Query psy7490
Match_columns 193
No_of_seqs 140 out of 559
Neff 5.1
Searched_HMMs 46136
Date Fri Aug 16 19:40:26 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy7490.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/7490hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK03988 translation initiatio 100.0 2.9E-54 6.2E-59 345.1 15.2 135 20-161 4-138 (138)
2 KOG2768|consensus 100.0 7.3E-55 1.6E-59 367.8 10.1 159 11-171 69-227 (231)
3 TIGR00311 aIF-2beta translatio 100.0 1.8E-53 4E-58 338.6 14.5 133 22-161 1-133 (133)
4 PRK12336 translation initiatio 100.0 2.7E-51 5.9E-56 344.9 14.9 137 21-164 1-137 (201)
5 smart00653 eIF2B_5 domain pres 100.0 2E-48 4.4E-53 300.9 12.6 109 47-155 2-110 (110)
6 PF01873 eIF-5_eIF-2B: Domain 100.0 7.3E-49 1.6E-53 309.3 10.1 121 36-156 4-124 (125)
7 COG1601 GCD7 Translation initi 100.0 1.3E-42 2.7E-47 281.5 7.7 144 19-167 4-147 (151)
8 KOG2767|consensus 100.0 5.2E-37 1.1E-41 274.5 5.0 119 43-161 10-133 (400)
9 KOG2768|consensus 98.6 7.9E-09 1.7E-13 88.5 1.1 43 145-193 180-222 (231)
10 PRK03988 translation initiatio 98.6 2.2E-08 4.8E-13 80.5 3.2 37 146-188 102-138 (138)
11 TIGR00311 aIF-2beta translatio 98.6 2.8E-08 6.1E-13 79.5 3.3 38 145-188 96-133 (133)
12 PRK12336 translation initiatio 98.4 1.2E-07 2.6E-12 80.2 3.3 39 146-190 98-136 (201)
13 COG1601 GCD7 Translation initi 98.0 7.3E-07 1.6E-11 72.8 -1.1 42 145-192 104-145 (151)
14 smart00653 eIF2B_5 domain pres 98.0 4.2E-06 9E-11 65.0 3.0 31 146-182 80-110 (110)
15 PF01873 eIF-5_eIF-2B: Domain 97.9 4E-06 8.7E-11 66.4 1.9 32 146-183 93-124 (125)
16 TIGR02443 conserved hypothetic 94.4 0.039 8.5E-07 38.7 2.6 39 120-159 5-44 (59)
17 PF09526 DUF2387: Probable met 94.3 0.034 7.4E-07 40.1 2.4 41 120-161 4-45 (71)
18 PF01253 SUI1: Translation ini 94.0 0.13 2.8E-06 37.5 4.9 56 63-122 20-79 (83)
19 COG1326 Uncharacterized archae 93.9 0.021 4.6E-07 48.7 0.7 36 123-158 4-42 (201)
20 PF12677 DUF3797: Domain of un 93.8 0.052 1.1E-06 36.7 2.3 32 122-154 10-46 (49)
21 PF14354 Lar_restr_allev: Rest 92.8 0.086 1.9E-06 35.8 2.2 28 127-154 5-37 (61)
22 PF04216 FdhE: Protein involve 92.7 0.063 1.4E-06 47.3 1.8 36 126-161 173-212 (290)
23 PRK00464 nrdR transcriptional 91.9 0.13 2.8E-06 42.2 2.5 30 127-156 2-38 (154)
24 PRK09710 lar restriction allev 91.8 0.17 3.7E-06 36.1 2.7 35 127-161 8-42 (64)
25 PRK03564 formate dehydrogenase 91.8 0.15 3.2E-06 46.2 3.0 36 125-160 187-226 (309)
26 TIGR01562 FdhE formate dehydro 91.4 0.12 2.7E-06 46.6 2.2 37 125-161 184-225 (305)
27 cd00474 SUI1_eIF1 The SUI1/eIF 91.4 0.4 8.8E-06 34.9 4.4 51 62-117 14-64 (77)
28 COG1997 RPL43A Ribosomal prote 89.1 0.56 1.2E-05 35.4 3.6 42 111-156 22-63 (89)
29 PF01096 TFIIS_C: Transcriptio 89.0 0.37 7.9E-06 30.6 2.2 30 126-155 1-37 (39)
30 PRK00939 translation initiatio 88.8 0.96 2.1E-05 34.5 4.8 54 60-119 36-89 (99)
31 PF13719 zinc_ribbon_5: zinc-r 88.6 0.2 4.4E-06 31.4 0.8 28 126-155 3-34 (37)
32 smart00440 ZnF_C2C2 C2C2 Zinc 88.0 0.52 1.1E-05 30.1 2.5 29 127-155 2-37 (40)
33 PF08271 TF_Zn_Ribbon: TFIIB z 87.3 0.38 8.2E-06 30.9 1.5 29 127-157 2-30 (43)
34 TIGR01158 SUI1_rel translation 87.1 1.8 3.9E-05 33.1 5.4 50 60-114 37-86 (101)
35 TIGR03655 anti_R_Lar restricti 86.9 0.73 1.6E-05 30.9 2.8 32 127-158 3-38 (53)
36 COG1198 PriA Primosomal protei 86.6 0.55 1.2E-05 47.1 2.9 52 125-191 435-492 (730)
37 COG3058 FdhE Uncharacterized p 86.3 0.25 5.3E-06 44.6 0.3 31 126-156 186-221 (308)
38 COG0023 SUI1 Translation initi 85.3 2.3 5E-05 32.9 5.2 57 58-119 37-93 (104)
39 TIGR01159 DRP1 density-regulat 84.9 1.8 3.8E-05 36.3 4.8 55 63-121 104-162 (173)
40 PF12898 Stc1: Stc1 domain; I 83.8 0.94 2E-05 33.4 2.4 70 102-182 7-84 (84)
41 PF04760 IF2_N: Translation in 82.9 1.1 2.3E-05 29.8 2.2 27 68-94 5-31 (54)
42 COG2956 Predicted N-acetylgluc 82.1 0.83 1.8E-05 42.4 1.8 79 72-190 305-385 (389)
43 PRK00415 rps27e 30S ribosomal 81.9 1 2.2E-05 31.6 1.9 30 125-156 11-40 (59)
44 TIGR01160 SUI1_MOF2 translatio 81.8 1.9 4E-05 33.7 3.5 54 62-120 40-97 (110)
45 cd04762 HTH_MerR-trunc Helix-T 81.6 4.4 9.6E-05 24.7 4.6 46 68-118 2-47 (49)
46 COG2051 RPS27A Ribosomal prote 80.9 0.91 2E-05 32.6 1.3 28 125-154 19-46 (67)
47 PF06573 Churchill: Churchill 80.4 2.1 4.5E-05 33.5 3.3 59 121-181 23-93 (112)
48 TIGR00244 transcriptional regu 80.0 1.6 3.5E-05 35.8 2.7 31 127-157 2-39 (147)
49 PRK11788 tetratricopeptide rep 80.0 1.1 2.4E-05 39.1 1.9 29 148-189 356-384 (389)
50 TIGR02159 PA_CoA_Oxy4 phenylac 79.9 0.86 1.9E-05 37.0 1.1 31 125-155 105-139 (146)
51 TIGR03655 anti_R_Lar restricti 79.8 1.7 3.6E-05 29.1 2.3 38 147-186 2-39 (53)
52 PHA02998 RNA polymerase subuni 79.1 2.1 4.5E-05 36.4 3.1 86 69-162 87-187 (195)
53 smart00834 CxxC_CXXC_SSSS Puta 79.0 0.89 1.9E-05 28.1 0.7 28 127-154 7-34 (41)
54 PRK00564 hypA hydrogenase nick 78.5 1.2 2.7E-05 34.5 1.6 58 79-156 40-98 (117)
55 PF14353 CpXC: CpXC protein 78.2 0.78 1.7E-05 35.5 0.3 18 142-159 34-51 (128)
56 PF14354 Lar_restr_allev: Rest 78.1 1.8 3.9E-05 29.2 2.1 34 147-181 4-37 (61)
57 PRK00420 hypothetical protein; 78.0 2.7 5.8E-05 32.9 3.3 32 125-160 23-54 (112)
58 PRK14714 DNA polymerase II lar 77.7 1.5 3.2E-05 46.6 2.2 23 125-156 667-689 (1337)
59 PRK14892 putative transcriptio 77.3 1.5 3.3E-05 33.6 1.6 36 123-158 19-54 (99)
60 PF11331 DUF3133: Protein of u 77.3 0.86 1.9E-05 30.4 0.3 31 125-155 6-40 (46)
61 PRK05580 primosome assembly pr 76.9 1.7 3.7E-05 42.9 2.3 45 125-183 381-431 (679)
62 PRK03824 hypA hydrogenase nick 76.8 1.6 3.4E-05 34.8 1.7 43 74-132 35-77 (135)
63 PRK06266 transcription initiat 76.6 4 8.7E-05 34.0 4.2 103 67-182 37-145 (178)
64 smart00401 ZnF_GATA zinc finge 76.5 1.4 3E-05 29.6 1.1 30 127-156 5-35 (52)
65 PRK09710 lar restriction allev 76.3 3 6.5E-05 29.7 2.8 34 147-186 7-40 (64)
66 PRK12380 hydrogenase nickel in 76.2 1.5 3.3E-05 33.8 1.5 26 79-106 40-65 (113)
67 COG3529 Predicted nucleic-acid 76.0 0.58 1.3E-05 33.2 -0.8 37 119-156 5-42 (66)
68 PF13717 zinc_ribbon_4: zinc-r 75.7 1.2 2.7E-05 27.8 0.7 9 146-154 25-33 (36)
69 TIGR00100 hypA hydrogenase nic 75.7 1.7 3.8E-05 33.6 1.6 57 79-156 40-96 (115)
70 COG1594 RPB9 DNA-directed RNA 75.6 3.5 7.7E-05 32.0 3.4 33 127-160 4-36 (113)
71 PF09297 zf-NADH-PPase: NADH p 75.5 1.3 2.9E-05 26.6 0.8 10 172-181 20-29 (32)
72 TIGR00595 priA primosomal prot 75.1 2.2 4.8E-05 40.7 2.5 39 128-183 225-263 (505)
73 cd00202 ZnF_GATA Zinc finger D 74.5 1.2 2.7E-05 30.2 0.5 30 127-156 1-31 (54)
74 smart00531 TFIIE Transcription 74.4 7.1 0.00015 31.2 4.9 27 68-94 17-47 (147)
75 PF12760 Zn_Tnp_IS1595: Transp 74.4 2.9 6.2E-05 27.1 2.2 27 126-154 19-45 (46)
76 PF14803 Nudix_N_2: Nudix N-te 73.1 2.2 4.7E-05 26.6 1.3 28 127-155 2-31 (34)
77 PF14599 zinc_ribbon_6: Zinc-r 73.0 1.3 2.9E-05 31.1 0.3 32 142-182 26-57 (61)
78 PF05129 Elf1: Transcription e 72.6 2.7 6E-05 30.8 2.0 35 123-157 20-57 (81)
79 COG4888 Uncharacterized Zn rib 72.4 2.7 5.8E-05 32.6 1.9 35 123-157 20-57 (104)
80 PF14205 Cys_rich_KTR: Cystein 72.1 3.5 7.5E-05 28.6 2.2 37 124-160 3-42 (55)
81 PF13453 zf-TFIIB: Transcripti 71.7 3.7 8E-05 26.0 2.2 27 127-154 1-27 (41)
82 PF00641 zf-RanBP: Zn-finger i 71.6 1.8 3.9E-05 25.6 0.7 9 176-184 21-29 (30)
83 PF01921 tRNA-synt_1f: tRNA sy 71.2 4.9 0.00011 37.3 3.7 52 111-162 151-215 (360)
84 TIGR00100 hypA hydrogenase nic 70.8 2.9 6.3E-05 32.4 1.8 20 125-144 86-105 (115)
85 PF14353 CpXC: CpXC protein 70.7 3.5 7.6E-05 31.8 2.3 19 168-186 33-51 (128)
86 PF02150 RNA_POL_M_15KD: RNA p 70.6 3.3 7.2E-05 25.7 1.7 31 127-159 3-33 (35)
87 TIGR02098 MJ0042_CXXC MJ0042 f 70.1 1.8 3.9E-05 26.6 0.5 8 147-154 26-33 (38)
88 PRK00398 rpoP DNA-directed RNA 70.1 2.8 6.1E-05 27.1 1.4 11 146-156 21-31 (46)
89 PRK08665 ribonucleotide-diphos 69.7 5.8 0.00012 40.0 4.1 41 111-156 688-750 (752)
90 PF08274 PhnA_Zn_Ribbon: PhnA 69.4 2.5 5.4E-05 25.7 0.9 26 126-155 3-28 (30)
91 PRK00564 hypA hydrogenase nick 69.1 3.3 7.1E-05 32.2 1.8 20 125-144 88-107 (117)
92 PRK03681 hypA hydrogenase nick 69.0 3.1 6.7E-05 32.2 1.6 25 79-105 40-64 (114)
93 COG2051 RPS27A Ribosomal prote 68.1 4.4 9.6E-05 29.1 2.2 33 142-182 15-47 (67)
94 PRK14873 primosome assembly pr 68.1 4.5 9.8E-05 40.2 3.0 23 146-183 410-432 (665)
95 PLN00209 ribosomal protein S27 68.0 3.7 7.9E-05 30.9 1.8 30 125-156 36-65 (86)
96 PF08996 zf-DNA_Pol: DNA Polym 67.1 2.1 4.6E-05 35.6 0.4 44 145-188 17-60 (188)
97 TIGR00373 conserved hypothetic 66.8 8.3 0.00018 31.4 3.8 102 67-181 29-136 (158)
98 smart00661 RPOL9 RNA polymeras 66.7 3.6 7.9E-05 26.6 1.4 32 127-160 2-34 (52)
99 PF12773 DZR: Double zinc ribb 66.5 3 6.5E-05 27.0 1.0 11 146-156 12-22 (50)
100 PF12172 DUF35_N: Rubredoxin-l 65.7 3.6 7.8E-05 25.3 1.2 16 141-156 6-21 (37)
101 PF04606 Ogr_Delta: Ogr/Delta- 65.7 5.2 0.00011 26.1 2.0 35 148-183 1-37 (47)
102 cd04761 HTH_MerR-SF Helix-Turn 65.6 14 0.00031 22.9 4.1 45 68-117 2-46 (49)
103 PRK14559 putative protein seri 65.5 4.1 8.8E-05 40.5 2.1 9 126-134 2-10 (645)
104 PTZ00083 40S ribosomal protein 65.3 4.6 9.9E-05 30.3 1.8 30 125-156 35-64 (85)
105 PRK03681 hypA hydrogenase nick 64.7 4.3 9.2E-05 31.4 1.7 19 126-144 88-106 (114)
106 PRK07451 translation initiatio 64.7 18 0.0004 28.4 5.2 51 61-116 52-102 (115)
107 COG1645 Uncharacterized Zn-fin 64.6 4.3 9.2E-05 32.7 1.7 24 127-155 30-53 (131)
108 PF05180 zf-DNL: DNL zinc fing 64.6 3.6 7.9E-05 29.4 1.1 32 127-158 6-41 (66)
109 PF01667 Ribosomal_S27e: Ribos 64.5 2.6 5.5E-05 29.2 0.3 29 125-155 7-35 (55)
110 smart00709 Zpr1 Duplicated dom 64.5 9.9 0.00021 31.3 3.9 32 127-158 2-41 (160)
111 PF00320 GATA: GATA zinc finge 64.3 1.9 4E-05 26.8 -0.3 28 128-155 1-29 (36)
112 TIGR03826 YvyF flagellar opero 64.2 7.7 0.00017 31.3 3.1 56 67-154 47-102 (137)
113 PRK09019 translation initiatio 63.8 13 0.00028 29.0 4.2 50 62-116 46-95 (108)
114 PF01155 HypA: Hydrogenase exp 63.3 3.4 7.3E-05 31.8 0.9 16 146-161 70-85 (113)
115 COG1545 Predicted nucleic-acid 63.1 4.2 9E-05 32.6 1.4 31 140-183 23-53 (140)
116 PRK00762 hypA hydrogenase nick 63.1 4.6 0.0001 31.7 1.6 25 79-105 40-64 (124)
117 PRK00762 hypA hydrogenase nick 63.0 5.2 0.00011 31.4 1.9 20 125-144 92-111 (124)
118 COG2835 Uncharacterized conser 62.7 4.1 8.8E-05 28.7 1.1 35 121-158 4-38 (60)
119 TIGR01384 TFS_arch transcripti 62.4 7.6 0.00017 28.9 2.6 31 125-155 62-99 (104)
120 PRK03824 hypA hydrogenase nick 62.1 5 0.00011 31.9 1.7 20 125-144 107-126 (135)
121 TIGR00467 lysS_arch lysyl-tRNA 61.7 9.6 0.00021 36.8 3.8 72 88-161 113-205 (515)
122 smart00659 RPOLCX RNA polymera 61.2 4.4 9.6E-05 26.5 1.0 27 127-157 4-30 (44)
123 KOG4577|consensus 61.0 3.4 7.3E-05 37.8 0.6 55 124-180 59-124 (383)
124 PRK12380 hydrogenase nickel in 61.0 5.6 0.00012 30.7 1.7 20 125-144 86-105 (113)
125 PF03604 DNA_RNApol_7kD: DNA d 60.8 5.8 0.00013 24.4 1.4 25 127-155 2-26 (32)
126 PF00165 HTH_AraC: Bacterial r 60.7 11 0.00024 23.3 2.8 28 67-94 9-36 (42)
127 PF09723 Zn-ribbon_8: Zinc rib 60.6 7.6 0.00016 24.8 2.0 28 127-154 7-34 (42)
128 PRK12496 hypothetical protein; 60.2 5.9 0.00013 32.5 1.8 39 134-183 115-153 (164)
129 PF13936 HTH_38: Helix-turn-he 60.0 8.6 0.00019 24.6 2.2 22 67-88 21-42 (44)
130 COG1327 Predicted transcriptio 59.9 6.2 0.00013 32.7 1.9 31 127-157 2-39 (156)
131 COG4888 Uncharacterized Zn rib 59.5 8 0.00017 30.0 2.3 37 146-185 22-58 (104)
132 TIGR00340 zpr1_rel ZPR1-relate 59.1 8 0.00017 32.0 2.4 30 128-157 1-39 (163)
133 KOG2767|consensus 58.7 3.2 7E-05 38.6 0.1 70 109-186 37-131 (400)
134 PRK14973 DNA topoisomerase I; 58.6 14 0.0003 38.4 4.5 61 126-191 589-652 (936)
135 PF07191 zinc-ribbons_6: zinc- 58.4 7.7 0.00017 28.1 1.9 26 126-156 2-27 (70)
136 TIGR02605 CxxC_CxxC_SSSS putat 58.2 4.3 9.4E-05 26.5 0.6 28 127-154 7-34 (52)
137 PF05379 Peptidase_C23: Carlav 57.7 10 0.00022 28.2 2.6 61 69-138 7-68 (89)
138 PRK06824 translation initiatio 57.6 19 0.00042 28.4 4.3 53 60-117 54-106 (118)
139 PF04810 zf-Sec23_Sec24: Sec23 57.6 7.5 0.00016 24.6 1.6 32 126-159 3-37 (40)
140 PF13248 zf-ribbon_3: zinc-rib 57.6 5.6 0.00012 22.9 0.9 7 127-133 4-10 (26)
141 PRK00423 tfb transcription ini 57.5 6.1 0.00013 35.3 1.6 29 125-155 11-39 (310)
142 PF08792 A2L_zn_ribbon: A2L zi 57.2 7.7 0.00017 23.9 1.5 27 126-155 4-30 (33)
143 COG1779 C4-type Zn-finger prot 56.7 15 0.00032 31.6 3.7 52 124-178 13-73 (201)
144 COG3058 FdhE Uncharacterized p 56.2 3.6 7.8E-05 37.3 -0.1 36 147-183 186-221 (308)
145 PF06322 Phage_NinH: Phage Nin 55.5 16 0.00034 26.1 3.0 37 67-110 17-53 (64)
146 PF05180 zf-DNL: DNL zinc fing 55.4 3.7 7.9E-05 29.4 -0.2 39 145-185 3-41 (66)
147 PF03367 zf-ZPR1: ZPR1 zinc-fi 55.3 11 0.00024 30.8 2.7 32 126-157 2-41 (161)
148 PHA00626 hypothetical protein 54.7 8.3 0.00018 27.0 1.5 34 127-161 2-38 (59)
149 PF01927 Mut7-C: Mut7-C RNAse 53.8 15 0.00032 29.3 3.1 37 102-138 62-104 (147)
150 PRK00432 30S ribosomal protein 53.4 7.4 0.00016 26.1 1.1 27 125-155 20-46 (50)
151 COG0375 HybF Zn finger protein 52.6 10 0.00022 29.9 1.9 18 88-105 47-64 (115)
152 KOG2907|consensus 52.4 7.3 0.00016 30.8 1.1 31 127-157 76-113 (116)
153 cd00674 LysRS_core_class_I cat 52.4 15 0.00032 33.9 3.3 90 70-161 90-207 (353)
154 PF11023 DUF2614: Protein of u 52.2 6.2 0.00013 31.1 0.7 36 124-164 68-103 (114)
155 PHA02540 61 DNA primase; Provi 51.9 16 0.00034 33.6 3.3 42 145-186 26-68 (337)
156 PF07227 DUF1423: Protein of u 51.9 12 0.00027 35.7 2.7 55 127-184 130-194 (446)
157 PF08535 KorB: KorB domain; I 51.6 13 0.00028 27.1 2.3 20 69-88 6-25 (93)
158 PRK04023 DNA polymerase II lar 51.6 11 0.00024 39.5 2.5 20 127-155 628-647 (1121)
159 smart00422 HTH_MERR helix_turn 51.5 33 0.00071 22.9 4.2 46 68-117 2-47 (70)
160 PF09756 DDRGK: DDRGK domain; 51.3 27 0.00058 29.6 4.4 48 66-116 113-163 (188)
161 PF09855 DUF2082: Nucleic-acid 51.3 11 0.00025 26.6 1.8 12 127-138 2-13 (64)
162 PRK02935 hypothetical protein; 51.1 8.7 0.00019 30.1 1.3 35 125-164 70-104 (110)
163 TIGR01562 FdhE formate dehydro 51.0 10 0.00022 34.4 1.9 43 146-189 184-226 (305)
164 PRK11827 hypothetical protein; 50.6 9.1 0.0002 26.8 1.2 36 121-159 4-39 (60)
165 COG2093 DNA-directed RNA polym 50.4 7.6 0.00017 27.7 0.8 11 127-137 20-30 (64)
166 COG3478 Predicted nucleic-acid 50.4 11 0.00023 27.2 1.5 12 125-136 4-15 (68)
167 PRK05667 dnaG DNA primase; Val 50.3 36 0.00079 33.3 5.7 63 107-185 2-69 (580)
168 COG1384 LysS Lysyl-tRNA synthe 49.8 21 0.00045 34.8 3.9 49 112-161 149-209 (521)
169 TIGR00310 ZPR1_znf ZPR1 zinc f 49.7 15 0.00032 31.2 2.6 32 127-158 2-42 (192)
170 PRK00241 nudC NADH pyrophospha 49.4 14 0.00031 32.2 2.6 39 116-157 90-128 (256)
171 PF05129 Elf1: Transcription e 49.3 11 0.00024 27.6 1.6 38 146-186 22-59 (81)
172 PRK03564 formate dehydrogenase 49.3 12 0.00027 33.9 2.2 42 146-189 187-228 (309)
173 TIGR01391 dnaG DNA primase, ca 49.0 36 0.00077 31.7 5.2 43 137-185 25-67 (415)
174 TIGR01385 TFSII transcription 48.9 15 0.00032 33.2 2.6 12 103-114 207-218 (299)
175 PRK12775 putative trifunctiona 48.7 12 0.00027 38.7 2.4 47 126-182 797-847 (1006)
176 PF10058 DUF2296: Predicted in 48.5 11 0.00024 25.6 1.4 33 145-182 21-53 (54)
177 PF01396 zf-C4_Topoisom: Topoi 48.4 18 0.00039 22.8 2.2 31 126-158 2-36 (39)
178 TIGR02494 PFLE_PFLC glycyl-rad 47.6 11 0.00023 32.7 1.5 42 121-162 20-66 (295)
179 COG3741 HutG N-formylglutamate 47.5 3.8 8.1E-05 36.7 -1.4 65 61-125 62-129 (272)
180 PF04216 FdhE: Protein involve 47.2 10 0.00022 33.3 1.4 42 146-189 172-213 (290)
181 PF06677 Auto_anti-p27: Sjogre 47.2 27 0.00059 22.5 3.0 34 116-153 8-41 (41)
182 PF05876 Terminase_GpA: Phage 46.8 17 0.00036 35.3 2.8 43 141-183 195-239 (557)
183 PF07282 OrfB_Zn_ribbon: Putat 46.6 11 0.00024 25.9 1.1 26 127-155 30-55 (69)
184 PHA02893 hypothetical protein; 46.5 11 0.00023 28.4 1.1 9 174-182 70-78 (88)
185 PF01155 HypA: Hydrogenase exp 45.6 17 0.00036 27.9 2.1 54 79-144 40-105 (113)
186 PRK06319 DNA topoisomerase I/S 45.1 31 0.00067 35.4 4.5 35 126-160 593-630 (860)
187 KOG3507|consensus 45.1 12 0.00025 26.5 1.1 25 127-155 22-46 (62)
188 COG0551 TopA Zn-finger domain 45.0 27 0.00058 27.4 3.3 52 123-185 58-113 (140)
189 COG1997 RPL43A Ribosomal prote 44.9 15 0.00033 27.7 1.8 28 147-183 36-63 (89)
190 smart00647 IBR In Between Ring 44.5 35 0.00077 22.3 3.4 37 116-155 6-49 (64)
191 PF04502 DUF572: Family of unk 44.4 19 0.00041 32.5 2.6 15 172-186 76-90 (324)
192 COG1163 DRG Predicted GTPase [ 44.3 17 0.00036 33.9 2.2 59 15-81 269-328 (365)
193 PF03966 Trm112p: Trm112p-like 44.3 13 0.00029 25.8 1.3 10 124-133 6-15 (68)
194 cd01106 HTH_TipAL-Mta Helix-Tu 44.2 45 0.00099 24.6 4.3 46 68-117 2-47 (103)
195 PRK11823 DNA repair protein Ra 44.1 13 0.00027 35.0 1.5 12 146-157 21-32 (446)
196 PF06044 DRP: Dam-replacing fa 44.1 17 0.00037 32.3 2.2 55 108-162 13-69 (254)
197 smart00249 PHD PHD zinc finger 44.0 17 0.00037 21.8 1.7 27 127-159 1-27 (47)
198 TIGR00416 sms DNA repair prote 43.3 13 0.00029 35.0 1.5 27 127-160 9-35 (454)
199 PF05077 DUF678: Protein of un 43.1 18 0.00038 26.5 1.8 10 173-182 57-66 (74)
200 cd02983 P5_C P5 family, C-term 43.0 33 0.00072 26.7 3.5 42 83-124 71-117 (130)
201 COG1096 Predicted RNA-binding 42.9 16 0.00035 31.1 1.8 48 121-182 124-174 (188)
202 COG1499 NMD3 NMD protein affec 42.7 17 0.00037 33.7 2.1 47 126-184 7-54 (355)
203 PF14768 RPA_interact_C: Repli 41.9 54 0.0012 23.8 4.2 54 103-157 23-81 (82)
204 PRK12286 rpmF 50S ribosomal pr 41.6 15 0.00033 25.3 1.2 27 122-156 24-50 (57)
205 PRK00750 lysK lysyl-tRNA synth 41.4 33 0.00071 33.0 3.8 49 112-162 153-215 (510)
206 cd01410 SIRT7 SIRT7: Eukaryoti 41.3 13 0.00028 31.3 1.0 49 132-182 80-129 (206)
207 COG2331 Uncharacterized protei 41.3 5 0.00011 29.8 -1.3 12 145-156 11-22 (82)
208 PRK14714 DNA polymerase II lar 41.2 18 0.0004 38.8 2.2 39 127-183 681-719 (1337)
209 COG5631 Predicted transcriptio 41.1 23 0.0005 30.0 2.4 31 68-98 100-130 (199)
210 TIGR01206 lysW lysine biosynth 40.9 18 0.00039 24.8 1.5 11 147-157 23-33 (54)
211 PF14116 YyzF: YyzF-like prote 40.4 44 0.00096 22.4 3.3 40 111-155 3-42 (48)
212 cd01406 SIR2-like Sir2-like: P 40.1 2.2E+02 0.0048 23.8 8.4 95 21-125 103-205 (242)
213 KOG2703|consensus 40.0 29 0.00063 33.1 3.2 31 127-157 260-298 (460)
214 TIGR02609 doc_partner putative 39.8 1.3E+02 0.0028 21.3 5.9 58 56-125 3-65 (74)
215 PHA02998 RNA polymerase subuni 39.7 33 0.00071 29.3 3.1 35 145-184 142-182 (195)
216 PRK03954 ribonuclease P protei 39.6 23 0.0005 28.1 2.1 32 127-158 66-105 (121)
217 cd01408 SIRT1 SIRT1: Eukaryoti 39.5 12 0.00026 32.2 0.5 48 131-181 100-148 (235)
218 KOG2907|consensus 39.2 22 0.00047 28.1 1.9 51 135-185 63-114 (116)
219 PRK07562 ribonucleotide-diphos 38.9 20 0.00044 38.2 2.2 15 80-94 1063-1077(1220)
220 PF02591 DUF164: Putative zinc 38.6 21 0.00045 23.9 1.5 24 108-133 31-54 (56)
221 cd03031 GRX_GRX_like Glutaredo 38.6 26 0.00056 28.3 2.3 33 143-181 107-141 (147)
222 PF15616 TerY-C: TerY-C metal 38.3 36 0.00079 27.3 3.1 45 123-167 75-126 (131)
223 PF12324 HTH_15: Helix-turn-he 38.2 55 0.0012 24.1 3.8 34 69-104 41-74 (77)
224 PF04423 Rad50_zn_hook: Rad50 38.0 19 0.00041 23.9 1.2 19 118-136 9-31 (54)
225 COG1405 SUA7 Transcription ini 37.9 19 0.0004 32.4 1.5 33 127-161 3-35 (285)
226 TIGR00280 L37a ribosomal prote 37.7 39 0.00084 25.7 3.0 43 109-156 20-63 (91)
227 PF03811 Zn_Tnp_IS1: InsA N-te 37.5 28 0.00062 21.8 1.9 11 125-135 5-15 (36)
228 PF11242 DUF2774: Protein of u 37.2 26 0.00056 24.9 1.8 44 67-110 14-57 (63)
229 PF02146 SIR2: Sir2 family; I 37.1 7.6 0.00017 31.4 -1.0 42 137-181 96-137 (178)
230 smart00342 HTH_ARAC helix_turn 37.0 47 0.001 21.9 3.1 28 67-94 51-79 (84)
231 TIGR01764 excise DNA binding d 36.7 97 0.0021 18.6 4.7 46 67-118 2-47 (49)
232 smart00497 IENR1 Intron encode 36.4 90 0.002 19.7 4.3 25 65-89 16-40 (53)
233 KOG3239|consensus 36.1 74 0.0016 27.1 4.7 47 75-121 124-174 (193)
234 PRK14295 chaperone protein Dna 36.0 28 0.00062 32.1 2.4 37 122-162 163-199 (389)
235 PRK14284 chaperone protein Dna 36.0 32 0.00069 31.8 2.8 33 123-159 156-188 (391)
236 PF14376 Haem_bd: Haem-binding 35.4 26 0.00056 27.8 1.8 25 109-139 31-55 (137)
237 PF13240 zinc_ribbon_2: zinc-r 35.4 21 0.00045 20.2 0.9 8 149-156 2-9 (23)
238 PRK14279 chaperone protein Dna 35.4 32 0.00069 31.8 2.7 35 122-160 170-204 (392)
239 PRK13130 H/ACA RNA-protein com 35.4 19 0.00042 24.9 0.9 11 175-185 19-29 (56)
240 PRK14873 primosome assembly pr 35.4 23 0.00051 35.2 1.9 39 124-183 382-420 (665)
241 PRK04136 rpl40e 50S ribosomal 35.3 22 0.00048 24.0 1.2 16 146-161 14-29 (48)
242 COG1497 Predicted transcriptio 35.1 52 0.0011 29.4 3.8 71 48-125 12-87 (260)
243 cd01279 HTH_HspR-like Helix-Tu 34.7 72 0.0016 23.6 4.1 45 68-117 3-47 (98)
244 TIGR00595 priA primosomal prot 34.6 28 0.0006 33.3 2.2 41 125-186 213-253 (505)
245 COG1996 RPC10 DNA-directed RNA 34.5 20 0.00043 24.3 0.9 32 127-161 8-39 (49)
246 PTZ00255 60S ribosomal protein 34.4 48 0.001 25.1 3.0 44 108-156 20-64 (90)
247 PF13411 MerR_1: MerR HTH fami 34.1 1E+02 0.0022 20.5 4.4 45 68-117 2-46 (69)
248 PRK10219 DNA-binding transcrip 34.1 48 0.001 24.2 3.0 27 68-94 23-49 (107)
249 cd01409 SIRT4 SIRT4: Eukaryoti 34.0 13 0.00028 32.5 -0.1 24 137-160 109-132 (260)
250 PF09332 Mcm10: Mcm10 replicat 33.9 20 0.00043 33.1 1.1 49 124-181 251-311 (344)
251 PLN03165 chaperone protein dna 33.8 55 0.0012 25.5 3.4 18 176-193 89-106 (111)
252 TIGR01031 rpmF_bact ribosomal 33.7 24 0.00052 24.1 1.2 25 123-155 24-48 (55)
253 TIGR02349 DnaJ_bact chaperone 33.6 35 0.00077 30.8 2.6 34 122-159 140-173 (354)
254 PRK14138 NAD-dependent deacety 33.6 15 0.00033 31.7 0.3 43 136-181 109-151 (244)
255 PF14446 Prok-RING_1: Prokaryo 33.4 20 0.00044 24.7 0.8 13 123-135 19-31 (54)
256 TIGR00373 conserved hypothetic 33.3 24 0.00052 28.6 1.4 35 60-94 69-104 (158)
257 PF01780 Ribosomal_L37ae: Ribo 33.3 30 0.00065 26.2 1.7 40 111-155 22-62 (90)
258 PRK14286 chaperone protein Dna 33.1 33 0.00071 31.5 2.3 36 122-161 147-182 (372)
259 cd01121 Sms Sms (bacterial rad 33.1 24 0.00053 32.5 1.5 14 145-158 13-26 (372)
260 KOG0712|consensus 33.0 29 0.00063 32.0 2.0 59 120-184 122-181 (337)
261 PRK08332 ribonucleotide-diphos 33.0 48 0.001 36.9 3.8 40 115-157 1695-1737(1740)
262 TIGR01385 TFSII transcription 33.0 37 0.00081 30.6 2.6 29 126-154 259-294 (299)
263 KOG2593|consensus 32.7 30 0.00065 33.0 2.0 66 64-155 93-162 (436)
264 cd01407 SIR2-fam SIR2 family o 32.7 21 0.00046 29.9 1.0 44 136-182 99-142 (218)
265 PF13289 SIR2_2: SIR2-like dom 32.2 2.1E+02 0.0046 21.2 9.2 97 21-125 6-112 (143)
266 PF02082 Rrf2: Transcriptional 32.0 1.1E+02 0.0024 21.5 4.6 52 67-118 26-80 (83)
267 PF05907 DUF866: Eukaryotic pr 31.9 24 0.00052 29.0 1.1 15 171-185 62-76 (161)
268 PF03833 PolC_DP2: DNA polymer 31.7 16 0.00034 37.7 0.0 21 127-156 657-677 (900)
269 PRK06599 DNA topoisomerase I; 31.6 52 0.0011 32.7 3.6 31 127-158 587-621 (675)
270 PRK14277 chaperone protein Dna 31.4 35 0.00076 31.4 2.2 33 122-158 152-184 (386)
271 PRK01310 hypothetical protein; 31.3 1.1E+02 0.0025 23.4 4.7 40 81-122 55-102 (104)
272 PF04161 Arv1: Arv1-like famil 31.2 24 0.00052 29.8 1.1 29 127-155 2-33 (208)
273 PRK07219 DNA topoisomerase I; 31.1 43 0.00093 34.1 3.0 33 126-159 603-639 (822)
274 PF05315 ICEA: ICEA Protein; 31.1 31 0.00067 30.1 1.7 61 77-140 45-116 (230)
275 PRK11788 tetratricopeptide rep 30.9 32 0.00069 29.9 1.8 44 112-162 339-384 (389)
276 KOG1603|consensus 30.8 1.2E+02 0.0027 21.0 4.6 40 81-120 20-61 (73)
277 PF04032 Rpr2: RNAse P Rpr2/Rp 30.6 60 0.0013 22.8 2.9 12 169-180 73-84 (85)
278 PRK10767 chaperone protein Dna 30.5 46 0.00099 30.4 2.8 35 122-160 139-173 (371)
279 PF05502 Dynactin_p62: Dynacti 30.5 31 0.00067 33.1 1.8 55 127-181 28-94 (483)
280 PF08772 NOB1_Zn_bind: Nin one 30.4 29 0.00062 25.2 1.2 18 167-184 3-20 (73)
281 PRK12496 hypothetical protein; 30.3 33 0.00071 28.1 1.7 25 161-185 115-139 (164)
282 PF01807 zf-CHC2: CHC2 zinc fi 30.2 47 0.001 24.6 2.4 44 136-185 23-66 (97)
283 PHA02554 13 neck protein; Prov 30.2 98 0.0021 28.4 4.8 41 77-126 5-45 (311)
284 cd01104 HTH_MlrA-CarA Helix-Tu 30.0 1.6E+02 0.0034 19.4 4.8 45 68-117 2-47 (68)
285 PF14255 Cys_rich_CPXG: Cystei 29.8 59 0.0013 22.0 2.6 36 126-161 1-39 (52)
286 COG2956 Predicted N-acetylgluc 29.7 1.3E+02 0.0027 28.4 5.5 32 124-163 354-385 (389)
287 smart00778 Prim_Zn_Ribbon Zinc 29.6 34 0.00075 21.6 1.3 30 125-154 3-33 (37)
288 PRK14973 DNA topoisomerase I; 29.6 35 0.00077 35.4 2.1 31 127-157 637-668 (936)
289 PRK14298 chaperone protein Dna 29.6 43 0.00092 30.9 2.5 34 122-159 138-171 (377)
290 PRK09678 DNA-binding transcrip 29.3 33 0.00071 24.8 1.3 29 127-156 3-39 (72)
291 COG1149 MinD superfamily P-loo 29.2 27 0.00059 31.6 1.1 28 82-109 21-52 (284)
292 PRK11511 DNA-binding transcrip 28.9 64 0.0014 24.7 3.0 28 67-94 26-53 (127)
293 COG1066 Sms Predicted ATP-depe 28.7 31 0.00067 33.1 1.4 14 145-158 20-33 (456)
294 TIGR03830 CxxCG_CxxCG_HTH puta 28.7 52 0.0011 24.6 2.5 10 128-137 1-10 (127)
295 COG1552 RPL40A Ribosomal prote 28.6 18 0.00038 24.6 -0.2 16 146-161 14-29 (50)
296 PF13408 Zn_ribbon_recom: Reco 28.5 41 0.0009 21.7 1.7 29 125-153 5-33 (58)
297 cd01411 SIR2H SIR2H: Uncharact 28.4 34 0.00074 29.1 1.5 37 136-181 108-144 (225)
298 PF13098 Thioredoxin_2: Thiore 28.4 71 0.0015 22.9 3.1 35 84-118 71-112 (112)
299 PF12728 HTH_17: Helix-turn-he 27.7 1.6E+02 0.0035 18.5 4.4 47 67-119 2-48 (51)
300 COG2023 RPR2 RNase P subunit R 27.7 51 0.0011 25.6 2.2 33 127-159 58-95 (105)
301 PRK05333 NAD-dependent deacety 27.6 21 0.00045 31.5 0.1 23 137-159 119-141 (285)
302 PRK07562 ribonucleotide-diphos 27.6 33 0.00072 36.7 1.6 11 172-182 1206-1216(1220)
303 PRK14282 chaperone protein Dna 27.6 54 0.0012 30.0 2.8 34 122-159 149-182 (369)
304 cd00592 HTH_MerR-like Helix-Tu 27.6 99 0.0022 22.3 3.7 45 68-117 2-46 (100)
305 COG1656 Uncharacterized conser 27.5 33 0.00071 28.7 1.2 71 76-156 52-140 (165)
306 PRK06393 rpoE DNA-directed RNA 27.2 25 0.00053 25.1 0.4 9 148-156 19-27 (64)
307 PF08281 Sigma70_r4_2: Sigma-7 27.2 81 0.0018 20.1 2.9 24 67-90 27-50 (54)
308 COG3677 Transposase and inacti 27.2 97 0.0021 24.5 3.8 39 120-159 25-66 (129)
309 PF07496 zf-CW: CW-type Zinc F 27.2 30 0.00065 22.8 0.8 15 172-186 2-16 (50)
310 PF08209 Sgf11: Sgf11 (transcr 27.1 24 0.00052 21.9 0.3 11 124-134 3-13 (33)
311 PF00352 TBP: Transcription fa 26.8 1.1E+02 0.0025 21.9 3.9 25 99-123 56-80 (86)
312 PF01783 Ribosomal_L32p: Ribos 26.7 27 0.00058 23.7 0.5 24 124-155 25-48 (56)
313 KOG1597|consensus 26.3 40 0.00086 30.8 1.6 29 127-156 2-31 (308)
314 PF13597 NRDD: Anaerobic ribon 26.2 94 0.002 30.2 4.3 46 103-156 458-514 (546)
315 PRK14704 anaerobic ribonucleos 25.9 1.1E+02 0.0024 30.4 4.7 40 109-156 533-582 (618)
316 PTZ00410 NAD-dependent SIR2; P 25.9 32 0.00069 31.8 1.0 48 131-181 131-179 (349)
317 cd04764 HTH_MlrA-like_sg1 Heli 25.8 2E+02 0.0043 19.2 4.7 46 68-118 2-47 (67)
318 COG0675 Transposase and inacti 25.8 36 0.00078 28.9 1.2 22 126-155 310-331 (364)
319 cd01412 SIRT5_Af1_CobB SIRT5_A 25.7 34 0.00073 28.7 1.0 42 135-182 98-139 (224)
320 KOG3084|consensus 25.6 59 0.0013 30.1 2.6 24 113-136 138-161 (345)
321 PF04981 NMD3: NMD3 family ; 25.6 31 0.00067 29.6 0.8 30 127-156 15-45 (236)
322 PF13384 HTH_23: Homeodomain-l 25.3 56 0.0012 20.5 1.8 27 67-93 18-46 (50)
323 PRK14278 chaperone protein Dna 25.2 55 0.0012 30.1 2.4 36 122-161 136-171 (378)
324 COG0484 DnaJ DnaJ-class molecu 24.9 61 0.0013 30.3 2.6 56 102-161 119-174 (371)
325 cd01413 SIR2_Af2 SIR2_Af2: Arc 24.8 29 0.00063 29.4 0.5 44 135-182 102-145 (222)
326 COG1779 C4-type Zn-finger prot 24.7 57 0.0012 28.1 2.2 41 144-184 12-54 (201)
327 PRK07726 DNA topoisomerase III 24.7 90 0.0019 30.9 3.9 8 127-134 612-619 (658)
328 TIGR01051 topA_bact DNA topois 24.7 70 0.0015 31.4 3.1 23 104-126 537-559 (610)
329 PF10825 DUF2752: Protein of u 24.6 11 0.00024 25.2 -1.7 19 171-189 7-25 (52)
330 PRK12366 replication factor A; 24.6 45 0.00098 33.0 1.8 35 140-185 526-560 (637)
331 smart00717 SANT SANT SWI3, AD 24.4 1E+02 0.0023 18.1 2.9 24 67-90 22-46 (49)
332 PRK13501 transcriptional activ 24.4 78 0.0017 27.1 3.0 28 67-94 193-220 (290)
333 COG1198 PriA Primosomal protei 24.2 60 0.0013 32.9 2.6 43 144-186 433-475 (730)
334 COG1096 Predicted RNA-binding 24.2 54 0.0012 28.0 2.0 27 125-156 149-175 (188)
335 PRK14281 chaperone protein Dna 23.9 56 0.0012 30.3 2.2 34 122-160 160-193 (397)
336 cd04476 RPA1_DBD_C RPA1_DBD_C: 23.9 65 0.0014 25.6 2.3 26 125-155 34-60 (166)
337 COG1439 Predicted nucleic acid 23.8 41 0.0009 28.4 1.2 30 140-182 133-162 (177)
338 KOG0481|consensus 23.5 1.4E+02 0.003 29.9 4.8 96 70-165 74-180 (729)
339 smart00731 SprT SprT homologue 23.5 1.2E+02 0.0026 23.9 3.8 63 108-182 80-142 (146)
340 cd00167 SANT 'SWI3, ADA2, N-Co 23.4 1E+02 0.0022 17.9 2.7 23 67-89 20-43 (45)
341 PRK14285 chaperone protein Dna 23.4 73 0.0016 29.2 2.8 34 122-159 143-176 (365)
342 PRK14291 chaperone protein Dna 23.3 63 0.0014 29.7 2.4 33 122-158 153-185 (382)
343 smart00504 Ubox Modified RING 23.2 79 0.0017 20.6 2.3 24 109-136 23-46 (63)
344 TIGR01464 hemE uroporphyrinoge 23.1 64 0.0014 28.6 2.3 57 78-139 264-327 (338)
345 PF15288 zf-CCHC_6: Zinc knuck 23.1 40 0.00087 21.9 0.8 15 147-161 2-16 (40)
346 PF02742 Fe_dep_repr_C: Iron d 22.9 11 0.00023 26.4 -2.2 62 70-132 5-66 (71)
347 KOG1296|consensus 22.9 24 0.00053 29.2 -0.3 15 146-160 64-78 (161)
348 PF11781 RRN7: RNA polymerase 22.8 59 0.0013 20.3 1.5 24 127-154 10-33 (36)
349 PF09538 FYDLN_acid: Protein o 22.8 39 0.00084 26.1 0.8 29 127-159 11-39 (108)
350 smart00132 LIM Zinc-binding do 22.8 54 0.0012 18.9 1.3 6 128-133 2-7 (39)
351 PF04472 DUF552: Protein of un 22.7 1.1E+02 0.0024 21.3 3.1 33 63-98 23-56 (73)
352 cd04763 HTH_MlrA-like Helix-Tu 22.5 2.2E+02 0.0047 19.0 4.5 46 68-118 2-48 (68)
353 PRK07220 DNA topoisomerase I; 22.4 69 0.0015 32.3 2.6 9 127-135 637-645 (740)
354 KOG2691|consensus 22.3 75 0.0016 25.0 2.3 62 106-182 47-110 (113)
355 PF15494 SRCR_2: Scavenger rec 22.3 60 0.0013 23.8 1.7 14 82-95 27-40 (98)
356 PF13921 Myb_DNA-bind_6: Myb-l 22.2 1E+02 0.0022 20.1 2.7 25 68-92 19-44 (60)
357 COG1571 Predicted DNA-binding 22.2 44 0.00096 31.8 1.2 36 121-160 346-381 (421)
358 PRK14296 chaperone protein Dna 22.2 79 0.0017 29.1 2.8 34 122-159 146-179 (372)
359 PRK14293 chaperone protein Dna 22.1 68 0.0015 29.4 2.4 34 122-159 140-173 (374)
360 PRK14301 chaperone protein Dna 22.0 72 0.0016 29.3 2.5 34 122-159 141-174 (373)
361 PRK14283 chaperone protein Dna 22.0 70 0.0015 29.3 2.4 33 123-159 144-176 (378)
362 PF14122 YokU: YokU-like prote 22.0 81 0.0018 23.8 2.3 36 148-183 1-45 (87)
363 PRK14287 chaperone protein Dna 21.9 74 0.0016 29.2 2.6 33 122-158 135-167 (371)
364 PF05046 Img2: Mitochondrial l 21.8 2.1E+02 0.0046 20.9 4.6 52 62-117 27-81 (87)
365 PRK14297 chaperone protein Dna 21.7 77 0.0017 29.1 2.6 33 122-158 145-177 (380)
366 PLN03086 PRLI-interacting fact 21.7 36 0.00078 33.5 0.5 11 123-133 405-415 (567)
367 PF10668 Phage_terminase: Phag 21.5 81 0.0018 22.0 2.1 22 67-88 23-44 (60)
368 PF03833 PolC_DP2: DNA polymer 21.5 31 0.00067 35.7 0.0 25 144-183 653-677 (900)
369 KOG2906|consensus 21.4 70 0.0015 24.8 1.9 30 127-159 3-34 (105)
370 PRK14288 chaperone protein Dna 21.3 1E+02 0.0022 28.2 3.4 45 126-180 141-185 (369)
371 PF03119 DNA_ligase_ZBD: NAD-d 21.3 39 0.00085 19.9 0.4 8 127-134 1-8 (28)
372 PF01399 PCI: PCI domain; Int 21.2 2.5E+02 0.0055 19.5 4.8 39 67-105 61-103 (105)
373 smart00547 ZnF_RBZ Zinc finger 20.9 56 0.0012 18.1 1.0 9 148-156 4-12 (26)
374 TIGR02297 HpaA 4-hydroxyphenyl 20.8 1.1E+02 0.0023 25.9 3.1 28 67-94 203-230 (287)
375 PF09567 RE_MamI: MamI restric 20.7 37 0.0008 30.6 0.3 29 123-158 80-108 (314)
376 PRK14280 chaperone protein Dna 20.7 70 0.0015 29.3 2.2 34 122-159 140-173 (376)
377 PF00249 Myb_DNA-binding: Myb- 20.7 1.1E+02 0.0023 19.3 2.5 22 68-89 23-46 (48)
378 PRK13503 transcriptional activ 20.7 1E+02 0.0022 25.8 3.0 28 67-94 188-215 (278)
379 TIGR01391 dnaG DNA primase, ca 20.6 89 0.0019 29.1 2.8 31 126-158 35-67 (415)
380 PHA02942 putative transposase; 20.5 59 0.0013 30.1 1.6 11 146-156 325-335 (383)
381 PRK13502 transcriptional activ 20.2 1.1E+02 0.0023 25.9 3.0 27 68-94 194-220 (282)
382 PF01418 HTH_6: Helix-turn-hel 20.1 1.1E+02 0.0024 21.4 2.7 28 67-95 35-62 (77)
383 PF02701 zf-Dof: Dof domain, z 20.1 61 0.0013 23.1 1.2 31 124-154 4-38 (63)
384 PHA02705 hypothetical protein; 20.1 87 0.0019 22.1 2.0 27 64-90 3-29 (72)
No 1
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=100.00 E-value=2.9e-54 Score=345.12 Aligned_cols=135 Identities=44% Similarity=0.838 Sum_probs=128.2
Q ss_pred CccHHHHHHHHHHHHHhcCCCcccCcceeeecCCCeEEEecCeeeEEeccHHHHHHcCCChHHHHHHHHHhhcCceeecC
Q psy7490 20 DYTYEELLSRVFEIMREKNPDMVAGKKQKFVMRPPQVVRIGTKKTSFANFTEICKTLHRLPKHLLDFLLAELGTSGSVDG 99 (193)
Q Consensus 20 ~~~Y~~LL~R~~~~L~~~~p~~~~~~~~R~~mP~p~v~~~Gg~KTvi~Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id~ 99 (193)
+|+|++||+|||+.| |+.. ++.+||+||+|+|.++| +||+|+||.|||++|||+|+||+|||++||||+|+++
T Consensus 4 ~~~Y~~lL~R~~~~l----p~~~-~~~~R~~~p~~~v~~eG-~kTvi~Nf~~I~~~L~R~~~hv~ky~~~ELgt~g~i~- 76 (138)
T PRK03988 4 YYDYEELLDRAYEKL----PEKV-FKESRFEVPKPDVRIEG-NRTIIRNFKEIADRLNRDPKHVAKFLLKELGTAGNIE- 76 (138)
T ss_pred ccCHHHHHHHHHHHC----cccc-CCCcceeCCCCeEEEEc-CcEEEecHHHHHHHHCCCHHHHHHHHHHHhCCceeec-
Confidence 589999999999998 8875 46789999999999997 5899999999999999999999999999999999995
Q ss_pred CCeEEEEeeccHHHHHHHHHHHhhhccccCCCCCCcceeEecCceeeccccccccccccccc
Q psy7490 100 NSQLIIKGRFQQKQIENVLRRYIKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVASI 161 (193)
Q Consensus 100 ~~~lii~G~~~~~~iq~~L~~yI~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~~~ 161 (193)
+|+++|+|+|++++||++|++||++||+|++|+||||.|+|++|+++++|+|||+.+||+++
T Consensus 77 ~~~lii~G~~~~~~i~~~L~~yI~~yVlC~~C~spdT~l~k~~r~~~l~C~ACGa~~~V~~~ 138 (138)
T PRK03988 77 GGRLILQGKFSPRVINEKIDRYVKEYVICPECGSPDTKLIKEGRIWVLKCEACGAETPVKPL 138 (138)
T ss_pred CCEEEEEEeeCHHHHHHHHHHHHHhcEECCCCCCCCcEEEEcCCeEEEEcccCCCCCcCCcC
Confidence 79999999999999999999999999999999999999999999999999999999999764
No 2
>KOG2768|consensus
Probab=100.00 E-value=7.3e-55 Score=367.77 Aligned_cols=159 Identities=72% Similarity=1.244 Sum_probs=152.8
Q ss_pred cCccccCCCCccHHHHHHHHHHHHHhcCCCcccCcceeeecCCCeEEEecCeeeEEeccHHHHHHcCCChHHHHHHHHHh
Q psy7490 11 SHTWIGSDRDYTYEELLSRVFEIMREKNPDMVAGKKQKFVMRPPQVVRIGTKKTSFANFTEICKTLHRLPKHLLDFLLAE 90 (193)
Q Consensus 11 ~~~~~~~~~~~~Y~~LL~R~~~~L~~~~p~~~~~~~~R~~mP~p~v~~~Gg~KTvi~Nf~dIak~L~R~p~hv~ky~~~E 90 (193)
+..|.+++++|.|++||.|+|.+|+++|||.+ +.+.+|.|+||||.++| +||+++||.|||+.|||.|+||++||++|
T Consensus 69 ~~~~~g~e~dy~Y~ElL~rvf~ilreknpe~a-Ge~~k~v~~PPqvlReg-kkT~f~Nf~Dick~mhR~pdHv~~FLlAE 146 (231)
T KOG2768|consen 69 GVSWVGSEPDYTYYELLSRVFNILREKNPELA-GEKRKFVMKPPQVLREG-KKTVFVNFADICKTMHRSPDHVMQFLLAE 146 (231)
T ss_pred cccccccCCCccHHHHHHHHHHHHHhcCchhc-ccccceeeCCHHHHhhc-cceeeeeHHHHHHHhccChHHHHHHHHHH
Confidence 36799999999999999999999999999986 46778999999999997 89999999999999999999999999999
Q ss_pred hcCceeecCCCeEEEEeeccHHHHHHHHHHHhhhccccCCCCCCcceeEecCceeecccccccccccccccccceeeecc
Q psy7490 91 LGTSGSVDGNSQLIIKGRFQQKQIENVLRRYIKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVASIKSGFQKDTR 170 (193)
Q Consensus 91 Lgt~g~id~~~~lii~G~~~~~~iq~~L~~yI~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~~~k~~~~~~~r 170 (193)
|||.||+|++++|+|+|+|++++||++|++||++||+|..|+||||.|.+++||+|++|++||+.++|..|++||+|...
