Query psy10712
Match_columns 75
No_of_seqs 102 out of 225
Neff 4.3
Searched_HMMs 46136
Date Fri Aug 16 16:41:57 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10712.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10712hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF09538 FYDLN_acid: Protein o 92.2 0.094 2E-06 34.9 1.7 33 15-48 6-39 (108)
2 smart00714 LITAF Possible memb 91.7 0.086 1.9E-06 31.4 1.0 18 15-32 49-66 (67)
3 PRK00398 rpoP DNA-directed RNA 90.3 0.37 7.9E-06 26.8 2.7 27 19-45 4-31 (46)
4 PF10601 zf-LITAF-like: LITAF- 90.2 0.16 3.4E-06 30.7 1.2 18 15-32 55-72 (73)
5 TIGR02300 FYDLN_acid conserved 90.0 0.21 4.5E-06 34.7 1.7 35 15-50 6-41 (129)
6 PF12773 DZR: Double zinc ribb 87.2 0.34 7.3E-06 26.9 1.1 32 16-48 10-42 (50)
7 PF12760 Zn_Tnp_IS1595: Transp 85.7 0.55 1.2E-05 26.2 1.5 14 13-27 14-27 (46)
8 PF13408 Zn_ribbon_recom: Reco 82.4 1.2 2.6E-05 24.7 2.0 21 15-36 2-22 (58)
9 PF10571 UPF0547: Uncharacteri 81.8 0.98 2.1E-05 23.1 1.3 21 20-44 2-23 (26)
10 PF13717 zinc_ribbon_4: zinc-r 81.4 0.92 2E-05 24.5 1.2 11 18-28 2-12 (36)
11 PF09862 DUF2089: Protein of u 79.6 0.74 1.6E-05 31.1 0.5 27 21-51 1-28 (113)
12 PF13248 zf-ribbon_3: zinc-rib 77.5 0.86 1.9E-05 22.9 0.3 13 16-28 14-26 (26)
13 PF13719 zinc_ribbon_5: zinc-r 77.4 1.5 3.2E-05 23.7 1.2 10 18-27 2-11 (37)
14 PRK00420 hypothetical protein; 76.8 1.7 3.6E-05 29.3 1.6 26 19-45 24-50 (112)
15 smart00531 TFIIE Transcription 76.5 1.4 3E-05 29.9 1.1 18 15-32 120-137 (147)
16 TIGR02098 MJ0042_CXXC MJ0042 f 76.0 1.8 3.8E-05 22.8 1.3 13 16-28 23-35 (38)
17 PF13240 zinc_ribbon_2: zinc-r 75.6 1.3 2.8E-05 22.0 0.6 21 20-44 1-22 (23)
18 PF03966 Trm112p: Trm112p-like 73.9 1.7 3.7E-05 25.9 1.0 14 13-26 48-61 (68)
19 PF11781 RRN7: RNA polymerase 72.7 1.3 2.9E-05 24.1 0.3 24 19-44 9-34 (36)
20 PF06750 DiS_P_DiS: Bacterial 71.8 3.4 7.4E-05 26.4 2.0 34 14-47 29-70 (92)
21 PRK03681 hypA hydrogenase nick 71.7 4.2 9E-05 26.8 2.5 37 14-54 66-103 (114)
22 PRK12380 hydrogenase nickel in 70.8 4.6 0.0001 26.5 2.5 36 14-54 66-102 (113)
23 PF03604 DNA_RNApol_7kD: DNA d 70.7 2.7 5.8E-05 22.5 1.1 24 21-45 3-27 (32)
24 smart00659 RPOLCX RNA polymera 70.4 2.5 5.4E-05 23.9 1.1 13 16-28 17-29 (44)
25 PRK11823 DNA repair protein Ra 70.4 2.8 6E-05 33.1 1.7 25 17-45 6-31 (446)
26 PF03119 DNA_ligase_ZBD: NAD-d 69.2 2 4.3E-05 22.2 0.4 10 20-29 1-10 (28)
27 PF07282 OrfB_Zn_ribbon: Putat 66.5 3.1 6.7E-05 24.3 0.9 25 19-44 29-55 (69)
28 PF08996 zf-DNA_Pol: DNA Polym 66.3 1.6 3.5E-05 30.7 -0.3 32 16-48 16-58 (188)
29 cd00065 FYVE FYVE domain; Zinc 66.1 4.3 9.4E-05 22.6 1.5 31 19-51 3-34 (57)
30 cd01121 Sms Sms (bacterial rad 65.6 3.6 7.7E-05 32.0 1.3 22 20-45 2-24 (372)
31 TIGR00100 hypA hydrogenase nic 65.4 5.9 0.00013 26.0 2.2 36 14-54 66-102 (115)
32 PF14599 zinc_ribbon_6: Zinc-r 63.4 4 8.7E-05 24.7 1.0 31 15-46 27-59 (61)
33 TIGR00416 sms DNA repair prote 61.9 4.8 0.0001 32.0 1.5 25 17-45 6-31 (454)
34 COG1645 Uncharacterized Zn-fin 61.2 4.7 0.0001 28.0 1.2 12 15-26 41-52 (131)
35 PRK05638 threonine synthase; V 58.9 6.7 0.00015 30.7 1.8 28 18-48 1-28 (442)
36 PF13453 zf-TFIIB: Transcripti 58.1 4.4 9.6E-05 21.9 0.5 17 20-37 1-17 (41)
37 PRK00564 hypA hydrogenase nick 57.2 14 0.00031 24.3 2.9 36 15-54 68-104 (117)
38 PF14471 DUF4428: Domain of un 56.7 2.2 4.8E-05 24.8 -0.9 34 20-53 1-38 (51)
39 PRK08351 DNA-directed RNA poly 56.6 5.7 0.00012 24.2 0.9 17 20-37 17-33 (61)
40 PF06044 DRP: Dam-replacing fa 56.5 3.1 6.8E-05 31.8 -0.4 31 13-43 26-61 (254)
41 PRK00432 30S ribosomal protein 56.2 6.8 0.00015 22.6 1.1 25 18-43 20-45 (50)
42 cd04476 RPA1_DBD_C RPA1_DBD_C: 55.8 8.6 0.00019 25.9 1.8 38 19-57 35-76 (166)
43 PRK14714 DNA polymerase II lar 55.1 9.9 0.00021 34.9 2.4 27 17-49 666-693 (1337)
44 PRK11827 hypothetical protein; 53.9 7.6 0.00017 23.5 1.1 15 17-32 7-21 (60)
45 TIGR00354 polC DNA polymerase, 53.7 11 0.00024 33.9 2.5 49 2-57 999-1048(1095)
46 smart00834 CxxC_CXXC_SSSS Puta 53.7 6.5 0.00014 20.5 0.7 13 16-28 24-36 (41)
47 PF08271 TF_Zn_Ribbon: TFIIB z 53.4 7 0.00015 21.3 0.8 18 15-32 16-33 (43)
48 cd01411 SIR2H SIR2H: Uncharact 52.3 19 0.00041 25.8 3.1 39 16-57 116-158 (225)
49 COG1571 Predicted DNA-binding 52.2 8.5 0.00018 31.2 1.4 30 15-45 347-377 (421)
50 PRK14559 putative protein seri 52.1 9.8 0.00021 32.1 1.8 27 16-48 13-40 (645)
51 PRK00241 nudC NADH pyrophospha 51.4 7.6 0.00016 28.7 1.0 35 13-47 94-129 (256)
52 TIGR00622 ssl1 transcription f 50.5 7.7 0.00017 26.2 0.8 31 20-54 3-34 (112)
53 COG2093 DNA-directed RNA polym 50.0 7.8 0.00017 24.1 0.7 20 17-37 17-36 (64)
54 COG1198 PriA Primosomal protei 49.8 8.7 0.00019 33.0 1.2 31 19-49 445-476 (730)
55 PF06677 Auto_anti-p27: Sjogre 49.4 10 0.00022 21.3 1.1 11 15-25 31-41 (41)
56 COG5629 Predicted metal-bindin 49.1 6.4 0.00014 30.9 0.3 39 16-54 167-214 (321)
57 smart00064 FYVE Protein presen 48.9 9.3 0.0002 22.1 0.9 28 19-48 11-39 (68)
58 KOG1088|consensus 48.9 13 0.00028 25.8 1.7 16 13-28 93-108 (124)
59 PRK03824 hypA hydrogenase nick 48.5 18 0.00038 24.5 2.3 13 15-27 67-79 (135)
60 PF07754 DUF1610: Domain of un 48.1 11 0.00024 19.1 1.0 10 16-25 14-23 (24)
61 KOG3092|consensus 47.4 9.4 0.0002 28.6 0.9 12 15-26 131-142 (216)
62 PRK08329 threonine synthase; V 47.2 13 0.00029 28.1 1.7 28 18-48 1-28 (347)
63 PF14205 Cys_rich_KTR: Cystein 47.0 11 0.00025 22.7 1.1 9 19-27 5-13 (55)
64 PRK04023 DNA polymerase II lar 47.0 16 0.00035 33.1 2.4 49 2-57 1024-1073(1121)
65 PRK14714 DNA polymerase II lar 46.8 16 0.00035 33.6 2.4 39 14-56 1249-1288(1337)
66 PF03226 Yippee-Mis18: Yippee 46.7 9.5 0.00021 23.7 0.8 15 16-30 55-69 (96)
67 PF11648 RIG-I_C-RD: C-termina 46.4 8.2 0.00018 25.7 0.5 26 15-40 57-82 (123)
68 PF14353 CpXC: CpXC protein 46.3 20 0.00043 23.2 2.3 13 16-28 36-48 (128)
69 PF04606 Ogr_Delta: Ogr/Delta- 45.6 9.3 0.0002 21.4 0.5 9 20-28 1-9 (47)
70 PRK12495 hypothetical protein; 45.0 14 0.00031 27.8 1.6 40 4-46 29-69 (226)
71 cd01412 SIRT5_Af1_CobB SIRT5_A 44.9 26 0.00056 24.7 2.8 41 16-56 107-151 (224)
72 COG1996 RPC10 DNA-directed RNA 44.8 12 0.00025 22.0 0.9 13 16-28 22-34 (49)
73 PF10122 Mu-like_Com: Mu-like 44.7 15 0.00033 21.8 1.4 14 13-26 19-32 (51)
74 PF13790 DUF4182: Domain of un 44.1 14 0.00029 20.8 1.0 17 17-33 2-18 (38)
75 PRK06835 DNA replication prote 44.1 14 0.0003 28.3 1.5 25 16-44 96-120 (329)
76 TIGR00595 priA primosomal prot 44.0 14 0.0003 29.7 1.5 25 19-43 223-248 (505)
77 PRK14873 primosome assembly pr 43.5 19 0.0004 30.4 2.2 26 19-44 393-419 (665)
78 PF01096 TFIIS_C: Transcriptio 43.4 11 0.00023 20.5 0.6 12 20-31 2-13 (39)
79 PF03811 Zn_Tnp_IS1: InsA N-te 43.0 14 0.00031 20.0 1.0 14 18-31 5-18 (36)
80 PF01363 FYVE: FYVE zinc finge 42.9 6.1 0.00013 22.9 -0.5 35 2-46 1-36 (69)
81 PF04810 zf-Sec23_Sec24: Sec23 42.7 15 0.00032 20.0 1.0 17 37-53 3-20 (40)
82 TIGR02605 CxxC_CxxC_SSSS putat 42.5 11 0.00025 20.8 0.6 11 16-26 24-34 (52)
83 PF10005 DUF2248: Uncharacteri 42.1 17 0.00036 28.9 1.6 22 20-45 1-23 (343)
84 PF14803 Nudix_N_2: Nudix N-te 41.8 11 0.00024 20.3 0.4 9 20-28 2-10 (34)
85 PTZ00396 Casein kinase II subu 41.6 12 0.00026 28.3 0.8 12 15-26 145-156 (251)
86 PF01214 CK_II_beta: Casein ki 40.6 13 0.00029 26.6 0.8 11 15-25 124-134 (184)
87 COG3877 Uncharacterized protei 39.6 15 0.00032 25.3 0.9 30 19-52 7-37 (122)
88 PTZ00409 Sir2 (Silent Informat 39.4 29 0.00063 25.9 2.5 42 16-57 135-186 (271)
89 TIGR03844 cysteate_syn cysteat 38.7 27 0.00058 27.4 2.3 28 18-48 2-30 (398)
90 PRK11088 rrmA 23S rRNA methylt 38.5 14 0.00031 26.6 0.7 23 19-43 3-25 (272)
91 PF08772 NOB1_Zn_bind: Nin one 37.9 13 0.00028 23.3 0.3 12 16-27 22-33 (73)
92 PF01396 zf-C4_Topoisom: Topoi 37.5 15 0.00033 19.9 0.6 9 20-28 3-11 (39)
93 COG3478 Predicted nucleic-acid 37.5 17 0.00037 22.8 0.8 11 17-27 3-13 (68)
94 PRK09401 reverse gyrase; Revie 37.4 14 0.00031 33.0 0.7 26 18-43 7-33 (1176)
95 PTZ00408 NAD-dependent deacety 37.2 25 0.00055 25.8 1.9 36 16-54 115-158 (242)
96 PF13695 zf-3CxxC: Zinc-bindin 35.6 45 0.00098 21.1 2.6 36 15-50 2-53 (98)
97 PF04438 zf-HIT: HIT zinc fing 35.1 17 0.00037 18.9 0.5 13 16-28 11-23 (30)
98 PRK06450 threonine synthase; V 35.1 31 0.00067 26.3 2.1 29 18-49 3-32 (338)
99 PF13878 zf-C2H2_3: zinc-finge 34.8 17 0.00036 20.0 0.4 15 12-26 7-21 (41)
100 PHA00626 hypothetical protein 34.5 17 0.00037 22.3 0.5 44 19-62 1-50 (59)
101 PF13005 zf-IS66: zinc-finger 34.2 19 0.00041 19.5 0.6 10 20-29 4-13 (47)
102 PRK00481 NAD-dependent deacety 34.2 38 0.00082 24.3 2.3 39 16-57 120-164 (242)
103 cd01410 SIRT7 SIRT7: Eukaryoti 34.0 32 0.00069 24.4 1.9 38 17-55 94-140 (206)
104 PRK14890 putative Zn-ribbon RN 33.6 26 0.00056 21.4 1.2 12 16-27 23-34 (59)
105 COG3809 Uncharacterized protei 33.5 17 0.00038 23.7 0.5 39 19-63 2-44 (88)
106 PF00130 C1_1: Phorbol esters/ 33.4 14 0.0003 20.3 -0.0 28 17-45 10-38 (53)
107 PF08209 Sgf11: Sgf11 (transcr 33.3 22 0.00047 19.1 0.7 12 18-29 4-15 (33)
108 PHA02325 hypothetical protein 33.2 18 0.0004 22.8 0.5 14 20-33 5-20 (72)
109 PRK05580 primosome assembly pr 33.0 25 0.00055 29.3 1.4 11 19-29 391-401 (679)
110 PF02591 DUF164: Putative zinc 32.5 31 0.00067 19.6 1.4 13 16-28 44-56 (56)
111 PRK06393 rpoE DNA-directed RNA 32.4 20 0.00044 22.1 0.6 17 20-37 19-35 (64)
112 PRK14138 NAD-dependent deacety 32.2 49 0.0011 24.1 2.7 38 16-56 117-164 (244)
113 PF02318 FYVE_2: FYVE-type zin 31.7 16 0.00034 23.9 -0.0 35 17-52 53-88 (118)
114 TIGR01206 lysW lysine biosynth 31.7 26 0.00056 20.7 0.9 14 17-30 21-34 (54)
115 cd01408 SIRT1 SIRT1: Eukaryoti 31.1 33 0.00072 24.8 1.6 38 16-56 114-161 (235)
116 PRK06418 transcription elongat 30.9 12 0.00026 26.6 -0.7 16 18-33 13-30 (166)
117 PRK14715 DNA polymerase II lar 30.9 41 0.00089 31.6 2.4 39 14-57 1538-1577(1627)
118 PF09723 Zn-ribbon_8: Zinc rib 30.4 24 0.00052 19.2 0.6 11 16-26 24-34 (42)
119 smart00109 C1 Protein kinase C 30.3 31 0.00068 17.9 1.1 25 19-45 12-37 (49)
120 PRK07218 replication factor A; 30.2 30 0.00066 27.8 1.4 18 20-43 299-317 (423)
121 cd01413 SIR2_Af2 SIR2_Af2: Arc 30.1 55 0.0012 23.3 2.6 39 16-57 111-158 (222)
122 PF02943 FeThRed_B: Ferredoxin 29.9 22 0.00047 23.7 0.4 33 16-49 42-91 (108)
123 COG2816 NPY1 NTP pyrophosphohy 29.2 32 0.00069 26.5 1.3 46 14-59 107-157 (279)
124 PRK06260 threonine synthase; V 29.0 47 0.001 25.5 2.2 30 18-49 3-33 (397)
125 PF10955 DUF2757: Protein of u 28.9 30 0.00066 21.9 1.0 16 18-33 4-19 (76)
126 PF08600 Rsm1: Rsm1-like; Int 28.5 37 0.0008 21.4 1.3 21 16-37 17-37 (91)
