Query psy4748
Match_columns 136
No_of_seqs 127 out of 743
Neff 6.0
Searched_HMMs 46136
Date Fri Aug 16 16:37:28 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4748.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4748hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2906|consensus 100.0 5.2E-34 1.1E-38 199.7 4.0 96 11-136 1-99 (105)
2 KOG2907|consensus 100.0 1.1E-33 2.4E-38 202.3 4.0 103 8-136 4-108 (116)
3 COG1594 RPB9 DNA-directed RNA 100.0 1.2E-30 2.6E-35 188.3 6.6 101 10-136 1-106 (113)
4 TIGR01384 TFS_arch transcripti 100.0 1.6E-29 3.4E-34 178.4 8.6 95 12-136 1-96 (104)
5 KOG2691|consensus 99.9 6.9E-28 1.5E-32 171.2 3.9 100 9-136 2-107 (113)
6 smart00440 ZnF_C2C2 C2C2 Zinc 99.8 1.3E-20 2.8E-25 113.2 4.2 34 103-136 1-34 (40)
7 PF01096 TFIIS_C: Transcriptio 99.8 1.8E-19 3.8E-24 107.6 4.4 34 103-136 1-34 (39)
8 PHA02998 RNA polymerase subuni 99.7 3.8E-17 8.1E-22 125.7 4.3 39 98-136 138-177 (195)
9 TIGR01385 TFSII transcription 99.4 1.7E-13 3.6E-18 113.3 3.9 37 100-136 256-292 (299)
10 PF02150 RNA_POL_M_15KD: RNA p 99.1 1.7E-11 3.7E-16 71.5 1.1 32 11-42 1-33 (35)
11 smart00661 RPOL9 RNA polymeras 98.5 7.2E-08 1.6E-12 59.6 3.2 31 12-42 1-33 (52)
12 KOG1105|consensus 98.2 1.1E-06 2.3E-11 72.8 3.2 40 97-136 249-289 (296)
13 PRK00432 30S ribosomal protein 97.8 1.2E-05 2.7E-10 50.2 2.1 32 7-40 16-48 (50)
14 PF14803 Nudix_N_2: Nudix N-te 97.2 0.00018 3.8E-09 41.7 1.5 28 12-39 1-32 (34)
15 COG1998 RPS31 Ribosomal protei 96.4 0.0021 4.6E-08 40.2 1.9 33 7-41 15-49 (51)
16 PF09297 zf-NADH-PPase: NADH p 96.4 0.0023 5E-08 36.0 1.9 29 11-39 3-31 (32)
17 PRK03564 formate dehydrogenase 96.1 0.016 3.4E-07 48.6 5.9 32 10-41 186-224 (309)
18 TIGR01562 FdhE formate dehydro 96.0 0.02 4.2E-07 47.9 6.0 32 10-41 183-222 (305)
19 PF04216 FdhE: Protein involve 95.9 0.0085 1.8E-07 49.0 3.4 30 12-41 173-209 (290)
20 PF12773 DZR: Double zinc ribb 95.2 0.0091 2E-07 36.3 1.1 33 8-41 9-41 (50)
21 PHA00626 hypothetical protein 95.0 0.021 4.5E-07 36.7 2.3 31 12-42 1-36 (59)
22 PF07754 DUF1610: Domain of un 94.8 0.028 6E-07 30.1 2.2 24 14-37 1-24 (24)
23 PF10571 UPF0547: Uncharacteri 94.6 0.018 3.9E-07 31.3 1.1 24 13-40 2-25 (26)
24 PRK00398 rpoP DNA-directed RNA 94.6 0.045 9.8E-07 33.0 3.0 32 12-43 4-35 (46)
25 PF13240 zinc_ribbon_2: zinc-r 94.5 0.017 3.6E-07 30.5 0.8 22 13-38 1-22 (23)
26 PF13248 zf-ribbon_3: zinc-rib 94.3 0.024 5.2E-07 30.5 1.2 24 11-38 2-25 (26)
27 cd00350 rubredoxin_like Rubred 94.2 0.027 5.8E-07 31.9 1.3 16 102-117 17-32 (33)
28 PF09855 DUF2082: Nucleic-acid 93.5 0.11 2.4E-06 34.0 3.4 15 101-115 35-49 (64)
29 PF08274 PhnA_Zn_Ribbon: PhnA 93.4 0.037 8.1E-07 31.1 0.9 27 13-40 4-30 (30)
30 PF08271 TF_Zn_Ribbon: TFIIB z 93.2 0.082 1.8E-06 31.4 2.3 30 12-41 1-31 (43)
31 TIGR00595 priA primosomal prot 93.2 0.1 2.2E-06 46.1 3.7 28 14-41 225-252 (505)
32 TIGR02098 MJ0042_CXXC MJ0042 f 92.8 0.079 1.7E-06 30.4 1.7 29 13-41 4-37 (38)
33 PF13719 zinc_ribbon_5: zinc-r 92.7 0.086 1.9E-06 30.6 1.8 28 13-40 4-36 (37)
34 PF00301 Rubredoxin: Rubredoxi 92.7 0.11 2.4E-06 32.0 2.4 14 29-42 1-14 (47)
35 cd00730 rubredoxin Rubredoxin; 92.6 0.064 1.4E-06 33.4 1.2 15 102-116 34-48 (50)
36 COG2816 NPY1 NTP pyrophosphohy 92.6 0.075 1.6E-06 44.0 2.0 34 7-40 107-140 (279)
37 PRK00241 nudC NADH pyrophospha 92.4 0.092 2E-06 42.6 2.3 35 7-41 95-129 (256)
38 COG1997 RPL43A Ribosomal prote 92.1 0.12 2.5E-06 36.0 2.1 34 10-43 34-67 (89)
39 COG1198 PriA Primosomal protei 92.0 0.17 3.8E-06 46.8 3.8 16 103-118 476-491 (730)
40 cd00729 rubredoxin_SM Rubredox 92.0 0.11 2.4E-06 29.7 1.6 14 103-116 19-32 (34)
41 PF01396 zf-C4_Topoisom: Topoi 92.0 0.15 3.3E-06 29.9 2.3 31 12-42 2-37 (39)
42 PF07282 OrfB_Zn_ribbon: Putat 91.9 0.12 2.6E-06 33.2 2.0 33 10-42 27-59 (69)
43 COG2888 Predicted Zn-ribbon RN 91.9 0.1 2.2E-06 33.8 1.6 25 12-36 10-34 (61)
44 TIGR01053 LSD1 zinc finger dom 91.8 0.17 3.8E-06 28.5 2.3 27 13-39 3-29 (31)
45 PRK14973 DNA topoisomerase I; 91.6 0.26 5.7E-06 46.8 4.6 29 102-136 635-663 (936)
46 PF11781 RRN7: RNA polymerase 91.3 0.13 2.9E-06 29.9 1.5 29 10-39 7-35 (36)
47 COG1592 Rubrerythrin [Energy p 91.3 0.086 1.9E-06 40.6 0.9 15 27-41 132-146 (166)
48 PRK04023 DNA polymerase II lar 91.3 0.12 2.7E-06 49.3 2.1 24 9-38 624-647 (1121)
49 TIGR01206 lysW lysine biosynth 90.9 0.24 5.3E-06 31.4 2.6 29 13-41 4-34 (54)
50 PRK14559 putative protein seri 90.9 0.12 2.7E-06 47.1 1.6 13 103-115 42-54 (645)
51 PHA00626 hypothetical protein 90.6 0.23 4.9E-06 32.0 2.2 28 104-136 2-29 (59)
52 COG1773 Rubredoxin [Energy pro 90.6 0.26 5.7E-06 31.4 2.5 17 102-118 36-52 (55)
53 PF12760 Zn_Tnp_IS1595: Transp 90.5 0.2 4.4E-06 30.2 1.9 25 103-136 19-43 (46)
54 PRK05580 primosome assembly pr 90.5 0.3 6.4E-06 44.7 3.7 28 14-41 393-420 (679)
55 PRK14873 primosome assembly pr 90.4 0.29 6.4E-06 44.8 3.6 25 14-38 395-419 (665)
56 PRK14890 putative Zn-ribbon RN 90.2 0.21 4.5E-06 32.3 1.8 25 13-37 9-33 (59)
57 PRK14714 DNA polymerase II lar 90.2 0.22 4.7E-06 48.7 2.6 14 103-116 710-723 (1337)
58 COG2835 Uncharacterized conser 89.6 0.4 8.7E-06 31.1 2.7 44 8-51 5-48 (60)
59 PRK12286 rpmF 50S ribosomal pr 89.6 0.27 5.9E-06 31.4 2.0 28 9-41 25-52 (57)
60 COG1645 Uncharacterized Zn-fin 89.1 0.32 6.9E-06 36.2 2.3 28 12-41 29-56 (131)
61 PF08772 NOB1_Zn_bind: Nin one 88.6 0.17 3.8E-06 33.9 0.6 14 7-20 20-33 (73)
62 PRK10220 hypothetical protein; 88.4 0.49 1.1E-05 34.2 2.8 34 9-43 1-34 (111)
63 TIGR00686 phnA alkylphosphonat 88.2 0.34 7.3E-06 34.9 1.9 31 11-42 2-32 (109)
64 PF01780 Ribosomal_L37ae: Ribo 88.1 0.22 4.8E-06 34.8 0.8 31 11-41 35-65 (90)
65 PRK07220 DNA topoisomerase I; 88.0 1.1 2.3E-05 41.6 5.5 28 13-40 591-624 (740)
66 smart00647 IBR In Between Ring 87.6 0.68 1.5E-05 28.6 2.8 32 10-41 17-52 (64)
67 PF06943 zf-LSD1: LSD1 zinc fi 87.6 0.54 1.2E-05 25.3 2.0 25 14-38 1-25 (25)
68 COG2051 RPS27A Ribosomal prote 87.5 0.43 9.3E-06 31.6 1.9 23 99-121 16-38 (67)
69 PF01485 IBR: IBR domain; Int 87.4 0.31 6.7E-06 30.1 1.2 32 10-41 17-52 (64)
70 PF08792 A2L_zn_ribbon: A2L zi 87.2 0.65 1.4E-05 26.4 2.3 31 10-40 2-32 (33)
71 PF13717 zinc_ribbon_4: zinc-r 86.9 0.48 1E-05 27.3 1.7 27 13-39 4-35 (36)
72 PRK05452 anaerobic nitric oxid 86.8 0.55 1.2E-05 41.2 2.8 22 21-42 417-438 (479)
73 smart00659 RPOLCX RNA polymera 86.8 0.57 1.2E-05 28.3 2.0 28 13-41 4-31 (44)
74 PRK11827 hypothetical protein; 86.6 0.86 1.9E-05 29.5 2.9 39 10-48 7-45 (60)
75 PF09082 DUF1922: Domain of un 86.1 0.46 9.9E-06 31.6 1.4 29 13-43 5-33 (68)
76 PF13453 zf-TFIIB: Transcripti 85.8 1.1 2.4E-05 26.2 2.9 25 104-136 1-25 (41)
77 TIGR01031 rpmF_bact ribosomal 85.6 0.57 1.2E-05 29.6 1.7 27 9-40 24-50 (55)
78 PF03119 DNA_ligase_ZBD: NAD-d 85.3 0.51 1.1E-05 25.9 1.2 21 13-33 1-21 (28)
79 COG1996 RPC10 DNA-directed RNA 85.3 0.55 1.2E-05 29.3 1.4 31 12-42 7-37 (49)
80 TIGR00515 accD acetyl-CoA carb 84.7 0.23 4.9E-06 41.2 -0.6 31 11-41 26-57 (285)
81 PF04606 Ogr_Delta: Ogr/Delta- 84.4 0.6 1.3E-05 28.3 1.3 28 14-41 2-39 (47)
82 PF06677 Auto_anti-p27: Sjogre 84.4 0.79 1.7E-05 27.4 1.8 24 12-36 18-41 (41)
83 COG1499 NMD3 NMD protein affec 84.4 0.86 1.9E-05 39.0 2.7 23 102-124 129-153 (355)
84 PF03811 Zn_Tnp_IS1: InsA N-te 84.2 1.4 3E-05 25.6 2.7 34 99-136 2-35 (36)
85 smart00834 CxxC_CXXC_SSSS Puta 84.2 0.56 1.2E-05 26.9 1.1 25 13-37 7-34 (41)
86 COG2023 RPR2 RNase P subunit R 84.0 0.64 1.4E-05 33.3 1.5 30 12-41 57-94 (105)
87 CHL00174 accD acetyl-CoA carbo 83.6 0.25 5.5E-06 41.2 -0.8 33 10-42 37-70 (296)
88 PF03604 DNA_RNApol_7kD: DNA d 83.3 0.45 9.8E-06 27.0 0.4 25 14-39 3-27 (32)
89 KOG3507|consensus 83.3 0.7 1.5E-05 30.0 1.3 28 11-39 20-47 (62)
90 PF07295 DUF1451: Protein of u 83.1 1.1 2.5E-05 33.6 2.6 15 27-41 110-124 (146)
91 PRK05654 acetyl-CoA carboxylas 82.8 0.3 6.6E-06 40.5 -0.6 32 11-42 27-59 (292)
92 TIGR03655 anti_R_Lar restricti 82.1 2.4 5.1E-05 26.2 3.4 31 103-136 2-32 (53)
93 TIGR00280 L37a ribosomal prote 81.7 0.9 1.9E-05 31.8 1.5 33 10-42 34-66 (91)
94 PF10122 Mu-like_Com: Mu-like 81.7 0.65 1.4E-05 29.2 0.7 32 12-43 5-38 (51)
95 KOG3084|consensus 81.5 0.91 2E-05 38.5 1.8 31 11-41 150-185 (345)
96 PRK00423 tfb transcription ini 81.5 1.1 2.4E-05 37.1 2.3 31 10-40 10-41 (310)
97 COG0777 AccD Acetyl-CoA carbox 81.5 0.47 1E-05 39.5 0.1 33 10-42 27-60 (294)
98 PF14446 Prok-RING_1: Prokaryo 81.4 1.3 2.8E-05 28.1 2.1 29 12-42 6-34 (54)
99 PF09526 DUF2387: Probable met 81.4 1.2 2.5E-05 29.7 1.9 31 13-43 10-44 (71)
100 PF12760 Zn_Tnp_IS1595: Transp 81.4 2 4.3E-05 25.8 2.8 27 12-38 19-46 (46)
101 PRK11032 hypothetical protein; 81.4 1.4 3E-05 33.8 2.6 14 28-41 123-136 (160)
102 PRK14892 putative transcriptio 80.6 1.3 2.7E-05 31.4 2.0 33 10-42 20-55 (99)
103 PF09538 FYDLN_acid: Protein o 80.6 1.3 2.8E-05 31.8 2.0 34 8-42 6-39 (108)
104 COG3478 Predicted nucleic-acid 80.5 1.1 2.3E-05 29.6 1.5 27 103-131 5-31 (68)
105 PTZ00255 60S ribosomal protein 80.2 1.2 2.7E-05 31.0 1.8 32 10-41 35-66 (90)
106 PRK00420 hypothetical protein; 80.0 1.7 3.7E-05 31.4 2.6 30 12-42 24-53 (112)
107 PRK09678 DNA-binding transcrip 79.0 1.8 4E-05 28.9 2.2 32 11-42 1-42 (72)
108 PRK07219 DNA topoisomerase I; 78.8 4.9 0.00011 37.7 5.8 11 101-111 732-742 (822)
109 PF04032 Rpr2: RNAse P Rpr2/Rp 78.7 0.98 2.1E-05 29.9 0.9 28 10-37 45-85 (85)
110 PRK14890 putative Zn-ribbon RN 78.5 2.6 5.5E-05 27.3 2.7 28 11-38 25-57 (59)
111 PF01783 Ribosomal_L32p: Ribos 78.5 0.58 1.3E-05 29.5 -0.3 27 10-41 25-51 (56)
112 PF14353 CpXC: CpXC protein 78.2 1.4 3.1E-05 31.5 1.7 13 30-42 2-14 (128)
113 COG1096 Predicted RNA-binding 78.1 1.8 3.8E-05 34.1 2.2 29 11-41 149-177 (188)
114 PF02591 DUF164: Putative zinc 77.7 0.99 2.1E-05 28.1 0.6 12 10-21 45-56 (56)
115 PF13408 Zn_ribbon_recom: Reco 77.6 1.4 3.1E-05 26.7 1.3 29 9-37 3-34 (58)
116 PF05876 Terminase_GpA: Phage 77.4 2 4.4E-05 38.4 2.8 36 101-136 199-235 (557)
117 PRK03976 rpl37ae 50S ribosomal 77.2 1.5 3.2E-05 30.6 1.4 32 10-41 35-66 (90)
118 PF01599 Ribosomal_S27: Riboso 77.0 1.6 3.4E-05 27.0 1.3 33 6-38 13-47 (47)
119 PRK06319 DNA topoisomerase I/S 76.9 3.9 8.4E-05 38.7 4.5 30 12-41 593-628 (860)
120 TIGR02443 conserved hypothetic 76.9 2.2 4.9E-05 27.5 2.1 31 13-43 11-45 (59)
121 PF01667 Ribosomal_S27e: Ribos 76.5 0.75 1.6E-05 29.3 -0.2 20 101-120 6-25 (55)
122 PF14354 Lar_restr_allev: Rest 76.2 3.9 8.5E-05 25.4 3.1 32 103-136 4-35 (61)
123 PF11792 Baculo_LEF5_C: Baculo 75.8 0.13 2.7E-06 31.3 -3.7 28 108-136 13-40 (43)
124 COG1571 Predicted DNA-binding 75.4 1.5 3.2E-05 38.4 1.3 30 12-42 351-380 (421)
125 PRK00415 rps27e 30S ribosomal 75.3 1.9 4.1E-05 27.8 1.5 21 100-120 9-29 (59)
126 TIGR02605 CxxC_CxxC_SSSS putat 75.1 1.5 3.3E-05 26.5 1.0 26 13-38 7-35 (52)
127 PF04810 zf-Sec23_Sec24: Sec23 74.9 3.5 7.6E-05 24.1 2.5 32 11-42 2-37 (40)
128 COG0675 Transposase and inacti 74.4 2.2 4.7E-05 33.9 2.0 31 8-43 306-336 (364)
129 COG2051 RPS27A Ribosomal prote 73.8 2.3 5E-05 28.1 1.6 30 13-42 21-51 (67)
130 COG2888 Predicted Zn-ribbon RN 73.8 3.3 7.1E-05 26.9 2.3 27 12-38 28-59 (61)
131 PHA02942 putative transposase; 73.7 2.7 5.8E-05 36.0 2.5 32 10-42 324-355 (383)
132 PRK12495 hypothetical protein; 73.3 2.7 5.9E-05 33.9 2.2 32 8-41 39-70 (226)
133 COG4640 Predicted membrane pro 72.4 2 4.2E-05 37.6 1.3 26 11-40 1-26 (465)
134 PF12172 DUF35_N: Rubredoxin-l 72.0 2 4.2E-05 24.5 0.9 23 11-37 11-33 (37)
135 PF01155 HypA: Hydrogenase exp 71.6 3.4 7.5E-05 29.4 2.3 15 27-41 68-82 (113)
136 PF00628 PHD: PHD-finger; Int 71.0 5.3 0.00012 23.7 2.7 26 13-41 1-26 (51)
137 PF09862 DUF2089: Protein of u 70.5 3.4 7.4E-05 29.9 2.0 24 14-41 1-24 (113)
138 PF06827 zf-FPG_IleRS: Zinc fi 70.4 2.4 5.1E-05 23.0 0.9 25 13-37 3-29 (30)
139 COG1779 C4-type Zn-finger prot 69.8 1.9 4.2E-05 34.1 0.7 30 11-40 14-54 (201)
140 PRK07219 DNA topoisomerase I; 68.3 12 0.00025 35.2 5.6 32 11-42 602-639 (822)
141 PF06044 DRP: Dam-replacing fa 66.7 3.7 8E-05 33.6 1.7 33 10-42 30-66 (254)
142 PF12677 DUF3797: Domain of un 66.7 2.9 6.3E-05 26.0 0.8 12 102-113 13-24 (49)
143 COG0333 RpmF Ribosomal protein 66.6 4.4 9.5E-05 26.0 1.7 27 10-41 26-52 (57)
144 PF06750 DiS_P_DiS: Bacterial 66.3 3.6 7.7E-05 28.4 1.4 36 6-41 28-70 (92)
145 TIGR00155 pqiA_fam integral me 65.9 5.1 0.00011 34.6 2.5 35 7-41 9-45 (403)
146 smart00531 TFIIE Transcription 65.7 2.4 5.2E-05 31.4 0.4 33 10-42 98-136 (147)
147 PRK09521 exosome complex RNA-b 65.0 6 0.00013 30.3 2.5 31 11-42 149-179 (189)
148 PRK04136 rpl40e 50S ribosomal 64.9 4.6 9.9E-05 25.1 1.5 26 9-38 12-37 (48)
149 PLN00209 ribosomal protein S27 64.9 4.3 9.4E-05 28.1 1.5 22 99-120 33-54 (86)
150 PTZ00083 40S ribosomal protein 63.6 4.8 0.0001 27.8 1.6 22 99-120 32-53 (85)
151 PRK00564 hypA hydrogenase nick 63.3 3.3 7.2E-05 29.7 0.8 28 11-39 71-98 (117)
152 TIGR02300 FYDLN_acid conserved 62.0 5.8 0.00013 29.4 1.8 34 8-42 6-39 (129)
153 PF01927 Mut7-C: Mut7-C RNAse 61.6 5.9 0.00013 29.3 1.9 31 11-41 91-136 (147)
154 PRK00222 methionine sulfoxide 61.6 9.5 0.00021 28.7 3.0 20 97-116 87-106 (142)
155 PRK01110 rpmF 50S ribosomal pr 61.4 4.9 0.00011 25.8 1.2 26 10-41 26-51 (60)
156 COG4332 Uncharacterized protei 61.3 8.5 0.00018 30.4 2.7 40 97-136 12-55 (203)
157 PF13005 zf-IS66: zinc-finger 61.2 9 0.00019 22.5 2.3 14 11-24 2-15 (47)
158 PF03966 Trm112p: Trm112p-like 60.9 8.3 0.00018 24.8 2.3 37 7-43 3-67 (68)
159 KOG3799|consensus 60.1 3.2 6.8E-05 31.4 0.2 33 9-41 87-119 (169)
160 COG1326 Uncharacterized archae 59.1 5.9 0.00013 31.4 1.5 29 12-41 7-42 (201)
161 TIGR00100 hypA hydrogenase nic 58.9 4.6 0.0001 28.8 0.9 27 11-39 70-96 (115)
162 PRK15103 paraquat-inducible me 58.9 7.9 0.00017 33.6 2.5 32 10-41 9-42 (419)
163 COG1656 Uncharacterized conser 58.8 5.5 0.00012 30.7 1.3 31 11-41 97-142 (165)
164 PF11672 DUF3268: Protein of u 58.7 9.9 0.00021 27.0 2.5 33 103-136 3-37 (102)
165 PF00130 C1_1: Phorbol esters/ 58.0 11 0.00024 22.5 2.4 32 9-41 9-40 (53)
166 PF09723 Zn-ribbon_8: Zinc rib 57.9 4.8 0.0001 23.7 0.7 25 13-37 7-34 (42)
167 PRK12380 hydrogenase nickel in 57.5 4.9 0.00011 28.6 0.8 26 11-38 70-95 (113)
168 PF08882 Acetone_carb_G: Aceto 57.5 4.2 9.2E-05 29.4 0.5 13 13-25 76-88 (112)
169 TIGR00357 methionine-R-sulfoxi 57.2 14 0.00031 27.5 3.2 19 98-116 85-103 (134)
170 COG4888 Uncharacterized Zn rib 57.0 8.3 0.00018 27.5 1.9 31 13-43 24-60 (104)
171 COG1779 C4-type Zn-finger prot 56.8 15 0.00033 29.1 3.5 35 101-136 13-49 (201)
172 TIGR00340 zpr1_rel ZPR1-relate 56.6 5.8 0.00013 30.3 1.1 28 14-41 1-40 (163)
173 COG1545 Predicted nucleic-acid 56.3 6.1 0.00013 29.2 1.2 23 13-39 31-53 (140)
174 COG2176 PolC DNA polymerase II 56.1 9.3 0.0002 37.8 2.6 25 19-43 901-928 (1444)
175 COG2824 PhnA Uncharacterized Z 54.9 10 0.00022 27.4 2.1 31 10-41 2-32 (112)
176 COG1405 SUA7 Transcription ini 54.7 8.6 0.00019 31.9 1.9 30 12-41 2-32 (285)
177 PF14369 zf-RING_3: zinc-finge 54.5 8.7 0.00019 21.9 1.4 27 11-37 2-29 (35)
178 PF04828 GFA: Glutathione-depe 54.4 3.8 8.3E-05 26.6 -0.2 15 10-24 47-61 (92)
179 PRK03681 hypA hydrogenase nick 54.4 6.2 0.00013 28.2 0.9 27 11-38 70-96 (114)
180 KOG1812|consensus 53.4 7.4 0.00016 33.5 1.4 30 10-40 305-334 (384)
181 PRK06266 transcription initiat 53.1 3.8 8.3E-05 31.6 -0.4 31 11-41 117-148 (178)
182 TIGR00373 conserved hypothetic 52.4 3.9 8.4E-05 30.8 -0.4 32 10-41 108-140 (158)
183 PRK14559 putative protein seri 52.1 8.2 0.00018 35.5 1.5 25 10-40 14-38 (645)
184 PRK00464 nrdR transcriptional 52.1 12 0.00025 28.4 2.1 31 13-43 2-42 (154)
185 cd00029 C1 Protein kinase C co 52.1 11 0.00023 21.9 1.6 31 10-41 10-40 (50)
186 PF10080 DUF2318: Predicted me 51.6 10 0.00022 26.9 1.6 39 3-42 27-65 (102)
187 PF14205 Cys_rich_KTR: Cystein 51.6 8.8 0.00019 24.4 1.1 13 103-115 29-41 (55)
188 PF07191 zinc-ribbons_6: zinc- 51.5 11 0.00023 25.2 1.6 27 13-41 3-29 (70)
189 PF09151 DUF1936: Domain of un 51.0 32 0.0007 19.6 3.3 27 103-134 2-28 (36)
190 COG3791 Uncharacterized conser 50.1 7 0.00015 28.5 0.6 17 10-26 68-84 (133)
191 smart00109 C1 Protein kinase C 49.2 12 0.00026 21.4 1.5 31 9-41 9-39 (49)
192 PF11331 DUF3133: Protein of u 48.3 9.2 0.0002 23.4 0.8 32 10-41 5-43 (46)
193 smart00709 Zpr1 Duplicated dom 48.0 9.2 0.0002 29.1 1.0 29 13-41 2-41 (160)
194 PF10058 DUF2296: Predicted in 47.5 15 0.00032 23.0 1.7 29 102-136 22-50 (54)
195 TIGR00310 ZPR1_znf ZPR1 zinc f 46.6 12 0.00026 29.3 1.5 28 14-41 3-42 (192)
196 PF06044 DRP: Dam-replacing fa 46.3 12 0.00026 30.7 1.4 29 102-136 31-59 (254)
197 COG4416 Com Mu-like prophage p 46.1 5.6 0.00012 25.5 -0.4 30 12-41 5-36 (60)
198 KOG0696|consensus 46.1 4.3 9.3E-05 36.4 -1.2 29 9-38 119-147 (683)
199 COG0229 Conserved domain frequ 45.5 22 0.00047 26.7 2.6 24 16-40 30-53 (140)
200 KOG0402|consensus 45.4 8.9 0.00019 26.6 0.5 32 10-41 35-66 (92)
201 PF05191 ADK_lid: Adenylate ki 45.4 5.6 0.00012 22.9 -0.4 26 12-37 2-29 (36)
202 PRK03954 ribonuclease P protei 44.8 15 0.00033 26.8 1.7 31 11-41 64-105 (121)
203 COG4647 AcxC Acetone carboxyla 44.6 8.9 0.00019 28.9 0.4 14 13-26 122-135 (165)
204 PF05180 zf-DNL: DNL zinc fing 44.6 12 0.00026 24.6 1.0 31 103-136 5-35 (66)
205 TIGR02820 formald_GSH S-(hydro 44.1 10 0.00022 29.6 0.7 15 10-24 88-102 (182)
206 PF02132 RecR: RecR protein; 44.0 7.5 0.00016 22.7 -0.0 13 10-22 16-28 (41)
207 PF01873 eIF-5_eIF-2B: Domain 43.4 35 0.00075 24.9 3.4 27 103-136 94-120 (125)
208 PF03367 zf-ZPR1: ZPR1 zinc-fi 43.4 10 0.00022 28.7 0.7 28 13-40 3-41 (161)
209 PRK05417 glutathione-dependent 43.1 11 0.00023 29.7 0.7 14 11-24 93-106 (191)
210 PF10005 DUF2248: Uncharacteri 42.7 15 0.00032 31.5 1.5 25 14-42 2-26 (343)
211 PF08646 Rep_fac-A_C: Replicat 42.2 17 0.00038 26.3 1.7 27 13-40 20-48 (146)
212 PRK11032 hypothetical protein; 42.0 14 0.0003 28.3 1.2 34 8-41 121-154 (160)
213 PRK03824 hypA hydrogenase nick 41.4 13 0.00028 27.3 0.9 29 10-38 69-116 (135)
214 PRK08579 anaerobic ribonucleos 41.4 15 0.00033 33.7 1.5 27 7-37 564-590 (625)
215 KOG3362|consensus 40.6 10 0.00022 28.8 0.3 30 5-41 112-141 (156)
216 PF05129 Elf1: Transcription e 40.0 52 0.0011 22.1 3.7 17 102-118 22-38 (81)
217 PRK08402 replication factor A; 39.8 19 0.0004 30.8 1.7 30 11-40 212-241 (355)
218 COG3809 Uncharacterized protei 39.6 23 0.00051 24.3 1.9 31 11-41 1-33 (88)
219 PF06397 Desulfoferrod_N: Desu 39.5 11 0.00024 21.9 0.2 22 11-32 6-28 (36)
220 COG3364 Zn-ribbon containing p 38.8 16 0.00035 26.3 1.0 21 103-123 21-41 (112)
221 KOG2463|consensus 38.6 13 0.00028 31.9 0.6 12 9-20 255-266 (376)
222 PRK05508 methionine sulfoxide 38.2 43 0.00092 24.5 3.2 19 98-116 75-93 (119)
223 TIGR00155 pqiA_fam integral me 38.1 18 0.00039 31.3 1.4 29 10-41 214-242 (403)
224 TIGR00311 aIF-2beta translatio 37.8 42 0.0009 24.8 3.1 27 103-136 98-124 (133)
225 PF14690 zf-ISL3: zinc-finger 37.8 15 0.00032 21.4 0.6 24 103-126 3-29 (47)
226 smart00532 LIGANc Ligase N fam 37.8 18 0.0004 31.7 1.4 30 10-39 398-429 (441)
227 PRK09710 lar restriction allev 37.5 52 0.0011 21.6 3.2 27 103-136 7-33 (64)
228 PRK03988 translation initiatio 37.2 44 0.00096 24.8 3.2 27 103-136 103-129 (138)
229 smart00778 Prim_Zn_Ribbon Zinc 36.8 32 0.00068 20.0 1.9 25 13-37 5-33 (37)
230 cd00674 LysRS_core_class_I cat 36.5 36 0.00078 29.0 2.9 30 101-134 168-197 (353)
231 PF08273 Prim_Zn_Ribbon: Zinc- 35.9 26 0.00056 20.7 1.4 24 14-37 6-34 (40)
232 cd04476 RPA1_DBD_C RPA1_DBD_C: 35.7 27 0.00059 25.8 1.9 27 12-39 35-61 (166)
233 PF08063 PADR1: PADR1 (NUC008) 35.5 18 0.00039 22.7 0.8 16 102-117 14-29 (55)
234 PF01641 SelR: SelR domain; I 35.5 29 0.00063 25.5 1.9 21 97-117 81-101 (124)
235 PRK14810 formamidopyrimidine-D 35.4 34 0.00074 27.8 2.6 27 102-136 244-270 (272)
236 PF06839 zf-GRF: GRF zinc fing 35.3 68 0.0015 18.8 3.3 14 122-135 17-30 (45)
237 KOG1842|consensus 34.9 9.7 0.00021 33.9 -0.7 29 9-39 178-206 (505)
238 TIGR03670 rpoB_arch DNA-direct 34.4 22 0.00049 32.4 1.5 30 10-39 537-566 (599)
239 PRK07218 replication factor A; 33.2 21 0.00046 31.2 1.1 25 11-41 297-321 (423)
240 PRK04023 DNA polymerase II lar 32.7 23 0.0005 34.5 1.3 13 30-42 664-676 (1121)
241 TIGR03826 YvyF flagellar opero 32.5 14 0.00031 27.5 -0.1 29 9-40 1-29 (137)
242 PF14311 DUF4379: Domain of un 32.4 19 0.00042 22.0 0.5 11 100-110 26-36 (55)
243 PF05876 Terminase_GpA: Phage 32.2 34 0.00073 30.8 2.2 30 12-41 201-241 (557)
244 COG2995 PqiA Uncharacterized p 31.3 39 0.00084 29.7 2.3 37 6-42 13-51 (418)
245 COG1552 RPL40A Ribosomal prote 31.2 12 0.00026 23.4 -0.6 26 12-41 15-40 (50)
246 PRK12336 translation initiatio 31.0 60 0.0013 25.4 3.2 27 103-136 99-125 (201)
247 PRK12366 replication factor A; 30.8 30 0.00065 31.7 1.7 26 12-39 533-558 (637)
248 COG3877 Uncharacterized protei 30.4 34 0.00073 24.9 1.5 26 11-40 6-31 (122)
249 PF01907 Ribosomal_L37e: Ribos 29.7 33 0.00072 21.8 1.2 29 10-41 14-42 (55)
250 PRK07225 DNA-directed RNA poly 29.3 34 0.00073 31.4 1.7 31 10-40 543-573 (605)
251 COG2260 Predicted Zn-ribbon RN 29.1 26 0.00057 22.6 0.7 14 100-113 15-28 (59)
252 PF01921 tRNA-synt_1f: tRNA sy 29.1 40 0.00086 29.0 2.0 31 101-136 173-205 (360)
253 TIGR01405 polC_Gram_pos DNA po 29.0 33 0.00072 33.9 1.7 15 28-42 682-696 (1213)
254 PRK00448 polC DNA polymerase I 28.7 34 0.00074 34.5 1.7 15 28-42 907-921 (1437)
255 PF13824 zf-Mss51: Zinc-finger 28.7 37 0.0008 21.6 1.3 26 13-41 1-26 (55)
256 PRK04179 rpl37e 50S ribosomal 28.6 30 0.00066 22.5 1.0 26 10-38 16-41 (62)
257 PF04194 PDCD2_C: Programmed c 28.6 56 0.0012 24.6 2.6 33 103-135 98-143 (164)
258 PF02012 BNR: BNR/Asp-box repe 28.3 24 0.00052 15.8 0.3 8 121-128 2-9 (12)
259 PRK05978 hypothetical protein; 27.9 28 0.0006 26.3 0.8 14 101-114 32-45 (148)
260 PRK00762 hypA hydrogenase nick 27.9 29 0.00063 25.1 0.9 26 11-37 70-100 (124)
261 PF00684 DnaJ_CXXCXGXG: DnaJ c 27.6 1.4E+02 0.0031 18.7 4.1 17 103-119 16-32 (66)
262 PRK14811 formamidopyrimidine-D 27.3 57 0.0012 26.5 2.6 27 102-136 235-261 (269)
263 smart00653 eIF2B_5 domain pres 27.2 86 0.0019 22.3 3.2 27 103-136 81-107 (110)
264 PRK08271 anaerobic ribonucleos 27.2 38 0.00083 31.1 1.7 27 7-37 562-588 (623)
265 PRK14018 trifunctional thiored 27.2 65 0.0014 29.0 3.1 19 97-115 462-481 (521)
266 smart00249 PHD PHD zinc finger 27.2 79 0.0017 17.3 2.5 26 13-41 1-26 (47)
267 PF01412 ArfGap: Putative GTPa 26.4 29 0.00062 24.5 0.6 27 102-136 13-39 (116)
268 PRK14714 DNA polymerase II lar 26.2 39 0.00084 33.8 1.6 23 13-40 681-703 (1337)
269 TIGR00467 lysS_arch lysyl-tRNA 26.2 62 0.0013 29.0 2.8 28 101-133 167-194 (515)
270 COG4311 SoxD Sarcosine oxidase 25.8 31 0.00067 24.4 0.7 11 9-19 1-11 (97)
271 PRK10445 endonuclease VIII; Pr 25.7 63 0.0014 26.1 2.5 27 102-136 235-261 (263)
272 PRK13945 formamidopyrimidine-D 25.1 67 0.0014 26.2 2.6 27 102-136 254-280 (282)
273 PF06353 DUF1062: Protein of u 25.1 43 0.00094 25.0 1.4 15 27-41 11-25 (142)
274 PF13894 zf-C2H2_4: C2H2-type 24.9 45 0.00097 15.7 1.0 12 30-41 1-12 (24)
275 PF14319 Zn_Tnp_IS91: Transpos 23.5 55 0.0012 23.2 1.6 34 7-41 38-72 (111)
276 KOG3002|consensus 23.2 42 0.00092 28.1 1.1 31 6-36 43-76 (299)
277 PRK08173 DNA topoisomerase III 23.0 56 0.0012 31.1 2.0 26 12-39 625-650 (862)
278 PRK13264 3-hydroxyanthranilate 23.0 28 0.00062 27.1 0.1 32 11-42 120-170 (177)
279 COG4481 Uncharacterized protei 22.9 43 0.00094 21.5 0.9 18 96-113 28-45 (60)
280 KOG0006|consensus 22.6 59 0.0013 28.1 1.8 32 10-41 314-348 (446)
281 KOG4537|consensus 22.5 23 0.00049 27.4 -0.6 27 12-39 41-67 (178)
282 PF15616 TerY-C: TerY-C metal 22.4 63 0.0014 23.9 1.8 29 12-41 78-117 (131)
283 TIGR01057 topA_arch DNA topois 22.4 60 0.0013 29.5 2.0 25 103-135 590-614 (618)
284 COG3529 Predicted nucleic-acid 22.4 25 0.00054 23.0 -0.3 11 102-112 32-42 (66)
285 COG1675 TFA1 Transcription ini 22.1 36 0.00077 26.4 0.4 14 13-26 134-147 (176)
286 PF05495 zf-CHY: CHY zinc fing 22.1 55 0.0012 21.3 1.3 26 11-36 41-68 (71)
287 KOG2703|consensus 22.0 66 0.0014 28.4 2.1 29 102-133 68-96 (460)
288 TIGR00577 fpg formamidopyrimid 22.0 83 0.0018 25.5 2.6 27 102-136 245-271 (272)
289 PF07649 C1_3: C1-like domain; 21.9 66 0.0014 17.1 1.4 25 13-40 2-26 (30)
290 TIGR00375 conserved hypothetic 21.8 34 0.00073 29.5 0.3 28 11-39 240-268 (374)
291 PF05605 zf-Di19: Drought indu 21.7 38 0.00082 20.6 0.4 27 12-38 3-40 (54)
292 COG3677 Transposase and inacti 21.3 60 0.0013 23.7 1.5 34 10-43 29-67 (129)
293 PF09845 DUF2072: Zn-ribbon co 21.2 35 0.00075 25.4 0.2 27 13-39 3-29 (131)
294 KOG2462|consensus 21.0 59 0.0013 27.1 1.5 32 10-41 129-173 (279)
295 PRK01103 formamidopyrimidine/5 20.9 99 0.0021 25.0 2.8 27 102-136 245-271 (274)
296 PHA02325 hypothetical protein 20.8 79 0.0017 20.9 1.8 22 103-124 4-28 (72)
297 PF14206 Cys_rich_CPCC: Cystei 20.7 79 0.0017 21.3 1.9 29 13-41 3-32 (78)
298 PF04438 zf-HIT: HIT zinc fing 20.7 57 0.0012 17.9 1.0 21 12-39 3-23 (30)
299 PF14255 Cys_rich_CPXG: Cystei 20.4 1.4E+02 0.0031 18.5 2.9 11 103-113 25-35 (52)
300 PF15135 UPF0515: Uncharacteri 20.3 47 0.001 27.5 0.8 22 100-121 153-174 (278)
301 smart00714 LITAF Possible memb 20.1 51 0.0011 20.9 0.8 12 10-21 51-62 (67)
No 1
>KOG2906|consensus
Probab=100.00 E-value=5.2e-34 Score=199.68 Aligned_cols=96 Identities=24% Similarity=0.445 Sum_probs=81.1
Q ss_pred ccccccCCCccccCCCC--CeEEcCCCCCceecCCCCCCcCCCchhhhhcccccchhhHHHHhhheeeEeEeecceeec-
Q psy4748 11 SEFCSKCGTILPLFDFK--GDVKCYVCKTSYGTQEQQPLLLGPDILFLKRFKGHFNLFLAVFEEIKAEYTIHFNTVEKE- 87 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~~--~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~e~~- 87 (136)
|.|||.|||||...++. ..+.|++|+|..++.. +|..++.+..++.+
T Consensus 1 m~FCP~Cgn~Live~g~~~~rf~C~tCpY~~~I~~------------------------------ei~~r~~~~~Kevd~ 50 (105)
T KOG2906|consen 1 MLFCPTCGNMLIVESGESCNRFSCRTCPYVFPISR------------------------------EISSRKYPKLKEVDD 50 (105)
T ss_pred CcccCCCCCEEEEecCCeEeeEEcCCCCceeeEee------------------------------eeeccccCchhhhhh
Confidence 68999999999999763 6899999999999842 24445555556655
Q ss_pred cccccccccCCCceeccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 88 KQKDKTEIADGPIVERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 88 ~~~~~~~~~~~~~~~~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
+++.+++++....+++.||+|||++|||+|+|+||||||||+||+|.+|
T Consensus 51 vlgg~~a~~nv~~t~~~Cp~Cgh~rayF~qlQtRSADEPmT~FYkC~~C 99 (105)
T KOG2906|consen 51 VLGGDEAWENVDQTEATCPTCGHERAYFMQLQTRSADEPMTTFYKCCKC 99 (105)
T ss_pred hcCCcccccchhhccCcCCCCCCCceEEEEeeeccCCCcHhHhhhhhcc
Confidence 5556667888888999999999999999999999999999999999998
No 2
>KOG2907|consensus
Probab=99.98 E-value=1.1e-33 Score=202.28 Aligned_cols=103 Identities=40% Similarity=0.799 Sum_probs=83.4
Q ss_pred CccccccccCCCccccCCCCCeEEcCCCCCceecCCCCCCcCCCchhhhhcccccchhhHHHHhhheeeEeEeecceeec
Q psy4748 8 NVESEFCSKCGTILPLFDFKGDVKCYVCKTSYGTQEQQPLLLGPDILFLKRFKGHFNLFLAVFEEIKAEYTIHFNTVEKE 87 (136)
Q Consensus 8 ~~~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~e~~ 87 (136)
++++.||++||+||+.+.....+.|..|+..++. .+|.+.++...+.+......