T Consensus 147 LgTsGSidg~~rLviKGrfq~kq~e~VLRrYI~eyV~C~~CkSpdt~L~kenRLfFL~C~~cgs~~sv~~Iktgf~A~~~ 226 (231)
T KOG2768|consen 147 LGTSGSIDGQQRLVIKGRFQQKQFENVLRRYIKEYVTCKTCKSPDTILQKENRLFFLRCEKCGSRCSVASIKTGFQAVVG 226 (231)
T ss_pred hccccccCCCceEEEeccccHHHHHHHHHHHHHHheEeeecCChhHHhhhhcceEEEEecCCCCeeeeeeeecccEEecc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999765
Q ss_pred E
Q psy7490 171 L 171 (193)
Q Consensus 171 l 171 (193)
.
T Consensus 227 k 227 (231)
T KOG2768|consen 227 K 227 (231)
T ss_pred c
Confidence 3
No 3
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=100.00 E-value=1.8e-53 Score=338.63 Aligned_cols=133 Identities=36% Similarity=0.764 Sum_probs=125.7
Q ss_pred cHHHHHHHHHHHHHhcCCCcccCcceeeecCCCeEEEecCeeeEEeccHHHHHHcCCChHHHHHHHHHhhcCceeecCCC
Q psy7490 22 TYEELLSRVFEIMREKNPDMVAGKKQKFVMRPPQVVRIGTKKTSFANFTEICKTLHRLPKHLLDFLLAELGTSGSVDGNS 101 (193)
Q Consensus 22 ~Y~~LL~R~~~~L~~~~p~~~~~~~~R~~mP~p~v~~~Gg~KTvi~Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id~~~ 101 (193)
+|++||+|||+.| |+... +.+||+||+|++.++| +||+|+||.|||++|||+|+||+|||++||||+|++| +|
T Consensus 1 ~Y~~lL~R~~~~l----~~~~~-~~~R~~mP~~~v~~eG-~kTvi~Nf~~Ia~~L~R~~~~v~ky~~~ELgt~g~i~-~~ 73 (133)
T TIGR00311 1 DYEKLLERAIDQL----PDEVF-ETKRFEVPKAYIVIEG-NRTIIQNFREVAKALNRDEQHLLKYLLKELGTAGNLE-GG 73 (133)
T ss_pred CHHHHHHHHHHHC----ccccC-CCccccCCCceEEEEc-CcEEEecHHHHHHHHCCCHHHHHHHHHHHhCCCceec-CC
Confidence 5999999999998 77653 5789999999999986 5899999999999999999999999999999999997 58
Q ss_pred eEEEEeeccHHHHHHHHHHHhhhccccCCCCCCcceeEecCceeeccccccccccccccc
Q psy7490 102 QLIIKGRFQQKQIENVLRRYIKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVASI 161 (193)
Q Consensus 102 ~lii~G~~~~~~iq~~L~~yI~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~~~ 161 (193)
+++|+|+|++++||++|++||++||+|++|+||||.|+|++|+++++|+|||+.+||++|
T Consensus 74 rlii~G~~~~~~i~~~L~~yI~~yVlC~~C~sPdT~l~k~~r~~~l~C~ACGa~~~v~~~ 133 (133)
T TIGR00311 74 RLILQGKFTHFLLNERIEDYVRKYVICRECNRPDTRIIKEGRVSLLKCEACGAKAPLRNI 133 (133)
T ss_pred EEEEEeecCHHHHHHHHHHHHhheEECCCCCCCCcEEEEeCCeEEEecccCCCCCccCcC
Confidence 999999999999999999999999999999999999999999999999999999999764
No 4
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=100.00 E-value=2.7e-51 Score=344.93 Aligned_cols=137 Identities=36% Similarity=0.759 Sum_probs=129.8
Q ss_pred ccHHHHHHHHHHHHHhcCCCcccCcceeeecCCCeEEEecCeeeEEeccHHHHHHcCCChHHHHHHHHHhhcCceeecCC
Q psy7490 21 YTYEELLSRVFEIMREKNPDMVAGKKQKFVMRPPQVVRIGTKKTSFANFTEICKTLHRLPKHLLDFLLAELGTSGSVDGN 100 (193)
Q Consensus 21 ~~Y~~LL~R~~~~L~~~~p~~~~~~~~R~~mP~p~v~~~Gg~KTvi~Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id~~ 100 (193)
|+|++||+|||+.| |+.. ++.+||+||+|++.++| +||+|+||.|||++|||+|+||+|||++||||+|++| +
T Consensus 1 ~~Y~~lL~r~~~~l----~~~~-~~~~R~~~p~~~v~~eG-~kT~i~N~~~i~~~l~R~~~~~~ky~~~ELgt~~~~~-~ 73 (201)
T PRK12336 1 MDYESLLDRAMEVL----PEPT-KSGERFSIPEPKIFIEG-KTTILTNFGEIADALNRDPDHLMKFLQRELGTAGKIE-G 73 (201)
T ss_pred CCHHHHHHHHHHHC----Cccc-CCccceecCCceEEEEc-CcEEEecHHHHHHHHCCCHHHHHHHHHHHhCCcceec-C
Confidence 57999999999998 8865 46789999999999887 7999999999999999999999999999999999998 5
Q ss_pred CeEEEEeeccHHHHHHHHHHHhhhccccCCCCCCcceeEecCceeecccccccccccccccccc
Q psy7490 101 SQLIIKGRFQQKQIENVLRRYIKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVASIKSG 164 (193)
Q Consensus 101 ~~lii~G~~~~~~iq~~L~~yI~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~~~k~~ 164 (193)
|+++|||+|++++||++|++||++||+|++|+||||.|++++|+++++|+|||+.+||+++++.
T Consensus 74 ~~~ii~G~~~~~~i~~~l~~yi~~yV~C~~C~~pdT~l~k~~~~~~l~C~aCGa~~~v~~~~~~ 137 (201)
T PRK12336 74 GRAVFNGKFTEEDIQAAIDAYVDEYVICSECGLPDTRLVKEDRVLMLRCDACGAHRPVKKRKAS 137 (201)
T ss_pred CEEEEEeeeCHHHHHHHHHHHHHheEECCCCCCCCcEEEEcCCeEEEEcccCCCCccccccccc
Confidence 7999999999999999999999999999999999999999999999999999999999988743
No 5
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=100.00 E-value=2e-48 Score=300.88 Aligned_cols=109 Identities=59% Similarity=1.079 Sum_probs=106.2
Q ss_pred eeeecCCCeEEEecCeeeEEeccHHHHHHcCCChHHHHHHHHHhhcCceeecCCCeEEEEeeccHHHHHHHHHHHhhhcc
Q psy7490 47 QKFVMRPPQVVRIGTKKTSFANFTEICKTLHRLPKHLLDFLLAELGTSGSVDGNSQLIIKGRFQQKQIENVLRRYIKEYV 126 (193)
Q Consensus 47 ~R~~mP~p~v~~~Gg~KTvi~Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id~~~~lii~G~~~~~~iq~~L~~yI~~YV 126 (193)
+||+||+|++.++|.+||+|+||.|||++|||+|+||+|||++||||+|++|++|+++|+|+|++++||++|++||++||
T Consensus 2 ~R~~~p~~~v~~eG~~kTvi~Nf~~I~~~L~R~p~hv~kyl~~ELgt~g~id~~~rlii~G~~~~~~i~~~l~~yI~~yV 81 (110)
T smart00653 2 YRFKMPPPQVLREGKGKTVIVNFADIAKALNRPPDHVLKFLLAELGTQGSIDGKGRLIVNGRFTPKKLQDLLRRYIKEYV 81 (110)
T ss_pred CccccCCCeEEEEcCCeEEEEcHHHHHHHHCCCHHHHHHHHHHHhCCceeECCCCeEEEEEeeCHHHHHHHHHHHHHhcE
Confidence 68999999999998669999999999999999999999999999999999998899999999999999999999999999
Q ss_pred ccCCCCCCcceeEecCceeeccccccccc
Q psy7490 127 TCHTCRSPDTILQKDTRLFFLQCETCGSR 155 (193)
Q Consensus 127 lC~~C~sPdT~L~k~~rl~~l~C~aCGa~ 155 (193)
+|++|+||||.|++++|+++++|+|||++
T Consensus 82 lC~~C~spdT~l~k~~r~~~l~C~aCGa~ 110 (110)
T smart00653 82 LCPECGSPDTELIKENRLFFLKCEACGAR 110 (110)
T ss_pred ECCCCCCCCcEEEEeCCeEEEEccccCCC
Confidence 99999999999999999999999999984
No 6
>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=100.00 E-value=7.3e-49 Score=309.32 Aligned_cols=121 Identities=51% Similarity=0.929 Sum_probs=110.6
Q ss_pred hcCCCcccCcceeeecCCCeEEEecCeeeEEeccHHHHHHcCCChHHHHHHHHHhhcCceeecCCCeEEEEeeccHHHHH
Q psy7490 36 EKNPDMVAGKKQKFVMRPPQVVRIGTKKTSFANFTEICKTLHRLPKHLLDFLLAELGTSGSVDGNSQLIIKGRFQQKQIE 115 (193)
Q Consensus 36 ~~~p~~~~~~~~R~~mP~p~v~~~Gg~KTvi~Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id~~~~lii~G~~~~~~iq 115 (193)
++||+.......||+||+|++.++|.+||+|+||.|||++|||+|+||+|||++||||+|++|++|+|||+|+|++++||
T Consensus 4 ~~np~~~~~~~~R~kmP~~~v~~eG~~KTvi~Nf~dI~~~L~R~p~~~~ky~~~ELgt~~~id~~~~lii~G~~~~~~i~ 83 (125)
T PF01873_consen 4 EKNPERSNSDKFRYKMPPPQVKIEGKKKTVIVNFVDICKALNRDPEHVLKYFGKELGTQGSIDGKGRLIINGRFSSKQIQ 83 (125)
T ss_dssp CSSTTTSCSSSSS-CCCT--EEEETSTEEEETTHHHHHHHHTSSHHHHHHHHHHHSSSEEEEETTTEEEEESSSSCCHHH
T ss_pred HhCcCcccCCCcceecCCCeEEEEccceeeeecHHHHHHHHCCCHHHHHHHHHHHHCCceEECCCCEEEEEEecCHHHHH
Confidence 34799543344699999999999987899999999999999999999999999999999999988999999999999999
Q ss_pred HHHHHHhhhccccCCCCCCcceeEecCceeecccccccccc
Q psy7490 116 NVLRRYIKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRC 156 (193)
Q Consensus 116 ~~L~~yI~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~ 156 (193)
++|++||++||+|++|+||||.|++++|+++++|.|||+.+
T Consensus 84 ~~L~~fI~~yVlC~~C~spdT~l~k~~r~~~l~C~aCGa~~ 124 (125)
T PF01873_consen 84 DLLDKFIKEYVLCPECGSPDTELIKEGRLIFLKCKACGASR 124 (125)
T ss_dssp HHHHHHHCHHSSCTSTSSSSEEEEEETTCCEEEETTTSCEE
T ss_pred HHHHHHHHHEEEcCCCCCCccEEEEcCCEEEEEecccCCcC
Confidence 99999999999999999999999999999999999999975
No 7
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.3e-42 Score=281.47 Aligned_cols=144 Identities=41% Similarity=0.779 Sum_probs=133.2
Q ss_pred CCccHHHHHHHHHHHHHhcCCCcccCcceeeecCCCeEEEecCeeeEEeccHHHHHHcCCChHHHHHHHHHhhcCceeec
Q psy7490 19 RDYTYEELLSRVFEIMREKNPDMVAGKKQKFVMRPPQVVRIGTKKTSFANFTEICKTLHRLPKHLLDFLLAELGTSGSVD 98 (193)
Q Consensus 19 ~~~~Y~~LL~R~~~~L~~~~p~~~~~~~~R~~mP~p~v~~~Gg~KTvi~Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id 98 (193)
..++|++||+|+|+.| |+.....+.||.||+|.+.++| .+|++.||.|||++|||||+|+++||.+||||+|++|
T Consensus 4 ~~~~yeelLeR~~~~l----P~~~~~~~~R~~ip~~~i~~~g-~~Ti~~Nf~dia~~l~rDp~h~~k~l~kel~t~g~~d 78 (151)
T COG1601 4 MEDDYEELLERAYSEL----PEKEVKNDERFRIPEPEINREG-NRTIIRNFGDIAEALNRDPEHLVKFLKKELGTAGSID 78 (151)
T ss_pred hhhhHHHHHHHHHHhC----CccccccccceecCCcceeccc-chhHHHhHHHHHHHhcCCHHHHHHHHHHHhccccccC
Confidence 3568999999999775 9986433449999999999885 5999999999999999999999999999999999999
Q ss_pred CCCeEEEEeeccHHHHHHHHHHHhhhccccCCCCCCcceeEecCceeecccccccccccccccccceee
Q psy7490 99 GNSQLIIKGRFQQKQIENVLRRYIKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVASIKSGFQK 167 (193)
Q Consensus 99 ~~~~lii~G~~~~~~iq~~L~~yI~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~~~k~~~~~ 167 (193)
++++|+|+|+|+++.|++.|++||..||.|++|++|||.|++++|+++++|.|||+.+||..++.+...
T Consensus 79 ~~~rlvl~g~f~~~~i~~~i~~yi~~yv~C~~c~s~dt~l~~~~R~~~l~c~acGa~~pv~~~~~~~~~ 147 (151)
T COG1601 79 GKGRLVLQGKFSDSEIVNEIERYIAEYVKCKECGSPDTELIKEERLLFLKCEACGAIRPVKLMKEYNLD 147 (151)
T ss_pred CcceEEEEecccHHHHHHHHHHHHHheeEeccCCCCchhhhhhhhhHhhHHHHhCCcccchhhhhcchh
Confidence 889999999999999999999999999999999999999999999999999999999999988876544
No 8
>KOG2767|consensus
Probab=100.00 E-value=5.2e-37 Score=274.53 Aligned_cols=119 Identities=28% Similarity=0.480 Sum_probs=112.5
Q ss_pred cCcceeeecCCCeEEEec---CeeeEEeccHHHHHHcCCChHHHHHHHHHhhcCceeecC-CCeEEEEeeccHHHHHHHH
Q psy7490 43 AGKKQKFVMRPPQVVRIG---TKKTSFANFTEICKTLHRLPKHLLDFLLAELGTSGSVDG-NSQLIIKGRFQQKQIENVL 118 (193)
Q Consensus 43 ~~~~~R~~mP~p~v~~~G---g~KTvi~Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id~-~~~lii~G~~~~~~iq~~L 118 (193)
.+..|||+||+++...+| |+||+|+|+.|||+||+|||.|++|||++|||+|+.||. +||+++||.|.+.+||++|
T Consensus 10 ~D~FYRYKMPrl~aKvEGKGNGIKTvIvNm~eIakAL~RPp~Y~tKyFGcELGAQT~fd~kn~ryiVNG~Hd~~KLqdlL 89 (400)
T KOG2767|consen 10 RDPFYRYKMPRLQAKVEGKGNGIKTVIVNMVEIAKALGRPPLYPTKYFGCELGAQTKFDVKNGRYIVNGAHEASKLQDLL 89 (400)
T ss_pred cchhhhhccchhhhhccccCCCeeeeeecHHHHHHHhCCCCCcccccceeeccccccccccCCeeeecccccHHHHHHHH
Confidence 467899999999998887 999999999999999999999999999999999999994 8999999999999999999
Q ss_pred HHHhhhccccCCCCCCcceeEec-Cceeeccccccccccccccc
Q psy7490 119 RRYIKEYVTCHTCRSPDTILQKD-TRLFFLQCETCGSRCSVASI 161 (193)
Q Consensus 119 ~~yI~~YVlC~~C~sPdT~L~k~-~rl~~l~C~aCGa~~~V~~~ 161 (193)
+.||++||+||+|+||||.|+.. +..+.+.|.|||.++.++..
T Consensus 90 dgFIkKFVlC~~C~NPETel~itk~q~i~~~CkACG~r~~~d~r 133 (400)
T KOG2767|consen 90 DGFIKKFVLCPSCENPETELIITKKQTISLKCKACGFRSDMDLR 133 (400)
T ss_pred HHHHHHheeCcCCCCCceeEEecccchhhhHHHHcCCcccccch
Confidence 99999999999999999999864 67789999999999999874
No 9
>KOG2768|consensus
Probab=98.64 E-value=7.9e-09 Score=88.45 Aligned_cols=43 Identities=63% Similarity=1.160 Sum_probs=40.2
Q ss_pred eecccccccccccccccccceeeeccEEEEEecccCCCccccccccCCC
Q psy7490 145 FFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRCSVASIKSGFQ 193 (193)
Q Consensus 145 ~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~~v~~~~~~~~ 193 (193)
.|+.|..|.++. +.+++.+|||||+|+.||+.++|.+||+||+
T Consensus 180 eyV~C~~CkSpd------t~L~kenRLfFL~C~~cgs~~sv~~Iktgf~ 222 (231)
T KOG2768|consen 180 EYVTCKTCKSPD------TILQKENRLFFLRCEKCGSRCSVASIKTGFQ 222 (231)
T ss_pred HheEeeecCChh------HHhhhhcceEEEEecCCCCeeeeeeeecccE
Confidence 489999999998 7778889999999999999999999999996
No 10
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=98.62 E-value=2.2e-08 Score=80.51 Aligned_cols=37 Identities=32% Similarity=0.860 Sum_probs=34.9
Q ss_pred ecccccccccccccccccceeeeccEEEEEecccCCCcccccc
Q psy7490 146 FLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRCSVASI 188 (193)
Q Consensus 146 ~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~~v~~~ 188 (193)
|+.|..||++. |.+.+..|+|+++|+||||++||++|
T Consensus 102 yVlC~~C~spd------T~l~k~~r~~~l~C~ACGa~~~V~~~ 138 (138)
T PRK03988 102 YVICPECGSPD------TKLIKEGRIWVLKCEACGAETPVKPL 138 (138)
T ss_pred cEECCCCCCCC------cEEEEcCCeEEEEcccCCCCCcCCcC
Confidence 89999999998 88888999999999999999999875
No 11
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=98.61 E-value=2.8e-08 Score=79.49 Aligned_cols=38 Identities=26% Similarity=0.713 Sum_probs=35.2
Q ss_pred eecccccccccccccccccceeeeccEEEEEecccCCCcccccc
Q psy7490 145 FFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRCSVASI 188 (193)
Q Consensus 145 ~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~~v~~~ 188 (193)
.|+.|..||++. |.+.+..|+|+++|+||||++||++|
T Consensus 96 ~yVlC~~C~sPd------T~l~k~~r~~~l~C~ACGa~~~v~~~ 133 (133)
T TIGR00311 96 KYVICRECNRPD------TRIIKEGRVSLLKCEACGAKAPLRNI 133 (133)
T ss_pred heEECCCCCCCC------cEEEEeCCeEEEecccCCCCCccCcC
Confidence 379999999998 88888999999999999999999875
No 12
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=98.45 E-value=1.2e-07 Score=80.19 Aligned_cols=39 Identities=28% Similarity=0.759 Sum_probs=36.4
Q ss_pred ecccccccccccccccccceeeeccEEEEEecccCCCcccccccc
Q psy7490 146 FLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRCSVASIKS 190 (193)
Q Consensus 146 ~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~~v~~~~~ 190 (193)
|+.|..||++. |.+.+..|+|+++|.||||++||.++|.
T Consensus 98 yV~C~~C~~pd------T~l~k~~~~~~l~C~aCGa~~~v~~~~~ 136 (201)
T PRK12336 98 YVICSECGLPD------TRLVKEDRVLMLRCDACGAHRPVKKRKA 136 (201)
T ss_pred eEECCCCCCCC------cEEEEcCCeEEEEcccCCCCcccccccc
Confidence 89999999998 8888889999999999999999998764
No 13
>COG1601 GCD7 Translation initiation factor 2, beta subunit (eIF-2beta)/eIF-5 N-terminal domain [Translation, ribosomal structure and biogenesis]
Probab=98.01 E-value=7.3e-07 Score=72.83 Aligned_cols=42 Identities=36% Similarity=0.742 Sum_probs=37.7
Q ss_pred eecccccccccccccccccceeeeccEEEEEecccCCCccccccccCC
Q psy7490 145 FFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRCSVASIKSGF 192 (193)
Q Consensus 145 ~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~~v~~~~~~~ 192 (193)
.|++|..||+.. +.++...|+|+++|+||||.+||..++.|.
T Consensus 104 ~yv~C~~c~s~d------t~l~~~~R~~~l~c~acGa~~pv~~~~~~~ 145 (151)
T COG1601 104 EYVKCKECGSPD------TELIKEERLLFLKCEACGAIRPVKLMKEYN 145 (151)
T ss_pred heeEeccCCCCc------hhhhhhhhhHhhHHHHhCCcccchhhhhcc
Confidence 489999999998 777888999999999999999999777664
No 14
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=98.00 E-value=4.2e-06 Score=65.02 Aligned_cols=31 Identities=48% Similarity=1.153 Sum_probs=29.3
Q ss_pred ecccccccccccccccccceeeeccEEEEEecccCCC
Q psy7490 146 FLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSR 182 (193)
Q Consensus 146 ~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~ 182 (193)
|+.|..||++. |.+.+..|+|+++|+||||+
T Consensus 80 yVlC~~C~spd------T~l~k~~r~~~l~C~aCGa~ 110 (110)
T smart00653 80 YVLCPECGSPD------TELIKENRLFFLKCEACGAR 110 (110)
T ss_pred cEECCCCCCCC------cEEEEeCCeEEEEccccCCC
Confidence 79999999998 88999999999999999995
No 15
>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=97.94 E-value=4e-06 Score=66.42 Aligned_cols=32 Identities=38% Similarity=0.940 Sum_probs=30.2
Q ss_pred ecccccccccccccccccceeeeccEEEEEecccCCCc
Q psy7490 146 FLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRC 183 (193)
Q Consensus 146 ~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~ 183 (193)
|+.|..|+++. |.+++..|+|+++|.||||++
T Consensus 93 yVlC~~C~spd------T~l~k~~r~~~l~C~aCGa~~ 124 (125)
T PF01873_consen 93 YVLCPECGSPD------TELIKEGRLIFLKCKACGASR 124 (125)
T ss_dssp HSSCTSTSSSS------EEEEEETTCCEEEETTTSCEE
T ss_pred EEEcCCCCCCc------cEEEEcCCEEEEEecccCCcC
Confidence 79999999998 889899999999999999986
No 16
>TIGR02443 conserved hypothetical metal-binding protein. Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various Proteobacteria.
Probab=94.36 E-value=0.039 Score=38.69 Aligned_cols=39 Identities=26% Similarity=0.646 Sum_probs=31.1
Q ss_pred HHhhhccccCCCCCCccee-EecCceeeccccccccccccc
Q psy7490 120 RYIKEYVTCHTCRSPDTIL-QKDTRLFFLQCETCGSRCSVA 159 (193)
Q Consensus 120 ~yI~~YVlC~~C~sPdT~L-~k~~rl~~l~C~aCGa~~~V~ 159 (193)
+||.- ..||.|+..||.. .+++++.++.|-.||.....+
T Consensus 5 RFIAG-A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~~~~ 44 (59)
T TIGR02443 5 RFIAG-AVCPACSAQDTLAMWKENNIELVECVECGYQEQQK 44 (59)
T ss_pred eEecc-ccCCCCcCccEEEEEEeCCceEEEeccCCCccccC
Confidence 34443 4799999999965 578999999999999987543
No 17
>PF09526 DUF2387: Probable metal-binding protein (DUF2387); InterPro: IPR012658 Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=94.33 E-value=0.034 Score=40.15 Aligned_cols=41 Identities=24% Similarity=0.643 Sum_probs=32.0
Q ss_pred HHhhhccccCCCCCCcceeE-ecCceeeccccccccccccccc
Q psy7490 120 RYIKEYVTCHTCRSPDTILQ-KDTRLFFLQCETCGSRCSVASI 161 (193)
Q Consensus 120 ~yI~~YVlC~~C~sPdT~L~-k~~rl~~l~C~aCGa~~~V~~~ 161 (193)
+||.- ..||.|++-||... +++++.++.|-+||.....+.-
T Consensus 4 rFIAG-a~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~~~~~ 45 (71)
T PF09526_consen 4 RFIAG-AVCPKCQAMDTIMMWRENGVEYVECVECGYTERQPDQ 45 (71)
T ss_pred eEecC-ccCCCCcCccEEEEEEeCCceEEEecCCCCeeccCCc
Confidence 34443 47999999999664 7888999999999998755433
No 18
>PF01253 SUI1: Translation initiation factor SUI1; InterPro: IPR001950 In Saccharomyces cerevisiae (Baker's yeast), SUI1 is a translation initiation factor that functions in concert with eIF-2 and the initiator tRNA-Met in directing the ribosome to the proper start site of translation []. SUI1 is a protein of 108 residues. Close homologs of SUI1 have been found [] in mammals, insects and plants. SUI1 is also evolutionary related to hypothetical proteins from Escherichia coli (yciH), Haemophilus influenzae (HI1225) and Methanococcus vannielii.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2OGH_A 1D1R_A 2IF1_A 2XZN_F 2XZM_F.
Probab=93.97 E-value=0.13 Score=37.46 Aligned_cols=56 Identities=16% Similarity=0.149 Sum_probs=41.3
Q ss_pred eeEEeccHHHHHHcCCChHHHHHHHHHhhcCceeecC----CCeEEEEeeccHHHHHHHHHHHh
Q psy7490 63 KTSFANFTEICKTLHRLPKHLLDFLLAELGTSGSVDG----NSQLIIKGRFQQKQIENVLRRYI 122 (193)
Q Consensus 63 KTvi~Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id~----~~~lii~G~~~~~~iq~~L~~yI 122 (193)
=|+|.||. .-.=+++-+++.|...+|++|++.. ...+.|+|.|...-.+-++.+|+
T Consensus 20 vT~V~gl~----~~~~d~~~lak~lkk~~ac~~sv~~~~~k~~~I~iQGd~~~~i~~~L~~~~~ 79 (83)
T PF01253_consen 20 VTIVSGLE----LFGIDLKELAKELKKKFACGGSVTKDPGKGEEIQIQGDHRDEIKDLLVEKGG 79 (83)
T ss_dssp EEEEES------STTSHHHHHHHHHHHHHTS-EEEEE-TTTSSEEEEESS-HHHHHHHHHHHCS
T ss_pred EEEEECCc----ccccCHHHHHHHHHHhccCceEEeecCCCCCEEEECCcHHHHHHHHHHHhCC
Confidence 37788888 3455889999999999999999942 45699999999887776666654
No 19
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=93.91 E-value=0.021 Score=48.69 Aligned_cols=36 Identities=28% Similarity=0.679 Sum_probs=29.9
Q ss_pred hhccccCCCCCCcc--eeEec-Cceeecccccccccccc
Q psy7490 123 KEYVTCHTCRSPDT--ILQKD-TRLFFLQCETCGSRCSV 158 (193)
Q Consensus 123 ~~YVlC~~C~sPdT--~L~k~-~rl~~l~C~aCGa~~~V 158 (193)
..|..||+|++-|| +++|+ ++-..++|..||.-.|.
T Consensus 4 ~iy~~Cp~Cg~eev~hEVik~~g~~~lvrC~eCG~V~~~ 42 (201)
T COG1326 4 EIYIECPSCGSEEVSHEVIKERGREPLVRCEECGTVHPA 42 (201)
T ss_pred eEEEECCCCCcchhhHHHHHhcCCceEEEccCCCcEeec
Confidence 35889999999999 88886 55567999999998854
No 20
>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=93.81 E-value=0.052 Score=36.70 Aligned_cols=32 Identities=25% Similarity=0.638 Sum_probs=25.3
Q ss_pred hhhccccCCCCCC-----cceeEecCceeecccccccc
Q psy7490 122 IKEYVTCHTCRSP-----DTILQKDTRLFFLQCETCGS 154 (193)
Q Consensus 122 I~~YVlC~~C~sP-----dT~L~k~~rl~~l~C~aCGa 154 (193)
..+|+.||.|+|- |-.|+.+..++...|+ ||-
T Consensus 10 ~~kY~~Cp~CGN~~vGngEG~liV~edtfkRtCk-CGf 46 (49)
T PF12677_consen 10 SNKYCKCPKCGNDKVGNGEGTLIVEEDTFKRTCK-CGF 46 (49)
T ss_pred hhhhccCcccCCcEeecCcceEEEeccceeeeec-ccc
Confidence 4569999999974 4577888888888887 774
No 21
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=92.79 E-value=0.086 Score=35.78 Aligned_cols=28 Identities=29% Similarity=1.005 Sum_probs=19.6
Q ss_pred ccCCCCCCcceeEecCce-----eecccccccc
Q psy7490 127 TCHTCRSPDTILQKDTRL-----FFLQCETCGS 154 (193)
Q Consensus 127 lC~~C~sPdT~L~k~~rl-----~~l~C~aCGa 154 (193)
-||-|++++..+...... +++.|..||+
T Consensus 5 PCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 5 PCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 599997777666654332 6788888887
No 22
>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=92.70 E-value=0.063 Score=47.32 Aligned_cols=36 Identities=25% Similarity=0.552 Sum_probs=18.2
Q ss_pred cccCCCCCC-cceeEec-C--ceeeccccccccccccccc
Q psy7490 126 VTCHTCRSP-DTILQKD-T--RLFFLQCETCGSRCSVASI 161 (193)
Q Consensus 126 VlC~~C~sP-dT~L~k~-~--rl~~l~C~aCGa~~~V~~~ 161 (193)
-.||.||++ ....++. + +.-|+.|.-||..-....+
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~ 212 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRI 212 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE--TT
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCC
Confidence 489999995 5555543 3 5678999999987655444
No 23
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=91.86 E-value=0.13 Score=42.23 Aligned_cols=30 Identities=33% Similarity=0.695 Sum_probs=23.1
Q ss_pred ccCCCCCCcceeEe-----cCcee--ecccccccccc
Q psy7490 127 TCHTCRSPDTILQK-----DTRLF--FLQCETCGSRC 156 (193)
Q Consensus 127 lC~~C~sPdT~L~k-----~~rl~--~l~C~aCGa~~ 156 (193)
.||.|++|+|..+. ++.+. +-+|..||.+-
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence 69999999998875 22122 48999999876
No 24
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=91.76 E-value=0.17 Score=36.06 Aligned_cols=35 Identities=20% Similarity=0.525 Sum_probs=26.8
Q ss_pred ccCCCCCCcceeEecCceeeccccccccccccccc
Q psy7490 127 TCHTCRSPDTILQKDTRLFFLQCETCGSRCSVASI 161 (193)
Q Consensus 127 lC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~~~ 161 (193)
-||-|+-.+-.+.-.++-+++.|..||+..+...-
T Consensus 8 PCPFCG~~~~~v~~~~g~~~v~C~~CgA~~~~~~t 42 (64)
T PRK09710 8 PCPFCGCPSVTVKAISGYYRAKCNGCESRTGYGGS 42 (64)
T ss_pred CCCCCCCceeEEEecCceEEEEcCCCCcCcccccC
Confidence 48888888777776777777888888888766543
No 25
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=91.76 E-value=0.15 Score=46.23 Aligned_cols=36 Identities=28% Similarity=0.560 Sum_probs=25.3
Q ss_pred ccccCCCCC-CcceeEe---cCceeecccccccccccccc
Q psy7490 125 YVTCHTCRS-PDTILQK---DTRLFFLQCETCGSRCSVAS 160 (193)
Q Consensus 125 YVlC~~C~s-PdT~L~k---~~rl~~l~C~aCGa~~~V~~ 160 (193)
--.||.|++ |...+++ +++.-|++|.-|+..-.+..
T Consensus 187 ~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R 226 (309)
T PRK03564 187 RQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVR 226 (309)
T ss_pred CCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccC
Confidence 478999999 4445443 35677898888887765543
No 26
>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=91.40 E-value=0.12 Score=46.62 Aligned_cols=37 Identities=24% Similarity=0.622 Sum_probs=25.4
Q ss_pred ccccCCCCCCcc-eeEe----cCceeeccccccccccccccc
Q psy7490 125 YVTCHTCRSPDT-ILQK----DTRLFFLQCETCGSRCSVASI 161 (193)
Q Consensus 125 YVlC~~C~sPdT-~L~k----~~rl~~l~C~aCGa~~~V~~~ 161 (193)
--.||.|+++=+ .+++ +++.-|+.|.-|+..-.+..+
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~ 225 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRV 225 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCc
Confidence 448999999543 4443 356778999888887655433
No 27
>cd00474 SUI1_eIF1 The SUI1/eIF1 (eukaryotic initiation factor 1) fold is found in eukaryotes, archaea, and some bacteria and is thought to play an important role in accurate initiator codon recognition during translation initiation. This fold, which includes two antiparallel alpha helices packed against the same side of a five-strand beta sheet, is structurally similar to other RNA-binding domains suggesting that SUI1/eIF1 may bind RNA. Point mutations in the yeast eIF1 implicate the protein in maintaining accurate start-site selection but its mechanism of action is unknown.
Probab=91.35 E-value=0.4 Score=34.88 Aligned_cols=51 Identities=18% Similarity=0.148 Sum_probs=40.7
Q ss_pred eeeEEeccHHHHHHcCCChHHHHHHHHHhhcCceeecCCCeEEEEeeccHHHHHHH
Q psy7490 62 KKTSFANFTEICKTLHRLPKHLLDFLLAELGTSGSVDGNSQLIIKGRFQQKQIENV 117 (193)
Q Consensus 62 ~KTvi~Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id~~~~lii~G~~~~~~iq~~ 117 (193)
.=|+|.+|..-.. +++-+.+.|.+.+|+.|++. ++.+.|+|.+...-.+-+
T Consensus 14 ~VT~I~Gl~~~~~----dlk~l~k~lKk~~~cggtv~-~~~I~lQGD~r~~v~~~L 64 (77)
T cd00474 14 TVTTVQGLDLEYA----DLKKLAKELKKKCACGGTVK-DEVIELQGDQRKKIKEFL 64 (77)
T ss_pred cEEEEECCCCchH----hHHHHHHHHHHHcCCCcEEe-cCEEEEeCcHHHHHHHHH
Confidence 4578888864322 78999999999999999997 579999999987655443
No 28
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=89.08 E-value=0.56 Score=35.41 Aligned_cols=42 Identities=17% Similarity=0.559 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHhhhccccCCCCCCcceeEecCceeecccccccccc
Q psy7490 111 QKQIENVLRRYIKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRC 156 (193)
Q Consensus 111 ~~~iq~~L~~yI~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~ 156 (193)
...+.++...=.+.| .||.|+++ |.-....++| .|..||+.-
T Consensus 22 Rrrv~~ie~~~~~~~-~Cp~C~~~-~VkR~a~GIW--~C~kCg~~f 63 (89)
T COG1997 22 RRRVKEIEAQQRAKH-VCPFCGRT-TVKRIATGIW--KCRKCGAKF 63 (89)
T ss_pred HHHHHHHHHHHhcCC-cCCCCCCc-ceeeeccCeE--EcCCCCCee
Confidence 345555555555666 79999999 5444456775 799999864
No 29
>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=88.97 E-value=0.37 Score=30.64 Aligned_cols=30 Identities=23% Similarity=0.770 Sum_probs=17.6
Q ss_pred cccCCCCCCcceeEe-------cCceeeccccccccc
Q psy7490 126 VTCHTCRSPDTILQK-------DTRLFFLQCETCGSR 155 (193)
Q Consensus 126 VlC~~C~sPdT~L~k-------~~rl~~l~C~aCGa~ 155 (193)
+.||.|++.++...- +.-..|..|..||..
T Consensus 1 ~~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~ 37 (39)
T PF01096_consen 1 IKCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHR 37 (39)
T ss_dssp S--SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEE
T ss_pred CCCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCe
Confidence 358888888876652 233667778778753
No 30
>PRK00939 translation initiation factor Sui1; Reviewed
Probab=88.81 E-value=0.96 Score=34.52 Aligned_cols=54 Identities=19% Similarity=0.273 Sum_probs=41.0
Q ss_pred cCeeeEEeccHHHHHHcCCChHHHHHHHHHhhcCceeecCCCeEEEEeeccHHHHHHHHH
Q psy7490 60 GTKKTSFANFTEICKTLHRLPKHLLDFLLAELGTSGSVDGNSQLIIKGRFQQKQIENVLR 119 (193)
Q Consensus 60 Gg~KTvi~Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id~~~~lii~G~~~~~~iq~~L~ 119 (193)
|..=|+|.||..- .=+++-+++.|.+.+|+.|++. ++.+.|+|.|...-. ++|.
T Consensus 36 gK~VTiI~Gl~~~----~~~lk~l~k~lKk~~gcGgsvk-~~~I~iQGD~r~~v~-~~L~ 89 (99)
T PRK00939 36 GKEVTIIEGIDPK----DIDLKELAKKLKSKLACGGTVK-DGRIELQGDHRERVK-ELLI 89 (99)
T ss_pred CceEEEEeCCCCc----chhHHHHHHHHHHHhCCCceEE-CCEEEEeCcHHHHHH-HHHH
Confidence 3445889999642 2257889999999999999996 568999999987654 4443
No 31
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=88.62 E-value=0.2 Score=31.45 Aligned_cols=28 Identities=36% Similarity=0.896 Sum_probs=18.0
Q ss_pred cccCCCCC----CcceeEecCceeeccccccccc
Q psy7490 126 VTCHTCRS----PDTILQKDTRLFFLQCETCGSR 155 (193)
Q Consensus 126 VlC~~C~s----PdT~L~k~~rl~~l~C~aCGa~ 155 (193)
+.||.|+. ||..|...++ .++|..||..
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~--~vrC~~C~~~ 34 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGR--KVRCPKCGHV 34 (37)
T ss_pred EECCCCCceEEcCHHHcccCCc--EEECCCCCcE
Confidence 56777774 5555554444 4777777764
No 32
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=88.03 E-value=0.52 Score=30.13 Aligned_cols=29 Identities=24% Similarity=0.738 Sum_probs=20.8
Q ss_pred ccCCCCCCcceeEe-------cCceeeccccccccc
Q psy7490 127 TCHTCRSPDTILQK-------DTRLFFLQCETCGSR 155 (193)
Q Consensus 127 lC~~C~sPdT~L~k-------~~rl~~l~C~aCGa~ 155 (193)
.||.|++.+....- +.-..|..|..||..
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~ 37 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHR 37 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCE
Confidence 68999988887642 233667888888864
No 33
>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=87.30 E-value=0.38 Score=30.85 Aligned_cols=29 Identities=28% Similarity=0.511 Sum_probs=18.7
Q ss_pred ccCCCCCCcceeEecCceeeccccccccccc
Q psy7490 127 TCHTCRSPDTILQKDTRLFFLQCETCGSRCS 157 (193)
Q Consensus 127 lC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~ 157 (193)
.||.|++.+ ++-+...-.+.|..||..-.
T Consensus 2 ~Cp~Cg~~~--~~~D~~~g~~vC~~CG~Vl~ 30 (43)
T PF08271_consen 2 KCPNCGSKE--IVFDPERGELVCPNCGLVLE 30 (43)
T ss_dssp SBTTTSSSE--EEEETTTTEEEETTT-BBEE
T ss_pred CCcCCcCCc--eEEcCCCCeEECCCCCCEee
Confidence 599999977 33333333568999997643
No 34
>TIGR01158 SUI1_rel translation initation factor SUI1, putative, prokaryotic. This family of archaeal and bacterial proteins is homologous to the eukaryotic translation intiation factor SUI1 involved in directing the ribosome to the proper start site of translation by functioning in concert with eIF-2 and the initiator tRNA-Met.
Probab=87.07 E-value=1.8 Score=33.05 Aligned_cols=50 Identities=20% Similarity=0.203 Sum_probs=39.9
Q ss_pred cCeeeEEeccHHHHHHcCCChHHHHHHHHHhhcCceeecCCCeEEEEeeccHHHH
Q psy7490 60 GTKKTSFANFTEICKTLHRLPKHLLDFLLAELGTSGSVDGNSQLIIKGRFQQKQI 114 (193)
Q Consensus 60 Gg~KTvi~Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id~~~~lii~G~~~~~~i 114 (193)
|..=|+|.||..-. -+++-+++.|.+.+|+.|++. ++.+.|+|.|...-.
T Consensus 37 gK~VTvV~Gl~~~~----~~l~~l~k~LKk~~gcGgtvk-~~~IeiQGD~~~~v~ 86 (101)
T TIGR01158 37 GKGVTIIEGLDLSD----IDLKELAKELKSKCGCGGTVK-DGVIEIQGDHRDRVK 86 (101)
T ss_pred CCEEEEEeCCcCch----hhHHHHHHHHHHHhcCCeeEe-CCEEEEeCcHHHHHH
Confidence 34568999995322 367889999999999999995 679999999987644
No 35
>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=86.87 E-value=0.73 Score=30.87 Aligned_cols=32 Identities=31% Similarity=0.789 Sum_probs=17.9
Q ss_pred ccCCCCCCcceeEe--c--Cceeecccccccccccc
Q psy7490 127 TCHTCRSPDTILQK--D--TRLFFLQCETCGSRCSV 158 (193)
Q Consensus 127 lC~~C~sPdT~L~k--~--~rl~~l~C~aCGa~~~V 158 (193)
-||-|++.+-.+.. + +...+..|..||+..++
T Consensus 3 PCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~~ 38 (53)
T TIGR03655 3 PCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGPV 38 (53)
T ss_pred CCCCCCCcceeeEeccCCCCCEEEEECCCCCCCccc
Confidence 37888875554431 1 12223367777777665
No 36
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=86.59 E-value=0.55 Score=47.12 Aligned_cols=52 Identities=23% Similarity=0.547 Sum_probs=34.2
Q ss_pred ccccCCCCCCc------ceeEecCceeecccccccccccccccccceeeeccEEEEEecccCCCccccccccC
Q psy7490 125 YVTCHTCRSPD------TILQKDTRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRCSVASIKSG 191 (193)
Q Consensus 125 YVlC~~C~sPd------T~L~k~~rl~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~~v~~~~~~ 191 (193)
+|+|..|+..- ..|.-....-.++|.-||+..+++ .+|..||+. .+.....|
T Consensus 435 ~l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p--------------~~Cp~Cgs~-~L~~~G~G 492 (730)
T COG1198 435 LLLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIP--------------QSCPECGSE-HLRAVGPG 492 (730)
T ss_pred eeecccCCCcccCCCCCcceEEecCCCeeEeCCCCCCCCCC--------------CCCCCCCCC-eeEEeccc
Confidence 78888887632 233333223458999999986443 369999998 55555444
No 37
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=86.27 E-value=0.25 Score=44.55 Aligned_cols=31 Identities=26% Similarity=0.584 Sum_probs=23.8
Q ss_pred cccCCCCC-CcceeEec----Cceeecccccccccc
Q psy7490 126 VTCHTCRS-PDTILQKD----TRLFFLQCETCGSRC 156 (193)
Q Consensus 126 VlC~~C~s-PdT~L~k~----~rl~~l~C~aCGa~~ 156 (193)
-.||.|+| |=+.++.. .++-|++|.-|-..-
T Consensus 186 ~~CPvCGS~PvaSmV~~g~~~~GlRYL~CslC~teW 221 (308)
T COG3058 186 QYCPVCGSMPVASMVQIGETEQGLRYLHCSLCETEW 221 (308)
T ss_pred ccCCCcCCCCcceeeeecCccccchhhhhhhHHHHH
Confidence 37999998 77888764 478888888776544
No 38
>COG0023 SUI1 Translation initiation factor 1 (eIF-1/SUI1) and related proteins [Translation, ribosomal structure and biogenesis]
Probab=85.27 E-value=2.3 Score=32.94 Aligned_cols=57 Identities=21% Similarity=0.244 Sum_probs=44.9
Q ss_pred EecCeeeEEeccHHHHHHcCCChHHHHHHHHHhhcCceeecCCCeEEEEeeccHHHHHHHHH
Q psy7490 58 RIGTKKTSFANFTEICKTLHRLPKHLLDFLLAELGTSGSVDGNSQLIIKGRFQQKQIENVLR 119 (193)
Q Consensus 58 ~~Gg~KTvi~Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id~~~~lii~G~~~~~~iq~~L~ 119 (193)
+-|..-|+|.+|.. -.-+++-+++.|-+.+|+.|++. +|...|+|.|..+-.+-++.
T Consensus 37 r~gK~VTiI~Gld~----~~~dlk~Lak~LKk~cacGGtvk-~~~IeiQGdhr~~v~~~L~~ 93 (104)
T COG0023 37 RKGKTVTIIEGLDL----KDIDLKKLAKELKKKCACGGTVK-DGEIEIQGDHRDKVKELLIK 93 (104)
T ss_pred cCCcEEEEEeCccc----chhhHHHHHHHHHHHcCCCceec-CCEEEEeChHHHHHHHHHHH
Confidence 34555788999887 33467889999999999999996 66999999998776555443
No 39
>TIGR01159 DRP1 density-regulated protein DRP1. This protein family shows weak but suggestive similarity to translation initiation factor SUI1 and its prokaryotic homologs.
Probab=84.94 E-value=1.8 Score=36.33 Aligned_cols=55 Identities=15% Similarity=0.232 Sum_probs=45.2
Q ss_pred eeEEeccHHHHHHcCCChHHHHHHHHHhhcCceeec----CCCeEEEEeeccHHHHHHHHHHH
Q psy7490 63 KTSFANFTEICKTLHRLPKHLLDFLLAELGTSGSVD----GNSQLIIKGRFQQKQIENVLRRY 121 (193)
Q Consensus 63 KTvi~Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id----~~~~lii~G~~~~~~iq~~L~~y 121 (193)
=|+|.+|... .-++.-+.|+|...+++.+++. +++.++|+|.|...-.+=++.+|
T Consensus 104 VT~V~GLe~f----~idlk~laK~lkkkfacG~SV~k~~~~~~eI~IQGD~~~~v~e~L~~~~ 162 (173)
T TIGR01159 104 VTVIKGLETF----DIDLKKASKTFAQKFATGCSVSKSVTGKEEIVIQGDVMDDIEDYIHEKW 162 (173)
T ss_pred EEEEeCCcCC----CcCHHHHHHHHHHHhCCCCccccCCCCCCEEEecCCHHHHHHHHHHHHc
Confidence 4888998763 4589999999999999998763 36799999999998887776666
No 40
>PF12898 Stc1: Stc1 domain; InterPro: IPR024630 The domain contains 8 conserved cysteines that may bind to zinc. In S. pombe, proteins containing the domain act as protein linkers, which link the chromatin modifying CLRC complex to RNAi by tethering it to the RITS complex. This domain has a slightly different arrangement of its CxxC pairs from the LIM domain, hence it is not part of that family []. The tandem zinc-finger structure could mediate protein-protein interactions.
Probab=83.77 E-value=0.94 Score=33.37 Aligned_cols=70 Identities=19% Similarity=0.427 Sum_probs=45.4
Q ss_pred eEEEEeeccHHHHHHHHHHHhhh-------ccccCCCCCCcceeEecCceeeccccccccccccccc-ccceeeeccEEE
Q psy7490 102 QLIIKGRFQQKQIENVLRRYIKE-------YVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVASI-KSGFQKDTRLFF 173 (193)
Q Consensus 102 ~lii~G~~~~~~iq~~L~~yI~~-------YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~~~-k~~~~~~~rl~~ 173 (193)
...-.+.|+..+++.+-..-... ++.|.+|.+..+ ..+.|..|+...|++.. |+.......-
T Consensus 7 ~~k~~~~FS~~Ql~~~~~~~~~~~~~~~~~~i~C~~ct~~q~--------~El~C~~C~~~k~ld~FSK~QR~~~~~a-- 76 (84)
T PF12898_consen 7 KWKPLSAFSKNQLEKLRKQIRANRVDPANSGIRCRECTGGQV--------VELTCSPCGKTKPLDEFSKNQRRKPDPA-- 76 (84)
T ss_pred eECChHHcCHHHHHHHHHHHhhccCccCCCCCCCccCCCCCc--------CcCEeccCCCCcCHHHHhHHhhcCCCcc--
Confidence 33445688998888865544444 699999987543 34599999999999876 3332222111
Q ss_pred EEecccCCC
Q psy7490 174 LQCETCGSR 182 (193)
Q Consensus 174 ~~c~~Cga~ 182 (193)
.|..|-+|
T Consensus 77 -~C~~Cv~~ 84 (84)
T PF12898_consen 77 -RCKDCVQW 84 (84)
T ss_pred -cchhhhcC
Confidence 67666543
No 41
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=82.91 E-value=1.1 Score=29.78 Aligned_cols=27 Identities=30% Similarity=0.431 Sum_probs=22.8
Q ss_pred ccHHHHHHcCCChHHHHHHHHHhhcCc
Q psy7490 68 NFTEICKTLHRLPKHLLDFLLAELGTS 94 (193)
Q Consensus 68 Nf~dIak~L~R~p~hv~ky~~~ELgt~ 94 (193)
...|+|+.|+.++..|.+.+..++|..
T Consensus 5 ~V~elAk~l~v~~~~ii~~l~~~~Gi~ 31 (54)
T PF04760_consen 5 RVSELAKELGVPSKEIIKKLFKELGIM 31 (54)
T ss_dssp -TTHHHHHHSSSHHHHHHHH-HHHTS-
T ss_pred EHHHHHHHHCcCHHHHHHHHHHhCCcC
Confidence 357999999999999999999999987
No 42
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=82.09 E-value=0.83 Score=42.36 Aligned_cols=79 Identities=13% Similarity=0.370 Sum_probs=46.6
Q ss_pred HHHHcCCChHHHH--HHHHHhhcCceeecCCCeEEEEeeccHHHHHHHHHHHhhhccccCCCCCCcceeEecCceeeccc
Q psy7490 72 ICKTLHRLPKHLL--DFLLAELGTSGSVDGNSQLIIKGRFQQKQIENVLRRYIKEYVTCHTCRSPDTILQKDTRLFFLQC 149 (193)
Q Consensus 72 Iak~L~R~p~hv~--ky~~~ELgt~g~id~~~~lii~G~~~~~~iq~~L~~yI~~YVlC~~C~sPdT~L~k~~rl~~l~C 149 (193)
+-+.|+|.|.... +++..+|.-. ++|+ ++-+-..+.+++..=|.. ...-+|
T Consensus 305 l~~Ql~r~Pt~~gf~rl~~~~l~da----eeg~----~k~sL~~lr~mvge~l~~-------------------~~~YRC 357 (389)
T COG2956 305 LTRQLRRKPTMRGFHRLMDYHLADA----EEGR----AKESLDLLRDMVGEQLRR-------------------KPRYRC 357 (389)
T ss_pred HHHHHhhCCcHHHHHHHHHhhhccc----cccc----hhhhHHHHHHHHHHHHhh-------------------cCCcee
Confidence 4467888887543 4444444321 1333 444445555555543332 234578
Q ss_pred ccccccccccccccceeeeccEEEEEecccCCCcccccccc
Q psy7490 150 ETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRCSVASIKS 190 (193)
Q Consensus 150 ~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~~v~~~~~ 190 (193)
..||... ++++-+|.+|.+|-||+.|+.
T Consensus 358 ~~CGF~a-------------~~l~W~CPsC~~W~TikPir~ 385 (389)
T COG2956 358 QNCGFTA-------------HTLYWHCPSCRAWETIKPIRG 385 (389)
T ss_pred cccCCcc-------------eeeeeeCCCcccccccCCccc
Confidence 8888753 567788888888888887763
No 43
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=81.86 E-value=1 Score=31.58 Aligned_cols=30 Identities=20% Similarity=0.657 Sum_probs=21.7
Q ss_pred ccccCCCCCCcceeEecCceeecccccccccc
Q psy7490 125 YVTCHTCRSPDTILQKDTRLFFLQCETCGSRC 156 (193)
Q Consensus 125 YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~ 156 (193)
-|.||.|++..|..-.-.. .+.|..||..=
T Consensus 11 ~VkCp~C~n~q~vFsha~t--~V~C~~Cg~~L 40 (59)
T PRK00415 11 KVKCPDCGNEQVVFSHAST--VVRCLVCGKTL 40 (59)
T ss_pred EEECCCCCCeEEEEecCCc--EEECcccCCCc
Confidence 4788888888777766554 37888888753
No 44
>TIGR01160 SUI1_MOF2 translation initiation factor SUI1, eukaryotic. Alternate name: MOF2. A similar protein family (see TIGRFAMs model TIGR01158) is found in prokaryotes. The human proteins complements a yeast SUI1 mutatation.
Probab=81.76 E-value=1.9 Score=33.71 Aligned_cols=54 Identities=15% Similarity=0.218 Sum_probs=40.5
Q ss_pred eeeEEeccHHHHHHcCCChHHHHHHHHHhhcCceeecC----CCeEEEEeeccHHHHHHHHHH
Q psy7490 62 KKTSFANFTEICKTLHRLPKHLLDFLLAELGTSGSVDG----NSQLIIKGRFQQKQIENVLRR 120 (193)
Q Consensus 62 ~KTvi~Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id~----~~~lii~G~~~~~~iq~~L~~ 120 (193)
.=|+|.+|.+ .=+-.-++|.|.+.+|+.|++.+ ++.+.|+|.|..+-.+-+...