127 COG1933 Archaeal DNA polymeras 28.3 35 0.00075 26.2 1.4 39 15-57 164-203 (253)
128 PF09855 DUF2082: Nucleic-acid 28.3 29 0.00062 21.1 0.8 8 20-27 2-9 (64)
129 PF10272 Tmpp129: Putative tra 28.1 23 0.00051 28.0 0.4 17 12-28 334-350 (358)
130 PF01485 IBR: IBR domain; Int 27.9 48 0.001 18.1 1.6 27 19-45 19-50 (64)
131 COG5041 SKB2 Casein kinase II, 27.6 27 0.00059 26.5 0.7 12 15-26 146-157 (242)
132 cd01407 SIR2-fam SIR2 family o 27.3 78 0.0017 22.3 2.9 41 16-57 107-155 (218)
133 PRK07591 threonine synthase; V 27.0 50 0.0011 25.8 2.1 29 18-49 18-47 (421)
134 PF06054 CoiA: Competence prot 26.9 35 0.00076 26.5 1.2 13 16-28 28-40 (375)
135 PRK06386 replication factor A; 26.5 49 0.0011 26.1 2.0 26 20-53 238-264 (358)
136 smart00647 IBR In Between Ring 26.5 63 0.0014 17.7 1.9 29 16-44 16-49 (64)
137 PF08646 Rep_fac-A_C: Replicat 26.3 30 0.00066 22.8 0.7 25 19-45 19-47 (146)
138 cd00162 RING RING-finger (Real 26.1 33 0.00071 16.9 0.7 12 17-28 34-45 (45)
139 TIGR00155 pqiA_fam integral me 26.0 41 0.00089 26.6 1.5 15 16-30 31-45 (403)
140 PRK08402 replication factor A; 25.8 45 0.00098 26.1 1.6 10 19-28 213-222 (355)
141 TIGR01374 soxD sarcosine oxida 25.8 32 0.00069 22.2 0.7 44 19-68 2-50 (84)
142 PF09814 HECT_2: HECT-like Ubi 25.8 66 0.0014 23.9 2.4 32 17-60 192-223 (354)
143 PRK08197 threonine synthase; V 25.3 49 0.0011 25.4 1.7 26 18-45 7-32 (394)
144 COG2888 Predicted Zn-ribbon RN 25.2 39 0.00086 20.8 1.0 11 15-25 24-34 (61)
145 PF07503 zf-HYPF: HypF finger; 25.2 36 0.00078 18.4 0.7 11 18-28 21-31 (35)
146 PF03884 DUF329: Domain of unk 25.2 36 0.00078 20.4 0.8 12 18-29 2-13 (57)
147 COG1066 Sms Predicted ATP-depe 25.0 55 0.0012 27.0 2.1 25 17-45 6-31 (456)
148 PF06906 DUF1272: Protein of u 25.0 35 0.00075 20.8 0.7 10 19-28 42-51 (57)
149 PF15616 TerY-C: TerY-C metal 24.8 26 0.00057 24.1 0.2 16 14-29 73-88 (131)
150 PHA02942 putative transposase; 24.8 36 0.00078 26.6 0.9 25 19-44 326-351 (383)
151 TIGR02443 conserved hypothetic 24.8 34 0.00074 20.8 0.6 9 19-27 10-18 (59)
152 KOG2807|consensus 24.7 27 0.00058 28.1 0.2 36 16-55 274-310 (378)
153 COG1096 Predicted RNA-binding 24.6 38 0.00082 24.9 0.9 25 19-45 150-175 (188)
154 smart00661 RPOL9 RNA polymeras 24.3 39 0.00084 18.3 0.8 24 20-43 2-28 (52)
155 PRK09521 exosome complex RNA-b 24.3 41 0.00089 23.4 1.1 27 17-44 146-175 (189)
156 COG1867 TRM1 N2,N2-dimethylgua 24.3 52 0.0011 26.5 1.7 26 18-44 240-266 (380)
157 KOG0801|consensus 24.2 42 0.00091 24.8 1.1 16 31-47 134-150 (205)
158 COG0143 MetG Methionyl-tRNA sy 24.0 45 0.00098 27.8 1.4 26 19-49 143-169 (558)
159 COG2956 Predicted N-acetylgluc 24.0 46 0.00099 27.0 1.4 26 16-45 352-378 (389)
160 PF14169 YdjO: Cold-inducible 23.7 32 0.0007 20.9 0.4 22 3-28 28-49 (59)
161 PRK09678 DNA-binding transcrip 23.6 37 0.00081 21.1 0.7 10 19-28 2-11 (72)
162 PF09889 DUF2116: Uncharacteri 23.5 39 0.00085 20.3 0.7 10 20-29 5-14 (59)
163 TIGR03655 anti_R_Lar restricti 23.4 41 0.00088 19.0 0.8 26 20-45 3-36 (53)
164 PF14255 Cys_rich_CPXG: Cystei 23.4 34 0.00075 20.0 0.5 10 19-28 1-10 (52)
165 cd00029 C1 Protein kinase C co 23.4 34 0.00073 18.0 0.4 26 19-45 12-38 (50)
166 cd00246 RabGEF Nucleotide exch 23.3 43 0.00092 22.4 0.9 11 18-28 2-12 (103)
167 PF09151 DUF1936: Domain of un 23.2 43 0.00093 18.5 0.8 9 19-27 2-10 (36)
168 PF10083 DUF2321: Uncharacteri 23.2 50 0.0011 23.7 1.3 13 19-31 40-52 (158)
169 PRK12366 replication factor A; 23.2 52 0.0011 27.5 1.6 29 19-50 533-562 (637)
170 PF14690 zf-ISL3: zinc-finger 23.1 41 0.0009 17.9 0.7 10 19-28 3-12 (47)
171 PF09526 DUF2387: Probable met 22.9 39 0.00084 20.9 0.6 27 19-45 9-40 (71)
172 COG1905 NuoE NADH:ubiquinone o 22.7 52 0.0011 23.4 1.3 24 27-53 113-138 (160)
173 PF12387 Peptidase_C74: Pestiv 22.5 54 0.0012 24.3 1.4 28 15-47 159-187 (200)
174 COG3677 Transposase and inacti 22.3 37 0.0008 22.9 0.5 32 14-45 26-63 (129)
175 COG0675 Transposase and inacti 22.1 41 0.00088 23.6 0.7 31 18-53 309-344 (364)
176 PRK14701 reverse gyrase; Provi 21.5 39 0.00085 31.5 0.6 24 19-42 7-31 (1638)
177 smart00440 ZnF_C2C2 C2C2 Zinc 21.4 57 0.0012 17.7 1.0 12 20-31 2-13 (40)
178 PF06170 DUF983: Protein of un 21.2 41 0.0009 21.3 0.5 19 15-33 5-23 (86)
179 PRK13130 H/ACA RNA-protein com 21.0 51 0.0011 19.7 0.9 12 17-28 16-27 (56)
180 TIGR00373 conserved hypothetic 21.0 44 0.00096 23.0 0.7 8 21-28 112-119 (158)
181 PF13913 zf-C2HC_2: zinc-finge 20.9 46 0.00099 16.3 0.6 11 19-29 3-13 (25)
182 PF04475 DUF555: Protein of un 20.6 50 0.0011 22.2 0.9 13 16-28 45-57 (102)
183 PRK12496 hypothetical protein; 20.5 45 0.00097 23.2 0.6 10 20-29 145-154 (164)
184 TIGR01054 rgy reverse gyrase. 20.5 47 0.001 29.8 0.9 25 19-43 8-33 (1171)
185 PRK11788 tetratricopeptide rep 20.4 87 0.0019 22.6 2.1 27 16-46 352-379 (389)
186 cd00729 rubredoxin_SM Rubredox 20.2 41 0.00088 17.7 0.3 13 19-31 19-31 (34)
No 1
>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=92.18 E-value=0.094 Score=34.87 Aligned_cols=33 Identities=27% Similarity=0.651 Sum_probs=27.3
Q ss_pred ccceeeCCCCCCccceeecCCCCCCC-CCCcccce
Q psy10712 15 LKDKLKCPNCSTNLGAFDYVSGHKCP-CKQQCVPF 48 (75)
Q Consensus 15 ~~GKL~CP~C~aKLGsf~wv~G~kCs-CG~~v~Pa 48 (75)
+--|-.||+|++|.=-+|= .-.-|+ ||+-+.|.
T Consensus 6 lGtKR~Cp~CG~kFYDLnk-~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 6 LGTKRTCPSCGAKFYDLNK-DPIVCPKCGTEFPPE 39 (108)
T ss_pred cCCcccCCCCcchhccCCC-CCccCCCCCCccCcc
Confidence 3457889999999877777 678898 99988777
No 2
>smart00714 LITAF Possible membrane-associated motif in LPS-induced tumor necrosis factor alpha factor (LITAF), also known as PIG7, and other animal proteins.
Probab=91.75 E-value=0.086 Score=31.40 Aligned_cols=18 Identities=33% Similarity=0.798 Sum_probs=15.4
Q ss_pred ccceeeCCCCCCccceee
Q psy10712 15 LKDKLKCPNCSTNLGAFD 32 (75)
Q Consensus 15 ~~GKL~CP~C~aKLGsf~ 32 (75)
.+-.-+||+|++.||.|+
T Consensus 49 kd~~H~Cp~C~~~lg~~~ 66 (67)
T smart00714 49 KDVNHYCPNCGAFLGTYN 66 (67)
T ss_pred cCccEECCCCCCEeEEec
Confidence 456689999999999985
No 3
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=90.32 E-value=0.37 Score=26.84 Aligned_cols=27 Identities=30% Similarity=0.832 Sum_probs=18.4
Q ss_pred eeCCCCCCccceeecCCCCCCC-CCCcc
Q psy10712 19 LKCPNCSTNLGAFDYVSGHKCP-CKQQC 45 (75)
Q Consensus 19 L~CP~C~aKLGsf~wv~G~kCs-CG~~v 45 (75)
..||+|++.+=.-.-....+|+ ||.-+
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~~ 31 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYRI 31 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCeE
Confidence 5799999987433332367898 99654
No 4
>PF10601 zf-LITAF-like: LITAF-like zinc ribbon domain; InterPro: IPR006629 Members of this family display a conserved zinc ribbon structure [] with the motif C-XX-C- separated from the more C-terminal HX-C(P)X-C-X4-G-R motif by a variable region of usually 25-30 (hydrophobic) residues. Although it belongs to one of the zinc finger's fold groups (zinc ribbon), this particular domain was first identified in LPS-induced tumour necrosis alpha factor (LITAF) which is produced in mammalian cells after being challenged with lipopolysaccharide (LPS). The hydrophobic region probably inserts into the membrane rather than traversing it. Such an insertion brings together the N- and C-terminal C-XX-C motifs to form a compact Zn2+-binding structure [].
Probab=90.21 E-value=0.16 Score=30.67 Aligned_cols=18 Identities=33% Similarity=0.713 Sum_probs=15.2
Q ss_pred ccceeeCCCCCCccceee
Q psy10712 15 LKDKLKCPNCSTNLGAFD 32 (75)
Q Consensus 15 ~~GKL~CP~C~aKLGsf~ 32 (75)
.+=..+||+|++.||.|+
T Consensus 55 kd~~H~Cp~C~~~lg~~~ 72 (73)
T PF10601_consen 55 KDVYHYCPNCGAFLGTYK 72 (73)
T ss_pred cCceEECCCCCCEeEEEe
Confidence 455688999999999985
No 5
>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=89.96 E-value=0.21 Score=34.70 Aligned_cols=35 Identities=23% Similarity=0.295 Sum_probs=28.4
Q ss_pred ccceeeCCCCCCccceeecCCCCCCC-CCCcccceEE
Q psy10712 15 LKDKLKCPNCSTNLGAFDYVSGHKCP-CKQQCVPFIH 50 (75)
Q Consensus 15 ~~GKL~CP~C~aKLGsf~wv~G~kCs-CG~~v~Paf~ 50 (75)
+--|-.||+|++|.=-.|= .-.-|+ ||+-+.|...
T Consensus 6 lGtKr~Cp~cg~kFYDLnk-~p~vcP~cg~~~~~~~~ 41 (129)
T TIGR02300 6 LGTKRICPNTGSKFYDLNR-RPAVSPYTGEQFPPEEA 41 (129)
T ss_pred hCccccCCCcCccccccCC-CCccCCCcCCccCcchh
Confidence 3457889999999877777 788997 9999888843
No 6
>PF12773 DZR: Double zinc ribbon
Probab=87.16 E-value=0.34 Score=26.92 Aligned_cols=32 Identities=38% Similarity=0.694 Sum_probs=23.5
Q ss_pred cceeeCCCCCCccceeecCCCCCCC-CCCcccce
Q psy10712 16 KDKLKCPNCSTNLGAFDYVSGHKCP-CKQQCVPF 48 (75)
Q Consensus 16 ~GKL~CP~C~aKLGsf~wv~G~kCs-CG~~v~Pa 48 (75)
.+...||+|+++|....= ....|+ ||+-+.+.
T Consensus 10 ~~~~fC~~CG~~l~~~~~-~~~~C~~Cg~~~~~~ 42 (50)
T PF12773_consen 10 DDAKFCPHCGTPLPPPDQ-SKKICPNCGAENPPN 42 (50)
T ss_pred ccccCChhhcCChhhccC-CCCCCcCCcCCCcCC
Confidence 456789999999984444 467895 99876554
No 7
>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=85.69 E-value=0.55 Score=26.23 Aligned_cols=14 Identities=21% Similarity=0.873 Sum_probs=11.2
Q ss_pred ccccceeeCCCCCCc
Q psy10712 13 NFLKDKLKCPNCSTN 27 (75)
Q Consensus 13 ~~~~GKL~CP~C~aK 27 (75)
-|-+| ..||+|++.
T Consensus 14 RW~~g-~~CP~Cg~~ 27 (46)
T PF12760_consen 14 RWPDG-FVCPHCGST 27 (46)
T ss_pred cCCCC-CCCCCCCCe
Confidence 46677 779999997
No 8
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=82.38 E-value=1.2 Score=24.72 Aligned_cols=21 Identities=24% Similarity=0.594 Sum_probs=18.1
Q ss_pred ccceeeCCCCCCccceeecCCC
Q psy10712 15 LKDKLKCPNCSTNLGAFDYVSG 36 (75)
Q Consensus 15 ~~GKL~CP~C~aKLGsf~wv~G 36 (75)
..|+|.|+.|+.++-...+ .+
T Consensus 2 l~g~l~C~~CG~~m~~~~~-~~ 22 (58)
T PF13408_consen 2 LSGLLRCGHCGSKMTRRKR-KG 22 (58)
T ss_pred CCCcEEcccCCcEeEEEEC-CC
Confidence 5789999999999998888 44
No 9
>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=81.80 E-value=0.98 Score=23.14 Aligned_cols=21 Identities=33% Similarity=0.936 Sum_probs=15.0
Q ss_pred eCCCCCCccceeecCCCCCCC-CCCc
Q psy10712 20 KCPNCSTNLGAFDYVSGHKCP-CKQQ 44 (75)
Q Consensus 20 ~CP~C~aKLGsf~wv~G~kCs-CG~~ 44 (75)
.||.|++.+ -++-..|+ ||.-
T Consensus 2 ~CP~C~~~V----~~~~~~Cp~CG~~ 23 (26)
T PF10571_consen 2 TCPECGAEV----PESAKFCPHCGYD 23 (26)
T ss_pred cCCCCcCCc----hhhcCcCCCCCCC
Confidence 488888888 22567787 8863
No 10
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=81.40 E-value=0.92 Score=24.51 Aligned_cols=11 Identities=36% Similarity=1.114 Sum_probs=8.9
Q ss_pred eeeCCCCCCcc
Q psy10712 18 KLKCPNCSTNL 28 (75)
Q Consensus 18 KL~CP~C~aKL 28 (75)
+|.||+|+++.
