Q ss_pred HHHHhCcee-----ecCCCCcceeeeeEEEEccCccccccccCccccCCCCCC
Q 032998 47 VILQMGLRL-----LAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 47 Vl~~lGL~~-----~s~~g~~I~~~k~W~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
-+.++||.+ +.-.|..|-++-.-+.+ ..... +. ++ ..||.||++
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 355677765 44558888887664442 22222 21 22 579999998
No 361
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=35.13 E-value=27 Score=19.14 Aligned_cols=22 Identities=32% Similarity=0.759 Sum_probs=14.1
Q ss_pred EccCccccccccCccccCCCCCC
Q 032998 72 KCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 72 rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
.|..|...-. .....|-.||.+
T Consensus 6 ~C~~C~~~N~-~~~~~C~~C~~~ 27 (30)
T PF00641_consen 6 KCPSCTFMNP-ASRSKCVACGAP 27 (30)
T ss_dssp EETTTTEEEE-SSSSB-TTT--B
T ss_pred cCCCCcCCch-HHhhhhhCcCCC
Confidence 5899996544 356889999976
No 362
>PRK00076 recR recombination protein RecR; Reviewed
Probab=35.03 E-value=20 Score=28.77 Aligned_cols=29 Identities=21% Similarity=0.505 Sum_probs=23.7
Q ss_pred ceeeeeEEEEccCccccccccCccccCCCCCC
Q 032998 63 IRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 63 I~~~k~W~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
|...+.-+..|.-|+.++.. .-|+.|-++
T Consensus 46 i~~~~~~i~~C~~C~~lse~---~~C~IC~d~ 74 (196)
T PRK00076 46 LEEAKEKIKHCSVCGNLTEQ---DPCEICSDP 74 (196)
T ss_pred HHHHHHcCCcCCCCCCcCCC---CcCCCCCCC
Confidence 55666778899999998765 679999987
No 363
>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=34.94 E-value=35 Score=26.17 Aligned_cols=23 Identities=22% Similarity=0.560 Sum_probs=12.6
Q ss_pred ccCCCCCCCceeEEE-EEeCCCceE
Q 032998 87 FCPKCGNGGTLRKVA-VTVGENGIV 110 (129)
Q Consensus 87 fCp~CG~~~tL~rv~-v~v~~~G~~ 110 (129)
.||+||.+ ...|+. +.+=--|.+
T Consensus 3 ~Cp~C~~~-~~~~~~~~~IP~F~ev 26 (161)
T PF03367_consen 3 LCPNCGEN-GTTRILLTDIPYFKEV 26 (161)
T ss_dssp E-TTTSSC-CEEEEEEEEETTTEEE
T ss_pred cCCCCCCC-cEEEEEEEcCCCCceE
Confidence 49999998 444443 333334655
No 364
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=34.89 E-value=23 Score=17.73 Aligned_cols=12 Identities=25% Similarity=0.492 Sum_probs=8.3
Q ss_pred EEccCccccccc
Q 032998 71 LKCHACYTITAE 82 (129)
Q Consensus 71 ~rC~~C~k~~~~ 82 (129)
+.|.-|++.|..
T Consensus 1 y~C~~C~~~f~~ 12 (23)
T PF00096_consen 1 YKCPICGKSFSS 12 (23)
T ss_dssp EEETTTTEEESS
T ss_pred CCCCCCCCccCC
Confidence 467778777654
No 365
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=34.28 E-value=24 Score=23.12 Aligned_cols=20 Identities=10% Similarity=-0.091 Sum_probs=13.2
Q ss_pred EEccCccccccccCccccCCCCC
Q 032998 71 LKCHACYTITAEIGRIFCPKCGN 93 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG~ 93 (129)
-.|..|+.... +.-.|| ||.
T Consensus 28 ~~c~~cg~~~~--pH~vc~-cG~ 47 (60)
T PRK01110 28 SVDKTTGEYHL--PHHVSP-KGY 47 (60)
T ss_pred eEcCCCCceec--cceecC-Ccc
Confidence 56888886443 346688 884
No 366
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=34.16 E-value=26 Score=22.14 Aligned_cols=27 Identities=30% Similarity=0.717 Sum_probs=16.5
Q ss_pred eeEEEEcc--Cccc---cccccCccccCCCCC
Q 032998 67 HRWILKCH--ACYT---ITAEIGRIFCPKCGN 93 (129)
Q Consensus 67 k~W~~rC~--~C~k---~~~~~~~~fCp~CG~ 93 (129)
.+-...|+ .|+. +.....+..|.+||.
T Consensus 15 ~r~rk~CP~~~CG~GvFMA~H~dR~~CGKCg~ 46 (47)
T PF01599_consen 15 KRLRKECPSPRCGAGVFMAEHKDRHYCGKCGY 46 (47)
T ss_dssp EESSEE-TSTTTTSSSEEEE-SSEEEETTTSS
T ss_pred EEhhhcCCCcccCCceEeeecCCCccCCCccc
Confidence 33446788 7775 334455888999985
No 367
>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=34.13 E-value=21 Score=33.34 Aligned_cols=32 Identities=28% Similarity=0.598 Sum_probs=18.2
Q ss_pred eeEEEEccCccccccc-cCccccCCCCCCCceeEEE
Q 032998 67 HRWILKCHACYTITAE-IGRIFCPKCGNGGTLRKVA 101 (129)
Q Consensus 67 k~W~~rC~~C~k~~~~-~~~~fCp~CG~~~tL~rv~ 101 (129)
+.|. | +|+|.-.. ....||+.||-.-|..||.
T Consensus 60 k~~e--C-~CGkyk~~~~~~~~C~~CgvE~t~s~vR 92 (619)
T TIGR02387 60 KDWE--C-HCGKYKRVRHRGIVCERCGVEVTESRVR 92 (619)
T ss_pred cCcE--E-eCCCccccCcCCcCCCCCCCEEchhhhH
Confidence 4454 5 67753321 1247999999763444443
No 368
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=34.11 E-value=17 Score=28.69 Aligned_cols=25 Identities=28% Similarity=0.607 Sum_probs=16.3
Q ss_pred EEEccCccccc-cc---cCccccCCCCCC
Q 032998 70 ILKCHACYTIT-AE---IGRIFCPKCGNG 94 (129)
Q Consensus 70 ~~rC~~C~k~~-~~---~~~~fCp~CG~~ 94 (129)
-|.|+-|.-.+ .+ ...-.||.||+.
T Consensus 113 ~y~C~~~~~r~sfdeA~~~~F~Cp~Cg~~ 141 (176)
T COG1675 113 YYVCPNCHVKYSFDEAMELGFTCPKCGED 141 (176)
T ss_pred ceeCCCCCCcccHHHHHHhCCCCCCCCch
Confidence 48897777333 22 113569999997
No 369
>PRK12268 methionyl-tRNA synthetase; Reviewed
Probab=33.78 E-value=57 Score=28.88 Aligned_cols=30 Identities=20% Similarity=0.208 Sum_probs=21.7
Q ss_pred ceeeeeEEEEccCccccccccC-ccccCCCC
Q 032998 63 IRQLHRWILKCHACYTITAEIG-RIFCPKCG 92 (129)
Q Consensus 63 I~~~k~W~~rC~~C~k~~~~~~-~~fCp~CG 92 (129)
|-+...-++.|+.|.+...+.. ...||.||
T Consensus 118 ~y~~~~~~~~~~~~~~~l~~~~v~g~cp~c~ 148 (556)
T PRK12268 118 IYKKTIEQAYCPSDGRFLPDRYVEGTCPYCG 148 (556)
T ss_pred eEEeeeEEEecCCCCcCcCccceeccCCCCC
Confidence 4455677899999998776544 35588887
No 370
>KOG0806 consensus Carbon-nitrogen hydrolase [Amino acid transport and metabolism]
Probab=33.75 E-value=85 Score=26.84 Aligned_cols=75 Identities=15% Similarity=0.198 Sum_probs=46.2
Q ss_pred HHHHHHHHHhCceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCCCceeEEEEEeCCCceEEeecCCccccC
Q 032998 42 YAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGENGIVLASRRPRITLR 121 (129)
Q Consensus 42 yamQNVl~~lGL~~~s~~g~~I~~~k~W~~rC~~C~k~~~~~~~~fCp~CG~~~tL~rv~v~v~~~G~~~~~~~~~~n~R 121 (129)
+.||||++++.+.++ .|. |.+. - .|.+.|.....--||.=|-. ..|..+-.|.||.....-++..-++
T Consensus 84 ~~ls~va~~~~~~~i--~g~-i~~~-----~--~~~k~yns~~~~~~~g~l~~--~yrk~hlFD~d~~~~~ry~e~~~~~ 151 (298)
T KOG0806|consen 84 QGLSEVAERLSCYII--GGS-IEEE-----A--LGDKLYNSCADSSCPGDGLA--KYRKNHLFDTDGPGVIRYRESHLLS 151 (298)
T ss_pred HHhHHHHhhceEEEe--cCc-chhh-----c--ccccccCcccccCCCcchhh--eeeeeEEeccCCccceeeeeeeccC
Confidence 569999999988875 332 3321 1 35555554444557776765 4555666788887765544433333
Q ss_pred -ceeecCC
Q 032998 122 -GTKVSIS 128 (129)
Q Consensus 122 -G~~ySlP 128 (129)
|..|.+|
T Consensus 152 ~g~~f~~~ 159 (298)
T KOG0806|consen 152 PGDQFTVV 159 (298)
T ss_pred CCcCCCcc
Confidence 7777765
No 371
>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=33.72 E-value=22 Score=22.61 Aligned_cols=10 Identities=20% Similarity=0.461 Sum_probs=2.9
Q ss_pred EEEEccCccc
Q 032998 69 WILKCHACYT 78 (129)
Q Consensus 69 W~~rC~~C~k 78 (129)
.+.-|..||+
T Consensus 24 rrhhCr~CG~ 33 (69)
T PF01363_consen 24 RRHHCRNCGR 33 (69)
T ss_dssp -EEE-TTT--
T ss_pred eeEccCCCCC
Confidence 3444555553
No 372
>CHL00018 rpoC1 RNA polymerase beta' subunit
Probab=33.69 E-value=20 Score=33.67 Aligned_cols=30 Identities=30% Similarity=0.466 Sum_probs=17.6
Q ss_pred EccCccccccc----cCccccCCCCCCCceeEEEE
Q 032998 72 KCHACYTITAE----IGRIFCPKCGNGGTLRKVAV 102 (129)
Q Consensus 72 rC~~C~k~~~~----~~~~fCp~CG~~~tL~rv~v 102 (129)
.| +|++.-.. ....||+.||-.-|..||..
T Consensus 68 ~C-~CGkyk~~~~~~~~~~~C~~CgVE~t~s~vRR 101 (663)
T CHL00018 68 IC-ACGNYRVIGDEKEDPKFCEQCGVEFTDSRVRR 101 (663)
T ss_pred EE-eCCCccccCccccCCCccCCcCCEechhhhhH
Confidence 45 67753321 12469999997744455443
No 373
>PRK14894 glycyl-tRNA synthetase; Provisional
Probab=33.50 E-value=27 Score=32.14 Aligned_cols=34 Identities=21% Similarity=0.472 Sum_probs=22.9
Q ss_pred eeeeeEEEEccCcccccccc-CccccCCCCCCCcee
Q 032998 64 RQLHRWILKCHACYTITAEI-GRIFCPKCGNGGTLR 98 (129)
Q Consensus 64 ~~~k~W~~rC~~C~k~~~~~-~~~fCp~CG~~~tL~ 98 (129)
...--|...|..|++.+.-- -...||.||+. .|.
T Consensus 82 ~~F~DpmV~CkkCk~ryRaD~LiikCP~CGs~-dLT 116 (539)
T PRK14894 82 ETFNDPLVDCRDCKMRWRADHIQGVCPNCGSR-DLT 116 (539)
T ss_pred CCCCCceeECCCCCccccCccceeeCCCCCCc-CCC
Confidence 34455678999999887521 12469999974 454
No 374
>PRK02625 rpoC1 DNA-directed RNA polymerase subunit gamma; Provisional
Probab=33.43 E-value=22 Score=33.25 Aligned_cols=23 Identities=26% Similarity=0.644 Sum_probs=14.1
Q ss_pred EEccCccccccc-cCccccCCCCCC
Q 032998 71 LKCHACYTITAE-IGRIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~~~-~~~~fCp~CG~~ 94 (129)
+.| +|+|.-.. ....||+.||-+
T Consensus 69 ~eC-~CGkyk~~~~~~~~C~~CgvE 92 (627)
T PRK02625 69 WEC-HCGKYKRVRHRGIVCERCGVE 92 (627)
T ss_pred cEE-eCCCccccCcCCcCCCCCCcE
Confidence 345 67753322 124799999976
No 375
>PF11682 DUF3279: Protein of unknown function (DUF3279); InterPro: IPR021696 This family of proteins with unknown function appears to be restricted to Enterobacteriaceae.