T Consensus 40 ~VTiI~Gl~~-----~~dlk~l~K~lKkk~~cGGsVk~~~~~~~~IelQGD~re~v~~~L~~~ 97 (110)
T TIGR01160 40 TLTTVQGLPK-----EYDLKKIVKALKKEFACNGTVIEDPEMGEVIQLQGDQRKNVCEFLISQ 97 (110)
T ss_pred cEEEEeccCC-----hHHHHHHHHHHHHHhCCCceEEeCCCCCCEEEEeCcHHHHHHHHHHHc
Confidence 3477888873 23457899999999999999864 257899999987766655444
No 45
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=81.59 E-value=4.4 Score=24.70 Aligned_cols=46 Identities=17% Similarity=0.201 Sum_probs=33.5
Q ss_pred ccHHHHHHcCCChHHHHHHHHHhhcCceeecCCCeEEEEeeccHHHHHHHH
Q psy7490 68 NFTEICKTLHRLPKHLLDFLLAELGTSGSVDGNSQLIIKGRFQQKQIENVL 118 (193)
Q Consensus 68 Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id~~~~lii~G~~~~~~iq~~L 118 (193)
+..|+|+.|+.++..|.+|........... ++++. .|+.++|..++
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~g~~~~~~~-~~~~~----~~~~~ei~~~~ 47 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKEGKLKAIRT-PGGHR----RFPEEDLERLL 47 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcCCCCceeC-CCCce----ecCHHHHHHHH
Confidence 578999999999999999998766543322 23333 47888887765
No 46
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=80.90 E-value=0.91 Score=32.63 Aligned_cols=28 Identities=21% Similarity=0.695 Sum_probs=14.4
Q ss_pred ccccCCCCCCcceeEecCceeecccccccc
Q psy7490 125 YVTCHTCRSPDTILQKDTRLFFLQCETCGS 154 (193)
Q Consensus 125 YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa 154 (193)
+|.||.|++--|..-.-. ..++|..||.
T Consensus 19 ~VkCpdC~N~q~vFshas--t~V~C~~CG~ 46 (67)
T COG2051 19 RVKCPDCGNEQVVFSHAS--TVVTCLICGT 46 (67)
T ss_pred EEECCCCCCEEEEeccCc--eEEEeccccc
Confidence 456666665554443332 2355666654
No 47
>PF06573 Churchill: Churchill protein; InterPro: IPR009508 This family consists of several eukaryotic Churchill proteins. This protein contains a novel zinc binding region that mediates FGF signalling during neural development. The slow induction by FGF of a transcription factor (Churchill) in the neural plate in turn induces expression of Sip1 (Smad interacting protein-1), which inhibits mesodermal genes and sensitizes cells to later neural inducing factors [].; GO: 0008270 zinc ion binding, 0007275 multicellular organismal development, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2JOX_A.
Probab=80.41 E-value=2.1 Score=33.55 Aligned_cols=59 Identities=24% Similarity=0.610 Sum_probs=34.0
Q ss_pred HhhhccccCCCCCCcceeEe------cCc----eeeccccccccccccccccccee--eeccEEEEEecccCC
Q psy7490 121 YIKEYVTCHTCRSPDTILQK------DTR----LFFLQCETCGSRCSVASIKSGFQ--KDTRLFFLQCETCGS 181 (193)
Q Consensus 121 yI~~YVlC~~C~sPdT~L~k------~~r----l~~l~C~aCGa~~~V~~~k~~~~--~~~rl~~~~c~~Cga 181 (193)
|+-.|+-|.+|++-|-.++. +++ .+.-.|..|+.. |+.+-=.|. -..+-|-+.|..||.
T Consensus 23 yllN~~~Ca~C~krdfv~i~nk~~~eedgeEivTY~HvC~nC~Hv--IA~HEYtF~V~~~yQeY~M~ClLCG~ 93 (112)
T PF06573_consen 23 YLLNFVGCASCQKRDFVLISNKSIEEEDGEEIVTYDHVCKNCHHV--IARHEYTFSVVDDYQEYTMLCLLCGK 93 (112)
T ss_dssp -TTTB---SSS--SS-EEEEEEEEEEETTEEEEEEEEEETTT--E--EEEEEEEEEEETTEEEEEEEETTTEE
T ss_pred eeeechhhhccCCCCcEEEecccccccCCcEEEEeeeccCccceE--EEeeeEEEEEeccchhhhHHHHHhCC
Confidence 67789999999999977663 222 556788888864 233333332 356779999999996
No 48
>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=79.99 E-value=1.6 Score=35.79 Aligned_cols=31 Identities=23% Similarity=0.508 Sum_probs=23.1
Q ss_pred ccCCCCCCcceeEe-----cCcee--eccccccccccc
Q psy7490 127 TCHTCRSPDTILQK-----DTRLF--FLQCETCGSRCS 157 (193)
Q Consensus 127 lC~~C~sPdT~L~k-----~~rl~--~l~C~aCGa~~~ 157 (193)
.||-|+++||..+- ++..+ --.|.+||.+-+
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFT 39 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFT 39 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccc
Confidence 59999999998873 33222 367999999873
No 49
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=79.95 E-value=1.1 Score=39.15 Aligned_cols=29 Identities=24% Similarity=0.818 Sum_probs=20.8
Q ss_pred ccccccccccccccccceeeeccEEEEEecccCCCccccccc
Q psy7490 148 QCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRCSVASIK 189 (193)
Q Consensus 148 ~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~~v~~~~ 189 (193)
.|..||... ..|+..|..||++-|++.|+
T Consensus 356 ~c~~cg~~~-------------~~~~~~c~~c~~~~~~~~~~ 384 (389)
T PRK11788 356 RCRNCGFTA-------------RTLYWHCPSCKAWETIKPIR 384 (389)
T ss_pred ECCCCCCCC-------------ccceeECcCCCCccCcCCcc
Confidence 377777654 56888888888887776554
No 50
>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=79.92 E-value=0.86 Score=36.96 Aligned_cols=31 Identities=26% Similarity=0.544 Sum_probs=23.0
Q ss_pred ccccCCCCCCcceeEec-Cce---eeccccccccc
Q psy7490 125 YVTCHTCRSPDTILQKD-TRL---FFLQCETCGSR 155 (193)
Q Consensus 125 YVlC~~C~sPdT~L~k~-~rl---~~l~C~aCGa~ 155 (193)
-|.||.|+|.+|+++-. +.. -..+|.+|..+
T Consensus 105 ~~~cp~c~s~~t~~~s~fg~t~cka~~~c~~c~ep 139 (146)
T TIGR02159 105 SVQCPRCGSADTTITSIFGPTACKALYRCRACKEP 139 (146)
T ss_pred CCcCCCCCCCCcEeecCCCChhhHHHhhhhhhCCc
Confidence 38999999999999875 211 13578888765
No 51
>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=79.83 E-value=1.7 Score=29.11 Aligned_cols=38 Identities=26% Similarity=0.640 Sum_probs=23.0
Q ss_pred cccccccccccccccccceeeeccEEEEEecccCCCcccc
Q psy7490 147 LQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRCSVA 186 (193)
Q Consensus 147 l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~~v~ 186 (193)
.-|..||...- .++.++.-...-.+..|..|||..++.
T Consensus 2 kPCPfCGg~~~--~~~~~~~~~~~~~~~~C~~Cga~~~~~ 39 (53)
T TIGR03655 2 KPCPFCGGADV--YLRRGFDPLDLSHYFECSTCGASGPVE 39 (53)
T ss_pred CCCCCCCCcce--eeEeccCCCCCEEEEECCCCCCCcccc
Confidence 35999999753 122222222222233999999999883
No 52
>PHA02998 RNA polymerase subunit; Provisional
Probab=79.05 E-value=2.1 Score=36.45 Aligned_cols=86 Identities=21% Similarity=0.447 Sum_probs=50.6
Q ss_pred cHHHHHHcC---CChHHHHHHHHHhh-----cCceeecCCCeEEEEeeccHHHHHHHHHHHhhhccccCCCCCCcceeE-
Q psy7490 69 FTEICKTLH---RLPKHLLDFLLAEL-----GTSGSVDGNSQLIIKGRFQQKQIENVLRRYIKEYVTCHTCRSPDTILQ- 139 (193)
Q Consensus 69 f~dIak~L~---R~p~hv~ky~~~EL-----gt~g~id~~~~lii~G~~~~~~iq~~L~~yI~~YVlC~~C~sPdT~L~- 139 (193)
..|||..++ =-...+++|++.-+ |+.-.||.=. .++-+.-=+++.. +.-|.||.|++.++...
T Consensus 87 y~~lc~~ir~tng~eke~lry~lfgikcv~~~veydid~~~------d~~y~~yfnvlpk--kt~v~CPkCg~~~A~f~q 158 (195)
T PHA02998 87 YKDLCDMIRGTNGTEKEILRYLLFGIKCIKKGVEYDIDKIP------DVDYDDYFNVLDE--KYNTPCPNCKSKNTTPMM 158 (195)
T ss_pred HHHHHHHHHhcCCchHHHHHHHHHHHHHHhcCCccchhhcc------cccchhheeccCc--ccCCCCCCCCCCceEEEE
Confidence 467887664 45678899997655 3333333200 0111111112221 14589999999998653
Q ss_pred ---e---cCceeecccccccccccccccc
Q psy7490 140 ---K---DTRLFFLQCETCGSRCSVASIK 162 (193)
Q Consensus 140 ---k---~~rl~~l~C~aCGa~~~V~~~k 162 (193)
+ |.-+.|.+|..||..-.-+..+
T Consensus 159 lQTRSADEPmT~FYkC~~CG~~wkppkf~ 187 (195)
T PHA02998 159 IQTRAADEPPLVRHACRDCKKHFKPPKFR 187 (195)
T ss_pred EeeccCCCCceEEEEcCCCCCccCCcccc
Confidence 2 3458899999999876555544
No 53
>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=79.00 E-value=0.89 Score=28.10 Aligned_cols=28 Identities=29% Similarity=0.599 Sum_probs=12.2
Q ss_pred ccCCCCCCcceeEecCceeecccccccc
Q psy7490 127 TCHTCRSPDTILQKDTRLFFLQCETCGS 154 (193)
Q Consensus 127 lC~~C~sPdT~L~k~~rl~~l~C~aCGa 154 (193)
.|++|+..=+.+.....-....|..||+
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 7 RCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 4555555433333221122345555555
No 54
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=78.54 E-value=1.2 Score=34.54 Aligned_cols=58 Identities=22% Similarity=0.231 Sum_probs=29.4
Q ss_pred ChHHHHHHHHHhhcCcee-ecCCCeEEEEeeccHHHHHHHHHHHhhhccccCCCCCCcceeEecCceeecccccccccc
Q psy7490 79 LPKHLLDFLLAELGTSGS-VDGNSQLIIKGRFQQKQIENVLRRYIKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRC 156 (193)
Q Consensus 79 ~p~hv~ky~~~ELgt~g~-id~~~~lii~G~~~~~~iq~~L~~yI~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~ 156 (193)
+|+.|.-.| +.-+.|+ +-++-+|.|.- +.--+.|..|+...+. + ...+.+|..||+++
T Consensus 40 ~pe~L~faf--~~~~~~T~~~ega~L~Ie~--------------vp~~~~C~~Cg~~~~~---~-~~~~~~CP~Cgs~~ 98 (117)
T PRK00564 40 DKSLFVSAF--ETFREESLVCKDAILDIVD--------------EKVELECKDCSHVFKP---N-ALDYGVCEKCHSKN 98 (117)
T ss_pred CHHHHHHHH--HHHhcCCcccCCCEEEEEe--------------cCCEEEhhhCCCcccc---C-CccCCcCcCCCCCc
Confidence 455444443 2345566 55566676642 2335567777732211 1 11234677777664
No 55
>PF14353 CpXC: CpXC protein
Probab=78.17 E-value=0.78 Score=35.48 Aligned_cols=18 Identities=28% Similarity=0.792 Sum_probs=12.7
Q ss_pred Cceeeccccccccccccc
Q psy7490 142 TRLFFLQCETCGSRCSVA 159 (193)
Q Consensus 142 ~rl~~l~C~aCGa~~~V~ 159 (193)
+.++...|..||+...+.
T Consensus 34 g~l~~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 34 GSLFSFTCPSCGHKFRLE 51 (128)
T ss_pred CCcCEEECCCCCCceecC
Confidence 556677777777777664
No 56
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=78.13 E-value=1.8 Score=29.20 Aligned_cols=34 Identities=26% Similarity=0.763 Sum_probs=20.1
Q ss_pred cccccccccccccccccceeeeccEEEEEecccCC
Q psy7490 147 LQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGS 181 (193)
Q Consensus 147 l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga 181 (193)
.-|.-||..........++.... .+++.|..|||
T Consensus 4 kPCPFCG~~~~~~~~~~~~~~~~-~~~V~C~~Cga 37 (61)
T PF14354_consen 4 KPCPFCGSADVLIRQDEGFDYGM-YYYVECTDCGA 37 (61)
T ss_pred cCCCCCCCcceEeecccCCCCCC-EEEEEcCCCCC
Confidence 45999987753322221111110 19999999999
No 57
>PRK00420 hypothetical protein; Validated
Probab=78.02 E-value=2.7 Score=32.95 Aligned_cols=32 Identities=31% Similarity=0.443 Sum_probs=24.3
Q ss_pred ccccCCCCCCcceeEecCceeecccccccccccccc
Q psy7490 125 YVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVAS 160 (193)
Q Consensus 125 YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~~ 160 (193)
--.||.|++|=+.+ +++. ..|..||..-.|..
T Consensus 23 ~~~CP~Cg~pLf~l-k~g~---~~Cp~Cg~~~~v~~ 54 (112)
T PRK00420 23 SKHCPVCGLPLFEL-KDGE---VVCPVHGKVYIVKS 54 (112)
T ss_pred cCCCCCCCCcceec-CCCc---eECCCCCCeeeecc
Confidence 35899999998888 5554 46999999766643
No 58
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=77.66 E-value=1.5 Score=46.55 Aligned_cols=23 Identities=22% Similarity=0.621 Sum_probs=13.9
Q ss_pred ccccCCCCCCcceeEecCceeecccccccccc
Q psy7490 125 YVTCHTCRSPDTILQKDTRLFFLQCETCGSRC 156 (193)
Q Consensus 125 YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~ 156 (193)
...||.|+.+-. ...|..||++.
T Consensus 667 ~rkCPkCG~~t~---------~~fCP~CGs~t 689 (1337)
T PRK14714 667 RRRCPSCGTETY---------ENRCPDCGTHT 689 (1337)
T ss_pred EEECCCCCCccc---------cccCcccCCcC
Confidence 457888887521 12666666664
No 59
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=77.28 E-value=1.5 Score=33.59 Aligned_cols=36 Identities=14% Similarity=0.451 Sum_probs=24.9
Q ss_pred hhccccCCCCCCcceeEecCceeecccccccccccc
Q psy7490 123 KEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSV 158 (193)
Q Consensus 123 ~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V 158 (193)
..++.||.|+++--.+..+++...+.|..||....-
T Consensus 19 pt~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 19 PKIFECPRCGKVSISVKIKKNIAIITCGNCGLYTEF 54 (99)
T ss_pred CcEeECCCCCCeEeeeecCCCcceEECCCCCCccCE
Confidence 467889999964222334456778999999987643
No 60
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=77.26 E-value=0.86 Score=30.43 Aligned_cols=31 Identities=23% Similarity=0.591 Sum_probs=22.3
Q ss_pred ccccCCCCC----CcceeEecCceeeccccccccc
Q psy7490 125 YVTCHTCRS----PDTILQKDTRLFFLQCETCGSR 155 (193)
Q Consensus 125 YVlC~~C~s----PdT~L~k~~rl~~l~C~aCGa~ 155 (193)
||.|.+|.. |......+++..-++|.+|...
T Consensus 6 Fv~C~~C~~lLqlP~~~~~~~k~~~klrCGaCs~v 40 (46)
T PF11331_consen 6 FVVCSSCFELLQLPAKFSLSKKNQQKLRCGACSEV 40 (46)
T ss_pred EeECccHHHHHcCCCccCCCccceeEEeCCCCcee
Confidence 788999964 6666655555677888888754
No 61
>PRK05580 primosome assembly protein PriA; Validated
Probab=76.94 E-value=1.7 Score=42.94 Aligned_cols=45 Identities=27% Similarity=0.599 Sum_probs=26.7
Q ss_pred ccccCCCCCC------cceeEecCceeecccccccccccccccccceeeeccEEEEEecccCCCc
Q psy7490 125 YVTCHTCRSP------DTILQKDTRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRC 183 (193)
Q Consensus 125 YVlC~~C~sP------dT~L~k~~rl~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~ 183 (193)
||.|..|+.+ |..|.-...--.+.|..||...+++. .|..||+..
T Consensus 381 ~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~~~--------------~Cp~Cg~~~ 431 (679)
T PRK05580 381 FLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPIPK--------------ACPECGSTD 431 (679)
T ss_pred ceEhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCCCCCC--------------CCCCCcCCe
Confidence 5666666643 23333221222488999998864443 388998864
No 62
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=76.84 E-value=1.6 Score=34.79 Aligned_cols=43 Identities=16% Similarity=0.241 Sum_probs=21.2
Q ss_pred HHcCCChHHHHHHHHHhhcCceeecCCCeEEEEeeccHHHHHHHHHHHhhhccccCCCC
Q psy7490 74 KTLHRLPKHLLDFLLAELGTSGSVDGNSQLIIKGRFQQKQIENVLRRYIKEYVTCHTCR 132 (193)
Q Consensus 74 k~L~R~p~hv~ky~~~ELgt~g~id~~~~lii~G~~~~~~iq~~L~~yI~~YVlC~~C~ 132 (193)
+.=.-.|+.+...|. .+ ++|++-++-+|.|.- +.-...|+.|+
T Consensus 35 ~ls~V~pe~L~fafe-~l-~~gt~~ega~L~i~~--------------~p~~~~C~~CG 77 (135)
T PRK03824 35 ELQDVDKEIVEFALN-EL-LKGTILEGAEIIFEE--------------EEAVLKCRNCG 77 (135)
T ss_pred hhhhhhHHHHHHHHH-HH-HcCCcccCCEEEEEe--------------cceEEECCCCC
Confidence 333445555555552 23 344443444666532 23456777776
No 63
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=76.60 E-value=4 Score=33.98 Aligned_cols=103 Identities=14% Similarity=0.256 Sum_probs=61.4
Q ss_pred eccHHHHHHcCCChHHHHHHH--HHhhcCceee---c-CCCeEEEEeeccHHHHHHHHHHHhhhccccCCCCCCcceeEe
Q psy7490 67 ANFTEICKTLHRLPKHLLDFL--LAELGTSGSV---D-GNSQLIIKGRFQQKQIENVLRRYIKEYVTCHTCRSPDTILQK 140 (193)
Q Consensus 67 ~Nf~dIak~L~R~p~hv~ky~--~~ELgt~g~i---d-~~~~lii~G~~~~~~iq~~L~~yI~~YVlC~~C~sPdT~L~k 140 (193)
..-.|+|+.|+-.+..|-+-+ +.|-|.-..- + +.|++..-=+++.+++.++|..=+..-+ +.-.-.|..
T Consensus 37 ~tdeeLA~~Lgi~~~~VRk~L~~L~e~gLv~~~r~r~~~~Gr~~y~w~l~~~~i~d~ik~~~~~~~-----~klk~~l~~ 111 (178)
T PRK06266 37 VTDEEIAEQTGIKLNTVRKILYKLYDARLADYKREKDEETNWYTYTWKPELEKLPEIIKKKKMEEL-----KKLKEQLEE 111 (178)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHHCCCeEEeeeeccCCCcEEEEEEeCHHHHHHHHHHHHHHHH-----HHHHHHhhh
Confidence 557899999999999998866 5666665421 2 3466666566777777777665333221 112223333
Q ss_pred cCceeecccccccccccccccccceeeeccEEEEEecccCCC
Q psy7490 141 DTRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSR 182 (193)
Q Consensus 141 ~~rl~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~ 182 (193)
+..-.+-.|..||.+-+.. .|.. +-+.|..||+.
T Consensus 112 e~~~~~Y~Cp~C~~rytf~------eA~~--~~F~Cp~Cg~~ 145 (178)
T PRK06266 112 EENNMFFFCPNCHIRFTFD------EAME--YGFRCPQCGEM 145 (178)
T ss_pred ccCCCEEECCCCCcEEeHH------HHhh--cCCcCCCCCCC
Confidence 3333456777777766432 2222 35678888764
No 64
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=76.53 E-value=1.4 Score=29.63 Aligned_cols=30 Identities=23% Similarity=0.478 Sum_probs=22.7
Q ss_pred ccCCCCCCcceeEecCcee-ecccccccccc
Q psy7490 127 TCHTCRSPDTILQKDTRLF-FLQCETCGSRC 156 (193)
Q Consensus 127 lC~~C~sPdT~L~k~~rl~-~l~C~aCGa~~ 156 (193)
.|..|+..+|.+-+.+..- -+.|++||-.-
T Consensus 5 ~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~ 35 (52)
T smart00401 5 SCSNCGTTETPLWRRGPSGNKTLCNACGLYY 35 (52)
T ss_pred CcCCCCCCCCCccccCCCCCCcEeecccHHH
Confidence 6999999999887754332 37899998654
No 65
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=76.31 E-value=3 Score=29.74 Aligned_cols=34 Identities=21% Similarity=0.503 Sum_probs=24.3
Q ss_pred cccccccccccccccccceeeeccEEEEEecccCCCcccc
Q psy7490 147 LQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRCSVA 186 (193)
Q Consensus 147 l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~~v~ 186 (193)
.-|.-||...-. ..+..+-|+..|..|||.-+..
T Consensus 7 KPCPFCG~~~~~------v~~~~g~~~v~C~~CgA~~~~~ 40 (64)
T PRK09710 7 KPCPFCGCPSVT------VKAISGYYRAKCNGCESRTGYG 40 (64)
T ss_pred cCCCCCCCceeE------EEecCceEEEEcCCCCcCcccc
Confidence 469999988622 2234556669999999988775
No 66
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=76.21 E-value=1.5 Score=33.85 Aligned_cols=26 Identities=19% Similarity=0.110 Sum_probs=14.0
Q ss_pred ChHHHHHHHHHhhcCceeecCCCeEEEE
Q psy7490 79 LPKHLLDFLLAELGTSGSVDGNSQLIIK 106 (193)
Q Consensus 79 ~p~hv~ky~~~ELgt~g~id~~~~lii~ 106 (193)
+|+.|.-.| +.-+.|++=++-+|.|.
T Consensus 40 ~pe~L~f~f--~~~~~~T~~egA~L~I~ 65 (113)
T PRK12380 40 EESAVRFSF--EIVCHGTVAQGCDLHIV 65 (113)
T ss_pred CHHHHHHHH--HHHhCCCccCCCEEEEE
Confidence 455555444 34455665455566663
No 67
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=76.00 E-value=0.58 Score=33.21 Aligned_cols=37 Identities=24% Similarity=0.724 Sum_probs=30.9
Q ss_pred HHHhhhccccCCCCCCcc-eeEecCceeecccccccccc
Q psy7490 119 RRYIKEYVTCHTCRSPDT-ILQKDTRLFFLQCETCGSRC 156 (193)
Q Consensus 119 ~~yI~~YVlC~~C~sPdT-~L~k~~rl~~l~C~aCGa~~ 156 (193)
.+||.-- .||.|..-|| .+-+++.+-.+.|-+||...
T Consensus 5 KRFIAGA-~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~ 42 (66)
T COG3529 5 KRFIAGA-VCPACQAQDTLAMWRENNVEIVECVKCGHHM 42 (66)
T ss_pred hhhhccC-CCcccchhhHHHHHHhcCCceEehhhcchHh
Confidence 4677665 6999999999 45689999999999999865
No 68
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=75.72 E-value=1.2 Score=27.78 Aligned_cols=9 Identities=33% Similarity=1.099 Sum_probs=4.7
Q ss_pred ecccccccc
Q psy7490 146 FLQCETCGS 154 (193)
Q Consensus 146 ~l~C~aCGa 154 (193)
.++|..||.
T Consensus 25 ~v~C~~C~~ 33 (36)
T PF13717_consen 25 KVRCSKCGH 33 (36)
T ss_pred EEECCCCCC
Confidence 355555554
No 69
>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=75.70 E-value=1.7 Score=33.60 Aligned_cols=57 Identities=19% Similarity=0.332 Sum_probs=28.9
Q ss_pred ChHHHHHHHHHhhcCceeecCCCeEEEEeeccHHHHHHHHHHHhhhccccCCCCCCcceeEecCceeecccccccccc
Q psy7490 79 LPKHLLDFLLAELGTSGSVDGNSQLIIKGRFQQKQIENVLRRYIKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRC 156 (193)
Q Consensus 79 ~p~hv~ky~~~ELgt~g~id~~~~lii~G~~~~~~iq~~L~~yI~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~ 156 (193)
+|+.|.-.| +.-+.|++-++-+|.|.= +.--..|+.|+..- .... ++..|..||+..
T Consensus 40 ~p~~L~faf--~~~~~~t~~ega~L~I~~--------------~p~~~~C~~Cg~~~---~~~~--~~~~CP~Cgs~~ 96 (115)
T TIGR00100 40 NPSQLQFAF--EVVREGTVAEGAKLNIED--------------EPVECECEDCSEEV---SPEI--DLYRCPKCHGIM 96 (115)
T ss_pred CHHHHHHHH--HHHhCCCccCCCEEEEEe--------------eCcEEEcccCCCEE---ecCC--cCccCcCCcCCC
Confidence 555554444 234556655555666632 23345677777211 1111 145677777664
No 70
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=75.63 E-value=3.5 Score=32.00 Aligned_cols=33 Identities=24% Similarity=0.369 Sum_probs=21.6
Q ss_pred ccCCCCCCcceeEecCceeecccccccccccccc
Q psy7490 127 TCHTCRSPDTILQKDTRLFFLQCETCGSRCSVAS 160 (193)
Q Consensus 127 lC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~~ 160 (193)
-||.|+|-=..=.++.+. .+.|..||...++..
T Consensus 4 FCp~Cgsll~p~~~~~~~-~l~C~kCgye~~~~~ 36 (113)
T COG1594 4 FCPKCGSLLYPKKDDEGG-KLVCRKCGYEEEASN 36 (113)
T ss_pred ccCCccCeeEEeEcCCCc-EEECCCCCcchhccc
Confidence 499999742111111222 799999999988875
No 71
>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=75.53 E-value=1.3 Score=26.60 Aligned_cols=10 Identities=30% Similarity=1.032 Sum_probs=3.9
Q ss_pred EEEEecccCC
Q psy7490 172 FFLQCETCGS 181 (193)
Q Consensus 172 ~~~~c~~Cga 181 (193)
|-.+|..||.
T Consensus 20 ~~r~C~~Cg~ 29 (32)
T PF09297_consen 20 WARRCPSCGH 29 (32)
T ss_dssp S-EEESSSS-
T ss_pred CEeECCCCcC
Confidence 4444555543
No 72
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=75.06 E-value=2.2 Score=40.67 Aligned_cols=39 Identities=31% Similarity=0.704 Sum_probs=24.0
Q ss_pred cCCCCCCcceeEecCceeecccccccccccccccccceeeeccEEEEEecccCCCc
Q psy7490 128 CHTCRSPDTILQKDTRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRC 183 (193)
Q Consensus 128 C~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~ 183 (193)
||.|..|=|. .+..+ .++|.-||...+++. .|..||+..
T Consensus 225 C~~C~~~l~~-h~~~~--~l~Ch~Cg~~~~~~~--------------~Cp~C~s~~ 263 (505)
T TIGR00595 225 CPNCDVSLTY-HKKEG--KLRCHYCGYQEPIPK--------------TCPQCGSED 263 (505)
T ss_pred CCCCCCceEE-ecCCC--eEEcCCCcCcCCCCC--------------CCCCCCCCe
Confidence 5555444332 23333 478999998865443 588888853
No 73
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=74.50 E-value=1.2 Score=30.23 Aligned_cols=30 Identities=23% Similarity=0.412 Sum_probs=23.1
Q ss_pred ccCCCCCCcceeEecCc-eeecccccccccc
Q psy7490 127 TCHTCRSPDTILQKDTR-LFFLQCETCGSRC 156 (193)
Q Consensus 127 lC~~C~sPdT~L~k~~r-l~~l~C~aCGa~~ 156 (193)
.|..|+..+|.+-+.+. --...|+|||-.-
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~ 31 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYW 31 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHH
Confidence 59999999998877542 3357899998654
No 74
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=74.45 E-value=7.1 Score=31.18 Aligned_cols=27 Identities=22% Similarity=0.178 Sum_probs=21.5
Q ss_pred ccHHHHHHcCCChHHHHHHH--HHh--hcCc
Q psy7490 68 NFTEICKTLHRLPKHLLDFL--LAE--LGTS 94 (193)
Q Consensus 68 Nf~dIak~L~R~p~hv~ky~--~~E--Lgt~ 94 (193)
-=.|+|+.|+-++..|-+.+ +.| ++..
T Consensus 17 ~dedLa~~l~i~~n~vRkiL~~L~ed~~~~~ 47 (147)
T smart00531 17 TEEDLAELLGIKQKQLRKILYLLYDEKLIKI 47 (147)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHhhhcchh
Confidence 35799999999999999877 666 6544
No 75
>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=74.36 E-value=2.9 Score=27.13 Aligned_cols=27 Identities=22% Similarity=0.471 Sum_probs=17.1
Q ss_pred cccCCCCCCcceeEecCceeecccccccc
Q psy7490 126 VTCHTCRSPDTILQKDTRLFFLQCETCGS 154 (193)
Q Consensus 126 VlC~~C~sPdT~L~k~~rl~~l~C~aCGa 154 (193)
+.||.|++. ......+ ...-+|.+|+.
T Consensus 19 ~~CP~Cg~~-~~~~~~~-~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGST-KHYRLKT-RGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCe-eeEEeCC-CCeEECCCCCC
Confidence 459999988 3333333 23468888875
No 76
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=73.12 E-value=2.2 Score=26.63 Aligned_cols=28 Identities=32% Similarity=0.534 Sum_probs=14.2
Q ss_pred ccCCCCCCcceeEe--cCceeeccccccccc
Q psy7490 127 TCHTCRSPDTILQK--DTRLFFLQCETCGSR 155 (193)
Q Consensus 127 lC~~C~sPdT~L~k--~~rl~~l~C~aCGa~ 155 (193)
-||.|+.|=+..+- |++ .-..|.+||.-
T Consensus 2 fC~~CG~~l~~~ip~gd~r-~R~vC~~Cg~I 31 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDR-ERLVCPACGFI 31 (34)
T ss_dssp B-TTT--B-EEE--TT-SS--EEEETTTTEE
T ss_pred ccccccChhhhhcCCCCCc-cceECCCCCCE
Confidence 49999999444444 444 35789999863
No 77
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=72.99 E-value=1.3 Score=31.09 Aligned_cols=32 Identities=22% Similarity=0.675 Sum_probs=12.4
Q ss_pred CceeecccccccccccccccccceeeeccEEEEEecccCCC
Q psy7490 142 TRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSR 182 (193)
Q Consensus 142 ~rl~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~ 182 (193)
+....+.|+.|++.+.|+ --.+.+||..|||=
T Consensus 26 ~~~v~IlCNDC~~~s~v~---------fH~lg~KC~~C~SY 57 (61)
T PF14599_consen 26 NKKVWILCNDCNAKSEVP---------FHFLGHKCSHCGSY 57 (61)
T ss_dssp --EEEEEESSS--EEEEE-----------TT----TTTS--
T ss_pred CCEEEEECCCCCCcccee---------eeHhhhcCCCCCCc
Confidence 334457777777765332 33455777777764
No 78
>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=72.59 E-value=2.7 Score=30.83 Aligned_cols=35 Identities=20% Similarity=0.526 Sum_probs=17.7
Q ss_pred hhccccCCCCCCcceeEe---cCceeeccccccccccc
Q psy7490 123 KEYVTCHTCRSPDTILQK---DTRLFFLQCETCGSRCS 157 (193)
Q Consensus 123 ~~YVlC~~C~sPdT~L~k---~~rl~~l~C~aCGa~~~ 157 (193)
...-.||-|+..++.-++ +.++-.+.|..||....
T Consensus 20 ~~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~ 57 (81)
T PF05129_consen 20 PKVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQ 57 (81)
T ss_dssp SS----TTT--SS-EEEEEETTTTEEEEEESSS--EEE
T ss_pred CceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEE
Confidence 345578888888775543 45677788888877653
No 79
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=72.41 E-value=2.7 Score=32.60 Aligned_cols=35 Identities=20% Similarity=0.438 Sum_probs=22.8
Q ss_pred hhccccCCCCCCcce---eEecCceeeccccccccccc
Q psy7490 123 KEYVTCHTCRSPDTI---LQKDTRLFFLQCETCGSRCS 157 (193)
Q Consensus 123 ~~YVlC~~C~sPdT~---L~k~~rl~~l~C~aCGa~~~ 157 (193)
+++-.||-|+.-.-. +.|......+.|..||.+.-
T Consensus 20 ~k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e 57 (104)
T COG4888 20 PKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFE 57 (104)
T ss_pred CceEecCccCCeeeeEEEEEecCceeEEEcccCcceEE
Confidence 445578888765433 55566667777888877653
No 80
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=72.11 E-value=3.5 Score=28.60 Aligned_cols=37 Identities=24% Similarity=0.594 Sum_probs=25.1
Q ss_pred hccccCCCCCCc-ceeEecC--ceeecccccccccccccc
Q psy7490 124 EYVTCHTCRSPD-TILQKDT--RLFFLQCETCGSRCSVAS 160 (193)
Q Consensus 124 ~YVlC~~C~sPd-T~L~k~~--rl~~l~C~aCGa~~~V~~ 160 (193)
+.++||.|++.- +.+..|. .-+-+-|..|....-+..
T Consensus 3 ~Wi~CP~CgnKTR~kir~DT~LkNfPlyCpKCK~EtlI~v 42 (55)
T PF14205_consen 3 EWILCPICGNKTRLKIREDTVLKNFPLYCPKCKQETLIDV 42 (55)
T ss_pred eEEECCCCCCccceeeecCceeccccccCCCCCceEEEEe
Confidence 578999999753 3333333 235688999999876543
No 81
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=71.69 E-value=3.7 Score=25.96 Aligned_cols=27 Identities=19% Similarity=0.442 Sum_probs=16.9
Q ss_pred ccCCCCCCcceeEecCceeecccccccc
Q psy7490 127 TCHTCRSPDTILQKDTRLFFLQCETCGS 154 (193)
Q Consensus 127 lC~~C~sPdT~L~k~~rl~~l~C~aCGa 154 (193)
.||.|+.+ -....-+.+..-.|.+||.
T Consensus 1 ~CP~C~~~-l~~~~~~~~~id~C~~C~G 27 (41)
T PF13453_consen 1 KCPRCGTE-LEPVRLGDVEIDVCPSCGG 27 (41)
T ss_pred CcCCCCcc-cceEEECCEEEEECCCCCe
Confidence 48888873 3222335566777888874
No 82
>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=71.56 E-value=1.8 Score=25.56 Aligned_cols=9 Identities=33% Similarity=0.988 Sum_probs=3.1
Q ss_pred ecccCCCcc
Q psy7490 176 CETCGSRCS 184 (193)
Q Consensus 176 c~~Cga~~~ 184 (193)
|.+||+.+|
T Consensus 21 C~~C~~~rp 29 (30)
T PF00641_consen 21 CVACGAPRP 29 (30)
T ss_dssp -TTT--BTT
T ss_pred hhCcCCCCc
Confidence 555555543
No 83
>PF01921 tRNA-synt_1f: tRNA synthetases class I (K); InterPro: IPR002904 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. Lysyl-tRNA synthetase (6.1.1.6 from EC) is an alpha 2 homodimer that belong to both class I and class II. In eubacteria and eukaryota lysyl-tRNA synthetases belong to class II in the same family as aspartyl tRNA synthetase. The class Ic lysyl-tRNA synthetase family is present in archaea and in a number of bacterial groups that include the alphaproteobacteria and spirochaetes[]. A refined crystal structures shows that the active site of LysU is shaped to position the substrates for the nucleophilic attack of the lysine carboxylate on the ATP alpha-phosphate. No residues are directly involved in catalysis, but a number of highly conserved amino acids and three metal ions coordinate the substrates and stabilise the pentavalent transition state. A loop close to the catalytic pocket, disordered in the lysine-bound structure, becomes ordered upon adenine binding [].; GO: 0000166 nucleotide binding, 0004824 lysine-tRNA ligase activity, 0005524 ATP binding, 0006430 lysyl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 1IRX_A.
Probab=71.15 E-value=4.9 Score=37.32 Aligned_cols=52 Identities=25% Similarity=0.502 Sum_probs=31.9
Q ss_pred HHHHHHHHHHHhhh---------ccccCCCCCCcc-eeEe-c--Cceeecccccccccccccccc
Q psy7490 111 QKQIENVLRRYIKE---------YVTCHTCRSPDT-ILQK-D--TRLFFLQCETCGSRCSVASIK 162 (193)
Q Consensus 111 ~~~iq~~L~~yI~~---------YVlC~~C~sPdT-~L~k-~--~rl~~l~C~aCGa~~~V~~~k 162 (193)
.+.|.++|..|..+ .++|+.|+.-+| .++. + +..+.-+|..||....++-.+
T Consensus 151 ~~~I~~Il~~~~~~~~~~~y~Pf~piC~~cGri~tt~v~~~d~~~~~v~Y~c~~cG~~g~~~i~~ 215 (360)
T PF01921_consen 151 RDEIREILNEYRGRERPETYSPFLPICEKCGRIDTTEVTEYDPEGGTVTYRCEECGHEGEVDITG 215 (360)
T ss_dssp HHHHHHHHHHHHHHT--TT--SEEEEETTTEE--EEEEEEE--SSSEEEEE--TTS---EEETTT
T ss_pred HHHHHHHHHHhcCcCCCCCeeeeeeeccccCCcccceeeEeecCCCEEEEEecCCCCEEEEecCC
Confidence 46777888877443 489999999665 4332 3 677788999999998776554
No 84
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=70.77 E-value=2.9 Score=32.35 Aligned_cols=20 Identities=15% Similarity=0.341 Sum_probs=16.4
Q ss_pred ccccCCCCCCcceeEecCce
Q psy7490 125 YVTCHTCRSPDTILQKDTRL 144 (193)
Q Consensus 125 YVlC~~C~sPdT~L~k~~rl 144 (193)
+..||.|+|+++.+..-+.+
T Consensus 86 ~~~CP~Cgs~~~~i~~G~El 105 (115)
T TIGR00100 86 LYRCPKCHGIMLQVRAGKEL 105 (115)
T ss_pred CccCcCCcCCCcEEecCCeE
Confidence 56899999999998875543
No 85
>PF14353 CpXC: CpXC protein
Probab=70.67 E-value=3.5 Score=31.81 Aligned_cols=19 Identities=32% Similarity=0.833 Sum_probs=13.5
Q ss_pred eccEEEEEecccCCCcccc
Q psy7490 168 DTRLFFLQCETCGSRCSVA 186 (193)
Q Consensus 168 ~~rl~~~~c~~Cga~~~v~ 186 (193)
...+|...|..||+...+.
T Consensus 33 ~g~l~~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 33 DGSLFSFTCPSCGHKFRLE 51 (128)
T ss_pred cCCcCEEECCCCCCceecC
Confidence 5567777888888776653
No 86
>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=70.64 E-value=3.3 Score=25.73 Aligned_cols=31 Identities=19% Similarity=0.455 Sum_probs=16.3
Q ss_pred ccCCCCCCcceeEecCceeeccccccccccccc
Q psy7490 127 TCHTCRSPDTILQKDTRLFFLQCETCGSRCSVA 159 (193)
Q Consensus 127 lC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~ 159 (193)
-||+|+|.=..-..+... . .|..||...++.
T Consensus 3 FCp~C~nlL~p~~~~~~~-~-~C~~C~Y~~~~~ 33 (35)
T PF02150_consen 3 FCPECGNLLYPKEDKEKR-V-ACRTCGYEEPIS 33 (35)
T ss_dssp BETTTTSBEEEEEETTTT-E-EESSSS-EEE-S
T ss_pred eCCCCCccceEcCCCccC-c-CCCCCCCccCCC
Confidence 489998753211111222 2 888888876543
No 87
>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=70.11 E-value=1.8 Score=26.64 Aligned_cols=8 Identities=38% Similarity=1.331 Sum_probs=4.1
Q ss_pred cccccccc
Q psy7490 147 LQCETCGS 154 (193)
Q Consensus 147 l~C~aCGa 154 (193)
++|..||.
T Consensus 26 v~C~~C~~ 33 (38)
T TIGR02098 26 VRCGKCGH 33 (38)
T ss_pred EECCCCCC
Confidence 44555554
No 88
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=70.05 E-value=2.8 Score=27.08 Aligned_cols=11 Identities=36% Similarity=0.818 Sum_probs=5.9
Q ss_pred ecccccccccc
Q psy7490 146 FLQCETCGSRC 156 (193)
Q Consensus 146 ~l~C~aCGa~~ 156 (193)
..+|..||++-
T Consensus 21 ~~~Cp~CG~~~ 31 (46)
T PRK00398 21 GVRCPYCGYRI 31 (46)
T ss_pred ceECCCCCCeE
Confidence 35566665543
No 89
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=69.65 E-value=5.8 Score=40.00 Aligned_cols=41 Identities=24% Similarity=0.477 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHhhhc----------------------cccCCCCCCcceeEecCceeecccccccccc
Q psy7490 111 QKQIENVLRRYIKEY----------------------VTCHTCRSPDTILQKDTRLFFLQCETCGSRC 156 (193)
Q Consensus 111 ~~~iq~~L~~yI~~Y----------------------VlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~ 156 (193)
++.|-++|.+++..- ..||+|++ | |+.+.+- +.|..||.+.
T Consensus 688 pDaI~kaL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~Cg~--~-l~~~~GC--~~C~~CG~sk 750 (752)
T PRK08665 688 PDAIAKVLEKHYLGGGKDVGAGNGTGSAGIEAPAPERGACPECGS--I-LEHEEGC--VVCHSCGYSK 750 (752)
T ss_pred HHHHHHHHHHHHHhccccccccccccccccccccCCCCCCCCCCc--c-cEECCCC--CcCCCCCCCC
Confidence 468888888776640 35999984 3 6666653 6899999864
No 90
>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=69.42 E-value=2.5 Score=25.75 Aligned_cols=26 Identities=38% Similarity=0.763 Sum_probs=12.1
Q ss_pred cccCCCCCCcceeEecCceeeccccccccc
Q psy7490 126 VTCHTCRSPDTILQKDTRLFFLQCETCGSR 155 (193)
Q Consensus 126 VlC~~C~sPdT~L~k~~rl~~l~C~aCGa~ 155 (193)
-.||.|+|..|- .++.+ +.|..||..
T Consensus 3 p~Cp~C~se~~y--~D~~~--~vCp~C~~e 28 (30)
T PF08274_consen 3 PKCPLCGSEYTY--EDGEL--LVCPECGHE 28 (30)
T ss_dssp ---TTT-----E--E-SSS--EEETTTTEE
T ss_pred CCCCCCCCccee--ccCCE--EeCCccccc
Confidence 469999998887 44443 678888864
No 91
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=69.13 E-value=3.3 Score=32.17 Aligned_cols=20 Identities=25% Similarity=0.742 Sum_probs=16.1
Q ss_pred ccccCCCCCCcceeEecCce
Q psy7490 125 YVTCHTCRSPDTILQKDTRL 144 (193)
Q Consensus 125 YVlC~~C~sPdT~L~k~~rl 144 (193)
|..||.|+||+..++..+.+
T Consensus 88 ~~~CP~Cgs~~~~i~~G~El 107 (117)
T PRK00564 88 YGVCEKCHSKNVIITQGNEM 107 (117)
T ss_pred CCcCcCCCCCceEEecCCEE
Confidence 45699999999998876554
No 92
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=69.03 E-value=3.1 Score=32.19 Aligned_cols=25 Identities=20% Similarity=0.131 Sum_probs=12.8
Q ss_pred ChHHHHHHHHHhhcCceeecCCCeEEE
Q psy7490 79 LPKHLLDFLLAELGTSGSVDGNSQLII 105 (193)
Q Consensus 79 ~p~hv~ky~~~ELgt~g~id~~~~lii 105 (193)
+|+.|.-.|. .-+.|++=++-+|.|
T Consensus 40 ~p~~L~f~f~--~~~~~t~~egA~L~i 64 (114)
T PRK03681 40 ETSSLAFCFD--LVCRGTVAEGCKLHL 64 (114)
T ss_pred CHHHHHHHHH--HHhCCCccCCCEEEE
Confidence 4555544442 234555545556666
No 93
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=68.10 E-value=4.4 Score=29.12 Aligned_cols=33 Identities=27% Similarity=0.638 Sum_probs=25.0
Q ss_pred CceeecccccccccccccccccceeeeccEEEEEecccCCC
Q psy7490 142 TRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSR 182 (193)
Q Consensus 142 ~rl~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~ 182 (193)
++.+.++|..||....|=+.- -..+.|..||+-
T Consensus 15 s~Fl~VkCpdC~N~q~vFsha--------st~V~C~~CG~~ 47 (67)
T COG2051 15 SRFLRVKCPDCGNEQVVFSHA--------STVVTCLICGTT 47 (67)
T ss_pred ceEEEEECCCCCCEEEEeccC--------ceEEEecccccE
Confidence 567899999999998665542 235789999963
No 94
>PRK14873 primosome assembly protein PriA; Provisional
Probab=68.06 E-value=4.5 Score=40.18 Aligned_cols=23 Identities=30% Similarity=0.671 Sum_probs=16.7
Q ss_pred ecccccccccccccccccceeeeccEEEEEecccCCCc
Q psy7490 146 FLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRC 183 (193)
Q Consensus 146 ~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~ 183 (193)
.++|..||... . -..|..||+..
T Consensus 410 ~l~Ch~CG~~~-~--------------p~~Cp~Cgs~~ 432 (665)
T PRK14873 410 TPRCRWCGRAA-P--------------DWRCPRCGSDR 432 (665)
T ss_pred eeECCCCcCCC-c--------------CccCCCCcCCc
Confidence 48899999853 1 12699999875
No 95
>PLN00209 ribosomal protein S27; Provisional
Probab=68.01 E-value=3.7 Score=30.89 Aligned_cols=30 Identities=20% Similarity=0.542 Sum_probs=22.9
Q ss_pred ccccCCCCCCcceeEecCceeecccccccccc
Q psy7490 125 YVTCHTCRSPDTILQKDTRLFFLQCETCGSRC 156 (193)
Q Consensus 125 YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~ 156 (193)
-|.||.|.+.-|..-.... .+.|..||..=
T Consensus 36 ~VkCp~C~n~q~VFShA~t--~V~C~~Cg~~L 65 (86)
T PLN00209 36 DVKCQGCFNITTVFSHSQT--VVVCGSCQTVL 65 (86)
T ss_pred EEECCCCCCeeEEEecCce--EEEccccCCEe
Confidence 4889999998887776554 47899888753
No 96
>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=67.14 E-value=2.1 Score=35.63 Aligned_cols=44 Identities=27% Similarity=0.461 Sum_probs=17.9
Q ss_pred eecccccccccccccccccceeeeccEEEEEecccCCCcccccc
Q psy7490 145 FFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRCSVASI 188 (193)
Q Consensus 145 ~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~~v~~~ 188 (193)
+.+.|..||...+.+.+-.+-......-.+.|..|++..|++.|
T Consensus 17 l~~~C~~C~~~~~f~g~~~~~~~~~~~~~~~C~~C~~~~~~~~l 60 (188)
T PF08996_consen 17 LKLTCPSCGTEFEFPGVFEEDGDDVSPSGLQCPNCSTPLSPASL 60 (188)
T ss_dssp EEEE-TTT--EEEE-SSS--SSEEEETTEEEETTT--B--HHHH
T ss_pred eEeECCCCCCCccccccccCCccccccCcCcCCCCCCcCCHHHH
Confidence 35667777777666655322112222335667777776665544
No 97
>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=66.82 E-value=8.3 Score=31.37 Aligned_cols=102 Identities=20% Similarity=0.244 Sum_probs=55.3
Q ss_pred eccHHHHHHcCCChHHHHHHH--HHhhcCceee---c-CCCeEEEEeeccHHHHHHHHHHHhhhccccCCCCCCcceeEe
Q psy7490 67 ANFTEICKTLHRLPKHLLDFL--LAELGTSGSV---D-GNSQLIIKGRFQQKQIENVLRRYIKEYVTCHTCRSPDTILQK 140 (193)
Q Consensus 67 ~Nf~dIak~L~R~p~hv~ky~--~~ELgt~g~i---d-~~~~lii~G~~~~~~iq~~L~~yI~~YVlC~~C~sPdT~L~k 140 (193)
..=.|||+.|+-+...|-+-+ +.|.|..... | ++|++..-=.++..++-+.|..=+..-+. .-.-.|..
T Consensus 29 ~tdEeLa~~Lgi~~~~VRk~L~~L~e~~Lv~~~r~r~~~~gw~~Y~w~i~~~~i~d~Ik~~~~~~~~-----~lk~~l~~ 103 (158)
T TIGR00373 29 FTDEEISLELGIKLNEVRKALYALYDAGLADYKRRKDDETGWYEYTWRINYEKALDVLKRKLEETAK-----KLREKLEF 103 (158)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHCCCceeeeeeecCCCcEEEEEEeCHHHHHHHHHHHHHHHHH-----HHHHHHhh
Confidence 456899999999999998866 6777776321 2 24555444456666666555443322110 11122222
Q ss_pred cCceeecccccccccccccccccceeeeccEEEEEecccCC
Q psy7490 141 DTRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGS 181 (193)
Q Consensus 141 ~~rl~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga 181 (193)
+..-.+-.|..|+.+-+.. .|.. +-..|..||+
T Consensus 104 e~~~~~Y~Cp~c~~r~tf~------eA~~--~~F~Cp~Cg~ 136 (158)
T TIGR00373 104 ETNNMFFICPNMCVRFTFN------EAME--LNFTCPRCGA 136 (158)
T ss_pred ccCCCeEECCCCCcEeeHH------HHHH--cCCcCCCCCC
Confidence 3223355666666655332 1111 3456777765
No 98
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=66.68 E-value=3.6 Score=26.62 Aligned_cols=32 Identities=19% Similarity=0.443 Sum_probs=19.5
Q ss_pred ccCCCCCCcceeEecC-ceeecccccccccccccc
Q psy7490 127 TCHTCRSPDTILQKDT-RLFFLQCETCGSRCSVAS 160 (193)
Q Consensus 127 lC~~C~sPdT~L~k~~-rl~~l~C~aCGa~~~V~~ 160 (193)
.||.|++.= ..++. .-....|..||....+.+
T Consensus 2 FCp~Cg~~l--~~~~~~~~~~~vC~~Cg~~~~~~~ 34 (52)
T smart00661 2 FCPKCGNML--IPKEGKEKRRFVCRKCGYEEPIEQ 34 (52)
T ss_pred CCCCCCCcc--ccccCCCCCEEECCcCCCeEECCC
Confidence 499999832 12222 112567999998876643
No 99
>PF12773 DZR: Double zinc ribbon
Probab=66.46 E-value=3 Score=26.97 Aligned_cols=11 Identities=27% Similarity=0.634 Sum_probs=5.8
Q ss_pred ecccccccccc
Q psy7490 146 FLQCETCGSRC 156 (193)
Q Consensus 146 ~l~C~aCGa~~ 156 (193)
...|..||..-
T Consensus 12 ~~fC~~CG~~l 22 (50)
T PF12773_consen 12 AKFCPHCGTPL 22 (50)
T ss_pred ccCChhhcCCh
Confidence 34455565554
No 100
>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=65.72 E-value=3.6 Score=25.32 Aligned_cols=16 Identities=31% Similarity=0.675 Sum_probs=9.2
Q ss_pred cCceeecccccccccc
Q psy7490 141 DTRLFFLQCETCGSRC 156 (193)
Q Consensus 141 ~~rl~~l~C~aCGa~~ 156 (193)
++++...+|.+||...
T Consensus 6 ~~~l~~~rC~~Cg~~~ 21 (37)
T PF12172_consen 6 EGRLLGQRCRDCGRVQ 21 (37)
T ss_dssp TT-EEEEE-TTT--EE
T ss_pred CCEEEEEEcCCCCCEe
Confidence 5678888888888864
No 101
>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=65.66 E-value=5.2 Score=26.14 Aligned_cols=35 Identities=29% Similarity=0.747 Sum_probs=20.7
Q ss_pred ccccccccccccccccceeeeccEEEEEecc--cCCCc
Q psy7490 148 QCETCGSRCSVASIKSGFQKDTRLFFLQCET--CGSRC 183 (193)
Q Consensus 148 ~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~--Cga~~ 183 (193)
+|..||++.-+.... ......+-.+.+|.. ||+..