T Consensus 2 ~i~Cp~C~~~y 12 (36)
T PF13717_consen 2 IITCPNCQAKY 12 (36)
T ss_pred EEECCCCCCEE
Confidence 58899999863
No 11
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=79.59 E-value=0.74 Score=31.08 Aligned_cols=27 Identities=37% Similarity=0.800 Sum_probs=15.4
Q ss_pred CCCCCCccceeecCCCCCCC-CCCcccceEEE
Q psy10712 21 CPNCSTNLGAFDYVSGHKCP-CKQQCVPFIHL 51 (75)
Q Consensus 21 CP~C~aKLGsf~wv~G~kCs-CG~~v~Paf~i 51 (75)
||.|+.+| =|+..+|+ |++-|.=.|.+
T Consensus 1 CPvCg~~l----~vt~l~C~~C~t~i~G~F~l 28 (113)
T PF09862_consen 1 CPVCGGEL----VVTRLKCPSCGTEIEGEFEL 28 (113)
T ss_pred CCCCCCce----EEEEEEcCCCCCEEEeeecc
Confidence 66666655 23556664 66666555544
No 12
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=77.49 E-value=0.86 Score=22.88 Aligned_cols=13 Identities=46% Similarity=0.986 Sum_probs=8.4
Q ss_pred cceeeCCCCCCcc
Q psy10712 16 KDKLKCPNCSTNL 28 (75)
Q Consensus 16 ~GKL~CP~C~aKL 28 (75)
.+--.||+|+++|
T Consensus 14 ~~~~fC~~CG~~L 26 (26)
T PF13248_consen 14 PDAKFCPNCGAKL 26 (26)
T ss_pred cccccChhhCCCC
Confidence 3445677777765
No 13
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=77.42 E-value=1.5 Score=23.70 Aligned_cols=10 Identities=50% Similarity=1.271 Sum_probs=8.0
Q ss_pred eeeCCCCCCc
Q psy10712 18 KLKCPNCSTN 27 (75)
Q Consensus 18 KL~CP~C~aK 27 (75)
++.||+|+++
T Consensus 2 ~i~CP~C~~~ 11 (37)
T PF13719_consen 2 IITCPNCQTR 11 (37)
T ss_pred EEECCCCCce
Confidence 4789999874
No 14
>PRK00420 hypothetical protein; Validated
Probab=76.78 E-value=1.7 Score=29.28 Aligned_cols=26 Identities=23% Similarity=0.459 Sum_probs=20.0
Q ss_pred eeCCCCCCccceeecCCCCCCC-CCCcc
Q psy10712 19 LKCPNCSTNLGAFDYVSGHKCP-CKQQC 45 (75)
Q Consensus 19 L~CP~C~aKLGsf~wv~G~kCs-CG~~v 45 (75)
-+||.|++.|=.++= .-..|+ ||..+
T Consensus 24 ~~CP~Cg~pLf~lk~-g~~~Cp~Cg~~~ 50 (112)
T PRK00420 24 KHCPVCGLPLFELKD-GEVVCPVHGKVY 50 (112)
T ss_pred CCCCCCCCcceecCC-CceECCCCCCee
Confidence 679999998866655 567886 99854
No 15
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=76.51 E-value=1.4 Score=29.87 Aligned_cols=18 Identities=28% Similarity=0.761 Sum_probs=13.6
Q ss_pred ccceeeCCCCCCccceee
Q psy10712 15 LKDKLKCPNCSTNLGAFD 32 (75)
Q Consensus 15 ~~GKL~CP~C~aKLGsf~ 32 (75)
.+|++.||+|++.|=.++
T Consensus 120 ~~~~f~Cp~Cg~~l~~~d 137 (147)
T smart00531 120 MDGTFTCPRCGEELEEDD 137 (147)
T ss_pred CCCcEECCCCCCEEEEcC
Confidence 368899999998885543
No 16
>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=76.00 E-value=1.8 Score=22.84 Aligned_cols=13 Identities=23% Similarity=0.670 Sum_probs=10.4
Q ss_pred cceeeCCCCCCcc
Q psy10712 16 KDKLKCPNCSTNL 28 (75)
Q Consensus 16 ~GKL~CP~C~aKL 28 (75)
.+++.||+|+..+
T Consensus 23 ~~~v~C~~C~~~~ 35 (38)
T TIGR02098 23 GGKVRCGKCGHVW 35 (38)
T ss_pred CCEEECCCCCCEE
Confidence 4589999999865
No 17
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=75.59 E-value=1.3 Score=21.96 Aligned_cols=21 Identities=33% Similarity=1.007 Sum_probs=13.4
Q ss_pred eCCCCCCccceeecCCCCCCC-CCCc
Q psy10712 20 KCPNCSTNLGAFDYVSGHKCP-CKQQ 44 (75)
Q Consensus 20 ~CP~C~aKLGsf~wv~G~kCs-CG~~ 44 (75)
.||+|+++|=. ...-|+ ||+-
T Consensus 1 ~Cp~CG~~~~~----~~~fC~~CG~~ 22 (23)
T PF13240_consen 1 YCPNCGAEIED----DAKFCPNCGTP 22 (23)
T ss_pred CCcccCCCCCC----cCcchhhhCCc
Confidence 48999988831 345565 7653
No 18
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=73.87 E-value=1.7 Score=25.89 Aligned_cols=14 Identities=29% Similarity=0.947 Sum_probs=11.7
Q ss_pred ccccceeeCCCCCC
Q psy10712 13 NFLKDKLKCPNCST 26 (75)
Q Consensus 13 ~~~~GKL~CP~C~a 26 (75)
+..+|.|.||+|+.
T Consensus 48 ~i~eg~L~Cp~c~r 61 (68)
T PF03966_consen 48 EIVEGELICPECGR 61 (68)
T ss_dssp ETTTTEEEETTTTE
T ss_pred cccCCEEEcCCCCC
Confidence 45789999999974
No 19
>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=72.72 E-value=1.3 Score=24.09 Aligned_cols=24 Identities=33% Similarity=0.704 Sum_probs=15.8
Q ss_pred eeCCCCCCccceeecCCC-CCC-CCCCc
Q psy10712 19 LKCPNCSTNLGAFDYVSG-HKC-PCKQQ 44 (75)
Q Consensus 19 L~CP~C~aKLGsf~wv~G-~kC-sCG~~ 44 (75)
+.|+.|+++ .|....| .-| +||.-
T Consensus 9 ~~C~~C~~~--~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 9 EPCPVCGSR--WFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CcCCCCCCe--EeEccCCEEEhhhCceE
Confidence 569999999 4544444 357 77753
No 20
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=71.76 E-value=3.4 Score=26.37 Aligned_cols=34 Identities=24% Similarity=0.664 Sum_probs=25.4
Q ss_pred cccceeeCCCCCCccceeecC-------CCCCCC-CCCcccc
Q psy10712 14 FLKDKLKCPNCSTNLGAFDYV-------SGHKCP-CKQQCVP 47 (75)
Q Consensus 14 ~~~GKL~CP~C~aKLGsf~wv-------~G~kCs-CG~~v~P 47 (75)
...++=.||+|+.+|.-++-| ..-+|. |++-+.+
T Consensus 29 i~~~rS~C~~C~~~L~~~~lIPi~S~l~lrGrCr~C~~~I~~ 70 (92)
T PF06750_consen 29 IIFPRSHCPHCGHPLSWWDLIPILSYLLLRGRCRYCGAPIPP 70 (92)
T ss_pred ccCCCCcCcCCCCcCcccccchHHHHHHhCCCCcccCCCCCh
Confidence 345678999999999876643 477886 8877654
No 21
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=71.71 E-value=4.2 Score=26.77 Aligned_cols=37 Identities=16% Similarity=0.500 Sum_probs=23.9
Q ss_pred cccceeeCCCCCCccceeecCCCCCCC-CCCcccceEEEEcC
Q psy10712 14 FLKDKLKCPNCSTNLGAFDYVSGHKCP-CKQQCVPFIHLVKS 54 (75)
Q Consensus 14 ~~~GKL~CP~C~aKLGsf~wv~G~kCs-CG~~v~Paf~i~kS 54 (75)
+..++..|+.|+...-.-.+ .-..|+ ||.. .+.|...
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~-~~~~CP~Cgs~---~~~i~~G 103 (114)
T PRK03681 66 EQEAECWCETCQQYVTLLTQ-RVRRCPQCHGD---MLRIVAD 103 (114)
T ss_pred eeCcEEEcccCCCeeecCCc-cCCcCcCcCCC---CcEEccC
Confidence 46789999999975443333 236798 9954 4555443
No 22
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=70.78 E-value=4.6 Score=26.52 Aligned_cols=36 Identities=17% Similarity=0.466 Sum_probs=23.1
Q ss_pred cccceeeCCCCCCccceeecCCCCCCC-CCCcccceEEEEcC
Q psy10712 14 FLKDKLKCPNCSTNLGAFDYVSGHKCP-CKQQCVPFIHLVKS 54 (75)
Q Consensus 14 ~~~GKL~CP~C~aKLGsf~wv~G~kCs-CG~~v~Paf~i~kS 54 (75)
+..++..|+.|+.....-.+ ...|+ ||.. .+.|...
T Consensus 66 ~vp~~~~C~~Cg~~~~~~~~--~~~CP~Cgs~---~~~i~~G 102 (113)
T PRK12380 66 YKPAQAWCWDCSQVVEIHQH--DAQCPHCHGE---RLRVDTG 102 (113)
T ss_pred eeCcEEEcccCCCEEecCCc--CccCcCCCCC---CcEEccC
Confidence 36789999999964433222 34598 9953 5555544
No 23
>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=70.73 E-value=2.7 Score=22.52 Aligned_cols=24 Identities=21% Similarity=0.720 Sum_probs=11.8
Q ss_pred CCCCCCccceeecCCCCCCC-CCCcc
Q psy10712 21 CPNCSTNLGAFDYVSGHKCP-CKQQC 45 (75)
Q Consensus 21 CP~C~aKLGsf~wv~G~kCs-CG~~v 45 (75)
|..|++.+- +..-...+|. ||..|
T Consensus 3 C~~Cg~~~~-~~~~~~irC~~CG~RI 27 (32)
T PF03604_consen 3 CGECGAEVE-LKPGDPIRCPECGHRI 27 (32)
T ss_dssp ESSSSSSE--BSTSSTSSBSSSS-SE
T ss_pred CCcCCCeeE-cCCCCcEECCcCCCeE
Confidence 556666655 2232456665 66554
No 24
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=70.44 E-value=2.5 Score=23.91 Aligned_cols=13 Identities=31% Similarity=0.905 Sum_probs=10.8
Q ss_pred cceeeCCCCCCcc
Q psy10712 16 KDKLKCPNCSTNL 28 (75)
Q Consensus 16 ~GKL~CP~C~aKL 28 (75)
.+.+.||+|+.|+
T Consensus 17 ~~~irC~~CG~rI 29 (44)
T smart00659 17 KDVVRCRECGYRI 29 (44)
T ss_pred CCceECCCCCceE
Confidence 4679999999886
No 25
>PRK11823 DNA repair protein RadA; Provisional
Probab=70.38 E-value=2.8 Score=33.15 Aligned_cols=25 Identities=20% Similarity=0.567 Sum_probs=20.7
Q ss_pred ceeeCCCCCCccceeecCCCCCCC-CCCcc
Q psy10712 17 DKLKCPNCSTNLGAFDYVSGHKCP-CKQQC 45 (75)
Q Consensus 17 GKL~CP~C~aKLGsf~wv~G~kCs-CG~~v 45 (75)
-.-.|.+|+..-..|-| ||+ |++|=
T Consensus 6 ~~y~C~~Cg~~~~~~~g----~Cp~C~~w~ 31 (446)
T PRK11823 6 TAYVCQECGAESPKWLG----RCPECGAWN 31 (446)
T ss_pred CeEECCcCCCCCcccCe----eCcCCCCcc
Confidence 34679999999888777 796 99996
No 26
>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=69.16 E-value=2 Score=22.17 Aligned_cols=10 Identities=40% Similarity=1.062 Sum_probs=5.4
Q ss_pred eCCCCCCccc
Q psy10712 20 KCPNCSTNLG 29 (75)
Q Consensus 20 ~CP~C~aKLG 29 (75)
.||.|+++|=
T Consensus 1 ~CP~C~s~l~ 10 (28)
T PF03119_consen 1 TCPVCGSKLV 10 (28)
T ss_dssp B-TTT--BEE
T ss_pred CcCCCCCEeE
Confidence 4899998885
No 27
>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=66.49 E-value=3.1 Score=24.29 Aligned_cols=25 Identities=24% Similarity=0.583 Sum_probs=19.3
Q ss_pred eeCCCCCCccce-eecCCCCCCC-CCCc
Q psy10712 19 LKCPNCSTNLGA-FDYVSGHKCP-CKQQ 44 (75)
Q Consensus 19 L~CP~C~aKLGs-f~wv~G~kCs-CG~~ 44 (75)
-.||.|+.+... .+. ....|+ ||..
T Consensus 29 q~C~~CG~~~~~~~~~-r~~~C~~Cg~~ 55 (69)
T PF07282_consen 29 QTCPRCGHRNKKRRSG-RVFTCPNCGFE 55 (69)
T ss_pred cCccCccccccccccc-ceEEcCCCCCE
Confidence 359999999987 555 578888 8874
No 28
>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=66.33 E-value=1.6 Score=30.69 Aligned_cols=32 Identities=44% Similarity=0.989 Sum_probs=15.8
Q ss_pred cceeeCCCCCCcc---ceee-------cCCCCCCC-CCCcccce
Q psy10712 16 KDKLKCPNCSTNL---GAFD-------YVSGHKCP-CKQQCVPF 48 (75)
Q Consensus 16 ~GKL~CP~C~aKL---Gsf~-------wv~G~kCs-CG~~v~Pa 48 (75)
.=++.||+|+... |.|. + +|..|+ |++.+.|+
T Consensus 16 ~l~~~C~~C~~~~~f~g~~~~~~~~~~~-~~~~C~~C~~~~~~~ 58 (188)
T PF08996_consen 16 PLKLTCPSCGTEFEFPGVFEEDGDDVSP-SGLQCPNCSTPLSPA 58 (188)
T ss_dssp -EEEE-TTT--EEEE-SSS--SSEEEET-TEEEETTT--B--HH
T ss_pred ceEeECCCCCCCccccccccCCcccccc-CcCcCCCCCCcCCHH
Confidence 3468999998764 3333 5 688897 99866544
No 29
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=66.05 E-value=4.3 Score=22.59 Aligned_cols=31 Identities=16% Similarity=0.357 Sum_probs=23.5
Q ss_pred eeCCCCCCccceeecCCCCCCC-CCCcccceEEE
Q psy10712 19 LKCPNCSTNLGAFDYVSGHKCP-CKQQCVPFIHL 51 (75)
Q Consensus 19 L~CP~C~aKLGsf~wv~G~kCs-CG~~v~Paf~i 51 (75)
-.|+.|+.++|.|.. ...|. ||..+-..-.-
T Consensus 3 ~~C~~C~~~F~~~~r--k~~Cr~Cg~~~C~~C~~ 34 (57)
T cd00065 3 SSCMGCGKPFTLTRR--RHHCRNCGRIFCSKCSS 34 (57)
T ss_pred CcCcccCccccCCcc--ccccCcCcCCcChHHcC
Confidence 368999999999887 67785 99887654433
No 30
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=65.55 E-value=3.6 Score=32.03 Aligned_cols=22 Identities=27% Similarity=0.611 Sum_probs=17.9
Q ss_pred eCCCCCCccceeecCCCCCCC-CCCcc
Q psy10712 20 KCPNCSTNLGAFDYVSGHKCP-CKQQC 45 (75)
Q Consensus 20 ~CP~C~aKLGsf~wv~G~kCs-CG~~v 45 (75)
.|.+|+..-..|-| ||+ ||+|=
T Consensus 2 ~c~~cg~~~~~~~g----~cp~c~~w~ 24 (372)
T cd01121 2 VCSECGYVSPKWLG----KCPECGEWN 24 (372)
T ss_pred CCCCCCCCCCCccE----ECcCCCCce
Confidence 48999998777666 786 99996
No 31
>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=65.44 E-value=5.9 Score=26.02 Aligned_cols=36 Identities=17% Similarity=0.488 Sum_probs=22.8
Q ss_pred cccceeeCCCCCCccceeecCCCCCCC-CCCcccceEEEEcC
Q psy10712 14 FLKDKLKCPNCSTNLGAFDYVSGHKCP-CKQQCVPFIHLVKS 54 (75)
Q Consensus 14 ~~~GKL~CP~C~aKLGsf~wv~G~kCs-CG~~v~Paf~i~kS 54 (75)
+...+..|++|+..... .. ....|+ ||.. .+.|...
T Consensus 66 ~~p~~~~C~~Cg~~~~~-~~-~~~~CP~Cgs~---~~~i~~G 102 (115)
T TIGR00100 66 DEPVECECEDCSEEVSP-EI-DLYRCPKCHGI---MLQVRAG 102 (115)
T ss_pred eeCcEEEcccCCCEEec-CC-cCccCcCCcCC---CcEEecC
Confidence 35788999999955433 22 256796 9964 3444443
No 32
>PF14599 zinc_ribbon_6: Zinc-ribbon; PDB: 2K2D_A.
Probab=63.37 E-value=4 Score=24.74 Aligned_cols=31 Identities=29% Similarity=0.695 Sum_probs=13.9
Q ss_pred ccceeeCCCCCCccc-eeecCCCCCCC-CCCccc
Q psy10712 15 LKDKLKCPNCSTNLG-AFDYVSGHKCP-CKQQCV 46 (75)
Q Consensus 15 ~~GKL~CP~C~aKLG-sf~wv~G~kCs-CG~~v~ 46 (75)
....|.|--|++|== .|-| =|.||+ ||.+-|
T Consensus 27 ~~v~IlCNDC~~~s~v~fH~-lg~KC~~C~SYNT 59 (61)
T PF14599_consen 27 KKVWILCNDCNAKSEVPFHF-LGHKCSHCGSYNT 59 (61)
T ss_dssp -EEEEEESSS--EEEEE--T-T----TTTS---E
T ss_pred CEEEEECCCCCCccceeeeH-hhhcCCCCCCccc
Confidence 356799977998754 5777 499997 998743
No 33
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=61.92 E-value=4.8 Score=32.00 Aligned_cols=25 Identities=28% Similarity=0.764 Sum_probs=20.3
Q ss_pred ceeeCCCCCCccceeecCCCCCCC-CCCcc
Q psy10712 17 DKLKCPNCSTNLGAFDYVSGHKCP-CKQQC 45 (75)
Q Consensus 17 GKL~CP~C~aKLGsf~wv~G~kCs-CG~~v 45 (75)
-.-.|.+|+..=-.|-| ||+ |++|=
T Consensus 6 ~~y~C~~Cg~~~~~~~g----~Cp~C~~w~ 31 (454)
T TIGR00416 6 SKFVCQHCGADSPKWQG----KCPACHAWN 31 (454)
T ss_pred CeEECCcCCCCCccccE----ECcCCCCcc
Confidence 34789999999777766 896 99995
No 34
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=61.24 E-value=4.7 Score=27.98 Aligned_cols=12 Identities=25% Similarity=0.697 Sum_probs=9.6
Q ss_pred ccceeeCCCCCC
Q psy10712 15 LKDKLKCPNCST 26 (75)
Q Consensus 15 ~~GKL~CP~C~a 26 (75)
.+|+++||.|+-
T Consensus 41 KdG~v~CPvC~~ 52 (131)
T COG1645 41 KDGEVFCPVCGY 52 (131)
T ss_pred eCCeEECCCCCc
Confidence 578888888874
No 35
>PRK05638 threonine synthase; Validated
Probab=58.93 E-value=6.7 Score=30.66 Aligned_cols=28 Identities=25% Similarity=0.597 Sum_probs=21.2
Q ss_pred eeeCCCCCCccceeecCCCCCCCCCCcccce
Q psy10712 18 KLKCPNCSTNLGAFDYVSGHKCPCKQQCVPF 48 (75)
Q Consensus 18 KL~CP~C~aKLGsf~wv~G~kCsCG~~v~Pa 48 (75)
||.|++|+..... ++ . ..|.||..+...
