Query 024241
Match_columns 270
No_of_seqs 183 out of 426
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 03:07:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024241.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024241hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2768 Translation initiation 100.0 1.9E-71 4.1E-76 493.0 12.3 215 50-268 16-230 (231)
2 PRK03988 translation initiatio 100.0 4.7E-55 1E-59 368.2 15.7 135 115-255 4-138 (138)
3 TIGR00311 aIF-2beta translatio 100.0 3.8E-54 8.3E-59 360.7 15.4 133 117-255 1-133 (133)
4 PRK12336 translation initiatio 100.0 4.5E-52 9.7E-57 368.2 15.8 137 116-258 1-137 (201)
5 smart00653 eIF2B_5 domain pres 100.0 2.2E-48 4.8E-53 316.6 13.3 109 141-249 2-110 (110)
6 PF01873 eIF-5_eIF-2B: Domain 100.0 1.2E-48 2.7E-53 324.3 10.0 120 131-250 4-124 (125)
7 COG1601 GCD7 Translation initi 100.0 6E-44 1.3E-48 304.6 6.6 147 113-264 3-150 (151)
8 KOG2767 Translation initiation 100.0 2.1E-33 4.6E-38 264.6 4.1 124 137-260 10-140 (400)
9 PF09526 DUF2387: Probable met 95.4 0.013 2.9E-07 44.8 2.7 42 213-255 3-45 (71)
10 TIGR02443 conserved hypothetic 95.2 0.017 3.8E-07 42.8 2.8 40 213-253 4-44 (59)
11 PF01253 SUI1: Translation ini 93.6 0.26 5.7E-06 37.9 6.3 58 156-217 19-80 (83)
12 PF14354 Lar_restr_allev: Rest 92.8 0.032 7E-07 40.1 0.1 28 221-248 5-37 (61)
13 PRK09710 lar restriction allev 92.6 0.045 9.7E-07 41.3 0.6 36 221-256 8-43 (64)
14 PF01096 TFIIS_C: Transcriptio 90.9 0.23 5E-06 33.5 2.6 31 220-250 1-38 (39)
15 smart00440 ZnF_C2C2 C2C2 Zinc 90.0 0.42 9E-06 32.4 3.3 30 221-250 2-38 (40)
16 PF12677 DUF3797: Domain of un 89.5 0.3 6.5E-06 35.1 2.3 32 216-248 10-46 (49)
17 TIGR03655 anti_R_Lar restricti 89.1 0.42 9.2E-06 33.9 2.9 32 221-253 3-39 (53)
18 PRK00939 translation initiatio 88.8 0.84 1.8E-05 36.9 4.8 57 152-214 34-90 (99)
19 cd00474 SUI1_eIF1 The SUI1/eIF 88.3 0.93 2E-05 35.0 4.5 55 154-213 12-66 (77)
20 PHA02998 RNA polymerase subuni 88.2 0.54 1.2E-05 42.2 3.5 86 163-256 87-187 (195)
21 PF13719 zinc_ribbon_5: zinc-r 87.4 0.43 9.4E-06 31.7 1.9 32 219-252 2-37 (37)
22 COG4888 Uncharacterized Zn rib 87.0 0.73 1.6E-05 37.8 3.3 37 216-252 19-58 (104)
23 PF14353 CpXC: CpXC protein 86.7 0.55 1.2E-05 38.4 2.6 18 236-253 34-51 (128)
24 TIGR01158 SUI1_rel translation 86.0 1.7 3.6E-05 35.2 5.0 53 152-209 35-87 (101)
25 PF08271 TF_Zn_Ribbon: TFIIB z 84.9 0.73 1.6E-05 31.3 2.1 35 221-257 2-36 (43)
26 PF04216 FdhE: Protein involve 84.3 0.66 1.4E-05 43.3 2.2 37 220-256 173-213 (290)
27 PRK14892 putative transcriptio 83.6 1.1 2.4E-05 36.3 2.9 37 216-252 18-54 (99)
28 COG2051 RPS27A Ribosomal prote 82.4 1.1 2.4E-05 34.1 2.3 30 219-250 19-48 (67)
29 PF14803 Nudix_N_2: Nudix N-te 81.9 1.1 2.3E-05 29.7 1.9 28 221-249 2-31 (34)
30 PRK03564 formate dehydrogenase 81.3 1.2 2.7E-05 42.7 2.8 38 219-256 187-228 (309)
31 PF05129 Elf1: Transcription e 80.6 2 4.2E-05 33.5 3.2 38 216-253 19-59 (81)
32 PF11331 DUF3133: Protein of u 80.5 1.2 2.6E-05 31.5 1.8 33 219-251 6-42 (46)
33 TIGR01159 DRP1 density-regulat 80.4 4.1 9E-05 36.1 5.6 56 156-215 103-162 (173)
34 PRK11788 tetratricopeptide rep 79.8 2.3 5.1E-05 39.2 4.1 44 206-256 339-384 (389)
35 COG0023 SUI1 Translation initi 79.2 5.6 0.00012 32.7 5.6 60 149-213 34-93 (104)
36 PF01921 tRNA-synt_1f: tRNA sy 78.0 3.3 7.2E-05 40.6 4.6 42 215-256 170-215 (360)
37 PF12760 Zn_Tnp_IS1595: Transp 77.9 1.9 4.1E-05 29.7 2.1 31 216-249 16-46 (46)
38 PRK08665 ribonucleotide-diphos 77.1 2 4.4E-05 45.6 3.1 42 205-251 688-751 (752)
39 COG1997 RPL43A Ribosomal prote 76.5 2.3 5E-05 34.0 2.6 42 206-251 23-64 (89)
40 PRK00415 rps27e 30S ribosomal 76.5 2.5 5.3E-05 31.5 2.5 30 219-250 11-40 (59)
41 COG3478 Predicted nucleic-acid 76.2 2.5 5.5E-05 32.2 2.6 35 218-252 3-52 (68)
42 smart00401 ZnF_GATA zinc finge 75.8 1.3 2.8E-05 31.6 0.8 33 220-252 4-37 (52)
43 TIGR00244 transcriptional regu 75.7 2.4 5.2E-05 36.8 2.6 31 221-251 2-39 (147)
44 PF05180 zf-DNL: DNL zinc fing 75.6 2.3 5E-05 32.3 2.2 35 219-253 4-42 (66)
45 PF13453 zf-TFIIB: Transcripti 75.4 3.5 7.6E-05 27.7 2.9 29 221-250 1-29 (41)
46 cd04762 HTH_MerR-trunc Helix-T 75.4 8.6 0.00019 24.8 4.8 47 162-213 2-48 (49)
47 TIGR01160 SUI1_MOF2 translatio 74.8 3.9 8.4E-05 33.9 3.5 60 151-215 34-98 (110)
48 PF09297 zf-NADH-PPase: NADH p 74.6 2 4.3E-05 27.4 1.5 26 221-249 5-30 (32)
49 PF04760 IF2_N: Translation in 74.5 3 6.5E-05 29.3 2.5 27 162-188 5-31 (54)
50 COG1096 Predicted RNA-binding 74.2 3 6.4E-05 37.6 2.9 27 219-250 149-175 (188)
51 PRK00420 hypothetical protein; 73.1 2.4 5.1E-05 35.2 1.9 31 219-253 23-53 (112)
52 TIGR01384 TFS_arch transcripti 73.1 4 8.6E-05 32.2 3.2 33 219-251 62-101 (104)
53 COG2835 Uncharacterized conser 72.7 2.7 5.8E-05 31.4 1.9 36 214-252 3-38 (60)
54 TIGR01385 TFSII transcription 72.5 3.5 7.6E-05 39.3 3.2 32 219-250 258-296 (299)
55 COG1779 C4-type Zn-finger prot 72.4 3.5 7.6E-05 37.5 3.0 33 218-251 13-54 (201)
56 TIGR00467 lysS_arch lysyl-tRNA 72.2 5.9 0.00013 40.5 4.9 73 181-255 112-205 (515)
57 PF02150 RNA_POL_M_15KD: RNA p 72.2 3.5 7.7E-05 27.2 2.2 30 221-253 3-33 (35)
58 cd00202 ZnF_GATA Zinc finger D 71.6 1 2.2E-05 32.5 -0.5 31 221-251 1-32 (54)
59 cd00674 LysRS_core_class_I cat 71.2 5.7 0.00012 38.7 4.4 92 163-255 89-207 (353)
60 TIGR01562 FdhE formate dehydro 71.1 2.8 6E-05 40.2 2.1 38 219-256 184-226 (305)
61 smart00661 RPOL9 RNA polymeras 70.2 3.2 6.9E-05 28.5 1.8 33 221-255 2-35 (52)
62 PF14205 Cys_rich_KTR: Cystein 69.4 3.8 8.2E-05 30.1 2.0 37 218-254 3-42 (55)
63 PF09855 DUF2082: Nucleic-acid 68.8 4.9 0.00011 30.2 2.6 32 221-252 2-48 (64)
64 PRK03954 ribonuclease P protei 68.1 4.5 9.9E-05 34.0 2.6 35 221-255 66-108 (121)
65 TIGR00100 hypA hydrogenase nic 68.0 4.4 9.6E-05 33.2 2.4 26 173-200 40-65 (115)
66 PF13717 zinc_ribbon_4: zinc-r 67.3 3.7 8E-05 27.2 1.5 30 219-250 2-35 (36)
67 COG3058 FdhE Uncharacterized p 67.2 2.3 5E-05 40.7 0.7 34 219-252 185-223 (308)
68 PF10058 DUF2296: Predicted in 65.1 5.6 0.00012 28.8 2.2 30 220-249 23-53 (54)
69 smart00531 TFIIE Transcription 64.8 6.6 0.00014 33.2 3.0 68 156-249 61-132 (147)
70 PF12898 Stc1: Stc1 domain; I 64.5 5.3 0.00012 31.1 2.2 52 196-255 7-65 (84)
71 PRK00241 nudC NADH pyrophospha 64.2 5.3 0.00011 37.0 2.5 39 211-252 91-129 (256)
72 PRK03824 hypA hydrogenase nick 63.9 8.4 0.00018 32.5 3.4 63 172-250 39-117 (135)
73 PF01927 Mut7-C: Mut7-C RNAse 63.5 8.3 0.00018 32.6 3.4 53 197-249 63-133 (147)
74 PRK00423 tfb transcription ini 63.4 4.5 9.7E-05 38.3 1.9 28 220-249 12-39 (310)
75 TIGR02098 MJ0042_CXXC MJ0042 f 63.3 4.5 9.7E-05 26.4 1.3 32 219-251 2-36 (38)
76 PRK07451 translation initiatio 63.2 16 0.00035 30.5 4.9 58 149-211 43-103 (115)
77 PRK00750 lysK lysyl-tRNA synth 62.6 13 0.00028 37.8 5.1 50 206-256 153-215 (510)
78 PRK00564 hypA hydrogenase nick 62.3 6.1 0.00013 32.5 2.2 57 174-250 41-98 (117)
79 PRK00398 rpoP DNA-directed RNA 62.2 8.2 0.00018 26.4 2.6 30 220-252 4-33 (46)
80 COG3529 Predicted nucleic-acid 62.2 1.5 3.3E-05 33.0 -1.2 37 213-250 5-42 (66)
81 KOG3507 DNA-directed RNA polym 62.1 3.3 7.1E-05 31.0 0.6 29 220-252 21-49 (62)
82 PLN00209 ribosomal protein S27 61.9 7.6 0.00017 31.0 2.6 30 219-250 36-65 (86)
83 PF08274 PhnA_Zn_Ribbon: PhnA 61.8 4.9 0.00011 26.0 1.2 27 220-250 3-29 (30)
84 PRK00564 hypA hydrogenase nick 61.1 9.1 0.0002 31.5 3.1 18 219-236 88-105 (117)
85 KOG2703 C4-type Zn-finger prot 60.6 5.9 0.00013 39.7 2.2 33 219-251 258-298 (460)
86 TIGR02159 PA_CoA_Oxy4 phenylac 60.5 9.7 0.00021 32.7 3.2 29 220-248 106-138 (146)
87 COG2956 Predicted N-acetylgluc 60.4 19 0.00042 35.6 5.6 79 165-256 304-384 (389)
88 COG1198 PriA Primosomal protei 60.3 7.1 0.00015 41.7 2.9 35 219-253 435-475 (730)
89 PRK12380 hydrogenase nickel in 60.3 15 0.00033 30.0 4.2 56 173-249 40-95 (113)
90 COG1163 DRG Predicted GTPase [ 60.2 9.4 0.0002 37.5 3.4 52 113-175 272-328 (365)
91 PF00320 GATA: GATA zinc finge 60.1 1.9 4.2E-05 28.4 -0.9 28 222-249 1-29 (36)
92 COG1594 RPB9 DNA-directed RNA 59.5 9.5 0.00021 31.4 2.9 33 219-251 72-111 (113)
93 PF07282 OrfB_Zn_ribbon: Putat 59.3 6.3 0.00014 28.7 1.7 28 220-250 29-56 (69)
94 PTZ00083 40S ribosomal protein 59.0 9.5 0.00021 30.4 2.7 30 219-250 35-64 (85)
95 PF01396 zf-C4_Topoisom: Topoi 58.9 8.5 0.00018 25.9 2.1 31 220-253 2-37 (39)
96 PRK09019 translation initiatio 58.7 26 0.00056 29.0 5.3 54 154-212 44-97 (108)
97 smart00834 CxxC_CXXC_SSSS Puta 58.5 6.1 0.00013 25.7 1.3 28 221-248 7-34 (41)
98 smart00659 RPOLCX RNA polymera 58.2 5.3 0.00012 27.7 1.0 30 221-254 4-33 (44)
99 COG1384 LysS Lysyl-tRNA synthe 57.4 16 0.00035 37.6 4.7 79 175-254 106-208 (521)
100 PRK03681 hypA hydrogenase nick 57.3 7.9 0.00017 31.7 2.1 58 173-250 40-97 (114)
101 PRK00762 hypA hydrogenase nick 56.5 9.1 0.0002 31.8 2.4 26 173-200 40-65 (124)
102 PF04194 PDCD2_C: Programmed c 56.2 2.1 4.5E-05 37.0 -1.6 18 163-180 60-77 (164)
103 PRK03681 hypA hydrogenase nick 54.9 19 0.00042 29.4 4.0 15 220-234 88-102 (114)
104 PRK00432 30S ribosomal protein 54.6 8 0.00017 27.5 1.5 28 219-250 20-47 (50)
105 PF08792 A2L_zn_ribbon: A2L zi 54.5 16 0.00034 24.0 2.7 29 219-251 3-32 (33)
106 PRK03824 hypA hydrogenase nick 54.5 10 0.00022 32.0 2.3 18 219-236 107-124 (135)
107 PF01667 Ribosomal_S27e: Ribos 53.6 6.2 0.00013 29.0 0.8 30 219-250 7-36 (55)
108 KOG0481 DNA replication licens 53.5 31 0.00067 36.2 6.0 140 117-260 24-181 (729)
109 PF00165 HTH_AraC: Bacterial r 53.3 19 0.00042 23.6 3.2 28 161-188 9-36 (42)
110 TIGR00100 hypA hydrogenase nic 53.2 15 0.00033 30.0 3.1 15 220-234 87-101 (115)
111 PF09723 Zn-ribbon_8: Zinc rib 52.2 10 0.00022 25.7 1.7 30 221-250 7-36 (42)
112 cd04761 HTH_MerR-SF Helix-Turn 51.5 34 0.00074 22.5 4.2 45 162-211 2-46 (49)
113 PRK12380 hydrogenase nickel in 51.5 11 0.00025 30.7 2.1 18 219-236 86-103 (113)
114 PF06322 Phage_NinH: Phage Nin 51.4 21 0.00046 27.0 3.3 37 161-204 17-53 (64)
115 PRK05580 primosome assembly pr 51.4 10 0.00022 39.8 2.2 34 219-252 381-420 (679)
116 PF04032 Rpr2: RNAse P Rpr2/Rp 51.3 18 0.0004 27.0 3.1 29 220-248 47-85 (85)
117 PRK11827 hypothetical protein; 50.7 8.1 0.00018 28.8 1.1 34 216-252 5-38 (60)
118 COG0375 HybF Zn finger protein 50.4 16 0.00034 30.6 2.8 22 177-199 43-64 (115)
119 PRK08332 ribonucleotide-diphos 49.6 17 0.00036 42.5 3.7 41 209-252 1695-1738(1740)
120 PHA00626 hypothetical protein 48.3 19 0.0004 26.9 2.6 35 221-255 2-38 (59)
121 PRK12286 rpmF 50S ribosomal pr 47.9 14 0.00031 27.0 1.9 28 215-250 23-50 (57)
122 PF03604 DNA_RNApol_7kD: DNA d 47.8 6.7 0.00015 25.6 0.2 27 221-251 2-28 (32)
123 PF13936 HTH_38: Helix-turn-he 47.1 20 0.00043 24.4 2.4 22 161-182 21-42 (44)
124 COG0375 HybF Zn finger protein 46.9 26 0.00057 29.3 3.6 17 222-238 89-105 (115)
125 PF05077 DUF678: Protein of un 46.8 9.8 0.00021 29.6 1.0 11 239-249 56-66 (74)
126 PRK06556 vitamin B12-dependent 46.8 18 0.00039 39.8 3.3 44 203-251 908-951 (953)
127 PRK07562 ribonucleotide-diphos 46.1 15 0.00032 41.4 2.6 39 207-251 1180-1218(1220)
128 TIGR01391 dnaG DNA primase, ca 44.6 28 0.00061 34.3 4.0 33 220-252 35-67 (415)
129 cd03031 GRX_GRX_like Glutaredo 44.4 25 0.00053 30.2 3.2 79 145-250 59-143 (147)
130 PF12172 DUF35_N: Rubredoxin-l 44.4 15 0.00033 23.8 1.5 17 235-251 6-22 (37)
131 PRK06824 translation initiatio 44.4 33 0.00072 28.7 3.9 55 153-212 53-107 (118)
132 COG2023 RPR2 RNase P subunit R 44.2 23 0.00049 29.3 2.8 35 221-255 58-97 (105)
133 COG5631 Predicted transcriptio 44.2 20 0.00043 32.2 2.6 32 162-193 100-131 (199)
134 PF04606 Ogr_Delta: Ogr/Delta- 44.1 24 0.00053 24.4 2.6 30 221-250 1-37 (47)
135 TIGR01206 lysW lysine biosynth 44.0 12 0.00026 27.2 1.1 33 220-255 3-37 (54)
136 TIGR00373 conserved hypothetic 43.9 15 0.00032 31.7 1.8 60 120-187 43-103 (158)
137 PF08535 KorB: KorB domain; I 43.3 21 0.00045 27.7 2.4 21 162-182 5-25 (93)
138 TIGR03830 CxxCG_CxxCG_HTH puta 43.3 23 0.00049 28.2 2.7 31 222-252 1-43 (127)
139 PF13248 zf-ribbon_3: zinc-rib 43.1 9.6 0.00021 23.3 0.4 23 220-249 3-25 (26)
140 PF11781 RRN7: RNA polymerase 43.0 16 0.00034 24.4 1.4 25 221-249 10-34 (36)
141 PF09862 DUF2089: Protein of u 42.9 19 0.00041 30.0 2.2 21 222-249 1-21 (113)
142 PF03966 Trm112p: Trm112p-like 42.4 17 0.00037 26.8 1.7 14 240-253 53-66 (68)
143 PF06044 DRP: Dam-replacing fa 41.0 18 0.0004 34.0 2.0 59 201-259 12-72 (254)
144 PF13597 NRDD: Anaerobic ribon 40.5 45 0.00098 34.2 4.9 68 183-261 447-526 (546)
145 TIGR00595 priA primosomal prot 40.4 19 0.00042 36.4 2.2 66 172-253 182-253 (505)
146 PRK05667 dnaG DNA primase; Val 40.3 34 0.00073 35.5 4.0 35 218-252 34-69 (580)
147 smart00647 IBR In Between Ring 40.3 34 0.00074 23.8 2.9 39 210-251 6-51 (64)
148 COG1594 RPB9 DNA-directed RNA 39.8 24 0.00052 29.0 2.3 31 221-254 4-36 (113)
149 PRK00762 hypA hydrogenase nick 39.5 36 0.00079 28.2 3.4 15 119-133 8-22 (124)
150 PHA02942 putative transposase; 39.4 19 0.00041 35.4 1.9 27 220-250 326-352 (383)
151 COG0675 Transposase and inacti 39.4 17 0.00036 32.7 1.5 22 220-249 310-331 (364)
152 KOG2768 Translation initiation 39.0 12 0.00027 34.6 0.5 21 14-34 20-40 (231)
153 COG3741 HutG N-formylglutamate 38.9 4.9 0.00011 38.1 -2.1 79 156-234 63-161 (272)
154 TIGR01031 rpmF_bact ribosomal 38.8 22 0.00048 25.7 1.8 25 217-249 24-48 (55)
155 PF06107 DUF951: Bacterial pro 38.7 34 0.00074 25.4 2.7 31 223-253 14-44 (57)
156 COG2093 DNA-directed RNA polym 38.6 14 0.00031 27.9 0.7 11 221-231 20-30 (64)
157 KOG2907 RNA polymerase I trans 38.4 20 0.00043 30.1 1.6 33 220-252 75-114 (116)
158 COG5349 Uncharacterized protei 37.9 9.9 0.00021 32.3 -0.2 26 220-253 22-53 (126)
159 TIGR03826 YvyF flagellar opero 37.6 37 0.00081 29.0 3.2 55 161-247 47-101 (137)
160 PF10080 DUF2318: Predicted me 36.7 32 0.0007 28.0 2.6 35 218-256 34-68 (102)
161 PF13597 NRDD: Anaerobic ribon 36.7 21 0.00045 36.7 1.8 39 219-266 504-542 (546)
162 KOG2593 Transcription initiati 36.5 41 0.00089 34.0 3.8 97 120-249 58-162 (436)
163 TIGR03831 YgiT_finger YgiT-typ 35.7 38 0.00081 22.2 2.4 8 242-249 34-41 (46)
164 PF05876 Terminase_GpA: Phage 35.4 32 0.00069 35.4 2.9 34 219-252 200-241 (557)
165 smart00497 IENR1 Intron encode 35.1 95 0.0021 20.8 4.5 25 159-183 16-40 (53)
166 smart00422 HTH_MERR helix_turn 35.1 83 0.0018 22.2 4.3 46 162-211 2-47 (70)
167 PHA02893 hypothetical protein; 35.0 17 0.00036 29.1 0.6 11 239-249 68-78 (88)
168 PF08394 Arc_trans_TRASH: Arch 34.9 35 0.00076 23.1 2.1 27 222-248 1-31 (37)
169 PF04810 zf-Sec23_Sec24: Sec23 34.5 17 0.00038 24.3 0.6 33 220-254 3-38 (40)
170 PF06573 Churchill: Churchill 34.5 42 0.00092 28.0 2.9 36 214-249 22-67 (112)
171 PF01155 HypA: Hydrogenase exp 34.3 40 0.00086 27.4 2.8 26 173-200 40-65 (113)
172 TIGR00686 phnA alkylphosphonat 34.2 26 0.00056 29.1 1.7 31 220-254 3-33 (109)
173 PF15494 SRCR_2: Scavenger rec 34.1 27 0.00059 27.2 1.8 15 236-250 84-98 (98)
174 COG1656 Uncharacterized conser 34.1 20 0.00043 31.8 1.0 71 170-250 52-140 (165)
175 PF03811 Zn_Tnp_IS1: InsA N-te 34.1 44 0.00095 22.3 2.5 27 219-246 5-35 (36)
176 PF02591 DUF164: Putative zinc 33.8 40 0.00086 23.9 2.4 23 203-227 32-54 (56)
177 PF04216 FdhE: Protein involve 33.6 29 0.00064 32.3 2.2 31 219-249 211-247 (290)
178 PF14599 zinc_ribbon_6: Zinc-r 32.9 19 0.00042 26.8 0.7 13 219-231 48-60 (61)
179 PF07191 zinc-ribbons_6: zinc- 32.8 27 0.00058 26.9 1.4 8 221-228 3-10 (70)
180 cd01896 DRG The developmentall 32.8 1.7E+02 0.0036 26.2 6.8 95 120-228 92-189 (233)
181 PF04981 NMD3: NMD3 family ; 32.7 19 0.00042 32.6 0.8 33 220-252 14-47 (236)
182 COG3677 Transposase and inacti 32.4 49 0.0011 27.8 3.1 41 213-254 24-67 (129)
183 PF05379 Peptidase_C23: Carlav 32.3 46 0.00099 26.3 2.7 63 163-234 7-70 (89)
184 PRK07220 DNA topoisomerase I; 32.3 37 0.00081 36.1 2.9 34 220-253 636-670 (740)
185 PRK01310 hypothetical protein; 31.9 96 0.0021 25.3 4.6 41 174-216 54-102 (104)
186 PRK09678 DNA-binding transcrip 31.7 47 0.001 25.5 2.6 30 221-251 3-40 (72)
187 TIGR01764 excise DNA binding d 31.5 1.2E+02 0.0027 19.3 4.4 48 160-213 1-48 (49)
188 smart00342 HTH_ARAC helix_turn 31.5 67 0.0014 22.5 3.3 28 161-188 51-79 (84)
189 PF08209 Sgf11: Sgf11 (transcr 31.5 24 0.00052 23.3 0.9 11 218-228 3-13 (33)
190 PF15616 TerY-C: TerY-C metal 31.4 62 0.0014 27.6 3.6 46 217-262 75-127 (131)
191 TIGR01566 ZF_HD_prot_N ZF-HD h 31.2 22 0.00048 26.0 0.7 16 237-252 33-48 (53)
192 PRK14704 anaerobic ribonucleos 31.0 36 0.00079 35.7 2.5 51 203-261 533-597 (618)
193 cd01106 HTH_TipAL-Mta Helix-Tu 30.5 98 0.0021 24.2 4.4 46 162-211 2-47 (103)
194 PF13408 Zn_ribbon_recom: Reco 30.3 49 0.0011 22.6 2.4 30 218-247 4-33 (58)
195 TIGR01051 topA_bact DNA topois 30.1 29 0.00063 36.0 1.6 55 196-252 535-609 (610)
196 PRK14973 DNA topoisomerase I; 30.1 30 0.00065 38.0 1.8 33 221-253 637-670 (936)
197 KOG2906 RNA polymerase III sub 29.9 45 0.00098 27.5 2.4 30 221-253 3-34 (105)
198 PF04423 Rad50_zn_hook: Rad50 29.8 17 0.00036 25.6 -0.1 8 221-228 22-29 (54)
199 PF11023 DUF2614: Protein of u 29.5 26 0.00057 29.3 1.0 35 219-258 69-103 (114)
200 COG1545 Predicted nucleic-acid 29.4 30 0.00066 29.3 1.4 35 206-250 16-53 (140)
201 TIGR02827 RNR_anaer_Bdell anae 28.8 59 0.0013 34.0 3.6 58 199-263 502-570 (586)
202 KOG2691 RNA polymerase II subu 28.7 59 0.0013 27.2 2.9 32 219-251 73-112 (113)
203 PF14353 CpXC: CpXC protein 28.2 50 0.0011 26.8 2.5 32 196-228 16-47 (128)
204 PF14446 Prok-RING_1: Prokaryo 28.1 32 0.00068 25.2 1.1 12 218-229 20-31 (54)
205 PRK10219 DNA-binding transcrip 28.1 75 0.0016 24.6 3.3 47 118-188 3-49 (107)
206 TIGR02609 doc_partner putative 27.9 1.5E+02 0.0033 22.2 4.9 58 150-219 3-65 (74)
207 PRK08402 replication factor A; 27.6 43 0.00094 32.8 2.3 47 197-253 197-243 (355)
208 PF09332 Mcm10: Mcm10 replicat 27.5 25 0.00054 34.5 0.6 53 199-251 229-296 (344)
209 cd01279 HTH_HspR-like Helix-Tu 27.4 1.1E+02 0.0024 24.0 4.2 45 162-211 3-47 (98)
210 PF00641 zf-RanBP: Zn-finger i 27.0 25 0.00054 21.9 0.3 25 220-251 5-29 (30)
211 PRK10220 hypothetical protein; 26.6 42 0.00091 28.0 1.7 31 220-254 4-34 (111)
212 TIGR03829 YokU_near_AblA uncha 26.6 50 0.0011 26.5 2.0 11 240-250 35-45 (89)
213 PF05315 ICEA: ICEA Protein; 26.2 35 0.00076 31.5 1.2 64 171-234 45-116 (230)
214 PF06677 Auto_anti-p27: Sjogre 26.0 53 0.0012 22.6 1.9 34 210-247 8-41 (41)
215 PF14116 YyzF: YyzF-like prote 25.8 54 0.0012 23.4 1.9 40 205-249 3-42 (48)
216 KOG3084 NADH pyrophosphatase I 25.8 42 0.00091 32.9 1.8 22 208-229 139-160 (345)
217 PF10083 DUF2321: Uncharacteri 25.8 41 0.00088 29.7 1.5 33 220-252 40-80 (158)
218 PRK02935 hypothetical protein; 25.6 49 0.0011 27.5 1.9 34 220-258 71-104 (110)
219 TIGR02605 CxxC_CxxC_SSSS putat 25.5 46 0.001 22.9 1.5 29 221-249 7-35 (52)
220 PF01783 Ribosomal_L32p: Ribos 25.1 22 0.00047 25.7 -0.2 24 218-249 25-48 (56)
221 PF08772 NOB1_Zn_bind: Nin one 24.9 41 0.00088 25.9 1.2 17 235-251 4-20 (73)
222 PF04135 Nop10p: Nucleolar RNA 24.9 66 0.0014 23.4 2.2 17 237-253 12-30 (53)
223 cd04476 RPA1_DBD_C RPA1_DBD_C: 24.8 88 0.0019 26.4 3.4 27 219-250 34-61 (166)
224 PF03119 DNA_ligase_ZBD: NAD-d 24.6 33 0.00071 21.6 0.6 21 221-244 1-21 (28)
225 PRK11788 tetratricopeptide rep 24.6 37 0.00081 31.3 1.2 16 219-234 368-383 (389)
226 PRK11511 DNA-binding transcrip 24.5 89 0.0019 25.4 3.3 29 161-189 26-54 (127)
227 PF12728 HTH_17: Helix-turn-he 24.5 1.8E+02 0.004 19.4 4.4 47 161-213 2-48 (51)
228 PF09538 FYDLN_acid: Protein o 24.3 33 0.00072 28.1 0.7 33 220-256 10-43 (108)
229 PF14768 RPA_interact_C: Repli 24.1 92 0.002 23.9 3.1 55 197-252 23-82 (82)
230 PRK14714 DNA polymerase II lar 24.1 41 0.0009 38.3 1.6 8 242-249 694-701 (1337)
231 cd02983 P5_C P5 family, C-term 24.1 99 0.0021 25.5 3.5 42 177-218 71-117 (130)
232 COG5242 TFB4 RNA polymerase II 23.9 1.3E+02 0.0027 28.6 4.4 48 141-192 180-233 (296)
233 PTZ00073 60S ribosomal protein 23.9 27 0.0006 28.1 0.1 31 218-256 15-45 (91)
234 PRK06266 transcription initiat 23.6 31 0.00067 30.4 0.4 30 218-249 116-145 (178)
235 TIGR02487 NrdD anaerobic ribon 23.6 39 0.00084 35.0 1.2 53 203-262 498-561 (579)
236 COG1996 RPC10 DNA-directed RNA 23.5 40 0.00086 24.2 0.9 34 221-257 8-41 (49)
237 cd01104 HTH_MlrA-CarA Helix-Tu 23.4 2.2E+02 0.0048 19.9 4.8 46 162-212 2-48 (68)
238 PF10263 SprT-like: SprT-like 23.0 75 0.0016 26.2 2.6 16 161-176 86-101 (157)
239 PRK14873 primosome assembly pr 22.8 58 0.0013 34.4 2.3 33 218-250 382-420 (665)
240 COG5595 Zn-ribbon-containing, 22.4 48 0.001 30.7 1.4 77 165-248 155-247 (256)
241 PF09332 Mcm10: Mcm10 replicat 22.4 80 0.0017 31.0 3.0 32 216-250 282-313 (344)
242 TIGR01562 FdhE formate dehydro 22.3 83 0.0018 30.3 3.0 27 104-130 84-112 (305)
243 KOG3277 Uncharacterized conser 22.2 63 0.0014 28.6 2.0 35 219-253 79-117 (165)
244 PF04502 DUF572: Family of unk 22.1 80 0.0017 30.3 2.9 48 219-266 40-105 (324)
245 smart00342 HTH_ARAC helix_turn 22.0 1.3E+02 0.0028 21.0 3.4 27 162-188 3-29 (84)
246 PRK04296 thymidine kinase; Pro 22.0 96 0.0021 26.8 3.2 44 204-247 125-185 (190)
247 PRK06319 DNA topoisomerase I/S 21.9 70 0.0015 34.8 2.7 35 220-254 593-630 (860)
248 smart00249 PHD PHD zinc finger 21.9 64 0.0014 20.4 1.6 26 221-252 1-26 (47)
249 PF15288 zf-CCHC_6: Zinc knuck 21.6 42 0.00091 23.2 0.7 16 241-256 2-17 (40)
250 PRK12366 replication factor A; 21.6 63 0.0014 33.9 2.2 29 219-252 532-560 (637)
251 PRK03564 formate dehydrogenase 21.6 84 0.0018 30.4 2.9 18 113-130 98-115 (309)
252 PHA02540 61 DNA primase; Provi 21.2 87 0.0019 30.6 3.0 34 220-253 28-68 (337)
253 PRK13501 transcriptional activ 21.2 1E+02 0.0022 28.0 3.3 29 161-189 193-221 (290)
254 KOG2422 Uncharacterized conser 21.2 83 0.0018 33.3 2.9 20 117-136 169-188 (665)
255 cd01675 RNR_III Class III ribo 20.9 92 0.002 32.1 3.2 40 203-250 492-542 (555)
256 TIGR02487 NrdD anaerobic ribon 20.9 83 0.0018 32.6 2.9 29 221-258 540-568 (579)
257 PRK05978 hypothetical protein; 20.8 44 0.00095 29.0 0.8 42 207-253 24-65 (148)
258 COG1645 Uncharacterized Zn-fin 20.6 54 0.0012 28.1 1.3 26 221-251 30-55 (131)
259 KOG3239 Density-regulated prot 20.4 1.7E+02 0.0037 26.5 4.4 47 169-215 124-174 (193)
260 PF04770 ZF-HD_dimer: ZF-HD pr 20.4 48 0.001 24.9 0.8 17 236-252 36-52 (60)
261 KOG1814 Predicted E3 ubiquitin 20.1 57 0.0012 33.0 1.5 46 201-249 344-395 (445)
No 1
>KOG2768 consensus Translation initiation factor 2, beta subunit (eIF-2beta) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.9e-71 Score=492.98 Aligned_cols=215 Identities=65% Similarity=1.000 Sum_probs=181.8
Q ss_pred cccccCccccccccccccCCCccccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCccHHHHHHHHHHHH
Q 024241 50 LSVSEGLESTFTGLKKKKKKPVESSLLNDEIGDAGDDLDGHVGEDDEADGSGGPRQRYPWEGSDRDYEYEELLGRVFNIL 129 (270)
Q Consensus 50 ~~~~~~~~~~~~~~KKKKKk~~~~~~~~~e~~~~~e~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~YeeLL~R~~~~l 129 (270)
.+++++++..+.++||||||++....++++...+.+..++...++.+. ...++.++|.|++++|.|++||.|+|++|
T Consensus 16 ~~~~~~l~~~~~~kKKKKkk~k~~s~~ee~~~~~~e~~~e~~~~~~e~---~~~~~~~~~~g~e~dy~Y~ElL~rvf~il 92 (231)
T KOG2768|consen 16 DEASERLDFLSLKKKKKKKKSKSLSALEEEDVNAGEFADEDKDPDKEV---RQNQQGVSWVGSEPDYTYYELLSRVFNIL 92 (231)
T ss_pred cchhhcccccccccccccCCCCchhhhHHHHHhccchhhhccChhhcc---ccccccccccccCCCccHHHHHHHHHHHH
Confidence 344555555556666666666544433333222233222221111111 13334499999999999999999999999
Q ss_pred hhcCCCcccCcceeecCCCeEEEeCceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHH
Q 024241 130 RENNPELAGDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFE 209 (270)
Q Consensus 130 ~~~np~~~~~~~R~~mP~p~V~~eG~kKTvi~Nf~dI~k~L~R~p~hv~kyl~~ELGt~gsid~~~rlii~G~f~~k~ie 209 (270)
+++|||++|++.+|.|+||||.|+| +||+|+||+|||+.|||+|+||++||++||||+||||+++||||+|+|++++||
T Consensus 93 reknpe~aGe~~k~v~~PPqvlReg-kkT~f~Nf~Dick~mhR~pdHv~~FLlAELgTsGSidg~~rLviKGrfq~kq~e 171 (231)
T KOG2768|consen 93 REKNPELAGEKRKFVMKPPQVLREG-KKTVFVNFADICKTMHRSPDHVMQFLLAELGTSGSIDGQQRLVIKGRFQQKQFE 171 (231)
T ss_pred HhcCchhcccccceeeCCHHHHhhc-cceeeeeHHHHHHHhccChHHHHHHHHHHhccccccCCCceEEEeccccHHHHH
Confidence 9999999999999999999999999 999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHhccceEeeCCCCCCcceEEEcCcEEEeEeccCCCcccccccccceEEEeeeccC
Q 024241 210 GILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKCGSGRSVAPIKAGFQARVGRRNA 268 (270)
Q Consensus 210 ~~L~~YI~eYVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V~~ik~gf~a~~~kr~~ 268 (270)
++||+||.+||+|.+|+||||.|.++||||||+|..||++++|.+|++||+|.+|+|+.