T Consensus 1 ~CP~Cg~~a~ir~S~-~~s~~~~~~Y~qC~N~~Cg~tf 37 (47)
T PF04606_consen 1 RCPHCGSKARIRTSR-QLSPLTRELYCQCTNPECGHTF 37 (47)
T ss_pred CcCCCCCeeEEEEch-hhCcceEEEEEEECCCcCCCEE
Confidence 366777766554432 223455667777777 77654
No 102
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=65.57 E-value=14 Score=22.91 Aligned_cols=45 Identities=13% Similarity=0.113 Sum_probs=32.9
Q ss_pred ccHHHHHHcCCChHHHHHHHHHhhcCceeecCCCeEEEEeeccHHHHHHH
Q psy7490 68 NFTEICKTLHRLPKHLLDFLLAELGTSGSVDGNSQLIIKGRFQQKQIENV 117 (193)
Q Consensus 68 Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id~~~~lii~G~~~~~~iq~~ 117 (193)
+..|+|+.++-++..|-.|....+.. ...+++|.. .|+.++|..+
T Consensus 2 ~~~e~a~~~gv~~~tlr~~~~~g~l~-~~~~~~~~~----~y~~~~v~~l 46 (49)
T cd04761 2 TIGELAKLTGVSPSTLRYYERIGLLS-PARTEGGYR----LYSDADLERL 46 (49)
T ss_pred cHHHHHHHHCcCHHHHHHHHHCCCCC-CCcCCCCCE----EeCHHHHHHh
Confidence 46899999999999999998877765 333333332 4788887765
No 103
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=65.54 E-value=4.1 Score=40.46 Aligned_cols=9 Identities=22% Similarity=0.789 Sum_probs=5.7
Q ss_pred cccCCCCCC
Q psy7490 126 VTCHTCRSP 134 (193)
Q Consensus 126 VlC~~C~sP 134 (193)
+.||.|+.+
T Consensus 2 ~~Cp~Cg~~ 10 (645)
T PRK14559 2 LICPQCQFE 10 (645)
T ss_pred CcCCCCCCc
Confidence 367777754
No 104
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=65.32 E-value=4.6 Score=30.32 Aligned_cols=30 Identities=23% Similarity=0.565 Sum_probs=22.4
Q ss_pred ccccCCCCCCcceeEecCceeecccccccccc
Q psy7490 125 YVTCHTCRSPDTILQKDTRLFFLQCETCGSRC 156 (193)
Q Consensus 125 YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~ 156 (193)
-|.|+.|.+.-|..-.... .+.|..||..=
T Consensus 35 ~VkCp~C~n~q~VFShA~t--~V~C~~Cg~~L 64 (85)
T PTZ00083 35 DVKCPGCSQITTVFSHAQT--VVLCGGCSSQL 64 (85)
T ss_pred EEECCCCCCeeEEEecCce--EEEccccCCEe
Confidence 4889999988887766554 37888888753
No 105
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=64.69 E-value=4.3 Score=31.41 Aligned_cols=19 Identities=21% Similarity=0.385 Sum_probs=12.7
Q ss_pred cccCCCCCCcceeEecCce
Q psy7490 126 VTCHTCRSPDTILQKDTRL 144 (193)
Q Consensus 126 VlC~~C~sPdT~L~k~~rl 144 (193)
..||.|+|+++.++.-+.+
T Consensus 88 ~~CP~Cgs~~~~i~~G~El 106 (114)
T PRK03681 88 RRCPQCHGDMLRIVADDGL 106 (114)
T ss_pred CcCcCcCCCCcEEccCCeE
Confidence 4688888877777664443
No 106
>PRK07451 translation initiation factor Sui1; Validated
Probab=64.65 E-value=18 Score=28.43 Aligned_cols=51 Identities=25% Similarity=0.361 Sum_probs=38.1
Q ss_pred CeeeEEeccHHHHHHcCCChHHHHHHHHHhhcCceeecCCCeEEEEeeccHHHHHH
Q psy7490 61 TKKTSFANFTEICKTLHRLPKHLLDFLLAELGTSGSVDGNSQLIIKGRFQQKQIEN 116 (193)
Q Consensus 61 g~KTvi~Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id~~~~lii~G~~~~~~iq~ 116 (193)
..-|+|.+|..-.. +-.-+.|.|-..+|+.|++. ++.+.|+|.|..+-.+-
T Consensus 52 K~VTvV~Gl~~~~~----dlk~LaK~LK~k~gcGGtvk-d~~IelQGD~r~~v~~~ 102 (115)
T PRK07451 52 KTVTVITGFQHKPE----TLAKLLKQLKTQCGSGGTVK-DNTIEIQGDHRQKILEI 102 (115)
T ss_pred CeEEEEeCCCCCHH----HHHHHHHHHHHHhcCCceEc-CCEEEEcCcHHHHHHHH
Confidence 34588888863222 34678899999999999994 66899999997664443
No 107
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=64.64 E-value=4.3 Score=32.73 Aligned_cols=24 Identities=38% Similarity=0.826 Sum_probs=18.7
Q ss_pred ccCCCCCCcceeEecCceeeccccccccc
Q psy7490 127 TCHTCRSPDTILQKDTRLFFLQCETCGSR 155 (193)
Q Consensus 127 lC~~C~sPdT~L~k~~rl~~l~C~aCGa~ 155 (193)
-||.|+.|=.. |++.+ .|..||.+
T Consensus 30 hCp~Cg~PLF~--KdG~v---~CPvC~~~ 53 (131)
T COG1645 30 HCPKCGTPLFR--KDGEV---FCPVCGYR 53 (131)
T ss_pred hCcccCCccee--eCCeE---ECCCCCce
Confidence 69999999665 66665 49999954
No 108
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=64.55 E-value=3.6 Score=29.40 Aligned_cols=32 Identities=22% Similarity=0.607 Sum_probs=19.8
Q ss_pred ccCCCCCCcceeEe----cCceeecccccccccccc
Q psy7490 127 TCHTCRSPDTILQK----DTRLFFLQCETCGSRCSV 158 (193)
Q Consensus 127 lC~~C~sPdT~L~k----~~rl~~l~C~aCGa~~~V 158 (193)
.|..|+...+..+. ++++..++|..|++..-+
T Consensus 6 TC~~C~~Rs~~~~sk~aY~~GvViv~C~gC~~~HlI 41 (66)
T PF05180_consen 6 TCNKCGTRSAKMFSKQAYHKGVVIVQCPGCKNRHLI 41 (66)
T ss_dssp EETTTTEEEEEEEEHHHHHTSEEEEE-TTS--EEES
T ss_pred EcCCCCCccceeeCHHHHhCCeEEEECCCCcceeee
Confidence 57777777776654 367777888888776544
No 109
>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=64.52 E-value=2.6 Score=29.16 Aligned_cols=29 Identities=24% Similarity=0.660 Sum_probs=16.1
Q ss_pred ccccCCCCCCcceeEecCceeeccccccccc
Q psy7490 125 YVTCHTCRSPDTILQKDTRLFFLQCETCGSR 155 (193)
Q Consensus 125 YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~ 155 (193)
-|.||.|.+.-|..-.-.. .+.|..||..
T Consensus 7 ~VkCp~C~~~q~vFSha~t--~V~C~~Cg~~ 35 (55)
T PF01667_consen 7 DVKCPGCYNIQTVFSHAQT--VVKCVVCGTV 35 (55)
T ss_dssp EEE-TTT-SEEEEETT-SS---EE-SSSTSE
T ss_pred EEECCCCCCeeEEEecCCe--EEEcccCCCE
Confidence 3788888887666544433 4778888764
No 110
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=64.49 E-value=9.9 Score=31.26 Aligned_cols=32 Identities=25% Similarity=0.621 Sum_probs=21.4
Q ss_pred ccCCCCCCcc-eeEec-----Cc--eeecccccccccccc
Q psy7490 127 TCHTCRSPDT-ILQKD-----TR--LFFLQCETCGSRCSV 158 (193)
Q Consensus 127 lC~~C~sPdT-~L~k~-----~r--l~~l~C~aCGa~~~V 158 (193)
.||.|+.+-+ .+... +. +....|..||.+++-
T Consensus 2 ~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~e 41 (160)
T smart00709 2 DCPSCGGNGTTRMLLTSIPYFREVIIMSFECEHCGYRNNE 41 (160)
T ss_pred cCCCCCCCCEEEEEEecCCCcceEEEEEEECCCCCCccce
Confidence 6999997654 33321 23 447889999998753
No 111
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 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 GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=64.27 E-value=1.9 Score=26.84 Aligned_cols=28 Identities=21% Similarity=0.449 Sum_probs=15.5
Q ss_pred cCCCCCCcceeEecCce-eeccccccccc
Q psy7490 128 CHTCRSPDTILQKDTRL-FFLQCETCGSR 155 (193)
Q Consensus 128 C~~C~sPdT~L~k~~rl-~~l~C~aCGa~ 155 (193)
|..|+..+|.+-+.+.. ....|++||-.
T Consensus 1 C~~C~tt~t~~WR~~~~g~~~LCn~Cg~~ 29 (36)
T PF00320_consen 1 CSNCGTTETPQWRRGPNGNRTLCNACGLY 29 (36)
T ss_dssp -TTT--ST-SSEEEETTSEE-EEHHHHHH
T ss_pred CcCCcCCCCchhhcCCCCCCHHHHHHHHH
Confidence 78899999888774331 12379998854
No 112
>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=64.16 E-value=7.7 Score=31.30 Aligned_cols=56 Identities=27% Similarity=0.550 Sum_probs=38.0
Q ss_pred eccHHHHHHcCCChHHHHHHHHHhhcCceeecCCCeEEEEeeccHHHHHHHHHHHhhhccccCCCCCCcceeEecCceee
Q psy7490 67 ANFTEICKTLHRLPKHLLDFLLAELGTSGSVDGNSQLIIKGRFQQKQIENVLRRYIKEYVTCHTCRSPDTILQKDTRLFF 146 (193)
Q Consensus 67 ~Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id~~~~lii~G~~~~~~iq~~L~~yI~~YVlC~~C~sPdT~L~k~~rl~~ 146 (193)
.|+.+|++++.-+++.|.+||- .|||.|.+ + =+-+..|..||.| ++.+++
T Consensus 47 ati~eV~e~tgVs~~~I~~~Ir-----------eGRL~~~~-~------------~nl~~~CE~CG~~----I~~Gr~-- 96 (137)
T TIGR03826 47 ATVSEIVEETGVSEKLILKFIR-----------EGRLQLKH-F------------PNLGYPCERCGTS----IREGRL-- 96 (137)
T ss_pred CCHHHHHHHHCcCHHHHHHHHH-----------cCCeeccC-C------------CCCcCcccccCCc----CCCCCc--
Confidence 4678999999999999999983 45666543 1 1335678888765 334433
Q ss_pred cccccccc
Q psy7490 147 LQCETCGS 154 (193)
Q Consensus 147 l~C~aCGa 154 (193)
|..|..
T Consensus 97 --C~~C~~ 102 (137)
T TIGR03826 97 --CDSCAG 102 (137)
T ss_pred --cHHHHH
Confidence 666654
No 113
>PRK09019 translation initiation factor Sui1; Validated
Probab=63.84 E-value=13 Score=28.96 Aligned_cols=50 Identities=16% Similarity=0.059 Sum_probs=37.7
Q ss_pred eeeEEeccHHHHHHcCCChHHHHHHHHHhhcCceeecCCCeEEEEeeccHHHHHH
Q psy7490 62 KKTSFANFTEICKTLHRLPKHLLDFLLAELGTSGSVDGNSQLIIKGRFQQKQIEN 116 (193)
Q Consensus 62 ~KTvi~Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id~~~~lii~G~~~~~~iq~ 116 (193)
.-|+|..|..-.. +-+-+.|.|-..+|+.|++. ++.+.|+|.|...-.+-
T Consensus 46 ~VTiI~Gl~~~~~----dlk~l~K~lKkk~gcGGtvk-~~~IelQGD~r~~v~~~ 95 (108)
T PRK09019 46 GVCLITGLDLDDA----ELKKLAAELKKKCGCGGAVK-DGVIEIQGDKRDLLKSL 95 (108)
T ss_pred eEEEEeCCcCCHH----HHHHHHHHHHHHhcCCCeEE-cCEEEEcCcHHHHHHHH
Confidence 4588888852111 13678999999999999996 67999999997765443
No 114
>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=63.33 E-value=3.4 Score=31.80 Aligned_cols=16 Identities=19% Similarity=0.538 Sum_probs=7.9
Q ss_pred eccccccccccccccc
Q psy7490 146 FLQCETCGSRCSVASI 161 (193)
Q Consensus 146 ~l~C~aCGa~~~V~~~ 161 (193)
..+|..||...++...
T Consensus 70 ~~~C~~Cg~~~~~~~~ 85 (113)
T PF01155_consen 70 RARCRDCGHEFEPDEF 85 (113)
T ss_dssp EEEETTTS-EEECHHC
T ss_pred cEECCCCCCEEecCCC
Confidence 3556666665544433
No 115
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=63.11 E-value=4.2 Score=32.57 Aligned_cols=31 Identities=29% Similarity=0.652 Sum_probs=20.4
Q ss_pred ecCceeecccccccccccccccccceeeeccEEEEEecccCCCc
Q psy7490 140 KDTRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRC 183 (193)
Q Consensus 140 k~~rl~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~ 183 (193)
++++++..+|..||+..- ++. -.|..||++.
T Consensus 23 ~~~kl~g~kC~~CG~v~~-PPr------------~~Cp~C~~~~ 53 (140)
T COG1545 23 KEGKLLGTKCKKCGRVYF-PPR------------AYCPKCGSET 53 (140)
T ss_pred hhCcEEEEEcCCCCeEEc-CCc------------ccCCCCCCCC
Confidence 357788888888887642 222 2477888774
No 116
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=63.09 E-value=4.6 Score=31.65 Aligned_cols=25 Identities=24% Similarity=0.394 Sum_probs=13.9
Q ss_pred ChHHHHHHHHHhhcCceeecCCCeEEE
Q psy7490 79 LPKHLLDFLLAELGTSGSVDGNSQLII 105 (193)
Q Consensus 79 ~p~hv~ky~~~ELgt~g~id~~~~lii 105 (193)
+|+.|.-.|. .-+.|++=++-.|.|
T Consensus 40 ~pe~L~faf~--~~~~gT~~egA~L~I 64 (124)
T PRK00762 40 NPEQLRFMLD--VLAEGTIAEDADLIV 64 (124)
T ss_pred CHHHHHHHHH--HHhCCCCcCCCEEEE
Confidence 5666655553 345566655556666
No 117
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=63.04 E-value=5.2 Score=31.35 Aligned_cols=20 Identities=10% Similarity=0.336 Sum_probs=14.4
Q ss_pred ccccCCCCCCcceeEecCce
Q psy7490 125 YVTCHTCRSPDTILQKDTRL 144 (193)
Q Consensus 125 YVlC~~C~sPdT~L~k~~rl 144 (193)
|..||.|+|++..+...+.+
T Consensus 92 ~~~CP~Cgs~~~~i~~G~El 111 (124)
T PRK00762 92 VIECPVCGNKRAHILGGREC 111 (124)
T ss_pred CCcCcCCCCCCCEEecCCeE
Confidence 45688888888887765443
No 118
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=62.66 E-value=4.1 Score=28.71 Aligned_cols=35 Identities=20% Similarity=0.617 Sum_probs=24.7
Q ss_pred HhhhccccCCCCCCcceeEecCceeecccccccccccc
Q psy7490 121 YIKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSV 158 (193)
Q Consensus 121 yI~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V 158 (193)
.+-+-+-||.|+.| -.+..+++ .+.|..||-..|+
T Consensus 4 ~LLeiLaCP~~kg~-L~~~~~~~--~L~c~~~~~aYpI 38 (60)
T COG2835 4 RLLEILACPVCKGP-LVYDEEKQ--ELICPRCKLAYPI 38 (60)
T ss_pred hhheeeeccCcCCc-ceEeccCC--EEEecccCceeec
Confidence 34556889999999 44444454 5778888887765
No 119
>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=62.37 E-value=7.6 Score=28.87 Aligned_cols=31 Identities=23% Similarity=0.564 Sum_probs=21.6
Q ss_pred ccccCCCCCCcceeEe-------cCceeeccccccccc
Q psy7490 125 YVTCHTCRSPDTILQK-------DTRLFFLQCETCGSR 155 (193)
Q Consensus 125 YVlC~~C~sPdT~L~k-------~~rl~~l~C~aCGa~ 155 (193)
.+.||.|++.+....- +.-..|-.|..||..
T Consensus 62 ~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~ 99 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYV 99 (104)
T ss_pred cCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCe
Confidence 4689999888865531 234667788888865
No 120
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=62.14 E-value=5 Score=31.92 Aligned_cols=20 Identities=25% Similarity=0.572 Sum_probs=16.0
Q ss_pred ccccCCCCCCcceeEecCce
Q psy7490 125 YVTCHTCRSPDTILQKDTRL 144 (193)
Q Consensus 125 YVlC~~C~sPdT~L~k~~rl 144 (193)
+..||.|+|+++.+..-+.+
T Consensus 107 ~~~CP~Cgs~~~~i~~G~el 126 (135)
T PRK03824 107 FLKCPKCGSRDFEIVKGRGV 126 (135)
T ss_pred CcCCcCCCCCCcEEecCceE
Confidence 56799999999988875544
No 121
>TIGR00467 lysS_arch lysyl-tRNA synthetase, archaeal and spirochete. This model represents the lysyl-tRNA synthetases that are class I amino-acyl tRNA synthetases. It includes archaeal and spirochete examples of the enzyme. All other known examples are class IIc amino-acyl tRNA synthetases and seem to form a separate orthologous set.
Probab=61.70 E-value=9.6 Score=36.82 Aligned_cols=72 Identities=28% Similarity=0.508 Sum_probs=46.2
Q ss_pred HHhhcCceeecCCCeEEEEeeccH---------HHHHHHHHHHhhh---------ccccCCCCCCcceeEe-c--Cceee
Q psy7490 88 LAELGTSGSVDGNSQLIIKGRFQQ---------KQIENVLRRYIKE---------YVTCHTCRSPDTILQK-D--TRLFF 146 (193)
Q Consensus 88 ~~ELgt~g~id~~~~lii~G~~~~---------~~iq~~L~~yI~~---------YVlC~~C~sPdT~L~k-~--~rl~~ 146 (193)
+.+||..-.+-.+..+.=+|+|.. ++|.++|..|... .++|+.|+.-.|.++. + ..+.|
T Consensus 113 l~~~gi~~e~~s~te~Y~sG~~~~~i~~~L~~~~~I~~il~~~~~~~~~~~~~P~~pic~~cGrv~~~~~~~~~~~~v~Y 192 (515)
T TIGR00467 113 LPVLGINPEFIRASKQYTSGLYASQIKIALDHRKEISEILNEYRTSKLEENWYPISVFCENCGRDTTTVNNYDNEYSIEY 192 (515)
T ss_pred HHHcCCeEEEEEHHHhhhcCChHHHHHHHHHhHHHHHHHHHHhcCCccCCCceeeeeecCCcCccCceEEEecCCceEEE
Confidence 455666533322334445666654 5677888888743 3689999998876553 2 34555
Q ss_pred ccccccccccccccc
Q psy7490 147 LQCETCGSRCSVASI 161 (193)
Q Consensus 147 l~C~aCGa~~~V~~~ 161 (193)
.|+ ||....++-.
T Consensus 193 -~c~-cG~~g~~~~~ 205 (515)
T TIGR00467 193 -SCE-CGNQESVDIY 205 (515)
T ss_pred -EcC-CCCEEEEeec
Confidence 896 9998877653
No 122
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=61.15 E-value=4.4 Score=26.51 Aligned_cols=27 Identities=22% Similarity=0.639 Sum_probs=15.4
Q ss_pred ccCCCCCCcceeEecCceeeccccccccccc
Q psy7490 127 TCHTCRSPDTILQKDTRLFFLQCETCGSRCS 157 (193)
Q Consensus 127 lC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~ 157 (193)
+|..|+..-+ +. ...-++|..||++=-
T Consensus 4 ~C~~Cg~~~~-~~---~~~~irC~~CG~rIl 30 (44)
T smart00659 4 ICGECGRENE-IK---SKDVVRCRECGYRIL 30 (44)
T ss_pred ECCCCCCEee-cC---CCCceECCCCCceEE
Confidence 5777776422 22 223477777777643
No 123
>KOG4577|consensus
Probab=61.05 E-value=3.4 Score=37.76 Aligned_cols=55 Identities=16% Similarity=0.522 Sum_probs=33.4
Q ss_pred hccccCCCCC--CcceeEecCce---------eecccccccccccccccccceeeeccEEEEEecccC
Q psy7490 124 EYVTCHTCRS--PDTILQKDTRL---------FFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCG 180 (193)
Q Consensus 124 ~YVlC~~C~s--PdT~L~k~~rl---------~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cg 180 (193)
.-..|..|+- -|+-+.+++.+ +-.+|.||.---|-....- .|+.-+|.|+|-+|-
T Consensus 59 ~CLkCs~C~~qL~drCFsR~~s~yCkedFfKrfGTKCsaC~~GIpPtqVVR--kAqd~VYHl~CF~C~ 124 (383)
T KOG4577|consen 59 SCLKCSDCHDQLADRCFSREGSVYCKEDFFKRFGTKCSACQEGIPPTQVVR--KAQDFVYHLHCFACF 124 (383)
T ss_pred hhcchhhhhhHHHHHHhhcCCceeehHHHHHHhCCcchhhcCCCChHHHHH--HhhcceeehhhhhhH
Confidence 3567888875 34444444433 3568999976433322211 267788999998884
No 124
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=61.01 E-value=5.6 Score=30.70 Aligned_cols=20 Identities=15% Similarity=0.370 Sum_probs=12.9
Q ss_pred ccccCCCCCCcceeEecCce
Q psy7490 125 YVTCHTCRSPDTILQKDTRL 144 (193)
Q Consensus 125 YVlC~~C~sPdT~L~k~~rl 144 (193)
+..||.|+|++..++.-..+
T Consensus 86 ~~~CP~Cgs~~~~i~~G~El 105 (113)
T PRK12380 86 DAQCPHCHGERLRVDTGDSL 105 (113)
T ss_pred CccCcCCCCCCcEEccCCeE
Confidence 33588888887777654443
No 125
>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=60.85 E-value=5.8 Score=24.39 Aligned_cols=25 Identities=28% Similarity=0.753 Sum_probs=13.6
Q ss_pred ccCCCCCCcceeEecCceeeccccccccc
Q psy7490 127 TCHTCRSPDTILQKDTRLFFLQCETCGSR 155 (193)
Q Consensus 127 lC~~C~sPdT~L~k~~rl~~l~C~aCGa~ 155 (193)
+|..|+.... |...+ -++|..||.+
T Consensus 2 ~C~~Cg~~~~-~~~~~---~irC~~CG~R 26 (32)
T PF03604_consen 2 ICGECGAEVE-LKPGD---PIRCPECGHR 26 (32)
T ss_dssp BESSSSSSE--BSTSS---TSSBSSSS-S
T ss_pred CCCcCCCeeE-cCCCC---cEECCcCCCe
Confidence 5777776655 22222 3578878775
No 126
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=60.71 E-value=11 Score=23.33 Aligned_cols=28 Identities=14% Similarity=0.217 Sum_probs=23.1
Q ss_pred eccHHHHHHcCCChHHHHHHHHHhhcCc
Q psy7490 67 ANFTEICKTLHRLPKHLLDFLLAELGTS 94 (193)
Q Consensus 67 ~Nf~dIak~L~R~p~hv~ky~~~ELgt~ 94 (193)
..+.|||+.++=++.|+.+-|..++|..
T Consensus 9 ~~l~~iA~~~g~S~~~f~r~Fk~~~g~t 36 (42)
T PF00165_consen 9 LTLEDIAEQAGFSPSYFSRLFKKETGMT 36 (42)
T ss_dssp --HHHHHHHHTS-HHHHHHHHHHHTSS-
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHCcC
Confidence 3578999999999999999999999974
No 127
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB []. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=60.59 E-value=7.6 Score=24.80 Aligned_cols=28 Identities=29% Similarity=0.540 Sum_probs=15.2
Q ss_pred ccCCCCCCcceeEecCceeecccccccc
Q psy7490 127 TCHTCRSPDTILQKDTRLFFLQCETCGS 154 (193)
Q Consensus 127 lC~~C~sPdT~L~k~~rl~~l~C~aCGa 154 (193)
.|..|+..-..+..-..-....|..||+
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 4666666555555422233466666666
No 128
>PRK12496 hypothetical protein; Provisional
Probab=60.18 E-value=5.9 Score=32.51 Aligned_cols=39 Identities=23% Similarity=0.257 Sum_probs=24.7
Q ss_pred CcceeEecCceeecccccccccccccccccceeeeccEEEEEecccCCCc
Q psy7490 134 PDTILQKDTRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRC 183 (193)
Q Consensus 134 PdT~L~k~~rl~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~ 183 (193)
..|.=+++.+.|-.+|.+||...+...- .--|.-||++-
T Consensus 115 ~~~~~i~~~~~w~~~C~gC~~~~~~~~~-----------~~~C~~CG~~~ 153 (164)
T PRK12496 115 IKTKGIKKVIKWRKVCKGCKKKYPEDYP-----------DDVCEICGSPV 153 (164)
T ss_pred cccccchhheeeeEECCCCCccccCCCC-----------CCcCCCCCChh
Confidence 3344455667788889999976543221 12589999763
No 129
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=59.95 E-value=8.6 Score=24.60 Aligned_cols=22 Identities=27% Similarity=0.208 Sum_probs=16.3
Q ss_pred eccHHHHHHcCCChHHHHHHHH
Q psy7490 67 ANFTEICKTLHRLPKHLLDFLL 88 (193)
Q Consensus 67 ~Nf~dIak~L~R~p~hv~ky~~ 88 (193)
..+.+||+.|+|++.-|.+++-
T Consensus 21 ~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 21 MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp --HHHHHHHTT--HHHHHHHHH
T ss_pred CCHHHHHHHHCcCcHHHHHHHh
Confidence 4578999999999999998874
No 130
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=59.90 E-value=6.2 Score=32.68 Aligned_cols=31 Identities=26% Similarity=0.580 Sum_probs=23.0
Q ss_pred ccCCCCCCcceeEe-----cCcee--eccccccccccc
Q psy7490 127 TCHTCRSPDTILQK-----DTRLF--FLQCETCGSRCS 157 (193)
Q Consensus 127 lC~~C~sPdT~L~k-----~~rl~--~l~C~aCGa~~~ 157 (193)
.||-|+++||..+- ++..+ --.|..||.+-+
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFT 39 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFT 39 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccc
Confidence 59999999998874 23221 357999999873
No 131
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=59.46 E-value=8 Score=30.00 Aligned_cols=37 Identities=19% Similarity=0.442 Sum_probs=29.3
Q ss_pred ecccccccccccccccccceeeeccEEEEEecccCCCccc
Q psy7490 146 FLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRCSV 185 (193)
Q Consensus 146 ~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~~v 185 (193)
...|..||+...+.-. ..+.....++.|-.||.+.-.
T Consensus 22 ~FtCp~Cghe~vs~ct---vkk~~~~g~~~Cg~CGls~e~ 58 (104)
T COG4888 22 TFTCPRCGHEKVSSCT---VKKTVNIGTAVCGNCGLSFEC 58 (104)
T ss_pred eEecCccCCeeeeEEE---EEecCceeEEEcccCcceEEE
Confidence 4689999999877533 347788999999999998643
No 132
>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=59.12 E-value=8 Score=31.99 Aligned_cols=30 Identities=33% Similarity=0.648 Sum_probs=20.5
Q ss_pred cCCCCCC-cceeEe--c----Cc--eeeccccccccccc
Q psy7490 128 CHTCRSP-DTILQK--D----TR--LFFLQCETCGSRCS 157 (193)
Q Consensus 128 C~~C~sP-dT~L~k--~----~r--l~~l~C~aCGa~~~ 157 (193)
||.|+.+ .+.+.. + +. +....|..||.++.
T Consensus 1 CP~Cg~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~ 39 (163)
T TIGR00340 1 CPVCGSRTLKAVTYDYDIPYFGKIMLSTYICEKCGYRST 39 (163)
T ss_pred CCCCCCcceEeeeEeccCCCcceEEEEEEECCCCCCchh
Confidence 9999987 343222 1 23 34788999999875
No 133
>KOG2767|consensus
Probab=58.74 E-value=3.2 Score=38.64 Aligned_cols=70 Identities=23% Similarity=0.513 Sum_probs=46.2
Q ss_pred ccHHHHHHHHHH---HhhhccccCCCCCCcceeEec-C-----------c---e------eecccccccccccccccccc
Q psy7490 109 FQQKQIENVLRR---YIKEYVTCHTCRSPDTILQKD-T-----------R---L------FFLQCETCGSRCSVASIKSG 164 (193)
Q Consensus 109 ~~~~~iq~~L~~---yI~~YVlC~~C~sPdT~L~k~-~-----------r---l------~~l~C~aCGa~~~V~~~k~~ 164 (193)
.+-.+|.+.|.+ |+-+|-=|-- ..-|.+-.+ + + + -|+.|..|+.+- |.
T Consensus 37 vNm~eIakAL~RPp~Y~tKyFGcEL--GAQT~fd~kn~ryiVNG~Hd~~KLqdlLdgFIkKFVlC~~C~NPE------Te 108 (400)
T KOG2767|consen 37 VNMVEIAKALGRPPLYPTKYFGCEL--GAQTKFDVKNGRYIVNGAHEASKLQDLLDGFIKKFVLCPSCENPE------TE 108 (400)
T ss_pred ecHHHHHHHhCCCCCcccccceeec--cccccccccCCeeeecccccHHHHHHHHHHHHHHheeCcCCCCCc------ee
Confidence 456778888875 8888865532 233433211 1 1 1 279999999997 44
Q ss_pred eeee-ccEEEEEecccCCCcccc
Q psy7490 165 FQKD-TRLFFLQCETCGSRCSVA 186 (193)
Q Consensus 165 ~~~~-~rl~~~~c~~Cga~~~v~ 186 (193)
+... +.-.-++|.|||-+..+.
T Consensus 109 l~itk~q~i~~~CkACG~r~~~d 131 (400)
T KOG2767|consen 109 LIITKKQTISLKCKACGFRSDMD 131 (400)
T ss_pred EEecccchhhhHHHHcCCccccc
Confidence 4433 667789999999988775
No 134
>PRK14973 DNA topoisomerase I; Provisional
Probab=58.59 E-value=14 Score=38.36 Aligned_cols=61 Identities=18% Similarity=0.302 Sum_probs=28.3
Q ss_pred cccCCCCCCcceeEecCceeeccccc---ccccccccccccceeeeccEEEEEecccCCCccccccccC
Q psy7490 126 VTCHTCRSPDTILQKDTRLFFLQCET---CGSRCSVASIKSGFQKDTRLFFLQCETCGSRCSVASIKSG 191 (193)
Q Consensus 126 VlC~~C~sPdT~L~k~~rl~~l~C~a---CGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~~v~~~~~~ 191 (193)
..||.|+.+ ..+.+...-.|+.|.. |+...++..-..|=...+ --.|..||+. -+..+|.|
T Consensus 589 ~~CP~CG~~-l~ik~~k~gkFigCS~Yp~Ck~t~~L~~~~~g~~~~~---~~~Cp~CG~p-~~~~~r~G 652 (936)
T PRK14973 589 GPCPVCGKD-LRIKHIGSSQFIGCSGYPDCTFNIGLPGTTWGWAIRT---DEVCPIHHLN-HVRLIRKG 652 (936)
T ss_pred ccCCccccc-ceeecccCceeEECCCCCCCCccccCCccccccCCCC---CCCCCCCCCC-ceEEeecC
Confidence 469999863 2222111112566765 776655542111100000 1257777774 34444444
No 135
>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=58.39 E-value=7.7 Score=28.09 Aligned_cols=26 Identities=27% Similarity=0.632 Sum_probs=14.1
Q ss_pred cccCCCCCCcceeEecCceeecccccccccc
Q psy7490 126 VTCHTCRSPDTILQKDTRLFFLQCETCGSRC 156 (193)
Q Consensus 126 VlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~ 156 (193)
..||.|+.| |...++. .+|.+|+..-
T Consensus 2 ~~CP~C~~~---L~~~~~~--~~C~~C~~~~ 27 (70)
T PF07191_consen 2 NTCPKCQQE---LEWQGGH--YHCEACQKDY 27 (70)
T ss_dssp -B-SSS-SB---EEEETTE--EEETTT--EE
T ss_pred CcCCCCCCc---cEEeCCE--EECccccccc
Confidence 379999887 6666643 4677777653
No 136
>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=58.18 E-value=4.3 Score=26.49 Aligned_cols=28 Identities=29% Similarity=0.596 Sum_probs=11.9
Q ss_pred ccCCCCCCcceeEecCceeecccccccc
Q psy7490 127 TCHTCRSPDTILQKDTRLFFLQCETCGS 154 (193)
Q Consensus 127 lC~~C~sPdT~L~k~~rl~~l~C~aCGa 154 (193)
.|+.|+..=..+..-..-....|..||+
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 7 RCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 4666664222332211112345666665
No 137
>PF05379 Peptidase_C23: Carlavirus endopeptidase ; InterPro: IPR008041 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. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C23 (clan CA). The type example is Carlavirus (apple stem pitting virus) endopeptidase, this thought to play a role in the post-translational cleavage of the high molecular weight primary translation products of the virus.; GO: 0003968 RNA-directed RNA polymerase activity, 0016817 hydrolase activity, acting on acid anhydrides
Probab=57.68 E-value=10 Score=28.25 Aligned_cols=61 Identities=15% Similarity=0.299 Sum_probs=39.5
Q ss_pred cHHHHHHcCCChHHHHHHHHHhhcCceeecCCCeEEEEe-eccHHHHHHHHHHHhhhccccCCCCCCccee
Q psy7490 69 FTEICKTLHRLPKHLLDFLLAELGTSGSVDGNSQLIIKG-RFQQKQIENVLRRYIKEYVTCHTCRSPDTIL 138 (193)
Q Consensus 69 f~dIak~L~R~p~hv~ky~~~ELgt~g~id~~~~lii~G-~~~~~~iq~~L~~yI~~YVlC~~C~sPdT~L 138 (193)
+..||++|+|++..|++.+....+.. -++ -+..| =++..+++.+ .+-|=+|-.|.-.+..+
T Consensus 7 i~AiA~aL~R~~~dVl~Vl~~~~~~~-~~~----~l~~G~Gl~l~~le~~----f~~F~I~A~v~~~g~~~ 68 (89)
T PF05379_consen 7 IRAIAEALGRREQDVLAVLSRKCGEE-LLE----ELWSGEGLDLEDLEEL----FELFDICAHVNFGGETF 68 (89)
T ss_pred hHHHHHHhCCCHHHHHHHHHhccCHH-HHH----HHHcCCCcCHHHHHHH----HHHcCeEEEEEECCEEE
Confidence 46799999999999999999877743 111 11122 2444555554 55678888886544433
No 138
>PRK06824 translation initiation factor Sui1; Validated
Probab=57.62 E-value=19 Score=28.38 Aligned_cols=53 Identities=19% Similarity=0.247 Sum_probs=38.6
Q ss_pred cCeeeEEeccHHHHHHcCCChHHHHHHHHHhhcCceeecCCCeEEEEeeccHHHHHHH
Q psy7490 60 GTKKTSFANFTEICKTLHRLPKHLLDFLLAELGTSGSVDGNSQLIIKGRFQQKQIENV 117 (193)
Q Consensus 60 Gg~KTvi~Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id~~~~lii~G~~~~~~iq~~ 117 (193)
|..=|+|..|..-... -.-+.|.|...+|+.|++. ++.+.|+|.|...-.+-+
T Consensus 54 gK~VTvI~Gl~~~~~d----lk~l~K~LKkk~gcGGtvk-d~~IeiQGD~r~~v~~~L 106 (118)
T PRK06824 54 GKTVTVITGVPLAEDA----LKELAKELKRRCGTGGTLK-DGVIEIQGDHVELLLAEL 106 (118)
T ss_pred CceEEEEeCCcCCHHH----HHHHHHHHHHHhcCCceEe-cCEEEEcCcHHHHHHHHH
Confidence 3445788888522222 3578999999999999995 679999999987654433
No 139
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=57.58 E-value=7.5 Score=24.58 Aligned_cols=32 Identities=25% Similarity=0.703 Sum_probs=13.1
Q ss_pred cccCCCCC---CcceeEecCceeeccccccccccccc
Q psy7490 126 VTCHTCRS---PDTILQKDTRLFFLQCETCGSRCSVA 159 (193)
Q Consensus 126 VlC~~C~s---PdT~L~k~~rl~~l~C~aCGa~~~V~ 159 (193)
|.|..|++ |=..+...++. -.|.-|+...+++
T Consensus 3 ~rC~~C~aylNp~~~~~~~~~~--w~C~~C~~~N~lp 37 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDDGGKT--WICNFCGTKNPLP 37 (40)
T ss_dssp -B-TTT--BS-TTSEEETTTTE--EEETTT--EEE--
T ss_pred cccCCCCCEECCcceEcCCCCE--EECcCCCCcCCCC
Confidence 45666663 44455444444 3566666665543
No 140
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=57.58 E-value=5.6 Score=22.90 Aligned_cols=7 Identities=29% Similarity=0.966 Sum_probs=3.6
Q ss_pred ccCCCCC
Q psy7490 127 TCHTCRS 133 (193)
Q Consensus 127 lC~~C~s 133 (193)
.||.|+.
T Consensus 4 ~Cp~Cg~ 10 (26)
T PF13248_consen 4 FCPNCGA 10 (26)
T ss_pred CCcccCC
Confidence 4555554
No 141
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=57.52 E-value=6.1 Score=35.33 Aligned_cols=29 Identities=28% Similarity=0.445 Sum_probs=20.2
Q ss_pred ccccCCCCCCcceeEecCceeeccccccccc
Q psy7490 125 YVTCHTCRSPDTILQKDTRLFFLQCETCGSR 155 (193)
Q Consensus 125 YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~ 155 (193)
-..||.|+++ .++.+..--.+.|..||.-
T Consensus 11 ~~~Cp~Cg~~--~iv~d~~~Ge~vC~~CG~V 39 (310)
T PRK00423 11 KLVCPECGSD--KLIYDYERGEIVCADCGLV 39 (310)
T ss_pred CCcCcCCCCC--CeeEECCCCeEeecccCCc
Confidence 3579999984 4555433445789999973
No 142
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=57.19 E-value=7.7 Score=23.93 Aligned_cols=27 Identities=26% Similarity=0.648 Sum_probs=12.7
Q ss_pred cccCCCCCCcceeEecCceeeccccccccc
Q psy7490 126 VTCHTCRSPDTILQKDTRLFFLQCETCGSR 155 (193)
Q Consensus 126 VlC~~C~sPdT~L~k~~rl~~l~C~aCGa~ 155 (193)
..|+.|+++--.. +++. +..|..||+.
T Consensus 4 ~~C~~C~~~~i~~-~~~~--~~~C~~Cg~~ 30 (33)
T PF08792_consen 4 KKCSKCGGNGIVN-KEDD--YEVCIFCGSS 30 (33)
T ss_pred eEcCCCCCCeEEE-ecCC--eEEcccCCcE
Confidence 4566666655221 2222 3445555554
No 143
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=56.68 E-value=15 Score=31.63 Aligned_cols=52 Identities=19% Similarity=0.357 Sum_probs=31.4
Q ss_pred hccccCCCCCCcceeEe-------cCc--eeecccccccccccccccccceeeeccEEEEEecc
Q psy7490 124 EYVTCHTCRSPDTILQK-------DTR--LFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCET 178 (193)
Q Consensus 124 ~YVlC~~C~sPdT~L~k-------~~r--l~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~ 178 (193)
.-+-||.|++ .-.++- -++ +....|+.||.+..--. ..=...-+.++++++.
T Consensus 13 ~~~~CPvCg~-~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~DV~--~~e~~eP~r~~lkve~ 73 (201)
T COG1779 13 TRIDCPVCGG-TLKAHMYLYDIPYFGEVLISTGVCERCGYRSTDVK--TLEEREPRRYTLKVES 73 (201)
T ss_pred eeecCCcccc-eeeEEEeeecCCccceEEEEEEEccccCCccccee--ecccCCCeEEEEEeCC
Confidence 3468999999 322221 144 34789999999874211 1113455778887764
No 144
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=56.16 E-value=3.6 Score=37.27 Aligned_cols=36 Identities=22% Similarity=0.484 Sum_probs=26.6
Q ss_pred cccccccccccccccccceeeeccEEEEEecccCCCc
Q psy7490 147 LQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRC 183 (193)
Q Consensus 147 l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~ 183 (193)
..|.+||+.-.+..+ .++....++=|++|.-|-..-
T Consensus 186 ~~CPvCGS~PvaSmV-~~g~~~~GlRYL~CslC~teW 221 (308)
T COG3058 186 QYCPVCGSMPVASMV-QIGETEQGLRYLHCSLCETEW 221 (308)
T ss_pred ccCCCcCCCCcceee-eecCccccchhhhhhhHHHHH
Confidence 479999997544444 455678899999998886543
No 145
>PF06322 Phage_NinH: Phage NinH protein; InterPro: IPR010454 This entry is represented by Bacteriophage 933W, NinH. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=55.51 E-value=16 Score=26.06 Aligned_cols=37 Identities=19% Similarity=0.253 Sum_probs=29.5
Q ss_pred eccHHHHHHcCCChHHHHHHHHHhhcCceeecCCCeEEEEeecc
Q psy7490 67 ANFTEICKTLHRLPKHLLDFLLAELGTSGSVDGNSQLIIKGRFQ 110 (193)
Q Consensus 67 ~Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id~~~~lii~G~~~ 110 (193)
-|..|+|..|+-.-..|.||... .++...+|+||.+.
T Consensus 17 GnqtEvaR~l~c~R~TVrKY~~D-------~~a~~HaIvNgvLM 53 (64)
T PF06322_consen 17 GNQTEVARRLGCNRATVRKYSRD-------KDAKRHAIVNGVLM 53 (64)
T ss_pred CcHHHHHHHhcccHHHHHHHhcc-------cccceEEEEcCEEE
Confidence 48999999999999999999753 33456788888653
No 146
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=55.35 E-value=3.7 Score=29.38 Aligned_cols=39 Identities=23% Similarity=0.635 Sum_probs=24.0
Q ss_pred eecccccccccccccccccceeeeccEEEEEecccCCCccc
Q psy7490 145 FFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRCSV 185 (193)
Q Consensus 145 ~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~~v 185 (193)
+...|+.|+.++.-.-.|..| ..++-+++|..|+++--+
T Consensus 3 l~FTC~~C~~Rs~~~~sk~aY--~~GvViv~C~gC~~~HlI 41 (66)
T PF05180_consen 3 LTFTCNKCGTRSAKMFSKQAY--HKGVVIVQCPGCKNRHLI 41 (66)
T ss_dssp EEEEETTTTEEEEEEEEHHHH--HTSEEEEE-TTS--EEES
T ss_pred EEEEcCCCCCccceeeCHHHH--hCCeEEEECCCCcceeee
Confidence 356799999877432223222 467899999999987554
No 147
>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=55.29 E-value=11 Score=30.84 Aligned_cols=32 Identities=25% Similarity=0.636 Sum_probs=17.6
Q ss_pred cccCCCCCCc-ceeEe-c----Cc--eeeccccccccccc
Q psy7490 126 VTCHTCRSPD-TILQK-D----TR--LFFLQCETCGSRCS 157 (193)
Q Consensus 126 VlC~~C~sPd-T~L~k-~----~r--l~~l~C~aCGa~~~ 157 (193)
..||.|+.+- |.+.. + +. +....|..||.++.
T Consensus 2 s~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~ 41 (161)
T PF03367_consen 2 SLCPNCGENGTTRILLTDIPYFKEVIIMSFECEHCGYKNN 41 (161)
T ss_dssp EE-TTTSSCCEEEEEEEEETTTEEEEEEEEE-TTT--EEE
T ss_pred CcCCCCCCCcEEEEEEEcCCCCceEEEEEeECCCCCCEee
Confidence 3799999875 44422 1 22 44668999999874
No 148
>PHA00626 hypothetical protein
Probab=54.71 E-value=8.3 Score=27.01 Aligned_cols=34 Identities=21% Similarity=0.361 Sum_probs=23.1
Q ss_pred ccCCCCCCcceeE---ecCceeeccccccccccccccc
Q psy7490 127 TCHTCRSPDTILQ---KDTRLFFLQCETCGSRCSVASI 161 (193)
Q Consensus 127 lC~~C~sPdT~L~---k~~rl~~l~C~aCGa~~~V~~~ 161 (193)
.||.|+|-+-..- ++-+- --.|..||...+-++.
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~sn-rYkCkdCGY~ft~~~~ 38 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSD-DYVCCDCGYNDSKDAF 38 (59)
T ss_pred CCCCCCCceeeeeceecccCc-ceEcCCCCCeechhhh
Confidence 6999999765432 22122 2479999999887765
No 149
>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=53.81 E-value=15 Score=29.28 Aligned_cols=37 Identities=22% Similarity=0.517 Sum_probs=24.9
Q ss_pred eEEEEeeccHHHHHHHHHHHhhh------ccccCCCCCCccee
Q psy7490 102 QLIIKGRFQQKQIENVLRRYIKE------YVTCHTCRSPDTIL 138 (193)
Q Consensus 102 ~lii~G~~~~~~iq~~L~~yI~~------YVlC~~C~sPdT~L 138 (193)
.+.|...-..+++..+++.|=-. +-.|+.|+++=..+
T Consensus 62 ~~li~~~~~~~QL~ev~~~~~l~~~~~~~~sRC~~CN~~L~~v 104 (147)
T PF01927_consen 62 VILIRSDDPEEQLREVLERFGLKLRLDPIFSRCPKCNGPLRPV 104 (147)
T ss_pred EEEEcCCCHHHHHHHHHHHcCCccccCCCCCccCCCCcEeeec
Confidence 35566777778888888877422 56788888743333
No 150
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=53.37 E-value=7.4 Score=26.10 Aligned_cols=27 Identities=22% Similarity=0.540 Sum_probs=15.5
Q ss_pred ccccCCCCCCcceeEecCceeeccccccccc
Q psy7490 125 YVTCHTCRSPDTILQKDTRLFFLQCETCGSR 155 (193)
Q Consensus 125 YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~ 155 (193)
.-.||.|++- .|..... ...|..||..
T Consensus 20 ~~fCP~Cg~~--~m~~~~~--r~~C~~Cgyt 46 (50)
T PRK00432 20 NKFCPRCGSG--FMAEHLD--RWHCGKCGYT 46 (50)
T ss_pred cCcCcCCCcc--hheccCC--cEECCCcCCE
Confidence 3468888763 3433332 3467777764
No 151
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=52.59 E-value=10 Score=29.93 Aligned_cols=18 Identities=22% Similarity=0.344 Sum_probs=11.3
Q ss_pred HHhhcCceeecCCCeEEE
Q psy7490 88 LAELGTSGSVDGNSQLII 105 (193)
Q Consensus 88 ~~ELgt~g~id~~~~lii 105 (193)
..|.-+.|++-++.+++|
T Consensus 47 aFev~~egT~aega~l~I 64 (115)
T COG0375 47 AFEVVAEGTIAEGAELHI 64 (115)
T ss_pred HHHHHhccCcccCCEEEE
Confidence 345555677765667777
No 152
>KOG2907|consensus
Probab=52.37 E-value=7.3 Score=30.77 Aligned_cols=31 Identities=16% Similarity=0.608 Sum_probs=23.0
Q ss_pred ccCCCCCCcceeE----e---cCceeeccccccccccc
Q psy7490 127 TCHTCRSPDTILQ----K---DTRLFFLQCETCGSRCS 157 (193)
Q Consensus 127 lC~~C~sPdT~L~----k---~~rl~~l~C~aCGa~~~ 157 (193)
.||.|+.++-.+. + ++...|-.|..|+.+.+
T Consensus 76 kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k~~ 113 (116)
T KOG2907|consen 76 KCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYKFT 113 (116)
T ss_pred cCcccCCchhhhhhhhcccccCCceEEEEcCccceeee
Confidence 7999998875442 2 57788888988887754
No 153
>cd00674 LysRS_core_class_I catalytic core domain of class I lysyl tRNA synthetase. Class I lysyl tRNA synthetase (LysRS) catalytic core domain. This class I enzyme is a monomer which aminoacylates the 2'-OH of the nucleotide at the 3' of the appropriate tRNA. The core domain is based on the Rossman fold and is responsible for the ATP-dependent formation of the enzyme bound aminoacyl-adenylate. It contains the characteristic class I HIGH and KMSKS motifs, which are involved in ATP binding. The class I LysRS is found only in archaea and some bacteria and has evolved separately from class II LysRS, as the two do not share structural or sequence similarity.
Probab=52.37 E-value=15 Score=33.85 Aligned_cols=90 Identities=21% Similarity=0.407 Sum_probs=51.8
Q ss_pred HHHHHHcCCChHHHHHH---H---HHhhcCceeecCCCeEEEEeeccH---------HHHHHHHHHHhhh---------c
Q psy7490 70 TEICKTLHRLPKHLLDF---L---LAELGTSGSVDGNSQLIIKGRFQQ---------KQIENVLRRYIKE---------Y 125 (193)
Q Consensus 70 ~dIak~L~R~p~hv~ky---~---~~ELgt~g~id~~~~lii~G~~~~---------~~iq~~L~~yI~~---------Y 125 (193)
.+|++.....|++.-.| | +..||.+-.+=..-.+--+|.|.. ..|.++|..|... .
T Consensus 90 ~~ip~p~g~~~~~~d~~~~~f~~~l~~lgi~~d~~~~T~~y~~g~~~~~i~~~L~~~~~I~~i~~~~~~~~~~~~~~P~~ 169 (353)
T cd00674 90 SSVPDPFGCCESYAEHFERPFEESLEKLGIEVEFISQSQMYKSGLYDENILIALEKRDEIMAILNEYRGRELQETWYPFM 169 (353)
T ss_pred hhchhhcCCCHHHHHHHHHHHHHHHHHcCCeeeeeecCCchhhchHHHHHHHHHHHCChHHHHHHHhcCCccCCCceeee
Confidence 34444444445444444 2 445666432212334555666654 3566777777764 4
Q ss_pred cccCCCCCCcceeEe-c--Cc-eeeccccccccccccccc
Q psy7490 126 VTCHTCRSPDTILQK-D--TR-LFFLQCETCGSRCSVASI 161 (193)
Q Consensus 126 VlC~~C~sPdT~L~k-~--~r-l~~l~C~aCGa~~~V~~~ 161 (193)
++|+.|+.-.|.++. + .+ +.| .|+ ||....++-.
T Consensus 170 p~c~~cg~~~~~v~~~d~~~~~v~y-~c~-cG~~g~~~~~ 207 (353)
T cd00674 170 PYCEKCGKDTTTVEAYDAKAGTVTY-KCE-CGHEETVDIR 207 (353)
T ss_pred eecCCcCcceeEEEEEeCCCCeEEE-EcC-CCCEEEEeec
Confidence 689999966565542 2 34 545 896 9998877554
No 154
>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=52.16 E-value=6.2 Score=31.11 Aligned_cols=36 Identities=19% Similarity=0.426 Sum_probs=25.2
Q ss_pred hccccCCCCCCcceeEecCceeecccccccccccccccccc
Q psy7490 124 EYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVASIKSG 164 (193)
Q Consensus 124 ~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~~~k~~ 164 (193)
.-|.||+|+.+---|-+. -.|--|+.+=++++-.+|
T Consensus 68 v~V~CP~C~K~TKmLGr~-----D~CM~C~~pLTLd~~leg 103 (114)
T PF11023_consen 68 VQVECPNCGKQTKMLGRV-----DACMHCKEPLTLDPSLEG 103 (114)
T ss_pred eeeECCCCCChHhhhchh-----hccCcCCCcCccCchhhc
Confidence 357899999874333333 279999999888776543
No 155
>PHA02540 61 DNA primase; Provisional
Probab=51.93 E-value=16 Score=33.63 Aligned_cols=42 Identities=17% Similarity=0.441 Sum_probs=28.9
Q ss_pred eecccccccccccccccccceee-eccEEEEEecccCCCcccc
Q psy7490 145 FFLQCETCGSRCSVASIKSGFQK-DTRLFFLQCETCGSRCSVA 186 (193)
Q Consensus 145 ~~l~C~aCGa~~~V~~~k~~~~~-~~rl~~~~c~~Cga~~~v~ 186 (193)
+.-.|.-||...+-..--+.++. .++-++.||-.|||...+-
T Consensus 26 ~~~~CPf~~ds~~~~~kpsF~V~p~k~~~~yhCFgCGa~Gd~i 68 (337)
T PHA02540 26 YNFRCPICGDSQKDKNKARGWIYEKKDGGVFKCHNCGYHRPFG 68 (337)
T ss_pred EEecCCCCCCccccCcCCcEEEeccCCceEEEecCCCCCCCHH
Confidence 88999999986643333233333 2335788999999988764
No 156
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=51.89 E-value=12 Score=35.67 Aligned_cols=55 Identities=18% Similarity=0.567 Sum_probs=33.3
Q ss_pred ccCCCCCCcceeEecCceeeccccccccccccc-ccccceee----ecc-----EEEEEecccCCCcc
Q psy7490 127 TCHTCRSPDTILQKDTRLFFLQCETCGSRCSVA-SIKSGFQK----DTR-----LFFLQCETCGSRCS 184 (193)
Q Consensus 127 lC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~-~~k~~~~~----~~r-----l~~~~c~~Cga~~~ 184 (193)
.|..|+.-|.. .|.-.++.|..||.+...+ +++.++.. ..+ =--.+|.+||...-
T Consensus 130 ~C~iC~kfD~~---~n~~~Wi~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~se 194 (446)
T PF07227_consen 130 MCCICSKFDDN---KNTCSWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKTSE 194 (446)
T ss_pred CccccCCcccC---CCCeeEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCChhh
Confidence 45556554332 2455579999999998875 55544321 111 12468999998653
No 157
>PF08535 KorB: KorB domain; InterPro: IPR013741 This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon []. This domain includes the DNA-binding HTH motif []. ; PDB: 1R71_C.
Probab=51.59 E-value=13 Score=27.15 Aligned_cols=20 Identities=25% Similarity=0.245 Sum_probs=16.5
Q ss_pred cHHHHHHcCCChHHHHHHHH
Q psy7490 69 FTEICKTLHRLPKHLLDFLL 88 (193)
Q Consensus 69 f~dIak~L~R~p~hv~ky~~ 88 (193)
-.|||+.|.+++.||.+|+.
T Consensus 6 q~eIA~~lGks~s~Vs~~l~ 25 (93)
T PF08535_consen 6 QEEIAKRLGKSRSWVSNHLA 25 (93)
T ss_dssp HHHHHHHTT--HHHHHHHHG
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 47999999999999999995
No 158
>PRK04023 DNA polymerase II large subunit; Validated
Probab=51.56 E-value=11 Score=39.54 Aligned_cols=20 Identities=30% Similarity=1.019 Sum_probs=14.9
Q ss_pred ccCCCCCCcceeEecCceeeccccccccc
Q psy7490 127 TCHTCRSPDTILQKDTRLFFLQCETCGSR 155 (193)
Q Consensus 127 lC~~C~sPdT~L~k~~rl~~l~C~aCGa~ 155 (193)
.|++|+.. .....|..||+.