T Consensus 1 ~l~C~~Cg~~~~~-~~-~-~~C~c~~~l~~~ 28 (442)
T PRK05638 1 KMKCPKCGREYNS-YI-P-PFCICGELLEII 28 (442)
T ss_pred CeEeCCCCCCCCC-CC-c-eecCCCCcEEEE
Confidence 7899999999873 45 3 779999776444
No 36
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=58.13 E-value=4.4 Score=21.94 Aligned_cols=17 Identities=35% Similarity=0.778 Sum_probs=13.6
Q ss_pred eCCCCCCccceeecCCCC
Q psy10712 20 KCPNCSTNLGAFDYVSGH 37 (75)
Q Consensus 20 ~CP~C~aKLGsf~wv~G~ 37 (75)
+||+|+..|-.... .+.
T Consensus 1 ~CP~C~~~l~~~~~-~~~ 17 (41)
T PF13453_consen 1 KCPRCGTELEPVRL-GDV 17 (41)
T ss_pred CcCCCCcccceEEE-CCE
Confidence 59999999988877 554
No 37
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=57.20 E-value=14 Score=24.31 Aligned_cols=36 Identities=19% Similarity=0.450 Sum_probs=22.2
Q ss_pred ccceeeCCCCCCccceeecCCCCCCC-CCCcccceEEEEcC
Q psy10712 15 LKDKLKCPNCSTNLGAFDYVSGHKCP-CKQQCVPFIHLVKS 54 (75)
Q Consensus 15 ~~GKL~CP~C~aKLGsf~wv~G~kCs-CG~~v~Paf~i~kS 54 (75)
...+..|+.|+... ......-.+|+ ||.. .+.|...
T Consensus 68 vp~~~~C~~Cg~~~-~~~~~~~~~CP~Cgs~---~~~i~~G 104 (117)
T PRK00564 68 EKVELECKDCSHVF-KPNALDYGVCEKCHSK---NVIITQG 104 (117)
T ss_pred cCCEEEhhhCCCcc-ccCCccCCcCcCCCCC---ceEEecC
Confidence 57889999999543 33220234697 9964 4555543
No 38
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=56.75 E-value=2.2 Score=24.77 Aligned_cols=34 Identities=32% Similarity=0.693 Sum_probs=24.4
Q ss_pred eCCCCCCccceee---cCCCCCCC-CCCcccceEEEEc
Q psy10712 20 KCPNCSTNLGAFD---YVSGHKCP-CKQQCVPFIHLVK 53 (75)
Q Consensus 20 ~CP~C~aKLGsf~---wv~G~kCs-CG~~v~Paf~i~k 53 (75)
.|+-|+.|+|-|. ...|.-|. |-..++|.+...+
T Consensus 1 ~C~iCg~kigl~~~~k~~DG~iC~~C~~Kl~~~~~~~~ 38 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDGYICKDCLKKLSGFFSDVK 38 (51)
T ss_pred CCCccccccccccceeccCccchHHHHHHhcCcccchh
Confidence 3888999999887 65677784 7777766664433
No 39
>PRK08351 DNA-directed RNA polymerase subunit E''; Validated
Probab=56.56 E-value=5.7 Score=24.22 Aligned_cols=17 Identities=18% Similarity=0.466 Sum_probs=14.3
Q ss_pred eCCCCCCccceeecCCCC
Q psy10712 20 KCPNCSTNLGAFDYVSGH 37 (75)
Q Consensus 20 ~CP~C~aKLGsf~wv~G~ 37 (75)
.||+|++..=+.+| .|.
T Consensus 17 ~CP~Cgs~~~T~~W-~G~ 33 (61)
T PRK08351 17 RCPVCGSRDLSDEW-FDL 33 (61)
T ss_pred cCCCCcCCcccccc-ccE
Confidence 59999999888999 563
No 40
>PF06044 DRP: Dam-replacing family; InterPro: IPR010324 Dam-replacing protein (DRP) is a restriction endonuclease that is flanked by pseudo-transposable small repeat elements. The replacement of Dam-methylase by DRP allows phase variation through slippage-like mechanisms in several pathogenic isolates of Neisseria meningitidis [].; PDB: 4ESJ_A.
Probab=56.45 E-value=3.1 Score=31.76 Aligned_cols=31 Identities=32% Similarity=1.034 Sum_probs=12.8
Q ss_pred ccccceeeCCCCCCc-cceeec---CCCCCCC-CCC
Q psy10712 13 NFLKDKLKCPNCSTN-LGAFDY---VSGHKCP-CKQ 43 (75)
Q Consensus 13 ~~~~GKL~CP~C~aK-LGsf~w---v~G~kCs-CG~ 43 (75)
.|+....+||+|+++ |-.|.= |....|. |+.
T Consensus 26 ~Wv~~n~yCP~Cg~~~L~~f~NN~PVaDF~C~~C~e 61 (254)
T PF06044_consen 26 DWVAENMYCPNCGSKPLSKFENNRPVADFYCPNCNE 61 (254)
T ss_dssp HHHHHH---TTT--SS-EE--------EEE-TTT--
T ss_pred HHHHHCCcCCCCCChhHhhccCCCccceeECCCCch
Confidence 588999999999999 777743 1233453 665
No 41
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=56.15 E-value=6.8 Score=22.62 Aligned_cols=25 Identities=24% Similarity=0.586 Sum_probs=13.1
Q ss_pred eeeCCCCCCccceeecCCCCCCC-CCC
Q psy10712 18 KLKCPNCSTNLGAFDYVSGHKCP-CKQ 43 (75)
Q Consensus 18 KL~CP~C~aKLGsf~wv~G~kCs-CG~ 43 (75)
+-.||+|++.+=.-.- ....|. ||.
T Consensus 20 ~~fCP~Cg~~~m~~~~-~r~~C~~Cgy 45 (50)
T PRK00432 20 NKFCPRCGSGFMAEHL-DRWHCGKCGY 45 (50)
T ss_pred cCcCcCCCcchheccC-CcEECCCcCC
Confidence 3489999873111122 345564 553
No 42
>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=55.85 E-value=8.6 Score=25.86 Aligned_cols=38 Identities=18% Similarity=0.362 Sum_probs=23.2
Q ss_pred eeCCCCCCccceeecCCCCCCC-CCCcc---cceEEEEcCccc
Q psy10712 19 LKCPNCSTNLGAFDYVSGHKCP-CKQQC---VPFIHLVKSKID 57 (75)
Q Consensus 19 L~CP~C~aKLGsf~wv~G~kCs-CG~~v---~Paf~i~kSkVD 57 (75)
..||+|+.||=..+= ....|. |+..+ .|-+.|+-.=.|
T Consensus 35 ~aC~~C~kkv~~~~~-~~~~C~~C~~~~~~~~~ry~l~~~i~D 76 (166)
T cd04476 35 PACPGCNKKVVEEGN-GTYRCEKCNKSVPNPEYRYILSLNVAD 76 (166)
T ss_pred ccccccCcccEeCCC-CcEECCCCCCcCCCccEEEEEEEEEEe
Confidence 469999999854431 346775 88764 444555444333
No 43
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=55.12 E-value=9.9 Score=34.92 Aligned_cols=27 Identities=30% Similarity=0.894 Sum_probs=18.6
Q ss_pred ceeeCCCCCCccceeecCCCCCCC-CCCcccceE
Q psy10712 17 DKLKCPNCSTNLGAFDYVSGHKCP-CKQQCVPFI 49 (75)
Q Consensus 17 GKL~CP~C~aKLGsf~wv~G~kCs-CG~~v~Paf 49 (75)
+...||+|++..-. ..|+ ||+...|.+
T Consensus 666 ~~rkCPkCG~~t~~------~fCP~CGs~te~vy 693 (1337)
T PRK14714 666 GRRRCPSCGTETYE------NRCPDCGTHTEPVY 693 (1337)
T ss_pred EEEECCCCCCcccc------ccCcccCCcCCCce
Confidence 56899999986421 2677 888776554
No 44
>PRK11827 hypothetical protein; Provisional
Probab=53.95 E-value=7.6 Score=23.54 Aligned_cols=15 Identities=27% Similarity=0.882 Sum_probs=11.7
Q ss_pred ceeeCCCCCCccceee
Q psy10712 17 DKLKCPNCSTNLGAFD 32 (75)
Q Consensus 17 GKL~CP~C~aKLGsf~ 32 (75)
.-|.||.|+.+| .|+
T Consensus 7 eILaCP~ckg~L-~~~ 21 (60)
T PRK11827 7 EIIACPVCNGKL-WYN 21 (60)
T ss_pred hheECCCCCCcC-eEc
Confidence 348999999998 454
No 45
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.
Probab=53.72 E-value=11 Score=33.88 Aligned_cols=49 Identities=18% Similarity=0.467 Sum_probs=33.7
Q ss_pred chhhhHHHhcCccccceeeCCCCCCccceeecCCCCCCC-CCCcccceEEEEcCccc
Q psy10712 2 SDWMRTAVEEGNFLKDKLKCPNCSTNLGAFDYVSGHKCP-CKQQCVPFIHLVKSKID 57 (75)
Q Consensus 2 m~WM~~~i~~~~~~~GKL~CP~C~aKLGsf~wv~G~kCs-CG~~v~Paf~i~kSkVD 57 (75)
|+-|.+ +.. +..-+.-|.+|++|-=.--- .-+|. ||..|.+ .+|+.-|.
T Consensus 999 PDl~GN-LRa--FsrQ~fRC~kC~~kYRR~PL--~G~C~kCGg~lil--TV~~GsV~ 1048 (1095)
T TIGR00354 999 PDIIGN-LRA--FSRQEVRCTKCNTKYRRIPL--VGKCLKCGNNLTL--TVSKGSVM 1048 (1095)
T ss_pred hHhhhh-Hhh--hhccceeecccCCccccCCC--CCcccccCCeEEE--EEecchhH
Confidence 444444 333 35677899999999887777 35896 9999955 45565553
No 46
>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=53.67 E-value=6.5 Score=20.52 Aligned_cols=13 Identities=23% Similarity=0.805 Sum_probs=9.5
Q ss_pred cceeeCCCCCCcc
Q psy10712 16 KDKLKCPNCSTNL 28 (75)
Q Consensus 16 ~GKL~CP~C~aKL 28 (75)
...+.||.|++.+
T Consensus 24 ~~~~~CP~Cg~~~ 36 (41)
T smart00834 24 DPLATCPECGGDV 36 (41)
T ss_pred CCCCCCCCCCCcc
Confidence 4467899999853
No 47
>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=53.37 E-value=7 Score=21.29 Aligned_cols=18 Identities=33% Similarity=0.577 Sum_probs=12.6
Q ss_pred ccceeeCCCCCCccceee
Q psy10712 15 LKDKLKCPNCSTNLGAFD 32 (75)
Q Consensus 15 ~~GKL~CP~C~aKLGsf~ 32 (75)
..|.+.|++|+.-|....
T Consensus 16 ~~g~~vC~~CG~Vl~e~~ 33 (43)
T PF08271_consen 16 ERGELVCPNCGLVLEENI 33 (43)
T ss_dssp TTTEEEETTT-BBEE-TT
T ss_pred CCCeEECCCCCCEeeccc
Confidence 578999999988776443
No 48
>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=52.26 E-value=19 Score=25.82 Aligned_cols=39 Identities=18% Similarity=0.356 Sum_probs=27.4
Q ss_pred cceeeCCCCCCccceeecC---CCCCCC-CCCcccceEEEEcCccc
Q psy10712 16 KDKLKCPNCSTNLGAFDYV---SGHKCP-CKQQCVPFIHLVKSKID 57 (75)
Q Consensus 16 ~GKL~CP~C~aKLGsf~wv---~G~kCs-CG~~v~Paf~i~kSkVD 57 (75)
-.++.|.+|+.. |+|. ..-.|+ ||..+.|.+-+.-..++
T Consensus 116 ~~~~~C~~C~~~---~~~~~~~~~p~C~~Cgg~lrP~vv~fge~~~ 158 (225)
T cd01411 116 LYRIYCTVCGKT---VDWEEYLKSPYHAKCGGVIRPDIVLYEEMLN 158 (225)
T ss_pred cCeeEeCCCCCc---cchhhcCCCCCCCCCCCEeCCCEEEcCCCCC
Confidence 346789999654 4431 246796 99999999987665554
No 49
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=52.24 E-value=8.5 Score=31.23 Aligned_cols=30 Identities=20% Similarity=0.628 Sum_probs=23.8
Q ss_pred ccceeeCCCCCCccceeecCCCCCCC-CCCcc
Q psy10712 15 LKDKLKCPNCSTNLGAFDYVSGHKCP-CKQQC 45 (75)
Q Consensus 15 ~~GKL~CP~C~aKLGsf~wv~G~kCs-CG~~v 45 (75)
..-+-.||.|+.++=|=-= +|.+|. ||+-.
T Consensus 347 ~~~~p~Cp~Cg~~m~S~G~-~g~rC~kCg~~~ 377 (421)
T COG1571 347 ERVNPVCPRCGGRMKSAGR-NGFRCKKCGTRA 377 (421)
T ss_pred EEcCCCCCccCCchhhcCC-CCcccccccccC
Confidence 3445689999999977666 589998 99875
No 50
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=52.08 E-value=9.8 Score=32.08 Aligned_cols=27 Identities=26% Similarity=0.629 Sum_probs=16.1
Q ss_pred cceeeCCCCCCccceeecCCCCCCC-CCCcccce
Q psy10712 16 KDKLKCPNCSTNLGAFDYVSGHKCP-CKQQCVPF 48 (75)
Q Consensus 16 ~GKL~CP~C~aKLGsf~wv~G~kCs-CG~~v~Pa 48 (75)
++--.||+|+++|.. ..|+ ||+-+.+.
T Consensus 13 ~~akFC~~CG~~l~~------~~Cp~CG~~~~~~ 40 (645)
T PRK14559 13 NNNRFCQKCGTSLTH------KPCPQCGTEVPVD 40 (645)
T ss_pred CCCccccccCCCCCC------CcCCCCCCCCCcc
Confidence 455578888888742 3453 66655443
No 51
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=51.41 E-value=7.6 Score=28.68 Aligned_cols=35 Identities=20% Similarity=0.546 Sum_probs=25.0
Q ss_pred ccccceeeCCCCCCccceeecCCCCCCC-CCCcccc
Q psy10712 13 NFLKDKLKCPNCSTNLGAFDYVSGHKCP-CKQQCVP 47 (75)
Q Consensus 13 ~~~~GKL~CP~C~aKLGsf~wv~G~kCs-CG~~v~P 47 (75)
.|....-.||.|++++-...--....|+ ||...-|
T Consensus 94 ~w~~~~~fC~~CG~~~~~~~~~~~~~C~~c~~~~yp 129 (256)
T PRK00241 94 EFYRSHRFCGYCGHPMHPSKTEWAMLCPHCRERYYP 129 (256)
T ss_pred HHhhcCccccccCCCCeecCCceeEECCCCCCEECC
Confidence 4667778999999998655432356786 9977644
No 52
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=50.48 E-value=7.7 Score=26.21 Aligned_cols=31 Identities=29% Similarity=0.725 Sum_probs=23.7
Q ss_pred eCCCCCCccceeecCCCCCCC-CCCcccceEEEEcC
Q psy10712 20 KCPNCSTNLGAFDYVSGHKCP-CKQQCVPFIHLVKS 54 (75)
Q Consensus 20 ~CP~C~aKLGsf~wv~G~kCs-CG~~v~Paf~i~kS 54 (75)
.||.|++|+=+. -..|+ ||-.++-+-+|.||
T Consensus 3 ~CPrC~skvC~L----P~~CpiCgLtLVss~HLARS 34 (112)
T TIGR00622 3 FCPQCRAKVCEL----PVECPICGLTLILSTHLARS 34 (112)
T ss_pred cCCCCCCCccCC----CCcCCcCCCEEeccchHHHh
Confidence 599999998554 57897 99888666666655
No 53
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=49.97 E-value=7.8 Score=24.10 Aligned_cols=20 Identities=25% Similarity=0.463 Sum_probs=15.8
Q ss_pred ceeeCCCCCCccceeecCCCC
Q psy10712 17 DKLKCPNCSTNLGAFDYVSGH 37 (75)
Q Consensus 17 GKL~CP~C~aKLGsf~wv~G~ 37 (75)
+.-.||.|++.==+++| .|+
T Consensus 17 d~e~CP~Cgs~~~te~W-~G~ 36 (64)
T COG2093 17 DTEICPVCGSTDLTEEW-FGL 36 (64)
T ss_pred CCccCCCCCCcccchhh-ccE
Confidence 34569999999669999 674
No 54
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=49.78 E-value=8.7 Score=32.96 Aligned_cols=31 Identities=26% Similarity=0.477 Sum_probs=19.9
Q ss_pred eeCCCCCCccceeecCCCCCCC-CCCcccceE
Q psy10712 19 LKCPNCSTNLGAFDYVSGHKCP-CKQQCVPFI 49 (75)
Q Consensus 19 L~CP~C~aKLGsf~wv~G~kCs-CG~~v~Paf 49 (75)
..||+|...|--..--..++|. ||.-..+.+
T Consensus 445 ~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~ 476 (730)
T COG1198 445 AECPNCDSPLTLHKATGQLRCHYCGYQEPIPQ 476 (730)
T ss_pred ccCCCCCcceEEecCCCeeEeCCCCCCCCCCC
Confidence 5678888877655554567775 777644333
No 55
>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=49.41 E-value=10 Score=21.28 Aligned_cols=11 Identities=27% Similarity=0.755 Sum_probs=8.7
Q ss_pred ccceeeCCCCC
Q psy10712 15 LKDKLKCPNCS 25 (75)
Q Consensus 15 ~~GKL~CP~C~ 25 (75)
.+|++.||.|+
T Consensus 31 k~g~~~Cv~C~ 41 (41)
T PF06677_consen 31 KDGKIYCVSCG 41 (41)
T ss_pred cCCCEECCCCC
Confidence 47888999885
No 56
>COG5629 Predicted metal-binding protein [Function unknown]
Probab=49.10 E-value=6.4 Score=30.89 Aligned_cols=39 Identities=26% Similarity=0.269 Sum_probs=25.7
Q ss_pred cceeeCCCCCCcccee---------ecCCCCCCCCCCcccceEEEEcC
Q psy10712 16 KDKLKCPNCSTNLGAF---------DYVSGHKCPCKQQCVPFIHLVKS 54 (75)
Q Consensus 16 ~GKL~CP~C~aKLGsf---------~wv~G~kCsCG~~v~Paf~i~kS 54 (75)
+.||+|-+|+|+||-= .|--..-|+=.+.+.|.+-|.-|
T Consensus 167 NfklhCsfCnA~lGlpn~~s~~kl~r~~k~~I~~g~tKihP~~dia~s 214 (321)
T COG5629 167 NFKLHCSFCNARLGLPNDSSIRKLFRYNKEVIPNGCTKIHPHEDLAYS 214 (321)
T ss_pred CcceeeehhhhhhCCCCchhhhhhhhcchheecCCCcccCchHHHHHH
Confidence 5689999999999843 34224556644567776655433
No 57
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the KOG1088|consensus
Probab=48.94 E-value=13 Score=25.77 Aligned_cols=16 Identities=19% Similarity=0.613 Sum_probs=13.1
Q ss_pred ccccceeeCCCCCCcc
Q psy10712 13 NFLKDKLKCPNCSTNL 28 (75)
Q Consensus 13 ~~~~GKL~CP~C~aKL 28 (75)
...+|+|.||+|+...
