Query psy2574
Match_columns 115
No_of_seqs 107 out of 233
Neff 3.2
Searched_HMMs 46136
Date Fri Aug 16 19:39:51 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2574.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2574hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00083 40S ribosomal protein 100.0 4.5E-48 9.8E-53 271.3 7.4 79 2-80 3-81 (85)
2 PLN00209 ribosomal protein S27 100.0 1.4E-47 3E-52 269.3 7.6 78 3-80 5-82 (86)
3 KOG1779|consensus 100.0 2.7E-44 5.9E-49 251.4 7.2 80 1-80 1-80 (84)
4 PF01667 Ribosomal_S27e: Ribos 100.0 8E-34 1.7E-38 185.4 4.1 52 28-79 1-52 (55)
5 PRK00415 rps27e 30S ribosomal 100.0 2.6E-32 5.6E-37 180.7 5.3 52 24-75 1-52 (59)
6 COG2051 RPS27A Ribosomal prote 100.0 1.3E-29 2.9E-34 171.6 5.3 56 22-77 6-62 (67)
7 PF08271 TF_Zn_Ribbon: TFIIB z 97.2 0.00037 8.1E-09 42.1 2.7 31 36-66 2-32 (43)
8 TIGR02098 MJ0042_CXXC MJ0042 f 95.7 0.014 3E-07 33.9 2.9 32 33-64 1-36 (38)
9 PRK00423 tfb transcription ini 95.2 0.012 2.6E-07 48.0 2.2 32 35-66 12-43 (310)
10 PRK00398 rpoP DNA-directed RNA 95.0 0.033 7.2E-07 33.9 3.1 36 33-69 2-37 (46)
11 PF13719 zinc_ribbon_5: zinc-r 93.1 0.11 2.4E-06 30.8 2.7 31 33-63 1-35 (37)
12 PF13248 zf-ribbon_3: zinc-rib 92.5 0.039 8.4E-07 30.5 0.1 26 33-63 1-26 (26)
13 smart00834 CxxC_CXXC_SSSS Puta 91.5 0.27 5.8E-06 28.3 3.0 31 33-63 4-36 (41)
14 PF13717 zinc_ribbon_4: zinc-r 89.1 0.46 9.9E-06 28.1 2.6 31 33-63 1-35 (36)
15 PF11023 DUF2614: Protein of u 88.9 0.17 3.7E-06 37.7 0.8 34 30-66 65-98 (114)
16 COG1405 SUA7 Transcription ini 87.9 0.42 9.1E-06 39.6 2.5 30 36-65 3-32 (285)
17 PF01096 TFIIS_C: Transcriptio 87.5 0.64 1.4E-05 27.8 2.5 28 35-62 1-37 (39)
18 PRK14892 putative transcriptio 87.4 0.72 1.6E-05 33.2 3.1 29 35-63 22-52 (99)
19 TIGR02605 CxxC_CxxC_SSSS putat 87.1 0.74 1.6E-05 28.0 2.7 29 33-61 4-34 (52)
20 PF09723 Zn-ribbon_8: Zinc rib 84.3 1.4 3.1E-05 26.5 3.0 30 32-61 3-34 (42)
21 PRK03681 hypA hydrogenase nick 83.5 0.93 2E-05 32.5 2.2 37 33-72 69-106 (114)
22 TIGR01206 lysW lysine biosynth 83.4 1.2 2.6E-05 29.0 2.4 32 33-64 1-33 (54)
23 TIGR01384 TFS_arch transcripti 83.2 1.2 2.5E-05 30.6 2.5 29 33-61 61-98 (104)
24 smart00659 RPOLCX RNA polymera 82.7 1.8 3.9E-05 26.8 3.0 30 33-64 1-30 (44)
25 PF05907 DUF866: Eukaryotic pr 82.7 1.8 3.9E-05 33.0 3.6 37 27-63 23-74 (161)
26 PF13240 zinc_ribbon_2: zinc-r 82.5 0.48 1E-05 25.8 0.3 23 36-63 1-23 (23)
27 PRK12380 hydrogenase nickel in 82.0 1 2.2E-05 32.3 1.9 36 33-71 69-104 (113)
28 smart00440 ZnF_C2C2 C2C2 Zinc 81.7 2.2 4.7E-05 25.7 3.0 27 36-62 2-37 (40)
29 TIGR00100 hypA hydrogenase nic 81.2 1.1 2.4E-05 32.1 1.9 36 33-71 69-104 (115)
30 PF02150 RNA_POL_M_15KD: RNA p 81.2 1.8 3.9E-05 25.5 2.5 28 36-63 3-30 (35)
31 PRK02935 hypothetical protein; 80.5 1 2.2E-05 33.5 1.5 36 29-67 65-100 (110)
32 COG2888 Predicted Zn-ribbon RN 77.6 3 6.5E-05 28.3 2.9 34 27-60 20-57 (61)
33 COG4888 Uncharacterized Zn rib 75.5 3.9 8.5E-05 30.2 3.3 28 35-62 23-55 (104)
34 PRK00420 hypothetical protein; 75.1 2.3 5.1E-05 31.3 2.1 35 33-69 22-56 (112)
35 PRK03824 hypA hydrogenase nick 74.7 2.5 5.5E-05 31.1 2.2 37 33-72 69-126 (135)
36 TIGR00311 aIF-2beta translatio 74.6 3.3 7.2E-05 30.9 2.8 28 35-62 98-127 (133)
37 PF10571 UPF0547: Uncharacteri 73.7 1.5 3.2E-05 24.7 0.6 23 36-63 2-24 (26)
38 smart00653 eIF2B_5 domain pres 73.2 4 8.7E-05 29.5 2.9 27 35-61 81-109 (110)
39 TIGR01053 LSD1 zinc finger dom 72.6 2.1 4.6E-05 25.0 1.1 18 54-71 2-19 (31)
40 PRK00432 30S ribosomal protein 72.5 3.3 7.1E-05 26.2 2.0 29 34-64 20-48 (50)
41 PRK03988 translation initiatio 71.9 4.4 9.5E-05 30.5 2.9 28 35-62 103-132 (138)
42 COG1594 RPB9 DNA-directed RNA 71.8 3.6 7.8E-05 29.8 2.4 29 34-62 72-109 (113)
43 KOG1597|consensus 71.7 3 6.6E-05 35.7 2.3 42 36-82 2-45 (308)
44 COG4416 Com Mu-like prophage p 70.1 3 6.5E-05 28.1 1.5 26 24-49 14-39 (60)
45 PHA00626 hypothetical protein 68.0 5.2 0.00011 27.0 2.3 31 36-66 2-36 (59)
46 PRK00564 hypA hydrogenase nick 67.9 2.6 5.7E-05 30.3 1.0 36 33-71 70-106 (117)
47 KOG3507|consensus 67.8 5.4 0.00012 27.1 2.4 34 28-63 14-47 (62)
48 PF14319 Zn_Tnp_IS91: Transpos 67.8 4.8 0.0001 28.8 2.3 36 26-62 34-69 (111)
49 PF08792 A2L_zn_ribbon: A2L zi 67.8 9 0.00019 22.5 3.1 29 34-63 3-31 (33)
50 PRK12336 translation initiatio 67.5 5.9 0.00013 31.0 2.9 28 35-62 99-128 (201)
51 PF09855 DUF2082: Nucleic-acid 66.1 5.9 0.00013 26.5 2.3 8 53-60 36-43 (64)
52 PF03604 DNA_RNApol_7kD: DNA d 65.4 2.1 4.5E-05 25.2 0.0 25 36-62 2-26 (32)
53 PRK14890 putative Zn-ribbon RN 65.3 9.4 0.0002 25.6 3.2 34 27-60 18-55 (59)
54 PRK00762 hypA hydrogenase nick 65.2 3.5 7.6E-05 29.9 1.2 39 33-72 69-111 (124)
55 PRK08197 threonine synthase; V 64.3 5.8 0.00013 33.1 2.5 32 28-63 1-32 (394)
56 PF13453 zf-TFIIB: Transcripti 64.1 9 0.0002 22.6 2.6 27 36-62 1-28 (41)
57 PF10263 SprT-like: SprT-like 63.2 12 0.00025 26.7 3.6 35 31-65 120-155 (157)
58 smart00531 TFIIE Transcription 62.5 5.2 0.00011 29.4 1.7 40 23-65 90-135 (147)
59 PF03884 DUF329: Domain of unk 61.7 5.7 0.00012 26.2 1.6 14 33-46 1-14 (57)
60 smart00647 IBR In Between Ring 61.6 9.8 0.00021 22.9 2.6 31 35-65 19-52 (64)
61 PRK05978 hypothetical protein; 61.4 3.2 6.9E-05 31.8 0.4 39 28-66 27-65 (148)
62 PF12760 Zn_Tnp_IS1595: Transp 60.7 11 0.00024 22.7 2.7 27 35-61 19-45 (46)
63 PF08274 PhnA_Zn_Ribbon: PhnA 60.7 7.7 0.00017 22.6 1.8 25 36-62 4-28 (30)
64 PRK07591 threonine synthase; V 60.4 6.6 0.00014 33.3 2.2 31 30-64 14-44 (421)
65 PHA02998 RNA polymerase subuni 59.4 7.6 0.00016 31.4 2.2 35 33-67 142-185 (195)
66 PF05191 ADK_lid: Adenylate ki 59.2 4.3 9.2E-05 24.2 0.6 31 35-65 2-33 (36)
67 PF08063 PADR1: PADR1 (NUC008) 58.9 7.8 0.00017 24.9 1.9 21 35-57 15-35 (55)
68 PF01873 eIF-5_eIF-2B: Domain 58.8 9.1 0.0002 28.2 2.4 28 35-62 94-123 (125)
69 PF10122 Mu-like_Com: Mu-like 58.8 8.6 0.00019 25.2 2.0 19 30-48 20-38 (51)
70 PF01485 IBR: IBR domain; Int 57.9 4.5 9.7E-05 24.4 0.6 47 20-69 7-56 (64)
71 PRK12496 hypothetical protein; 57.7 4.6 9.9E-05 30.7 0.7 28 35-65 128-155 (164)
72 PF01155 HypA: Hydrogenase exp 56.5 3.4 7.3E-05 29.4 -0.2 35 33-70 69-103 (113)
73 COG0675 Transposase and inacti 56.4 13 0.00028 28.2 2.9 36 21-62 296-331 (364)
74 PF09862 DUF2089: Protein of u 56.0 13 0.00028 27.4 2.8 22 37-63 1-22 (113)
75 PF14354 Lar_restr_allev: Rest 56.0 15 0.00033 22.7 2.8 25 37-61 6-37 (61)
76 smart00661 RPOL9 RNA polymeras 54.9 10 0.00022 22.6 1.8 27 37-63 3-30 (52)
77 TIGR02443 conserved hypothetic 54.7 19 0.00041 24.1 3.2 35 35-69 10-47 (59)
78 PF09082 DUF1922: Domain of un 53.8 17 0.00037 24.9 2.9 29 32-64 1-30 (68)
79 PF06827 zf-FPG_IleRS: Zinc fi 53.7 18 0.00039 19.9 2.6 26 36-61 3-29 (30)
80 TIGR01385 TFSII transcription 53.4 12 0.00026 31.3 2.5 28 34-61 258-294 (299)
81 PF11781 RRN7: RNA polymerase 52.6 15 0.00033 21.8 2.3 26 36-63 10-35 (36)
82 PF05129 Elf1: Transcription e 51.8 18 0.0004 24.7 2.9 39 22-63 13-56 (81)
83 PF03811 Zn_Tnp_IS1: InsA N-te 51.2 12 0.00025 22.5 1.6 19 33-51 4-22 (36)
84 COG1326 Uncharacterized archae 50.4 13 0.00028 30.3 2.2 31 33-63 5-40 (201)
85 COG3877 Uncharacterized protei 50.4 13 0.00028 28.1 2.1 29 30-63 2-30 (122)
86 PF06943 zf-LSD1: LSD1 zinc fi 49.5 12 0.00025 21.2 1.3 15 56-70 1-15 (25)
87 PF07295 DUF1451: Protein of u 49.4 11 0.00024 28.5 1.6 28 35-63 113-140 (146)
88 PF09332 Mcm10: Mcm10 replicat 49.0 8 0.00017 33.2 0.9 33 35-68 286-318 (344)
89 PRK13130 H/ACA RNA-protein com 48.5 14 0.00031 24.2 1.8 22 35-63 6-27 (56)
90 PF12773 DZR: Double zinc ribb 48.4 8.6 0.00019 23.0 0.7 12 53-64 12-23 (50)
91 PF08996 zf-DNA_Pol: DNA Polym 47.7 19 0.00042 27.5 2.7 32 33-64 17-56 (188)
92 PF13901 DUF4206: Domain of un 47.2 9.9 0.00021 29.5 1.1 28 36-63 154-182 (202)
93 PF09526 DUF2387: Probable met 46.9 27 0.00058 23.7 3.0 34 35-68 9-45 (71)
94 PF10080 DUF2318: Predicted me 46.9 49 0.0011 23.8 4.5 30 47-78 46-75 (102)
95 PF05180 zf-DNL: DNL zinc fing 46.0 13 0.00029 25.1 1.4 18 32-49 27-44 (66)
96 TIGR00319 desulf_FeS4 desulfof 45.0 28 0.00061 19.7 2.5 22 35-56 8-29 (34)
97 cd00974 DSRD Desulforedoxin (D 44.6 28 0.00061 19.8 2.5 22 35-56 5-26 (34)
98 PRK14873 primosome assembly pr 44.1 29 0.00062 31.9 3.7 48 22-79 370-418 (665)
99 PF05077 DUF678: Protein of un 44.0 18 0.00038 25.4 1.8 48 15-65 8-69 (74)
100 PF06677 Auto_anti-p27: Sjogre 43.3 21 0.00046 21.9 1.9 26 33-60 16-41 (41)
101 PF01780 Ribosomal_L37ae: Ribo 43.3 29 0.00062 24.9 2.9 29 35-64 36-64 (90)
102 PF03119 DNA_ligase_ZBD: NAD-d 43.1 16 0.00034 20.6 1.2 18 55-72 1-18 (28)
103 COG1997 RPL43A Ribosomal prote 42.7 29 0.00062 25.1 2.8 30 35-65 36-65 (89)
104 PRK11032 hypothetical protein; 42.0 17 0.00037 28.1 1.7 28 35-63 125-152 (160)
105 PF15288 zf-CCHC_6: Zinc knuck 41.7 8.8 0.00019 23.9 0.0 22 34-59 1-22 (40)
106 PF07282 OrfB_Zn_ribbon: Putat 40.6 26 0.00056 22.1 2.1 33 30-63 24-56 (69)
107 TIGR01562 FdhE formate dehydro 39.9 21 0.00046 30.0 2.0 35 29-63 219-262 (305)
108 PF09538 FYDLN_acid: Protein o 39.8 13 0.00027 27.0 0.6 27 36-64 11-37 (108)
109 COG3677 Transposase and inacti 39.3 24 0.00051 26.0 2.0 39 33-72 29-72 (129)
110 PRK05580 primosome assembly pr 38.5 35 0.00076 31.0 3.3 45 19-63 365-418 (679)
111 PF09272 Hepsin-SRCR: Hepsin, 37.2 19 0.00041 26.9 1.2 18 26-43 90-107 (110)
112 PF03117 Herpes_UL49_1: UL49 f 36.9 37 0.00081 28.2 3.0 41 24-67 126-172 (245)
113 PTZ00255 60S ribosomal protein 36.7 41 0.00089 24.1 2.8 29 35-64 37-65 (90)
114 PRK06260 threonine synthase; V 36.4 23 0.00049 29.7 1.7 28 33-63 2-29 (397)
115 PF07754 DUF1610: Domain of un 35.6 27 0.00059 19.5 1.4 15 28-42 10-24 (24)
116 smart00746 TRASH metallochaper 35.5 34 0.00074 16.9 1.7 30 56-90 1-30 (39)
117 PRK06450 threonine synthase; V 35.2 23 0.00049 29.4 1.5 27 33-63 2-28 (338)
118 smart00132 LIM Zinc-binding do 34.3 31 0.00067 18.4 1.5 9 55-63 29-37 (39)
119 KOG2906|consensus 33.8 52 0.0011 24.4 3.0 29 36-64 3-32 (105)
120 PF12677 DUF3797: Domain of un 33.8 21 0.00047 23.2 0.9 13 34-46 13-25 (49)
121 PF08646 Rep_fac-A_C: Replicat 33.7 65 0.0014 23.0 3.5 35 31-67 15-51 (146)
122 PF14599 zinc_ribbon_6: Zinc-r 33.4 40 0.00086 22.3 2.2 32 29-61 25-56 (61)
123 PF14446 Prok-RING_1: Prokaryo 33.0 28 0.0006 22.9 1.3 32 31-65 2-33 (54)
124 PHA02893 hypothetical protein; 33.0 29 0.00063 25.0 1.5 31 35-65 35-81 (88)
125 PF05876 Terminase_GpA: Phage 32.4 27 0.00059 31.1 1.6 34 32-65 198-241 (557)
126 PRK05654 acetyl-CoA carboxylas 32.1 13 0.00028 30.9 -0.4 31 33-63 26-56 (292)
127 smart00614 ZnF_BED BED zinc fi 32.1 42 0.0009 20.3 2.0 16 52-67 17-32 (50)
128 TIGR00280 L37a ribosomal prote 32.1 56 0.0012 23.5 2.9 29 35-64 36-64 (91)
129 PRK14714 DNA polymerase II lar 32.0 26 0.00056 35.3 1.5 23 34-63 667-689 (1337)
130 KOG1296|consensus 31.8 28 0.0006 27.5 1.4 64 27-98 23-89 (161)
131 PF09297 zf-NADH-PPase: NADH p 31.7 45 0.00097 18.7 1.9 22 56-77 6-27 (32)
132 TIGR00320 dfx_rbo desulfoferro 31.7 48 0.001 24.4 2.6 27 35-63 8-34 (125)
133 TIGR00373 conserved hypothetic 30.7 16 0.00034 27.5 -0.1 41 22-65 99-140 (158)
134 PF11331 DUF3133: Protein of u 30.7 26 0.00057 22.2 0.9 17 47-63 25-41 (46)
135 PRK00464 nrdR transcriptional 30.4 42 0.0009 25.7 2.1 28 36-63 2-38 (154)
136 PF01927 Mut7-C: Mut7-C RNAse 29.6 61 0.0013 23.7 2.8 52 50-115 88-139 (147)
137 PF00236 Hormone_6: Glycoprote 29.6 13 0.00028 27.2 -0.7 41 28-68 2-44 (96)
138 KOG2907|consensus 29.4 15 0.00032 27.7 -0.4 50 8-62 53-111 (116)
139 KOG1598|consensus 29.3 24 0.00053 32.2 0.8 36 36-71 2-43 (521)
140 PF06397 Desulfoferrod_N: Desu 29.2 58 0.0013 19.7 2.2 22 35-56 7-28 (36)
141 PF09814 HECT_2: HECT-like Ubi 29.1 50 0.0011 26.7 2.5 52 21-75 159-216 (354)
142 COG1996 RPC10 DNA-directed RNA 29.0 72 0.0016 20.5 2.7 34 32-66 4-38 (49)
143 PF09963 DUF2197: Uncharacteri 28.4 19 0.00041 23.8 -0.0 35 33-67 1-45 (56)
144 PRK06266 transcription initiat 28.3 19 0.00041 27.7 -0.0 40 23-65 108-148 (178)
145 cd04476 RPA1_DBD_C RPA1_DBD_C: 28.2 63 0.0014 23.5 2.7 35 31-67 31-65 (166)
146 PRK09710 lar restriction allev 27.7 76 0.0016 21.6 2.8 26 37-62 9-36 (64)
147 PRK14559 putative protein seri 27.5 27 0.00059 32.1 0.8 24 35-63 2-25 (645)
148 PF15616 TerY-C: TerY-C metal 27.5 1E+02 0.0023 23.2 3.8 23 36-66 79-101 (131)
149 PF08150 FerB: FerB (NUC096) d 27.3 27 0.00058 24.3 0.6 10 40-49 43-52 (76)
150 PF02591 DUF164: Putative zinc 27.3 34 0.00073 21.2 1.0 28 36-63 24-56 (56)
151 COG0777 AccD Acetyl-CoA carbox 27.0 30 0.00065 29.6 0.9 31 33-63 27-57 (294)
152 COG3088 CcmH Uncharacterized p 26.8 27 0.00059 27.3 0.6 37 5-51 25-61 (153)
153 PRK03564 formate dehydrogenase 26.7 48 0.001 28.1 2.1 35 29-63 221-262 (309)
154 PHA02942 putative transposase; 26.7 49 0.0011 28.2 2.1 29 33-63 324-352 (383)
155 cd00729 rubredoxin_SM Rubredox 26.5 53 0.0011 19.0 1.7 24 35-61 3-26 (34)
156 PF12172 DUF35_N: Rubredoxin-l 26.3 63 0.0014 18.4 2.0 28 29-61 6-33 (37)
157 COG2023 RPR2 RNase P subunit R 26.2 93 0.002 22.9 3.2 33 36-68 58-97 (105)
158 TIGR03655 anti_R_Lar restricti 26.1 86 0.0019 19.3 2.7 29 36-64 3-37 (53)
159 TIGR02300 FYDLN_acid conserved 25.5 33 0.00071 26.2 0.8 26 36-63 11-36 (129)
160 PF14206 Cys_rich_CPCC: Cystei 25.0 54 0.0012 22.7 1.7 26 35-60 2-27 (78)
161 PRK00241 nudC NADH pyrophospha 24.9 59 0.0013 26.1 2.2 27 36-63 101-127 (256)
162 COG5347 GTPase-activating prot 24.8 22 0.00047 30.2 -0.3 59 35-108 21-80 (319)
163 PF09947 DUF2180: Uncharacteri 24.7 17 0.00037 24.9 -0.8 27 36-65 2-28 (68)
164 COG5349 Uncharacterized protei 24.2 31 0.00067 26.3 0.4 57 25-86 12-68 (126)
165 smart00336 BBOX B-Box-type zin 24.1 56 0.0012 18.1 1.5 28 35-62 4-32 (42)
166 PRK15103 paraquat-inducible me 23.9 68 0.0015 27.8 2.5 35 35-69 11-46 (419)
167 PF14353 CpXC: CpXC protein 23.8 57 0.0012 22.9 1.7 18 29-46 33-50 (128)
168 PF02892 zf-BED: BED zinc fing 23.6 54 0.0012 18.9 1.3 22 49-70 12-33 (45)
169 PF06221 zf-C2HC5: Putative zi 23.1 44 0.00096 22.0 1.0 17 53-69 18-34 (57)
170 PF08209 Sgf11: Sgf11 (transcr 23.0 73 0.0016 18.8 1.8 14 51-64 2-15 (33)
171 PF08772 NOB1_Zn_bind: Nin one 23.0 39 0.00084 23.1 0.7 23 35-61 10-32 (73)
172 cd00021 BBOX B-Box-type zinc f 22.9 47 0.001 18.2 0.9 25 36-60 2-27 (39)
173 PF04828 GFA: Glutathione-depe 22.6 86 0.0019 19.7 2.3 17 48-64 43-59 (92)
174 PRK12286 rpmF 50S ribosomal pr 22.6 69 0.0015 20.7 1.8 21 35-61 28-48 (57)
175 smart00547 ZnF_RBZ Zinc finger 22.4 33 0.00072 18.0 0.2 23 35-62 3-25 (26)
176 COG0375 HybF Zn finger protein 22.3 70 0.0015 23.7 2.0 36 34-72 70-105 (115)
177 TIGR03831 YgiT_finger YgiT-typ 22.1 1.3E+02 0.0028 16.9 2.8 10 56-65 35-44 (46)
178 TIGR00515 accD acetyl-CoA carb 22.1 23 0.00051 29.3 -0.6 29 33-63 25-55 (285)
179 COG0846 SIR2 NAD-dependent pro 21.9 53 0.0011 26.8 1.4 39 29-67 117-160 (250)
180 cd00674 LysRS_core_class_I cat 21.7 2E+02 0.0042 24.6 4.8 45 29-74 163-214 (353)
181 PF05280 FlhC: Flagellar trans 21.6 67 0.0015 24.9 1.9 30 32-61 132-162 (175)
182 COG1644 RPB10 DNA-directed RNA 21.5 32 0.0007 23.4 0.1 13 52-64 3-15 (63)
183 PRK14559 putative protein seri 21.3 44 0.00096 30.8 0.9 32 36-74 29-60 (645)
184 PRK05638 threonine synthase; V 21.2 56 0.0012 27.8 1.5 26 34-64 1-26 (442)
185 cd01411 SIR2H SIR2H: Uncharact 21.0 45 0.00098 26.0 0.8 38 25-63 109-146 (225)
186 PRK07218 replication factor A; 20.7 56 0.0012 28.7 1.4 27 28-62 292-318 (423)
187 PRK07562 ribonucleotide-diphos 20.6 80 0.0017 31.7 2.5 28 33-62 1189-1216(1220)
188 PF08821 CGGC: CGGC domain; I 20.6 63 0.0014 23.1 1.4 13 96-108 36-48 (107)
189 PF01396 zf-C4_Topoisom: Topoi 20.1 48 0.001 19.7 0.6 13 55-67 3-15 (39)
190 PF09845 DUF2072: Zn-ribbon co 20.1 41 0.00088 25.6 0.4 20 55-77 3-22 (131)
No 1
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=100.00 E-value=4.5e-48 Score=271.27 Aligned_cols=79 Identities=68% Similarity=1.118 Sum_probs=76.6
Q ss_pred CcccccCCCCHHHHHHhhcccccccCCCCceeEEeCCCCCceeEEeeecceeEEcCCCCeeeecccCCceeeccCCCCc
Q psy2574 2 PLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLTEDDTGD 80 (115)
Q Consensus 2 ~l~~DLl~Ps~e~ek~k~K~krLV~~PnS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PTGGKA~l~egc~f~ 80 (115)
.|+.|||||++|+|++|||+|||||+||||||+||||+|+|||||||||||+|.|.+||++||+||||||+|+|||+|.