T Consensus 4 ~~~~~FC~~CG~ll~~~~~~~~~~C~~Ck~~~~v--------------------------~~~~~~~v~~~~~~~~~~~A 57 (116)
T KOG2907|consen 4 NGDLDFCSDCGSLLEEPSAQSTVLCIRCKIEYPV--------------------------SQFSGLVVETKSLFDEFTSA 57 (116)
T ss_pred ccCcchhhhhhhhcccccccCceEeccccccCCH--------------------------HHhCCeeEEEEEeecccchh
Confidence 4489999999999999988788889999999987 45555556555555543222
Q ss_pred --cccccccccCCCceeccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 88 --KQKDKTEIADGPIVERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 88 --~~~~~~~~~~~~~~~~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
...+.+....+|+|+++||||||++|.|.|+|||||||||||||+|++|
T Consensus 58 ~~~~ve~~~~~~ga~I~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC 108 (116)
T KOG2907|consen 58 LAEKVENESSADGAVIKHKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKC 108 (116)
T ss_pred hhhhhcccccccccchhccCcccCCchhhhhhhhcccccCCceEEEEcCcc
Confidence 1122334457899999999999999999999999999999999999998
No 3
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=99.96 E-value=1.2e-30 Score=188.28 Aligned_cols=101 Identities=28% Similarity=0.521 Sum_probs=71.2
Q ss_pred cccccccCCCccccCCC--CCeEEcCCCCCceecCCCCCCcCCCchhhhhcccccchhhHHHHhhheeeEeEeecceeec
Q psy4748 10 ESEFCSKCGTILPLFDF--KGDVKCYVCKTSYGTQEQQPLLLGPDILFLKRFKGHFNLFLAVFEEIKAEYTIHFNTVEKE 87 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~--~~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~e~~ 87 (136)
.|+|||+|||||+|+.+ +..++|+.|||...+.+- .+|+ .......+.....
T Consensus 1 ~m~FCp~Cgsll~p~~~~~~~~l~C~kCgye~~~~~~-----------------------~~~~---~~~~~~~~~~~~~ 54 (113)
T COG1594 1 SMRFCPKCGSLLYPKKDDEGGKLVCRKCGYEEEASNK-----------------------KVYR---YSVKEAVEKKKEV 54 (113)
T ss_pred CccccCCccCeeEEeEcCCCcEEECCCCCcchhcccc-----------------------ceeE---EEEeeccCCccee
Confidence 47999999999999864 469999999999998530 1111 0011111111111
Q ss_pred ccc---ccccccCCCceeccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 88 KQK---DKTEIADGPIVERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 88 ~~~---~~~~~~~~~~~~~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
+.. +....+..++..+.||+|||++|+|||+|+||||||||+||+|++|
T Consensus 55 ~~~~~~~~~~~~~~~~~~~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~C 106 (113)
T COG1594 55 VLVVEDETQGAKTLPTAKEKCPKCGNKEAYYWQLQTRSADEPETRFYKCTRC 106 (113)
T ss_pred eeeecccccCccccccccccCCCCCCceeEEEeeehhccCCCceEEEEeccc
Confidence 111 2223344555578999999999999999999999999999999998
No 4
>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=99.96 E-value=1.6e-29 Score=178.39 Aligned_cols=95 Identities=28% Similarity=0.542 Sum_probs=69.7
Q ss_pred cccccCCCccccCCCCCeEEcCCCCCceecCCCCCCcCCCchhhhhcccccchhhHHHHhhheeeEeEeecceeec-ccc
Q psy4748 12 EFCSKCGTILPLFDFKGDVKCYVCKTSYGTQEQQPLLLGPDILFLKRFKGHFNLFLAVFEEIKAEYTIHFNTVEKE-KQK 90 (136)
Q Consensus 12 ~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~e~~-~~~ 90 (136)
.|||.||+||.+.+ +.+.|+.|+|....... ..| +.+..+..+..+ +..
T Consensus 1 ~fC~~Cg~~l~~~~--~~~~C~~C~~~~~~~~~-----------------------~~~-----v~~~~~~~~~~~~~~~ 50 (104)
T TIGR01384 1 KFCPKCGSLMTPKN--GVYVCPSCGYEKEKKPE-----------------------DDY-----KVTEKVKHKIKETIII 50 (104)
T ss_pred CCCcccCcccccCC--CeEECcCCCCccccccc-----------------------ccc-----EEEEEeccccccceee
Confidence 49999999998853 58999999999876310 011 111122222111 222
Q ss_pred ccccccCCCceeccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 91 DKTEIADGPIVERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 91 ~~~~~~~~~~~~~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
..+..+++|++++.||+|||++|+|||+|+||||||||+||+|++|
T Consensus 51 ~~~~~~~~~~~~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C 96 (104)
T TIGR01384 51 REEDSETLPTTRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKC 96 (104)
T ss_pred ccccccCCCcccCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCC
Confidence 2233477888899999999999999999999999999999999998
No 5
>KOG2691|consensus
Probab=99.94 E-value=6.9e-28 Score=171.22 Aligned_cols=100 Identities=21% Similarity=0.404 Sum_probs=79.8
Q ss_pred ccccccccCCCccccCCC----CCeEEcCCCCCceecCCCCCCcCCCchhhhhcccccchhhHHHHhhheeeEeEeecce
Q psy4748 9 VESEFCSKCGTILPLFDF----KGDVKCYVCKTSYGTQEQQPLLLGPDILFLKRFKGHFNLFLAVFEEIKAEYTIHFNTV 84 (136)
Q Consensus 9 ~~~~FCp~CgnlL~~~~~----~~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~~~~~~~~ 84 (136)
++++||++|||||||+++ .+.++||+|.|++.+... .+|. ..+..+..
T Consensus 2 ~~~rfC~eCNNmLYPkEDked~~L~laCrnCd~ve~A~s~-----------------------~vY~-----~~~~~e~d 53 (113)
T KOG2691|consen 2 VGIRFCRECNNMLYPKEDKEDRILLLACRNCDYVEEADSS-----------------------RVYV-----NELSHEHD 53 (113)
T ss_pred CccchhhhhhccccccccccccEEEEEecCCcceEecCCc-----------------------ceEc-----CCcccchh
Confidence 468999999999999987 368999999999998641 3443 12222222
Q ss_pred eec-cccccccccCCCc-eeccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 85 EKE-KQKDKTEIADGPI-VERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 85 e~~-~~~~~~~~~~~~~-~~~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
|.. ++.+...|+++|. .+..||||||++|+|||.|+|.|||+|++||+|+.|
T Consensus 54 E~t~ii~Dl~~DPTLPrts~~~C~~C~~~eavffQ~~~~r~d~~m~l~yvC~~C 107 (113)
T KOG2691|consen 54 ELTQIIMDLASDPTLPRTSDKHCPKCGHREAVFFQAQTRRADEAMRLFYVCCSC 107 (113)
T ss_pred hHHHHHHhhccCCCcCccccccCCccCCcceEEEecccccccceEEEEEEeccc
Confidence 322 4456778999996 678999999999999999999999999999999987
No 6
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=99.82 E-value=1.3e-20 Score=113.16 Aligned_cols=34 Identities=47% Similarity=0.961 Sum_probs=32.7
Q ss_pred ccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 103 RKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 103 ~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
.+||+|||++|+|+|+|+||||||||+||+|++|
T Consensus 1 ~~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C 34 (40)
T smart00440 1 APCPKCGNREATFFQLQTRSADEPMTVFYVCTKC 34 (40)
T ss_pred CcCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCC
Confidence 3699999999999999999999999999999998
No 7
>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=99.78 E-value=1.8e-19 Score=107.61 Aligned_cols=34 Identities=38% Similarity=0.888 Sum_probs=30.0
Q ss_pred ccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 103 RKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 103 ~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
.+||+|||++|+|+|+|+||||||||+||+|.+|
T Consensus 1 ~~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C 34 (39)
T PF01096_consen 1 IKCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNC 34 (39)
T ss_dssp S--SSS-SSEEEEEEESSSSSSSSSEEEEEESSS
T ss_pred CCCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCC
Confidence 3799999999999999999999999999999988
No 8
>PHA02998 RNA polymerase subunit; Provisional
Probab=99.67 E-value=3.8e-17 Score=125.70 Aligned_cols=39 Identities=23% Similarity=0.466 Sum_probs=36.8
Q ss_pred CCc-eeccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 98 GPI-VERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 98 ~~~-~~~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
+++ ++..||+|||++|+|||+|+||||||||+||+|.+|
T Consensus 138 lpkkt~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~C 177 (195)
T PHA02998 138 LDEKYNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDC 177 (195)
T ss_pred cCcccCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCC
Confidence 455 789999999999999999999999999999999998
No 9
>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=99.40 E-value=1.7e-13 Score=113.30 Aligned_cols=37 Identities=41% Similarity=0.716 Sum_probs=34.6
Q ss_pred ceeccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 100 IVERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 100 ~~~~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
+....||+|||++++|||+|+||||||||+||+|++|
T Consensus 256 t~~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~C 292 (299)
T TIGR01385 256 TDLFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEEC 292 (299)
T ss_pred cccccCCCCCCccceEEEecccCCCCCCeEEEEcCCC
Confidence 3356999999999999999999999999999999998
No 10
>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=99.12 E-value=1.7e-11 Score=71.51 Aligned_cols=32 Identities=28% Similarity=0.547 Sum_probs=23.8
Q ss_pred ccccccCCCccccCCCC-CeEEcCCCCCceecC
Q psy4748 11 SEFCSKCGTILPLFDFK-GDVKCYVCKTSYGTQ 42 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~~-~~~~C~~C~~~~~~~ 42 (136)
|.|||+|||||+++++. ...+|++|+|+++++
T Consensus 1 m~FCp~C~nlL~p~~~~~~~~~C~~C~Y~~~~~ 33 (35)
T PF02150_consen 1 MRFCPECGNLLYPKEDKEKRVACRTCGYEEPIS 33 (35)
T ss_dssp --BETTTTSBEEEEEETTTTEEESSSS-EEE-S
T ss_pred CeeCCCCCccceEcCCCccCcCCCCCCCccCCC
Confidence 68999999999999763 334999999999984
No 11
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=98.54 E-value=7.2e-08 Score=59.58 Aligned_cols=31 Identities=29% Similarity=0.554 Sum_probs=27.0
Q ss_pred cccccCCCccccCCCC--CeEEcCCCCCceecC
Q psy4748 12 EFCSKCGTILPLFDFK--GDVKCYVCKTSYGTQ 42 (136)
Q Consensus 12 ~FCp~CgnlL~~~~~~--~~~~C~~C~~~~~~~ 42 (136)
.|||+||+||++++.. ..++|+.|||...+.
T Consensus 1 ~FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~~~~~ 33 (52)
T smart00661 1 KFCPKCGNMLIPKEGKEKRRFVCRKCGYEEPIE 33 (52)
T ss_pred CCCCCCCCccccccCCCCCEEECCcCCCeEECC
Confidence 4999999999998652 489999999999884
No 12
>KOG1105|consensus
Probab=98.19 E-value=1.1e-06 Score=72.82 Aligned_cols=40 Identities=43% Similarity=0.797 Sum_probs=35.2
Q ss_pred CCCce-eccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 97 DGPIV-ERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 97 ~~~~~-~~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
.+..+ ..+|-+|+.....|+|+|+||||||||.|-.|..|
T Consensus 249 ~gt~td~fkcgkckk~~cty~q~Qtrs~DePmtTfv~C~ec 289 (296)
T KOG1105|consen 249 QGTQTDLFKCGKCKKKNCTYTQLQTRSADEPMTTFVTCNEC 289 (296)
T ss_pred ccccccceeeccccccceeEEeeccCCCCCCcceeeeeccc
Confidence 33434 45899999999999999999999999999999887
No 13
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=97.81 E-value=1.2e-05 Score=50.24 Aligned_cols=32 Identities=19% Similarity=0.483 Sum_probs=26.1
Q ss_pred cCccccccccCCC-ccccCCCCCeEEcCCCCCcee
Q psy4748 7 FNVESEFCSKCGT-ILPLFDFKGDVKCYVCKTSYG 40 (136)
Q Consensus 7 ~~~~~~FCp~Cgn-lL~~~~~~~~~~C~~C~~~~~ 40 (136)
+.....|||.||+ +|.+.. +.+.|+.|||.+-
T Consensus 16 v~~~~~fCP~Cg~~~m~~~~--~r~~C~~Cgyt~~ 48 (50)
T PRK00432 16 VKRKNKFCPRCGSGFMAEHL--DRWHCGKCGYTEF 48 (50)
T ss_pred EEEccCcCcCCCcchheccC--CcEECCCcCCEEe
Confidence 4456779999999 888854 6999999999864
No 14
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=97.21 E-value=0.00018 Score=41.66 Aligned_cols=28 Identities=29% Similarity=0.580 Sum_probs=17.9
Q ss_pred cccccCCCccccC----CCCCeEEcCCCCCce
Q psy4748 12 EFCSKCGTILPLF----DFKGDVKCYVCKTSY 39 (136)
Q Consensus 12 ~FCp~CgnlL~~~----~~~~~~~C~~C~~~~ 39 (136)
.|||.||.-|... ++..+++|..||+.+
T Consensus 1 kfC~~CG~~l~~~ip~gd~r~R~vC~~Cg~Ih 32 (34)
T PF14803_consen 1 KFCPQCGGPLERRIPEGDDRERLVCPACGFIH 32 (34)
T ss_dssp -B-TTT--B-EEE--TT-SS-EEEETTTTEEE
T ss_pred CccccccChhhhhcCCCCCccceECCCCCCEE
Confidence 5999999999875 225699999999875
No 15
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=96.43 E-value=0.0021 Score=40.20 Aligned_cols=33 Identities=21% Similarity=0.497 Sum_probs=25.4
Q ss_pred cCccccccccCC--CccccCCCCCeEEcCCCCCceec
Q psy4748 7 FNVESEFCSKCG--TILPLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 7 ~~~~~~FCp~Cg--nlL~~~~~~~~~~C~~C~~~~~~ 41 (136)
+.....|||.|| .+|-- -.+++.|..|||.+-.
T Consensus 15 v~rk~~~CPrCG~gvfmA~--H~dR~~CGkCgyTe~~ 49 (51)
T COG1998 15 VKRKNRFCPRCGPGVFMAD--HKDRWACGKCGYTEFK 49 (51)
T ss_pred EEEccccCCCCCCcchhhh--cCceeEeccccceEee
Confidence 455678999999 45544 4569999999998754
No 16
>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=96.41 E-value=0.0023 Score=36.03 Aligned_cols=29 Identities=21% Similarity=0.418 Sum_probs=20.1
Q ss_pred ccccccCCCccccCCCCCeEEcCCCCCce
Q psy4748 11 SEFCSKCGTILPLFDFKGDVKCYVCKTSY 39 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~~~~~~C~~C~~~~ 39 (136)
-+||+.||.-+.+....-..+|..|+..+
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCGHEH 31 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS-EE
T ss_pred CcccCcCCccccCCCCcCEeECCCCcCEe
Confidence 47999999999998877789999999764
No 17
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=96.06 E-value=0.016 Score=48.57 Aligned_cols=32 Identities=19% Similarity=0.631 Sum_probs=23.1
Q ss_pred cccccccCCCcc-----ccCC-C-CCeEEcCCCCCceec
Q psy4748 10 ESEFCSKCGTIL-----PLFD-F-KGDVKCYVCKTSYGT 41 (136)
Q Consensus 10 ~~~FCp~CgnlL-----~~~~-~-~~~~~C~~C~~~~~~ 41 (136)
...+||-||+.= .... . .-++.|..|+..+..
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~ 224 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHV 224 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccc
Confidence 457999999972 2211 1 237899999999887
No 18
>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=95.96 E-value=0.02 Score=47.93 Aligned_cols=32 Identities=19% Similarity=0.478 Sum_probs=22.9
Q ss_pred cccccccCCCccccC-------CCC-CeEEcCCCCCceec
Q psy4748 10 ESEFCSKCGTILPLF-------DFK-GDVKCYVCKTSYGT 41 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~-------~~~-~~~~C~~C~~~~~~ 41 (136)
...+||-||+.=... .++ -++.|..|+..+..
T Consensus 183 ~~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~ 222 (305)
T TIGR01562 183 SRTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHY 222 (305)
T ss_pred CCCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccc
Confidence 345999999973221 122 37899999999987
No 19
>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=95.86 E-value=0.0085 Score=49.03 Aligned_cols=30 Identities=27% Similarity=0.593 Sum_probs=15.6
Q ss_pred cccccCCCccccC-----C--CCCeEEcCCCCCceec
Q psy4748 12 EFCSKCGTILPLF-----D--FKGDVKCYVCKTSYGT 41 (136)
Q Consensus 12 ~FCp~CgnlL~~~-----~--~~~~~~C~~C~~~~~~ 41 (136)
..||-||+.=... + +.-++.|..|++.+..
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~ 209 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRF 209 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE-
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeee
Confidence 6999999863332 2 1237899999999987
No 20
>PF12773 DZR: Double zinc ribbon
Probab=95.23 E-value=0.0091 Score=36.31 Aligned_cols=33 Identities=27% Similarity=0.534 Sum_probs=25.5
Q ss_pred CccccccccCCCccccCCCCCeEEcCCCCCceec
Q psy4748 8 NVESEFCSKCGTILPLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 8 ~~~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~ 41 (136)
..+..||+.||..|... ....+.|+.||+..+.
T Consensus 9 ~~~~~fC~~CG~~l~~~-~~~~~~C~~Cg~~~~~ 41 (50)
T PF12773_consen 9 PDDAKFCPHCGTPLPPP-DQSKKICPNCGAENPP 41 (50)
T ss_pred CccccCChhhcCChhhc-cCCCCCCcCCcCCCcC
Confidence 34678999999999932 3457899999998654
No 21
>PHA00626 hypothetical protein
Probab=94.99 E-value=0.021 Score=36.71 Aligned_cols=31 Identities=23% Similarity=0.429 Sum_probs=23.4
Q ss_pred cccccCCCccccCC-----CCCeEEcCCCCCceecC
Q psy4748 12 EFCSKCGTILPLFD-----FKGDVKCYVCKTSYGTQ 42 (136)
Q Consensus 12 ~FCp~CgnlL~~~~-----~~~~~~C~~C~~~~~~~ 42 (136)
+.||.||+--.... ..+.|.|..|||....+
T Consensus 1 m~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 1 MSCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSKD 36 (59)
T ss_pred CCCCCCCCceeeeeceecccCcceEcCCCCCeechh
Confidence 47999999533342 24799999999998764
No 22
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=94.84 E-value=0.028 Score=30.14 Aligned_cols=24 Identities=21% Similarity=0.495 Sum_probs=21.2
Q ss_pred cccCCCccccCCCCCeEEcCCCCC
Q psy4748 14 CSKCGTILPLFDFKGDVKCYVCKT 37 (136)
Q Consensus 14 Cp~CgnlL~~~~~~~~~~C~~C~~ 37 (136)
|..||-.|.+.+....|.|+.||+
T Consensus 1 C~sC~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTSCGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred CccCCCcccCcccCceEeCCCCCC
Confidence 778999999988667999999985
No 23
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=94.60 E-value=0.018 Score=31.28 Aligned_cols=24 Identities=25% Similarity=0.627 Sum_probs=19.2
Q ss_pred ccccCCCccccCCCCCeEEcCCCCCcee
Q psy4748 13 FCSKCGTILPLFDFKGDVKCYVCKTSYG 40 (136)
Q Consensus 13 FCp~CgnlL~~~~~~~~~~C~~C~~~~~ 40 (136)
=||+|+..+... .-.|+.|||...
T Consensus 2 ~CP~C~~~V~~~----~~~Cp~CG~~F~ 25 (26)
T PF10571_consen 2 TCPECGAEVPES----AKFCPHCGYDFE 25 (26)
T ss_pred cCCCCcCCchhh----cCcCCCCCCCCc
Confidence 399999999763 448999999764
No 24
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=94.57 E-value=0.045 Score=32.98 Aligned_cols=32 Identities=25% Similarity=0.527 Sum_probs=26.1
Q ss_pred cccccCCCccccCCCCCeEEcCCCCCceecCC
Q psy4748 12 EFCSKCGTILPLFDFKGDVKCYVCKTSYGTQE 43 (136)
Q Consensus 12 ~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~~~ 43 (136)
.=|+.||..+...+....+.|+.||.......
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~~~~~ 35 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRILFKE 35 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeEEEcc
Confidence 45999999999987655899999998776543
No 25
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=94.51 E-value=0.017 Score=30.47 Aligned_cols=22 Identities=27% Similarity=0.634 Sum_probs=16.7
Q ss_pred ccccCCCccccCCCCCeEEcCCCCCc
Q psy4748 13 FCSKCGTILPLFDFKGDVKCYVCKTS 38 (136)
Q Consensus 13 FCp~CgnlL~~~~~~~~~~C~~C~~~ 38 (136)
|||.||+-|... .-.|+.||+.
T Consensus 1 ~Cp~CG~~~~~~----~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIEDD----AKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCCc----CcchhhhCCc
Confidence 799999988652 3369999864
No 26
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=94.30 E-value=0.024 Score=30.47 Aligned_cols=24 Identities=25% Similarity=0.636 Sum_probs=17.9
Q ss_pred ccccccCCCccccCCCCCeEEcCCCCCc
Q psy4748 11 SEFCSKCGTILPLFDFKGDVKCYVCKTS 38 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~~~~~~C~~C~~~ 38 (136)
..+||.||..+.. +.-.|+.||..
T Consensus 2 ~~~Cp~Cg~~~~~----~~~fC~~CG~~ 25 (26)
T PF13248_consen 2 EMFCPNCGAEIDP----DAKFCPNCGAK 25 (26)
T ss_pred cCCCcccCCcCCc----ccccChhhCCC
Confidence 3689999996544 24489999964
No 27
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=94.22 E-value=0.027 Score=31.94 Aligned_cols=16 Identities=13% Similarity=0.385 Sum_probs=12.3
Q ss_pred eccccccCCCceEEEE
Q psy4748 102 ERKCKRCNNDTMSYAT 117 (136)
Q Consensus 102 ~~~CpkCg~~~a~f~~ 117 (136)
.+.||.||+++..|..
T Consensus 17 ~~~CP~Cg~~~~~F~~ 32 (33)
T cd00350 17 PWVCPVCGAPKDKFEK 32 (33)
T ss_pred CCcCcCCCCcHHHcEE
Confidence 4689999998877653
No 28
>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=93.46 E-value=0.11 Score=33.98 Aligned_cols=15 Identities=13% Similarity=0.399 Sum_probs=10.9
Q ss_pred eeccccccCCCceEE
Q psy4748 101 VERKCKRCNNDTMSY 115 (136)
Q Consensus 101 ~~~~CpkCg~~~a~f 115 (136)
+-..|++||+-|.|-
T Consensus 35 ~~v~C~~CGYTE~Y~ 49 (64)
T PF09855_consen 35 TTVSCTNCGYTEFYK 49 (64)
T ss_pred EEEECCCCCCEEEEe
Confidence 346788888887765
No 29
>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=93.41 E-value=0.037 Score=31.10 Aligned_cols=27 Identities=19% Similarity=0.379 Sum_probs=15.5
Q ss_pred ccccCCCccccCCCCCeEEcCCCCCcee
Q psy4748 13 FCSKCGTILPLFDFKGDVKCYVCKTSYG 40 (136)
Q Consensus 13 FCp~CgnlL~~~~~~~~~~C~~C~~~~~ 40 (136)
=||.||+--... ++..++|+.|++++.
T Consensus 4 ~Cp~C~se~~y~-D~~~~vCp~C~~ew~ 30 (30)
T PF08274_consen 4 KCPLCGSEYTYE-DGELLVCPECGHEWN 30 (30)
T ss_dssp --TTT-----EE--SSSEEETTTTEEE-
T ss_pred CCCCCCCcceec-cCCEEeCCcccccCC
Confidence 499999887774 457999999998763
No 30
>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=93.25 E-value=0.082 Score=31.42 Aligned_cols=30 Identities=20% Similarity=0.431 Sum_probs=20.9
Q ss_pred cccccCCCcc-ccCCCCCeEEcCCCCCceec
Q psy4748 12 EFCSKCGTIL-PLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 12 ~FCp~CgnlL-~~~~~~~~~~C~~C~~~~~~ 41 (136)
+.||.||+-. ......+.++|+.||.....
T Consensus 1 m~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 1 MKCPNCGSKEIVFDPERGELVCPNCGLVLEE 31 (43)
T ss_dssp ESBTTTSSSEEEEETTTTEEEETTT-BBEE-
T ss_pred CCCcCCcCCceEEcCCCCeEECCCCCCEeec
Confidence 3699999954 22234578999999998765
No 31
>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=93.18 E-value=0.1 Score=46.10 Aligned_cols=28 Identities=21% Similarity=0.578 Sum_probs=17.3
Q ss_pred cccCCCccccCCCCCeEEcCCCCCceec
Q psy4748 14 CSKCGTILPLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 14 Cp~CgnlL~~~~~~~~~~C~~C~~~~~~ 41 (136)
||.|+--|..-.....+.|..||+..+.
T Consensus 225 C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~ 252 (505)
T TIGR00595 225 CPNCDVSLTYHKKEGKLRCHYCGYQEPI 252 (505)
T ss_pred CCCCCCceEEecCCCeEEcCCCcCcCCC
Confidence 5555544544444457788888877665
No 32
>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=92.76 E-value=0.079 Score=30.44 Aligned_cols=29 Identities=28% Similarity=0.619 Sum_probs=22.7
Q ss_pred ccccCCCccccCCC-----CCeEEcCCCCCceec
Q psy4748 13 FCSKCGTILPLFDF-----KGDVKCYVCKTSYGT 41 (136)
Q Consensus 13 FCp~CgnlL~~~~~-----~~~~~C~~C~~~~~~ 41 (136)
=||.||....+..+ +..+.|++|+....+
T Consensus 4 ~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~~ 37 (38)
T TIGR02098 4 QCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWYA 37 (38)
T ss_pred ECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEEe
Confidence 49999998888743 347999999987653
No 33
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=92.74 E-value=0.086 Score=30.60 Aligned_cols=28 Identities=25% Similarity=0.534 Sum_probs=23.4
Q ss_pred ccccCCCccccCCC-----CCeEEcCCCCCcee
Q psy4748 13 FCSKCGTILPLFDF-----KGDVKCYVCKTSYG 40 (136)
Q Consensus 13 FCp~CgnlL~~~~~-----~~~~~C~~C~~~~~ 40 (136)
=||.|+....++++ +..+.|..|++.+.
T Consensus 4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f~ 36 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVFR 36 (37)
T ss_pred ECCCCCceEEcCHHHcccCCcEEECCCCCcEee
Confidence 49999999998854 45899999998764
No 34
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=92.72 E-value=0.11 Score=31.97 Aligned_cols=14 Identities=29% Similarity=0.712 Sum_probs=11.9
Q ss_pred eEEcCCCCCceecC
Q psy4748 29 DVKCYVCKTSYGTQ 42 (136)
Q Consensus 29 ~~~C~~C~~~~~~~ 42 (136)
.+.|+.|||++.-.
T Consensus 1 ky~C~~CgyvYd~~ 14 (47)
T PF00301_consen 1 KYQCPVCGYVYDPE 14 (47)
T ss_dssp EEEETTTSBEEETT
T ss_pred CcCCCCCCEEEcCC
Confidence 47999999999864
No 35
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=92.61 E-value=0.064 Score=33.44 Aligned_cols=15 Identities=13% Similarity=0.505 Sum_probs=12.6
Q ss_pred eccccccCCCceEEE
Q psy4748 102 ERKCKRCNNDTMSYA 116 (136)
Q Consensus 102 ~~~CpkCg~~~a~f~ 116 (136)
++.||.||..+..|-
T Consensus 34 ~w~CP~C~a~K~~F~ 48 (50)
T cd00730 34 DWVCPVCGAGKDDFE 48 (50)
T ss_pred CCCCCCCCCcHHHcE
Confidence 789999999887664
No 36
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=92.60 E-value=0.075 Score=44.03 Aligned_cols=34 Identities=21% Similarity=0.284 Sum_probs=29.7
Q ss_pred cCccccccccCCCccccCCCCCeEEcCCCCCcee
Q psy4748 7 FNVESEFCSKCGTILPLFDFKGDVKCYVCKTSYG 40 (136)
Q Consensus 7 ~~~~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~ 40 (136)
|....+||+.||.=+++.+.+....|+.||+.+.