T Consensus 172 ~VLRrYI~eyV~C~~CkSpdt~L~kenRLfFL~C~~cgs~~sv~~Iktgf~A~~~kr~~ 230 (231)
T KOG2768|consen 172 NVLRRYIKEYVTCKTCKSPDTILQKENRLFFLRCEKCGSRCSVASIKTGFQAVVGKRAM 230 (231)
T ss_pred HHHHHHHHHheEeeecCChhHHhhhhcceEEEEecCCCCeeeeeeeecccEEecccccc
Confidence 99999999999999999999999999999999999999999999999999999999975
No 2
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=100.00 E-value=4.7e-55 Score=368.16 Aligned_cols=135 Identities=44% Similarity=0.852 Sum_probs=130.2
Q ss_pred CccHHHHHHHHHHHHhhcCCCcccCcceeecCCCeEEEeCceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecCC
Q 024241 115 DYEYEELLGRVFNILRENNPELAGDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQ 194 (270)
Q Consensus 115 ~~~YeeLL~R~~~~l~~~np~~~~~~~R~~mP~p~V~~eG~kKTvi~Nf~dI~k~L~R~p~hv~kyl~~ELGt~gsid~~ 194 (270)
+|+|++||+|||+.| |+..++.+||+||+|+|.++| +||+|+||.|||++|||+|+||++||++||||+|+|+ +
T Consensus 4 ~~~Y~~lL~R~~~~l----p~~~~~~~R~~~p~~~v~~eG-~kTvi~Nf~~I~~~L~R~~~hv~ky~~~ELgt~g~i~-~ 77 (138)
T PRK03988 4 YYDYEELLDRAYEKL----PEKVFKESRFEVPKPDVRIEG-NRTIIRNFKEIADRLNRDPKHVAKFLLKELGTAGNIE-G 77 (138)
T ss_pred ccCHHHHHHHHHHHC----ccccCCCcceeCCCCeEEEEc-CcEEEecHHHHHHHHCCCHHHHHHHHHHHhCCceeec-C
Confidence 689999999999999 777778889999999999999 7899999999999999999999999999999999996 5
Q ss_pred ceEEEEeecChHHHHHHHHHhccceEeeCCCCCCcceEEEcCcEEEeEeccCCCccccccc
Q 024241 195 QRLVVKGRFAPKNFEGILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKCGSGRSVAPI 255 (270)
Q Consensus 195 ~rlii~G~f~~k~ie~~L~~YI~eYVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V~~i 255 (270)
++|||+|+|++++|+++|++||++||+|++|+||||.|++++|+++++|+||||++||++|
T Consensus 78 ~~lii~G~~~~~~i~~~L~~yI~~yVlC~~C~spdT~l~k~~r~~~l~C~ACGa~~~V~~~ 138 (138)
T PRK03988 78 GRLILQGKFSPRVINEKIDRYVKEYVICPECGSPDTKLIKEGRIWVLKCEACGAETPVKPL 138 (138)
T ss_pred CEEEEEEeeCHHHHHHHHHHHHHhcEECCCCCCCCcEEEEcCCeEEEEcccCCCCCcCCcC
Confidence 7999999999999999999999999999999999999999999999999999999999875
No 3
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=100.00 E-value=3.8e-54 Score=360.68 Aligned_cols=133 Identities=36% Similarity=0.740 Sum_probs=128.0
Q ss_pred cHHHHHHHHHHHHhhcCCCcccCcceeecCCCeEEEeCceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecCCce
Q 024241 117 EYEELLGRVFNILRENNPELAGDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQR 196 (270)
Q Consensus 117 ~YeeLL~R~~~~l~~~np~~~~~~~R~~mP~p~V~~eG~kKTvi~Nf~dI~k~L~R~p~hv~kyl~~ELGt~gsid~~~r 196 (270)
+|++||+|||+.| |+..++.+||+||+|+|.++| +||+|.||.+||++|||+|+||++||++||||+|+|++ ++
T Consensus 1 ~Y~~lL~R~~~~l----~~~~~~~~R~~mP~~~v~~eG-~kTvi~Nf~~Ia~~L~R~~~~v~ky~~~ELgt~g~i~~-~r 74 (133)
T TIGR00311 1 DYEKLLERAIDQL----PDEVFETKRFEVPKAYIVIEG-NRTIIQNFREVAKALNRDEQHLLKYLLKELGTAGNLEG-GR 74 (133)
T ss_pred CHHHHHHHHHHHC----ccccCCCccccCCCceEEEEc-CcEEEecHHHHHHHHCCCHHHHHHHHHHHhCCCceecC-CE
Confidence 5999999999999 776677889999999999999 78999999999999999999999999999999999985 69
Q ss_pred EEEEeecChHHHHHHHHHhccceEeeCCCCCCcceEEEcCcEEEeEeccCCCccccccc
Q 024241 197 LVVKGRFAPKNFEGILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKCGSGRSVAPI 255 (270)
Q Consensus 197 lii~G~f~~k~ie~~L~~YI~eYVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V~~i 255 (270)
|||+|+|++++|+++|++||++||+|++|+||||.|++++|+++++|+||||++||.+|
T Consensus 75 lii~G~~~~~~i~~~L~~yI~~yVlC~~C~sPdT~l~k~~r~~~l~C~ACGa~~~v~~~ 133 (133)
T TIGR00311 75 LILQGKFTHFLLNERIEDYVRKYVICRECNRPDTRIIKEGRVSLLKCEACGAKAPLRNI 133 (133)
T ss_pred EEEEeecCHHHHHHHHHHHHhheEECCCCCCCCcEEEEeCCeEEEecccCCCCCccCcC
Confidence 99999999999999999999999999999999999999999999999999999999876
No 4
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=100.00 E-value=4.5e-52 Score=368.23 Aligned_cols=137 Identities=42% Similarity=0.827 Sum_probs=132.2
Q ss_pred ccHHHHHHHHHHHHhhcCCCcccCcceeecCCCeEEEeCceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecCCc
Q 024241 116 YEYEELLGRVFNILRENNPELAGDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQ 195 (270)
Q Consensus 116 ~~YeeLL~R~~~~l~~~np~~~~~~~R~~mP~p~V~~eG~kKTvi~Nf~dI~k~L~R~p~hv~kyl~~ELGt~gsid~~~ 195 (270)
|+|++||+|+|+.| |+..++.+||+||+|+|.++| +||+|+||.|||++|||+|+||++||++||||+|+|++ +
T Consensus 1 ~~Y~~lL~r~~~~l----~~~~~~~~R~~~p~~~v~~eG-~kT~i~N~~~i~~~l~R~~~~~~ky~~~ELgt~~~~~~-~ 74 (201)
T PRK12336 1 MDYESLLDRAMEVL----PEPTKSGERFSIPEPKIFIEG-KTTILTNFGEIADALNRDPDHLMKFLQRELGTAGKIEG-G 74 (201)
T ss_pred CCHHHHHHHHHHHC----CcccCCccceecCCceEEEEc-CcEEEecHHHHHHHHCCCHHHHHHHHHHHhCCcceecC-C
Confidence 68999999999999 888888899999999999999 89999999999999999999999999999999999986 5
Q ss_pred eEEEEeecChHHHHHHHHHhccceEeeCCCCCCcceEEEcCcEEEeEeccCCCcccccccccc
Q 024241 196 RLVVKGRFAPKNFEGILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKCGSGRSVAPIKAG 258 (270)
Q Consensus 196 rlii~G~f~~k~ie~~L~~YI~eYVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V~~ik~g 258 (270)
+|||+|+|++++||++|++||++||+|++|+||||.|++++|+++|+|+||||+++|.++|+-
T Consensus 75 ~~ii~G~~~~~~i~~~l~~yi~~yV~C~~C~~pdT~l~k~~~~~~l~C~aCGa~~~v~~~~~~ 137 (201)
T PRK12336 75 RAVFNGKFTEEDIQAAIDAYVDEYVICSECGLPDTRLVKEDRVLMLRCDACGAHRPVKKRKAS 137 (201)
T ss_pred EEEEEeeeCHHHHHHHHHHHHHheEECCCCCCCCcEEEEcCCeEEEEcccCCCCccccccccc
Confidence 999999999999999999999999999999999999999999999999999999999998743
No 5
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=100.00 E-value=2.2e-48 Score=316.61 Aligned_cols=109 Identities=63% Similarity=1.136 Sum_probs=106.5
Q ss_pred ceeecCCCeEEEeCceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHHHhccceE
Q 024241 141 RRTVMRPPQVLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILRRYVNEYV 220 (270)
Q Consensus 141 ~R~~mP~p~V~~eG~kKTvi~Nf~dI~k~L~R~p~hv~kyl~~ELGt~gsid~~~rlii~G~f~~k~ie~~L~~YI~eYV 220 (270)
+||+||+|+|.++|++||+|.||.|||++|||+|+||++||++||||+|+||++++|||+|+|++++||++|++||++||
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 68999999999999659999999999999999999999999999999999999889999999999999999999999999
Q ss_pred eeCCCCCCcceEEEcCcEEEeEeccCCCc
Q 024241 221 ICLGCKSPDTILSKENRLFFLRCEKCGSG 249 (270)
Q Consensus 221 lC~~C~sPDT~L~ke~rl~~l~C~aCGa~ 249 (270)
+|++|+||||.|++++|+++|+|+||||+
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 99999999999999999999999999985
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=1.2e-48 Score=324.31 Aligned_cols=120 Identities=52% Similarity=1.000 Sum_probs=111.6
Q ss_pred hcCCCc-ccCcceeecCCCeEEEeCceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHH
Q 024241 131 ENNPEL-AGDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFE 209 (270)
Q Consensus 131 ~~np~~-~~~~~R~~mP~p~V~~eG~kKTvi~Nf~dI~k~L~R~p~hv~kyl~~ELGt~gsid~~~rlii~G~f~~k~ie 209 (270)
++||+. .++..||+||+|+|.++|++||+|+||.|||++|||+|+||++||++||||+|+||++++|||+|+|++++||
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 467984 5555699999999999999999999999999999999999999999999999999997899999999999999
Q ss_pred HHHHHhccceEeeCCCCCCcceEEEcCcEEEeEeccCCCcc
Q 024241 210 GILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKCGSGR 250 (270)
Q Consensus 210 ~~L~~YI~eYVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~ 250 (270)
++|++||++||+|++|+||||.|++++|+++++|.||||++
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 99999999999999999999999999999999999999986
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=6e-44 Score=304.55 Aligned_cols=147 Identities=42% Similarity=0.761 Sum_probs=139.0
Q ss_pred CCCccHHHHHHHHHHHHhhcCCCcccCcc-eeecCCCeEEEeCceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceee
Q 024241 113 DRDYEYEELLGRVFNILRENNPELAGDRR-RTVMRPPQVLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSL 191 (270)
Q Consensus 113 ~~~~~YeeLL~R~~~~l~~~np~~~~~~~-R~~mP~p~V~~eG~kKTvi~Nf~dI~k~L~R~p~hv~kyl~~ELGt~gsi 191 (270)
...++|++||+|+|..+ |+...... ||.||+|.|.++| ++|++.||.|||++|||+|+|+++||.+||||+|++
T Consensus 3 ~~~~~yeelLeR~~~~l----P~~~~~~~~R~~ip~~~i~~~g-~~Ti~~Nf~dia~~l~rDp~h~~k~l~kel~t~g~~ 77 (151)
T COG1601 3 EMEDDYEELLERAYSEL----PEKEVKNDERFRIPEPEINREG-NRTIIRNFGDIAEALNRDPEHLVKFLKKELGTAGSI 77 (151)
T ss_pred hhhhhHHHHHHHHHHhC----CccccccccceecCCcceeccc-chhHHHhHHHHHHHhcCCHHHHHHHHHHHhcccccc
Confidence 34678999999999766 99877665 9999999999999 999999999999999999999999999999999999
Q ss_pred cCCceEEEEeecChHHHHHHHHHhccceEeeCCCCCCcceEEEcCcEEEeEeccCCCcccccccccceEEEee
Q 024241 192 DGQQRLVVKGRFAPKNFEGILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKCGSGRSVAPIKAGFQARVG 264 (270)
Q Consensus 192 d~~~rlii~G~f~~k~ie~~L~~YI~eYVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V~~ik~gf~a~~~ 264 (270)
++.++|||+|+|++++|++.|++||..||.|++|+||||.|++++|+|+|+|.||||.+||..++.|.++.++
T Consensus 78 d~~~rlvl~g~f~~~~i~~~i~~yi~~yv~C~~c~s~dt~l~~~~R~~~l~c~acGa~~pv~~~~~~~~~~~~ 150 (151)
T COG1601 78 DGKGRLVLQGKFSDSEIVNEIERYIAEYVKCKECGSPDTELIKEERLLFLKCEACGAIRPVKLMKEYNLDFVS 150 (151)
T ss_pred CCcceEEEEecccHHHHHHHHHHHHHheeEeccCCCCchhhhhhhhhHhhHHHHhCCcccchhhhhcchhhhc
Confidence 9988999999999999999999999999999999999999999999999999999999999999988877553
No 8
>KOG2767 consensus Translation initiation factor 5 (eIF-5) [Translation, ribosomal structure and biogenesis]
Probab=99.97 E-value=2.1e-33 Score=264.60 Aligned_cols=124 Identities=26% Similarity=0.471 Sum_probs=114.5
Q ss_pred ccCcceeecCCCeEEEeC---ceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecC-CceEEEEeecChHHHHHHH
Q 024241 137 AGDRRRTVMRPPQVLREG---TKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDG-QQRLVVKGRFAPKNFEGIL 212 (270)
Q Consensus 137 ~~~~~R~~mP~p~V~~eG---~kKTvi~Nf~dI~k~L~R~p~hv~kyl~~ELGt~gsid~-~~rlii~G~f~~k~ie~~L 212 (270)
....|||+||++++..|| ++||+|+|+.|||++|+|+|-|+++||++|||+|++||. ++|+++||.|.+..||.+|
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 355799999999999999 499999999999999999999999999999999999995 7899999999999999999
Q ss_pred HHhccceEeeCCCCCCcceEEEc-CcEEEeEeccCCCcccccccc--cceE
Q 024241 213 RRYVNEYVICLGCKSPDTILSKE-NRLFFLRCEKCGSGRSVAPIK--AGFQ 260 (270)
Q Consensus 213 ~~YI~eYVlC~~C~sPDT~L~ke-~rl~~l~C~aCGa~~~V~~ik--~gf~ 260 (270)
+.||++||+|+.|.+|+|.|+.. +..+.+.|.|||.++.+.... ++|.
T Consensus 90 dgFIkKFVlC~~C~NPETel~itk~q~i~~~CkACG~r~~~d~rhKLs~fI 140 (400)
T KOG2767|consen 90 DGFIKKFVLCPSCENPETELIITKKQTISLKCKACGFRSDMDLRHKLSTFI 140 (400)
T ss_pred HHHHHHheeCcCCCCCceeEEecccchhhhHHHHcCCcccccchhhhccee
Confidence 99999999999999999999985 788899999999999987532 5554
No 9
>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=95.40 E-value=0.013 Score=44.77 Aligned_cols=42 Identities=26% Similarity=0.688 Sum_probs=34.5
Q ss_pred HHhccceEeeCCCCCCcceEE-EcCcEEEeEeccCCCccccccc
Q 024241 213 RRYVNEYVICLGCKSPDTILS-KENRLFFLRCEKCGSGRSVAPI 255 (270)
Q Consensus 213 ~~YI~eYVlC~~C~sPDT~L~-ke~rl~~l~C~aCGa~~~V~~i 255 (270)
++||-- ..||.|++.||... +++.+-.+.|-+||++-....-
T Consensus 3 krFIAG-a~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~~~~~ 45 (71)
T PF09526_consen 3 KRFIAG-AVCPKCQAMDTIMMWRENGVEYVECVECGYTERQPDQ 45 (71)
T ss_pred ceEecC-ccCCCCcCccEEEEEEeCCceEEEecCCCCeeccCCc
Confidence 456665 78999999999876 5888999999999998766544
No 10
>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=95.24 E-value=0.017 Score=42.83 Aligned_cols=40 Identities=28% Similarity=0.717 Sum_probs=33.1
Q ss_pred HHhccceEeeCCCCCCcceEE-EcCcEEEeEeccCCCccccc
Q 024241 213 RRYVNEYVICLGCKSPDTILS-KENRLFFLRCEKCGSGRSVA 253 (270)
Q Consensus 213 ~~YI~eYVlC~~C~sPDT~L~-ke~rl~~l~C~aCGa~~~V~ 253 (270)
++||-- ..||.|+..||... +++.+-...|-.||++-...
T Consensus 4 KRFIAG-A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~~~~ 44 (59)
T TIGR02443 4 KRFIAG-AVCPACSAQDTLAMWKENNIELVECVECGYQEQQK 44 (59)
T ss_pred ceEecc-ccCCCCcCccEEEEEEeCCceEEEeccCCCccccC
Confidence 466665 78999999999876 58999999999999986543
No 11
>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=93.62 E-value=0.26 Score=37.92 Aligned_cols=58 Identities=9% Similarity=0.065 Sum_probs=44.0
Q ss_pred eeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeec----CCceEEEEeecChHHHHHHHHHhcc
Q 024241 156 KKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLD----GQQRLVVKGRFAPKNFEGILRRYVN 217 (270)
Q Consensus 156 kKTvi~Nf~dI~k~L~R~p~hv~kyl~~ELGt~gsid----~~~rlii~G~f~~k~ie~~L~~YI~ 217 (270)
.-|++.||. .-.=+++-+++.|...+|++|++. ....+.|+|.|...-.+-++.+|+.
T Consensus 19 ~vT~V~gl~----~~~~d~~~lak~lkk~~ac~~sv~~~~~k~~~I~iQGd~~~~i~~~L~~~~~~ 80 (83)
T PF01253_consen 19 FVTIVSGLE----LFGIDLKELAKELKKKFACGGSVTKDPGKGEEIQIQGDHRDEIKDLLVEKGGI 80 (83)
T ss_dssp EEEEEES------STTSHHHHHHHHHHHHHTS-EEEEE-TTTSSEEEEESS-HHHHHHHHHHHCSS
T ss_pred EEEEEECCc----ccccCHHHHHHHHHHhccCceEEeecCCCCCEEEECCcHHHHHHHHHHHhCCC
Confidence 568888988 345579999999999999999993 1457999999999988888788753
No 12
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=92.79 E-value=0.032 Score=40.08 Aligned_cols=28 Identities=25% Similarity=0.880 Sum_probs=21.7
Q ss_pred eeCCCCCCcceEEEcCcE-----EEeEeccCCC
Q 024241 221 ICLGCKSPDTILSKENRL-----FFLRCEKCGS 248 (270)
Q Consensus 221 lC~~C~sPDT~L~ke~rl-----~~l~C~aCGa 248 (270)
-||-|+++...+...... +++.|..||+
T Consensus 5 PCPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 5 PCPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 499997777666654333 8999999999
No 13
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=92.56 E-value=0.045 Score=41.29 Aligned_cols=36 Identities=17% Similarity=0.391 Sum_probs=29.8
Q ss_pred eeCCCCCCcceEEEcCcEEEeEeccCCCcccccccc
Q 024241 221 ICLGCKSPDTILSKENRLFFLRCEKCGSGRSVAPIK 256 (270)
Q Consensus 221 lC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V~~ik 256 (270)
-||-|+-.+-.+.-.++.|+..|..||+..+..+-.
T Consensus 8 PCPFCG~~~~~v~~~~g~~~v~C~~CgA~~~~~~te 43 (64)
T PRK09710 8 PCPFCGCPSVTVKAISGYYRAKCNGCESRTGYGGSE 43 (64)
T ss_pred CCCCCCCceeEEEecCceEEEEcCCCCcCcccccCH
Confidence 499999988766667888899999999988776544
No 14
>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=90.94 E-value=0.23 Score=33.46 Aligned_cols=31 Identities=23% Similarity=0.611 Sum_probs=22.4
Q ss_pred EeeCCCCCCcceEEE-------cCcEEEeEeccCCCcc
Q 024241 220 VICLGCKSPDTILSK-------ENRLFFLRCEKCGSGR 250 (270)
Q Consensus 220 VlC~~C~sPDT~L~k-------e~rl~~l~C~aCGa~~ 250 (270)
+.||.|++.++...- |.-.+|..|..||.+.
T Consensus 1 ~~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~w 38 (39)
T PF01096_consen 1 IKCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHRW 38 (39)
T ss_dssp S--SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEEE
T ss_pred CCCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCee
Confidence 469999999988773 3468899999999763
No 15
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=90.05 E-value=0.42 Score=32.44 Aligned_cols=30 Identities=27% Similarity=0.601 Sum_probs=24.5
Q ss_pred eeCCCCCCcceEEE-------cCcEEEeEeccCCCcc
Q 024241 221 ICLGCKSPDTILSK-------ENRLFFLRCEKCGSGR 250 (270)
Q Consensus 221 lC~~C~sPDT~L~k-------e~rl~~l~C~aCGa~~ 250 (270)
.||.|++.+..... |.-.+|..|..||.+.
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~w 38 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHRW 38 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCEe
Confidence 69999999988753 3458899999999864
No 16
>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=89.49 E-value=0.3 Score=35.06 Aligned_cols=32 Identities=31% Similarity=0.647 Sum_probs=24.3
Q ss_pred ccceEeeCCCCCC-----cceEEEcCcEEEeEeccCCC
Q 024241 216 VNEYVICLGCKSP-----DTILSKENRLFFLRCEKCGS 248 (270)
Q Consensus 216 I~eYVlC~~C~sP-----DT~L~ke~rl~~l~C~aCGa 248 (270)
..+|+.||.|++- +-.|+.+.-.|.-.|. ||-
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 3458999999874 5567777777888887 773
No 17
>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=89.08 E-value=0.42 Score=33.94 Aligned_cols=32 Identities=28% Similarity=0.701 Sum_probs=23.1
Q ss_pred eeCCCCCCcceEEE-----cCcEEEeEeccCCCccccc
Q 024241 221 ICLGCKSPDTILSK-----ENRLFFLRCEKCGSGRSVA 253 (270)
Q Consensus 221 lC~~C~sPDT~L~k-----e~rl~~l~C~aCGa~~~V~ 253 (270)
-||-|++-+-.+.. +..-++ .|..||+..++.
T Consensus 3 PCPfCGg~~~~~~~~~~~~~~~~~~-~C~~Cga~~~~~ 39 (53)
T TIGR03655 3 PCPFCGGADVYLRRGFDPLDLSHYF-ECSTCGASGPVE 39 (53)
T ss_pred CCCCCCCcceeeEeccCCCCCEEEE-ECCCCCCCcccc
Confidence 49999997765542 223333 999999999883
No 18
>PRK00939 translation initiation factor Sui1; Reviewed
Probab=88.80 E-value=0.84 Score=36.90 Aligned_cols=57 Identities=16% Similarity=0.233 Sum_probs=43.1
Q ss_pred EeCceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHHH
Q 024241 152 REGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILRR 214 (270)
Q Consensus 152 ~eG~kKTvi~Nf~dI~k~L~R~p~hv~kyl~~ELGt~gsid~~~rlii~G~f~~k~ie~~L~~ 214 (270)
+-|..-|+|.||..- .=++.-+++.|...+|+.|++.+ +.+.|+|.|...-. .+|..
T Consensus 34 ~~gK~VTiI~Gl~~~----~~~lk~l~k~lKk~~gcGgsvk~-~~I~iQGD~r~~v~-~~L~~ 90 (99)
T PRK00939 34 RYGKEVTIIEGIDPK----DIDLKELAKKLKSKLACGGTVKD-GRIELQGDHRERVK-ELLIK 90 (99)
T ss_pred CCCceEEEEeCCCCc----chhHHHHHHHHHHHhCCCceEEC-CEEEEeCcHHHHHH-HHHHH
Confidence 445577899999631 12578899999999999999975 47999999977655 44443
No 19
>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=88.33 E-value=0.93 Score=34.96 Aligned_cols=55 Identities=13% Similarity=0.106 Sum_probs=43.0
Q ss_pred CceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHH
Q 024241 154 GTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILR 213 (270)
Q Consensus 154 G~kKTvi~Nf~dI~k~L~R~p~hv~kyl~~ELGt~gsid~~~rlii~G~f~~k~ie~~L~ 213 (270)
|..-|+|.+|..-.. +++-+++.|...+|+.|++.. +.+.|+|.+...-.+-++.
T Consensus 12 ~K~VT~I~Gl~~~~~----dlk~l~k~lKk~~~cggtv~~-~~I~lQGD~r~~v~~~L~~ 66 (77)
T cd00474 12 GKTVTTVQGLDLEYA----DLKKLAKELKKKCACGGTVKD-EVIELQGDQRKKIKEFLIK 66 (77)
T ss_pred CccEEEEECCCCchH----hHHHHHHHHHHHcCCCcEEec-CEEEEeCcHHHHHHHHHHH
Confidence 346788899864222 789999999999999999985 5999999998776654443
No 20
>PHA02998 RNA polymerase subunit; Provisional
Probab=88.17 E-value=0.54 Score=42.19 Aligned_cols=86 Identities=19% Similarity=0.346 Sum_probs=53.4
Q ss_pred hHHHHHHhC---CChHHHHHHHHHhhc-----CceeecCCceEEEEeecChHHHHHHHHHhccceEeeCCCCCCcceEEE
Q 024241 163 FMDLCKTMH---RQPDHVMTFLLAELG-----TSGSLDGQQRLVVKGRFAPKNFEGILRRYVNEYVICLGCKSPDTILSK 234 (270)
Q Consensus 163 f~dI~k~L~---R~p~hv~kyl~~ELG-----t~gsid~~~rlii~G~f~~k~ie~~L~~YI~eYVlC~~C~sPDT~L~k 234 (270)
..+||..++ --...+++||+.-+- +.-.||.=. .+.-..-=+++..= .-|.||.|++..+....
T Consensus 87 y~~lc~~ir~tng~eke~lry~lfgikcv~~~veydid~~~------d~~y~~yfnvlpkk--t~v~CPkCg~~~A~f~q 158 (195)
T PHA02998 87 YKDLCDMIRGTNGTEKEILRYLLFGIKCIKKGVEYDIDKIP------DVDYDDYFNVLDEK--YNTPCPNCKSKNTTPMM 158 (195)
T ss_pred HHHHHHHHHhcCCchHHHHHHHHHHHHHHhcCCccchhhcc------cccchhheeccCcc--cCCCCCCCCCCceEEEE
Confidence 567887764 456788899987653 333333200 11111111222221 34899999999987543
Q ss_pred -------cCcEEEeEeccCCCcccccccc
Q 024241 235 -------ENRLFFLRCEKCGSGRSVAPIK 256 (270)
Q Consensus 235 -------e~rl~~l~C~aCGa~~~V~~ik 256 (270)
|.-..|.+|..||.+..-+.++
T Consensus 159 lQTRSADEPmT~FYkC~~CG~~wkppkf~ 187 (195)
T PHA02998 159 IQTRAADEPPLVRHACRDCKKHFKPPKFR 187 (195)
T ss_pred EeeccCCCCceEEEEcCCCCCccCCcccc
Confidence 4568899999999988776655
No 21
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=87.43 E-value=0.43 Score=31.73 Aligned_cols=32 Identities=38% Similarity=0.796 Sum_probs=24.5
Q ss_pred eEeeCCCCC----CcceEEEcCcEEEeEeccCCCcccc
Q 024241 219 YVICLGCKS----PDTILSKENRLFFLRCEKCGSGRSV 252 (270)
Q Consensus 219 YVlC~~C~s----PDT~L~ke~rl~~l~C~aCGa~~~V 252 (270)
.+.||.|+. |++.|...++ .++|..||+...|
T Consensus 2 ~i~CP~C~~~f~v~~~~l~~~~~--~vrC~~C~~~f~v 37 (37)
T PF13719_consen 2 IITCPNCQTRFRVPDDKLPAGGR--KVRCPKCGHVFRV 37 (37)
T ss_pred EEECCCCCceEEcCHHHcccCCc--EEECCCCCcEeeC
Confidence 589999975 6777765555 7899999987543
No 22
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=86.96 E-value=0.73 Score=37.77 Aligned_cols=37 Identities=16% Similarity=0.330 Sum_probs=30.0
Q ss_pred ccceEeeCCCCCCcce---EEEcCcEEEeEeccCCCcccc
Q 024241 216 VNEYVICLGCKSPDTI---LSKENRLFFLRCEKCGSGRSV 252 (270)
Q Consensus 216 I~eYVlC~~C~sPDT~---L~ke~rl~~l~C~aCGa~~~V 252 (270)
+..+..||-|+.-.-. +.+...+.++.|..||.+.-+
T Consensus 19 L~k~FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~ 58 (104)
T COG4888 19 LPKTFTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFEC 58 (104)
T ss_pred CCceEecCccCCeeeeEEEEEecCceeEEEcccCcceEEE
Confidence 4567899999887654 666788999999999997654
No 23
>PF14353 CpXC: CpXC protein
Probab=86.72 E-value=0.55 Score=38.44 Aligned_cols=18 Identities=28% Similarity=0.676 Sum_probs=13.5
Q ss_pred CcEEEeEeccCCCccccc
Q 024241 236 NRLFFLRCEKCGSGRSVA 253 (270)
Q Consensus 236 ~rl~~l~C~aCGa~~~V~ 253 (270)
+.++...|..||+...+.
T Consensus 34 g~l~~~~CP~Cg~~~~~~ 51 (128)
T PF14353_consen 34 GSLFSFTCPSCGHKFRLE 51 (128)
T ss_pred CCcCEEECCCCCCceecC
Confidence 567788888888877663
No 24
>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=86.04 E-value=1.7 Score=35.21 Aligned_cols=53 Identities=13% Similarity=0.193 Sum_probs=41.8
Q ss_pred EeCceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHH
Q 024241 152 REGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFE 209 (270)
Q Consensus 152 ~eG~kKTvi~Nf~dI~k~L~R~p~hv~kyl~~ELGt~gsid~~~rlii~G~f~~k~ie 209 (270)
|-|+.-|+|.||..- .-+++-++++|...+|+.|++. ++.+.|+|.|...-.+
T Consensus 35 r~gK~VTvV~Gl~~~----~~~l~~l~k~LKk~~gcGgtvk-~~~IeiQGD~~~~v~~ 87 (101)
T TIGR01158 35 RKGKGVTIIEGLDLS----DIDLKELAKELKSKCGCGGTVK-DGVIEIQGDHRDRVKD 87 (101)
T ss_pred CCCCEEEEEeCCcCc----hhhHHHHHHHHHHHhcCCeeEe-CCEEEEeCcHHHHHHH
Confidence 445678999999622 2367889999999999999997 4589999999776553
No 25
>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=84.90 E-value=0.73 Score=31.28 Aligned_cols=35 Identities=23% Similarity=0.342 Sum_probs=22.1
Q ss_pred eeCCCCCCcceEEEcCcEEEeEeccCCCccccccccc
Q 024241 221 ICLGCKSPDTILSKENRLFFLRCEKCGSGRSVAPIKA 257 (270)
Q Consensus 221 lC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V~~ik~ 257 (270)
.||.|++.. ++-+...-.+.|..||..-.-..|-.
T Consensus 2 ~Cp~Cg~~~--~~~D~~~g~~vC~~CG~Vl~e~~i~~ 36 (43)
T PF08271_consen 2 KCPNCGSKE--IVFDPERGELVCPNCGLVLEENIIDE 36 (43)
T ss_dssp SBTTTSSSE--EEEETTTTEEEETTT-BBEE-TTBSC
T ss_pred CCcCCcCCc--eEEcCCCCeEECCCCCCEeecccccC
Confidence 599999977 44443223669999998755554443
No 26
>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=84.34 E-value=0.66 Score=43.26 Aligned_cols=37 Identities=27% Similarity=0.497 Sum_probs=19.7
Q ss_pred EeeCCCCCC-cceEEE-cC--cEEEeEeccCCCcccccccc
Q 024241 220 VICLGCKSP-DTILSK-EN--RLFFLRCEKCGSGRSVAPIK 256 (270)
Q Consensus 220 VlC~~C~sP-DT~L~k-e~--rl~~l~C~aCGa~~~V~~ik 256 (270)
-.||.|+|+ .-..++ +. +.-+|+|.-||..+....++
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~ 213 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIK 213 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCC
Confidence 589999997 444444 33 56899999999998876665
No 27
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=83.57 E-value=1.1 Score=36.35 Aligned_cols=37 Identities=14% Similarity=0.394 Sum_probs=27.2
Q ss_pred ccceEeeCCCCCCcceEEEcCcEEEeEeccCCCcccc
Q 024241 216 VNEYVICLGCKSPDTILSKENRLFFLRCEKCGSGRSV 252 (270)
Q Consensus 216 I~eYVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V 252 (270)
+..++.||.|+++--.+.+......+.|..||....-
T Consensus 18 lpt~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~~~ 54 (99)
T PRK14892 18 LPKIFECPRCGKVSISVKIKKNIAIITCGNCGLYTEF 54 (99)
T ss_pred CCcEeECCCCCCeEeeeecCCCcceEECCCCCCccCE
Confidence 3468999999975322334557789999999987654
No 28
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=82.36 E-value=1.1 Score=34.14 Aligned_cols=30 Identities=23% Similarity=0.542 Sum_probs=23.2
Q ss_pred eEeeCCCCCCcceEEEcCcEEEeEeccCCCcc
Q 024241 219 YVICLGCKSPDTILSKENRLFFLRCEKCGSGR 250 (270)
Q Consensus 219 YVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~ 250 (270)
+|.|+.|++--|....- -...+|..||..=
T Consensus 19 ~VkCpdC~N~q~vFsha--st~V~C~~CG~~l 48 (67)
T COG2051 19 RVKCPDCGNEQVVFSHA--STVVTCLICGTTL 48 (67)
T ss_pred EEECCCCCCEEEEeccC--ceEEEecccccEE
Confidence 79999999877665543 3478999999753
No 29
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=81.89 E-value=1.1 Score=29.73 Aligned_cols=28 Identities=29% Similarity=0.505 Sum_probs=15.0
Q ss_pred eeCCCCCCcceEEE--cCcEEEeEeccCCCc
Q 024241 221 ICLGCKSPDTILSK--ENRLFFLRCEKCGSG 249 (270)
Q Consensus 221 lC~~C~sPDT~L~k--e~rl~~l~C~aCGa~ 249 (270)
.|+.|++|=+..+- ++| .-+.|.+||..
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 47889999964
No 30
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=81.34 E-value=1.2 Score=42.71 Aligned_cols=38 Identities=26% Similarity=0.481 Sum_probs=28.4
Q ss_pred eEeeCCCCCCc-ceEEE---cCcEEEeEeccCCCcccccccc
Q 024241 219 YVICLGCKSPD-TILSK---ENRLFFLRCEKCGSGRSVAPIK 256 (270)
Q Consensus 219 YVlC~~C~sPD-T~L~k---e~rl~~l~C~aCGa~~~V~~ik 256 (270)
--.||.|+|+= ..+++ .++.-+|+|.-||..+.+..++
T Consensus 187 ~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~ 228 (309)
T PRK03564 187 RQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVK 228 (309)
T ss_pred CCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCcc
Confidence 47899999964 44443 3577899999999988876554
No 31
>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=80.63 E-value=2 Score=33.51 Aligned_cols=38 Identities=18% Similarity=0.414 Sum_probs=22.1
Q ss_pred ccceEeeCCCCCCcceEEE---cCcEEEeEeccCCCccccc
Q 024241 216 VNEYVICLGCKSPDTILSK---ENRLFFLRCEKCGSGRSVA 253 (270)
Q Consensus 216 I~eYVlC~~C~sPDT~L~k---e~rl~~l~C~aCGa~~~V~ 253 (270)
+..+-.||-|+...|.-++ ..++-.+.|..||......
T Consensus 19 l~~~F~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~ 59 (81)
T PF05129_consen 19 LPKVFDCPFCNHEKSVSVKIDKKEGIGILSCRVCGESFQTK 59 (81)
T ss_dssp -SS----TTT--SS-EEEEEETTTTEEEEEESSS--EEEEE
T ss_pred CCceEcCCcCCCCCeEEEEEEccCCEEEEEecCCCCeEEEc
Confidence 4567899999998887775 4689999999999876543
No 32
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=80.47 E-value=1.2 Score=31.53 Aligned_cols=33 Identities=27% Similarity=0.550 Sum_probs=25.0
Q ss_pred eEeeCCCC----CCcceEEEcCcEEEeEeccCCCccc
Q 024241 219 YVICLGCK----SPDTILSKENRLFFLRCEKCGSGRS 251 (270)
Q Consensus 219 YVlC~~C~----sPDT~L~ke~rl~~l~C~aCGa~~~ 251 (270)
||+|+.|- -|........+..-|+|-+|...-.