T Consensus 93 ~v~EG~l~CpetG~vf 108 (124)
T KOG1088|consen 93 DVIEGELVCPETGRVF 108 (124)
T ss_pred hhccceEecCCCCcEe
Confidence 3568999999998764
No 59
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=48.52 E-value=18 Score=24.46 Aligned_cols=13 Identities=38% Similarity=0.802 Sum_probs=10.1
Q ss_pred ccceeeCCCCCCc
Q psy10712 15 LKDKLKCPNCSTN 27 (75)
Q Consensus 15 ~~GKL~CP~C~aK 27 (75)
...+..|++|+..
T Consensus 67 ~p~~~~C~~CG~~ 79 (135)
T PRK03824 67 EEAVLKCRNCGNE 79 (135)
T ss_pred cceEEECCCCCCE
Confidence 4578999999944
No 60
>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=48.11 E-value=11 Score=19.13 Aligned_cols=10 Identities=40% Similarity=1.075 Sum_probs=7.8
Q ss_pred cceeeCCCCC
Q psy10712 16 KDKLKCPNCS 25 (75)
Q Consensus 16 ~GKL~CP~C~ 25 (75)
.-...||||+
T Consensus 14 ~v~f~CPnCG 23 (24)
T PF07754_consen 14 AVPFPCPNCG 23 (24)
T ss_pred CceEeCCCCC
Confidence 4467899997
No 61
>KOG3092|consensus
Probab=47.41 E-value=9.4 Score=28.59 Aligned_cols=12 Identities=42% Similarity=0.886 Sum_probs=9.8
Q ss_pred ccceeeCCCCCC
Q psy10712 15 LKDKLKCPNCST 26 (75)
Q Consensus 15 ~~GKL~CP~C~a 26 (75)
..=||+||+|..
T Consensus 131 ~~VklYCP~C~d 142 (216)
T KOG3092|consen 131 STVKLYCPSCED 142 (216)
T ss_pred ceEEEeCCCccc
Confidence 467999999963
No 62
>PRK08329 threonine synthase; Validated
Probab=47.17 E-value=13 Score=28.09 Aligned_cols=28 Identities=18% Similarity=0.600 Sum_probs=20.8
Q ss_pred eeeCCCCCCccceeecCCCCCCCCCCcccce
Q psy10712 18 KLKCPNCSTNLGAFDYVSGHKCPCKQQCVPF 48 (75)
Q Consensus 18 KL~CP~C~aKLGsf~wv~G~kCsCG~~v~Pa 48 (75)
+|.|++|+..... ++ . ..|.||..+...
T Consensus 1 ~l~C~~Cg~~~~~-~~-~-~~C~c~~~l~~~ 28 (347)
T PRK08329 1 MLRCTKCGRTYEE-KF-K-LRCDCGGTLLVE 28 (347)
T ss_pred CcCcCCCCCCcCC-CC-c-eecCCCCcEEEE
Confidence 4789999999874 45 3 789999765444
No 63
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=47.03 E-value=11 Score=22.71 Aligned_cols=9 Identities=33% Similarity=1.117 Sum_probs=7.4
Q ss_pred eeCCCCCCc
Q psy10712 19 LKCPNCSTN 27 (75)
Q Consensus 19 L~CP~C~aK 27 (75)
|.||.|+.|
T Consensus 5 i~CP~CgnK 13 (55)
T PF14205_consen 5 ILCPICGNK 13 (55)
T ss_pred EECCCCCCc
Confidence 789999865
No 64
>PRK04023 DNA polymerase II large subunit; Validated
Probab=47.01 E-value=16 Score=33.06 Aligned_cols=49 Identities=18% Similarity=0.560 Sum_probs=33.4
Q ss_pred chhhhHHHhcCccccceeeCCCCCCccceeecCCCCCCC-CCCcccceEEEEcCccc
Q psy10712 2 SDWMRTAVEEGNFLKDKLKCPNCSTNLGAFDYVSGHKCP-CKQQCVPFIHLVKSKID 57 (75)
Q Consensus 2 m~WM~~~i~~~~~~~GKL~CP~C~aKLGsf~wv~G~kCs-CG~~v~Paf~i~kSkVD 57 (75)
|+-|.+ +.. +..-+.-|.+|++|-=.-=- .-+|. ||..|.+ .+|+.-|.
T Consensus 1024 PDl~GN-LRa--FsrQ~fRC~kC~~kYRR~PL--~G~C~kCGg~lil--TVh~GsV~ 1073 (1121)
T PRK04023 1024 PDLIGN-LRA--FSRQEFRCTKCGAKYRRPPL--SGKCPKCGGNLIL--TVHKGSVE 1073 (1121)
T ss_pred hhhhhh-hhh--hcccceeecccCcccccCCC--CCcCccCCCeEEE--EEecchHH
Confidence 444444 333 35677899999999877777 35885 9999955 45555553
No 65
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=46.82 E-value=16 Score=33.63 Aligned_cols=39 Identities=18% Similarity=0.554 Sum_probs=29.6
Q ss_pred cccceeeCCCCCCccceeecCCCCCCC-CCCcccceEEEEcCcc
Q psy10712 14 FLKDKLKCPNCSTNLGAFDYVSGHKCP-CKQQCVPFIHLVKSKI 56 (75)
Q Consensus 14 ~~~GKL~CP~C~aKLGsf~wv~G~kCs-CG~~v~Paf~i~kSkV 56 (75)
+..-+.-|.+|++|-=.-=- .-+|. ||..|.+. +|+.-|
T Consensus 1249 FsrQ~~RC~kC~~kyRR~PL--~G~C~kCGg~iilT--v~~Gsv 1288 (1337)
T PRK14714 1249 FSRQEFRCLKCGTKYRRMPL--AGKCRKCGGRIILT--VHEGSV 1288 (1337)
T ss_pred hhccceeecccCcccccCCC--CCcccccCCeEEEE--EecchH
Confidence 45678899999999887777 35896 99999554 555555
No 66
>PF03226 Yippee-Mis18: Yippee zinc-binding/DNA-binding /Mis18, centromere assembly; InterPro: IPR004910 This entry represents the Yippee-like (YPEL) family of putative zinc-binding proteins which is highly conserved among eukaryotes. The first protein in this family to be characterised, the Yippee protein from Drosophila, was identified by yeast interaction trap screen as a protein that physically interacts with moth hemolin []. It was subsequently found to be a member of a highly conserved family of proteins found in diverse eukaryotes including plants, animals and fungi []. Mammals contain five members of this family, YPEL1 to YPEL5, while other organisms tend to contain only two or three members. The mammalian proteins all appear to localise in the nucleus. YPEL1-4 are located in an unknown structure located on or close to the mitotic apparatus in the mitotic phase, whereas in the interphase they are located in the nuclei and nucleoli. In contrast, YPEL5 is localised to the centrosome and nucleus during interphase and at the mitotic spindle during mitosis, suggesting a function distinct from that of YPEL1-4. The localisation of the YPEL proteins suggests a novel, thopugh still unknown, function involved in cell division.
Probab=46.69 E-value=9.5 Score=23.68 Aligned_cols=15 Identities=40% Similarity=0.680 Sum_probs=12.6
Q ss_pred cceeeCCCCCCccce
Q psy10712 16 KDKLKCPNCSTNLGA 30 (75)
Q Consensus 16 ~GKL~CP~C~aKLGs 30 (75)
--.|.|.+|++.||-
T Consensus 55 ~~~l~C~~C~~~lGw 69 (96)
T PF03226_consen 55 VRDLFCSGCNTILGW 69 (96)
T ss_pred EEEeEcccCChhHCc
Confidence 346999999999993
No 67
>PF11648 RIG-I_C-RD: C-terminal domain of RIG-I; InterPro: IPR021673 This family of proteins represents the regulatory domain RD of RIG-I, a protein which initiates a signalling cascade that provides essential antiviral protection for the host. The RD domain binds viral RNA, activating the RIG-I ATPase by RNA-dependent dimerisation. The structure of RD contains a zinc-binding domain and is thought to confer ligand specificity []. ; GO: 0016817 hydrolase activity, acting on acid anhydrides; PDB: 2RQB_A 3GA3_A 2W4R_D 3EQT_A 2RQA_A 2RMJ_A 3NCU_A 2QFD_C 2QFB_D 3TMI_A ....
Probab=46.42 E-value=8.2 Score=25.72 Aligned_cols=26 Identities=27% Similarity=0.597 Sum_probs=19.4
Q ss_pred ccceeeCCCCCCccceeecCCCCCCC
Q psy10712 15 LKDKLKCPNCSTNLGAFDYVSGHKCP 40 (75)
Q Consensus 15 ~~GKL~CP~C~aKLGsf~wv~G~kCs 40 (75)
..|+|.|-+|+..+|..-=..|...+
T Consensus 57 ~~~~I~C~~C~~~wG~~m~yk~~~LP 82 (123)
T PF11648_consen 57 PNGKIHCKNCGQDWGIMMKYKGVELP 82 (123)
T ss_dssp EEEEEEETSTSBEEEEEEEETTEEEE
T ss_pred eCCEEEcCCCChHhhhheEECCcccc
Confidence 57999999999999965433565543
No 68
>PF14353 CpXC: CpXC protein
Probab=46.34 E-value=20 Score=23.22 Aligned_cols=13 Identities=23% Similarity=0.769 Sum_probs=8.0
Q ss_pred cceeeCCCCCCcc
Q psy10712 16 KDKLKCPNCSTNL 28 (75)
Q Consensus 16 ~GKL~CP~C~aKL 28 (75)
-....||+|+.+.
T Consensus 36 l~~~~CP~Cg~~~ 48 (128)
T PF14353_consen 36 LFSFTCPSCGHKF 48 (128)
T ss_pred cCEEECCCCCCce
Confidence 3456677777654
No 69
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=45.62 E-value=9.3 Score=21.37 Aligned_cols=9 Identities=33% Similarity=1.331 Sum_probs=6.7
Q ss_pred eCCCCCCcc
Q psy10712 20 KCPNCSTNL 28 (75)
Q Consensus 20 ~CP~C~aKL 28 (75)
.||.|+++.
T Consensus 1 ~CP~Cg~~a 9 (47)
T PF04606_consen 1 RCPHCGSKA 9 (47)
T ss_pred CcCCCCCee
Confidence 488888764
No 70
>PRK12495 hypothetical protein; Provisional
Probab=45.02 E-value=14 Score=27.83 Aligned_cols=40 Identities=23% Similarity=0.469 Sum_probs=27.9
Q ss_pred hhhHHHhcCccccceeeCCCCCCccceeecCCCCCCC-CCCccc
Q psy10712 4 WMRTAVEEGNFLKDKLKCPNCSTNLGAFDYVSGHKCP-CKQQCV 46 (75)
Q Consensus 4 WM~~~i~~~~~~~GKL~CP~C~aKLGsf~wv~G~kCs-CG~~v~ 46 (75)
=|...|.++. ...-.+|+.|+.-|=.+..+ ..|. |+..|.
T Consensus 29 ~ma~lL~~ga-tmsa~hC~~CG~PIpa~pG~--~~Cp~CQ~~~~ 69 (226)
T PRK12495 29 RMSELLLQGA-TMTNAHCDECGDPIFRHDGQ--EFCPTCQQPVT 69 (226)
T ss_pred HHHHHHHhhc-ccchhhcccccCcccCCCCe--eECCCCCCccc
Confidence 3566666543 56778899999999766442 5574 998764
No 71
>cd01412 SIRT5_Af1_CobB SIRT5_Af1_CobB: Eukaryotic, archaeal and prokaryotic group (class3) which includes human sirtuin SIRT5, Archaeoglobus fulgidus Sir2-Af1, and E. coli CobB; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. CobB is a bacterial sirtuin that deacetylates acetyl-CoA synthetase at an active site lysine to stimulate its enzymatic activity.
Probab=44.85 E-value=26 Score=24.72 Aligned_cols=41 Identities=15% Similarity=0.303 Sum_probs=27.8
Q ss_pred cceeeCCCCCCccce---eecCCCCCCC-CCCcccceEEEEcCcc
Q psy10712 16 KDKLKCPNCSTNLGA---FDYVSGHKCP-CKQQCVPFIHLVKSKI 56 (75)
Q Consensus 16 ~GKL~CP~C~aKLGs---f~wv~G~kCs-CG~~v~Paf~i~kSkV 56 (75)
-..+.|.+|+.+.-. .+-....+|+ ||..+.|.+-+.-..+
T Consensus 107 ~~~~~C~~C~~~~~~~~~~~~~~~p~C~~Cgg~lrp~Vv~fge~~ 151 (224)
T cd01412 107 LFRVRCSSCGYVGENNEEIPEEELPRCPKCGGLLRPGVVWFGESL 151 (224)
T ss_pred cCccccCCCCCCCCcchhhhccCCCCCCCCCCccCCceEECCCCC
Confidence 456889999987521 1111246896 9999999997665544
No 72
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=44.84 E-value=12 Score=22.03 Aligned_cols=13 Identities=23% Similarity=0.984 Sum_probs=10.6
Q ss_pred cceeeCCCCCCcc
Q psy10712 16 KDKLKCPNCSTNL 28 (75)
Q Consensus 16 ~GKL~CP~C~aKL 28 (75)
..-+-||.|+.|+
T Consensus 22 ~~~irCp~Cg~rI 34 (49)
T COG1996 22 TRGIRCPYCGSRI 34 (49)
T ss_pred cCceeCCCCCcEE
Confidence 4558899999986
No 73
>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=44.71 E-value=15 Score=21.82 Aligned_cols=14 Identities=36% Similarity=0.992 Sum_probs=10.1
Q ss_pred ccccceeeCCCCCC
Q psy10712 13 NFLKDKLKCPNCST 26 (75)
Q Consensus 13 ~~~~GKL~CP~C~a 26 (75)
...+..|.||+|++
T Consensus 19 ~~~~leIKCpRC~t 32 (51)
T PF10122_consen 19 EVIELEIKCPRCKT 32 (51)
T ss_pred CccEEEEECCCCCc
Confidence 34567888998864
No 74
>PF13790 DUF4182: Domain of unknown function (DUF4182)
Probab=44.15 E-value=14 Score=20.82 Aligned_cols=17 Identities=18% Similarity=0.716 Sum_probs=14.8
Q ss_pred ceeeCCCCCCccceeec
Q psy10712 17 DKLKCPNCSTNLGAFDY 33 (75)
Q Consensus 17 GKL~CP~C~aKLGsf~w 33 (75)
|.|.|..|++-++.|.=
T Consensus 2 GtIvCq~C~~~Id~~e~ 18 (38)
T PF13790_consen 2 GTIVCQHCNETIDHFET 18 (38)
T ss_pred CEEEeccccceeeeecC
Confidence 77999999999999863
No 75
>PRK06835 DNA replication protein DnaC; Validated
Probab=44.14 E-value=14 Score=28.31 Aligned_cols=25 Identities=40% Similarity=1.007 Sum_probs=19.3
Q ss_pred cceeeCCCCCCccceeecCCCCCCCCCCc
Q psy10712 16 KDKLKCPNCSTNLGAFDYVSGHKCPCKQQ 44 (75)
Q Consensus 16 ~GKL~CP~C~aKLGsf~wv~G~kCsCG~~ 44 (75)
+-+-.||+|+-. |-+ .|.+|+|-..