T Consensus 107 w~~~~RFCg~CG~~~~~~~~g~~~~C~~cg~~~f 140 (279)
T COG2816 107 WYRSHRFCGRCGTKTYPREGGWARVCPKCGHEHF 140 (279)
T ss_pred HHhhCcCCCCCCCcCccccCceeeeCCCCCCccC
Confidence 4557789999999999998888999999999763
No 37
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=92.43 E-value=0.092 Score=42.56 Aligned_cols=35 Identities=23% Similarity=0.491 Sum_probs=28.6
Q ss_pred cCccccccccCCCccccCCCCCeEEcCCCCCceec
Q psy4748 7 FNVESEFCSKCGTILPLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 7 ~~~~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~ 41 (136)
+....+|||.||+-|..........|..|+..+..
T Consensus 95 w~~~~~fC~~CG~~~~~~~~~~~~~C~~c~~~~yp 129 (256)
T PRK00241 95 FYRSHRFCGYCGHPMHPSKTEWAMLCPHCRERYYP 129 (256)
T ss_pred HhhcCccccccCCCCeecCCceeEECCCCCCEECC
Confidence 34567899999999988766678899999987754
No 38
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=92.07 E-value=0.12 Score=36.02 Aligned_cols=34 Identities=21% Similarity=0.375 Sum_probs=26.6
Q ss_pred cccccccCCCccccCCCCCeEEcCCCCCceecCC
Q psy4748 10 ESEFCSKCGTILPLFDFKGDVKCYVCKTSYGTQE 43 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~~~ 43 (136)
...-||.||.--.-+...++|.|+.||+...-..
T Consensus 34 ~~~~Cp~C~~~~VkR~a~GIW~C~kCg~~fAGga 67 (89)
T COG1997 34 AKHVCPFCGRTTVKRIATGIWKCRKCGAKFAGGA 67 (89)
T ss_pred cCCcCCCCCCcceeeeccCeEEcCCCCCeecccc
Confidence 4457999999955445678999999999986543
No 39
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=91.97 E-value=0.17 Score=46.84 Aligned_cols=16 Identities=13% Similarity=0.526 Sum_probs=10.2
Q ss_pred ccccccCCCceEEEEe
Q psy4748 103 RKCKRCNNDTMSYATL 118 (136)
Q Consensus 103 ~~CpkCg~~~a~f~~~ 118 (136)
..||+||.....++-.
T Consensus 476 ~~Cp~Cgs~~L~~~G~ 491 (730)
T COG1198 476 QSCPECGSEHLRAVGP 491 (730)
T ss_pred CCCCCCCCCeeEEecc
Confidence 4577777776655544
No 40
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=91.97 E-value=0.11 Score=29.71 Aligned_cols=14 Identities=21% Similarity=0.627 Sum_probs=11.1
Q ss_pred ccccccCCCceEEE
Q psy4748 103 RKCKRCNNDTMSYA 116 (136)
Q Consensus 103 ~~CpkCg~~~a~f~ 116 (136)
..||-||++...|.
T Consensus 19 ~~CP~Cg~~~~~F~ 32 (34)
T cd00729 19 EKCPICGAPKEKFE 32 (34)
T ss_pred CcCcCCCCchHHcE
Confidence 47999999877664
No 41
>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=91.95 E-value=0.15 Score=29.92 Aligned_cols=31 Identities=32% Similarity=0.401 Sum_probs=25.7
Q ss_pred cccccCCCccccCCC--CCeEEcCC---CCCceecC
Q psy4748 12 EFCSKCGTILPLFDF--KGDVKCYV---CKTSYGTQ 42 (136)
Q Consensus 12 ~FCp~CgnlL~~~~~--~~~~~C~~---C~~~~~~~ 42 (136)
.-||.||..|..+.. +..+.|.. |.|.....
T Consensus 2 ~~CP~Cg~~lv~r~~k~g~F~~Cs~yP~C~~~~~~~ 37 (39)
T PF01396_consen 2 EKCPKCGGPLVLRRGKKGKFLGCSNYPECKYTEPLP 37 (39)
T ss_pred cCCCCCCceeEEEECCCCCEEECCCCCCcCCeEeCC
Confidence 469999999999854 46889997 99988764
No 42
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=91.93 E-value=0.12 Score=33.25 Aligned_cols=33 Identities=18% Similarity=0.304 Sum_probs=27.7
Q ss_pred cccccccCCCccccCCCCCeEEcCCCCCceecC
Q psy4748 10 ESEFCSKCGTILPLFDFKGDVKCYVCKTSYGTQ 42 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~~ 42 (136)
+..=||.||..+........+.|..||+....+
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~~~rD 59 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFEMDRD 59 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCEECcH
Confidence 557799999999985555699999999998875
No 43
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=91.86 E-value=0.1 Score=33.84 Aligned_cols=25 Identities=20% Similarity=0.493 Sum_probs=13.2
Q ss_pred cccccCCCccccCCCCCeEEcCCCC
Q psy4748 12 EFCSKCGTILPLFDFKGDVKCYVCK 36 (136)
Q Consensus 12 ~FCp~CgnlL~~~~~~~~~~C~~C~ 36 (136)
.-|..||-.|.+.+....+.|++||
T Consensus 10 ~~CtSCg~~i~p~e~~v~F~CPnCG 34 (61)
T COG2888 10 PVCTSCGREIAPGETAVKFPCPNCG 34 (61)
T ss_pred ceeccCCCEeccCCceeEeeCCCCC
Confidence 4455555555554444455555555
No 44
>TIGR01053 LSD1 zinc finger domain, LSD1 subclass. This model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC
Probab=91.84 E-value=0.17 Score=28.51 Aligned_cols=27 Identities=30% Similarity=0.615 Sum_probs=23.4
Q ss_pred ccccCCCccccCCCCCeEEcCCCCCce
Q psy4748 13 FCSKCGTILPLFDFKGDVKCYVCKTSY 39 (136)
Q Consensus 13 FCp~CgnlL~~~~~~~~~~C~~C~~~~ 39 (136)
-|.-|+++|..+.+...+.|..|....
T Consensus 3 ~C~~C~t~L~yP~gA~~vrCs~C~~vt 29 (31)
T TIGR01053 3 VCGGCRTLLMYPRGASSVRCALCQTVN 29 (31)
T ss_pred CcCCCCcEeecCCCCCeEECCCCCeEe
Confidence 489999999999877799999998654
No 45
>PRK14973 DNA topoisomerase I; Provisional
Probab=91.60 E-value=0.26 Score=46.82 Aligned_cols=29 Identities=14% Similarity=0.291 Sum_probs=18.3
Q ss_pred eccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 102 ERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 102 ~~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
+..||+||.+. .+-+|...-|+ |.-|++|
T Consensus 635 ~~~Cp~CG~p~----~~~~r~Gr~g~--fl~CP~C 663 (936)
T PRK14973 635 DEVCPIHHLNH----VRLIRKGARPW--DIGCPLC 663 (936)
T ss_pred CCCCCCCCCCc----eEEeecCCCcc--cccCccc
Confidence 45788888862 33445555566 6667766
No 46
>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=91.33 E-value=0.13 Score=29.86 Aligned_cols=29 Identities=28% Similarity=0.398 Sum_probs=22.6
Q ss_pred cccccccCCCccccCCCCCeEEcCCCCCce
Q psy4748 10 ESEFCSKCGTILPLFDFKGDVKCYVCKTSY 39 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~ 39 (136)
...=|+.||+.+....+ +.+.|..||++.
T Consensus 7 ~~~~C~~C~~~~~~~~d-G~~yC~~cG~~~ 35 (36)
T PF11781_consen 7 PNEPCPVCGSRWFYSDD-GFYYCDRCGHQS 35 (36)
T ss_pred CCCcCCCCCCeEeEccC-CEEEhhhCceEc
Confidence 33459999999766654 699999999763
No 47
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=91.32 E-value=0.086 Score=40.59 Aligned_cols=15 Identities=20% Similarity=0.186 Sum_probs=11.9
Q ss_pred CCeEEcCCCCCceec
Q psy4748 27 KGDVKCYVCKTSYGT 41 (136)
Q Consensus 27 ~~~~~C~~C~~~~~~ 41 (136)
+..|+|+.|||....
T Consensus 132 ~~~~vC~vCGy~~~g 146 (166)
T COG1592 132 GKVWVCPVCGYTHEG 146 (166)
T ss_pred CCEEEcCCCCCcccC
Confidence 348999999987765
No 48
>PRK04023 DNA polymerase II large subunit; Validated
Probab=91.25 E-value=0.12 Score=49.28 Aligned_cols=24 Identities=25% Similarity=0.546 Sum_probs=19.2
Q ss_pred ccccccccCCCccccCCCCCeEEcCCCCCc
Q psy4748 9 VESEFCSKCGTILPLFDFKGDVKCYVCKTS 38 (136)
Q Consensus 9 ~~~~FCp~CgnlL~~~~~~~~~~C~~C~~~ 38 (136)
.+.+|||.||..+ ....|+.||..
T Consensus 624 Vg~RfCpsCG~~t------~~frCP~CG~~ 647 (1121)
T PRK04023 624 IGRRKCPSCGKET------FYRRCPFCGTH 647 (1121)
T ss_pred ccCccCCCCCCcC------CcccCCCCCCC
Confidence 3667999999985 35689999976
No 49
>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=90.92 E-value=0.24 Score=31.35 Aligned_cols=29 Identities=24% Similarity=0.437 Sum_probs=24.8
Q ss_pred ccccCCCccccCCC--CCeEEcCCCCCceec
Q psy4748 13 FCSKCGTILPLFDF--KGDVKCYVCKTSYGT 41 (136)
Q Consensus 13 FCp~CgnlL~~~~~--~~~~~C~~C~~~~~~ 41 (136)
=||.||.-+.++.+ +..+.|..||....+
T Consensus 4 ~CP~CG~~iev~~~~~GeiV~Cp~CGaeleV 34 (54)
T TIGR01206 4 ECPDCGAEIELENPELGELVICDECGAELEV 34 (54)
T ss_pred CCCCCCCEEecCCCccCCEEeCCCCCCEEEE
Confidence 59999999998754 568999999998876
No 50
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=90.87 E-value=0.12 Score=47.15 Aligned_cols=13 Identities=23% Similarity=0.649 Sum_probs=6.4
Q ss_pred ccccccCCCceEE
Q psy4748 103 RKCKRCNNDTMSY 115 (136)
Q Consensus 103 ~~CpkCg~~~a~f 115 (136)
..||+||+.-...
T Consensus 42 ~fC~~CG~~~~~~ 54 (645)
T PRK14559 42 AHCPNCGAETGTI 54 (645)
T ss_pred ccccccCCcccch
Confidence 3455555544333
No 51
>PHA00626 hypothetical protein
Probab=90.64 E-value=0.23 Score=31.95 Aligned_cols=28 Identities=21% Similarity=0.724 Sum_probs=14.2
Q ss_pred cccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 104 KCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 104 ~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
.||+||+.+.+ ---..| ++.--|+|.+|
T Consensus 2 ~CP~CGS~~Iv-rcg~cr----~~snrYkCkdC 29 (59)
T PHA00626 2 SCPKCGSGNIA-KEKTMR----GWSDDYVCCDC 29 (59)
T ss_pred CCCCCCCceee-eeceec----ccCcceEcCCC
Confidence 47777776554 211222 23344677665
No 52
>COG1773 Rubredoxin [Energy production and conversion]
Probab=90.57 E-value=0.26 Score=31.40 Aligned_cols=17 Identities=12% Similarity=0.530 Sum_probs=13.9
Q ss_pred eccccccCCCceEEEEe
Q psy4748 102 ERKCKRCNNDTMSYATL 118 (136)
Q Consensus 102 ~~~CpkCg~~~a~f~~~ 118 (136)
++.||.||-.+..|-.+
T Consensus 36 ~w~CP~Cg~~K~~F~~~ 52 (55)
T COG1773 36 DWVCPECGVGKKDFEMI 52 (55)
T ss_pred ccCCCCCCCCHhHeeec
Confidence 78999999988877554
No 53
>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=90.52 E-value=0.2 Score=30.15 Aligned_cols=25 Identities=16% Similarity=0.425 Sum_probs=18.2
Q ss_pred ccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 103 RKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 103 ~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
..||+||+.+++.... ..-|.|.+|
T Consensus 19 ~~CP~Cg~~~~~~~~~---------~~~~~C~~C 43 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKT---------RGRYRCKAC 43 (46)
T ss_pred CCCCCCCCeeeEEeCC---------CCeEECCCC
Confidence 5699999996665543 345888777
No 54
>PRK05580 primosome assembly protein PriA; Validated
Probab=90.51 E-value=0.3 Score=44.65 Aligned_cols=28 Identities=25% Similarity=0.636 Sum_probs=15.3
Q ss_pred cccCCCccccCCCCCeEEcCCCCCceec
Q psy4748 14 CSKCGTILPLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 14 Cp~CgnlL~~~~~~~~~~C~~C~~~~~~ 41 (136)
||.|+.-|........+.|..||+....
T Consensus 393 C~~C~~~l~~h~~~~~l~Ch~Cg~~~~~ 420 (679)
T PRK05580 393 CPHCDASLTLHRFQRRLRCHHCGYQEPI 420 (679)
T ss_pred CCCCCCceeEECCCCeEECCCCcCCCCC
Confidence 3333333333333456778888877654
No 55
>PRK14873 primosome assembly protein PriA; Provisional
Probab=90.37 E-value=0.29 Score=44.82 Aligned_cols=25 Identities=28% Similarity=0.590 Sum_probs=12.7
Q ss_pred cccCCCccccCCCCCeEEcCCCCCc
Q psy4748 14 CSKCGTILPLFDFKGDVKCYVCKTS 38 (136)
Q Consensus 14 Cp~CgnlL~~~~~~~~~~C~~C~~~ 38 (136)
||.|+.-|........+.|..||+.
T Consensus 395 C~~C~~~L~~h~~~~~l~Ch~CG~~ 419 (665)
T PRK14873 395 CRHCTGPLGLPSAGGTPRCRWCGRA 419 (665)
T ss_pred CCCCCCceeEecCCCeeECCCCcCC
Confidence 4444444444333346666666664
No 56
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=90.22 E-value=0.21 Score=32.33 Aligned_cols=25 Identities=20% Similarity=0.440 Sum_probs=10.6
Q ss_pred ccccCCCccccCCCCCeEEcCCCCC
Q psy4748 13 FCSKCGTILPLFDFKGDVKCYVCKT 37 (136)
Q Consensus 13 FCp~CgnlL~~~~~~~~~~C~~C~~ 37 (136)
.|..||-.|.+.+....+.|+.||.
T Consensus 9 ~CtSCg~~i~~~~~~~~F~CPnCG~ 33 (59)
T PRK14890 9 KCTSCGIEIAPREKAVKFLCPNCGE 33 (59)
T ss_pred cccCCCCcccCCCccCEeeCCCCCC
Confidence 3444444444433223444444443
No 57
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=90.19 E-value=0.22 Score=48.66 Aligned_cols=14 Identities=29% Similarity=0.835 Sum_probs=9.4
Q ss_pred ccccccCCCceEEE
Q psy4748 103 RKCKRCNNDTMSYA 116 (136)
Q Consensus 103 ~~CpkCg~~~a~f~ 116 (136)
..||+||.+-..+-
T Consensus 710 ~~CP~CGtplv~~~ 723 (1337)
T PRK14714 710 VECPRCDVELTPYQ 723 (1337)
T ss_pred ccCCCCCCcccccc
Confidence 46888888665543
No 58
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=89.59 E-value=0.4 Score=31.10 Aligned_cols=44 Identities=27% Similarity=0.428 Sum_probs=36.6
Q ss_pred CccccccccCCCccccCCCCCeEEcCCCCCceecCCCCCCcCCC
Q psy4748 8 NVESEFCSKCGTILPLFDFKGDVKCYVCKTSYGTQEQQPLLLGP 51 (136)
Q Consensus 8 ~~~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~~~~~~~~~~~ 51 (136)
-.++.-||.|..-|...+.+..++|+.|+-.+++.++=|.++.+
T Consensus 5 LLeiLaCP~~kg~L~~~~~~~~L~c~~~~~aYpI~dGIPvlL~~ 48 (60)
T COG2835 5 LLEILACPVCKGPLVYDEEKQELICPRCKLAYPIRDGIPVLLPD 48 (60)
T ss_pred hheeeeccCcCCcceEeccCCEEEecccCceeecccCccccCch
Confidence 35678899999999998888899999999999998765555533
No 59
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=89.58 E-value=0.27 Score=31.39 Aligned_cols=28 Identities=21% Similarity=0.310 Sum_probs=22.8
Q ss_pred ccccccccCCCccccCCCCCeEEcCCCCCceec
Q psy4748 9 VESEFCSKCGTILPLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 9 ~~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~ 41 (136)
-.+..||.||++..+ ..+|..|||....
T Consensus 25 ~~l~~C~~CG~~~~~-----H~vC~~CG~Y~gr 52 (57)
T PRK12286 25 PGLVECPNCGEPKLP-----HRVCPSCGYYKGR 52 (57)
T ss_pred CcceECCCCCCccCC-----eEECCCCCcCCCE
Confidence 356789999999877 7899999976554
No 60
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=89.09 E-value=0.32 Score=36.16 Aligned_cols=28 Identities=39% Similarity=0.630 Sum_probs=22.8
Q ss_pred cccccCCCccccCCCCCeEEcCCCCCceec
Q psy4748 12 EFCSKCGTILPLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 12 ~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~ 41 (136)
.-||.||.=|.- ..+.+.|+.|+|....
T Consensus 29 ~hCp~Cg~PLF~--KdG~v~CPvC~~~~~~ 56 (131)
T COG1645 29 KHCPKCGTPLFR--KDGEVFCPVCGYREVV 56 (131)
T ss_pred hhCcccCCccee--eCCeEECCCCCceEEE
Confidence 469999998887 4469999999986654
No 61
>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=88.60 E-value=0.17 Score=33.92 Aligned_cols=14 Identities=36% Similarity=1.001 Sum_probs=6.3
Q ss_pred cCccccccccCCCc
Q psy4748 7 FNVESEFCSKCGTI 20 (136)
Q Consensus 7 ~~~~~~FCp~Cgnl 20 (136)
..++..|||.|||-
T Consensus 20 ~~~~k~FCp~CGn~ 33 (73)
T PF08772_consen 20 KDMTKQFCPKCGNA 33 (73)
T ss_dssp S-SS--S-SSS--S
T ss_pred CCCCceeCcccCCC
Confidence 35778899999985
No 62
>PRK10220 hypothetical protein; Provisional
Probab=88.43 E-value=0.49 Score=34.18 Aligned_cols=34 Identities=24% Similarity=0.514 Sum_probs=27.5
Q ss_pred ccccccccCCCccccCCCCCeEEcCCCCCceecCC
Q psy4748 9 VESEFCSKCGTILPLFDFKGDVKCYVCKTSYGTQE 43 (136)
Q Consensus 9 ~~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~~~ 43 (136)
|++-=||.|++-...+. +..|+|+-|+|++...+
T Consensus 1 m~lP~CP~C~seytY~d-~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 1 MSLPHCPKCNSEYTYED-NGMYICPECAHEWNDAE 34 (111)
T ss_pred CCCCcCCCCCCcceEcC-CCeEECCcccCcCCccc
Confidence 35667999999888764 46899999999998653
No 63
>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=88.23 E-value=0.34 Score=34.93 Aligned_cols=31 Identities=19% Similarity=0.460 Sum_probs=25.4
Q ss_pred ccccccCCCccccCCCCCeEEcCCCCCceecC
Q psy4748 11 SEFCSKCGTILPLFDFKGDVKCYVCKTSYGTQ 42 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~~ 42 (136)
+-=||.|++-...+. +..++|+-|+|.+...
T Consensus 2 lp~CP~C~seytY~d-g~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 2 LPPCPKCNSEYTYHD-GTQLICPSCLYEWNEN 32 (109)
T ss_pred CCcCCcCCCcceEec-CCeeECcccccccccc
Confidence 346999999888864 4689999999999764
No 64
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=88.07 E-value=0.22 Score=34.76 Aligned_cols=31 Identities=23% Similarity=0.359 Sum_probs=25.3
Q ss_pred ccccccCCCccccCCCCCeEEcCCCCCceec
Q psy4748 11 SEFCSKCGTILPLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~ 41 (136)
-.+||.||..-.-+...++|.|+.|++...-
T Consensus 35 ky~Cp~Cgk~~vkR~a~GIW~C~~C~~~~AG 65 (90)
T PF01780_consen 35 KYTCPFCGKTSVKRVATGIWKCKKCGKKFAG 65 (90)
T ss_dssp -BEESSSSSSEEEEEETTEEEETTTTEEEE-
T ss_pred CCcCCCCCCceeEEeeeEEeecCCCCCEEeC
Confidence 4589999999866666789999999998865
No 65
>PRK07220 DNA topoisomerase I; Validated
Probab=88.01 E-value=1.1 Score=41.56 Aligned_cols=28 Identities=25% Similarity=0.376 Sum_probs=17.2
Q ss_pred ccccCCCccccCCC---CCeEEcCC---CCCcee
Q psy4748 13 FCSKCGTILPLFDF---KGDVKCYV---CKTSYG 40 (136)
Q Consensus 13 FCp~CgnlL~~~~~---~~~~~C~~---C~~~~~ 40 (136)
=||.||.-|..+.. +..+.|.. |++..+
T Consensus 591 ~CP~Cg~~l~~r~~r~g~~f~gCs~yp~C~~~~~ 624 (740)
T PRK07220 591 KCPLCGSDLMVRRSKRGSRFIGCEGYPECTFSLP 624 (740)
T ss_pred ccccCCCeeeEEecCCCceEEEcCCCCCCCceee
Confidence 59999876655422 23588864 664443
No 66
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=87.59 E-value=0.68 Score=28.60 Aligned_cols=32 Identities=19% Similarity=0.476 Sum_probs=25.7
Q ss_pred cccccc--cCCCccccCC--CCCeEEcCCCCCceec
Q psy4748 10 ESEFCS--KCGTILPLFD--FKGDVKCYVCKTSYGT 41 (136)
Q Consensus 10 ~~~FCp--~CgnlL~~~~--~~~~~~C~~C~~~~~~ 41 (136)
.+.+|| .|+.++...+ ....+.|..|++..-.
T Consensus 17 ~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~ 52 (64)
T smart00647 17 DLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCF 52 (64)
T ss_pred CccCCCCCCCcceEEecCCCCCCeeECCCCCCeECC
Confidence 577999 9999999974 3468999999987643
No 67
>PF06943 zf-LSD1: LSD1 zinc finger; InterPro: IPR005735 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 model describes a putative zinc finger domain found in three closely spaced copies in Arabidopsis protein LSD1 and in two copies in other proteins from the same species. The motif resembles CxxCRxxLMYxxGASxVxCxxC []. This domain may play a role in the regulation of transcription, via either repression of a prodeath pathway or activation of an antideath pathway, in response to signals emanating from cells undergoing pathogen-induced hypersensitive cell death. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].
Probab=87.56 E-value=0.54 Score=25.34 Aligned_cols=25 Identities=32% Similarity=0.619 Sum_probs=21.2
Q ss_pred cccCCCccccCCCCCeEEcCCCCCc
Q psy4748 14 CSKCGTILPLFDFKGDVKCYVCKTS 38 (136)
Q Consensus 14 Cp~CgnlL~~~~~~~~~~C~~C~~~ 38 (136)
|..|..+|..+.....+.|..|.+.
T Consensus 1 C~~Cr~~L~yp~GA~sVrCa~C~~V 25 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAPSVRCACCHTV 25 (25)
T ss_pred CCCCCceEEcCCCCCCeECCccCcC
Confidence 6789999999877779999999863
No 68
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=87.45 E-value=0.43 Score=31.57 Aligned_cols=23 Identities=17% Similarity=0.504 Sum_probs=18.4
Q ss_pred CceeccccccCCCceEEEEeecc
Q psy4748 99 PIVERKCKRCNNDTMSYATLQLR 121 (136)
Q Consensus 99 ~~~~~~CpkCg~~~a~f~~~Q~R 121 (136)
.-.+.+||+|||.+.+|--.|++
T Consensus 16 ~Fl~VkCpdC~N~q~vFshast~ 38 (67)
T COG2051 16 RFLRVKCPDCGNEQVVFSHASTV 38 (67)
T ss_pred eEEEEECCCCCCEEEEeccCceE
Confidence 34588999999999999776554
No 69
>PF01485 IBR: IBR domain; InterPro: IPR002867 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=87.40 E-value=0.31 Score=30.12 Aligned_cols=32 Identities=25% Similarity=0.488 Sum_probs=19.3
Q ss_pred ccccccc--CCCccccCCCCCe--EEcCCCCCceec
Q psy4748 10 ESEFCSK--CGTILPLFDFKGD--VKCYVCKTSYGT 41 (136)
Q Consensus 10 ~~~FCp~--CgnlL~~~~~~~~--~~C~~C~~~~~~ 41 (136)
.+++||. |+.++........ +.|+.|++..-.
T Consensus 17 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~ 52 (64)
T PF01485_consen 17 NIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCF 52 (64)
T ss_dssp -CC--TTSST---ECS-SSTTS--CCTTSCCSEECS
T ss_pred CccCCCCCCCcccEEecCCCCCCeeECCCCCCcCcc
Confidence 4579977 9999999876444 899999987644
No 70
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=87.21 E-value=0.65 Score=26.44 Aligned_cols=31 Identities=26% Similarity=0.418 Sum_probs=23.9
Q ss_pred cccccccCCCccccCCCCCeEEcCCCCCcee
Q psy4748 10 ESEFCSKCGTILPLFDFKGDVKCYVCKTSYG 40 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~ 40 (136)
.+.-|+.||.-+......++++|.-||...+
T Consensus 2 ~~~~C~~C~~~~i~~~~~~~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 2 NLKKCSKCGGNGIVNKEDDYEVCIFCGSSFP 32 (33)
T ss_pred CceEcCCCCCCeEEEecCCeEEcccCCcEee
Confidence 3566999998777744457999999998764
No 71
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=86.88 E-value=0.48 Score=27.34 Aligned_cols=27 Identities=22% Similarity=0.552 Sum_probs=21.3
Q ss_pred ccccCCCccccCCC-----CCeEEcCCCCCce
Q psy4748 13 FCSKCGTILPLFDF-----KGDVKCYVCKTSY 39 (136)
Q Consensus 13 FCp~CgnlL~~~~~-----~~~~~C~~C~~~~ 39 (136)
=||.|+.-..+++. +..+.|+.|++.+
T Consensus 4 ~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 49999998887743 3579999999865
No 72
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=86.79 E-value=0.55 Score=41.23 Aligned_cols=22 Identities=23% Similarity=0.463 Sum_probs=16.2
Q ss_pred cccCCCCCeEEcCCCCCceecC
Q psy4748 21 LPLFDFKGDVKCYVCKTSYGTQ 42 (136)
Q Consensus 21 L~~~~~~~~~~C~~C~~~~~~~ 42 (136)
|.+......|.|+.|||.+.-.
T Consensus 417 ~~~~~~~~~~~c~~c~~~yd~~ 438 (479)
T PRK05452 417 TTTADLGPRMQCSVCQWIYDPA 438 (479)
T ss_pred ccccCCCCeEEECCCCeEECCC
Confidence 4444345689999999999764
No 73
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=86.75 E-value=0.57 Score=28.33 Aligned_cols=28 Identities=25% Similarity=0.494 Sum_probs=22.6
Q ss_pred ccccCCCccccCCCCCeEEcCCCCCceec
Q psy4748 13 FCSKCGTILPLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 13 FCp~CgnlL~~~~~~~~~~C~~C~~~~~~ 41 (136)
-|.+||.-..++. .+.+.|+.||+..-.
T Consensus 4 ~C~~Cg~~~~~~~-~~~irC~~CG~rIly 31 (44)
T smart00659 4 ICGECGRENEIKS-KDVVRCRECGYRILY 31 (44)
T ss_pred ECCCCCCEeecCC-CCceECCCCCceEEE
Confidence 4999999888763 578999999987654
No 74
>PRK11827 hypothetical protein; Provisional
Probab=86.57 E-value=0.86 Score=29.50 Aligned_cols=39 Identities=21% Similarity=0.332 Sum_probs=31.7
Q ss_pred cccccccCCCccccCCCCCeEEcCCCCCceecCCCCCCc
Q psy4748 10 ESEFCSKCGTILPLFDFKGDVKCYVCKTSYGTQEQQPLL 48 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~~~~~~~~ 48 (136)
++.-||.|+.=|....+...++|..|+-.+++.++=|.+
T Consensus 7 eILaCP~ckg~L~~~~~~~~Lic~~~~laYPI~dgIPVl 45 (60)
T PRK11827 7 EIIACPVCNGKLWYNQEKQELICKLDNLAFPLRDGIPVL 45 (60)
T ss_pred hheECCCCCCcCeEcCCCCeEECCccCeeccccCCcccc
Confidence 567899999999887666789999999999997654433
No 75
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=86.07 E-value=0.46 Score=31.56 Aligned_cols=29 Identities=31% Similarity=0.584 Sum_probs=21.3
Q ss_pred ccccCCCccccCCCCCeEEcCCCCCceecCC
Q psy4748 13 FCSKCGTILPLFDFKGDVKCYVCKTSYGTQE 43 (136)
Q Consensus 13 FCp~CgnlL~~~~~~~~~~C~~C~~~~~~~~ 43 (136)
=| +||+.|+.+++..+-.| .||+...+.+
T Consensus 5 rC-~Cgr~lya~e~~kTkkC-~CG~~l~vk~ 33 (68)
T PF09082_consen 5 RC-DCGRYLYAKEGAKTKKC-VCGKTLKVKE 33 (68)
T ss_dssp EE-TTS--EEEETT-SEEEE-TTTEEEE--S
T ss_pred Ee-cCCCEEEecCCcceeEe-cCCCeeeeee
Confidence 48 89999999988778899 9999998864
No 76
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=85.85 E-value=1.1 Score=26.20 Aligned_cols=25 Identities=32% Similarity=0.792 Sum_probs=15.7
Q ss_pred cccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 104 KCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 104 ~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
+||+|++ .|.=..+ +-...+.|.+|
T Consensus 1 ~CP~C~~-~l~~~~~-------~~~~id~C~~C 25 (41)
T PF13453_consen 1 KCPRCGT-ELEPVRL-------GDVEIDVCPSC 25 (41)
T ss_pred CcCCCCc-ccceEEE-------CCEEEEECCCC
Confidence 5999988 4432222 33667888877
No 77
>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=85.60 E-value=0.57 Score=29.63 Aligned_cols=27 Identities=22% Similarity=0.426 Sum_probs=21.5
Q ss_pred ccccccccCCCccccCCCCCeEEcCCCCCcee
Q psy4748 9 VESEFCSKCGTILPLFDFKGDVKCYVCKTSYG 40 (136)
Q Consensus 9 ~~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~ 40 (136)
-.+..||.||++..+ ..+|..|||-..
T Consensus 24 p~l~~C~~cG~~~~~-----H~vc~~cG~Y~g 50 (55)
T TIGR01031 24 PTLVVCPNCGEFKLP-----HRVCPSCGYYKG 50 (55)
T ss_pred CcceECCCCCCcccC-----eeECCccCeECC
Confidence 356689999998766 789999997654
No 78
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=85.34 E-value=0.51 Score=25.86 Aligned_cols=21 Identities=29% Similarity=0.570 Sum_probs=12.0
Q ss_pred ccccCCCccccCCCCCeEEcC
Q psy4748 13 FCSKCGTILPLFDFKGDVKCY 33 (136)
Q Consensus 13 FCp~CgnlL~~~~~~~~~~C~ 33 (136)
+||.||+-|.-.++.-.+.|.
T Consensus 1 ~CP~C~s~l~~~~~ev~~~C~ 21 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDIRCP 21 (28)
T ss_dssp B-TTT--BEEE-CCTTCEEE-
T ss_pred CcCCCCCEeEcCCCCEeEECC
Confidence 699999999966554466665
No 79
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=85.29 E-value=0.55 Score=29.27 Aligned_cols=31 Identities=19% Similarity=0.460 Sum_probs=25.2
Q ss_pred cccccCCCccccCCCCCeEEcCCCCCceecC
Q psy4748 12 EFCSKCGTILPLFDFKGDVKCYVCKTSYGTQ 42 (136)
Q Consensus 12 ~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~~ 42 (136)
.-|..||..+...+....+.|+.||+..-..
T Consensus 7 Y~C~~Cg~~~~~~~~~~~irCp~Cg~rIl~K 37 (49)
T COG1996 7 YKCARCGREVELDQETRGIRCPYCGSRILVK 37 (49)
T ss_pred EEhhhcCCeeehhhccCceeCCCCCcEEEEe
Confidence 4599999999765556789999999987664
No 80
>TIGR00515 accD acetyl-CoA carboxylase, carboxyl transferase, beta subunit. The enzyme acetyl-CoA carboxylase contains a biotin carboxyl carrier protein or domain, a biotin carboxylase, and a carboxyl transferase. This model represents the beta chain of the carboxyl transferase for cases in which the architecture of the protein is as in E. coli, in which the carboxyltransferase portion consists of two non-identical subnits, alpha and beta.
Probab=84.73 E-value=0.23 Score=41.18 Aligned_cols=31 Identities=23% Similarity=0.458 Sum_probs=25.8
Q ss_pred ccccccCCCccccCCC-CCeEEcCCCCCceec
Q psy4748 11 SEFCSKCGTILPLFDF-KGDVKCYVCKTSYGT 41 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~-~~~~~C~~C~~~~~~ 41 (136)
+.=||.||.+|+.++- .+..+|+.|+|-...