T Consensus 6 Fv~C~~C~~lLqlP~~~~~~~k~~~klrCGaCs~vl~ 42 (46)
T PF11331_consen 6 FVVCSSCFELLQLPAKFSLSKKNQQKLRCGACSEVLS 42 (46)
T ss_pred EeECccHHHHHcCCCccCCCccceeEEeCCCCceeEE
Confidence 89999994 4766666565688999999986543
No 33
>TIGR01159 DRP1 density-regulated protein DRP1. This protein family shows weak but suggestive similarity to translation initiation factor SUI1 and its prokaryotic homologs.
Probab=80.44 E-value=4.1 Score=36.14 Aligned_cols=56 Identities=14% Similarity=0.204 Sum_probs=46.6
Q ss_pred eeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeec----CCceEEEEeecChHHHHHHHHHh
Q 024241 156 KKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLD----GQQRLVVKGRFAPKNFEGILRRY 215 (270)
Q Consensus 156 kKTvi~Nf~dI~k~L~R~p~hv~kyl~~ELGt~gsid----~~~rlii~G~f~~k~ie~~L~~Y 215 (270)
.-|+|.+|.. -.-++.-+.++|...++++||+. +++.++|+|.|...-++=++.+|
T Consensus 103 ~VT~V~GLe~----f~idlk~laK~lkkkfacG~SV~k~~~~~~eI~IQGD~~~~v~e~L~~~~ 162 (173)
T TIGR01159 103 FVTVIKGLET----FDIDLKKASKTFAQKFATGCSVSKSVTGKEEIVIQGDVMDDIEDYIHEKW 162 (173)
T ss_pred eEEEEeCCcC----CCcCHHHHHHHHHHHhCCCCccccCCCCCCEEEecCCHHHHHHHHHHHHc
Confidence 4688999974 24579999999999999998772 35799999999998887777777
No 34
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=79.81 E-value=2.3 Score=39.23 Aligned_cols=44 Identities=16% Similarity=0.467 Sum_probs=34.0
Q ss_pred HHHHHHHHHhcc--ceEeeCCCCCCcceEEEcCcEEEeEeccCCCcccccccc
Q 024241 206 KNFEGILRRYVN--EYVICLGCKSPDTILSKENRLFFLRCEKCGSGRSVAPIK 256 (270)
Q Consensus 206 k~ie~~L~~YI~--eYVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V~~ik 256 (270)
..++.++++.|. -...|..|+.-- ..|+..|..||+..+..+|+
T Consensus 339 ~~~~~~~~~~~~~~p~~~c~~cg~~~-------~~~~~~c~~c~~~~~~~~~~ 384 (389)
T PRK11788 339 LLLRDLVGEQLKRKPRYRCRNCGFTA-------RTLYWHCPSCKAWETIKPIR 384 (389)
T ss_pred HHHHHHHHHHHhCCCCEECCCCCCCC-------ccceeECcCCCCccCcCCcc
Confidence 446777776653 234499999765 56899999999999999987
No 35
>COG0023 SUI1 Translation initiation factor 1 (eIF-1/SUI1) and related proteins [Translation, ribosomal structure and biogenesis]
Probab=79.21 E-value=5.6 Score=32.72 Aligned_cols=60 Identities=13% Similarity=0.176 Sum_probs=47.8
Q ss_pred eEEEeCceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHH
Q 024241 149 QVLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILR 213 (270)
Q Consensus 149 ~V~~eG~kKTvi~Nf~dI~k~L~R~p~hv~kyl~~ELGt~gsid~~~rlii~G~f~~k~ie~~L~ 213 (270)
+-.|-|.--|+|.+|.. -.-+++-|++.|-+.+|+.|++-.+ ...|+|.|..+-.+=++.
T Consensus 34 e~rr~gK~VTiI~Gld~----~~~dlk~Lak~LKk~cacGGtvk~~-~IeiQGdhr~~v~~~L~~ 93 (104)
T COG0023 34 ETRRKGKTVTIIEGLDL----KDIDLKKLAKELKKKCACGGTVKDG-EIEIQGDHRDKVKELLIK 93 (104)
T ss_pred EeecCCcEEEEEeCccc----chhhHHHHHHHHHHHcCCCceecCC-EEEEeChHHHHHHHHHHH
Confidence 33466767899999985 3446788999999999999999755 999999998877665554
No 36
>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=77.99 E-value=3.3 Score=40.64 Aligned_cols=42 Identities=29% Similarity=0.502 Sum_probs=24.5
Q ss_pred hccceEeeCCCCCCcc-eEEE-c--CcEEEeEeccCCCcccccccc
Q 024241 215 YVNEYVICLGCKSPDT-ILSK-E--NRLFFLRCEKCGSGRSVAPIK 256 (270)
Q Consensus 215 YI~eYVlC~~C~sPDT-~L~k-e--~rl~~l~C~aCGa~~~V~~ik 256 (270)
|+==.++|+.|+..+| .++. + +..+.-+|..||....+.-..
T Consensus 170 y~Pf~piC~~cGri~tt~v~~~d~~~~~v~Y~c~~cG~~g~~~i~~ 215 (360)
T PF01921_consen 170 YSPFLPICEKCGRIDTTEVTEYDPEGGTVTYRCEECGHEGEVDITG 215 (360)
T ss_dssp --SEEEEETTTEE--EEEEEEE--SSSEEEEE--TTS---EEETTT
T ss_pred eeeeeeeccccCCcccceeeEeecCCCEEEEEecCCCCEEEEecCC
Confidence 4555799999999654 4433 3 688899999999998886544
No 37
>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=77.91 E-value=1.9 Score=29.72 Aligned_cols=31 Identities=19% Similarity=0.395 Sum_probs=20.7
Q ss_pred ccceEeeCCCCCCcceEEEcCcEEEeEeccCCCc
Q 024241 216 VNEYVICLGCKSPDTILSKENRLFFLRCEKCGSG 249 (270)
Q Consensus 216 I~eYVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~ 249 (270)
-+. +.||.|++. ......+ ....+|.+|+.+
T Consensus 16 ~~g-~~CP~Cg~~-~~~~~~~-~~~~~C~~C~~q 46 (46)
T PF12760_consen 16 PDG-FVCPHCGST-KHYRLKT-RGRYRCKACRKQ 46 (46)
T ss_pred CCC-CCCCCCCCe-eeEEeCC-CCeEECCCCCCc
Confidence 344 559999998 3333333 446799999864
No 38
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=77.10 E-value=2 Score=45.64 Aligned_cols=42 Identities=24% Similarity=0.491 Sum_probs=29.7
Q ss_pred hHHHHHHHHHhccce----------------------EeeCCCCCCcceEEEcCcEEEeEeccCCCccc
Q 024241 205 PKNFEGILRRYVNEY----------------------VICLGCKSPDTILSKENRLFFLRCEKCGSGRS 251 (270)
Q Consensus 205 ~k~ie~~L~~YI~eY----------------------VlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~ 251 (270)
+..|-.+|.+|+..- ..||+|++ | |+.+.+ .+.|.+||.+..
T Consensus 688 pDaI~kaL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Cp~Cg~--~-l~~~~G--C~~C~~CG~skC 751 (752)
T PRK08665 688 PDAIAKVLEKHYLGGGKDVGAGNGTGSAGIEAPAPERGACPECGS--I-LEHEEG--CVVCHSCGYSKC 751 (752)
T ss_pred HHHHHHHHHHHHHhccccccccccccccccccccCCCCCCCCCCc--c-cEECCC--CCcCCCCCCCCC
Confidence 667788888776530 35999984 3 666555 569999998753
No 39
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=76.53 E-value=2.3 Score=34.05 Aligned_cols=42 Identities=19% Similarity=0.468 Sum_probs=25.6
Q ss_pred HHHHHHHHHhccceEeeCCCCCCcceEEEcCcEEEeEeccCCCccc
Q 024241 206 KNFEGILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKCGSGRS 251 (270)
Q Consensus 206 k~ie~~L~~YI~eYVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~ 251 (270)
..+..+.-.-...| .||.|+++ |.-..-.++| .|..||+.-.
T Consensus 23 rrv~~ie~~~~~~~-~Cp~C~~~-~VkR~a~GIW--~C~kCg~~fA 64 (89)
T COG1997 23 RRVKEIEAQQRAKH-VCPFCGRT-TVKRIATGIW--KCRKCGAKFA 64 (89)
T ss_pred HHHHHHHHHHhcCC-cCCCCCCc-ceeeeccCeE--EcCCCCCeec
Confidence 34444444434444 69999999 4333345765 7999998643
No 40
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=76.53 E-value=2.5 Score=31.51 Aligned_cols=30 Identities=27% Similarity=0.637 Sum_probs=24.2
Q ss_pred eEeeCCCCCCcceEEEcCcEEEeEeccCCCcc
Q 024241 219 YVICLGCKSPDTILSKENRLFFLRCEKCGSGR 250 (270)
Q Consensus 219 YVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~ 250 (270)
.|.|+.|.+.-|....-.. ...|..||..=
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 5999999998887776543 68999999753
No 41
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=76.21 E-value=2.5 Score=32.17 Aligned_cols=35 Identities=26% Similarity=0.576 Sum_probs=24.5
Q ss_pred ceEeeCCCCCCc----------ceEEE-----cCcEEEeEeccCCCcccc
Q 024241 218 EYVICLGCKSPD----------TILSK-----ENRLFFLRCEKCGSGRSV 252 (270)
Q Consensus 218 eYVlC~~C~sPD----------T~L~k-----e~rl~~l~C~aCGa~~~V 252 (270)
.+-.||.|++-+ |.|.+ .++.+...|..||.+-.-
T Consensus 3 ~~~kCpKCgn~~~~ekei~~tg~~lskifdvq~n~f~~itCk~CgYtEfY 52 (68)
T COG3478 3 NAFKCPKCGNTNYEEKEIAATGGGLSKIFDVQNNKFIVITCKNCGYTEFY 52 (68)
T ss_pred ccccCCCcCCcchhhceeeccCCCcceeEEecccEEEEEEeccCCchhhe
Confidence 345699999865 23332 368889999999987543
No 42
>smart00401 ZnF_GATA zinc finger binding to DNA consensus sequence [AT]GATA[AG].
Probab=75.75 E-value=1.3 Score=31.63 Aligned_cols=33 Identities=21% Similarity=0.308 Sum_probs=24.6
Q ss_pred EeeCCCCCCcceEEEcCcEE-EeEeccCCCcccc
Q 024241 220 VICLGCKSPDTILSKENRLF-FLRCEKCGSGRSV 252 (270)
Q Consensus 220 VlC~~C~sPDT~L~ke~rl~-~l~C~aCGa~~~V 252 (270)
..|..|+..+|.+-+.+..- .+-|+|||-....
T Consensus 4 ~~C~~C~~~~T~~WR~g~~g~~~LCnaCgl~~~k 37 (52)
T smart00401 4 RSCSNCGTTETPLWRRGPSGNKTLCNACGLYYKK 37 (52)
T ss_pred CCcCCCCCCCCCccccCCCCCCcEeecccHHHHH
Confidence 36999999999998864222 4789999965443
No 43
>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=75.69 E-value=2.4 Score=36.84 Aligned_cols=31 Identities=16% Similarity=0.345 Sum_probs=23.0
Q ss_pred eeCCCCCCcceEEE-----cCcEE--EeEeccCCCccc
Q 024241 221 ICLGCKSPDTILSK-----ENRLF--FLRCEKCGSGRS 251 (270)
Q Consensus 221 lC~~C~sPDT~L~k-----e~rl~--~l~C~aCGa~~~ 251 (270)
.||-|+++||..+= ++..+ --.|.+||.+-+
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFT 39 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFT 39 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccc
Confidence 59999999999874 33222 257999998754
No 44
>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=75.63 E-value=2.3 Score=32.25 Aligned_cols=35 Identities=14% Similarity=0.436 Sum_probs=26.3
Q ss_pred eEeeCCCCCCcceEEE----cCcEEEeEeccCCCccccc
Q 024241 219 YVICLGCKSPDTILSK----ENRLFFLRCEKCGSGRSVA 253 (270)
Q Consensus 219 YVlC~~C~sPDT~L~k----e~rl~~l~C~aCGa~~~V~ 253 (270)
.-+|..|+...+..+. ++++.+.+|..|.+..-++
T Consensus 4 ~FTC~~C~~Rs~~~~sk~aY~~GvViv~C~gC~~~HlIa 42 (66)
T PF05180_consen 4 TFTCNKCGTRSAKMFSKQAYHKGVVIVQCPGCKNRHLIA 42 (66)
T ss_dssp EEEETTTTEEEEEEEEHHHHHTSEEEEE-TTS--EEES-
T ss_pred EEEcCCCCCccceeeCHHHHhCCeEEEECCCCcceeeeh
Confidence 3589999998888876 4799999999999987664
No 45
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=75.41 E-value=3.5 Score=27.66 Aligned_cols=29 Identities=17% Similarity=0.306 Sum_probs=20.5
Q ss_pred eeCCCCCCcceEEEcCcEEEeEeccCCCcc
Q 024241 221 ICLGCKSPDTILSKENRLFFLRCEKCGSGR 250 (270)
Q Consensus 221 lC~~C~sPDT~L~ke~rl~~l~C~aCGa~~ 250 (270)
.||.|+.+=. ...-..+..-.|.+||...
T Consensus 1 ~CP~C~~~l~-~~~~~~~~id~C~~C~G~W 29 (41)
T PF13453_consen 1 KCPRCGTELE-PVRLGDVEIDVCPSCGGIW 29 (41)
T ss_pred CcCCCCcccc-eEEECCEEEEECCCCCeEE
Confidence 4999998422 2222568899999999654
No 46
>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=75.39 E-value=8.6 Score=24.78 Aligned_cols=47 Identities=11% Similarity=0.132 Sum_probs=34.3
Q ss_pred ehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHH
Q 024241 162 NFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILR 213 (270)
Q Consensus 162 Nf~dI~k~L~R~p~hv~kyl~~ELGt~gsid~~~rlii~G~f~~k~ie~~L~ 213 (270)
+..|+|+.|+.++.+|.+|+........... +++. +|+..+|..++.
T Consensus 2 s~~e~a~~lgvs~~tl~~~~~~g~~~~~~~~-~~~~----~~~~~ei~~~~~ 48 (49)
T cd04762 2 TTKEAAELLGVSPSTLRRWVKEGKLKAIRTP-GGHR----RFPEEDLERLLG 48 (49)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcCCCCceeCC-CCce----ecCHHHHHHHHh
Confidence 5789999999999999999988665443322 2333 478888877653
No 47
>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=74.83 E-value=3.9 Score=33.85 Aligned_cols=60 Identities=13% Similarity=0.165 Sum_probs=45.2
Q ss_pred EEeC-ceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecC----CceEEEEeecChHHHHHHHHHh
Q 024241 151 LREG-TKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDG----QQRLVVKGRFAPKNFEGILRRY 215 (270)
Q Consensus 151 ~~eG-~kKTvi~Nf~dI~k~L~R~p~hv~kyl~~ELGt~gsid~----~~rlii~G~f~~k~ie~~L~~Y 215 (270)
.|-| ..-|+|.+|.+ .=+-.-+++.|.+.+|+.|++-. +..+.|+|.|..+-.+-+....
T Consensus 34 qR~grK~VTiI~Gl~~-----~~dlk~l~K~lKkk~~cGGsVk~~~~~~~~IelQGD~re~v~~~L~~~g 98 (110)
T TIGR01160 34 QRNGRKTLTTVQGLPK-----EYDLKKIVKALKKEFACNGTVIEDPEMGEVIQLQGDQRKNVCEFLISQG 98 (110)
T ss_pred EccCCccEEEEeccCC-----hHHHHHHHHHHHHHhCCCceEEeCCCCCCEEEEeCcHHHHHHHHHHHcC
Confidence 4555 35678888862 23457789999999999999953 3579999999988777776665
No 48
>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=74.65 E-value=2 Score=27.44 Aligned_cols=26 Identities=27% Similarity=0.658 Sum_probs=13.9
Q ss_pred eeCCCCCCcceEEEcCcEEEeEeccCCCc
Q 024241 221 ICLGCKSPDTILSKENRLFFLRCEKCGSG 249 (270)
Q Consensus 221 lC~~C~sPDT~L~ke~rl~~l~C~aCGa~ 249 (270)
.|+.|++|-+ +... =+.++|.+||..
T Consensus 5 fC~~CG~~t~-~~~~--g~~r~C~~Cg~~ 30 (32)
T PF09297_consen 5 FCGRCGAPTK-PAPG--GWARRCPSCGHE 30 (32)
T ss_dssp B-TTT--BEE-E-SS--SS-EEESSSS-E
T ss_pred ccCcCCcccc-CCCC--cCEeECCCCcCE
Confidence 5999999843 2222 358899999974
No 49
>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=74.52 E-value=3 Score=29.26 Aligned_cols=27 Identities=22% Similarity=0.372 Sum_probs=23.0
Q ss_pred ehHHHHHHhCCChHHHHHHHHHhhcCc
Q 024241 162 NFMDLCKTMHRQPDHVMTFLLAELGTS 188 (270)
Q Consensus 162 Nf~dI~k~L~R~p~hv~kyl~~ELGt~ 188 (270)
.+.|+|+.|+.++..|++.|..++|..
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 467999999999999999999999998
No 50
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=74.21 E-value=3 Score=37.60 Aligned_cols=27 Identities=37% Similarity=1.027 Sum_probs=21.9
Q ss_pred eEeeCCCCCCcceEEEcCcEEEeEeccCCCcc
Q 024241 219 YVICLGCKSPDTILSKENRLFFLRCEKCGSGR 250 (270)
Q Consensus 219 YVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~ 250 (270)
|-+|+.|+.| |+++++ .|+|..||+.-
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 7899999976 777543 89999999853
No 51
>PRK00420 hypothetical protein; Validated
Probab=73.13 E-value=2.4 Score=35.22 Aligned_cols=31 Identities=26% Similarity=0.307 Sum_probs=23.8
Q ss_pred eEeeCCCCCCcceEEEcCcEEEeEeccCCCccccc
Q 024241 219 YVICLGCKSPDTILSKENRLFFLRCEKCGSGRSVA 253 (270)
Q Consensus 219 YVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V~ 253 (270)
--.||.|++|=+.+ +.+. ..|-+||..-.|.
T Consensus 23 ~~~CP~Cg~pLf~l-k~g~---~~Cp~Cg~~~~v~ 53 (112)
T PRK00420 23 SKHCPVCGLPLFEL-KDGE---VVCPVHGKVYIVK 53 (112)
T ss_pred cCCCCCCCCcceec-CCCc---eECCCCCCeeeec
Confidence 35799999998777 5554 5799999966654
No 52
>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=73.09 E-value=4 Score=32.23 Aligned_cols=33 Identities=27% Similarity=0.484 Sum_probs=26.4
Q ss_pred eEeeCCCCCCcceEEE-------cCcEEEeEeccCCCccc
Q 024241 219 YVICLGCKSPDTILSK-------ENRLFFLRCEKCGSGRS 251 (270)
Q Consensus 219 YVlC~~C~sPDT~L~k-------e~rl~~l~C~aCGa~~~ 251 (270)
.+.|+.|++.+..... +.-.+|-.|..||.++.
T Consensus 62 ~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~~w~ 101 (104)
T TIGR01384 62 RVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGYVWR 101 (104)
T ss_pred cCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCCeeE
Confidence 5899999999965542 35678999999998764
No 53
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=72.70 E-value=2.7 Score=31.43 Aligned_cols=36 Identities=25% Similarity=0.547 Sum_probs=26.2
Q ss_pred HhccceEeeCCCCCCcceEEEcCcEEEeEeccCCCcccc
Q 024241 214 RYVNEYVICLGCKSPDTILSKENRLFFLRCEKCGSGRSV 252 (270)
Q Consensus 214 ~YI~eYVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V 252 (270)
..+-+-+-||.|+.| -.+..+++ .|.|..||-..++
T Consensus 3 ~~LLeiLaCP~~kg~-L~~~~~~~--~L~c~~~~~aYpI 38 (60)
T COG2835 3 YRLLEILACPVCKGP-LVYDEEKQ--ELICPRCKLAYPI 38 (60)
T ss_pred hhhheeeeccCcCCc-ceEeccCC--EEEecccCceeec
Confidence 344567899999999 33333444 8899999988775
No 54
>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=72.48 E-value=3.5 Score=39.35 Aligned_cols=32 Identities=28% Similarity=0.600 Sum_probs=25.7
Q ss_pred eEeeCCCCCCcceEEE-------cCcEEEeEeccCCCcc
Q 024241 219 YVICLGCKSPDTILSK-------ENRLFFLRCEKCGSGR 250 (270)
Q Consensus 219 YVlC~~C~sPDT~L~k-------e~rl~~l~C~aCGa~~ 250 (270)
-+.|+.|+..++.... +.=..|..|..||+++
T Consensus 258 ~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~~w 296 (299)
T TIGR01385 258 LFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGNRW 296 (299)
T ss_pred cccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCCee
Confidence 5899999999986653 2347799999999875
No 55
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=72.42 E-value=3.5 Score=37.49 Aligned_cols=33 Identities=18% Similarity=0.309 Sum_probs=22.6
Q ss_pred ceEeeCCCCCCcceEEE-------cCc--EEEeEeccCCCccc
Q 024241 218 EYVICLGCKSPDTILSK-------ENR--LFFLRCEKCGSGRS 251 (270)
Q Consensus 218 eYVlC~~C~sPDT~L~k-------e~r--l~~l~C~aCGa~~~ 251 (270)
.-+.||.|++ .-.++- -++ +....|+.||.+.+
T Consensus 13 ~~~~CPvCg~-~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~ 54 (201)
T COG1779 13 TRIDCPVCGG-TLKAHMYLYDIPYFGEVLISTGVCERCGYRST 54 (201)
T ss_pred eeecCCcccc-eeeEEEeeecCCccceEEEEEEEccccCCccc
Confidence 3578999999 322221 144 44789999999875
No 56
>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=72.21 E-value=5.9 Score=40.51 Aligned_cols=73 Identities=26% Similarity=0.485 Sum_probs=49.0
Q ss_pred HHHhhcCceeecCCceEEEEeecCh---------HHHHHHHHHhccc---------eEeeCCCCCCcceEEE-c--CcEE
Q 024241 181 LLAELGTSGSLDGQQRLVVKGRFAP---------KNFEGILRRYVNE---------YVICLGCKSPDTILSK-E--NRLF 239 (270)
Q Consensus 181 l~~ELGt~gsid~~~rlii~G~f~~---------k~ie~~L~~YI~e---------YVlC~~C~sPDT~L~k-e--~rl~ 239 (270)
++.+||..-.+-.+..+.=+|+|.. ..|.++|..|... .++|+.|+.-.|.++. + ..+.
T Consensus 112 ~l~~~gi~~e~~s~te~Y~sG~~~~~i~~~L~~~~~I~~il~~~~~~~~~~~~~P~~pic~~cGrv~~~~~~~~~~~~v~ 191 (515)
T TIGR00467 112 SLPVLGINPEFIRASKQYTSGLYASQIKIALDHRKEISEILNEYRTSKLEENWYPISVFCENCGRDTTTVNNYDNEYSIE 191 (515)
T ss_pred HHHHcCCeEEEEEHHHhhhcCChHHHHHHHHHhHHHHHHHHHHhcCCccCCCceeeeeecCCcCccCceEEEecCCceEE
Confidence 3456666544433445666677754 5677888888743 4799999999876663 2 3444
Q ss_pred EeEeccCCCccccccc
Q 024241 240 FLRCEKCGSGRSVAPI 255 (270)
Q Consensus 240 ~l~C~aCGa~~~V~~i 255 (270)
+ +|+ ||....+...
T Consensus 192 Y-~c~-cG~~g~~~~~ 205 (515)
T TIGR00467 192 Y-SCE-CGNQESVDIY 205 (515)
T ss_pred E-EcC-CCCEEEEeec
Confidence 4 897 9999888653
No 57
>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=72.20 E-value=3.5 Score=27.20 Aligned_cols=30 Identities=23% Similarity=0.565 Sum_probs=18.0
Q ss_pred eeCCCCCCcceEEEcC-cEEEeEeccCCCccccc
Q 024241 221 ICLGCKSPDTILSKEN-RLFFLRCEKCGSGRSVA 253 (270)
Q Consensus 221 lC~~C~sPDT~L~ke~-rl~~l~C~aCGa~~~V~ 253 (270)
-||.|++.= +.+++ .... .|..||+..++.
T Consensus 3 FCp~C~nlL--~p~~~~~~~~-~C~~C~Y~~~~~ 33 (35)
T PF02150_consen 3 FCPECGNLL--YPKEDKEKRV-ACRTCGYEEPIS 33 (35)
T ss_dssp BETTTTSBE--EEEEETTTTE-EESSSS-EEE-S
T ss_pred eCCCCCccc--eEcCCCccCc-CCCCCCCccCCC
Confidence 599999863 22322 1112 999999987764
No 58
>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=71.64 E-value=1 Score=32.53 Aligned_cols=31 Identities=23% Similarity=0.333 Sum_probs=23.7
Q ss_pred eeCCCCCCcceEEEcCc-EEEeEeccCCCccc
Q 024241 221 ICLGCKSPDTILSKENR-LFFLRCEKCGSGRS 251 (270)
Q Consensus 221 lC~~C~sPDT~L~ke~r-l~~l~C~aCGa~~~ 251 (270)
.|..|+..+|-+-+.+. --..-|+|||-...
T Consensus 1 ~C~~C~~~~Tp~WR~g~~~~~~LCNaCgl~~~ 32 (54)
T cd00202 1 ACSNCGTTTTPLWRRGPSGGSTLCNACGLYWK 32 (54)
T ss_pred CCCCCCCCCCcccccCCCCcchHHHHHHHHHH
Confidence 59999999999988642 33568999986543
No 59
>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=71.25 E-value=5.7 Score=38.70 Aligned_cols=92 Identities=18% Similarity=0.320 Sum_probs=56.3
Q ss_pred hHHHHHHhCCChHHHHHH------HHHhhcCceeecCCceEEEEeecCh---------HHHHHHHHHhccc---------
Q 024241 163 FMDLCKTMHRQPDHVMTF------LLAELGTSGSLDGQQRLVVKGRFAP---------KNFEGILRRYVNE--------- 218 (270)
Q Consensus 163 f~dI~k~L~R~p~hv~ky------l~~ELGt~gsid~~~rlii~G~f~~---------k~ie~~L~~YI~e--------- 218 (270)
+..|+.-....|+++..| ++..||.+-.+=..-.+.-+|.|.+ ..|.++|..|...
T Consensus 89 i~~ip~p~g~~~~~~d~~~~~f~~~l~~lgi~~d~~~~T~~y~~g~~~~~i~~~L~~~~~I~~i~~~~~~~~~~~~~~P~ 168 (353)
T cd00674 89 LSSVPDPFGCCESYAEHFERPFEESLEKLGIEVEFISQSQMYKSGLYDENILIALEKRDEIMAILNEYRGRELQETWYPF 168 (353)
T ss_pred chhchhhcCCCHHHHHHHHHHHHHHHHHcCCeeeeeecCCchhhchHHHHHHHHHHHCChHHHHHHHhcCCccCCCceee
Confidence 334444444455554444 3445666544323345666677765 4567778777765
Q ss_pred eEeeCCCCCCcceEEE-c--CcEEEeEeccCCCccccccc
Q 024241 219 YVICLGCKSPDTILSK-E--NRLFFLRCEKCGSGRSVAPI 255 (270)
Q Consensus 219 YVlC~~C~sPDT~L~k-e--~rl~~l~C~aCGa~~~V~~i 255 (270)
.++|+.|+...|.++- + .+.+.-+|. ||....+...
T Consensus 169 ~p~c~~cg~~~~~v~~~d~~~~~v~y~c~-cG~~g~~~~~ 207 (353)
T cd00674 169 MPYCEKCGKDTTTVEAYDAKAGTVTYKCE-CGHEETVDIR 207 (353)
T ss_pred eeecCCcCcceeEEEEEeCCCCeEEEEcC-CCCEEEEeec
Confidence 4799999976666653 3 354555996 9998887654
No 60
>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=71.08 E-value=2.8 Score=40.23 Aligned_cols=38 Identities=26% Similarity=0.620 Sum_probs=28.4
Q ss_pred eEeeCCCCCCcc-eEEE----cCcEEEeEeccCCCcccccccc
Q 024241 219 YVICLGCKSPDT-ILSK----ENRLFFLRCEKCGSGRSVAPIK 256 (270)
Q Consensus 219 YVlC~~C~sPDT-~L~k----e~rl~~l~C~aCGa~~~V~~ik 256 (270)
--.||.|+|+=+ .+++ +++.-+|+|.-|+..+.+..++
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~ 226 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRVK 226 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCcc
Confidence 458999999753 3333 3577899999999988876655
No 61
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=70.16 E-value=3.2 Score=28.53 Aligned_cols=33 Identities=24% Similarity=0.490 Sum_probs=21.2
Q ss_pred eeCCCCCCcceEEEcC-cEEEeEeccCCCccccccc
Q 024241 221 ICLGCKSPDTILSKEN-RLFFLRCEKCGSGRSVAPI 255 (270)
Q Consensus 221 lC~~C~sPDT~L~ke~-rl~~l~C~aCGa~~~V~~i 255 (270)
.||.|++.= ..++. .-..+.|..||....+.+.
T Consensus 2 FCp~Cg~~l--~~~~~~~~~~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 2 FCPKCGNML--IPKEGKEKRRFVCRKCGYEEPIEQK 35 (52)
T ss_pred CCCCCCCcc--ccccCCCCCEEECCcCCCeEECCCc
Confidence 499999832 22222 1126689999998777543
No 62
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=69.37 E-value=3.8 Score=30.15 Aligned_cols=37 Identities=22% Similarity=0.545 Sum_probs=26.8
Q ss_pred ceEeeCCCCCCc-ceEEEcC--cEEEeEeccCCCcccccc
Q 024241 218 EYVICLGCKSPD-TILSKEN--RLFFLRCEKCGSGRSVAP 254 (270)
Q Consensus 218 eYVlC~~C~sPD-T~L~ke~--rl~~l~C~aCGa~~~V~~ 254 (270)
+.++||.|++.- +.+..+. .-|-|-|..|-..+-+..
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 579999999863 4444444 457889999998877653
No 63
>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=68.83 E-value=4.9 Score=30.20 Aligned_cols=32 Identities=22% Similarity=0.476 Sum_probs=22.3
Q ss_pred eeCCCCCCcceE----------EE-----cCcEEEeEeccCCCcccc
Q 024241 221 ICLGCKSPDTIL----------SK-----ENRLFFLRCEKCGSGRSV 252 (270)
Q Consensus 221 lC~~C~sPDT~L----------~k-----e~rl~~l~C~aCGa~~~V 252 (270)
.||.|++-+.+. .+ .++.+.+.|..||.+-.-
T Consensus 2 ~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~CGYTE~Y 48 (64)
T PF09855_consen 2 KCPKCGNEEYESGEVRATGGGLSKIFDVQNKKFTTVSCTNCGYTEFY 48 (64)
T ss_pred CCCCCCCcceecceEEccCCeeEEEEEecCcEEEEEECCCCCCEEEE
Confidence 499999876543 11 246778899999987443
No 64
>PRK03954 ribonuclease P protein component 4; Validated
Probab=68.07 E-value=4.5 Score=33.97 Aligned_cols=35 Identities=20% Similarity=0.444 Sum_probs=22.6
Q ss_pred eeCCCCCC-----cceEEE-cCc--EEEeEeccCCCccccccc
Q 024241 221 ICLGCKSP-----DTILSK-ENR--LFFLRCEKCGSGRSVAPI 255 (270)
Q Consensus 221 lC~~C~sP-----DT~L~k-e~r--l~~l~C~aCGa~~~V~~i 255 (270)
+|..|.+| ...+.. .++ .+.+.|..||..+-.+-.
T Consensus 66 ~CK~C~t~LiPG~n~~vRi~~~~~~~vvitCl~CG~~kR~P~~ 108 (121)
T PRK03954 66 YCKRCHSFLVPGVNARVRLRQKRMPHVVITCLECGHIMRYPYL 108 (121)
T ss_pred HhhcCCCeeecCCceEEEEecCCcceEEEECccCCCEEeeccc
Confidence 58888776 323322 332 568999999998766443
No 65
>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=67.96 E-value=4.4 Score=33.20 Aligned_cols=26 Identities=12% Similarity=0.299 Sum_probs=16.0
Q ss_pred ChHHHHHHHHHhhcCceeecCCceEEEE
Q 024241 173 QPDHVMTFLLAELGTSGSLDGQQRLVVK 200 (270)
Q Consensus 173 ~p~hv~kyl~~ELGt~gsid~~~rlii~ 200 (270)
+|+.|.-.| . +-+.|++-.+-+|.|.
T Consensus 40 ~p~~L~faf-~-~~~~~t~~ega~L~I~ 65 (115)
T TIGR00100 40 NPSQLQFAF-E-VVREGTVAEGAKLNIE 65 (115)
T ss_pred CHHHHHHHH-H-HHhCCCccCCCEEEEE
Confidence 366665554 3 4466777556688884
No 66
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=67.27 E-value=3.7 Score=27.20 Aligned_cols=30 Identities=30% Similarity=0.730 Sum_probs=20.3
Q ss_pred eEeeCCCCC----CcceEEEcCcEEEeEeccCCCcc
Q 024241 219 YVICLGCKS----PDTILSKENRLFFLRCEKCGSGR 250 (270)
Q Consensus 219 YVlC~~C~s----PDT~L~ke~rl~~l~C~aCGa~~ 250 (270)
.+.|+.|+. ||..|--.++ .++|..||...
T Consensus 2 ~i~Cp~C~~~y~i~d~~ip~~g~--~v~C~~C~~~f 35 (36)
T PF13717_consen 2 IITCPNCQAKYEIDDEKIPPKGR--KVRCSKCGHVF 35 (36)
T ss_pred EEECCCCCCEEeCCHHHCCCCCc--EEECCCCCCEe
Confidence 478999975 3444432333 89999999753
No 67
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=67.21 E-value=2.3 Score=40.65 Aligned_cols=34 Identities=24% Similarity=0.461 Sum_probs=25.3
Q ss_pred eEeeCCCCC-CcceEEEc----CcEEEeEeccCCCcccc
Q 024241 219 YVICLGCKS-PDTILSKE----NRLFFLRCEKCGSGRSV 252 (270)
Q Consensus 219 YVlC~~C~s-PDT~L~ke----~rl~~l~C~aCGa~~~V 252 (270)
--.||.|+| |=+.++.. .++-||+|.-|-..+-+
T Consensus 185 ~~~CPvCGS~PvaSmV~~g~~~~GlRYL~CslC~teW~~ 223 (308)
T COG3058 185 RQYCPVCGSMPVASMVQIGETEQGLRYLHCSLCETEWHY 223 (308)
T ss_pred cccCCCcCCCCcceeeeecCccccchhhhhhhHHHHHHH
Confidence 357999999 57888873 48889988877655444
No 68
>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=65.13 E-value=5.6 Score=28.79 Aligned_cols=30 Identities=30% Similarity=0.582 Sum_probs=23.6
Q ss_pred EeeCCCCCCcceE-EEcCcEEEeEeccCCCc
Q 024241 220 VICLGCKSPDTIL-SKENRLFFLRCEKCGSG 249 (270)
Q Consensus 220 VlC~~C~sPDT~L-~ke~rl~~l~C~aCGa~ 249 (270)
++|+.|++..=.. ..+..-+.-+|-.||+.
T Consensus 23 LIC~~C~~hNGla~~~~~~~i~y~C~~Cg~~ 53 (54)
T PF10058_consen 23 LICSKCFSHNGLAPKEEFEEIQYRCPYCGAL 53 (54)
T ss_pred EECcccchhhcccccccCCceEEEcCCCCCc
Confidence 6899999987544 45667678999999975
No 69
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=64.83 E-value=6.6 Score=33.23 Aligned_cols=68 Identities=22% Similarity=0.368 Sum_probs=43.5
Q ss_pred eeEEE-EehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHHHhccceEeeCCCCCCcceEE-
Q 024241 156 KKTVF-VNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILRRYVNEYVICLGCKSPDTILS- 233 (270)
Q Consensus 156 kKTvi-~Nf~dI~k~L~R~p~hv~kyl~~ELGt~gsid~~~rlii~G~f~~k~ie~~L~~YI~eYVlC~~C~sPDT~L~- 233 (270)
..+.| .|+..|..+|...-.++.+=|..+|--..+ ..+..||.|+.-=|.+.
T Consensus 61 ~~~yw~i~y~~~~~vik~r~~~~~~~L~~~l~~e~~--------------------------~~~Y~Cp~C~~~y~~~ea 114 (147)
T smart00531 61 YRYYWYINYDTLLDVVKYKLDKMRKRLEDKLEDETN--------------------------NAYYKCPNCQSKYTFLEA 114 (147)
T ss_pred EEEEEEecHHHHHHHHHHHHHHHHHHHHHHHhcccC--------------------------CcEEECcCCCCEeeHHHH
Confidence 45566 999999999998888888877776644322 13778999974322111
Q ss_pred --EcCcEEEeEeccCCCc
Q 024241 234 --KENRLFFLRCEKCGSG 249 (270)
Q Consensus 234 --ke~rl~~l~C~aCGa~ 249 (270)
-.+-.-...|..||+.