T Consensus 3 ~~~~DLl~p~~~~e~~khK~k~Lv~~PnS~Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~PTGGKa~l~~gc~fr 81 (85)
T PTZ00083 3 FMDVDLLYPDPESEARKHKLKRLVQGPNSYFMDVKCPGCSQITTVFSHAQTVVLCGGCSSQLCQPTGGKAKLTEGCSFR 81 (85)
T ss_pred cchhhhcCCCHHHHHhhhhceeEecCCCCeEEEEECCCCCCeeEEEecCceEEEccccCCEeeccCCCCeEecCCceEE
Confidence 3577999999999999999999999999999999999999999999999999999999999999999999999999983
No 2
>PLN00209 ribosomal protein S27; Provisional
Probab=100.00 E-value=1.4e-47 Score=269.32 Aligned_cols=78 Identities=67% Similarity=1.121 Sum_probs=75.9
Q ss_pred cccccCCCCHHHHHHhhcccccccCCCCceeEEeCCCCCceeEEeeecceeEEcCCCCeeeecccCCceeeccCCCCc
Q psy2574 3 LAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLTEDDTGD 80 (115)
Q Consensus 3 l~~DLl~Ps~e~ek~k~K~krLV~~PnS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PTGGKA~l~egc~f~ 80 (115)
++.|||||++|+|++|||+|||||+||||||+||||+|+|||||||||||+|.|.+||++||+||||||+|+|||+|-
T Consensus 5 ~~~DLl~P~~~~e~~khK~k~Lv~~PnS~Fm~VkCp~C~n~q~VFShA~t~V~C~~Cg~~L~~PTGGKa~l~~gc~fr 82 (86)
T PLN00209 5 NDIDLLNPPAELEKRKHKLKRLVQSPNSFFMDVKCQGCFNITTVFSHSQTVVVCGSCQTVLCQPTGGKARLTEGCSFR 82 (86)
T ss_pred cchhccCCCHHHHHhhhhceeeecCCCCEEEEEECCCCCCeeEEEecCceEEEccccCCEeeccCCCCeEecCCceEE
Confidence 467999999999999999999999999999999999999999999999999999999999999999999999999983
No 3
>KOG1779|consensus
Probab=100.00 E-value=2.7e-44 Score=251.42 Aligned_cols=80 Identities=80% Similarity=1.331 Sum_probs=79.0
Q ss_pred CCcccccCCCCHHHHHHhhcccccccCCCCceeEEeCCCCCceeEEeeecceeEEcCCCCeeeecccCCceeeccCCCCc
Q psy2574 1 MPLAKDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLTEDDTGD 80 (115)
Q Consensus 1 m~l~~DLl~Ps~e~ek~k~K~krLV~~PnS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PTGGKA~l~egc~f~ 80 (115)
|+|++|||||++|+|+|+||+|||||+||||||+|||++|.||++|||||||+|.|.+|+++|++||||||+++|||+|-
T Consensus 1 m~la~dllhPs~e~e~r~hK~krLvq~~nsyFm~VkC~gc~~iT~vfSHaqtvVvc~~c~~il~~~tggra~ls~~csfr 80 (84)
T KOG1779|consen 1 MPLAKDLLHPSPEKEKRKHKLKRLVQSPNSYFMDVKCPGCFKITTVFSHAQTVVVCEGCSTILCQPTGGKAKLSEGCSFR 80 (84)
T ss_pred CccchhhcCCCHHHHhhhhhhhhheeCCCceEEEEEcCCceEEEEEeecCceEEEcCCCceEEEEecCCcEEecCCCcce
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999983
No 4
>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=100.00 E-value=8e-34 Score=185.38 Aligned_cols=52 Identities=73% Similarity=1.252 Sum_probs=42.3
Q ss_pred CCCceeEEeCCCCCceeEEeeecceeEEcCCCCeeeecccCCceeeccCCCC
Q psy2574 28 PNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLTEDDTG 79 (115)
Q Consensus 28 PnS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PTGGKA~l~egc~f 79 (115)
|||||||||||+|+|+|+||||||++|.|.+||++|++||||||+|.+||.|
T Consensus 1 P~S~Fm~VkCp~C~~~q~vFSha~t~V~C~~Cg~~L~~PtGGKa~l~~~~~~ 52 (55)
T PF01667_consen 1 PNSYFMDVKCPGCYNIQTVFSHAQTVVKCVVCGTVLAQPTGGKARLTEGCSF 52 (55)
T ss_dssp -S--EEEEE-TTT-SEEEEETT-SS-EE-SSSTSEEEEE-SSSEEESSSEEE
T ss_pred CCccEEEEECCCCCCeeEEEecCCeEEEcccCCCEecCCCCcCeEEeCCeEE
Confidence 8999999999999999999999999999999999999999999999999976
No 5
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=99.97 E-value=2.6e-32 Score=180.75 Aligned_cols=52 Identities=46% Similarity=0.916 Sum_probs=50.4
Q ss_pred cccCCCCceeEEeCCCCCceeEEeeecceeEEcCCCCeeeecccCCceeecc
Q psy2574 24 LVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLTE 75 (115)
Q Consensus 24 LV~~PnS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PTGGKA~l~e 75 (115)
|||+|||+||+||||+|+|+|+||||||++|.|.+||++|++||||||+|..
T Consensus 1 li~~p~S~F~~VkCp~C~n~q~vFsha~t~V~C~~Cg~~L~~PtGGKa~i~~ 52 (59)
T PRK00415 1 LIPQPRSRFLKVKCPDCGNEQVVFSHASTVVRCLVCGKTLAEPTGGKAKIKG 52 (59)
T ss_pred CCCCCCCeEEEEECCCCCCeEEEEecCCcEEECcccCCCcccCCCcceeeeh
Confidence 7999999999999999999999999999999999999999999999999963
No 6
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=99.96 E-value=1.3e-29 Score=171.60 Aligned_cols=56 Identities=45% Similarity=0.819 Sum_probs=52.2
Q ss_pred ccccc-CCCCceeEEeCCCCCceeEEeeecceeEEcCCCCeeeecccCCceeeccCC
Q psy2574 22 KRLVQ-HPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLTEDD 77 (115)
Q Consensus 22 krLV~-~PnS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PTGGKA~l~egc 77 (115)
|-++| .|||+||+||||||+|+|+|||||||+|.|.+||++|++||||||+|.+..
T Consensus 6 k~~~p~~p~s~Fl~VkCpdC~N~q~vFshast~V~C~~CG~~l~~PTGGka~i~~~i 62 (67)
T COG2051 6 KVKIPKEPRSRFLRVKCPDCGNEQVVFSHASTVVTCLICGTTLAEPTGGKAKISGKI 62 (67)
T ss_pred eeeecCCCCceEEEEECCCCCCEEEEeccCceEEEecccccEEEecCCCeEEeeeee
Confidence 44555 999999999999999999999999999999999999999999999998864
No 7
>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=97.18 E-value=0.00037 Score=42.08 Aligned_cols=31 Identities=29% Similarity=0.752 Sum_probs=27.2
Q ss_pred eCCCCCceeEEeeecceeEEcCCCCeeeecc
Q psy2574 36 KCPGCYKITTVFSHAQSVVICAGCSTILCQP 66 (115)
Q Consensus 36 KCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~P 66 (115)
+||.|+...++|.+++..+.|..||.+|-+-
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl~e~ 32 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCGLVLEEN 32 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-BBEE-T
T ss_pred CCcCCcCCceEEcCCCCeEECCCCCCEeecc
Confidence 7999999999999999999999999999653
No 8
>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=95.67 E-value=0.014 Score=33.88 Aligned_cols=32 Identities=25% Similarity=0.619 Sum_probs=23.9
Q ss_pred eEEeCCCCCceeEEee----ecceeEEcCCCCeeee
Q psy2574 33 MDVKCPGCYKITTVFS----HAQSVVICAGCSTILC 64 (115)
Q Consensus 33 m~VKCp~C~n~q~VFS----HAqt~V~C~~Cg~vL~ 64 (115)
|+++||.|+..--|=+ .+...|.|..||+++-
T Consensus 1 M~~~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 1 MRIQCPNCKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred CEEECCCCCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 7899999998644432 2345799999999873
No 9
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=95.24 E-value=0.012 Score=48.02 Aligned_cols=32 Identities=19% Similarity=0.646 Sum_probs=29.5
Q ss_pred EeCCCCCceeEEeeecceeEEcCCCCeeeecc
Q psy2574 35 VKCPGCYKITTVFSHAQSVVICAGCSTILCQP 66 (115)
Q Consensus 35 VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~P 66 (115)
.+||+|+...+|+++++..+.|..||.||.+-
T Consensus 12 ~~Cp~Cg~~~iv~d~~~Ge~vC~~CG~Vl~e~ 43 (310)
T PRK00423 12 LVCPECGSDKLIYDYERGEIVCADCGLVIEEN 43 (310)
T ss_pred CcCcCCCCCCeeEECCCCeEeecccCCccccc
Confidence 47999999999999999999999999999663
No 10
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=94.97 E-value=0.033 Score=33.86 Aligned_cols=36 Identities=17% Similarity=0.296 Sum_probs=26.5
Q ss_pred eEEeCCCCCceeEEeeecceeEEcCCCCeeeecccCC
Q psy2574 33 MDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGG 69 (115)
Q Consensus 33 m~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PTGG 69 (115)
+..+|++|+.+..+ ....+.+.|..||..+..-..+
T Consensus 2 ~~y~C~~CG~~~~~-~~~~~~~~Cp~CG~~~~~~~~~ 37 (46)
T PRK00398 2 AEYKCARCGREVEL-DEYGTGVRCPYCGYRILFKERP 37 (46)
T ss_pred CEEECCCCCCEEEE-CCCCCceECCCCCCeEEEccCC
Confidence 56899999996554 4444589999999987654433
No 11
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=93.11 E-value=0.11 Score=30.80 Aligned_cols=31 Identities=26% Similarity=0.577 Sum_probs=23.9
Q ss_pred eEEeCCCCCceeEEee----ecceeEEcCCCCeee
Q psy2574 33 MDVKCPGCYKITTVFS----HAQSVVICAGCSTIL 63 (115)
Q Consensus 33 m~VKCp~C~n~q~VFS----HAqt~V~C~~Cg~vL 63 (115)
|.+.||.|...--|=. -+...|+|..|+.+.
T Consensus 1 M~i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 1 MIITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred CEEECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 7899999987655433 356799999999875
No 12
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=92.47 E-value=0.039 Score=30.50 Aligned_cols=26 Identities=27% Similarity=0.680 Sum_probs=20.8
Q ss_pred eEEeCCCCCceeEEeeecceeEEcCCCCeee
Q psy2574 33 MDVKCPGCYKITTVFSHAQSVVICAGCSTIL 63 (115)
Q Consensus 33 m~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL 63 (115)
|.+.||.|+++ +......|..||+.|
T Consensus 1 m~~~Cp~Cg~~-----~~~~~~fC~~CG~~L 26 (26)
T PF13248_consen 1 MEMFCPNCGAE-----IDPDAKFCPNCGAKL 26 (26)
T ss_pred CcCCCcccCCc-----CCcccccChhhCCCC
Confidence 56889999983 366778899999865
No 13
>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=91.54 E-value=0.27 Score=28.27 Aligned_cols=31 Identities=13% Similarity=0.443 Sum_probs=22.2
Q ss_pred eEEeCCCCCcee-EEeeec-ceeEEcCCCCeee
Q psy2574 33 MDVKCPGCYKIT-TVFSHA-QSVVICAGCSTIL 63 (115)
Q Consensus 33 m~VKCp~C~n~q-~VFSHA-qt~V~C~~Cg~vL 63 (115)
++-+|++|+++- +..+-+ ...+.|..||..+
T Consensus 4 Y~y~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~ 36 (41)
T smart00834 4 YEYRCEDCGHTFEVLQKISDDPLATCPECGGDV 36 (41)
T ss_pred EEEEcCCCCCEEEEEEecCCCCCCCCCCCCCcc
Confidence 467999999944 444333 6688899999843
No 14
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=89.13 E-value=0.46 Score=28.13 Aligned_cols=31 Identities=23% Similarity=0.564 Sum_probs=21.3
Q ss_pred eEEeCCCCCceeEEee----ecceeEEcCCCCeee
Q psy2574 33 MDVKCPGCYKITTVFS----HAQSVVICAGCSTIL 63 (115)
Q Consensus 33 m~VKCp~C~n~q~VFS----HAqt~V~C~~Cg~vL 63 (115)
|+|.||.|...--|=+ -....|.|..||.+.
T Consensus 1 M~i~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 1 MIITCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred CEEECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 7788888877654433 234578888888764
No 15
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=88.95 E-value=0.17 Score=37.75 Aligned_cols=34 Identities=26% Similarity=0.583 Sum_probs=29.1
Q ss_pred CceeEEeCCCCCceeEEeeecceeEEcCCCCeeeecc
Q psy2574 30 SYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQP 66 (115)
Q Consensus 30 S~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~P 66 (115)
.+...|+||+|++.+-+.++.+ .|--|+++|.-.
T Consensus 65 tkav~V~CP~C~K~TKmLGr~D---~CM~C~~pLTLd 98 (114)
T PF11023_consen 65 TKAVQVECPNCGKQTKMLGRVD---ACMHCKEPLTLD 98 (114)
T ss_pred ccceeeECCCCCChHhhhchhh---ccCcCCCcCccC
Confidence 3457899999999999999986 899999998643
No 16
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=87.91 E-value=0.42 Score=39.58 Aligned_cols=30 Identities=23% Similarity=0.670 Sum_probs=28.4
Q ss_pred eCCCCCceeEEeeecceeEEcCCCCeeeec
Q psy2574 36 KCPGCYKITTVFSHAQSVVICAGCSTILCQ 65 (115)
Q Consensus 36 KCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~ 65 (115)
.||.|+...++.++....+.|..||.+|-.
T Consensus 3 ~CpeCg~~~~~~d~~~ge~VC~~CG~Vi~~ 32 (285)
T COG1405 3 SCPECGSTNIITDYERGEIVCADCGLVLED 32 (285)
T ss_pred CCCCCCCccceeeccCCeEEeccCCEEecc
Confidence 699999999999999999999999999965
No 17
>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=87.52 E-value=0.64 Score=27.80 Aligned_cols=28 Identities=32% Similarity=0.785 Sum_probs=19.4
Q ss_pred EeCCCCCceeEEeeecce---------eEEcCCCCee
Q psy2574 35 VKCPGCYKITTVFSHAQS---------VVICAGCSTI 62 (115)
Q Consensus 35 VKCp~C~n~q~VFSHAqt---------~V~C~~Cg~v 62 (115)
++||.|++..++|-..|+ ...|..||..
T Consensus 1 ~~Cp~Cg~~~a~~~~~Q~rsaDE~~T~fy~C~~C~~~ 37 (39)
T PF01096_consen 1 IKCPKCGHNEAVFFQIQTRSADEPMTLFYVCCNCGHR 37 (39)
T ss_dssp S--SSS-SSEEEEEEESSSSSSSSSEEEEEESSSTEE
T ss_pred CCCcCCCCCeEEEEEeeccCCCCCCeEEEEeCCCCCe
Confidence 589999999999986654 4678888764
No 18
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=87.37 E-value=0.72 Score=33.18 Aligned_cols=29 Identities=21% Similarity=0.685 Sum_probs=21.4
Q ss_pred EeCCCCCceeE--EeeecceeEEcCCCCeee
Q psy2574 35 VKCPGCYKITT--VFSHAQSVVICAGCSTIL 63 (115)
Q Consensus 35 VKCp~C~n~q~--VFSHAqt~V~C~~Cg~vL 63 (115)
+.||.|++..+ -+.+-...+.|..||.--
T Consensus 22 f~CP~Cge~~v~v~~~k~~~h~~C~~CG~y~ 52 (99)
T PRK14892 22 FECPRCGKVSISVKIKKNIAIITCGNCGLYT 52 (99)
T ss_pred eECCCCCCeEeeeecCCCcceEECCCCCCcc
Confidence 68999995322 256767789999999753
No 19
>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=87.06 E-value=0.74 Score=27.99 Aligned_cols=29 Identities=14% Similarity=0.494 Sum_probs=20.4
Q ss_pred eEEeCCCCCcee-EEee-ecceeEEcCCCCe
Q psy2574 33 MDVKCPGCYKIT-TVFS-HAQSVVICAGCST 61 (115)
Q Consensus 33 m~VKCp~C~n~q-~VFS-HAqt~V~C~~Cg~ 61 (115)
++-+|++|+++- +..+ +....+.|..||.
T Consensus 4 Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 4 YEYRCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EEEEeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 467999999944 4433 2235678999997
No 20
>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=84.35 E-value=1.4 Score=26.50 Aligned_cols=30 Identities=20% Similarity=0.562 Sum_probs=21.8
Q ss_pred eeEEeCCCCCceeEEeee-cc-eeEEcCCCCe
Q psy2574 32 FMDVKCPGCYKITTVFSH-AQ-SVVICAGCST 61 (115)
Q Consensus 32 Fm~VKCp~C~n~q~VFSH-Aq-t~V~C~~Cg~ 61 (115)
..+-+|++|++.--++-. +. ..+.|..||.
T Consensus 3 ~Yey~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 3 IYEYRCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred CEEEEeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 357799999955444433 33 5899999998
No 21
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=83.47 E-value=0.93 Score=32.53 Aligned_cols=37 Identities=14% Similarity=0.293 Sum_probs=27.1
Q ss_pred eEEeCCCCCceeEEeeecce-eEEcCCCCeeeecccCCcee
Q psy2574 33 MDVKCPGCYKITTVFSHAQS-VVICAGCSTILCQPTGGRAR 72 (115)
Q Consensus 33 m~VKCp~C~n~q~VFSHAqt-~V~C~~Cg~vL~~PTGGKA~ 72 (115)
...+|++|++ .|..... ...|+.||..-.+-.+|+--
T Consensus 69 ~~~~C~~Cg~---~~~~~~~~~~~CP~Cgs~~~~i~~G~El 106 (114)
T PRK03681 69 AECWCETCQQ---YVTLLTQRVRRCPQCHGDMLRIVADDGL 106 (114)
T ss_pred cEEEcccCCC---eeecCCccCCcCcCcCCCCcEEccCCeE
Confidence 3589999996 4555433 36799999887788888753
No 22
>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=83.42 E-value=1.2 Score=28.99 Aligned_cols=32 Identities=28% Similarity=0.597 Sum_probs=21.9
Q ss_pred eEEeCCCCCceeEE-eeecceeEEcCCCCeeee
Q psy2574 33 MDVKCPGCYKITTV-FSHAQSVVICAGCSTILC 64 (115)
Q Consensus 33 m~VKCp~C~n~q~V-FSHAqt~V~C~~Cg~vL~ 64 (115)
|..+||.|+..-.+ =+..-..|.|..||..|=
T Consensus 1 ~~~~CP~CG~~iev~~~~~GeiV~Cp~CGaele 33 (54)
T TIGR01206 1 MQFECPDCGAEIELENPELGELVICDECGAELE 33 (54)
T ss_pred CccCCCCCCCEEecCCCccCCEEeCCCCCCEEE
Confidence 35689999985433 112346889999998773
No 23
>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=83.25 E-value=1.2 Score=30.61 Aligned_cols=29 Identities=24% Similarity=0.551 Sum_probs=22.3
Q ss_pred eEEeCCCCCceeEEeeecce---------eEEcCCCCe
Q psy2574 33 MDVKCPGCYKITTVFSHAQS---------VVICAGCST 61 (115)
Q Consensus 33 m~VKCp~C~n~q~VFSHAqt---------~V~C~~Cg~ 61 (115)
.+++||.|++...+|.-.|+ .-.|..||.
T Consensus 61 ~~~~Cp~Cg~~~a~f~~~Q~RsadE~~T~fy~C~~C~~ 98 (104)
T TIGR01384 61 TRVECPKCGHKEAYYWLLQTRRADEPETRFYKCTKCGY 98 (104)
T ss_pred ccCCCCCCCCCeeEEEEeccCCCCCCcEEEEEeCCCCC
Confidence 36899999999999986654 456777764
No 24
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=82.74 E-value=1.8 Score=26.79 Aligned_cols=30 Identities=23% Similarity=0.452 Sum_probs=23.2
Q ss_pred eEEeCCCCCceeEEeeecceeEEcCCCCeeee
Q psy2574 33 MDVKCPGCYKITTVFSHAQSVVICAGCSTILC 64 (115)
Q Consensus 33 m~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~ 64 (115)
|.-+|.+|+.+..+- ....|.|..||.-+.
T Consensus 1 ~~Y~C~~Cg~~~~~~--~~~~irC~~CG~rIl 30 (44)
T smart00659 1 MIYICGECGRENEIK--SKDVVRCRECGYRIL 30 (44)
T ss_pred CEEECCCCCCEeecC--CCCceECCCCCceEE
Confidence 345899999987764 568899999997553
No 25
>PF05907 DUF866: Eukaryotic protein of unknown function (DUF866); InterPro: IPR008584 This family consists of a number of hypothetical eukaryotic proteins of unknown function with an average length of around 165 residues.; PDB: 1ZSO_B.
Probab=82.72 E-value=1.8 Score=32.97 Aligned_cols=37 Identities=24% Similarity=0.494 Sum_probs=21.9
Q ss_pred CCCCceeEEeCCCCCcee---EEee------------ecceeEEcCCCCeee
Q psy2574 27 HPNSYFMDVKCPGCYKIT---TVFS------------HAQSVVICAGCSTIL 63 (115)
Q Consensus 27 ~PnS~Fm~VKCp~C~n~q---~VFS------------HAqt~V~C~~Cg~vL 63 (115)
.|-.||++|||..|+.+. |.++ -|..+.+|..|++..