Probab=32.91 E-value=26 Score=26.41 Aligned_cols=22 Identities=36% Similarity=0.937 Sum_probs=18.6
Q ss_pred EEccCccccccccCccccCCCCCC
Q 032998 71 LKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
..|.-|+.-|.. ..+||.||.-
T Consensus 98 W~Cv~C~~~Y~G--eK~C~~C~tG 119 (128)
T PF11682_consen 98 WHCVMCGNHYHG--EKYCPKCGTG 119 (128)
T ss_pred EEEecCCCccCc--CEecCCCCCc
Confidence 479999998865 5899999986
No 376
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=32.62 E-value=20 Score=23.57 Aligned_cols=10 Identities=40% Similarity=1.102 Sum_probs=8.2
Q ss_pred ccccCCCCCC
Q 032998 85 RIFCPKCGNG 94 (129)
Q Consensus 85 ~~fCp~CG~~ 94 (129)
..-||.||.+
T Consensus 3 HkHC~~CG~~ 12 (59)
T PF09889_consen 3 HKHCPVCGKP 12 (59)
T ss_pred CCcCCcCCCc
Confidence 3569999987
No 377
>PF04296 DUF448: Protein of unknown function (DUF448); InterPro: IPR007393 This entry represents a group of uncharacterised proteins. Some member sequences retain zinc-binding residues. The structure of the hypothetical cytosolic protein SP0554 from Streptococcus pneumoniae revealed an alpha+beta fold that could have evolved from a glucocorticoid receptor-like zinc finger domain [].; PDB: 1G2R_A.
Probab=32.33 E-value=55 Score=21.98 Aligned_cols=37 Identities=16% Similarity=0.343 Sum_probs=17.6
Q ss_pred EccCccccccccCccccCCCCCCCceeEEEEEeCCCceEEeecCCccccCc
Q 032998 72 KCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGENGIVLASRRPRITLRG 122 (129)
Q Consensus 72 rC~~C~k~~~~~~~~fCp~CG~~~tL~rv~v~v~~~G~~~~~~~~~~n~RG 122 (129)
.|-+|.+.++. ..|.|+.+ .++|.+.+....+..-||
T Consensus 3 ~Cv~cr~~~~k------------~~LlR~v~--~~~~~i~~D~~~k~~GRG 39 (78)
T PF04296_consen 3 TCVVCRKRFPK------------KELLRFVR--TPDGEIVPDPSGKLPGRG 39 (78)
T ss_dssp B-TTT--B--G------------GGEEEEEE---TTS-EEEETTS---SEE
T ss_pred eecccCCCcCh------------HHcEEEEE--eCCCEEEECCCCCCCCCe
Confidence 58899987764 24666554 678887777554445555
No 378
>PLN02189 cellulose synthase
Probab=32.16 E-value=18 Score=35.67 Aligned_cols=27 Identities=26% Similarity=0.806 Sum_probs=20.7
Q ss_pred EccCccccccccCccccCCCCCCCceeEE
Q 032998 72 KCHACYTITAEIGRIFCPKCGNGGTLRKV 100 (129)
Q Consensus 72 rC~~C~k~~~~~~~~fCp~CG~~~tL~rv 100 (129)
.|..|+........+-||.|+.+ -+|+
T Consensus 63 vCr~Cyeyer~eg~q~CpqCkt~--Y~r~ 89 (1040)
T PLN02189 63 VCRPCYEYERREGTQNCPQCKTR--YKRL 89 (1040)
T ss_pred cccchhhhhhhcCCccCcccCCc--hhhc
Confidence 67888877666668999999987 5544
No 379
>PRK10996 thioredoxin 2; Provisional
Probab=31.99 E-value=35 Score=24.69 Aligned_cols=24 Identities=25% Similarity=0.634 Sum_probs=17.9
Q ss_pred EEccCccccccccC-----ccccCCCCCC
Q 032998 71 LKCHACYTITAEIG-----RIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~~~~~-----~~fCp~CG~~ 94 (129)
-.|++|+-++.-+. .--||.||..
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 31 (139)
T PRK10996 3 TVCTSCQAINRLPDERIEDAAKCGRCGHD 31 (139)
T ss_pred EECCCCCCcCCCCCccccCCCcCCCCCCc
Confidence 47999998876432 3569999986
No 380
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=31.97 E-value=22 Score=31.70 Aligned_cols=32 Identities=31% Similarity=0.634 Sum_probs=21.5
Q ss_pred ceeeeeEEE---EccCccccccccCc--cccCCCCCC
Q 032998 63 IRQLHRWIL---KCHACYTITAEIGR--IFCPKCGNG 94 (129)
Q Consensus 63 I~~~k~W~~---rC~~C~k~~~~~~~--~fCp~CG~~ 94 (129)
|.++-.|.. +|+-|+.......+ --||+||..
T Consensus 340 v~~l~~~~~~~p~Cp~Cg~~m~S~G~~g~rC~kCg~~ 376 (421)
T COG1571 340 VLKLARYERVNPVCPRCGGRMKSAGRNGFRCKKCGTR 376 (421)
T ss_pred EEEeeeeEEcCCCCCccCCchhhcCCCCccccccccc
Confidence 444444553 89999987654332 469999975
No 381
>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=31.63 E-value=61 Score=20.08 Aligned_cols=9 Identities=44% Similarity=1.069 Sum_probs=7.5
Q ss_pred cccCCCCCC
Q 032998 86 IFCPKCGNG 94 (129)
Q Consensus 86 ~fCp~CG~~ 94 (129)
.-||.||++
T Consensus 2 kPCPfCGg~ 10 (53)
T TIGR03655 2 KPCPFCGGA 10 (53)
T ss_pred CCCCCCCCc
Confidence 349999997
No 382
>PRK14526 adenylate kinase; Provisional
Probab=31.52 E-value=25 Score=27.68 Aligned_cols=25 Identities=20% Similarity=0.430 Sum_probs=18.1
Q ss_pred EEEccCccccccc-----cCccccCCCCCC
Q 032998 70 ILKCHACYTITAE-----IGRIFCPKCGNG 94 (129)
Q Consensus 70 ~~rC~~C~k~~~~-----~~~~fCp~CG~~ 94 (129)
+..|+.|+++|.. ....-|+.||.+
T Consensus 122 R~~~~~~g~~y~~~~~pp~~~~~~~~~~~~ 151 (211)
T PRK14526 122 RRICKSCNNIFNIYTLPTKEKGICDVCKGD 151 (211)
T ss_pred CCcccccCCccccccCCCCccCcCCCCCCe
Confidence 4569999998842 123569999987
No 383
>PF08458 PH_2: Plant pleckstrin homology-like region; InterPro: IPR013666 This domain describes a pleckstrin homology (PH)-like region found in several plant proteins of unknown function.
Probab=31.50 E-value=70 Score=23.60 Aligned_cols=29 Identities=17% Similarity=0.271 Sum_probs=21.9
Q ss_pred ccCCCCCCCceeEEEEEeCCCceEEeecCC
Q 032998 87 FCPKCGNGGTLRKVAVTVGENGIVLASRRP 116 (129)
Q Consensus 87 fCp~CG~~~tL~rv~v~v~~~G~~~~~~~~ 116 (129)
-|-.||.- -++.|+|+++..|++.+-.|+
T Consensus 5 k~tr~G~l-~~k~Vsvyink~~qVilKmKs 33 (110)
T PF08458_consen 5 KRTRKGDL-HWKTVSVYINKKGQVILKMKS 33 (110)
T ss_pred EecCCCce-EEEEEEEEECCCcEEEEEeec
Confidence 35667776 689999999999988665443
No 384
>TIGR00339 sopT ATP sulphurylase. Members of this family also include the dissimilatory sulfate adenylyltransferase (sat) of the sulfate reducer Archaeoglobus fulgidus.
Probab=31.49 E-value=59 Score=28.34 Aligned_cols=45 Identities=11% Similarity=0.178 Sum_probs=32.5
Q ss_pred EeechHHHHHHHH----HhCceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCC
Q 032998 37 CITGDYAMQNVIL----QMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGN 93 (129)
Q Consensus 37 ~~TdDyamQNVl~----~lGL~~~s~~g~~I~~~k~W~~rC~~C~k~~~~~~~~fCp~CG~ 93 (129)
-+=+.|..|.++. .|||+.+.+ .+..+|..|+++.+. ..||+-..
T Consensus 300 ~~Y~~~~aq~i~~~~~~~l~I~~v~~---------~~~~Yc~~c~~~~~~---~~cph~~~ 348 (383)
T TIGR00339 300 DFYGPYDAQELFEKYKAELGIKIVPF---------EHVAYCPDEDEYAPA---DQAGHTNL 348 (383)
T ss_pred cCCCcchHHHHHHhCccccCceEEec---------ceeEEEcccCcEeec---ccCCCCcc
Confidence 6778899999994 455665544 577899999987654 57888433
No 385
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=31.44 E-value=13 Score=22.01 Aligned_cols=22 Identities=27% Similarity=0.658 Sum_probs=11.7
Q ss_pred ccCccccccccC-------ccccCCCCCC
Q 032998 73 CHACYTITAEIG-------RIFCPKCGNG 94 (129)
Q Consensus 73 C~~C~k~~~~~~-------~~fCp~CG~~ 94 (129)
|..|.+.+.++. ..-|+.||=+
T Consensus 2 C~~C~~Ey~~p~~RR~~~~~isC~~CGPr 30 (35)
T PF07503_consen 2 CDDCLKEYFDPSNRRFHYQFISCTNCGPR 30 (35)
T ss_dssp -HHHHHHHCSTTSTTTT-TT--BTTCC-S
T ss_pred CHHHHHHHcCCCCCcccCcCccCCCCCCC
Confidence 666776664322 2459999976
No 386
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=31.42 E-value=18 Score=35.76 Aligned_cols=26 Identities=27% Similarity=0.866 Sum_probs=20.6
Q ss_pred EccCccccccccCccccCCCCCCCceeE
Q 032998 72 KCHACYTITAEIGRIFCPKCGNGGTLRK 99 (129)
Q Consensus 72 rC~~C~k~~~~~~~~fCp~CG~~~tL~r 99 (129)
.|+.|+........+-||.|+.+ -+|
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 68888977666668999999987 454
No 387
>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=31.13 E-value=37 Score=31.43 Aligned_cols=32 Identities=34% Similarity=0.813 Sum_probs=20.9
Q ss_pred EEEEccCccccccc---cCccccCCCCCCCceeEE
Q 032998 69 WILKCHACYTITAE---IGRIFCPKCGNGGTLRKV 100 (129)
Q Consensus 69 W~~rC~~C~k~~~~---~~~~fCp~CG~~~tL~rv 100 (129)
=.+.|..|+.+... ....+|+.|++.+.+.++
T Consensus 537 ~~~vC~~CG~~~~~~~~~~~~~C~~c~~~~~i~~v 571 (599)
T TIGR03670 537 VVYVCENCGHIAWEDKRKGTAYCPVCGETGDISPV 571 (599)
T ss_pred eEEeecccCceeehhcccCceeccccCCCCceeee
Confidence 34679999987531 124579999986335444
No 388
>PRK08764 ferredoxin; Provisional
Probab=30.97 E-value=42 Score=24.57 Aligned_cols=40 Identities=15% Similarity=0.165 Sum_probs=24.3
Q ss_pred echHHHHHHHHHhCceeecCCCCcc----eeee-eEEEEccCccc
Q 032998 39 TGDYAMQNVILQMGLRLLAPGGMQI----RQLH-RWILKCHACYT 78 (129)
Q Consensus 39 TdDyamQNVl~~lGL~~~s~~g~~I----~~~k-~W~~rC~~C~k 78 (129)
..+-.+|+++..||+...+++...- .++. ....+|.+|++
T Consensus 48 ~G~c~lq~~a~~~gv~~~~~~~~~~~~~~~~~~~~~~~~Ci~C~~ 92 (135)
T PRK08764 48 GGDAGARALAQVLGVPARPYDRSRGTHKLPQVAWIVEADCIGCTK 92 (135)
T ss_pred CCHHHHHHHHHHhCCCccccccccCCCCCCeeEEECcccCcCcch
Confidence 3456799999999998765442211 1111 12357888875
No 389
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=30.95 E-value=33 Score=28.07 Aligned_cols=16 Identities=31% Similarity=0.735 Sum_probs=12.9
Q ss_pred ccccCCCCCCCceeEEEE
Q 032998 85 RIFCPKCGNGGTLRKVAV 102 (129)
Q Consensus 85 ~~fCp~CG~~~tL~rv~v 102 (129)
.+-||.||.+ ++|..+
T Consensus 245 g~pC~~Cg~~--I~~~~~ 260 (272)
T TIGR00577 245 GEPCRRCGTP--IEKIKV 260 (272)
T ss_pred CCCCCCCCCe--eEEEEE
Confidence 4679999997 888765
No 390
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=30.67 E-value=20 Score=21.59 Aligned_cols=29 Identities=21% Similarity=0.509 Sum_probs=19.7
Q ss_pred EEEEccCccccccccCccccCCCCCCCceeEE
Q 032998 69 WILKCHACYTITAEIGRIFCPKCGNGGTLRKV 100 (129)
Q Consensus 69 W~~rC~~C~k~~~~~~~~fCp~CG~~~tL~rv 100 (129)
....|..|...... ....||.|-.+ +.+|
T Consensus 22 H~~~C~~C~~~~~~-~~~~CP~Cr~~--i~~V 50 (50)
T PF13920_consen 22 HLCFCEECAERLLK-RKKKCPICRQP--IESV 50 (50)
T ss_dssp EEEEEHHHHHHHHH-TTSBBTTTTBB---SEE
T ss_pred ChHHHHHHhHHhcc-cCCCCCcCChh--hcCC
Confidence 34578888865543 45789999987 6554
No 391
>PRK00418 DNA gyrase inhibitor; Reviewed
Probab=30.63 E-value=25 Score=23.46 Aligned_cols=9 Identities=22% Similarity=0.689 Sum_probs=5.0
Q ss_pred EEccCcccc
Q 032998 71 LKCHACYTI 79 (129)
Q Consensus 71 ~rC~~C~k~ 79 (129)
.+|+.|++.