T Consensus 115 ~~~~d~~~~f~Cp~Cg~~ 132 (147)
T smart00531 115 NQLLDMDGTFTCPRCGEE 132 (147)
T ss_pred HHhcCCCCcEECCCCCCE
Confidence 0000112789999875
No 70
>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=64.53 E-value=5.3 Score=31.13 Aligned_cols=52 Identities=15% Similarity=0.400 Sum_probs=37.1
Q ss_pred eEEEEeecChHHHHHHHHHhccc-------eEeeCCCCCCcceEEEcCcEEEeEeccCCCccccccc
Q 024241 196 RLVVKGRFAPKNFEGILRRYVNE-------YVICLGCKSPDTILSKENRLFFLRCEKCGSGRSVAPI 255 (270)
Q Consensus 196 rlii~G~f~~k~ie~~L~~YI~e-------YVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V~~i 255 (270)
...-.+.|+..|++.+-..-... ++.|..|-+..+ .-+.|..||-..++..+
T Consensus 7 ~~k~~~~FS~~Ql~~~~~~~~~~~~~~~~~~i~C~~ct~~q~--------~El~C~~C~~~k~ld~F 65 (84)
T PF12898_consen 7 KWKPLSAFSKNQLEKLRKQIRANRVDPANSGIRCRECTGGQV--------VELTCSPCGKTKPLDEF 65 (84)
T ss_pred eECChHHcCHHHHHHHHHHHhhccCccCCCCCCCccCCCCCc--------CcCEeccCCCCcCHHHH
Confidence 34445789999988776544444 799999976532 23499999998888654
No 71
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=64.19 E-value=5.3 Score=36.98 Aligned_cols=39 Identities=18% Similarity=0.352 Sum_probs=28.5
Q ss_pred HHHHhccceEeeCCCCCCcceEEEcCcEEEeEeccCCCcccc
Q 024241 211 ILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKCGSGRSV 252 (270)
Q Consensus 211 ~L~~YI~eYVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V 252 (270)
.|-.|-..+-.|+.|++| |... +.+ +.+.|.+||...-.
T Consensus 91 ~l~~w~~~~~fC~~CG~~-~~~~-~~~-~~~~C~~c~~~~yp 129 (256)
T PRK00241 91 QLAEFYRSHRFCGYCGHP-MHPS-KTE-WAMLCPHCRERYYP 129 (256)
T ss_pred HHHHHhhcCccccccCCC-Ceec-CCc-eeEECCCCCCEECC
Confidence 356788889999999998 3333 233 46889999976654
No 72
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=63.90 E-value=8.4 Score=32.48 Aligned_cols=63 Identities=24% Similarity=0.374 Sum_probs=36.0
Q ss_pred CChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHHHhccceEeeCCCCCCcceE----------------EEc
Q 024241 172 RQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILRRYVNEYVICLGCKSPDTIL----------------SKE 235 (270)
Q Consensus 172 R~p~hv~kyl~~ELGt~gsid~~~rlii~G~f~~k~ie~~L~~YI~eYVlC~~C~sPDT~L----------------~ke 235 (270)
-.|+.+...| ..+ +.|++-.+-+|.|. .+.-...|+.|+..-+.- .-+
T Consensus 39 V~pe~L~faf-e~l-~~gt~~ega~L~i~--------------~~p~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~ 102 (135)
T PRK03824 39 VDKEIVEFAL-NEL-LKGTILEGAEIIFE--------------EEEAVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPE 102 (135)
T ss_pred hhHHHHHHHH-HHH-HcCCcccCCEEEEE--------------ecceEEECCCCCCEEeccccccccccccccccccccc
Confidence 3455555544 334 45665445578874 344579999998432111 001
Q ss_pred CcEEEeEeccCCCcc
Q 024241 236 NRLFFLRCEKCGSGR 250 (270)
Q Consensus 236 ~rl~~l~C~aCGa~~ 250 (270)
--.++++|..||+..
T Consensus 103 ~~~~~~~CP~Cgs~~ 117 (135)
T PRK03824 103 VVHAFLKCPKCGSRD 117 (135)
T ss_pred ccccCcCCcCCCCCC
Confidence 113567899999764
No 73
>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=63.52 E-value=8.3 Score=32.56 Aligned_cols=53 Identities=25% Similarity=0.510 Sum_probs=37.6
Q ss_pred EEEEeecChHHHHHHHHHhccc------eEeeCCCCCCcceEEEc------------CcEEEeEeccCCCc
Q 024241 197 LVVKGRFAPKNFEGILRRYVNE------YVICLGCKSPDTILSKE------------NRLFFLRCEKCGSG 249 (270)
Q Consensus 197 lii~G~f~~k~ie~~L~~YI~e------YVlC~~C~sPDT~L~ke------------~rl~~l~C~aCGa~ 249 (270)
+.|...-..+|+..+++.|=-. +-.|+.|.++=..+.++ .---|-+|..||..
T Consensus 63 ~li~~~~~~~QL~ev~~~~~l~~~~~~~~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~ki 133 (147)
T PF01927_consen 63 ILIRSDDPEEQLREVLERFGLKLRLDPIFSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKI 133 (147)
T ss_pred EEEcCCCHHHHHHHHHHHcCCccccCCCCCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCE
Confidence 4567777788999999888422 67999999964444443 11238999999964
No 74
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=63.43 E-value=4.5 Score=38.30 Aligned_cols=28 Identities=25% Similarity=0.466 Sum_probs=20.4
Q ss_pred EeeCCCCCCcceEEEcCcEEEeEeccCCCc
Q 024241 220 VICLGCKSPDTILSKENRLFFLRCEKCGSG 249 (270)
Q Consensus 220 VlC~~C~sPDT~L~ke~rl~~l~C~aCGa~ 249 (270)
..||.|+++ .++.+-.-=.+.|..||..
T Consensus 12 ~~Cp~Cg~~--~iv~d~~~Ge~vC~~CG~V 39 (310)
T PRK00423 12 LVCPECGSD--KLIYDYERGEIVCADCGLV 39 (310)
T ss_pred CcCcCCCCC--CeeEECCCCeEeecccCCc
Confidence 579999984 4655433347899999983
No 75
>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=63.29 E-value=4.5 Score=26.36 Aligned_cols=32 Identities=28% Similarity=0.446 Sum_probs=20.0
Q ss_pred eEeeCCCCCC---cceEEEcCcEEEeEeccCCCccc
Q 024241 219 YVICLGCKSP---DTILSKENRLFFLRCEKCGSGRS 251 (270)
Q Consensus 219 YVlC~~C~sP---DT~L~ke~rl~~l~C~aCGa~~~ 251 (270)
.+.||.|+.- +....-.++. .++|..||+.-.
T Consensus 2 ~~~CP~C~~~~~v~~~~~~~~~~-~v~C~~C~~~~~ 36 (38)
T TIGR02098 2 RIQCPNCKTSFRVVDSQLGANGG-KVRCGKCGHVWY 36 (38)
T ss_pred EEECCCCCCEEEeCHHHcCCCCC-EEECCCCCCEEE
Confidence 4789999872 2222222222 688999998643
No 76
>PRK07451 translation initiation factor Sui1; Validated
Probab=63.21 E-value=16 Score=30.50 Aligned_cols=58 Identities=21% Similarity=0.339 Sum_probs=41.3
Q ss_pred eEEEeC---ceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHH
Q 024241 149 QVLREG---TKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGI 211 (270)
Q Consensus 149 ~V~~eG---~kKTvi~Nf~dI~k~L~R~p~hv~kyl~~ELGt~gsid~~~rlii~G~f~~k~ie~~ 211 (270)
++.+.| ..-|+|.+|..-.. +-.-|++.|-..+|+.|++..+ .+.|+|.|..+-.+-+
T Consensus 43 ~~~r~gR~GK~VTvV~Gl~~~~~----dlk~LaK~LK~k~gcGGtvkd~-~IelQGD~r~~v~~~L 103 (115)
T PRK07451 43 QATRSGRKGKTVTVITGFQHKPE----TLAKLLKQLKTQCGSGGTVKDN-TIEIQGDHRQKILEIL 103 (115)
T ss_pred EEEecCCCCCeEEEEeCCCCCHH----HHHHHHHHHHHHhcCCceEcCC-EEEEcCcHHHHHHHHH
Confidence 344444 36788998863211 2467889999999999999644 8999999977655444
No 77
>PRK00750 lysK lysyl-tRNA synthetase; Reviewed
Probab=62.59 E-value=13 Score=37.80 Aligned_cols=50 Identities=26% Similarity=0.394 Sum_probs=34.6
Q ss_pred HHHHHHHHHhccc---------eEeeCCCCCCcceEEE--c--CcEEEeEeccCCCcccccccc
Q 024241 206 KNFEGILRRYVNE---------YVICLGCKSPDTILSK--E--NRLFFLRCEKCGSGRSVAPIK 256 (270)
Q Consensus 206 k~ie~~L~~YI~e---------YVlC~~C~sPDT~L~k--e--~rl~~l~C~aCGa~~~V~~ik 256 (270)
..|.++|..|... .++|+.|+.-.|..+. + .+.+.-.|. ||....+.-..
T Consensus 153 ~~i~~il~~~~~~~~~~~~~P~~pic~~cg~~~~~~~~~~d~~~~~v~y~~~-cG~~~~~~~~~ 215 (510)
T PRK00750 153 DEIMEILLPYLGEERQATYSPFLPICPKCGKVLTTPVISYDAEAGTVTYDCE-CGHEGEVPVTG 215 (510)
T ss_pred HHHHHHHHHhcCCccCCCeeeeeeeCCCCCccceEEEEEEeCCCCEEEEEcC-CCCEEEEecCC
Confidence 4566677766443 4799999999987763 2 344444787 99998876544
No 78
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=62.28 E-value=6.1 Score=32.52 Aligned_cols=57 Identities=18% Similarity=0.150 Sum_probs=30.7
Q ss_pred hHHHHHHHHHhhcCcee-ecCCceEEEEeecChHHHHHHHHHhccceEeeCCCCCCcceEEEcCcEEEeEeccCCCcc
Q 024241 174 PDHVMTFLLAELGTSGS-LDGQQRLVVKGRFAPKNFEGILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKCGSGR 250 (270)
Q Consensus 174 p~hv~kyl~~ELGt~gs-id~~~rlii~G~f~~k~ie~~L~~YI~eYVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~ 250 (270)
|+.|.-.| .. -+.|+ +-.+-+|.|.- +.-.+.|..|+..-+.- ...+.+|..||+..
T Consensus 41 pe~L~faf-~~-~~~~T~~~ega~L~Ie~--------------vp~~~~C~~Cg~~~~~~----~~~~~~CP~Cgs~~ 98 (117)
T PRK00564 41 KSLFVSAF-ET-FREESLVCKDAILDIVD--------------EKVELECKDCSHVFKPN----ALDYGVCEKCHSKN 98 (117)
T ss_pred HHHHHHHH-HH-HhcCCcccCCCEEEEEe--------------cCCEEEhhhCCCccccC----CccCCcCcCCCCCc
Confidence 55554444 33 46677 66566888842 33456777777322111 11244677777653
No 79
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=62.22 E-value=8.2 Score=26.38 Aligned_cols=30 Identities=20% Similarity=0.356 Sum_probs=20.2
Q ss_pred EeeCCCCCCcceEEEcCcEEEeEeccCCCcccc
Q 024241 220 VICLGCKSPDTILSKENRLFFLRCEKCGSGRSV 252 (270)
Q Consensus 220 VlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V 252 (270)
..|+.|+.. +..+...-.++|..||+.-..
T Consensus 4 y~C~~CG~~---~~~~~~~~~~~Cp~CG~~~~~ 33 (46)
T PRK00398 4 YKCARCGRE---VELDEYGTGVRCPYCGYRILF 33 (46)
T ss_pred EECCCCCCE---EEECCCCCceECCCCCCeEEE
Confidence 579999873 333333226899999986554
No 80
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=62.15 E-value=1.5 Score=32.98 Aligned_cols=37 Identities=30% Similarity=0.774 Sum_probs=30.7
Q ss_pred HHhccceEeeCCCCCCcceE-EEcCcEEEeEeccCCCcc
Q 024241 213 RRYVNEYVICLGCKSPDTIL-SKENRLFFLRCEKCGSGR 250 (270)
Q Consensus 213 ~~YI~eYVlC~~C~sPDT~L-~ke~rl~~l~C~aCGa~~ 250 (270)
.+||.- -.||.|..-||.- -+|+.+-...|-+||..-
T Consensus 5 KRFIAG-A~CP~C~~~Dtl~mW~En~ve~vECV~CG~~~ 42 (66)
T COG3529 5 KRFIAG-AVCPACQAQDTLAMWRENNVEIVECVKCGHHM 42 (66)
T ss_pred hhhhcc-CCCcccchhhHHHHHHhcCCceEehhhcchHh
Confidence 467766 5699999999864 479999999999999864
No 81
>KOG3507 consensus DNA-directed RNA polymerase, subunit RPB7.0 [Transcription]
Probab=62.14 E-value=3.3 Score=31.01 Aligned_cols=29 Identities=28% Similarity=0.659 Sum_probs=21.1
Q ss_pred EeeCCCCCCcceEEEcCcEEEeEeccCCCcccc
Q 024241 220 VICLGCKSPDTILSKENRLFFLRCEKCGSGRSV 252 (270)
Q Consensus 220 VlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V 252 (270)
-+|..|++-+|.=.++ .++|.-||.+=..
T Consensus 21 YiCgdC~~en~lk~~D----~irCReCG~RIly 49 (62)
T KOG3507|consen 21 YICGDCGQENTLKRGD----VIRCRECGYRILY 49 (62)
T ss_pred EEeccccccccccCCC----cEehhhcchHHHH
Confidence 4799999988653333 6799999986443
No 82
>PLN00209 ribosomal protein S27; Provisional
Probab=61.90 E-value=7.6 Score=30.97 Aligned_cols=30 Identities=27% Similarity=0.532 Sum_probs=24.3
Q ss_pred eEeeCCCCCCcceEEEcCcEEEeEeccCCCcc
Q 024241 219 YVICLGCKSPDTILSKENRLFFLRCEKCGSGR 250 (270)
Q Consensus 219 YVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~ 250 (270)
.|.|+.|.+.-|....-. ....|..||..=
T Consensus 36 ~VkCp~C~n~q~VFShA~--t~V~C~~Cg~~L 65 (86)
T PLN00209 36 DVKCQGCFNITTVFSHSQ--TVVVCGSCQTVL 65 (86)
T ss_pred EEECCCCCCeeEEEecCc--eEEEccccCCEe
Confidence 599999999988777654 368899999753
No 83
>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=61.76 E-value=4.9 Score=26.01 Aligned_cols=27 Identities=30% Similarity=0.598 Sum_probs=13.7
Q ss_pred EeeCCCCCCcceEEEcCcEEEeEeccCCCcc
Q 024241 220 VICLGCKSPDTILSKENRLFFLRCEKCGSGR 250 (270)
Q Consensus 220 VlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~ 250 (270)
-.|+.|+|..|- .++. .+.|..||+..
T Consensus 3 p~Cp~C~se~~y--~D~~--~~vCp~C~~ew 29 (30)
T PF08274_consen 3 PKCPLCGSEYTY--EDGE--LLVCPECGHEW 29 (30)
T ss_dssp ---TTT-----E--E-SS--SEEETTTTEEE
T ss_pred CCCCCCCCccee--ccCC--EEeCCcccccC
Confidence 469999999987 4444 57899999754
No 84
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=61.15 E-value=9.1 Score=31.49 Aligned_cols=18 Identities=33% Similarity=0.813 Sum_probs=12.3
Q ss_pred eEeeCCCCCCcceEEEcC
Q 024241 219 YVICLGCKSPDTILSKEN 236 (270)
Q Consensus 219 YVlC~~C~sPDT~L~ke~ 236 (270)
|..||.|+|+++.++.-.
T Consensus 88 ~~~CP~Cgs~~~~i~~G~ 105 (117)
T PRK00564 88 YGVCEKCHSKNVIITQGN 105 (117)
T ss_pred CCcCcCCCCCceEEecCC
Confidence 345888888887776633
No 85
>KOG2703 consensus C4-type Zn-finger protein [General function prediction only]
Probab=60.62 E-value=5.9 Score=39.69 Aligned_cols=33 Identities=21% Similarity=0.607 Sum_probs=25.0
Q ss_pred eEeeCCCCCC-cceEEEcC-------cEEEeEeccCCCccc
Q 024241 219 YVICLGCKSP-DTILSKEN-------RLFFLRCEKCGSGRS 251 (270)
Q Consensus 219 YVlC~~C~sP-DT~L~ke~-------rl~~l~C~aCGa~~~ 251 (270)
--.||.|..| +|.|.--+ =++-..|.+||+++.
T Consensus 258 ~t~Cp~C~~pcet~Mk~~~IPhFkeVIiMst~Cd~CGyksn 298 (460)
T KOG2703|consen 258 PTTCPSCTAPCETNMKLTDIPHFKEVIIMSTVCDRCGYKSN 298 (460)
T ss_pred cCCCCCCCCchhccceeccCCcceeEEEEeecccccCCccc
Confidence 3469999999 89887522 344678999999875
No 86
>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=60.48 E-value=9.7 Score=32.71 Aligned_cols=29 Identities=31% Similarity=0.630 Sum_probs=22.0
Q ss_pred EeeCCCCCCcceEEEc-Cc---EEEeEeccCCC
Q 024241 220 VICLGCKSPDTILSKE-NR---LFFLRCEKCGS 248 (270)
Q Consensus 220 VlC~~C~sPDT~L~ke-~r---l~~l~C~aCGa 248 (270)
|.||.|+|.+|+++-. +. --..+|.+|..
T Consensus 106 ~~cp~c~s~~t~~~s~fg~t~cka~~~c~~c~e 138 (146)
T TIGR02159 106 VQCPRCGSADTTITSIFGPTACKALYRCRACKE 138 (146)
T ss_pred CcCCCCCCCCcEeecCCCChhhHHHhhhhhhCC
Confidence 8999999999999975 21 11457888864
No 87
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=60.38 E-value=19 Score=35.56 Aligned_cols=79 Identities=14% Similarity=0.322 Sum_probs=53.9
Q ss_pred HHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHHHhccce--EeeCCCCCCcceEEEcCcEEEeE
Q 024241 165 DLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILRRYVNEY--VICLGCKSPDTILSKENRLFFLR 242 (270)
Q Consensus 165 dI~k~L~R~p~hv~kyl~~ELGt~gsid~~~rlii~G~f~~k~ie~~L~~YI~eY--VlC~~C~sPDT~L~ke~rl~~l~ 242 (270)
-+-..|+|.|....-|=+-++-.+--= .++ ++-+-..+..++..=|..- -.|..|+--- +.++-+
T Consensus 304 ~l~~Ql~r~Pt~~gf~rl~~~~l~dae--eg~----~k~sL~~lr~mvge~l~~~~~YRC~~CGF~a-------~~l~W~ 370 (389)
T COG2956 304 YLTRQLRRKPTMRGFHRLMDYHLADAE--EGR----AKESLDLLRDMVGEQLRRKPRYRCQNCGFTA-------HTLYWH 370 (389)
T ss_pred HHHHHHhhCCcHHHHHHHHHhhhcccc--ccc----hhhhHHHHHHHHHHHHhhcCCceecccCCcc-------eeeeee
Confidence 456789999987655544444332211 122 4555666777776666543 3799998643 778999
Q ss_pred eccCCCcccccccc
Q 024241 243 CEKCGSGRSVAPIK 256 (270)
Q Consensus 243 C~aCGa~~~V~~ik 256 (270)
|.+|.++.+++||+
T Consensus 371 CPsC~~W~TikPir 384 (389)
T COG2956 371 CPSCRAWETIKPIR 384 (389)
T ss_pred CCCcccccccCCcc
Confidence 99999999999998
No 88
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=60.34 E-value=7.1 Score=41.65 Aligned_cols=35 Identities=26% Similarity=0.537 Sum_probs=24.0
Q ss_pred eEeeCCCCCC------cceEEEcCcEEEeEeccCCCccccc
Q 024241 219 YVICLGCKSP------DTILSKENRLFFLRCEKCGSGRSVA 253 (270)
Q Consensus 219 YVlC~~C~sP------DT~L~ke~rl~~l~C~aCGa~~~V~ 253 (270)
+|+|+.|+.. |..|+-....-.|+|.-||+..++.
T Consensus 435 ~l~C~~Cg~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p 475 (730)
T COG1198 435 LLLCRDCGYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIP 475 (730)
T ss_pred eeecccCCCcccCCCCCcceEEecCCCeeEeCCCCCCCCCC
Confidence 7888888753 3445544333578999999986664
No 89
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=60.33 E-value=15 Score=30.01 Aligned_cols=56 Identities=16% Similarity=0.305 Sum_probs=33.9
Q ss_pred ChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHHHhccceEeeCCCCCCcceEEEcCcEEEeEeccCCCc
Q 024241 173 QPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKCGSG 249 (270)
Q Consensus 173 ~p~hv~kyl~~ELGt~gsid~~~rlii~G~f~~k~ie~~L~~YI~eYVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~ 249 (270)
.|+.|.-.| ++-+.|++-.+-+|.|. .+.--+.|+.|+.. ...+. ++..|..||+.
T Consensus 40 ~pe~L~f~f--~~~~~~T~~egA~L~I~--------------~vp~~~~C~~Cg~~---~~~~~--~~~~CP~Cgs~ 95 (113)
T PRK12380 40 EESAVRFSF--EIVCHGTVAQGCDLHIV--------------YKPAQAWCWDCSQV---VEIHQ--HDAQCPHCHGE 95 (113)
T ss_pred CHHHHHHHH--HHHhCCCccCCCEEEEE--------------eeCcEEEcccCCCE---EecCC--cCccCcCCCCC
Confidence 377666555 35567777656688884 34456788888822 11221 23448888865
No 90
>COG1163 DRG Predicted GTPase [General function prediction only]
Probab=60.16 E-value=9.4 Score=37.54 Aligned_cols=52 Identities=25% Similarity=0.514 Sum_probs=37.9
Q ss_pred CCCccHHHHHHHHHHHHhhcCCCcc-----cCcceeecCCCeEEEeCceeEEEEehHHHHHHhCCChH
Q 024241 113 DRDYEYEELLGRVFNILRENNPELA-----GDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTMHRQPD 175 (270)
Q Consensus 113 ~~~~~YeeLL~R~~~~l~~~np~~~-----~~~~R~~mP~p~V~~eG~kKTvi~Nf~dI~k~L~R~p~ 175 (270)
.++++-++|++++|..| .+. .....-..++|.|.+.| ....|+|..|||+--
T Consensus 272 ~~~~nld~L~e~i~~~L-----~liRVYtK~~g~~pd~~~PlIlr~G------sTV~Dvc~~IH~~l~ 328 (365)
T COG1163 272 KKGINLDELKERIWDVL-----GLIRVYTKPPGEEPDFDEPLILRRG------STVGDVCRKIHRDLV 328 (365)
T ss_pred ccCCCHHHHHHHHHHhh-----CeEEEEecCCCCCCCCCCCeEEeCC------CcHHHHHHHHHHHHH
Confidence 44667899999999999 221 01122345789999999 568999999999743
No 91
>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=60.09 E-value=1.9 Score=28.43 Aligned_cols=28 Identities=21% Similarity=0.381 Sum_probs=16.7
Q ss_pred eCCCCCCcceEEEcCc-EEEeEeccCCCc
Q 024241 222 CLGCKSPDTILSKENR-LFFLRCEKCGSG 249 (270)
Q Consensus 222 C~~C~sPDT~L~ke~r-l~~l~C~aCGa~ 249 (270)
|..|+..+|.+-+.+. --..-|++||-.
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 8899999999998532 112379999854
No 92
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=59.49 E-value=9.5 Score=31.40 Aligned_cols=33 Identities=21% Similarity=0.499 Sum_probs=24.7
Q ss_pred eEeeCCCCCCcceEEE-------cCcEEEeEeccCCCccc
Q 024241 219 YVICLGCKSPDTILSK-------ENRLFFLRCEKCGSGRS 251 (270)
Q Consensus 219 YVlC~~C~sPDT~L~k-------e~rl~~l~C~aCGa~~~ 251 (270)
-+.||.|++-+-.+.- +.-..|-+|..||.++.
T Consensus 72 ~~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~wr 111 (113)
T COG1594 72 KEKCPKCGNKEAYYWQLQTRSADEPETRFYKCTRCGYRWR 111 (113)
T ss_pred cccCCCCCCceeEEEeeehhccCCCceEEEEecccCCEee
Confidence 3789999998744432 34577999999998764
No 93
>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=59.30 E-value=6.3 Score=28.69 Aligned_cols=28 Identities=21% Similarity=0.595 Sum_probs=20.4
Q ss_pred EeeCCCCCCcceEEEcCcEEEeEeccCCCcc
Q 024241 220 VICLGCKSPDTILSKENRLFFLRCEKCGSGR 250 (270)
Q Consensus 220 VlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~ 250 (270)
-+||.|+.+.-. ...+| ...|..||...
T Consensus 29 q~C~~CG~~~~~-~~~~r--~~~C~~Cg~~~ 56 (69)
T PF07282_consen 29 QTCPRCGHRNKK-RRSGR--VFTCPNCGFEM 56 (69)
T ss_pred cCccCccccccc-ccccc--eEEcCCCCCEE
Confidence 469999998765 22334 67899999863
No 94
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=59.04 E-value=9.5 Score=30.39 Aligned_cols=30 Identities=30% Similarity=0.607 Sum_probs=24.4
Q ss_pred eEeeCCCCCCcceEEEcCcEEEeEeccCCCcc
Q 024241 219 YVICLGCKSPDTILSKENRLFFLRCEKCGSGR 250 (270)
Q Consensus 219 YVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~ 250 (270)
.|.|+.|.+.-|....-.. ...|..||..=
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 5999999999888777543 67899999753
No 95
>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=58.89 E-value=8.5 Score=25.86 Aligned_cols=31 Identities=23% Similarity=0.618 Sum_probs=21.3
Q ss_pred EeeCCCCCCcceEEEc--CcEEEeEecc---CCCccccc
Q 024241 220 VICLGCKSPDTILSKE--NRLFFLRCEK---CGSGRSVA 253 (270)
Q Consensus 220 VlC~~C~sPDT~L~ke--~rl~~l~C~a---CGa~~~V~ 253 (270)
+.||.|+++ .+.|. .+ .|+-|.. |....++.
T Consensus 2 ~~CP~Cg~~--lv~r~~k~g-~F~~Cs~yP~C~~~~~~~ 37 (39)
T PF01396_consen 2 EKCPKCGGP--LVLRRGKKG-KFLGCSNYPECKYTEPLP 37 (39)
T ss_pred cCCCCCCce--eEEEECCCC-CEEECCCCCCcCCeEeCC
Confidence 579999943 23332 34 7999987 88877664
No 96
>PRK09019 translation initiation factor Sui1; Validated
Probab=58.66 E-value=26 Score=28.98 Aligned_cols=54 Identities=9% Similarity=0.013 Sum_probs=39.3
Q ss_pred CceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHH
Q 024241 154 GTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGIL 212 (270)
Q Consensus 154 G~kKTvi~Nf~dI~k~L~R~p~hv~kyl~~ELGt~gsid~~~rlii~G~f~~k~ie~~L 212 (270)
|..-|+|..|..-.. +-.-|++.|-..+|+.|++.+ +.+.|+|.|..+-.+-+.
T Consensus 44 GK~VTiI~Gl~~~~~----dlk~l~K~lKkk~gcGGtvk~-~~IelQGD~r~~v~~~L~ 97 (108)
T PRK09019 44 GKGVCLITGLDLDDA----ELKKLAAELKKKCGCGGAVKD-GVIEIQGDKRDLLKSLLE 97 (108)
T ss_pred CCeEEEEeCCcCCHH----HHHHHHHHHHHHhcCCCeEEc-CEEEEcCcHHHHHHHHHH
Confidence 335688888851111 146789999999999999974 489999999776555443
No 97
>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=58.48 E-value=6.1 Score=25.73 Aligned_cols=28 Identities=25% Similarity=0.524 Sum_probs=20.6
Q ss_pred eeCCCCCCcceEEEcCcEEEeEeccCCC
Q 024241 221 ICLGCKSPDTILSKENRLFFLRCEKCGS 248 (270)
Q Consensus 221 lC~~C~sPDT~L~ke~rl~~l~C~aCGa 248 (270)
.|+.|+..=+.+..-..--...|-.||+
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 7 RCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 7999999766665532234678999998
No 98
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=58.17 E-value=5.3 Score=27.74 Aligned_cols=30 Identities=23% Similarity=0.517 Sum_probs=21.0
Q ss_pred eeCCCCCCcceEEEcCcEEEeEeccCCCcccccc
Q 024241 221 ICLGCKSPDTILSKENRLFFLRCEKCGSGRSVAP 254 (270)
Q Consensus 221 lC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V~~ 254 (270)
+|..|+..-+ +. ..-.++|..||++=-.+.
T Consensus 4 ~C~~Cg~~~~-~~---~~~~irC~~CG~rIlyK~ 33 (44)
T smart00659 4 ICGECGRENE-IK---SKDVVRCRECGYRILYKK 33 (44)
T ss_pred ECCCCCCEee-cC---CCCceECCCCCceEEEEe
Confidence 6999998543 22 334689999999765543
No 99
>COG1384 LysS Lysyl-tRNA synthetase (class I) [Translation, ribosomal structure and biogenesis]
Probab=57.39 E-value=16 Score=37.57 Aligned_cols=79 Identities=23% Similarity=0.359 Sum_probs=50.9
Q ss_pred HHHHHHHHHhhcCce---eecCCceEEEEeecCh---------HHHHHHHHHhccc---------eEeeCCCCCCc-ceE
Q 024241 175 DHVMTFLLAELGTSG---SLDGQQRLVVKGRFAP---------KNFEGILRRYVNE---------YVICLGCKSPD-TIL 232 (270)
Q Consensus 175 ~hv~kyl~~ELGt~g---sid~~~rlii~G~f~~---------k~ie~~L~~YI~e---------YVlC~~C~sPD-T~L 232 (270)
+|..+=|...|..-| .+-....+.=.|.|.. ..|..+|..|-.. -++|+.|+..+ |.+
T Consensus 106 ~hf~~~f~~~l~~~Gi~~E~~s~se~Yk~G~~~~~i~~ale~rdeI~~il~~~~~~~~~e~~~P~~piC~kcGri~~t~v 185 (521)
T COG1384 106 EHFLRPFEEFLDEFGIEVEFVSATELYKSGLYDEAIRIALERRDEIMEILNEYRGRELEEDWSPFMPICEKCGRILTTPV 185 (521)
T ss_pred HHHHHHHHHHHHhcCCceEEEEhHHhhhcccHHHHHHHHHhhHHHHHHHHHHhcCCcccCCceeccccccccCCcceeEE
Confidence 455555555555544 2212334555566654 5678888887766 47999999955 444
Q ss_pred EE-cCc-EEEeEeccCCCcccccc
Q 024241 233 SK-ENR-LFFLRCEKCGSGRSVAP 254 (270)
Q Consensus 233 ~k-e~r-l~~l~C~aCGa~~~V~~ 254 (270)
.. +.. .+.-+|+ ||+...|.-
T Consensus 186 ~~~d~~~~v~Y~Ce-~Gh~g~v~i 208 (521)
T COG1384 186 IEWDGEGTVEYRCE-CGHEGEVDI 208 (521)
T ss_pred EEecCCceEEEEec-CCccceeec
Confidence 44 443 7788998 999988854
No 100
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=57.29 E-value=7.9 Score=31.72 Aligned_cols=58 Identities=14% Similarity=0.197 Sum_probs=33.1
Q ss_pred ChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHHHhccceEeeCCCCCCcceEEEcCcEEEeEeccCCCcc
Q 024241 173 QPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKCGSGR 250 (270)
Q Consensus 173 ~p~hv~kyl~~ELGt~gsid~~~rlii~G~f~~k~ie~~L~~YI~eYVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~ 250 (270)
.|+.|.-.|- +-+.|++-.+-+|.|. .+.--..|+.|+..- ... ..++..|..||+..
T Consensus 40 ~p~~L~f~f~--~~~~~t~~egA~L~i~--------------~~p~~~~C~~Cg~~~---~~~-~~~~~~CP~Cgs~~ 97 (114)
T PRK03681 40 ETSSLAFCFD--LVCRGTVAEGCKLHLE--------------EQEAECWCETCQQYV---TLL-TQRVRRCPQCHGDM 97 (114)
T ss_pred CHHHHHHHHH--HHhCCCccCCCEEEEE--------------eeCcEEEcccCCCee---ecC-CccCCcCcCcCCCC
Confidence 3666655553 3466777666688884 344457788888421 111 11235688888653
No 101
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=56.48 E-value=9.1 Score=31.80 Aligned_cols=26 Identities=19% Similarity=0.409 Sum_probs=16.9
Q ss_pred ChHHHHHHHHHhhcCceeecCCceEEEE
Q 024241 173 QPDHVMTFLLAELGTSGSLDGQQRLVVK 200 (270)
Q Consensus 173 ~p~hv~kyl~~ELGt~gsid~~~rlii~ 200 (270)
.|+.|.-+|- +-+.|++-.+-.|.|.
T Consensus 40 ~pe~L~faf~--~~~~gT~~egA~L~I~ 65 (124)
T PRK00762 40 NPEQLRFMLD--VLAEGTIAEDADLIVE 65 (124)
T ss_pred CHHHHHHHHH--HHhCCCCcCCCEEEEE
Confidence 4777766663 4567777656688874
No 102
>PF04194 PDCD2_C: Programmed cell death protein 2, C-terminal putative domain ; InterPro: IPR007320 PDCD2 is localized predominantly in the cytosol of cells situated at the opposite pole of the germinal centre from the centroblasts as well as in cells in the mantle zone. It has been shown to interact with BCL6, an evolutionarily conserved Kruppel-type zinc finger protein that functions as a strong transcriptional repressor and is required for germinal centre development. The rat homologue, Rp8, is associated with programmed cell death in thymocytes.; GO: 0005737 cytoplasm
Probab=56.21 E-value=2.1 Score=37.05 Aligned_cols=18 Identities=28% Similarity=0.805 Sum_probs=12.6
Q ss_pred hHHHHHHhCCChHHHHHH
Q 024241 163 FMDLCKTMHRQPDHVMTF 180 (270)
Q Consensus 163 f~dI~k~L~R~p~hv~ky 180 (270)
|....++|.|.|++|++|
T Consensus 60 f~~F~~rl~~~P~QvlRY 77 (164)
T PF04194_consen 60 FLKFQKRLSRNPEQVLRY 77 (164)
T ss_pred HHHHHHHHhcCCCeEEEE
Confidence 555566777777777777
No 103
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=54.91 E-value=19 Score=29.41 Aligned_cols=15 Identities=13% Similarity=0.231 Sum_probs=9.6
Q ss_pred EeeCCCCCCcceEEE
Q 024241 220 VICLGCKSPDTILSK 234 (270)
Q Consensus 220 VlC~~C~sPDT~L~k 234 (270)
..||.|+|+++.++.
T Consensus 88 ~~CP~Cgs~~~~i~~ 102 (114)
T PRK03681 88 RRCPQCHGDMLRIVA 102 (114)
T ss_pred CcCcCcCCCCcEEcc
Confidence 457777777666654
No 104
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=54.60 E-value=8 Score=27.53 Aligned_cols=28 Identities=25% Similarity=0.553 Sum_probs=19.0
Q ss_pred eEeeCCCCCCcceEEEcCcEEEeEeccCCCcc
Q 024241 219 YVICLGCKSPDTILSKENRLFFLRCEKCGSGR 250 (270)
Q Consensus 219 YVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~ 250 (270)
.-.||.|++- .|..... .+.|..||.+.
T Consensus 20 ~~fCP~Cg~~--~m~~~~~--r~~C~~Cgyt~ 47 (50)
T PRK00432 20 NKFCPRCGSG--FMAEHLD--RWHCGKCGYTE 47 (50)
T ss_pred cCcCcCCCcc--hheccCC--cEECCCcCCEE
Confidence 4579999984 4444332 45899999753
No 105
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=54.49 E-value=16 Score=23.97 Aligned_cols=29 Identities=28% Similarity=0.560 Sum_probs=21.3
Q ss_pred eEeeCCCCCCcceEE-EcCcEEEeEeccCCCccc
Q 024241 219 YVICLGCKSPDTILS-KENRLFFLRCEKCGSGRS 251 (270)
Q Consensus 219 YVlC~~C~sPDT~L~-ke~rl~~l~C~aCGa~~~ 251 (270)
..+|+.|+++- |. ++.. .+.|.-||+..+
T Consensus 3 ~~~C~~C~~~~--i~~~~~~--~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 3 LKKCSKCGGNG--IVNKEDD--YEVCIFCGSSFP 32 (33)
T ss_pred ceEcCCCCCCe--EEEecCC--eEEcccCCcEee
Confidence 57899999987 33 4443 678999998654
No 106
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=54.45 E-value=10 Score=31.98 Aligned_cols=18 Identities=28% Similarity=0.536 Sum_probs=14.7
Q ss_pred eEeeCCCCCCcceEEEcC
Q 024241 219 YVICLGCKSPDTILSKEN 236 (270)
Q Consensus 219 YVlC~~C~sPDT~L~ke~ 236 (270)
|..||.|+|+++.+..-.