T Consensus 26 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~rl 57 (285)
T TIGR00515 26 WTKCPKCGQVLYTKELERNLEVCPKCDHHMRM 57 (285)
T ss_pred eeECCCCcchhhHHHHHhhCCCCCCCCCcCcC
Confidence 5679999999999742 457899999997765
No 81
>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=84.43 E-value=0.6 Score=28.31 Aligned_cols=28 Identities=18% Similarity=0.496 Sum_probs=23.1
Q ss_pred cccCCCccccCCC--------CCeEEcCC--CCCceec
Q psy4748 14 CSKCGTILPLFDF--------KGDVKCYV--CKTSYGT 41 (136)
Q Consensus 14 Cp~CgnlL~~~~~--------~~~~~C~~--C~~~~~~ 41 (136)
||.||+.+..... ..++.|.+ ||+...+
T Consensus 2 CP~Cg~~a~ir~S~~~s~~~~~~Y~qC~N~~Cg~tfv~ 39 (47)
T PF04606_consen 2 CPHCGSKARIRTSRQLSPLTRELYCQCTNPECGHTFVA 39 (47)
T ss_pred cCCCCCeeEEEEchhhCcceEEEEEEECCCcCCCEEEE
Confidence 9999999888743 24789998 9998876
No 82
>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=84.39 E-value=0.79 Score=27.40 Aligned_cols=24 Identities=38% Similarity=0.732 Sum_probs=19.2
Q ss_pred cccccCCCccccCCCCCeEEcCCCC
Q psy4748 12 EFCSKCGTILPLFDFKGDVKCYVCK 36 (136)
Q Consensus 12 ~FCp~CgnlL~~~~~~~~~~C~~C~ 36 (136)
.-||.||.-|.-..+ +.+.|..|+
T Consensus 18 ~~Cp~C~~PL~~~k~-g~~~Cv~C~ 41 (41)
T PF06677_consen 18 EHCPDCGTPLMRDKD-GKIYCVSCG 41 (41)
T ss_pred CccCCCCCeeEEecC-CCEECCCCC
Confidence 579999999988444 478899986
No 83
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=84.36 E-value=0.86 Score=38.95 Aligned_cols=23 Identities=30% Similarity=0.560 Sum_probs=18.5
Q ss_pred eccccccCCCceEEEE--eeccccC
Q psy4748 102 ERKCKRCNNDTMSYAT--LQLRSAD 124 (136)
Q Consensus 102 ~~~CpkCg~~~a~f~~--~Q~RSAD 124 (136)
...||.|+.....||. +|+|+.-
T Consensus 129 ~~~Cp~C~r~~~~y~eAivQvR~~~ 153 (355)
T COG1499 129 RTLCPRCSRFTGGYYEAIVQVRAKG 153 (355)
T ss_pred EeEChhhhccccceeEEEEEEEecc
Confidence 5689999998888875 5999763
No 84
>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=84.20 E-value=1.4 Score=25.62 Aligned_cols=34 Identities=18% Similarity=0.478 Sum_probs=22.3
Q ss_pred CceeccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 99 PIVERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 99 ~~~~~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
++|+..||.|+..+.++---+.. .| ..-|.|..|
T Consensus 2 a~i~v~CP~C~s~~~v~k~G~~~---~G-~qryrC~~C 35 (36)
T PF03811_consen 2 AKIDVHCPRCQSTEGVKKNGKSP---SG-HQRYRCKDC 35 (36)
T ss_pred CcEeeeCCCCCCCCcceeCCCCC---CC-CEeEecCcC
Confidence 57899999999999665432221 22 234777766
No 85
>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=84.17 E-value=0.56 Score=26.86 Aligned_cols=25 Identities=20% Similarity=0.518 Sum_probs=18.7
Q ss_pred ccccCCCccccCC---CCCeEEcCCCCC
Q psy4748 13 FCSKCGTILPLFD---FKGDVKCYVCKT 37 (136)
Q Consensus 13 FCp~CgnlL~~~~---~~~~~~C~~C~~ 37 (136)
.|++||+...... +.....|+.||.
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (41)
T smart00834 7 RCEDCGHTFEVLQKISDDPLATCPECGG 34 (41)
T ss_pred EcCCCCCEEEEEEecCCCCCCCCCCCCC
Confidence 6999999655432 245789999997
No 86
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=84.02 E-value=0.64 Score=33.34 Aligned_cols=30 Identities=30% Similarity=0.348 Sum_probs=24.9
Q ss_pred cccccCCCccccCCC--------CCeEEcCCCCCceec
Q psy4748 12 EFCSKCGTILPLFDF--------KGDVKCYVCKTSYGT 41 (136)
Q Consensus 12 ~FCp~CgnlL~~~~~--------~~~~~C~~C~~~~~~ 41 (136)
.||..|+++|.|-.+ ...+.|..||+....
T Consensus 57 ~~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~~R~ 94 (105)
T COG2023 57 TICKKCYTPLVPGKNARVRLRKGRVVVTCLECGTIRRY 94 (105)
T ss_pred HhccccCcccccCcceEEEEcCCeEEEEecCCCcEEEe
Confidence 599999999999744 147899999998765
No 87
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=83.65 E-value=0.25 Score=41.22 Aligned_cols=33 Identities=12% Similarity=0.032 Sum_probs=26.5
Q ss_pred cccccccCCCccccCCC-CCeEEcCCCCCceecC
Q psy4748 10 ESEFCSKCGTILPLFDF-KGDVKCYVCKTSYGTQ 42 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~-~~~~~C~~C~~~~~~~ 42 (136)
-+.=||.|+.+|+.++- .+.++|+.|+|-....
T Consensus 37 lw~kc~~C~~~~~~~~l~~~~~vcp~c~~h~rlt 70 (296)
T CHL00174 37 LWVQCENCYGLNYKKFLKSKMNICEQCGYHLKMS 70 (296)
T ss_pred CeeECCCccchhhHHHHHHcCCCCCCCCCCcCCC
Confidence 35679999999999853 4578999999976653
No 88
>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=83.29 E-value=0.45 Score=27.00 Aligned_cols=25 Identities=24% Similarity=0.669 Sum_probs=18.6
Q ss_pred cccCCCccccCCCCCeEEcCCCCCce
Q psy4748 14 CSKCGTILPLFDFKGDVKCYVCKTSY 39 (136)
Q Consensus 14 Cp~CgnlL~~~~~~~~~~C~~C~~~~ 39 (136)
|.+||....++. .+.+.|+.||+..
T Consensus 3 C~~Cg~~~~~~~-~~~irC~~CG~RI 27 (32)
T PF03604_consen 3 CGECGAEVELKP-GDPIRCPECGHRI 27 (32)
T ss_dssp ESSSSSSE-BST-SSTSSBSSSS-SE
T ss_pred CCcCCCeeEcCC-CCcEECCcCCCeE
Confidence 889999888764 3578999999864
No 89
>KOG3507|consensus
Probab=83.27 E-value=0.7 Score=29.97 Aligned_cols=28 Identities=21% Similarity=0.466 Sum_probs=22.9
Q ss_pred ccccccCCCccccCCCCCeEEcCCCCCce
Q psy4748 11 SEFCSKCGTILPLFDFKGDVKCYVCKTSY 39 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~~~~~~C~~C~~~~ 39 (136)
+.-|.+||.-+.++. ++.+.||-|||..
T Consensus 20 iYiCgdC~~en~lk~-~D~irCReCG~RI 47 (62)
T KOG3507|consen 20 IYICGDCGQENTLKR-GDVIRCRECGYRI 47 (62)
T ss_pred EEEeccccccccccC-CCcEehhhcchHH
Confidence 357999999888865 4799999999864
No 90
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=83.10 E-value=1.1 Score=33.65 Aligned_cols=15 Identities=20% Similarity=0.441 Sum_probs=12.0
Q ss_pred CCeEEcCCCCCceec
Q psy4748 27 KGDVKCYVCKTSYGT 41 (136)
Q Consensus 27 ~~~~~C~~C~~~~~~ 41 (136)
.+.++|..||+....
T Consensus 110 ~G~l~C~~Cg~~~~~ 124 (146)
T PF07295_consen 110 PGTLVCENCGHEVEL 124 (146)
T ss_pred CceEecccCCCEEEe
Confidence 368999999987665
No 91
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=82.76 E-value=0.3 Score=40.52 Aligned_cols=32 Identities=19% Similarity=0.352 Sum_probs=26.2
Q ss_pred ccccccCCCccccCCC-CCeEEcCCCCCceecC
Q psy4748 11 SEFCSKCGTILPLFDF-KGDVKCYVCKTSYGTQ 42 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~-~~~~~C~~C~~~~~~~ 42 (136)
+.=||.|+.+|+.++- .+..+|+.|+|-....
T Consensus 27 ~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~rl~ 59 (292)
T PRK05654 27 WTKCPSCGQVLYRKELEANLNVCPKCGHHMRIS 59 (292)
T ss_pred eeECCCccchhhHHHHHhcCCCCCCCCCCeeCC
Confidence 6789999999999853 3568999999987653
No 92
>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=82.09 E-value=2.4 Score=26.17 Aligned_cols=31 Identities=16% Similarity=0.511 Sum_probs=18.3
Q ss_pred ccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 103 RKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 103 ~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
+.||.||.....+.- +..|-+-.-+|.|.+|
T Consensus 2 kPCPfCGg~~~~~~~---~~~~~~~~~~~~C~~C 32 (53)
T TIGR03655 2 KPCPFCGGADVYLRR---GFDPLDLSHYFECSTC 32 (53)
T ss_pred CCCCCCCCcceeeEe---ccCCCCCEEEEECCCC
Confidence 468999886554421 1234445555678776
No 93
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=81.74 E-value=0.9 Score=31.79 Aligned_cols=33 Identities=18% Similarity=0.346 Sum_probs=25.2
Q ss_pred cccccccCCCccccCCCCCeEEcCCCCCceecC
Q psy4748 10 ESEFCSKCGTILPLFDFKGDVKCYVCKTSYGTQ 42 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~~ 42 (136)
....||.||..=.-+...++|.|+.|++...--
T Consensus 34 a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGG 66 (91)
T TIGR00280 34 AKYVCPFCGKKTVKRGSTGIWTCRKCGAKFAGG 66 (91)
T ss_pred cCccCCCCCCCceEEEeeEEEEcCCCCCEEeCC
Confidence 446899999755444556899999999998653
No 94
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=81.70 E-value=0.65 Score=29.18 Aligned_cols=32 Identities=25% Similarity=0.499 Sum_probs=25.5
Q ss_pred cccccCCCccccCC-C-CCeEEcCCCCCceecCC
Q psy4748 12 EFCSKCGTILPLFD-F-KGDVKCYVCKTSYGTQE 43 (136)
Q Consensus 12 ~FCp~CgnlL~~~~-~-~~~~~C~~C~~~~~~~~ 43 (136)
.=|+.||.+|---. . ...+.|+.|+..+.+..
T Consensus 5 iRC~~CnklLa~~g~~~~leIKCpRC~tiN~~~a 38 (51)
T PF10122_consen 5 IRCGHCNKLLAKAGEVIELEIKCPRCKTINHVRA 38 (51)
T ss_pred eeccchhHHHhhhcCccEEEEECCCCCccceEec
Confidence 45999999998843 2 36899999999988753
No 95
>KOG3084|consensus
Probab=81.54 E-value=0.91 Score=38.50 Aligned_cols=31 Identities=23% Similarity=0.567 Sum_probs=23.8
Q ss_pred ccccccCCCccccCCCCCeEEcC--CCC---Cceec
Q psy4748 11 SEFCSKCGTILPLFDFKGDVKCY--VCK---TSYGT 41 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~~~~~~C~--~C~---~~~~~ 41 (136)
..|||-||+-+-+.+.+....|+ .|. +.++.
T Consensus 150 ykFCp~CG~~tkp~e~g~k~~Cs~~~C~~~n~~yPr 185 (345)
T KOG3084|consen 150 YKFCPGCGSPTKPEEAGTKLQCSDETCPSCNVIYPR 185 (345)
T ss_pred hccCcccCCCcccccCCccceeecccCCcCCeeccC
Confidence 47999999999999887777776 565 44444
No 96
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=81.52 E-value=1.1 Score=37.09 Aligned_cols=31 Identities=26% Similarity=0.519 Sum_probs=21.7
Q ss_pred cccccccCCC-ccccCCCCCeEEcCCCCCcee
Q psy4748 10 ESEFCSKCGT-ILPLFDFKGDVKCYVCKTSYG 40 (136)
Q Consensus 10 ~~~FCp~Cgn-lL~~~~~~~~~~C~~C~~~~~ 40 (136)
....||+||+ -+......+.++|..||+...
T Consensus 10 ~~~~Cp~Cg~~~iv~d~~~Ge~vC~~CG~Vl~ 41 (310)
T PRK00423 10 EKLVCPECGSDKLIYDYERGEIVCADCGLVIE 41 (310)
T ss_pred cCCcCcCCCCCCeeEECCCCeEeecccCCccc
Confidence 3458999998 222223357999999999754
No 97
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=81.45 E-value=0.47 Score=39.46 Aligned_cols=33 Identities=18% Similarity=0.316 Sum_probs=27.2
Q ss_pred cccccccCCCccccCCC-CCeEEcCCCCCceecC
Q psy4748 10 ESEFCSKCGTILPLFDF-KGDVKCYVCKTSYGTQ 42 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~-~~~~~C~~C~~~~~~~ 42 (136)
-+.=||.||.|||.++- .+..+|..|+|-..+.
T Consensus 27 lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ri~ 60 (294)
T COG0777 27 LWTKCPSCGEMLYRKELESNLKVCPKCGHHMRIS 60 (294)
T ss_pred ceeECCCccceeeHHHHHhhhhcccccCcccccC
Confidence 34679999999999863 5689999999987764
No 98
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=81.44 E-value=1.3 Score=28.11 Aligned_cols=29 Identities=24% Similarity=0.411 Sum_probs=23.9
Q ss_pred cccccCCCccccCCCCCeEEcCCCCCceecC
Q psy4748 12 EFCSKCGTILPLFDFKGDVKCYVCKTSYGTQ 42 (136)
Q Consensus 12 ~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~~ 42 (136)
.-|+.||--|.+. .+.++|..||..+...
T Consensus 6 ~~C~~Cg~~~~~~--dDiVvCp~CgapyHR~ 34 (54)
T PF14446_consen 6 CKCPVCGKKFKDG--DDIVVCPECGAPYHRD 34 (54)
T ss_pred ccChhhCCcccCC--CCEEECCCCCCcccHH
Confidence 4599999888773 4699999999998873
No 99
>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=81.43 E-value=1.2 Score=29.72 Aligned_cols=31 Identities=19% Similarity=0.462 Sum_probs=23.5
Q ss_pred ccccCCCccccC----CCCCeEEcCCCCCceecCC
Q psy4748 13 FCSKCGTILPLF----DFKGDVKCYVCKTSYGTQE 43 (136)
Q Consensus 13 FCp~CgnlL~~~----~~~~~~~C~~C~~~~~~~~ 43 (136)
-||.|+.|=.+. .+..+..|-.|||......
T Consensus 10 ~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~~~~ 44 (71)
T PF09526_consen 10 VCPKCQAMDTIMMWRENGVEYVECVECGYTERQPD 44 (71)
T ss_pred cCCCCcCccEEEEEEeCCceEEEecCCCCeeccCC
Confidence 499999874333 3456899999999988753
No 100
>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=81.38 E-value=2 Score=25.75 Aligned_cols=27 Identities=22% Similarity=0.669 Sum_probs=19.3
Q ss_pred cccccCCCccccC-CCCCeEEcCCCCCc
Q psy4748 12 EFCSKCGTILPLF-DFKGDVKCYVCKTS 38 (136)
Q Consensus 12 ~FCp~CgnlL~~~-~~~~~~~C~~C~~~ 38 (136)
..||.||+.=... .....+.|..|+++
T Consensus 19 ~~CP~Cg~~~~~~~~~~~~~~C~~C~~q 46 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKTRGRYRCKACRKQ 46 (46)
T ss_pred CCCCCCCCeeeEEeCCCCeEECCCCCCc
Confidence 4599999972222 23479999999874
No 101
>PRK11032 hypothetical protein; Provisional
Probab=81.38 E-value=1.4 Score=33.76 Aligned_cols=14 Identities=21% Similarity=0.617 Sum_probs=11.3
Q ss_pred CeEEcCCCCCceec
Q psy4748 28 GDVKCYVCKTSYGT 41 (136)
Q Consensus 28 ~~~~C~~C~~~~~~ 41 (136)
+.++|..||+....
T Consensus 123 G~LvC~~Cg~~~~~ 136 (160)
T PRK11032 123 GNLVCEKCHHHLAF 136 (160)
T ss_pred ceEEecCCCCEEEe
Confidence 68899999977665
No 102
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=80.62 E-value=1.3 Score=31.39 Aligned_cols=33 Identities=15% Similarity=0.342 Sum_probs=22.7
Q ss_pred cccccccCCCc-cccC--CCCCeEEcCCCCCceecC
Q psy4748 10 ESEFCSKCGTI-LPLF--DFKGDVKCYVCKTSYGTQ 42 (136)
Q Consensus 10 ~~~FCp~Cgnl-L~~~--~~~~~~~C~~C~~~~~~~ 42 (136)
.+.-||.||+. |..+ .....++|+.||+.....
T Consensus 20 t~f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~~~~ 55 (99)
T PRK14892 20 KIFECPRCGKVSISVKIKKNIAIITCGNCGLYTEFE 55 (99)
T ss_pred cEeECCCCCCeEeeeecCCCcceEECCCCCCccCEE
Confidence 34569999953 3222 234689999999988664
No 103
>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=80.57 E-value=1.3 Score=31.77 Aligned_cols=34 Identities=21% Similarity=0.478 Sum_probs=27.3
Q ss_pred CccccccccCCCccccCCCCCeEEcCCCCCceecC
Q psy4748 8 NVESEFCSKCGTILPLFDFKGDVKCYVCKTSYGTQ 42 (136)
Q Consensus 8 ~~~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~~ 42 (136)
+|.-+.||.||.-.|=-. +.-++|+.||..+...
T Consensus 6 lGtKR~Cp~CG~kFYDLn-k~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 6 LGTKRTCPSCGAKFYDLN-KDPIVCPKCGTEFPPE 39 (108)
T ss_pred cCCcccCCCCcchhccCC-CCCccCCCCCCccCcc
Confidence 456789999999877643 3578999999999875
No 104
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=80.54 E-value=1.1 Score=29.62 Aligned_cols=27 Identities=26% Similarity=0.651 Sum_probs=18.4
Q ss_pred ccccccCCCceEEEEeeccccCCCceEEE
Q psy4748 103 RKCKRCNNDTMSYATLQLRSADEGQTIFF 131 (136)
Q Consensus 103 ~~CpkCg~~~a~f~~~Q~RSADEg~TvFY 131 (136)
.+|||||+.+ |.+-|++-..++..-||
T Consensus 5 ~kCpKCgn~~--~~ekei~~tg~~lskif 31 (68)
T COG3478 5 FKCPKCGNTN--YEEKEIAATGGGLSKIF 31 (68)
T ss_pred ccCCCcCCcc--hhhceeeccCCCcceeE
Confidence 4599999986 45666666666655443
No 105
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=80.20 E-value=1.2 Score=31.02 Aligned_cols=32 Identities=25% Similarity=0.430 Sum_probs=24.4
Q ss_pred cccccccCCCccccCCCCCeEEcCCCCCceec
Q psy4748 10 ESEFCSKCGTILPLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~ 41 (136)
....||.||..=.-+...++|.|+.|++...-
T Consensus 35 a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AG 66 (90)
T PTZ00255 35 AKYFCPFCGKHAVKRQAVGIWRCKGCKKTVAG 66 (90)
T ss_pred CCccCCCCCCCceeeeeeEEEEcCCCCCEEeC
Confidence 44689999865444445679999999999865
No 106
>PRK00420 hypothetical protein; Validated
Probab=80.02 E-value=1.7 Score=31.39 Aligned_cols=30 Identities=30% Similarity=0.558 Sum_probs=23.5
Q ss_pred cccccCCCccccCCCCCeEEcCCCCCceecC
Q psy4748 12 EFCSKCGTILPLFDFKGDVKCYVCKTSYGTQ 42 (136)
Q Consensus 12 ~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~~ 42 (136)
.-||.||.-|.-.. .+...|+.||......
T Consensus 24 ~~CP~Cg~pLf~lk-~g~~~Cp~Cg~~~~v~ 53 (112)
T PRK00420 24 KHCPVCGLPLFELK-DGEVVCPVHGKVYIVK 53 (112)
T ss_pred CCCCCCCCcceecC-CCceECCCCCCeeeec
Confidence 57999998777642 3589999999977654
No 107
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=78.97 E-value=1.8 Score=28.90 Aligned_cols=32 Identities=16% Similarity=0.251 Sum_probs=25.4
Q ss_pred ccccccCCCccccCCC--------CCeEEcC--CCCCceecC
Q psy4748 11 SEFCSKCGTILPLFDF--------KGDVKCY--VCKTSYGTQ 42 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~--------~~~~~C~--~C~~~~~~~ 42 (136)
|+.||.||.-...... ..+..|. .||+.....
T Consensus 1 mm~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF~t~ 42 (72)
T PRK09678 1 MFHCPLCQHAAHARTSRYITDTTKERYHQCQNVNCSATFITY 42 (72)
T ss_pred CccCCCCCCccEEEEChhcChhhheeeeecCCCCCCCEEEEE
Confidence 5789999999876643 2478999 899988773
No 108
>PRK07219 DNA topoisomerase I; Validated
Probab=78.84 E-value=4.9 Score=37.70 Aligned_cols=11 Identities=27% Similarity=0.782 Sum_probs=8.9
Q ss_pred eeccccccCCC
Q psy4748 101 VERKCKRCNND 111 (136)
Q Consensus 101 ~~~~CpkCg~~ 111 (136)
++..||+||.+
T Consensus 732 ~~~~CpkCg~~ 742 (822)
T PRK07219 732 TDEKCPECGLP 742 (822)
T ss_pred ccCCCCCCCCe
Confidence 46789999975
No 109
>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=78.74 E-value=0.98 Score=29.86 Aligned_cols=28 Identities=25% Similarity=0.415 Sum_probs=15.9
Q ss_pred cccccccCCCccccCCC-------------CCeEEcCCCCC
Q psy4748 10 ESEFCSKCGTILPLFDF-------------KGDVKCYVCKT 37 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~-------------~~~~~C~~C~~ 37 (136)
...||..||++|.|-.. ...+.|..||.
T Consensus 45 kr~~Ck~C~~~liPG~~~~vri~~~~~~~~~l~~~C~~C~~ 85 (85)
T PF04032_consen 45 KRTICKKCGSLLIPGVNCSVRIRKKKKKKNFLVYTCLNCGH 85 (85)
T ss_dssp CCTB-TTT--B--CTTTEEEEEE---SSS-EEEEEETTTTE
T ss_pred hcccccCCCCEEeCCCccEEEEEecCCCCCEEEEEccccCC
Confidence 45799999999999632 12577888873
No 110
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=78.54 E-value=2.6 Score=27.27 Aligned_cols=28 Identities=18% Similarity=0.443 Sum_probs=20.8
Q ss_pred ccccccCCCccccCC-----CCCeEEcCCCCCc
Q psy4748 11 SEFCSKCGTILPLFD-----FKGDVKCYVCKTS 38 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~-----~~~~~~C~~C~~~ 38 (136)
...||.||..+..+- ....|.|+.||+.
T Consensus 25 ~F~CPnCG~~~I~RC~~CRk~~~~Y~CP~CGF~ 57 (59)
T PRK14890 25 KFLCPNCGEVIIYRCEKCRKQSNPYTCPKCGFE 57 (59)
T ss_pred EeeCCCCCCeeEeechhHHhcCCceECCCCCCc
Confidence 347999999865552 2468999999985
No 111
>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=78.51 E-value=0.58 Score=29.51 Aligned_cols=27 Identities=22% Similarity=0.372 Sum_probs=20.4
Q ss_pred cccccccCCCccccCCCCCeEEcCCCCCceec
Q psy4748 10 ESEFCSKCGTILPLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~ 41 (136)
.+..||.||.+-.+ ..+|..|||....
T Consensus 25 ~l~~c~~cg~~~~~-----H~vc~~cG~y~~r 51 (56)
T PF01783_consen 25 NLVKCPNCGEPKLP-----HRVCPSCGYYKGR 51 (56)
T ss_dssp SEEESSSSSSEEST-----TSBCTTTBBSSSS
T ss_pred ceeeeccCCCEecc-----cEeeCCCCeECCE
Confidence 56789999987666 4589999876544
No 112
>PF14353 CpXC: CpXC protein
Probab=78.20 E-value=1.4 Score=31.49 Aligned_cols=13 Identities=15% Similarity=0.608 Sum_probs=10.9
Q ss_pred EEcCCCCCceecC
Q psy4748 30 VKCYVCKTSYGTQ 42 (136)
Q Consensus 30 ~~C~~C~~~~~~~ 42 (136)
+.|+.|++....+
T Consensus 2 itCP~C~~~~~~~ 14 (128)
T PF14353_consen 2 ITCPHCGHEFEFE 14 (128)
T ss_pred cCCCCCCCeeEEE
Confidence 6899999988873
No 113
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=78.09 E-value=1.8 Score=34.07 Aligned_cols=29 Identities=24% Similarity=0.375 Sum_probs=24.7
Q ss_pred ccccccCCCccccCCCCCeEEcCCCCCceec
Q psy4748 11 SEFCSKCGTILPLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~ 41 (136)
.--|+.|+..|.. ....+.|+.||+.+..
T Consensus 149 ~A~CsrC~~~L~~--~~~~l~Cp~Cg~tEkR 177 (188)
T COG1096 149 YARCSRCRAPLVK--KGNMLKCPNCGNTEKR 177 (188)
T ss_pred EEEccCCCcceEE--cCcEEECCCCCCEEee
Confidence 3479999999999 4569999999998865
No 114
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=77.74 E-value=0.99 Score=28.10 Aligned_cols=12 Identities=58% Similarity=1.262 Sum_probs=10.6
Q ss_pred cccccccCCCcc
Q psy4748 10 ESEFCSKCGTIL 21 (136)
Q Consensus 10 ~~~FCp~CgnlL 21 (136)
.+.|||.||-||
T Consensus 45 ~i~~Cp~CgRiL 56 (56)
T PF02591_consen 45 EIVFCPNCGRIL 56 (56)
T ss_pred CeEECcCCCccC
Confidence 578999999987
No 115
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=77.59 E-value=1.4 Score=26.73 Aligned_cols=29 Identities=14% Similarity=0.212 Sum_probs=22.2
Q ss_pred ccccccccCCCccccCCC---CCeEEcCCCCC
Q psy4748 9 VESEFCSKCGTILPLFDF---KGDVKCYVCKT 37 (136)
Q Consensus 9 ~~~~FCp~CgnlL~~~~~---~~~~~C~~C~~ 37 (136)
.++.+|+.||.-|..... ...|.|+....
T Consensus 3 ~g~l~C~~CG~~m~~~~~~~~~~yy~C~~~~~ 34 (58)
T PF13408_consen 3 SGLLRCGHCGSKMTRRKRKGKYRYYRCSNRRR 34 (58)
T ss_pred CCcEEcccCCcEeEEEECCCCceEEEcCCCcC
Confidence 468899999999998743 25788887653
No 116
>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=77.39 E-value=2 Score=38.45 Aligned_cols=36 Identities=17% Similarity=0.588 Sum_probs=24.4
Q ss_pred eeccccccCCCc-eEEEEeeccccCCCceEEEEecCC
Q psy4748 101 VERKCKRCNNDT-MSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 101 ~~~~CpkCg~~~-a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
=-..||.||+.. +.|-.++--.-..+.++.|+|+.|
T Consensus 199 ~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~C 235 (557)
T PF05876_consen 199 YYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHC 235 (557)
T ss_pred EEccCCCCCCCccccccceeecCCCCccceEEECCCC
Confidence 357999999944 444444441111579999999988
No 117
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=77.25 E-value=1.5 Score=30.65 Aligned_cols=32 Identities=19% Similarity=0.354 Sum_probs=25.0
Q ss_pred cccccccCCCccccCCCCCeEEcCCCCCceec
Q psy4748 10 ESEFCSKCGTILPLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~ 41 (136)
.-..||.||..=.-+...++|.|+.|++...-
T Consensus 35 a~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AG 66 (90)
T PRK03976 35 AKHVCPVCGRPKVKRVGTGIWECRKCGAKFAG 66 (90)
T ss_pred cCccCCCCCCCceEEEEEEEEEcCCCCCEEeC
Confidence 34689999866555556689999999999865
No 118
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=76.98 E-value=1.6 Score=27.00 Aligned_cols=33 Identities=18% Similarity=0.362 Sum_probs=22.6
Q ss_pred ccCccccccc--cCCCccccCCCCCeEEcCCCCCc
Q psy4748 6 YFNVESEFCS--KCGTILPLFDFKGDVKCYVCKTS 38 (136)
Q Consensus 6 ~~~~~~~FCp--~CgnlL~~~~~~~~~~C~~C~~~ 38 (136)
........|| +||.-..+.+-.+++.|..|++.
T Consensus 13 kv~r~rk~CP~~~CG~GvFMA~H~dR~~CGKCg~T 47 (47)
T PF01599_consen 13 KVKRLRKECPSPRCGAGVFMAEHKDRHYCGKCGYT 47 (47)
T ss_dssp EEEESSEE-TSTTTTSSSEEEE-SSEEEETTTSS-
T ss_pred cEEEhhhcCCCcccCCceEeeecCCCccCCCcccC
Confidence 3445567999 99996555444679999999974
No 119
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=76.88 E-value=3.9 Score=38.66 Aligned_cols=30 Identities=20% Similarity=0.192 Sum_probs=20.7
Q ss_pred cccccCCC-ccccCC--CCCeEEcCC---CCCceec
Q psy4748 12 EFCSKCGT-ILPLFD--FKGDVKCYV---CKTSYGT 41 (136)
Q Consensus 12 ~FCp~Cgn-lL~~~~--~~~~~~C~~---C~~~~~~ 41 (136)
.=||.||. +|..+. .+..+.|.. |+|..+.
T Consensus 593 ~~CP~Cg~~~L~~k~gr~G~Fl~Cs~yP~C~~t~~~ 628 (860)
T PRK06319 593 IDCPKCHKGKLVKIWAKNRYFYGCSEYPECDYKTSE 628 (860)
T ss_pred cccCCCCCcceeEEecCCCceeeccCCccccccCCc
Confidence 56999964 565542 356889976 8877665
No 120
>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=76.87 E-value=2.2 Score=27.53 Aligned_cols=31 Identities=19% Similarity=0.372 Sum_probs=23.0
Q ss_pred ccccCCCccccC----CCCCeEEcCCCCCceecCC
Q psy4748 13 FCSKCGTILPLF----DFKGDVKCYVCKTSYGTQE 43 (136)
Q Consensus 13 FCp~CgnlL~~~----~~~~~~~C~~C~~~~~~~~ 43 (136)
-||.|+.|=.+. .+...+.|-.|||.....+
T Consensus 11 ~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~~~~~ 45 (59)
T TIGR02443 11 VCPACSAQDTLAMWKENNIELVECVECGYQEQQKD 45 (59)
T ss_pred cCCCCcCccEEEEEEeCCceEEEeccCCCccccCC
Confidence 499999874443 2346899999999987643
No 121
>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=76.54 E-value=0.75 Score=29.31 Aligned_cols=20 Identities=25% Similarity=0.501 Sum_probs=13.6
Q ss_pred eeccccccCCCceEEEEeec
Q psy4748 101 VERKCKRCNNDTMSYATLQL 120 (136)
Q Consensus 101 ~~~~CpkCg~~~a~f~~~Q~ 120 (136)
++.+||+|++...+|-..|+
T Consensus 6 m~VkCp~C~~~q~vFSha~t 25 (55)
T PF01667_consen 6 MDVKCPGCYNIQTVFSHAQT 25 (55)
T ss_dssp EEEE-TTT-SEEEEETT-SS
T ss_pred EEEECCCCCCeeEEEecCCe
Confidence 57899999999999866554
No 122
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=76.18 E-value=3.9 Score=25.42 Aligned_cols=32 Identities=22% Similarity=0.533 Sum_probs=17.2
Q ss_pred ccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 103 RKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 103 ~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
..||-||.......+ ...-+.++..+-.|.+|
T Consensus 4 kPCPFCG~~~~~~~~--~~~~~~~~~~~V~C~~C 35 (61)
T PF14354_consen 4 KPCPFCGSADVLIRQ--DEGFDYGMYYYVECTDC 35 (61)
T ss_pred cCCCCCCCcceEeec--ccCCCCCCEEEEEcCCC
Confidence 468888776665544 22223333333447666
No 123
>PF11792 Baculo_LEF5_C: Baculoviridae late expression factor 5 C-terminal domain; InterPro: IPR021758 This C-terminal domain is likely to be a zinc-binding domain.
Probab=75.76 E-value=0.13 Score=31.31 Aligned_cols=28 Identities=32% Similarity=0.635 Sum_probs=18.9
Q ss_pred cCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 108 CNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 108 Cg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
|.|.=. ....|+|+.||--+.+=.|.+|
T Consensus 13 C~H~f~-~~E~Q~RAGDE~VSfI~~C~~C 40 (43)
T PF11792_consen 13 CKHKFV-TIEKQLRAGDEAVSFIKYCQKC 40 (43)
T ss_pred ceeeee-ehhhhhcccchHHHHHHHHHHh
Confidence 666544 4557999999976655556555
No 124
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=75.45 E-value=1.5 Score=38.38 Aligned_cols=30 Identities=20% Similarity=0.493 Sum_probs=25.5
Q ss_pred cccccCCCccccCCCCCeEEcCCCCCceecC
Q psy4748 12 EFCSKCGTILPLFDFKGDVKCYVCKTSYGTQ 42 (136)
Q Consensus 12 ~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~~ 42 (136)
--||.||.-|.....+ -|.|+.||+..+..
T Consensus 351 p~Cp~Cg~~m~S~G~~-g~rC~kCg~~~~~~ 380 (421)
T COG1571 351 PVCPRCGGRMKSAGRN-GFRCKKCGTRARET 380 (421)
T ss_pred CCCCccCCchhhcCCC-CcccccccccCCcc
Confidence 4799999999887655 89999999988764
No 125
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=75.30 E-value=1.9 Score=27.84 Aligned_cols=21 Identities=19% Similarity=0.610 Sum_probs=16.1
Q ss_pred ceeccccccCCCceEEEEeec
Q psy4748 100 IVERKCKRCNNDTMSYATLQL 120 (136)
Q Consensus 100 ~~~~~CpkCg~~~a~f~~~Q~ 120 (136)
=.+.+||+|+|....|--.|+
T Consensus 9 F~~VkCp~C~n~q~vFsha~t 29 (59)
T PRK00415 9 FLKVKCPDCGNEQVVFSHAST 29 (59)
T ss_pred EEEEECCCCCCeEEEEecCCc
Confidence 357889999999988866553
No 126
>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=75.09 E-value=1.5 Score=26.50 Aligned_cols=26 Identities=23% Similarity=0.522 Sum_probs=18.3
Q ss_pred ccccCCC---ccccCCCCCeEEcCCCCCc
Q psy4748 13 FCSKCGT---ILPLFDFKGDVKCYVCKTS 38 (136)
Q Consensus 13 FCp~Cgn---lL~~~~~~~~~~C~~C~~~ 38 (136)
.|++||. +|....+.....|+.||..
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~ 35 (52)
T TIGR02605 7 RCTACGHRFEVLQKMSDDPLATCPECGGE 35 (52)
T ss_pred EeCCCCCEeEEEEecCCCCCCCCCCCCCC
Confidence 6999999 4443333456789999973
No 127
>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=74.88 E-value=3.5 Score=24.08 Aligned_cols=32 Identities=22% Similarity=0.323 Sum_probs=18.5
Q ss_pred ccccccCCCccccCC----CCCeEEcCCCCCceecC
Q psy4748 11 SEFCSKCGTILPLFD----FKGDVKCYVCKTSYGTQ 42 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~----~~~~~~C~~C~~~~~~~ 42 (136)
+.-|..|+..|.|-- ++..+.|..|+......
T Consensus 2 p~rC~~C~aylNp~~~~~~~~~~w~C~~C~~~N~lp 37 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQFDDGGKTWICNFCGTKNPLP 37 (40)
T ss_dssp S-B-TTT--BS-TTSEEETTTTEEEETTT--EEE--
T ss_pred ccccCCCCCEECCcceEcCCCCEEECcCCCCcCCCC
Confidence 456999999999873 24699999999988763
No 128
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=74.37 E-value=2.2 Score=33.91 Aligned_cols=31 Identities=23% Similarity=0.283 Sum_probs=24.4
Q ss_pred CccccccccCCCccccCCCCCeEEcCCCCCceecCC
Q psy4748 8 NVESEFCSKCGTILPLFDFKGDVKCYVCKTSYGTQE 43 (136)
Q Consensus 8 ~~~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~~~ 43 (136)
..+..=||.||. .....+.|+.||+...++.