T Consensus 7 v~CP~C~k~ 15 (62)
T PRK00418 7 VNCPTCGKP 15 (62)
T ss_pred ccCCCCCCc
Confidence 456666654
No 392
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=30.45 E-value=24 Score=21.11 Aligned_cols=9 Identities=44% Similarity=1.128 Sum_probs=7.6
Q ss_pred cccCCCCCC
Q 032998 86 IFCPKCGNG 94 (129)
Q Consensus 86 ~fCp~CG~~ 94 (129)
.-||.||..
T Consensus 4 ~pCP~CGG~ 12 (37)
T smart00778 4 GPCPNCGGS 12 (37)
T ss_pred cCCCCCCCc
Confidence 459999997
No 393
>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=30.43 E-value=4.3 Score=31.78 Aligned_cols=32 Identities=25% Similarity=0.402 Sum_probs=18.7
Q ss_pred CCCcceeeeeEE-----EEccCccccccccCccccCCCCCC
Q 032998 59 GGMQIRQLHRWI-----LKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 59 ~g~~I~~~k~W~-----~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
.|+.|..-..|- ..|.-||+.+= .-||.|+.+
T Consensus 12 NGH~~t~~~~~~p~~~~~fC~kCG~~tI----~~Cp~C~~~ 48 (158)
T PF10083_consen 12 NGHVITDSYDKNPELREKFCSKCGAKTI----TSCPNCSTP 48 (158)
T ss_pred CccccccccccCchHHHHHHHHhhHHHH----HHCcCCCCC
Confidence 455554433332 45777886442 458888887
No 394
>PHA02325 hypothetical protein
Probab=30.09 E-value=24 Score=24.12 Aligned_cols=14 Identities=43% Similarity=0.907 Sum_probs=10.4
Q ss_pred CccccCCCCCCCcee
Q 032998 84 GRIFCPKCGNGGTLR 98 (129)
Q Consensus 84 ~~~fCp~CG~~~tL~ 98 (129)
....||+||.. =|.
T Consensus 2 ~~k~CPkC~A~-Wld 15 (72)
T PHA02325 2 DTKICPKCGAR-WLD 15 (72)
T ss_pred CccccCccCCE-eEc
Confidence 35789999986 554
No 395
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=29.98 E-value=25 Score=19.36 Aligned_cols=21 Identities=24% Similarity=0.467 Sum_probs=5.4
Q ss_pred EccCccccccccCccccCCCC
Q 032998 72 KCHACYTITAEIGRIFCPKCG 92 (129)
Q Consensus 72 rC~~C~k~~~~~~~~fCp~CG 92 (129)
+|.+|++.........|+.|.
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cd 22 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECD 22 (30)
T ss_dssp --TTTS----S--EEE-TTT-
T ss_pred cCCcCCCcCCCCceEECccCC
Confidence 455555544331234455553
No 396
>KOG0402 consensus 60S ribosomal protein L37 [Translation, ribosomal structure and biogenesis]
Probab=29.81 E-value=16 Score=26.10 Aligned_cols=17 Identities=35% Similarity=0.784 Sum_probs=11.0
Q ss_pred ccccCCCCCCCceeEEEE
Q 032998 85 RIFCPKCGNGGTLRKVAV 102 (129)
Q Consensus 85 ~~fCp~CG~~~tL~rv~v 102 (129)
+.+|+-||.. +++|-++
T Consensus 36 ky~CsfCGK~-~vKR~Av 52 (92)
T KOG0402|consen 36 KYTCSFCGKK-TVKRKAV 52 (92)
T ss_pred hhhhhhcchh-hhhhhce
Confidence 4567777766 6666555
No 397
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=29.77 E-value=24 Score=21.50 Aligned_cols=23 Identities=30% Similarity=0.755 Sum_probs=9.4
Q ss_pred EccC--ccccccccC---c--cccCCCCCC
Q 032998 72 KCHA--CYTITAEIG---R--IFCPKCGNG 94 (129)
Q Consensus 72 rC~~--C~k~~~~~~---~--~fCp~CG~~ 94 (129)
.|+. |..+..... . ..|+.||..
T Consensus 20 ~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~ 49 (64)
T PF01485_consen 20 WCPNPDCEYIIEKDDGCNSPIVTCPSCGTE 49 (64)
T ss_dssp --TTSST---ECS-SSTTS--CCTTSCCSE
T ss_pred CCCCCCCcccEEecCCCCCCeeECCCCCCc
Confidence 7766 776653221 1 467777753
No 398
>KOG2264 consensus Exostosin EXT1L [Signal transduction mechanisms]
Probab=29.75 E-value=63 Score=30.76 Aligned_cols=34 Identities=24% Similarity=0.514 Sum_probs=21.9
Q ss_pred chHHHHHHHHHhCceeecCCCCcceeeeeEEEEccCcccc
Q 032998 40 GDYAMQNVILQMGLRLLAPGGMQIRQLHRWILKCHACYTI 79 (129)
Q Consensus 40 dDyamQNVl~~lGL~~~s~~g~~I~~~k~W~~rC~~C~k~ 79 (129)
.|-||-=...|+- .-.-|+-..+|.+||+||-.-
T Consensus 820 EDIAMNfLVSHiT------RKPPiKvTSRWTfrCPgCp~s 853 (907)
T KOG2264|consen 820 EDIAMNFLVSHIT------RKPPIKVTSRWTFRCPGCPES 853 (907)
T ss_pred HHHHHHHHHHHhc------cCCCceeeceeEEeCCCCchh
Confidence 4556655555531 123367777999999999743
No 399
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=29.71 E-value=36 Score=27.81 Aligned_cols=16 Identities=25% Similarity=0.634 Sum_probs=12.7
Q ss_pred ccccCCCCCCCceeEEEE
Q 032998 85 RIFCPKCGNGGTLRKVAV 102 (129)
Q Consensus 85 ~~fCp~CG~~~tL~rv~v 102 (129)
..-||.||.+ |.|+.+
T Consensus 245 g~pC~~Cg~~--I~~~~~ 260 (274)
T PRK01103 245 GEPCRRCGTP--IEKIKQ 260 (274)
T ss_pred CCCCCCCCCe--eEEEEE
Confidence 4679999986 887665
No 400
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 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. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=29.68 E-value=33 Score=22.78 Aligned_cols=24 Identities=33% Similarity=0.679 Sum_probs=15.2
Q ss_pred EEEccCcccccccc-----CccccCCCCC
Q 032998 70 ILKCHACYTITAEI-----GRIFCPKCGN 93 (129)
Q Consensus 70 ~~rC~~C~k~~~~~-----~~~fCp~CG~ 93 (129)
...|..|.+..... ...+||.|+.
T Consensus 41 ~v~Cg~C~~~~~~~~~~c~~~~~C~~C~~ 69 (71)
T PF05495_consen 41 RVICGKCRTEQPIDEYSCGADYFCPICGL 69 (71)
T ss_dssp EEEETTT--EEES-SBTT--SEEETTTTE
T ss_pred CeECCCCCCccChhhhhcCCCccCcCcCC
Confidence 67899998765432 1468999985
No 401
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=29.51 E-value=36 Score=27.93 Aligned_cols=22 Identities=27% Similarity=0.712 Sum_probs=15.2
Q ss_pred ccccccCccccCCCCCCCceeEEEE
Q 032998 78 TITAEIGRIFCPKCGNGGTLRKVAV 102 (129)
Q Consensus 78 k~~~~~~~~fCp~CG~~~tL~rv~v 102 (129)
++|.. ..+-||.||.+ +.|+.+
T Consensus 229 ~Vy~R-~g~pC~~Cg~~--I~~~~~ 250 (269)
T PRK14811 229 AVYGR-EGQPCPRCGTP--IEKIVV 250 (269)
T ss_pred EecCC-CcCCCCcCCCe--eEEEEE
Confidence 34532 24679999986 888766
No 402
>PRK04149 sat sulfate adenylyltransferase; Reviewed
Probab=29.42 E-value=65 Score=28.28 Aligned_cols=48 Identities=23% Similarity=0.427 Sum_probs=34.1
Q ss_pred CceeeEeechHHHHHHHHHh-----CceeecCCCCcceeeeeEEEEccCccccccccCccccCCC
Q 032998 32 ESTVACITGDYAMQNVILQM-----GLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKC 91 (129)
Q Consensus 32 ~~~va~~TdDyamQNVl~~l-----GL~~~s~~g~~I~~~k~W~~rC~~C~k~~~~~~~~fCp~C 91 (129)
+..+.-+=+.|..|.++... ||+++. ..+..+|..|+++.+. .+||+-
T Consensus 290 HAG~g~~Y~~~~aq~i~~~~~~~~l~I~~v~---------~~~~~Yc~~c~~~~~~---~~cphg 342 (391)
T PRK04149 290 HAGVGDYYGPYDAQEIFDEFTEEELGITPLK---------FEEAFYCPKCGGMASE---KTCPHG 342 (391)
T ss_pred CCCccccCCCchHHHHHHhCCcccCCceEEe---------cceeEEecCCCeEEEc---ccCCCC
Confidence 44555677889999999885 233333 3677899999987654 589983
No 403
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=29.21 E-value=21 Score=24.86 Aligned_cols=15 Identities=27% Similarity=0.631 Sum_probs=11.5
Q ss_pred ccccCCCCCCCceeEEE
Q 032998 85 RIFCPKCGNGGTLRKVA 101 (129)
Q Consensus 85 ~~fCp~CG~~~tL~rv~ 101 (129)
.+.|++||.+ +.+..
T Consensus 8 ~~~C~~CG~d--~~~~~ 22 (86)
T PF06170_consen 8 APRCPHCGLD--YSHAR 22 (86)
T ss_pred CCcccccCCc--cccCC
Confidence 4679999998 66655
No 405
>cd00517 ATPS ATP-sulfurylase. ATP-sulfurylase (ATPS), also known as sulfate adenylate transferase, catalyzes the transfer of an adenylyl group from ATP to sulfate, forming adenosine 5'-phosphosulfate (APS). This reaction is generally accompanied by a further reaction, catalyzed by APS kinase, in which APS is phosphorylated to yield 3'-phospho-APS (PAPS). In some organisms the APS kinase is a separate protein, while in others it is incorporated with ATP sulfurylase in a bifunctional enzyme that catalyzes both reactions. In bifunctional proteins, the domain that performs the kinase activity can be attached at the N-terminal end of the sulfurylase unit or at the C-terminal end, depending on the organism. While the reaction is ubiquitous among organisms, the physiological role of the reaction varies. In some organisms it is used to generate APS from sulfate and ATP, while in others it proceeds in the opposite direction to generate ATP from APS and pyrophosphate. ATP sulfurylase can be
Probab=29.17 E-value=86 Score=27.08 Aligned_cols=41 Identities=24% Similarity=0.468 Sum_probs=28.9
Q ss_pred EeechHHHHHHHHHh----CceeecCCCCcceeeeeEEEEccCccccccccCccccC
Q 032998 37 CITGDYAMQNVILQM----GLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCP 89 (129)
Q Consensus 37 ~~TdDyamQNVl~~l----GL~~~s~~g~~I~~~k~W~~rC~~C~k~~~~~~~~fCp 89 (129)
-.=+.|+.|.+...+ ||+++.+ .+..+|..|+.+.+. ..||
T Consensus 270 ~yY~~y~aq~i~~~~~~~l~I~~v~~---------~~~~Yc~~c~~~~~~---~~cp 314 (353)
T cd00517 270 DYYGPYDAQEIFKKLAPELGIEPVPF---------REAAYCPKCDGMASE---DTCP 314 (353)
T ss_pred ccCCcchhHHHHHhCcccCCceEEec---------ceeEEecCCCeEEec---ccCC
Confidence 566889999998876 3443333 455669999987654 6799
No 406
>KOG3940 consensus Uncharacterized conserved protein [Function unknown]
Probab=29.02 E-value=29 Score=30.18 Aligned_cols=53 Identities=19% Similarity=0.136 Sum_probs=33.8
Q ss_pred HHHHHHHHHhCceeecCCCCcceeeeeEE-EEccCccccccccC-ccccCCCCCC
Q 032998 42 YAMQNVILQMGLRLLAPGGMQIRQLHRWI-LKCHACYTITAEIG-RIFCPKCGNG 94 (129)
Q Consensus 42 yamQNVl~~lGL~~~s~~g~~I~~~k~W~-~rC~~C~k~~~~~~-~~fCp~CG~~ 94 (129)
|+-.-|..++|=.-...++--+.-...-- ..|+-|++-|.+.. -.|||.|++.
T Consensus 293 ~~~~~v~~~~g~~as~~~~~~~~gse~~s~~~Cp~cg~r~~~~~~ak~~~~c~~r 347 (351)
T KOG3940|consen 293 RAAKQVKAHLGRGASLSDLPPPPGSENPSYVQCPHCGRRFNEQAAAKHIPKCVNR 347 (351)
T ss_pred HHHHHHhhhcCCccccccCCCCCCCCCCCcccCccccccchHHHHHhhccccccc
Confidence 55566777887555444433333333333 56999998887443 6889999986
No 407
>PF11706 zf-CGNR: CGNR zinc finger; InterPro: IPR021005 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 C-terminal zinc finger domain. It seems likely to be DNA-binding given the conservation of many positively charged residues. The domain is named after a highly conserved motif found in many members of the family. ; PDB: 3H0N_A.
Probab=28.98 E-value=14 Score=22.92 Aligned_cols=24 Identities=29% Similarity=0.819 Sum_probs=11.4
Q ss_pred EEc--cCcccccccc----CccccC--CCCCC
Q 032998 71 LKC--HACYTITAEI----GRIFCP--KCGNG 94 (129)
Q Consensus 71 ~rC--~~C~k~~~~~----~~~fCp--~CG~~ 94 (129)
.+| +.|..+|-|. .+.+|. .|||.