T Consensus 107 ~~~CP~Cgs~~~~i~~G~ 124 (135)
T PRK03824 107 FLKCPKCGSRDFEIVKGR 124 (135)
T ss_pred CcCCcCCCCCCcEEecCc
Confidence 567999999998887643
No 107
>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=53.62 E-value=6.2 Score=28.96 Aligned_cols=30 Identities=30% Similarity=0.649 Sum_probs=18.5
Q ss_pred eEeeCCCCCCcceEEEcCcEEEeEeccCCCcc
Q 024241 219 YVICLGCKSPDTILSKENRLFFLRCEKCGSGR 250 (270)
Q Consensus 219 YVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~ 250 (270)
-|.|+.|.+.-|....-. ....|..||..=
T Consensus 7 ~VkCp~C~~~q~vFSha~--t~V~C~~Cg~~L 36 (55)
T PF01667_consen 7 DVKCPGCYNIQTVFSHAQ--TVVKCVVCGTVL 36 (55)
T ss_dssp EEE-TTT-SEEEEETT-S--S-EE-SSSTSEE
T ss_pred EEECCCCCCeeEEEecCC--eEEEcccCCCEe
Confidence 599999998876654433 368999999753
No 108
>KOG0481 consensus DNA replication licensing factor, MCM5 component [Replication, recombination and repair]
Probab=53.54 E-value=31 Score=36.24 Aligned_cols=140 Identities=14% Similarity=0.248 Sum_probs=86.3
Q ss_pred cHHHHHHHHHHHHhhcCCCcccCcceeecCCCeEEEeCceeEEEEeh-------HHHHHHhCCChHHHHHHHHHh-----
Q 024241 117 EYEELLGRVFNILRENNPELAGDRRRTVMRPPQVLREGTKKTVFVNF-------MDLCKTMHRQPDHVMTFLLAE----- 184 (270)
Q Consensus 117 ~YeeLL~R~~~~l~~~np~~~~~~~R~~mP~p~V~~eG~kKTvi~Nf-------~dI~k~L~R~p~hv~kyl~~E----- 184 (270)
.|+.++.++-+.++.-+-+-. -.||-.+..-. -.| ....-+|+ .+++..|++.|...+..|..-
T Consensus 24 ~~~~v~~~fkefir~f~~~~~-f~Yrd~L~~N~--~~~-~y~L~v~le~L~~fdedl~~~L~~~P~~~lp~fEeAa~~Va 99 (729)
T KOG0481|consen 24 RKSQVKTKFKEFIRQFRTGTD-FKYRDQLKRNY--NLG-EYSLEVELEDLISFDEDLADKLSKQPADHLPLFEEAAKEVA 99 (729)
T ss_pred cHHHHHHHHHHHHHHhccccc-cchHHHHHhcc--ccc-ceEEEEEHHHhhccchHHHHHHHhChHhHHHHHHHHHHHHH
Confidence 577888777776653221100 11222222111 112 33333444 468999999999888887654
Q ss_pred --h---cCcee-ecCCceEEEEeecChHHHHHHHHHhccceEeeCCCCCCcceEEEcCcEEEeEeccCCCcccccccccc
Q 024241 185 --L---GTSGS-LDGQQRLVVKGRFAPKNFEGILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKCGSGRSVAPIKAG 258 (270)
Q Consensus 185 --L---Gt~gs-id~~~rlii~G~f~~k~ie~~L~~YI~eYVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V~~ik~g 258 (270)
+ +.+|. .-.+=+++++-.-.+-.|.++=-.+|..-|.=+.=--.-..+.-.-.-++|.|..|-+++++-..+.|
T Consensus 100 d~i~~~~~~~E~~~~d~Qv~L~sda~p~~iR~l~s~~vsklVki~GIiiaAS~v~~kat~l~l~CrnC~~t~~~~~~~pg 179 (729)
T KOG0481|consen 100 DEITRPRPSGEEVLHDIQVLLTSDANPISIRQLKSDHVSKLVKISGIIIAASAVSAKATRLSLVCRNCRHTRPNVIMRPG 179 (729)
T ss_pred hhhcCCCcCCCccceeeEEEEecCCCcccHhHhhhHhhhhheeeccEEEEeeeeeecceEEEEEeccccccccceecCCC
Confidence 2 33331 01134788888888999999999999998876653222222222334569999999999999888877
Q ss_pred eE
Q 024241 259 FQ 260 (270)
Q Consensus 259 f~ 260 (270)
+.
T Consensus 180 l~ 181 (729)
T KOG0481|consen 180 LE 181 (729)
T ss_pred cc
Confidence 64
No 109
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=53.31 E-value=19 Score=23.58 Aligned_cols=28 Identities=14% Similarity=0.265 Sum_probs=23.2
Q ss_pred EehHHHHHHhCCChHHHHHHHHHhhcCc
Q 024241 161 VNFMDLCKTMHRQPDHVMTFLLAELGTS 188 (270)
Q Consensus 161 ~Nf~dI~k~L~R~p~hv~kyl~~ELGt~ 188 (270)
..+.+||..++=++.|+.+-|..++|.+
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 3588999999999999999999999974
No 110
>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=53.16 E-value=15 Score=30.04 Aligned_cols=15 Identities=13% Similarity=0.213 Sum_probs=7.3
Q ss_pred EeeCCCCCCcceEEE
Q 024241 220 VICLGCKSPDTILSK 234 (270)
Q Consensus 220 VlC~~C~sPDT~L~k 234 (270)
..||.|+|+++.+..
T Consensus 87 ~~CP~Cgs~~~~i~~ 101 (115)
T TIGR00100 87 YRCPKCHGIMLQVRA 101 (115)
T ss_pred ccCcCCcCCCcEEec
Confidence 445555555544443
No 111
>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=52.23 E-value=10 Score=25.71 Aligned_cols=30 Identities=23% Similarity=0.412 Sum_probs=22.7
Q ss_pred eeCCCCCCcceEEEcCcEEEeEeccCCCcc
Q 024241 221 ICLGCKSPDTILSKENRLFFLRCEKCGSGR 250 (270)
Q Consensus 221 lC~~C~sPDT~L~ke~rl~~l~C~aCGa~~ 250 (270)
.|..|+..-..+..-..--...|.+||+..
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~ 36 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISEDDPVPCPECGSTE 36 (42)
T ss_pred EeCCCCCEEEEEEEcCCCCCCcCCCCCCCc
Confidence 699999887777763335578999999843
No 112
>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=51.51 E-value=34 Score=22.49 Aligned_cols=45 Identities=11% Similarity=0.090 Sum_probs=33.1
Q ss_pred ehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHH
Q 024241 162 NFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGI 211 (270)
Q Consensus 162 Nf~dI~k~L~R~p~hv~kyl~~ELGt~gsid~~~rlii~G~f~~k~ie~~ 211 (270)
+..++|+.++-++..|-.|....+.. .....+++. .|+..+|..+
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 46899999999999999998888766 333333332 4788887765
No 113
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=51.47 E-value=11 Score=30.73 Aligned_cols=18 Identities=11% Similarity=0.279 Sum_probs=14.4
Q ss_pred eEeeCCCCCCcceEEEcC
Q 024241 219 YVICLGCKSPDTILSKEN 236 (270)
Q Consensus 219 YVlC~~C~sPDT~L~ke~ 236 (270)
+..||.|+|+++.++.-.
T Consensus 86 ~~~CP~Cgs~~~~i~~G~ 103 (113)
T PRK12380 86 DAQCPHCHGERLRVDTGD 103 (113)
T ss_pred CccCcCCCCCCcEEccCC
Confidence 456999999998887643
No 114
>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=51.42 E-value=21 Score=27.00 Aligned_cols=37 Identities=14% Similarity=0.227 Sum_probs=30.0
Q ss_pred EehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecC
Q 024241 161 VNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFA 204 (270)
Q Consensus 161 ~Nf~dI~k~L~R~p~hv~kyl~~ELGt~gsid~~~rlii~G~f~ 204 (270)
-|..|+|..|+-.-..|.+|.. -.++...+|+||.+.
T Consensus 17 GnqtEvaR~l~c~R~TVrKY~~-------D~~a~~HaIvNgvLM 53 (64)
T PF06322_consen 17 GNQTEVARRLGCNRATVRKYSR-------DKDAKRHAIVNGVLM 53 (64)
T ss_pred CcHHHHHHHhcccHHHHHHHhc-------ccccceEEEEcCEEE
Confidence 4899999999999999999974 344556788888764
No 115
>PRK05580 primosome assembly protein PriA; Validated
Probab=51.39 E-value=10 Score=39.81 Aligned_cols=34 Identities=26% Similarity=0.599 Sum_probs=20.4
Q ss_pred eEeeCCCCCC------cceEEEcCcEEEeEeccCCCcccc
Q 024241 219 YVICLGCKSP------DTILSKENRLFFLRCEKCGSGRSV 252 (270)
Q Consensus 219 YVlC~~C~sP------DT~L~ke~rl~~l~C~aCGa~~~V 252 (270)
||.|..|+.+ +..|+-...--.|.|.-||.+.++
T Consensus 381 ~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~ 420 (679)
T PRK05580 381 FLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQEPI 420 (679)
T ss_pred ceEhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCCCC
Confidence 6667766643 344543222236889999988654
No 116
>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=51.32 E-value=18 Score=27.04 Aligned_cols=29 Identities=31% Similarity=0.805 Sum_probs=16.9
Q ss_pred EeeCCCCC---Cc-c---eEEE---cCcEEEeEeccCCC
Q 024241 220 VICLGCKS---PD-T---ILSK---ENRLFFLRCEKCGS 248 (270)
Q Consensus 220 VlC~~C~s---PD-T---~L~k---e~rl~~l~C~aCGa 248 (270)
-+|..|++ |- | .+.+ .++.+...|..||.
T Consensus 47 ~~Ck~C~~~liPG~~~~vri~~~~~~~~~l~~~C~~C~~ 85 (85)
T PF04032_consen 47 TICKKCGSLLIPGVNCSVRIRKKKKKKNFLVYTCLNCGH 85 (85)
T ss_dssp TB-TTT--B--CTTTEEEEEE---SSS-EEEEEETTTTE
T ss_pred ccccCCCCEEeCCCccEEEEEecCCCCCEEEEEccccCC
Confidence 58999998 42 2 2221 16888999999994
No 117
>PRK11827 hypothetical protein; Provisional
Probab=50.74 E-value=8.1 Score=28.77 Aligned_cols=34 Identities=18% Similarity=0.254 Sum_probs=22.9
Q ss_pred ccceEeeCCCCCCcceEEEcCcEEEeEeccCCCcccc
Q 024241 216 VNEYVICLGCKSPDTILSKENRLFFLRCEKCGSGRSV 252 (270)
Q Consensus 216 I~eYVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V 252 (270)
+-+-..||.|+.+=. +..+.. -|.|.+||-..+|
T Consensus 5 LLeILaCP~ckg~L~-~~~~~~--~Lic~~~~laYPI 38 (60)
T PRK11827 5 LLEIIACPVCNGKLW-YNQEKQ--ELICKLDNLAFPL 38 (60)
T ss_pred HHhheECCCCCCcCe-EcCCCC--eEECCccCeeccc
Confidence 345688999998632 222222 4679999987776
No 118
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=50.40 E-value=16 Score=30.56 Aligned_cols=22 Identities=18% Similarity=0.418 Sum_probs=12.1
Q ss_pred HHHHHHHhhcCceeecCCceEEE
Q 024241 177 VMTFLLAELGTSGSLDGQQRLVV 199 (270)
Q Consensus 177 v~kyl~~ELGt~gsid~~~rlii 199 (270)
.++|-+ +.-+.|++-.+.+|+|
T Consensus 43 ~l~FaF-ev~~egT~aega~l~I 64 (115)
T COG0375 43 ALRFAF-EVVAEGTIAEGAELHI 64 (115)
T ss_pred HHHHHH-HHHhccCcccCCEEEE
Confidence 334443 4445566655557777
No 119
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=49.59 E-value=17 Score=42.48 Aligned_cols=41 Identities=27% Similarity=0.498 Sum_probs=28.3
Q ss_pred HHHHHHhccceEeeCCCCCCcceE---EEcCcEEEeEeccCCCcccc
Q 024241 209 EGILRRYVNEYVICLGCKSPDTIL---SKENRLFFLRCEKCGSGRSV 252 (270)
Q Consensus 209 e~~L~~YI~eYVlC~~C~sPDT~L---~ke~rl~~l~C~aCGa~~~V 252 (270)
..+|..++. -+-||.|++++-.| ..+.+ ...|..||-+..+
T Consensus 1695 ~~~~~~~~~-~~~cp~c~~~~~~~~~~~~~~g--c~~c~~cg~s~c~ 1738 (1740)
T PRK08332 1695 EEKIRELLG-VVYCPVCYEKEGKLVELRMESG--CATCPVCGWSKCV 1738 (1740)
T ss_pred HHHHHHHhc-cCCCCCCCCCCCcceeeEecCC--ceeCCCCCCcccc
Confidence 555555542 24499999997554 44555 6799999987654
No 120
>PHA00626 hypothetical protein
Probab=48.34 E-value=19 Score=26.86 Aligned_cols=35 Identities=23% Similarity=0.309 Sum_probs=23.0
Q ss_pred eeCCCCCCcceEEE--cCcEEEeEeccCCCccccccc
Q 024241 221 ICLGCKSPDTILSK--ENRLFFLRCEKCGSGRSVAPI 255 (270)
Q Consensus 221 lC~~C~sPDT~L~k--e~rl~~l~C~aCGa~~~V~~i 255 (270)
.||.|+|-+-..-. .+.----+|..||..-+-.++
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~~~ 38 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSKDAF 38 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeechhhh
Confidence 59999997633211 111123589999999888765
No 121
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=47.94 E-value=14 Score=27.03 Aligned_cols=28 Identities=29% Similarity=0.562 Sum_probs=20.6
Q ss_pred hccceEeeCCCCCCcceEEEcCcEEEeEeccCCCcc
Q 024241 215 YVNEYVICLGCKSPDTILSKENRLFFLRCEKCGSGR 250 (270)
Q Consensus 215 YI~eYVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~ 250 (270)
.+-..|.|+.|+++- +--..|..||.-+
T Consensus 23 ~~~~l~~C~~CG~~~--------~~H~vC~~CG~Y~ 50 (57)
T PRK12286 23 KAPGLVECPNCGEPK--------LPHRVCPSCGYYK 50 (57)
T ss_pred cCCcceECCCCCCcc--------CCeEECCCCCcCC
Confidence 345679999999874 3366799999644
No 122
>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=47.78 E-value=6.7 Score=25.63 Aligned_cols=27 Identities=30% Similarity=0.636 Sum_probs=17.4
Q ss_pred eeCCCCCCcceEEEcCcEEEeEeccCCCccc
Q 024241 221 ICLGCKSPDTILSKENRLFFLRCEKCGSGRS 251 (270)
Q Consensus 221 lC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~ 251 (270)
+|..|+.... |.... .++|..||.+--
T Consensus 2 ~C~~Cg~~~~-~~~~~---~irC~~CG~RIl 28 (32)
T PF03604_consen 2 ICGECGAEVE-LKPGD---PIRCPECGHRIL 28 (32)
T ss_dssp BESSSSSSE--BSTSS---TSSBSSSS-SEE
T ss_pred CCCcCCCeeE-cCCCC---cEECCcCCCeEE
Confidence 6999998765 33222 469999998743
No 123
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=47.11 E-value=20 Score=24.35 Aligned_cols=22 Identities=18% Similarity=0.247 Sum_probs=16.5
Q ss_pred EehHHHHHHhCCChHHHHHHHH
Q 024241 161 VNFMDLCKTMHRQPDHVMTFLL 182 (270)
Q Consensus 161 ~Nf~dI~k~L~R~p~hv~kyl~ 182 (270)
..+.+||+.|+|++.-|.++|-
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 5688999999999999998875
No 124
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=46.88 E-value=26 Score=29.27 Aligned_cols=17 Identities=24% Similarity=0.438 Sum_probs=10.5
Q ss_pred eCCCCCCcceEEEcCcE
Q 024241 222 CLGCKSPDTILSKENRL 238 (270)
Q Consensus 222 C~~C~sPDT~L~ke~rl 238 (270)
||.|+|++..+..-+.+
T Consensus 89 CP~C~s~~~~i~~G~el 105 (115)
T COG0375 89 CPKCGSINLRIIGGDEL 105 (115)
T ss_pred CCCCCCCceEEecCCee
Confidence 77777777666654433
No 125
>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=46.83 E-value=9.8 Score=29.55 Aligned_cols=11 Identities=45% Similarity=0.887 Sum_probs=9.3
Q ss_pred EEeEeccCCCc
Q 024241 239 FFLRCEKCGSG 249 (270)
Q Consensus 239 ~~l~C~aCGa~ 249 (270)
-.|+|.|||+.
T Consensus 56 ~tLsCsACGS~ 66 (74)
T PF05077_consen 56 NTLSCSACGSE 66 (74)
T ss_pred CeEeehhcccc
Confidence 47999999985
No 126
>PRK06556 vitamin B12-dependent ribonucleotide reductase; Validated
Probab=46.76 E-value=18 Score=39.84 Aligned_cols=44 Identities=18% Similarity=0.399 Sum_probs=29.3
Q ss_pred cChHHHHHHHHHhccceEeeCCCCCCcceEEEcCcEEEeEeccCCCccc
Q 024241 203 FAPKNFEGILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKCGSGRS 251 (270)
Q Consensus 203 f~~k~ie~~L~~YI~eYVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~ 251 (270)
++...+-.....+.-.--+|++|+ |.+++.+- ...|+.||+++-
T Consensus 908 ~~~~~~~~~~~~~~~~~~~c~~c~---~~~~~~g~--c~~c~~cg~t~g 951 (953)
T PRK06556 908 HSSTELLELQLGEAADAPLCPTCG---TKMVRNGS--CYVCEGCGSTSG 951 (953)
T ss_pred CccHHHHHHhhcccccCCcCCCcc---CeeeECCc--eEeccCCCCCCC
Confidence 333444444445555557799995 67877765 568999999863
No 127
>PRK07562 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=46.13 E-value=15 Score=41.44 Aligned_cols=39 Identities=26% Similarity=0.580 Sum_probs=29.9
Q ss_pred HHHHHHHHhccceEeeCCCCCCcceEEEcCcEEEeEeccCCCccc
Q 024241 207 NFEGILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKCGSGRS 251 (270)
Q Consensus 207 ~ie~~L~~YI~eYVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~ 251 (270)
..+..+..| +=..|++|++ +.|++.+. .++|+.||+++-
T Consensus 1180 ~~~a~~~g~--~g~~c~~cg~--~~~vrngt--c~~c~~cg~t~g 1218 (1220)
T PRK07562 1180 RAEAKMQGY--TGEACSECGN--FTLVRNGT--CLKCDTCGSTTG 1218 (1220)
T ss_pred hhHHHhCCC--CCCcCCCcCC--eEEEeCCe--eeeccccCCCCC
Confidence 555666777 5567999997 55888765 789999999763
No 128
>TIGR01391 dnaG DNA primase, catalytic core. This protein contains a CHC2 zinc finger (Pfam:PF01807) and a Toprim domain (Pfam:PF01751).
Probab=44.58 E-value=28 Score=34.32 Aligned_cols=33 Identities=21% Similarity=0.382 Sum_probs=21.3
Q ss_pred EeeCCCCCCcceEEEcCcEEEeEeccCCCcccc
Q 024241 220 VICLGCKSPDTILSKENRLFFLRCEKCGSGRSV 252 (270)
Q Consensus 220 VlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V 252 (270)
..||-|.--...+.....--+-+|-+||....+
T Consensus 35 ~~CPfh~ek~pSf~v~~~k~~~~Cf~Cg~~Gd~ 67 (415)
T TIGR01391 35 GLCPFHHEKTPSFSVSPEKQFYHCFGCGAGGDA 67 (415)
T ss_pred eeCCCCCCCCCeEEEEcCCCcEEECCCCCCCCH
Confidence 489999654445555322225689999987654
No 129
>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=44.40 E-value=25 Score=30.19 Aligned_cols=79 Identities=18% Similarity=0.455 Sum_probs=45.6
Q ss_pred cCCCeEEEeCceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCc--ee-ecC-CceEEEEeecChHHHHHHHHHhccceE
Q 024241 145 MRPPQVLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTS--GS-LDG-QQRLVVKGRFAPKNFEGILRRYVNEYV 220 (270)
Q Consensus 145 mP~p~V~~eG~kKTvi~Nf~dI~k~L~R~p~hv~kyl~~ELGt~--gs-id~-~~rlii~G~f~~k~ie~~L~~YI~eYV 220 (270)
...|||.+.| ..|-...++-. ||.+-+ |.+.| ..+... +. =++ ++ ..||
T Consensus 59 ~tvPqVFI~G---~~IGG~del~~-L~e~G~-L~~lL-~~~~~~~~~~~C~~Cgg---------------------~rfv 111 (147)
T cd03031 59 VSLPRVFVDG---RYLGGAEEVLR-LNESGE-LRKLL-KGIRARAGGGVCEGCGG---------------------ARFV 111 (147)
T ss_pred CCCCEEEECC---EEEecHHHHHH-HHHcCC-HHHHH-hhcccccCCCCCCCCCC---------------------cCeE
Confidence 4678999999 25677777655 554433 33333 332111 11 121 11 1389
Q ss_pred eeCCCCCCcceEEEc--CcEEEeEeccCCCcc
Q 024241 221 ICLGCKSPDTILSKE--NRLFFLRCEKCGSGR 250 (270)
Q Consensus 221 lC~~C~sPDT~L~ke--~rl~~l~C~aCGa~~ 250 (270)
.|..|+..--.+..+ +...+++|..|..-.
T Consensus 112 ~C~~C~Gs~k~~~~~~~~~~~~~rC~~Cneng 143 (147)
T cd03031 112 PCSECNGSCKVFAENATAAGGFLRCPECNENG 143 (147)
T ss_pred ECCCCCCcceEEeccCcccccEEECCCCCccc
Confidence 999997765554444 245689999998654
No 130
>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=44.39 E-value=15 Score=23.85 Aligned_cols=17 Identities=41% Similarity=0.751 Sum_probs=10.2
Q ss_pred cCcEEEeEeccCCCccc
Q 024241 235 ENRLFFLRCEKCGSGRS 251 (270)
Q Consensus 235 e~rl~~l~C~aCGa~~~ 251 (270)
+++|+..+|.+||....
T Consensus 6 ~~~l~~~rC~~Cg~~~~ 22 (37)
T PF12172_consen 6 EGRLLGQRCRDCGRVQF 22 (37)
T ss_dssp TT-EEEEE-TTT--EEE
T ss_pred CCEEEEEEcCCCCCEec
Confidence 46899999999998743
No 131
>PRK06824 translation initiation factor Sui1; Validated
Probab=44.38 E-value=33 Score=28.74 Aligned_cols=55 Identities=18% Similarity=0.189 Sum_probs=40.2
Q ss_pred eCceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHH
Q 024241 153 EGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGIL 212 (270)
Q Consensus 153 eG~kKTvi~Nf~dI~k~L~R~p~hv~kyl~~ELGt~gsid~~~rlii~G~f~~k~ie~~L 212 (270)
-|..-|+|..|..-.. +-.-|++.|-..+|+.|++-. +.+.|+|.|...-.+-+.
T Consensus 53 ~gK~VTvI~Gl~~~~~----dlk~l~K~LKkk~gcGGtvkd-~~IeiQGD~r~~v~~~L~ 107 (118)
T PRK06824 53 GGKTVTVITGVPLAED----ALKELAKELKRRCGTGGTLKD-GVIEIQGDHVELLLAELL 107 (118)
T ss_pred CCceEEEEeCCcCCHH----HHHHHHHHHHHHhcCCceEec-CEEEEcCcHHHHHHHHHH
Confidence 4557788888852111 135788999999999999964 589999999776555443
No 132
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=44.23 E-value=23 Score=29.27 Aligned_cols=35 Identities=23% Similarity=0.472 Sum_probs=23.7
Q ss_pred eeCCCCCC---c--ceEEEcCcEEEeEeccCCCccccccc
Q 024241 221 ICLGCKSP---D--TILSKENRLFFLRCEKCGSGRSVAPI 255 (270)
Q Consensus 221 lC~~C~sP---D--T~L~ke~rl~~l~C~aCGa~~~V~~i 255 (270)
+|+.|.+| - -.+...+......|..||...-.+-.
T Consensus 58 ~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~~R~p~~ 97 (105)
T COG2023 58 ICKKCYTPLVPGKNARVRLRKGRVVVTCLECGTIRRYPYG 97 (105)
T ss_pred hccccCcccccCcceEEEEcCCeEEEEecCCCcEEEeccc
Confidence 69999994 2 22222455578999999987765543
No 133
>COG5631 Predicted transcription regulator, contains HTH domain (MarR family) [Transcription]
Probab=44.20 E-value=20 Score=32.17 Aligned_cols=32 Identities=25% Similarity=0.569 Sum_probs=28.9
Q ss_pred ehHHHHHHhCCChHHHHHHHHHhhcCceeecC
Q 024241 162 NFMDLCKTMHRQPDHVMTFLLAELGTSGSLDG 193 (270)
Q Consensus 162 Nf~dI~k~L~R~p~hv~kyl~~ELGt~gsid~ 193 (270)
-+.|||.+|||+.-|+..|-+..|-..|-|.+
T Consensus 100 ~laDic~~ln~eDth~itYslrKL~k~gLit~ 131 (199)
T COG5631 100 SLADICQMLNREDTHNITYSLRKLLKGGLITR 131 (199)
T ss_pred hHHHHHHHhccccchhHHHHHHHHHhccceec
Confidence 37899999999999999999999988888864
No 134
>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=44.10 E-value=24 Score=24.37 Aligned_cols=30 Identities=27% Similarity=0.587 Sum_probs=21.9
Q ss_pred eeCCCCCCcceEEE-----cCcEEEeEecc--CCCcc
Q 024241 221 ICLGCKSPDTILSK-----ENRLFFLRCEK--CGSGR 250 (270)
Q Consensus 221 lC~~C~sPDT~L~k-----e~rl~~l~C~a--CGa~~ 250 (270)
.||.|+++=..-.. .-+-++..|.. ||+.-
T Consensus 1 ~CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg~tf 37 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLSPLTRELYCQCTNPECGHTF 37 (47)
T ss_pred CcCCCCCeeEEEEchhhCcceEEEEEEECCCcCCCEE
Confidence 49999998644332 23778999998 99864
No 135
>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=44.05 E-value=12 Score=27.20 Aligned_cols=33 Identities=24% Similarity=0.560 Sum_probs=21.7
Q ss_pred EeeCCCCCCcceEEEcC--cEEEeEeccCCCccccccc
Q 024241 220 VICLGCKSPDTILSKEN--RLFFLRCEKCGSGRSVAPI 255 (270)
Q Consensus 220 VlC~~C~sPDT~L~ke~--rl~~l~C~aCGa~~~V~~i 255 (270)
..||.|+.. |.... +=..+.|..||+.--|-+.
T Consensus 3 ~~CP~CG~~---iev~~~~~GeiV~Cp~CGaeleVv~~ 37 (54)
T TIGR01206 3 FECPDCGAE---IELENPELGELVICDECGAELEVVSL 37 (54)
T ss_pred cCCCCCCCE---EecCCCccCCEEeCCCCCCEEEEEeC
Confidence 379999983 33221 1236699999998777443
No 136
>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=43.94 E-value=15 Score=31.70 Aligned_cols=60 Identities=15% Similarity=0.231 Sum_probs=38.4
Q ss_pred HHHHHHHHHHhhcCCCcccCcceeecCCCeEEEeCceeEEE-EehHHHHHHhCCChHHHHHHHHHhhcC
Q 024241 120 ELLGRVFNILRENNPELAGDRRRTVMRPPQVLREGTKKTVF-VNFMDLCKTMHRQPDHVMTFLLAELGT 187 (270)
Q Consensus 120 eLL~R~~~~l~~~np~~~~~~~R~~mP~p~V~~eG~kKTvi-~Nf~dI~k~L~R~p~hv~kyl~~ELGt 187 (270)
.-+.|+...|.++. ++. ..| ...+ ..|.....| .|..+|.++|...-..+.+=|..+|--
T Consensus 43 ~~VRk~L~~L~e~~--Lv~-~~r--~r~~---~~gw~~Y~w~i~~~~i~d~Ik~~~~~~~~~lk~~l~~ 103 (158)
T TIGR00373 43 NEVRKALYALYDAG--LAD-YKR--RKDD---ETGWYEYTWRINYEKALDVLKRKLEETAKKLREKLEF 103 (158)
T ss_pred HHHHHHHHHHHHCC--Cce-eee--eeec---CCCcEEEEEEeCHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 56778888886543 332 111 1111 124456665 899999999998888887777666654
No 137
>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=43.34 E-value=21 Score=27.65 Aligned_cols=21 Identities=14% Similarity=0.211 Sum_probs=16.7
Q ss_pred ehHHHHHHhCCChHHHHHHHH
Q 024241 162 NFMDLCKTMHRQPDHVMTFLL 182 (270)
Q Consensus 162 Nf~dI~k~L~R~p~hv~kyl~ 182 (270)
+-.+||+.|.|++.||.+||.
T Consensus 5 tq~eIA~~lGks~s~Vs~~l~ 25 (93)
T PF08535_consen 5 TQEEIAKRLGKSRSWVSNHLA 25 (93)
T ss_dssp -HHHHHHHTT--HHHHHHHHG
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 357999999999999999996
No 138
>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=43.28 E-value=23 Score=28.20 Aligned_cols=31 Identities=19% Similarity=0.309 Sum_probs=18.9
Q ss_pred eCCCCCCcceEEE-------cC-----cEEEeEeccCCCcccc
Q 024241 222 CLGCKSPDTILSK-------EN-----RLFFLRCEKCGSGRSV 252 (270)
Q Consensus 222 C~~C~sPDT~L~k-------e~-----rl~~l~C~aCGa~~~V 252 (270)
|+.|++.++.-.+ .+ .+-...|..||..-..
T Consensus 1 C~~C~~~~~~~~~~~~~~~~~G~~~~v~~~~~~C~~CGe~~~~ 43 (127)
T TIGR03830 1 CPICGSGELVRDVKDEPYTYKGESITIGVPGWYCPACGEELLD 43 (127)
T ss_pred CCCCCCccceeeeecceEEEcCEEEEEeeeeeECCCCCCEEEc
Confidence 9999876543222 12 2235689999986544
No 139
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=43.07 E-value=9.6 Score=23.32 Aligned_cols=23 Identities=22% Similarity=0.738 Sum_probs=14.9
Q ss_pred EeeCCCCCCcceEEEcCcEEEeEeccCCCc
Q 024241 220 VICLGCKSPDTILSKENRLFFLRCEKCGSG 249 (270)
Q Consensus 220 VlC~~C~sPDT~L~ke~rl~~l~C~aCGa~ 249 (270)
+.|+.|+.+ +..+ ..-|..||+.
T Consensus 3 ~~Cp~Cg~~---~~~~----~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPNCGAE---IDPD----AKFCPNCGAK 25 (26)
T ss_pred CCCcccCCc---CCcc----cccChhhCCC
Confidence 578889874 2222 4468888864
No 140
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=43.02 E-value=16 Score=24.36 Aligned_cols=25 Identities=28% Similarity=0.751 Sum_probs=16.9
Q ss_pred eeCCCCCCcceEEEcCcEEEeEeccCCCc
Q 024241 221 ICLGCKSPDTILSKENRLFFLRCEKCGSG 249 (270)
Q Consensus 221 lC~~C~sPDT~L~ke~rl~~l~C~aCGa~ 249 (270)
.|+.|++- ....+.+ +..|..||..
T Consensus 10 ~C~~C~~~--~~~~~dG--~~yC~~cG~~ 34 (36)
T PF11781_consen 10 PCPVCGSR--WFYSDDG--FYYCDRCGHQ 34 (36)
T ss_pred cCCCCCCe--EeEccCC--EEEhhhCceE
Confidence 69999998 3333344 4568888864
No 141
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=42.90 E-value=19 Score=29.99 Aligned_cols=21 Identities=29% Similarity=0.686 Sum_probs=15.7
Q ss_pred eCCCCCCcceEEEcCcEEEeEeccCCCc
Q 024241 222 CLGCKSPDTILSKENRLFFLRCEKCGSG 249 (270)
Q Consensus 222 C~~C~sPDT~L~ke~rl~~l~C~aCGa~ 249 (270)
||.|+++= .+--|+|..||..
T Consensus 1 CPvCg~~l-------~vt~l~C~~C~t~ 21 (113)
T PF09862_consen 1 CPVCGGEL-------VVTRLKCPSCGTE 21 (113)
T ss_pred CCCCCCce-------EEEEEEcCCCCCE
Confidence 99999763 2346899999853
No 142
>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=42.42 E-value=17 Score=26.79 Aligned_cols=14 Identities=29% Similarity=0.669 Sum_probs=11.8
Q ss_pred EeEeccCCCccccc
Q 024241 240 FLRCEKCGSGRSVA 253 (270)
Q Consensus 240 ~l~C~aCGa~~~V~ 253 (270)
.|.|..||...+|.
T Consensus 53 ~L~Cp~c~r~YPI~ 66 (68)
T PF03966_consen 53 ELICPECGREYPIR 66 (68)
T ss_dssp EEEETTTTEEEEEE
T ss_pred EEEcCCCCCEEeCC
Confidence 68999999988774
No 143
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=40.97 E-value=18 Score=33.98 Aligned_cols=59 Identities=17% Similarity=0.309 Sum_probs=30.0
Q ss_pred eecChHHHHHHH-HHhccceEeeCCCCCCcceEEEc-CcEEEeEeccCCCcccccccccce
Q 024241 201 GRFAPKNFEGIL-RRYVNEYVICLGCKSPDTILSKE-NRLFFLRCEKCGSGRSVAPIKAGF 259 (270)
Q Consensus 201 G~f~~k~ie~~L-~~YI~eYVlC~~C~sPDT~L~ke-~rl~~l~C~aCGa~~~V~~ik~gf 259 (270)
|-.+..|+-.+| ..+|.+.+.||.|++.-..=... ..+--..|..|+...-+++-+..+
T Consensus 12 ~YkS~sQ~aRVltE~Wv~~n~yCP~Cg~~~L~~f~NN~PVaDF~C~~C~eeyELKSk~~~l 72 (254)
T PF06044_consen 12 GYKSNSQIARVLTEDWVAENMYCPNCGSKPLSKFENNRPVADFYCPNCNEEYELKSKKKKL 72 (254)
T ss_dssp HTTT-TTHHHHHHHHHHHHH---TTT--SS-EE--------EEE-TTT--EEEEEEEESS-
T ss_pred hccChhhhhHHHHHHHHHHCCcCCCCCChhHhhccCCCccceeECCCCchHHhhhhhcccc
Confidence 334556666665 67899999999999986333333 468889999999988887766444
No 144
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=40.45 E-value=45 Score=34.25 Aligned_cols=68 Identities=24% Similarity=0.371 Sum_probs=29.2
Q ss_pred HhhcCceeecCCceEEEEeecChHHHHHHHHHhcc-----------ceEeeCCCCCCcceEEEcCcEEEeEeccCCCc-c
Q 024241 183 AELGTSGSLDGQQRLVVKGRFAPKNFEGILRRYVN-----------EYVICLGCKSPDTILSKENRLFFLRCEKCGSG-R 250 (270)
Q Consensus 183 ~ELGt~gsid~~~rlii~G~f~~k~ie~~L~~YI~-----------eYVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~-~ 250 (270)
..|-+.|.|- .+-+--+.+++.+++++++=.+ .+-+|+.|+.-.. . .-.|..||+. .
T Consensus 447 ~~~~~GG~I~---hv~l~e~~n~~al~~lv~~~~~~~~i~Y~~in~~~~~C~~CG~~~~------~--~~~CP~CGs~~~ 515 (546)
T PF13597_consen 447 QKLYTGGHIF---HVELGEKPNPEALEKLVRYAMENTGIPYFTINPPIDICPDCGYIGG------E--GDKCPKCGSENI 515 (546)
T ss_dssp HTTSTTB--E---EEE----T-HHHHHHHHHHHHH--H-SEEEEE--EEEETTT---S----------EEE-CCC----E
T ss_pred ccccCCceEE---EEEcCCCCCHHHHHHHHHHHHHhCCCCeEEEecCcccccCCCcCCC------C--CCCCCCCCCccc
Confidence 3455556653 3444445577888888877666 2357888886432 1 4568888887 3
Q ss_pred cccccccceEE
Q 024241 251 SVAPIKAGFQA 261 (270)
Q Consensus 251 ~V~~ik~gf~a 261 (270)
.|=..-.||..
T Consensus 516 ~~~~Rv~GYl~ 526 (546)
T PF13597_consen 516 EVYSRVTGYLR 526 (546)
T ss_dssp EEEB-SSSS-B
T ss_pred ceEEEeecccc
Confidence 33333345433
No 145
>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=40.43 E-value=19 Score=36.41 Aligned_cols=66 Identities=21% Similarity=0.411 Sum_probs=34.6
Q ss_pred CChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHHHhccceEeeCCCCCC------cceEEEcCcEEEeEecc
Q 024241 172 RQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILRRYVNEYVICLGCKSP------DTILSKENRLFFLRCEK 245 (270)
Q Consensus 172 R~p~hv~kyl~~ELGt~gsid~~~rlii~G~f~~k~ie~~L~~YI~eYVlC~~C~sP------DT~L~ke~rl~~l~C~a 245 (270)
+-++.+++.+...|....+ .|++-=+ +.| --++.|..|+.. +..|+-...--.|+|.-
T Consensus 182 ~ls~~l~~~i~~~l~~g~q-----vLvflnr----------rGy-a~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~ 245 (505)
T TIGR00595 182 FLSPELITAIEQTLAAGEQ-----SILFLNR----------RGY-SKNLLCRSCGYILCCPNCDVSLTYHKKEGKLRCHY 245 (505)
T ss_pred CccHHHHHHHHHHHHcCCc-----EEEEEeC----------CcC-CCeeEhhhCcCccCCCCCCCceEEecCCCeEEcCC
Confidence 4567778888777765322 3333111 111 135566555543 33344322222678999
Q ss_pred CCCccccc
Q 024241 246 CGSGRSVA 253 (270)
Q Consensus 246 CGa~~~V~ 253 (270)
||.+.++.