T Consensus 628 fCpsCG~~---------t~~frCP~CG~~ 647 (1121)
T PRK04023 628 KCPSCGKE---------TFYRRCPFCGTH 647 (1121)
T ss_pred cCCCCCCc---------CCcccCCCCCCC
Confidence 78888876 145678888876
No 159
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=51.53 E-value=33 Score=22.90 Aligned_cols=46 Identities=11% Similarity=0.048 Sum_probs=32.6
Q ss_pred ccHHHHHHcCCChHHHHHHHHHhhcCceeecCCCeEEEEeeccHHHHHHH
Q psy7490 68 NFTEICKTLHRLPKHLLDFLLAELGTSGSVDGNSQLIIKGRFQQKQIENV 117 (193)
Q Consensus 68 Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id~~~~lii~G~~~~~~iq~~ 117 (193)
+..|+|+.++.+|..|-.|....+-.+..-+++|+. .|+..+++.+
T Consensus 2 s~~eva~~~gvs~~tlr~~~~~gli~~~~~~~~g~r----~y~~~dl~~l 47 (70)
T smart00422 2 TIGEVAKLAGVSVRTLRYYERIGLLPPPIRTEGGYR----LYSDEDLERL 47 (70)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCCCCCCCccCCCCCE----ecCHHHHHHH
Confidence 468999999999999999987666544312234332 5888888764
No 160
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=51.30 E-value=27 Score=29.61 Aligned_cols=48 Identities=15% Similarity=0.333 Sum_probs=25.8
Q ss_pred EeccHHHHHHcCCChHHHHHHHH---HhhcCceeecCCCeEEEEeeccHHHHHH
Q psy7490 66 FANFTEICKTLHRLPKHLLDFLL---AELGTSGSVDGNSQLIIKGRFQQKQIEN 116 (193)
Q Consensus 66 i~Nf~dIak~L~R~p~hv~ky~~---~ELgt~g~id~~~~lii~G~~~~~~iq~ 116 (193)
++++.|+|..++=.++.+...|. .+=...|.+|+.|++|. +++..++.
T Consensus 113 vv~ledla~~f~l~t~~~i~ri~~L~~~g~ltGv~DdrGkfIy---Is~eE~~~ 163 (188)
T PF09756_consen 113 VVNLEDLAAEFGLRTQDVINRIQELEAEGRLTGVIDDRGKFIY---ISEEEMEA 163 (188)
T ss_dssp EE-HHHHHHHH-S-HHHHHHHHHHHHHHSSS-EEE-TT--EEE-----------
T ss_pred eeeHHHHHHHcCCCHHHHHHHHHHHHHCCCceeeEcCCCCeEE---ecHHHHHH
Confidence 57899999999999999988873 33334588888888886 34444444
No 161
>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=51.28 E-value=11 Score=26.59 Aligned_cols=12 Identities=17% Similarity=0.487 Sum_probs=8.8
Q ss_pred ccCCCCCCccee
Q psy7490 127 TCHTCRSPDTIL 138 (193)
Q Consensus 127 lC~~C~sPdT~L 138 (193)
.||.|++-+.+.
T Consensus 2 ~C~KCg~~~~e~ 13 (64)
T PF09855_consen 2 KCPKCGNEEYES 13 (64)
T ss_pred CCCCCCCcceec
Confidence 589999876643
No 162
>PRK02935 hypothetical protein; Provisional
Probab=51.08 E-value=8.7 Score=30.05 Aligned_cols=35 Identities=23% Similarity=0.595 Sum_probs=24.7
Q ss_pred ccccCCCCCCcceeEecCceeecccccccccccccccccc
Q psy7490 125 YVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVASIKSG 164 (193)
Q Consensus 125 YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~~~k~~ 164 (193)
-|.||+|+.|---|=+.+ .|--|+.+=+.++-..|
T Consensus 70 qV~CP~C~K~TKmLGrvD-----~CM~C~~PLTLd~~leg 104 (110)
T PRK02935 70 QVICPSCEKPTKMLGRVD-----ACMHCNQPLTLDRSLEG 104 (110)
T ss_pred eeECCCCCchhhhcccee-----ecCcCCCcCCcCccccc
Confidence 379999998744443333 68889998877766544
No 163
>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=51.03 E-value=10 Score=34.42 Aligned_cols=43 Identities=28% Similarity=0.604 Sum_probs=30.7
Q ss_pred ecccccccccccccccccceeeeccEEEEEecccCCCccccccc
Q psy7490 146 FLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRCSVASIK 189 (193)
Q Consensus 146 ~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~~v~~~~ 189 (193)
-..|..||+.-.+..++.+ ....+.=+++|..|+.+-.+..++
T Consensus 184 ~~~CPvCGs~P~~s~~~~~-~~~~G~RyL~CslC~teW~~~R~~ 226 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQG-GKETGLRYLSCSLCATEWHYVRVK 226 (305)
T ss_pred CCcCCCCCChhhhhhhccc-CCCCCceEEEcCCCCCcccccCcc
Confidence 3589999998755555432 134678899999999887776554
No 164
>PRK11827 hypothetical protein; Provisional
Probab=50.62 E-value=9.1 Score=26.84 Aligned_cols=36 Identities=14% Similarity=0.292 Sum_probs=22.8
Q ss_pred HhhhccccCCCCCCcceeEecCceeeccccccccccccc
Q psy7490 121 YIKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVA 159 (193)
Q Consensus 121 yI~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~ 159 (193)
.+-+-..||.|+.|=. +.++.. .+.|.+||-..||.
T Consensus 4 ~LLeILaCP~ckg~L~-~~~~~~--~Lic~~~~laYPI~ 39 (60)
T PRK11827 4 RLLEIIACPVCNGKLW-YNQEKQ--ELICKLDNLAFPLR 39 (60)
T ss_pred HHHhheECCCCCCcCe-EcCCCC--eEECCccCeecccc
Confidence 3445678999988533 323222 35688888877763
No 165
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=50.44 E-value=7.6 Score=27.67 Aligned_cols=11 Identities=36% Similarity=0.770 Sum_probs=9.1
Q ss_pred ccCCCCCCcce
Q psy7490 127 TCHTCRSPDTI 137 (193)
Q Consensus 127 lC~~C~sPdT~ 137 (193)
+||.|+|+|+.
T Consensus 20 ~CP~Cgs~~~t 30 (64)
T COG2093 20 ICPVCGSTDLT 30 (64)
T ss_pred cCCCCCCcccc
Confidence 69999999863
No 166
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=50.39 E-value=11 Score=27.19 Aligned_cols=12 Identities=17% Similarity=0.564 Sum_probs=7.8
Q ss_pred ccccCCCCCCcc
Q psy7490 125 YVTCHTCRSPDT 136 (193)
Q Consensus 125 YVlC~~C~sPdT 136 (193)
+-.||.|++-+-
T Consensus 4 ~~kCpKCgn~~~ 15 (68)
T COG3478 4 AFKCPKCGNTNY 15 (68)
T ss_pred cccCCCcCCcch
Confidence 345888887553
No 167
>PRK05667 dnaG DNA primase; Validated
Probab=50.35 E-value=36 Score=33.30 Aligned_cols=63 Identities=29% Similarity=0.443 Sum_probs=41.2
Q ss_pred eeccHHHHHHHHH-----HHhhhccccCCCCCCcceeEecCceeecccccccccccccccccceeeeccEEEEEecccCC
Q psy7490 107 GRFQQKQIENVLR-----RYIKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGS 181 (193)
Q Consensus 107 G~~~~~~iq~~L~-----~yI~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga 181 (193)
++++++.|+++.. .+|.+|| .|.+.++-+...|.-|+..+| .|......-+.+|-.||+
T Consensus 2 ~~i~~~~i~~i~~~~dI~~vi~~~v----------~Lkk~G~~~~~~CPfH~ektp------Sf~V~~~k~~~~CF~Cg~ 65 (580)
T PRK05667 2 GRIPPEFIEELRARVDIVDVIGEYV----------KLKKAGRNYKGLCPFHDEKTP------SFTVSPDKQFYHCFGCGA 65 (580)
T ss_pred CCCCHHHHHHHHhcCCHHHHHHHhc----------ceeecCCceeecCCCCCCCCC------ceEEECCCCeEEECCCCC
Confidence 4566777777655 5677764 356667767778888887763 244444445678888887
Q ss_pred Cccc
Q psy7490 182 RCSV 185 (193)
Q Consensus 182 ~~~v 185 (193)
.-.|
T Consensus 66 ~Gd~ 69 (580)
T PRK05667 66 GGDV 69 (580)
T ss_pred CCCH
Confidence 6544
No 168
>COG1384 LysS Lysyl-tRNA synthetase (class I) [Translation, ribosomal structure and biogenesis]
Probab=49.83 E-value=21 Score=34.82 Aligned_cols=49 Identities=24% Similarity=0.427 Sum_probs=36.5
Q ss_pred HHHHHHHHHHhhh---------ccccCCCCCCcc-eeEe-cCc-eeeccccccccccccccc
Q psy7490 112 KQIENVLRRYIKE---------YVTCHTCRSPDT-ILQK-DTR-LFFLQCETCGSRCSVASI 161 (193)
Q Consensus 112 ~~iq~~L~~yI~~---------YVlC~~C~sPdT-~L~k-~~r-l~~l~C~aCGa~~~V~~~ 161 (193)
+.|.++|..|-.. -++|+.|+..+| .+.. +.. ...-+|+ ||....|+-.
T Consensus 149 deI~~il~~~~~~~~~e~~~P~~piC~kcGri~~t~v~~~d~~~~v~Y~Ce-~Gh~g~v~ir 209 (521)
T COG1384 149 DEIMEILNEYRGRELEEDWSPFMPICEKCGRILTTPVIEWDGEGTVEYRCE-CGHEGEVDIR 209 (521)
T ss_pred HHHHHHHHHhcCCcccCCceeccccccccCCcceeEEEEecCCceEEEEec-CCccceeecc
Confidence 5788888888777 479999999554 4443 443 6677898 8999877654
No 169
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=49.73 E-value=15 Score=31.20 Aligned_cols=32 Identities=25% Similarity=0.520 Sum_probs=21.5
Q ss_pred ccCCCCCCc-ceeEecC------c--eeecccccccccccc
Q psy7490 127 TCHTCRSPD-TILQKDT------R--LFFLQCETCGSRCSV 158 (193)
Q Consensus 127 lC~~C~sPd-T~L~k~~------r--l~~l~C~aCGa~~~V 158 (193)
-||.|+.+- |.+..-+ . +....|..||.++.-
T Consensus 2 ~Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~e 42 (192)
T TIGR00310 2 DCPSCGGECETVMKTVNDIPYFGEVLETSTICEHCGYRSND 42 (192)
T ss_pred cCCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCCCccce
Confidence 599999764 4444322 2 346789999998753
No 170
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=49.41 E-value=14 Score=32.23 Aligned_cols=39 Identities=21% Similarity=0.444 Sum_probs=28.9
Q ss_pred HHHHHHhhhccccCCCCCCcceeEecCceeeccccccccccc
Q psy7490 116 NVLRRYIKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCS 157 (193)
Q Consensus 116 ~~L~~yI~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~ 157 (193)
..|..+-..+-.|+.|++| |... +++ .-..|.+||...-
T Consensus 90 ~~l~~w~~~~~fC~~CG~~-~~~~-~~~-~~~~C~~c~~~~y 128 (256)
T PRK00241 90 VQLAEFYRSHRFCGYCGHP-MHPS-KTE-WAMLCPHCRERYY 128 (256)
T ss_pred HHHHHHhhcCccccccCCC-Ceec-CCc-eeEECCCCCCEEC
Confidence 4577889999999999998 4433 333 3478999997654
No 171
>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=49.29 E-value=11 Score=27.57 Aligned_cols=38 Identities=24% Similarity=0.536 Sum_probs=22.0
Q ss_pred ecccccccccccccccccceeeeccEEEEEecccCCCcccc
Q psy7490 146 FLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRCSVA 186 (193)
Q Consensus 146 ~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~~v~ 186 (193)
...|.-||+..+|.-. ++...++-.+.|..||.++...
T Consensus 22 ~F~CPfC~~~~sV~v~---idkk~~~~~~~C~~Cg~~~~~~ 59 (81)
T PF05129_consen 22 VFDCPFCNHEKSVSVK---IDKKEGIGILSCRVCGESFQTK 59 (81)
T ss_dssp ----TTT--SS-EEEE---EETTTTEEEEEESSS--EEEEE
T ss_pred eEcCCcCCCCCeEEEE---EEccCCEEEEEecCCCCeEEEc
Confidence 5789999988877522 2355889999999999987654
No 172
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=49.27 E-value=12 Score=33.94 Aligned_cols=42 Identities=26% Similarity=0.493 Sum_probs=29.8
Q ss_pred ecccccccccccccccccceeeeccEEEEEecccCCCccccccc
Q psy7490 146 FLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRCSVASIK 189 (193)
Q Consensus 146 ~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~~v~~~~ 189 (193)
-..|..||+.-.+..++. ....+.=+++|..|+.+-.+..++
T Consensus 187 ~~~CPvCGs~P~~s~v~~--~~~~G~RyL~CslC~teW~~~R~~ 228 (309)
T PRK03564 187 RQFCPVCGSMPVSSVVQI--GTTQGLRYLHCNLCESEWHVVRVK 228 (309)
T ss_pred CCCCCCCCCcchhheeec--cCCCCceEEEcCCCCCcccccCcc
Confidence 478999999864443432 134678899999999887766543
No 173
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=49.03 E-value=36 Score=31.71 Aligned_cols=43 Identities=21% Similarity=0.385 Sum_probs=25.5
Q ss_pred eeEecCceeecccccccccccccccccceeeeccEEEEEecccCCCccc
Q psy7490 137 ILQKDTRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRCSV 185 (193)
Q Consensus 137 ~L~k~~rl~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~~v 185 (193)
.|.+.++-+...|.-|+..+| .|.....--+.+|-.||+.-.|
T Consensus 25 ~l~~~G~~~~~~CPfh~ek~p------Sf~v~~~k~~~~Cf~Cg~~Gd~ 67 (415)
T TIGR01391 25 KLKKKGRNYVGLCPFHHEKTP------SFSVSPEKQFYHCFGCGAGGDA 67 (415)
T ss_pred ceeecCCceEeeCCCCCCCCC------eEEEEcCCCcEEECCCCCCCCH
Confidence 456666666667888877653 2223333345678888875443
No 174
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=48.88 E-value=15 Score=33.21 Aligned_cols=12 Identities=8% Similarity=0.454 Sum_probs=7.7
Q ss_pred EEEEeeccHHHH
Q psy7490 103 LIIKGRFQQKQI 114 (193)
Q Consensus 103 lii~G~~~~~~i 114 (193)
-+++|.+++++|
T Consensus 207 ~vl~G~i~p~~l 218 (299)
T TIGR01385 207 NVLTGEITPEKL 218 (299)
T ss_pred HHHcCCCCHHHH
Confidence 366777776654
No 175
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=48.67 E-value=12 Score=38.71 Aligned_cols=47 Identities=28% Similarity=0.663 Sum_probs=33.6
Q ss_pred cccCCCCCCc---ceeE-ecCceeecccccccccccccccccceeeeccEEEEEecccCCC
Q psy7490 126 VTCHTCRSPD---TILQ-KDTRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSR 182 (193)
Q Consensus 126 VlC~~C~sPd---T~L~-k~~rl~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~ 182 (193)
-.||.|+.|= -.++ --+..+.-+|..||..+ .||..- +-.|.+||+.
T Consensus 797 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~~~~~----~~~~~~~~~~ 847 (1006)
T PRK12775 797 ATCPKCHRPLEGDEEYVCCATSELQWRCDDCGKVS------EGFAFP----YGMCPACGGK 847 (1006)
T ss_pred ccCcccCCCCCCCceeEEecCcceeeehhhhcccc------ccccCC----cCcCcccccc
Confidence 3699999983 2333 24555678999999987 666544 3479999987
No 176
>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=48.51 E-value=11 Score=25.64 Aligned_cols=33 Identities=27% Similarity=0.581 Sum_probs=17.7
Q ss_pred eecccccccccccccccccceeeeccEEEEEecccCCC
Q psy7490 145 FFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSR 182 (193)
Q Consensus 145 ~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~ 182 (193)
+-+.|..|.+.+-..+ + ....-..-.|..||+.
T Consensus 21 ~aLIC~~C~~hNGla~-~----~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 21 YALICSKCFSHNGLAP-K----EEFEEIQYRCPYCGAL 53 (54)
T ss_pred eeEECcccchhhcccc-c----ccCCceEEEcCCCCCc
Confidence 3566777766654444 2 2223335567777653
No 177
>PF01396 zf-C4_Topoisom: Topoisomerase DNA binding C4 zinc finger; InterPro: IPR013498 DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks []. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis [, ]. DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA []. Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA. This entry represents the zinc-finger domain found in type IA topoisomerases, including bacterial and archaeal topoisomerase I and III enzymes, and in eukaryotic topoisomerase III enzymes. Escherichia coli topoisomerase I proteins contain five copies of a zinc-ribbon-like domain at their C terminus, two of which have lost their cysteine residues and are therefore probably not able to bind zinc []. This domain is still considered to be a member of the zinc-ribbon superfamily despite not being able to bind zinc. More information about this protein can be found at Protein of the Month: DNA Topoisomerase [].; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0005694 chromosome
Probab=48.37 E-value=18 Score=22.82 Aligned_cols=31 Identities=26% Similarity=0.680 Sum_probs=16.0
Q ss_pred cccCCCCCCcceeEe-cCceeeccccc---ccccccc
Q psy7490 126 VTCHTCRSPDTILQK-DTRLFFLQCET---CGSRCSV 158 (193)
Q Consensus 126 VlC~~C~sPdT~L~k-~~rl~~l~C~a---CGa~~~V 158 (193)
+.||.|+++ -.+.. ..+ .|+-|.. |....++
T Consensus 2 ~~CP~Cg~~-lv~r~~k~g-~F~~Cs~yP~C~~~~~~ 36 (39)
T PF01396_consen 2 EKCPKCGGP-LVLRRGKKG-KFLGCSNYPECKYTEPL 36 (39)
T ss_pred cCCCCCCce-eEEEECCCC-CEEECCCCCCcCCeEeC
Confidence 468888832 22222 223 5677765 6655443
No 178
>TIGR02494 PFLE_PFLC glycyl-radical enzyme activating protein family. This subset of the radical-SAM family (pfam04055) includes a number of probable activating proteins acting on different enzymes all requiring an amino-acid-centered radical. The closest relatives to this family are the pyruvate-formate lyase activating enzyme (PflA, 1.97.1.4, TIGR02493) and the anaerobic ribonucleotide reductase activating enzyme (TIGR02491). Included within this subfamily are activators of hydroxyphenyl acetate decarboxylase (HdpA, ), benzylsuccinate synthase (BssD, ), gycerol dehydratase (DhaB2, ) as well as enzymes annotated in E. coli as activators of different isozymes of pyruvate-formate lyase (PFLC and PFLE) however, these appear to lack characterization and may activate enzymes with distinctive functions. Most of the sequence-level variability between these forms is concentrated within an N-terminal domain which follows a conserved group of three cysteines and contains a variable pattern of 0
Probab=47.64 E-value=11 Score=32.70 Aligned_cols=42 Identities=19% Similarity=0.539 Sum_probs=25.6
Q ss_pred Hhhh-ccccCCCCCCcceeEec----Cceeecccccccccccccccc
Q psy7490 121 YIKE-YVTCHTCRSPDTILQKD----TRLFFLQCETCGSRCSVASIK 162 (193)
Q Consensus 121 yI~~-YVlC~~C~sPdT~L~k~----~rl~~l~C~aCGa~~~V~~~k 162 (193)
|+.- -..|..|.+|++..... +.-....|..|-...|+.++.
T Consensus 20 f~~gc~~~C~~c~~p~~~~~~~~~~~~~~~C~~C~~C~~~Cp~~a~~ 66 (295)
T TIGR02494 20 FLKGCPLRCKWCSNPESQRKSPELLFKENRCLGCGKCVEVCPAGTAR 66 (295)
T ss_pred HhhcCCccCcccCCccccCCCceEEEccccCCCCchhhhhCcccccc
Confidence 4555 47899999999754211 111245667776666666653
No 179
>COG3741 HutG N-formylglutamate amidohydrolase [Amino acid transport and metabolism]
Probab=47.47 E-value=3.8 Score=36.72 Aligned_cols=65 Identities=22% Similarity=0.248 Sum_probs=52.1
Q ss_pred CeeeEEeccHHHHHHcCCChHHHHHH---HHHhhcCceeecCCCeEEEEeeccHHHHHHHHHHHhhhc
Q psy7490 61 TKKTSFANFTEICKTLHRLPKHLLDF---LLAELGTSGSVDGNSQLIIKGRFQQKQIENVLRRYIKEY 125 (193)
Q Consensus 61 g~KTvi~Nf~dIak~L~R~p~hv~ky---~~~ELgt~g~id~~~~lii~G~~~~~~iq~~L~~yI~~Y 125 (193)
|.-++-.||.-.+=.+||+|.+..-| --..||+...+|+.+.++--|+.++.++..-|..|-+=|
T Consensus 62 GA~~l~A~fsR~~vDvNR~p~~~~l~~~~~ttGL~~~~~fdge~l~~~g~~~~~~e~~~Rle~~~~PY 129 (272)
T COG3741 62 GATLLRANFSRAVVDVNREPDGASLYPGRVTTGLGPVTTFDGEPLYIYGGAPTPAEALARLETLWKPY 129 (272)
T ss_pred cchhhhccccceeEecCCCCCCCcCccccccCCccccccccCccccccCCCCCHHHHHHHHHHhhccH
Confidence 44555666777777799999999988 356788889999988888888999999998888776544
No 180
>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=47.18 E-value=10 Score=33.34 Aligned_cols=42 Identities=26% Similarity=0.551 Sum_probs=21.7
Q ss_pred ecccccccccccccccccceeeeccEEEEEecccCCCccccccc
Q psy7490 146 FLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRCSVASIK 189 (193)
Q Consensus 146 ~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~~v~~~~ 189 (193)
...|..||+.-.+..++.+=. .+.=+++|..||.+-....++
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~--~G~R~L~Cs~C~t~W~~~R~~ 213 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGER--EGKRYLHCSLCGTEWRFVRIK 213 (290)
T ss_dssp -SS-TTT---EEEEEEE--------EEEEEETTT--EEE--TTS
T ss_pred CCcCCCCCCcCceEEEecCCC--CccEEEEcCCCCCeeeecCCC
Confidence 378999999987777753311 366899999999887665543
No 181
>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=47.16 E-value=27 Score=22.54 Aligned_cols=34 Identities=26% Similarity=0.617 Sum_probs=19.9
Q ss_pred HHHHHHhhhccccCCCCCCcceeEecCceeeccccccc
Q psy7490 116 NVLRRYIKEYVTCHTCRSPDTILQKDTRLFFLQCETCG 153 (193)
Q Consensus 116 ~~L~~yI~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCG 153 (193)
-+|+.|---=-.||.|+.|=.. .+++++ .|.+|+
T Consensus 8 ~LL~G~~ML~~~Cp~C~~PL~~-~k~g~~---~Cv~C~ 41 (41)
T PF06677_consen 8 YLLQGWTMLDEHCPDCGTPLMR-DKDGKI---YCVSCG 41 (41)
T ss_pred HHHHhHhHhcCccCCCCCeeEE-ecCCCE---ECCCCC
Confidence 4555555555679999766444 234444 466654
No 182
>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=46.84 E-value=17 Score=35.30 Aligned_cols=43 Identities=19% Similarity=0.498 Sum_probs=26.8
Q ss_pred cCceeeccccccccccccccccccee--eeccEEEEEecccCCCc
Q psy7490 141 DTRLFFLQCETCGSRCSVASIKSGFQ--KDTRLFFLQCETCGSRC 183 (193)
Q Consensus 141 ~~rl~~l~C~aCGa~~~V~~~k~~~~--~~~rl~~~~c~~Cga~~ 183 (193)
+.+-+++.|..||....+.--.=.+. +....-.+.|..||..-
T Consensus 195 dqr~~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i 239 (557)
T PF05876_consen 195 DQRRYYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEI 239 (557)
T ss_pred CceEEEccCCCCCCCccccccceeecCCCCccceEEECCCCcCCC
Confidence 45678888888888877641111111 13556777888888753
No 183
>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=46.62 E-value=11 Score=25.86 Aligned_cols=26 Identities=27% Similarity=0.768 Sum_probs=15.7
Q ss_pred ccCCCCCCcceeEecCceeeccccccccc
Q psy7490 127 TCHTCRSPDTILQKDTRLFFLQCETCGSR 155 (193)
Q Consensus 127 lC~~C~sPdT~L~k~~rl~~l~C~aCGa~ 155 (193)
.||.|+.+.-. ...++ ...|..||..
T Consensus 30 ~C~~CG~~~~~-~~~~r--~~~C~~Cg~~ 55 (69)
T PF07282_consen 30 TCPRCGHRNKK-RRSGR--VFTCPNCGFE 55 (69)
T ss_pred CccCccccccc-ccccc--eEEcCCCCCE
Confidence 57888776655 22333 3567777765
No 184
>PHA02893 hypothetical protein; Provisional
Probab=46.53 E-value=11 Score=28.45 Aligned_cols=9 Identities=44% Similarity=1.250 Sum_probs=6.5
Q ss_pred EEecccCCC
Q psy7490 174 LQCETCGSR 182 (193)
Q Consensus 174 ~~c~~Cga~ 182 (193)
|+|.|||+.
T Consensus 70 L~CaACGS~ 78 (88)
T PHA02893 70 IKCIACGSS 78 (88)
T ss_pred eeehhhchh
Confidence 677777764
No 185
>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=45.60 E-value=17 Score=27.91 Aligned_cols=54 Identities=22% Similarity=0.412 Sum_probs=28.2
Q ss_pred ChHHHHHHHHHhhcCceeecCCCeEEEE------------eeccHHHHHHHHHHHhhhccccCCCCCCcceeEecCce
Q psy7490 79 LPKHLLDFLLAELGTSGSVDGNSQLIIK------------GRFQQKQIENVLRRYIKEYVTCHTCRSPDTILQKDTRL 144 (193)
Q Consensus 79 ~p~hv~ky~~~ELgt~g~id~~~~lii~------------G~~~~~~iq~~L~~yI~~YVlC~~C~sPdT~L~k~~rl 144 (193)
+|+.+.-.|. .-+.+++-++-+|.|. -.|+.+... ..||.|+|++..++.-+.+
T Consensus 40 ~pe~L~f~f~--~~~~~T~~e~a~L~Ie~~p~~~~C~~Cg~~~~~~~~~----------~~CP~Cgs~~~~i~~G~el 105 (113)
T PF01155_consen 40 EPEALRFAFE--VLAEGTILEGAELEIEEVPARARCRDCGHEFEPDEFD----------FSCPRCGSPDVEIISGREL 105 (113)
T ss_dssp -HHHHHHHHH--HHHCCSTTTT-EEEEEEE--EEEETTTS-EEECHHCC----------HH-SSSSSS-EEEEESS-E
T ss_pred CHHHHHHHHH--HHhCCCCccCCEEEEEecCCcEECCCCCCEEecCCCC----------CCCcCCcCCCcEEccCCeE
Confidence 5666554443 3345566556677763 233333322 2499999999988876554
No 186
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=45.13 E-value=31 Score=35.36 Aligned_cols=35 Identities=17% Similarity=0.496 Sum_probs=24.2
Q ss_pred cccCCCCCCcceeEecCceeeccccc---ccccccccc
Q psy7490 126 VTCHTCRSPDTILQKDTRLFFLQCET---CGSRCSVAS 160 (193)
Q Consensus 126 VlC~~C~sPdT~L~k~~rl~~l~C~a---CGa~~~V~~ 160 (193)
..||.|+++...+.....=.|+.|.. |....++..
T Consensus 593 ~~CP~Cg~~~L~~k~gr~G~Fl~Cs~yP~C~~t~~~~~ 630 (860)
T PRK06319 593 IDCPKCHKGKLVKIWAKNRYFYGCSEYPECDYKTSEEE 630 (860)
T ss_pred cccCCCCCcceeEEecCCCceeeccCCccccccCCccc
Confidence 35999999877765532224788866 877777653
No 187
>KOG3507|consensus
Probab=45.13 E-value=12 Score=26.52 Aligned_cols=25 Identities=32% Similarity=0.877 Sum_probs=11.4
Q ss_pred ccCCCCCCcceeEecCceeeccccccccc
Q psy7490 127 TCHTCRSPDTILQKDTRLFFLQCETCGSR 155 (193)
Q Consensus 127 lC~~C~sPdT~L~k~~rl~~l~C~aCGa~ 155 (193)
+|..|++-+|. |.+. -++|..||.+
T Consensus 22 iCgdC~~en~l--k~~D--~irCReCG~R 46 (62)
T KOG3507|consen 22 ICGDCGQENTL--KRGD--VIRCRECGYR 46 (62)
T ss_pred Eeccccccccc--cCCC--cEehhhcchH
Confidence 45555554432 1111 2455555554
No 188
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=44.96 E-value=27 Score=27.37 Aligned_cols=52 Identities=31% Similarity=0.516 Sum_probs=29.0
Q ss_pred hhccccCCCCCCcceeEecC-ceeeccccc---ccccccccccccceeeeccEEEEEecccCCCccc
Q psy7490 123 KEYVTCHTCRSPDTILQKDT-RLFFLQCET---CGSRCSVASIKSGFQKDTRLFFLQCETCGSRCSV 185 (193)
Q Consensus 123 ~~YVlC~~C~sPdT~L~k~~-rl~~l~C~a---CGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~~v 185 (193)
..=+.||.|+.++..+.+.. +..|..|.. |.......+.. ..|..||+...|
T Consensus 58 ~~~~~Cp~C~~~~~~~k~~~~~~~f~~~~~~Pkc~~~~~~~~~~-----------~~cp~c~~~~~~ 113 (140)
T COG0551 58 KTGVKCPKCGKGLLVLKKGRFGKNFLGCSNYPKCRFTEKPKPKE-----------KKCPKCGSRKLV 113 (140)
T ss_pred cCceeCCCCCCCceEEEeccCCceEEeecCCCcCceeecCCccc-----------ccCCcCCCceeE
Confidence 33479999999888777643 223444444 44433222221 228888874433
No 189
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=44.94 E-value=15 Score=27.74 Aligned_cols=28 Identities=32% Similarity=0.880 Sum_probs=21.5
Q ss_pred cccccccccccccccccceeeeccEEEEEecccCCCc
Q psy7490 147 LQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRC 183 (193)
Q Consensus 147 l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~ 183 (193)
-.|..||.. .|..+.+| +-+|.-||+..
T Consensus 36 ~~Cp~C~~~-~VkR~a~G--------IW~C~kCg~~f 63 (89)
T COG1997 36 HVCPFCGRT-TVKRIATG--------IWKCRKCGAKF 63 (89)
T ss_pred CcCCCCCCc-ceeeeccC--------eEEcCCCCCee
Confidence 579999999 77777655 34799998753
No 190
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=44.53 E-value=35 Score=22.29 Aligned_cols=37 Identities=19% Similarity=0.465 Sum_probs=23.4
Q ss_pred HHHHHHhhh---ccccC--CCCCCcceeEec--Cceeeccccccccc
Q psy7490 116 NVLRRYIKE---YVTCH--TCRSPDTILQKD--TRLFFLQCETCGSR 155 (193)
Q Consensus 116 ~~L~~yI~~---YVlC~--~C~sPdT~L~k~--~rl~~l~C~aCGa~ 155 (193)
-+++.||+. +.-|| .|+.. +..+ .+...+.|..||..
T Consensus 6 ~~~~~~i~~~~~~~~CP~~~C~~~---~~~~~~~~~~~v~C~~C~~~ 49 (64)
T smart00647 6 LLLESYVESNPDLKWCPAPDCSAA---IIVTEEEGCNRVTCPKCGFS 49 (64)
T ss_pred HHHHHHHhcCCCccCCCCCCCcce---EEecCCCCCCeeECCCCCCe
Confidence 455666654 77899 88652 3332 24457889888854
No 191
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=44.36 E-value=19 Score=32.54 Aligned_cols=15 Identities=20% Similarity=0.871 Sum_probs=10.7
Q ss_pred EEEEecccCCCcccc
Q psy7490 172 FFLQCETCGSRCSVA 186 (193)
Q Consensus 172 ~~~~c~~Cga~~~v~ 186 (193)
|+++|..|+++-.++
T Consensus 76 F~~kC~~C~~~i~~k 90 (324)
T PF04502_consen 76 FYIKCPRCSNEIEFK 90 (324)
T ss_pred EEEEcCCCCCEEeee
Confidence 577888888776654
No 192
>COG1163 DRG Predicted GTPase [General function prediction only]
Probab=44.30 E-value=17 Score=33.91 Aligned_cols=59 Identities=19% Similarity=0.416 Sum_probs=39.3
Q ss_pred ccCCCCccHHHHHHHHHHHHHhcCCCc-ccCcceeeecCCCeEEEecCeeeEEeccHHHHHHcCCChH
Q psy7490 15 IGSDRDYTYEELLSRVFEIMREKNPDM-VAGKKQKFVMRPPQVVRIGTKKTSFANFTEICKTLHRLPK 81 (193)
Q Consensus 15 ~~~~~~~~Y~~LL~R~~~~L~~~~p~~-~~~~~~R~~mP~p~v~~~Gg~KTvi~Nf~dIak~L~R~p~ 81 (193)
++...+.+-++|++++|+.|. .-.. -......-..++|.|++.|+ | ..|+|..|||+-.
T Consensus 269 isa~~~~nld~L~e~i~~~L~--liRVYtK~~g~~pd~~~PlIlr~Gs--T----V~Dvc~~IH~~l~ 328 (365)
T COG1163 269 ISAKKGINLDELKERIWDVLG--LIRVYTKPPGEEPDFDEPLILRRGS--T----VGDVCRKIHRDLV 328 (365)
T ss_pred EecccCCCHHHHHHHHHHhhC--eEEEEecCCCCCCCCCCCeEEeCCC--c----HHHHHHHHHHHHH
Confidence 445556788999999999982 1110 01112233457888899873 3 5899999999753
No 193
>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=44.27 E-value=13 Score=25.82 Aligned_cols=10 Identities=20% Similarity=0.919 Sum_probs=5.8
Q ss_pred hccccCCCCC
Q psy7490 124 EYVTCHTCRS 133 (193)
Q Consensus 124 ~YVlC~~C~s 133 (193)
++..||.|++
T Consensus 6 niL~Cp~ck~ 15 (68)
T PF03966_consen 6 NILACPVCKG 15 (68)
T ss_dssp GTBB-TTTSS
T ss_pred hhhcCCCCCC
Confidence 4556777776
No 194
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=44.17 E-value=45 Score=24.59 Aligned_cols=46 Identities=13% Similarity=0.094 Sum_probs=34.3
Q ss_pred ccHHHHHHcCCChHHHHHHHHHhhcCceeecCCCeEEEEeeccHHHHHHH
Q psy7490 68 NFTEICKTLHRLPKHLLDFLLAELGTSGSVDGNSQLIIKGRFQQKQIENV 117 (193)
Q Consensus 68 Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id~~~~lii~G~~~~~~iq~~ 117 (193)
+..|+|+.++-+|..|-.|....+..+...+++|. -.|+.++|+.+
T Consensus 2 ti~eva~~~gvs~~tlR~ye~~Gll~~~~~~~~g~----R~y~~~di~~l 47 (103)
T cd01106 2 TVGEVAKLTGVSVRTLHYYDEIGLLKPSRRTENGY----RLYTEEDLERL 47 (103)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCCCCCCCccCCCCc----eeeCHHHHHHH
Confidence 46899999999999999888776665544444443 24888888775
No 195
>PRK11823 DNA repair protein RadA; Provisional
Probab=44.15 E-value=13 Score=35.03 Aligned_cols=12 Identities=25% Similarity=0.758 Sum_probs=4.5
Q ss_pred eccccccccccc
Q psy7490 146 FLQCETCGSRCS 157 (193)
Q Consensus 146 ~l~C~aCGa~~~ 157 (193)
+-+|.+||++.+
T Consensus 21 ~g~Cp~C~~w~t 32 (446)
T PRK11823 21 LGRCPECGAWNT 32 (446)
T ss_pred CeeCcCCCCccc
Confidence 333333333333
No 196
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=44.09 E-value=17 Score=32.31 Aligned_cols=55 Identities=22% Similarity=0.409 Sum_probs=27.3
Q ss_pred eccHHHHHHHH-HHHhhhccccCCCCCCcc-eeEecCceeecccccccccccccccc
Q psy7490 108 RFQQKQIENVL-RRYIKEYVTCHTCRSPDT-ILQKDTRLFFLQCETCGSRCSVASIK 162 (193)
Q Consensus 108 ~~~~~~iq~~L-~~yI~~YVlC~~C~sPdT-~L~k~~rl~~l~C~aCGa~~~V~~~k 162 (193)
-.+.+++..+| +.++.+-+.||.|++... .+.-...+-...|..|+...-+++.+
T Consensus 13 YkS~sQ~aRVltE~Wv~~n~yCP~Cg~~~L~~f~NN~PVaDF~C~~C~eeyELKSk~ 69 (254)
T PF06044_consen 13 YKSNSQIARVLTEDWVAENMYCPNCGSKPLSKFENNRPVADFYCPNCNEEYELKSKK 69 (254)
T ss_dssp TTT-TTHHHHHHHHHHHHH---TTT--SS-EE--------EEE-TTT--EEEEEEEE
T ss_pred ccChhhhhHHHHHHHHHHCCcCCCCCChhHhhccCCCccceeECCCCchHHhhhhhc
Confidence 34455555554 789999999999999754 44445567788999999888776655
No 197
>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 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=43.28 E-value=13 Score=35.04 Aligned_cols=27 Identities=15% Similarity=0.553 Sum_probs=19.0
Q ss_pred ccCCCCCCcceeEecCceeecccccccccccccc
Q psy7490 127 TCHTCRSPDTILQKDTRLFFLQCETCGSRCSVAS 160 (193)
Q Consensus 127 lC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~~ 160 (193)
.|.+|+.- ...|+-+|.+||+++++..
T Consensus 9 ~C~~Cg~~-------~~~~~g~Cp~C~~w~t~~~ 35 (454)
T TIGR00416 9 VCQHCGAD-------SPKWQGKCPACHAWNTITE 35 (454)
T ss_pred ECCcCCCC-------CccccEECcCCCCccccch
Confidence 48888753 2457778888888887765
No 199
>PF05077 DUF678: Protein of unknown function (DUF678); InterPro: IPR007769 This family contains poxvirus proteins belonging to the A19 family. The proteins are of unknown function.
Probab=43.10 E-value=18 Score=26.54 Aligned_cols=10 Identities=50% Similarity=1.165 Sum_probs=5.5
Q ss_pred EEEecccCCC
Q psy7490 173 FLQCETCGSR 182 (193)
Q Consensus 173 ~~~c~~Cga~ 182 (193)
.|.|.|||+.
T Consensus 57 tLsCsACGS~ 66 (74)
T PF05077_consen 57 TLSCSACGSE 66 (74)
T ss_pred eEeehhcccc
Confidence 3556666653
No 200
>cd02983 P5_C P5 family, C-terminal redox inactive TRX-like domain; P5 is a protein disulfide isomerase (PDI)-related protein with a domain structure of aa'b (where a and a' are redox active TRX domains and b is a redox inactive TRX-like domain). Like PDI, P5 is located in the endoplasmic reticulum (ER) and displays both isomerase and chaperone activities, which are independent of each other. Compared to PDI, the isomerase and chaperone activities of P5 are lower. The first cysteine in the CXXC motif of both redox active domains in P5 is necessary for isomerase activity. The P5 gene was first isolated as an amplified gene from a hydroxyurea-resistant hamster cell line. The zebrafish P5 homolog has been implicated to play a critical role in establishing left/right asymmetries in the embryonic midline. The C-terminal domain is likely involved in substrate binding, similar to the b and b' domains of PDI.
Probab=43.01 E-value=33 Score=26.73 Aligned_cols=42 Identities=21% Similarity=0.333 Sum_probs=27.1
Q ss_pred HHHHHH-HhhcCcee--ecC-CCeEE-EEeeccHHHHHHHHHHHhhh
Q psy7490 83 LLDFLL-AELGTSGS--VDG-NSQLI-IKGRFQQKQIENVLRRYIKE 124 (193)
Q Consensus 83 v~ky~~-~ELgt~g~--id~-~~~li-i~G~~~~~~iq~~L~~yI~~ 124 (193)
+++||+ .+-+.+.- ++. ++++. ..|.|+.+.|.+-+.+|++.
T Consensus 71 ~~~~fgl~~~~~P~v~i~~~~~~KY~~~~~~~t~e~i~~Fv~~~l~G 117 (130)
T cd02983 71 LEEALNIGGFGYPAMVAINFRKMKFATLKGSFSEDGINEFLRELSYG 117 (130)
T ss_pred HHHHcCCCccCCCEEEEEecccCccccccCccCHHHHHHHHHHHHcC
Confidence 566664 22233322 343 33777 88999999998888887764
No 201
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=42.89 E-value=16 Score=31.11 Aligned_cols=48 Identities=21% Similarity=0.492 Sum_probs=30.9
Q ss_pred HhhhccccCCCCCCcceeEe---cCceeecccccccccccccccccceeeeccEEEEEecccCCC
Q psy7490 121 YIKEYVTCHTCRSPDTILQK---DTRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSR 182 (193)
Q Consensus 121 yI~~YVlC~~C~sPdT~L~k---~~rl~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~ 182 (193)
+|+-+|+=-. +--.|.. +=++++-.|..|++.- .. +=..|+|..||+.
T Consensus 124 ivrA~Vis~~---~~~~Lst~~~dlGVI~A~CsrC~~~L---------~~--~~~~l~Cp~Cg~t 174 (188)
T COG1096 124 IVRARVISTG---DPIQLSTKGNDLGVIYARCSRCRAPL---------VK--KGNMLKCPNCGNT 174 (188)
T ss_pred EEEEEEEecC---CCeEEEecCCcceEEEEEccCCCcce---------EE--cCcEEECCCCCCE
Confidence 4556676655 3334432 2368899999999874 11 4457899999974
No 202
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=42.67 E-value=17 Score=33.67 Aligned_cols=47 Identities=17% Similarity=0.334 Sum_probs=27.9
Q ss_pred cccCCCCCCcceeEecCceeecccccccccccccccccceeee-ccEEEEEecccCCCcc
Q psy7490 126 VTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVASIKSGFQKD-TRLFFLQCETCGSRCS 184 (193)
Q Consensus 126 VlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~~~k~~~~~~-~rl~~~~c~~Cga~~~ 184 (193)
.+|+.|+.|+= .+....|..|=... ...... .++=...|..|||-++
T Consensus 7 ~~C~~CGr~~~------~~~~~lC~dC~~~~------~~~~~ip~~~~v~~C~~Cga~~~ 54 (355)
T COG1499 7 ILCVRCGRSVD------PLIDGLCGDCYVET------TPLIEIPDEVNVEVCRHCGAYRI 54 (355)
T ss_pred cEeccCCCcCc------hhhccccHHHHhcc------CccccCCCceEEEECCcCCCccC
Confidence 47999997653 45556677776652 111222 2555667777776544
No 203
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=41.91 E-value=54 Score=23.76 Aligned_cols=54 Identities=13% Similarity=0.316 Sum_probs=38.5
Q ss_pred EEEEee---ccHHHHHHHHHHHhhhccccCCCCCCcceeEecC--ceeeccccccccccc
Q psy7490 103 LIIKGR---FQQKQIENVLRRYIKEYVTCHTCRSPDTILQKDT--RLFFLQCETCGSRCS 157 (193)
Q Consensus 103 lii~G~---~~~~~iq~~L~~yI~~YVlC~~C~sPdT~L~k~~--rl~~l~C~aCGa~~~ 157 (193)
+-|+.. .+.++|+..|.+=+.+.-.= -.+.|.-.+..+. .-.++.|.+|.....
T Consensus 23 l~l~~~~~~~tl~~l~~~L~~~~~~H~~~-C~~~p~F~v~~~~~~~~L~~~C~~Cd~~~v 81 (82)
T PF14768_consen 23 LRLNTQQDELTLEELRQLLEEAVTEHSDR-CSSTPQFSVEPGFGESSLYMSCEACDFLEV 81 (82)
T ss_pred cEEecCCCCCCHHHHHHHHHHHHHHHHHh-CCCCCEEEEecCCCchhheeECCCCCccee
Confidence 666665 88899999998888776544 1456887777542 256899999987643
No 204
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=41.60 E-value=15 Score=25.29 Aligned_cols=27 Identities=30% Similarity=0.634 Sum_probs=17.8
Q ss_pred hhhccccCCCCCCcceeEecCceeecccccccccc
Q psy7490 122 IKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRC 156 (193)
Q Consensus 122 I~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~ 156 (193)
+...+.|+.|+++- +-...|..||.-+
T Consensus 24 ~~~l~~C~~CG~~~--------~~H~vC~~CG~Y~ 50 (57)
T PRK12286 24 APGLVECPNCGEPK--------LPHRVCPSCGYYK 50 (57)
T ss_pred CCcceECCCCCCcc--------CCeEECCCCCcCC
Confidence 35567888888763 3456677777543
No 205
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=41.36 E-value=33 Score=32.97 Aligned_cols=49 Identities=24% Similarity=0.488 Sum_probs=32.1
Q ss_pred HHHHHHHHHHhhh---------ccccCCCCCCcceeEe----cCc-eeecccccccccccccccc
Q psy7490 112 KQIENVLRRYIKE---------YVTCHTCRSPDTILQK----DTR-LFFLQCETCGSRCSVASIK 162 (193)
Q Consensus 112 ~~iq~~L~~yI~~---------YVlC~~C~sPdT~L~k----~~r-l~~l~C~aCGa~~~V~~~k 162 (193)
..|.++|..|... .++|+.|+.-.|..+. +.+ +.| .|+ ||....++-.+
T Consensus 153 ~~i~~il~~~~~~~~~~~~~P~~pic~~cg~~~~~~~~~~d~~~~~v~y-~~~-cG~~~~~~~~~ 215 (510)
T PRK00750 153 DEIMEILLPYLGEERQATYSPFLPICPKCGKVLTTPVISYDAEAGTVTY-DCE-CGHEGEVPVTG 215 (510)
T ss_pred HHHHHHHHHhcCCccCCCeeeeeeeCCCCCccceEEEEEEeCCCCEEEE-EcC-CCCEEEEecCC
Confidence 4566666666443 3789999998886653 233 444 776 99988776543
No 206
>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=41.30 E-value=13 Score=31.33 Aligned_cols=49 Identities=16% Similarity=0.397 Sum_probs=29.3
Q ss_pred CCCc-ceeEecCceeecccccccccccccccccceeeeccEEEEEecccCCC
Q psy7490 132 RSPD-TILQKDTRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSR 182 (193)
Q Consensus 132 ~sPd-T~L~k~~rl~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~ 182 (193)
+.|. -.+.-.+.+..++|..|+...+.......+.... ...+|..||+.
T Consensus 80 G~~~~~vielHG~~~~~~C~~C~~~~~~~~~~~~~~~~~--~~p~C~~Cgg~ 129 (206)
T cd01410 80 GLPREKLSELHGNMFIEVCKSCGPEYVRDDVVETRGDKE--TGRRCHACGGI 129 (206)
T ss_pred CcCcccEEEecCCcCcccCCCCCCccchHHHHHHhhcCC--CCCcCCCCcCc
Confidence 4543 3555688888999999997765543322111110 13569999853
No 207
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.25 E-value=5 Score=29.76 Aligned_cols=12 Identities=33% Similarity=1.060 Sum_probs=5.5
Q ss_pred eecccccccccc
Q psy7490 145 FFLQCETCGSRC 156 (193)
Q Consensus 145 ~~l~C~aCGa~~ 156 (193)
+--+|..||.+.
T Consensus 11 Y~Y~c~~cg~~~ 22 (82)
T COG2331 11 YSYECTECGNRF 22 (82)
T ss_pred eEEeecccchHH
Confidence 334455555443
No 208
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=41.24 E-value=18 Score=38.76 Aligned_cols=39 Identities=21% Similarity=0.580 Sum_probs=25.9
Q ss_pred ccCCCCCCcceeEecCceeecccccccccccccccccceeeeccEEEEEecccCCCc
Q psy7490 127 TCHTCRSPDTILQKDTRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRC 183 (193)
Q Consensus 127 lC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~ 183 (193)
.||.|+++-+. . ..|..||+.-+-.. + + -..|..||...
T Consensus 681 fCP~CGs~te~-------v-y~CPsCGaev~~de--s-----~---a~~CP~CGtpl 719 (1337)
T PRK14714 681 RCPDCGTHTEP-------V-YVCPDCGAEVPPDE--S-----G---RVECPRCDVEL 719 (1337)
T ss_pred cCcccCCcCCC-------c-eeCccCCCccCCCc--c-----c---cccCCCCCCcc
Confidence 89999998321 2 29999999743322 1 1 22599999754
No 209
>COG5631 Predicted transcription regulator, contains HTH domain (MarR family) [Transcription]
Probab=41.08 E-value=23 Score=30.00 Aligned_cols=31 Identities=26% Similarity=0.540 Sum_probs=28.0
Q ss_pred ccHHHHHHcCCChHHHHHHHHHhhcCceeec
Q psy7490 68 NFTEICKTLHRLPKHLLDFLLAELGTSGSVD 98 (193)
Q Consensus 68 Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id 98 (193)
-+.|||.+|||+..|+..|=...|-..|-+.
T Consensus 100 ~laDic~~ln~eDth~itYslrKL~k~gLit 130 (199)
T COG5631 100 SLADICQMLNREDTHNITYSLRKLLKGGLIT 130 (199)
T ss_pred hHHHHHHHhccccchhHHHHHHHHHhcccee
Confidence 4789999999999999999999998877776
No 210
>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=40.86 E-value=18 Score=24.78 Aligned_cols=11 Identities=27% Similarity=0.978 Sum_probs=5.4
Q ss_pred ccccccccccc
Q psy7490 147 LQCETCGSRCS 157 (193)
Q Consensus 147 l~C~aCGa~~~ 157 (193)
+.|..||+.--
T Consensus 23 V~Cp~CGaele 33 (54)
T TIGR01206 23 VICDECGAELE 33 (54)
T ss_pred EeCCCCCCEEE
Confidence 35555555433
No 211
>PF14116 YyzF: YyzF-like protein
Probab=40.39 E-value=44 Score=22.37 Aligned_cols=40 Identities=23% Similarity=0.491 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHhhhccccCCCCCCcceeEecCceeeccccccccc
Q psy7490 111 QKQIENVLRRYIKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSR 155 (193)
Q Consensus 111 ~~~iq~~L~~yI~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~ 155 (193)
.+.|+-.|+.|+++|=. .|+..-..+....-.+|.-|+.+
T Consensus 3 ~EHie~AiD~~Vde~e~-----aP~i~~l~~~~~~~~~C~~C~~~ 42 (48)
T PF14116_consen 3 EEHIELAIDDFVDEYEQ-----APDIEKLEEVEKLPTTCEYCDQP 42 (48)
T ss_pred HHHHHHHHHHHHHhhcc-----CCCeEeccccCCCCCcchhhCCC
Confidence 36789999999999853 68877666555557889999775
No 212
>cd01406 SIR2-like Sir2-like: Prokaryotic group of uncharacterized Sir2-like proteins which lack certain key catalytic residues and conserved zinc binding cysteines; and are members of the SIR2 superfamily of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation.
Probab=40.06 E-value=2.2e+02 Score=23.82 Aligned_cols=95 Identities=17% Similarity=0.214 Sum_probs=59.1
Q ss_pred ccHHHHHHHHHHHHHhcCCCcccCc---ceeeecCCCeEEE-ec---CeeeEEeccHHHHHHcCCChHHHHHHHHHhhcC
Q psy7490 21 YTYEELLSRVFEIMREKNPDMVAGK---KQKFVMRPPQVVR-IG---TKKTSFANFTEICKTLHRLPKHLLDFLLAELGT 93 (193)
Q Consensus 21 ~~Y~~LL~R~~~~L~~~~p~~~~~~---~~R~~mP~p~v~~-~G---g~KTvi~Nf~dIak~L~R~p~hv~ky~~~ELgt 93 (193)
-+||.||++++.... .+-.+... ........+.|++ .| ...+++.--.|..+..... ..+.++|..-|.+
T Consensus 103 TNyD~llE~a~~~~~--~~~~~~~~~~~~~~~~~~~~~i~klHG~~~~~~~~VlT~~dY~~~~~~~-~~~~~~l~~ll~~ 179 (242)
T cd01406 103 TNYDRLLETALKEIN--KVVKVIVSVQLALSASARFNGVYKIHGDVDDDESIVLTKSDYERYYLKN-GWATKFLKSDLEK 179 (242)
T ss_pred cchHHHHHHHHHHcC--CCCCcccCccccccccCCCceEEEEecccCCCCceEecHHHHHHHHhcc-HHHHHHHHHHHhc
Confidence 479999999998752 11111100 0111122233333 35 2344566678888887777 5677777777763
Q ss_pred ceeecCCCeEEEEe-eccHHHHHHHHHHHhhhc
Q psy7490 94 SGSVDGNSQLIIKG-RFQQKQIENVLRRYIKEY 125 (193)
Q Consensus 94 ~g~id~~~~lii~G-~~~~~~iq~~L~~yI~~Y 125 (193)
..+++=| +++...|..+|+.....+
T Consensus 180 -------~~~LFiG~S~~D~~i~~ll~~~~~~~ 205 (242)
T cd01406 180 -------YTVLFIGYSLTDPNIRYLLERLRKNY 205 (242)
T ss_pred -------CcEEEEEcCCCCCcHHHHHHHHHHHh
Confidence 2456667 999999999999977775
No 213
>KOG2703|consensus
Probab=39.98 E-value=29 Score=33.05 Aligned_cols=31 Identities=26% Similarity=0.745 Sum_probs=20.3
Q ss_pred ccCCCCCC-cceeEec-------Cceeeccccccccccc
Q psy7490 127 TCHTCRSP-DTILQKD-------TRLFFLQCETCGSRCS 157 (193)
Q Consensus 127 lC~~C~sP-dT~L~k~-------~rl~~l~C~aCGa~~~ 157 (193)
-||+|..| ||.|.-- ==+....|..||.++.