T Consensus 23 ~~~~~~fkvkCt~CgE~~~k~V~i~~~e~~e~~gsrG~aNfv~KCk~C~re~ 74 (161)
T PF05907_consen 23 PDFEWFFKVKCTSCGEVHPKWVYINRFEKHEIPGSRGTANFVMKCKFCKRES 74 (161)
T ss_dssp TT--EEEEEEETTSS--EEEEEEE-TT-BEE-TTSS-EESEEE--SSSS--E
T ss_pred CCCEEEEEEEECCCCCccCcceEeecceEEecCCCccceEeEecCcCcCCcc
Confidence 467899999999999754 3444 467788999998743
No 26
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=82.46 E-value=0.48 Score=25.84 Aligned_cols=23 Identities=30% Similarity=0.725 Sum_probs=15.5
Q ss_pred eCCCCCceeEEeeecceeEEcCCCCeee
Q psy2574 36 KCPGCYKITTVFSHAQSVVICAGCSTIL 63 (115)
Q Consensus 36 KCp~C~n~q~VFSHAqt~V~C~~Cg~vL 63 (115)
+||.|+++. ......|..||+.|
T Consensus 1 ~Cp~CG~~~-----~~~~~fC~~CG~~l 23 (23)
T PF13240_consen 1 YCPNCGAEI-----EDDAKFCPNCGTPL 23 (23)
T ss_pred CCcccCCCC-----CCcCcchhhhCCcC
Confidence 478888764 23455588888764
No 27
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=81.98 E-value=1 Score=32.33 Aligned_cols=36 Identities=19% Similarity=0.309 Sum_probs=26.0
Q ss_pred eEEeCCCCCceeEEeeecceeEEcCCCCeeeecccCCce
Q psy2574 33 MDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRA 71 (115)
Q Consensus 33 m~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PTGGKA 71 (115)
..++|++|++ .|........|+.||..=.+-.+|+-
T Consensus 69 ~~~~C~~Cg~---~~~~~~~~~~CP~Cgs~~~~i~~G~E 104 (113)
T PRK12380 69 AQAWCWDCSQ---VVEIHQHDAQCPHCHGERLRVDTGDS 104 (113)
T ss_pred cEEEcccCCC---EEecCCcCccCcCCCCCCcEEccCCe
Confidence 4589999994 45555555669999987666677764
No 28
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=81.68 E-value=2.2 Score=25.68 Aligned_cols=27 Identities=26% Similarity=0.642 Sum_probs=20.8
Q ss_pred eCCCCCceeEEeeecc---------eeEEcCCCCee
Q psy2574 36 KCPGCYKITTVFSHAQ---------SVVICAGCSTI 62 (115)
Q Consensus 36 KCp~C~n~q~VFSHAq---------t~V~C~~Cg~v 62 (115)
+||.|++..++|-..| ....|..||..
T Consensus 2 ~Cp~C~~~~a~~~q~Q~RsaDE~mT~fy~C~~C~~~ 37 (40)
T smart00440 2 PCPKCGNREATFFQLQTRSADEPMTVFYVCTKCGHR 37 (40)
T ss_pred cCCCCCCCeEEEEEEcccCCCCCCeEEEEeCCCCCE
Confidence 7999999999997554 35677777753
No 29
>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=81.24 E-value=1.1 Score=32.10 Aligned_cols=36 Identities=22% Similarity=0.559 Sum_probs=25.5
Q ss_pred eEEeCCCCCceeEEeeecceeEEcCCCCeeeecccCCce
Q psy2574 33 MDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRA 71 (115)
Q Consensus 33 m~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PTGGKA 71 (115)
...+|++|++ .|+.......|+.||..-.+-.+|+-
T Consensus 69 ~~~~C~~Cg~---~~~~~~~~~~CP~Cgs~~~~i~~G~E 104 (115)
T TIGR00100 69 VECECEDCSE---EVSPEIDLYRCPKCHGIMLQVRAGKE 104 (115)
T ss_pred cEEEcccCCC---EEecCCcCccCcCCcCCCcEEecCCe
Confidence 3589999994 45555556789999987655566653
No 30
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=81.16 E-value=1.8 Score=25.52 Aligned_cols=28 Identities=21% Similarity=0.414 Sum_probs=20.7
Q ss_pred eCCCCCceeEEeeecceeEEcCCCCeee
Q psy2574 36 KCPGCYKITTVFSHAQSVVICAGCSTIL 63 (115)
Q Consensus 36 KCp~C~n~q~VFSHAqt~V~C~~Cg~vL 63 (115)
-||.|+|+=.+=......+.|..|+..-
T Consensus 3 FCp~C~nlL~p~~~~~~~~~C~~C~Y~~ 30 (35)
T PF02150_consen 3 FCPECGNLLYPKEDKEKRVACRTCGYEE 30 (35)
T ss_dssp BETTTTSBEEEEEETTTTEEESSSS-EE
T ss_pred eCCCCCccceEcCCCccCcCCCCCCCcc
Confidence 3888988888777776666888888653
No 31
>PRK02935 hypothetical protein; Provisional
Probab=80.50 E-value=1 Score=33.53 Aligned_cols=36 Identities=25% Similarity=0.540 Sum_probs=29.4
Q ss_pred CCceeEEeCCCCCceeEEeeecceeEEcCCCCeeeeccc
Q psy2574 29 NSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPT 67 (115)
Q Consensus 29 nS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PT 67 (115)
..+...|.||+|++.+-+-.+.. .|--|+++|.-+.
T Consensus 65 StkavqV~CP~C~K~TKmLGrvD---~CM~C~~PLTLd~ 100 (110)
T PRK02935 65 STKAVQVICPSCEKPTKMLGRVD---ACMHCNQPLTLDR 100 (110)
T ss_pred cccceeeECCCCCchhhhcccee---ecCcCCCcCCcCc
Confidence 45678899999999998887754 8999999986543
No 32
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=77.60 E-value=3 Score=28.27 Aligned_cols=34 Identities=18% Similarity=0.464 Sum_probs=24.8
Q ss_pred CCCCceeEEeCCCCCceeEEeeec----ceeEEcCCCC
Q psy2574 27 HPNSYFMDVKCPGCYKITTVFSHA----QSVVICAGCS 60 (115)
Q Consensus 27 ~PnS~Fm~VKCp~C~n~q~VFSHA----qt~V~C~~Cg 60 (115)
.|...+..-.||+|+++.|.=.+. ...-.|..||
T Consensus 20 ~p~e~~v~F~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CG 57 (61)
T COG2888 20 APGETAVKFPCPNCGEVEIYRCAKCRKLGNPYRCPKCG 57 (61)
T ss_pred ccCCceeEeeCCCCCceeeehhhhHHHcCCceECCCcC
Confidence 377888899999999988875432 3455677776
No 33
>COG4888 Uncharacterized Zn ribbon-containing protein [General function prediction only]
Probab=75.52 E-value=3.9 Score=30.22 Aligned_cols=28 Identities=18% Similarity=0.551 Sum_probs=18.9
Q ss_pred EeCCCCCceeEE---eee--cceeEEcCCCCee
Q psy2574 35 VKCPGCYKITTV---FSH--AQSVVICAGCSTI 62 (115)
Q Consensus 35 VKCp~C~n~q~V---FSH--Aqt~V~C~~Cg~v 62 (115)
-.||-|+.+.++ -.. .--.+.|.+||--
T Consensus 23 FtCp~Cghe~vs~ctvkk~~~~g~~~Cg~CGls 55 (104)
T COG4888 23 FTCPRCGHEKVSSCTVKKTVNIGTAVCGNCGLS 55 (104)
T ss_pred EecCccCCeeeeEEEEEecCceeEEEcccCcce
Confidence 479999999887 222 2235678888753
No 34
>PRK00420 hypothetical protein; Validated
Probab=75.14 E-value=2.3 Score=31.25 Aligned_cols=35 Identities=17% Similarity=0.425 Sum_probs=26.4
Q ss_pred eEEeCCCCCceeEEeeecceeEEcCCCCeeeecccCC
Q psy2574 33 MDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGG 69 (115)
Q Consensus 33 m~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PTGG 69 (115)
+.-.||.|+. ..|.=-+..+.|+.||.++.--.|=
T Consensus 22 l~~~CP~Cg~--pLf~lk~g~~~Cp~Cg~~~~v~~~e 56 (112)
T PRK00420 22 LSKHCPVCGL--PLFELKDGEVVCPVHGKVYIVKSDE 56 (112)
T ss_pred ccCCCCCCCC--cceecCCCceECCCCCCeeeeccHH
Confidence 5578999994 4555478899999999988654443
No 35
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=74.70 E-value=2.5 Score=31.11 Aligned_cols=37 Identities=22% Similarity=0.436 Sum_probs=26.3
Q ss_pred eEEeCCCCCceeEEeeec---------------------ceeEEcCCCCeeeecccCCcee
Q psy2574 33 MDVKCPGCYKITTVFSHA---------------------QSVVICAGCSTILCQPTGGRAR 72 (115)
Q Consensus 33 m~VKCp~C~n~q~VFSHA---------------------qt~V~C~~Cg~vL~~PTGGKA~ 72 (115)
...+|++|+.+ |+.. .....|+.||..-.+-.+|+-.
T Consensus 69 ~~~~C~~CG~~---~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G~el 126 (135)
T PRK03824 69 AVLKCRNCGNE---WSLKEVKESLDEEIREAIHFIPEVVHAFLKCPKCGSRDFEIVKGRGV 126 (135)
T ss_pred eEEECCCCCCE---EecccccccccccccccccccccccccCcCCcCCCCCCcEEecCceE
Confidence 45899999954 4443 4557799999876666677643
No 36
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=74.55 E-value=3.3 Score=30.94 Aligned_cols=28 Identities=25% Similarity=0.551 Sum_probs=22.8
Q ss_pred EeCCCCCceeEEeeec--ceeEEcCCCCee
Q psy2574 35 VKCPGCYKITTVFSHA--QSVVICAGCSTI 62 (115)
Q Consensus 35 VKCp~C~n~q~VFSHA--qt~V~C~~Cg~v 62 (115)
|.|+.|++.-+.+..- -....|..||..
T Consensus 98 VlC~~C~sPdT~l~k~~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 98 VICRECNRPDTRIIKEGRVSLLKCEACGAK 127 (133)
T ss_pred EECCCCCCCCcEEEEeCCeEEEecccCCCC
Confidence 9999999998888873 334699999964
No 37
>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=73.66 E-value=1.5 Score=24.67 Aligned_cols=23 Identities=26% Similarity=0.652 Sum_probs=17.8
Q ss_pred eCCCCCceeEEeeecceeEEcCCCCeee
Q psy2574 36 KCPGCYKITTVFSHAQSVVICAGCSTIL 63 (115)
Q Consensus 36 KCp~C~n~q~VFSHAqt~V~C~~Cg~vL 63 (115)
+||+|+.+- +.....|..||..+
T Consensus 2 ~CP~C~~~V-----~~~~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEV-----PESAKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCc-----hhhcCcCCCCCCCC
Confidence 589998765 66778898888765
No 38
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=73.23 E-value=4 Score=29.54 Aligned_cols=27 Identities=26% Similarity=0.560 Sum_probs=23.2
Q ss_pred EeCCCCCceeEEeee--cceeEEcCCCCe
Q psy2574 35 VKCPGCYKITTVFSH--AQSVVICAGCST 61 (115)
Q Consensus 35 VKCp~C~n~q~VFSH--Aqt~V~C~~Cg~ 61 (115)
|.|+.|++.-+.+.. -.....|..||.
T Consensus 81 VlC~~C~spdT~l~k~~r~~~l~C~aCGa 109 (110)
T smart00653 81 VLCPECGSPDTELIKENRLFFLKCEACGA 109 (110)
T ss_pred EECCCCCCCCcEEEEeCCeEEEEccccCC
Confidence 999999999888886 556778999995
No 39
>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=72.57 E-value=2.1 Score=24.99 Aligned_cols=18 Identities=44% Similarity=1.082 Sum_probs=15.7
Q ss_pred EEcCCCCeeeecccCCce
Q psy2574 54 VICAGCSTILCQPTGGRA 71 (115)
Q Consensus 54 V~C~~Cg~vL~~PTGGKA 71 (115)
+.|..|++.|.-|.|-+.
T Consensus 2 ~~C~~C~t~L~yP~gA~~ 19 (31)
T TIGR01053 2 VVCGGCRTLLMYPRGASS 19 (31)
T ss_pred cCcCCCCcEeecCCCCCe
Confidence 689999999999998654
No 40
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=72.47 E-value=3.3 Score=26.22 Aligned_cols=29 Identities=21% Similarity=0.356 Sum_probs=22.5
Q ss_pred EEeCCCCCceeEEeeecceeEEcCCCCeeee
Q psy2574 34 DVKCPGCYKITTVFSHAQSVVICAGCSTILC 64 (115)
Q Consensus 34 ~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~ 64 (115)
.--||.|++. +...|. ....|..||-+.-
T Consensus 20 ~~fCP~Cg~~-~m~~~~-~r~~C~~Cgyt~~ 48 (50)
T PRK00432 20 NKFCPRCGSG-FMAEHL-DRWHCGKCGYTEF 48 (50)
T ss_pred cCcCcCCCcc-hheccC-CcEECCCcCCEEe
Confidence 3479999998 777776 6778999997753
No 41
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=71.88 E-value=4.4 Score=30.46 Aligned_cols=28 Identities=29% Similarity=0.540 Sum_probs=23.4
Q ss_pred EeCCCCCceeEEeee--cceeEEcCCCCee
Q psy2574 35 VKCPGCYKITTVFSH--AQSVVICAGCSTI 62 (115)
Q Consensus 35 VKCp~C~n~q~VFSH--Aqt~V~C~~Cg~v 62 (115)
|.|+.|++.-|.+.. -.....|..||..
T Consensus 103 VlC~~C~spdT~l~k~~r~~~l~C~ACGa~ 132 (138)
T PRK03988 103 VICPECGSPDTKLIKEGRIWVLKCEACGAE 132 (138)
T ss_pred EECCCCCCCCcEEEEcCCeEEEEcccCCCC
Confidence 999999999988876 3357899999964
No 42
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=71.79 E-value=3.6 Score=29.77 Aligned_cols=29 Identities=24% Similarity=0.517 Sum_probs=25.5
Q ss_pred EEeCCCCCceeEEeeeccee---------EEcCCCCee
Q psy2574 34 DVKCPGCYKITTVFSHAQSV---------VICAGCSTI 62 (115)
Q Consensus 34 ~VKCp~C~n~q~VFSHAqt~---------V~C~~Cg~v 62 (115)
+++||.|++....|=-.|+- ..|..||.+
T Consensus 72 ~~~CpkCg~~ea~y~~~QtRsaDEp~T~Fy~C~~Cg~~ 109 (113)
T COG1594 72 KEKCPKCGNKEAYYWQLQTRSADEPETRFYKCTRCGYR 109 (113)
T ss_pred cccCCCCCCceeEEEeeehhccCCCceEEEEecccCCE
Confidence 67999999999999887775 899999875
No 43
>KOG1597|consensus
Probab=71.68 E-value=3 Score=35.66 Aligned_cols=42 Identities=21% Similarity=0.512 Sum_probs=30.6
Q ss_pred eCCCCCcee--EEeeecceeEEcCCCCeeeecccCCceeeccCCCCccE
Q psy2574 36 KCPGCYKIT--TVFSHAQSVVICAGCSTILCQPTGGRARLTEDDTGDSM 82 (115)
Q Consensus 36 KCp~C~n~q--~VFSHAqt~V~C~~Cg~vL~~PTGGKA~l~egc~f~s~ 82 (115)
.|++|..-+ +|.+|...-..|..||-+|- --.|-++-.+.|.
T Consensus 2 ~c~~C~~~~~~~V~d~~~gdtvC~~CGlVl~-----~r~Id~~sEwrtf 45 (308)
T KOG1597|consen 2 TCPDCKRHPENLVEDHSAGDTVCSECGLVLE-----DRIIDEGSEWRTF 45 (308)
T ss_pred CCCCCCCCCCCeeeeccCCceecccCCeeec-----ccccccccccccc
Confidence 477776544 79999999999999999993 3345555555444
No 44
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=70.08 E-value=3 Score=28.13 Aligned_cols=26 Identities=19% Similarity=0.657 Sum_probs=20.8
Q ss_pred cccCCCCceeEEeCCCCCceeEEeee
Q psy2574 24 LVQHPNSYFMDVKCPGCYKITTVFSH 49 (115)
Q Consensus 24 LV~~PnS~Fm~VKCp~C~n~q~VFSH 49 (115)
|...--+.++.+|||.|..++-+++.
T Consensus 14 La~a~~~~yle~KCPrCK~vN~~~~~ 39 (60)
T COG4416 14 LAEAEGQAYLEKKCPRCKEVNEFYIK 39 (60)
T ss_pred HHhcccceeeeecCCccceeeeeecc
Confidence 44445667999999999999988875
No 45
>PHA00626 hypothetical protein
Probab=67.98 E-value=5.2 Score=26.97 Aligned_cols=31 Identities=16% Similarity=0.381 Sum_probs=22.8
Q ss_pred eCCCCCceeEEeeec----ceeEEcCCCCeeeecc
Q psy2574 36 KCPGCYKITTVFSHA----QSVVICAGCSTILCQP 66 (115)
Q Consensus 36 KCp~C~n~q~VFSHA----qt~V~C~~Cg~vL~~P 66 (115)
+||.|+..+|+=+-. +..-.|..||-....-
T Consensus 2 ~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~ 36 (59)
T PHA00626 2 SCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSKD 36 (59)
T ss_pred CCCCCCCceeeeeceecccCcceEcCCCCCeechh
Confidence 699999998884321 4567899999877553
No 46
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=67.93 E-value=2.6 Score=30.34 Aligned_cols=36 Identities=19% Similarity=0.500 Sum_probs=24.1
Q ss_pred eEEeCCCCCceeEEeeeccee-EEcCCCCeeeecccCCce
Q psy2574 33 MDVKCPGCYKITTVFSHAQSV-VICAGCSTILCQPTGGRA 71 (115)
Q Consensus 33 m~VKCp~C~n~q~VFSHAqt~-V~C~~Cg~vL~~PTGGKA 71 (115)
..++|.+|++. |+-.... ..|+.||..-.+-.+|+-
T Consensus 70 ~~~~C~~Cg~~---~~~~~~~~~~CP~Cgs~~~~i~~G~E 106 (117)
T PRK00564 70 VELECKDCSHV---FKPNALDYGVCEKCHSKNVIITQGNE 106 (117)
T ss_pred CEEEhhhCCCc---cccCCccCCcCcCCCCCceEEecCCE
Confidence 45899999954 4443333 359999987766666653
No 47
>KOG3507|consensus
Probab=67.85 E-value=5.4 Score=27.14 Aligned_cols=34 Identities=24% Similarity=0.467 Sum_probs=28.3
Q ss_pred CCCceeEEeCCCCCceeEEeeecceeEEcCCCCeee
Q psy2574 28 PNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTIL 63 (115)
Q Consensus 28 PnS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL 63 (115)
|++.=|.--|.+|+.++++ .+.-+|.|..||--+
T Consensus 14 ~r~~~miYiCgdC~~en~l--k~~D~irCReCG~RI 47 (62)
T KOG3507|consen 14 PRTATMIYICGDCGQENTL--KRGDVIRCRECGYRI 47 (62)
T ss_pred CCcccEEEEeccccccccc--cCCCcEehhhcchHH
Confidence 4677789999999999998 456799999999643
No 48
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=67.81 E-value=4.8 Score=28.80 Aligned_cols=36 Identities=17% Similarity=0.385 Sum_probs=26.6
Q ss_pred cCCCCceeEEeCCCCCceeEEeeecceeEEcCCCCee
Q psy2574 26 QHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTI 62 (115)
Q Consensus 26 ~~PnS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~v 62 (115)
....--|+...|++|+.+.+++- +=-.-.|+.||..
T Consensus 34 rt~~~G~~~~~C~~Cg~~~~~~~-SCk~R~CP~C~~~ 69 (111)
T PF14319_consen 34 RTEALGFHRYRCEDCGHEKIVYN-SCKNRHCPSCQAK 69 (111)
T ss_pred CCccCCcceeecCCCCceEEecC-cccCcCCCCCCCh
Confidence 34566799999999999996653 3333388888865
No 49
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=67.77 E-value=9 Score=22.48 Aligned_cols=29 Identities=21% Similarity=0.366 Sum_probs=23.2
Q ss_pred EEeCCCCCceeEEeeecceeEEcCCCCeee
Q psy2574 34 DVKCPGCYKITTVFSHAQSVVICAGCSTIL 63 (115)
Q Consensus 34 ~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL 63 (115)
..+|.+|+..-+++ -.+.--.|..||.+-
T Consensus 3 ~~~C~~C~~~~i~~-~~~~~~~C~~Cg~~~ 31 (33)
T PF08792_consen 3 LKKCSKCGGNGIVN-KEDDYEVCIFCGSSF 31 (33)
T ss_pred ceEcCCCCCCeEEE-ecCCeEEcccCCcEe
Confidence 36899999988666 667778899999864
No 50
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=67.49 E-value=5.9 Score=30.99 Aligned_cols=28 Identities=21% Similarity=0.431 Sum_probs=23.4
Q ss_pred EeCCCCCceeEEeee--cceeEEcCCCCee
Q psy2574 35 VKCPGCYKITTVFSH--AQSVVICAGCSTI 62 (115)
Q Consensus 35 VKCp~C~n~q~VFSH--Aqt~V~C~~Cg~v 62 (115)
|.|+.|++.-|.+-. -.....|..||..
T Consensus 99 V~C~~C~~pdT~l~k~~~~~~l~C~aCGa~ 128 (201)
T PRK12336 99 VICSECGLPDTRLVKEDRVLMLRCDACGAH 128 (201)
T ss_pred EECCCCCCCCcEEEEcCCeEEEEcccCCCC
Confidence 999999999888876 4456799999974
No 51
>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=66.13 E-value=5.9 Score=26.48 Aligned_cols=8 Identities=38% Similarity=1.082 Sum_probs=3.6
Q ss_pred eEEcCCCC
Q psy2574 53 VVICAGCS 60 (115)
Q Consensus 53 ~V~C~~Cg 60 (115)
+|.|..||
T Consensus 36 ~v~C~~CG 43 (64)
T PF09855_consen 36 TVSCTNCG 43 (64)
T ss_pred EEECCCCC
Confidence 44444444
No 52
>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=65.44 E-value=2.1 Score=25.17 Aligned_cols=25 Identities=16% Similarity=0.384 Sum_probs=17.3
Q ss_pred eCCCCCceeEEeeecceeEEcCCCCee
Q psy2574 36 KCPGCYKITTVFSHAQSVVICAGCSTI 62 (115)
Q Consensus 36 KCp~C~n~q~VFSHAqt~V~C~~Cg~v 62 (115)
+|.+|+.+..+- +..+|.|..||.-
T Consensus 2 ~C~~Cg~~~~~~--~~~~irC~~CG~R 26 (32)
T PF03604_consen 2 ICGECGAEVELK--PGDPIRCPECGHR 26 (32)
T ss_dssp BESSSSSSE-BS--TSSTSSBSSSS-S
T ss_pred CCCcCCCeeEcC--CCCcEECCcCCCe
Confidence 588898887733 4567899999854
No 53
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=65.30 E-value=9.4 Score=25.59 Aligned_cols=34 Identities=18% Similarity=0.486 Sum_probs=20.6
Q ss_pred CCCCceeEEeCCCCCceeEEee----ecceeEEcCCCC
Q psy2574 27 HPNSYFMDVKCPGCYKITTVFS----HAQSVVICAGCS 60 (115)
Q Consensus 27 ~PnS~Fm~VKCp~C~n~q~VFS----HAqt~V~C~~Cg 60 (115)
.|+.++..-.||+|+++.|.=. .-+....|..||
T Consensus 18 ~~~~~~~~F~CPnCG~~~I~RC~~CRk~~~~Y~CP~CG 55 (59)
T PRK14890 18 APREKAVKFLCPNCGEVIIYRCEKCRKQSNPYTCPKCG 55 (59)
T ss_pred cCCCccCEeeCCCCCCeeEeechhHHhcCCceECCCCC
Confidence 4566678888999987544321 223445666665
No 54
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=65.21 E-value=3.5 Score=29.95 Aligned_cols=39 Identities=23% Similarity=0.434 Sum_probs=24.2
Q ss_pred eEEeCCCCCceeEE--eeecce--eEEcCCCCeeeecccCCcee
Q psy2574 33 MDVKCPGCYKITTV--FSHAQS--VVICAGCSTILCQPTGGRAR 72 (115)
Q Consensus 33 m~VKCp~C~n~q~V--FSHAqt--~V~C~~Cg~vL~~PTGGKA~ 72 (115)
...+| +|+..-.+ +..... ...|+.||..-.+-.+|+--
T Consensus 69 ~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~~~i~~G~El 111 (124)
T PRK00762 69 VEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKRAHILGGREC 111 (124)
T ss_pred eeEEe-eCcCcccccccchhccccCCcCcCCCCCCCEEecCCeE
Confidence 45899 99966222 222112 25799999777666666643
No 55
>PRK08197 threonine synthase; Validated
Probab=64.27 E-value=5.8 Score=33.09 Aligned_cols=32 Identities=28% Similarity=0.668 Sum_probs=23.9
Q ss_pred CCCceeEEeCCCCCceeEEeeecceeEEcCCCCeee
Q psy2574 28 PNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTIL 63 (115)
Q Consensus 28 PnS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL 63 (115)
|.++|...+|..|+.+ |+-......| .||-.|
T Consensus 1 ~~~~~~~~~C~~Cg~~---~~~~~~~~~C-~cg~~l 32 (394)
T PRK08197 1 PFSYVSHLECSKCGET---YDADQVHNLC-KCGKPL 32 (394)
T ss_pred CCceeeEEEECCCCCC---CCCCCcceec-CCCCee
Confidence 4577888999999987 5555556789 797654
No 56
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=64.05 E-value=9 Score=22.61 Aligned_cols=27 Identities=26% Similarity=0.624 Sum_probs=12.2
Q ss_pred eCCCCCceeEEeeec-ceeEEcCCCCee
Q psy2574 36 KCPGCYKITTVFSHA-QSVVICAGCSTI 62 (115)
Q Consensus 36 KCp~C~n~q~VFSHA-qt~V~C~~Cg~v 62 (115)
+||.|.+.-....-. -.+-.|..|+-+
T Consensus 1 ~CP~C~~~l~~~~~~~~~id~C~~C~G~ 28 (41)
T PF13453_consen 1 KCPRCGTELEPVRLGDVEIDVCPSCGGI 28 (41)
T ss_pred CcCCCCcccceEEECCEEEEECCCCCeE
Confidence 466666533222222 233346666543
No 57
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=63.24 E-value=12 Score=26.67 Aligned_cols=35 Identities=20% Similarity=0.376 Sum_probs=26.5
Q ss_pred ceeEEeCCCCCceeEEeeecce-eEEcCCCCeeeec
Q psy2574 31 YFMDVKCPGCYKITTVFSHAQS-VVICAGCSTILCQ 65 (115)
Q Consensus 31 ~Fm~VKCp~C~n~q~VFSHAqt-~V~C~~Cg~vL~~ 65 (115)
+-....|++|+.+......... .-.|..|+..|.+
T Consensus 120 ~~~~~~C~~C~~~~~r~~~~~~~~~~C~~C~~~l~~ 155 (157)
T PF10263_consen 120 KKYVYRCPSCGREYKRHRRSKRKRYRCGRCGGPLVQ 155 (157)
T ss_pred cceEEEcCCCCCEeeeecccchhhEECCCCCCEEEE
Confidence 5567899999998766666532 3479999998864
No 58
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=62.47 E-value=5.2 Score=29.38 Aligned_cols=40 Identities=28% Similarity=0.634 Sum_probs=26.4
Q ss_pred ccccCCCCceeEEeCCCCCceeEEeeeccee------EEcCCCCeeeec
Q psy2574 23 RLVQHPNSYFMDVKCPGCYKITTVFSHAQSV------VICAGCSTILCQ 65 (115)
Q Consensus 23 rLV~~PnS~Fm~VKCp~C~n~q~VFSHAqt~------V~C~~Cg~vL~~ 65 (115)
+|-+..+..| ..||.|+. +..|.-|... ..|+.||..|-.