T Consensus 96 ~~~y~Cp~C~dt-G~i---~~~~C~C~~q 120 (329)
T PRK06835 96 EMKYTCPKCKDT-GFI---NGKKCSCYKQ 120 (329)
T ss_pred CCCCCCCCCCCC-CCc---CCccccchhH
Confidence 455679999988 644 5789999865
No 76
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=43.99 E-value=14 Score=29.73 Aligned_cols=25 Identities=32% Similarity=0.711 Sum_probs=13.5
Q ss_pred eeCCCCCCccceeecCCCCCCC-CCC
Q psy10712 19 LKCPNCSTNLGAFDYVSGHKCP-CKQ 43 (75)
Q Consensus 19 L~CP~C~aKLGsf~wv~G~kCs-CG~ 43 (75)
+.||+|+..|--..--+-.+|. ||.
T Consensus 223 ~~C~~C~~~l~~h~~~~~l~Ch~Cg~ 248 (505)
T TIGR00595 223 LCCPNCDVSLTYHKKEGKLRCHYCGY 248 (505)
T ss_pred cCCCCCCCceEEecCCCeEEcCCCcC
Confidence 3488888777543322334454 443
No 77
>PRK14873 primosome assembly protein PriA; Provisional
Probab=43.46 E-value=19 Score=30.38 Aligned_cols=26 Identities=23% Similarity=0.617 Sum_probs=13.2
Q ss_pred eeCCCCCCccceeecCCCCCCC-CCCc
Q psy10712 19 LKCPNCSTNLGAFDYVSGHKCP-CKQQ 44 (75)
Q Consensus 19 L~CP~C~aKLGsf~wv~G~kCs-CG~~ 44 (75)
+.||+|+..|.-..--.-.+|. ||.-
T Consensus 393 ~~C~~C~~~L~~h~~~~~l~Ch~CG~~ 419 (665)
T PRK14873 393 ARCRHCTGPLGLPSAGGTPRCRWCGRA 419 (665)
T ss_pred eECCCCCCceeEecCCCeeECCCCcCC
Confidence 5566666666432221235565 6653
No 78
>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=43.44 E-value=11 Score=20.50 Aligned_cols=12 Identities=50% Similarity=1.201 Sum_probs=5.4
Q ss_pred eCCCCCCcccee
Q psy10712 20 KCPNCSTNLGAF 31 (75)
Q Consensus 20 ~CP~C~aKLGsf 31 (75)
.||+|+.+--.|
T Consensus 2 ~Cp~Cg~~~a~~ 13 (39)
T PF01096_consen 2 KCPKCGHNEAVF 13 (39)
T ss_dssp --SSS-SSEEEE
T ss_pred CCcCCCCCeEEE
Confidence 577777665444
No 79
>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=42.99 E-value=14 Score=20.05 Aligned_cols=14 Identities=29% Similarity=0.871 Sum_probs=10.4
Q ss_pred eeeCCCCCCcccee
Q psy10712 18 KLKCPNCSTNLGAF 31 (75)
Q Consensus 18 KL~CP~C~aKLGsf 31 (75)
.+.||.|++--+-+
T Consensus 5 ~v~CP~C~s~~~v~ 18 (36)
T PF03811_consen 5 DVHCPRCQSTEGVK 18 (36)
T ss_pred eeeCCCCCCCCcce
Confidence 48999999876433
No 80
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=42.89 E-value=6.1 Score=22.94 Aligned_cols=35 Identities=20% Similarity=0.663 Sum_probs=15.5
Q ss_pred chhhhHHHhcCccccceeeCCCCCCccceeecCCCCCCC-CCCccc
Q psy10712 2 SDWMRTAVEEGNFLKDKLKCPNCSTNLGAFDYVSGHKCP-CKQQCV 46 (75)
Q Consensus 2 m~WM~~~i~~~~~~~GKL~CP~C~aKLGsf~wv~G~kCs-CG~~v~ 46 (75)
|.|+.+. ..-.|+.|+.+.+-|.. -..|. ||..|-
T Consensus 1 ~~W~~d~--------~~~~C~~C~~~F~~~~r--rhhCr~CG~~vC 36 (69)
T PF01363_consen 1 PHWVPDS--------EASNCMICGKKFSLFRR--RHHCRNCGRVVC 36 (69)
T ss_dssp --SSSGG--------G-SB-TTT--B-BSSS---EEE-TTT--EEE
T ss_pred CCcCCCC--------CCCcCcCcCCcCCCcee--eEccCCCCCEEC
Confidence 5677751 22469999999876655 56675 887663
No 81
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=42.66 E-value=15 Score=19.97 Aligned_cols=17 Identities=24% Similarity=0.671 Sum_probs=9.4
Q ss_pred CCCC-CCCcccceEEEEc
Q psy10712 37 HKCP-CKQQCVPFIHLVK 53 (75)
Q Consensus 37 ~kCs-CG~~v~Paf~i~k 53 (75)
.+|+ |++++.|-.+|..
T Consensus 3 ~rC~~C~aylNp~~~~~~ 20 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDD 20 (40)
T ss_dssp -B-TTT--BS-TTSEEET
T ss_pred cccCCCCCEECCcceEcC
Confidence 4675 8888888888875
No 82
>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=42.46 E-value=11 Score=20.78 Aligned_cols=11 Identities=27% Similarity=0.830 Sum_probs=8.9
Q ss_pred cceeeCCCCCC
Q psy10712 16 KDKLKCPNCST 26 (75)
Q Consensus 16 ~GKL~CP~C~a 26 (75)
+..+.||.|++
T Consensus 24 ~~~~~CP~Cg~ 34 (52)
T TIGR02605 24 DPLATCPECGG 34 (52)
T ss_pred CCCCCCCCCCC
Confidence 45678999998
No 83
>PF10005 DUF2248: Uncharacterized protein conserved in bacteria (DUF2248); InterPro: IPR011201 This is a family of uncharacterised bacterial proteins.
Probab=42.09 E-value=17 Score=28.85 Aligned_cols=22 Identities=27% Similarity=0.945 Sum_probs=17.7
Q ss_pred eCCCCCCccceeecCCCCCC-CCCCcc
Q psy10712 20 KCPNCSTNLGAFDYVSGHKC-PCKQQC 45 (75)
Q Consensus 20 ~CP~C~aKLGsf~wv~G~kC-sCG~~v 45 (75)
.||+|+..| . | ....| +||.-+
T Consensus 1 ~C~~Cg~~v-~--F-eNt~C~~Cg~~L 23 (343)
T PF10005_consen 1 SCPNCGQPV-F--F-ENTRCLSCGSAL 23 (343)
T ss_pred CCCCCCCcc-e--e-CCCccccCCccc
Confidence 499999998 2 3 67899 899977
No 84
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=41.78 E-value=11 Score=20.29 Aligned_cols=9 Identities=44% Similarity=1.124 Sum_probs=3.7
Q ss_pred eCCCCCCcc
Q psy10712 20 KCPNCSTNL 28 (75)
Q Consensus 20 ~CP~C~aKL 28 (75)
.||+|+..|
T Consensus 2 fC~~CG~~l 10 (34)
T PF14803_consen 2 FCPQCGGPL 10 (34)
T ss_dssp B-TTT--B-
T ss_pred ccccccChh
Confidence 478888776
No 85
>PTZ00396 Casein kinase II subunit beta; Provisional
Probab=41.57 E-value=12 Score=28.28 Aligned_cols=12 Identities=33% Similarity=0.877 Sum_probs=9.8
Q ss_pred ccceeeCCCCCC
Q psy10712 15 LKDKLKCPNCST 26 (75)
Q Consensus 15 ~~GKL~CP~C~a 26 (75)
..=||+||+|+.
T Consensus 145 ~~VKlyCP~C~D 156 (251)
T PTZ00396 145 SRVKVYCPRCQE 156 (251)
T ss_pred CceeEeCCCchh
Confidence 567999999974
No 86
>PF01214 CK_II_beta: Casein kinase II regulatory subunit; InterPro: IPR000704 Protein phosphorylation, which plays a key role in most cellular activities, is a reversible process mediated by protein kinases and phosphoprotein phosphatases. Protein kinases catalyse the transfer of the gamma phosphate from nucleotide triphosphates (often ATP) to one or more amino acid residues in a protein substrate side chain, resulting in a conformational change affecting protein function. Phosphoprotein phosphatases catalyse the reverse process. Protein kinases fall into three broad classes, characterised with respect to substrate specificity []: Serine/threonine-protein kinases Tyrosine-protein kinases Dual specific protein kinases (e.g. MEK - phosphorylates both Thr and Tyr on target proteins) Protein kinase function has been evolutionarily conserved from Escherichia coli to human []. Protein kinases play a role in a multitude of cellular processes, including division, proliferation, apoptosis, and differentiation []. Phosphorylation usually results in a functional change of the target protein by changing enzyme activity, cellular location, or association with other proteins. The catalytic subunits of protein kinases are highly conserved, and several structures have been solved [], leading to large screens to develop kinase-specific inhibitors for the treatments of a number of diseases []. Casein kinase, a ubiquitous, well-conserved protein kinase involved in cell metabolism and differentiation, is characterised by its preference for Ser or Thr in acidic stretches of amino acids. The enzyme is a tetramer of 2 alpha- and 2 beta-subunits [, ]. However, some species (e.g., mammals) possess 2 related forms of the alpha-subunit (alpha and alpha'), while others (e.g., fungi) possess 2 related beta-subunits (beta and beta') []. The alpha-subunit is the catalytic unit and contains regions characteristic of serine/threonine protein kinases. The beta-subunit is believed to be regulatory, possessing an N-terminal auto-phosphorylation site, an internal acidic domain, and a potential metal-binding motif []. The beta subunit is a highly conserved protein of about 25kDa that contains, in its central section, a cysteine-rich motif, CX(n)C, that could be involved in binding a metal such as zinc []. The mammalian beta-subunit gene promoter shares common features with those of other mammalian protein kinases and is closely related to the promoter of the regulatory subunit of cAMP-dependent protein kinase [].; GO: 0019887 protein kinase regulator activity, 0005956 protein kinase CK2 complex; PDB: 2R6M_B 1RQF_K 1DS5_G 1QF8_B 3EED_A 4DGL_A 1JWH_D.
Probab=40.61 E-value=13 Score=26.58 Aligned_cols=11 Identities=45% Similarity=0.945 Sum_probs=9.1
Q ss_pred ccceeeCCCCC
Q psy10712 15 LKDKLKCPNCS 25 (75)
Q Consensus 15 ~~GKL~CP~C~ 25 (75)
..=||.||+|+
T Consensus 124 ~~vKlyCP~C~ 134 (184)
T PF01214_consen 124 STVKLYCPRCK 134 (184)
T ss_dssp -BBEEEETTTT
T ss_pred cceeEECCCCc
Confidence 56799999998
No 87
>COG3877 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.55 E-value=15 Score=25.32 Aligned_cols=30 Identities=27% Similarity=0.657 Sum_probs=23.1
Q ss_pred eeCCCCCCccceeecCCCCCCC-CCCcccceEEEE
Q psy10712 19 LKCPNCSTNLGAFDYVSGHKCP-CKQQCVPFIHLV 52 (75)
Q Consensus 19 L~CP~C~aKLGsf~wv~G~kCs-CG~~v~Paf~i~ 52 (75)
..||-|+.++ -|+..+|+ |++-|.-.|.+.
T Consensus 7 ~~cPvcg~~~----iVTeL~c~~~etTVrg~F~~s 37 (122)
T COG3877 7 NRCPVCGRKL----IVTELKCSNCETTVRGNFKMS 37 (122)
T ss_pred CCCCcccccc----eeEEEecCCCCceEecceecc
Confidence 4589998887 56788997 999887777654
No 88
>PTZ00409 Sir2 (Silent Information Regulator) protein; Provisional
Probab=39.37 E-value=29 Score=25.94 Aligned_cols=42 Identities=19% Similarity=0.434 Sum_probs=27.2
Q ss_pred cceeeCCCCCCcccee--------ecCC--CCCCCCCCcccceEEEEcCccc
Q psy10712 16 KDKLKCPNCSTNLGAF--------DYVS--GHKCPCKQQCVPFIHLVKSKID 57 (75)
Q Consensus 16 ~GKL~CP~C~aKLGsf--------~wv~--G~kCsCG~~v~Paf~i~kSkVD 57 (75)
-.++.|.+|+.+.-.- .+.. ..+|+||..+.|.+-+.--.++
T Consensus 135 l~~~~C~~C~~~~~~~~~~~~~~~~~~~~~~P~C~Cgg~lrP~VV~FGE~lp 186 (271)
T PTZ00409 135 VFEARCCTCRKTIQLNKIMLQKTSHFMHQLPPECPCGGIFKPNVILFGEVIP 186 (271)
T ss_pred cCcceeCCCCCCcccCHHHHhhhhhhccCCCCCCCCCCcccCcEEEeCCcCC
Confidence 3568899998763200 0001 2579999999999887655444
No 89
>TIGR03844 cysteate_syn cysteate synthase. Members of this family are cysteate synthase, an enzyme of alternate pathway to sulfopyruvate, a precursor of coenzyme M.
Probab=38.66 E-value=27 Score=27.36 Aligned_cols=28 Identities=29% Similarity=0.470 Sum_probs=19.6
Q ss_pred eeeCCCCCCccceeecCCCCCCC-CCCcccce
Q psy10712 18 KLKCPNCSTNLGAFDYVSGHKCP-CKQQCVPF 48 (75)
Q Consensus 18 KL~CP~C~aKLGsf~wv~G~kCs-CG~~v~Pa 48 (75)
+|.|++|+.... +. .-.+|+ |+..+...
T Consensus 2 ~l~C~~Cg~~~~--~~-~~~~C~~c~g~l~~~ 30 (398)
T TIGR03844 2 TLRCPGCGEVLP--DH-YTLSCPLDCGLLRAE 30 (398)
T ss_pred EEEeCCCCCccC--Cc-cccCCCCCCCceEEe
Confidence 589999999986 44 247896 87654433
No 90
>PRK11088 rrmA 23S rRNA methyltransferase A; Provisional
Probab=38.49 E-value=14 Score=26.56 Aligned_cols=23 Identities=26% Similarity=0.749 Sum_probs=16.8
Q ss_pred eeCCCCCCccceeecCCCCCCCCCC
Q psy10712 19 LKCPNCSTNLGAFDYVSGHKCPCKQ 43 (75)
Q Consensus 19 L~CP~C~aKLGsf~wv~G~kCsCG~ 43 (75)
+.||.|++.| ...= .+..|..|.
T Consensus 3 ~~CP~C~~~l-~~~~-~~~~C~~~h 25 (272)
T PRK11088 3 YQCPLCHQPL-TLEE-NSWICPQNH 25 (272)
T ss_pred ccCCCCCcch-hcCC-CEEEcCCCC
Confidence 6799999999 3333 567888765
No 91
>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=37.86 E-value=13 Score=23.27 Aligned_cols=12 Identities=33% Similarity=0.802 Sum_probs=5.9
Q ss_pred cceeeCCCCCCc
Q psy10712 16 KDKLKCPNCSTN 27 (75)
Q Consensus 16 ~GKL~CP~C~aK 27 (75)
..|+-||+|+.+
T Consensus 22 ~~k~FCp~CGn~ 33 (73)
T PF08772_consen 22 MTKQFCPKCGNA 33 (73)
T ss_dssp SS--S-SSS--S
T ss_pred CCceeCcccCCC
Confidence 578999999876
No 92
>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=37.52 E-value=15 Score=19.90 Aligned_cols=9 Identities=56% Similarity=1.368 Sum_probs=6.9
Q ss_pred eCCCCCCcc
Q psy10712 20 KCPNCSTNL 28 (75)
Q Consensus 20 ~CP~C~aKL 28 (75)
.||.|++.|
T Consensus 3 ~CP~Cg~~l 11 (39)
T PF01396_consen 3 KCPKCGGPL 11 (39)
T ss_pred CCCCCCcee
Confidence 599998654
No 93
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=37.52 E-value=17 Score=22.84 Aligned_cols=11 Identities=36% Similarity=1.204 Sum_probs=7.3
Q ss_pred ceeeCCCCCCc
Q psy10712 17 DKLKCPNCSTN 27 (75)
Q Consensus 17 GKL~CP~C~aK 27 (75)
++-.||+|+.+
T Consensus 3 ~~~kCpKCgn~ 13 (68)
T COG3478 3 NAFKCPKCGNT 13 (68)
T ss_pred ccccCCCcCCc
Confidence 34459999764
No 94
>PRK09401 reverse gyrase; Reviewed
Probab=37.45 E-value=14 Score=33.04 Aligned_cols=26 Identities=31% Similarity=0.736 Sum_probs=22.0
Q ss_pred eeeCCCCCCccceeecCCCCCCC-CCC
Q psy10712 18 KLKCPNCSTNLGAFDYVSGHKCP-CKQ 43 (75)
Q Consensus 18 KL~CP~C~aKLGsf~wv~G~kCs-CG~ 43 (75)
+-.||||+..+-+..-..|.-|. |=.