T Consensus 306 ~~tS~~C~~cg~-----~~~r~~~C~~cg~~~~rD~ 336 (364)
T COG0675 306 YYTSKTCPCCGH-----LSGRLFKCPRCGFVHDRDV 336 (364)
T ss_pred CCCcccccccCC-----ccceeEECCCCCCeehhhH
Confidence 345678999999 2345899999999998864
No 129
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=73.81 E-value=2.3 Score=28.13 Aligned_cols=30 Identities=27% Similarity=0.638 Sum_probs=23.6
Q ss_pred ccccCCCccccCC-CCCeEEcCCCCCceecC
Q psy4748 13 FCSKCGTILPLFD-FKGDVKCYVCKTSYGTQ 42 (136)
Q Consensus 13 FCp~CgnlL~~~~-~~~~~~C~~C~~~~~~~ 42 (136)
=||+|||.-..-. ....+.|..||......
T Consensus 21 kCpdC~N~q~vFshast~V~C~~CG~~l~~P 51 (67)
T COG2051 21 KCPDCGNEQVVFSHASTVVTCLICGTTLAEP 51 (67)
T ss_pred ECCCCCCEEEEeccCceEEEecccccEEEec
Confidence 4999999877764 35689999999887553
No 130
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=73.75 E-value=3.3 Score=26.89 Aligned_cols=27 Identities=19% Similarity=0.338 Sum_probs=19.7
Q ss_pred cccccCCCccccCCC-----CCeEEcCCCCCc
Q psy4748 12 EFCSKCGTILPLFDF-----KGDVKCYVCKTS 38 (136)
Q Consensus 12 ~FCp~CgnlL~~~~~-----~~~~~C~~C~~~ 38 (136)
.-||.||+.+..+-. +..|.|+.||+.
T Consensus 28 F~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CGF~ 59 (61)
T COG2888 28 FPCPNCGEVEIYRCAKCRKLGNPYRCPKCGFE 59 (61)
T ss_pred eeCCCCCceeeehhhhHHHcCCceECCCcCcc
Confidence 359999976666632 468899999875
No 131
>PHA02942 putative transposase; Provisional
Probab=73.72 E-value=2.7 Score=36.03 Aligned_cols=32 Identities=22% Similarity=0.401 Sum_probs=24.9
Q ss_pred cccccccCCCccccCCCCCeEEcCCCCCceecC
Q psy4748 10 ESEFCSKCGTILPLFDFKGDVKCYVCKTSYGTQ 42 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~~ 42 (136)
+..-||.||...... ..-.+.|..||+....+
T Consensus 324 TSq~Cs~CG~~~~~l-~~r~f~C~~CG~~~drD 355 (383)
T PHA02942 324 SSVSCPKCGHKMVEI-AHRYFHCPSCGYENDRD 355 (383)
T ss_pred CCccCCCCCCccCcC-CCCEEECCCCCCEeCcH
Confidence 558899999876422 23489999999999875
No 132
>PRK12495 hypothetical protein; Provisional
Probab=73.33 E-value=2.7 Score=33.86 Aligned_cols=32 Identities=19% Similarity=0.527 Sum_probs=25.7
Q ss_pred CccccccccCCCccccCCCCCeEEcCCCCCceec
Q psy4748 8 NVESEFCSKCGTILPLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 8 ~~~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~ 41 (136)
.+...+|+.||.-|+- ..+...|..|+.....
T Consensus 39 tmsa~hC~~CG~PIpa--~pG~~~Cp~CQ~~~~~ 70 (226)
T PRK12495 39 TMTNAHCDECGDPIFR--HDGQEFCPTCQQPVTE 70 (226)
T ss_pred ccchhhcccccCcccC--CCCeeECCCCCCcccc
Confidence 4567899999999983 3568999999987543
No 133
>COG4640 Predicted membrane protein [Function unknown]
Probab=72.42 E-value=2 Score=37.62 Aligned_cols=26 Identities=35% Similarity=0.910 Sum_probs=18.8
Q ss_pred ccccccCCCccccCCCCCeEEcCCCCCcee
Q psy4748 11 SEFCSKCGTILPLFDFKGDVKCYVCKTSYG 40 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~ 40 (136)
|+|||.||+-=. .+.+.|..||+...
T Consensus 1 M~fC~kcG~qk~----Ed~~qC~qCG~~~t 26 (465)
T COG4640 1 MKFCPKCGSQKA----EDDVQCTQCGHKFT 26 (465)
T ss_pred CCcccccccccc----cccccccccCCcCC
Confidence 789999996321 23455999998764
No 134
>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=72.02 E-value=2 Score=24.47 Aligned_cols=23 Identities=22% Similarity=0.504 Sum_probs=13.7
Q ss_pred ccccccCCCccccCCCCCeEEcCCCCC
Q psy4748 11 SEFCSKCGTILPLFDFKGDVKCYVCKT 37 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~~~~~~C~~C~~ 37 (136)
..-|+.||.+..|+. ..|+.|+.
T Consensus 11 ~~rC~~Cg~~~~pPr----~~Cp~C~s 33 (37)
T PF12172_consen 11 GQRCRDCGRVQFPPR----PVCPHCGS 33 (37)
T ss_dssp EEE-TTT--EEES------SEETTTT-
T ss_pred EEEcCCCCCEecCCC----cCCCCcCc
Confidence 457999999988864 38999973
No 135
>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=71.60 E-value=3.4 Score=29.35 Aligned_cols=15 Identities=13% Similarity=0.532 Sum_probs=8.7
Q ss_pred CCeEEcCCCCCceec
Q psy4748 27 KGDVKCYVCKTSYGT 41 (136)
Q Consensus 27 ~~~~~C~~C~~~~~~ 41 (136)
...+.|+.||+....
T Consensus 68 p~~~~C~~Cg~~~~~ 82 (113)
T PF01155_consen 68 PARARCRDCGHEFEP 82 (113)
T ss_dssp --EEEETTTS-EEEC
T ss_pred CCcEECCCCCCEEec
Confidence 346777777777665
No 136
>PF00628 PHD: PHD-finger; InterPro: IPR019787 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=71.00 E-value=5.3 Score=23.69 Aligned_cols=26 Identities=27% Similarity=0.648 Sum_probs=20.9
Q ss_pred ccccCCCccccCCCCCeEEcCCCCCceec
Q psy4748 13 FCSKCGTILPLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 13 FCp~CgnlL~~~~~~~~~~C~~C~~~~~~ 41 (136)
||+.||. ....+..+.|..|+..+..
T Consensus 1 ~C~vC~~---~~~~~~~i~C~~C~~~~H~ 26 (51)
T PF00628_consen 1 YCPVCGQ---SDDDGDMIQCDSCNRWYHQ 26 (51)
T ss_dssp EBTTTTS---SCTTSSEEEBSTTSCEEET
T ss_pred eCcCCCC---cCCCCCeEEcCCCChhhCc
Confidence 6889999 3344679999999988776
No 137
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=70.53 E-value=3.4 Score=29.91 Aligned_cols=24 Identities=33% Similarity=0.695 Sum_probs=20.7
Q ss_pred cccCCCccccCCCCCeEEcCCCCCceec
Q psy4748 14 CSKCGTILPLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 14 Cp~CgnlL~~~~~~~~~~C~~C~~~~~~ 41 (136)
||.||.=|.. ..+.|..|+....-
T Consensus 1 CPvCg~~l~v----t~l~C~~C~t~i~G 24 (113)
T PF09862_consen 1 CPVCGGELVV----TRLKCPSCGTEIEG 24 (113)
T ss_pred CCCCCCceEE----EEEEcCCCCCEEEe
Confidence 9999999888 48899999997653
No 138
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=70.39 E-value=2.4 Score=23.04 Aligned_cols=25 Identities=16% Similarity=0.513 Sum_probs=15.1
Q ss_pred ccccCCCccccCCC--CCeEEcCCCCC
Q psy4748 13 FCSKCGTILPLFDF--KGDVKCYVCKT 37 (136)
Q Consensus 13 FCp~CgnlL~~~~~--~~~~~C~~C~~ 37 (136)
=|+.|++.+..... ...+.|..|-.
T Consensus 3 ~C~rC~~~~~~~~~~~r~~~~C~rCq~ 29 (30)
T PF06827_consen 3 KCPRCWNYIEDIGINGRSTYLCPRCQK 29 (30)
T ss_dssp B-TTT--BBEEEEETTEEEEE-TTTCC
T ss_pred cCccCCCcceEeEecCCCCeECcCCcC
Confidence 38999999877643 45789999853
No 139
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=69.77 E-value=1.9 Score=34.14 Aligned_cols=30 Identities=20% Similarity=0.332 Sum_probs=22.7
Q ss_pred ccccccCCCccccCCC-------C----CeEEcCCCCCcee
Q psy4748 11 SEFCSKCGTILPLFDF-------K----GDVKCYVCKTSYG 40 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~-------~----~~~~C~~C~~~~~ 40 (136)
..=||-||.-|..... + ..+.|.+|||...
T Consensus 14 ~~~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~~ 54 (201)
T COG1779 14 RIDCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGYRST 54 (201)
T ss_pred eecCCcccceeeEEEeeecCCccceEEEEEEEccccCCccc
Confidence 4569999998776532 1 3689999999875
No 140
>PRK07219 DNA topoisomerase I; Validated
Probab=68.28 E-value=12 Score=35.24 Aligned_cols=32 Identities=22% Similarity=0.441 Sum_probs=21.6
Q ss_pred ccccccCCCccccCC--CC-CeEEcCC---CCCceecC
Q psy4748 11 SEFCSKCGTILPLFD--FK-GDVKCYV---CKTSYGTQ 42 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~--~~-~~~~C~~---C~~~~~~~ 42 (136)
..=||.||.-|.... .+ ..+.|.. |++..+..
T Consensus 602 ~~~CP~Cg~~l~~r~~~~g~~F~gCs~yp~C~~t~~lp 639 (822)
T PRK07219 602 IGKCPECGGDLIIIRTDKGSRFVGCSGYPDCRNTFPLP 639 (822)
T ss_pred cCcCCCCCCcceeeeccCCceeeecCCCcCCCCeeecC
Confidence 345999997554432 22 3589987 99887764
No 141
>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=66.69 E-value=3.7 Score=33.65 Aligned_cols=33 Identities=30% Similarity=0.747 Sum_probs=15.4
Q ss_pred cccccccCCCc-cccCCC---CCeEEcCCCCCceecC
Q psy4748 10 ESEFCSKCGTI-LPLFDF---KGDVKCYVCKTSYGTQ 42 (136)
Q Consensus 10 ~~~FCp~Cgnl-L~~~~~---~~~~~C~~C~~~~~~~ 42 (136)
.-.+||.||+. |..-++ .-.+.|..|+-.+...
T Consensus 30 ~n~yCP~Cg~~~L~~f~NN~PVaDF~C~~C~eeyELK 66 (254)
T PF06044_consen 30 ENMYCPNCGSKPLSKFENNRPVADFYCPNCNEEYELK 66 (254)
T ss_dssp HH---TTT--SS-EE--------EEE-TTT--EEEEE
T ss_pred HCCcCCCCCChhHhhccCCCccceeECCCCchHHhhh
Confidence 44699999998 666554 2579999999988764
No 142
>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=66.67 E-value=2.9 Score=26.03 Aligned_cols=12 Identities=42% Similarity=0.944 Sum_probs=9.8
Q ss_pred eccccccCCCce
Q psy4748 102 ERKCKRCNNDTM 113 (136)
Q Consensus 102 ~~~CpkCg~~~a 113 (136)
-..||+|||+..
T Consensus 13 Y~~Cp~CGN~~v 24 (49)
T PF12677_consen 13 YCKCPKCGNDKV 24 (49)
T ss_pred hccCcccCCcEe
Confidence 358999999865
No 143
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=66.58 E-value=4.4 Score=25.97 Aligned_cols=27 Identities=22% Similarity=0.480 Sum_probs=21.6
Q ss_pred cccccccCCCccccCCCCCeEEcCCCCCceec
Q psy4748 10 ESEFCSKCGTILPLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~ 41 (136)
.+..|+.||.+..+ .-+|..|||-...
T Consensus 26 ~~~~c~~cG~~~l~-----Hrvc~~cg~Y~g~ 52 (57)
T COG0333 26 TLSVCPNCGEYKLP-----HRVCLKCGYYKGR 52 (57)
T ss_pred cceeccCCCCcccC-----ceEcCCCCCccCe
Confidence 36799999998877 5589999987654
No 144
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=66.34 E-value=3.6 Score=28.43 Aligned_cols=36 Identities=19% Similarity=0.444 Sum_probs=28.2
Q ss_pred ccCccccccccCCCccccCCC-------CCeEEcCCCCCceec
Q psy4748 6 YFNVESEFCSKCGTILPLFDF-------KGDVKCYVCKTSYGT 41 (136)
Q Consensus 6 ~~~~~~~FCp~CgnlL~~~~~-------~~~~~C~~C~~~~~~ 41 (136)
.+..+.-+|+.|+..|...+. -..-.|+.|+...+.
T Consensus 28 ~i~~~rS~C~~C~~~L~~~~lIPi~S~l~lrGrCr~C~~~I~~ 70 (92)
T PF06750_consen 28 SIIFPRSHCPHCGHPLSWWDLIPILSYLLLRGRCRYCGAPIPP 70 (92)
T ss_pred CccCCCCcCcCCCCcCcccccchHHHHHHhCCCCcccCCCCCh
Confidence 455567899999999999865 145699999977665
No 145
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=65.92 E-value=5.1 Score=34.62 Aligned_cols=35 Identities=20% Similarity=0.404 Sum_probs=26.4
Q ss_pred cCccccccccCCCccccCC--CCCeEEcCCCCCceec
Q psy4748 7 FNVESEFCSKCGTILPLFD--FKGDVKCYVCKTSYGT 41 (136)
Q Consensus 7 ~~~~~~FCp~CgnlL~~~~--~~~~~~C~~C~~~~~~ 41 (136)
.-.++.=||+||.+...+. .+....|++||+.-..
T Consensus 9 ~~~~~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~~ 45 (403)
T TIGR00155 9 PAAKHILCSQCDMLVALPRIESGQKAACPRCGTTLTV 45 (403)
T ss_pred CCCCeeeCCCCCCcccccCCCCCCeeECCCCCCCCcC
Confidence 3344567999999987663 4568899999998754
No 146
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=65.74 E-value=2.4 Score=31.38 Aligned_cols=33 Identities=15% Similarity=0.439 Sum_probs=23.5
Q ss_pred cccccccCCCccccCCC------CCeEEcCCCCCceecC
Q psy4748 10 ESEFCSKCGTILPLFDF------KGDVKCYVCKTSYGTQ 42 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~------~~~~~C~~C~~~~~~~ 42 (136)
....||.||......+. .+.+.|+.||..-...
T Consensus 98 ~~Y~Cp~C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~~ 136 (147)
T smart00531 98 AYYKCPNCQSKYTFLEANQLLDMDGTFTCPRCGEELEED 136 (147)
T ss_pred cEEECcCCCCEeeHHHHHHhcCCCCcEECCCCCCEEEEc
Confidence 34579999987766432 1249999999887654
No 147
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=64.97 E-value=6 Score=30.33 Aligned_cols=31 Identities=26% Similarity=0.490 Sum_probs=25.2
Q ss_pred ccccccCCCccccCCCCCeEEcCCCCCceecC
Q psy4748 11 SEFCSKCGTILPLFDFKGDVKCYVCKTSYGTQ 42 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~~ 42 (136)
.-+|+.||..|.|.+ .+.+.|..|++.+...
T Consensus 149 ~a~~~~~g~~~~~~~-~~~~~c~~~~~~e~rk 179 (189)
T PRK09521 149 YAMCSRCRTPLVKKG-ENELKCPNCGNIETRK 179 (189)
T ss_pred EEEccccCCceEECC-CCEEECCCCCCEEeec
Confidence 348999999998854 3689999999988763
No 148
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=64.88 E-value=4.6 Score=25.06 Aligned_cols=26 Identities=23% Similarity=0.595 Sum_probs=21.1
Q ss_pred ccccccccCCCccccCCCCCeEEcCCCCCc
Q psy4748 9 VESEFCSKCGTILPLFDFKGDVKCYVCKTS 38 (136)
Q Consensus 9 ~~~~FCp~CgnlL~~~~~~~~~~C~~C~~~ 38 (136)
.....|-.|+..+++.. -.||.|||.
T Consensus 12 ~~k~ICrkC~ARnp~~A----~~CRKCg~~ 37 (48)
T PRK04136 12 FNKKICMRCNARNPWRA----TKCRKCGYK 37 (48)
T ss_pred hcccchhcccCCCCccc----cccccCCCC
Confidence 35678999999999953 479999984
No 149
>PLN00209 ribosomal protein S27; Provisional
Probab=64.86 E-value=4.3 Score=28.11 Aligned_cols=22 Identities=27% Similarity=0.443 Sum_probs=18.3
Q ss_pred CceeccccccCCCceEEEEeec
Q psy4748 99 PIVERKCKRCNNDTMSYATLQL 120 (136)
Q Consensus 99 ~~~~~~CpkCg~~~a~f~~~Q~ 120 (136)
-=++++||.|++...+|--.|+
T Consensus 33 ~Fm~VkCp~C~n~q~VFShA~t 54 (86)
T PLN00209 33 FFMDVKCQGCFNITTVFSHSQT 54 (86)
T ss_pred EEEEEECCCCCCeeEEEecCce
Confidence 3468999999999999977664
No 150
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=63.56 E-value=4.8 Score=27.81 Aligned_cols=22 Identities=23% Similarity=0.449 Sum_probs=18.4
Q ss_pred CceeccccccCCCceEEEEeec
Q psy4748 99 PIVERKCKRCNNDTMSYATLQL 120 (136)
Q Consensus 99 ~~~~~~CpkCg~~~a~f~~~Q~ 120 (136)
-=++++||.|++...+|--.|+
T Consensus 32 ~Fm~VkCp~C~n~q~VFShA~t 53 (85)
T PTZ00083 32 YFMDVKCPGCSQITTVFSHAQT 53 (85)
T ss_pred eEEEEECCCCCCeeEEEecCce
Confidence 3468999999999999987664
No 151
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=63.27 E-value=3.3 Score=29.72 Aligned_cols=28 Identities=14% Similarity=0.355 Sum_probs=19.2
Q ss_pred ccccccCCCccccCCCCCeEEcCCCCCce
Q psy4748 11 SEFCSKCGTILPLFDFKGDVKCYVCKTSY 39 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~~~~~~C~~C~~~~ 39 (136)
..+|..||+.-.+... ..+.|+.||-..
T Consensus 71 ~~~C~~Cg~~~~~~~~-~~~~CP~Cgs~~ 98 (117)
T PRK00564 71 ELECKDCSHVFKPNAL-DYGVCEKCHSKN 98 (117)
T ss_pred EEEhhhCCCccccCCc-cCCcCcCCCCCc
Confidence 4589999977666432 244699999643
No 152
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=62.03 E-value=5.8 Score=29.43 Aligned_cols=34 Identities=6% Similarity=0.115 Sum_probs=27.0
Q ss_pred CccccccccCCCccccCCCCCeEEcCCCCCceecC
Q psy4748 8 NVESEFCSKCGTILPLFDFKGDVKCYVCKTSYGTQ 42 (136)
Q Consensus 8 ~~~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~~ 42 (136)
++.-+-||.||.-.|=-. +.-++|+.||..++..
T Consensus 6 lGtKr~Cp~cg~kFYDLn-k~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 6 LGTKRICPNTGSKFYDLN-RRPAVSPYTGEQFPPE 39 (129)
T ss_pred hCccccCCCcCccccccC-CCCccCCCcCCccCcc
Confidence 456688999999887643 4678999999998764
No 153
>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=61.59 E-value=5.9 Score=29.25 Aligned_cols=31 Identities=23% Similarity=0.307 Sum_probs=23.2
Q ss_pred ccccccCCCccccCCC---------------CCeEEcCCCCCceec
Q psy4748 11 SEFCSKCGTILPLFDF---------------KGDVKCYVCKTSYGT 41 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~---------------~~~~~C~~C~~~~~~ 41 (136)
+.-|+.||..|.+-+. ...+.|+.||..+=.
T Consensus 91 ~sRC~~CN~~L~~v~~~~v~~~vp~~v~~~~~~f~~C~~C~kiyW~ 136 (147)
T PF01927_consen 91 FSRCPKCNGPLRPVSKEEVKDRVPPYVYETYDEFWRCPGCGKIYWE 136 (147)
T ss_pred CCccCCCCcEeeechhhccccccCccccccCCeEEECCCCCCEecc
Confidence 4689999998866522 126899999988744
No 154
>PRK00222 methionine sulfoxide reductase B; Provisional
Probab=61.55 E-value=9.5 Score=28.71 Aligned_cols=20 Identities=15% Similarity=0.247 Sum_probs=14.3
Q ss_pred CCCceeccccccCCCceEEE
Q psy4748 97 DGPIVERKCKRCNNDTMSYA 116 (136)
Q Consensus 97 ~~~~~~~~CpkCg~~~a~f~ 116 (136)
....+++.|.+||..--.-|
T Consensus 87 gm~RtEv~C~~Cg~HLGHVF 106 (142)
T PRK00222 87 GMVRTEVRCANCDSHLGHVF 106 (142)
T ss_pred CceEEEEEeCCCCCccCccc
Confidence 34478999999997655444
No 155
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=61.36 E-value=4.9 Score=25.81 Aligned_cols=26 Identities=8% Similarity=-0.199 Sum_probs=20.0
Q ss_pred cccccccCCCccccCCCCCeEEcCCCCCceec
Q psy4748 10 ESEFCSKCGTILPLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~ 41 (136)
.+..|+.||.+..+ .-+|. |||....
T Consensus 26 ~~~~c~~cg~~~~p-----H~vc~-cG~Y~gr 51 (60)
T PRK01110 26 TLSVDKTTGEYHLP-----HHVSP-KGYYKGR 51 (60)
T ss_pred ceeEcCCCCceecc-----ceecC-CcccCCe
Confidence 35689999999888 45799 9976654
No 156
>COG4332 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=61.30 E-value=8.5 Score=30.38 Aligned_cols=40 Identities=20% Similarity=0.602 Sum_probs=27.7
Q ss_pred CCCceeccccccCCCceEEEEeeccccCCCc----eEEEEecCC
Q psy4748 97 DGPIVERKCKRCNNDTMSYATLQLRSADEGQ----TIFFTCTKC 136 (136)
Q Consensus 97 ~~~~~~~~CpkCg~~~a~f~~~Q~RSADEg~----TvFY~C~~C 136 (136)
..|.+-..|++||..+++--.--.|---.|- =++|+|+.|
T Consensus 12 ~~pq~~k~C~~Cg~kr~f~cSg~fRvNAq~K~LDvWlIYkC~~C 55 (203)
T COG4332 12 GAPQPAKRCNSCGVKRAFTCSGKFRVNAQGKVLDVWLIYKCTHC 55 (203)
T ss_pred cCChhhhhCcccCCcceeeecCcEEEcCCCcEEEEEEEEEeecc
Confidence 4456667899999999876544444444442 268999988
No 157
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=61.22 E-value=9 Score=22.51 Aligned_cols=14 Identities=29% Similarity=0.638 Sum_probs=11.0
Q ss_pred ccccccCCCccccC
Q psy4748 11 SEFCSKCGTILPLF 24 (136)
Q Consensus 11 ~~FCp~CgnlL~~~ 24 (136)
...||.||.-|..-
T Consensus 2 ~~~C~~Cg~~l~~i 15 (47)
T PF13005_consen 2 PRACPDCGGELKEI 15 (47)
T ss_pred CCcCCCCCceeeEC
Confidence 35799999988854
No 158
>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=60.95 E-value=8.3 Score=24.79 Aligned_cols=37 Identities=19% Similarity=0.413 Sum_probs=25.5
Q ss_pred cCccccccccCCCcc------------------------c----cCCCCCeEEcCCCCCceecCC
Q psy4748 7 FNVESEFCSKCGTIL------------------------P----LFDFKGDVKCYVCKTSYGTQE 43 (136)
Q Consensus 7 ~~~~~~FCp~CgnlL------------------------~----~~~~~~~~~C~~C~~~~~~~~ 43 (136)
+-..+.-||.|.+=| . ..-..+.++|+.|+..+++.+
T Consensus 3 ~llniL~Cp~ck~pL~~~~l~~~~~~~~~~lp~~~~~~~~~l~~~~i~eg~L~Cp~c~r~YPI~d 67 (68)
T PF03966_consen 3 LLLNILACPVCKGPLDWEALVETAQLGLSELPKELPEDYHVLLEVEIVEGELICPECGREYPIRD 67 (68)
T ss_dssp GGCGTBB-TTTSSBEHHHHHHHHHHCCCCHCHHCHHCHCEHHCTEETTTTEEEETTTTEEEEEET
T ss_pred hHHhhhcCCCCCCcchHHHHHHHHHhCcccCCCCCccchhhhhcccccCCEEEcCCCCCEEeCCC
Confidence 345678899998855 1 111246999999999998853
No 159
>KOG3799|consensus
Probab=60.12 E-value=3.2 Score=31.43 Aligned_cols=33 Identities=24% Similarity=0.574 Sum_probs=29.1
Q ss_pred ccccccccCCCccccCCCCCeEEcCCCCCceec
Q psy4748 9 VESEFCSKCGTILPLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 9 ~~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~ 41 (136)
-.++||..||--..+++++-+|+|..|.....+
T Consensus 87 Cq~r~CARCGGrv~lrsNKv~wvcnlc~k~q~i 119 (169)
T KOG3799|consen 87 CQTRFCARCGGRVSLRSNKVMWVCNLCRKQQEI 119 (169)
T ss_pred hhhhHHHhcCCeeeeccCceEEeccCCcHHHHH
Confidence 457899999999999988889999999987765
No 160
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=59.09 E-value=5.9 Score=31.42 Aligned_cols=29 Identities=24% Similarity=0.360 Sum_probs=20.2
Q ss_pred cccccCCCcccc-------CCCCCeEEcCCCCCceec
Q psy4748 12 EFCSKCGTILPL-------FDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 12 ~FCp~CgnlL~~-------~~~~~~~~C~~C~~~~~~ 41 (136)
.-||.|| -... ......+.|..||+.+++
T Consensus 7 ~~Cp~Cg-~eev~hEVik~~g~~~lvrC~eCG~V~~~ 42 (201)
T COG1326 7 IECPSCG-SEEVSHEVIKERGREPLVRCEECGTVHPA 42 (201)
T ss_pred EECCCCC-cchhhHHHHHhcCCceEEEccCCCcEeec
Confidence 3599999 3322 112348999999999965
No 161
>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=58.93 E-value=4.6 Score=28.85 Aligned_cols=27 Identities=15% Similarity=0.251 Sum_probs=18.6
Q ss_pred ccccccCCCccccCCCCCeEEcCCCCCce
Q psy4748 11 SEFCSKCGTILPLFDFKGDVKCYVCKTSY 39 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~~~~~~C~~C~~~~ 39 (136)
..+|+.||..-.+.. ..+.|+.||-..
T Consensus 70 ~~~C~~Cg~~~~~~~--~~~~CP~Cgs~~ 96 (115)
T TIGR00100 70 ECECEDCSEEVSPEI--DLYRCPKCHGIM 96 (115)
T ss_pred EEEcccCCCEEecCC--cCccCcCCcCCC
Confidence 358999996666643 356799998543
No 162
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=58.86 E-value=7.9 Score=33.65 Aligned_cols=32 Identities=19% Similarity=0.492 Sum_probs=24.2
Q ss_pred cccccccCCCccccCC--CCCeEEcCCCCCceec
Q psy4748 10 ESEFCSKCGTILPLFD--FKGDVKCYVCKTSYGT 41 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~--~~~~~~C~~C~~~~~~ 41 (136)
+..=||+||.+...+. .+....|++||+.-..
T Consensus 9 ~~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~~ 42 (419)
T PRK15103 9 KHILCPQCDMLVALPRLEHGQKAACPRCGTTLTV 42 (419)
T ss_pred CcccCCCCCceeecCCCCCCCeeECCCCCCCCcC
Confidence 3455999999987653 3567899999998754
No 163
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=58.76 E-value=5.5 Score=30.71 Aligned_cols=31 Identities=19% Similarity=0.335 Sum_probs=23.0
Q ss_pred ccccccCCCccccCCC---------------CCeEEcCCCCCceec
Q psy4748 11 SEFCSKCGTILPLFDF---------------KGDVKCYVCKTSYGT 41 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~---------------~~~~~C~~C~~~~~~ 41 (136)
..=||+||.-|..-.. ...+.|..||..+=.
T Consensus 97 ~~RCp~CN~~L~~vs~eev~~~Vp~~~~~~~~~f~~C~~CgkiYW~ 142 (165)
T COG1656 97 FSRCPECNGELEKVSREEVKEKVPEKVYRNYEEFYRCPKCGKIYWK 142 (165)
T ss_pred cccCcccCCEeccCcHHHHhhccchhhhhcccceeECCCCcccccC
Confidence 4469999999876532 136789999988754
No 164
>PF11672 DUF3268: Protein of unknown function (DUF3268); InterPro: IPR021686 This entry is represented by Listeria phage P100, Gp150. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=58.67 E-value=9.9 Score=27.03 Aligned_cols=33 Identities=21% Similarity=0.493 Sum_probs=18.4
Q ss_pred ccccccCCCceEEEEee--ccccCCCceEEEEecCC
Q psy4748 103 RKCKRCNNDTMSYATLQ--LRSADEGQTIFFTCTKC 136 (136)
Q Consensus 103 ~~CpkCg~~~a~f~~~Q--~RSADEg~TvFY~C~~C 136 (136)
..||-||.+-..---.. -++.|++. .+|.|+.|
T Consensus 3 ~~CpYCg~~~~l~~~~~iYg~~~~~~~-~~y~C~~C 37 (102)
T PF11672_consen 3 IICPYCGGPAELVDGSEIYGHRYDDGP-YLYVCTPC 37 (102)
T ss_pred cccCCCCCeeEEcccchhcCccCCCCc-eeEECCCC
Confidence 46999998432110000 14555554 45999887
No 165
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=58.01 E-value=11 Score=22.50 Aligned_cols=32 Identities=19% Similarity=0.381 Sum_probs=23.6
Q ss_pred ccccccccCCCccccCCCCCeEEcCCCCCceec
Q psy4748 9 VESEFCSKCGTILPLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 9 ~~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~ 41 (136)
....+|..|+.+|.. ....-+.|..|++....
T Consensus 9 ~~~~~C~~C~~~i~g-~~~~g~~C~~C~~~~H~ 40 (53)
T PF00130_consen 9 SKPTYCDVCGKFIWG-LGKQGYRCSWCGLVCHK 40 (53)
T ss_dssp SSTEB-TTSSSBECS-SSSCEEEETTTT-EEET
T ss_pred CCCCCCcccCcccCC-CCCCeEEECCCCChHhh
Confidence 466799999999954 33468999999998765
No 166
>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=57.93 E-value=4.8 Score=23.70 Aligned_cols=25 Identities=24% Similarity=0.638 Sum_probs=16.7
Q ss_pred ccccCCCccccC---CCCCeEEcCCCCC
Q psy4748 13 FCSKCGTILPLF---DFKGDVKCYVCKT 37 (136)
Q Consensus 13 FCp~CgnlL~~~---~~~~~~~C~~C~~ 37 (136)
-|++||+..... .+.....|+.||.
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 488888544333 2246788999986
No 167
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=57.53 E-value=4.9 Score=28.65 Aligned_cols=26 Identities=19% Similarity=0.704 Sum_probs=17.7
Q ss_pred ccccccCCCccccCCCCCeEEcCCCCCc
Q psy4748 11 SEFCSKCGTILPLFDFKGDVKCYVCKTS 38 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~~~~~~C~~C~~~ 38 (136)
..+|+.||..-.+.. ..+.|+.||-.
T Consensus 70 ~~~C~~Cg~~~~~~~--~~~~CP~Cgs~ 95 (113)
T PRK12380 70 QAWCWDCSQVVEIHQ--HDAQCPHCHGE 95 (113)
T ss_pred EEEcccCCCEEecCC--cCccCcCCCCC
Confidence 458999996665532 35569999943
No 168
>PF08882 Acetone_carb_G: Acetone carboxylase gamma subunit; InterPro: IPR014979 Acetone carboxylase is the key enzyme of bacterial acetone metabolism, catalysing the condensation of acetone and CO2 to form acetoacetate [] according to the following reaction: CH3COCH3 + CO2 + ATP = CH3COCH2COO- + AMP + 2P(i) + H+ It has the subunit composition: (alpha(2)beta(2)gamma(2) multimers of 85kDa, 78kDa, and 20kDa subunits). It is expressed to high levels (17 to 25% of soluble protein) in cells grown with acetone as the carbon source but are not present at detectable levels in cells grown with other carbon sources []. Acetone carboxylase may enable Helicobacter pylori to survive off acetone in the stomach of humans and other mammals where it is the etiological agent of peptic ulcer disease []. This entry represents the family of gamma subunit-related acetone carboxylase proteins.
Probab=57.52 E-value=4.2 Score=29.45 Aligned_cols=13 Identities=38% Similarity=0.915 Sum_probs=11.4
Q ss_pred ccccCCCccccCC
Q psy4748 13 FCSKCGTILPLFD 25 (136)
Q Consensus 13 FCp~CgnlL~~~~ 25 (136)
+||.||+||..+-
T Consensus 76 yCP~Cgt~levE~ 88 (112)
T PF08882_consen 76 YCPGCGTQLEVEA 88 (112)
T ss_pred ECCCCcceeEEcc
Confidence 8999999998863
No 169
>TIGR00357 methionine-R-sulfoxide reductase. This model describes a domain found in PilB, a protein important for pilin expression, N-terminal to a domain coextensive to with the known peptide methionine sulfoxide reductase (MsrA), a protein repair enzyme, of E. coli. Among the early completed genomes, this module is found if and only if MsrA is also found, whether N-terminal to MsrA (as for Helicobacter pylori), C-terminal (as for Treponema pallidum), or in a separate polypeptide. Although the function of this region is not clear, an auxiliary function to MsrA is suggested.
Probab=57.16 E-value=14 Score=27.48 Aligned_cols=19 Identities=16% Similarity=0.277 Sum_probs=13.8
Q ss_pred CCceeccccccCCCceEEE
Q psy4748 98 GPIVERKCKRCNNDTMSYA 116 (136)
Q Consensus 98 ~~~~~~~CpkCg~~~a~f~ 116 (136)
...++..|.+||..--.-|
T Consensus 85 m~RtEv~C~~Cg~HLGHVF 103 (134)
T TIGR00357 85 MIRTEVRCRNCDAHLGHVF 103 (134)
T ss_pred cEEEEEEecCCCCccCccc
Confidence 3578999999997654444
No 170
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=57.02 E-value=8.3 Score=27.54 Aligned_cols=31 Identities=23% Similarity=0.386 Sum_probs=23.9
Q ss_pred ccccCCCccccC------CCCCeEEcCCCCCceecCC
Q psy4748 13 FCSKCGTILPLF------DFKGDVKCYVCKTSYGTQE 43 (136)
Q Consensus 13 FCp~CgnlL~~~------~~~~~~~C~~C~~~~~~~~ 43 (136)
=||.||...... .....+.|..||-....+.