T Consensus 90 ~l~~e~~~~~--Y~Cp~C~~-~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~ 135 (147)
T smart00531 90 KLEDETNNAY--YKCPNCQS-KYTFLEANQLLDMDGTFTCPRCGEELEE 135 (147)
T ss_pred HHhcccCCcE--EECcCCCC-EeeHHHHHHhcCCCCcEECCCCCCEEEE
Confidence 4555555554 57999974 4445444332 899999999854
No 59
>PF03884 DUF329: Domain of unknown function (DUF329); InterPro: IPR005584 The biological function of these short proteins is unknown, but they contain four conserved cysteines, suggesting that they all bind zinc. YacG (Q5X8H6 from SWISSPROT) from Escherichia coli has been shown to bind zinc and contains the structural motifs typical of zinc-binding proteins []. The conserved four cysteine motif in these proteins (-C-X(2)-C-X(15)-C-X(3)-C-) is not found in other zinc-binding proteins with known structures.; GO: 0008270 zinc ion binding; PDB: 1LV3_A.
Probab=61.74 E-value=5.7 Score=26.15 Aligned_cols=14 Identities=50% Similarity=0.736 Sum_probs=6.5
Q ss_pred eEEeCCCCCceeEE
Q psy2574 33 MDVKCPGCYKITTV 46 (115)
Q Consensus 33 m~VKCp~C~n~q~V 46 (115)
|.|+||.|++....
T Consensus 1 m~v~CP~C~k~~~~ 14 (57)
T PF03884_consen 1 MTVKCPICGKPVEW 14 (57)
T ss_dssp -EEE-TTT--EEE-
T ss_pred CcccCCCCCCeecc
Confidence 67888888776544
No 60
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=61.60 E-value=9.8 Score=22.93 Aligned_cols=31 Identities=26% Similarity=0.563 Sum_probs=22.8
Q ss_pred EeCC--CCCceeEEee-ecceeEEcCCCCeeeec
Q psy2574 35 VKCP--GCYKITTVFS-HAQSVVICAGCSTILCQ 65 (115)
Q Consensus 35 VKCp--~C~n~q~VFS-HAqt~V~C~~Cg~vL~~ 65 (115)
.-|| +|..+....+ -....|.|..|+...+-
T Consensus 19 ~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~ 52 (64)
T smart00647 19 KWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCF 52 (64)
T ss_pred cCCCCCCCcceEEecCCCCCCeeECCCCCCeECC
Confidence 4699 9988776652 24568999999887764
No 61
>PRK05978 hypothetical protein; Provisional
Probab=61.37 E-value=3.2 Score=31.79 Aligned_cols=39 Identities=18% Similarity=0.275 Sum_probs=29.6
Q ss_pred CCCceeEEeCCCCCceeEEeeecceeEEcCCCCeeeecc
Q psy2574 28 PNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQP 66 (115)
Q Consensus 28 PnS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~P 66 (115)
|=.+=++-|||.|++-.+-=+--...-.|..||..+-.=
T Consensus 27 ~~~rGl~grCP~CG~G~LF~g~Lkv~~~C~~CG~~~~~~ 65 (148)
T PRK05978 27 AMWRGFRGRCPACGEGKLFRAFLKPVDHCAACGEDFTHH 65 (148)
T ss_pred HHHHHHcCcCCCCCCCcccccccccCCCccccCCccccC
Confidence 333446789999999887666667888999999887543
No 62
>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=60.71 E-value=11 Score=22.73 Aligned_cols=27 Identities=19% Similarity=0.459 Sum_probs=20.1
Q ss_pred EeCCCCCceeEEeeecceeEEcCCCCe
Q psy2574 35 VKCPGCYKITTVFSHAQSVVICAGCST 61 (115)
Q Consensus 35 VKCp~C~n~q~VFSHAqt~V~C~~Cg~ 61 (115)
+.||.|++..+.+=.....-.|..|+.
T Consensus 19 ~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred CCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 559999999444444448889999975
No 63
>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=60.69 E-value=7.7 Score=22.59 Aligned_cols=25 Identities=28% Similarity=0.643 Sum_probs=13.0
Q ss_pred eCCCCCceeEEeeecceeEEcCCCCee
Q psy2574 36 KCPGCYKITTVFSHAQSVVICAGCSTI 62 (115)
Q Consensus 36 KCp~C~n~q~VFSHAqt~V~C~~Cg~v 62 (115)
|||.|+.+.+. +-.....|..|+..
T Consensus 4 ~Cp~C~se~~y--~D~~~~vCp~C~~e 28 (30)
T PF08274_consen 4 KCPLCGSEYTY--EDGELLVCPECGHE 28 (30)
T ss_dssp --TTT-----E--E-SSSEEETTTTEE
T ss_pred CCCCCCCccee--ccCCEEeCCccccc
Confidence 79999999888 55566778888864
No 64
>PRK07591 threonine synthase; Validated
Probab=60.45 E-value=6.6 Score=33.33 Aligned_cols=31 Identities=19% Similarity=0.382 Sum_probs=24.0
Q ss_pred CceeEEeCCCCCceeEEeeecceeEEcCCCCeeee
Q psy2574 30 SYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILC 64 (115)
Q Consensus 30 S~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~ 64 (115)
++|...+|..|+.+ |.-... ..|..||..|-
T Consensus 14 ~~~~~l~C~~Cg~~---~~~~~~-~~C~~cg~~l~ 44 (421)
T PRK07591 14 GPAVALKCRECGAE---YPLGPI-HVCEECFGPLE 44 (421)
T ss_pred cceeEEEeCCCCCc---CCCCCC-ccCCCCCCeEE
Confidence 77889999999987 443344 88999987663
No 65
>PHA02998 RNA polymerase subunit; Provisional
Probab=59.41 E-value=7.6 Score=31.43 Aligned_cols=35 Identities=23% Similarity=0.483 Sum_probs=28.9
Q ss_pred eEEeCCCCCceeEEeeecce---------eEEcCCCCeeeeccc
Q psy2574 33 MDVKCPGCYKITTVFSHAQS---------VVICAGCSTILCQPT 67 (115)
Q Consensus 33 m~VKCp~C~n~q~VFSHAqt---------~V~C~~Cg~vL~~PT 67 (115)
.+++||.|++....|-.-|+ -..|..||...-.|.
T Consensus 142 t~v~CPkCg~~~A~f~qlQTRSADEPmT~FYkC~~CG~~wkppk 185 (195)
T PHA02998 142 YNTPCPNCKSKNTTPMMIQTRAADEPPLVRHACRDCKKHFKPPK 185 (195)
T ss_pred cCCCCCCCCCCceEEEEEeeccCCCCceEEEEcCCCCCccCCcc
Confidence 45899999999999987665 468999999887664
No 66
>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=59.24 E-value=4.3 Score=24.20 Aligned_cols=31 Identities=29% Similarity=0.655 Sum_probs=23.5
Q ss_pred EeCCCCCceeEE-eeecceeEEcCCCCeeeec
Q psy2574 35 VKCPGCYKITTV-FSHAQSVVICAGCSTILCQ 65 (115)
Q Consensus 35 VKCp~C~n~q~V-FSHAqt~V~C~~Cg~vL~~ 65 (115)
.-|+.|+.+--+ |.-+...-.|..||..|.|
T Consensus 2 r~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~~L~q 33 (36)
T PF05191_consen 2 RICPKCGRIYHIEFNPPKVEGVCDNCGGELVQ 33 (36)
T ss_dssp EEETTTTEEEETTTB--SSTTBCTTTTEBEBE
T ss_pred cCcCCCCCccccccCCCCCCCccCCCCCeeEe
Confidence 468999987544 7777888999999998875
No 67
>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=58.93 E-value=7.8 Score=24.94 Aligned_cols=21 Identities=24% Similarity=0.472 Sum_probs=13.8
Q ss_pred EeCCCCCceeEEeeecceeEEcC
Q psy2574 35 VKCPGCYKITTVFSHAQSVVICA 57 (115)
Q Consensus 35 VKCp~C~n~q~VFSHAqt~V~C~ 57 (115)
-+||.|.+-|++|+.. ...|.
T Consensus 15 ~~Cp~C~~~~l~~~~~--~Y~C~ 35 (55)
T PF08063_consen 15 EPCPKCKGGQLYFDGS--GYKCT 35 (55)
T ss_dssp ---SSSSE-EEEEETT--EEEEE
T ss_pred CCCCCCCCCeEEecCC--ccEeC
Confidence 4799999999999877 45554
No 68
>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=58.77 E-value=9.1 Score=28.23 Aligned_cols=28 Identities=25% Similarity=0.502 Sum_probs=23.4
Q ss_pred EeCCCCCceeEEee--ecceeEEcCCCCee
Q psy2574 35 VKCPGCYKITTVFS--HAQSVVICAGCSTI 62 (115)
Q Consensus 35 VKCp~C~n~q~VFS--HAqt~V~C~~Cg~v 62 (115)
|.|+.|++..+.+. --.....|..||..
T Consensus 94 VlC~~C~spdT~l~k~~r~~~l~C~aCGa~ 123 (125)
T PF01873_consen 94 VLCPECGSPDTELIKEGRLIFLKCKACGAS 123 (125)
T ss_dssp SSCTSTSSSSEEEEEETTCCEEEETTTSCE
T ss_pred EEcCCCCCCccEEEEcCCEEEEEecccCCc
Confidence 89999999888876 35677899999964
No 69
>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=58.76 E-value=8.6 Score=25.16 Aligned_cols=19 Identities=32% Similarity=0.690 Sum_probs=15.0
Q ss_pred CceeEEeCCCCCceeEEee
Q psy2574 30 SYFMDVKCPGCYKITTVFS 48 (115)
Q Consensus 30 S~Fm~VKCp~C~n~q~VFS 48 (115)
-..+.+|||.|+.++.|=+
T Consensus 20 ~~~leIKCpRC~tiN~~~a 38 (51)
T PF10122_consen 20 VIELEIKCPRCKTINHVRA 38 (51)
T ss_pred ccEEEEECCCCCccceEec
Confidence 3458999999999987743
No 70
>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=57.94 E-value=4.5 Score=24.39 Aligned_cols=47 Identities=30% Similarity=0.515 Sum_probs=23.7
Q ss_pred cccccccCCCCceeEEeCCC--CCceeEEeeeccee-EEcCCCCeeeecccCC
Q psy2574 20 KLKRLVQHPNSYFMDVKCPG--CYKITTVFSHAQSV-VICAGCSTILCQPTGG 69 (115)
Q Consensus 20 K~krLV~~PnS~Fm~VKCp~--C~n~q~VFSHAqt~-V~C~~Cg~vL~~PTGG 69 (115)
+.++.|....+. ..||. |.....+-+..... |.|..|+...|-==++
T Consensus 7 ~~~~~~~~~~~~---~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~ 56 (64)
T PF01485_consen 7 LLKRYLESDPNI---RWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGE 56 (64)
T ss_dssp CCHS---S---C---C--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTS
T ss_pred HHHHHHHCCCCc---cCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCc
Confidence 345555433333 38977 99988877777764 9999999988754433
No 71
>PRK12496 hypothetical protein; Provisional
Probab=57.70 E-value=4.6 Score=30.67 Aligned_cols=28 Identities=21% Similarity=0.530 Sum_probs=20.2
Q ss_pred EeCCCCCceeEEeeecceeEEcCCCCeeeec
Q psy2574 35 VKCPGCYKITTVFSHAQSVVICAGCSTILCQ 65 (115)
Q Consensus 35 VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~ 65 (115)
-.|++|+++ |...-..-.|.+||..|-+
T Consensus 128 ~~C~gC~~~---~~~~~~~~~C~~CG~~~~r 155 (164)
T PRK12496 128 KVCKGCKKK---YPEDYPDDVCEICGSPVKR 155 (164)
T ss_pred EECCCCCcc---ccCCCCCCcCCCCCChhhh
Confidence 459999964 5544444579999998743
No 72
>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=56.55 E-value=3.4 Score=29.40 Aligned_cols=35 Identities=17% Similarity=0.347 Sum_probs=21.2
Q ss_pred eEEeCCCCCceeEEeeecceeEEcCCCCeeeecccCCc
Q psy2574 33 MDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGR 70 (115)
Q Consensus 33 m~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PTGGK 70 (115)
..++|.+|+.+-- -......|+.||..-.+=.+|+
T Consensus 69 ~~~~C~~Cg~~~~---~~~~~~~CP~Cgs~~~~i~~G~ 103 (113)
T PF01155_consen 69 ARARCRDCGHEFE---PDEFDFSCPRCGSPDVEIISGR 103 (113)
T ss_dssp -EEEETTTS-EEE---CHHCCHH-SSSSSS-EEEEESS
T ss_pred CcEECCCCCCEEe---cCCCCCCCcCCcCCCcEEccCC
Confidence 4689999998644 3334466999998765555554
No 73
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=56.38 E-value=13 Score=28.18 Aligned_cols=36 Identities=19% Similarity=0.485 Sum_probs=27.1
Q ss_pred ccccccCCCCceeEEeCCCCCceeEEeeecceeEEcCCCCee
Q psy2574 21 LKRLVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTI 62 (115)
Q Consensus 21 ~krLV~~PnS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~v 62 (115)
-..+|-..+.++-...|+-|+. -+.....|..||.+
T Consensus 296 ~~~~v~~~~~~~tS~~C~~cg~------~~~r~~~C~~cg~~ 331 (364)
T COG0675 296 GGIVVKVVPPYYTSKTCPCCGH------LSGRLFKCPRCGFV 331 (364)
T ss_pred CCeEEEECCCCCCcccccccCC------ccceeEECCCCCCe
Confidence 4455555566666789999999 34678899999986
No 74
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=56.00 E-value=13 Score=27.41 Aligned_cols=22 Identities=32% Similarity=0.720 Sum_probs=19.4
Q ss_pred CCCCCceeEEeeecceeEEcCCCCeee
Q psy2574 37 CPGCYKITTVFSHAQSVVICAGCSTIL 63 (115)
Q Consensus 37 Cp~C~n~q~VFSHAqt~V~C~~Cg~vL 63 (115)
||-|++.-+| |...|..|++.+
T Consensus 1 CPvCg~~l~v-----t~l~C~~C~t~i 22 (113)
T PF09862_consen 1 CPVCGGELVV-----TRLKCPSCGTEI 22 (113)
T ss_pred CCCCCCceEE-----EEEEcCCCCCEE
Confidence 8999988776 789999999987
No 75
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=55.96 E-value=15 Score=22.67 Aligned_cols=25 Identities=24% Similarity=0.644 Sum_probs=18.8
Q ss_pred CCCCCceeEEeeecc-------eeEEcCCCCe
Q psy2574 37 CPGCYKITTVFSHAQ-------SVVICAGCST 61 (115)
Q Consensus 37 Cp~C~n~q~VFSHAq-------t~V~C~~Cg~ 61 (115)
||=|+...+...... ..|.|..||.
T Consensus 6 CPFCG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 6 CPFCGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CCCCCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 888877776666533 5688999988
No 76
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=54.88 E-value=10 Score=22.57 Aligned_cols=27 Identities=19% Similarity=0.460 Sum_probs=14.7
Q ss_pred CCCCCceeEEeeecc-eeEEcCCCCeee
Q psy2574 37 CPGCYKITTVFSHAQ-SVVICAGCSTIL 63 (115)
Q Consensus 37 Cp~C~n~q~VFSHAq-t~V~C~~Cg~vL 63 (115)
||.|++.-..=.-.+ ....|..||...
T Consensus 3 Cp~Cg~~l~~~~~~~~~~~vC~~Cg~~~ 30 (52)
T smart00661 3 CPKCGNMLIPKEGKEKRRFVCRKCGYEE 30 (52)
T ss_pred CCCCCCccccccCCCCCEEECCcCCCeE
Confidence 777877332211222 256688887654
No 77
>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=54.67 E-value=19 Score=24.13 Aligned_cols=35 Identities=23% Similarity=0.373 Sum_probs=28.2
Q ss_pred EeCCCCCceeE---EeeecceeEEcCCCCeeeecccCC
Q psy2574 35 VKCPGCYKITT---VFSHAQSVVICAGCSTILCQPTGG 69 (115)
Q Consensus 35 VKCp~C~n~q~---VFSHAqt~V~C~~Cg~vL~~PTGG 69 (115)
.+||.|...-. ...+-.-.|.|..||-.-.+|+.+
T Consensus 10 A~CP~C~~~Dtl~~~~e~~~e~vECv~Cg~~~~~~~~~ 47 (59)
T TIGR02443 10 AVCPACSAQDTLAMWKENNIELVECVECGYQEQQKDQS 47 (59)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEeccCCCccccCCcc
Confidence 68999987544 345667789999999999999876
No 78
>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=53.84 E-value=17 Score=24.95 Aligned_cols=29 Identities=17% Similarity=0.615 Sum_probs=18.0
Q ss_pred eeEEeCCCCCceeEEeeec-ceeEEcCCCCeeee
Q psy2574 32 FMDVKCPGCYKITTVFSHA-QSVVICAGCSTILC 64 (115)
Q Consensus 32 Fm~VKCp~C~n~q~VFSHA-qt~V~C~~Cg~vL~ 64 (115)
|+-.+| +|++. ++++- +-.-.| .||++|-
T Consensus 1 ylifrC-~Cgr~--lya~e~~kTkkC-~CG~~l~ 30 (68)
T PF09082_consen 1 YLIFRC-DCGRY--LYAKEGAKTKKC-VCGKTLK 30 (68)
T ss_dssp EEEEEE-TTS----EEEETT-SEEEE-TTTEEEE
T ss_pred CEEEEe-cCCCE--EEecCCcceeEe-cCCCeee
Confidence 466789 89875 44543 344578 9999874
No 79
>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=53.69 E-value=18 Score=19.91 Aligned_cols=26 Identities=27% Similarity=0.783 Sum_probs=16.0
Q ss_pred eCCCCCceeEEeee-cceeEEcCCCCe
Q psy2574 36 KCPGCYKITTVFSH-AQSVVICAGCST 61 (115)
Q Consensus 36 KCp~C~n~q~VFSH-Aqt~V~C~~Cg~ 61 (115)
+|+-|.+...-... ......|..|..
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 68999987665554 667788888864
No 80
>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=53.42 E-value=12 Score=31.32 Aligned_cols=28 Identities=21% Similarity=0.558 Sum_probs=22.6
Q ss_pred EEeCCCCCceeEEeeecc---------eeEEcCCCCe
Q psy2574 34 DVKCPGCYKITTVFSHAQ---------SVVICAGCST 61 (115)
Q Consensus 34 ~VKCp~C~n~q~VFSHAq---------t~V~C~~Cg~ 61 (115)
.++|+.|++..++|-..| +.+.|..||.
T Consensus 258 ~~~C~~C~~~~~~~~q~QtrsaDEpmT~f~~C~~Cg~ 294 (299)
T TIGR01385 258 LFTCGKCKQKKCTYYQLQTRSADEPMTTFVTCEECGN 294 (299)
T ss_pred cccCCCCCCccceEEEecccCCCCCCeEEEEcCCCCC
Confidence 489999999999998765 4567888774
No 81
>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=52.62 E-value=15 Score=21.77 Aligned_cols=26 Identities=23% Similarity=0.511 Sum_probs=21.3
Q ss_pred eCCCCCceeEEeeecceeEEcCCCCeee
Q psy2574 36 KCPGCYKITTVFSHAQSVVICAGCSTIL 63 (115)
Q Consensus 36 KCp~C~n~q~VFSHAqt~V~C~~Cg~vL 63 (115)
.|+.|++. .|.-..-...|..||++.
T Consensus 10 ~C~~C~~~--~~~~~dG~~yC~~cG~~~ 35 (36)
T PF11781_consen 10 PCPVCGSR--WFYSDDGFYYCDRCGHQS 35 (36)
T ss_pred cCCCCCCe--EeEccCCEEEhhhCceEc
Confidence 49999988 777788888898888764
No 82
>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=51.84 E-value=18 Score=24.73 Aligned_cols=39 Identities=18% Similarity=0.432 Sum_probs=16.9
Q ss_pred cccccCCCCceeEEeCCCCCce---eEEeeec--ceeEEcCCCCeee
Q psy2574 22 KRLVQHPNSYFMDVKCPGCYKI---TTVFSHA--QSVVICAGCSTIL 63 (115)
Q Consensus 22 krLV~~PnS~Fm~VKCp~C~n~---q~VFSHA--qt~V~C~~Cg~vL 63 (115)
++..+.....| .||-|+++ .+.++.. ...+.|..||..-
T Consensus 13 kk~~~~l~~~F---~CPfC~~~~sV~v~idkk~~~~~~~C~~Cg~~~ 56 (81)
T PF05129_consen 13 KKKKPKLPKVF---DCPFCNHEKSVSVKIDKKEGIGILSCRVCGESF 56 (81)
T ss_dssp -------SS-------TTT--SS-EEEEEETTTTEEEEEESSS--EE
T ss_pred cCcCCCCCceE---cCCcCCCCCeEEEEEEccCCEEEEEecCCCCeE
Confidence 34445555665 79999954 4445543 6789999997654
No 83
>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=51.20 E-value=12 Score=22.45 Aligned_cols=19 Identities=32% Similarity=0.716 Sum_probs=14.5
Q ss_pred eEEeCCCCCceeEEeeecc
Q psy2574 33 MDVKCPGCYKITTVFSHAQ 51 (115)
Q Consensus 33 m~VKCp~C~n~q~VFSHAq 51 (115)
++|+||-|...+-|.-|-.