T Consensus 3 r~C~~~~C~~~F~D~sr~~~RrwCsm~~Cgnr 34 (44)
T PF11706_consen 3 RRCANPDCRWVFLDTSRNGRRRWCSMERCGNR 34 (44)
T ss_dssp EE--STT---EEE--SSS-----SS-HHHHHH
T ss_pred cccCCCCCceEEEeCCCCCCceecCcccccCH
Confidence 568 8899888653 378998 89986
No 408
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=28.91 E-value=22 Score=21.83 Aligned_cols=22 Identities=23% Similarity=0.436 Sum_probs=15.2
Q ss_pred EEccCccccccccCccccCCCC
Q 032998 71 LKCHACYTITAEIGRIFCPKCG 92 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG 92 (129)
.+|..|+.+.-..+-..||.=+
T Consensus 2 ~kC~~CG~~GH~~t~k~CP~~~ 23 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNKRCPMYC 23 (40)
T ss_pred ccccccccccccccCccCCCCC
Confidence 5799999876554557788533
No 409
>PF06061 Baculo_ME53: Baculoviridae ME53; InterPro: IPR010336 ME53 is one of the major early-transcribed genes. The ME53 protein is reported to contain a putative zinc finger motif [].; GO: 0003677 DNA binding, 0008270 zinc ion binding
Probab=28.83 E-value=23 Score=30.47 Aligned_cols=24 Identities=25% Similarity=0.699 Sum_probs=18.7
Q ss_pred EEccCcc--ccccccCccccCCCCCC
Q 032998 71 LKCHACY--TITAEIGRIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~--k~~~~~~~~fCp~CG~~ 94 (129)
.-|..|. |++...+..+|..||--
T Consensus 261 ~~C~~Ck~~K~yk~nPVLyCS~CGFT 286 (327)
T PF06061_consen 261 RECKYCKKNKLYKNNPVLYCSKCGFT 286 (327)
T ss_pred hhhhhccccceecCCceEEEcccCCC
Confidence 4599998 66765568999999963
No 410
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=28.65 E-value=55 Score=25.33 Aligned_cols=8 Identities=38% Similarity=1.082 Sum_probs=6.6
Q ss_pred ccCCCCCC
Q 032998 87 FCPKCGNG 94 (129)
Q Consensus 87 fCp~CG~~ 94 (129)
-||.||++
T Consensus 2 ~CP~C~~~ 9 (147)
T TIGR00244 2 HCPFCQHH 9 (147)
T ss_pred CCCCCCCC
Confidence 48999987
No 411
>cd07973 Spt4 Transcription elongation factor Spt4. Spt4 is a transcription elongation factor. Three transcription-elongation factors Spt4, Spt5, and Spt6, are conserved among eukaryotes and are essential for transcription via the modulation of chromatin structure. It is known that Spt4, Spt5, and Spt6 are general transcription-elongation factors, controlling transcription both positively and negatively in important regulatory and developmental roles. Spt4 functions entirely in the context of the Spt4-Spt5 heterodimer and it has been found only as a complex to Spt5 in Yeast and Human. Spt4 is a small protein that has zinc finger at the N-terminus. Spt5 is a large protein that has several interesting structural features of an acidic N-terminus, a single NGN domain, five or six KOW domains, and a set of simple C-termianl repeats. Spt4 binds to Spt5 NGN domain. Unlike Spt5, Spt4 is not essential for viability in yeast, however Spt4 is critical for normal function of the Spt4-Spt5 compl
Probab=28.50 E-value=31 Score=24.75 Aligned_cols=21 Identities=38% Similarity=0.735 Sum_probs=15.3
Q ss_pred EccCcccccccc--CccccCCCC
Q 032998 72 KCHACYTITAEI--GRIFCPKCG 92 (129)
Q Consensus 72 rC~~C~k~~~~~--~~~fCp~CG 92 (129)
.|..|+.+.... ...-||.||
T Consensus 5 AC~~C~~I~~~~qf~~~gCpnC~ 27 (98)
T cd07973 5 ACLLCSLIKTEDQFERDGCPNCE 27 (98)
T ss_pred hhccCCcccccccccCCCCCCCc
Confidence 799999887532 135699996
No 412
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=28.34 E-value=20 Score=27.98 Aligned_cols=14 Identities=43% Similarity=1.030 Sum_probs=11.4
Q ss_pred ccccCCCCCCCcee
Q 032998 85 RIFCPKCGNGGTLR 98 (129)
Q Consensus 85 ~~fCp~CG~~~tL~ 98 (129)
..||..||.+.+|+
T Consensus 89 ~r~CARCGGrv~lr 102 (169)
T KOG3799|consen 89 TRFCARCGGRVSLR 102 (169)
T ss_pred hhHHHhcCCeeeec
Confidence 47999999986666
No 413
>PF04959 ARS2: Arsenite-resistance protein 2; InterPro: IPR007042 This entry represents Arsenite-resistance protein 2 (also known as Serrate RNA effector molecule homolog) which is thought to play a role in arsenite resistance [], although does not directly confer arsenite resistance but rather modulates arsenic sensitivity []. Arsenite is a carcinogenic compound which can act as a comutagen by inhibiting DNA repair. It is also involved in cell cycle progression at S phase. ; PDB: 3AX1_A.
Probab=28.31 E-value=26 Score=28.39 Aligned_cols=22 Identities=9% Similarity=0.184 Sum_probs=15.0
Q ss_pred CcceeeeeEEEEccCccccccc
Q 032998 61 MQIRQLHRWILKCHACYTITAE 82 (129)
Q Consensus 61 ~~I~~~k~W~~rC~~C~k~~~~ 82 (129)
..+++.-.|+++|..|+|.|..
T Consensus 68 ~~~~e~~~~K~~C~lc~KlFkg 89 (214)
T PF04959_consen 68 KNTKEEDEDKWRCPLCGKLFKG 89 (214)
T ss_dssp EEE-SSSSEEEEE-SSS-EESS
T ss_pred HHHHHHcCCEECCCCCCcccCC
Confidence 3456677899999999999864
No 414
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=28.24 E-value=39 Score=27.79 Aligned_cols=16 Identities=25% Similarity=0.715 Sum_probs=12.7
Q ss_pred ccccCCCCCCCceeEEEE
Q 032998 85 RIFCPKCGNGGTLRKVAV 102 (129)
Q Consensus 85 ~~fCp~CG~~~tL~rv~v 102 (129)
..-||.||.+ |++..+
T Consensus 254 g~pC~~Cg~~--I~~~~~ 269 (282)
T PRK13945 254 GKPCRKCGTP--IERIKL 269 (282)
T ss_pred cCCCCcCCCe--eEEEEE
Confidence 4679999986 887666
No 415
>TIGR00398 metG methionyl-tRNA synthetase. The methionyl-tRNA synthetase (metG) is a class I amino acyl-tRNA ligase. This model appears to recognize the methionyl-tRNA synthetase of every species, including eukaryotic cytosolic and mitochondrial forms. The UPGMA difference tree calculated after search and alignment according to this model shows an unusual deep split between two families of MetG. One family contains forms from the Archaea, yeast cytosol, spirochetes, and E. coli, among others. The other family includes forms from yeast mitochondrion, Synechocystis sp., Bacillus subtilis, the Mycoplasmas, Aquifex aeolicus, and Helicobacter pylori. The E. coli enzyme is homodimeric, although monomeric forms can be prepared that are fully active. Activity of this enzyme in bacteria includes aminoacylation of fMet-tRNA with Met; subsequent formylation of the Met to fMet is catalyzed by a separate enzyme. Note that the protein from Aquifex aeolicus is split into an alpha (large) and beta (sma
Probab=28.20 E-value=81 Score=27.76 Aligned_cols=26 Identities=31% Similarity=0.565 Sum_probs=16.9
Q ss_pred eEEEEccCccccccccC-ccccCCCCC
Q 032998 68 RWILKCHACYTITAEIG-RIFCPKCGN 93 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~~~-~~fCp~CG~ 93 (129)
.=++.|..|.+...+.. ...||.||.
T Consensus 118 ~~v~~~~~~~~~l~~~~v~g~cp~c~~ 144 (530)
T TIGR00398 118 IKQLYCPECEMFLPDRYVEGTCPKCGS 144 (530)
T ss_pred eEEEecCCCCcCCchhhhcCCCCCCCC
Confidence 34688888887766543 455777665
No 416
>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=28.16 E-value=34 Score=25.93 Aligned_cols=11 Identities=45% Similarity=1.343 Sum_probs=9.1
Q ss_pred cccCCCCCCCc
Q 032998 86 IFCPKCGNGGT 96 (129)
Q Consensus 86 ~fCp~CG~~~t 96 (129)
.-||.||+.+|
T Consensus 106 ~~cp~c~s~~t 116 (146)
T TIGR02159 106 VQCPRCGSADT 116 (146)
T ss_pred CcCCCCCCCCc
Confidence 67999999843
No 417
>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=27.95 E-value=30 Score=22.71 Aligned_cols=11 Identities=45% Similarity=0.990 Sum_probs=4.9
Q ss_pred CccccCCCCCC
Q 032998 84 GRIFCPKCGNG 94 (129)
Q Consensus 84 ~~~fCp~CG~~ 94 (129)
.+.||..||+.
T Consensus 45 kr~~Ck~C~~~ 55 (85)
T PF04032_consen 45 KRTICKKCGSL 55 (85)
T ss_dssp CCTB-TTT--B
T ss_pred hcccccCCCCE
Confidence 35677777763
No 418
>smart00290 ZnF_UBP Ubiquitin Carboxyl-terminal Hydrolase-like zinc finger.
Probab=27.91 E-value=29 Score=20.72 Aligned_cols=19 Identities=37% Similarity=0.943 Sum_probs=12.7
Q ss_pred EccCccccccccCccccCCCCC
Q 032998 72 KCHACYTITAEIGRIFCPKCGN 93 (129)
Q Consensus 72 rC~~C~k~~~~~~~~fCp~CG~ 93 (129)
+|..|+.... ..+|..||.
T Consensus 1 ~C~~C~~~~~---l~~CL~C~~ 19 (50)
T smart00290 1 RCSVCGTIEN---LWLCLTCGQ 19 (50)
T ss_pred CcccCCCcCC---eEEecCCCC
Confidence 5788885432 467888875
No 419
>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=27.68 E-value=56 Score=19.52 Aligned_cols=20 Identities=35% Similarity=0.589 Sum_probs=7.7
Q ss_pred cccCCCCCCCceeEEEEEeCCCceE
Q 032998 86 IFCPKCGNGGTLRKVAVTVGENGIV 110 (129)
Q Consensus 86 ~fCp~CG~~~tL~rv~v~v~~~G~~ 110 (129)
..|.+|||- |.+..+..|.+
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 448888885 45544444543
No 420
>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=27.62 E-value=21 Score=24.80 Aligned_cols=14 Identities=29% Similarity=0.971 Sum_probs=6.6
Q ss_pred cccCccccCCCCCC
Q 032998 81 AEIGRIFCPKCGNG 94 (129)
Q Consensus 81 ~~~~~~fCp~CG~~ 94 (129)
.+|....||+||+.
T Consensus 61 ENMs~~~Cp~Cg~~ 74 (81)
T PF10609_consen 61 ENMSYFVCPHCGER 74 (81)
T ss_dssp ECT-EEE-TTT--E
T ss_pred ECCCccCCCCCCCe
Confidence 34566778888875
No 421
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=27.52 E-value=21 Score=34.03 Aligned_cols=24 Identities=33% Similarity=0.574 Sum_probs=17.6
Q ss_pred EEccCccccccccC-cc------ccCCCCCC
Q 032998 71 LKCHACYTITAEIG-RI------FCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~~~~~-~~------fCp~CG~~ 94 (129)
.-|..|.+.|.++. +. -||.||=+
T Consensus 152 ~lC~~C~~EY~dP~nRRfHAQp~aCp~CGP~ 182 (750)
T COG0068 152 PLCPFCDKEYKDPLNRRFHAQPIACPKCGPH 182 (750)
T ss_pred cCCHHHHHHhcCccccccccccccCcccCCC
Confidence 35888888887644 33 39999976
No 422
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=27.51 E-value=27 Score=29.10 Aligned_cols=24 Identities=38% Similarity=0.751 Sum_probs=16.2
Q ss_pred EEccCccccc---c-ccCccccCCCCCC
Q 032998 71 LKCHACYTIT---A-EIGRIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~---~-~~~~~fCp~CG~~ 94 (129)
++|+.|+... + .....+|..||.-
T Consensus 12 ~~Cp~Cg~~~iv~d~~~Ge~vC~~CG~V 39 (310)
T PRK00423 12 LVCPECGSDKLIYDYERGEIVCADCGLV 39 (310)
T ss_pred CcCcCCCCCCeeEECCCCeEeecccCCc
Confidence 4799998621 1 1236889999974
No 423
>PRK13844 recombination protein RecR; Provisional
Probab=27.51 E-value=30 Score=27.86 Aligned_cols=29 Identities=28% Similarity=0.529 Sum_probs=23.3
Q ss_pred ceeeeeEEEEccCccccccccCccccCCCCCC
Q 032998 63 IRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 63 I~~~k~W~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
|...+.-+..|.-|+.++.. .-|+.|-.+
T Consensus 50 i~~~~~~i~~C~~C~~lte~---~~C~IC~d~ 78 (200)
T PRK13844 50 LLDATANIKKCVYCQALTED---DVCNICSNT 78 (200)
T ss_pred HHHHHHhCCcCCCCCCCCCC---CCCCCCCCC
Confidence 45566677889999998865 669999987
No 424
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=27.37 E-value=40 Score=20.48 Aligned_cols=7 Identities=29% Similarity=0.747 Sum_probs=3.2
Q ss_pred ccCcccc
Q 032998 73 CHACYTI 79 (129)
Q Consensus 73 C~~C~k~ 79 (129)
|..|.+.