T Consensus 260 ~Cp~C~~pcet~Mk~~~IPhFkeVIiMst~Cd~CGyksn 298 (460)
T KOG2703|consen 260 TCPSCTAPCETNMKLTDIPHFKEVIIMSTVCDRCGYKSN 298 (460)
T ss_pred CCCCCCCchhccceeccCCcceeEEEEeecccccCCccc
Confidence 58888886 5766431 1244567888888764
No 214
>TIGR02609 doc_partner putative addiction module antidote. Members of this protein family are putative addiction module antidote proteins that appear recurringly in two-gene operons with members of the Doc (death-on-curing) family TIGR01550. Members of this family contain a SpoVT/AbrB-like domain (pfam04014). Note that the gene pairs with a member of this family tend to be found on bacterial chromosomes, not on plasmids.
Probab=39.82 E-value=1.3e+02 Score=21.26 Aligned_cols=58 Identities=22% Similarity=0.326 Sum_probs=33.5
Q ss_pred EEEecCeeeEEeccHHHHHHcCCChHHHHHHHHHhhcCceeec-CCCeEEEEeecc----HHHHHHHHHHHhhhc
Q psy7490 56 VVRIGTKKTSFANFTEICKTLHRLPKHLLDFLLAELGTSGSVD-GNSQLIIKGRFQ----QKQIENVLRRYIKEY 125 (193)
Q Consensus 56 v~~~Gg~KTvi~Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id-~~~~lii~G~~~----~~~iq~~L~~yI~~Y 125 (193)
|.+.|+...+.. |..+++-++-.-|..-.+. .+|.++|.=.-. ..++..++++.+++|
T Consensus 3 i~k~GNS~~vtI------------Pk~i~~~lgl~~Gd~v~v~~~~~~iii~~~~~~~~~~~~~~~~~~~~~~~y 65 (74)
T TIGR02609 3 IRKVGNSLVVTL------------PKEVLESLGLKEGDTLYVDEEEGGLKLKRFDEGKELEKKMQMAVERAMSKY 65 (74)
T ss_pred EEEECCeeEEEE------------CHHHHHHcCcCCCCEEEEEEECCEEEEEECCCCccHHHHHHHHHHHHHHHH
Confidence 556676554422 5555555555556555554 367788864433 355555667777666
No 215
>PHA02998 RNA polymerase subunit; Provisional
Probab=39.71 E-value=33 Score=29.33 Aligned_cols=35 Identities=23% Similarity=0.525 Sum_probs=25.2
Q ss_pred eecccccccccccccccccceeeecc------EEEEEecccCCCcc
Q psy7490 145 FFLQCETCGSRCSVASIKSGFQKDTR------LFFLQCETCGSRCS 184 (193)
Q Consensus 145 ~~l~C~aCGa~~~V~~~k~~~~~~~r------l~~~~c~~Cga~~~ 184 (193)
....|..||.....- ++.++| .-|..|..||-...
T Consensus 142 t~v~CPkCg~~~A~f-----~qlQTRSADEPmT~FYkC~~CG~~wk 182 (195)
T PHA02998 142 YNTPCPNCKSKNTTP-----MMIQTRAADEPPLVRHACRDCKKHFK 182 (195)
T ss_pred cCCCCCCCCCCceEE-----EEEeeccCCCCceEEEEcCCCCCccC
Confidence 458999999987432 234444 78999999997543
No 216
>PRK03954 ribonuclease P protein component 4; Validated
Probab=39.62 E-value=23 Score=28.06 Aligned_cols=32 Identities=22% Similarity=0.530 Sum_probs=18.5
Q ss_pred ccCCCCCC-----cceeEe-cCc--eeecccccccccccc
Q psy7490 127 TCHTCRSP-----DTILQK-DTR--LFFLQCETCGSRCSV 158 (193)
Q Consensus 127 lC~~C~sP-----dT~L~k-~~r--l~~l~C~aCGa~~~V 158 (193)
+|..|.+| ...+.. .++ -+.+.|..||...-.
T Consensus 66 ~CK~C~t~LiPG~n~~vRi~~~~~~~vvitCl~CG~~kR~ 105 (121)
T PRK03954 66 YCKRCHSFLVPGVNARVRLRQKRMPHVVITCLECGHIMRY 105 (121)
T ss_pred HhhcCCCeeecCCceEEEEecCCcceEEEECccCCCEEee
Confidence 79999875 223322 221 346778778776533
No 217
>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=39.51 E-value=12 Score=32.16 Aligned_cols=48 Identities=17% Similarity=0.447 Sum_probs=30.0
Q ss_pred CCCCc-ceeEecCceeecccccccccccccccccceeeeccEEEEEecccCC
Q psy7490 131 CRSPD-TILQKDTRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGS 181 (193)
Q Consensus 131 C~sPd-T~L~k~~rl~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga 181 (193)
.++|. -.+.-.+.+..++|..|+...+.......+.... .-+|..||+
T Consensus 100 aG~~~~~V~elHG~l~~~~C~~C~~~~~~~~~~~~~~~~~---~p~C~~Cgg 148 (235)
T cd01408 100 AGVPDDRIIEAHGSFATAHCIKCKHKYPGDWMREDIFNQE---VPKCPRCGG 148 (235)
T ss_pred cCCCccCEEEeCcCCCccccccCCCcCCHHHHHHHHhCCC---CccCCCCCC
Confidence 36554 3556689999999999998765433322211111 367999985
No 218
>KOG2907|consensus
Probab=39.23 E-value=22 Score=28.14 Aligned_cols=51 Identities=14% Similarity=0.343 Sum_probs=35.2
Q ss_pred cceeEecCceeeccccccccccccc-ccccceeeeccEEEEEecccCCCccc
Q psy7490 135 DTILQKDTRLFFLQCETCGSRCSVA-SIKSGFQKDTRLFFLQCETCGSRCSV 185 (193)
Q Consensus 135 dT~L~k~~rl~~l~C~aCGa~~~V~-~~k~~~~~~~rl~~~~c~~Cga~~~v 185 (193)
++...+++-++--+|.+||+....- .++.+---.-..-|--|..|+-+.+.
T Consensus 63 e~~~~~~ga~I~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 63 ENESSADGAVIKHKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYKFTE 114 (116)
T ss_pred cccccccccchhccCcccCCchhhhhhhhcccccCCceEEEEcCccceeeec
Confidence 4555567788899999999998763 23333323445667789999977654
No 219
>PRK07562 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=38.87 E-value=20 Score=38.22 Aligned_cols=15 Identities=33% Similarity=0.673 Sum_probs=11.6
Q ss_pred hHHHHHHHHHhhcCc
Q psy7490 80 PKHLLDFLLAELGTS 94 (193)
Q Consensus 80 p~hv~ky~~~ELgt~ 94 (193)
..-|+.|+..|||.+
T Consensus 1063 atSilDyifr~l~~~ 1077 (1220)
T PRK07562 1063 ATSILDYVFRELAVS 1077 (1220)
T ss_pred hhhHHHHHHHHHHHH
Confidence 456788999988865
No 220
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=38.64 E-value=21 Score=23.86 Aligned_cols=24 Identities=17% Similarity=0.531 Sum_probs=17.9
Q ss_pred eccHHHHHHHHHHHhhhccccCCCCC
Q psy7490 108 RFQQKQIENVLRRYIKEYVTCHTCRS 133 (193)
Q Consensus 108 ~~~~~~iq~~L~~yI~~YVlC~~C~s 133 (193)
..++..++++... ++-|.||+|+.
T Consensus 31 ~l~~~~~~~i~~~--~~i~~Cp~CgR 54 (56)
T PF02591_consen 31 ELPPQELNEIRKG--DEIVFCPNCGR 54 (56)
T ss_pred EcCHHHHHHHHcC--CCeEECcCCCc
Confidence 4567777777666 78888888875
No 221
>cd03031 GRX_GRX_like Glutaredoxin (GRX) family, GRX-like domain containing protein subfamily; composed of uncharacterized eukaryotic proteins containing a GRX-like domain having only one conserved cysteine, aligning to the C-terminal cysteine of the CXXC motif of GRXs. This subfamily is predominantly composed of plant proteins. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins via a redox active CXXC motif using a similar dithiol mechanism employed by TRXs. GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. Proteins containing only the C-terminal cysteine are generally redox inactive.
Probab=38.59 E-value=26 Score=28.34 Aligned_cols=33 Identities=30% Similarity=0.788 Sum_probs=18.8
Q ss_pred ceeecccccccccccccccccceeee--ccEEEEEecccCC
Q psy7490 143 RLFFLQCETCGSRCSVASIKSGFQKD--TRLFFLQCETCGS 181 (193)
Q Consensus 143 rl~~l~C~aCGa~~~V~~~k~~~~~~--~rl~~~~c~~Cga 181 (193)
+.-|+-|..|+-+.-+ |.+. ..--+++|..|+.
T Consensus 107 g~rfv~C~~C~Gs~k~------~~~~~~~~~~~~rC~~Cne 141 (147)
T cd03031 107 GARFVPCSECNGSCKV------FAENATAAGGFLRCPECNE 141 (147)
T ss_pred CcCeEECCCCCCcceE------EeccCcccccEEECCCCCc
Confidence 4557777777766533 2222 1233578888764
No 222
>PF15616 TerY-C: TerY-C metal binding domain
Probab=38.31 E-value=36 Score=27.34 Aligned_cols=45 Identities=22% Similarity=0.398 Sum_probs=25.6
Q ss_pred hhccccCCCCCC-cceeEecCcee------ecccccccccccccccccceee
Q psy7490 123 KEYVTCHTCRSP-DTILQKDTRLF------FLQCETCGSRCSVASIKSGFQK 167 (193)
Q Consensus 123 ~~YVlC~~C~sP-dT~L~k~~rl~------~l~C~aCGa~~~V~~~k~~~~~ 167 (193)
..+--||.|++. --.+-.=++++ .+.|..||...++.....+|+.
T Consensus 75 ~g~PgCP~CGn~~~fa~C~CGkl~Ci~g~~~~~CPwCg~~g~~~~~~~~fdv 126 (131)
T PF15616_consen 75 IGAPGCPHCGNQYAFAVCGCGKLFCIDGEGEVTCPWCGNEGSFGAGDGGFDV 126 (131)
T ss_pred cCCCCCCCCcChhcEEEecCCCEEEeCCCCCEECCCCCCeeeecccCCceEe
Confidence 345789999986 22221112222 3667777777666666555543
No 223
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=38.24 E-value=55 Score=24.09 Aligned_cols=34 Identities=12% Similarity=0.130 Sum_probs=25.9
Q ss_pred cHHHHHHcCCChHHHHHHHHHhhcCceeecCCCeEE
Q psy7490 69 FTEICKTLHRLPKHLLDFLLAELGTSGSVDGNSQLI 104 (193)
Q Consensus 69 f~dIak~L~R~p~hv~ky~~~ELgt~g~id~~~~li 104 (193)
..++|.+++++.+.|...|..-=+ ..+|++|+.|
T Consensus 41 ~~~LA~a~g~~~e~v~~~L~~~p~--tEyD~~GrIV 74 (77)
T PF12324_consen 41 VEQLAAALGWPVEEVRAALAAMPD--TEYDDQGRIV 74 (77)
T ss_dssp HHHHHHHHT--HHHHHHHHHH-TT--SEEETTSEEE
T ss_pred HHHHHHHHCCCHHHHHHHHHhCCC--ceEcCCCCee
Confidence 469999999999999999977644 4588888876
No 224
>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=38.03 E-value=19 Score=23.85 Aligned_cols=19 Identities=37% Similarity=0.821 Sum_probs=9.6
Q ss_pred HHHHhhhcc----ccCCCCCCcc
Q psy7490 118 LRRYIKEYV----TCHTCRSPDT 136 (193)
Q Consensus 118 L~~yI~~YV----lC~~C~sPdT 136 (193)
+.+||++.- .||.|++|=+
T Consensus 9 ~~k~i~~l~~~~~~CPlC~r~l~ 31 (54)
T PF04423_consen 9 LKKYIEELKEAKGCCPLCGRPLD 31 (54)
T ss_dssp HHHHHHHHTT-SEE-TTT--EE-
T ss_pred HHHHHHHHhcCCCcCCCCCCCCC
Confidence 455555554 8999998743
No 225
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=37.91 E-value=19 Score=32.36 Aligned_cols=33 Identities=24% Similarity=0.408 Sum_probs=20.9
Q ss_pred ccCCCCCCcceeEecCceeeccccccccccccccc
Q psy7490 127 TCHTCRSPDTILQKDTRLFFLQCETCGSRCSVASI 161 (193)
Q Consensus 127 lC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~~~ 161 (193)
.||+|++. .++.+-.--...|..||.----+.+
T Consensus 3 ~CpeCg~~--~~~~d~~~ge~VC~~CG~Vi~~~~i 35 (285)
T COG1405 3 SCPECGST--NIITDYERGEIVCADCGLVLEDSLI 35 (285)
T ss_pred CCCCCCCc--cceeeccCCeEEeccCCEEeccccc
Confidence 59999998 5665521124678888875443333
No 226
>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=37.68 E-value=39 Score=25.66 Aligned_cols=43 Identities=19% Similarity=0.561 Sum_probs=27.3
Q ss_pred ccHHHHHHHHHHHhhhccccCCCCCCcceeEec-Cceeecccccccccc
Q psy7490 109 FQQKQIENVLRRYIKEYVTCHTCRSPDTILQKD-TRLFFLQCETCGSRC 156 (193)
Q Consensus 109 ~~~~~iq~~L~~yI~~YVlC~~C~sPdT~L~k~-~rl~~l~C~aCGa~~ 156 (193)
.-.+.+.++-..=-..| .||.|+.+. +.+. .++ -+|..||..-
T Consensus 20 slRK~v~kie~~q~a~y-~CpfCgk~~--vkR~a~GI--W~C~~C~~~~ 63 (91)
T TIGR00280 20 KLRRQVKKIEIQQKAKY-VCPFCGKKT--VKRGSTGI--WTCRKCGAKF 63 (91)
T ss_pred HHHHHHHHHHHHHhcCc-cCCCCCCCc--eEEEeeEE--EEcCCCCCEE
Confidence 33455555555555667 799999644 4433 355 5899998764
No 227
>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=37.52 E-value=28 Score=21.81 Aligned_cols=11 Identities=36% Similarity=0.863 Sum_probs=6.6
Q ss_pred ccccCCCCCCc
Q psy7490 125 YVTCHTCRSPD 135 (193)
Q Consensus 125 YVlC~~C~sPd 135 (193)
.|.||.|++.+
T Consensus 5 ~v~CP~C~s~~ 15 (36)
T PF03811_consen 5 DVHCPRCQSTE 15 (36)
T ss_pred eeeCCCCCCCC
Confidence 35666666655
No 228
>PF11242 DUF2774: Protein of unknown function (DUF2774); InterPro: IPR021404 This entry is represented by Bacteriophage T4, Gp24.3; it is a family of uncharacterised viral proteins.
Probab=37.20 E-value=26 Score=24.95 Aligned_cols=44 Identities=11% Similarity=0.172 Sum_probs=31.0
Q ss_pred eccHHHHHHcCCChHHHHHHHHHhhcCceeecCCCeEEEEeecc
Q psy7490 67 ANFTEICKTLHRLPKHLLDFLLAELGTSGSVDGNSQLIIKGRFQ 110 (193)
Q Consensus 67 ~Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id~~~~lii~G~~~ 110 (193)
.||.|||+.++-.|..+.++...--++...+......+..-+|.
T Consensus 14 ~~FveIAr~~~i~a~e~a~~w~~Ve~Ak~kfk~rEkVVYRKr~~ 57 (63)
T PF11242_consen 14 LSFVEIARKIGITAKEVAKAWAEVETAKEKFKTREKVVYRKRLI 57 (63)
T ss_pred CcHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccCceeeehhhc
Confidence 68999999999999999998876555544443334555544443
No 229
>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=37.12 E-value=7.6 Score=31.43 Aligned_cols=42 Identities=24% Similarity=0.641 Sum_probs=25.1
Q ss_pred eeEecCceeecccccccccccccccccceeeeccEEEEEecccCC
Q psy7490 137 ILQKDTRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGS 181 (193)
Q Consensus 137 ~L~k~~rl~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga 181 (193)
.+.-.+.+..++|..|+...+...+........ .-+|..||.
T Consensus 96 vielHG~l~~~~C~~C~~~~~~~~~~~~~~~~~---~~~C~~C~~ 137 (178)
T PF02146_consen 96 VIELHGSLFRLRCSKCGKEYDREDIVDSIDEEE---PPRCPKCGG 137 (178)
T ss_dssp EEETTEEEEEEEETTTSBEEEGHHHHHHHHTTS---SCBCTTTSC
T ss_pred hHHHHhhhceeeecCCCccccchhhcccccccc---cccccccCc
Confidence 334478888888998988776544321111110 118888887
No 230
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=36.96 E-value=47 Score=21.91 Aligned_cols=28 Identities=14% Similarity=0.062 Sum_probs=25.6
Q ss_pred eccHHHHHHcCC-ChHHHHHHHHHhhcCc
Q psy7490 67 ANFTEICKTLHR-LPKHLLDFLLAELGTS 94 (193)
Q Consensus 67 ~Nf~dIak~L~R-~p~hv~ky~~~ELgt~ 94 (193)
.++.|||..++= ++.|+.+.|....|..
T Consensus 51 ~~~~~ia~~~g~~s~~~f~r~Fk~~~g~s 79 (84)
T smart00342 51 LSVTEIALRVGFSSQSYFSRAFKKLFGVT 79 (84)
T ss_pred CCHHHHHHHhCCCChHHHHHHHHHHHCcC
Confidence 578999999999 9999999999998864
No 231
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=36.69 E-value=97 Score=18.63 Aligned_cols=46 Identities=11% Similarity=0.117 Sum_probs=30.7
Q ss_pred eccHHHHHHcCCChHHHHHHHHHhhcCceeecCCCeEEEEeeccHHHHHHHH
Q psy7490 67 ANFTEICKTLHRLPKHLLDFLLAELGTSGSVDGNSQLIIKGRFQQKQIENVL 118 (193)
Q Consensus 67 ~Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id~~~~lii~G~~~~~~iq~~L 118 (193)
.++.|+|+.|+-++..+.+++.... .++...+ ++ -.+..++|++.+
T Consensus 2 lt~~e~a~~lgis~~ti~~~~~~g~-i~~~~~g-~~----~~~~~~~l~~~~ 47 (49)
T TIGR01764 2 LTVEEAAEYLGVSKDTVYRLIHEGE-LPAYRVG-RH----YRIPREDVDEYL 47 (49)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHcCC-CCeEEeC-Ce----EEEeHHHHHHHH
Confidence 5789999999999999999985432 2222222 22 246677776654
No 232
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=36.42 E-value=90 Score=19.65 Aligned_cols=25 Identities=20% Similarity=0.260 Sum_probs=22.9
Q ss_pred EEeccHHHHHHcCCChHHHHHHHHH
Q psy7490 65 SFANFTEICKTLHRLPKHLLDFLLA 89 (193)
Q Consensus 65 vi~Nf~dIak~L~R~p~hv~ky~~~ 89 (193)
.+..+.|.|+.|+.+..+|.+++-.
T Consensus 16 ~f~S~~eAa~~lg~~~~~I~~~~~~ 40 (53)
T smart00497 16 EFSSIREAAKYLGISHSSISKYLNT 40 (53)
T ss_pred EecCHHHHHHHhCCCHHHHHHHHhC
Confidence 5899999999999999999999864
No 233
>KOG3239|consensus
Probab=36.08 E-value=74 Score=27.14 Aligned_cols=47 Identities=17% Similarity=0.340 Sum_probs=37.6
Q ss_pred HcCCChHHHHHHHHHhhcCceeecC----CCeEEEEeeccHHHHHHHHHHH
Q psy7490 75 TLHRLPKHLLDFLLAELGTSGSVDG----NSQLIIKGRFQQKQIENVLRRY 121 (193)
Q Consensus 75 ~L~R~p~hv~ky~~~ELgt~g~id~----~~~lii~G~~~~~~iq~~L~~y 121 (193)
.+.-+-....|||..-++|..|+-+ .+..+|+|.+..+-+.=+.++|
T Consensus 124 ~FdIdlk~aaK~fa~KFAtGaSVtk~a~kkdEIvIQGDv~dDi~d~I~ekw 174 (193)
T KOG3239|consen 124 TFDIDLKKAAKFFAQKFATGASVTKNAEKKDEIVIQGDVKDDIFDFIPEKW 174 (193)
T ss_pred hccccHHHHHHHHHHhhccCccccCCCCccceEEEeccchHHHHHHHHHhc
Confidence 4566778889999999999999876 6899999999877665554443
No 234
>PRK14295 chaperone protein DnaJ; Provisional
Probab=36.01 E-value=28 Score=32.15 Aligned_cols=37 Identities=16% Similarity=0.348 Sum_probs=20.5
Q ss_pred hhhccccCCCCCCcceeEecCceeecccccccccccccccc
Q psy7490 122 IKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVASIK 162 (193)
Q Consensus 122 I~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~~~k 162 (193)
+...|.|+.|...-.. .+ .....|..|+-...+....
T Consensus 163 ~~r~~~C~~C~G~G~~---~~-~~~~~C~~C~G~G~~~~~~ 199 (389)
T PRK14295 163 LTSQAPCPACSGTGAK---NG-TTPRVCPTCSGTGQVSRNS 199 (389)
T ss_pred eeccccCCCCcccccC---CC-CCCcCCCCCCCEeEEEEEe
Confidence 4667889999764432 11 1124466666666554443
No 235
>PRK14284 chaperone protein DnaJ; Provisional
Probab=35.97 E-value=32 Score=31.75 Aligned_cols=33 Identities=18% Similarity=0.463 Sum_probs=18.9
Q ss_pred hhccccCCCCCCcceeEecCceeeccccccccccccc
Q psy7490 123 KEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVA 159 (193)
Q Consensus 123 ~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~ 159 (193)
...+.|+.|+..-..- + .-...|..|+-...|.
T Consensus 156 ~r~~~C~~C~G~G~~~---~-~~~~~C~~C~G~G~v~ 188 (391)
T PRK14284 156 SGYKSCDACSGSGANS---S-QGIKVCDRCKGSGQVV 188 (391)
T ss_pred eeeccCCCCcccccCC---C-CCCeecCccCCeeEEE
Confidence 5678999997654311 1 1123477777665444
No 236
>PF14376 Haem_bd: Haem-binding domain
Probab=35.42 E-value=26 Score=27.83 Aligned_cols=25 Identities=20% Similarity=0.495 Sum_probs=20.4
Q ss_pred ccHHHHHHHHHHHhhhccccCCCCCCcceeE
Q psy7490 109 FQQKQIENVLRRYIKEYVTCHTCRSPDTILQ 139 (193)
Q Consensus 109 ~~~~~iq~~L~~yI~~YVlC~~C~sPdT~L~ 139 (193)
-.++.++.+|++ -|.-|+|++|.+-
T Consensus 31 ~~p~~v~~il~~------~CydCHSn~T~~P 55 (137)
T PF14376_consen 31 KAPEEVKIILKN------SCYDCHSNNTRYP 55 (137)
T ss_pred cchHHHHHHHHc------cccccCCCCCCCc
Confidence 356788888877 8999999999873
No 237
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=35.42 E-value=21 Score=20.16 Aligned_cols=8 Identities=38% Similarity=1.248 Sum_probs=3.8
Q ss_pred cccccccc
Q psy7490 149 CETCGSRC 156 (193)
Q Consensus 149 C~aCGa~~ 156 (193)
|..||+.-
T Consensus 2 Cp~CG~~~ 9 (23)
T PF13240_consen 2 CPNCGAEI 9 (23)
T ss_pred CcccCCCC
Confidence 44455443
No 238
>PRK14279 chaperone protein DnaJ; Provisional
Probab=35.41 E-value=32 Score=31.85 Aligned_cols=35 Identities=17% Similarity=0.362 Sum_probs=20.9
Q ss_pred hhhccccCCCCCCcceeEecCceeecccccccccccccc
Q psy7490 122 IKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVAS 160 (193)
Q Consensus 122 I~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~~ 160 (193)
+..+|.|+.|...-..- +. ....|..|+-...+..
T Consensus 170 ~~~~~~C~~C~G~G~~~---~~-~~~~C~~C~G~G~~~~ 204 (392)
T PRK14279 170 LTSPAPCTTCHGSGARP---GT-SPKVCPTCNGSGVISR 204 (392)
T ss_pred eeccccCCCCccccccC---CC-CCCCCCCCcceEEEEE
Confidence 46789999998765421 11 1245667766655443
No 239
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=35.39 E-value=19 Score=24.86 Aligned_cols=11 Identities=27% Similarity=0.839 Sum_probs=5.8
Q ss_pred EecccCCCccc
Q psy7490 175 QCETCGSRCSV 185 (193)
Q Consensus 175 ~c~~Cga~~~v 185 (193)
.|..||+...+
T Consensus 19 ~CP~CG~~t~~ 29 (56)
T PRK13130 19 ICPVCGGKTKN 29 (56)
T ss_pred cCcCCCCCCCC
Confidence 45556655444
No 240
>PRK14873 primosome assembly protein PriA; Provisional
Probab=35.39 E-value=23 Score=35.23 Aligned_cols=39 Identities=21% Similarity=0.583 Sum_probs=26.4
Q ss_pred hccccCCCCCCcceeEecCceeecccccccccccccccccceeeeccEEEEEecccCCCc
Q psy7490 124 EYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRC 183 (193)
Q Consensus 124 ~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~ 183 (193)
-++.|..|+. ..+|..|+.+-.+. +..+ .++|.-||...
T Consensus 382 p~l~C~~Cg~------------~~~C~~C~~~L~~h-------~~~~--~l~Ch~CG~~~ 420 (665)
T PRK14873 382 PSLACARCRT------------PARCRHCTGPLGLP-------SAGG--TPRCRWCGRAA 420 (665)
T ss_pred CeeEhhhCcC------------eeECCCCCCceeEe-------cCCC--eeECCCCcCCC
Confidence 4778888873 46788888765332 2222 58999999864
No 241
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=35.26 E-value=22 Score=23.98 Aligned_cols=16 Identities=19% Similarity=0.326 Sum_probs=8.2
Q ss_pred eccccccccccccccc
Q psy7490 146 FLQCETCGSRCSVASI 161 (193)
Q Consensus 146 ~l~C~aCGa~~~V~~~ 161 (193)
...|..|+++.|+.+.
T Consensus 14 k~ICrkC~ARnp~~A~ 29 (48)
T PRK04136 14 KKICMRCNARNPWRAT 29 (48)
T ss_pred ccchhcccCCCCcccc
Confidence 3445555555555543
No 242
>COG1497 Predicted transcriptional regulator [Transcription]
Probab=35.07 E-value=52 Score=29.36 Aligned_cols=71 Identities=23% Similarity=0.342 Sum_probs=45.7
Q ss_pred eeecCCCeEEEecCeeeEEeccHHHHHHcCCChHHHHHHHHHhhcCceeecCCC--eEEEEee---ccHHHHHHHHHHHh
Q psy7490 48 KFVMRPPQVVRIGTKKTSFANFTEICKTLHRLPKHLLDFLLAELGTSGSVDGNS--QLIIKGR---FQQKQIENVLRRYI 122 (193)
Q Consensus 48 R~~mP~p~v~~~Gg~KTvi~Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id~~~--~lii~G~---~~~~~iq~~L~~yI 122 (193)
||.+-....++++. ++-.|||+.|.-.|+-|..|| +||=..|-++..| +|.|.-+ +-..++.+ |+.|+
T Consensus 12 ~fqIL~ei~~~qp~-----v~q~eIA~~lgiT~QaVsehi-K~Lv~eG~i~~~gR~~Y~iTkkG~e~l~~~~~d-lr~f~ 84 (260)
T COG1497 12 RFQILSEIAVRQPR-----VKQKEIAKKLGITLQAVSEHI-KELVKEGLIEKEGRGEYEITKKGAEWLLEQLSD-LRRFS 84 (260)
T ss_pred HHHHHHHHHHhCCC-----CCHHHHHHHcCCCHHHHHHHH-HHHHhccceeecCCeeEEEehhHHHHHHHHHHH-HHHHH
Confidence 44443333344443 567899999999999998887 6788888888644 5666433 33333333 56777
Q ss_pred hhc
Q psy7490 123 KEY 125 (193)
Q Consensus 123 ~~Y 125 (193)
++-
T Consensus 85 ~ev 87 (260)
T COG1497 85 EEV 87 (260)
T ss_pred HHH
Confidence 654
No 243
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=34.70 E-value=72 Score=23.55 Aligned_cols=45 Identities=13% Similarity=0.142 Sum_probs=31.7
Q ss_pred ccHHHHHHcCCChHHHHHHHHHhhcCceeecCCCeEEEEeeccHHHHHHH
Q psy7490 68 NFTEICKTLHRLPKHLLDFLLAELGTSGSVDGNSQLIIKGRFQQKQIENV 117 (193)
Q Consensus 68 Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id~~~~lii~G~~~~~~iq~~ 117 (193)
++.|+|+.++-++..|-.|....|..+. -+++|+- .|+..+|+.+
T Consensus 3 ~i~eva~~~gVs~~tLR~ye~~Gli~p~-r~~~g~R----~Ys~~dv~~l 47 (98)
T cd01279 3 PISVAAELLGIHPQTLRVYDRLGLVSPA-RTNGGGR----RYSNNDLELL 47 (98)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCCCCCCC-cCCCCCe----eECHHHHHHH
Confidence 6889999999999999999877766552 2223322 2666666654
No 244
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=34.57 E-value=28 Score=33.32 Aligned_cols=41 Identities=24% Similarity=0.644 Sum_probs=25.6
Q ss_pred ccccCCCCCCcceeEecCceeecccccccccccccccccceeeeccEEEEEecccCCCcccc
Q psy7490 125 YVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRCSVA 186 (193)
Q Consensus 125 YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~~v~ 186 (193)
++.|..|+. ..+|..|+.+-++ ++..+ .++|.-||...++.
T Consensus 213 ~~~C~~Cg~------------~~~C~~C~~~l~~-------h~~~~--~l~Ch~Cg~~~~~~ 253 (505)
T TIGR00595 213 NLLCRSCGY------------ILCCPNCDVSLTY-------HKKEG--KLRCHYCGYQEPIP 253 (505)
T ss_pred eeEhhhCcC------------ccCCCCCCCceEE-------ecCCC--eEEcCCCcCcCCCC
Confidence 456666653 3567777655322 22222 68999999988764
No 245
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=34.45 E-value=20 Score=24.26 Aligned_cols=32 Identities=28% Similarity=0.484 Sum_probs=15.4
Q ss_pred ccCCCCCCcceeEecCceeeccccccccccccccc
Q psy7490 127 TCHTCRSPDTILQKDTRLFFLQCETCGSRCSVASI 161 (193)
Q Consensus 127 lC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~~~ 161 (193)
.|..|+..-..+.. .-.++|.-||++--++..
T Consensus 8 ~C~~Cg~~~~~~~~---~~~irCp~Cg~rIl~K~R 39 (49)
T COG1996 8 KCARCGREVELDQE---TRGIRCPYCGSRILVKER 39 (49)
T ss_pred EhhhcCCeeehhhc---cCceeCCCCCcEEEEecc
Confidence 46666654422222 223566666665544433
No 246
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=34.44 E-value=48 Score=25.09 Aligned_cols=44 Identities=18% Similarity=0.436 Sum_probs=27.8
Q ss_pred eccHHHHHHHHHHHhhhccccCCCCCCcceeEec-Cceeecccccccccc
Q psy7490 108 RFQQKQIENVLRRYIKEYVTCHTCRSPDTILQKD-TRLFFLQCETCGSRC 156 (193)
Q Consensus 108 ~~~~~~iq~~L~~yI~~YVlC~~C~sPdT~L~k~-~rl~~l~C~aCGa~~ 156 (193)
..-.+.+.++-..=-..| .||.|+.+. +.+. .++ -+|..||..-
T Consensus 20 ~slRK~v~kie~~q~a~y-~CpfCgk~~--vkR~a~GI--W~C~~C~~~~ 64 (90)
T PTZ00255 20 ASLRKQIKKIEISQHAKY-FCPFCGKHA--VKRQAVGI--WRCKGCKKTV 64 (90)
T ss_pred HHHHHHHHHHHHHHhCCc-cCCCCCCCc--eeeeeeEE--EEcCCCCCEE
Confidence 333455555555555667 799999643 4443 355 4899998764
No 247
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=34.11 E-value=1e+02 Score=20.47 Aligned_cols=45 Identities=20% Similarity=0.270 Sum_probs=32.0
Q ss_pred ccHHHHHHcCCChHHHHHHHHHhhcCceeecCCCeEEEEeeccHHHHHHH
Q psy7490 68 NFTEICKTLHRLPKHLLDFLLAELGTSGSVDGNSQLIIKGRFQQKQIENV 117 (193)
Q Consensus 68 Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id~~~~lii~G~~~~~~iq~~ 117 (193)
.+.|+|+.++-++.-|-.|....+ .+...+++|+ ..|+.++|+.+
T Consensus 2 ti~eva~~~gvs~~tlr~y~~~gl-l~~~~~~~g~----r~y~~~dv~~l 46 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTLRYYEREGL-LPPPRDENGY----RYYSEEDVERL 46 (69)
T ss_dssp EHHHHHHHTTTTHHHHHHHHHTTS-STTBESTTSS----EEE-HHHHHHH
T ss_pred cHHHHHHHHCcCHHHHHHHHHhcC-cccccccCce----eeccHHHHHHH
Confidence 468999999999999988887777 4444454544 35777777765
No 248
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=34.09 E-value=48 Score=24.19 Aligned_cols=27 Identities=11% Similarity=-0.033 Sum_probs=25.2
Q ss_pred ccHHHHHHcCCChHHHHHHHHHhhcCc
Q psy7490 68 NFTEICKTLHRLPKHLLDFLLAELGTS 94 (193)
Q Consensus 68 Nf~dIak~L~R~p~hv~ky~~~ELgt~ 94 (193)
++.++|+.++-++.|+.+.|...+|.+
T Consensus 23 ~~~~lA~~~~~S~~~l~r~f~~~~g~s 49 (107)
T PRK10219 23 NIDVVAKKSGYSKWYLQRMFRTVTHQT 49 (107)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHCcC
Confidence 678999999999999999999999975
No 249
>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=34.04 E-value=13 Score=32.47 Aligned_cols=24 Identities=25% Similarity=0.491 Sum_probs=18.6
Q ss_pred eeEecCceeecccccccccccccc
Q psy7490 137 ILQKDTRLFFLQCETCGSRCSVAS 160 (193)
Q Consensus 137 ~L~k~~rl~~l~C~aCGa~~~V~~ 160 (193)
.+.-.+.+..++|..|+...+...
T Consensus 109 vielHG~~~~~~C~~C~~~~~~~~ 132 (260)
T cd01409 109 VVELHGSLHRVVCLSCGFRTPRAE 132 (260)
T ss_pred EEEEeeecCEEEeCCCcCccCHHH
Confidence 455678899999999999876443
No 250
>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=33.91 E-value=20 Score=33.13 Aligned_cols=49 Identities=33% Similarity=0.685 Sum_probs=0.0
Q ss_pred hccccCCCC------------CCcceeEecCceeecccccccccccccccccceeeeccEEEEEecccCC
Q psy7490 124 EYVTCHTCR------------SPDTILQKDTRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGS 181 (193)
Q Consensus 124 ~YVlC~~C~------------sPdT~L~k~~rl~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga 181 (193)
..|.|..|. .-.+.-..+.---|.+|..||.+. +...|+=.-+|..||.
T Consensus 251 kav~C~~C~yt~~~~~~~C~~~~H~l~~~~a~KRFFkC~~C~~Rt---------~sl~r~P~~~C~~Cg~ 311 (344)
T PF09332_consen 251 KAVTCKQCKYTAFKPSDRCKEEGHPLKWHDAVKRFFKCKDCGNRT---------ISLERLPKKHCSNCGS 311 (344)
T ss_dssp EEEEETTT--EESS--HHHHHTT--EEEEEEE-EEEE-T-TS-EE---------EESSSS--S--TTT-S
T ss_pred EEEEcCCCCCcccCcchhHHhcCCceEEeeeeeeeEECCCCCCee---------eecccCCCCCCCcCCc
No 251
>PLN03165 chaperone protein dnaJ-related; Provisional
Probab=33.75 E-value=55 Score=25.50 Aligned_cols=18 Identities=17% Similarity=0.272 Sum_probs=11.4
Q ss_pred ecccCCCccccccccCCC
Q psy7490 176 CETCGSRCSVASIKSGFQ 193 (193)
Q Consensus 176 c~~Cga~~~v~~~~~~~~ 193 (193)
|..|..+..++.--.||+
T Consensus 89 C~~C~G~G~~~~~~~~~~ 106 (111)
T PLN03165 89 CTTCQGSGIQPRYLDRRE 106 (111)
T ss_pred CCCCCCCEEEeeeecccc
Confidence 777777776665545543
No 252
>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=33.68 E-value=24 Score=24.07 Aligned_cols=25 Identities=28% Similarity=0.620 Sum_probs=15.8
Q ss_pred hhccccCCCCCCcceeEecCceeeccccccccc
Q psy7490 123 KEYVTCHTCRSPDTILQKDTRLFFLQCETCGSR 155 (193)
Q Consensus 123 ~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~ 155 (193)
-..|.|+.|+.+ .+-...|..||.-
T Consensus 24 p~l~~C~~cG~~--------~~~H~vc~~cG~Y 48 (55)
T TIGR01031 24 PTLVVCPNCGEF--------KLPHRVCPSCGYY 48 (55)
T ss_pred CcceECCCCCCc--------ccCeeECCccCeE
Confidence 346778888875 3445567777743
No 253
>TIGR02349 DnaJ_bact chaperone protein DnaJ. This model represents bacterial forms of DnaJ, part of the DnaK-DnaJ-GrpE chaperone system. The three components typically are encoded by consecutive genes. DnaJ homologs occur in many genomes, typically not near DnaK and GrpE-like genes; most such genes are not included by this family. Eukaryotic (mitochondrial and chloroplast) forms are not included in the scope of this family.
Probab=33.62 E-value=35 Score=30.81 Aligned_cols=34 Identities=26% Similarity=0.439 Sum_probs=19.3
Q ss_pred hhhccccCCCCCCcceeEecCceeeccccccccccccc
Q psy7490 122 IKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVA 159 (193)
Q Consensus 122 I~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~ 159 (193)
+...+.|+.|...-+.- ..-...|..|+-...+.
T Consensus 140 ~~r~~~C~~C~G~G~~~----~~~~~~C~~C~G~G~~~ 173 (354)
T TIGR02349 140 IPRKESCETCHGTGAKP----GTDPKTCPTCGGTGQVR 173 (354)
T ss_pred eecCCcCCCCCCCCCCC----CCCCccCCCCCCeeEEE
Confidence 45678999998755421 11124566666655443
No 254
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=33.56 E-value=15 Score=31.68 Aligned_cols=43 Identities=19% Similarity=0.493 Sum_probs=28.2
Q ss_pred ceeEecCceeecccccccccccccccccceeeeccEEEEEecccCC
Q psy7490 136 TILQKDTRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGS 181 (193)
Q Consensus 136 T~L~k~~rl~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga 181 (193)
-.+.-.+.+..++|..|+...+.......+... -.-+|..||+
T Consensus 109 ~VielHG~~~~~~C~~C~~~~~~~~~~~~~~~~---~~p~Cp~Cgg 151 (244)
T PRK14138 109 KVIELHGNVEEYYCVRCGKRYTVEDVIEKLEKS---DVPRCDDCSG 151 (244)
T ss_pred eEEEccCCcCeeEECCCCCcccHHHHHHHHhcC---CCCCCCCCCC
Confidence 355567889999999999887664442211111 1467999985
No 255
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=33.41 E-value=20 Score=24.70 Aligned_cols=13 Identities=31% Similarity=0.836 Sum_probs=10.1
Q ss_pred hhccccCCCCCCc
Q psy7490 123 KEYVTCHTCRSPD 135 (193)
Q Consensus 123 ~~YVlC~~C~sPd 135 (193)
+.-|.||.|+.|=
T Consensus 19 dDiVvCp~Cgapy 31 (54)
T PF14446_consen 19 DDIVVCPECGAPY 31 (54)
T ss_pred CCEEECCCCCCcc
Confidence 4568999999874
No 256
>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=33.34 E-value=24 Score=28.65 Aligned_cols=35 Identities=17% Similarity=0.175 Sum_probs=26.4
Q ss_pred cCeeeEE-eccHHHHHHcCCChHHHHHHHHHhhcCc
Q psy7490 60 GTKKTSF-ANFTEICKTLHRLPKHLLDFLLAELGTS 94 (193)
Q Consensus 60 Gg~KTvi-~Nf~dIak~L~R~p~hv~ky~~~ELgt~ 94 (193)
|-....| .|..++-++|...-..+.+=|..+|--.
T Consensus 69 gw~~Y~w~i~~~~i~d~Ik~~~~~~~~~lk~~l~~e 104 (158)
T TIGR00373 69 GWYEYTWRINYEKALDVLKRKLEETAKKLREKLEFE 104 (158)
T ss_pred CcEEEEEEeCHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 3344555 8999999999998888888777776643
No 257
>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=33.27 E-value=30 Score=26.20 Aligned_cols=40 Identities=23% Similarity=0.703 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHhhhccccCCCCCCcceeEe-cCceeeccccccccc
Q psy7490 111 QKQIENVLRRYIKEYVTCHTCRSPDTILQK-DTRLFFLQCETCGSR 155 (193)
Q Consensus 111 ~~~iq~~L~~yI~~YVlC~~C~sPdT~L~k-~~rl~~l~C~aCGa~ 155 (193)
.+.+.++...=-.+| .||.|+... +.+ .-++| +|..||..
T Consensus 22 RK~vkkie~~q~~ky-~Cp~Cgk~~--vkR~a~GIW--~C~~C~~~ 62 (90)
T PF01780_consen 22 RKRVKKIEISQHAKY-TCPFCGKTS--VKRVATGIW--KCKKCGKK 62 (90)
T ss_dssp HHHHHHHHHHHHS-B-EESSSSSSE--EEEEETTEE--EETTTTEE
T ss_pred HHHHHHHHHHHhCCC-cCCCCCCce--eEEeeeEEe--ecCCCCCE
Confidence 344555444444566 799999876 444 35664 89999865
No 258
>PRK14286 chaperone protein DnaJ; Provisional
Probab=33.06 E-value=33 Score=31.52 Aligned_cols=36 Identities=17% Similarity=0.417 Sum_probs=22.0
Q ss_pred hhhccccCCCCCCcceeEecCceeeccccccccccccccc
Q psy7490 122 IKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVASI 161 (193)
Q Consensus 122 I~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~~~ 161 (193)
+...|.|+.|...-.. .+. ....|..|+-...|...
T Consensus 147 ~~r~~~C~~C~G~G~~---~~~-~~~~C~~C~G~G~v~~~ 182 (372)
T PRK14286 147 IPRLESCVDCNGSGAS---KGS-SPTTCPDCGGSGQIRRT 182 (372)
T ss_pred eeccccCCCCcCCCcC---CCC-CCccCCCCcCeEEEEEE
Confidence 4668899999886542 211 12457777776655443
No 259
>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=33.05 E-value=24 Score=32.51 Aligned_cols=14 Identities=21% Similarity=0.757 Sum_probs=7.5
Q ss_pred eecccccccccccc
Q psy7490 145 FFLQCETCGSRCSV 158 (193)
Q Consensus 145 ~~l~C~aCGa~~~V 158 (193)
|+-+|.+||+++++
T Consensus 13 ~~g~cp~c~~w~~~ 26 (372)
T cd01121 13 WLGKCPECGEWNTL 26 (372)
T ss_pred ccEECcCCCCceee
Confidence 45555555555554
No 260
>KOG0712|consensus
Probab=33.03 E-value=29 Score=32.03 Aligned_cols=59 Identities=14% Similarity=0.285 Sum_probs=39.3
Q ss_pred HHhhhccccCCCCC-CcceeEecCceeecccccccccccccccccceeeeccEEEEEecccCCCcc
Q psy7490 120 RYIKEYVTCHTCRS-PDTILQKDTRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRCS 184 (193)
Q Consensus 120 ~yI~~YVlC~~C~s-PdT~L~k~~rl~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~~ 184 (193)
-++..=++|+.|.. +...-.. -.|..|..+.+-...+..-..+...+-+.|..|+=.--
T Consensus 122 l~l~~~~iCs~C~GsGgksg~~------~~C~~C~GsGv~~~~~~~gPg~~qs~q~~C~~C~G~G~ 181 (337)
T KOG0712|consen 122 LFLSRNFICSKCSGSGGKSGSA------PKCTTCRGSGVQTRTRQMGPGMVQSPQLVCDSCNGSGE 181 (337)
T ss_pred eecccCccCCcCCCCCCCCCCC------CCCCCCCCCCceeEEEeccccccccceeEeccCCCccc
Confidence 36677899999984 4443322 37999988876655543334466777788888875443
No 261
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=33.02 E-value=48 Score=36.87 Aligned_cols=40 Identities=23% Similarity=0.505 Sum_probs=27.3
Q ss_pred HHHHHHHhhhccccCCCCCCccee---EecCceeeccccccccccc
Q psy7490 115 ENVLRRYIKEYVTCHTCRSPDTIL---QKDTRLFFLQCETCGSRCS 157 (193)
Q Consensus 115 q~~L~~yI~~YVlC~~C~sPdT~L---~k~~rl~~l~C~aCGa~~~ 157 (193)
...++.++ .-+-||+|+.++-.| +-+.+ ...|..||-+..
T Consensus 1695 ~~~~~~~~-~~~~cp~c~~~~~~~~~~~~~~g--c~~c~~cg~s~c 1737 (1740)
T PRK08332 1695 EEKIRELL-GVVYCPVCYEKEGKLVELRMESG--CATCPVCGWSKC 1737 (1740)
T ss_pred HHHHHHHh-ccCCCCCCCCCCCcceeeEecCC--ceeCCCCCCccc
Confidence 55555554 334499999998555 44666 468999998754
No 262
>TIGR01385 TFSII transcription elongation factor S-II. This model represents eukaryotic transcription elongation factor S-II. This protein allows stalled RNA transcription complexes to perform a cleavage of the nascent RNA and restart at the newly generated 3-prime end.
Probab=33.02 E-value=37 Score=30.65 Aligned_cols=29 Identities=28% Similarity=0.761 Sum_probs=15.0
Q ss_pred cccCCCCCCcceeEe-------cCceeecccccccc
Q psy7490 126 VTCHTCRSPDTILQK-------DTRLFFLQCETCGS 154 (193)
Q Consensus 126 VlC~~C~sPdT~L~k-------~~rl~~l~C~aCGa 154 (193)
+.|+.|+..++.+.- +.=..|..|..||.
T Consensus 259 ~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~ 294 (299)
T TIGR01385 259 FTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGN 294 (299)
T ss_pred ccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCC
Confidence 566666666654431 11144555666654
No 263
>KOG2593|consensus
Probab=32.69 E-value=30 Score=33.04 Aligned_cols=66 Identities=21% Similarity=0.426 Sum_probs=50.0
Q ss_pred eEEeccHHHHHHcCCChHHHHHHHHHhhcCceeecCCCeEEEEeeccHHHHHHHHHHHhhhccccCCCCCCcceeEe---
Q psy7490 64 TSFANFTEICKTLHRLPKHLLDFLLAELGTSGSVDGNSQLIIKGRFQQKQIENVLRRYIKEYVTCHTCRSPDTILQK--- 140 (193)
Q Consensus 64 Tvi~Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id~~~~lii~G~~~~~~iq~~L~~yI~~YVlC~~C~sPdT~L~k--- 140 (193)
-.++|+..|.++++-.-.|+.|=|-.+|--..+. ..| .||.|.+-=|.|.-
T Consensus 93 YyyInY~~~idvVKyKlh~m~krled~~~d~t~~-------------------------~~Y-~Cp~C~kkyt~Lea~~L 146 (436)
T KOG2593|consen 93 YYYINYAQVIDVVKYKLHQMRKRLEDRLRDDTNV-------------------------AGY-VCPNCQKKYTSLEALQL 146 (436)
T ss_pred EEEeehHHHHHHHHHHHHHHHHHHHHHhhhcccc-------------------------ccc-cCCccccchhhhHHHHh
Confidence 3478999999999999999999998887755444 336 69999988777753
Q ss_pred -cCceeeccccccccc
Q psy7490 141 -DTRLFFLQCETCGSR 155 (193)
Q Consensus 141 -~~rl~~l~C~aCGa~ 155 (193)
+.-....+|.-||..
T Consensus 147 ~~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 147 LDNETGEFHCENCGGE 162 (436)
T ss_pred hcccCceEEEecCCCc
Confidence 332335789999865
No 264
>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=32.68 E-value=21 Score=29.92 Aligned_cols=44 Identities=20% Similarity=0.575 Sum_probs=27.5
Q ss_pred ceeEecCceeecccccccccccccccccceeeeccEEEEEecccCCC
Q psy7490 136 TILQKDTRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSR 182 (193)
Q Consensus 136 T~L~k~~rl~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~ 182 (193)
-.+.-.+.+..++|..|+...+.......+. .--..+|..||+.
T Consensus 99 ~v~elHG~~~~~~C~~C~~~~~~~~~~~~~~---~~~~p~C~~Cg~~ 142 (218)
T cd01407 99 KVIELHGSLFRVRCTKCGKEYPRDELQADID---REEVPRCPKCGGL 142 (218)
T ss_pred CEEECcCCcCcceeCCCcCCCcHHHHhHhhc---cCCCCcCCCCCCc
Confidence 3444578888999999998766543221111 1124679999864
No 265
>PF13289 SIR2_2: SIR2-like domain
Probab=32.19 E-value=2.1e+02 Score=21.18 Aligned_cols=97 Identities=15% Similarity=0.218 Sum_probs=55.7
Q ss_pred ccHHHHHHHHHHHHHhcCCC-cccCcc---eeeecCCCeEEE-ecCe----eeEEeccHHHHHHcCCChHHHHHHHHHhh
Q psy7490 21 YTYEELLSRVFEIMREKNPD-MVAGKK---QKFVMRPPQVVR-IGTK----KTSFANFTEICKTLHRLPKHLLDFLLAEL 91 (193)
Q Consensus 21 ~~Y~~LL~R~~~~L~~~~p~-~~~~~~---~R~~mP~p~v~~-~Gg~----KTvi~Nf~dIak~L~R~p~hv~ky~~~EL 91 (193)
.+|+.||++|+......... ...... ....-..+.+.+ .|.. .+++.--.|..+.++ ....+.+++...|
T Consensus 6 tNyD~llE~a~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~klHG~~~~~~~~~vlt~~~y~~~~~-~~~~~~~~l~~~l 84 (143)
T PF13289_consen 6 TNYDDLLEKALEEAGIPFIVWISDEDFSNESRSSSGRPPIYKLHGSLDWDPESIVLTEDDYEEYYS-SNPWFPNFLRSLL 84 (143)
T ss_pred CCHhHHHHHHHHHcCCCceeeeccccccccccccCCCcEEEEEecCcccCCCCEEEcHHHHHHHhh-hHHHHHHHHHHHH
Confidence 37999999999765221110 000000 112333444444 3643 345555667777774 4445677777666
Q ss_pred cCceeecCCCeEEEEe-eccHHHHHHHHHHHhhhc
Q psy7490 92 GTSGSVDGNSQLIIKG-RFQQKQIENVLRRYIKEY 125 (193)
Q Consensus 92 gt~g~id~~~~lii~G-~~~~~~iq~~L~~yI~~Y 125 (193)
.+ + .+++=| ++....|+.+|+...+..
T Consensus 85 ~~------~-~~lfiGys~~D~~i~~~l~~~~~~~ 112 (143)
T PF13289_consen 85 RS------K-TLLFIGYSFNDPDIRQLLRSALENS 112 (143)
T ss_pred cC------C-CEEEEEECCCCHHHHHHHHHHHHhc
Confidence 32 2 455557 899899999998776654
No 266
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=32.04 E-value=1.1e+02 Score=21.54 Aligned_cols=52 Identities=19% Similarity=0.224 Sum_probs=33.4
Q ss_pred eccHHHHHHcCCChHHHHHHH--HHhhcCceeecC-CCeEEEEeeccHHHHHHHH
Q psy7490 67 ANFTEICKTLHRLPKHLLDFL--LAELGTSGSVDG-NSQLIIKGRFQQKQIENVL 118 (193)
Q Consensus 67 ~Nf~dIak~L~R~p~hv~ky~--~~ELgt~g~id~-~~~lii~G~~~~~~iq~~L 118 (193)
.+..+||+.++-+|.++.+-+ +.+-|.=.+..| +|.+.+.-.-..=.|-+++
T Consensus 26 ~s~~eiA~~~~i~~~~l~kil~~L~~~Gli~s~~G~~GGy~L~~~~~~Itl~dI~ 80 (83)
T PF02082_consen 26 VSSKEIAERLGISPSYLRKILQKLKKAGLIESSRGRGGGYRLARPPEEITLLDIV 80 (83)
T ss_dssp BEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETSTTSEEEESS-CCGSBHHHHH
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHhhCCeeEecCCCCCceeecCCHHHCCHHHHH
Confidence 678899999999999999877 444454334434 5777776554444444443
No 267
>PF05907 DUF866: Eukaryotic protein of unknown function (DUF866); InterPro: IPR008584 This family consists of a number of hypothetical eukaryotic proteins of unknown function with an average length of around 165 residues.; PDB: 1ZSO_B.