T Consensus 4 i~v~CP~C~s~~~v~k~G~ 22 (36)
T PF03811_consen 4 IDVHCPRCQSTEGVKKNGK 22 (36)
T ss_pred EeeeCCCCCCCCcceeCCC
Confidence 6899999999885555543
No 84
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=50.44 E-value=13 Score=30.27 Aligned_cols=31 Identities=23% Similarity=0.557 Sum_probs=21.4
Q ss_pred eEEeCCCCCceeE-----EeeecceeEEcCCCCeee
Q psy2574 33 MDVKCPGCYKITT-----VFSHAQSVVICAGCSTIL 63 (115)
Q Consensus 33 m~VKCp~C~n~q~-----VFSHAqt~V~C~~Cg~vL 63 (115)
+...||.|+.+.+ -+---.-.|.|..||++-
T Consensus 5 iy~~Cp~Cg~eev~hEVik~~g~~~lvrC~eCG~V~ 40 (201)
T COG1326 5 IYIECPSCGSEEVSHEVIKERGREPLVRCEECGTVH 40 (201)
T ss_pred EEEECCCCCcchhhHHHHHhcCCceEEEccCCCcEe
Confidence 4578999995544 121223689999999976
No 85
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=50.42 E-value=13 Score=28.12 Aligned_cols=29 Identities=31% Similarity=0.668 Sum_probs=24.3
Q ss_pred CceeEEeCCCCCceeEEeeecceeEEcCCCCeee
Q psy2574 30 SYFMDVKCPGCYKITTVFSHAQSVVICAGCSTIL 63 (115)
Q Consensus 30 S~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL 63 (115)
||=|--+||.|+..-+| |...|..|++++
T Consensus 2 ~~~~~~~cPvcg~~~iV-----TeL~c~~~etTV 30 (122)
T COG3877 2 SYKVINRCPVCGRKLIV-----TELKCSNCETTV 30 (122)
T ss_pred CCCCCCCCCccccccee-----EEEecCCCCceE
Confidence 34456789999999987 788999999987
No 86
>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=49.54 E-value=12 Score=21.22 Aligned_cols=15 Identities=47% Similarity=1.114 Sum_probs=13.0
Q ss_pred cCCCCeeeecccCCc
Q psy2574 56 CAGCSTILCQPTGGR 70 (115)
Q Consensus 56 C~~Cg~vL~~PTGGK 70 (115)
|.+|.++|.-|.|-.
T Consensus 1 C~~Cr~~L~yp~GA~ 15 (25)
T PF06943_consen 1 CGGCRTLLMYPRGAP 15 (25)
T ss_pred CCCCCceEEcCCCCC
Confidence 789999999999854
No 87
>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=49.43 E-value=11 Score=28.54 Aligned_cols=28 Identities=18% Similarity=0.529 Sum_probs=22.6
Q ss_pred EeCCCCCceeEEeeecceeEEcCCCCeee
Q psy2574 35 VKCPGCYKITTVFSHAQSVVICAGCSTIL 63 (115)
Q Consensus 35 VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL 63 (115)
-.|..|+.... |.|+...-.|+.||..-
T Consensus 113 l~C~~Cg~~~~-~~~~~~l~~Cp~C~~~~ 140 (146)
T PF07295_consen 113 LVCENCGHEVE-LTHPERLPPCPKCGHTE 140 (146)
T ss_pred EecccCCCEEE-ecCCCcCCCCCCCCCCe
Confidence 47999987655 56899999999999753
No 88
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=49.03 E-value=8 Score=33.23 Aligned_cols=33 Identities=24% Similarity=0.491 Sum_probs=17.1
Q ss_pred EeCCCCCceeEEeeecceeEEcCCCCeeeecccC
Q psy2574 35 VKCPGCYKITTVFSHAQSVVICAGCSTILCQPTG 68 (115)
Q Consensus 35 VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PTG 68 (115)
.+|++|++-+|.|.. =-...|..||..--+.+|
T Consensus 286 FkC~~C~~Rt~sl~r-~P~~~C~~Cg~~~wer~~ 318 (344)
T PF09332_consen 286 FKCKDCGNRTISLER-LPKKHCSNCGSSKWERTG 318 (344)
T ss_dssp EE-T-TS-EEEESSS-S--S--TTT-S---EEE-
T ss_pred EECCCCCCeeeeccc-CCCCCCCcCCcCceeehh
Confidence 489999999999954 345899999987776664
No 89
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=48.48 E-value=14 Score=24.22 Aligned_cols=22 Identities=36% Similarity=0.634 Sum_probs=16.4
Q ss_pred EeCCCCCceeEEeeecceeEEcCCCCeee
Q psy2574 35 VKCPGCYKITTVFSHAQSVVICAGCSTIL 63 (115)
Q Consensus 35 VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL 63 (115)
.+|+.|+.-++ .-.|..||..+
T Consensus 6 r~C~~CgvYTL-------k~~CP~CG~~t 27 (56)
T PRK13130 6 RKCPKCGVYTL-------KEICPVCGGKT 27 (56)
T ss_pred eECCCCCCEEc-------cccCcCCCCCC
Confidence 57888887776 55688888765
No 90
>PF12773 DZR: Double zinc ribbon
Probab=48.43 E-value=8.6 Score=22.97 Aligned_cols=12 Identities=33% Similarity=0.625 Sum_probs=5.5
Q ss_pred eEEcCCCCeeee
Q psy2574 53 VVICAGCSTILC 64 (115)
Q Consensus 53 ~V~C~~Cg~vL~ 64 (115)
...|..||+.|.
T Consensus 12 ~~fC~~CG~~l~ 23 (50)
T PF12773_consen 12 AKFCPHCGTPLP 23 (50)
T ss_pred ccCChhhcCChh
Confidence 444444444443
No 91
>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.
Probab=47.73 E-value=19 Score=27.50 Aligned_cols=32 Identities=31% Similarity=0.648 Sum_probs=17.7
Q ss_pred eEEeCCCCCceeEE---ee-----ecceeEEcCCCCeeee
Q psy2574 33 MDVKCPGCYKITTV---FS-----HAQSVVICAGCSTILC 64 (115)
Q Consensus 33 m~VKCp~C~n~q~V---FS-----HAqt~V~C~~Cg~vL~ 64 (115)
+.++||.|+.+... |. ....-..|..|+..+.
T Consensus 17 l~~~C~~C~~~~~f~g~~~~~~~~~~~~~~~C~~C~~~~~ 56 (188)
T PF08996_consen 17 LKLTCPSCGTEFEFPGVFEEDGDDVSPSGLQCPNCSTPLS 56 (188)
T ss_dssp EEEE-TTT--EEEE-SSS--SSEEEETTEEEETTT--B--
T ss_pred eEeECCCCCCCccccccccCCccccccCcCcCCCCCCcCC
Confidence 67999999988765 44 3455788999988553
No 92
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=47.16 E-value=9.9 Score=29.52 Aligned_cols=28 Identities=21% Similarity=0.594 Sum_probs=25.1
Q ss_pred eCCCCCceeEEeeecc-eeEEcCCCCeee
Q psy2574 36 KCPGCYKITTVFSHAQ-SVVICAGCSTIL 63 (115)
Q Consensus 36 KCp~C~n~q~VFSHAq-t~V~C~~Cg~vL 63 (115)
-|.-|.+..+||.--. +++.|..|+++.
T Consensus 154 iCe~C~~~~~IfPF~~~~~~~C~~C~~v~ 182 (202)
T PF13901_consen 154 ICEICNSDDIIFPFQIDTTVRCPKCKSVF 182 (202)
T ss_pred CCccCCCCCCCCCCCCCCeeeCCcCcccc
Confidence 5888999999999877 999999999875
No 93
>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=46.88 E-value=27 Score=23.67 Aligned_cols=34 Identities=26% Similarity=0.544 Sum_probs=28.6
Q ss_pred EeCCCCCceeEE---eeecceeEEcCCCCeeeecccC
Q psy2574 35 VKCPGCYKITTV---FSHAQSVVICAGCSTILCQPTG 68 (115)
Q Consensus 35 VKCp~C~n~q~V---FSHAqt~V~C~~Cg~vL~~PTG 68 (115)
..||.|...-.| ..+-.-.|.|..||-.-.+|.-
T Consensus 9 a~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e~~~~~ 45 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRENGVEYVECVECGYTERQPDQ 45 (71)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEecCCCCeeccCCc
Confidence 689999976544 4677889999999999999986
No 94
>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=46.86 E-value=49 Score=23.79 Aligned_cols=30 Identities=17% Similarity=0.380 Sum_probs=23.9
Q ss_pred eeecceeEEcCCCCeeeecccCCceeeccCCC
Q psy2574 47 FSHAQSVVICAGCSTILCQPTGGRARLTEDDT 78 (115)
Q Consensus 47 FSHAqt~V~C~~Cg~vL~~PTGGKA~l~egc~ 78 (115)
|...--.+.|..|++.+..+|=| .+.-||.
T Consensus 46 Y~q~g~~lvC~~C~~~~~~~~ig--~~~GGCN 75 (102)
T PF10080_consen 46 YYQEGDQLVCKNCGVRFNLPTIG--GKSGGCN 75 (102)
T ss_pred eEEECCEEEEecCCCEEehhhcc--cccCCCC
Confidence 33677889999999999999966 4566884
No 95
>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=46.00 E-value=13 Score=25.12 Aligned_cols=18 Identities=28% Similarity=0.689 Sum_probs=10.2
Q ss_pred eeEEeCCCCCceeEEeee
Q psy2574 32 FMDVKCPGCYKITTVFSH 49 (115)
Q Consensus 32 Fm~VKCp~C~n~q~VFSH 49 (115)
-+-|+||+|.|.-.|=+|
T Consensus 27 vViv~C~gC~~~HlIaDn 44 (66)
T PF05180_consen 27 VVIVQCPGCKNRHLIADN 44 (66)
T ss_dssp EEEEE-TTS--EEES--S
T ss_pred eEEEECCCCcceeeehhh
Confidence 367999999998777555
No 96
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=45.02 E-value=28 Score=19.70 Aligned_cols=22 Identities=27% Similarity=0.625 Sum_probs=15.0
Q ss_pred EeCCCCCceeEEeeecceeEEc
Q psy2574 35 VKCPGCYKITTVFSHAQSVVIC 56 (115)
Q Consensus 35 VKCp~C~n~q~VFSHAqt~V~C 56 (115)
-||..|+|+-.+..-+...+.|
T Consensus 8 ykC~~Cgniv~v~~~~~~~l~C 29 (34)
T TIGR00319 8 YKCEVCGNIVEVLHAGGGQLVC 29 (34)
T ss_pred EEcCCCCcEEEEEECCCcceec
Confidence 4788888888777644444544
No 97
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=44.56 E-value=28 Score=19.77 Aligned_cols=22 Identities=27% Similarity=0.628 Sum_probs=15.1
Q ss_pred EeCCCCCceeEEeeecceeEEc
Q psy2574 35 VKCPGCYKITTVFSHAQSVVIC 56 (115)
Q Consensus 35 VKCp~C~n~q~VFSHAqt~V~C 56 (115)
-||..|+|+-.+..-+...+.|
T Consensus 5 ykC~~CGniv~v~~~~~~~l~C 26 (34)
T cd00974 5 YKCEICGNIVEVLNVGGGTLVC 26 (34)
T ss_pred EEcCCCCcEEEEEECCCcceee
Confidence 4788888888777655445555
No 98
>PRK14873 primosome assembly protein PriA; Provisional
Probab=44.14 E-value=29 Score=31.92 Aligned_cols=48 Identities=25% Similarity=0.411 Sum_probs=31.0
Q ss_pred cccccCC-CCceeEEeCCCCCceeEEeeecceeEEcCCCCeeeecccCCceeeccCCCC
Q psy2574 22 KRLVQHP-NSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLTEDDTG 79 (115)
Q Consensus 22 krLV~~P-nS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PTGGKA~l~egc~f 79 (115)
..|+.-| +.|.=-+.|.+|+. ++.|..|+-.|.....+..-.--.|.+
T Consensus 370 qvll~lnRrGyap~l~C~~Cg~----------~~~C~~C~~~L~~h~~~~~l~Ch~CG~ 418 (665)
T PRK14873 370 PVLVQVPRRGYVPSLACARCRT----------PARCRHCTGPLGLPSAGGTPRCRWCGR 418 (665)
T ss_pred cEEEEecCCCCCCeeEhhhCcC----------eeECCCCCCceeEecCCCeeECCCCcC
Confidence 6777766 55555668888885 466777777777665544444455544
No 99
>PF05077 DUF678: Protein of unknown function (DUF678); InterPro: IPR007769 This family contains poxvirus proteins belonging to the A19 family. The proteins are of unknown function.
Probab=43.99 E-value=18 Score=25.40 Aligned_cols=48 Identities=25% Similarity=0.508 Sum_probs=33.8
Q ss_pred HHHhhcccccccCC-CCceeEEeCCCCCceeEEeee-------------cceeEEcCCCCeeeec
Q psy2574 15 EKRKHKLKRLVQHP-NSYFMDVKCPGCYKITTVFSH-------------AQSVVICAGCSTILCQ 65 (115)
Q Consensus 15 ek~k~K~krLV~~P-nS~Fm~VKCp~C~n~q~VFSH-------------Aqt~V~C~~Cg~vL~~ 65 (115)
.+||+|-+.-|+.+ ... +-|.-|+..-+-||- ......|..||..|..
T Consensus 8 Krrkrk~~t~v~~~~d~c---~tCSsC~SkLV~~Sdvtk~sl~~~~~~g~~~tLsCsACGS~L~~ 69 (74)
T PF05077_consen 8 KRRKRKPKTTVDDEEDDC---TTCSSCQSKLVKFSDVTKVSLDEYKVAGKGNTLSCSACGSELRP 69 (74)
T ss_pred hhcccCCCceeecCCCCc---cchhhhhhheeeeecccceehhhhcccCCCCeEeehhcccccee
Confidence 34555556667776 333 778899998888883 2466789999988864
No 100
>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=43.33 E-value=21 Score=21.90 Aligned_cols=26 Identities=27% Similarity=0.828 Sum_probs=12.6
Q ss_pred eEEeCCCCCceeEEeeecceeEEcCCCC
Q psy2574 33 MDVKCPGCYKITTVFSHAQSVVICAGCS 60 (115)
Q Consensus 33 m~VKCp~C~n~q~VFSHAqt~V~C~~Cg 60 (115)
++-.||.|+ ...|---+..+.|+.|+
T Consensus 16 L~~~Cp~C~--~PL~~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 16 LDEHCPDCG--TPLMRDKDGKIYCVSCG 41 (41)
T ss_pred hcCccCCCC--CeeEEecCCCEECCCCC
Confidence 344566663 33444334455566553
No 101
>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=43.25 E-value=29 Score=24.86 Aligned_cols=29 Identities=28% Similarity=0.529 Sum_probs=24.9
Q ss_pred EeCCCCCceeEEeeecceeEEcCCCCeeee
Q psy2574 35 VKCPGCYKITTVFSHAQSVVICAGCSTILC 64 (115)
Q Consensus 35 VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~ 64 (115)
-.||-|++.. |=-.+.-.-.|..|+.+++
T Consensus 36 y~Cp~Cgk~~-vkR~a~GIW~C~~C~~~~A 64 (90)
T PF01780_consen 36 YTCPFCGKTS-VKRVATGIWKCKKCGKKFA 64 (90)
T ss_dssp BEESSSSSSE-EEEEETTEEEETTTTEEEE
T ss_pred CcCCCCCCce-eEEeeeEEeecCCCCCEEe
Confidence 4799999998 6677788899999999985
No 102
>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=43.12 E-value=16 Score=20.61 Aligned_cols=18 Identities=22% Similarity=0.468 Sum_probs=10.3
Q ss_pred EcCCCCeeeecccCCcee
Q psy2574 55 ICAGCSTILCQPTGGRAR 72 (115)
Q Consensus 55 ~C~~Cg~vL~~PTGGKA~ 72 (115)
.|.+||+.|.+.-|+.+.
T Consensus 1 ~CP~C~s~l~~~~~ev~~ 18 (28)
T PF03119_consen 1 TCPVCGSKLVREEGEVDI 18 (28)
T ss_dssp B-TTT--BEEE-CCTTCE
T ss_pred CcCCCCCEeEcCCCCEeE
Confidence 488899999887776654
No 103
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=42.69 E-value=29 Score=25.07 Aligned_cols=30 Identities=27% Similarity=0.477 Sum_probs=24.7
Q ss_pred EeCCCCCceeEEeeecceeEEcCCCCeeeec
Q psy2574 35 VKCPGCYKITTVFSHAQSVVICAGCSTILCQ 65 (115)
Q Consensus 35 VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~ 65 (115)
-.||.|+.. +|=-=+.-.-.|..||.+++-
T Consensus 36 ~~Cp~C~~~-~VkR~a~GIW~C~kCg~~fAG 65 (89)
T COG1997 36 HVCPFCGRT-TVKRIATGIWKCRKCGAKFAG 65 (89)
T ss_pred CcCCCCCCc-ceeeeccCeEEcCCCCCeecc
Confidence 479999999 666667778899999999863
No 104
>PRK11032 hypothetical protein; Provisional
Probab=41.97 E-value=17 Score=28.14 Aligned_cols=28 Identities=18% Similarity=0.501 Sum_probs=23.7
Q ss_pred EeCCCCCceeEEeeecceeEEcCCCCeee
Q psy2574 35 VKCPGCYKITTVFSHAQSVVICAGCSTIL 63 (115)
Q Consensus 35 VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL 63 (115)
..|..|+... .|.|+...-.|+.||..-
T Consensus 125 LvC~~Cg~~~-~~~~p~~i~pCp~C~~~~ 152 (160)
T PRK11032 125 LVCEKCHHHL-AFYTPEVLPLCPKCGHDQ 152 (160)
T ss_pred EEecCCCCEE-EecCCCcCCCCCCCCCCe
Confidence 5799999876 569999999999999754
No 105
>PF15288 zf-CCHC_6: Zinc knuckle
Probab=41.71 E-value=8.8 Score=23.91 Aligned_cols=22 Identities=32% Similarity=0.647 Sum_probs=18.2
Q ss_pred EEeCCCCCceeEEeeecceeEEcCCC
Q psy2574 34 DVKCPGCYKITTVFSHAQSVVICAGC 59 (115)
Q Consensus 34 ~VKCp~C~n~q~VFSHAqt~V~C~~C 59 (115)
+|||..|+. |.|..+.-.|..=
T Consensus 1 k~kC~~CG~----~GH~~t~k~CP~~ 22 (40)
T PF15288_consen 1 KVKCKNCGA----FGHMRTNKRCPMY 22 (40)
T ss_pred Ccccccccc----ccccccCccCCCC
Confidence 489999996 7899999888753
No 106
>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=40.63 E-value=26 Score=22.06 Aligned_cols=33 Identities=18% Similarity=0.501 Sum_probs=24.7
Q ss_pred CceeEEeCCCCCceeEEeeecceeEEcCCCCeee
Q psy2574 30 SYFMDVKCPGCYKITTVFSHAQSVVICAGCSTIL 63 (115)
Q Consensus 30 S~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL 63 (115)
.+|-.-.||.|+....- .-......|..||...
T Consensus 24 ~~~TSq~C~~CG~~~~~-~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 24 EAYTSQTCPRCGHRNKK-RRSGRVFTCPNCGFEM 56 (69)
T ss_pred CCCCccCccCccccccc-ccccceEEcCCCCCEE
Confidence 33356779999887776 6677788899998764
No 107
>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=39.88 E-value=21 Score=30.05 Aligned_cols=35 Identities=23% Similarity=0.502 Sum_probs=22.3
Q ss_pred CCceeEEeCCCCCceeEE--eeec-------ceeEEcCCCCeee
Q psy2574 29 NSYFMDVKCPGCYKITTV--FSHA-------QSVVICAGCSTIL 63 (115)
Q Consensus 29 nS~Fm~VKCp~C~n~q~V--FSHA-------qt~V~C~~Cg~vL 63 (115)
.=+|.+++|+.|+|..-+ |+-. --+-.|..|++=|
T Consensus 219 eW~~~R~~C~~Cg~~~~l~y~~~e~~~~~~~~r~e~C~~C~~Yl 262 (305)
T TIGR01562 219 EWHYVRVKCSHCEESKHLAYLSLEHDAEKAVLKAETCDSCQGYL 262 (305)
T ss_pred cccccCccCCCCCCCCceeeEeecCCCCCcceEEeeccccccch
Confidence 446788999999987644 3211 1344688887654
No 108
>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=39.79 E-value=13 Score=26.99 Aligned_cols=27 Identities=22% Similarity=0.661 Sum_probs=16.3
Q ss_pred eCCCCCceeEEeeecceeEEcCCCCeeee
Q psy2574 36 KCPGCYKITTVFSHAQSVVICAGCSTILC 64 (115)
Q Consensus 36 KCp~C~n~q~VFSHAqt~V~C~~Cg~vL~ 64 (115)
.||.|+.-= |.=-..+|.|..||+..-
T Consensus 11 ~Cp~CG~kF--YDLnk~PivCP~CG~~~~ 37 (108)
T PF09538_consen 11 TCPSCGAKF--YDLNKDPIVCPKCGTEFP 37 (108)
T ss_pred cCCCCcchh--ccCCCCCccCCCCCCccC
Confidence 466666543 333336777888887653
No 109
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=39.32 E-value=24 Score=26.00 Aligned_cols=39 Identities=23% Similarity=0.466 Sum_probs=29.4
Q ss_pred eEEeCCCCCceeEEeeecceeE-----EcCCCCeeeecccCCcee
Q psy2574 33 MDVKCPGCYKITTVFSHAQSVV-----ICAGCSTILCQPTGGRAR 72 (115)
Q Consensus 33 m~VKCp~C~n~q~VFSHAqt~V-----~C~~Cg~vL~~PTGGKA~ 72 (115)
.++.||-|.... ++-+..... +|..|+.+...=+|+-+.
T Consensus 29 ~~~~cP~C~s~~-~~k~g~~~~~~qRyrC~~C~~tf~~~~~~~~~ 72 (129)
T COG3677 29 TKVNCPRCKSSN-VVKIGGIRRGHQRYKCKSCGSTFTVETGSPLS 72 (129)
T ss_pred ccCcCCCCCccc-eeeECCccccccccccCCcCcceeeeccCccc
Confidence 458899999988 666555544 799999998877776543
No 110
>PRK05580 primosome assembly protein PriA; Validated
Probab=38.49 E-value=35 Score=30.98 Aligned_cols=45 Identities=16% Similarity=0.211 Sum_probs=26.8
Q ss_pred hcccccccCCC-CceeEEeCCCCCce--------eEEeeecceeEEcCCCCeee
Q psy2574 19 HKLKRLVQHPN-SYFMDVKCPGCYKI--------TTVFSHAQSVVICAGCSTIL 63 (115)
Q Consensus 19 ~K~krLV~~Pn-S~Fm~VKCp~C~n~--------q~VFSHAqt~V~C~~Cg~vL 63 (115)
++++.|+.-|+ .|.-.+.|..|+.. ..+|........|.-||..-
T Consensus 365 ~g~qvll~~nrrGy~~~~~C~~Cg~~~~C~~C~~~l~~h~~~~~l~Ch~Cg~~~ 418 (679)
T PRK05580 365 RGEQVLLFLNRRGYAPFLLCRDCGWVAECPHCDASLTLHRFQRRLRCHHCGYQE 418 (679)
T ss_pred cCCeEEEEEcCCCCCCceEhhhCcCccCCCCCCCceeEECCCCeEECCCCcCCC
Confidence 34456777664 44445666666654 45565556666666666554
No 111
>PF09272 Hepsin-SRCR: Hepsin, SRCR; InterPro: IPR015352 This entry represents the extracellular domain of the serine protease hepsin. The domain is formed primarily by three elements of regular secondary structure: a 12-residue alpha helix, a twisted five-stranded antiparallel beta sheet, and a second, two-stranded, antiparallel sheet. The two beta-sheets lie at roughly right angles to each other, with the helix nestled between the two, adopting an SRCR fold. The exact function of this domain has not been identified, though it probably may serve to orient the protease domain or place it in the vicinity of its substrate []. ; GO: 0004252 serine-type endopeptidase activity, 0070008 serine-type exopeptidase activity; PDB: 3T2N_B 1Z8G_A 1P57_A 1O5E_L 1O5F_L.