T Consensus 246 Cg~~~~~~ 253 (505)
T TIGR00595 246 CGYQEPIP 253 (505)
T ss_pred CcCcCCCC
Confidence 98887653
No 146
>PRK05667 dnaG DNA primase; Validated
Probab=40.34 E-value=34 Score=35.52 Aligned_cols=35 Identities=23% Similarity=0.475 Sum_probs=22.5
Q ss_pred ceE-eeCCCCCCcceEEEcCcEEEeEeccCCCcccc
Q 024241 218 EYV-ICLGCKSPDTILSKENRLFFLRCEKCGSGRSV 252 (270)
Q Consensus 218 eYV-lC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V 252 (270)
.|+ .||-|.--...+.....--+-+|-+||+...+
T Consensus 34 ~~~~~CPfH~ektpSf~V~~~k~~~~CF~Cg~~Gd~ 69 (580)
T PRK05667 34 NYKGLCPFHDEKTPSFTVSPDKQFYHCFGCGAGGDV 69 (580)
T ss_pred ceeecCCCCCCCCCceEEECCCCeEEECCCCCCCCH
Confidence 344 79999654445665432235789999987654
No 147
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=40.30 E-value=34 Score=23.76 Aligned_cols=39 Identities=23% Similarity=0.479 Sum_probs=24.6
Q ss_pred HHHHHhcc---ceEeeC--CCCCCcceEEEc--CcEEEeEeccCCCccc
Q 024241 210 GILRRYVN---EYVICL--GCKSPDTILSKE--NRLFFLRCEKCGSGRS 251 (270)
Q Consensus 210 ~~L~~YI~---eYVlC~--~C~sPDT~L~ke--~rl~~l~C~aCGa~~~ 251 (270)
-++++||+ .+.-|| .|... +... .....+.|..||..--
T Consensus 6 ~~~~~~i~~~~~~~~CP~~~C~~~---~~~~~~~~~~~v~C~~C~~~fC 51 (64)
T smart00647 6 LLLESYVESNPDLKWCPAPDCSAA---IIVTEEEGCNRVTCPKCGFSFC 51 (64)
T ss_pred HHHHHHHhcCCCccCCCCCCCcce---EEecCCCCCCeeECCCCCCeEC
Confidence 35566665 478899 89653 3332 2455788988886543
No 148
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=39.78 E-value=24 Score=29.04 Aligned_cols=31 Identities=29% Similarity=0.503 Sum_probs=22.3
Q ss_pred eeCCCCCCcceEEE--cCcEEEeEeccCCCcccccc
Q 024241 221 ICLGCKSPDTILSK--ENRLFFLRCEKCGSGRSVAP 254 (270)
Q Consensus 221 lC~~C~sPDT~L~k--e~rl~~l~C~aCGa~~~V~~ 254 (270)
-||.|+|. |+- ++.-..+.|..||+.-.+..
T Consensus 4 FCp~Cgsl---l~p~~~~~~~~l~C~kCgye~~~~~ 36 (113)
T COG1594 4 FCPKCGSL---LYPKKDDEGGKLVCRKCGYEEEASN 36 (113)
T ss_pred ccCCccCe---eEEeEcCCCcEEECCCCCcchhccc
Confidence 49999985 332 11112899999999999885
No 149
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=39.53 E-value=36 Score=28.21 Aligned_cols=15 Identities=27% Similarity=0.397 Sum_probs=8.0
Q ss_pred HHHHHHHHHHHhhcC
Q 024241 119 EELLGRVFNILRENN 133 (270)
Q Consensus 119 eeLL~R~~~~l~~~n 133 (270)
+.+|+.+.+..++++
T Consensus 8 ~~il~~v~~~a~~~~ 22 (124)
T PRK00762 8 CEIVEAVIDTAEKNN 22 (124)
T ss_pred HHHHHHHHHHHHHcC
Confidence 345566655555444
No 150
>PHA02942 putative transposase; Provisional
Probab=39.41 E-value=19 Score=35.35 Aligned_cols=27 Identities=26% Similarity=0.701 Sum_probs=19.7
Q ss_pred EeeCCCCCCcceEEEcCcEEEeEeccCCCcc
Q 024241 220 VICLGCKSPDTILSKENRLFFLRCEKCGSGR 250 (270)
Q Consensus 220 VlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~ 250 (270)
-+||.|+.....+ .+| ...|..||...
T Consensus 326 q~Cs~CG~~~~~l--~~r--~f~C~~CG~~~ 352 (383)
T PHA02942 326 VSCPKCGHKMVEI--AHR--YFHCPSCGYEN 352 (383)
T ss_pred ccCCCCCCccCcC--CCC--EEECCCCCCEe
Confidence 5799999876433 345 47899999864
No 151
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=39.35 E-value=17 Score=32.73 Aligned_cols=22 Identities=27% Similarity=0.768 Sum_probs=17.0
Q ss_pred EeeCCCCCCcceEEEcCcEEEeEeccCCCc
Q 024241 220 VICLGCKSPDTILSKENRLFFLRCEKCGSG 249 (270)
Q Consensus 220 VlC~~C~sPDT~L~ke~rl~~l~C~aCGa~ 249 (270)
+.|+.|+. ...| ...|..||..
T Consensus 310 ~~C~~cg~------~~~r--~~~C~~cg~~ 331 (364)
T COG0675 310 KTCPCCGH------LSGR--LFKCPRCGFV 331 (364)
T ss_pred ccccccCC------ccce--eEECCCCCCe
Confidence 67999999 2234 4689999986
No 152
>KOG2768 consensus Translation initiation factor 2, beta subunit (eIF-2beta) [Translation, ribosomal structure and biogenesis]
Probab=39.00 E-value=12 Score=34.58 Aligned_cols=21 Identities=38% Similarity=0.278 Sum_probs=15.6
Q ss_pred hccCCCCccccccccccccCC
Q 024241 14 AELAPFDPTKKKKKKKVVIQD 34 (270)
Q Consensus 14 ~~~~~fd~~kKKKKKK~~~~d 34 (270)
+.|..|+++|||||||.....
T Consensus 20 ~~l~~~~~~kKKKKkk~k~~s 40 (231)
T KOG2768|consen 20 ERLDFLSLKKKKKKKKSKSLS 40 (231)
T ss_pred hcccccccccccccCCCCchh
Confidence 447788888888888777553
No 153
>COG3741 HutG N-formylglutamate amidohydrolase [Amino acid transport and metabolism]
Probab=38.88 E-value=4.9 Score=38.10 Aligned_cols=79 Identities=18% Similarity=0.316 Sum_probs=61.2
Q ss_pred eeEEEEehHHHHHHhCCChHHHHHH---HHHhhcCceeecCCceEEEEeecChHHHHHHHHHhcc---------------
Q 024241 156 KKTVFVNFMDLCKTMHRQPDHVMTF---LLAELGTSGSLDGQQRLVVKGRFAPKNFEGILRRYVN--------------- 217 (270)
Q Consensus 156 kKTvi~Nf~dI~k~L~R~p~hv~ky---l~~ELGt~gsid~~~rlii~G~f~~k~ie~~L~~YI~--------------- 217 (270)
.-++-.||.-.+=-+||+|.++.-| --..||+...+|+.+.++--|+.+..++..-|..|-+
T Consensus 63 A~~l~A~fsR~~vDvNR~p~~~~l~~~~~ttGL~~~~~fdge~l~~~g~~~~~~e~~~Rle~~~~PYHaaL~~el~r~~a 142 (272)
T COG3741 63 ATLLRANFSRAVVDVNREPDGASLYPGRVTTGLGPVTTFDGEPLYIYGGAPTPAEALARLETLWKPYHAALRRELERLRA 142 (272)
T ss_pred chhhhccccceeEecCCCCCCCcCccccccCCccccccccCccccccCCCCCHHHHHHHHHHhhccHHHHHHHHHHHHHh
Confidence 5556667777777899999999988 4567888999999889999889999999888777644
Q ss_pred --ceEeeCCCCCCcceEEE
Q 024241 218 --EYVICLGCKSPDTILSK 234 (270)
Q Consensus 218 --eYVlC~~C~sPDT~L~k 234 (270)
-|++=..|+|.--.+-.
T Consensus 143 ~~G~avLiDcHSm~s~ip~ 161 (272)
T COG3741 143 IFGAAVLIDCHSMRSHIPR 161 (272)
T ss_pred hcCeEEEEecccccccccc
Confidence 56777778876544433
No 154
>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=38.78 E-value=22 Score=25.74 Aligned_cols=25 Identities=28% Similarity=0.584 Sum_probs=17.9
Q ss_pred cceEeeCCCCCCcceEEEcCcEEEeEeccCCCc
Q 024241 217 NEYVICLGCKSPDTILSKENRLFFLRCEKCGSG 249 (270)
Q Consensus 217 ~eYVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~ 249 (270)
-..|.|+.|+.+ .+---.|..||.-
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 356899999986 3345678888853
No 155
>PF06107 DUF951: Bacterial protein of unknown function (DUF951); InterPro: IPR009296 This family consists of several short hypothetical bacterial proteins of unknown function.
Probab=38.72 E-value=34 Score=25.36 Aligned_cols=31 Identities=16% Similarity=0.297 Sum_probs=25.7
Q ss_pred CCCCCCcceEEEcCcEEEeEeccCCCccccc
Q 024241 223 LGCKSPDTILSKENRLFFLRCEKCGSGRSVA 253 (270)
Q Consensus 223 ~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V~ 253 (270)
+-|++-+=++.+-+--+-++|..||..=.++
T Consensus 14 HPCG~~~Wei~R~GaDikikC~gCg~~imlp 44 (57)
T PF06107_consen 14 HPCGSNEWEIIRIGADIKIKCLGCGRQIMLP 44 (57)
T ss_pred CCCCCCEEEEEEccCcEEEEECCCCCEEEEe
Confidence 4699999899998888899999999875553
No 156
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=38.59 E-value=14 Score=27.94 Aligned_cols=11 Identities=45% Similarity=0.770 Sum_probs=9.1
Q ss_pred eeCCCCCCcce
Q 024241 221 ICLGCKSPDTI 231 (270)
Q Consensus 221 lC~~C~sPDT~ 231 (270)
+||.|+|+++.
T Consensus 20 ~CP~Cgs~~~t 30 (64)
T COG2093 20 ICPVCGSTDLT 30 (64)
T ss_pred cCCCCCCcccc
Confidence 59999999853
No 157
>KOG2907 consensus RNA polymerase I transcription factor TFIIS, subunit A12.2/RPA12 [Transcription]
Probab=38.42 E-value=20 Score=30.12 Aligned_cols=33 Identities=21% Similarity=0.442 Sum_probs=25.6
Q ss_pred EeeCCCCCCcceE----EE---cCcEEEeEeccCCCcccc
Q 024241 220 VICLGCKSPDTIL----SK---ENRLFFLRCEKCGSGRSV 252 (270)
Q Consensus 220 VlC~~C~sPDT~L----~k---e~rl~~l~C~aCGa~~~V 252 (270)
-.||.|+.++-.. .| |+...|-.|..|+.+-+.
T Consensus 75 ~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k~~e 114 (116)
T KOG2907|consen 75 HKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYKFTE 114 (116)
T ss_pred ccCcccCCchhhhhhhhcccccCCceEEEEcCccceeeec
Confidence 4799999886332 34 689999999999987654
No 158
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=37.94 E-value=9.9 Score=32.26 Aligned_cols=26 Identities=42% Similarity=0.836 Sum_probs=17.5
Q ss_pred EeeCCCCCCcceEEEcCcEE--E----eEeccCCCccccc
Q 024241 220 VICLGCKSPDTILSKENRLF--F----LRCEKCGSGRSVA 253 (270)
Q Consensus 220 VlC~~C~sPDT~L~ke~rl~--~----l~C~aCGa~~~V~ 253 (270)
-.||.|+. +||| | -.|.|||-...-.
T Consensus 22 grCP~CGe--------GrLF~gFLK~~p~C~aCG~dyg~~ 53 (126)
T COG5349 22 GRCPRCGE--------GRLFRGFLKVVPACEACGLDYGFA 53 (126)
T ss_pred CCCCCCCC--------chhhhhhcccCchhhhccccccCC
Confidence 47999984 3333 2 3699999876553
No 159
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=37.62 E-value=37 Score=29.03 Aligned_cols=55 Identities=24% Similarity=0.508 Sum_probs=39.6
Q ss_pred EehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHHHhccceEeeCCCCCCcceEEEcCcEEE
Q 024241 161 VNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILRRYVNEYVICLGCKSPDTILSKENRLFF 240 (270)
Q Consensus 161 ~Nf~dI~k~L~R~p~hv~kyl~~ELGt~gsid~~~rlii~G~f~~k~ie~~L~~YI~eYVlC~~C~sPDT~L~ke~rl~~ 240 (270)
.|+.+|+.++.-++++|.+||- .+||.|.+ + -+-+..|..|+.| ++.+|+
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 5688999999999999999985 34666643 1 1346888888875 345554
Q ss_pred eEeccCC
Q 024241 241 LRCEKCG 247 (270)
Q Consensus 241 l~C~aCG 247 (270)
|..|-
T Consensus 97 --C~~C~ 101 (137)
T TIGR03826 97 --CDSCA 101 (137)
T ss_pred --cHHHH
Confidence 66664
No 160
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=36.71 E-value=32 Score=28.00 Aligned_cols=35 Identities=23% Similarity=0.557 Sum_probs=27.2
Q ss_pred ceEeeCCCCCCcceEEEcCcEEEeEeccCCCcccccccc
Q 024241 218 EYVICLGCKSPDTILSKENRLFFLRCEKCGSGRSVAPIK 256 (270)
Q Consensus 218 eYVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V~~ik 256 (270)
-+=.|-.| ++..-.++.+ .+.|.+||-+....+|.
T Consensus 34 a~daCeiC-~~~GY~q~g~---~lvC~~C~~~~~~~~ig 68 (102)
T PF10080_consen 34 AFDACEIC-GPKGYYQEGD---QLVCKNCGVRFNLPTIG 68 (102)
T ss_pred EEEecccc-CCCceEEECC---EEEEecCCCEEehhhcc
Confidence 57889999 5655555555 57899999999888775
No 161
>PF13597 NRDD: Anaerobic ribonucleoside-triphosphate reductase; PDB: 1HK8_A 1H78_A 1H7A_A 1H79_A 1H7B_A.
Probab=36.66 E-value=21 Score=36.69 Aligned_cols=39 Identities=28% Similarity=0.315 Sum_probs=13.9
Q ss_pred eEeeCCCCCCcceEEEcCcEEEeEeccCCCcccccccccceEEEeeec
Q 024241 219 YVICLGCKSPDTILSKENRLFFLRCEKCGSGRSVAPIKAGFQARVGRR 266 (270)
Q Consensus 219 YVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V~~ik~gf~a~~~kr 266 (270)
.-.||.|+|+++... .|+ ||.-++|+..-.|=++-+..|
T Consensus 504 ~~~CP~CGs~~~~~~--~Rv-------~GYl~~v~~~n~gK~~E~~~R 542 (546)
T PF13597_consen 504 GDKCPKCGSENIEVY--SRV-------TGYLRPVSRWNKGKQAEFKDR 542 (546)
T ss_dssp EEE-CCC----EEEE--B-S-------SSS-BTTS-------------
T ss_pred CCCCCCCCCcccceE--EEe-------eccccCccccCHHHHHHHHHh
Confidence 567999999994433 454 999999988666655544333
No 162
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=36.51 E-value=41 Score=33.99 Aligned_cols=97 Identities=24% Similarity=0.447 Sum_probs=65.1
Q ss_pred HHHHHHHHHHhhcCCCcccCcceeecCCCeEEEeCc----eeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecCCc
Q 024241 120 ELLGRVFNILRENNPELAGDRRRTVMRPPQVLREGT----KKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQ 195 (270)
Q Consensus 120 eLL~R~~~~l~~~np~~~~~~~R~~mP~p~V~~eG~----kKTvi~Nf~dI~k~L~R~p~hv~kyl~~ELGt~gsid~~~ 195 (270)
..|..+...|++. -+..-..|..+++ .|+ ..-.++|+..|+..++---.|+.|=|-.+|--..+..+
T Consensus 58 KqLR~li~~Lred--KlI~~~~r~E~~~-----nGr~~~~~~YyyInY~~~idvVKyKlh~m~krled~~~d~t~~~~-- 128 (436)
T KOG2593|consen 58 KQLRKLIASLRED--KLIKIRTRTETAE-----NGRAVDKHTYYYINYAQVIDVVKYKLHQMRKRLEDRLRDDTNVAG-- 128 (436)
T ss_pred HHHHHHHHHhhhh--hhhhhhhhhhcCC-----CCcceeeeEEEEeehHHHHHHHHHHHHHHHHHHHHHhhhcccccc--
Confidence 4566667777532 1333333445554 452 13358999999999999999999999988876666543
Q ss_pred eEEEEeecChHHHHHHHHHhccceEeeCCCCCCcceEEE----cCcEEEeEeccCCCc
Q 024241 196 RLVVKGRFAPKNFEGILRRYVNEYVICLGCKSPDTILSK----ENRLFFLRCEKCGSG 249 (270)
Q Consensus 196 rlii~G~f~~k~ie~~L~~YI~eYVlC~~C~sPDT~L~k----e~rl~~l~C~aCGa~ 249 (270)
| .||.|.+-=|.|.- ++--...+|.-||..
T Consensus 129 -----------------------Y-~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~ge 162 (436)
T KOG2593|consen 129 -----------------------Y-VCPNCQKKYTSLEALQLLDNETGEFHCENCGGE 162 (436)
T ss_pred -----------------------c-cCCccccchhhhHHHHhhcccCceEEEecCCCc
Confidence 3 59999887777754 332336789999864
No 163
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=35.72 E-value=38 Score=22.21 Aligned_cols=8 Identities=38% Similarity=1.165 Sum_probs=6.6
Q ss_pred EeccCCCc
Q 024241 242 RCEKCGSG 249 (270)
Q Consensus 242 ~C~aCGa~ 249 (270)
.|..||..
T Consensus 34 ~C~~CGE~ 41 (46)
T TIGR03831 34 VCPQCGEE 41 (46)
T ss_pred ccccCCCE
Confidence 59999975
No 164
>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=35.44 E-value=32 Score=35.38 Aligned_cols=34 Identities=24% Similarity=0.482 Sum_probs=24.3
Q ss_pred eEeeCCCCCCcce----EEEc----CcEEEeEeccCCCcccc
Q 024241 219 YVICLGCKSPDTI----LSKE----NRLFFLRCEKCGSGRSV 252 (270)
Q Consensus 219 YVlC~~C~sPDT~----L~ke----~rl~~l~C~aCGa~~~V 252 (270)
||-||.|+-.-.. |.-+ .....+.|..||..-.=
T Consensus 200 ~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e 241 (557)
T PF05876_consen 200 YVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEE 241 (557)
T ss_pred EccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCH
Confidence 9999999876442 2212 25678999999987653
No 165
>smart00497 IENR1 Intron encoded nuclease repeat motif. Repeat of unknown function, but possibly DNA-binding via helix-turn-helix motif (Ponting, unpublished).
Probab=35.11 E-value=95 Score=20.80 Aligned_cols=25 Identities=12% Similarity=0.195 Sum_probs=23.2
Q ss_pred EEEehHHHHHHhCCChHHHHHHHHH
Q 024241 159 VFVNFMDLCKTMHRQPDHVMTFLLA 183 (270)
Q Consensus 159 vi~Nf~dI~k~L~R~p~hv~kyl~~ 183 (270)
.|..+.+.|+.|+.+..+|.+++-.
T Consensus 16 ~f~S~~eAa~~lg~~~~~I~~~~~~ 40 (53)
T smart00497 16 EFSSIREAAKYLGISHSSISKYLNT 40 (53)
T ss_pred EecCHHHHHHHhCCCHHHHHHHHhC
Confidence 6999999999999999999999875
No 166
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=35.09 E-value=83 Score=22.17 Aligned_cols=46 Identities=7% Similarity=-0.018 Sum_probs=32.7
Q ss_pred ehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHH
Q 024241 162 NFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGI 211 (270)
Q Consensus 162 Nf~dI~k~L~R~p~hv~kyl~~ELGt~gsid~~~rlii~G~f~~k~ie~~ 211 (270)
+..++|+.++.+|.+|-.|....+-.+..-+.+++. .|+..+|..+
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 468999999999999999987666554312233332 5888888765
No 167
>PHA02893 hypothetical protein; Provisional
Probab=35.03 E-value=17 Score=29.08 Aligned_cols=11 Identities=36% Similarity=0.869 Sum_probs=8.9
Q ss_pred EEeEeccCCCc
Q 024241 239 FFLRCEKCGSG 249 (270)
Q Consensus 239 ~~l~C~aCGa~ 249 (270)
-.|+|.|||+.
T Consensus 68 ~tL~CaACGS~ 78 (88)
T PHA02893 68 SNIKCIACGSS 78 (88)
T ss_pred Cceeehhhchh
Confidence 36899999974
No 168
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=34.92 E-value=35 Score=23.14 Aligned_cols=27 Identities=26% Similarity=0.706 Sum_probs=19.1
Q ss_pred eCCCCCC---cceEE-EcCcEEEeEeccCCC
Q 024241 222 CLGCKSP---DTILS-KENRLFFLRCEKCGS 248 (270)
Q Consensus 222 C~~C~sP---DT~L~-ke~rl~~l~C~aCGa 248 (270)
|.-|+++ +-... ..|++|+.=|..|-+
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~fCC~tC~~ 31 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYFCCPTCLS 31 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEEECHHHHH
Confidence 6678876 22233 378999999999854
No 169
>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=34.50 E-value=17 Score=24.34 Aligned_cols=33 Identities=24% Similarity=0.640 Sum_probs=17.7
Q ss_pred EeeCCCCC---CcceEEEcCcEEEeEeccCCCcccccc
Q 024241 220 VICLGCKS---PDTILSKENRLFFLRCEKCGSGRSVAP 254 (270)
Q Consensus 220 VlC~~C~s---PDT~L~ke~rl~~l~C~aCGa~~~V~~ 254 (270)
|.|..|++ |=..+...++ .-.|.-||...+|..
T Consensus 3 ~rC~~C~aylNp~~~~~~~~~--~w~C~~C~~~N~lp~ 38 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDDGGK--TWICNFCGTKNPLPP 38 (40)
T ss_dssp -B-TTT--BS-TTSEEETTTT--EEEETTT--EEE--G
T ss_pred cccCCCCCEECCcceEcCCCC--EEECcCCCCcCCCCC
Confidence 68999976 4555555555 468999999887753
No 170
>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=34.50 E-value=42 Score=27.97 Aligned_cols=36 Identities=22% Similarity=0.544 Sum_probs=19.3
Q ss_pred HhccceEeeCCCCCCcceEEEc------C----cEEEeEeccCCCc
Q 024241 214 RYVNEYVICLGCKSPDTILSKE------N----RLFFLRCEKCGSG 249 (270)
Q Consensus 214 ~YI~eYVlC~~C~sPDT~L~ke------~----rl~~l~C~aCGa~ 249 (270)
.|+-.|+-|..|++-|-.++.. + =.|-..|..|++.
T Consensus 22 SyllN~~~Ca~C~krdfv~i~nk~~~eedgeEivTY~HvC~nC~Hv 67 (112)
T PF06573_consen 22 SYLLNFVGCASCQKRDFVLISNKSIEEEDGEEIVTYDHVCKNCHHV 67 (112)
T ss_dssp --TTTB---SSS--SS-EEEEEEEEEEETTEEEEEEEEEETTT--E
T ss_pred ceeeechhhhccCCCCcEEEecccccccCCcEEEEeeeccCccceE
Confidence 3677899999999999777641 1 3567889999874
No 171
>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=34.32 E-value=40 Score=27.41 Aligned_cols=26 Identities=12% Similarity=0.206 Sum_probs=14.7
Q ss_pred ChHHHHHHHHHhhcCceeecCCceEEEE
Q 024241 173 QPDHVMTFLLAELGTSGSLDGQQRLVVK 200 (270)
Q Consensus 173 ~p~hv~kyl~~ELGt~gsid~~~rlii~ 200 (270)
.|+.|.-+|. .-+.|++-.+-+|.|.
T Consensus 40 ~pe~L~f~f~--~~~~~T~~e~a~L~Ie 65 (113)
T PF01155_consen 40 EPEALRFAFE--VLAEGTILEGAELEIE 65 (113)
T ss_dssp -HHHHHHHHH--HHHCCSTTTT-EEEEE
T ss_pred CHHHHHHHHH--HHhCCCCccCCEEEEE
Confidence 3666655443 3355777666688884
No 172
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=34.16 E-value=26 Score=29.14 Aligned_cols=31 Identities=23% Similarity=0.311 Sum_probs=22.8
Q ss_pred EeeCCCCCCcceEEEcCcEEEeEeccCCCcccccc
Q 024241 220 VICLGCKSPDTILSKENRLFFLRCEKCGSGRSVAP 254 (270)
Q Consensus 220 VlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V~~ 254 (270)
--||.|.|--|.- ++. .+.|..||+.++-..
T Consensus 3 p~CP~C~seytY~--dg~--~~iCpeC~~EW~~~~ 33 (109)
T TIGR00686 3 PPCPKCNSEYTYH--DGT--QLICPSCLYEWNENE 33 (109)
T ss_pred CcCCcCCCcceEe--cCC--eeECccccccccccc
Confidence 3599999987643 233 488999999987654
No 173
>PF15494 SRCR_2: Scavenger receptor cysteine-rich domain
Probab=34.15 E-value=27 Score=27.24 Aligned_cols=15 Identities=27% Similarity=0.756 Sum_probs=12.8
Q ss_pred CcEEEeEeccCCCcc
Q 024241 236 NRLFFLRCEKCGSGR 250 (270)
Q Consensus 236 ~rl~~l~C~aCGa~~ 250 (270)
++++-|+|.+||.+.
T Consensus 84 ~~vVsL~C~~CG~r~ 98 (98)
T PF15494_consen 84 GSVVSLQCSDCGKRT 98 (98)
T ss_pred CCEEEEECcccCCcC
Confidence 478999999999863
No 174
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=34.11 E-value=20 Score=31.82 Aligned_cols=71 Identities=24% Similarity=0.447 Sum_probs=41.7
Q ss_pred hCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHHHh------ccceEeeCCCCCCcceEEEcC---c---
Q 024241 170 MHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILRRY------VNEYVICLGCKSPDTILSKEN---R--- 237 (270)
Q Consensus 170 L~R~p~hv~kyl~~ELGt~gsid~~~rlii~G~f~~k~ie~~L~~Y------I~eYVlC~~C~sPDT~L~ke~---r--- 237 (270)
|-|+-+.+-++ -+|..+.+ |.-....+|+-.+|.+| -.++-.||.|+.|=-.+.++. +
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 44666655554 55654443 22333456666664432 134889999988744444432 1
Q ss_pred ------EEEeEeccCCCcc
Q 024241 238 ------LFFLRCEKCGSGR 250 (270)
Q Consensus 238 ------l~~l~C~aCGa~~ 250 (270)
--|.+|..||...
T Consensus 122 ~~~~~~~~f~~C~~CgkiY 140 (165)
T COG1656 122 KVYRNYEEFYRCPKCGKIY 140 (165)
T ss_pred hhhhcccceeECCCCcccc
Confidence 2288899999754
No 175
>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=34.06 E-value=44 Score=22.33 Aligned_cols=27 Identities=30% Similarity=0.614 Sum_probs=17.0
Q ss_pred eEeeCCCCCCcceEEE----cCcEEEeEeccC
Q 024241 219 YVICLGCKSPDTILSK----ENRLFFLRCEKC 246 (270)
Q Consensus 219 YVlC~~C~sPDT~L~k----e~rl~~l~C~aC 246 (270)
.|.||-|.|.+- +.| .++.---+|..|
T Consensus 5 ~v~CP~C~s~~~-v~k~G~~~~G~qryrC~~C 35 (36)
T PF03811_consen 5 DVHCPRCQSTEG-VKKNGKSPSGHQRYRCKDC 35 (36)
T ss_pred eeeCCCCCCCCc-ceeCCCCCCCCEeEecCcC
Confidence 588999988763 233 134445567776
No 176
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=33.83 E-value=40 Score=23.88 Aligned_cols=23 Identities=26% Similarity=0.684 Sum_probs=17.2
Q ss_pred cChHHHHHHHHHhccceEeeCCCCC
Q 024241 203 FAPKNFEGILRRYVNEYVICLGCKS 227 (270)
Q Consensus 203 f~~k~ie~~L~~YI~eYVlC~~C~s 227 (270)
.++..++.+... ++-|.||.|+.
T Consensus 32 l~~~~~~~i~~~--~~i~~Cp~CgR 54 (56)
T PF02591_consen 32 LPPQELNEIRKG--DEIVFCPNCGR 54 (56)
T ss_pred cCHHHHHHHHcC--CCeEECcCCCc
Confidence 467777777666 78888988875
No 177
>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=33.56 E-value=29 Score=32.30 Aligned_cols=31 Identities=29% Similarity=0.402 Sum_probs=15.0
Q ss_pred eEeeCCCCCCcceEE----E--cCcEEEeEeccCCCc
Q 024241 219 YVICLGCKSPDTILS----K--ENRLFFLRCEKCGSG 249 (270)
Q Consensus 219 YVlC~~C~sPDT~L~----k--e~rl~~l~C~aCGa~ 249 (270)
.+.|+.|++.+-.-. . +...-.-.|+.||+-
T Consensus 211 R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~Y 247 (290)
T PF04216_consen 211 RIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSY 247 (290)
T ss_dssp TTS-TTT---SS-EEE--------SEEEEEETTTTEE
T ss_pred CCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccch
Confidence 356788887754321 1 235667788888853
No 178
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=32.90 E-value=19 Score=26.80 Aligned_cols=13 Identities=31% Similarity=0.301 Sum_probs=5.3
Q ss_pred eEeeCCCCCCcce
Q 024241 219 YVICLGCKSPDTI 231 (270)
Q Consensus 219 YVlC~~C~sPDT~ 231 (270)
+..|+.|+|.+|.
T Consensus 48 g~KC~~C~SYNT~ 60 (61)
T PF14599_consen 48 GHKCSHCGSYNTR 60 (61)
T ss_dssp ----TTTS---EE
T ss_pred hhcCCCCCCcccC
Confidence 7899999999985
No 179
>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=32.78 E-value=27 Score=26.89 Aligned_cols=8 Identities=25% Similarity=0.841 Sum_probs=2.8
Q ss_pred eeCCCCCC
Q 024241 221 ICLGCKSP 228 (270)
Q Consensus 221 lC~~C~sP 228 (270)
+||.|..|
T Consensus 3 ~CP~C~~~ 10 (70)
T PF07191_consen 3 TCPKCQQE 10 (70)
T ss_dssp B-SSS-SB
T ss_pred cCCCCCCc
Confidence 34445444
No 180
>cd01896 DRG The developmentally regulated GTP-binding protein (DRG) subfamily is an uncharacterized member of the Obg family, an evolutionary branch of GTPase superfamily proteins. GTPases act as molecular switches regulating diverse cellular processes. DRG2 and DRG1 comprise the DRG subfamily in eukaryotes. In view of their widespread expression in various tissues and high conservation among distantly related species in eukaryotes and archaea, DRG proteins may regulate fundamental cellular processes. It is proposed that the DRG subfamily proteins play their physiological roles through RNA binding.
Probab=32.77 E-value=1.7e+02 Score=26.22 Aligned_cols=95 Identities=12% Similarity=0.117 Sum_probs=65.1
Q ss_pred HHHHHHHHHHhhcCCCcccCcceeecCCCeEEEeCceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEE
Q 024241 120 ELLGRVFNILRENNPELAGDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVV 199 (270)
Q Consensus 120 eLL~R~~~~l~~~np~~~~~~~R~~mP~p~V~~eG~kKTvi~Nf~dI~k~L~R~p~hv~kyl~~ELGt~gsid~~~rlii 199 (270)
..++++.+.|.... -++.-++|.|...+ +..-=.++.--.+..+=+.+.+.+ ++.|.|...- .+.|
T Consensus 92 ~~~~~~~~~l~~~g-------i~l~~~~~~v~~~~-~~~ggi~~~~~~~~~~~~~~~v~~-~l~~~~i~~~-----~v~~ 157 (233)
T cd01896 92 GHREILERELEGVG-------IRLNKRPPNITIKK-KKKGGINITSTVPLTKLDEKTIKA-ILREYKIHNA-----DVLI 157 (233)
T ss_pred hHHHHHHHHHHHcC-------ceecCCCCeEEEEE-EecCCEEEeccCCCCCCCHHHHHH-HHHHhCeeeE-----EEEE
Confidence 36666777774321 14566778888877 333333343445666667788877 5668887543 5688
Q ss_pred EeecChHHHHHHHH---HhccceEeeCCCCCC
Q 024241 200 KGRFAPKNFEGILR---RYVNEYVICLGCKSP 228 (270)
Q Consensus 200 ~G~f~~k~ie~~L~---~YI~eYVlC~~C~sP 228 (270)
.|..+-++|.++|. .|+...+....|-..
T Consensus 158 ~~~~~~~~~~~~~~~~~~y~p~iiV~NK~Dl~ 189 (233)
T cd01896 158 REDITVDDLIDVIEGNRVYIPCLYVYNKIDLI 189 (233)
T ss_pred ccCCCHHHHHHHHhCCceEeeEEEEEECccCC
Confidence 99999999999997 788888888888654
No 181
>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=32.72 E-value=19 Score=32.64 Aligned_cols=33 Identities=24% Similarity=0.413 Sum_probs=26.2
Q ss_pred EeeCCCCCCcceEEE-cCcEEEeEeccCCCcccc
Q 024241 220 VICLGCKSPDTILSK-ENRLFFLRCEKCGSGRSV 252 (270)
Q Consensus 220 VlC~~C~sPDT~L~k-e~rl~~l~C~aCGa~~~V 252 (270)
-+|+.|-.-.+.|.. ..++-...|..||+...-
T Consensus 14 ~lC~~C~~~~~~i~ei~~~i~v~~C~~Cg~~~~~ 47 (236)
T PF04981_consen 14 GLCPDCYLKRFDIIEIPDRIEVTICPKCGRYRIG 47 (236)
T ss_pred ccChHHhcccCCeeecCCccCceECCCCCCEECC
Confidence 478888877777766 567889999999997653
No 182
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=32.41 E-value=49 Score=27.81 Aligned_cols=41 Identities=27% Similarity=0.441 Sum_probs=28.4
Q ss_pred HHhccceEeeCCCCCCcceEEEc---CcEEEeEeccCCCcccccc
Q 024241 213 RRYVNEYVICLGCKSPDTILSKE---NRLFFLRCEKCGSGRSVAP 254 (270)
Q Consensus 213 ~~YI~eYVlC~~C~sPDT~L~ke---~rl~~l~C~aCGa~~~V~~ 254 (270)
.+....-+.||-|++.. ....- .+.---+|..||....+..
T Consensus 24 ~~~~~~~~~cP~C~s~~-~~k~g~~~~~~qRyrC~~C~~tf~~~~ 67 (129)
T COG3677 24 IRMQITKVNCPRCKSSN-VVKIGGIRRGHQRYKCKSCGSTFTVET 67 (129)
T ss_pred HhhhcccCcCCCCCccc-eeeECCccccccccccCCcCcceeeec
Confidence 34445558999999999 33331 2345568999999887753
No 183
>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=32.31 E-value=46 Score=26.31 Aligned_cols=63 Identities=14% Similarity=0.288 Sum_probs=41.0
Q ss_pred hHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEe-ecChHHHHHHHHHhccceEeeCCCCCCcceEEE
Q 024241 163 FMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKG-RFAPKNFEGILRRYVNEYVICLGCKSPDTILSK 234 (270)
Q Consensus 163 f~dI~k~L~R~p~hv~kyl~~ELGt~gsid~~~rlii~G-~f~~k~ie~~L~~YI~eYVlC~~C~sPDT~L~k 234 (270)
+.-||++|+|.+..|++.|....+.. -++ .+..| =++-.+++.++.-| =+|-.|......++-
T Consensus 7 i~AiA~aL~R~~~dVl~Vl~~~~~~~-~~~----~l~~G~Gl~l~~le~~f~~F----~I~A~v~~~g~~~~l 70 (89)
T PF05379_consen 7 IRAIAEALGRREQDVLAVLSRKCGEE-LLE----ELWSGEGLDLEDLEELFELF----DICAHVNFGGETFVL 70 (89)
T ss_pred hHHHHHHhCCCHHHHHHHHHhccCHH-HHH----HHHcCCCcCHHHHHHHHHHc----CeEEEEEECCEEEEE
Confidence 45799999999999999999988742 221 11111 25667777766655 677777555444443
No 184
>PRK07220 DNA topoisomerase I; Validated
Probab=32.30 E-value=37 Score=36.13 Aligned_cols=34 Identities=15% Similarity=0.206 Sum_probs=23.3
Q ss_pred EeeCCCCCCcceEEEcC-cEEEeEeccCCCccccc
Q 024241 220 VICLGCKSPDTILSKEN-RLFFLRCEKCGSGRSVA 253 (270)
Q Consensus 220 VlC~~C~sPDT~L~ke~-rl~~l~C~aCGa~~~V~ 253 (270)
..||.|+.+...+.+.+ +-||+.|..|.......