Probab=31.95 E-value=24 Score=28.97 Aligned_cols=15 Identities=27% Similarity=0.775 Sum_probs=5.5
Q ss_pred EEEEEecccCCCccc
Q psy7490 171 LFFLQCETCGSRCSV 185 (193)
Q Consensus 171 l~~~~c~~Cga~~~v 185 (193)
-|.++|..|+...++
T Consensus 62 Nfv~KCk~C~re~si 76 (161)
T PF05907_consen 62 NFVMKCKFCKRESSI 76 (161)
T ss_dssp SEEE--SSSS--EEE
T ss_pred EeEecCcCcCCccEE
Confidence 444555555555544
No 268
>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=31.73 E-value=16 Score=37.75 Aligned_cols=21 Identities=33% Similarity=0.967 Sum_probs=0.0
Q ss_pred ccCCCCCCcceeEecCceeecccccccccc
Q psy7490 127 TCHTCRSPDTILQKDTRLFFLQCETCGSRC 156 (193)
Q Consensus 127 lC~~C~sPdT~L~k~~rl~~l~C~aCGa~~ 156 (193)
.||.|+.+ .++.+|..||+.+
T Consensus 657 ~Cp~Cg~~---------t~~~~Cp~CG~~T 677 (900)
T PF03833_consen 657 RCPKCGKE---------TFYNRCPECGSHT 677 (900)
T ss_dssp ------------------------------
T ss_pred cCcccCCc---------chhhcCcccCCcc
Confidence 79999865 4566777777764
No 269
>PRK06599 DNA topoisomerase I; Validated
Probab=31.65 E-value=52 Score=32.68 Aligned_cols=31 Identities=26% Similarity=0.577 Sum_probs=17.8
Q ss_pred ccCCCCCCcceeEe-cCceeeccccc---ccccccc
Q psy7490 127 TCHTCRSPDTILQK-DTRLFFLQCET---CGSRCSV 158 (193)
Q Consensus 127 lC~~C~sPdT~L~k-~~rl~~l~C~a---CGa~~~V 158 (193)
.||.|+.-+..+.+ ..+ -|+.|.. |+...++
T Consensus 587 ~CP~C~~~~l~~k~~k~g-~F~~Cs~~p~C~~~~~~ 621 (675)
T PRK06599 587 TCPKCGGGPLVLKLGKNG-KFLGCSGYPECKYTKNI 621 (675)
T ss_pred cccccCCCcceEEecCCC-ceeeCCCCCccCCCCCC
Confidence 69999655554443 222 2677754 7655543
No 270
>PRK14277 chaperone protein DnaJ; Provisional
Probab=31.36 E-value=35 Score=31.44 Aligned_cols=33 Identities=15% Similarity=0.478 Sum_probs=18.8
Q ss_pred hhhccccCCCCCCcceeEecCceeecccccccccccc
Q psy7490 122 IKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSV 158 (193)
Q Consensus 122 I~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V 158 (193)
+...|+|+.|...-.. .+ .....|..|+-...+
T Consensus 152 ~~r~~~C~~C~G~G~~---~~-~~~~~C~~C~G~G~~ 184 (386)
T PRK14277 152 VERFEKCDVCKGSGAK---PG-SKPVTCPVCHGTGQV 184 (386)
T ss_pred EEeeccCCCCCCCCcC---CC-CCCccCCCCCCEEEE
Confidence 4667899999875542 11 112446666665543
No 271
>PRK01310 hypothetical protein; Validated
Probab=31.29 E-value=1.1e+02 Score=23.39 Aligned_cols=40 Identities=30% Similarity=0.473 Sum_probs=29.4
Q ss_pred HHHHHHHHHhhcCcee-e-------cCCCeEEEEeeccHHHHHHHHHHHh
Q psy7490 81 KHLLDFLLAELGTSGS-V-------DGNSQLIIKGRFQQKQIENVLRRYI 122 (193)
Q Consensus 81 ~hv~ky~~~ELgt~g~-i-------d~~~~lii~G~~~~~~iq~~L~~yI 122 (193)
+++++||...||++-+ | ...-.+.|.| +++++.+.|..++
T Consensus 55 ~ali~~LA~~l~v~ks~I~iv~G~tsR~K~v~I~~--~~~~l~~~l~~~~ 102 (104)
T PRK01310 55 RALIELLAKALGVPKSSVRLLSGATSRLKQLRIDG--DPEDLGEALRALT 102 (104)
T ss_pred HHHHHHHHHHhCCChhhEEEEecCCCCceEEEEeC--CHHHHHHHHHHHh
Confidence 6899999999997532 2 1234667777 7888888888765
No 272
>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=31.23 E-value=24 Score=29.79 Aligned_cols=29 Identities=24% Similarity=0.631 Sum_probs=22.1
Q ss_pred ccCCCCCCcceeEe---cCceeeccccccccc
Q psy7490 127 TCHTCRSPDTILQK---DTRLFFLQCETCGSR 155 (193)
Q Consensus 127 lC~~C~sPdT~L~k---~~rl~~l~C~aCGa~ 155 (193)
.|-+|+.|-..|-+ .+.+--.+|+.||..
T Consensus 2 iCIeCg~~v~~Ly~~Ys~~~irLt~C~~C~~v 33 (208)
T PF04161_consen 2 ICIECGHPVKSLYRQYSPGNIRLTKCPNCGKV 33 (208)
T ss_pred EeccCCCcchhhhhccCCCcEEEeeccccCCc
Confidence 59999999766654 345667899999965
No 273
>PRK07219 DNA topoisomerase I; Validated
Probab=31.15 E-value=43 Score=34.09 Aligned_cols=33 Identities=18% Similarity=0.493 Sum_probs=20.3
Q ss_pred cccCCCCCCcceeEec-Cceeeccccc---cccccccc
Q psy7490 126 VTCHTCRSPDTILQKD-TRLFFLQCET---CGSRCSVA 159 (193)
Q Consensus 126 VlC~~C~sPdT~L~k~-~rl~~l~C~a---CGa~~~V~ 159 (193)
..||.|+++ ..+.+. ++-.|+.|.. |+...+++
T Consensus 603 ~~CP~Cg~~-l~~r~~~~g~~F~gCs~yp~C~~t~~lp 639 (822)
T PRK07219 603 GKCPECGGD-LIIIRTDKGSRFVGCSGYPDCRNTFPLP 639 (822)
T ss_pred CcCCCCCCc-ceeeeccCCceeeecCCCcCCCCeeecC
Confidence 469999974 333332 2225788866 88776654
No 274
>PF05315 ICEA: ICEA Protein; InterPro: IPR007979 This family consists of several ICEA proteins from Helicobacter pylori, infection of which causes gastritis and peptic ulcer disease, and the bacteria is classified as a definite carcinogen of gastric cancer. ICEA1 is speculated to be associated with peptic ulcer disease and may have endonuclease activity [].
Probab=31.09 E-value=31 Score=30.07 Aligned_cols=61 Identities=21% Similarity=0.343 Sum_probs=46.8
Q ss_pred CCChHHHHHHHHHhhcCc----eeecCCCeEEEEeeccHHHHHHHHHHHhhhc------cccCCCCCCc-ceeEe
Q psy7490 77 HRLPKHLLDFLLAELGTS----GSVDGNSQLIIKGRFQQKQIENVLRRYIKEY------VTCHTCRSPD-TILQK 140 (193)
Q Consensus 77 ~R~p~hv~ky~~~ELgt~----g~id~~~~lii~G~~~~~~iq~~L~~yI~~Y------VlC~~C~sPd-T~L~k 140 (193)
-|....+.|++--|++-. .+| +++.+||--+...++.-|++=|+.| |+|..|++.+ |.|..
T Consensus 45 cR~~SsLak~y~lEfdk~~~~gnsI---d~IRLnG~n~~~~fnq~Ir~dIk~~yk~q~Cvm~g~~g~sent~iei 116 (230)
T PF05315_consen 45 CRSSSSLAKEYILEFDKRQTSGNSI---DRIRLNGFNTEKVFNQNIRQDIKNYYKQQCCVMCGVRGNSENTKIEI 116 (230)
T ss_pred cCCchHHHHHhhcccccccCCCccH---HHHHHcCcCchhhhhhHHHHHHHHHHHhcCeeeecccCCCccceeee
Confidence 478888888888887743 224 3888999888888888888888776 7888888755 67754
No 275
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=30.86 E-value=32 Score=29.94 Aligned_cols=44 Identities=16% Similarity=0.510 Sum_probs=31.7
Q ss_pred HHHHHHHHHHhh--hccccCCCCCCcceeEecCceeecccccccccccccccc
Q psy7490 112 KQIENVLRRYIK--EYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVASIK 162 (193)
Q Consensus 112 ~~iq~~L~~yI~--~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~~~k 162 (193)
..++.++++-|. -.-.|..|+.-- ..|+..|..||+..++.++.
T Consensus 339 ~~~~~~~~~~~~~~p~~~c~~cg~~~-------~~~~~~c~~c~~~~~~~~~~ 384 (389)
T PRK11788 339 LLLRDLVGEQLKRKPRYRCRNCGFTA-------RTLYWHCPSCKAWETIKPIR 384 (389)
T ss_pred HHHHHHHHHHHhCCCCEECCCCCCCC-------ccceeECcCCCCccCcCCcc
Confidence 446666665553 223599999643 35899999999999998884
No 276
>KOG1603|consensus
Probab=30.83 E-value=1.2e+02 Score=20.99 Aligned_cols=40 Identities=15% Similarity=0.307 Sum_probs=31.4
Q ss_pred HHHHHHHHHhhcCc-eeec-CCCeEEEEeeccHHHHHHHHHH
Q psy7490 81 KHLLDFLLAELGTS-GSVD-GNSQLIIKGRFQQKQIENVLRR 120 (193)
Q Consensus 81 ~hv~ky~~~ELgt~-g~id-~~~~lii~G~~~~~~iq~~L~~ 120 (193)
..+.+.|..--|.. ..+| +++++++.|.+++..+.+.|.+
T Consensus 20 ~kV~~~l~~~~GV~~v~id~~~~kvtV~g~~~p~~vl~~l~k 61 (73)
T KOG1603|consen 20 RKVKRVLQKLKGVESVDIDIKKQKVTVKGNVDPVKLLKKLKK 61 (73)
T ss_pred HHHHHHhhccCCeEEEEecCCCCEEEEEEecCHHHHHHHHHh
Confidence 36777777777743 4577 4789999999999999998887
No 277
>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=30.57 E-value=60 Score=22.80 Aligned_cols=12 Identities=25% Similarity=0.883 Sum_probs=6.2
Q ss_pred ccEEEEEecccC
Q psy7490 169 TRLFFLQCETCG 180 (193)
Q Consensus 169 ~rl~~~~c~~Cg 180 (193)
.+.....|..||
T Consensus 73 ~~~l~~~C~~C~ 84 (85)
T PF04032_consen 73 KNFLVYTCLNCG 84 (85)
T ss_dssp S-EEEEEETTTT
T ss_pred CCEEEEEccccC
Confidence 445555666665
No 278
>PRK10767 chaperone protein DnaJ; Provisional
Probab=30.54 E-value=46 Score=30.38 Aligned_cols=35 Identities=29% Similarity=0.427 Sum_probs=20.6
Q ss_pred hhhccccCCCCCCcceeEecCceeecccccccccccccc
Q psy7490 122 IKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVAS 160 (193)
Q Consensus 122 I~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~~ 160 (193)
+...|.|+.|...-..- + .....|..|+-...|..
T Consensus 139 ~~r~~~C~~C~G~G~~~---~-~~~~~C~~C~G~G~~~~ 173 (371)
T PRK10767 139 IPTLVTCDTCHGSGAKP---G-TSPKTCPTCHGAGQVRM 173 (371)
T ss_pred eeecccCCCCCCcccCC---C-CCCccCCCCCCeeEEEE
Confidence 46689999998754321 1 11245777776665443
No 279
>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=30.48 E-value=31 Score=33.08 Aligned_cols=55 Identities=22% Similarity=0.492 Sum_probs=36.8
Q ss_pred ccCCCC--CCcceeE-ecCce--eeccccccccccccccccc-------ceeeeccEEEEEecccCC
Q psy7490 127 TCHTCR--SPDTILQ-KDTRL--FFLQCETCGSRCSVASIKS-------GFQKDTRLFFLQCETCGS 181 (193)
Q Consensus 127 lC~~C~--sPdT~L~-k~~rl--~~l~C~aCGa~~~V~~~k~-------~~~~~~rl~~~~c~~Cga 181 (193)
.||.|- -|-.... +.+|- -...|..|++.=.|.+... .-......|+|.|..|-=
T Consensus 28 yCp~CL~~~p~~e~~~~~nrC~r~Cf~CP~C~~~L~~~~~~~~~~~~~~~~~~~~~~~~l~C~~C~W 94 (483)
T PF05502_consen 28 YCPNCLFEVPSSEARSEKNRCSRNCFDCPICFSPLSVRASDTPPSPPDPSSDSGGKPYYLSCSYCRW 94 (483)
T ss_pred ECccccccCChhhheeccceeccccccCCCCCCcceeEecccccccccccccCCCCCEEEECCCcee
Confidence 688885 3544442 33442 3578999998877765543 224567899999999963
No 280
>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=30.40 E-value=29 Score=25.20 Aligned_cols=18 Identities=22% Similarity=0.549 Sum_probs=7.8
Q ss_pred eeccEEEEEecccCCCcc
Q psy7490 167 KDTRLFFLQCETCGSRCS 184 (193)
Q Consensus 167 ~~~rl~~~~c~~Cga~~~ 184 (193)
...+.|.|+|.||-.-.+
T Consensus 3 k~~k~~vlrC~aCf~~t~ 20 (73)
T PF08772_consen 3 KRVKTWVLRCHACFKITK 20 (73)
T ss_dssp -----EEEE-SSS--EES
T ss_pred chhheeeEEccccccCcC
Confidence 456789999999876544
No 281
>PRK12496 hypothetical protein; Provisional
Probab=30.31 E-value=33 Score=28.11 Aligned_cols=25 Identities=20% Similarity=0.259 Sum_probs=19.4
Q ss_pred cccceeeeccEEEEEecccCCCccc
Q psy7490 161 IKSGFQKDTRLFFLQCETCGSRCSV 185 (193)
Q Consensus 161 ~k~~~~~~~rl~~~~c~~Cga~~~v 185 (193)
+.+.-.+..+.|-..|.+||..++.
T Consensus 115 ~~~~~i~~~~~w~~~C~gC~~~~~~ 139 (164)
T PRK12496 115 IKTKGIKKVIKWRKVCKGCKKKYPE 139 (164)
T ss_pred cccccchhheeeeEECCCCCccccC
Confidence 3333467888999999999998864
No 282
>PF01807 zf-CHC2: CHC2 zinc finger; InterPro: IPR002694 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents CycHisCysCys (CHC2) type zinc finger domains, which are found in bacteria and viruses. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0003896 DNA primase activity, 0008270 zinc ion binding, 0006260 DNA replication; PDB: 1D0Q_B 2AU3_A.
Probab=30.24 E-value=47 Score=24.64 Aligned_cols=44 Identities=23% Similarity=0.376 Sum_probs=19.7
Q ss_pred ceeEecCceeecccccccccccccccccceeeeccEEEEEecccCCCccc
Q psy7490 136 TILQKDTRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRCSV 185 (193)
Q Consensus 136 T~L~k~~rl~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~~v 185 (193)
+.|.+.++-+...|.-|+..+|--.+ ...++ ..+|-+||+.-.+
T Consensus 23 ~~l~~~G~~~~~~CPfH~d~~pS~~i----~~~k~--~~~Cf~Cg~~Gd~ 66 (97)
T PF01807_consen 23 IKLKRRGREYRCLCPFHDDKTPSFSI----NPDKN--RFKCFGCGKGGDV 66 (97)
T ss_dssp S--EEETTEEEE--SSS--SS--EEE----ETTTT--EEEETTT--EE-H
T ss_pred ccccccCCeEEEECcCCCCCCCceEE----ECCCC--eEEECCCCCCCcH
Confidence 35777777777888888876642111 12233 3578888876543
No 283
>PHA02554 13 neck protein; Provisional
Probab=30.21 E-value=98 Score=28.37 Aligned_cols=41 Identities=29% Similarity=0.519 Sum_probs=33.3
Q ss_pred CCChHHHHHHHHHhhcCceeecCCCeEEEEeeccHHHHHHHHHHHhhhcc
Q psy7490 77 HRLPKHLLDFLLAELGTSGSVDGNSQLIIKGRFQQKQIENVLRRYIKEYV 126 (193)
Q Consensus 77 ~R~p~hv~ky~~~ELgt~g~id~~~~lii~G~~~~~~iq~~L~~yI~~YV 126 (193)
-++|+.|..|++.-||++ ||+=..++++|.+.|++=|+-|-
T Consensus 5 ~~sp~eLkD~iLRrLGAP---------ii~Ievt~dQi~D~I~rALely~ 45 (311)
T PHA02554 5 PNNPRELKDYILRRLGAP---------IINVEVTEDQIYDCIQRALELYG 45 (311)
T ss_pred CCCHHHHHHHHHHhcCCC---------eeEeecCHHHHHHHHHHHHHHHH
Confidence 368999999999999997 45566788888888887776663
No 284
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=30.02 E-value=1.6e+02 Score=19.45 Aligned_cols=45 Identities=7% Similarity=0.166 Sum_probs=30.0
Q ss_pred ccHHHHHHcCCChHHHHHHHHHhhcCcee-ecCCCeEEEEeeccHHHHHHH
Q psy7490 68 NFTEICKTLHRLPKHLLDFLLAELGTSGS-VDGNSQLIIKGRFQQKQIENV 117 (193)
Q Consensus 68 Nf~dIak~L~R~p~hv~ky~~~ELgt~g~-id~~~~lii~G~~~~~~iq~~ 117 (193)
...|+|+.++-++..|-+|... .|.... -+++|. -.|++++++.+
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~-~g~~~~~r~~~~~----r~yt~~~v~~l 47 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERR-YGLPAPQRTDGGH----RLYSEADVARL 47 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh-CCCCCCCcCCCCC----eecCHHHHHHH
Confidence 3679999999999999998753 343322 222222 25788888765
No 285
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=29.78 E-value=59 Score=22.04 Aligned_cols=36 Identities=22% Similarity=0.537 Sum_probs=25.9
Q ss_pred cccCCCCCCcceeEe---cCceeeccccccccccccccc
Q psy7490 126 VTCHTCRSPDTILQK---DTRLFFLQCETCGSRCSVASI 161 (193)
Q Consensus 126 VlC~~C~sPdT~L~k---~~rl~~l~C~aCGa~~~V~~~ 161 (193)
|.||-|+-+-+.++- .+.-++--|..|-.+-.+...
T Consensus 1 i~CPyCge~~~~~iD~s~~~Q~yiEDC~vCC~PI~~~v~ 39 (52)
T PF14255_consen 1 IQCPYCGEPIEILIDPSAGDQEYIEDCQVCCRPIEVQVT 39 (52)
T ss_pred CCCCCCCCeeEEEEecCCCCeeEEeehhhcCCccEEEEE
Confidence 579999987766553 345778889999888655433
No 286
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=29.73 E-value=1.3e+02 Score=28.40 Aligned_cols=32 Identities=19% Similarity=0.705 Sum_probs=26.3
Q ss_pred hccccCCCCCCcceeEecCceeeccccccccccccccccc
Q psy7490 124 EYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVASIKS 163 (193)
Q Consensus 124 ~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~~~k~ 163 (193)
.| .|..|+-- .+++|-+|.+|.++.+++|++.
T Consensus 354 ~Y-RC~~CGF~-------a~~l~W~CPsC~~W~TikPir~ 385 (389)
T COG2956 354 RY-RCQNCGFT-------AHTLYWHCPSCRAWETIKPIRG 385 (389)
T ss_pred Cc-eecccCCc-------ceeeeeeCCCcccccccCCccc
Confidence 35 89999953 3567899999999999999973
No 287
>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=29.65 E-value=34 Score=21.65 Aligned_cols=30 Identities=23% Similarity=0.442 Sum_probs=15.6
Q ss_pred ccccCCCCCCcceeEec-Cceeecccccccc
Q psy7490 125 YVTCHTCRSPDTILQKD-TRLFFLQCETCGS 154 (193)
Q Consensus 125 YVlC~~C~sPdT~L~k~-~rl~~l~C~aCGa 154 (193)
-+-||.|++-|.-=..+ ++.=--.|..||+
T Consensus 3 ~~pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 3 HGPCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred ccCCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 35688888877533332 1111234666654
No 288
>PRK14973 DNA topoisomerase I; Provisional
Probab=29.61 E-value=35 Score=35.43 Aligned_cols=31 Identities=16% Similarity=0.265 Sum_probs=16.9
Q ss_pred ccCCCCCCcceeEecCc-eeeccccccccccc
Q psy7490 127 TCHTCRSPDTILQKDTR-LFFLQCETCGSRCS 157 (193)
Q Consensus 127 lC~~C~sPdT~L~k~~r-l~~l~C~aCGa~~~ 157 (193)
.||.|++|--.+.+.+| =+|+-|..|....+
T Consensus 637 ~Cp~CG~p~~~~~r~Gr~g~fl~CP~C~~~~~ 668 (936)
T PRK14973 637 VCPIHHLNHVRLIRKGARPWDIGCPLCSHIES 668 (936)
T ss_pred CCCCCCCCceEEeecCCCcccccCccccchhh
Confidence 47777776333334433 24666666666544
No 289
>PRK14298 chaperone protein DnaJ; Provisional
Probab=29.55 E-value=43 Score=30.86 Aligned_cols=34 Identities=24% Similarity=0.457 Sum_probs=20.1
Q ss_pred hhhccccCCCCCCcceeEecCceeeccccccccccccc
Q psy7490 122 IKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVA 159 (193)
Q Consensus 122 I~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~ 159 (193)
+...|.|+.|...-+. .+ .....|..|+-...|.
T Consensus 138 ~~r~~~C~~C~G~G~~---~~-~~~~~C~~C~G~G~~~ 171 (377)
T PRK14298 138 VPRAERCSTCSGTGAK---PG-TSPKRCPTCGGTGQVT 171 (377)
T ss_pred EEeeccCCCCCCCccc---CC-CCCCcCCCCCCccEEE
Confidence 4567899999876542 11 1234577776665443
No 290
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=29.34 E-value=33 Score=24.84 Aligned_cols=29 Identities=21% Similarity=0.588 Sum_probs=16.9
Q ss_pred ccCCCCCCcceeEec------Cceeecccc--cccccc
Q psy7490 127 TCHTCRSPDTILQKD------TRLFFLQCE--TCGSRC 156 (193)
Q Consensus 127 lC~~C~sPdT~L~k~------~rl~~l~C~--aCGa~~ 156 (193)
.||.|++++ .+.+. -+-.|-.|. .||.+.
T Consensus 3 ~CP~Cg~~a-~irtSr~~s~~~~~~Y~qC~N~eCg~tF 39 (72)
T PRK09678 3 HCPLCQHAA-HARTSRYITDTTKERYHQCQNVNCSATF 39 (72)
T ss_pred cCCCCCCcc-EEEEChhcChhhheeeeecCCCCCCCEE
Confidence 478888877 33321 123366776 777664
No 291
>COG1149 MinD superfamily P-loop ATPase containing an inserted ferredoxin domain [Energy production and conversion]
Probab=29.25 E-value=27 Score=31.56 Aligned_cols=28 Identities=18% Similarity=0.143 Sum_probs=14.5
Q ss_pred HHHHHHHHhhcCc---eeec-CCCeEEEEeec
Q psy7490 82 HLLDFLLAELGTS---GSVD-GNSQLIIKGRF 109 (193)
Q Consensus 82 hv~ky~~~ELgt~---g~id-~~~~lii~G~~ 109 (193)
++..+|..++.+. .-+| .|..+++.+.-
T Consensus 21 ~la~~l~~~~~~~l~DcDVe~PNl~l~l~~e~ 52 (284)
T COG1149 21 NLAVLLGDKYKLVLADCDVEAPNLHLLLGVEV 52 (284)
T ss_pred HHHHHhccccceEEEecCCCCCCcceEeccch
Confidence 4455555552222 2244 37788887654
No 292
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=28.91 E-value=64 Score=24.72 Aligned_cols=28 Identities=18% Similarity=0.186 Sum_probs=25.3
Q ss_pred eccHHHHHHcCCChHHHHHHHHHhhcCc
Q psy7490 67 ANFTEICKTLHRLPKHLLDFLLAELGTS 94 (193)
Q Consensus 67 ~Nf~dIak~L~R~p~hv~ky~~~ELgt~ 94 (193)
.++.++|+.++-+|.++.+.|..++|.+
T Consensus 26 ~sl~~lA~~~g~S~~~l~r~Fk~~~G~s 53 (127)
T PRK11511 26 LSLEKVSERSGYSKWHLQRMFKKETGHS 53 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence 3467999999999999999999999975
No 293
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=28.73 E-value=31 Score=33.08 Aligned_cols=14 Identities=21% Similarity=0.795 Sum_probs=8.3
Q ss_pred eecccccccccccc
Q psy7490 145 FFLQCETCGSRCSV 158 (193)
Q Consensus 145 ~~l~C~aCGa~~~V 158 (193)
|.-+|..||+++++
T Consensus 20 W~GkCp~Cg~Wns~ 33 (456)
T COG1066 20 WLGKCPACGAWNTL 33 (456)
T ss_pred ccccCCCCCCccce
Confidence 55666666666554
No 294
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=28.73 E-value=52 Score=24.61 Aligned_cols=10 Identities=30% Similarity=0.846 Sum_probs=7.0
Q ss_pred cCCCCCCcce
Q psy7490 128 CHTCRSPDTI 137 (193)
Q Consensus 128 C~~C~sPdT~ 137 (193)
||.|++.++.
T Consensus 1 C~~C~~~~~~ 10 (127)
T TIGR03830 1 CPICGSGELV 10 (127)
T ss_pred CCCCCCccce
Confidence 8888776554
No 295
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=28.60 E-value=18 Score=24.65 Aligned_cols=16 Identities=19% Similarity=0.301 Sum_probs=9.0
Q ss_pred eccccccccccccccc
Q psy7490 146 FLQCETCGSRCSVASI 161 (193)
Q Consensus 146 ~l~C~aCGa~~~V~~~ 161 (193)
...|..|++++|.++-
T Consensus 14 kkIC~rC~Arnp~~A~ 29 (50)
T COG1552 14 KKICRRCYARNPPRAT 29 (50)
T ss_pred HHHHHHhcCCCCcchh
Confidence 3456666666655554
No 296
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=28.46 E-value=41 Score=21.67 Aligned_cols=29 Identities=17% Similarity=0.427 Sum_probs=17.1
Q ss_pred ccccCCCCCCcceeEecCceeeccccccc
Q psy7490 125 YVTCHTCRSPDTILQKDTRLFFLQCETCG 153 (193)
Q Consensus 125 YVlC~~C~sPdT~L~k~~rl~~l~C~aCG 153 (193)
.|.|+.|+++=+.-...++..+..|...-
T Consensus 5 ~l~C~~CG~~m~~~~~~~~~~yy~C~~~~ 33 (58)
T PF13408_consen 5 LLRCGHCGSKMTRRKRKGKYRYYRCSNRR 33 (58)
T ss_pred cEEcccCCcEeEEEECCCCceEEEcCCCc
Confidence 46777777765554444444566666554
No 297
>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=28.39 E-value=34 Score=29.06 Aligned_cols=37 Identities=16% Similarity=0.432 Sum_probs=24.9
Q ss_pred ceeEecCceeecccccccccccccccccceeeeccEEEEEecccCC
Q psy7490 136 TILQKDTRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGS 181 (193)
Q Consensus 136 T~L~k~~rl~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga 181 (193)
-.+.-.+.+..++|..|+...+..... + ..+|..||+
T Consensus 108 ~v~elHG~~~~~~C~~C~~~~~~~~~~-------~--~p~C~~Cgg 144 (225)
T cd01411 108 NVVEFHGSLYRIYCTVCGKTVDWEEYL-------K--SPYHAKCGG 144 (225)
T ss_pred cEEEeCCCcCeeEeCCCCCccchhhcC-------C--CCCCCCCCC
Confidence 355567888889999998765443221 1 257999986
No 298
>PF13098 Thioredoxin_2: Thioredoxin-like domain; PDB: 1T3B_A 2L57_A 1EEJ_B 1TJD_A 1JZD_B 1JZO_A 1G0T_B 3GV1_A 1V58_A 2H0H_A ....
Probab=28.38 E-value=71 Score=22.85 Aligned_cols=35 Identities=20% Similarity=0.397 Sum_probs=21.9
Q ss_pred HHHHHHhhcCcee-----ecCCCeE--EEEeeccHHHHHHHH
Q psy7490 84 LDFLLAELGTSGS-----VDGNSQL--IIKGRFQQKQIENVL 118 (193)
Q Consensus 84 ~ky~~~ELgt~g~-----id~~~~l--ii~G~~~~~~iq~~L 118 (193)
.+-+...+|..|+ +|++|+. .+.|-.++++|.++|
T Consensus 71 ~~~l~~~~~v~gtPt~~~~d~~G~~v~~~~G~~~~~~l~~~L 112 (112)
T PF13098_consen 71 NKELAQRYGVNGTPTIVFLDKDGKIVYRIPGYLSPEELLKML 112 (112)
T ss_dssp HHHHHHHTT--SSSEEEECTTTSCEEEEEESS--HHHHHHHH
T ss_pred HHHHHHHcCCCccCEEEEEcCCCCEEEEecCCCCHHHHHhhC
Confidence 3457777777665 5656653 478999999999876
No 299
>PF12728 HTH_17: Helix-turn-helix domain
Probab=27.67 E-value=1.6e+02 Score=18.51 Aligned_cols=47 Identities=9% Similarity=0.094 Sum_probs=30.0
Q ss_pred eccHHHHHHcCCChHHHHHHHHHhhcCceeecCCCeEEEEeeccHHHHHHHHH
Q psy7490 67 ANFTEICKTLHRLPKHLLDFLLAELGTSGSVDGNSQLIIKGRFQQKQIENVLR 119 (193)
Q Consensus 67 ~Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id~~~~lii~G~~~~~~iq~~L~ 119 (193)
.+..|+|+.|+-++..+.+++...---...+ +++. .+..++|++.|+
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g~i~~~~~--g~~~----~~~~~~l~~~~~ 48 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQGKIPPFKI--GRKW----RIPKSDLDRWLE 48 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCCCeEEe--CCEE----EEeHHHHHHHHH
Confidence 4678999999999999999985442211111 1122 356666666554
No 300
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=27.66 E-value=51 Score=25.63 Aligned_cols=33 Identities=18% Similarity=0.478 Sum_probs=21.0
Q ss_pred ccCCCCCC---ccee--EecCceeeccccccccccccc
Q psy7490 127 TCHTCRSP---DTIL--QKDTRLFFLQCETCGSRCSVA 159 (193)
Q Consensus 127 lC~~C~sP---dT~L--~k~~rl~~l~C~aCGa~~~V~ 159 (193)
.|+.|.+| --.. .-+++...+.|..||...-.+
T Consensus 58 ~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~~R~p 95 (105)
T COG2023 58 ICKKCYTPLVPGKNARVRLRKGRVVVTCLECGTIRRYP 95 (105)
T ss_pred hccccCcccccCcceEEEEcCCeEEEEecCCCcEEEec
Confidence 69999984 3322 223443578999999875443
No 301
>PRK05333 NAD-dependent deacetylase; Provisional
Probab=27.61 E-value=21 Score=31.49 Aligned_cols=23 Identities=30% Similarity=0.564 Sum_probs=18.0
Q ss_pred eeEecCceeeccccccccccccc
Q psy7490 137 ILQKDTRLFFLQCETCGSRCSVA 159 (193)
Q Consensus 137 ~L~k~~rl~~l~C~aCGa~~~V~ 159 (193)
.+.-.+.+..++|..|+...+..
T Consensus 119 ViElHG~~~~~~C~~C~~~~~~~ 141 (285)
T PRK05333 119 VIELHGRLDGVRCMGCGARHPRA 141 (285)
T ss_pred EEeecCCcCEEEECCCCCcCCHH
Confidence 45567889999999999876644
No 302
>PRK07562 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=27.59 E-value=33 Score=36.68 Aligned_cols=11 Identities=55% Similarity=1.189 Sum_probs=6.7
Q ss_pred EEEEecccCCC
Q psy7490 172 FFLQCETCGSR 182 (193)
Q Consensus 172 ~~~~c~~Cga~ 182 (193)
..++|++||+.
T Consensus 1206 tc~~c~~cg~t 1216 (1220)
T PRK07562 1206 TCLKCDTCGST 1216 (1220)
T ss_pred eeeeccccCCC
Confidence 45666666654
No 303
>PRK14282 chaperone protein DnaJ; Provisional
Probab=27.58 E-value=54 Score=29.98 Aligned_cols=34 Identities=18% Similarity=0.458 Sum_probs=20.7
Q ss_pred hhhccccCCCCCCcceeEecCceeeccccccccccccc
Q psy7490 122 IKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVA 159 (193)
Q Consensus 122 I~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~ 159 (193)
+...|+|+.|...-.. .+ .-...|..|+-...|.
T Consensus 149 ~~r~~~C~~C~G~G~~---~~-~~~~~C~~C~G~G~~~ 182 (369)
T PRK14282 149 YDRYETCPHCGGTGVE---PG-SGYVTCPKCHGTGRIR 182 (369)
T ss_pred eeecccCCCCCccCCC---CC-CCCcCCCCCCCcCEEE
Confidence 4667899999875542 11 1124677777666543
No 304
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=27.55 E-value=99 Score=22.29 Aligned_cols=45 Identities=16% Similarity=0.147 Sum_probs=32.7
Q ss_pred ccHHHHHHcCCChHHHHHHHHHhhcCceeecCCCeEEEEeeccHHHHHHH
Q psy7490 68 NFTEICKTLHRLPKHLLDFLLAELGTSGSVDGNSQLIIKGRFQQKQIENV 117 (193)
Q Consensus 68 Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id~~~~lii~G~~~~~~iq~~ 117 (193)
+..|+|+.++-+|..|-.|....+-.+ ..+++|+. .|+.++|..+
T Consensus 2 ~~~eva~~~gi~~~tlr~~~~~Gll~~-~~~~~g~r----~y~~~dv~~l 46 (100)
T cd00592 2 TIGEVAKLLGVSVRTLRYYEEKGLLPP-ERSENGYR----LYSEEDLERL 46 (100)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCCCcCC-CcCCCCCc----ccCHHHHHHH
Confidence 568999999999999999987766543 33333333 4788888764
No 305
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=27.46 E-value=33 Score=28.72 Aligned_cols=71 Identities=21% Similarity=0.430 Sum_probs=37.8
Q ss_pred cCCChHHHHHHHHHhhcCceeecCCCeEEEEeeccHHHHHHHHHHH------hhhccccCCCCCCcceeEecC---c---
Q psy7490 76 LHRLPKHLLDFLLAELGTSGSVDGNSQLIIKGRFQQKQIENVLRRY------IKEYVTCHTCRSPDTILQKDT---R--- 143 (193)
Q Consensus 76 L~R~p~hv~ky~~~ELgt~g~id~~~~lii~G~~~~~~iq~~L~~y------I~~YVlC~~C~sPdT~L~k~~---r--- 143 (193)
|-||-+.+.+. .+|..+.+ |.-....+++-.+|..+ -.++-.||.|+.|=-.+.++. +
T Consensus 52 lTRDr~L~~r~---k~g~~~i~-------i~~~s~~~Ql~e~~~~~~l~~~~~~e~~RCp~CN~~L~~vs~eev~~~Vp~ 121 (165)
T COG1656 52 LTRDRELYKRA---KLGIKAIL-------IRSDSIEEQLAEFLARLGLKPRLFPEFSRCPECNGELEKVSREEVKEKVPE 121 (165)
T ss_pred EeccHHHHHHh---hccCceEE-------EeCCCHHHHHHHHHHHhccchhcccccccCcccCCEeccCcHHHHhhccch
Confidence 45776666555 55554433 22233344444443321 134889999987644443321 1
Q ss_pred ------eeecccccccccc
Q psy7490 144 ------LFFLQCETCGSRC 156 (193)
Q Consensus 144 ------l~~l~C~aCGa~~ 156 (193)
-.+-.|..||...
T Consensus 122 ~~~~~~~~f~~C~~CgkiY 140 (165)
T COG1656 122 KVYRNYEEFYRCPKCGKIY 140 (165)
T ss_pred hhhhcccceeECCCCcccc
Confidence 1256688887654
No 306
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=27.23 E-value=25 Score=25.06 Aligned_cols=9 Identities=22% Similarity=0.534 Sum_probs=5.7
Q ss_pred ccccccccc
Q psy7490 148 QCETCGSRC 156 (193)
Q Consensus 148 ~C~aCGa~~ 156 (193)
.|..||+..
T Consensus 19 ~Cp~Cgs~~ 27 (64)
T PRK06393 19 TCPVHGDEK 27 (64)
T ss_pred cCCCCCCCc
Confidence 566666654
No 307
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, 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 []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=27.20 E-value=81 Score=20.09 Aligned_cols=24 Identities=17% Similarity=0.133 Sum_probs=18.6
Q ss_pred eccHHHHHHcCCChHHHHHHHHHh
Q psy7490 67 ANFTEICKTLHRLPKHLLDFLLAE 90 (193)
Q Consensus 67 ~Nf~dIak~L~R~p~hv~ky~~~E 90 (193)
..+.|||+.|+.++.-+.+.+..-
T Consensus 27 ~s~~eIa~~l~~s~~~v~~~l~ra 50 (54)
T PF08281_consen 27 MSYAEIAEILGISESTVKRRLRRA 50 (54)
T ss_dssp --HHHHHHHCTS-HHHHHHHHHHH
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHH
Confidence 457899999999999999888654
No 308
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=27.19 E-value=97 Score=24.49 Aligned_cols=39 Identities=26% Similarity=0.571 Sum_probs=26.2
Q ss_pred HHhhhccccCCCCCCcceeEec---Cceeeccccccccccccc
Q psy7490 120 RYIKEYVTCHTCRSPDTILQKD---TRLFFLQCETCGSRCSVA 159 (193)
Q Consensus 120 ~yI~~YVlC~~C~sPdT~L~k~---~rl~~l~C~aCGa~~~V~ 159 (193)
.....-+-||-|++.. ..... .+.---+|..|++...+.
T Consensus 25 ~~~~~~~~cP~C~s~~-~~k~g~~~~~~qRyrC~~C~~tf~~~ 66 (129)
T COG3677 25 RMQITKVNCPRCKSSN-VVKIGGIRRGHQRYKCKSCGSTFTVE 66 (129)
T ss_pred hhhcccCcCCCCCccc-eeeECCccccccccccCCcCcceeee
Confidence 3444558999999999 33332 224456899999887654
No 309
>PF07496 zf-CW: CW-type Zinc Finger; InterPro: IPR011124 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 CW-type zinc finger motif, named for its conserved cysteine and tryptophan residues. It is predicted to be a highly specialised mononuclear four-cysteine (C4) zinc finger that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including chromatin methylation status and early embryonic development. Weak homology to members of IPR001965 from INTERPRO further evidences these predictions. The domain is found exclusively in vertebrates, vertebrate-infecting parasites and higher plants []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2RR4_A 2E61_A 2L7P_A.
Probab=27.18 E-value=30 Score=22.81 Aligned_cols=15 Identities=20% Similarity=0.760 Sum_probs=8.9
Q ss_pred EEEEecccCCCcccc
Q psy7490 172 FFLQCETCGSRCSVA 186 (193)
Q Consensus 172 ~~~~c~~Cga~~~v~ 186 (193)
+.++|..|+.+|.|.
T Consensus 2 ~WVQCd~C~KWR~lp 16 (50)
T PF07496_consen 2 YWVQCDSCLKWRRLP 16 (50)
T ss_dssp EEEE-TTT--EEEE-
T ss_pred eEEECCCCCceeeCC
Confidence 357899999999885
No 310
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=27.10 E-value=24 Score=21.87 Aligned_cols=11 Identities=45% Similarity=1.192 Sum_probs=6.7
Q ss_pred hccccCCCCCC
Q psy7490 124 EYVTCHTCRSP 134 (193)
Q Consensus 124 ~YVlC~~C~sP 134 (193)
.||.|+.|+.+
T Consensus 3 ~~~~C~nC~R~ 13 (33)
T PF08209_consen 3 PYVECPNCGRP 13 (33)
T ss_dssp -EEE-TTTSSE
T ss_pred CeEECCCCcCC
Confidence 47788888764
No 311
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=26.80 E-value=1.1e+02 Score=21.87 Aligned_cols=25 Identities=8% Similarity=0.393 Sum_probs=22.8
Q ss_pred CCCeEEEEeeccHHHHHHHHHHHhh
Q psy7490 99 GNSQLIIKGRFQQKQIENVLRRYIK 123 (193)
Q Consensus 99 ~~~~lii~G~~~~~~iq~~L~~yI~ 123 (193)
.+|++++.|.-+.++++..+++++.
T Consensus 56 ~sGki~itGaks~~~~~~a~~~i~~ 80 (86)
T PF00352_consen 56 SSGKIVITGAKSEEEAKKAIEKILP 80 (86)
T ss_dssp TTSEEEEEEESSHHHHHHHHHHHHH
T ss_pred cCCEEEEEecCCHHHHHHHHHHHHH
Confidence 5899999999999999999998865
No 312
>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=26.68 E-value=27 Score=23.70 Aligned_cols=24 Identities=33% Similarity=0.827 Sum_probs=15.1
Q ss_pred hccccCCCCCCcceeEecCceeeccccccccc
Q psy7490 124 EYVTCHTCRSPDTILQKDTRLFFLQCETCGSR 155 (193)
Q Consensus 124 ~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~ 155 (193)
..+.|+.|+.+ .+-...|..||.-
T Consensus 25 ~l~~c~~cg~~--------~~~H~vc~~cG~y 48 (56)
T PF01783_consen 25 NLVKCPNCGEP--------KLPHRVCPSCGYY 48 (56)
T ss_dssp SEEESSSSSSE--------ESTTSBCTTTBBS
T ss_pred ceeeeccCCCE--------ecccEeeCCCCeE
Confidence 46778888853 2334567777743
No 313
>KOG1597|consensus
Probab=26.26 E-value=40 Score=30.83 Aligned_cols=29 Identities=31% Similarity=0.606 Sum_probs=21.1
Q ss_pred ccCCCCC-CcceeEecCceeecccccccccc
Q psy7490 127 TCHTCRS-PDTILQKDTRLFFLQCETCGSRC 156 (193)
Q Consensus 127 lC~~C~s-PdT~L~k~~rl~~l~C~aCGa~~ 156 (193)
.|+.|+. |+ .++.+-+--...|..||-.-
T Consensus 2 ~c~~C~~~~~-~~V~d~~~gdtvC~~CGlVl 31 (308)
T KOG1597|consen 2 TCPDCKRHPE-NLVEDHSAGDTVCSECGLVL 31 (308)
T ss_pred CCCCCCCCCC-CeeeeccCCceecccCCeee
Confidence 5899997 55 67766555567899999654
No 314
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=26.17 E-value=94 Score=30.19 Aligned_cols=46 Identities=17% Similarity=0.366 Sum_probs=22.1
Q ss_pred EEEEeeccHHHHHHHHHHHhhh-----------ccccCCCCCCcceeEecCceeecccccccccc
Q psy7490 103 LIIKGRFQQKQIENVLRRYIKE-----------YVTCHTCRSPDTILQKDTRLFFLQCETCGSRC 156 (193)
Q Consensus 103 lii~G~~~~~~iq~~L~~yI~~-----------YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~ 156 (193)
+-+--+.+++.+++++++=.+. +-.|+.|+.-+. + .-.|..||++.
T Consensus 458 v~l~e~~n~~al~~lv~~~~~~~~i~Y~~in~~~~~C~~CG~~~~------~--~~~CP~CGs~~ 514 (546)
T PF13597_consen 458 VELGEKPNPEALEKLVRYAMENTGIPYFTINPPIDICPDCGYIGG------E--GDKCPKCGSEN 514 (546)
T ss_dssp EE----T-HHHHHHHHHHHHH--H-SEEEEE--EEEETTT---S----------EEE-CCC----
T ss_pred EEcCCCCCHHHHHHHHHHHHHhCCCCeEEEecCcccccCCCcCCC------C--CCCCCCCCCcc
Confidence 3343366788999988887772 347888886332 2 45688888884
No 315
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=25.93 E-value=1.1e+02 Score=30.39 Aligned_cols=40 Identities=15% Similarity=0.497 Sum_probs=27.2
Q ss_pred ccHHHHHHHHHHHhh----------hccccCCCCCCcceeEecCceeecccccccccc
Q psy7490 109 FQQKQIENVLRRYIK----------EYVTCHTCRSPDTILQKDTRLFFLQCETCGSRC 156 (193)
Q Consensus 109 ~~~~~iq~~L~~yI~----------~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~ 156 (193)
.+++.+.++++..-+ .+-.|++|+. .-.+ .-.|..||+..
T Consensus 533 ~n~~Al~~lvk~~~~~~i~Y~sin~~~~~C~~CGy-~g~~-------~~~CP~CG~~d 582 (618)
T PRK14704 533 HNKKALKQIVQAMAEHGVGYGSINHPVDRCKCCSY-HGVI-------GNECPSCGNED 582 (618)
T ss_pred CCHHHHHHHHHHHHhcCCceEEeCCCCeecCCCCC-CCCc-------CccCcCCCCCC
Confidence 588999999988444 1346888885 2121 26788888764
No 316
>PTZ00410 NAD-dependent SIR2; Provisional
Probab=25.89 E-value=32 Score=31.84 Aligned_cols=48 Identities=15% Similarity=0.388 Sum_probs=30.5
Q ss_pred CCCCc-ceeEecCceeecccccccccccccccccceeeeccEEEEEecccCC
Q psy7490 131 CRSPD-TILQKDTRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGS 181 (193)
Q Consensus 131 C~sPd-T~L~k~~rl~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga 181 (193)
.+.|. -.+.-.+.+..++|..|+...+........... . .-+|..||.
T Consensus 131 AG~~~~~ViElHGsl~~~~C~~C~~~~~~~~~~~~~~~~-~--vP~C~~CgG 179 (349)
T PTZ00410 131 AGVPPSLLVEAHGSFSAASCIECHTPYDIEQAYLEARSG-K--VPHCSTCGG 179 (349)
T ss_pred cCCCcccEEEeccCCCeeEeCCCCCCcchhHHHHHhhcC-C--CCCCCCCCC
Confidence 56664 455568999999999999776554332111111 1 357999985
No 317
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=25.81 E-value=2e+02 Score=19.15 Aligned_cols=46 Identities=15% Similarity=0.180 Sum_probs=30.4
Q ss_pred ccHHHHHHcCCChHHHHHHHHHhhcCceeecCCCeEEEEeeccHHHHHHHH
Q psy7490 68 NFTEICKTLHRLPKHLLDFLLAELGTSGSVDGNSQLIIKGRFQQKQIENVL 118 (193)
Q Consensus 68 Nf~dIak~L~R~p~hv~ky~~~ELgt~g~id~~~~lii~G~~~~~~iq~~L 118 (193)
+..|+|+.++-+|..|-.|-. +.+....-+++|+ -.|+.++|+.+.
T Consensus 2 ~i~evA~~~gvs~~tlR~~~~-~g~l~~~~~~~g~----R~y~~~~l~~l~ 47 (67)
T cd04764 2 TIKEVSEIIGVKPHTLRYYEK-EFNLYIPRTENGR----RYYTDEDIELLK 47 (67)
T ss_pred CHHHHHHHHCcCHHHHHHHHH-hcCCCCCCCCCCc----eeeCHHHHHHHH
Confidence 468999999999998887744 3333332333333 248888888653
No 318
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=25.75 E-value=36 Score=28.87 Aligned_cols=22 Identities=36% Similarity=0.827 Sum_probs=13.2
Q ss_pred cccCCCCCCcceeEecCceeeccccccccc
Q psy7490 126 VTCHTCRSPDTILQKDTRLFFLQCETCGSR 155 (193)
Q Consensus 126 VlC~~C~sPdT~L~k~~rl~~l~C~aCGa~ 155 (193)
..|+.|+. ...|. ..|..||..
T Consensus 310 ~~C~~cg~------~~~r~--~~C~~cg~~ 331 (364)
T COG0675 310 KTCPCCGH------LSGRL--FKCPRCGFV 331 (364)
T ss_pred ccccccCC------cccee--EECCCCCCe
Confidence 46777777 22333 467777764
No 319
>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=25.67 E-value=34 Score=28.74 Aligned_cols=42 Identities=19% Similarity=0.438 Sum_probs=26.3
Q ss_pred cceeEecCceeecccccccccccccccccceeeeccEEEEEecccCCC
Q psy7490 135 DTILQKDTRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSR 182 (193)
Q Consensus 135 dT~L~k~~rl~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~ 182 (193)
+-.+.-.+.+..++|..|+........ ...-..-+|..||+.
T Consensus 98 ~~v~e~HG~~~~~~C~~C~~~~~~~~~------~~~~~~p~C~~Cgg~ 139 (224)
T cd01412 98 RNVIELHGSLFRVRCSSCGYVGENNEE------IPEEELPRCPKCGGL 139 (224)
T ss_pred CceEeeCCCcCccccCCCCCCCCcchh------hhccCCCCCCCCCCc
Confidence 445556788888999999877544311 011124679999864
No 320
>KOG3084|consensus
Probab=25.64 E-value=59 Score=30.11 Aligned_cols=24 Identities=25% Similarity=0.636 Sum_probs=19.2
Q ss_pred HHHHHHHHHhhhccccCCCCCCcc
Q psy7490 113 QIENVLRRYIKEYVTCHTCRSPDT 136 (193)
Q Consensus 113 ~iq~~L~~yI~~YVlC~~C~sPdT 136 (193)
-.-..+-+++..|-.||.|++|--
T Consensus 138 a~ars~l~W~skykFCp~CG~~tk 161 (345)
T KOG3084|consen 138 AVARSLLDWVSKYKFCPGCGSPTK 161 (345)
T ss_pred HHHHHHHHHHHHhccCcccCCCcc
Confidence 344567788999999999999853
No 321
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=25.59 E-value=31 Score=29.56 Aligned_cols=30 Identities=20% Similarity=0.409 Sum_probs=19.2
Q ss_pred ccCCCCCCcceeEe-cCceeecccccccccc
Q psy7490 127 TCHTCRSPDTILQK-DTRLFFLQCETCGSRC 156 (193)
Q Consensus 127 lC~~C~sPdT~L~k-~~rl~~l~C~aCGa~~ 156 (193)
+|+.|---+..|.. .+++....|..||+..
T Consensus 15 lC~~C~~~~~~i~ei~~~i~v~~C~~Cg~~~ 45 (236)
T PF04981_consen 15 LCPDCYLKRFDIIEIPDRIEVTICPKCGRYR 45 (236)
T ss_pred cChHHhcccCCeeecCCccCceECCCCCCEE
Confidence 66666666665544 4556667777777764
No 322
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=25.32 E-value=56 Score=20.50 Aligned_cols=27 Identities=22% Similarity=0.223 Sum_probs=17.4
Q ss_pred eccHHHHHHcCCChHHHHHHHHH--hhcC
Q psy7490 67 ANFTEICKTLHRLPKHLLDFLLA--ELGT 93 (193)
Q Consensus 67 ~Nf~dIak~L~R~p~hv~ky~~~--ELgt 93 (193)
.+..+||+.|+.++..|.+++.. +-|.
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~kr~~~~G~ 46 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIKRYREEGL 46 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT-------
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHcccccc
Confidence 34689999999999999999854 4554
No 323
>PRK14278 chaperone protein DnaJ; Provisional
Probab=25.24 E-value=55 Score=30.09 Aligned_cols=36 Identities=28% Similarity=0.625 Sum_probs=20.8
Q ss_pred hhhccccCCCCCCcceeEecCceeeccccccccccccccc
Q psy7490 122 IKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVASI 161 (193)
Q Consensus 122 I~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~~~ 161 (193)
+...+.|+.|+..-+. .+ .....|..|+-...+...
T Consensus 136 ~~~~~~C~~C~G~G~~---~~-~~~~~C~~C~G~G~~~~~ 171 (378)
T PRK14278 136 VDTAVLCDRCHGKGTA---GD-SKPVTCDTCGGRGEVQTV 171 (378)
T ss_pred EEeeccCCCCcCccCC---CC-CCceecCCccCceEEEEE
Confidence 4667899999875542 11 122457777666644433
No 324
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=24.89 E-value=61 Score=30.33 Aligned_cols=56 Identities=16% Similarity=0.275 Sum_probs=31.2
Q ss_pred eEEEEeeccHHHHHHHHHHHhhhccccCCCCCCcceeEecCceeeccccccccccccccc
Q psy7490 102 QLIIKGRFQQKQIENVLRRYIKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVASI 161 (193)
Q Consensus 102 ~lii~G~~~~~~iq~~L~~yI~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~~~ 161 (193)
++.|.=.|...-.-.-..-=+...+.|+.|+.--. +.+.--..|..|+-...|...
T Consensus 119 ~~~l~isleEa~~G~~~~i~~~~~~~C~~C~GsGa----k~gt~~~tC~tC~G~G~v~~~ 174 (371)
T COG0484 119 RYNLEITLEEAVFGVKKEIRVTRSVTCSTCHGSGA----KPGTDPKTCPTCNGSGQVRTV 174 (371)
T ss_pred EEEEEeEhhhhccCceeeEecceeeECCcCCCCCC----CCCCCCCcCCCCCCcCeEEEE
Confidence 44444444443332222233577899999986311 111234788888888766544
No 325
>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=24.75 E-value=29 Score=29.39 Aligned_cols=44 Identities=23% Similarity=0.508 Sum_probs=28.3
Q ss_pred cceeEecCceeecccccccccccccccccceeeeccEEEEEecccCCC
Q psy7490 135 DTILQKDTRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSR 182 (193)
Q Consensus 135 dT~L~k~~rl~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~ 182 (193)
+-.+.-.+.+..++|..|+...+...+.. +.. . -.-+|..||+.