Probab=37.15 E-value=19 Score=26.91 Aligned_cols=18 Identities=22% Similarity=0.606 Sum_probs=9.7
Q ss_pred cCCCCceeEEeCCCCCce
Q psy2574 26 QHPNSYFMDVKCPGCYKI 43 (115)
Q Consensus 26 ~~PnS~Fm~VKCp~C~n~ 43 (115)
-=|+.+|+.+.|.||+.-
T Consensus 90 dCp~G~fLat~CQDCGRR 107 (110)
T PF09272_consen 90 DCPRGRFLATICQDCGRR 107 (110)
T ss_dssp --TT-EEEEEEE---S--
T ss_pred eCCCCceeehhhhhhCcc
Confidence 459999999999999864
No 112
>PF03117 Herpes_UL49_1: UL49 family; InterPro: IPR004339 UL49 proteins are present in the viral tegument at the surface of the nucleocapsid []. Many of the nonconserved tegument proteins of alpha-herpes viruses play important roles during different steps of the viral replication cycle, such as the shutoff of host cell functions by the vhs protein encoded by UL41 and the transcriptional activation of viral immediate-early genes by the UL48 gene product, VP16. UL49 of Human herpesvirus 1 (HHV-1) has been shown to directly interact with VP16. The UL49 gene products of HHV-1 and Bovine herpesvirus 1 exhibit virus-independent intercellular trafficking of unknown biological function but are dispensable for productive viral replication. Envelope glycoprotein M (gM) and the complex formed by glycoproteins E (gE) and I (gI) are involved in the secondary envelopment of Suid herpesvirus 1 (Pseudorabies virus, PrV) particles in the cytoplasm of infected cells. In the absence of the gE-gI complex and gM, envelopment is blocked and capsids surrounded by tegument proteins accumulate in the cytoplasm. The cytoplasmic domains of gE and gM specifically interact with the C-terminal part of the UL49 gene product of PrV suggesting a role for the protein in secondary envelopment during herpesvirus virion maturation [].; GO: 0016032 viral reproduction, 0019033 viral tegument
Probab=36.87 E-value=37 Score=28.25 Aligned_cols=41 Identities=15% Similarity=0.259 Sum_probs=33.5
Q ss_pred cccCCCCceeEEeCCCCCceeEEeeecceeEEcCCCCe------eeeccc
Q psy2574 24 LVQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCST------ILCQPT 67 (115)
Q Consensus 24 LV~~PnS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~------vL~~PT 67 (115)
..=+|||-|. |.|=.+.|++|++++-.|-|.-||. .|.++.
T Consensus 126 ~~F~pts~FY---~RDqkEK~v~~c~~tgriyCS~CGS~~l~~~~l~e~~ 172 (245)
T PF03117_consen 126 QNFPPTSMFY---YRDQKEKQVIYCATTGRIYCSLCGSQRLRKERLYEMY 172 (245)
T ss_pred cCcCCcceeE---eccccceeEEEeccCCCEEEccCCCCeeEEEeeeecc
Confidence 4456888876 6777889999999999999999996 466666
No 113
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=36.72 E-value=41 Score=24.08 Aligned_cols=29 Identities=31% Similarity=0.577 Sum_probs=24.5
Q ss_pred EeCCCCCceeEEeeecceeEEcCCCCeeee
Q psy2574 35 VKCPGCYKITTVFSHAQSVVICAGCSTILC 64 (115)
Q Consensus 35 VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~ 64 (115)
-.||-|+... +--.+.-...|..|+.+++
T Consensus 37 y~CpfCgk~~-vkR~a~GIW~C~~C~~~~A 65 (90)
T PTZ00255 37 YFCPFCGKHA-VKRQAVGIWRCKGCKKTVA 65 (90)
T ss_pred ccCCCCCCCc-eeeeeeEEEEcCCCCCEEe
Confidence 4799999755 6778889999999999984
No 114
>PRK06260 threonine synthase; Validated
Probab=36.40 E-value=23 Score=29.65 Aligned_cols=28 Identities=25% Similarity=0.593 Sum_probs=20.8
Q ss_pred eEEeCCCCCceeEEeeecceeEEcCCCCeee
Q psy2574 33 MDVKCPGCYKITTVFSHAQSVVICAGCSTIL 63 (115)
Q Consensus 33 m~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL 63 (115)
+..+|..|+.+ |+-......|..||..|
T Consensus 2 ~~~~C~~cg~~---~~~~~~~~~Cp~cg~~l 29 (397)
T PRK06260 2 YWLKCIECGKE---YDPDEIIYTCPECGGLL 29 (397)
T ss_pred CEEEECCCCCC---CCCCCccccCCCCCCeE
Confidence 45789999976 55555667899998654
No 115
>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=35.65 E-value=27 Score=19.51 Aligned_cols=15 Identities=27% Similarity=0.627 Sum_probs=10.9
Q ss_pred CCCceeEEeCCCCCc
Q psy2574 28 PNSYFMDVKCPGCYK 42 (115)
Q Consensus 28 PnS~Fm~VKCp~C~n 42 (115)
|+.+...-+||+|+.
T Consensus 10 ~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 10 PREQAVPFPCPNCGF 24 (24)
T ss_pred CcccCceEeCCCCCC
Confidence 556667778888874
No 116
>smart00746 TRASH metallochaperone-like domain.
Probab=35.46 E-value=34 Score=16.87 Aligned_cols=30 Identities=17% Similarity=0.371 Sum_probs=17.9
Q ss_pred cCCCCeeeecccCCceeeccCCCCccEEEEEeecC
Q psy2574 56 CAGCSTILCQPTGGRARLTEDDTGDSMTVRGCALD 90 (115)
Q Consensus 56 C~~Cg~vL~~PTGGKA~l~egc~f~s~~~~~ca~d 90 (115)
|..||..+..|+.+.....+| -...+|+..
T Consensus 1 c~~C~~~~~~~~~~~~~~~~g-----~~~~FCs~~ 30 (39)
T smart00746 1 CSFCGKDIYNPGTGIMVVNDG-----KVFYFCSSK 30 (39)
T ss_pred CCCCCCCccCCCCceEEEECC-----EEEEEeCHH
Confidence 778888887666555443444 333556543
No 117
>PRK06450 threonine synthase; Validated
Probab=35.15 E-value=23 Score=29.40 Aligned_cols=27 Identities=19% Similarity=0.328 Sum_probs=19.0
Q ss_pred eEEeCCCCCceeEEeeecceeEEcCCCCeee
Q psy2574 33 MDVKCPGCYKITTVFSHAQSVVICAGCSTIL 63 (115)
Q Consensus 33 m~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL 63 (115)
++.+|..|+.+ |+. .....|..||-.|
T Consensus 2 ~~~~C~~Cg~~---~~~-~~~~~C~~cg~~l 28 (338)
T PRK06450 2 VKEVCMKCGKE---RES-IYEIRCKKCGGPF 28 (338)
T ss_pred ceeEECCcCCc---CCC-cccccCCcCCCEe
Confidence 35789999987 333 4456899998654
No 118
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=34.35 E-value=31 Score=18.37 Aligned_cols=9 Identities=33% Similarity=0.844 Sum_probs=4.9
Q ss_pred EcCCCCeee
Q psy2574 55 ICAGCSTIL 63 (115)
Q Consensus 55 ~C~~Cg~vL 63 (115)
.|..|+..|
T Consensus 29 ~C~~C~~~L 37 (39)
T smart00132 29 KCSKCGKPL 37 (39)
T ss_pred CCcccCCcC
Confidence 455555555
No 119
>KOG2906|consensus
Probab=33.83 E-value=52 Score=24.45 Aligned_cols=29 Identities=24% Similarity=0.496 Sum_probs=24.9
Q ss_pred eCCCCCceeEEeeecc-eeEEcCCCCeeee
Q psy2574 36 KCPGCYKITTVFSHAQ-SVVICAGCSTILC 64 (115)
Q Consensus 36 KCp~C~n~q~VFSHAq-t~V~C~~Cg~vL~ 64 (115)
-||.|+|.-+|=+-++ ..-.|..|.-+..
T Consensus 3 FCP~Cgn~Live~g~~~~rf~C~tCpY~~~ 32 (105)
T KOG2906|consen 3 FCPTCGNMLIVESGESCNRFSCRTCPYVFP 32 (105)
T ss_pred ccCCCCCEEEEecCCeEeeEEcCCCCceee
Confidence 4999999999999888 7888999987654
No 120
>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=33.79 E-value=21 Score=23.22 Aligned_cols=13 Identities=31% Similarity=0.506 Sum_probs=9.8
Q ss_pred EEeCCCCCceeEE
Q psy2574 34 DVKCPGCYKITTV 46 (115)
Q Consensus 34 ~VKCp~C~n~q~V 46 (115)
.++||.|+|..|-
T Consensus 13 Y~~Cp~CGN~~vG 25 (49)
T PF12677_consen 13 YCKCPKCGNDKVG 25 (49)
T ss_pred hccCcccCCcEee
Confidence 3789999887653
No 121
>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=33.70 E-value=65 Score=23.00 Aligned_cols=35 Identities=20% Similarity=0.477 Sum_probs=24.9
Q ss_pred ceeEEeCC--CCCceeEEeeecceeEEcCCCCeeeeccc
Q psy2574 31 YFMDVKCP--GCYKITTVFSHAQSVVICAGCSTILCQPT 67 (115)
Q Consensus 31 ~Fm~VKCp--~C~n~q~VFSHAqt~V~C~~Cg~vL~~PT 67 (115)
.|.-.-|| .|.+- +... ....-.|..|+....+|.
T Consensus 15 ~~~Y~aC~~~~C~kK-v~~~-~~~~y~C~~C~~~~~~~~ 51 (146)
T PF08646_consen 15 NWYYPACPNEKCNKK-VTEN-GDGSYRCEKCNKTVENPK 51 (146)
T ss_dssp TTEEEE-TSTTTS-B--EEE-TTTEEEETTTTEEESS-E
T ss_pred CcEECCCCCccCCCE-eecC-CCcEEECCCCCCcCCCee
Confidence 67778999 99974 5555 667789999999987665
No 122
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=33.37 E-value=40 Score=22.33 Aligned_cols=32 Identities=19% Similarity=0.304 Sum_probs=17.3
Q ss_pred CCceeEEeCCCCCceeEEeeecceeEEcCCCCe
Q psy2574 29 NSYFMDVKCPGCYKITTVFSHAQSVVICAGCST 61 (115)
Q Consensus 29 nS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~ 61 (115)
+.....|.|.||++...++-|-- -.+|..||.
T Consensus 25 ~~~~v~IlCNDC~~~s~v~fH~l-g~KC~~C~S 56 (61)
T PF14599_consen 25 RNKKVWILCNDCNAKSEVPFHFL-GHKCSHCGS 56 (61)
T ss_dssp ---EEEEEESSS--EEEEE--TT-----TTTS-
T ss_pred hCCEEEEECCCCCCccceeeeHh-hhcCCCCCC
Confidence 55678999999999999998864 357888874
No 123
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=33.04 E-value=28 Score=22.88 Aligned_cols=32 Identities=28% Similarity=0.724 Sum_probs=23.0
Q ss_pred ceeEEeCCCCCceeEEeeecceeEEcCCCCeeeec
Q psy2574 31 YFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQ 65 (115)
Q Consensus 31 ~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~ 65 (115)
+|+..+|+.|+.. |-----.|.|..||++-=+
T Consensus 2 ~~~~~~C~~Cg~~---~~~~dDiVvCp~CgapyHR 33 (54)
T PF14446_consen 2 NYEGCKCPVCGKK---FKDGDDIVVCPECGAPYHR 33 (54)
T ss_pred CccCccChhhCCc---ccCCCCEEECCCCCCcccH
Confidence 4667889999874 4445567889999987643
No 124
>PHA02893 hypothetical protein; Provisional
Probab=32.99 E-value=29 Score=25.03 Aligned_cols=31 Identities=29% Similarity=0.700 Sum_probs=24.0
Q ss_pred EeCCCCCceeEEeee----------------cceeEEcCCCCeeeec
Q psy2574 35 VKCPGCYKITTVFSH----------------AQSVVICAGCSTILCQ 65 (115)
Q Consensus 35 VKCp~C~n~q~VFSH----------------Aqt~V~C~~Cg~vL~~ 65 (115)
+-|.-|+..-+-||- +.....|..||..|+.
T Consensus 35 ~TCSsC~SKLV~~Sdvtk~sl~~~~~~Gk~~~~~tL~CaACGS~L~~ 81 (88)
T PHA02893 35 TTCQICQSKLVMFSGVNKYKLKDYLNIGKAFSNSNIKCIACGSSLCH 81 (88)
T ss_pred cchhhhhcceeeeeccchhhhHHHHhccccCCCCceeehhhchhhhh
Confidence 578888888888883 2567788999988864
No 125
>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=32.42 E-value=27 Score=31.05 Aligned_cols=34 Identities=18% Similarity=0.479 Sum_probs=24.3
Q ss_pred eeEEeCCCCCceeEE-eee---------cceeEEcCCCCeeeec
Q psy2574 32 FMDVKCPGCYKITTV-FSH---------AQSVVICAGCSTILCQ 65 (115)
Q Consensus 32 Fm~VKCp~C~n~q~V-FSH---------Aqt~V~C~~Cg~vL~~ 65 (115)
..-|.||.|+..|+. |++ ......|..||..+-+
T Consensus 198 ~~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~~i~e 241 (557)
T PF05876_consen 198 RYYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGCEIEE 241 (557)
T ss_pred EEEccCCCCCCCccccccceeecCCCCccceEEECCCCcCCCCH
Confidence 457999999998864 232 2456678888887743
No 126
>PRK05654 acetyl-CoA carboxylase subunit beta; Validated
Probab=32.10 E-value=13 Score=30.87 Aligned_cols=31 Identities=19% Similarity=0.522 Sum_probs=20.5
Q ss_pred eEEeCCCCCceeEEeeecceeEEcCCCCeee
Q psy2574 33 MDVKCPGCYKITTVFSHAQSVVICAGCSTIL 63 (115)
Q Consensus 33 m~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL 63 (115)
+-+|||.|+++--.=.-....-.|..||.-+
T Consensus 26 ~~~~c~~c~~~~~~~~l~~~~~vc~~c~~h~ 56 (292)
T PRK05654 26 LWTKCPSCGQVLYRKELEANLNVCPKCGHHM 56 (292)
T ss_pred CeeECCCccchhhHHHHHhcCCCCCCCCCCe
Confidence 6799999997533222222335799998865
No 127
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=32.09 E-value=42 Score=20.35 Aligned_cols=16 Identities=19% Similarity=0.432 Sum_probs=13.8
Q ss_pred eeEEcCCCCeeeeccc
Q psy2574 52 SVVICAGCSTILCQPT 67 (115)
Q Consensus 52 t~V~C~~Cg~vL~~PT 67 (115)
..+.|.-|+.+|..++
T Consensus 17 ~~a~C~~C~~~l~~~~ 32 (50)
T smart00614 17 QRAKCKYCGKKLSRSS 32 (50)
T ss_pred eEEEecCCCCEeeeCC
Confidence 5789999999998775
No 128
>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=32.06 E-value=56 Score=23.46 Aligned_cols=29 Identities=28% Similarity=0.516 Sum_probs=24.1
Q ss_pred EeCCCCCceeEEeeecceeEEcCCCCeeee
Q psy2574 35 VKCPGCYKITTVFSHAQSVVICAGCSTILC 64 (115)
Q Consensus 35 VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~ 64 (115)
-.||-|++.. |=-.+.-.-.|..|+.+++
T Consensus 36 y~CpfCgk~~-vkR~a~GIW~C~~C~~~~A 64 (91)
T TIGR00280 36 YVCPFCGKKT-VKRGSTGIWTCRKCGAKFA 64 (91)
T ss_pred ccCCCCCCCc-eEEEeeEEEEcCCCCCEEe
Confidence 4799999766 5677888899999999984
No 129
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=32.04 E-value=26 Score=35.31 Aligned_cols=23 Identities=30% Similarity=0.736 Sum_probs=16.6
Q ss_pred EEeCCCCCceeEEeeecceeEEcCCCCeee
Q psy2574 34 DVKCPGCYKITTVFSHAQSVVICAGCSTIL 63 (115)
Q Consensus 34 ~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL 63 (115)
..+||.|+.+. |+ ..|..||..+
T Consensus 667 ~rkCPkCG~~t--~~-----~fCP~CGs~t 689 (1337)
T PRK14714 667 RRRCPSCGTET--YE-----NRCPDCGTHT 689 (1337)
T ss_pred EEECCCCCCcc--cc-----ccCcccCCcC
Confidence 46899999964 32 2788888776
No 130
>KOG1296|consensus
Probab=31.83 E-value=28 Score=27.54 Aligned_cols=64 Identities=16% Similarity=0.187 Sum_probs=38.4
Q ss_pred CCCCceeEEeCCCCCceeEEeeecceeEEcCCCCeeeeccc-CCceeeccCCCCc--cEEEEEeecCCCCCCccc
Q psy2574 27 HPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPT-GGRARLTEDDTGD--SMTVRGCALDSGTPTTDT 98 (115)
Q Consensus 27 ~PnS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PT-GGKA~l~egc~f~--s~~~~~ca~ds~~~~~d~ 98 (115)
.+-|+||+.||..|+.+. -.-.|+.=...++.|. -|-|.+..-|.|= --+|+-|+ ..+.|.|++
T Consensus 23 ~~~rf~~kLkCtnCgE~~-------dkw~~I~l~E~~~~pg~Rgta~~v~KCK~C~Rensv~iv~-~~~~pyt~e 89 (161)
T KOG1296|consen 23 PDFRFYLKLKCTNCGELS-------DKWQYITLNEEVAMPGSRGTASFVMKCKFCSRENSVTIVA-FEDKPYTAE 89 (161)
T ss_pred CCceeEEEeccccccccC-------CceEEEEeeeeecCCCCcchhhHhhhhhhhcccCcEEEec-CCCCccccc
Confidence 456789999999999864 1222333355666666 3677777777771 22333333 445555544
No 131
>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=31.68 E-value=45 Score=18.67 Aligned_cols=22 Identities=27% Similarity=0.453 Sum_probs=7.4
Q ss_pred cCCCCeeeecccCCceeeccCC
Q psy2574 56 CAGCSTILCQPTGGRARLTEDD 77 (115)
Q Consensus 56 C~~Cg~vL~~PTGGKA~l~egc 77 (115)
|..||..+..=.+|.++.=+.|
T Consensus 6 C~~CG~~t~~~~~g~~r~C~~C 27 (32)
T PF09297_consen 6 CGRCGAPTKPAPGGWARRCPSC 27 (32)
T ss_dssp -TTT--BEEE-SSSS-EEESSS
T ss_pred cCcCCccccCCCCcCEeECCCC
Confidence 4444444444444444443333
No 132
>TIGR00320 dfx_rbo desulfoferrodoxin. This protein is described in some articles as rubredoxin oxidoreductase (rbo), and its gene shares an operon with the rubredoxin gene in Desulfovibrio vulgaris Hildenborough.
Probab=31.67 E-value=48 Score=24.37 Aligned_cols=27 Identities=26% Similarity=0.667 Sum_probs=20.5
Q ss_pred EeCCCCCceeEEeeecceeEEcCCCCeee
Q psy2574 35 VKCPGCYKITTVFSHAQSVVICAGCSTIL 63 (115)
Q Consensus 35 VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL 63 (115)
-+|+.|+|+-.+.+-....+.| ||..|
T Consensus 8 YkC~~CGniv~v~~~g~~~l~C--Cge~m 34 (125)
T TIGR00320 8 YKCEVCGNIVEVLNAGIGQLVC--CNQPM 34 (125)
T ss_pred EECCCCCcEEEEEECCCcceee--CCccc
Confidence 5899999999888767777777 45533
No 133
>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=30.73 E-value=16 Score=27.48 Aligned_cols=41 Identities=24% Similarity=0.517 Sum_probs=26.0
Q ss_pred cccccCCCCceeEEeCCCCCceeEEeeecc-eeEEcCCCCeeeec
Q psy2574 22 KRLVQHPNSYFMDVKCPGCYKITTVFSHAQ-SVVICAGCSTILCQ 65 (115)
Q Consensus 22 krLV~~PnS~Fm~VKCp~C~n~q~VFSHAq-t~V~C~~Cg~vL~~ 65 (115)
++|-+.-+..|. .||.|. ...-|.-|. ..-.|+.||.+|-.
T Consensus 99 ~~l~~e~~~~~Y--~Cp~c~-~r~tf~eA~~~~F~Cp~Cg~~L~~ 140 (158)
T TIGR00373 99 EKLEFETNNMFF--ICPNMC-VRFTFNEAMELNFTCPRCGAMLDY 140 (158)
T ss_pred HHHhhccCCCeE--ECCCCC-cEeeHHHHHHcCCcCCCCCCEeee
Confidence 334444444443 599998 445555443 35689999999854
No 134
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=30.70 E-value=26 Score=22.24 Aligned_cols=17 Identities=29% Similarity=0.616 Sum_probs=10.0
Q ss_pred eeecceeEEcCCCCeee
Q psy2574 47 FSHAQSVVICAGCSTIL 63 (115)
Q Consensus 47 FSHAqt~V~C~~Cg~vL 63 (115)
..+-+..+.|-.|+.+|
T Consensus 25 ~~k~~~klrCGaCs~vl 41 (46)
T PF11331_consen 25 SKKNQQKLRCGACSEVL 41 (46)
T ss_pred CccceeEEeCCCCceeE
Confidence 33445566666666665
No 135
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=30.36 E-value=42 Score=25.67 Aligned_cols=28 Identities=21% Similarity=0.519 Sum_probs=18.4
Q ss_pred eCCCCCce--eEEeeeccee---E----EcCCCCeee
Q psy2574 36 KCPGCYKI--TTVFSHAQSV---V----ICAGCSTIL 63 (115)
Q Consensus 36 KCp~C~n~--q~VFSHAqt~---V----~C~~Cg~vL 63 (115)
|||-|++. +++=|..-.. | .|..||...
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence 79999963 5666663333 3 488888654
No 136
>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=29.62 E-value=61 Score=23.70 Aligned_cols=52 Identities=19% Similarity=0.378 Sum_probs=35.5
Q ss_pred cceeEEcCCCCeeeecccCCceeeccCCCCccEEEEEeecCCCCCCccceeEEeecccceeecCCC
Q psy2574 50 AQSVVICAGCSTILCQPTGGRARLTEDDTGDSMTVRGCALDSGTPTTDTELIRMSHCGGFYFDDSQ 115 (115)
Q Consensus 50 Aqt~V~C~~Cg~vL~~PTGGKA~l~egc~f~s~~~~~ca~ds~~~~~d~~~~~~~~~~~~~~~~~~ 115 (115)
....-+|..|+..|..-+ |..+.+- .|-+.+-..+|.-|=..||-.|+.|++
T Consensus 88 ~~~~sRC~~CN~~L~~v~--~~~v~~~------------vp~~v~~~~~~f~~C~~C~kiyW~GsH 139 (147)
T PF01927_consen 88 DPIFSRCPKCNGPLRPVS--KEEVKDR------------VPPYVYETYDEFWRCPGCGKIYWEGSH 139 (147)
T ss_pred CCCCCccCCCCcEeeech--hhccccc------------cCccccccCCeEEECCCCCCEeccccc
Confidence 333457888988775543 2322222 566677777788889999999999864
No 137
>PF00236 Hormone_6: Glycoprotein hormone; InterPro: IPR000476 Glycoprotein hormones [, ] (or gonadotropins) are a family of proteins, which include the mammalian hormones follitropin (FSH), lutropin (LSH), thyrotropin (TSH) placental chorionic gonadotropins hCG and eCG [] and chorionic gonadotropin (CG), as well as at least two forms of fish gonadotropins. These hormones are central to the complex endocrine system that regulates normal growth, sexual development, and reproductive function []. The hormones LH, FSH and TSH are secreted by the anterior pituitary gland, while hCG and eCG are secreted by the placenta []. All these hormones consist of two glycosylated chains (alpha and beta). The alpha subunit is common to each protein dimer (well conserved within species, but differing between them []), and a unique beta subunit, which confers biological specificity []. The alpha chains are highly conserved proteins of about 100 amino acid residues which contain ten conserved cysteines all involved in disulphide bonds [], as shown in the following schematic representation. +---------------------------+ +----------+| +-------------|--+ | || | | | xxxxCxCxxxxxxCxCCxxxxxxxxxxxxxCCxxxxxxxxxxCxCxxCx | | | | +------|-----------------+ | | | +----------------------------+ 'C': conserved cysteine involved in a disulphide bond. Intracellular levels of free alpha subunits are greater than those of the mature glycoprotein, implying that hormone assembly is limited by the appearance of the specific beta subunits, and hence that synthesis of alpha and beta is independently regulated [].; GO: 0005179 hormone activity, 0005576 extracellular region; PDB: 1HD4_A 1QFW_A 1XWD_D 1DZ7_A 1HCN_A 1E9J_A 1HRP_A 1FL7_A.