T Consensus 24 tCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls~e~ev 60 (104)
T COG4888 24 TCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLSFECEV 60 (104)
T ss_pred ecCccCCeeeeEEEEEecCceeEEEcccCcceEEEec
Confidence 399999988773 1246899999999887653
No 171
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=56.81 E-value=15 Score=29.13 Aligned_cols=35 Identities=17% Similarity=0.345 Sum_probs=22.5
Q ss_pred eeccccccCCCceEEEEeeccccCCCce--EEEEecCC
Q psy4748 101 VERKCKRCNNDTMSYATLQLRSADEGQT--IFFTCTKC 136 (136)
Q Consensus 101 ~~~~CpkCg~~~a~f~~~Q~RSADEg~T--vFY~C~~C 136 (136)
....||-||+ .++..+.+..---.|-- ..+.|.+|
T Consensus 13 ~~~~CPvCg~-~l~~~~~~~~IPyFG~V~i~t~~C~~C 49 (201)
T COG1779 13 TRIDCPVCGG-TLKAHMYLYDIPYFGEVLISTGVCERC 49 (201)
T ss_pred eeecCCcccc-eeeEEEeeecCCccceEEEEEEEcccc
Confidence 4567888888 77777776666666633 33456665
No 172
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=56.58 E-value=5.8 Score=30.32 Aligned_cols=28 Identities=29% Similarity=0.594 Sum_probs=18.5
Q ss_pred cccCCCc-cccC----C---CC----CeEEcCCCCCceec
Q psy4748 14 CSKCGTI-LPLF----D---FK----GDVKCYVCKTSYGT 41 (136)
Q Consensus 14 Cp~Cgnl-L~~~----~---~~----~~~~C~~C~~~~~~ 41 (136)
||.||+. |... . .+ ..+.|..|||....
T Consensus 1 CP~Cg~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~e 40 (163)
T TIGR00340 1 CPVCGSRTLKAVTYDYDIPYFGKIMLSTYICEKCGYRSTD 40 (163)
T ss_pred CCCCCCcceEeeeEeccCCCcceEEEEEEECCCCCCchhh
Confidence 9999964 2221 1 12 36899999998753
No 173
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=56.34 E-value=6.1 Score=29.24 Aligned_cols=23 Identities=26% Similarity=0.505 Sum_probs=19.5
Q ss_pred ccccCCCccccCCCCCeEEcCCCCCce
Q psy4748 13 FCSKCGTILPLFDFKGDVKCYVCKTSY 39 (136)
Q Consensus 13 FCp~CgnlL~~~~~~~~~~C~~C~~~~ 39 (136)
=|+.||++..|+.. .|..|+..-
T Consensus 31 kC~~CG~v~~PPr~----~Cp~C~~~~ 53 (140)
T COG1545 31 KCKKCGRVYFPPRA----YCPKCGSET 53 (140)
T ss_pred EcCCCCeEEcCCcc----cCCCCCCCC
Confidence 59999999999754 799999873
No 174
>COG2176 PolC DNA polymerase III, alpha subunit (gram-positive type) [DNA replication, recombination, and repair]
Probab=56.10 E-value=9.3 Score=37.84 Aligned_cols=25 Identities=20% Similarity=0.284 Sum_probs=17.9
Q ss_pred CccccCCC---CCeEEcCCCCCceecCC
Q psy4748 19 TILPLFDF---KGDVKCYVCKTSYGTQE 43 (136)
Q Consensus 19 nlL~~~~~---~~~~~C~~C~~~~~~~~ 43 (136)
||+-..+. .-.|.|+.|.|.+-.++
T Consensus 901 tm~gITEVNPL~PHY~Cp~Cky~Ef~~d 928 (1444)
T COG2176 901 TMIGITEVNPLPPHYLCPECKYSEFIDD 928 (1444)
T ss_pred HhhcccccCCCCccccCCCCceeeeecC
Confidence 55555553 23899999999988753
No 175
>COG2824 PhnA Uncharacterized Zn-ribbon-containing protein involved in phosphonate metabolism [Inorganic ion transport and metabolism]
Probab=54.91 E-value=10 Score=27.36 Aligned_cols=31 Identities=23% Similarity=0.478 Sum_probs=25.3
Q ss_pred cccccccCCCccccCCCCCeEEcCCCCCceec
Q psy4748 10 ESEFCSKCGTILPLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~ 41 (136)
.+.-||.|++-...... ..+.|+.|.+.+..
T Consensus 2 ~lp~cp~c~sEytYed~-~~~~cpec~~ew~~ 32 (112)
T COG2824 2 SLPPCPKCNSEYTYEDG-GQLICPECAHEWNE 32 (112)
T ss_pred CCCCCCccCCceEEecC-ceEeCchhcccccc
Confidence 45679999998777654 59999999999874
No 176
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=54.65 E-value=8.6 Score=31.88 Aligned_cols=30 Identities=23% Similarity=0.558 Sum_probs=22.5
Q ss_pred cccccCCCccccCC-CCCeEEcCCCCCceec
Q psy4748 12 EFCSKCGTILPLFD-FKGDVKCYVCKTSYGT 41 (136)
Q Consensus 12 ~FCp~CgnlL~~~~-~~~~~~C~~C~~~~~~ 41 (136)
+=||+||..--..+ ..+.++|..||.....
T Consensus 2 ~~CpeCg~~~~~~d~~~ge~VC~~CG~Vi~~ 32 (285)
T COG1405 2 MSCPECGSTNIITDYERGEIVCADCGLVLED 32 (285)
T ss_pred CCCCCCCCccceeeccCCeEEeccCCEEecc
Confidence 35999999944333 2579999999998754
No 177
>PF14369 zf-RING_3: zinc-finger
Probab=54.50 E-value=8.7 Score=21.94 Aligned_cols=27 Identities=22% Similarity=0.619 Sum_probs=19.2
Q ss_pred ccccccCCCccccCCC-CCeEEcCCCCC
Q psy4748 11 SEFCSKCGTILPLFDF-KGDVKCYVCKT 37 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~-~~~~~C~~C~~ 37 (136)
..||-.|.....+... .....|+.|+-
T Consensus 2 ~ywCh~C~~~V~~~~~~~~~~~CP~C~~ 29 (35)
T PF14369_consen 2 RYWCHQCNRFVRIAPSPDSDVACPRCHG 29 (35)
T ss_pred CEeCccCCCEeEeCcCCCCCcCCcCCCC
Confidence 4689999998887533 23346999983
No 178
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=54.43 E-value=3.8 Score=26.63 Aligned_cols=15 Identities=40% Similarity=0.687 Sum_probs=10.4
Q ss_pred cccccccCCCccccC
Q psy4748 10 ESEFCSKCGTILPLF 24 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~ 24 (136)
...||+.||+-|...
T Consensus 47 ~r~FC~~CGs~l~~~ 61 (92)
T PF04828_consen 47 ERYFCPTCGSPLFSE 61 (92)
T ss_dssp EEEEETTT--EEEEE
T ss_pred cCcccCCCCCeeecc
Confidence 456999999999963
No 179
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=54.40 E-value=6.2 Score=28.17 Aligned_cols=27 Identities=19% Similarity=0.530 Sum_probs=17.8
Q ss_pred ccccccCCCccccCCCCCeEEcCCCCCc
Q psy4748 11 SEFCSKCGTILPLFDFKGDVKCYVCKTS 38 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~~~~~~C~~C~~~ 38 (136)
..+|+.||..-..... ..+.|+.||-.
T Consensus 70 ~~~C~~Cg~~~~~~~~-~~~~CP~Cgs~ 96 (114)
T PRK03681 70 ECWCETCQQYVTLLTQ-RVRRCPQCHGD 96 (114)
T ss_pred EEEcccCCCeeecCCc-cCCcCcCcCCC
Confidence 3589999975555322 24679999944
No 180
>KOG1812|consensus
Probab=53.35 E-value=7.4 Score=33.46 Aligned_cols=30 Identities=20% Similarity=0.495 Sum_probs=24.9
Q ss_pred cccccccCCCccccCCCCCeEEcCCCCCcee
Q psy4748 10 ESEFCSKCGTILPLFDFKGDVKCYVCKTSYG 40 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~ 40 (136)
..+=||.|+.++...++=+.+.|| ||+..-
T Consensus 305 ~wr~CpkC~~~ie~~~GCnhm~Cr-C~~~fc 334 (384)
T KOG1812|consen 305 RWRQCPKCKFMIELSEGCNHMTCR-CGHQFC 334 (384)
T ss_pred hcCcCcccceeeeecCCcceEEee-ccccch
Confidence 467899999999887766799999 998653
No 181
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=53.07 E-value=3.8 Score=31.55 Aligned_cols=31 Identities=16% Similarity=0.379 Sum_probs=23.2
Q ss_pred ccccccCCCccccCCC-CCeEEcCCCCCceec
Q psy4748 11 SEFCSKCGTILPLFDF-KGDVKCYVCKTSYGT 41 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~-~~~~~C~~C~~~~~~ 41 (136)
...||.||.-....+. ...+.|+.||..-.-
T Consensus 117 ~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 117 FFFCPNCHIRFTFDEAMEYGFRCPQCGEMLEE 148 (178)
T ss_pred EEECCCCCcEEeHHHHhhcCCcCCCCCCCCee
Confidence 4569999977776654 357999999987644
No 182
>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=52.39 E-value=3.9 Score=30.82 Aligned_cols=32 Identities=9% Similarity=0.153 Sum_probs=23.4
Q ss_pred cccccccCCCccccCCC-CCeEEcCCCCCceec
Q psy4748 10 ESEFCSKCGTILPLFDF-KGDVKCYVCKTSYGT 41 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~-~~~~~C~~C~~~~~~ 41 (136)
....||.||.-....+. ...+.|+.||..-.-
T Consensus 108 ~~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 108 MFFICPNMCVRFTFNEAMELNFTCPRCGAMLDY 140 (158)
T ss_pred CeEECCCCCcEeeHHHHHHcCCcCCCCCCEeee
Confidence 33469999977666543 357999999987654
No 183
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=52.13 E-value=8.2 Score=35.53 Aligned_cols=25 Identities=40% Similarity=0.780 Sum_probs=15.6
Q ss_pred cccccccCCCccccCCCCCeEEcCCCCCcee
Q psy4748 10 ESEFCSKCGTILPLFDFKGDVKCYVCKTSYG 40 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~ 40 (136)
+..||+.||.-|... .|..||+..+
T Consensus 14 ~akFC~~CG~~l~~~------~Cp~CG~~~~ 38 (645)
T PRK14559 14 NNRFCQKCGTSLTHK------PCPQCGTEVP 38 (645)
T ss_pred CCccccccCCCCCCC------cCCCCCCCCC
Confidence 567888888887532 3555555433
No 184
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=52.11 E-value=12 Score=28.42 Aligned_cols=31 Identities=26% Similarity=0.589 Sum_probs=19.4
Q ss_pred ccccCCC----ccccC---C-C--CCeEEcCCCCCceecCC
Q psy4748 13 FCSKCGT----ILPLF---D-F--KGDVKCYVCKTSYGTQE 43 (136)
Q Consensus 13 FCp~Cgn----lL~~~---~-~--~~~~~C~~C~~~~~~~~ 43 (136)
=||.||+ ..... + + .-...|+.||+....-+
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f~~~e 42 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRFTTFE 42 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcceEeE
Confidence 4999996 22222 1 1 12489999999876543
No 185
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=52.08 E-value=11 Score=21.92 Aligned_cols=31 Identities=26% Similarity=0.611 Sum_probs=24.0
Q ss_pred cccccccCCCccccCCCCCeEEcCCCCCceec
Q psy4748 10 ESEFCSKCGTILPLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~ 41 (136)
...||..|+.+|... ....+.|+.|++....
T Consensus 10 ~~~~C~~C~~~i~~~-~~~~~~C~~C~~~~H~ 40 (50)
T cd00029 10 KPTFCDVCRKSIWGL-FKQGLRCSWCKVKCHK 40 (50)
T ss_pred CCCChhhcchhhhcc-ccceeEcCCCCCchhh
Confidence 467999999999864 2357899999987654
No 186
>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=51.56 E-value=10 Score=26.86 Aligned_cols=39 Identities=18% Similarity=0.462 Sum_probs=31.6
Q ss_pred CCCccCccccccccCCCccccCCCCCeEEcCCCCCceecC
Q psy4748 3 SEGYFNVESEFCSKCGTILPLFDFKGDVKCYVCKTSYGTQ 42 (136)
Q Consensus 3 ~~~~~~~~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~~ 42 (136)
+.+.+...+..|.-||..=|..+ ++.++|..|+......
T Consensus 27 ~dg~~~va~daCeiC~~~GY~q~-g~~lvC~~C~~~~~~~ 65 (102)
T PF10080_consen 27 PDGSYRVAFDACEICGPKGYYQE-GDQLVCKNCGVRFNLP 65 (102)
T ss_pred CCCCEEEEEEeccccCCCceEEE-CCEEEEecCCCEEehh
Confidence 45667778889999988887743 5799999999998774
No 187
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=51.55 E-value=8.8 Score=24.45 Aligned_cols=13 Identities=23% Similarity=0.659 Sum_probs=9.0
Q ss_pred ccccccCCCceEE
Q psy4748 103 RKCKRCNNDTMSY 115 (136)
Q Consensus 103 ~~CpkCg~~~a~f 115 (136)
.-||||.+....-
T Consensus 29 lyCpKCK~EtlI~ 41 (55)
T PF14205_consen 29 LYCPKCKQETLID 41 (55)
T ss_pred ccCCCCCceEEEE
Confidence 4688888876544
No 188
>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=51.49 E-value=11 Score=25.17 Aligned_cols=27 Identities=30% Similarity=0.701 Sum_probs=18.1
Q ss_pred ccccCCCccccCCCCCeEEcCCCCCceec
Q psy4748 13 FCSKCGTILPLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 13 FCp~CgnlL~~~~~~~~~~C~~C~~~~~~ 41 (136)
-||.|++-|.+.. +.+.|..|+..+..
T Consensus 3 ~CP~C~~~L~~~~--~~~~C~~C~~~~~~ 29 (70)
T PF07191_consen 3 TCPKCQQELEWQG--GHYHCEACQKDYKK 29 (70)
T ss_dssp B-SSS-SBEEEET--TEEEETTT--EEEE
T ss_pred cCCCCCCccEEeC--CEEECcccccccee
Confidence 4999999998854 68899999876554
No 189
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=51.03 E-value=32 Score=19.59 Aligned_cols=27 Identities=22% Similarity=0.573 Sum_probs=15.3
Q ss_pred ccccccCCCceEEEEeeccccCCCceEEEEec
Q psy4748 103 RKCKRCNNDTMSYATLQLRSADEGQTIFFTCT 134 (136)
Q Consensus 103 ~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~ 134 (136)
.-|||||-.-..=.--| .|....|.|.
T Consensus 2 hlcpkcgvgvl~pvy~~-----kgeikvfrcs 28 (36)
T PF09151_consen 2 HLCPKCGVGVLEPVYNQ-----KGEIKVFRCS 28 (36)
T ss_dssp -B-TTTSSSBEEEEE-T-----TS-EEEEEES
T ss_pred ccCCccCceEEEEeecC-----CCcEEEEEcC
Confidence 35999998766543333 3666777775
No 190
>COG3791 Uncharacterized conserved protein [Function unknown]
Probab=50.14 E-value=7 Score=28.49 Aligned_cols=17 Identities=29% Similarity=0.526 Sum_probs=13.8
Q ss_pred cccccccCCCccccCCC
Q psy4748 10 ESEFCSKCGTILPLFDF 26 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~ 26 (136)
...||+.||+-|.-+..
T Consensus 68 ~r~FC~~CGs~l~~~~~ 84 (133)
T COG3791 68 GRGFCPTCGSPLFWRGP 84 (133)
T ss_pred CCeecccCCCceEEecC
Confidence 34599999999999843
No 191
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=49.21 E-value=12 Score=21.38 Aligned_cols=31 Identities=16% Similarity=0.269 Sum_probs=23.6
Q ss_pred ccccccccCCCccccCCCCCeEEcCCCCCceec
Q psy4748 9 VESEFCSKCGTILPLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 9 ~~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~ 41 (136)
....||..|+..|.... ..+.|+.|++....
T Consensus 9 ~~~~~C~~C~~~i~~~~--~~~~C~~C~~~~H~ 39 (49)
T smart00109 9 KKPTKCCVCRKSIWGSF--QGLRCSWCKVKCHK 39 (49)
T ss_pred CCCCCccccccccCcCC--CCcCCCCCCchHHH
Confidence 34679999999998643 36889999987654
No 192
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=48.28 E-value=9.2 Score=23.43 Aligned_cols=32 Identities=22% Similarity=0.417 Sum_probs=24.9
Q ss_pred cccccccCCCccccCCC-------CCeEEcCCCCCceec
Q psy4748 10 ESEFCSKCGTILPLFDF-------KGDVKCYVCKTSYGT 41 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~-------~~~~~C~~C~~~~~~ 41 (136)
+...|..|.++|..+.+ ...+.|..|......
T Consensus 5 PFv~C~~C~~lLqlP~~~~~~~k~~~klrCGaCs~vl~~ 43 (46)
T PF11331_consen 5 PFVVCSSCFELLQLPAKFSLSKKNQQKLRCGACSEVLSF 43 (46)
T ss_pred CEeECccHHHHHcCCCccCCCccceeEEeCCCCceeEEE
Confidence 45689999999999864 247999999876543
No 193
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=48.04 E-value=9.2 Score=29.06 Aligned_cols=29 Identities=21% Similarity=0.368 Sum_probs=19.4
Q ss_pred ccccCCCccccCC-------CC----CeEEcCCCCCceec
Q psy4748 13 FCSKCGTILPLFD-------FK----GDVKCYVCKTSYGT 41 (136)
Q Consensus 13 FCp~CgnlL~~~~-------~~----~~~~C~~C~~~~~~ 41 (136)
-||.||......- .+ ..+.|..|||....
T Consensus 2 ~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~e 41 (160)
T smart00709 2 DCPSCGGNGTTRMLLTSIPYFREVIIMSFECEHCGYRNNE 41 (160)
T ss_pred cCCCCCCCCEEEEEEecCCCcceEEEEEEECCCCCCccce
Confidence 4999986544221 11 36899999998753
No 194
>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=47.51 E-value=15 Score=23.03 Aligned_cols=29 Identities=21% Similarity=0.487 Sum_probs=19.8
Q ss_pred eccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 102 ERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 102 ~~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
-..|++|...--.+. ..|..-+-|+|..|
T Consensus 22 aLIC~~C~~hNGla~------~~~~~~i~y~C~~C 50 (54)
T PF10058_consen 22 ALICSKCFSHNGLAP------KEEFEEIQYRCPYC 50 (54)
T ss_pred eEECcccchhhcccc------cccCCceEEEcCCC
Confidence 456999986443222 45677778999887
No 195
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=46.61 E-value=12 Score=29.30 Aligned_cols=28 Identities=21% Similarity=0.502 Sum_probs=18.5
Q ss_pred cccCCCccccC----C----CC----CeEEcCCCCCceec
Q psy4748 14 CSKCGTILPLF----D----FK----GDVKCYVCKTSYGT 41 (136)
Q Consensus 14 Cp~CgnlL~~~----~----~~----~~~~C~~C~~~~~~ 41 (136)
||.||...... . .+ ..+.|..|||....
T Consensus 3 Cp~C~~~~~~~~~~~~~IP~F~evii~sf~C~~CGyr~~e 42 (192)
T TIGR00310 3 CPSCGGECETVMKTVNDIPYFGEVLETSTICEHCGYRSND 42 (192)
T ss_pred CCCCCCCCEEEEEEEcCCCCcceEEEEEEECCCCCCccce
Confidence 99998543221 1 11 36899999998753
No 196
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=46.33 E-value=12 Score=30.73 Aligned_cols=29 Identities=28% Similarity=0.597 Sum_probs=9.5
Q ss_pred eccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 102 ERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 102 ~~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
..-||.||+....=|..=..+|| |-|..|
T Consensus 31 n~yCP~Cg~~~L~~f~NN~PVaD------F~C~~C 59 (254)
T PF06044_consen 31 NMYCPNCGSKPLSKFENNRPVAD------FYCPNC 59 (254)
T ss_dssp H---TTT--SS-EE--------E------EE-TTT
T ss_pred CCcCCCCCChhHhhccCCCccce------eECCCC
Confidence 45799999886665555555554 556666
No 197
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=46.09 E-value=5.6 Score=25.45 Aligned_cols=30 Identities=27% Similarity=0.427 Sum_probs=23.6
Q ss_pred cccccCCCccccCCCC--CeEEcCCCCCceec
Q psy4748 12 EFCSKCGTILPLFDFK--GDVKCYVCKTSYGT 41 (136)
Q Consensus 12 ~FCp~CgnlL~~~~~~--~~~~C~~C~~~~~~ 41 (136)
.-|..||.+|---+.. +...|+.|......
T Consensus 5 iRC~~CnKlLa~a~~~~yle~KCPrCK~vN~~ 36 (60)
T COG4416 5 IRCAKCNKLLAEAEGQAYLEKKCPRCKEVNEF 36 (60)
T ss_pred eehHHHhHHHHhcccceeeeecCCccceeeee
Confidence 4589999999876543 56799999987765
No 198
>KOG0696|consensus
Probab=46.05 E-value=4.3 Score=36.40 Aligned_cols=29 Identities=28% Similarity=0.701 Sum_probs=21.5
Q ss_pred ccccccccCCCccccCCCCCeEEcCCCCCc
Q psy4748 9 VESEFCSKCGTILPLFDFKGDVKCYVCKTS 38 (136)
Q Consensus 9 ~~~~FCp~CgnlL~~~~~~~~~~C~~C~~~ 38 (136)
.+..||.+||+|||---- .-+.|..|.--
T Consensus 119 ssPTFCDhCGsLLyGl~H-QGmKC~~C~mN 147 (683)
T KOG0696|consen 119 SSPTFCDHCGSLLYGLIH-QGMKCDTCDMN 147 (683)
T ss_pred CCCchhhhHHHHHHHHHh-cccccccccch
Confidence 467899999999997422 24688888753
No 199
>COG0229 Conserved domain frequently associated with peptide methionine sulfoxide reductase [Posttranslational modification, protein turnover, chaperones]
Probab=45.54 E-value=22 Score=26.74 Aligned_cols=24 Identities=29% Similarity=0.343 Sum_probs=15.5
Q ss_pred cCCCccccCCCCCeEEcCCCCCcee
Q psy4748 16 KCGTILPLFDFKGDVKCYVCKTSYG 40 (136)
Q Consensus 16 ~CgnlL~~~~~~~~~~C~~C~~~~~ 40 (136)
..|-++...+ .++|+|..||..-.
T Consensus 30 ft~~y~~~~~-~GiY~c~~cg~pLF 53 (140)
T COG0229 30 FTGEYLDNKE-KGIYVCIVCGEPLF 53 (140)
T ss_pred CCChhhcccC-CceEEeecCCCccc
Confidence 3455555554 36899999996543
No 200
>KOG0402|consensus
Probab=45.39 E-value=8.9 Score=26.61 Aligned_cols=32 Identities=28% Similarity=0.333 Sum_probs=26.6
Q ss_pred cccccccCCCccccCCCCCeEEcCCCCCceec
Q psy4748 10 ESEFCSKCGTILPLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~ 41 (136)
+-.+|+.||..-.-++..++|.|+.|.....-
T Consensus 35 aky~CsfCGK~~vKR~AvGiW~C~~C~kv~ag 66 (92)
T KOG0402|consen 35 AKYTCSFCGKKTVKRKAVGIWKCGSCKKVVAG 66 (92)
T ss_pred hhhhhhhcchhhhhhhceeEEecCCccceecc
Confidence 44689999998887777789999999987654
No 201
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=45.38 E-value=5.6 Score=22.93 Aligned_cols=26 Identities=31% Similarity=0.539 Sum_probs=15.3
Q ss_pred cccccCCCccccCCC--CCeEEcCCCCC
Q psy4748 12 EFCSKCGTILPLFDF--KGDVKCYVCKT 37 (136)
Q Consensus 12 ~FCp~CgnlL~~~~~--~~~~~C~~C~~ 37 (136)
+.|+.||.+....-+ ...-+|..||-
T Consensus 2 r~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~ 29 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNPPKVEGVCDNCGG 29 (36)
T ss_dssp EEETTTTEEEETTTB--SSTTBCTTTTE
T ss_pred cCcCCCCCccccccCCCCCCCccCCCCC
Confidence 357777776655422 23347777774
No 202
>PRK03954 ribonuclease P protein component 4; Validated
Probab=44.84 E-value=15 Score=26.80 Aligned_cols=31 Identities=19% Similarity=0.387 Sum_probs=23.7
Q ss_pred ccccccCCCccccCCC-------C----CeEEcCCCCCceec
Q psy4748 11 SEFCSKCGTILPLFDF-------K----GDVKCYVCKTSYGT 41 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~-------~----~~~~C~~C~~~~~~ 41 (136)
..||-.|+++|.|-.+ + ..+.|-.||+....
T Consensus 64 R~~CK~C~t~LiPG~n~~vRi~~~~~~~vvitCl~CG~~kR~ 105 (121)
T PRK03954 64 RRYCKRCHSFLVPGVNARVRLRQKRMPHVVITCLECGHIMRY 105 (121)
T ss_pred HHHhhcCCCeeecCCceEEEEecCCcceEEEECccCCCEEee
Confidence 3599999999998421 1 35789999998765
No 203
>COG4647 AcxC Acetone carboxylase, gamma subunit [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=44.56 E-value=8.9 Score=28.85 Aligned_cols=14 Identities=21% Similarity=0.650 Sum_probs=12.1
Q ss_pred ccccCCCccccCCC
Q psy4748 13 FCSKCGTILPLFDF 26 (136)
Q Consensus 13 FCp~CgnlL~~~~~ 26 (136)
|||+||.|+..+..
T Consensus 122 icpecg~l~eveaa 135 (165)
T COG4647 122 ICPECGILHEVEAA 135 (165)
T ss_pred hCccccceeeeccC
Confidence 89999999998743
No 204
>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=44.56 E-value=12 Score=24.64 Aligned_cols=31 Identities=19% Similarity=0.523 Sum_probs=15.5
Q ss_pred ccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 103 RKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 103 ~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
-.|.+|+++.+.-+..| |=+-=+|+-.|++|
T Consensus 5 FTC~~C~~Rs~~~~sk~---aY~~GvViv~C~gC 35 (66)
T PF05180_consen 5 FTCNKCGTRSAKMFSKQ---AYHKGVVIVQCPGC 35 (66)
T ss_dssp EEETTTTEEEEEEEEHH---HHHTSEEEEE-TTS
T ss_pred EEcCCCCCccceeeCHH---HHhCCeEEEECCCC
Confidence 34666666555544422 34444566666555
No 205
>TIGR02820 formald_GSH S-(hydroxymethyl)glutathione synthase. The formation of S-(hydroxymethyl)glutathione synthase from glutathione and formaldehyde occurs naturally, but this enzyme speeds its formation in some species as part of a pathway of formaldehyde detoxification.
Probab=44.10 E-value=10 Score=29.56 Aligned_cols=15 Identities=27% Similarity=0.459 Sum_probs=12.2
Q ss_pred cccccccCCCccccC
Q psy4748 10 ESEFCSKCGTILPLF 24 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~ 24 (136)
...||+.||+-|+..
T Consensus 88 ~R~FC~~CGS~L~~~ 102 (182)
T TIGR02820 88 QRHACKGCGTHMYGR 102 (182)
T ss_pred EeecCCCCCCccccc
Confidence 345999999999765
No 206
>PF02132 RecR: RecR protein; InterPro: IPR023628 The bacterial protein RecR seems to play a role in a recombinational process of DNA repair []. It may act with RecF and RecO. RecR's structure consists of a N-terminal helix-hairpin-helix (HhH) motif, followed by a Cys4 zinc-finger motif, a Toprim domain and a Walker B motif []. This entry represents the C4-type zinc finger.; PDB: 1VDD_D 2V1C_B.
Probab=43.97 E-value=7.5 Score=22.75 Aligned_cols=13 Identities=38% Similarity=0.966 Sum_probs=6.8
Q ss_pred cccccccCCCccc
Q psy4748 10 ESEFCSKCGTILP 22 (136)
Q Consensus 10 ~~~FCp~CgnlL~ 22 (136)
.+.+|+.|||+=.
T Consensus 16 ~i~~C~~C~nlse 28 (41)
T PF02132_consen 16 NIKFCSICGNLSE 28 (41)
T ss_dssp H-EE-SSS--EES
T ss_pred cCCccCCCCCcCC
Confidence 4679999999754
No 207
>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=43.42 E-value=35 Score=24.91 Aligned_cols=27 Identities=26% Similarity=0.716 Sum_probs=21.2
Q ss_pred ccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 103 RKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 103 ~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
+.||.|++++-.+.-. +-+.|-.|..|
T Consensus 94 VlC~~C~spdT~l~k~-------~r~~~l~C~aC 120 (125)
T PF01873_consen 94 VLCPECGSPDTELIKE-------GRLIFLKCKAC 120 (125)
T ss_dssp SSCTSTSSSSEEEEEE-------TTCCEEEETTT
T ss_pred EEcCCCCCCccEEEEc-------CCEEEEEeccc
Confidence 5899999999876543 56788888877
No 208
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=43.37 E-value=10 Score=28.71 Aligned_cols=28 Identities=25% Similarity=0.479 Sum_probs=15.9
Q ss_pred ccccCCCccccCC-------CC----CeEEcCCCCCcee
Q psy4748 13 FCSKCGTILPLFD-------FK----GDVKCYVCKTSYG 40 (136)
Q Consensus 13 FCp~CgnlL~~~~-------~~----~~~~C~~C~~~~~ 40 (136)
-||.||......- .+ ..+.|..|||...
T Consensus 3 ~Cp~C~~~~~~~~~~~~IP~F~evii~sf~C~~CGyk~~ 41 (161)
T PF03367_consen 3 LCPNCGENGTTRILLTDIPYFKEVIIMSFECEHCGYKNN 41 (161)
T ss_dssp E-TTTSSCCEEEEEEEEETTTEEEEEEEEE-TTT--EEE
T ss_pred cCCCCCCCcEEEEEEEcCCCCceEEEEEeECCCCCCEee
Confidence 4999998754431 11 3589999999875
No 209
>PRK05417 glutathione-dependent formaldehyde-activating enzyme; Provisional
Probab=43.12 E-value=11 Score=29.66 Aligned_cols=14 Identities=21% Similarity=0.446 Sum_probs=12.3
Q ss_pred ccccccCCCccccC
Q psy4748 11 SEFCSKCGTILPLF 24 (136)
Q Consensus 11 ~~FCp~CgnlL~~~ 24 (136)
..||+.||+-|+..
T Consensus 93 R~FC~~CGS~L~~~ 106 (191)
T PRK05417 93 RHACKECGVHMYGR 106 (191)
T ss_pred eeeCCCCCCccccc
Confidence 45999999999886
No 210
>PF10005 DUF2248: Uncharacterized protein conserved in bacteria (DUF2248); InterPro: IPR011201 This is a family of uncharacterised bacterial proteins.
Probab=42.66 E-value=15 Score=31.46 Aligned_cols=25 Identities=24% Similarity=0.744 Sum_probs=20.6
Q ss_pred cccCCCccccCCCCCeEEcCCCCCceecC
Q psy4748 14 CSKCGTILPLFDFKGDVKCYVCKTSYGTQ 42 (136)
Q Consensus 14 Cp~CgnlL~~~~~~~~~~C~~C~~~~~~~ 42 (136)
|+.||+.|+.+.. .|-.||..-.-.
T Consensus 2 C~~Cg~~v~FeNt----~C~~Cg~~LGf~ 26 (343)
T PF10005_consen 2 CPNCGQPVFFENT----RCLSCGSALGFD 26 (343)
T ss_pred CCCCCCcceeCCC----ccccCCccccCC
Confidence 9999999999644 799999876543
No 211
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=42.18 E-value=17 Score=26.30 Aligned_cols=27 Identities=22% Similarity=0.517 Sum_probs=19.0
Q ss_pred ccc--cCCCccccCCCCCeEEcCCCCCcee
Q psy4748 13 FCS--KCGTILPLFDFKGDVKCYVCKTSYG 40 (136)
Q Consensus 13 FCp--~CgnlL~~~~~~~~~~C~~C~~~~~ 40 (136)
=|| .|+.-+... +.+.|.|..|+...+
T Consensus 20 aC~~~~C~kKv~~~-~~~~y~C~~C~~~~~ 48 (146)
T PF08646_consen 20 ACPNEKCNKKVTEN-GDGSYRCEKCNKTVE 48 (146)
T ss_dssp E-TSTTTS-B-EEE-TTTEEEETTTTEEES
T ss_pred CCCCccCCCEeecC-CCcEEECCCCCCcCC
Confidence 499 999987776 346899999997753
No 212
>PRK11032 hypothetical protein; Provisional
Probab=41.98 E-value=14 Score=28.25 Aligned_cols=34 Identities=18% Similarity=0.297 Sum_probs=28.2
Q ss_pred CccccccccCCCccccCCCCCeEEcCCCCCceec
Q psy4748 8 NVESEFCSKCGTILPLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 8 ~~~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~ 41 (136)
..+.+-|..||..+......-+-.|+.||..+..
T Consensus 121 g~G~LvC~~Cg~~~~~~~p~~i~pCp~C~~~~F~ 154 (160)
T PRK11032 121 GLGNLVCEKCHHHLAFYTPEVLPLCPKCGHDQFQ 154 (160)
T ss_pred ecceEEecCCCCEEEecCCCcCCCCCCCCCCeee
Confidence 3467899999999999766567799999988775
No 213
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=41.44 E-value=13 Score=27.32 Aligned_cols=29 Identities=24% Similarity=0.508 Sum_probs=18.7
Q ss_pred cccccccCCCccccCC-------------------CCCeEEcCCCCCc
Q psy4748 10 ESEFCSKCGTILPLFD-------------------FKGDVKCYVCKTS 38 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~-------------------~~~~~~C~~C~~~ 38 (136)
....|+.||..-.+.+ ....+.|+.||..
T Consensus 69 ~~~~C~~CG~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~ 116 (135)
T PRK03824 69 AVLKCRNCGNEWSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSR 116 (135)
T ss_pred eEEECCCCCCEEecccccccccccccccccccccccccCcCCcCCCCC
Confidence 3457899997765542 0235679999854
No 214
>PRK08579 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=41.40 E-value=15 Score=33.68 Aligned_cols=27 Identities=22% Similarity=0.530 Sum_probs=20.1
Q ss_pred cCccccccccCCCccccCCCCCeEEcCCCCC
Q psy4748 7 FNVESEFCSKCGTILPLFDFKGDVKCYVCKT 37 (136)
Q Consensus 7 ~~~~~~FCp~CgnlL~~~~~~~~~~C~~C~~ 37 (136)
|+..+.+|+.||..+ .+....|+.||.
T Consensus 564 inp~~~~C~~CG~~~----~g~~~~CP~CGs 590 (625)
T PRK08579 564 YTPAITVCNKCGRST----TGLYTRCPRCGS 590 (625)
T ss_pred eCCCCccCCCCCCcc----CCCCCcCcCCCC
Confidence 445778999999944 233679999995
No 215
>KOG3362|consensus
Probab=40.62 E-value=10 Score=28.82 Aligned_cols=30 Identities=30% Similarity=0.658 Sum_probs=22.4
Q ss_pred CccCccccccccCCCccccCCCCCeEEcCCCCCceec
Q psy4748 5 GYFNVESEFCSKCGTILPLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 5 ~~~~~~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~ 41 (136)
-+|.-...||..||. . ..+.|-.||..+-.