T Consensus 102 ~~v~elHG~l~~~~C~~C~~~~~~~~~~~-~~~--~-~~p~C~~Cgg~ 145 (222)
T cd01413 102 KNVIELHGTLQTAYCVNCGSKYDLEEVKY-AKK--H-EVPRCPKCGGI 145 (222)
T ss_pred CcEEEccCCcCcceECCCCCCcchhHHHH-hcc--C-CCCcCCCCCCc
Confidence 34556678888999999998776654421 111 1 13579999863
No 326
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=24.74 E-value=57 Score=28.14 Aligned_cols=41 Identities=20% Similarity=0.393 Sum_probs=26.9
Q ss_pred eeeccccccccccccc--ccccceeeeccEEEEEecccCCCcc
Q psy7490 144 LFFLQCETCGSRCSVA--SIKSGFQKDTRLFFLQCETCGSRCS 184 (193)
Q Consensus 144 l~~l~C~aCGa~~~V~--~~k~~~~~~~rl~~~~c~~Cga~~~ 184 (193)
...+.|..||+.--.- ....-|....=+....|+.||-+.+
T Consensus 12 ~~~~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~ 54 (201)
T COG1779 12 ETRIDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGYRST 54 (201)
T ss_pred eeeecCCcccceeeEEEeeecCCccceEEEEEEEccccCCccc
Confidence 3467899999932111 1123445566678899999998764
No 327
>PRK07726 DNA topoisomerase III; Provisional
Probab=24.73 E-value=90 Score=30.95 Aligned_cols=8 Identities=38% Similarity=1.194 Sum_probs=5.7
Q ss_pred ccCCCCCC
Q psy7490 127 TCHTCRSP 134 (193)
Q Consensus 127 lC~~C~sP 134 (193)
.||.|+.+
T Consensus 612 ~CP~C~~~ 619 (658)
T PRK07726 612 KCPDCGKP 619 (658)
T ss_pred cccccCcc
Confidence 48888765
No 328
>TIGR01051 topA_bact DNA topoisomerase I, bacterial. This model describes DNA topoisomerase I among the members of bacteria. DNA topoisomerase I transiently cleaves one DNA strand and thus relaxes negatively supercoiled DNA during replication, transcription and recombination events.
Probab=24.65 E-value=70 Score=31.41 Aligned_cols=23 Identities=17% Similarity=0.160 Sum_probs=13.4
Q ss_pred EEEeeccHHHHHHHHHHHhhhcc
Q psy7490 104 IIKGRFQQKQIENVLRRYIKEYV 126 (193)
Q Consensus 104 ii~G~~~~~~iq~~L~~yI~~YV 126 (193)
|-.|+.+.+++-+-+.+++.+.|
T Consensus 537 I~~G~~~~~~~l~~~~~~~~~~v 559 (610)
T TIGR01051 537 IAEGKAEWKPVLKNFYTGFSSKV 559 (610)
T ss_pred HHcCCCCHHHHHHHHHHHHHHHH
Confidence 33577777666655555555444
No 329
>PF10825 DUF2752: Protein of unknown function (DUF2752); InterPro: IPR021215 This family is conserved in bacteria. Many members are annotated as being putative membrane proteins.
Probab=24.62 E-value=11 Score=25.22 Aligned_cols=19 Identities=21% Similarity=0.450 Sum_probs=12.4
Q ss_pred EEEEEecccCCCccccccc
Q psy7490 171 LFFLQCETCGSRCSVASIK 189 (193)
Q Consensus 171 l~~~~c~~Cga~~~v~~~~ 189 (193)
++-+.|.+||..|++..+-
T Consensus 7 ltG~~CPgCG~tRa~~~ll 25 (52)
T PF10825_consen 7 LTGIPCPGCGMTRAFIALL 25 (52)
T ss_pred hhCCCCCCCcHHHHHHHHH
Confidence 4445677888777775543
No 330
>PRK12366 replication factor A; Reviewed
Probab=24.56 E-value=45 Score=32.96 Aligned_cols=35 Identities=20% Similarity=0.579 Sum_probs=21.8
Q ss_pred ecCceeecccccccccccccccccceeeeccEEEEEecccCCCccc
Q psy7490 140 KDTRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRCSV 185 (193)
Q Consensus 140 k~~rl~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~~v 185 (193)
+++..+|-.|..|+..= +...+.| +|+.||...|.
T Consensus 526 ~~~~~~y~aCp~CnkKv---------~~~~g~~--~C~~c~~~~p~ 560 (637)
T PRK12366 526 RKQKIILYLCPNCRKRV---------EEVDGEY--ICEFCGEVEPN 560 (637)
T ss_pred eCCCEEEecccccCeEe---------EcCCCcE--ECCCCCCCCCc
Confidence 35677888898885531 1122333 58888876554
No 331
>smart00717 SANT SANT SWI3, ADA2, N-CoR and TFIIIB'' DNA-binding domains.
Probab=24.44 E-value=1e+02 Score=18.13 Aligned_cols=24 Identities=21% Similarity=0.194 Sum_probs=19.5
Q ss_pred eccHHHHHHcC-CChHHHHHHHHHh
Q psy7490 67 ANFTEICKTLH-RLPKHLLDFLLAE 90 (193)
Q Consensus 67 ~Nf~dIak~L~-R~p~hv~ky~~~E 90 (193)
.|+..||+.|. |.+..+..++..-
T Consensus 22 ~~w~~Ia~~~~~rt~~~~~~~~~~~ 46 (49)
T smart00717 22 NNWEKIAKELPGRTAEQCRERWNNL 46 (49)
T ss_pred CCHHHHHHHcCCCCHHHHHHHHHHH
Confidence 57889999998 9999888887543
No 332
>PRK13501 transcriptional activator RhaR; Provisional
Probab=24.38 E-value=78 Score=27.09 Aligned_cols=28 Identities=14% Similarity=0.368 Sum_probs=26.2
Q ss_pred eccHHHHHHcCCChHHHHHHHHHhhcCc
Q psy7490 67 ANFTEICKTLHRLPKHLLDFLLAELGTS 94 (193)
Q Consensus 67 ~Nf~dIak~L~R~p~hv~ky~~~ELgt~ 94 (193)
.++.++|++++-+|.|+.+.|.+++|..
T Consensus 193 ~sl~~lA~~~~lS~~~l~r~Fk~~~G~T 220 (290)
T PRK13501 193 FDMADFCHKNQLVERSLKQLFRQQTGMS 220 (290)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence 4799999999999999999999999975
No 333
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=24.22 E-value=60 Score=32.93 Aligned_cols=43 Identities=21% Similarity=0.402 Sum_probs=28.6
Q ss_pred eeecccccccccccccccccceeeeccEEEEEecccCCCcccc
Q psy7490 144 LFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRCSVA 186 (193)
Q Consensus 144 l~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~~v~ 186 (193)
.-++.|..||..--=+.=..-+.-+..-=.++|.-||...++.
T Consensus 433 s~~l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p 475 (730)
T COG1198 433 APLLLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIP 475 (730)
T ss_pred cceeecccCCCcccCCCCCcceEEecCCCeeEeCCCCCCCCCC
Confidence 4478999999865443333344444444678999999987664
No 334
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=24.18 E-value=54 Score=27.97 Aligned_cols=27 Identities=41% Similarity=1.030 Sum_probs=21.1
Q ss_pred ccccCCCCCCcceeEecCceeecccccccccc
Q psy7490 125 YVTCHTCRSPDTILQKDTRLFFLQCETCGSRC 156 (193)
Q Consensus 125 YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~ 156 (193)
|-.|+.|+.| |++++. .++|..||+.-
T Consensus 149 ~A~CsrC~~~---L~~~~~--~l~Cp~Cg~tE 175 (188)
T COG1096 149 YARCSRCRAP---LVKKGN--MLKCPNCGNTE 175 (188)
T ss_pred EEEccCCCcc---eEEcCc--EEECCCCCCEE
Confidence 6789999865 777554 58999999863
No 335
>PRK14281 chaperone protein DnaJ; Provisional
Probab=23.92 E-value=56 Score=30.27 Aligned_cols=34 Identities=26% Similarity=0.514 Sum_probs=21.4
Q ss_pred hhhccccCCCCCCcceeEecCceeecccccccccccccc
Q psy7490 122 IKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVAS 160 (193)
Q Consensus 122 I~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~~ 160 (193)
+...|.|+.|...-.. .+. ...|..|+-...+..
T Consensus 160 ~~r~~~C~~C~G~G~~---~~~--~~~C~~C~G~G~~~~ 193 (397)
T PRK14281 160 IKKQVPCKECNGTGSK---TGA--TETCPTCHGSGEVRQ 193 (397)
T ss_pred EEeeecCCCCCCcccC---CCC--CccCCCCCCCcEEEE
Confidence 3557899999876543 121 346888877765533
No 336
>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=23.88 E-value=65 Score=25.63 Aligned_cols=26 Identities=23% Similarity=0.724 Sum_probs=17.1
Q ss_pred ccccCCCCCCcceeEecC-ceeeccccccccc
Q psy7490 125 YVTCHTCRSPDTILQKDT-RLFFLQCETCGSR 155 (193)
Q Consensus 125 YVlC~~C~sPdT~L~k~~-rl~~l~C~aCGa~ 155 (193)
|.-||.|+.. +..++ +. -.|..|+..
T Consensus 34 Y~aC~~C~kk---v~~~~~~~--~~C~~C~~~ 60 (166)
T cd04476 34 YPACPGCNKK---VVEEGNGT--YRCEKCNKS 60 (166)
T ss_pred EccccccCcc---cEeCCCCc--EECCCCCCc
Confidence 8888888763 33332 33 478888876
No 337
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=23.83 E-value=41 Score=28.40 Aligned_cols=30 Identities=30% Similarity=0.627 Sum_probs=20.9
Q ss_pred ecCceeecccccccccccccccccceeeeccEEEEEecccCCC
Q psy7490 140 KDTRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSR 182 (193)
Q Consensus 140 k~~rl~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~ 182 (193)
++-+-|..+|..|+..-+ .+.+ -|..||++
T Consensus 133 ~~v~~w~~rC~GC~~~f~-~~~~------------~Cp~CG~~ 162 (177)
T COG1439 133 KKVRKWRLRCHGCKRIFP-EPKD------------FCPICGSP 162 (177)
T ss_pred ceEeeeeEEEecCceecC-CCCC------------cCCCCCCc
Confidence 344567888999988876 2222 48888887
No 338
>KOG0481|consensus
Probab=23.49 E-value=1.4e+02 Score=29.92 Aligned_cols=96 Identities=14% Similarity=0.257 Sum_probs=59.2
Q ss_pred HHHHHHcCCChHHHHHHHHHh-------h---cCcee-ecCCCeEEEEeeccHHHHHHHHHHHhhhccccCCCCCCccee
Q psy7490 70 TEICKTLHRLPKHLLDFLLAE-------L---GTSGS-VDGNSQLIIKGRFQQKQIENVLRRYIKEYVTCHTCRSPDTIL 138 (193)
Q Consensus 70 ~dIak~L~R~p~hv~ky~~~E-------L---gt~g~-id~~~~lii~G~~~~~~iq~~L~~yI~~YVlC~~C~sPdT~L 138 (193)
+|+++.|++.|...+-.|..- + +.+|. .-.+=+++++-.-.+-.|..+=-.++.+-|.=+.=--.-..+
T Consensus 74 edl~~~L~~~P~~~lp~fEeAa~~Vad~i~~~~~~~E~~~~d~Qv~L~sda~p~~iR~l~s~~vsklVki~GIiiaAS~v 153 (729)
T KOG0481|consen 74 EDLADKLSKQPADHLPLFEEAAKEVADEITRPRPSGEEVLHDIQVLLTSDANPISIRQLKSDHVSKLVKISGIIIAASAV 153 (729)
T ss_pred hHHHHHHHhChHhHHHHHHHHHHHHHhhhcCCCcCCCccceeeEEEEecCCCcccHhHhhhHhhhhheeeccEEEEeeee
Confidence 468999999998888877543 2 22220 001236788888888888888888888877544321111111
Q ss_pred EecCceeecccccccccccccccccce
Q psy7490 139 QKDTRLFFLQCETCGSRCSVASIKSGF 165 (193)
Q Consensus 139 ~k~~rl~~l~C~aCGa~~~V~~~k~~~ 165 (193)
.-+-.-.++.|..|.+..++-..+.||
T Consensus 154 ~~kat~l~l~CrnC~~t~~~~~~~pgl 180 (729)
T KOG0481|consen 154 SAKATRLSLVCRNCRHTRPNVIMRPGL 180 (729)
T ss_pred eecceEEEEEeccccccccceecCCCc
Confidence 112233478888888888777666554
No 339
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=23.49 E-value=1.2e+02 Score=23.85 Aligned_cols=63 Identities=14% Similarity=0.389 Sum_probs=40.9
Q ss_pred eccHHHHHHHHHHHhhhccccCCCCCCcceeEecCceeecccccccccccccccccceeeeccEEEEEecccCCC
Q psy7490 108 RFQQKQIENVLRRYIKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSR 182 (193)
Q Consensus 108 ~~~~~~iq~~L~~yI~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~ 182 (193)
.|. ..++.++.+.-..+-- .|++.+.+-+ +.+.-+|..||.... ..+ ...++....|..||.+
T Consensus 80 ~Hg-~~f~~~~~~~~~~~~~--~~h~~~~~~~---~~~~y~C~~C~~~~~--~~r----r~~~~~~y~C~~C~g~ 142 (146)
T smart00731 80 GHG-DEWKRWMRQVNGLFPE--RCHTFLIESV---KKYPYRCTGCGQRYL--RVR----RSNNVSRYRCGKCGGK 142 (146)
T ss_pred CcC-HHHHHHHHHHcCCCcc--eEcCCccccc---ceEEEECCCCCCCCc--eEc----cccCcceEEcCCCCCE
Confidence 455 7888888887666531 4555554433 567889999997652 111 2223377899999875
No 340
>cd00167 SANT 'SWI3, ADA2, N-CoR and TFIIIB' DNA-binding domains. Tandem copies of the domain bind telomeric DNA tandem repeatsas part of the capping complex. Binding is sequence dependent for repeats which contain the G/C rich motif [C2-3 A (CA)1-6]. The domain is also found in regulatory transcriptional repressor complexes where it also binds DNA.
Probab=23.41 E-value=1e+02 Score=17.94 Aligned_cols=23 Identities=30% Similarity=0.388 Sum_probs=18.7
Q ss_pred eccHHHHHHcC-CChHHHHHHHHH
Q psy7490 67 ANFTEICKTLH-RLPKHLLDFLLA 89 (193)
Q Consensus 67 ~Nf~dIak~L~-R~p~hv~ky~~~ 89 (193)
.|+..||+.+. |++..+..++..
T Consensus 20 ~~w~~Ia~~~~~rs~~~~~~~~~~ 43 (45)
T cd00167 20 NNWEKIAKELPGRTPKQCRERWRN 43 (45)
T ss_pred CCHHHHHhHcCCCCHHHHHHHHHH
Confidence 57889999996 999888887653
No 341
>PRK14285 chaperone protein DnaJ; Provisional
Probab=23.38 E-value=73 Score=29.16 Aligned_cols=34 Identities=18% Similarity=0.365 Sum_probs=19.6
Q ss_pred hhhccccCCCCCCcceeEecCceeeccccccccccccc
Q psy7490 122 IKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVA 159 (193)
Q Consensus 122 I~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~ 159 (193)
+...|.|+.|...-.. ++ .....|..|+-...+.
T Consensus 143 ~~r~~~C~~C~G~G~~---~~-~~~~~C~~C~G~G~~~ 176 (365)
T PRK14285 143 ITRNMLCESCLGKKSE---KG-TSPSICNMCNGSGRVM 176 (365)
T ss_pred eeecccCCCCCCcccC---CC-CCCccCCCccCceeEE
Confidence 4567899999875431 11 1124577776665443
No 342
>PRK14291 chaperone protein DnaJ; Provisional
Probab=23.25 E-value=63 Score=29.70 Aligned_cols=33 Identities=24% Similarity=0.492 Sum_probs=18.6
Q ss_pred hhhccccCCCCCCcceeEecCceeecccccccccccc
Q psy7490 122 IKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSV 158 (193)
Q Consensus 122 I~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V 158 (193)
+...|.|+.|...-+. .+ .-...|..|+-...+
T Consensus 153 ~~r~~~C~~C~G~G~~---~~-~~~~~C~~C~G~G~~ 185 (382)
T PRK14291 153 VPRYVPCEACGGTGYD---PG-SGEKVCPTCGGSGEI 185 (382)
T ss_pred EeeeccCCCCccccCC---CC-CCCccCCCCCCceEE
Confidence 4567889999875542 11 112446666655543
No 343
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=23.16 E-value=79 Score=20.60 Aligned_cols=24 Identities=25% Similarity=0.227 Sum_probs=15.9
Q ss_pred ccHHHHHHHHHHHhhhccccCCCCCCcc
Q psy7490 109 FQQKQIENVLRRYIKEYVTCHTCRSPDT 136 (193)
Q Consensus 109 ~~~~~iq~~L~~yI~~YVlC~~C~sPdT 136 (193)
|..+-|++.+ ++...||.|+.|-|
T Consensus 23 ~~~~~i~~~~----~~~~~cP~~~~~~~ 46 (63)
T smart00504 23 YERRAIEKWL----LSHGTDPVTGQPLT 46 (63)
T ss_pred EeHHHHHHHH----HHCCCCCCCcCCCC
Confidence 4555555544 44778999998754
No 344
>TIGR01464 hemE uroporphyrinogen decarboxylase. This model represents uroporphyrinogen decarboxylase (HemE), which converts uroporphyrinogen III to coproporphyrinogen III. This step takes the pathway toward protoporphyrin IX, a common precursor of both heme and chlorophyll, rather than toward precorrin 2 and its products.
Probab=23.15 E-value=64 Score=28.61 Aligned_cols=57 Identities=14% Similarity=0.190 Sum_probs=38.8
Q ss_pred CChHHHHHHHHHhhcCceeecCCCeEEEEeeccHHHHHHHHHHHhhh------ccccCCCCC-CcceeE
Q psy7490 78 RLPKHLLDFLLAELGTSGSVDGNSQLIIKGRFQQKQIENVLRRYIKE------YVTCHTCRS-PDTILQ 139 (193)
Q Consensus 78 R~p~hv~ky~~~ELgt~g~id~~~~lii~G~~~~~~iq~~L~~yI~~------YVlC~~C~s-PdT~L~ 139 (193)
-+.....+-++.....+|++|. . ++ .| ++++|++..++.|++ |++.+.|+- |+|.+.
T Consensus 264 ~dl~e~~~~~~~~~~i~Gni~p-~-~l-~g--t~e~i~~~v~~~l~~~~~~~g~Il~~Gc~i~~~tp~e 327 (338)
T TIGR01464 264 VDLKEARKRVGPGVAIQGNLDP-A-VL-YA--PEEALEEKVEKILEAFGGKSRYIFNLGHGILPDTPPE 327 (338)
T ss_pred CCHHHHHHHhCCCeeEEeCCCh-H-Hh-cC--CHHHHHHHHHHHHHHhccCCCceecCCCcCCCCcCHH
Confidence 3444455555555666788864 2 33 56 788888888888885 899999995 577643
No 345
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=23.08 E-value=40 Score=21.88 Aligned_cols=15 Identities=20% Similarity=0.667 Sum_probs=10.8
Q ss_pred ccccccccccccccc
Q psy7490 147 LQCETCGSRCSVASI 161 (193)
Q Consensus 147 l~C~aCGa~~~V~~~ 161 (193)
++|.+||+-......
T Consensus 2 ~kC~~CG~~GH~~t~ 16 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTN 16 (40)
T ss_pred ccccccccccccccC
Confidence 578889887765544
No 346
>PF02742 Fe_dep_repr_C: Iron dependent repressor, metal binding and dimerisation domain; InterPro: IPR001367 The diphtheria toxin repressor protein (DTXR) is a member of this group []. In Corynebacterium diphtheriae where it has been studied in some detail this protein acts as an iron-binding repressor of dipheteria toxin gene expression and may serve as a global regulator of gene expression. The N terminus may be involved in iron binding and may associate with the Tox operator. Binding of DTXR to Tox operator requires a divalent metal ion such as cobalt, ferric, manganese and nickel whereas zinc shows weak activation [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0005506 iron ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2X4H_D 2H09_A 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A 2F5D_A 3R61_A ....
Probab=22.93 E-value=11 Score=26.38 Aligned_cols=62 Identities=19% Similarity=0.245 Sum_probs=41.5
Q ss_pred HHHHHHcCCChHHHHHHHHHhhcCceeecCCCeEEEEeeccHHHHHHHHHHHhhhccccCCCC
Q psy7490 70 TEICKTLHRLPKHLLDFLLAELGTSGSVDGNSQLIIKGRFQQKQIENVLRRYIKEYVTCHTCR 132 (193)
Q Consensus 70 ~dIak~L~R~p~hv~ky~~~ELgt~g~id~~~~lii~G~~~~~~iq~~L~~yI~~YVlC~~C~ 132 (193)
.++|+.+.|.=..+..||..-||.+...-....--|- .+-+....+.|.+|++..-.||.++
T Consensus 5 ~~~A~~i~~rH~~le~fl~~~lgv~~~~a~~~A~~iE-H~is~e~~~~l~~~l~~~~~~P~~~ 66 (71)
T PF02742_consen 5 REIAERILRRHRILEEFLVEVLGVDEEEAEEEACRIE-HVISPETIERLCKFLGFPETCPHGN 66 (71)
T ss_dssp HHHHHHHHHHHHHHHHHHHHTTT--HHHHHHHHHHHG-CCS-HHHHHHHHHHTTCTSBETTSC
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCCHHHHHHHHHHHH-ccCCHHHHHHHHHHhcCCCcCcCCC
Confidence 3678888888889999999999987654111111111 2344566677899999999999876
No 347
>KOG1296|consensus
Probab=22.93 E-value=24 Score=29.21 Aligned_cols=15 Identities=27% Similarity=0.658 Sum_probs=8.0
Q ss_pred ecccccccccccccc
Q psy7490 146 FLQCETCGSRCSVAS 160 (193)
Q Consensus 146 ~l~C~aCGa~~~V~~ 160 (193)
..+|+-|+...+|.-
T Consensus 64 v~KCK~C~Rensv~i 78 (161)
T KOG1296|consen 64 VMKCKFCSRENSVTI 78 (161)
T ss_pred hhhhhhhcccCcEEE
Confidence 455555555555543
No 348
>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=22.85 E-value=59 Score=20.27 Aligned_cols=24 Identities=29% Similarity=0.789 Sum_probs=13.5
Q ss_pred ccCCCCCCcceeEecCceeecccccccc
Q psy7490 127 TCHTCRSPDTILQKDTRLFFLQCETCGS 154 (193)
Q Consensus 127 lC~~C~sPdT~L~k~~rl~~l~C~aCGa 154 (193)
.|+.|++- ....+++. .-|..||.
T Consensus 10 ~C~~C~~~--~~~~~dG~--~yC~~cG~ 33 (36)
T PF11781_consen 10 PCPVCGSR--WFYSDDGF--YYCDRCGH 33 (36)
T ss_pred cCCCCCCe--EeEccCCE--EEhhhCce
Confidence 58888877 33334443 33666664
No 349
>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=22.82 E-value=39 Score=26.13 Aligned_cols=29 Identities=28% Similarity=0.570 Sum_probs=16.0
Q ss_pred ccCCCCCCcceeEecCceeeccccccccccccc
Q psy7490 127 TCHTCRSPDTILQKDTRLFFLQCETCGSRCSVA 159 (193)
Q Consensus 127 lC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~ 159 (193)
+||+|+.-=-.|-| . -+.|..||+..++.
T Consensus 11 ~Cp~CG~kFYDLnk-~---PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 11 TCPSCGAKFYDLNK-D---PIVCPKCGTEFPPE 39 (108)
T ss_pred cCCCCcchhccCCC-C---CccCCCCCCccCcc
Confidence 57777653333333 2 24477777766655
No 350
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=22.76 E-value=54 Score=18.90 Aligned_cols=6 Identities=33% Similarity=1.121 Sum_probs=2.6
Q ss_pred cCCCCC
Q psy7490 128 CHTCRS 133 (193)
Q Consensus 128 C~~C~s 133 (193)
|..|+.
T Consensus 2 C~~C~~ 7 (39)
T smart00132 2 CAGCGK 7 (39)
T ss_pred ccccCC
Confidence 444443
No 351
>PF04472 DUF552: Protein of unknown function (DUF552); InterPro: IPR007561 This entry represents a cell division protein, designated SepF, which is conserved in Gram-positive bacteria. SepF accumulates at the cell division site in an FtsZ-dependent manner and is required for proper septum formation []. Mutants are viable but the formation of the septum is much slower and occurs with a very abnormal morphology. This entry also includes archaeal related proteins of unknown function.; GO: 0000917 barrier septum formation; PDB: 3P04_A.
Probab=22.74 E-value=1.1e+02 Score=21.32 Aligned_cols=33 Identities=24% Similarity=0.388 Sum_probs=22.8
Q ss_pred eeEEeccHHHHHHcCCChHHHHHHH-HHhhcCceeec
Q psy7490 63 KTSFANFTEICKTLHRLPKHLLDFL-LAELGTSGSVD 98 (193)
Q Consensus 63 KTvi~Nf~dIak~L~R~p~hv~ky~-~~ELgt~g~id 98 (193)
++++.||..+-+.. .+.+..|+ +.-.+..|.+.
T Consensus 23 ~~Vivnl~~l~~~~---~~Ri~Dfl~G~~~al~G~i~ 56 (73)
T PF04472_consen 23 KIVIVNLENLDDEE---AQRILDFLSGAVYALDGDIQ 56 (73)
T ss_dssp --EEEE-TTS-HHH---HHHHHHHHHHHHHHTT-EEE
T ss_pred CEEEEECCCCCHHH---HHHHHHHHhchheeeCCEEE
Confidence 89999999999888 78899999 56666667765
No 352
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=22.48 E-value=2.2e+02 Score=19.04 Aligned_cols=46 Identities=17% Similarity=0.245 Sum_probs=30.9
Q ss_pred ccHHHHHHcCCChHHHHHHHHHhhcCcee-ecCCCeEEEEeeccHHHHHHHH
Q psy7490 68 NFTEICKTLHRLPKHLLDFLLAELGTSGS-VDGNSQLIIKGRFQQKQIENVL 118 (193)
Q Consensus 68 Nf~dIak~L~R~p~hv~ky~~~ELgt~g~-id~~~~lii~G~~~~~~iq~~L 118 (193)
+..|+|+.++.+|..|-.| ..++|.... -+++|+ ..|+.++|+.+.
T Consensus 2 ~i~e~A~~~gVs~~tlr~y-e~~~gl~~~~r~~~g~----R~yt~~di~~l~ 48 (68)
T cd04763 2 TIGEVALLTGIKPHVLRAW-EREFGLLKPQRSDGGH----RLFNDADIDRIL 48 (68)
T ss_pred CHHHHHHHHCcCHHHHHHH-HHhcCCCCCCcCCCCC----cccCHHHHHHHH
Confidence 5689999999999998877 444454422 223332 258888888653
No 353
>PRK07220 DNA topoisomerase I; Validated
Probab=22.39 E-value=69 Score=32.29 Aligned_cols=9 Identities=11% Similarity=0.283 Sum_probs=4.4
Q ss_pred ccCCCCCCc
Q psy7490 127 TCHTCRSPD 135 (193)
Q Consensus 127 lC~~C~sPd 135 (193)
.||.|+.+.
T Consensus 637 ~Cp~Cg~~~ 645 (740)
T PRK07220 637 VCEAHGLNH 645 (740)
T ss_pred CCCCCCCce
Confidence 355555443
No 354
>KOG2691|consensus
Probab=22.33 E-value=75 Score=25.01 Aligned_cols=62 Identities=24% Similarity=0.529 Sum_probs=29.8
Q ss_pred EeeccHHHHHHHHHHHhhhccccCCCCCCcceeEecCceeecccccccccccc--cccccceeeeccEEEEEecccCCC
Q psy7490 106 KGRFQQKQIENVLRRYIKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSV--ASIKSGFQKDTRLFFLQCETCGSR 182 (193)
Q Consensus 106 ~G~~~~~~iq~~L~~yI~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V--~~~k~~~~~~~rl~~~~c~~Cga~ 182 (193)
+|.++...+..++..-+ ||-.|- ++.-..|..||.+-.| ++....=...-+|||+=|. ||-.
T Consensus 47 ~~~~e~dE~t~ii~Dl~-----------~DPTLP---rts~~~C~~C~~~eavffQ~~~~r~d~~m~l~yvC~~-C~h~ 110 (113)
T KOG2691|consen 47 ELSHEHDELTQIIMDLA-----------SDPTLP---RTSDKHCPKCGHREAVFFQAQTRRADEAMRLFYVCCS-CGHR 110 (113)
T ss_pred CcccchhhHHHHHHhhc-----------cCCCcC---ccccccCCccCCcceEEEecccccccceEEEEEEecc-cccc
Confidence 45666666666655422 232222 2233567777776654 1111111234456665444 7643
No 355
>PF15494 SRCR_2: Scavenger receptor cysteine-rich domain
Probab=22.29 E-value=60 Score=23.80 Aligned_cols=14 Identities=29% Similarity=0.226 Sum_probs=8.9
Q ss_pred HHHHHHHHhhcCce
Q psy7490 82 HLLDFLLAELGTSG 95 (193)
Q Consensus 82 hv~ky~~~ELgt~g 95 (193)
++.+.....||-.+
T Consensus 27 ~~s~~~C~qLGy~~ 40 (98)
T PF15494_consen 27 ALSKAACQQLGYSS 40 (98)
T ss_pred HHHHHHHHHhCCCC
Confidence 44577777777643
No 356
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=22.23 E-value=1e+02 Score=20.10 Aligned_cols=25 Identities=24% Similarity=0.348 Sum_probs=20.6
Q ss_pred ccHHHHHHcC-CChHHHHHHHHHhhc
Q psy7490 68 NFTEICKTLH-RLPKHLLDFLLAELG 92 (193)
Q Consensus 68 Nf~dIak~L~-R~p~hv~ky~~~ELg 92 (193)
|..+||+.|+ |.|..+..-+..-|.
T Consensus 19 ~W~~Ia~~l~~Rt~~~~~~r~~~~l~ 44 (60)
T PF13921_consen 19 DWKKIAEHLGNRTPKQCRNRWRNHLR 44 (60)
T ss_dssp -HHHHHHHSTTS-HHHHHHHHHHTTS
T ss_pred CHHHHHHHHCcCCHHHHHHHHHHHCc
Confidence 7899999999 999999988888665
No 357
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=22.21 E-value=44 Score=31.78 Aligned_cols=36 Identities=22% Similarity=0.541 Sum_probs=23.5
Q ss_pred HhhhccccCCCCCCcceeEecCceeecccccccccccccc
Q psy7490 121 YIKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVAS 160 (193)
Q Consensus 121 yI~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~~ 160 (193)
|...--+||.|+. .|.-.++- ..+|..||.+-+-..
T Consensus 346 ~~~~~p~Cp~Cg~---~m~S~G~~-g~rC~kCg~~~~~~~ 381 (421)
T COG1571 346 YERVNPVCPRCGG---RMKSAGRN-GFRCKKCGTRARETL 381 (421)
T ss_pred eEEcCCCCCccCC---chhhcCCC-CcccccccccCCccc
Confidence 5555557888873 45555555 788888887765433
No 358
>PRK14296 chaperone protein DnaJ; Provisional
Probab=22.21 E-value=79 Score=29.07 Aligned_cols=34 Identities=15% Similarity=0.335 Sum_probs=20.3
Q ss_pred hhhccccCCCCCCcceeEecCceeeccccccccccccc
Q psy7490 122 IKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVA 159 (193)
Q Consensus 122 I~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~ 159 (193)
+...+.|+.|....+.- +. ....|..|+-...+.
T Consensus 146 ~~~~~~C~~C~G~G~~~---~~-~~~~C~~C~G~G~~~ 179 (372)
T PRK14296 146 LDLLTNCSKCFGSGAES---NS-DIHICNNCHGTGEVL 179 (372)
T ss_pred EeeeeccCCCCCCccCC---CC-CCccCCCCCCCceEE
Confidence 46678999999766521 11 124577777666443
No 359
>PRK14293 chaperone protein DnaJ; Provisional
Probab=22.13 E-value=68 Score=29.37 Aligned_cols=34 Identities=32% Similarity=0.526 Sum_probs=19.6
Q ss_pred hhhccccCCCCCCcceeEecCceeeccccccccccccc
Q psy7490 122 IKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVA 159 (193)
Q Consensus 122 I~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~ 159 (193)
+...+.|+.|....+.- +. ..-.|..|+-...+.
T Consensus 140 ~~r~~~C~~C~G~G~~~---~~-~~~~C~~C~G~G~~~ 173 (374)
T PRK14293 140 IPHLETCETCRGSGAKP---GT-GPTTCSTCGGAGQVR 173 (374)
T ss_pred eeccccCCCCCCcCCCC---CC-CCeeCCCCCCcceEE
Confidence 35578999998766532 11 123466666665443
No 360
>PRK14301 chaperone protein DnaJ; Provisional
Probab=22.03 E-value=72 Score=29.29 Aligned_cols=34 Identities=26% Similarity=0.497 Sum_probs=20.8
Q ss_pred hhhccccCCCCCCcceeEecCceeeccccccccccccc
Q psy7490 122 IKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVA 159 (193)
Q Consensus 122 I~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~ 159 (193)
+...|.|+.|...-+. .+ .....|..|+-...|.
T Consensus 141 ~~r~~~C~~C~G~G~~---~~-~~~~~C~~C~G~G~v~ 174 (373)
T PRK14301 141 IPKNVTCDDCGGSGAA---PG-TSPETCRHCGGSGQVR 174 (373)
T ss_pred eeecccCCCCCCcccC---CC-CCCcccCCccCeeEEE
Confidence 4567899999876542 11 1124577777766554
No 361
>PRK14283 chaperone protein DnaJ; Provisional
Probab=21.99 E-value=70 Score=29.35 Aligned_cols=33 Identities=21% Similarity=0.440 Sum_probs=19.5
Q ss_pred hhccccCCCCCCcceeEecCceeeccccccccccccc
Q psy7490 123 KEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVA 159 (193)
Q Consensus 123 ~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~ 159 (193)
...+.|+.|..+... . +.-...|..|+....+.
T Consensus 144 ~r~~~C~~C~G~G~~---~-~~~~~~C~~C~G~G~~~ 176 (378)
T PRK14283 144 RHTKKCPVCNGSRAE---P-GSEVKTCPTCGGTGQVK 176 (378)
T ss_pred eeeccCCCCCccccC---C-CCCCccCCCcCCccEEE
Confidence 446889999876642 1 11224577776666554
No 362
>PF14122 YokU: YokU-like protein
Probab=21.97 E-value=81 Score=23.80 Aligned_cols=36 Identities=28% Similarity=0.409 Sum_probs=17.4
Q ss_pred ccccccccccccccccc---------eeeeccEEEEEecccCCCc
Q psy7490 148 QCETCGSRCSVASIKSG---------FQKDTRLFFLQCETCGSRC 183 (193)
Q Consensus 148 ~C~aCGa~~~V~~~k~~---------~~~~~rl~~~~c~~Cga~~ 183 (193)
+|..||+...+....+- -...+..=.+-|..||.-+
T Consensus 1 ~C~wC~~~~a~~~~~tvyWeLpdGtraIeI~~tP~i~C~~CgmvY 45 (87)
T PF14122_consen 1 KCEWCGSEEASESESTVYWELPDGTRAIEITDTPAIICSNCGMVY 45 (87)
T ss_pred CcccccCcccccccceEEEEcCCCceEEEecCCceeeecCCCcEE
Confidence 36666665444333221 2233444455666666543
No 363
>PRK14287 chaperone protein DnaJ; Provisional
Probab=21.91 E-value=74 Score=29.18 Aligned_cols=33 Identities=24% Similarity=0.441 Sum_probs=19.4
Q ss_pred hhhccccCCCCCCcceeEecCceeecccccccccccc
Q psy7490 122 IKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSV 158 (193)
Q Consensus 122 I~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V 158 (193)
+...|.|+.|...-.. .+. ....|..|+-...+
T Consensus 135 ~~r~~~C~~C~G~G~~---~~~-~~~~C~~C~G~G~~ 167 (371)
T PRK14287 135 IPREETCGTCHGSGAK---PGT-KPETCSHCGGSGQL 167 (371)
T ss_pred EeeeccCCCCCCcccC---CCC-CCcccCCCCCEEEE
Confidence 4567899999865542 111 12457777666544
No 364
>PF05046 Img2: Mitochondrial large subunit ribosomal protein (Img2); InterPro: IPR007740 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 proteins has been identified as part of the mitochondrial large ribosomal subunit in Saccharomyces cerevisiae [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome
Probab=21.82 E-value=2.1e+02 Score=20.89 Aligned_cols=52 Identities=21% Similarity=0.208 Sum_probs=32.8
Q ss_pred eeeEEeccHHHHHHcCCChHHHHHHHHHhhc--CceeecC-CCeEEEEeeccHHHHHHH
Q psy7490 62 KKTSFANFTEICKTLHRLPKHLLDFLLAELG--TSGSVDG-NSQLIIKGRFQQKQIENV 117 (193)
Q Consensus 62 ~KTvi~Nf~dIak~L~R~p~hv~ky~~~ELg--t~g~id~-~~~lii~G~~~~~~iq~~ 117 (193)
.-|+|.+++-=..+|. +.|.++|....+ -...+++ .|.++|+|.|.. +|.+.
T Consensus 27 ~~T~IrkI~GD~~aL~---~dL~~~l~~~~~~~~~~~V~~~~g~i~IkG~~~~-~Vk~w 81 (87)
T PF05046_consen 27 KITVIRKIEGDIWALK---KDLRKFLGEKPKKKIDVRVNELTGHIEIKGDHVE-EVKKW 81 (87)
T ss_pred eEEEEEeecCCHHHHH---HHHHHHhhhhcCCCcceEEeecCCEEEEcCccHH-HHHHH
Confidence 4677777754444443 345666666665 3455665 789999999944 34433
No 365
>PRK14297 chaperone protein DnaJ; Provisional
Probab=21.74 E-value=77 Score=29.08 Aligned_cols=33 Identities=18% Similarity=0.497 Sum_probs=20.2
Q ss_pred hhhccccCCCCCCcceeEecCceeecccccccccccc
Q psy7490 122 IKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSV 158 (193)
Q Consensus 122 I~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V 158 (193)
+...|.|+.|...-.. .+.....|..|+-...+
T Consensus 145 ~~r~~~C~~C~G~G~~----~~~~~~~C~~C~G~G~~ 177 (380)
T PRK14297 145 VTRNENCETCNGTGAK----PGTSPKTCDKCGGTGQI 177 (380)
T ss_pred eeeeccCCCccccccc----CCCcCccCCCccCeEEE
Confidence 4668899999875542 11123457777766544
No 366
>PLN03086 PRLI-interacting factor K; Provisional
Probab=21.73 E-value=36 Score=33.53 Aligned_cols=11 Identities=27% Similarity=0.878 Sum_probs=6.8
Q ss_pred hhccccCCCCC
Q psy7490 123 KEYVTCHTCRS 133 (193)
Q Consensus 123 ~~YVlC~~C~s 133 (193)
...|.|+.|+.
T Consensus 405 ~~~V~C~NC~~ 415 (567)
T PLN03086 405 VDTVECRNCKH 415 (567)
T ss_pred CCeEECCCCCC
Confidence 34666777764
No 367
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=21.53 E-value=81 Score=22.04 Aligned_cols=22 Identities=9% Similarity=0.137 Sum_probs=18.7
Q ss_pred eccHHHHHHcCCChHHHHHHHH
Q psy7490 67 ANFTEICKTLHRLPKHLLDFLL 88 (193)
Q Consensus 67 ~Nf~dIak~L~R~p~hv~ky~~ 88 (193)
..+.|||+.|+-++..|-++=.
T Consensus 23 i~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 23 IKLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred ccHHHHHHHHCCCHHHHHHHhh
Confidence 4678999999999999988743
No 368
>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=21.50 E-value=31 Score=35.66 Aligned_cols=25 Identities=32% Similarity=0.863 Sum_probs=0.0
Q ss_pred eeecccccccccccccccccceeeeccEEEEEecccCCCc
Q psy7490 144 LFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCGSRC 183 (193)
Q Consensus 144 l~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cga~~ 183 (193)
+...+|..||..+ |+.+|..||+.+
T Consensus 653 i~~r~Cp~Cg~~t---------------~~~~Cp~CG~~T 677 (900)
T PF03833_consen 653 IGRRRCPKCGKET---------------FYNRCPECGSHT 677 (900)
T ss_dssp ----------------------------------------
T ss_pred eecccCcccCCcc---------------hhhcCcccCCcc
Confidence 3456788888765 566777777763
No 369
>KOG2906|consensus
Probab=21.43 E-value=70 Score=24.84 Aligned_cols=30 Identities=23% Similarity=0.457 Sum_probs=22.2
Q ss_pred ccCCCCCCcceeEec--Cceeeccccccccccccc
Q psy7490 127 TCHTCRSPDTILQKD--TRLFFLQCETCGSRCSVA 159 (193)
Q Consensus 127 lC~~C~sPdT~L~k~--~rl~~l~C~aCGa~~~V~ 159 (193)
.||+|+|- |+.+ ....-+.|.+|+...++.
T Consensus 3 FCP~Cgn~---Live~g~~~~rf~C~tCpY~~~I~ 34 (105)
T KOG2906|consen 3 FCPTCGNM---LIVESGESCNRFSCRTCPYVFPIS 34 (105)
T ss_pred ccCCCCCE---EEEecCCeEeeEEcCCCCceeeEe
Confidence 59999983 4432 335678999999988874
No 370
>PRK14288 chaperone protein DnaJ; Provisional
Probab=21.27 E-value=1e+02 Score=28.21 Aligned_cols=45 Identities=27% Similarity=0.657 Sum_probs=0.0
Q ss_pred cccCCCCCCcceeEecCceeecccccccccccccccccceeeeccEEEEEecccC
Q psy7490 126 VTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVASIKSGFQKDTRLFFLQCETCG 180 (193)
Q Consensus 126 VlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~~~k~~~~~~~rl~~~~c~~Cg 180 (193)
++|+.|+..-. +.+ -...|..|+-...|.... |+. .+...|..|+
T Consensus 141 ~~C~~C~G~G~---~~~--~~~~C~~C~G~G~~~~~~-g~~----~~~~~C~~C~ 185 (369)
T PRK14288 141 SVCESCDGTGA---KDK--ALETCKQCNGQGQVFMRQ-GFM----SFAQTCGACQ 185 (369)
T ss_pred ccCCCCCCccc---CCC--CCcCCCCCCCCcEEEEEe-ceE----EEEEecCCCC
No 371
>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=21.27 E-value=39 Score=19.91 Aligned_cols=8 Identities=50% Similarity=1.041 Sum_probs=3.7
Q ss_pred ccCCCCCC
Q psy7490 127 TCHTCRSP 134 (193)
Q Consensus 127 lC~~C~sP 134 (193)
.||+|+++
T Consensus 1 ~CP~C~s~ 8 (28)
T PF03119_consen 1 TCPVCGSK 8 (28)
T ss_dssp B-TTT--B
T ss_pred CcCCCCCE
Confidence 38999875
No 372
>PF01399 PCI: PCI domain; InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) []. Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 []; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 [, ]; Arabidopsis COP9 and FUS6/COP11 []; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; GO: 0005515 protein binding; PDB: 3TXM_A 3TXN_A 1UFM_A 3CHM_A 3T5X_A 3T5V_B.
Probab=21.21 E-value=2.5e+02 Score=19.50 Aligned_cols=39 Identities=18% Similarity=0.338 Sum_probs=29.3
Q ss_pred eccHHHHHHcCCChHHHHHHHHHhhc---CceeecC-CCeEEE
Q psy7490 67 ANFTEICKTLHRLPKHLLDFLLAELG---TSGSVDG-NSQLII 105 (193)
Q Consensus 67 ~Nf~dIak~L~R~p~hv~ky~~~ELg---t~g~id~-~~~lii 105 (193)
..+.+||++|+=+.+.+-.++..-.. ..|.||. +|.+++
T Consensus 61 i~~~~ia~~l~~~~~~vE~~l~~~I~~~~i~~~ID~~~~~v~~ 103 (105)
T PF01399_consen 61 ISISEIAKALQLSEEEVESILIDLISNGLIKAKIDQVNGVVVF 103 (105)
T ss_dssp EEHHHHHHHHTCCHHHHHHHHHHHHHTTSSEEEEETTTTEEEE
T ss_pred cchHHHHHHhccchHHHHHHHHHHHHCCCEEEEEECCCCEEEe
Confidence 56899999999999999988865443 3478885 455554
No 373
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=20.86 E-value=56 Score=18.12 Aligned_cols=9 Identities=22% Similarity=0.626 Sum_probs=4.1
Q ss_pred ccccccccc
Q psy7490 148 QCETCGSRC 156 (193)
Q Consensus 148 ~C~aCGa~~ 156 (193)
.|.+|+..+
T Consensus 4 ~C~~C~~~N 12 (26)
T smart00547 4 ECPACTFLN 12 (26)
T ss_pred cCCCCCCcC
Confidence 344554443
No 374
>TIGR02297 HpaA 4-hydroxyphenylacetate catabolism regulatory protein HpaA. This putative transcriptional regulator, which contains both the substrate-binding, dimerization domain (pfam02311) and the helix-turn-helix DNA-binding domain (pfam00165) of the AraC famil, is located proximal to genes of the 4-hydroxyphenylacetate catabolism pathway.
Probab=20.80 E-value=1.1e+02 Score=25.92 Aligned_cols=28 Identities=18% Similarity=0.014 Sum_probs=25.9
Q ss_pred eccHHHHHHcCCChHHHHHHHHHhhcCc
Q psy7490 67 ANFTEICKTLHRLPKHLLDFLLAELGTS 94 (193)
Q Consensus 67 ~Nf~dIak~L~R~p~hv~ky~~~ELgt~ 94 (193)
.++.++|+.++-++.|+.+.|....|.+
T Consensus 203 ~sl~~lA~~~~~S~~~l~r~Fk~~~G~t 230 (287)
T TIGR02297 203 LRLPEYADRLGISESRLNDICRRFSALS 230 (287)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHhCCC
Confidence 4789999999999999999999999975
No 375
>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=20.75 E-value=37 Score=30.64 Aligned_cols=29 Identities=21% Similarity=0.454 Sum_probs=19.5
Q ss_pred hhccccCCCCCCcceeEecCceeecccccccccccc
Q psy7490 123 KEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSV 158 (193)
Q Consensus 123 ~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V 158 (193)
++--.|..|++-= ..+...|.+||+.+--
T Consensus 80 DQl~~C~~CGa~V-------~~~e~~Cp~C~StnI~ 108 (314)
T PF09567_consen 80 DQLGKCNNCGANV-------SRLEESCPNCGSTNIK 108 (314)
T ss_pred hhhhhhcccccee-------eehhhcCCCCCccccc
Confidence 4556788888632 2356789999987643
No 376
>PRK14280 chaperone protein DnaJ; Provisional
Probab=20.73 E-value=70 Score=29.34 Aligned_cols=34 Identities=26% Similarity=0.479 Sum_probs=20.4
Q ss_pred hhhccccCCCCCCcceeEecCceeeccccccccccccc
Q psy7490 122 IKEYVTCHTCRSPDTILQKDTRLFFLQCETCGSRCSVA 159 (193)
Q Consensus 122 I~~YVlC~~C~sPdT~L~k~~rl~~l~C~aCGa~~~V~ 159 (193)
+...|.|+.|...-+. .+ .....|..|+-...+.
T Consensus 140 ~~r~~~C~~C~G~G~~---~~-~~~~~C~~C~G~G~~~ 173 (376)
T PRK14280 140 IPKEETCDTCHGSGAK---PG-TSKETCSHCGGSGQVS 173 (376)
T ss_pred EeeeccCCCCCCcccC---CC-CCCccCCCCCCEEEEE
Confidence 4567899999876532 11 1124577777666543
No 377
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=20.66 E-value=1.1e+02 Score=19.33 Aligned_cols=22 Identities=23% Similarity=0.270 Sum_probs=18.8
Q ss_pred ccHHHHHHcC--CChHHHHHHHHH
Q psy7490 68 NFTEICKTLH--RLPKHLLDFLLA 89 (193)
Q Consensus 68 Nf~dIak~L~--R~p~hv~ky~~~ 89 (193)
|+..||+.+. |.+..+..++..
T Consensus 23 ~W~~Ia~~~~~~Rt~~qc~~~~~~ 46 (48)
T PF00249_consen 23 NWKKIAKRMPGGRTAKQCRSRYQN 46 (48)
T ss_dssp HHHHHHHHHSSSSTHHHHHHHHHH
T ss_pred HHHHHHHHcCCCCCHHHHHHHHHh
Confidence 8999999998 999988877643
No 378
>PRK13503 transcriptional activator RhaS; Provisional
Probab=20.65 E-value=1e+02 Score=25.77 Aligned_cols=28 Identities=14% Similarity=0.203 Sum_probs=26.0
Q ss_pred eccHHHHHHcCCChHHHHHHHHHhhcCc
Q psy7490 67 ANFTEICKTLHRLPKHLLDFLLAELGTS 94 (193)
Q Consensus 67 ~Nf~dIak~L~R~p~hv~ky~~~ELgt~ 94 (193)
..+.|+|+.++=+|.|+.+.|.++.|.+
T Consensus 188 ~tl~~lA~~~~lS~~~l~r~Fk~~~G~S 215 (278)
T PRK13503 188 VNWEALADQFSLSLRTLHRQLKQQTGLT 215 (278)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHhCcC
Confidence 4589999999999999999999999986
No 379
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=20.57 E-value=89 Score=29.09 Aligned_cols=31 Identities=16% Similarity=0.400 Sum_probs=20.0
Q ss_pred cccCCCCCCcceeEe--cCceeecccccccccccc
Q psy7490 126 VTCHTCRSPDTILQK--DTRLFFLQCETCGSRCSV 158 (193)
Q Consensus 126 VlC~~C~sPdT~L~k--~~rl~~l~C~aCGa~~~V 158 (193)
..||-|.--.-.+.. +++ .-+|-+||....+
T Consensus 35 ~~CPfh~ek~pSf~v~~~k~--~~~Cf~Cg~~Gd~ 67 (415)
T TIGR01391 35 GLCPFHHEKTPSFSVSPEKQ--FYHCFGCGAGGDA 67 (415)
T ss_pred eeCCCCCCCCCeEEEEcCCC--cEEECCCCCCCCH
Confidence 389999743334444 444 4689999987644
No 380
>PHA02942 putative transposase; Provisional
Probab=20.48 E-value=59 Score=30.13 Aligned_cols=11 Identities=27% Similarity=0.908 Sum_probs=6.1
Q ss_pred ecccccccccc
Q psy7490 146 FLQCETCGSRC 156 (193)
Q Consensus 146 ~l~C~aCGa~~ 156 (193)
...|..||+..
T Consensus 325 Sq~Cs~CG~~~ 335 (383)
T PHA02942 325 SVSCPKCGHKM 335 (383)
T ss_pred CccCCCCCCcc
Confidence 34566666543
No 381
>PRK13502 transcriptional activator RhaR; Provisional
Probab=20.19 E-value=1.1e+02 Score=25.94 Aligned_cols=27 Identities=15% Similarity=0.251 Sum_probs=25.2
Q ss_pred ccHHHHHHcCCChHHHHHHHHHhhcCc
Q psy7490 68 NFTEICKTLHRLPKHLLDFLLAELGTS 94 (193)
Q Consensus 68 Nf~dIak~L~R~p~hv~ky~~~ELgt~ 94 (193)
...++|++++-+|.|+.+.|..++|..
T Consensus 194 ~~~~lA~~~~iS~~~L~r~fk~~~G~t 220 (282)
T PRK13502 194 ALDAFCQQEQCSERVLRQQFRAQTGMT 220 (282)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHCcC
Confidence 468999999999999999999999986
No 382
>PF01418 HTH_6: Helix-turn-helix domain, rpiR family; InterPro: IPR000281 This domain contains a helix-turn-helix motif []. Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2O3F_B 3IWF_B.
Probab=20.12 E-value=1.1e+02 Score=21.39 Aligned_cols=28 Identities=25% Similarity=0.431 Sum_probs=22.0
Q ss_pred eccHHHHHHcCCChHHHHHHHHHhhcCce
Q psy7490 67 ANFTEICKTLHRLPKHLLDFLLAELGTSG 95 (193)
Q Consensus 67 ~Nf~dIak~L~R~p~hv~ky~~~ELgt~g 95 (193)
.+..|||+..+-+|.-|.+|..+ ||-.|
T Consensus 35 ~si~elA~~~~vS~sti~Rf~kk-LG~~g 62 (77)
T PF01418_consen 35 MSISELAEKAGVSPSTIVRFCKK-LGFSG 62 (77)
T ss_dssp --HHHHHHHCTS-HHHHHHHHHH-CTTTC
T ss_pred ccHHHHHHHcCCCHHHHHHHHHH-hCCCC
Confidence 56889999999999999998765 88765
No 383
>PF02701 zf-Dof: Dof domain, zinc finger; InterPro: IPR003851 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 consists of proteins containing a Dof domain, which is a zinc finger DNA-binding domain that shows resemblance to the Cys2 zinc finger, although it has a longer putative loop where an extra Cys residue is conserved []. AOBP, a DNA-binding protein in pumpkin (Cucurbita maxima), contains a 52 amino acid Dof domain, which is highly conserved in several DNA-binding proteins of higher plants. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent
Probab=20.12 E-value=61 Score=23.06 Aligned_cols=31 Identities=19% Similarity=0.384 Sum_probs=20.1
Q ss_pred hccccCCCCCCcceeEecC--c--eeecccccccc
Q psy7490 124 EYVTCHTCRSPDTILQKDT--R--LFFLQCETCGS 154 (193)
Q Consensus 124 ~YVlC~~C~sPdT~L~k~~--r--l~~l~C~aCGa 154 (193)
+-+.||-|.|.+|..-=-+ . .---.|.+|..
T Consensus 4 ~~~~CPRC~S~nTKFcYyNNy~~~QPR~~Ck~C~r 38 (63)
T PF02701_consen 4 QPLPCPRCDSTNTKFCYYNNYNLSQPRYFCKSCRR 38 (63)
T ss_pred cCCCCCCcCCCCCEEEeecCCCCCCcchhhHHHHH
Confidence 4578999999999886421 1 11235777754
No 384
>PHA02705 hypothetical protein; Provisional
Probab=20.09 E-value=87 Score=22.14 Aligned_cols=27 Identities=26% Similarity=0.347 Sum_probs=22.2
Q ss_pred eEEeccHHHHHHcCCChHHHHHHHHHh
Q psy7490 64 TSFANFTEICKTLHRLPKHLLDFLLAE 90 (193)
Q Consensus 64 Tvi~Nf~dIak~L~R~p~hv~ky~~~E 90 (193)
|-+.|..||-..+.|+.+.++|-..-|
T Consensus 3 tdvanvedimneidrekeeilknveme 29 (72)
T PHA02705 3 TDVANVEDIMNEIDREKEEILKNVEME 29 (72)
T ss_pred cchhhHHHHHHHHHHHHHHHHHhhhhh
Confidence 567899999999999999988876444
Done!