Probab=29.58 E-value=13 Score=27.20 Aligned_cols=41 Identities=34% Similarity=0.681 Sum_probs=27.3
Q ss_pred CCCceeEEeCCCCC-ceeEEeee-cceeEEcCCCCeeeecccC
Q psy2574 28 PNSYFMDVKCPGCY-KITTVFSH-AQSVVICAGCSTILCQPTG 68 (115)
Q Consensus 28 PnS~Fm~VKCp~C~-n~q~VFSH-Aqt~V~C~~Cg~vL~~PTG 68 (115)
||..|+..-|++|. +++..||+ -.-+-.|.+|----|-||-
T Consensus 2 p~~d~~~~gC~eC~L~~N~~fs~~~~piyQC~GCCFSrAYPTP 44 (96)
T PF00236_consen 2 PNGDFSNQGCPECKLKENKFFSRLGAPIYQCMGCCFSRAYPTP 44 (96)
T ss_dssp -------TBS-BSEEEEETTTEBTTBEEEEEEEEEEEEEEE-S
T ss_pred cccccccCCCCccCcccCccccCCCCceeEeeeeeeccccCCc
Confidence 78889999999995 78889999 5666789999998898984
No 138
>KOG2907|consensus
Probab=29.41 E-value=15 Score=27.65 Aligned_cols=50 Identities=20% Similarity=0.341 Sum_probs=32.3
Q ss_pred CCCCHHHHHHhhcccccccCCCCceeEEeCCCCCceeEEeeecce---------eEEcCCCCee
Q psy2574 8 LHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQS---------VVICAGCSTI 62 (115)
Q Consensus 8 l~Ps~e~ek~k~K~krLV~~PnS~Fm~VKCp~C~n~q~VFSHAqt---------~V~C~~Cg~v 62 (115)
.+|++..++...-.+. ..-=++-|||.|+++...|.-.|+ --.|..|+.-
T Consensus 53 ~~~~A~~~~ve~~~~~-----~ga~I~~kCpkCghe~m~Y~T~QlRSADEGQTVFYTC~kC~~k 111 (116)
T KOG2907|consen 53 EFTSALAEKVENESSA-----DGAVIKHKCPKCGHEEMSYHTLQLRSADEGQTVFYTCPKCKYK 111 (116)
T ss_pred ccchhhhhhhcccccc-----cccchhccCcccCCchhhhhhhhcccccCCceEEEEcCcccee
Confidence 4566666653221111 345688999999999999985553 2468888753
No 139
>KOG1598|consensus
Probab=29.33 E-value=24 Score=32.18 Aligned_cols=36 Identities=22% Similarity=0.366 Sum_probs=29.7
Q ss_pred eCCCCCceeEEeeecceeEEcCCCCeee------ecccCCce
Q psy2574 36 KCPGCYKITTVFSHAQSVVICAGCSTIL------CQPTGGRA 71 (115)
Q Consensus 36 KCp~C~n~q~VFSHAqt~V~C~~Cg~vL------~~PTGGKA 71 (115)
-|++|+...+-=.-|+-...|..||++| ++=|+++.
T Consensus 2 ~C~~C~~s~fe~d~a~g~~~C~~CG~v~E~~~ivsev~F~e~ 43 (521)
T KOG1598|consen 2 VCKNCGGSNFERDEATGNLYCTACGTVLEYNNIVAEVTFVEG 43 (521)
T ss_pred cCCCCCCCCcccccccCCceeccccceeeccceeEEeeeecc
Confidence 5999999888888899999999999987 44555554
No 140
>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=29.21 E-value=58 Score=19.66 Aligned_cols=22 Identities=27% Similarity=0.638 Sum_probs=10.8
Q ss_pred EeCCCCCceeEEeeecceeEEc
Q psy2574 35 VKCPGCYKITTVFSHAQSVVIC 56 (115)
Q Consensus 35 VKCp~C~n~q~VFSHAqt~V~C 56 (115)
-||..|+|+--|..-..-...|
T Consensus 7 YkC~~CGniVev~~~g~g~lvC 28 (36)
T PF06397_consen 7 YKCEHCGNIVEVVHDGGGPLVC 28 (36)
T ss_dssp EE-TTT--EEEEEE--SS-EEE
T ss_pred EEccCCCCEEEEEECCCCCEEe
Confidence 4788888887766655555555
No 141
>PF09814 HECT_2: HECT-like Ubiquitin-conjugating enzyme (E2)-binding; InterPro: IPR019193 This entry consists of E3 ubiquitin-protein ligases which accept ubiquitin from specific E2 ubiquitin-conjugating enzymes, and transfer it to substrates, generally promoting their degradation by the proteasome [].
Probab=29.11 E-value=50 Score=26.68 Aligned_cols=52 Identities=15% Similarity=0.183 Sum_probs=34.7
Q ss_pred ccccccCCCCceeEEeC-----CCCCceeEEeeecceeEEcCCCCeeee-cccCCceeecc
Q psy2574 21 LKRLVQHPNSYFMDVKC-----PGCYKITTVFSHAQSVVICAGCSTILC-QPTGGRARLTE 75 (115)
Q Consensus 21 ~krLV~~PnS~Fm~VKC-----p~C~n~q~VFSHAqt~V~C~~Cg~vL~-~PTGGKA~l~e 75 (115)
...+.|.++.-|+..-- .+|.+..+... ..|.|..|+..|. .+.++-.+|-.
T Consensus 159 ~~~l~p~~~~~lvg~~~~l~~~~~~~~~~~~~~---~~v~C~~C~~~LG~~~~~~~~rL~K 216 (354)
T PF09814_consen 159 NNSLKPREGDILVGDSYFLLHESDLQGDVIRIE---RIVRCKRCSSQLGEKFSDNTVRLYK 216 (354)
T ss_pred ccccccCCCcEEEechhheecchhcccccccCC---cEEEeCCCCceeCCCccCCeEEEEe
Confidence 37788888876655432 33444444444 7899999999998 66655555544
No 142
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=28.97 E-value=72 Score=20.53 Aligned_cols=34 Identities=24% Similarity=0.571 Sum_probs=22.5
Q ss_pred eeEEeCCCCCceeEEeeecceeEEcCCCCe-eeecc
Q psy2574 32 FMDVKCPGCYKITTVFSHAQSVVICAGCST-ILCQP 66 (115)
Q Consensus 32 Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~-vL~~P 66 (115)
-|.-+|..|+.+- --.-....|.|.-||. +|..|
T Consensus 4 ~~~Y~C~~Cg~~~-~~~~~~~~irCp~Cg~rIl~K~ 38 (49)
T COG1996 4 MMEYKCARCGREV-ELDQETRGIRCPYCGSRILVKE 38 (49)
T ss_pred eEEEEhhhcCCee-ehhhccCceeCCCCCcEEEEec
Confidence 3566888888875 2234667888998875 44444
No 143
>PF09963 DUF2197: Uncharacterized protein conserved in bacteria (DUF2197); InterPro: IPR019241 This family represents various hypothetical bacterial proteins with no known function.
Probab=28.42 E-value=19 Score=23.84 Aligned_cols=35 Identities=26% Similarity=0.453 Sum_probs=26.0
Q ss_pred eEEeCCCCCceeEEee----------ecceeEEcCCCCeeeeccc
Q psy2574 33 MDVKCPGCYKITTVFS----------HAQSVVICAGCSTILCQPT 67 (115)
Q Consensus 33 m~VKCp~C~n~q~VFS----------HAqt~V~C~~Cg~vL~~PT 67 (115)
|+|+|.=|.++-.|=. ++-..--|.-|..-|..+|
T Consensus 1 m~vkC~lCdk~~~Id~~~~~aKrLrnrPi~tYmC~eC~~RI~~~t 45 (56)
T PF09963_consen 1 MRVKCILCDKKEEIDEDTPEAKRLRNRPIHTYMCDECKERIREET 45 (56)
T ss_pred CeeEEEecCCEEEeccCCHHHHHhhcCCCcceeChhHHHHHhHHH
Confidence 6788888888877765 5556667888877777666
No 144
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=28.34 E-value=19 Score=27.72 Aligned_cols=40 Identities=28% Similarity=0.562 Sum_probs=25.2
Q ss_pred ccccCCCCceeEEeCCCCCceeEEeeecc-eeEEcCCCCeeeec
Q psy2574 23 RLVQHPNSYFMDVKCPGCYKITTVFSHAQ-SVVICAGCSTILCQ 65 (115)
Q Consensus 23 rLV~~PnS~Fm~VKCp~C~n~q~VFSHAq-t~V~C~~Cg~vL~~ 65 (115)
+|-+.-+..| -.||.|+. ...|.-|- ..-.|..||.+|.+
T Consensus 108 ~l~~e~~~~~--Y~Cp~C~~-rytf~eA~~~~F~Cp~Cg~~L~~ 148 (178)
T PRK06266 108 QLEEEENNMF--FFCPNCHI-RFTFDEAMEYGFRCPQCGEMLEE 148 (178)
T ss_pred HhhhccCCCE--EECCCCCc-EEeHHHHhhcCCcCCCCCCCCee
Confidence 3444444444 36999983 44444333 35789999999965
No 145
>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=28.15 E-value=63 Score=23.51 Aligned_cols=35 Identities=26% Similarity=0.602 Sum_probs=25.7
Q ss_pred ceeEEeCCCCCceeEEeeecceeEEcCCCCeeeeccc
Q psy2574 31 YFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPT 67 (115)
Q Consensus 31 ~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PT 67 (115)
.|...-||.|.+- ++ ......-.|..|+....+|.
T Consensus 31 ~~~Y~aC~~C~kk-v~-~~~~~~~~C~~C~~~~~~~~ 65 (166)
T cd04476 31 NWWYPACPGCNKK-VV-EEGNGTYRCEKCNKSVPNPE 65 (166)
T ss_pred CeEEccccccCcc-cE-eCCCCcEECCCCCCcCCCcc
Confidence 6888999999885 33 33337788999998875554
No 146
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=27.74 E-value=76 Score=21.58 Aligned_cols=26 Identities=23% Similarity=0.530 Sum_probs=18.7
Q ss_pred CCCCCceeEEeeecce--eEEcCCCCee
Q psy2574 37 CPGCYKITTVFSHAQS--VVICAGCSTI 62 (115)
Q Consensus 37 Cp~C~n~q~VFSHAqt--~V~C~~Cg~v 62 (115)
||-|+...+..-|... .|.|.+|+..
T Consensus 9 CPFCG~~~~~v~~~~g~~~v~C~~CgA~ 36 (64)
T PRK09710 9 CPFCGCPSVTVKAISGYYRAKCNGCESR 36 (64)
T ss_pred CCCCCCceeEEEecCceEEEEcCCCCcC
Confidence 8888887777776543 3678888873
No 147
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=27.49 E-value=27 Score=32.15 Aligned_cols=24 Identities=29% Similarity=0.661 Sum_probs=12.3
Q ss_pred EeCCCCCceeEEeeecceeEEcCCCCeee
Q psy2574 35 VKCPGCYKITTVFSHAQSVVICAGCSTIL 63 (115)
Q Consensus 35 VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL 63 (115)
++||.|+.+. +.....|..||+.|
T Consensus 2 ~~Cp~Cg~~n-----~~~akFC~~CG~~l 25 (645)
T PRK14559 2 LICPQCQFEN-----PNNNRFCQKCGTSL 25 (645)
T ss_pred CcCCCCCCcC-----CCCCccccccCCCC
Confidence 3566666542 34444555555555
No 148
>PF15616 TerY-C: TerY-C metal binding domain
Probab=27.45 E-value=1e+02 Score=23.23 Aligned_cols=23 Identities=30% Similarity=1.003 Sum_probs=13.7
Q ss_pred eCCCCCceeEEeeecceeEEcCCCCeeeecc
Q psy2574 36 KCPGCYKITTVFSHAQSVVICAGCSTILCQP 66 (115)
Q Consensus 36 KCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~P 66 (115)
-||-|+|.. -.+.| .||+++|--
T Consensus 79 gCP~CGn~~-------~fa~C-~CGkl~Ci~ 101 (131)
T PF15616_consen 79 GCPHCGNQY-------AFAVC-GCGKLFCID 101 (131)
T ss_pred CCCCCcChh-------cEEEe-cCCCEEEeC
Confidence 488888752 34555 566666643
No 149
>PF08150 FerB: FerB (NUC096) domain; InterPro: IPR012561 The ferlin gene family are characterised by multiple tandem C2 domains and a C-terminal transmembrane domain. They are found in a wide range of species and their function remains unknown, however, mutations in its two most well-characterised members, dysferlin and otoferlin, have been implicated in human disease []. This is central domain B in proteins of the Ferlin family [].; GO: 0016021 integral to membrane
Probab=27.27 E-value=27 Score=24.27 Aligned_cols=10 Identities=50% Similarity=0.816 Sum_probs=8.2
Q ss_pred CCceeEEeee
Q psy2574 40 CYKITTVFSH 49 (115)
Q Consensus 40 C~n~q~VFSH 49 (115)
|+++|++|=.
T Consensus 43 CGk~qt~flk 52 (76)
T PF08150_consen 43 CGKIQTLFLK 52 (76)
T ss_pred cCeeEEEEEE
Confidence 8899988854
No 150
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=27.26 E-value=34 Score=21.23 Aligned_cols=28 Identities=29% Similarity=0.763 Sum_probs=17.3
Q ss_pred eCCCCCceeE--Ee---eecceeEEcCCCCeee
Q psy2574 36 KCPGCYKITT--VF---SHAQSVVICAGCSTIL 63 (115)
Q Consensus 36 KCp~C~n~q~--VF---SHAqt~V~C~~Cg~vL 63 (115)
.|.+|+-.=- .+ -.....+.|..||..|
T Consensus 24 ~C~gC~~~l~~~~~~~i~~~~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 24 TCSGCHMELPPQELNEIRKGDEIVFCPNCGRIL 56 (56)
T ss_pred ccCCCCEEcCHHHHHHHHcCCCeEECcCCCccC
Confidence 7888863210 01 1224789999999876
No 151
>COG0777 AccD Acetyl-CoA carboxylase beta subunit [Lipid metabolism]
Probab=27.03 E-value=30 Score=29.61 Aligned_cols=31 Identities=19% Similarity=0.522 Sum_probs=20.5
Q ss_pred eEEeCCCCCceeEEeeecceeEEcCCCCeee
Q psy2574 33 MDVKCPGCYKITTVFSHAQSVVICAGCSTIL 63 (115)
Q Consensus 33 m~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL 63 (115)
+-+|||.|+..---=.=-+..-.|..|+.-.
T Consensus 27 lw~KCp~c~~~~y~~eL~~n~~vcp~c~~h~ 57 (294)
T COG0777 27 LWTKCPSCGEMLYRKELESNLKVCPKCGHHM 57 (294)
T ss_pred ceeECCCccceeeHHHHHhhhhcccccCccc
Confidence 5589999986432222345567799998765
No 152
>COG3088 CcmH Uncharacterized protein involved in biosynthesis of c-type cytochromes [Posttranslational modification, protein turnover, chaperones]
Probab=26.82 E-value=27 Score=27.31 Aligned_cols=37 Identities=24% Similarity=0.438 Sum_probs=27.7
Q ss_pred cccCCCCHHHHHHhhcccccccCCCCceeEEeCCCCCceeEEeeecc
Q psy2574 5 KDLLHPSQAEEKRKHKLKRLVQHPNSYFMDVKCPGCYKITTVFSHAQ 51 (115)
Q Consensus 5 ~DLl~Ps~e~ek~k~K~krLV~~PnS~Fm~VKCp~C~n~q~VFSHAq 51 (115)
.+....++++|+|.+-.- =..+||.|.|..|.=|.|.
T Consensus 25 d~~~f~~~~qe~ra~~Lt----------~~LRCp~CQNqsIadSnA~ 61 (153)
T COG3088 25 DTEQFADPAQEQRARALT----------EELRCPQCQNQSIADSNAP 61 (153)
T ss_pred CcccCCCHHHHHHHHHHH----------HhcCCCcCCCCChhhhccH
Confidence 366778899998877321 2378999999999877764
No 153
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=26.74 E-value=48 Score=28.09 Aligned_cols=35 Identities=29% Similarity=0.535 Sum_probs=19.2
Q ss_pred CCceeEEeCCCCCceeEE--eee-----cceeEEcCCCCeee
Q psy2574 29 NSYFMDVKCPGCYKITTV--FSH-----AQSVVICAGCSTIL 63 (115)
Q Consensus 29 nS~Fm~VKCp~C~n~q~V--FSH-----Aqt~V~C~~Cg~vL 63 (115)
.=+|.+++|+.|++..-+ |+- +--+-.|..|++=|
T Consensus 221 eW~~~R~~C~~Cg~~~~l~y~~~~~~~~~~r~e~C~~C~~Yl 262 (309)
T PRK03564 221 EWHVVRVKCSNCEQSGKLHYWSLDSEQAAVKAESCGDCGTYL 262 (309)
T ss_pred cccccCccCCCCCCCCceeeeeecCCCcceEeeecccccccc
Confidence 345778888888875322 211 11334566666544
No 154
>PHA02942 putative transposase; Provisional
Probab=26.68 E-value=49 Score=28.20 Aligned_cols=29 Identities=24% Similarity=0.469 Sum_probs=20.2
Q ss_pred eEEeCCCCCceeEEeeecceeEEcCCCCeee
Q psy2574 33 MDVKCPGCYKITTVFSHAQSVVICAGCSTIL 63 (115)
Q Consensus 33 m~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL 63 (115)
=.-.||.|+.+.. +.+.-...|..||..+
T Consensus 324 TSq~Cs~CG~~~~--~l~~r~f~C~~CG~~~ 352 (383)
T PHA02942 324 SSVSCPKCGHKMV--EIAHRYFHCPSCGYEN 352 (383)
T ss_pred CCccCCCCCCccC--cCCCCEEECCCCCCEe
Confidence 4567888887653 3345578888888764
No 155
>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=26.51 E-value=53 Score=19.02 Aligned_cols=24 Identities=25% Similarity=0.473 Sum_probs=15.0
Q ss_pred EeCCCCCceeEEeeecceeEEcCCCCe
Q psy2574 35 VKCPGCYKITTVFSHAQSVVICAGCST 61 (115)
Q Consensus 35 VKCp~C~n~q~VFSHAqt~V~C~~Cg~ 61 (115)
-+|+.|+.+-.- ....-.|.+||.
T Consensus 3 ~~C~~CG~i~~g---~~~p~~CP~Cg~ 26 (34)
T cd00729 3 WVCPVCGYIHEG---EEAPEKCPICGA 26 (34)
T ss_pred EECCCCCCEeEC---CcCCCcCcCCCC
Confidence 468888876332 223457888876
No 156
>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=26.31 E-value=63 Score=18.38 Aligned_cols=28 Identities=14% Similarity=0.603 Sum_probs=14.0
Q ss_pred CCceeEEeCCCCCceeEEeeecceeEEcCCCCe
Q psy2574 29 NSYFMDVKCPGCYKITTVFSHAQSVVICAGCST 61 (115)
Q Consensus 29 nS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~ 61 (115)
+..++--+|.+|+.++. .- ...|..|+.
T Consensus 6 ~~~l~~~rC~~Cg~~~~----pP-r~~Cp~C~s 33 (37)
T PF12172_consen 6 EGRLLGQRCRDCGRVQF----PP-RPVCPHCGS 33 (37)
T ss_dssp TT-EEEEE-TTT--EEE----S---SEETTTT-
T ss_pred CCEEEEEEcCCCCCEec----CC-CcCCCCcCc
Confidence 45678888999987732 21 255677764
No 157
>COG2023 RPR2 RNase P subunit RPR2 [Translation, ribosomal structure and biogenesis]
Probab=26.20 E-value=93 Score=22.94 Aligned_cols=33 Identities=33% Similarity=0.667 Sum_probs=24.7
Q ss_pred eCCCCCce-------eEEeeecceeEEcCCCCeeeecccC
Q psy2574 36 KCPGCYKI-------TTVFSHAQSVVICAGCSTILCQPTG 68 (115)
Q Consensus 36 KCp~C~n~-------q~VFSHAqt~V~C~~Cg~vL~~PTG 68 (115)
-|.+|+.. .+-+--...+|.|..||...--|-|
T Consensus 58 ~CkkC~t~Lvpg~n~rvR~~~~~v~vtC~~CG~~~R~p~~ 97 (105)
T COG2023 58 ICKKCYTPLVPGKNARVRLRKGRVVVTCLECGTIRRYPYG 97 (105)
T ss_pred hccccCcccccCcceEEEEcCCeEEEEecCCCcEEEeccc
Confidence 48888763 4555555688999999998877776
No 158
>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=26.12 E-value=86 Score=19.32 Aligned_cols=29 Identities=17% Similarity=0.344 Sum_probs=17.3
Q ss_pred eCCCCCceeEEee------ecceeEEcCCCCeeee
Q psy2574 36 KCPGCYKITTVFS------HAQSVVICAGCSTILC 64 (115)
Q Consensus 36 KCp~C~n~q~VFS------HAqt~V~C~~Cg~vL~ 64 (115)
-||-|+.....|- .-...+.|..||....
T Consensus 3 PCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~ 37 (53)
T TIGR03655 3 PCPFCGGADVYLRRGFDPLDLSHYFECSTCGASGP 37 (53)
T ss_pred CCCCCCCcceeeEeccCCCCCEEEEECCCCCCCcc
Confidence 3788887666342 2233447888877643
No 159
>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=25.49 E-value=33 Score=26.19 Aligned_cols=26 Identities=8% Similarity=0.144 Sum_probs=15.2
Q ss_pred eCCCCCceeEEeeecceeEEcCCCCeee
Q psy2574 36 KCPGCYKITTVFSHAQSVVICAGCSTIL 63 (115)
Q Consensus 36 KCp~C~n~q~VFSHAqt~V~C~~Cg~vL 63 (115)
.||.|+..- |.-...++.|..||++.
T Consensus 11 ~Cp~cg~kF--YDLnk~p~vcP~cg~~~ 36 (129)
T TIGR02300 11 ICPNTGSKF--YDLNRRPAVSPYTGEQF 36 (129)
T ss_pred cCCCcCccc--cccCCCCccCCCcCCcc
Confidence 366665432 33344677777777764
No 160
>PF14206 Cys_rich_CPCC: Cysteine-rich CPCC
Probab=25.05 E-value=54 Score=22.73 Aligned_cols=26 Identities=27% Similarity=0.406 Sum_probs=13.5
Q ss_pred EeCCCCCceeEEeeecceeEEcCCCC
Q psy2574 35 VKCPGCYKITTVFSHAQSVVICAGCS 60 (115)
Q Consensus 35 VKCp~C~n~q~VFSHAqt~V~C~~Cg 60 (115)
++||=|+..++-=.-..+--.|.+|+
T Consensus 2 ~~CPCCg~~Tl~~~~~~~ydIC~VC~ 27 (78)
T PF14206_consen 2 YPCPCCGYYTLEERGEGTYDICPVCF 27 (78)
T ss_pred ccCCCCCcEEeccCCCcCceECCCCC
Confidence 46776666554322222344566664
No 161
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=24.93 E-value=59 Score=26.11 Aligned_cols=27 Identities=19% Similarity=0.383 Sum_probs=18.2
Q ss_pred eCCCCCceeEEeeecceeEEcCCCCeee
Q psy2574 36 KCPGCYKITTVFSHAQSVVICAGCSTIL 63 (115)
Q Consensus 36 KCp~C~n~q~VFSHAqt~V~C~~Cg~vL 63 (115)
-|+.|+....+ .+....-.|..||...
T Consensus 101 fC~~CG~~~~~-~~~~~~~~C~~c~~~~ 127 (256)
T PRK00241 101 FCGYCGHPMHP-SKTEWAMLCPHCRERY 127 (256)
T ss_pred cccccCCCCee-cCCceeEECCCCCCEE
Confidence 48888876544 4566777788887544
No 162
>COG5347 GTPase-activating protein that regulates ARFs (ADP-ribosylation factors), involved in ARF-mediated vesicular transport [Intracellular trafficking and secretion]
Probab=24.84 E-value=22 Score=30.23 Aligned_cols=59 Identities=29% Similarity=0.498 Sum_probs=41.2
Q ss_pred EeCCCCCceeEEeeec-ceeEEcCCCCeeeecccCCceeeccCCCCccEEEEEeecCCCCCCccceeEEeecccc
Q psy2574 35 VKCPGCYKITTVFSHA-QSVVICAGCSTILCQPTGGRARLTEDDTGDSMTVRGCALDSGTPTTDTELIRMSHCGG 108 (115)
Q Consensus 35 VKCp~C~n~q~VFSHA-qt~V~C~~Cg~vL~~PTGGKA~l~egc~f~s~~~~~ca~ds~~~~~d~~~~~~~~~~~ 108 (115)
-+|-||++....+.-- =-++.|..|..+.- .|+-.- --++.-.+|. |+.+||.||-| ||
T Consensus 21 k~CaDCga~~P~W~S~nlGvfiCi~CagvHR-------sLGvhi----S~VKSitLD~---wt~~~l~~m~~-gG 80 (319)
T COG5347 21 KKCADCGAPNPTWASVNLGVFLCIDCAGVHR-------SLGVHI----SKVKSLTLDN---WTEEELRRMEV-GG 80 (319)
T ss_pred CccccCCCCCCceEecccCeEEEeecchhhh-------ccccce----eeeeeeeccc---CCHHHHHHHHH-hc
Confidence 4799999998777543 34778999988761 122221 2255556665 99999999998 65
No 163
>PF09947 DUF2180: Uncharacterized protein conserved in archaea (DUF2180); InterPro: IPR017211 This group represents a predicted zinc finger protein, AF1427 type.