T Consensus 7 ~~~cpnc~g~i~~~rl~~g~~c~~cl~ 33 (1176)
T PRK09401 7 KNSCPNCGGDISDERLEKGLPCEKCLP 33 (1176)
T ss_pred cccCCCCCCcCcHhHHhcCCcChhhCC
Confidence 34699999999999998899996 754
No 95
>PTZ00408 NAD-dependent deacetylase; Provisional
Probab=37.25 E-value=25 Score=25.76 Aligned_cols=36 Identities=22% Similarity=0.503 Sum_probs=24.0
Q ss_pred cceeeCCCCCCccceeecC-----CCCCCC-CC--CcccceEEEEcC
Q psy10712 16 KDKLKCPNCSTNLGAFDYV-----SGHKCP-CK--QQCVPFIHLVKS 54 (75)
Q Consensus 16 ~GKL~CP~C~aKLGsf~wv-----~G~kCs-CG--~~v~Paf~i~kS 54 (75)
--++.|.+|+.+ |+|. .-.+|+ || ..+.|.|-+.--
T Consensus 115 ~~~~~C~~C~~~---~~~~~~~~~~~p~C~~Cg~~g~lrP~vV~FGE 158 (242)
T PTZ00408 115 LLKVRCTATGHV---FDWTEDVVHGSSRCKCCGCVGTLRPHIVWFGE 158 (242)
T ss_pred cceEEECCCCcc---cCchhhhhcCCCccccCCCCCCCCCCEEEcCC
Confidence 345789999875 5551 115685 77 789998877443
No 96
>PF13695 zf-3CxxC: Zinc-binding domain
Probab=35.59 E-value=45 Score=21.11 Aligned_cols=36 Identities=19% Similarity=0.655 Sum_probs=25.4
Q ss_pred ccceeeCCCCCCccceee-cC--------------CCCCCC-CCCcccceEE
Q psy10712 15 LKDKLKCPNCSTNLGAFD-YV--------------SGHKCP-CKQQCVPFIH 50 (75)
Q Consensus 15 ~~GKL~CP~C~aKLGsf~-wv--------------~G~kCs-CG~~v~Paf~ 50 (75)
..|++.|++|+..=+|=+ || -|.+|. |+....|-|.
T Consensus 2 ~~grF~C~~C~~~W~S~~v~i~f~~~~~g~v~~rv~~Q~C~~C~~~~~P~~~ 53 (98)
T PF13695_consen 2 AFGRFQCSKCSRGWTSAKVWILFHMYRGGQVNMRVFGQRCKKCNPLERPYFS 53 (98)
T ss_pred cEEEEECCCCCCCCccCEEEEEEEEcCCCeEEEEEECCCCCCCCCCCCccCc
Confidence 468889999965544311 11 288995 9999999996
No 97
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=35.14 E-value=17 Score=18.94 Aligned_cols=13 Identities=31% Similarity=0.953 Sum_probs=8.3
Q ss_pred cceeeCCCCCCcc
Q psy10712 16 KDKLKCPNCSTNL 28 (75)
Q Consensus 16 ~GKL~CP~C~aKL 28 (75)
.+|-.||+|+.+.
T Consensus 11 ~~kY~Cp~C~~~~ 23 (30)
T PF04438_consen 11 PAKYRCPRCGARY 23 (30)
T ss_dssp EESEE-TTT--EE
T ss_pred CCEEECCCcCCce
Confidence 6788999999874
No 98
>PRK06450 threonine synthase; Validated
Probab=35.11 E-value=31 Score=26.28 Aligned_cols=29 Identities=24% Similarity=0.508 Sum_probs=20.6
Q ss_pred eeeCCCCCCccceeecCCCCCCC-CCCcccceE
Q psy10712 18 KLKCPNCSTNLGAFDYVSGHKCP-CKQQCVPFI 49 (75)
Q Consensus 18 KL~CP~C~aKLGsf~wv~G~kCs-CG~~v~Paf 49 (75)
+|.|+.|+..... .+ -.+|+ ||..+...+
T Consensus 3 ~~~C~~Cg~~~~~-~~--~~~C~~cg~~l~~~~ 32 (338)
T PRK06450 3 KEVCMKCGKERES-IY--EIRCKKCGGPFEILI 32 (338)
T ss_pred eeEECCcCCcCCC-cc--cccCCcCCCEeEEee
Confidence 4899999998765 44 36896 997664443
No 99
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=34.78 E-value=17 Score=20.03 Aligned_cols=15 Identities=27% Similarity=0.623 Sum_probs=10.3
Q ss_pred CccccceeeCCCCCC
Q psy10712 12 GNFLKDKLKCPNCST 26 (75)
Q Consensus 12 ~~~~~GKL~CP~C~a 26 (75)
||...|...||.|+-
T Consensus 7 gq~~~~~~~C~~CgM 21 (41)
T PF13878_consen 7 GQKSFGATTCPTCGM 21 (41)
T ss_pred CCCccCCcCCCCCCC
Confidence 454557788888863
No 100
>PHA00626 hypothetical protein
Probab=34.51 E-value=17 Score=22.26 Aligned_cols=44 Identities=16% Similarity=0.291 Sum_probs=25.7
Q ss_pred eeCCCCCCc----cce-eecCCCCCCC-CCCcccceEEEEcCccceeecc
Q psy10712 19 LKCPNCSTN----LGA-FDYVSGHKCP-CKQQCVPFIHLVKSKIDIQYAN 62 (75)
Q Consensus 19 L~CP~C~aK----LGs-f~wv~G~kCs-CG~~v~Paf~i~kSkVD~~~~~ 62 (75)
+.||+|++. -|. ..|.+-.+|. ||...+---.=.+.|-+.+.+.
T Consensus 1 m~CP~CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~~~~~~~~~~~~~~~ 50 (59)
T PHA00626 1 MSCPKCGSGNIAKEKTMRGWSDDYVCCDCGYNDSKDAFGERGKNEFVRIN 50 (59)
T ss_pred CCCCCCCCceeeeeceecccCcceEcCCCCCeechhhhhhccccceEEec
Confidence 369999984 232 2344567786 9987765433344454544443
No 101
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=34.19 E-value=19 Score=19.48 Aligned_cols=10 Identities=40% Similarity=1.182 Sum_probs=7.5
Q ss_pred eCCCCCCccc
Q psy10712 20 KCPNCSTNLG 29 (75)
Q Consensus 20 ~CP~C~aKLG 29 (75)
.||.|++.|.
T Consensus 4 ~C~~Cg~~l~ 13 (47)
T PF13005_consen 4 ACPDCGGELK 13 (47)
T ss_pred cCCCCCceee
Confidence 5888888776
No 102
>PRK00481 NAD-dependent deacetylase; Provisional
Probab=34.18 E-value=38 Score=24.32 Aligned_cols=39 Identities=21% Similarity=0.524 Sum_probs=27.1
Q ss_pred cceeeCCCCCCccceeecC-----CCCCCC-CCCcccceEEEEcCccc
Q psy10712 16 KDKLKCPNCSTNLGAFDYV-----SGHKCP-CKQQCVPFIHLVKSKID 57 (75)
Q Consensus 16 ~GKL~CP~C~aKLGsf~wv-----~G~kCs-CG~~v~Paf~i~kSkVD 57 (75)
-.++.|.+|+.. |.+- .-.+|+ ||..+.|.+-+.-..++
T Consensus 120 ~~~~~C~~C~~~---~~~~~~~~~~~p~C~~Cgg~lrP~Vv~fge~~~ 164 (242)
T PRK00481 120 LLRARCTKCGQT---YDLDEYLKPEPPRCPKCGGILRPDVVLFGEMLP 164 (242)
T ss_pred cCceeeCCCCCC---cChhhhccCCCCCCCCCCCccCCCeEECCCCCC
Confidence 456889999654 3321 123597 99999999987766553
No 103
>cd01410 SIRT7 SIRT7: Eukaryotic and prokaryotic group (class4) which includes human sirtuin SIRT6, SIRT7, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span.
Probab=33.99 E-value=32 Score=24.45 Aligned_cols=38 Identities=21% Similarity=0.313 Sum_probs=25.6
Q ss_pred ceeeCCCCCCccceeecC--------CCCCCC-CCCcccceEEEEcCc
Q psy10712 17 DKLKCPNCSTNLGAFDYV--------SGHKCP-CKQQCVPFIHLVKSK 55 (75)
Q Consensus 17 GKL~CP~C~aKLGsf~wv--------~G~kCs-CG~~v~Paf~i~kSk 55 (75)
-++.|++|+...- ++.+ ...+|+ ||..+.|.+-+.--.
T Consensus 94 ~~~~C~~C~~~~~-~~~~~~~~~~~~~~p~C~~Cgg~lrP~VV~FgE~ 140 (206)
T cd01410 94 FIEVCKSCGPEYV-RDDVVETRGDKETGRRCHACGGILKDTIVDFGER 140 (206)
T ss_pred CcccCCCCCCccc-hHHHHHHhhcCCCCCcCCCCcCccCCcEEECCCC
Confidence 4678999996532 1111 236796 999999998776543
No 104
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=33.55 E-value=26 Score=21.38 Aligned_cols=12 Identities=42% Similarity=0.897 Sum_probs=9.8
Q ss_pred cceeeCCCCCCc
Q psy10712 16 KDKLKCPNCSTN 27 (75)
Q Consensus 16 ~GKL~CP~C~aK 27 (75)
.-+..||+|++-
T Consensus 23 ~~~F~CPnCG~~ 34 (59)
T PRK14890 23 AVKFLCPNCGEV 34 (59)
T ss_pred cCEeeCCCCCCe
Confidence 457899999876
No 105
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.55 E-value=17 Score=23.73 Aligned_cols=39 Identities=31% Similarity=0.575 Sum_probs=28.0
Q ss_pred eeCCCCCCccceeecCCCC---CCC-CCCcccceEEEEcCccceeeccC
Q psy10712 19 LKCPNCSTNLGAFDYVSGH---KCP-CKQQCVPFIHLVKSKIDIQYANR 63 (75)
Q Consensus 19 L~CP~C~aKLGsf~wv~G~---kCs-CG~~v~Paf~i~kSkVD~~~~~~ 63 (75)
+.||+|++-|=.-.= +|. .|+ |+ .++|.+.-+|.+....
T Consensus 2 llCP~C~v~l~~~~r-s~vEiD~CPrCr-----GVWLDrGELdKli~r~ 44 (88)
T COG3809 2 LLCPICGVELVMSVR-SGVEIDYCPRCR-----GVWLDRGELDKLIERS 44 (88)
T ss_pred cccCcCCceeeeeee-cCceeeeCCccc-----cEeecchhHHHHHHHh
Confidence 579999998865444 443 565 54 6789999998876544
No 106
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=33.37 E-value=14 Score=20.28 Aligned_cols=28 Identities=21% Similarity=0.611 Sum_probs=18.8
Q ss_pred ceeeCCCCCCccceeecCCCCCCC-CCCcc
Q psy10712 17 DKLKCPNCSTNLGAFDYVSGHKCP-CKQQC 45 (75)
Q Consensus 17 GKL~CP~C~aKLGsf~wv~G~kCs-CG~~v 45 (75)
.--.|-.|+..|-.+.- +|.+|+ |+..+
T Consensus 10 ~~~~C~~C~~~i~g~~~-~g~~C~~C~~~~ 38 (53)
T PF00130_consen 10 KPTYCDVCGKFIWGLGK-QGYRCSWCGLVC 38 (53)
T ss_dssp STEB-TTSSSBECSSSS-CEEEETTTT-EE
T ss_pred CCCCCcccCcccCCCCC-CeEEECCCCChH
Confidence 34578889999944444 899997 77643
No 107
>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=33.28 E-value=22 Score=19.15 Aligned_cols=12 Identities=33% Similarity=1.024 Sum_probs=8.3
Q ss_pred eeeCCCCCCccc
Q psy10712 18 KLKCPNCSTNLG 29 (75)
Q Consensus 18 KL~CP~C~aKLG 29 (75)
.+.||+|+-.+.
T Consensus 4 ~~~C~nC~R~v~ 15 (33)
T PF08209_consen 4 YVECPNCGRPVA 15 (33)
T ss_dssp EEE-TTTSSEEE
T ss_pred eEECCCCcCCcc
Confidence 478999987764
No 108
>PHA02325 hypothetical protein
Probab=33.23 E-value=18 Score=22.80 Aligned_cols=14 Identities=29% Similarity=0.892 Sum_probs=11.0
Q ss_pred eCCCCCCcc--ceeec
Q psy10712 20 KCPNCSTNL--GAFDY 33 (75)
Q Consensus 20 ~CP~C~aKL--Gsf~w 33 (75)
.||+|+|+- |.-.|
T Consensus 5 ~CPkC~A~WldgqhYW 20 (72)
T PHA02325 5 ICPKCGARWLDGQHYW 20 (72)
T ss_pred ccCccCCEeEcceeee
Confidence 599999984 66667
No 109
>PRK05580 primosome assembly protein PriA; Validated
Probab=33.03 E-value=25 Score=29.26 Aligned_cols=11 Identities=36% Similarity=1.111 Sum_probs=8.0
Q ss_pred eeCCCCCCccc
Q psy10712 19 LKCPNCSTNLG 29 (75)
Q Consensus 19 L~CP~C~aKLG 29 (75)
+.||+|+..|-
T Consensus 391 ~~C~~C~~~l~ 401 (679)
T PRK05580 391 AECPHCDASLT 401 (679)
T ss_pred cCCCCCCCcee
Confidence 56888887774
No 110
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=32.47 E-value=31 Score=19.59 Aligned_cols=13 Identities=38% Similarity=0.907 Sum_probs=10.0
Q ss_pred cceeeCCCCCCcc
Q psy10712 16 KDKLKCPNCSTNL 28 (75)
Q Consensus 16 ~GKL~CP~C~aKL 28 (75)
+.-+.||+|+.-|
T Consensus 44 ~~i~~Cp~CgRiL 56 (56)
T PF02591_consen 44 DEIVFCPNCGRIL 56 (56)
T ss_pred CCeEECcCCCccC
Confidence 5679999998643
No 111
>PRK06393 rpoE DNA-directed RNA polymerase subunit E''; Validated
Probab=32.42 E-value=20 Score=22.06 Aligned_cols=17 Identities=18% Similarity=0.446 Sum_probs=13.9
Q ss_pred eCCCCCCccceeecCCCC
Q psy10712 20 KCPNCSTNLGAFDYVSGH 37 (75)
Q Consensus 20 ~CP~C~aKLGsf~wv~G~ 37 (75)
.||.|++.==|-|| .|+
T Consensus 19 ~Cp~Cgs~~~S~~w-~G~ 35 (64)
T PRK06393 19 TCPVHGDEKTTTEW-FGF 35 (64)
T ss_pred cCCCCCCCcCCcCc-ceE
Confidence 79999998667888 665
No 112
>PRK14138 NAD-dependent deacetylase; Provisional
Probab=32.25 E-value=49 Score=24.07 Aligned_cols=38 Identities=16% Similarity=0.441 Sum_probs=26.2
Q ss_pred cceeeCCCCCCccceeecC---------CCCCCC-CCCcccceEEEEcCcc
Q psy10712 16 KDKLKCPNCSTNLGAFDYV---------SGHKCP-CKQQCVPFIHLVKSKI 56 (75)
Q Consensus 16 ~GKL~CP~C~aKLGsf~wv---------~G~kCs-CG~~v~Paf~i~kSkV 56 (75)
-.++.|.+|+.+ |++. ...+|+ ||..+.|.+-+.---+
T Consensus 117 ~~~~~C~~C~~~---~~~~~~~~~~~~~~~p~Cp~Cgg~lrP~Vv~FgE~~ 164 (244)
T PRK14138 117 VEEYYCVRCGKR---YTVEDVIEKLEKSDVPRCDDCSGLIRPNIVFFGEAL 164 (244)
T ss_pred cCeeEECCCCCc---ccHHHHHHHHhcCCCCCCCCCCCeECCCEEECCCcC
Confidence 345779999975 4431 236795 9999999887764433
No 113
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=31.65 E-value=16 Score=23.87 Aligned_cols=35 Identities=20% Similarity=0.496 Sum_probs=24.6
Q ss_pred ceeeCCCCCCccceeecCCCCCCC-CCCcccceEEEE
Q psy10712 17 DKLKCPNCSTNLGAFDYVSGHKCP-CKQQCVPFIHLV 52 (75)
Q Consensus 17 GKL~CP~C~aKLGsf~wv~G~kCs-CG~~v~Paf~i~ 52 (75)
+.-.|..|...+|-+.- .|..|. |...|...-.+.
T Consensus 53 ~~~~C~~C~~~fg~l~~-~~~~C~~C~~~VC~~C~~~ 88 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFN-RGRVCVDCKHRVCKKCGVY 88 (118)
T ss_dssp CCSB-TTTS-BCSCTST-TCEEETTTTEEEETTSEEE
T ss_pred CCcchhhhCCcccccCC-CCCcCCcCCccccCccCCc
Confidence 55589999999996655 799996 888876655444
No 114
>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=31.65 E-value=26 Score=20.70 Aligned_cols=14 Identities=21% Similarity=0.684 Sum_probs=10.1
Q ss_pred ceeeCCCCCCccce
Q psy10712 17 DKLKCPNCSTNLGA 30 (75)
Q Consensus 17 GKL~CP~C~aKLGs 30 (75)
--+.||.|++.|=-
T Consensus 21 eiV~Cp~CGaeleV 34 (54)
T TIGR01206 21 ELVICDECGAELEV 34 (54)
T ss_pred CEEeCCCCCCEEEE
Confidence 35689999987643
No 115
>cd01408 SIRT1 SIRT1: Eukaryotic group (class1) which includes human sirtuins SIRT1-3 and yeast Hst1-4; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The nuclear SIRT1 has been shown to target the p53 tumor suppressor protein for deacetylation to suppress DNA damage, and the cytoplasmic SIRT2 homolog has been shown to target alpha-tubulin for deacetylation for the maintenance of cell integrity.