T Consensus 112 p~~KP~r~fCaVCG~---~----S~ysC~~CG~kyCs 141 (156)
T KOG3362|consen 112 PSFKPLRKFCAVCGY---D----SKYSCVNCGTKYCS 141 (156)
T ss_pred CCCCCcchhhhhcCC---C----chhHHHhcCCceee
Confidence 355556679999993 2 46789999988865
No 216
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=40.03 E-value=52 Score=22.13 Aligned_cols=17 Identities=18% Similarity=0.415 Sum_probs=7.5
Q ss_pred eccccccCCCceEEEEe
Q psy4748 102 ERKCKRCNNDTMSYATL 118 (136)
Q Consensus 102 ~~~CpkCg~~~a~f~~~ 118 (136)
.-.||.|||..++-..+
T Consensus 22 ~F~CPfC~~~~sV~v~i 38 (81)
T PF05129_consen 22 VFDCPFCNHEKSVSVKI 38 (81)
T ss_dssp ----TTT--SS-EEEEE
T ss_pred eEcCCcCCCCCeEEEEE
Confidence 46788888888776666
No 217
>PRK08402 replication factor A; Reviewed
Probab=39.85 E-value=19 Score=30.82 Aligned_cols=30 Identities=10% Similarity=0.087 Sum_probs=23.3
Q ss_pred ccccccCCCccccCCCCCeEEcCCCCCcee
Q psy4748 11 SEFCSKCGTILPLFDFKGDVKCYVCKTSYG 40 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~ 40 (136)
..=||.|+.-+......+.|.|..||...+
T Consensus 212 y~aCp~CnKkv~~~~~~~~~~Ce~~~~v~p 241 (355)
T PRK08402 212 YDACPECRRKVDYDPATDTWICPEHGEVEP 241 (355)
T ss_pred EecCCCCCeEEEEecCCCCEeCCCCCCcCc
Confidence 357999999987665567899999986443
No 218
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.64 E-value=23 Score=24.33 Aligned_cols=31 Identities=19% Similarity=0.281 Sum_probs=24.2
Q ss_pred ccccccCCCccccCCC--CCeEEcCCCCCceec
Q psy4748 11 SEFCSKCGTILPLFDF--KGDVKCYVCKTSYGT 41 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~--~~~~~C~~C~~~~~~ 41 (136)
|+-||.||--|.++.- ...-.|+.|+-++-.
T Consensus 1 ~llCP~C~v~l~~~~rs~vEiD~CPrCrGVWLD 33 (88)
T COG3809 1 MLLCPICGVELVMSVRSGVEIDYCPRCRGVWLD 33 (88)
T ss_pred CcccCcCCceeeeeeecCceeeeCCccccEeec
Confidence 4679999999998743 345689999988754
No 219
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=39.46 E-value=11 Score=21.88 Aligned_cols=22 Identities=27% Similarity=0.631 Sum_probs=10.4
Q ss_pred ccccccCCCccccCCC-CCeEEc
Q psy4748 11 SEFCSKCGTILPLFDF-KGDVKC 32 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~-~~~~~C 32 (136)
..-|..|||+...-.+ ...++|
T Consensus 6 ~YkC~~CGniVev~~~g~g~lvC 28 (36)
T PF06397_consen 6 FYKCEHCGNIVEVVHDGGGPLVC 28 (36)
T ss_dssp EEE-TTT--EEEEEE--SS-EEE
T ss_pred EEEccCCCCEEEEEECCCCCEEe
Confidence 4568888888766543 335555
No 220
>COG3364 Zn-ribbon containing protein [General function prediction only]
Probab=38.76 E-value=16 Score=26.25 Aligned_cols=21 Identities=24% Similarity=0.580 Sum_probs=17.0
Q ss_pred ccccccCCCceEEEEeecccc
Q psy4748 103 RKCKRCNNDTMSYATLQLRSA 123 (136)
Q Consensus 103 ~~CpkCg~~~a~f~~~Q~RSA 123 (136)
.-||+||.+.-.|.---.|-|
T Consensus 21 ~GCp~CG~nkF~yv~~e~rpa 41 (112)
T COG3364 21 SGCPKCGCNKFLYVPEEKRPA 41 (112)
T ss_pred ccCccccchheEecccccccc
Confidence 469999999999887766655
No 221
>KOG2463|consensus
Probab=38.61 E-value=13 Score=31.94 Aligned_cols=12 Identities=33% Similarity=1.071 Sum_probs=10.1
Q ss_pred ccccccccCCCc
Q psy4748 9 VESEFCSKCGTI 20 (136)
Q Consensus 9 ~~~~FCp~Cgnl 20 (136)
++..|||.||+-
T Consensus 255 m~k~FCp~CG~~ 266 (376)
T KOG2463|consen 255 MPKDFCPSCGHK 266 (376)
T ss_pred cchhcccccCCC
Confidence 467899999986
No 222
>PRK05508 methionine sulfoxide reductase B; Provisional
Probab=38.19 E-value=43 Score=24.50 Aligned_cols=19 Identities=21% Similarity=0.326 Sum_probs=14.3
Q ss_pred CCceeccccccCCCceEEE
Q psy4748 98 GPIVERKCKRCNNDTMSYA 116 (136)
Q Consensus 98 ~~~~~~~CpkCg~~~a~f~ 116 (136)
+..++..|.+||..--.-|
T Consensus 75 ~~RtEv~C~~C~~HLGHVF 93 (119)
T PRK05508 75 GRRTEIVCANCGGHLGHVF 93 (119)
T ss_pred CcEEEEEeCCCCCccCccc
Confidence 4578999999997655444
No 223
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=38.12 E-value=18 Score=31.26 Aligned_cols=29 Identities=24% Similarity=0.402 Sum_probs=21.7
Q ss_pred cccccccCCCccccCCCCCeEEcCCCCCceec
Q psy4748 10 ESEFCSKCGTILPLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~ 41 (136)
++.=||+||-.+.+ +....|++||+.-..
T Consensus 214 ~~~~C~~Cd~~~~~---~~~a~CpRC~~~L~~ 242 (403)
T TIGR00155 214 KLRSCSACHTTILP---AQEPVCPRCSTPLYV 242 (403)
T ss_pred CCCcCCCCCCccCC---CCCcCCcCCCCcccC
Confidence 35569999997754 345689999998654
No 224
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=37.83 E-value=42 Score=24.80 Aligned_cols=27 Identities=26% Similarity=0.737 Sum_probs=20.2
Q ss_pred ccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 103 RKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 103 ~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
+.||.||+++-.+.- ++-..|-.|..|
T Consensus 98 VlC~~C~sPdT~l~k-------~~r~~~l~C~AC 124 (133)
T TIGR00311 98 VICRECNRPDTRIIK-------EGRVSLLKCEAC 124 (133)
T ss_pred EECCCCCCCCcEEEE-------eCCeEEEecccC
Confidence 579999999987642 345667788877
No 225
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=37.83 E-value=15 Score=21.38 Aligned_cols=24 Identities=25% Similarity=0.650 Sum_probs=15.6
Q ss_pred ccccccCCCceE---EEEeeccccCCC
Q psy4748 103 RKCKRCNNDTMS---YATLQLRSADEG 126 (136)
Q Consensus 103 ~~CpkCg~~~a~---f~~~Q~RSADEg 126 (136)
..||.||....+ +.+..+|-.+=+
T Consensus 3 ~~Cp~Cg~~~~~~~g~~~r~i~~l~~~ 29 (47)
T PF14690_consen 3 PRCPHCGSPSVHRHGYKTRRIRHLPIG 29 (47)
T ss_pred ccCCCcCCCceECCceEEEEEeecccC
Confidence 469999988755 455555544444
No 226
>smart00532 LIGANc Ligase N family.
Probab=37.77 E-value=18 Score=31.71 Aligned_cols=30 Identities=23% Similarity=0.523 Sum_probs=22.3
Q ss_pred cccccccCCCccccCCCCCeEEcCC--CCCce
Q psy4748 10 ESEFCSKCGTILPLFDFKGDVKCYV--CKTSY 39 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~~~~~~C~~--C~~~~ 39 (136)
-..+||.||+-|...++...+.|.+ |..+.
T Consensus 398 ~P~~CP~C~s~l~~~~~~~~~~C~n~~C~aq~ 429 (441)
T smart00532 398 MPTHCPSCGSELVREEGEVDIRCPNPLCPAQL 429 (441)
T ss_pred CCCCCCCCCCEeEecCCceEEEeCCCCCHHHH
Confidence 4579999999998765555788974 66443
No 227
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=37.54 E-value=52 Score=21.56 Aligned_cols=27 Identities=15% Similarity=0.407 Sum_probs=15.5
Q ss_pred ccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 103 RKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 103 ~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
+.||-||-+.+..-. + +-.-+++|.+|
T Consensus 7 KPCPFCG~~~~~v~~------~-~g~~~v~C~~C 33 (64)
T PRK09710 7 KPCPFCGCPSVTVKA------I-SGYYRAKCNGC 33 (64)
T ss_pred cCCCCCCCceeEEEe------c-CceEEEEcCCC
Confidence 567777777665542 1 22344566665
No 228
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=37.20 E-value=44 Score=24.81 Aligned_cols=27 Identities=22% Similarity=0.644 Sum_probs=21.3
Q ss_pred ccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 103 RKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 103 ~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
+.|+.||+++-.+.- |+.+.|-.|..|
T Consensus 103 VlC~~C~spdT~l~k-------~~r~~~l~C~AC 129 (138)
T PRK03988 103 VICPECGSPDTKLIK-------EGRIWVLKCEAC 129 (138)
T ss_pred EECCCCCCCCcEEEE-------cCCeEEEEcccC
Confidence 579999999976632 366888889877
No 229
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=36.82 E-value=32 Score=20.01 Aligned_cols=25 Identities=32% Similarity=0.599 Sum_probs=16.2
Q ss_pred ccccCCCccccC--C--CCCeEEcCCCCC
Q psy4748 13 FCSKCGTILPLF--D--FKGDVKCYVCKT 37 (136)
Q Consensus 13 FCp~CgnlL~~~--~--~~~~~~C~~C~~ 37 (136)
=||.||.-=..+ . ....+.|+.|+.
T Consensus 5 pCP~CGG~DrFr~~d~~g~G~~~C~~Cg~ 33 (37)
T smart00778 5 PCPNCGGSDRFRFDDKDGRGTWFCSVCGA 33 (37)
T ss_pred CCCCCCCccccccccCCCCcCEEeCCCCC
Confidence 488888732222 1 236899999974
No 230
>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=36.49 E-value=36 Score=29.02 Aligned_cols=30 Identities=23% Similarity=0.602 Sum_probs=17.9
Q ss_pred eeccccccCCCceEEEEeeccccCCCceEEEEec
Q psy4748 101 VERKCKRCNNDTMSYATLQLRSADEGQTIFFTCT 134 (136)
Q Consensus 101 ~~~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~ 134 (136)
..-.||+||... .++=-. -.+.-||.|+|.
T Consensus 168 ~~p~c~~cg~~~---~~v~~~-d~~~~~v~y~c~ 197 (353)
T cd00674 168 FMPYCEKCGKDT---TTVEAY-DAKAGTVTYKCE 197 (353)
T ss_pred eeeecCCcCcce---eEEEEE-eCCCCeEEEEcC
Confidence 356899999332 222112 224569999993
No 231
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=35.88 E-value=26 Score=20.71 Aligned_cols=24 Identities=29% Similarity=0.559 Sum_probs=13.1
Q ss_pred cccCCCccccC-----CCCCeEEcCCCCC
Q psy4748 14 CSKCGTILPLF-----DFKGDVKCYVCKT 37 (136)
Q Consensus 14 Cp~CgnlL~~~-----~~~~~~~C~~C~~ 37 (136)
||.||.--... .....+.|+.|+.
T Consensus 6 CP~CGG~DrFri~~d~~~~G~~~C~~C~~ 34 (40)
T PF08273_consen 6 CPICGGKDRFRIFDDKDGRGTWICRQCGG 34 (40)
T ss_dssp -TTTT-TTTEEEETT----S-EEETTTTB
T ss_pred CCCCcCccccccCcCcccCCCEECCCCCC
Confidence 88898754333 1247899999953
No 232
>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=35.74 E-value=27 Score=25.80 Aligned_cols=27 Identities=22% Similarity=0.458 Sum_probs=21.5
Q ss_pred cccccCCCccccCCCCCeEEcCCCCCce
Q psy4748 12 EFCSKCGTILPLFDFKGDVKCYVCKTSY 39 (136)
Q Consensus 12 ~FCp~CgnlL~~~~~~~~~~C~~C~~~~ 39 (136)
.-||.|+.-|....+ +.+.|..|+...
T Consensus 35 ~aC~~C~kkv~~~~~-~~~~C~~C~~~~ 61 (166)
T cd04476 35 PACPGCNKKVVEEGN-GTYRCEKCNKSV 61 (166)
T ss_pred ccccccCcccEeCCC-CcEECCCCCCcC
Confidence 469999998876432 689999999875
No 233
>PF08063 PADR1: PADR1 (NUC008) domain; InterPro: IPR012982 This domain is found in poly(ADP-ribose)-synthetases []. The function of this domain is unknown.; GO: 0003950 NAD+ ADP-ribosyltransferase activity, 0005634 nucleus; PDB: 2JVN_A 4DQY_E 2RIQ_A.
Probab=35.47 E-value=18 Score=22.69 Aligned_cols=16 Identities=13% Similarity=0.584 Sum_probs=9.5
Q ss_pred eccccccCCCceEEEE
Q psy4748 102 ERKCKRCNNDTMSYAT 117 (136)
Q Consensus 102 ~~~CpkCg~~~a~f~~ 117 (136)
-..||+|++...+|..
T Consensus 14 l~~Cp~C~~~~l~~~~ 29 (55)
T PF08063_consen 14 LEPCPKCKGGQLYFDG 29 (55)
T ss_dssp E---SSSSE-EEEEET
T ss_pred CCCCCCCCCCeEEecC
Confidence 3689999999888743
No 234
>PF01641 SelR: SelR domain; InterPro: IPR002579 Peptide methionine sulphoxide reductase (Msr) reverses the inactivation of many proteins due to the oxidation of critical methionine residues by reducing methionine sulphoxide, Met(O), to methionine []. It is present in most living organisms, and the cognate structural gene belongs to the so-called minimum gene set [, ]. The domains: MsrA and MsrB, reduce different epimeric forms of methionine sulphoxide. This group represents MsrB, the crystal structure of which has been determined to 1.8A []. The overall structure shows no resemblance to the structures of MsrA (IPR002569 from INTERPRO) from other organisms; though the active sites show approximate mirror symmetry. In each case, conserved amino acid motifs mediate the stereo-specific recognition and reduction of the substrate. Unlike the MsrA domain, the MsrB domain activates the cysteine or selenocysteine nucleophile through a unique Cys-Arg-Asp/Glu catalytic triad. The collapse of the reaction intermediate most likely results in the formation of a sulphenic or selenenic acid moiety. Regeneration of the active site occurs through a series of thiol-disulphide exchange steps involving another active site Cys residue and thioredoxin. In a number of pathogenic bacteria, including Neisseria gonorrhoeae, the MsrA and MsrB domains are fused; the MsrA being N-terminal to MsrB. This arrangement is reversed in Treponema pallidum. In N. gonorrhoeae and Neisseria meningitidis, a thioredoxin domain is fused to the N terminus. This may function to reduce the active sites of the downstream MsrA and MsrB domains. ; GO: 0008113 peptide-methionine-(S)-S-oxide reductase activity, 0055114 oxidation-reduction process; PDB: 1L1D_A 3E0O_D 2KZN_A 3HCG_B 3HCH_A 2L1U_A 3MAO_A 2K8D_A 3HCJ_A 3HCI_A ....
Probab=35.47 E-value=29 Score=25.46 Aligned_cols=21 Identities=19% Similarity=0.276 Sum_probs=15.5
Q ss_pred CCCceeccccccCCCceEEEE
Q psy4748 97 DGPIVERKCKRCNNDTMSYAT 117 (136)
Q Consensus 97 ~~~~~~~~CpkCg~~~a~f~~ 117 (136)
....+++.|.+||..--.-|.
T Consensus 81 g~~R~Ev~C~~Cg~HLGHVF~ 101 (124)
T PF01641_consen 81 GMVRTEVRCARCGSHLGHVFD 101 (124)
T ss_dssp SSEEEEEEETTTCCEEEEEES
T ss_pred CceEEEEEecCCCCccccEeC
Confidence 355789999999986655543
No 235
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=35.38 E-value=34 Score=27.82 Aligned_cols=27 Identities=15% Similarity=0.396 Sum_probs=16.0
Q ss_pred eccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 102 ERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 102 ~~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
.+.||+||..=..-.+. .-.-|-|++|
T Consensus 244 g~pCprCG~~I~~~~~~--------gR~t~~CP~C 270 (272)
T PRK14810 244 GEPCLNCKTPIRRVVVA--------GRSSHYCPHC 270 (272)
T ss_pred CCcCCCCCCeeEEEEEC--------CCccEECcCC
Confidence 56899999754332221 2233668887
No 236
>PF06839 zf-GRF: GRF zinc finger; InterPro: IPR010666 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This presumed zinc-binding domain is found in a variety of DNA-binding proteins. It seems likely that this domain is involved in nucleic acid binding. It is named GRF after three conserved residues in the centre of the alignment of the domain. This zinc finger may be related to IPR000380 from INTERPRO. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=35.31 E-value=68 Score=18.81 Aligned_cols=14 Identities=14% Similarity=0.515 Sum_probs=8.9
Q ss_pred ccCCCceEEEEecC
Q psy4748 122 SADEGQTIFFTCTK 135 (136)
Q Consensus 122 SADEg~TvFY~C~~ 135 (136)
..+.+==+||.|..
T Consensus 17 ~~~N~GR~Fy~C~~ 30 (45)
T PF06839_consen 17 TGPNPGRRFYKCPN 30 (45)
T ss_pred CCCCCCCcceECCC
Confidence 34555568888863
No 237
>KOG1842|consensus
Probab=34.90 E-value=9.7 Score=33.85 Aligned_cols=29 Identities=21% Similarity=0.555 Sum_probs=19.8
Q ss_pred ccccccccCCCccccCCCCCeEEcCCCCCce
Q psy4748 9 VESEFCSKCGTILPLFDFKGDVKCYVCKTSY 39 (136)
Q Consensus 9 ~~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~ 39 (136)
.+..|||.|+|-..+..- .--||.||-+.
T Consensus 178 s~V~~CP~Ca~~F~l~rR--rHHCRLCG~Vm 206 (505)
T KOG1842|consen 178 SSVQFCPECANSFGLTRR--RHHCRLCGRVM 206 (505)
T ss_pred CcccccccccchhhhHHH--hhhhhhcchHH
Confidence 356799999998777422 34677776654
No 238
>TIGR03670 rpoB_arch DNA-directed RNA polymerase subunit B. This model represents the archaeal version of DNA-directed RNA polymerase subunit B (rpoB) and is observed in all archaeal genomes.
Probab=34.36 E-value=22 Score=32.44 Aligned_cols=30 Identities=30% Similarity=0.445 Sum_probs=22.6
Q ss_pred cccccccCCCccccCCCCCeEEcCCCCCce
Q psy4748 10 ESEFCSKCGTILPLFDFKGDVKCYVCKTSY 39 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~ 39 (136)
....|..||.++........+.|+.|+...
T Consensus 537 ~~~vC~~CG~~~~~~~~~~~~~C~~c~~~~ 566 (599)
T TIGR03670 537 VVYVCENCGHIAWEDKRKGTAYCPVCGETG 566 (599)
T ss_pred eEEeecccCceeehhcccCceeccccCCCC
Confidence 346899999999764334578899998754
No 239
>PRK07218 replication factor A; Provisional
Probab=33.23 E-value=21 Score=31.24 Aligned_cols=25 Identities=24% Similarity=0.549 Sum_probs=20.0
Q ss_pred ccccccCCCccccCCCCCeEEcCCCCCceec
Q psy4748 11 SEFCSKCGTILPLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~ 41 (136)
+.=||.|+..|.. ..|+.||...+.
T Consensus 297 i~rCP~C~r~v~~------~~C~~hG~ve~~ 321 (423)
T PRK07218 297 IERCPECGRVIQK------GQCRSHGAVEGE 321 (423)
T ss_pred eecCcCccccccC------CcCCCCCCcCCe
Confidence 3579999999933 699999988665
No 240
>PRK04023 DNA polymerase II large subunit; Validated
Probab=32.66 E-value=23 Score=34.55 Aligned_cols=13 Identities=15% Similarity=0.258 Sum_probs=8.5
Q ss_pred EEcCCCCCceecC
Q psy4748 30 VKCYVCKTSYGTQ 42 (136)
Q Consensus 30 ~~C~~C~~~~~~~ 42 (136)
+.|..||......
T Consensus 664 y~CPKCG~El~~~ 676 (1121)
T PRK04023 664 DECEKCGREPTPY 676 (1121)
T ss_pred CcCCCCCCCCCcc
Confidence 4577777766543
No 241
>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=32.53 E-value=14 Score=27.46 Aligned_cols=29 Identities=28% Similarity=0.539 Sum_probs=22.1
Q ss_pred ccccccccCCCccccCCCCCeEEcCCCCCcee
Q psy4748 9 VESEFCSKCGTILPLFDFKGDVKCYVCKTSYG 40 (136)
Q Consensus 9 ~~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~ 40 (136)
|++.-||.||.+.... ..-.|+.|.....
T Consensus 1 m~l~nC~~CgklF~~~---~~~iCp~C~~~~e 29 (137)
T TIGR03826 1 MELANCPKCGRLFVKT---GRDVCPSCYEEEE 29 (137)
T ss_pred CCCccccccchhhhhc---CCccCHHHhHHHH
Confidence 5678999999987772 3457999987554
No 242
>PF14311 DUF4379: Domain of unknown function (DUF4379)
Probab=32.40 E-value=19 Score=22.00 Aligned_cols=11 Identities=36% Similarity=0.767 Sum_probs=9.3
Q ss_pred ceeccccccCC
Q psy4748 100 IVERKCKRCNN 110 (136)
Q Consensus 100 ~~~~~CpkCg~ 110 (136)
.+-.+|++|||
T Consensus 26 ~v~W~C~~Cgh 36 (55)
T PF14311_consen 26 KVWWKCPKCGH 36 (55)
T ss_pred EEEEECCCCCC
Confidence 45689999998
No 243
>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=32.23 E-value=34 Score=30.76 Aligned_cols=30 Identities=20% Similarity=0.335 Sum_probs=22.4
Q ss_pred cccccCCCccccC-C----------CCCeEEcCCCCCceec
Q psy4748 12 EFCSKCGTILPLF-D----------FKGDVKCYVCKTSYGT 41 (136)
Q Consensus 12 ~FCp~CgnlL~~~-~----------~~~~~~C~~C~~~~~~ 41 (136)
.=||.||-+-.+. + ..-.|+|..||.....
T Consensus 201 vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e 241 (557)
T PF05876_consen 201 VPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEE 241 (557)
T ss_pred ccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCH
Confidence 3599999887775 1 1247999999998764
No 244
>COG2995 PqiA Uncharacterized paraquat-inducible protein A [Function unknown]
Probab=31.29 E-value=39 Score=29.67 Aligned_cols=37 Identities=14% Similarity=0.253 Sum_probs=28.6
Q ss_pred ccCccccccccCCCccccCC--CCCeEEcCCCCCceecC
Q psy4748 6 YFNVESEFCSKCGTILPLFD--FKGDVKCYVCKTSYGTQ 42 (136)
Q Consensus 6 ~~~~~~~FCp~CgnlL~~~~--~~~~~~C~~C~~~~~~~ 42 (136)
.-.+...-||+|+-+...+. .+..-.|++||+.-...
T Consensus 13 ~~~~~~~~C~eCd~~~~~P~l~~~q~A~CPRC~~~l~~~ 51 (418)
T COG2995 13 LPPGHLILCPECDMLVSLPRLDSGQSAYCPRCGHTLTRG 51 (418)
T ss_pred CCccceecCCCCCceeccccCCCCCcccCCCCCCccccC
Confidence 34456778999999988874 35678999999987653
No 245
>COG1552 RPL40A Ribosomal protein L40E [Translation, ribosomal structure and biogenesis]
Probab=31.19 E-value=12 Score=23.36 Aligned_cols=26 Identities=23% Similarity=0.443 Sum_probs=18.8
Q ss_pred cccccCCCccccCCCCCeEEcCCCCCceec
Q psy4748 12 EFCSKCGTILPLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 12 ~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~ 41 (136)
.-|-.||...++. .-.||.|+|..-.
T Consensus 15 kIC~rC~Arnp~~----A~kCRkC~~k~LR 40 (50)
T COG1552 15 KICRRCYARNPPR----ATKCRKCGYKNLR 40 (50)
T ss_pred HHHHHhcCCCCcc----hhHHhhccCCCcc
Confidence 3588888887774 3479999887643
No 246
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=31.05 E-value=60 Score=25.39 Aligned_cols=27 Identities=19% Similarity=0.612 Sum_probs=20.9
Q ss_pred ccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 103 RKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 103 ~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
+.|+.||+++-.+.- ++.+.|-.|..|
T Consensus 99 V~C~~C~~pdT~l~k-------~~~~~~l~C~aC 125 (201)
T PRK12336 99 VICSECGLPDTRLVK-------EDRVLMLRCDAC 125 (201)
T ss_pred EECCCCCCCCcEEEE-------cCCeEEEEcccC
Confidence 579999999977642 256888889877
No 247
>PRK12366 replication factor A; Reviewed
Probab=30.78 E-value=30 Score=31.68 Aligned_cols=26 Identities=19% Similarity=0.525 Sum_probs=21.2
Q ss_pred cccccCCCccccCCCCCeEEcCCCCCce
Q psy4748 12 EFCSKCGTILPLFDFKGDVKCYVCKTSY 39 (136)
Q Consensus 12 ~FCp~CgnlL~~~~~~~~~~C~~C~~~~ 39 (136)
.=||.|+.-|.. ..+.|.|..|+...
T Consensus 533 ~aCp~CnkKv~~--~~g~~~C~~c~~~~ 558 (637)
T PRK12366 533 YLCPNCRKRVEE--VDGEYICEFCGEVE 558 (637)
T ss_pred ecccccCeEeEc--CCCcEECCCCCCCC
Confidence 469999998864 45799999999873
No 248
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.44 E-value=34 Score=24.86 Aligned_cols=26 Identities=31% Similarity=0.689 Sum_probs=20.8
Q ss_pred ccccccCCCccccCCCCCeEEcCCCCCcee
Q psy4748 11 SEFCSKCGTILPLFDFKGDVKCYVCKTSYG 40 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~ 40 (136)
+.=||.||.-|.. ..+.|++|+....
T Consensus 6 ~~~cPvcg~~~iV----TeL~c~~~etTVr 31 (122)
T COG3877 6 INRCPVCGRKLIV----TELKCSNCETTVR 31 (122)
T ss_pred CCCCCccccccee----EEEecCCCCceEe
Confidence 3469999988877 4789999998654
No 249
>PF01907 Ribosomal_L37e: Ribosomal protein L37e; InterPro: IPR001569 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A19_A 4A1D_A 4A18_A 4A1B_A 1S1I_Y 3O5H_d 3IZS_l 3O58_d 2ZKR_2 3IZR_l ....
Probab=29.66 E-value=33 Score=21.82 Aligned_cols=29 Identities=21% Similarity=0.478 Sum_probs=19.8
Q ss_pred cccccccCCCccccCCCCCeEEcCCCCCceec
Q psy4748 10 ESEFCSKCGTILPLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~~ 41 (136)
.-..|..||..-+..... .|..|||....
T Consensus 14 tH~~CrRCG~~syH~qK~---~CasCGyp~~k 42 (55)
T PF01907_consen 14 THTLCRRCGRRSYHIQKK---TCASCGYPAAK 42 (55)
T ss_dssp SEEE-TTTSSEEEETTTT---EETTTBTTTSS
T ss_pred cEeeecccCCeeeecCCC---cccccCCCccc
Confidence 345788888887775443 88888886654
No 250
>PRK07225 DNA-directed RNA polymerase subunit B'; Validated
Probab=29.30 E-value=34 Score=31.37 Aligned_cols=31 Identities=26% Similarity=0.480 Sum_probs=22.9
Q ss_pred cccccccCCCccccCCCCCeEEcCCCCCcee
Q psy4748 10 ESEFCSKCGTILPLFDFKGDVKCYVCKTSYG 40 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~~~~~~C~~C~~~~~ 40 (136)
....|..||.++........+.|+.|+....
T Consensus 543 ~~~vC~~CG~~~~~~~~~~~~~C~~C~~~~~ 573 (605)
T PRK07225 543 EIYVCAKCGMIAIYDKKRNRKYCPICGEETD 573 (605)
T ss_pred eEEeecCcCcceehhcccCceeecccCCCCc
Confidence 3467999999997654345778999986543
No 251
>COG2260 Predicted Zn-ribbon RNA-binding protein [Translation, ribosomal structure and biogenesis]
Probab=29.11 E-value=26 Score=22.59 Aligned_cols=14 Identities=36% Similarity=0.786 Sum_probs=10.8
Q ss_pred ceeccccccCCCce
Q psy4748 100 IVERKCKRCNNDTM 113 (136)
Q Consensus 100 ~~~~~CpkCg~~~a 113 (136)
|..++||.||....
T Consensus 15 TLke~Cp~CG~~t~ 28 (59)
T COG2260 15 TLKEKCPVCGGDTK 28 (59)
T ss_pred eecccCCCCCCccc
Confidence 45689999998654
No 252
>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=29.10 E-value=40 Score=29.04 Aligned_cols=31 Identities=32% Similarity=0.779 Sum_probs=19.5
Q ss_pred eeccccccCC-CceEEEEeeccccC-CCceEEEEecCC
Q psy4748 101 VERKCKRCNN-DTMSYATLQLRSAD-EGQTIFFTCTKC 136 (136)
Q Consensus 101 ~~~~CpkCg~-~~a~f~~~Q~RSAD-Eg~TvFY~C~~C 136 (136)
....|++||. ....-. +-| ++-||.|+|..|
T Consensus 173 f~piC~~cGri~tt~v~-----~~d~~~~~v~Y~c~~c 205 (360)
T PF01921_consen 173 FLPICEKCGRIDTTEVT-----EYDPEGGTVTYRCEEC 205 (360)
T ss_dssp EEEEETTTEE--EEEEE-----EE--SSSEEEEE--TT
T ss_pred eeeeccccCCcccceee-----EeecCCCEEEEEecCC
Confidence 4668999998 554322 345 788999999776
No 253
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha chain, Gram-positive type. The N-terminal region of about 200 amino acids is rich in low-complexity sequence, poorly alignable, and not included n this model.
Probab=29.01 E-value=33 Score=33.94 Aligned_cols=15 Identities=27% Similarity=0.186 Sum_probs=12.1
Q ss_pred CeEEcCCCCCceecC
Q psy4748 28 GDVKCYVCKTSYGTQ 42 (136)
Q Consensus 28 ~~~~C~~C~~~~~~~ 42 (136)
-+|.|+.|.|.+-..
T Consensus 682 phy~c~~c~~~ef~~ 696 (1213)
T TIGR01405 682 PHYLCPNCKYSEFIT 696 (1213)
T ss_pred ccccCcccccccccc
Confidence 378999999888764
No 254
>PRK00448 polC DNA polymerase III PolC; Validated
Probab=28.68 E-value=34 Score=34.49 Aligned_cols=15 Identities=27% Similarity=0.160 Sum_probs=12.2
Q ss_pred CeEEcCCCCCceecC
Q psy4748 28 GDVKCYVCKTSYGTQ 42 (136)
Q Consensus 28 ~~~~C~~C~~~~~~~ 42 (136)
-+|.|+.|.|.+-..
T Consensus 907 phy~C~~C~~~ef~~ 921 (1437)
T PRK00448 907 PHYVCPNCKYSEFFT 921 (1437)
T ss_pred ccccCcccccccccc
Confidence 378999999888764
No 255
>PF13824 zf-Mss51: Zinc-finger of mitochondrial splicing suppressor 51
Probab=28.67 E-value=37 Score=21.55 Aligned_cols=26 Identities=23% Similarity=0.539 Sum_probs=19.6
Q ss_pred ccccCCCccccCCCCCeEEcCCCCCceec
Q psy4748 13 FCSKCGTILPLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 13 FCp~CgnlL~~~~~~~~~~C~~C~~~~~~ 41 (136)
+||.|+.-+.. ...+.|+.||....-
T Consensus 1 ~Cpv~~~~~~~---~v~~~Cp~cGipthc 26 (55)
T PF13824_consen 1 LCPVCKKDLPA---HVNFECPDCGIPTHC 26 (55)
T ss_pred CCCCCcccccc---ccCCcCCCCCCcCcc
Confidence 68888887632 347899999987654
No 256
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=28.64 E-value=30 Score=22.53 Aligned_cols=26 Identities=19% Similarity=0.383 Sum_probs=19.9
Q ss_pred cccccccCCCccccCCCCCeEEcCCCCCc
Q psy4748 10 ESEFCSKCGTILPLFDFKGDVKCYVCKTS 38 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~~~~~~C~~C~~~ 38 (136)
.-..|..||..-+... .-.|..|||-
T Consensus 16 tHt~CrRCG~~syh~q---K~~CasCGyg 41 (62)
T PRK04179 16 THIRCRRCGRHSYNVR---KKYCAACGFG 41 (62)
T ss_pred ccchhcccCccccccc---ccchhhcCCC
Confidence 4568999999876643 4489999993
No 257
>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=28.63 E-value=56 Score=24.55 Aligned_cols=33 Identities=27% Similarity=0.571 Sum_probs=22.6
Q ss_pred ccccccCCCceEEEEe------ecccc-------CCCceEEEEecC
Q psy4748 103 RKCKRCNNDTMSYATL------QLRSA-------DEGQTIFFTCTK 135 (136)
Q Consensus 103 ~~CpkCg~~~a~f~~~------Q~RSA-------DEg~TvFY~C~~ 135 (136)
-.|+.||.++..=||+ .++.. |=|.-++|+|.+
T Consensus 98 p~C~~Cg~~R~FEfQlmP~li~~L~~~~~~~~~~dwgtv~VyTCs~ 143 (164)
T PF04194_consen 98 PKCENCGSPRVFEFQLMPQLIYYLEVDDEGSDSMDWGTVLVYTCSA 143 (164)
T ss_pred CCCccCCCccEEEEEechHHHHHhhccccCCCCceeeEEEEEEehH
Confidence 3799999998876665 23333 445668899963
No 258
>PF02012 BNR: BNR/Asp-box repeat; InterPro: IPR002860 Members of this entry contain multiple BNR (bacterial neuraminidase repeat) repeats or Asp-boxes. The repeats are short, however the repeats are never found closer than 40 residues together suggesting that the repeat is structurally longer. These repeats are found in a variety of non-homologous proteins, including bacterial ribonucleases, sulphite oxidases, reelin, netrins, sialidases, neuraminidases, some lipoprotein receptors, and a variety of glycosyl hydrolases [].; PDB: 2JKB_A 2VW0_A 2VW2_A 2VW1_A 2CN2_D 2CN3_B 2VK7_B 2VK5_A 2VK6_A 2BF6_A ....