T Consensus 5 C~~C~~~ 11 (57)
T cd00065 5 CMGCGKP 11 (57)
T ss_pred CcccCcc
Confidence 4445443
No 425
>PLN02436 cellulose synthase A
Probab=27.34 E-value=25 Score=34.89 Aligned_cols=27 Identities=26% Similarity=0.838 Sum_probs=21.0
Q ss_pred EccCccccccccCccccCCCCCCCceeEE
Q 032998 72 KCHACYTITAEIGRIFCPKCGNGGTLRKV 100 (129)
Q Consensus 72 rC~~C~k~~~~~~~~fCp~CG~~~tL~rv 100 (129)
.|..|+........+-||.|+.+ -+|+
T Consensus 65 vCr~Cyeyer~eg~~~Cpqckt~--Y~r~ 91 (1094)
T PLN02436 65 VCRPCYEYERREGNQACPQCKTR--YKRI 91 (1094)
T ss_pred cccchhhhhhhcCCccCcccCCc--hhhc
Confidence 68888977666668999999987 5544
No 426
>PF14149 YhfH: YhfH-like protein
Probab=27.28 E-value=14 Score=22.44 Aligned_cols=15 Identities=20% Similarity=0.532 Sum_probs=9.6
Q ss_pred ccccCccccCCCCCC
Q 032998 80 TAEIGRIFCPKCGNG 94 (129)
Q Consensus 80 ~~~~~~~fCp~CG~~ 94 (129)
|...+.+.|+.||..
T Consensus 8 frnLp~K~C~~CG~~ 22 (37)
T PF14149_consen 8 FRNLPPKKCTECGKE 22 (37)
T ss_pred HHhCCCcccHHHHHH
Confidence 444555678888764
No 427
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=27.23 E-value=22 Score=35.26 Aligned_cols=23 Identities=30% Similarity=0.847 Sum_probs=19.1
Q ss_pred EccCccccccccCccccCCCCCC
Q 032998 72 KCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 72 rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
.|+.|+.+......+-||.|+.+
T Consensus 46 VCrpCYEYEr~eG~q~CPqCktr 68 (1079)
T PLN02638 46 VCRPCYEYERKDGNQSCPQCKTK 68 (1079)
T ss_pred cccchhhhhhhcCCccCCccCCc
Confidence 68888977666668999999987
No 428
>PF04161 Arv1: Arv1-like family ; InterPro: IPR007290 Arv1 is a transmembrane protein, with potential zinc-binding motifs, that mediates sterol homeostasis. Its action is important in lipid homeostasis, which prevents free sterol toxicity []. Arv1 contains a homology domain (AHD), which consists of an N-terminal cysteine-rich subdomain with a putative zinc-binding motif, followed by a C-terminal subdomain of 33 amino acids. The C-terminal subdomain of the AHD is critical for the protein's function []. In yeast, Arv1p is important for the delivery of an early glycosylphosphatidylinositol GPI intermediate, GlcN-acylPI, to the first mannosyltransferase of GPI synthesis in the ER lumen []. It is important for the traffic of sterol in yeast and in humans. In eukaryotic cells, it may fuction in the sphingolipid metabolic pathway as a transporter of ceramides between the ER and Golgi [].
Probab=27.22 E-value=27 Score=27.56 Aligned_cols=24 Identities=29% Similarity=0.650 Sum_probs=15.9
Q ss_pred EEccCccccccc---------cCccccCCCCCC
Q 032998 71 LKCHACYTITAE---------IGRIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~~~---------~~~~fCp~CG~~ 94 (129)
++|-.|+..-+. .-...||+||..
T Consensus 1 miCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~v 33 (208)
T PF04161_consen 1 MICIECGHPVKSLYRQYSPGNIRLTKCPNCGKV 33 (208)
T ss_pred CEeccCCCcchhhhhccCCCcEEEeeccccCCc
Confidence 478888864321 113679999987
No 429
>PRK00939 translation initiation factor Sui1; Reviewed
Probab=27.13 E-value=32 Score=24.61 Aligned_cols=9 Identities=44% Similarity=1.080 Sum_probs=6.7
Q ss_pred cccCCCCCC
Q 032998 86 IFCPKCGNG 94 (129)
Q Consensus 86 ~fCp~CG~~ 94 (129)
+.||.||.+
T Consensus 2 ~~c~~c~~~ 10 (99)
T PRK00939 2 EICPVCGLP 10 (99)
T ss_pred CcCccCCCC
Confidence 458888876
No 430
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=26.73 E-value=36 Score=19.27 Aligned_cols=20 Identities=35% Similarity=0.918 Sum_probs=11.4
Q ss_pred EEccCccccccccCccccCCCCCC
Q 032998 71 LKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
..|..|+. .. +.-||.||.+
T Consensus 3 ~~C~vC~~-~~---kY~Cp~C~~~ 22 (30)
T PF04438_consen 3 KLCSVCGN-PA---KYRCPRCGAR 22 (30)
T ss_dssp EEETSSSS-EE---SEE-TTT--E
T ss_pred CCCccCcC-CC---EEECCCcCCc
Confidence 46888887 32 4668888865
No 431
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.53 E-value=32 Score=24.44 Aligned_cols=28 Identities=25% Similarity=0.582 Sum_probs=16.0
Q ss_pred EEccCccccc-----cccCccccCCCCCCCceeE
Q 032998 71 LKCHACYTIT-----AEIGRIFCPKCGNGGTLRK 99 (129)
Q Consensus 71 ~rC~~C~k~~-----~~~~~~fCp~CG~~~tL~r 99 (129)
+.|+.|+--- .....+.||.|+.- -|.|
T Consensus 2 llCP~C~v~l~~~~rs~vEiD~CPrCrGV-WLDr 34 (88)
T COG3809 2 LLCPICGVELVMSVRSGVEIDYCPRCRGV-WLDR 34 (88)
T ss_pred cccCcCCceeeeeeecCceeeeCCccccE-eecc
Confidence 4577777321 12335778888875 4443
No 432
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=26.19 E-value=30 Score=18.63 Aligned_cols=9 Identities=44% Similarity=1.243 Sum_probs=7.1
Q ss_pred cccCCCCCC
Q 032998 86 IFCPKCGNG 94 (129)
Q Consensus 86 ~fCp~CG~~ 94 (129)
.-||.||..
T Consensus 3 ~~C~~CgR~ 11 (25)
T PF13913_consen 3 VPCPICGRK 11 (25)
T ss_pred CcCCCCCCE
Confidence 569999974
No 433
>COG5319 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.13 E-value=19 Score=27.61 Aligned_cols=16 Identities=38% Similarity=0.893 Sum_probs=11.9
Q ss_pred cCccccCCCCCCCceeE
Q 032998 83 IGRIFCPKCGNGGTLRK 99 (129)
Q Consensus 83 ~~~~fCp~CG~~~tL~r 99 (129)
+....||+||+. ++.|
T Consensus 30 rgLv~CPvCgs~-~VsK 45 (142)
T COG5319 30 RGLVTCPVCGST-EVSK 45 (142)
T ss_pred cCceeCCCCCcH-HHHH
Confidence 445789999996 6654
No 434
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=25.99 E-value=55 Score=19.89 Aligned_cols=9 Identities=33% Similarity=0.822 Sum_probs=4.4
Q ss_pred cccCCCCCC
Q 032998 86 IFCPKCGNG 94 (129)
Q Consensus 86 ~fCp~CG~~ 94 (129)
.||-.||.+
T Consensus 49 ~fC~~C~~~ 57 (64)
T smart00647 49 SFCFRCKVP 57 (64)
T ss_pred eECCCCCCc
Confidence 445555543
No 435
>cd00279 YlxR Ylxr homologs; group of conserved hypothetical bacterial proteins of unknown function; structure revealed putative RNA binding cleft; proteins are encoded by an operon that includes other proteins involved in transcription and/or translation
Probab=25.64 E-value=86 Score=21.36 Aligned_cols=38 Identities=21% Similarity=0.343 Sum_probs=23.6
Q ss_pred EEccCccccccccCccccCCCCCCCceeEEEEEeCCCceEEeecCCccccCc
Q 032998 71 LKCHACYTITAEIGRIFCPKCGNGGTLRKVAVTVGENGIVLASRRPRITLRG 122 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG~~~tL~rv~v~v~~~G~~~~~~~~~~n~RG 122 (129)
-+|-+|.+.++.. .|.|+.. +.+|.+.+....+.+-||
T Consensus 3 R~CI~cr~~~~k~------------~LiR~v~--~~~g~i~~D~~~k~~GRG 40 (79)
T cd00279 3 RKCIVTGEMKPKK------------ELIRFVA--GPEGEVVPDPTGKLPGRG 40 (79)
T ss_pred eeeeecCCCCChH------------HCEEEEE--cCCCeEEECCCCCCCCCe
Confidence 3688999876542 4666554 567877776544344555
No 436
>PLN02195 cellulose synthase A
Probab=25.55 E-value=31 Score=33.94 Aligned_cols=23 Identities=35% Similarity=0.852 Sum_probs=19.1
Q ss_pred EccCccccccccCccccCCCCCC
Q 032998 72 KCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 72 rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
.|..|+.+......+-||.|+.+
T Consensus 35 vCrpCyeyer~eg~q~CpqCkt~ 57 (977)
T PLN02195 35 LCKACLEYEIKEGRKVCLRCGGP 57 (977)
T ss_pred cccchhhhhhhcCCccCCccCCc
Confidence 68888977666667999999987
No 437
>PF02348 CTP_transf_3: Cytidylyltransferase; InterPro: IPR003329 Synonym(s): CMP-N-acetylneuraminic acid synthetase Acylneuraminate cytidylyltransferase (2.7.7.43 from EC) (CMP-NeuAc synthetase) catalyzes the reaction of CTP and NeuAc to form CMP-NeuAc, which is the nucleotide sugar donor used by sialyltransferases []. The outer membrane lipooligosaccharides of some microorganisms contain terminal sialic acid attached to N-acetyllactosamine and so this modification may be important in pathogenesis.; GO: 0009103 lipopolysaccharide biosynthetic process; PDB: 3K8D_C 1VH1_B 3K8E_C 1QWJ_A 3EWI_A 1VIC_B 3DUV_A 1VH3_C 3TQD_A 2Y6P_C ....
Probab=25.55 E-value=1e+02 Score=23.04 Aligned_cols=25 Identities=12% Similarity=0.327 Sum_probs=22.3
Q ss_pred ceeeEeechHHHHHHHHHhCceeec
Q 032998 33 STVACITGDYAMQNVILQMGLRLLA 57 (129)
Q Consensus 33 ~~va~~TdDyamQNVl~~lGL~~~s 57 (129)
..|++-|||-.+.+++.+.|..+.-
T Consensus 41 d~IvVaTd~~~i~~~~~~~g~~v~~ 65 (217)
T PF02348_consen 41 DEIVVATDDEEIDDIAEEYGAKVIF 65 (217)
T ss_dssp SEEEEEESSHHHHHHHHHTTSEEEE
T ss_pred CeEEEeCCCHHHHHHHHHcCCeeEE
Confidence 4689999999999999999988853
No 438
>PRK10246 exonuclease subunit SbcC; Provisional
Probab=25.52 E-value=29 Score=33.65 Aligned_cols=9 Identities=44% Similarity=1.080 Sum_probs=5.3
Q ss_pred cccCCCCCC
Q 032998 86 IFCPKCGNG 94 (129)
Q Consensus 86 ~fCp~CG~~ 94 (129)
.-||+||+.
T Consensus 504 ePCPVCGS~ 512 (1047)
T PRK10246 504 QPCPLCGST 512 (1047)
T ss_pred CCcCCCCcc
Confidence 446666654
No 439
>PF05743 UEV: UEV domain; InterPro: IPR008883 The N-terminal ubiquitin E2 variant (UEV) domain is ~145 amino acid residues in length and shows significant sequence similarity to E2 ubiquitin ligases but is unable to catalyze ubiquitin transfer as it lacks the active site cysteine that forms the transient thioester bond with the C terminus of ubiquitin (Ub). Nevertheless, at least some UEVs have retained the ability to bind Ub, and appear to act either as cofactors in ubiquitylation reactions, or as ubiquitin sensors. UEV domains also frequently contain other protein recognition motifs, and may generally serve to couple protein and Ub binding functions to facilitate the formation of multiprotein complexes [, , , ]. The UEV domain consists of a twisted four-stranded antiparallel beta-sheet having a meander topology, with four alpha-helices packed against one face of the sheet. The UEV fold is generally similar to canonical E2 ligases in the hydrophobic core and 'active site' regions, but differs significantly at both its N- and C-termini [, ]. The UEV domain is found in the eukaryotic tumour susceptibility gene 101 protein (TSG101). Altered transcripts of this gene have been detected in sporadic breast cancers and many other Homo sapiens malignancies. However, the involvement of this gene in neoplastic transformation and tumourigenesis is still elusive. TSG101 is required for normal cell function of embryonic and adult tissues but this gene is not a tumour suppressor for sporadic forms of breast cancer [].; GO: 0006464 protein modification process, 0015031 protein transport; PDB: 3R3Q_A 3R42_A 1UZX_A 3OBX_A 3OBS_A 3P9H_A 2F0R_A 3P9G_A 3OBQ_A 3OBU_A ....