T Consensus 636 ~~Cp~Cg~~~~k~~~~g~~~~~~~Cp~C~~~~~~~ 670 (740)
T PRK07220 636 KVCEAHGLNHIRIINGGKRPWDLGCPQCNFIEWQK 670 (740)
T ss_pred CCCCCCCCceEEEEecCCccceeeCCCCCCccccC
Confidence 36999998865555443 45688999998754333
No 185
>PRK01310 hypothetical protein; Validated
Probab=31.86 E-value=96 Score=25.32 Aligned_cols=41 Identities=22% Similarity=0.399 Sum_probs=30.7
Q ss_pred hHHHHHHHHHhhcCcee--------ecCCceEEEEeecChHHHHHHHHHhc
Q 024241 174 PDHVMTFLLAELGTSGS--------LDGQQRLVVKGRFAPKNFEGILRRYV 216 (270)
Q Consensus 174 p~hv~kyl~~ELGt~gs--------id~~~rlii~G~f~~k~ie~~L~~YI 216 (270)
=++|+.||...||++-+ -.....+.|.| +++++...|..|+
T Consensus 54 N~ali~~LA~~l~v~ks~I~iv~G~tsR~K~v~I~~--~~~~l~~~l~~~~ 102 (104)
T PRK01310 54 NRALIELLAKALGVPKSSVRLLSGATSRLKQLRIDG--DPEDLGEALRALT 102 (104)
T ss_pred HHHHHHHHHHHhCCChhhEEEEecCCCCceEEEEeC--CHHHHHHHHHHHh
Confidence 36899999999997432 22245677877 7889999888775
No 186
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=31.73 E-value=47 Score=25.52 Aligned_cols=30 Identities=13% Similarity=0.417 Sum_probs=21.1
Q ss_pred eeCCCCCCcceEEE-----c-CcEEEeEec--cCCCccc
Q 024241 221 ICLGCKSPDTILSK-----E-NRLFFLRCE--KCGSGRS 251 (270)
Q Consensus 221 lC~~C~sPDT~L~k-----e-~rl~~l~C~--aCGa~~~ 251 (270)
.||.|+++. .+.. + -+-.+-.|. .||++-.
T Consensus 3 ~CP~Cg~~a-~irtSr~~s~~~~~~Y~qC~N~eCg~tF~ 40 (72)
T PRK09678 3 HCPLCQHAA-HARTSRYITDTTKERYHQCQNVNCSATFI 40 (72)
T ss_pred cCCCCCCcc-EEEEChhcChhhheeeeecCCCCCCCEEE
Confidence 599999999 3333 1 244578898 8998654
No 187
>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=31.55 E-value=1.2e+02 Score=19.30 Aligned_cols=48 Identities=10% Similarity=0.169 Sum_probs=31.9
Q ss_pred EEehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHH
Q 024241 160 FVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILR 213 (270)
Q Consensus 160 i~Nf~dI~k~L~R~p~hv~kyl~~ELGt~gsid~~~rlii~G~f~~k~ie~~L~ 213 (270)
|.++.|+|+.|+-++..|.+++..-. .++...|+ + -+|...+|+..|.
T Consensus 1 ~lt~~e~a~~lgis~~ti~~~~~~g~-i~~~~~g~-~----~~~~~~~l~~~~~ 48 (49)
T TIGR01764 1 YLTVEEAAEYLGVSKDTVYRLIHEGE-LPAYRVGR-H----YRIPREDVDEYLE 48 (49)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHcCC-CCeEEeCC-e----EEEeHHHHHHHHh
Confidence 35789999999999999999986533 23332232 2 2456677666553
No 188
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=31.50 E-value=67 Score=22.47 Aligned_cols=28 Identities=4% Similarity=0.052 Sum_probs=25.8
Q ss_pred EehHHHHHHhCC-ChHHHHHHHHHhhcCc
Q 024241 161 VNFMDLCKTMHR-QPDHVMTFLLAELGTS 188 (270)
Q Consensus 161 ~Nf~dI~k~L~R-~p~hv~kyl~~ELGt~ 188 (270)
.++.+||..++= ++.|+.+.|....|.+
T Consensus 51 ~~~~~ia~~~g~~s~~~f~r~Fk~~~g~s 79 (84)
T smart00342 51 LSVTEIALRVGFSSQSYFSRAFKKLFGVT 79 (84)
T ss_pred CCHHHHHHHhCCCChHHHHHHHHHHHCcC
Confidence 579999999999 9999999999999875
No 189
>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=31.50 E-value=24 Score=23.27 Aligned_cols=11 Identities=45% Similarity=1.071 Sum_probs=7.1
Q ss_pred ceEeeCCCCCC
Q 024241 218 EYVICLGCKSP 228 (270)
Q Consensus 218 eYVlC~~C~sP 228 (270)
.||.|+.|+.+
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 57888888764
No 190
>PF15616 TerY-C: TerY-C metal binding domain
Probab=31.40 E-value=62 Score=27.61 Aligned_cols=46 Identities=22% Similarity=0.403 Sum_probs=32.8
Q ss_pred cceEeeCCCCCC-cceEEEcCcEEE------eEeccCCCcccccccccceEEE
Q 024241 217 NEYVICLGCKSP-DTILSKENRLFF------LRCEKCGSGRSVAPIKAGFQAR 262 (270)
Q Consensus 217 ~eYVlC~~C~sP-DT~L~ke~rl~~------l~C~aCGa~~~V~~ik~gf~a~ 262 (270)
..+--||.|++. --.+--=++|+- ..|..||...++.....+|...
T Consensus 75 ~g~PgCP~CGn~~~fa~C~CGkl~Ci~g~~~~~CPwCg~~g~~~~~~~~fdv~ 127 (131)
T PF15616_consen 75 IGAPGCPHCGNQYAFAVCGCGKLFCIDGEGEVTCPWCGNEGSFGAGDGGFDVN 127 (131)
T ss_pred cCCCCCCCCcChhcEEEecCCCEEEeCCCCCEECCCCCCeeeecccCCceEec
Confidence 345789999886 322222245554 8999999999999888888763
No 191
>TIGR01566 ZF_HD_prot_N ZF-HD homeobox protein Cys/His-rich dimerization domain. This model describes a 54-residue domain found in the N-terminal region of plant proteins, the vast majority of which contain a ZF-HD class homeobox domain toward the C-terminus. The region between the two domains typically is rich in low complexity sequence. The companion ZF-HD homeobox domain is described in model TIGR01565.
Probab=31.17 E-value=22 Score=25.95 Aligned_cols=16 Identities=31% Similarity=0.586 Sum_probs=12.6
Q ss_pred cEEEeEeccCCCcccc
Q 024241 237 RLFFLRCEKCGSGRSV 252 (270)
Q Consensus 237 rl~~l~C~aCGa~~~V 252 (270)
-.--|+|.|||..|..
T Consensus 33 ~~~al~CaACgCHRnF 48 (53)
T TIGR01566 33 DPESLTCAACGCHRNF 48 (53)
T ss_pred CCcceeeeecCccccc
Confidence 3447999999998864
No 192
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=30.96 E-value=36 Score=35.68 Aligned_cols=51 Identities=16% Similarity=0.335 Sum_probs=34.8
Q ss_pred cChHHHHHHHHHhcc----------ceEeeCCCCCCcceEEEcCcEEEeEeccCCCcc----cccccccceEE
Q 024241 203 FAPKNFEGILRRYVN----------EYVICLGCKSPDTILSKENRLFFLRCEKCGSGR----SVAPIKAGFQA 261 (270)
Q Consensus 203 f~~k~ie~~L~~YI~----------eYVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~----~V~~ik~gf~a 261 (270)
.+++.+.++++..-+ .+-.|+.|+. .-.+ .-.|..||+.. .|-..-.||..
T Consensus 533 ~n~~Al~~lvk~~~~~~i~Y~sin~~~~~C~~CGy-~g~~-------~~~CP~CG~~d~~~~~v~~Ri~GYl~ 597 (618)
T PRK14704 533 HNKKALKQIVQAMAEHGVGYGSINHPVDRCKCCSY-HGVI-------GNECPSCGNEDEANIERIRRITGYLV 597 (618)
T ss_pred CCHHHHHHHHHHHHhcCCceEEeCCCCeecCCCCC-CCCc-------CccCcCCCCCCcchhHHHHHHHhHhc
Confidence 489999999998544 2457999996 2222 27899999874 33333467764
No 193
>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=30.50 E-value=98 Score=24.19 Aligned_cols=46 Identities=7% Similarity=0.010 Sum_probs=34.7
Q ss_pred ehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHH
Q 024241 162 NFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGI 211 (270)
Q Consensus 162 Nf~dI~k~L~R~p~hv~kyl~~ELGt~gsid~~~rlii~G~f~~k~ie~~ 211 (270)
++.++|+.++-+|..|-.|....+..+...+++++ -.|+..+|+.+
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 56899999999999999998776665555554432 24888888776
No 194
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=30.32 E-value=49 Score=22.65 Aligned_cols=30 Identities=20% Similarity=0.381 Sum_probs=22.5
Q ss_pred ceEeeCCCCCCcceEEEcCcEEEeEeccCC
Q 024241 218 EYVICLGCKSPDTILSKENRLFFLRCEKCG 247 (270)
Q Consensus 218 eYVlC~~C~sPDT~L~ke~rl~~l~C~aCG 247 (270)
..|.|+.|+++=+.-...++..+.+|..+-
T Consensus 4 g~l~C~~CG~~m~~~~~~~~~~yy~C~~~~ 33 (58)
T PF13408_consen 4 GLLRCGHCGSKMTRRKRKGKYRYYRCSNRR 33 (58)
T ss_pred CcEEcccCCcEeEEEECCCCceEEEcCCCc
Confidence 468999999997765555555778888774
No 195
>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=30.06 E-value=29 Score=36.03 Aligned_cols=55 Identities=20% Similarity=0.267 Sum_probs=29.8
Q ss_pred eEEEEeecChHHHHHHHHHhccce----------------EeeCCCCCCcceEEEcC-cEEEeEecc---CCCcccc
Q 024241 196 RLVVKGRFAPKNFEGILRRYVNEY----------------VICLGCKSPDTILSKEN-RLFFLRCEK---CGSGRSV 252 (270)
Q Consensus 196 rlii~G~f~~k~ie~~L~~YI~eY----------------VlC~~C~sPDT~L~ke~-rl~~l~C~a---CGa~~~V 252 (270)
..|-.|+.+..++-+-+..|+... ..||.|+++ .+.+.+ +--|..|.. |+...+|
T Consensus 535 ~~I~~G~~~~~~~l~~~~~~~~~~v~~~~~~~~~~~~~~~~~CP~Cg~~--~~~~~~~~gkf~gCs~y~~C~~~~~l 609 (610)
T TIGR01051 535 DEIAEGKAEWKPVLKNFYTGFSSKVKKLRNMRIIVDFKTSQDCPLCGRP--MVVKLGKYGPFLACSNFPECKYTKSI 609 (610)
T ss_pred HHHHcCCCCHHHHHHHHHHHHHHHHHHhhhcccccccccCCCCCCCCCe--eEEEecCCCceeeCCCCCCCCCCCCC
Confidence 345557777665554444443322 249999874 232221 113678877 7765543
No 196
>PRK14973 DNA topoisomerase I; Provisional
Probab=30.06 E-value=30 Score=38.05 Aligned_cols=33 Identities=15% Similarity=0.241 Sum_probs=25.1
Q ss_pred eeCCCCCCcceEEEcCc-EEEeEeccCCCccccc
Q 024241 221 ICLGCKSPDTILSKENR-LFFLRCEKCGSGRSVA 253 (270)
Q Consensus 221 lC~~C~sPDT~L~ke~r-l~~l~C~aCGa~~~V~ 253 (270)
.||.|++|--.+.+.+| =||+-|..|.+..+..
T Consensus 637 ~Cp~CG~p~~~~~r~Gr~g~fl~CP~C~~~~~~~ 670 (936)
T PRK14973 637 VCPIHHLNHVRLIRKGARPWDIGCPLCSHIESNT 670 (936)
T ss_pred CCCCCCCCceEEeecCCCcccccCccccchhhcc
Confidence 69999999555556654 4699999999877743
No 197
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=29.94 E-value=45 Score=27.48 Aligned_cols=30 Identities=20% Similarity=0.389 Sum_probs=23.2
Q ss_pred eeCCCCCCcceEEEc--CcEEEeEeccCCCccccc
Q 024241 221 ICLGCKSPDTILSKE--NRLFFLRCEKCGSGRSVA 253 (270)
Q Consensus 221 lC~~C~sPDT~L~ke--~rl~~l~C~aCGa~~~V~ 253 (270)
.||+|++. |+.+ ....-+.|.+|+...++.
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 59999985 5543 346789999999988875
No 198
>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=29.84 E-value=17 Score=25.62 Aligned_cols=8 Identities=38% Similarity=0.895 Sum_probs=4.6
Q ss_pred eeCCCCCC
Q 024241 221 ICLGCKSP 228 (270)
Q Consensus 221 lC~~C~sP 228 (270)
.||.|++|
T Consensus 22 ~CPlC~r~ 29 (54)
T PF04423_consen 22 CCPLCGRP 29 (54)
T ss_dssp E-TTT--E
T ss_pred cCCCCCCC
Confidence 99999987
No 199
>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=29.54 E-value=26 Score=29.30 Aligned_cols=35 Identities=23% Similarity=0.499 Sum_probs=24.7
Q ss_pred eEeeCCCCCCcceEEEcCcEEEeEeccCCCcccccccccc
Q 024241 219 YVICLGCKSPDTILSKENRLFFLRCEKCGSGRSVAPIKAG 258 (270)
Q Consensus 219 YVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V~~ik~g 258 (270)
.|.||+|+.+---|-+. -.|--|+..=++.+-.+|
T Consensus 69 ~V~CP~C~K~TKmLGr~-----D~CM~C~~pLTLd~~leg 103 (114)
T PF11023_consen 69 QVECPNCGKQTKMLGRV-----DACMHCKEPLTLDPSLEG 103 (114)
T ss_pred eeECCCCCChHhhhchh-----hccCcCCCcCccCchhhc
Confidence 58999999875444443 269999988777665544
No 200
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=29.37 E-value=30 Score=29.27 Aligned_cols=35 Identities=31% Similarity=0.531 Sum_probs=20.5
Q ss_pred HHHHHHHHHhccceEeeCCCCCCcceEEEcCcEEE---eEeccCCCcc
Q 024241 206 KNFEGILRRYVNEYVICLGCKSPDTILSKENRLFF---LRCEKCGSGR 250 (270)
Q Consensus 206 k~ie~~L~~YI~eYVlC~~C~sPDT~L~ke~rl~~---l~C~aCGa~~ 250 (270)
..+-+.|+++---+..|+.|+ +++| ..|..||+..
T Consensus 16 ~~f~~~l~~~kl~g~kC~~CG----------~v~~PPr~~Cp~C~~~~ 53 (140)
T COG1545 16 SKFFKGLKEGKLLGTKCKKCG----------RVYFPPRAYCPKCGSET 53 (140)
T ss_pred hHHhhhhhhCcEEEEEcCCCC----------eEEcCCcccCCCCCCCC
Confidence 344445555555667777775 4443 4677777764
No 201
>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.
Probab=28.80 E-value=59 Score=34.04 Aligned_cols=58 Identities=26% Similarity=0.562 Sum_probs=36.6
Q ss_pred EEeecChHHHHHHHHHhccc----------eEeeCCCCCCcceEEEcCcEEEeEeccCCCcc-cccccccceEEEe
Q 024241 199 VKGRFAPKNFEGILRRYVNE----------YVICLGCKSPDTILSKENRLFFLRCEKCGSGR-SVAPIKAGFQARV 263 (270)
Q Consensus 199 i~G~f~~k~ie~~L~~YI~e----------YVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~-~V~~ik~gf~a~~ 263 (270)
+-.+.+++.+.++++.=.+. +-+|+.|+... +++ .-.|..||+.. .|-+.-.||.-.|
T Consensus 502 l~e~~n~ea~~~lv~~~~~~~i~Y~tin~~~siC~~CGy~~------g~~-~~~CP~CGs~~~ev~sRv~GYl~~v 570 (586)
T TIGR02827 502 LEESLSEDGYRKLLRVAADTGCNYFCFNIKITICNDCHHID------KRT-LHRCPVCGSANIDYGTRVIGYLKRV 570 (586)
T ss_pred cCCCCCHHHHHHHHHHHHhcCCceEEeCCCCeecCCCCCcC------CCc-CCcCcCCCCccceEEEeecceecCc
Confidence 33355888999998875553 56899999832 111 36899999642 2333335665433
No 202
>KOG2691 consensus RNA polymerase II subunit 9 [Transcription]
Probab=28.69 E-value=59 Score=27.17 Aligned_cols=32 Identities=25% Similarity=0.719 Sum_probs=22.2
Q ss_pred eEeeCCCCCCcceEEE------c-C-cEEEeEeccCCCccc
Q 024241 219 YVICLGCKSPDTILSK------E-N-RLFFLRCEKCGSGRS 251 (270)
Q Consensus 219 YVlC~~C~sPDT~L~k------e-~-rl~~l~C~aCGa~~~ 251 (270)
-.-||.|+.-+-.... + . +||++-| +||.+++
T Consensus 73 ~~~C~~C~~~eavffQ~~~~r~d~~m~l~yvC~-~C~h~wt 112 (113)
T KOG2691|consen 73 DKHCPKCGHREAVFFQAQTRRADEAMRLFYVCC-SCGHRWT 112 (113)
T ss_pred cccCCccCCcceEEEecccccccceEEEEEEec-ccccccc
Confidence 4679999998877754 1 1 6655544 5998764
No 203
>PF14353 CpXC: CpXC protein
Probab=28.19 E-value=50 Score=26.83 Aligned_cols=32 Identities=19% Similarity=0.246 Sum_probs=26.9
Q ss_pred eEEEEeecChHHHHHHHHHhccceEeeCCCCCC
Q 024241 196 RLVVKGRFAPKNFEGILRRYVNEYVICLGCKSP 228 (270)
Q Consensus 196 rlii~G~f~~k~ie~~L~~YI~eYVlC~~C~sP 228 (270)
-.+|+...+++-.+.+|+.=+.. +.||.|+..
T Consensus 16 ~~~I~~~~~p~l~e~il~g~l~~-~~CP~Cg~~ 47 (128)
T PF14353_consen 16 WTSINADEDPELKEKILDGSLFS-FTCPSCGHK 47 (128)
T ss_pred EeEEcCcCCHHHHHHHHcCCcCE-EECCCCCCc
Confidence 56788899999999999887776 689999864
No 204
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=28.13 E-value=32 Score=25.24 Aligned_cols=12 Identities=33% Similarity=0.922 Sum_probs=10.1
Q ss_pred ceEeeCCCCCCc
Q 024241 218 EYVICLGCKSPD 229 (270)
Q Consensus 218 eYVlC~~C~sPD 229 (270)
.-|.||.|+.|=
T Consensus 20 DiVvCp~Cgapy 31 (54)
T PF14446_consen 20 DIVVCPECGAPY 31 (54)
T ss_pred CEEECCCCCCcc
Confidence 469999999984
No 205
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=28.06 E-value=75 Score=24.58 Aligned_cols=47 Identities=6% Similarity=0.036 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHHhhcCCCcccCcceeecCCCeEEEeCceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCc
Q 024241 118 YEELLGRVFNILRENNPELAGDRRRTVMRPPQVLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTS 188 (270)
Q Consensus 118 YeeLL~R~~~~l~~~np~~~~~~~R~~mP~p~V~~eG~kKTvi~Nf~dI~k~L~R~p~hv~kyl~~ELGt~ 188 (270)
...++.++...+..+ +. -| .++.+||+.++-++.|+.+.|...+|.+
T Consensus 3 ~~~~~~~~~~~i~~~-~~---------~~--------------~~~~~lA~~~~~S~~~l~r~f~~~~g~s 49 (107)
T PRK10219 3 HQKIIQTLIAWIDEH-ID---------QP--------------LNIDVVAKKSGYSKWYLQRMFRTVTHQT 49 (107)
T ss_pred hHHHHHHHHHHHHHh-cC---------CC--------------CCHHHHHHHHCCCHHHHHHHHHHHHCcC
Confidence 467788888888432 21 01 2688999999999999999999999874
No 206
>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=27.93 E-value=1.5e+02 Score=22.22 Aligned_cols=58 Identities=21% Similarity=0.248 Sum_probs=35.9
Q ss_pred EEEeCceeEEEEehHHHHHHhCCChHHHHHHHHHhhcCceeec-CCceEEEEeecC----hHHHHHHHHHhccce
Q 024241 150 VLREGTKKTVFVNFMDLCKTMHRQPDHVMTFLLAELGTSGSLD-GQQRLVVKGRFA----PKNFEGILRRYVNEY 219 (270)
Q Consensus 150 V~~eG~kKTvi~Nf~dI~k~L~R~p~hv~kyl~~ELGt~gsid-~~~rlii~G~f~----~k~ie~~L~~YI~eY 219 (270)
|.+-|+...+.. |..++.-|.-.-|..-.+. .++.++|.=.-. ...|..++++.+++|
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 566675555444 7777777777777777775 356788864333 344444555555555
No 207
>PRK08402 replication factor A; Reviewed
Probab=27.59 E-value=43 Score=32.76 Aligned_cols=47 Identities=17% Similarity=0.287 Sum_probs=27.5
Q ss_pred EEEEeecChHHHHHHHHHhccceEeeCCCCCCcceEEEcCcEEEeEeccCCCccccc
Q 024241 197 LVVKGRFAPKNFEGILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKCGSGRSVA 253 (270)
Q Consensus 197 lii~G~f~~k~ie~~L~~YI~eYVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V~ 253 (270)
+.|.|.... |.. .+ -|-.||+|+. .++.+..--.-+|..||...|+.
T Consensus 197 v~v~g~Iv~--i~~---~~--~y~aCp~CnK---kv~~~~~~~~~~Ce~~~~v~p~~ 243 (355)
T PRK08402 197 VEVRGTIAK--VYR---VL--VYDACPECRR---KVDYDPATDTWICPEHGEVEPIK 243 (355)
T ss_pred EEEEEEEEE--Eec---Ce--eEecCCCCCe---EEEEecCCCCEeCCCCCCcCcce
Confidence 566675543 111 23 3999999976 44432211134899999765543
No 208
>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=27.51 E-value=25 Score=34.45 Aligned_cols=53 Identities=19% Similarity=0.331 Sum_probs=17.4
Q ss_pred EEeecChHHHHHHHHHhc---cceEeeCCCCCCc-----------ceEEE-cCcEEEeEeccCCCccc
Q 024241 199 VKGRFAPKNFEGILRRYV---NEYVICLGCKSPD-----------TILSK-ENRLFFLRCEKCGSGRS 251 (270)
Q Consensus 199 i~G~f~~k~ie~~L~~YI---~eYVlC~~C~sPD-----------T~L~k-e~rl~~l~C~aCGa~~~ 251 (270)
++.--..++++..|..=- -.+|.|.+|...- -.|.. +.---|.+|..||.+..
T Consensus 229 f~~Le~kEkmeekm~~i~e~k~kav~C~~C~yt~~~~~~~C~~~~H~l~~~~a~KRFFkC~~C~~Rt~ 296 (344)
T PF09332_consen 229 FEKLEKKEKMEEKMESIREVKCKAVTCKQCKYTAFKPSDRCKEEGHPLKWHDAVKRFFKCKDCGNRTI 296 (344)
T ss_dssp ---------------S-S--EEEEEEETTT--EESS--HHHHHTT--EEEEEEE-EEEE-T-TS-EEE
T ss_pred HHHHHHHHHHHHHHhhCcEEEEEEEEcCCCCCcccCcchhHHhcCCceEEeeeeeeeEECCCCCCeee
Confidence 334444445554443221 3578999996321 11222 32233889999998754
No 209
>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=27.45 E-value=1.1e+02 Score=24.01 Aligned_cols=45 Identities=11% Similarity=0.177 Sum_probs=32.2
Q ss_pred ehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHH
Q 024241 162 NFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGI 211 (270)
Q Consensus 162 Nf~dI~k~L~R~p~hv~kyl~~ELGt~gsid~~~rlii~G~f~~k~ie~~ 211 (270)
++.++|+.++-++.+|-.|....|..+..-+++ +. .|+..+|..+
T Consensus 3 ~i~eva~~~gVs~~tLR~ye~~Gli~p~r~~~g-~R----~Ys~~dv~~l 47 (98)
T cd01279 3 PISVAAELLGIHPQTLRVYDRLGLVSPARTNGG-GR----RYSNNDLELL 47 (98)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCCCCCCCcCCCC-Ce----eECHHHHHHH
Confidence 789999999999999999988777665322223 22 2677776654
No 210
>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=27.02 E-value=25 Score=21.87 Aligned_cols=25 Identities=28% Similarity=0.527 Sum_probs=13.8
Q ss_pred EeeCCCCCCcceEEEcCcEEEeEeccCCCccc
Q 024241 220 VICLGCKSPDTILSKENRLFFLRCEKCGSGRS 251 (270)
Q Consensus 220 VlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~ 251 (270)
=.|+.|..- |...-.+|.+||+.++
T Consensus 5 W~C~~C~~~-------N~~~~~~C~~C~~~rp 29 (30)
T PF00641_consen 5 WKCPSCTFM-------NPASRSKCVACGAPRP 29 (30)
T ss_dssp EEETTTTEE-------EESSSSB-TTT--BTT
T ss_pred ccCCCCcCC-------chHHhhhhhCcCCCCc
Confidence 467777532 2333568999999876
No 211
>PRK10220 hypothetical protein; Provisional
Probab=26.64 E-value=42 Score=27.99 Aligned_cols=31 Identities=26% Similarity=0.426 Sum_probs=22.9
Q ss_pred EeeCCCCCCcceEEEcCcEEEeEeccCCCcccccc
Q 024241 220 VICLGCKSPDTILSKENRLFFLRCEKCGSGRSVAP 254 (270)
Q Consensus 220 VlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V~~ 254 (270)
--||.|.|--|. +.+- .+.|..||+.++-..
T Consensus 4 P~CP~C~seytY---~d~~-~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 4 PHCPKCNSEYTY---EDNG-MYICPECAHEWNDAE 34 (111)
T ss_pred CcCCCCCCcceE---cCCC-eEECCcccCcCCccc
Confidence 469999987653 3332 478999999998765
No 212
>TIGR03829 YokU_near_AblA uncharacterized protein, YokU family. Members of this protein family occur in various species of the genus Bacillus, always next to the gene (kamA or ablA) for lysine 2,3-aminomutase. Members have a pair of CXXC motifs, and share homology to the amino-terminal region of a family of putative transcription factors for which the C-terminal is modeled by pfam01381, a helix-turn-helix domain model. This family, however, is shorter and lacks the helix-turn-helix region. The function of this protein family is unknown, but a regulatory role in compatible solute biosynthesis is suggested by local genome context.
Probab=26.59 E-value=50 Score=26.50 Aligned_cols=11 Identities=27% Similarity=0.794 Sum_probs=8.5
Q ss_pred EeEeccCCCcc
Q 024241 240 FLRCEKCGSGR 250 (270)
Q Consensus 240 ~l~C~aCGa~~ 250 (270)
-+.|..||...
T Consensus 35 a~~C~~CGe~y 45 (89)
T TIGR03829 35 SISCSHCGMEY 45 (89)
T ss_pred cccccCCCcEe
Confidence 35799999764
No 213
>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=26.21 E-value=35 Score=31.54 Aligned_cols=64 Identities=17% Similarity=0.264 Sum_probs=48.1
Q ss_pred CCChHHHHHHHHHhhcCceeecC-CceEEEEeecChHHHHHHHHHhccce------EeeCCCCCC-cceEEE
Q 024241 171 HRQPDHVMTFLLAELGTSGSLDG-QQRLVVKGRFAPKNFEGILRRYVNEY------VICLGCKSP-DTILSK 234 (270)
Q Consensus 171 ~R~p~hv~kyl~~ELGt~gsid~-~~rlii~G~f~~k~ie~~L~~YI~eY------VlC~~C~sP-DT~L~k 234 (270)
.|....|.+++--|++-.-+... =+++.++|--+...|..-||.=|+.| |+|..|++. .|.|..
T Consensus 45 cR~~SsLak~y~lEfdk~~~~gnsId~IRLnG~n~~~~fnq~Ir~dIk~~yk~q~Cvm~g~~g~sent~iei 116 (230)
T PF05315_consen 45 CRSSSSLAKEYILEFDKRQTSGNSIDRIRLNGFNTEKVFNQNIRQDIKNYYKQQCCVMCGVRGNSENTKIEI 116 (230)
T ss_pred cCCchHHHHHhhcccccccCCCccHHHHHHcCcCchhhhhhHHHHHHHHHHHhcCeeeecccCCCccceeee
Confidence 47788888888888875322111 14889999999999999998888776 888888665 677765
No 214
>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=25.98 E-value=53 Score=22.56 Aligned_cols=34 Identities=24% Similarity=0.546 Sum_probs=19.6
Q ss_pred HHHHHhccceEeeCCCCCCcceEEEcCcEEEeEeccCC
Q 024241 210 GILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKCG 247 (270)
Q Consensus 210 ~~L~~YI~eYVlC~~C~sPDT~L~ke~rl~~l~C~aCG 247 (270)
-+|+-|-----.||.|+.|=.+ .+++++ .|-+|+
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 3445554455679999766432 134444 577775
No 215
>PF14116 YyzF: YyzF-like protein
Probab=25.85 E-value=54 Score=23.36 Aligned_cols=40 Identities=25% Similarity=0.405 Sum_probs=26.9
Q ss_pred hHHHHHHHHHhccceEeeCCCCCCcceEEEcCcEEEeEeccCCCc
Q 024241 205 PKNFEGILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKCGSG 249 (270)
Q Consensus 205 ~k~ie~~L~~YI~eYVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~ 249 (270)
.++|+-.|+.||.+|=+ .|+..-..+..-.--+|.-|+..
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 46899999999999864 56655444443445567777643
No 216
>KOG3084 consensus NADH pyrophosphatase I of the Nudix family of hydrolases [Replication, recombination and repair]
Probab=25.83 E-value=42 Score=32.87 Aligned_cols=22 Identities=36% Similarity=0.780 Sum_probs=18.0
Q ss_pred HHHHHHHhccceEeeCCCCCCc
Q 024241 208 FEGILRRYVNEYVICLGCKSPD 229 (270)
Q Consensus 208 ie~~L~~YI~eYVlC~~C~sPD 229 (270)
.-..+-.++..|-.||.|++|-
T Consensus 139 ~ars~l~W~skykFCp~CG~~t 160 (345)
T KOG3084|consen 139 VARSLLDWVSKYKFCPGCGSPT 160 (345)
T ss_pred HHHHHHHHHHHhccCcccCCCc
Confidence 3455667889999999999995
No 217
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=25.77 E-value=41 Score=29.68 Aligned_cols=33 Identities=21% Similarity=0.441 Sum_probs=22.4
Q ss_pred EeeCCCCCC-cceEEEcCcEEE-------eEeccCCCcccc
Q 024241 220 VICLGCKSP-DTILSKENRLFF-------LRCEKCGSGRSV 252 (270)
Q Consensus 220 VlC~~C~sP-DT~L~ke~rl~~-------l~C~aCGa~~~V 252 (270)
..||.|+.| -=....++-+.+ --|..||...|-
T Consensus 40 ~~Cp~C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpyPW 80 (158)
T PF10083_consen 40 TSCPNCSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPYPW 80 (158)
T ss_pred HHCcCCCCCCCCceecCCeeeeCCCCCCChhHHhCCCCCch
Confidence 579999887 333444544433 479999988764
No 218
>PRK02935 hypothetical protein; Provisional
Probab=25.61 E-value=49 Score=27.54 Aligned_cols=34 Identities=26% Similarity=0.686 Sum_probs=23.4
Q ss_pred EeeCCCCCCcceEEEcCcEEEeEeccCCCcccccccccc
Q 024241 220 VICLGCKSPDTILSKENRLFFLRCEKCGSGRSVAPIKAG 258 (270)
Q Consensus 220 VlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V~~ik~g 258 (270)
|.||+|+.|---|-|.+ .|--|+..=+..+-..|
T Consensus 71 V~CP~C~K~TKmLGrvD-----~CM~C~~PLTLd~~leg 104 (110)
T PRK02935 71 VICPSCEKPTKMLGRVD-----ACMHCNQPLTLDRSLEG 104 (110)
T ss_pred eECCCCCchhhhcccee-----ecCcCCCcCCcCccccc
Confidence 89999998855554444 58888877666554433
No 219
>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=25.47 E-value=46 Score=22.86 Aligned_cols=29 Identities=24% Similarity=0.516 Sum_probs=18.1
Q ss_pred eeCCCCCCcceEEEcCcEEEeEeccCCCc
Q 024241 221 ICLGCKSPDTILSKENRLFFLRCEKCGSG 249 (270)
Q Consensus 221 lC~~C~sPDT~L~ke~rl~~l~C~aCGa~ 249 (270)
.|..|+..=..+..-..--...|-.||+.
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~ 35 (52)
T TIGR02605 7 RCTACGHRFEVLQKMSDDPLATCPECGGE 35 (52)
T ss_pred EeCCCCCEeEEEEecCCCCCCCCCCCCCC
Confidence 69999874444443211224679999984
No 220
>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=25.12 E-value=22 Score=25.65 Aligned_cols=24 Identities=29% Similarity=0.646 Sum_probs=16.2
Q ss_pred ceEeeCCCCCCcceEEEcCcEEEeEeccCCCc
Q 024241 218 EYVICLGCKSPDTILSKENRLFFLRCEKCGSG 249 (270)
Q Consensus 218 eYVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~ 249 (270)
..+.|+.|+.+ ..- -..|.+||.-
T Consensus 25 ~l~~c~~cg~~----~~~----H~vc~~cG~y 48 (56)
T PF01783_consen 25 NLVKCPNCGEP----KLP----HRVCPSCGYY 48 (56)
T ss_dssp SEEESSSSSSE----EST----TSBCTTTBBS
T ss_pred ceeeeccCCCE----ecc----cEeeCCCCeE
Confidence 57899999953 222 3458888843
No 221
>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=24.91 E-value=41 Score=25.93 Aligned_cols=17 Identities=24% Similarity=0.497 Sum_probs=7.5
Q ss_pred cCcEEEeEeccCCCccc
Q 024241 235 ENRLFFLRCEKCGSGRS 251 (270)
Q Consensus 235 e~rl~~l~C~aCGa~~~ 251 (270)
.-|.|.|+|.||-...+
T Consensus 4 ~~k~~vlrC~aCf~~t~ 20 (73)
T PF08772_consen 4 RVKTWVLRCHACFKITK 20 (73)
T ss_dssp ----EEEE-SSS--EES
T ss_pred hhheeeEEccccccCcC
Confidence 34678888888866554
No 222
>PF04135 Nop10p: Nucleolar RNA-binding protein, Nop10p family; InterPro: IPR007264 H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs. More than 100 mammalian H/ACA RNAs form an equal number of ribonucleoproteins (RNPs) by associating with the same four core proteins: Cbf5, Gar1, Nhp2 and Nop10. The function of these H/ACA RNPs is essential for biogenesis of the ribosome, splicing of precursor mRNAs (pre-mRNAs), maintenance of telomeres and probably for additional cellular processes []. Recent crystal structures of archaeal H/ACA protein complexes show how the same four proteins accommodate >100 distinct but related H/ACA RNAs []. The complex contains a stable core composed of Cbf5 and Nop10, to which Gar1 and Nhp2 subsequently bind, the complex interacts with snoRNAs []. In eukaryotes Nop10 is a nucleolar protein that is specifically associated with H/ACA snoRNAs. It is essential for normal 18S rRNA production and rRNA pseudouridylation by the ribonucleoprotein particles containing H/ACA snoRNAs (H/ACA snoRNPs). Nop10 is probably necessary for the stability of these RNPs [].; PDB: 2RFK_B 3LWR_B 2HVY_C 3HAX_C 3MQK_B 3LWO_B 3LWV_B 3HAY_C 3HJY_B 2EY4_E ....
Probab=24.90 E-value=66 Score=23.43 Aligned_cols=17 Identities=35% Similarity=0.878 Sum_probs=12.3
Q ss_pred cEEEeE--eccCCCccccc
Q 024241 237 RLFFLR--CEKCGSGRSVA 253 (270)
Q Consensus 237 rl~~l~--C~aCGa~~~V~ 253 (270)
++|.|+ |..||....++
T Consensus 12 ~~YTLk~~cp~cG~~T~~a 30 (53)
T PF04135_consen 12 RVYTLKDKCPPCGGPTESA 30 (53)
T ss_dssp CEEESSSBBTTTSSBSEES
T ss_pred CcEeCCCccCCCCCCCcCC
Confidence 367776 99999876653
No 223
>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=24.76 E-value=88 Score=26.39 Aligned_cols=27 Identities=37% Similarity=0.851 Sum_probs=19.7
Q ss_pred eEeeCCCCCCcceEEEcC-cEEEeEeccCCCcc
Q 024241 219 YVICLGCKSPDTILSKEN-RLFFLRCEKCGSGR 250 (270)
Q Consensus 219 YVlC~~C~sPDT~L~ke~-rl~~l~C~aCGa~~ 250 (270)
|.-||.|+.. +...+ + .-.|..|+...