Probab=28.35 E-value=24 Score=15.76 Aligned_cols=8 Identities=50% Similarity=0.646 Sum_probs=6.4
Q ss_pred cccCCCce
Q psy4748 121 RSADEGQT 128 (136)
Q Consensus 121 RSADEg~T 128 (136)
+|.|.|+|
T Consensus 2 ~S~D~G~T 9 (12)
T PF02012_consen 2 YSTDGGKT 9 (12)
T ss_dssp EESSTTSS
T ss_pred EeCCCccc
Confidence 67888887
No 259
>PRK05978 hypothetical protein; Provisional
Probab=27.94 E-value=28 Score=26.32 Aligned_cols=14 Identities=14% Similarity=0.608 Sum_probs=11.8
Q ss_pred eeccccccCCCceE
Q psy4748 101 VERKCKRCNNDTMS 114 (136)
Q Consensus 101 ~~~~CpkCg~~~a~ 114 (136)
..-+||+||..++.
T Consensus 32 l~grCP~CG~G~LF 45 (148)
T PRK05978 32 FRGRCPACGEGKLF 45 (148)
T ss_pred HcCcCCCCCCCccc
Confidence 36799999999985
No 260
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=27.92 E-value=29 Score=25.06 Aligned_cols=26 Identities=23% Similarity=0.448 Sum_probs=16.3
Q ss_pred ccccccCCCccccCCCC-----CeEEcCCCCC
Q psy4748 11 SEFCSKCGTILPLFDFK-----GDVKCYVCKT 37 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~~-----~~~~C~~C~~ 37 (136)
..+| .||..-.+.... ..+.|+.||-
T Consensus 70 ~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs 100 (124)
T PRK00762 70 EIEC-ECGYEGVVDEDEIDHYAAVIECPVCGN 100 (124)
T ss_pred eEEe-eCcCcccccccchhccccCCcCcCCCC
Confidence 3589 999765543211 1267999983
No 261
>PF00684 DnaJ_CXXCXGXG: DnaJ central domain; InterPro: IPR001305 The hsp70 chaperone machine performs many diverse roles in the cell, including folding of nascent proteins, translocation of polypeptides across organelle membranes, coordinating responses to stress, and targeting selected proteins for degradation. DnaJ is a member of the hsp40 family of molecular chaperones, which is also called the J-protein family, the members of which regulate the activity of hsp70s. DnaJ (hsp40) binds to DnaK (hsp70) and stimulates its ATPase activity, generating the ADP-bound state of DnaK, which interacts stably with the polypeptide substrate []. Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation []. DnaJ consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acid residues, a glycine and phenylalanine-rich domain ('G/F' domain), a central cysteine rich domain (CR-type zinc finger) containing four repeats of a CXXCXGXG motif which can coordinate two zinc atom and a C-terminal domain (CTD) []. This entry represents the central cysteine-rich (CR) domain of DnaJ proteins. This central cysteine rich domain (CR-type zinc finger) has an overall V-shaped extended beta-hairpin topology and contains four repeats of the motif CXXCXGXG where X is any amino acid. The isolated cysteine rich domain folds in zinc dependent fashion. Each set of two repeats binds one unit of zinc. Although this domain has been implicated in substrate binding, no evidence of specific interaction between the isolated DnaJ cysteine rich domain and various hydrophobic peptides has been found [].; GO: 0031072 heat shock protein binding, 0051082 unfolded protein binding; PDB: 1NLT_A 2CTT_A 1EXK_A.
Probab=27.56 E-value=1.4e+02 Score=18.74 Aligned_cols=17 Identities=24% Similarity=0.524 Sum_probs=12.1
Q ss_pred ccccccCCCceEEEEee
Q psy4748 103 RKCKRCNNDTMSYATLQ 119 (136)
Q Consensus 103 ~~CpkCg~~~a~f~~~Q 119 (136)
..|+.|+-...+..+.|
T Consensus 16 ~~C~~C~G~G~~~~~~~ 32 (66)
T PF00684_consen 16 KTCPQCNGSGQVTRRQQ 32 (66)
T ss_dssp EE-TTSSSSSEEEEEEE
T ss_pred cCCcCCCCeeEEEEEEe
Confidence 47888888888777665
No 262
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=27.34 E-value=57 Score=26.48 Aligned_cols=27 Identities=22% Similarity=0.565 Sum_probs=16.5
Q ss_pred eccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 102 ERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 102 ~~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
.+.||.||..=..-.. .-|+ + |-|+.|
T Consensus 235 g~pC~~Cg~~I~~~~~-~gR~------t-y~Cp~C 261 (269)
T PRK14811 235 GQPCPRCGTPIEKIVV-GGRG------T-HFCPQC 261 (269)
T ss_pred cCCCCcCCCeeEEEEE-CCCC------c-EECCCC
Confidence 4689999986544333 2232 3 668777
No 263
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=27.25 E-value=86 Score=22.34 Aligned_cols=27 Identities=19% Similarity=0.600 Sum_probs=20.3
Q ss_pred ccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 103 RKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 103 ~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
+.|+.|++++-.+..- +-+.|-.|..|
T Consensus 81 VlC~~C~spdT~l~k~-------~r~~~l~C~aC 107 (110)
T smart00653 81 VLCPECGSPDTELIKE-------NRLFFLKCEAC 107 (110)
T ss_pred EECCCCCCCCcEEEEe-------CCeEEEEcccc
Confidence 5899999999766432 45777788776
No 264
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=27.21 E-value=38 Score=31.13 Aligned_cols=27 Identities=30% Similarity=0.741 Sum_probs=19.9
Q ss_pred cCccccccccCCCccccCCCCCeEEcCCCCC
Q psy4748 7 FNVESEFCSKCGTILPLFDFKGDVKCYVCKT 37 (136)
Q Consensus 7 ~~~~~~FCp~CgnlL~~~~~~~~~~C~~C~~ 37 (136)
|+..+..|+.||.+. .+....|+.||.
T Consensus 562 in~~~~iC~~CG~~~----~g~~~~CP~CGs 588 (623)
T PRK08271 562 FNVKITICNDCHHID----KRTGKRCPICGS 588 (623)
T ss_pred eCCCCccCCCCCCcC----CCCCcCCcCCCC
Confidence 345677899999762 234679999985
No 265
>PRK14018 trifunctional thioredoxin/methionine sulfoxide reductase A/B protein; Provisional
Probab=27.20 E-value=65 Score=29.01 Aligned_cols=19 Identities=5% Similarity=0.135 Sum_probs=13.5
Q ss_pred CCCceeccccccCCC-ceEE
Q psy4748 97 DGPIVERKCKRCNND-TMSY 115 (136)
Q Consensus 97 ~~~~~~~~CpkCg~~-~a~f 115 (136)
....++..|.+||.+ +.+|
T Consensus 462 g~~R~Ev~c~~c~~HLGHvf 481 (521)
T PRK14018 462 NMRRTEVRSRAADSHLGHVF 481 (521)
T ss_pred CceEEEEEECCCCCcCCccc
Confidence 345789999999954 4444
No 266
>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 PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=26.36 E-value=29 Score=24.52 Aligned_cols=27 Identities=26% Similarity=0.796 Sum_probs=16.0
Q ss_pred eccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 102 ERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 102 ~~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
+..|..||.....|..+.+. .|.|.+|
T Consensus 13 N~~CaDCg~~~p~w~s~~~G--------iflC~~C 39 (116)
T PF01412_consen 13 NKVCADCGAPNPTWASLNYG--------IFLCLEC 39 (116)
T ss_dssp CTB-TTT-SBS--EEETTTT--------EEE-HHH
T ss_pred cCcCCCCCCCCCCEEEeecC--------hhhhHHH
Confidence 57899999999988876653 4666554
No 268
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=26.22 E-value=39 Score=33.76 Aligned_cols=23 Identities=26% Similarity=0.462 Sum_probs=14.6
Q ss_pred ccccCCCccccCCCCCeEEcCCCCCcee
Q psy4748 13 FCSKCGTILPLFDFKGDVKCYVCKTSYG 40 (136)
Q Consensus 13 FCp~CgnlL~~~~~~~~~~C~~C~~~~~ 40 (136)
|||.||.-+.+ .+.|+.||...+
T Consensus 681 fCP~CGs~te~-----vy~CPsCGaev~ 703 (1337)
T PRK14714 681 RCPDCGTHTEP-----VYVCPDCGAEVP 703 (1337)
T ss_pred cCcccCCcCCC-----ceeCccCCCccC
Confidence 77777776643 346777776543
No 269
>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=26.18 E-value=62 Score=29.01 Aligned_cols=28 Identities=25% Similarity=0.583 Sum_probs=18.4
Q ss_pred eeccccccCCCceEEEEeeccccCCCceEEEEe
Q psy4748 101 VERKCKRCNNDTMSYATLQLRSADEGQTIFFTC 133 (136)
Q Consensus 101 ~~~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C 133 (136)
..-.||+||.-.- -.. +-|..-||.|+|
T Consensus 167 ~~pic~~cGrv~~--~~~---~~~~~~~v~Y~c 194 (515)
T TIGR00467 167 ISVFCENCGRDTT--TVN---NYDNEYSIEYSC 194 (515)
T ss_pred eeeecCCcCccCc--eEE---EecCCceEEEEc
Confidence 4668999999743 112 334333899999
No 270
>COG4311 SoxD Sarcosine oxidase delta subunit [Amino acid transport and metabolism]
Probab=25.82 E-value=31 Score=24.39 Aligned_cols=11 Identities=27% Similarity=0.546 Sum_probs=8.8
Q ss_pred ccccccccCCC
Q psy4748 9 VESEFCSKCGT 19 (136)
Q Consensus 9 ~~~~FCp~Cgn 19 (136)
|.+..||.||-
T Consensus 1 mlLI~CP~Cg~ 11 (97)
T COG4311 1 MLLIPCPYCGE 11 (97)
T ss_pred CceecCCCCCC
Confidence 45778999997
No 271
>PRK10445 endonuclease VIII; Provisional
Probab=25.69 E-value=63 Score=26.13 Aligned_cols=27 Identities=19% Similarity=0.578 Sum_probs=15.8
Q ss_pred eccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 102 ERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 102 ~~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
.+.||.||..=..-.. - |=++ |-|++|
T Consensus 235 g~~Cp~Cg~~I~~~~~-~------gR~t-~~CP~C 261 (263)
T PRK10445 235 GEACERCGGIIEKTTL-S------SRPF-YWCPGC 261 (263)
T ss_pred CCCCCCCCCEeEEEEE-C------CCCc-EECCCC
Confidence 4789999975432222 2 2233 668877
No 272
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=25.11 E-value=67 Score=26.22 Aligned_cols=27 Identities=19% Similarity=0.568 Sum_probs=16.4
Q ss_pred eccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 102 ERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 102 ~~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
.+.||.||..=..-.. --| ++ |-|+.|
T Consensus 254 g~pC~~Cg~~I~~~~~-~gR------~t-~~CP~C 280 (282)
T PRK13945 254 GKPCRKCGTPIERIKL-AGR------ST-HWCPNC 280 (282)
T ss_pred cCCCCcCCCeeEEEEE-CCC------cc-EECCCC
Confidence 4689999976543322 223 33 668877
No 273
>PF06353 DUF1062: Protein of unknown function (DUF1062); InterPro: IPR009412 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=25.06 E-value=43 Score=25.02 Aligned_cols=15 Identities=13% Similarity=0.279 Sum_probs=13.4
Q ss_pred CCeEEcCCCCCceec
Q psy4748 27 KGDVKCYVCKTSYGT 41 (136)
Q Consensus 27 ~~~~~C~~C~~~~~~ 41 (136)
-+.|.|..|++.+..
T Consensus 11 WLIYrC~~C~~TwN~ 25 (142)
T PF06353_consen 11 WLIYRCEKCDYTWNM 25 (142)
T ss_pred EEEEEcccCcCcccc
Confidence 468999999999988
No 274
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=24.86 E-value=45 Score=15.72 Aligned_cols=12 Identities=25% Similarity=0.872 Sum_probs=7.7
Q ss_pred EEcCCCCCceec
Q psy4748 30 VKCYVCKTSYGT 41 (136)
Q Consensus 30 ~~C~~C~~~~~~ 41 (136)
+.|..|++....
T Consensus 1 ~~C~~C~~~~~~ 12 (24)
T PF13894_consen 1 FQCPICGKSFRS 12 (24)
T ss_dssp EE-SSTS-EESS
T ss_pred CCCcCCCCcCCc
Confidence 578899988765
No 275
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=23.48 E-value=55 Score=23.16 Aligned_cols=34 Identities=18% Similarity=0.465 Sum_probs=24.3
Q ss_pred cCccccccccCCCccccCCC-CCeEEcCCCCCceec
Q psy4748 7 FNVESEFCSKCGTILPLFDF-KGDVKCYVCKTSYGT 41 (136)
Q Consensus 7 ~~~~~~FCp~CgnlL~~~~~-~~~~~C~~C~~~~~~ 41 (136)
.++...-|+.||..-..... +++ .|+.|+.....
T Consensus 38 ~G~~~~~C~~Cg~~~~~~~SCk~R-~CP~C~~~~~~ 72 (111)
T PF14319_consen 38 LGFHRYRCEDCGHEKIVYNSCKNR-HCPSCQAKATE 72 (111)
T ss_pred CCcceeecCCCCceEEecCcccCc-CCCCCCChHHH
Confidence 44555689999988776643 445 89999987654
No 276
>KOG3002|consensus
Probab=23.23 E-value=42 Score=28.05 Aligned_cols=31 Identities=19% Similarity=0.385 Sum_probs=25.4
Q ss_pred ccCccccccccCCCccccCC---CCCeEEcCCCC
Q psy4748 6 YFNVESEFCSKCGTILPLFD---FKGDVKCYVCK 36 (136)
Q Consensus 6 ~~~~~~~FCp~CgnlL~~~~---~~~~~~C~~C~ 36 (136)
.+..++.=||.|.+-|.++- +.+.++|..|-
T Consensus 43 ~~~~~lleCPvC~~~l~~Pi~QC~nGHlaCssC~ 76 (299)
T KOG3002|consen 43 LLDLDLLDCPVCFNPLSPPIFQCDNGHLACSSCR 76 (299)
T ss_pred ccchhhccCchhhccCcccceecCCCcEehhhhh
Confidence 45677888999999999983 35789999887
No 277
>PRK08173 DNA topoisomerase III; Validated
Probab=23.02 E-value=56 Score=31.13 Aligned_cols=26 Identities=23% Similarity=0.546 Sum_probs=19.2
Q ss_pred cccccCCCccccCCCCCeEEcCCCCCce
Q psy4748 12 EFCSKCGTILPLFDFKGDVKCYVCKTSY 39 (136)
Q Consensus 12 ~FCp~CgnlL~~~~~~~~~~C~~C~~~~ 39 (136)
.-||.||.-| ......|.|..|++..
T Consensus 625 ~~CP~Cg~~~--~~~~~~~~Cs~C~f~~ 650 (862)
T PRK08173 625 TPCPNCGGVV--KENYRRFACTKCDFSI 650 (862)
T ss_pred ccCCcccccc--cccCceeEcCCCCccc
Confidence 4699999865 2234469999999765
No 278
>PRK13264 3-hydroxyanthranilate 3,4-dioxygenase; Provisional
Probab=23.01 E-value=28 Score=27.05 Aligned_cols=32 Identities=16% Similarity=0.356 Sum_probs=23.9
Q ss_pred ccccccCCCccccCCC-------------------CCeEEcCCCCCceecC
Q psy4748 11 SEFCSKCGTILPLFDF-------------------KGDVKCYVCKTSYGTQ 42 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~-------------------~~~~~C~~C~~~~~~~ 42 (136)
.-||+.|+.+|+-... ...-.|..||...+..
T Consensus 120 ~wyc~~c~~~~~e~~f~~~d~~~~~~~~~~~f~~~~e~rtC~~CG~v~~~~ 170 (177)
T PRK13264 120 QWYCDECNHKVHEVEVQLTDIETDLPPVFAAFYASEELRTCDNCGTVHPGK 170 (177)
T ss_pred EEECCCCCCeEEEEEEEecChhhhhHHHHHHHhcCHhhccCCcCCcccCcc
Confidence 3599999999985421 1245899999998875
No 279
>COG4481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=22.93 E-value=43 Score=21.45 Aligned_cols=18 Identities=28% Similarity=0.660 Sum_probs=14.0
Q ss_pred cCCCceeccccccCCCce
Q psy4748 96 ADGPIVERKCKRCNNDTM 113 (136)
Q Consensus 96 ~~~~~~~~~CpkCg~~~a 113 (136)
.-++.+..+|.+|||--|
T Consensus 28 RvGaDIkikC~nC~h~vm 45 (60)
T COG4481 28 RVGADIKIKCENCGHSVM 45 (60)
T ss_pred EecCcEEEEecCCCcEEE
Confidence 345677899999999654
No 280
>KOG0006|consensus
Probab=22.58 E-value=59 Score=28.10 Aligned_cols=32 Identities=22% Similarity=0.389 Sum_probs=23.0
Q ss_pred ccccc--ccCCCccccCCCCCeEEcCC-CCCceec
Q psy4748 10 ESEFC--SKCGTILPLFDFKGDVKCYV-CKTSYGT 41 (136)
Q Consensus 10 ~~~FC--p~CgnlL~~~~~~~~~~C~~-C~~~~~~ 41 (136)
+-.-| |-||.=|.++.+...+.|.. |||..-.
T Consensus 314 gGVlCP~pgCG~gll~EPD~rkvtC~~gCgf~FCR 348 (446)
T KOG0006|consen 314 GGVLCPRPGCGAGLLPEPDQRKVTCEGGCGFAFCR 348 (446)
T ss_pred CCEecCCCCCCcccccCCCCCcccCCCCchhHhHH
Confidence 34467 46998888887766788887 8887643
No 281
>KOG4537|consensus
Probab=22.55 E-value=23 Score=27.39 Aligned_cols=27 Identities=30% Similarity=0.524 Sum_probs=21.2
Q ss_pred cccccCCCccccCCCCCeEEcCCCCCce
Q psy4748 12 EFCSKCGTILPLFDFKGDVKCYVCKTSY 39 (136)
Q Consensus 12 ~FCp~CgnlL~~~~~~~~~~C~~C~~~~ 39 (136)
..||.|+.+|.-..+ ..+.|-.|.-..
T Consensus 41 e~Cp~C~~Ilm~dr~-~~~~CVsC~~~~ 67 (178)
T KOG4537|consen 41 EICPKCEKILMRDRD-NPMFCVSCINDL 67 (178)
T ss_pred hhcchHHHHHHhhcc-CceEEEeeeccc
Confidence 589999999877554 578899997654
No 282
>PF15616 TerY-C: TerY-C metal binding domain
Probab=22.41 E-value=63 Score=23.93 Aligned_cols=29 Identities=24% Similarity=0.505 Sum_probs=18.4
Q ss_pred cccccCCCcc-----------ccCCCCCeEEcCCCCCceec
Q psy4748 12 EFCSKCGTIL-----------PLFDFKGDVKCYVCKTSYGT 41 (136)
Q Consensus 12 ~FCp~CgnlL-----------~~~~~~~~~~C~~C~~~~~~ 41 (136)
-=||.|||.. -... ...+.|+-|+..-..
T Consensus 78 PgCP~CGn~~~fa~C~CGkl~Ci~g-~~~~~CPwCg~~g~~ 117 (131)
T PF15616_consen 78 PGCPHCGNQYAFAVCGCGKLFCIDG-EGEVTCPWCGNEGSF 117 (131)
T ss_pred CCCCCCcChhcEEEecCCCEEEeCC-CCCEECCCCCCeeee
Confidence 3577777763 3322 347888888877655
No 283
>TIGR01057 topA_arch DNA topoisomerase I, archaeal. This model describes topoisomerase I from archaea. These enzymes are involved in the control of DNA topology. DNA topoisomerase I belongs to the type I topoisomerases, which are ATP-independent.
Probab=22.39 E-value=60 Score=29.47 Aligned_cols=25 Identities=32% Similarity=0.772 Sum_probs=15.2
Q ss_pred ccccccCCCceEEEEeeccccCCCceEEEEecC
Q psy4748 103 RKCKRCNNDTMSYATLQLRSADEGQTIFFTCTK 135 (136)
Q Consensus 103 ~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~ 135 (136)
.+||+||++ +-.|...-| .||-|.+
T Consensus 590 ~~CPkCg~~------l~~~~~k~g--~f~gCs~ 614 (618)
T TIGR01057 590 GKCPKCGGK------LVSKYAKKG--RFVGCSN 614 (618)
T ss_pred CCCCcCCCe------eeeeecCCc--cEEECCC
Confidence 579999975 222222223 5899976
No 284
>COG3529 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=22.37 E-value=25 Score=23.00 Aligned_cols=11 Identities=18% Similarity=0.664 Sum_probs=8.9
Q ss_pred eccccccCCCc
Q psy4748 102 ERKCKRCNNDT 112 (136)
Q Consensus 102 ~~~CpkCg~~~ 112 (136)
-..|-+|||..
T Consensus 32 ~vECV~CG~~~ 42 (66)
T COG3529 32 IVECVKCGHHM 42 (66)
T ss_pred eEehhhcchHh
Confidence 36899999965
No 285
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=22.12 E-value=36 Score=26.45 Aligned_cols=14 Identities=43% Similarity=0.828 Sum_probs=11.5
Q ss_pred ccccCCCccccCCC
Q psy4748 13 FCSKCGTILPLFDF 26 (136)
Q Consensus 13 FCp~CgnlL~~~~~ 26 (136)
=||.||+.|....+
T Consensus 134 ~Cp~Cg~~L~~~d~ 147 (176)
T COG1675 134 TCPKCGEDLEEYDS 147 (176)
T ss_pred CCCCCCchhhhccc
Confidence 49999999988644
No 286
>PF05495 zf-CHY: CHY zinc finger; InterPro: IPR008913 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Pirh2 is an eukaryotic ubiquitin protein ligase, which has been shown to promote p53 degradation in mammals. Pirh2 physically interacts with p53 and promotes ubiquitination of p53 independently of MDM2. Like MDM2, Pirh2 is thought to participate in an autoregulatory feedback loop that controls p53 function. Pirh2 proteins contain three distinct zinc fingers, the CHY-type, the CTCHY-type which is C-terminal to the CHY-type zinc finger and a RING finger. The CHY-type zinc finger has no currently known function []. As well as Pirh2, the CHY-type zinc finger is also found in the following proteins: Yeast helper of Tim protein 13. Hot13 may have a role in the assembly and recycling of the small Tims, a complex of the mitochondrial intermembrane space that participates in the TIM22 import pathway for assembly of the inner membrane [] Several plant hypothetical proteins that also contain haemerythrin cation binding domains Several protozoan hypothetical proteins that also contain a Myb domain The solution structure of this zinc finger has been solved and binds 3 zinc atoms as shown in the following schematic representation: ++---------+-----+ || | | CXHYxxxxxxxxxCCxxxxxCxxCHxxxxxHxxxxxxxxxxxCxxCxxxxxxxxxCxxC | | | | | | | | +-+-----------------+--+ +--+---------+--+ 'C': conserved cysteine involved in the binding of one zinc atom. 'H': conserved histidine involved in the binding of one zinc atom. More information about these proteins can be found at Protein of the Month: Zinc Fingers []; GO: 0008270 zinc ion binding; PDB: 2DKT_A 2K2C_A.
Probab=22.10 E-value=55 Score=21.25 Aligned_cols=26 Identities=31% Similarity=0.759 Sum_probs=11.1
Q ss_pred ccccccCCCccccCCCC--CeEEcCCCC
Q psy4748 11 SEFCSKCGTILPLFDFK--GDVKCYVCK 36 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~~--~~~~C~~C~ 36 (136)
...|..|++.+.+.+.. ..+.|+.|+
T Consensus 41 ~v~Cg~C~~~~~~~~~~c~~~~~C~~C~ 68 (71)
T PF05495_consen 41 RVICGKCRTEQPIDEYSCGADYFCPICG 68 (71)
T ss_dssp EEEETTT--EEES-SBTT--SEEETTTT
T ss_pred CeECCCCCCccChhhhhcCCCccCcCcC
Confidence 44555555555554321 135555554
No 287
>KOG2703|consensus
Probab=22.04 E-value=66 Score=28.44 Aligned_cols=29 Identities=10% Similarity=0.221 Sum_probs=20.6
Q ss_pred eccccccCCCceEEEEeeccccCCCceEEEEe
Q psy4748 102 ERKCKRCNNDTMSYATLQLRSADEGQTIFFTC 133 (136)
Q Consensus 102 ~~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C 133 (136)
...||+|||+... +|--+++...-+-|+|
T Consensus 68 SF~CpHCG~kN~e---iQ~a~~iQ~~Gvri~l 96 (460)
T KOG2703|consen 68 SFECPHCGHKNNE---IQSAEEIQEGGVRIEL 96 (460)
T ss_pred EeecCccCCcccc---ccchhccccCceEEEE
Confidence 5689999998875 4556666666666665
No 288
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=22.03 E-value=83 Score=25.52 Aligned_cols=27 Identities=22% Similarity=0.595 Sum_probs=16.5
Q ss_pred eccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 102 ERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 102 ~~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
.+.||.||..=..- .+--| ++ |-|+.|
T Consensus 245 g~pC~~Cg~~I~~~-~~~gR------~t-~~CP~C 271 (272)
T TIGR00577 245 GEPCRRCGTPIEKI-KVGGR------GT-HFCPQC 271 (272)
T ss_pred CCCCCCCCCeeEEE-EECCC------CC-EECCCC
Confidence 46899999765442 22223 33 558777
No 289
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=21.93 E-value=66 Score=17.13 Aligned_cols=25 Identities=20% Similarity=0.405 Sum_probs=8.7
Q ss_pred ccccCCCccccCCCCCeEEcCCCCCcee
Q psy4748 13 FCSKCGTILPLFDFKGDVKCYVCKTSYG 40 (136)
Q Consensus 13 FCp~CgnlL~~~~~~~~~~C~~C~~~~~ 40 (136)
.|..||.-+.. ...|.|..|++...
T Consensus 2 ~C~~C~~~~~~---~~~Y~C~~Cdf~lH 26 (30)
T PF07649_consen 2 RCDACGKPIDG---GWFYRCSECDFDLH 26 (30)
T ss_dssp --TTTS----S-----EEE-TTT-----
T ss_pred cCCcCCCcCCC---CceEECccCCCccC
Confidence 36667765554 35889999987653
No 290
>TIGR00375 conserved hypothetical protein TIGR00375. The member of this family from Methanococcus jannaschii, MJ0043, is considerably longer and appears to contain an intein N-terminal to the region of homology.
Probab=21.78 E-value=34 Score=29.52 Aligned_cols=28 Identities=21% Similarity=0.394 Sum_probs=22.3
Q ss_pred ccccccCCCccccCCC-CCeEEcCCCCCce
Q psy4748 11 SEFCSKCGTILPLFDF-KGDVKCYVCKTSY 39 (136)
Q Consensus 11 ~~FCp~CgnlL~~~~~-~~~~~C~~C~~~~ 39 (136)
+.+|..|+..|.+.+. ...+.|+ ||...
T Consensus 240 ~~~c~~C~~~~~~~~~~~~~~~Cp-CG~~i 268 (374)
T TIGR00375 240 QTACEACGEPAVSEDAETACANCP-CGGRI 268 (374)
T ss_pred hhhhcccCCcCCchhhhhcCCCCC-CCCcc
Confidence 4589999999998764 3457999 99873
No 291
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=21.74 E-value=38 Score=20.56 Aligned_cols=27 Identities=22% Similarity=0.471 Sum_probs=17.8
Q ss_pred cccccCCCccccCC-----------CCCeEEcCCCCCc
Q psy4748 12 EFCSKCGTILPLFD-----------FKGDVKCYVCKTS 38 (136)
Q Consensus 12 ~FCp~CgnlL~~~~-----------~~~~~~C~~C~~~ 38 (136)
.-||.||.-+...+ +...++|+.|...
T Consensus 3 f~CP~C~~~~~~~~L~~H~~~~H~~~~~~v~CPiC~~~ 40 (54)
T PF05605_consen 3 FTCPYCGKGFSESSLVEHCEDEHRSESKNVVCPICSSR 40 (54)
T ss_pred cCCCCCCCccCHHHHHHHHHhHCcCCCCCccCCCchhh
Confidence 35999998444321 1246899999863
No 292
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=21.28 E-value=60 Score=23.67 Aligned_cols=34 Identities=15% Similarity=0.327 Sum_probs=24.7
Q ss_pred cccccccCCCccccCCC-----CCeEEcCCCCCceecCC
Q psy4748 10 ESEFCSKCGTILPLFDF-----KGDVKCYVCKTSYGTQE 43 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~-----~~~~~C~~C~~~~~~~~ 43 (136)
.+.-||.|+.-....-+ ...+.|..|++......
T Consensus 29 ~~~~cP~C~s~~~~k~g~~~~~~qRyrC~~C~~tf~~~~ 67 (129)
T COG3677 29 TKVNCPRCKSSNVVKIGGIRRGHQRYKCKSCGSTFTVET 67 (129)
T ss_pred ccCcCCCCCccceeeECCccccccccccCCcCcceeeec
Confidence 45679999998822211 35899999999887653
No 293
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=21.24 E-value=35 Score=25.40 Aligned_cols=27 Identities=22% Similarity=0.363 Sum_probs=18.6
Q ss_pred ccccCCCccccCCCCCeEEcCCCCCce
Q psy4748 13 FCSKCGTILPLFDFKGDVKCYVCKTSY 39 (136)
Q Consensus 13 FCp~CgnlL~~~~~~~~~~C~~C~~~~ 39 (136)
=|..||.+..--+....--|+.||-..
T Consensus 3 ~Ct~Cg~~f~dgs~eil~GCP~CGg~k 29 (131)
T PF09845_consen 3 QCTKCGRVFEDGSKEILSGCPECGGNK 29 (131)
T ss_pred ccCcCCCCcCCCcHHHHccCcccCCcc
Confidence 488999988754433455799988543
No 294
>KOG2462|consensus
Probab=21.02 E-value=59 Score=27.12 Aligned_cols=32 Identities=22% Similarity=0.442 Sum_probs=20.6
Q ss_pred cccccccCCCccccCCC-------------CCeEEcCCCCCceec
Q psy4748 10 ESEFCSKCGTILPLFDF-------------KGDVKCYVCKTSYGT 41 (136)
Q Consensus 10 ~~~FCp~CgnlL~~~~~-------------~~~~~C~~C~~~~~~ 41 (136)
...-|++||..+--..+ +....|..||..+..
T Consensus 129 ~r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~YvS 173 (279)
T KOG2462|consen 129 PRYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVYVS 173 (279)
T ss_pred CceeccccccccccccccchhhcccccccccccccCCCCCceeee
Confidence 34468888887766543 235677777776643
No 295
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=20.91 E-value=99 Score=25.03 Aligned_cols=27 Identities=26% Similarity=0.687 Sum_probs=16.0
Q ss_pred eccccccCCCceEEEEeeccccCCCceEEEEecCC
Q psy4748 102 ERKCKRCNNDTMSYATLQLRSADEGQTIFFTCTKC 136 (136)
Q Consensus 102 ~~~CpkCg~~~a~f~~~Q~RSADEg~TvFY~C~~C 136 (136)
.+.||.||..=.. ..+--| ++ |-|+.|
T Consensus 245 g~pC~~Cg~~I~~-~~~~gR------~t-~~CP~C 271 (274)
T PRK01103 245 GEPCRRCGTPIEK-IKQGGR------ST-FFCPRC 271 (274)
T ss_pred CCCCCCCCCeeEE-EEECCC------Cc-EECcCC
Confidence 4679999976443 222223 33 568777
No 296
>PHA02325 hypothetical protein
Probab=20.83 E-value=79 Score=20.93 Aligned_cols=22 Identities=18% Similarity=0.465 Sum_probs=14.2
Q ss_pred ccccccCC---CceEEEEeeccccC
Q psy4748 103 RKCKRCNN---DTMSYATLQLRSAD 124 (136)
Q Consensus 103 ~~CpkCg~---~~a~f~~~Q~RSAD 124 (136)
..|||||. +.-.||.---|-++
T Consensus 4 k~CPkC~A~WldgqhYWsgTgk~g~ 28 (72)
T PHA02325 4 KICPKCGARWLDGQHYWSGTGKKGN 28 (72)
T ss_pred cccCccCCEeEcceeeeccCCCcCC
Confidence 57999998 55566664444443
No 297
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=20.75 E-value=79 Score=21.35 Aligned_cols=29 Identities=21% Similarity=0.093 Sum_probs=22.2
Q ss_pred ccccCCCccccCCC-CCeEEcCCCCCceec
Q psy4748 13 FCSKCGTILPLFDF-KGDVKCYVCKTSYGT 41 (136)
Q Consensus 13 FCp~CgnlL~~~~~-~~~~~C~~C~~~~~~ 41 (136)
-||-||..-..... ...-+|..|.-+...
T Consensus 3 ~CPCCg~~Tl~~~~~~~ydIC~VC~WEdD~ 32 (78)
T PF14206_consen 3 PCPCCGYYTLEERGEGTYDICPVCFWEDDG 32 (78)
T ss_pred cCCCCCcEEeccCCCcCceECCCCCcccCC
Confidence 59999998776644 358899999977654
No 298
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=20.70 E-value=57 Score=17.89 Aligned_cols=21 Identities=33% Similarity=0.937 Sum_probs=12.5
Q ss_pred cccccCCCccccCCCCCeEEcCCCCCce
Q psy4748 12 EFCSKCGTILPLFDFKGDVKCYVCKTSY 39 (136)
Q Consensus 12 ~FCp~CgnlL~~~~~~~~~~C~~C~~~~ 39 (136)
.+|..||+ . ..|.|+.|+...
T Consensus 3 ~~C~vC~~---~----~kY~Cp~C~~~~ 23 (30)
T PF04438_consen 3 KLCSVCGN---P----AKYRCPRCGARY 23 (30)
T ss_dssp EEETSSSS---E----ESEE-TTT--EE
T ss_pred CCCccCcC---C----CEEECCCcCCce
Confidence 57888887 2 267898888654
No 299
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=20.42 E-value=1.4e+02 Score=18.50 Aligned_cols=11 Identities=18% Similarity=0.564 Sum_probs=5.6
Q ss_pred ccccccCCCce
Q psy4748 103 RKCKRCNNDTM 113 (136)
Q Consensus 103 ~~CpkCg~~~a 113 (136)
+.|+-|-++=.
T Consensus 25 EDC~vCC~PI~ 35 (52)
T PF14255_consen 25 EDCQVCCRPIE 35 (52)
T ss_pred eehhhcCCccE
Confidence 44555555443
No 300
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=20.32 E-value=47 Score=27.51 Aligned_cols=22 Identities=23% Similarity=0.616 Sum_probs=15.1
Q ss_pred ceeccccccCCCceEEEEeecc
Q psy4748 100 IVERKCKRCNNDTMSYATLQLR 121 (136)
Q Consensus 100 ~~~~~CpkCg~~~a~f~~~Q~R 121 (136)
.-+..||+|+|.=--|-|+-.+
T Consensus 153 ~aef~C~~C~h~F~G~~qm~v~ 174 (278)
T PF15135_consen 153 IAEFHCPKCRHNFRGFAQMGVP 174 (278)
T ss_pred eeeeecccccccchhhhhcCCC
Confidence 3467899999976666555444
No 301
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=20.10 E-value=51 Score=20.88 Aligned_cols=12 Identities=33% Similarity=1.135 Sum_probs=6.6
Q ss_pred cccccccCCCcc
Q psy4748 10 ESEFCSKCGTIL 21 (136)
Q Consensus 10 ~~~FCp~CgnlL 21 (136)
...+||.||+.|
T Consensus 51 ~~H~Cp~C~~~l 62 (67)
T smart00714 51 VNHYCPNCGAFL 62 (67)
T ss_pred ccEECCCCCCEe
Confidence 344566666554
Done!