Probab=25.50 E-value=47 Score=24.17 Aligned_cols=31 Identities=19% Similarity=0.252 Sum_probs=20.8
Q ss_pred EEEEEeCCCceE--Eeec--CCccccCceeecCCC
Q 032998 99 KVAVTVGENGIV--LASR--RPRITLRGTKVSISL 129 (129)
Q Consensus 99 rv~v~v~~~G~~--~~~~--~~~~n~RG~~ySlP~ 129 (129)
|..+.+.+||.. ++.. .-.+..+|+.|+||+
T Consensus 18 ~~~~ft~~~G~~~~LL~L~Gtipi~y~g~~y~iPi 52 (121)
T PF05743_consen 18 RTDTFTFNDGSSKLLLCLYGTIPITYKGSTYNIPI 52 (121)
T ss_dssp EEEEEESTTSTEEEEEEEEEEEEECCTTCCEEEEE
T ss_pred eeeeeEcCCCChheEEEEecCcccccCCcccceeE
Confidence 455667788853 3332 224789999999984
No 440
>TIGR00615 recR recombination protein RecR. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=25.42 E-value=19 Score=28.87 Aligned_cols=29 Identities=17% Similarity=0.516 Sum_probs=23.6
Q ss_pred ceeeeeEEEEccCccccccccCccccCCCCCC
Q 032998 63 IRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 63 I~~~k~W~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
|.+.+.-+..|.-|+.++.. .-|+.|-.+
T Consensus 46 i~~~~~~i~~C~~C~~lse~---~~C~IC~d~ 74 (195)
T TIGR00615 46 LLEAKENLRTCSVCGAISDQ---EVCNICSDE 74 (195)
T ss_pred HHHHHHcCCcCCCCCCCCCC---CcCCCCCCC
Confidence 55666777899999988765 669999998
No 441
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=25.38 E-value=44 Score=19.76 Aligned_cols=13 Identities=31% Similarity=1.094 Sum_probs=9.8
Q ss_pred cccCCCCCCCc-eeE
Q 032998 86 IFCPKCGNGGT-LRK 99 (129)
Q Consensus 86 ~fCp~CG~~~t-L~r 99 (129)
.-||.|++. . +.|
T Consensus 6 v~CP~C~s~-~~v~k 19 (36)
T PF03811_consen 6 VHCPRCQST-EGVKK 19 (36)
T ss_pred eeCCCCCCC-Cccee
Confidence 569999997 4 554
No 442
>KOG0856 consensus Predicted pilin-like transcription factor [Posttranslational modification, protein turnover, chaperones]
Probab=25.09 E-value=67 Score=24.91 Aligned_cols=47 Identities=19% Similarity=0.277 Sum_probs=32.8
Q ss_pred HHHHhCceeecCCCCcceeeeeEEEEccCccccccccCccccCCCCCC
Q 032998 47 VILQMGLRLLAPGGMQIRQLHRWILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 47 Vl~~lGL~~~s~~g~~I~~~k~W~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
|+++.|.+- +..|.-.+....=+|.|-+|+..-.....+|+..||=|
T Consensus 32 v~RekgTE~-p~tGey~~~~e~GvY~C~~C~~pLykS~tKfdsgcGWP 78 (146)
T KOG0856|consen 32 VLREKGTER-PGTGEYTKHFEEGVYVCAGCGTPLYKSTTKFDSGCGWP 78 (146)
T ss_pred hhHhhcccC-CCCcccccccCCceEEEeecCCccccccccccCCCCCc
Confidence 677877764 23344444555668999999976444456899999976
No 443
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=24.94 E-value=34 Score=24.87 Aligned_cols=10 Identities=50% Similarity=1.099 Sum_probs=8.6
Q ss_pred ccccCCCCCC
Q 032998 85 RIFCPKCGNG 94 (129)
Q Consensus 85 ~~fCp~CG~~ 94 (129)
...||.||.+
T Consensus 3 LI~CP~Cg~R 12 (97)
T COG4311 3 LIPCPYCGER 12 (97)
T ss_pred eecCCCCCCC
Confidence 5789999987
No 444
>PRK09401 reverse gyrase; Reviewed
Probab=24.82 E-value=34 Score=33.96 Aligned_cols=27 Identities=26% Similarity=0.555 Sum_probs=20.8
Q ss_pred eeEEEEccCccccccccCccccCCCCCC
Q 032998 67 HRWILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 67 k~W~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
..-..+|..|+..+.+. ...||.||++
T Consensus 675 y~~~k~c~~~g~~f~~~-~~~~~~c~~~ 701 (1176)
T PRK09401 675 YDTIKRCRDCGYQFTDE-SDKCPRCGST 701 (1176)
T ss_pred eeeeccccccccccccc-cccccccccc
Confidence 34557899999888764 4689999963
No 445
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=24.65 E-value=35 Score=25.34 Aligned_cols=26 Identities=23% Similarity=0.723 Sum_probs=17.9
Q ss_pred EEEEccCcccc--ccccCccccCCCCCC
Q 032998 69 WILKCHACYTI--TAEIGRIFCPKCGNG 94 (129)
Q Consensus 69 W~~rC~~C~k~--~~~~~~~fCp~CG~~ 94 (129)
|.--|+-|... |.+.....||.|+++
T Consensus 2 ~lp~cp~c~sEytYed~~~~~cpec~~e 29 (112)
T COG2824 2 SLPPCPKCNSEYTYEDGGQLICPECAHE 29 (112)
T ss_pred CCCCCCccCCceEEecCceEeCchhccc
Confidence 34468888633 455556789999987
No 446
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=24.62 E-value=33 Score=25.64 Aligned_cols=10 Identities=50% Similarity=1.265 Sum_probs=8.2
Q ss_pred ccccCCCCCC
Q 032998 85 RIFCPKCGNG 94 (129)
Q Consensus 85 ~~fCp~CG~~ 94 (129)
+.-||+||++
T Consensus 74 ~~kCpkCghe 83 (116)
T KOG2907|consen 74 KHKCPKCGHE 83 (116)
T ss_pred hccCcccCCc
Confidence 4569999997
No 447
>PRK00124 hypothetical protein; Validated
Probab=24.60 E-value=1e+02 Score=23.79 Aligned_cols=43 Identities=23% Similarity=0.325 Sum_probs=32.7
Q ss_pred CCCCceeeecCCCceeeEeechHHHHHHHHHhCceeecCCCCcc
Q 032998 20 CSEQSWMLRSLSESTVACITGDYAMQNVILQMGLRLLAPGGMQI 63 (129)
Q Consensus 20 ~~~~~wi~~~~~~~~va~~TdDyamQNVl~~lGL~~~s~~g~~I 63 (129)
+....||-... +..-.++|.||.|--.++.-|..++++.|...
T Consensus 55 D~AD~~Iv~~~-~~gDiVIT~Di~LAa~~l~Kga~vl~prG~~y 97 (151)
T PRK00124 55 DAADNEIVQLA-EKGDIVITQDYGLAALALEKGAIVLNPRGYIY 97 (151)
T ss_pred ChHHHHHHHhC-CCCCEEEeCCHHHHHHHHHCCCEEECCCCcCC
Confidence 34445665442 34468999999999999999999999988643
No 448
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=24.56 E-value=33 Score=30.87 Aligned_cols=26 Identities=23% Similarity=0.562 Sum_probs=19.8
Q ss_pred EEEEccCccccccc----------cCccccCCCCCC
Q 032998 69 WILKCHACYTITAE----------IGRIFCPKCGNG 94 (129)
Q Consensus 69 W~~rC~~C~k~~~~----------~~~~fCp~CG~~ 94 (129)
=.|+|+.|.+.|.. ...--|..||.+
T Consensus 127 ~~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 127 AGYVCPNCQKKYTSLEALQLLDNETGEFHCENCGGE 162 (436)
T ss_pred ccccCCccccchhhhHHHHhhcccCceEEEecCCCc
Confidence 35899999998752 234569999998
No 449
>PRK07418 acetolactate synthase 3 catalytic subunit; Reviewed
Probab=24.52 E-value=35 Score=30.76 Aligned_cols=23 Identities=30% Similarity=0.837 Sum_probs=16.8
Q ss_pred EEccCccccccccCccccCCCCCC
Q 032998 71 LKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
..|+.|+..- .+...||+.||..
T Consensus 593 ~~~~~~~~~~-~~~~~f~~~~g~~ 615 (616)
T PRK07418 593 IYCSNCGAKN-PSTHRFCPECGTK 615 (616)
T ss_pred ccCCCCCCcC-ccccccchhhCCC
Confidence 5789999742 2336899999985
No 450
>COG1671 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.30 E-value=92 Score=24.19 Aligned_cols=47 Identities=19% Similarity=0.354 Sum_probs=35.5
Q ss_pred ccCCCCCCCceeeecCCCceeeEeechHHHHHHHHHhCceeecCCCCc
Q 032998 15 YVDDECSEQSWMLRSLSESTVACITGDYAMQNVILQMGLRLLAPGGMQ 62 (129)
Q Consensus 15 ~~~~~~~~~~wi~~~~~~~~va~~TdDyamQNVl~~lGL~~~s~~g~~ 62 (129)
.+..-+....||-.- .+..-.++|.|+.+--.++-.|..+++..|..
T Consensus 49 V~~g~DaaD~~Iv~~-a~~gDlVVT~Di~LA~~ll~kg~~v~~prGr~ 95 (150)
T COG1671 49 VDAGFDAADDWIVNL-AEKGDLVVTADIPLASLLLDKGAAVLNPRGRL 95 (150)
T ss_pred ecCCcchHHHHHHHh-CCCCCEEEECchHHHHHHHhcCCEEECCCCcc
Confidence 333445556677632 35566899999999999999999999998863
No 451
>smart00259 ZnF_A20 A20-like zinc fingers. A20- (an inhibitor of cell death)-like zinc fingers. The zinc finger mediates self-association in A20. These fingers also mediate IL-1-induced NF-kappaB activation.
Probab=24.29 E-value=30 Score=19.17 Aligned_cols=20 Identities=30% Similarity=0.713 Sum_probs=15.0
Q ss_pred Ecc--CccccccccCccccCCC
Q 032998 72 KCH--ACYTITAEIGRIFCPKC 91 (129)
Q Consensus 72 rC~--~C~k~~~~~~~~fCp~C 91 (129)
.|. +|+......+..+|++|
T Consensus 3 ~C~~~~CgF~G~~~t~~~CskC 24 (26)
T smart00259 3 KCRRPGCGFFGNPATEGLCSKC 24 (26)
T ss_pred ccccCCCCCcCChhhcccCHhh
Confidence 366 88877766667888887
No 452
>PF14952 zf-tcix: Putative treble-clef, zinc-finger, Zn-binding
Probab=24.24 E-value=32 Score=21.63 Aligned_cols=9 Identities=56% Similarity=1.154 Sum_probs=7.0
Q ss_pred cccCCCCCC
Q 032998 86 IFCPKCGNG 94 (129)
Q Consensus 86 ~fCp~CG~~ 94 (129)
.-||.||.-
T Consensus 12 rkCp~CGt~ 20 (44)
T PF14952_consen 12 RKCPKCGTY 20 (44)
T ss_pred ccCCcCcCc
Confidence 459999964
No 453
>COG4049 Uncharacterized protein containing archaeal-type C2H2 Zn-finger [General function prediction only]
Probab=24.05 E-value=27 Score=23.40 Aligned_cols=14 Identities=21% Similarity=0.496 Sum_probs=11.3
Q ss_pred EEEEccCccccccc
Q 032998 69 WILKCHACYTITAE 82 (129)
Q Consensus 69 W~~rC~~C~k~~~~ 82 (129)
-.++|+.|+.++..
T Consensus 16 ~~lrCPRC~~~FR~ 29 (65)
T COG4049 16 EFLRCPRCGMVFRR 29 (65)
T ss_pred eeeeCCchhHHHHH
Confidence 35899999998875
No 454
>PF11822 DUF3342: Domain of unknown function (DUF3342); InterPro: IPR021777 This family of proteins are functionally uncharacterised. This family is found in bacteria. This presumed domain is typically between 170 to 303 amino acids in length. The N-terminal half of this family is a BTB-like domain.
Probab=23.93 E-value=96 Score=26.76 Aligned_cols=48 Identities=25% Similarity=0.513 Sum_probs=29.4
Q ss_pred eEEEEccCccccccccC--cccc------CCCCCCCceeEEEEEeCCCceEEe-e-cCCcccc
Q 032998 68 RWILKCHACYTITAEIG--RIFC------PKCGNGGTLRKVAVTVGENGIVLA-S-RRPRITL 120 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~~~--~~fC------p~CG~~~tL~rv~v~v~~~G~~~~-~-~~~~~n~ 120 (129)
.-.+||..|++.+.... +.-| |.|.+. .| ..||..|+++. | +.+.|++
T Consensus 178 ~tL~rC~~C~~Ll~~~~~~~i~C~~~~~~~~~P~~---~k--~~Vd~~G~li~~H~~d~~W~l 235 (317)
T PF11822_consen 178 ATLYRCSLCGKLLTQEEERRIPCRYRNSFPLCPGL---AK--ISVDRRGELISTHVRDKSWDL 235 (317)
T ss_pred ceEEEecccccccChhhHhhccccccccccccccc---cc--eEECCCCCEEEEEeccCCcch
Confidence 46899999999886533 3445 445442 23 34588998743 2 4444544
No 455
>TIGR00143 hypF [NiFe] hydrogenase maturation protein HypF. A previously described regulatory effect of HypF mutatation is attributable to loss of activity of a regulatory hydrogenase. A zinc finger-like region CXXCX(18)CXXCX(24)CXXCX(18)CXXC region further supported the regulatory hypothesis. However, more recent work (PUBMED:11375153) shows the direct effect is on the activity of expressed hydrogenases with nickel/iron centers, rather than on expression.