Probab=24.70 E-value=17 Score=24.89 Aligned_cols=27 Identities=30% Similarity=0.716 Sum_probs=20.8
Q ss_pred eCCCCCceeEEeeecceeEEcCCCCeeeec
Q psy2574 36 KCPGCYKITTVFSHAQSVVICAGCSTILCQ 65 (115)
Q Consensus 36 KCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~ 65 (115)
||-+|..+.. -+..+-.|.+||.-||.
T Consensus 2 kCY~Ca~~gk---dt~AVavCivCG~GlC~ 28 (68)
T PF09947_consen 2 KCYDCAEEGK---DTDAVAVCIVCGAGLCM 28 (68)
T ss_pred cchhhhhcCC---CccceehHHhcCchhhH
Confidence 6777777766 34677889999998874
No 164
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.17 E-value=31 Score=26.31 Aligned_cols=57 Identities=19% Similarity=0.263 Sum_probs=39.1
Q ss_pred ccCCCCceeEEeCCCCCceeEEeeecceeEEcCCCCeeeecccCCceeeccCCCCccEEEEE
Q psy2574 25 VQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLTEDDTGDSMTVRG 86 (115)
Q Consensus 25 V~~PnS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PTGGKA~l~egc~f~s~~~~~ 86 (115)
+..|=..=++-.||.|++=..-=.--..+-.|..||.-+ |.++-.+|=.|-++.|.|
T Consensus 12 ~~~pi~~Gl~grCP~CGeGrLF~gFLK~~p~C~aCG~dy-----g~~~a~DgPa~fvI~IvG 68 (126)
T COG5349 12 VVTPIKRGLRGRCPRCGEGRLFRGFLKVVPACEACGLDY-----GFADADDGPAYFVILIVG 68 (126)
T ss_pred cCcHHHHHhcCCCCCCCCchhhhhhcccCchhhhccccc-----cCCcccCCCcEEEEEeec
Confidence 334444446788999998655433445567899999887 667777777777776655
No 165
>smart00336 BBOX B-Box-type zinc finger.
Probab=24.07 E-value=56 Score=18.10 Aligned_cols=28 Identities=18% Similarity=0.449 Sum_probs=20.2
Q ss_pred EeCCCCC-ceeEEeeecceeEEcCCCCee
Q psy2574 35 VKCPGCY-KITTVFSHAQSVVICAGCSTI 62 (115)
Q Consensus 35 VKCp~C~-n~q~VFSHAqt~V~C~~Cg~v 62 (115)
..|+.+. +.-.+|...-..+.|..|-..
T Consensus 4 ~~C~~h~~~~~~~~C~~c~~~iC~~C~~~ 32 (42)
T smart00336 4 PKCDSHGDEPAEFFCEECGALLCRTCDEA 32 (42)
T ss_pred CcCCCCCCCceEEECCCCCcccccccChh
Confidence 4588887 555778888777888887643
No 166
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=23.88 E-value=68 Score=27.83 Aligned_cols=35 Identities=20% Similarity=0.434 Sum_probs=24.1
Q ss_pred EeCCCCCceeEEee-ecceeEEcCCCCeeeecccCC
Q psy2574 35 VKCPGCYKITTVFS-HAQSVVICAGCSTILCQPTGG 69 (115)
Q Consensus 35 VKCp~C~n~q~VFS-HAqt~V~C~~Cg~vL~~PTGG 69 (115)
+-|++|....-+=. .......|.-||.+|.+...+
T Consensus 11 ~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~~~~~~ 46 (419)
T PRK15103 11 ILCPQCDMLVALPRLEHGQKAACPRCGTTLTVRWDE 46 (419)
T ss_pred ccCCCCCceeecCCCCCCCeeECCCCCCCCcCCCCC
Confidence 66999998754332 223357799999999766543
No 167
>PF14353 CpXC: CpXC protein
Probab=23.79 E-value=57 Score=22.93 Aligned_cols=18 Identities=17% Similarity=0.554 Sum_probs=14.6
Q ss_pred CCceeEEeCCCCCceeEE
Q psy2574 29 NSYFMDVKCPGCYKITTV 46 (115)
Q Consensus 29 nS~Fm~VKCp~C~n~q~V 46 (115)
+..|..+.||.|+....+
T Consensus 33 ~g~l~~~~CP~Cg~~~~~ 50 (128)
T PF14353_consen 33 DGSLFSFTCPSCGHKFRL 50 (128)
T ss_pred cCCcCEEECCCCCCceec
Confidence 778888999999987643
No 168
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 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 predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=23.63 E-value=54 Score=18.93 Aligned_cols=22 Identities=18% Similarity=0.480 Sum_probs=12.4
Q ss_pred ecceeEEcCCCCeeeecccCCc
Q psy2574 49 HAQSVVICAGCSTILCQPTGGR 70 (115)
Q Consensus 49 HAqt~V~C~~Cg~vL~~PTGGK 70 (115)
.....+.|..|+.++....||-
T Consensus 12 ~~~~~a~C~~C~~~~~~~~~~t 33 (45)
T PF02892_consen 12 GDKKKAKCKYCGKVIKYSSGGT 33 (45)
T ss_dssp GCSS-EEETTTTEE-----SST
T ss_pred CCcCeEEeCCCCeEEeeCCCcH
Confidence 4567889999999998875554
No 169
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=23.09 E-value=44 Score=21.96 Aligned_cols=17 Identities=29% Similarity=0.841 Sum_probs=13.2
Q ss_pred eEEcCCCCeeeecccCC
Q psy2574 53 VVICAGCSTILCQPTGG 69 (115)
Q Consensus 53 ~V~C~~Cg~vL~~PTGG 69 (115)
.-+|..||+++|.--|.
T Consensus 18 ~~NCl~CGkIiC~~Eg~ 34 (57)
T PF06221_consen 18 APNCLNCGKIICEQEGP 34 (57)
T ss_pred cccccccChhhcccccC
Confidence 45788888888887764
No 170
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=22.98 E-value=73 Score=18.82 Aligned_cols=14 Identities=21% Similarity=0.567 Sum_probs=8.2
Q ss_pred ceeEEcCCCCeeee
Q psy2574 51 QSVVICAGCSTILC 64 (115)
Q Consensus 51 qt~V~C~~Cg~vL~ 64 (115)
+..+.|..|+..++
T Consensus 2 ~~~~~C~nC~R~v~ 15 (33)
T PF08209_consen 2 SPYVECPNCGRPVA 15 (33)
T ss_dssp S-EEE-TTTSSEEE
T ss_pred CCeEECCCCcCCcc
Confidence 34577777777764
No 171
>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=22.96 E-value=39 Score=23.12 Aligned_cols=23 Identities=30% Similarity=0.911 Sum_probs=10.9
Q ss_pred EeCCCCCceeEEeeecceeEEcCCCCe
Q psy2574 35 VKCPGCYKITTVFSHAQSVVICAGCST 61 (115)
Q Consensus 35 VKCp~C~n~q~VFSHAqt~V~C~~Cg~ 61 (115)
.+|-.|++++- -.+.+.|..||.
T Consensus 10 lrC~aCf~~t~----~~~k~FCp~CGn 32 (73)
T PF08772_consen 10 LRCHACFKITK----DMTKQFCPKCGN 32 (73)
T ss_dssp EE-SSS--EES-----SS--S-SSS--
T ss_pred EEccccccCcC----CCCceeCcccCC
Confidence 57888988775 457788999985
No 172
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=22.85 E-value=47 Score=18.20 Aligned_cols=25 Identities=16% Similarity=0.539 Sum_probs=18.4
Q ss_pred eCCCCCc-eeEEeeecceeEEcCCCC
Q psy2574 36 KCPGCYK-ITTVFSHAQSVVICAGCS 60 (115)
Q Consensus 36 KCp~C~n-~q~VFSHAqt~V~C~~Cg 60 (115)
.|+.+.+ .-.+|..+-....|..|.
T Consensus 2 ~C~~H~~~~~~~fC~~~~~~iC~~C~ 27 (39)
T cd00021 2 LCDEHGEEPLSLFCETDRALLCVDCD 27 (39)
T ss_pred CCCccCCcceEEEeCccChhhhhhcC
Confidence 5777866 557787777777777775
No 173
>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=22.63 E-value=86 Score=19.65 Aligned_cols=17 Identities=18% Similarity=0.448 Sum_probs=12.0
Q ss_pred eecceeEEcCCCCeeee
Q psy2574 48 SHAQSVVICAGCSTILC 64 (115)
Q Consensus 48 SHAqt~V~C~~Cg~vL~ 64 (115)
+.......|..||+.|.
T Consensus 43 ~~~~~r~FC~~CGs~l~ 59 (92)
T PF04828_consen 43 GKGVERYFCPTCGSPLF 59 (92)
T ss_dssp TSSCEEEEETTT--EEE
T ss_pred CCcCcCcccCCCCCeee
Confidence 45556788999999998
No 174
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=22.59 E-value=69 Score=20.75 Aligned_cols=21 Identities=29% Similarity=0.805 Sum_probs=16.0
Q ss_pred EeCCCCCceeEEeeecceeEEcCCCCe
Q psy2574 35 VKCPGCYKITTVFSHAQSVVICAGCST 61 (115)
Q Consensus 35 VKCp~C~n~q~VFSHAqt~V~C~~Cg~ 61 (115)
+.||.|++... .-..|..||.
T Consensus 28 ~~C~~CG~~~~------~H~vC~~CG~ 48 (57)
T PRK12286 28 VECPNCGEPKL------PHRVCPSCGY 48 (57)
T ss_pred eECCCCCCccC------CeEECCCCCc
Confidence 78999998653 3467888884
No 175
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=22.39 E-value=33 Score=17.97 Aligned_cols=23 Identities=26% Similarity=0.609 Sum_probs=14.6
Q ss_pred EeCCCCCceeEEeeecceeEEcCCCCee
Q psy2574 35 VKCPGCYKITTVFSHAQSVVICAGCSTI 62 (115)
Q Consensus 35 VKCp~C~n~q~VFSHAqt~V~C~~Cg~v 62 (115)
..|+.|...+ ......|..|++.
T Consensus 3 W~C~~C~~~N-----~~~~~~C~~C~~p 25 (26)
T smart00547 3 WECPACTFLN-----FASRSKCFACGAP 25 (26)
T ss_pred ccCCCCCCcC-----hhhhccccccCCc
Confidence 4688887544 2344578888764
No 176
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=22.34 E-value=70 Score=23.73 Aligned_cols=36 Identities=19% Similarity=0.362 Sum_probs=23.0
Q ss_pred EEeCCCCCceeEEeeecceeEEcCCCCeeeecccCCcee
Q psy2574 34 DVKCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRAR 72 (115)
Q Consensus 34 ~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PTGGKA~ 72 (115)
..+|.+|... |.--.....|+.||..-.+=.+|+.-
T Consensus 70 ~~~C~~C~~~---~~~e~~~~~CP~C~s~~~~i~~G~el 105 (115)
T COG0375 70 ECWCLDCGQE---VELEELDYRCPKCGSINLRIIGGDEL 105 (115)
T ss_pred EEEeccCCCe---ecchhheeECCCCCCCceEEecCCee
Confidence 5789999433 23223334499999877666666643
No 177
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=22.13 E-value=1.3e+02 Score=16.95 Aligned_cols=10 Identities=20% Similarity=0.644 Sum_probs=5.6
Q ss_pred cCCCCeeeec
Q psy2574 56 CAGCSTILCQ 65 (115)
Q Consensus 56 C~~Cg~vL~~ 65 (115)
|..||..+..
T Consensus 35 C~~CGE~~~~ 44 (46)
T TIGR03831 35 CPQCGEEYLD 44 (46)
T ss_pred cccCCCEeeC
Confidence 6666665543
No 178
>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=22.12 E-value=23 Score=29.34 Aligned_cols=29 Identities=21% Similarity=0.771 Sum_probs=20.7
Q ss_pred eEEeCCCCCceeEEeee--cceeEEcCCCCeee
Q psy2574 33 MDVKCPGCYKITTVFSH--AQSVVICAGCSTIL 63 (115)
Q Consensus 33 m~VKCp~C~n~q~VFSH--Aqt~V~C~~Cg~vL 63 (115)
+-+|||.|+++ +|.. ...--.|..||.-+
T Consensus 25 ~~~~c~~c~~~--~~~~~l~~~~~vc~~c~~h~ 55 (285)
T TIGR00515 25 VWTKCPKCGQV--LYTKELERNLEVCPKCDHHM 55 (285)
T ss_pred CeeECCCCcch--hhHHHHHhhCCCCCCCCCcC
Confidence 67999999975 4443 23446799999864
No 179
>COG0846 SIR2 NAD-dependent protein deacetylases, SIR2 family [Transcription]
Probab=21.85 E-value=53 Score=26.82 Aligned_cols=39 Identities=18% Similarity=0.405 Sum_probs=26.9
Q ss_pred CCceeEEeCCCCCceeE-----EeeecceeEEcCCCCeeeeccc
Q psy2574 29 NSYFMDVKCPGCYKITT-----VFSHAQSVVICAGCSTILCQPT 67 (115)
Q Consensus 29 nS~Fm~VKCp~C~n~q~-----VFSHAqt~V~C~~Cg~vL~~PT 67 (115)
...+..+.|..|++..- .+-+..-+..|..||..+.+|.
T Consensus 117 HGsl~~~~C~~C~~~~~~~~~~~~~~~~~~p~C~~Cg~~~lrP~ 160 (250)
T COG0846 117 HGSLKRVRCSKCGNQYYDEDVIKFIEDGLIPRCPKCGGPVLRPD 160 (250)
T ss_pred ccceeeeEeCCCcCccchhhhhhhcccCCCCcCccCCCccccCC
Confidence 35678899999986543 2333334678999999655664
No 180
>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=21.68 E-value=2e+02 Score=24.61 Aligned_cols=45 Identities=24% Similarity=0.405 Sum_probs=26.4
Q ss_pred CCce-eEEeCCCCCceeEEe-eec----ceeEEcCCCCeeeec-ccCCceeec
Q psy2574 29 NSYF-MDVKCPGCYKITTVF-SHA----QSVVICAGCSTILCQ-PTGGRARLT 74 (115)
Q Consensus 29 nS~F-m~VKCp~C~n~q~VF-SHA----qt~V~C~~Cg~vL~~-PTGGKA~l~ 74 (115)
..++ ..+.|+.|+.+|+.- +.- ...-.| .||..-.. +++|+++|.
T Consensus 163 ~~~~P~~p~c~~cg~~~~~v~~~d~~~~~v~y~c-~cG~~g~~~~~~g~~KL~ 214 (353)
T cd00674 163 ETWYPFMPYCEKCGKDTTTVEAYDAKAGTVTYKC-ECGHEETVDIRTGRGKLT 214 (353)
T ss_pred CCceeeeeecCCcCcceeEEEEEeCCCCeEEEEc-CCCCEEEEeecCCCcccC
Confidence 4333 578999999775432 332 223345 48866544 567776664
No 181
>PF05280 FlhC: Flagellar transcriptional activator (FlhC); InterPro: IPR007944 This family consists of several bacterial flagellar transcriptional activator (FlhC) proteins. FlhC combines with FlhD to form a regulatory complex in Escherichia coli, this complex has been shown to be a global regulator involved in many cellular processes as well as a flagellar transcriptional activator [].; GO: 0003677 DNA binding, 0030092 regulation of flagellum assembly, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2AVU_E.
Probab=21.61 E-value=67 Score=24.92 Aligned_cols=30 Identities=17% Similarity=0.409 Sum_probs=15.5
Q ss_pred eeEEeCCCCCceeEEeeec-ceeEEcCCCCe
Q psy2574 32 FMDVKCPGCYKITTVFSHA-QSVVICAGCST 61 (115)
Q Consensus 32 Fm~VKCp~C~n~q~VFSHA-qt~V~C~~Cg~ 61 (115)
..-..|..|+..-|+-.|. ...+.|..|..
T Consensus 132 l~l~~C~~C~~~fv~~~~~~~~~~~Cp~C~~ 162 (175)
T PF05280_consen 132 LQLAPCRRCGGHFVTHAHDPRHSFVCPFCQP 162 (175)
T ss_dssp EEEEE-TTT--EEEEESS--SS----TT---
T ss_pred ccccCCCCCCCCeECcCCCCCcCcCCCCCCC
Confidence 4567899999999987776 67899999994
No 182
>COG1644 RPB10 DNA-directed RNA polymerase, subunit N (RpoN/RPB10) [Transcription]
Probab=21.50 E-value=32 Score=23.45 Aligned_cols=13 Identities=23% Similarity=0.588 Sum_probs=10.9
Q ss_pred eeEEcCCCCeeee
Q psy2574 52 SVVICAGCSTILC 64 (115)
Q Consensus 52 t~V~C~~Cg~vL~ 64 (115)
.+|+|-.||++++
T Consensus 3 iPiRCFsCGkvi~ 15 (63)
T COG1644 3 IPVRCFSCGKVIG 15 (63)
T ss_pred CceEeecCCCCHH
Confidence 4789999999885
No 183
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=21.32 E-value=44 Score=30.82 Aligned_cols=32 Identities=19% Similarity=0.310 Sum_probs=19.3
Q ss_pred eCCCCCceeEEeeecceeEEcCCCCeeeecccCCceeec
Q psy2574 36 KCPGCYKITTVFSHAQSVVICAGCSTILCQPTGGRARLT 74 (115)
Q Consensus 36 KCp~C~n~q~VFSHAqt~V~C~~Cg~vL~~PTGGKA~l~ 74 (115)
+||.|+.+ -+...-.|..||+.+.++ ..|.|+
T Consensus 29 ~Cp~CG~~-----~~~~~~fC~~CG~~~~~~--~~~~~~ 60 (645)
T PRK14559 29 PCPQCGTE-----VPVDEAHCPNCGAETGTI--WWAIIA 60 (645)
T ss_pred cCCCCCCC-----CCcccccccccCCcccch--hhhhcc
Confidence 47777666 234445677777776555 555554
No 184
>PRK05638 threonine synthase; Validated
Probab=21.23 E-value=56 Score=27.81 Aligned_cols=26 Identities=27% Similarity=0.697 Sum_probs=17.8
Q ss_pred EEeCCCCCceeEEeeecceeEEcCCCCeeee
Q psy2574 34 DVKCPGCYKITTVFSHAQSVVICAGCSTILC 64 (115)
Q Consensus 34 ~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL~ 64 (115)
+.+|..|+.+ |+ ......| .||-.|-
T Consensus 1 ~l~C~~Cg~~---~~-~~~~~~C-~c~~~l~ 26 (442)
T PRK05638 1 KMKCPKCGRE---YN-SYIPPFC-ICGELLE 26 (442)
T ss_pred CeEeCCCCCC---CC-CCCceec-CCCCcEE
Confidence 3689999987 44 3334789 7986653
No 185
>cd01411 SIR2H SIR2H: Uncharacterized prokaryotic Sir2 homologs from several gram positive bacterial species and Fusobacteria; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=21.00 E-value=45 Score=25.99 Aligned_cols=38 Identities=16% Similarity=0.264 Sum_probs=22.5
Q ss_pred ccCCCCceeEEeCCCCCceeEEeeecceeEEcCCCCeee
Q psy2574 25 VQHPNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTIL 63 (115)
Q Consensus 25 V~~PnS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~vL 63 (115)
|=+.-..+..++|..|.... .+.-...+-.|..||.+|
T Consensus 109 v~elHG~~~~~~C~~C~~~~-~~~~~~~~p~C~~Cgg~l 146 (225)
T cd01411 109 VVEFHGSLYRIYCTVCGKTV-DWEEYLKSPYHAKCGGVI 146 (225)
T ss_pred EEEeCCCcCeeEeCCCCCcc-chhhcCCCCCCCCCCCEe
Confidence 33455667778999996542 222222346798897543
No 186
>PRK07218 replication factor A; Provisional
Probab=20.73 E-value=56 Score=28.70 Aligned_cols=27 Identities=19% Similarity=0.571 Sum_probs=17.4
Q ss_pred CCCceeEEeCCCCCceeEEeeecceeEEcCCCCee
Q psy2574 28 PNSYFMDVKCPGCYKITTVFSHAQSVVICAGCSTI 62 (115)
Q Consensus 28 PnS~Fm~VKCp~C~n~q~VFSHAqt~V~C~~Cg~v 62 (115)
+.|-|++ +||.|.+.- ..-.|..||.+
T Consensus 292 ~gsgli~-rCP~C~r~v-------~~~~C~~hG~v 318 (423)
T PRK07218 292 DGSGLIE-RCPECGRVI-------QKGQCRSHGAV 318 (423)
T ss_pred cCCccee-cCcCccccc-------cCCcCCCCCCc
Confidence 3445443 788887754 22578888876
No 187
>PRK07562 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=20.59 E-value=80 Score=31.72 Aligned_cols=28 Identities=21% Similarity=0.544 Sum_probs=23.2
Q ss_pred eEEeCCCCCceeEEeeecceeEEcCCCCee
Q psy2574 33 MDVKCPGCYKITTVFSHAQSVVICAGCSTI 62 (115)
Q Consensus 33 m~VKCp~C~n~q~VFSHAqt~V~C~~Cg~v 62 (115)
.-.-|+.|+|.++| +--|-..|..||.+
T Consensus 1189 ~g~~c~~cg~~~~v--rngtc~~c~~cg~t 1216 (1220)
T PRK07562 1189 TGEACSECGNFTLV--RNGTCLKCDTCGST 1216 (1220)
T ss_pred CCCcCCCcCCeEEE--eCCeeeeccccCCC
Confidence 55669999999987 66788889999975
No 188
>PF08821 CGGC: CGGC domain; InterPro: IPR014925 Proteins in this entry are a quite highly conserved sequence of CGGC in its central region. The region has many conserved cysteines and histidines suggestive of a zinc binding function.
Probab=20.56 E-value=63 Score=23.12 Aligned_cols=13 Identities=46% Similarity=0.961 Sum_probs=11.7
Q ss_pred ccceeEEeecccc
Q psy2574 96 TDTELIRMSHCGG 108 (115)
Q Consensus 96 ~d~~~~~~~~~~~ 108 (115)
.|.|||=|.+|||
T Consensus 36 ~~~elvgf~~CgG 48 (107)
T PF08821_consen 36 EDVELVGFFTCGG 48 (107)
T ss_pred CCeEEEEEeeCCC
Confidence 4799999999998
No 189
>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=20.15 E-value=48 Score=19.66 Aligned_cols=13 Identities=23% Similarity=0.465 Sum_probs=6.1
Q ss_pred EcCCCCeeeeccc
Q psy2574 55 ICAGCSTILCQPT 67 (115)
Q Consensus 55 ~C~~Cg~vL~~PT 67 (115)
.|..||..|.+=+
T Consensus 3 ~CP~Cg~~lv~r~ 15 (39)
T PF01396_consen 3 KCPKCGGPLVLRR 15 (39)
T ss_pred CCCCCCceeEEEE
Confidence 4445554444444
No 190
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=20.10 E-value=41 Score=25.64 Aligned_cols=20 Identities=15% Similarity=0.562 Sum_probs=12.9
Q ss_pred EcCCCCeeeecccCCceeeccCC
Q psy2574 55 ICAGCSTILCQPTGGRARLTEDD 77 (115)
Q Consensus 55 ~C~~Cg~vL~~PTGGKA~l~egc 77 (115)
.|..||+++ +.|-+- |..||
T Consensus 3 ~Ct~Cg~~f--~dgs~e-il~GC 22 (131)
T PF09845_consen 3 QCTKCGRVF--EDGSKE-ILSGC 22 (131)
T ss_pred ccCcCCCCc--CCCcHH-HHccC
Confidence 477777777 554443 67777
Done!