T Consensus 34 Y~aC~~C~kk---v~~~~~~--~~~C~~C~~~~ 61 (166)
T cd04476 34 YPACPGCNKK---VVEEGNG--TYRCEKCNKSV 61 (166)
T ss_pred EccccccCcc---cEeCCCC--cEECCCCCCcC
Confidence 9999999873 44332 3 46799999874
No 224
>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=24.58 E-value=33 Score=21.57 Aligned_cols=21 Identities=33% Similarity=0.600 Sum_probs=8.9
Q ss_pred eeCCCCCCcceEEEcCcEEEeEec
Q 024241 221 ICLGCKSPDTILSKENRLFFLRCE 244 (270)
Q Consensus 221 lC~~C~sPDT~L~ke~rl~~l~C~ 244 (270)
.||.|+|+ |+++..-..++|.
T Consensus 1 ~CP~C~s~---l~~~~~ev~~~C~ 21 (28)
T PF03119_consen 1 TCPVCGSK---LVREEGEVDIRCP 21 (28)
T ss_dssp B-TTT--B---EEE-CCTTCEEE-
T ss_pred CcCCCCCE---eEcCCCCEeEECC
Confidence 48999876 5553322255553
No 225
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=24.55 E-value=37 Score=31.27 Aligned_cols=16 Identities=38% Similarity=0.600 Sum_probs=13.7
Q ss_pred eEeeCCCCCCcceEEE
Q 024241 219 YVICLGCKSPDTILSK 234 (270)
Q Consensus 219 YVlC~~C~sPDT~L~k 234 (270)
|-.||.|++.+|..-+
T Consensus 368 ~~~c~~c~~~~~~~~~ 383 (389)
T PRK11788 368 YWHCPSCKAWETIKPI 383 (389)
T ss_pred eeECcCCCCccCcCCc
Confidence 7899999999997654
No 226
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=24.54 E-value=89 Score=25.38 Aligned_cols=29 Identities=14% Similarity=0.117 Sum_probs=25.7
Q ss_pred EehHHHHHHhCCChHHHHHHHHHhhcCce
Q 024241 161 VNFMDLCKTMHRQPDHVMTFLLAELGTSG 189 (270)
Q Consensus 161 ~Nf~dI~k~L~R~p~hv~kyl~~ELGt~g 189 (270)
.++.++|..++-+|.|+.+.|..++|.+=
T Consensus 26 ~sl~~lA~~~g~S~~~l~r~Fk~~~G~s~ 54 (127)
T PRK11511 26 LSLEKVSERSGYSKWHLQRMFKKETGHSL 54 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHCcCH
Confidence 34679999999999999999999999753
No 227
>PF12728 HTH_17: Helix-turn-helix domain
Probab=24.49 E-value=1.8e+02 Score=19.44 Aligned_cols=47 Identities=9% Similarity=0.110 Sum_probs=30.5
Q ss_pred EehHHHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHH
Q 024241 161 VNFMDLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILR 213 (270)
Q Consensus 161 ~Nf~dI~k~L~R~p~hv~kyl~~ELGt~gsid~~~rlii~G~f~~k~ie~~L~ 213 (270)
.+..|+|..|+-++..|.+++....- +..-.|. ++ +|...+|++.|.
T Consensus 2 lt~~e~a~~l~is~~tv~~~~~~g~i-~~~~~g~-~~----~~~~~~l~~~~~ 48 (51)
T PF12728_consen 2 LTVKEAAELLGISRSTVYRWIRQGKI-PPFKIGR-KW----RIPKSDLDRWLE 48 (51)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCC-CeEEeCC-EE----EEeHHHHHHHHH
Confidence 47889999999999999999865422 2221111 22 356667666654
No 228
>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=24.32 E-value=33 Score=28.14 Aligned_cols=33 Identities=30% Similarity=0.581 Sum_probs=23.9
Q ss_pred EeeCCCCCCcceEEEcCcEEEeEeccCCCccccc-ccc
Q 024241 220 VICLGCKSPDTILSKENRLFFLRCEKCGSGRSVA-PIK 256 (270)
Q Consensus 220 VlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V~-~ik 256 (270)
-+|++|+.-=--|-|. -+.|-.||+..++. ..+
T Consensus 10 R~Cp~CG~kFYDLnk~----PivCP~CG~~~~~~~~~k 43 (108)
T PF09538_consen 10 RTCPSCGAKFYDLNKD----PIVCPKCGTEFPPEPPLK 43 (108)
T ss_pred ccCCCCcchhccCCCC----CccCCCCCCccCcccccc
Confidence 3799998754446552 35799999999988 444
No 229
>PF14768 RPA_interact_C: Replication protein A interacting C-terminal
Probab=24.14 E-value=92 Score=23.94 Aligned_cols=55 Identities=16% Similarity=0.265 Sum_probs=39.7
Q ss_pred EEEEee---cChHHHHHHHHHhccceEeeCCCCCCcceEEEcC--cEEEeEeccCCCcccc
Q 024241 197 LVVKGR---FAPKNFEGILRRYVNEYVICLGCKSPDTILSKEN--RLFFLRCEKCGSGRSV 252 (270)
Q Consensus 197 lii~G~---f~~k~ie~~L~~YI~eYVlC~~C~sPDT~L~ke~--rl~~l~C~aCGa~~~V 252 (270)
|.|+.. .+..+|+..|..=+.+.-.= -...|.-.+.-.. ..+++.|.+|+....|
T Consensus 23 l~l~~~~~~~tl~~l~~~L~~~~~~H~~~-C~~~p~F~v~~~~~~~~L~~~C~~Cd~~~vV 82 (82)
T PF14768_consen 23 LRLNTQQDELTLEELRQLLEEAVTEHSDR-CSSTPQFSVEPGFGESSLYMSCEACDFLEVV 82 (82)
T ss_pred cEEecCCCCCCHHHHHHHHHHHHHHHHHh-CCCCCEEEEecCCCchhheeECCCCCcceeC
Confidence 666666 78899999998887765543 1466776666532 3779999999987654
No 230
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=24.12 E-value=41 Score=38.27 Aligned_cols=8 Identities=38% Similarity=1.161 Sum_probs=5.1
Q ss_pred EeccCCCc
Q 024241 242 RCEKCGSG 249 (270)
Q Consensus 242 ~C~aCGa~ 249 (270)
.|..||+.
T Consensus 694 ~CPsCGae 701 (1337)
T PRK14714 694 VCPDCGAE 701 (1337)
T ss_pred eCccCCCc
Confidence 66666664
No 231
>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=24.06 E-value=99 Score=25.51 Aligned_cols=42 Identities=17% Similarity=0.298 Sum_probs=27.7
Q ss_pred HHHHHH-HhhcCcee--ecCC-ceEE-EEeecChHHHHHHHHHhccc
Q 024241 177 VMTFLL-AELGTSGS--LDGQ-QRLV-VKGRFAPKNFEGILRRYVNE 218 (270)
Q Consensus 177 v~kyl~-~ELGt~gs--id~~-~rli-i~G~f~~k~ie~~L~~YI~e 218 (270)
++.||+ .+-+.+.- ++.+ +++. ..|.|+.+.|..-+..|+.-
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 666665 22244332 2332 3776 88999999999988888764
No 232
>COG5242 TFB4 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit TFB4 [Transcription / DNA replication, recombination, and repair]
Probab=23.89 E-value=1.3e+02 Score=28.61 Aligned_cols=48 Identities=19% Similarity=0.295 Sum_probs=36.0
Q ss_pred ceeecCCCeEEEeCceeEEEEehHHHHHHhC------CChHHHHHHHHHhhcCceeec
Q 024241 141 RRTVMRPPQVLREGTKKTVFVNFMDLCKTMH------RQPDHVMTFLLAELGTSGSLD 192 (270)
Q Consensus 141 ~R~~mP~p~V~~eG~kKTvi~Nf~dI~k~L~------R~p~hv~kyl~~ELGt~gsid 192 (270)
.++.+|--.+.+.|+.++ +.+-|++-+ -+|+-+++||+.-|++-|++-
T Consensus 180 qk~~ipI~v~~i~g~s~f----l~Q~~daTgG~Yl~ve~~eGllqyL~~~lf~d~~lr 233 (296)
T COG5242 180 QKFGIPISVFSIFGNSKF----LLQCCDATGGDYLTVEDTEGLLQYLLSLLFTDGELR 233 (296)
T ss_pred hhcCCceEEEEecCccHH----HHHHhhccCCeeEeecCchhHHHHHHHHhcCCCCcc
Confidence 467888878888885333 456666654 368999999999999988764
No 233
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=23.86 E-value=27 Score=28.13 Aligned_cols=31 Identities=26% Similarity=0.643 Sum_probs=23.0
Q ss_pred ceEeeCCCCCCcceEEEcCcEEEeEeccCCCcccccccc
Q 024241 218 EYVICLGCKSPDTILSKENRLFFLRCEKCGSGRSVAPIK 256 (270)
Q Consensus 218 eYVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V~~ik 256 (270)
..++|.-|++---.+.+. .|.+||. |.+.++
T Consensus 15 tHtlCrRCG~~syH~qK~------~CasCGy--psak~R 45 (91)
T PTZ00073 15 THTLCRRCGKRSFHVQKK------RCASCGY--PSAKMR 45 (91)
T ss_pred CcchhcccCccccccccc------cchhcCC--chhhcc
Confidence 468999999887767665 3999999 444444
No 234
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=23.64 E-value=31 Score=30.42 Aligned_cols=30 Identities=23% Similarity=0.565 Sum_probs=17.9
Q ss_pred ceEeeCCCCCCcceEEEcCcEEEeEeccCCCc
Q 024241 218 EYVICLGCKSPDTILSKENRLFFLRCEKCGSG 249 (270)
Q Consensus 218 eYVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~ 249 (270)
.|-.||.|+.-=|-+.--+ +...|..||+.
T Consensus 116 ~~Y~Cp~C~~rytf~eA~~--~~F~Cp~Cg~~ 145 (178)
T PRK06266 116 MFFFCPNCHIRFTFDEAME--YGFRCPQCGEM 145 (178)
T ss_pred CEEECCCCCcEEeHHHHhh--cCCcCCCCCCC
Confidence 5788998884322222111 35688888874
No 235
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=23.56 E-value=39 Score=35.01 Aligned_cols=53 Identities=23% Similarity=0.443 Sum_probs=33.1
Q ss_pred cChHHHHHHHHHhccc----------eEeeCCCCCCcceEEEcCcEEEeEeccCCCcc-cccccccceEEE
Q 024241 203 FAPKNFEGILRRYVNE----------YVICLGCKSPDTILSKENRLFFLRCEKCGSGR-SVAPIKAGFQAR 262 (270)
Q Consensus 203 f~~k~ie~~L~~YI~e----------YVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~-~V~~ik~gf~a~ 262 (270)
.+++.+.++++.=.+. +-+|+.|+...-.+ .-.|..||+.. .|-..-.||.-.
T Consensus 498 ~n~eal~~lv~~a~~~~i~Y~~~n~~~~~C~~CG~~g~~~-------~~~CP~Cgs~~~~~~~Rv~GYl~~ 561 (579)
T TIGR02487 498 PDPEALKDITKKAMKNGIGYFGINPPVDVCEDCGYTGEGL-------NDKCPKCGSHDIEVISRITGYLGP 561 (579)
T ss_pred CCHHHHHHHHHHHHhcCCceEEeccCCccCCCCCCCCCCC-------CCcCcCCCCccceehhhhhhhhcc
Confidence 4788999998875554 34799998622111 14799999763 233333677643
No 236
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=23.51 E-value=40 Score=24.25 Aligned_cols=34 Identities=24% Similarity=0.387 Sum_probs=24.3
Q ss_pred eeCCCCCCcceEEEcCcEEEeEeccCCCccccccccc
Q 024241 221 ICLGCKSPDTILSKENRLFFLRCEKCGSGRSVAPIKA 257 (270)
Q Consensus 221 lC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V~~ik~ 257 (270)
.|..|+..-..+.... -++|.-||++--++....
T Consensus 8 ~C~~Cg~~~~~~~~~~---~irCp~Cg~rIl~K~R~~ 41 (49)
T COG1996 8 KCARCGREVELDQETR---GIRCPYCGSRILVKERPK 41 (49)
T ss_pred EhhhcCCeeehhhccC---ceeCCCCCcEEEEeccCC
Confidence 6999998764333333 579999999988765543
No 237
>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=23.42 E-value=2.2e+02 Score=19.91 Aligned_cols=46 Identities=7% Similarity=0.114 Sum_probs=30.6
Q ss_pred ehHHHHHHhCCChHHHHHHHHHhhcCcee-ecCCceEEEEeecChHHHHHHH
Q 024241 162 NFMDLCKTMHRQPDHVMTFLLAELGTSGS-LDGQQRLVVKGRFAPKNFEGIL 212 (270)
Q Consensus 162 Nf~dI~k~L~R~p~hv~kyl~~ELGt~gs-id~~~rlii~G~f~~k~ie~~L 212 (270)
.+.|+|+.+.-++..|.+|... .|.... -+.+++ -.|++.+|+.+.
T Consensus 2 s~~eva~~~gvs~~tlr~w~~~-~g~~~~~r~~~~~----r~yt~~~v~~l~ 48 (68)
T cd01104 2 TIGAVARLTGVSPDTLRAWERR-YGLPAPQRTDGGH----RLYSEADVARLR 48 (68)
T ss_pred CHHHHHHHHCcCHHHHHHHHHh-CCCCCCCcCCCCC----eecCHHHHHHHH
Confidence 3679999999999999998754 344332 222221 247888887653
No 238
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=23.03 E-value=75 Score=26.24 Aligned_cols=16 Identities=13% Similarity=0.339 Sum_probs=12.3
Q ss_pred EehHHHHHHhCCChHH
Q 024241 161 VNFMDLCKTMHRQPDH 176 (270)
Q Consensus 161 ~Nf~dI~k~L~R~p~h 176 (270)
.+|..++..|+-.|.+
T Consensus 86 ~~fk~~~~~ig~~~~~ 101 (157)
T PF10263_consen 86 KEFKQWARRIGASPPR 101 (157)
T ss_pred HHHHHHHHHHCCcccc
Confidence 4788888888887776
No 239
>PRK14873 primosome assembly protein PriA; Provisional
Probab=22.82 E-value=58 Score=34.41 Aligned_cols=33 Identities=24% Similarity=0.470 Sum_probs=19.1
Q ss_pred ceEeeCCCCCC------cceEEEcCcEEEeEeccCCCcc
Q 024241 218 EYVICLGCKSP------DTILSKENRLFFLRCEKCGSGR 250 (270)
Q Consensus 218 eYVlC~~C~sP------DT~L~ke~rl~~l~C~aCGa~~ 250 (270)
-++.|..|+.+ +..|+-...--.++|.-||...
T Consensus 382 p~l~C~~Cg~~~~C~~C~~~L~~h~~~~~l~Ch~CG~~~ 420 (665)
T PRK14873 382 PSLACARCRTPARCRHCTGPLGLPSAGGTPRCRWCGRAA 420 (665)
T ss_pred CeeEhhhCcCeeECCCCCCceeEecCCCeeECCCCcCCC
Confidence 46666666543 3344432222268999999864
No 240
>COG5595 Zn-ribbon-containing, possibly nucleic-acid-binding protein [General function prediction only]
Probab=22.44 E-value=48 Score=30.68 Aligned_cols=77 Identities=21% Similarity=0.380 Sum_probs=55.2
Q ss_pred HHHHHhCCChHHHHHHHHHhhcCceeecCCceEEEEeecChHHHHHHHHHhc--------------cceEeeCCCCCCcc
Q 024241 165 DLCKTMHRQPDHVMTFLLAELGTSGSLDGQQRLVVKGRFAPKNFEGILRRYV--------------NEYVICLGCKSPDT 230 (270)
Q Consensus 165 dI~k~L~R~p~hv~kyl~~ELGt~gsid~~~rlii~G~f~~k~ie~~L~~YI--------------~eYVlC~~C~sPDT 230 (270)
.-|+.|.-.-..+-++.++|+.-. +..|.++||...+.||..+..=. +.|--||.|+.-=
T Consensus 155 qacdqlqmnga~leq~al~eIsd~-----dSdLsk~Gr~l~~rIek~t~iptyYylyrVgGnSlAqek~r~CPsC~k~W- 228 (256)
T COG5595 155 QACDQLQMNGAVLEQQALAEISDL-----DSDLSKHGRYLSKRIEKCTGIPTYYYLYRVGGNSLAQEKYRCCPSCGKDW- 228 (256)
T ss_pred HHHHHHHhhhHHHHHHHHHHHhcc-----cchHHHHHHHHHHHHHHHhCCCceEEEEEecCchhhhhccCCCCcccccc-
Confidence 468888888888888988888643 33688889999999998875411 3456799998531
Q ss_pred eEEEcC--cEEEeEeccCCC
Q 024241 231 ILSKEN--RLFFLRCEKCGS 248 (270)
Q Consensus 231 ~L~ke~--rl~~l~C~aCGa 248 (270)
..+++ -+|..+|+.|--
T Consensus 229 -qlk~~i~d~fhfkcd~crl 247 (256)
T COG5595 229 -QLKNPIFDTFHFKCDTCRL 247 (256)
T ss_pred -eeccchhhheeeeccccee
Confidence 22332 678889999943
No 241
>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=22.38 E-value=80 Score=30.98 Aligned_cols=32 Identities=31% Similarity=0.689 Sum_probs=16.6
Q ss_pred ccceEeeCCCCCCcceEEEcCcEEEeEeccCCCcc
Q 024241 216 VNEYVICLGCKSPDTILSKENRLFFLRCEKCGSGR 250 (270)
Q Consensus 216 I~eYVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~ 250 (270)
++.|..|..|+.--|.| .|+=..+|..||...
T Consensus 282 ~KRFFkC~~C~~Rt~sl---~r~P~~~C~~Cg~~~ 313 (344)
T PF09332_consen 282 VKRFFKCKDCGNRTISL---ERLPKKHCSNCGSSK 313 (344)
T ss_dssp E-EEEE-T-TS-EEEES---SSS--S--TTT-S--
T ss_pred eeeeEECCCCCCeeeec---ccCCCCCCCcCCcCc
Confidence 57799999999986555 467678999999753
No 242
>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=22.28 E-value=83 Score=30.30 Aligned_cols=27 Identities=11% Similarity=0.009 Sum_probs=19.7
Q ss_pred CCCCCCCC--CCCCccHHHHHHHHHHHHh
Q 024241 104 RQRYPWEG--SDRDYEYEELLGRVFNILR 130 (270)
Q Consensus 104 ~~~~~~~~--~~~~~~YeeLL~R~~~~l~ 130 (270)
++.+|... ..++..+.++|.++++.|+
T Consensus 84 ~g~PpL~~~~~~~d~~w~~~l~~LL~~l~ 112 (305)
T TIGR01562 84 HGMPPLDYDLLVREGAWLPWLDALLAGYP 112 (305)
T ss_pred cCCCCCChhhcccCHHHHHHHHHHHHHhc
Confidence 34455553 4567788999999999995
No 243
>KOG3277 consensus Uncharacterized conserved protein [Function unknown]
Probab=22.18 E-value=63 Score=28.63 Aligned_cols=35 Identities=20% Similarity=0.443 Sum_probs=27.9
Q ss_pred eEeeCCCCCCcceEEE----cCcEEEeEeccCCCccccc
Q 024241 219 YVICLGCKSPDTILSK----ENRLFFLRCEKCGSGRSVA 253 (270)
Q Consensus 219 YVlC~~C~sPDT~L~k----e~rl~~l~C~aCGa~~~V~ 253 (270)
--+|..|..-.|.-+- ++++.++.|..|.-..-++
T Consensus 79 ~yTCkvCntRs~ktisk~AY~~GvVivqC~gC~~~Hlia 117 (165)
T KOG3277|consen 79 AYTCKVCNTRSTKTISKQAYEKGVVIVQCPGCKNHHLIA 117 (165)
T ss_pred EEEeeccCCccccccChhhhhCceEEEECCCCccceeeh
Confidence 4689999988886553 5799999999998766554
No 244
>PF04502 DUF572: Family of unknown function (DUF572) ; InterPro: IPR007590 This entry represents eukaryotic proteins with undetermined function belonging to the CWC16 family.
Probab=22.09 E-value=80 Score=30.26 Aligned_cols=48 Identities=23% Similarity=0.587 Sum_probs=30.6
Q ss_pred eEeeCCCCCCc---ceE--EEc---C------cE--EEeEeccCCCccccc--ccccceEEEeeec
Q 024241 219 YVICLGCKSPD---TIL--SKE---N------RL--FFLRCEKCGSGRSVA--PIKAGFQARVGRR 266 (270)
Q Consensus 219 YVlC~~C~sPD---T~L--~ke---~------rl--~~l~C~aCGa~~~V~--~ik~gf~a~~~kr 266 (270)
-|.|.+|+.+= |.. .|+ + ++ |+++|..|++.=.+. |--+.|+..-|=|
T Consensus 40 ~i~C~~C~~~I~kG~rFNA~Ke~v~~E~Yls~~I~rF~~kC~~C~~~i~~kTDPkn~dY~~~~Ga~ 105 (324)
T PF04502_consen 40 NIWCNTCGEYIYKGVRFNARKEKVGNEKYLSTPIYRFYIKCPRCSNEIEFKTDPKNTDYVVESGAR 105 (324)
T ss_pred cCcCCCCccccccceeeeeeeEecCCCccccceEEEEEEEcCCCCCEEeeecCCCCCCeeeecCee
Confidence 48899998871 111 111 1 23 489999999988775 4467887755433
No 245
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=22.03 E-value=1.3e+02 Score=20.97 Aligned_cols=27 Identities=26% Similarity=0.491 Sum_probs=24.4
Q ss_pred ehHHHHHHhCCChHHHHHHHHHhhcCc
Q 024241 162 NFMDLCKTMHRQPDHVMTFLLAELGTS 188 (270)
Q Consensus 162 Nf~dI~k~L~R~p~hv~kyl~~ELGt~ 188 (270)
++.+||..++-++.++.+.|....|.+
T Consensus 3 ~~~~la~~~~~s~~~l~~~f~~~~~~s 29 (84)
T smart00342 3 TLEDLAEALGMSPRHLQRLFKKETGTT 29 (84)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHhCcC
Confidence 578999999999999999999988874
No 246
>PRK04296 thymidine kinase; Provisional
Probab=22.01 E-value=96 Score=26.83 Aligned_cols=44 Identities=16% Similarity=0.307 Sum_probs=32.6
Q ss_pred ChHHHHHHHHHhccceEeeCCCCCCcceEEE--c---------------CcEEEeEeccCC
Q 024241 204 APKNFEGILRRYVNEYVICLGCKSPDTILSK--E---------------NRLFFLRCEKCG 247 (270)
Q Consensus 204 ~~k~ie~~L~~YI~eYVlC~~C~sPDT~L~k--e---------------~rl~~l~C~aCG 247 (270)
.+..|-.+.+.-++---.|..|+.+-|.=.| + +-.|.-+|..|=
T Consensus 125 ~~~~L~~~aD~V~~l~~vC~~Cg~~a~~~~r~~~~~~~~~~~~~~~ig~~e~Y~~~Cr~c~ 185 (190)
T PRK04296 125 GSPYLLALADKVTELKAICVHCGRKATMNQRLIDGGPAVYEGPQVLVGGNESYEAVCRKHY 185 (190)
T ss_pred hHHHHHHhcCeEEEeeEEccccCCccceEEEEeCCCCccCCCCEEEECCcCcEEehhHHhh
Confidence 5678888888888889999999988765333 1 125777888774
No 247
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=21.94 E-value=70 Score=34.77 Aligned_cols=35 Identities=17% Similarity=0.420 Sum_probs=24.5
Q ss_pred EeeCCCCCCcceEEEcCcEEEeEecc---CCCcccccc
Q 024241 220 VICLGCKSPDTILSKENRLFFLRCEK---CGSGRSVAP 254 (270)
Q Consensus 220 VlC~~C~sPDT~L~ke~rl~~l~C~a---CGa~~~V~~ 254 (270)
..||.|+++...+..-..=.|+.|.. |...+++..
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 46999998876665432225888976 888777653
No 248
>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 PF15288 zf-CCHC_6: Zinc knuckle
Probab=21.64 E-value=42 Score=23.21 Aligned_cols=16 Identities=25% Similarity=0.673 Sum_probs=11.4
Q ss_pred eEeccCCCcccccccc
Q 024241 241 LRCEKCGSGRSVAPIK 256 (270)
Q Consensus 241 l~C~aCGa~~~V~~ik 256 (270)
++|.+||+......-+
T Consensus 2 ~kC~~CG~~GH~~t~k 17 (40)
T PF15288_consen 2 VKCKNCGAFGHMRTNK 17 (40)
T ss_pred ccccccccccccccCc
Confidence 5899999876665433
No 250
>PRK12366 replication factor A; Reviewed
Probab=21.63 E-value=63 Score=33.89 Aligned_cols=29 Identities=21% Similarity=0.516 Sum_probs=19.6
Q ss_pred eEeeCCCCCCcceEEEcCcEEEeEeccCCCcccc
Q 024241 219 YVICLGCKSPDTILSKENRLFFLRCEKCGSGRSV 252 (270)
Q Consensus 219 YVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V 252 (270)
|-.||+|+. .++...+ .-+|..||...+.
T Consensus 532 y~aCp~Cnk---Kv~~~~g--~~~C~~c~~~~p~ 560 (637)
T PRK12366 532 LYLCPNCRK---RVEEVDG--EYICEFCGEVEPN 560 (637)
T ss_pred EecccccCe---EeEcCCC--cEECCCCCCCCCc
Confidence 788999965 3443333 3479999988443
No 251
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=21.59 E-value=84 Score=30.37 Aligned_cols=18 Identities=28% Similarity=0.453 Sum_probs=14.5
Q ss_pred CCCccHHHHHHHHHHHHh
Q 024241 113 DRDYEYEELLGRVFNILR 130 (270)
Q Consensus 113 ~~~~~YeeLL~R~~~~l~ 130 (270)
.++-.+..+|.++.+.+.
T Consensus 98 ~r~~~w~~~L~~Ll~~l~ 115 (309)
T PRK03564 98 PRDKHWQKLLMALIAELK 115 (309)
T ss_pred ccChHHHHHHHHHHHHhc
Confidence 455678999999999884
No 252
>PHA02540 61 DNA primase; Provisional
Probab=21.22 E-value=87 Score=30.58 Aligned_cols=34 Identities=18% Similarity=0.326 Sum_probs=23.3
Q ss_pred EeeCCCCCCc-----ceEEE--cCcEEEeEeccCCCccccc
Q 024241 220 VICLGCKSPD-----TILSK--ENRLFFLRCEKCGSGRSVA 253 (270)
Q Consensus 220 VlC~~C~sPD-----T~L~k--e~rl~~l~C~aCGa~~~V~ 253 (270)
-+||-|+=-. +.... +++-++-+|-.||+...+-
T Consensus 28 ~~CPf~~ds~~~~~kpsF~V~p~k~~~~yhCFgCGa~Gd~i 68 (337)
T PHA02540 28 FRCPICGDSQKDKNKARGWIYEKKDGGVFKCHNCGYHRPFG 68 (337)
T ss_pred ecCCCCCCccccCcCCcEEEeccCCceEEEecCCCCCCCHH
Confidence 4799997522 12333 4555688999999998773
No 253
>PRK13501 transcriptional activator RhaR; Provisional
Probab=21.21 E-value=1e+02 Score=27.97 Aligned_cols=29 Identities=14% Similarity=0.260 Sum_probs=26.5
Q ss_pred EehHHHHHHhCCChHHHHHHHHHhhcCce
Q 024241 161 VNFMDLCKTMHRQPDHVMTFLLAELGTSG 189 (270)
Q Consensus 161 ~Nf~dI~k~L~R~p~hv~kyl~~ELGt~g 189 (270)
.++.++|.+++-+|.||.+.|-.++|.+=
T Consensus 193 ~sl~~lA~~~~lS~~~l~r~Fk~~~G~T~ 221 (290)
T PRK13501 193 FDMADFCHKNQLVERSLKQLFRQQTGMSI 221 (290)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHCcCH
Confidence 37999999999999999999999999853
No 254
>KOG2422 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.15 E-value=83 Score=33.31 Aligned_cols=20 Identities=15% Similarity=0.245 Sum_probs=14.8
Q ss_pred cHHHHHHHHHHHHhhcCCCc
Q 024241 117 EYEELLGRVFNILRENNPEL 136 (270)
Q Consensus 117 ~YeeLL~R~~~~l~~~np~~ 136 (270)
.|..-+.++|.-.+.-||+.
T Consensus 169 ~l~~k~~k~~v~~~~lnpdt 188 (665)
T KOG2422|consen 169 SLGSKSCKLFVDFKKLNPDT 188 (665)
T ss_pred hHHHHHHHHHHhhhccCCCc
Confidence 57777888886667778874
No 255
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=20.85 E-value=92 Score=32.10 Aligned_cols=40 Identities=25% Similarity=0.500 Sum_probs=28.2
Q ss_pred cChHHHHHHHHHhccc-----------eEeeCCCCCCcceEEEcCcEEEeEeccCCCcc
Q 024241 203 FAPKNFEGILRRYVNE-----------YVICLGCKSPDTILSKENRLFFLRCEKCGSGR 250 (270)
Q Consensus 203 f~~k~ie~~L~~YI~e-----------YVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~ 250 (270)
.+++.+.++++.=.+. + +|+.|+.-.. -..-.|..||++.
T Consensus 492 ~n~~al~~lv~~a~~~~~~y~~~~~p~~-~C~~CG~~~~-------~~~~~CP~CGs~~ 542 (555)
T cd01675 492 PNPEALEALVKKAAKRGVIYFGINTPID-ICNDCGYIGE-------GEGFKCPKCGSED 542 (555)
T ss_pred CCHHHHHHHHHHHHHcCCceEEEecCCc-cCCCCCCCCc-------CCCCCCcCCCCcC
Confidence 4788898888773333 3 7999996432 1247899999874
No 256
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=20.85 E-value=83 Score=32.63 Aligned_cols=29 Identities=28% Similarity=0.417 Sum_probs=20.7
Q ss_pred eeCCCCCCcceEEEcCcEEEeEeccCCCcccccccccc
Q 024241 221 ICLGCKSPDTILSKENRLFFLRCEKCGSGRSVAPIKAG 258 (270)
Q Consensus 221 lC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V~~ik~g 258 (270)
.||.|+|.+ +.+=.|+ ||.-++|...-.|
T Consensus 540 ~CP~Cgs~~--~~~~~Rv-------~GYl~~v~~~n~g 568 (579)
T TIGR02487 540 KCPKCGSHD--IEVISRI-------TGYLGPVENWNDG 568 (579)
T ss_pred cCcCCCCcc--ceehhhh-------hhhhccccccccc
Confidence 699999987 4444565 8888887654433
No 257
>PRK05978 hypothetical protein; Provisional
Probab=20.77 E-value=44 Score=29.04 Aligned_cols=42 Identities=17% Similarity=0.241 Sum_probs=25.9
Q ss_pred HHHHHHHHhccceEeeCCCCCCcceEEEcCcEEEeEeccCCCccccc
Q 024241 207 NFEGILRRYVNEYVICLGCKSPDTILSKENRLFFLRCEKCGSGRSVA 253 (270)
Q Consensus 207 ~ie~~L~~YI~eYVlC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~V~ 253 (270)
-.+.+++-+ .-.||.|+.-. |.+.==-.--+|.+||..-...
T Consensus 24 ~~~~~~rGl---~grCP~CG~G~--LF~g~Lkv~~~C~~CG~~~~~~ 65 (148)
T PRK05978 24 VGRAMWRGF---RGRCPACGEGK--LFRAFLKPVDHCAACGEDFTHH 65 (148)
T ss_pred hHHHHHHHH---cCcCCCCCCCc--ccccccccCCCccccCCccccC
Confidence 445666666 56899998764 3321011245799999876543
No 258
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=20.63 E-value=54 Score=28.08 Aligned_cols=26 Identities=27% Similarity=0.590 Sum_probs=18.6
Q ss_pred eeCCCCCCcceEEEcCcEEEeEeccCCCccc
Q 024241 221 ICLGCKSPDTILSKENRLFFLRCEKCGSGRS 251 (270)
Q Consensus 221 lC~~C~sPDT~L~ke~rl~~l~C~aCGa~~~ 251 (270)
.||.|+.|=-. +++.+ .|-.||.+-.
T Consensus 30 hCp~Cg~PLF~--KdG~v---~CPvC~~~~~ 55 (131)
T COG1645 30 HCPKCGTPLFR--KDGEV---FCPVCGYREV 55 (131)
T ss_pred hCcccCCccee--eCCeE---ECCCCCceEE
Confidence 69999999533 55654 5999996433
No 259
>KOG3239 consensus Density-regulated protein related to translation initiation factor 1 (eIF-1/SUI1) [General function prediction only]
Probab=20.38 E-value=1.7e+02 Score=26.52 Aligned_cols=47 Identities=17% Similarity=0.348 Sum_probs=38.7
Q ss_pred HhCCChHHHHHHHHHhhcCceeecC----CceEEEEeecChHHHHHHHHHh
Q 024241 169 TMHRQPDHVMTFLLAELGTSGSLDG----QQRLVVKGRFAPKNFEGILRRY 215 (270)
Q Consensus 169 ~L~R~p~hv~kyl~~ELGt~gsid~----~~rlii~G~f~~k~ie~~L~~Y 215 (270)
...-+-....+||..-+.|..|+-+ .+.++|+|.+...-+.=+...|
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 4566778889999999999999976 6799999999888776666555
No 260
>PF04770 ZF-HD_dimer: ZF-HD protein dimerisation region; InterPro: IPR006456 The homeodomain (HD) is a 60-amino acid DNA-binding domain found in many transcription factors. HD-containing proteins are found in diverse organisms such as humans, Drosophila, nematode worms, and plants, where they play important roles in development. Zinc-finger-homeodomain (ZF- HD) subfamily proteins have only been identified in plants, and likely play plant specific roles. ZF-HD proteins are expressed predominantly or exclusively in floral tissue, indicating a likely regulatory role during floral development []. The ZF-HD class of homeodomain proteins may also be involved in the photosynthesis-related mesophyll-specific gene expression of phosphoenolpyruvate carboxylase in C4 species [] and in pathogen signaling and plant defense mechanisms []. These proteins share three domains of high sequence similarity: the homeodomain (II) located at the carboxy-terminus, and two other segments (Ia and Ib) located in the amino-terminal part. These N-terminal domains contain five conserved cysteine residues and at least three conserved histidine residues whose spacing ressembles zinc-binding domains involved in dimerization of transcription factors. Although the two domains contain at least eight potential zinc-binding amino-acids, the unique spacing of the conserved cysteine and histidine residues within domain Ib suggests that both domains form one rather than two zinc finger structures. The two conserved motifs Ia and Ib constitute a dimerization domain which is sufficient for the formation of homo- and heterodimers []. This entry represents the N-terminal Cysteine/Histidine-rich dimerization domain. The companion ZF-HD homeobox domain is described in IPR006455 from INTERPRO.
Probab=20.38 E-value=48 Score=24.86 Aligned_cols=17 Identities=29% Similarity=0.628 Sum_probs=13.9
Q ss_pred CcEEEeEeccCCCcccc
Q 024241 236 NRLFFLRCEKCGSGRSV 252 (270)
Q Consensus 236 ~rl~~l~C~aCGa~~~V 252 (270)
+..-.|+|.|||..|..
T Consensus 36 g~~~al~CaACgCHRnF 52 (60)
T PF04770_consen 36 GTPEALKCAACGCHRNF 52 (60)
T ss_pred CCcccceecccCcchhc
Confidence 45668999999998865
No 261
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=20.14 E-value=57 Score=32.97 Aligned_cols=46 Identities=22% Similarity=0.525 Sum_probs=34.3
Q ss_pred eecChHHHHHHHHHhccceE------eeCCCCCCcceEEEcCcEEEeEeccCCCc
Q 024241 201 GRFAPKNFEGILRRYVNEYV------ICLGCKSPDTILSKENRLFFLRCEKCGSG 249 (270)
Q Consensus 201 G~f~~k~ie~~L~~YI~eYV------lC~~C~sPDT~L~ke~rl~~l~C~aCGa~ 249 (270)
-|+-...|+.++.+|..+-+ .||+|+.+ +.|..+---++|..||.-
T Consensus 344 ~Ryg~rvve~~vn~~lsekwl~~N~krCP~C~v~---IEr~eGCnKM~C~~c~~~ 395 (445)
T KOG1814|consen 344 KRYGKRVVEELVNDFLSEKWLESNSKRCPKCKVV---IERSEGCNKMHCTKCGTY 395 (445)
T ss_pred HHhhHHHHHHHHHHHHHHHHHHhcCCCCCcccce---eecCCCccceeecccccc
Confidence 45555588888888887433 69999865 677666778899999875
Done!