Probab=23.86 E-value=27 Score=32.81 Aligned_cols=27 Identities=30% Similarity=0.597 Sum_probs=19.5
Q ss_pred eEEEEccCccccccccC-ccc------cCCCCCC
Q 032998 68 RWILKCHACYTITAEIG-RIF------CPKCGNG 94 (129)
Q Consensus 68 ~W~~rC~~C~k~~~~~~-~~f------Cp~CG~~ 94 (129)
.-.-.|..|.+.|.++. +.| ||.||=+
T Consensus 116 ~~f~~C~~C~~ey~~p~~rr~h~~~~~C~~Cgp~ 149 (711)
T TIGR00143 116 ADFPLCPDCAKEYKDPLDRRFHAQPIACPRCGPQ 149 (711)
T ss_pred CCCcCCHHHHHHhcCCccccCCCCCccCCCCCcE
Confidence 33457999998886643 444 9999986
No 456
>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=23.76 E-value=78 Score=23.08 Aligned_cols=19 Identities=37% Similarity=0.700 Sum_probs=10.5
Q ss_pred cccCCCCCCCceeEEEEEeCCCce
Q 032998 86 IFCPKCGNGGTLRKVAVTVGENGI 109 (129)
Q Consensus 86 ~fCp~CG~~~tL~rv~v~v~~~G~ 109 (129)
-.||.||.+ |.++++.+|.
T Consensus 40 S~cp~tg~p-----I~l~v~~~~i 58 (127)
T PF03243_consen 40 SRCPATGEP-----IRLTVDPGGI 58 (127)
T ss_dssp EE-TTT--E-----EEEEE-SSSE
T ss_pred EcCCCCCCe-----EEEEEeCCce
Confidence 569999998 5666676664
No 457
>PF12225 MTHFR_C: Methylene-tetrahydrofolate reductase C terminal; InterPro: IPR022026 This family is found in bacteria and archaea, and is approximately 100 amino acids in length. There is a conserved NGPCGG sequence motif. This family is the C-terminal of methylene-tetrahydrofolate reductase. This protein reduces FAD using the reducing equivalents from reduced FAD, subsequently reduces tetrahydrofolate. The C-terminal of MTHFR contains the FAD binding site and is the catalytic portion of the enzyme.
Probab=23.62 E-value=43 Score=24.10 Aligned_cols=28 Identities=21% Similarity=0.449 Sum_probs=21.7
Q ss_pred ceeeeeEEEEccCccccccccCccccCC
Q 032998 63 IRQLHRWILKCHACYTITAEIGRIFCPK 90 (129)
Q Consensus 63 I~~~k~W~~rC~~C~k~~~~~~~~fCp~ 90 (129)
.+..+.|..+|.+|+.=.-..+-..||.
T Consensus 13 ~~~~~~~~~~C~~CG~C~L~~TggiCP~ 40 (97)
T PF12225_consen 13 EREVKVFLERCRACGDCVLGDTGGICPM 40 (97)
T ss_pred eeeccchhccCCCCCCcccccccccCcc
Confidence 5778899999999997555545567876
No 458
>PLN02400 cellulose synthase
Probab=23.58 E-value=38 Score=33.66 Aligned_cols=28 Identities=29% Similarity=0.752 Sum_probs=21.9
Q ss_pred EEccCccccccccCccccCCCCCCCceeEE
Q 032998 71 LKCHACYTITAEIGRIFCPKCGNGGTLRKV 100 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG~~~tL~rv 100 (129)
-.|+.|+.+......+-||.|+.+ -+|.
T Consensus 64 PVCRpCYEYERkeGnq~CPQCkTr--YkR~ 91 (1085)
T PLN02400 64 PVCRPCYEYERKDGTQCCPQCKTR--YRRH 91 (1085)
T ss_pred ccccchhheecccCCccCcccCCc--cccc
Confidence 378899987777678999999987 4544
No 459
>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=23.50 E-value=85 Score=22.56 Aligned_cols=23 Identities=30% Similarity=0.585 Sum_probs=18.9
Q ss_pred ccccCCCCCCCceeEEEEEeCCCceE
Q 032998 85 RIFCPKCGNGGTLRKVAVTVGENGIV 110 (129)
Q Consensus 85 ~~fCp~CG~~~tL~rv~v~v~~~G~~ 110 (129)
..+||.|+.+ .||..-+++||+.
T Consensus 71 ~lv~p~~~k~---~rv~~~~~~~g~k 93 (104)
T TIGR01079 71 MLFDPKTGKA---TRVGIRFEEDGKK 93 (104)
T ss_pred EEEcCcCCCC---eEEEEEEccCCcE
Confidence 4789999998 4888888888864
No 460
>COG1631 RPL42A Ribosomal protein L44E [Translation, ribosomal structure and biogenesis]
Probab=23.44 E-value=52 Score=23.79 Aligned_cols=18 Identities=39% Similarity=0.861 Sum_probs=14.4
Q ss_pred ccccCCCCCCCceeEEEEE
Q 032998 85 RIFCPKCGNGGTLRKVAVT 103 (129)
Q Consensus 85 ~~fCp~CG~~~tL~rv~v~ 103 (129)
+-+||.|... |+..|+-.
T Consensus 8 ~tyCp~Ckkh-T~H~V~~~ 25 (94)
T COG1631 8 RTYCPYCKKH-TIHKVERV 25 (94)
T ss_pred eecCcccccc-eeeeeeeh
Confidence 5789999997 88877753
No 461
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=23.32 E-value=45 Score=21.65 Aligned_cols=42 Identities=17% Similarity=0.052 Sum_probs=23.0
Q ss_pred chHHHHHHHHHhCceeecCCC-Cc-----ceeeeeEEEEccCccccccc
Q 032998 40 GDYAMQNVILQMGLRLLAPGG-MQ-----IRQLHRWILKCHACYTITAE 82 (129)
Q Consensus 40 dDyamQNVl~~lGL~~~s~~g-~~-----I~~~k~W~~rC~~C~k~~~~ 82 (129)
+-.++-.++. +|+.-++-.- .. -.++..=.+.|+.|++.|+.
T Consensus 18 ~~~~l~~~~~-~~~~~lp~~~~~~~~~l~~~~i~eg~L~Cp~c~r~YPI 65 (68)
T PF03966_consen 18 DWEALVETAQ-LGLSELPKELPEDYHVLLEVEIVEGELICPECGREYPI 65 (68)
T ss_dssp HHHHHHHHHH-CCCCHCHHCHHCHCEHHCTEETTTTEEEETTTTEEEEE
T ss_pred hHHHHHHHHH-hCcccCCCCCccchhhhhcccccCCEEEcCCCCCEEeC
Confidence 3445666666 6666422100 00 01233346999999999875
No 462
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=23.20 E-value=51 Score=24.05 Aligned_cols=17 Identities=35% Similarity=0.800 Sum_probs=12.1
Q ss_pred ccCccccCCCCCCCceeE
Q 032998 82 EIGRIFCPKCGNGGTLRK 99 (129)
Q Consensus 82 ~~~~~fCp~CG~~~tL~r 99 (129)
.++...||.||.+ ++.+
T Consensus 14 ~~~~~~Cp~Cg~~-m~~~ 30 (140)
T COG0551 14 LKTGQICPKCGKN-MVKK 30 (140)
T ss_pred cccCccCCcCCCe-eEEE
Confidence 3456789999998 4443
No 463
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=23.08 E-value=25 Score=23.77 Aligned_cols=12 Identities=25% Similarity=0.661 Sum_probs=4.2
Q ss_pred ccCCCCCCCcee
Q 032998 87 FCPKCGNGGTLR 98 (129)
Q Consensus 87 fCp~CG~~~tL~ 98 (129)
.||.|-.|+..+
T Consensus 42 ~CPvC~~Paw~q 53 (65)
T PF14835_consen 42 ECPVCHTPAWIQ 53 (65)
T ss_dssp B-SSS--B-S-S
T ss_pred CCCCcCChHHHH
Confidence 377777774443
No 464
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=22.90 E-value=51 Score=29.01 Aligned_cols=27 Identities=22% Similarity=0.395 Sum_probs=18.9
Q ss_pred eeEEEEccCccccccccCccccCCCCCC
Q 032998 67 HRWILKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 67 k~W~~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
..=.|.|+.|+...=..+ ..||.||--
T Consensus 273 ~~~Gy~CP~CkakvCsLP-~eCpiC~lt 299 (378)
T KOG2807|consen 273 SGGGYFCPQCKAKVCSLP-IECPICSLT 299 (378)
T ss_pred ccCceeCCcccCeeecCC-ccCCcccee
Confidence 344589999995544443 679999973
No 465
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=22.73 E-value=37 Score=24.59 Aligned_cols=13 Identities=46% Similarity=1.058 Sum_probs=9.8
Q ss_pred cccCCCCCCCcee
Q 032998 86 IFCPKCGNGGTLR 98 (129)
Q Consensus 86 ~fCp~CG~~~tL~ 98 (129)
..||.||.++.|.
T Consensus 3 ~~CpYCg~~~~l~ 15 (102)
T PF11672_consen 3 IICPYCGGPAELV 15 (102)
T ss_pred cccCCCCCeeEEc
Confidence 5699999984443
No 466
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=22.70 E-value=49 Score=20.42 Aligned_cols=10 Identities=30% Similarity=1.075 Sum_probs=7.1
Q ss_pred ccccCCCCCC
Q 032998 85 RIFCPKCGNG 94 (129)
Q Consensus 85 ~~fCp~CG~~ 94 (129)
...||.|...
T Consensus 31 ~v~CPiC~~~ 40 (54)
T PF05605_consen 31 NVVCPICSSR 40 (54)
T ss_pred CccCCCchhh
Confidence 4678888763
No 467
>PF10005 DUF2248: Uncharacterized protein conserved in bacteria (DUF2248); InterPro: IPR011201 This is a family of uncharacterised bacterial proteins.
Probab=22.65 E-value=48 Score=28.89 Aligned_cols=21 Identities=29% Similarity=0.670 Sum_probs=15.9
Q ss_pred EccCcc-ccccccCccccCCCCCC
Q 032998 72 KCHACY-TITAEIGRIFCPKCGNG 94 (129)
Q Consensus 72 rC~~C~-k~~~~~~~~fCp~CG~~ 94 (129)
.|..|+ .+|.+. ..|..||+.
T Consensus 1 ~C~~Cg~~v~FeN--t~C~~Cg~~ 22 (343)
T PF10005_consen 1 SCPNCGQPVFFEN--TRCLSCGSA 22 (343)
T ss_pred CCCCCCCcceeCC--CccccCCcc
Confidence 489999 456664 569999986
No 468
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=22.65 E-value=42 Score=23.42 Aligned_cols=10 Identities=50% Similarity=1.338 Sum_probs=8.7
Q ss_pred ccccCCCCCC
Q 032998 85 RIFCPKCGNG 94 (129)
Q Consensus 85 ~~fCp~CG~~ 94 (129)
+.+||+||++
T Consensus 33 rS~C~~C~~~ 42 (92)
T PF06750_consen 33 RSHCPHCGHP 42 (92)
T ss_pred CCcCcCCCCc
Confidence 6889999997
No 469
>TIGR00269 conserved hypothetical protein TIGR00269.
Probab=22.64 E-value=37 Score=23.90 Aligned_cols=9 Identities=33% Similarity=0.944 Sum_probs=4.2
Q ss_pred cccCCCCCC
Q 032998 86 IFCPKCGNG 94 (129)
Q Consensus 86 ~fCp~CG~~ 94 (129)
..|..||.+
T Consensus 81 ~~C~~CG~p 89 (104)
T TIGR00269 81 RRCERCGEP 89 (104)
T ss_pred CcCCcCcCc
Confidence 345555544
No 470
>PRK03922 hypothetical protein; Provisional
Probab=22.55 E-value=67 Score=23.92 Aligned_cols=18 Identities=39% Similarity=0.936 Sum_probs=12.7
Q ss_pred cCccccCCCCCCCceeEEEE
Q 032998 83 IGRIFCPKCGNGGTLRKVAV 102 (129)
Q Consensus 83 ~~~~fCp~CG~~~tL~rv~v 102 (129)
+....||.||.+ +.-+-+
T Consensus 47 vG~~~cP~cge~--~~~afv 64 (113)
T PRK03922 47 VGLTICPKCGEP--FDSAFV 64 (113)
T ss_pred cCcccCCCCCCc--CCcEEE
Confidence 345679999998 665544
No 471
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=22.46 E-value=73 Score=19.70 Aligned_cols=25 Identities=24% Similarity=0.385 Sum_probs=15.4
Q ss_pred eeEEEEccCccccccc----c--CccccCCC
Q 032998 67 HRWILKCHACYTITAE----I--GRIFCPKC 91 (129)
Q Consensus 67 k~W~~rC~~C~k~~~~----~--~~~fCp~C 91 (129)
++.--+|..|+..+.. . ....||.|
T Consensus 25 ~~v~W~C~~Cgh~w~~~v~~R~~~~~~CP~C 55 (55)
T PF14311_consen 25 KKVWWKCPKCGHEWKASVNDRTRRGKGCPYC 55 (55)
T ss_pred CEEEEECCCCCCeeEccHhhhccCCCCCCCC
Confidence 3444689999866542 1 24567776
No 472
>PRK14906 DNA-directed RNA polymerase subunit beta'/alpha domain fusion protein; Provisional
Probab=22.34 E-value=32 Score=35.17 Aligned_cols=31 Identities=32% Similarity=0.461 Sum_probs=18.6
Q ss_pred EEccCccccccccC-ccccCCCCCCCceeEEEE
Q 032998 71 LKCHACYTITAEIG-RIFCPKCGNGGTLRKVAV 102 (129)
Q Consensus 71 ~rC~~C~k~~~~~~-~~fCp~CG~~~tL~rv~v 102 (129)
+.| +|+|+-.... ..+|+.||-.-|..||..
T Consensus 60 ~eC-~CGKyk~~~~~g~~C~~CGVEvt~s~vRR 91 (1460)
T PRK14906 60 WEC-ACGKYKRIRFKGIVCERCGVEVTRAKVRR 91 (1460)
T ss_pred cEE-eCccccccCcCCeEcCCCCcEecchHHHH
Confidence 456 6886433222 479999998734444443
No 473
>PRK06824 translation initiation factor Sui1; Validated
Probab=22.07 E-value=47 Score=24.65 Aligned_cols=16 Identities=25% Similarity=0.654 Sum_probs=11.5
Q ss_pred cccccCccccCCCCCC
Q 032998 79 ITAEIGRIFCPKCGNG 94 (129)
Q Consensus 79 ~~~~~~~~fCp~CG~~ 94 (129)
+|+.....|||.||.+
T Consensus 10 vySt~~g~~c~~cg~~ 25 (118)
T PRK06824 10 VYSTEHGRHCPDCGQP 25 (118)
T ss_pred EEECCCCccCcccCCc
Confidence 4544345899999997
No 474
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=22.01 E-value=64 Score=26.23 Aligned_cols=18 Identities=44% Similarity=0.790 Sum_probs=12.2
Q ss_pred ccccCCCCCCCceeEEEEEe
Q 032998 85 RIFCPKCGNGGTLRKVAVTV 104 (129)
Q Consensus 85 ~~fCp~CG~~~tL~rv~v~v 104 (129)
+..||+||+ +|+-+....
T Consensus 14 ~~~CPvCg~--~l~~~~~~~ 31 (201)
T COG1779 14 RIDCPVCGG--TLKAHMYLY 31 (201)
T ss_pred eecCCcccc--eeeEEEeee
Confidence 467999998 476555433
No 475
>PRK05580 primosome assembly protein PriA; Validated
Probab=21.84 E-value=44 Score=30.88 Aligned_cols=9 Identities=33% Similarity=0.770 Sum_probs=5.8
Q ss_pred EEccCcccc
Q 032998 71 LKCHACYTI 79 (129)
Q Consensus 71 ~rC~~C~k~ 79 (129)
..|..|+.+
T Consensus 382 ~~C~~Cg~~ 390 (679)
T PRK05580 382 LLCRDCGWV 390 (679)
T ss_pred eEhhhCcCc
Confidence 567777753
No 476
>KOG1253 consensus tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=21.84 E-value=66 Score=29.63 Aligned_cols=14 Identities=14% Similarity=0.508 Sum_probs=11.7
Q ss_pred eeEEEEccCccccc
Q 032998 67 HRWILKCHACYTIT 80 (129)
Q Consensus 67 k~W~~rC~~C~k~~ 80 (129)
..|++.|.+|+...
T Consensus 299 ~~~v~hC~gC~s~~ 312 (525)
T KOG1253|consen 299 YGLVYHCSGCGSFH 312 (525)
T ss_pred eeEEEEecCcchhh
Confidence 57999999999755
No 477
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=21.65 E-value=11 Score=32.61 Aligned_cols=19 Identities=26% Similarity=0.611 Sum_probs=13.0
Q ss_pred EEccCccccccccCccccCCCCCC
Q 032998 71 LKCHACYTITAEIGRIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~~~~~~~fCp~CG~~ 94 (129)
--|+-||+.. .+||+|-..
T Consensus 322 VtCt~CGkrm-----~eCPICRqy 340 (350)
T KOG4275|consen 322 VTCTKCGKRM-----NECPICRQY 340 (350)
T ss_pred Eeehhhcccc-----ccCchHHHH
Confidence 4567777633 379999876
No 478
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=21.50 E-value=64 Score=23.63 Aligned_cols=17 Identities=47% Similarity=1.023 Sum_probs=11.8
Q ss_pred CccccCCCCCCCceeEEEE
Q 032998 84 GRIFCPKCGNGGTLRKVAV 102 (129)
Q Consensus 84 ~~~fCp~CG~~~tL~rv~v 102 (129)
....||.||.+ |.-+-+
T Consensus 46 G~~~cP~Cge~--~~~a~v 62 (102)
T PF04475_consen 46 GDTICPKCGEE--LDSAFV 62 (102)
T ss_pred CcccCCCCCCc--cCceEE
Confidence 34679999998 665444
No 479
>PRK11595 DNA utilization protein GntX; Provisional
Probab=21.45 E-value=35 Score=26.98 Aligned_cols=8 Identities=50% Similarity=1.385 Sum_probs=4.1
Q ss_pred ccCCCCCC
Q 032998 87 FCPKCGNG 94 (129)
Q Consensus 87 fCp~CG~~ 94 (129)
.|+.||.+
T Consensus 36 ~C~~Cg~~ 43 (227)
T PRK11595 36 CCPQCGLP 43 (227)
T ss_pred cCccCCCc
Confidence 45555543
No 480
>PF00703 Glyco_hydro_2: Glycosyl hydrolases family 2; InterPro: IPR006102 O-Glycosyl hydrolases 3.2.1. from EC are a widespread group of enzymes that hydrolyse the glycosidic bond between two or more carbohydrates, or between a carbohydrate and a non-carbohydrate moiety. A classification system for glycosyl hydrolases, based on sequence similarity, has led to the definition of 85 different families [, ]. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. Glycoside hydrolase family 2 GH2 from CAZY comprises enzymes with several known activities: beta-galactosidase (3.2.1.23 from EC); beta-mannosidase (3.2.1.25 from EC); beta-glucuronidase (3.2.1.31 from EC). These enzymes contain a conserved glutamic acid residue which has been shown [], in Escherichia coli lacZ (P00722 from SWISSPROT), to be the general acid/base catalyst in the active site of the enzyme. This entry describes the immunoglobulin-like beta-sandwich domain [].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 3FN9_C 3DEC_A 3OB8_A 3OBA_A 3CMG_A 3GM8_A 3HN3_E 1BHG_A 2VZU_A 2X09_A ....
Probab=21.21 E-value=88 Score=20.29 Aligned_cols=21 Identities=29% Similarity=0.403 Sum_probs=17.2
Q ss_pred CCCCceeEEEEEeCCCceEEee
Q 032998 92 GNGGTLRKVAVTVGENGIVLAS 113 (129)
Q Consensus 92 G~~~tL~rv~v~v~~~G~~~~~ 113 (129)
|.| .|.++.+++..+|...-.
T Consensus 82 ~~P-~LY~l~v~l~~~g~~~d~ 102 (110)
T PF00703_consen 82 EDP-YLYTLEVELDDDGEVLDS 102 (110)
T ss_dssp SSB-SEEEEEEEEEETTEEEEE
T ss_pred CCc-eEEEEEEEEEeCCEEEEE
Confidence 888 899999999888876533
No 481
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=21.20 E-value=58 Score=25.61 Aligned_cols=24 Identities=25% Similarity=0.812 Sum_probs=14.8
Q ss_pred EEEccCccccccc--cCccccCCCCC
Q 032998 70 ILKCHACYTITAE--IGRIFCPKCGN 93 (129)
Q Consensus 70 ~~rC~~C~k~~~~--~~~~fCp~CG~ 93 (129)
..+|..|+.++-. ..+.-||+|.-
T Consensus 172 ~~~C~~C~~v~H~~C~~~~~CpkC~R 197 (202)
T PF13901_consen 172 TVRCPKCKSVFHKSCFRKKSCPKCAR 197 (202)
T ss_pred eeeCCcCccccchhhcCCCCCCCcHh
Confidence 4678888777642 11356888864
No 482
>PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=20.55 E-value=63 Score=28.99 Aligned_cols=15 Identities=33% Similarity=0.436 Sum_probs=10.5
Q ss_pred ccCCCCCCCceeEEEEE
Q 032998 87 FCPKCGNGGTLRKVAVT 103 (129)
Q Consensus 87 fCp~CG~~~tL~rv~v~ 103 (129)
.||.|+++ |.-++..
T Consensus 54 ~CP~C~~~--L~~~~~~ 68 (483)
T PF05502_consen 54 DCPICFSP--LSVRASD 68 (483)
T ss_pred cCCCCCCc--ceeEecc
Confidence 39999996 6654444
No 483
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=20.49 E-value=66 Score=25.52 Aligned_cols=16 Identities=38% Similarity=0.960 Sum_probs=10.8
Q ss_pred ccccCCCCCCCceeEEEE
Q 032998 85 RIFCPKCGNGGTLRKVAV 102 (129)
Q Consensus 85 ~~fCp~CG~~~tL~rv~v 102 (129)
+..||+||+. .+...|
T Consensus 5 ~~~CPvC~~~--F~~~~v 20 (214)
T PF09986_consen 5 KITCPVCGKE--FKTKKV 20 (214)
T ss_pred ceECCCCCCe--eeeeEE
Confidence 3679999997 444333
No 484
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=20.38 E-value=33 Score=22.74 Aligned_cols=24 Identities=29% Similarity=0.787 Sum_probs=16.6
Q ss_pred EEccCccccccccC-----ccccCCCCCC
Q 032998 71 LKCHACYTITAEIG-----RIFCPKCGNG 94 (129)
Q Consensus 71 ~rC~~C~k~~~~~~-----~~fCp~CG~~ 94 (129)
.||.-|.++-.... ..-||.|-.-
T Consensus 5 iRC~~CnKlLa~a~~~~yle~KCPrCK~v 33 (60)
T COG4416 5 IRCAKCNKLLAEAEGQAYLEKKCPRCKEV 33 (60)
T ss_pred eehHHHhHHHHhcccceeeeecCCcccee
Confidence 68999998754321 3569999753
No 485
>PF06054 CoiA: Competence protein CoiA-like family; InterPro: IPR010330 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. Many of the members of this family are described as transcription factors. CoiA falls within a competence-specific operon in Streptococcus. CoiA is an uncharacterised protein.
Probab=20.35 E-value=57 Score=28.09 Aligned_cols=10 Identities=50% Similarity=1.477 Sum_probs=8.9
Q ss_pred ccccCCCCCC
Q 032998 85 RIFCPKCGNG 94 (129)
Q Consensus 85 ~~fCp~CG~~ 94 (129)
.-+||.||.+
T Consensus 30 ~~~CP~C~~~ 39 (375)
T PF06054_consen 30 KYFCPGCGEP 39 (375)
T ss_pred cEECCCCCCe
Confidence 5789999998
No 486
>COG1138 CcmF Cytochrome c biogenesis factor [Posttranslational modification, protein turnover, chaperones]
Probab=20.12 E-value=48 Score=31.25 Aligned_cols=18 Identities=22% Similarity=0.344 Sum_probs=14.5
Q ss_pred eeEeechHHHHHHHHHhC
Q 032998 35 VACITGDYAMQNVILQMG 52 (129)
Q Consensus 35 va~~TdDyamQNVl~~lG 52 (129)
-+-+++||++|||+.|=.
T Consensus 59 ~afv~~DFSv~yVa~nS~ 76 (648)
T COG1138 59 YAFVVSDFSVQYVAQNSN 76 (648)
T ss_pred HHHHhccHHHHHHHHhcc
Confidence 356789999999998844
No 487
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=20.08 E-value=49 Score=18.04 Aligned_cols=9 Identities=33% Similarity=0.877 Sum_probs=7.3
Q ss_pred cccCCCCCC
Q 032998 86 IFCPKCGNG 94 (129)
Q Consensus 86 ~fCp~CG~~ 94 (129)
..||+|+..
T Consensus 2 v~CPiC~~~ 10 (26)
T smart00734 2 VQCPVCFRE 10 (26)
T ss_pred CcCCCCcCc
Confidence 359999986
No 489
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=20.04 E-value=59 Score=20.46 Aligned_cols=7 Identities=43% Similarity=1.308 Sum_probs=5.9
Q ss_pred cCCCCCC
Q 032998 88 CPKCGNG 94 (129)
Q Consensus 88 Cp~CG~~ 94 (129)
|+.||++
T Consensus 2 C~iCg~k 8 (51)
T PF14471_consen 2 CAICGKK 8 (51)
T ss_pred CCccccc
Confidence 8888887
No 490
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.02 E-value=30 Score=29.67 Aligned_cols=28 Identities=32% Similarity=0.661 Sum_probs=18.9
Q ss_pred EccCccccccccCccccCCCCCCCceeEEE
Q 032998 72 KCHACYTITAEIGRIFCPKCGNGGTLRKVA 101 (129)
Q Consensus 72 rC~~C~k~~~~~~~~fCp~CG~~~tL~rv~ 101 (129)
.|.+|-..........||.|+.+ |++-.
T Consensus 30 ~C~sCv~~l~~~~~~~CP~C~~~--lrk~~ 57 (309)
T TIGR00570 30 LCESCVDLLFVRGSGSCPECDTP--LRKNN 57 (309)
T ss_pred ccHHHHHHHhcCCCCCCCCCCCc--cchhh
Confidence 58888755332234679999986 77654
Done!