Probab=31.07 E-value=33 Score=24.79 Aligned_cols=38 Identities=21% Similarity=0.427 Sum_probs=26.4
Q ss_pred cceeeCCCCCCccceeecC---------CCCCCC-CCCcccceEEEEcCcc
Q psy10712 16 KDKLKCPNCSTNLGAFDYV---------SGHKCP-CKQQCVPFIHLVKSKI 56 (75)
Q Consensus 16 ~GKL~CP~C~aKLGsf~wv---------~G~kCs-CG~~v~Paf~i~kSkV 56 (75)
-.++.|.+|+.. |++- ...+|+ ||..+.|.+-+.--.+
T Consensus 114 l~~~~C~~C~~~---~~~~~~~~~~~~~~~p~C~~Cgg~lrP~Vv~FGE~l 161 (235)
T cd01408 114 FATAHCIKCKHK---YPGDWMREDIFNQEVPKCPRCGGLVKPDIVFFGESL 161 (235)
T ss_pred CCccccccCCCc---CCHHHHHHHHhCCCCccCCCCCCCccCcEEECCCCC
Confidence 356789999984 4430 135796 9999999987765443
No 116
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=30.90 E-value=12 Score=26.64 Aligned_cols=16 Identities=38% Similarity=0.800 Sum_probs=11.9
Q ss_pred eeeCCCCCCcc--ceeec
Q psy10712 18 KLKCPNCSTNL--GAFDY 33 (75)
Q Consensus 18 KL~CP~C~aKL--Gsf~w 33 (75)
-|.||+|..+| |.+.+
T Consensus 13 ~ilC~~c~~~~~~G~v~~ 30 (166)
T PRK06418 13 GLLCPRCQSLLDSGEVTE 30 (166)
T ss_pred CccChhHHhHhhcCceEE
Confidence 58899999998 44444
No 117
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=30.85 E-value=41 Score=31.65 Aligned_cols=39 Identities=21% Similarity=0.715 Sum_probs=29.0
Q ss_pred cccceeeCCCCCCccceeecCCCCCCC-CCCcccceEEEEcCccc
Q psy10712 14 FLKDKLKCPNCSTNLGAFDYVSGHKCP-CKQQCVPFIHLVKSKID 57 (75)
Q Consensus 14 ~~~GKL~CP~C~aKLGsf~wv~G~kCs-CG~~v~Paf~i~kSkVD 57 (75)
+...+.-| +|++|-=.--- .-+|. ||..+. ..+++.-|.
T Consensus 1538 FsrQ~~RC-kC~~kyRR~PL--~G~C~kCGg~~i--lTV~kGsv~ 1577 (1627)
T PRK14715 1538 FSRQEFRC-KCGAKYRRVPL--KGKCPKCGSKLI--LTVSKGAVE 1577 (1627)
T ss_pred hhccceee-cCCCccccCCC--CCcCcccCCeEE--EEEecchHH
Confidence 35667899 99999887777 35796 999995 455666554
No 118
>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=30.38 E-value=24 Score=19.23 Aligned_cols=11 Identities=36% Similarity=1.186 Sum_probs=9.0
Q ss_pred cceeeCCCCCC
Q psy10712 16 KDKLKCPNCST 26 (75)
Q Consensus 16 ~GKL~CP~C~a 26 (75)
...+.||+|++
T Consensus 24 ~~~~~CP~Cg~ 34 (42)
T PF09723_consen 24 DDPVPCPECGS 34 (42)
T ss_pred CCCCcCCCCCC
Confidence 45688999998
No 119
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=30.26 E-value=31 Score=17.88 Aligned_cols=25 Identities=32% Similarity=0.774 Sum_probs=18.4
Q ss_pred eeCCCCCCccceeecCCCCCCC-CCCcc
Q psy10712 19 LKCPNCSTNLGAFDYVSGHKCP-CKQQC 45 (75)
Q Consensus 19 L~CP~C~aKLGsf~wv~G~kCs-CG~~v 45 (75)
..|--|+..|..+. +|.+|+ |+..+
T Consensus 12 ~~C~~C~~~i~~~~--~~~~C~~C~~~~ 37 (49)
T smart00109 12 TKCCVCRKSIWGSF--QGLRCSWCKVKC 37 (49)
T ss_pred CCccccccccCcCC--CCcCCCCCCchH
Confidence 46877999987653 689998 76544
No 120
>PRK07218 replication factor A; Provisional
Probab=30.24 E-value=30 Score=27.78 Aligned_cols=18 Identities=22% Similarity=0.772 Sum_probs=14.6
Q ss_pred eCCCCCCccceeecCCCCCCC-CCC
Q psy10712 20 KCPNCSTNLGAFDYVSGHKCP-CKQ 43 (75)
Q Consensus 20 ~CP~C~aKLGsf~wv~G~kCs-CG~ 43 (75)
.||.|+-+|.. .+|+ ||.
T Consensus 299 rCP~C~r~v~~------~~C~~hG~ 317 (423)
T PRK07218 299 RCPECGRVIQK------GQCRSHGA 317 (423)
T ss_pred cCcCccccccC------CcCCCCCC
Confidence 59999999943 4797 886
No 121
>cd01413 SIR2_Af2 SIR2_Af2: Archaeal and prokaryotic group which includes Archaeoglobus fulgidus Sir2-Af2, Sulfolobus solfataricus ssSir2, and several bacterial homologs; and are members of the SIR2 family of proteins, silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation. Sir2 proteins have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The Sir2 homolog from the archaea Sulfolobus solftaricus deacetylates the non-specific DNA protein Alba to mediate transcription repression.
Probab=30.06 E-value=55 Score=23.35 Aligned_cols=39 Identities=23% Similarity=0.531 Sum_probs=27.5
Q ss_pred cceeeCCCCCCccceeecC--------CCCCCC-CCCcccceEEEEcCccc
Q psy10712 16 KDKLKCPNCSTNLGAFDYV--------SGHKCP-CKQQCVPFIHLVKSKID 57 (75)
Q Consensus 16 ~GKL~CP~C~aKLGsf~wv--------~G~kCs-CG~~v~Paf~i~kSkVD 57 (75)
-.++.|.+|+.. |.|. .-.+|+ ||..+.|.+-+.-..++
T Consensus 111 l~~~~C~~C~~~---~~~~~~~~~~~~~~p~C~~Cgg~lrP~Vv~fgE~lp 158 (222)
T cd01413 111 LQTAYCVNCGSK---YDLEEVKYAKKHEVPRCPKCGGIIRPDVVLFGEPLP 158 (222)
T ss_pred cCcceECCCCCC---cchhHHHHhccCCCCcCCCCCCccCCCEEECCCCCC
Confidence 456889999864 4441 135796 99999998887665555
No 122
>PF02943 FeThRed_B: Ferredoxin thioredoxin reductase catalytic beta chain; InterPro: IPR004209 Ferredoxin thioredoxin reductase is a [4FE-4S] protein present in organisms performing oxygenic photosynthesis, and plays an important role in the ferredoxin/thioredoxin regulatory chain. It converts an electron signal (photoreduced ferredoxin) to a thiol signal (reduced thioredoxin), regulating enzymes by reduction of specific disulphide groups. It catalyses the light-dependent activation of several photosynthetis enzymes. Ferredoxin thioredoxin reductase is a heterodimer of subunit alpha and subunit beta. Subunit alpha is the variable subunit, and beta is the catalytic chain []. The structure of the beta subunit has been determined and found to fold around the FeS cluster [].; GO: 0008937 ferredoxin-NAD(P) reductase activity, 0055114 oxidation-reduction process; PDB: 2PUK_E 2PVD_A 2PVG_A 2PUO_A 2PU9_A 1DJ7_A 2PVO_A.
Probab=29.87 E-value=22 Score=23.72 Aligned_cols=33 Identities=24% Similarity=0.430 Sum_probs=15.3
Q ss_pred cceeeCCCCCCccc------eeecCCCCC-----------CCCCCcccceE
Q psy10712 16 KDKLKCPNCSTNLG------AFDYVSGHK-----------CPCKQQCVPFI 49 (75)
Q Consensus 16 ~GKL~CP~C~aKLG------sf~wv~G~k-----------CsCG~~v~Paf 49 (75)
-|+-+|| |...-| .-+||---. |.||-+++|.+
T Consensus 42 yG~~~CP-Cr~~~~~~ee~~d~~iiCPC~~~r~~~~~~G~ChC~Lf~~~e~ 91 (108)
T PF02943_consen 42 YGYPYCP-CRLASGKEEEVKDRDIICPCVPYREDDIEYGHCHCGLFVSPEY 91 (108)
T ss_dssp HSS-B-S-SC--S-HHHHHHH-TTBSS-HHHHHH-------TTSSSB-TTS
T ss_pred hCCCCCC-CCCCCCchhhhccCCeecCCHHHHhhccccccceEeeeECccc
Confidence 3566666 665555 234544444 89999998876
No 123
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=29.17 E-value=32 Score=26.54 Aligned_cols=46 Identities=17% Similarity=0.314 Sum_probs=28.2
Q ss_pred cccceeeCCCCCCccceeecCCCCCCC-CCCcc----cceEEEEcCcccee
Q psy10712 14 FLKDKLKCPNCSTNLGAFDYVSGHKCP-CKQQC----VPFIHLVKSKIDIQ 59 (75)
Q Consensus 14 ~~~GKL~CP~C~aKLGsf~wv~G~kCs-CG~~v----~Paf~i~kSkVD~~ 59 (75)
|...--.||+|+.|.=...==-..+|+ ||... .|++=+--.|-|++
T Consensus 107 w~~~~RFCg~CG~~~~~~~~g~~~~C~~cg~~~fPR~dP~vIv~v~~~~~i 157 (279)
T COG2816 107 WYRSHRFCGRCGTKTYPREGGWARVCPKCGHEHFPRIDPCVIVAVIRGDEI 157 (279)
T ss_pred HHhhCcCCCCCCCcCccccCceeeeCCCCCCccCCCCCCeEEEEEecCCce
Confidence 555556799999987433221146776 88765 45555555555553
No 124
>PRK06260 threonine synthase; Validated
Probab=29.00 E-value=47 Score=25.53 Aligned_cols=30 Identities=20% Similarity=0.352 Sum_probs=19.9
Q ss_pred eeeCCCCCCccceeecCCCCCC-CCCCcccceE
Q psy10712 18 KLKCPNCSTNLGAFDYVSGHKC-PCKQQCVPFI 49 (75)
Q Consensus 18 KL~CP~C~aKLGsf~wv~G~kC-sCG~~v~Paf 49 (75)
+|.|++|+.....=.+ -.+| .||..+...+
T Consensus 3 ~~~C~~cg~~~~~~~~--~~~Cp~cg~~l~~~y 33 (397)
T PRK06260 3 WLKCIECGKEYDPDEI--IYTCPECGGLLEVIY 33 (397)
T ss_pred EEEECCCCCCCCCCCc--cccCCCCCCeEEEEe
Confidence 4889999998753323 2578 4987654443
No 125
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=28.90 E-value=30 Score=21.91 Aligned_cols=16 Identities=31% Similarity=0.812 Sum_probs=13.8
Q ss_pred eeeCCCCCCccceeec
Q psy10712 18 KLKCPNCSTNLGAFDY 33 (75)
Q Consensus 18 KL~CP~C~aKLGsf~w 33 (75)
.-.|-.|+.|||+.+-
T Consensus 4 ~Y~CRHCg~~IG~i~~ 19 (76)
T PF10955_consen 4 HYYCRHCGTKIGTIDA 19 (76)
T ss_pred EEEecCCCCEEEEeec
Confidence 3579899999999987
No 126
>PF08600 Rsm1: Rsm1-like; InterPro: IPR013909 This entry contains Nuclear-interacting partner of ALK (NIPA) and NIPA like proteins, as well as mRNA export factor Rsm1, all of which contain a C3HC-type zinc finger. The domain represented in this entry is found C-terminal to the zinc-finger like domain IPR012935 from INTERPRO. Rsm1 is involved in mRNA export from the nucleus []. NIPA is an essential component of an SCF-type E3 ligase complex, SCF(NIPA), a complex that controls mitotic entry by mediating ubiquitination and subsequent degradation of cyclin B1 (CCNB1). Its cell-cycle-dependent phosphorylation regulates the assembly of the SCF(NIPA) complex, restricting CCNB1 ubiquitination activity to interphase. Its inactivation results in nuclear accumulation of CCNB1 in interphase and premature mitotic entry [].
Probab=28.50 E-value=37 Score=21.43 Aligned_cols=21 Identities=24% Similarity=0.564 Sum_probs=17.9
Q ss_pred cceeeCCCCCCccceeecCCCC
Q psy10712 16 KDKLKCPNCSTNLGAFDYVSGH 37 (75)
Q Consensus 16 ~GKL~CP~C~aKLGsf~wv~G~ 37 (75)
.+-|.|--|.-|||=|++ ...
T Consensus 17 ~~~~~C~~C~Rr~GLW~f-~~~ 37 (91)
T PF08600_consen 17 LGLLSCSYCFRRLGLWMF-KSK 37 (91)
T ss_pred cCeEEccccCcEeeeeec-ccC
Confidence 468999999999999999 443
No 127
>COG1933 Archaeal DNA polymerase II, large subunit [DNA replication, recombination, and repair]
Probab=28.34 E-value=35 Score=26.19 Aligned_cols=39 Identities=23% Similarity=0.640 Sum_probs=30.0
Q ss_pred ccceeeCCCCCCccceeecCCCCCCC-CCCcccceEEEEcCccc
Q psy10712 15 LKDKLKCPNCSTNLGAFDYVSGHKCP-CKQQCVPFIHLVKSKID 57 (75)
Q Consensus 15 ~~GKL~CP~C~aKLGsf~wv~G~kCs-CG~~v~Paf~i~kSkVD 57 (75)
.--+..|-+|++|+|.--- + .+|. ||..+ ..-+++.+|-
T Consensus 164 ~rq~~rc~~c~~k~rr~pl-~-g~c~kcg~~~--~ltv~~g~v~ 203 (253)
T COG1933 164 TRQEFRCVKCNTKFRRPPL-D-GKCPICGGKI--VLTVSKGAIE 203 (253)
T ss_pred hhheeehHhhhhhhcCCCc-c-ccccccCCeE--EEEEeccHHH
Confidence 4556889999999999988 3 5787 99955 6666776653
No 128
>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=28.33 E-value=29 Score=21.14 Aligned_cols=8 Identities=50% Similarity=1.514 Sum_probs=6.2
Q ss_pred eCCCCCCc
Q psy10712 20 KCPNCSTN 27 (75)
Q Consensus 20 ~CP~C~aK 27 (75)
.||||+.+
T Consensus 2 ~C~KCg~~ 9 (64)
T PF09855_consen 2 KCPKCGNE 9 (64)
T ss_pred CCCCCCCc
Confidence 48999875
No 129
>PF10272 Tmpp129: Putative transmembrane protein precursor; InterPro: IPR018801 This entry consists of proteins conserved from worms to humans. They are purported to be transmembrane protein-precursors but their function is unknown.
Probab=28.14 E-value=23 Score=28.01 Aligned_cols=17 Identities=29% Similarity=0.841 Sum_probs=14.9
Q ss_pred CccccceeeCCCCCCcc
Q psy10712 12 GNFLKDKLKCPNCSTNL 28 (75)
Q Consensus 12 ~~~~~GKL~CP~C~aKL 28 (75)
..|+.||-.||-|.+|.
T Consensus 334 ~~Wl~~~~~CPtCRa~F 350 (358)
T PF10272_consen 334 ETWLSGKCPCPTCRAKF 350 (358)
T ss_pred hhhhcCCCCCCCCcccc
Confidence 46999999999999974
No 130
>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=27.94 E-value=48 Score=18.14 Aligned_cols=27 Identities=30% Similarity=0.640 Sum_probs=12.9
Q ss_pred eeCCC--CCCccceeecCCC--CCCC-CCCcc
Q psy10712 19 LKCPN--CSTNLGAFDYVSG--HKCP-CKQQC 45 (75)
Q Consensus 19 L~CP~--C~aKLGsf~wv~G--~kCs-CG~~v 45 (75)
..||+ |+.-+-.-+=... ++|+ |+...
T Consensus 19 ~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~f 50 (64)
T PF01485_consen 19 RWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEF 50 (64)
T ss_dssp C--TTSST---ECS-SSTTS--CCTTSCCSEE
T ss_pred cCCCCCCCcccEEecCCCCCCeeECCCCCCcC
Confidence 48988 9887754444223 6888 88643
No 131
>COG5041 SKB2 Casein kinase II, beta subunit [Signal transduction mechanisms / Cell division and chromosome partitioning / Transcription]
Probab=27.56 E-value=27 Score=26.50 Aligned_cols=12 Identities=42% Similarity=0.886 Sum_probs=9.9
Q ss_pred ccceeeCCCCCC
Q psy10712 15 LKDKLKCPNCST 26 (75)
Q Consensus 15 ~~GKL~CP~C~a 26 (75)
..-||+||+|..
T Consensus 146 ~~vkLyCpsC~d 157 (242)
T COG5041 146 SSVKLYCPSCED 157 (242)
T ss_pred ceeEEecCchhh
Confidence 567999999964
No 132
>cd01407 SIR2-fam SIR2 family of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer.
Probab=27.30 E-value=78 Score=22.30 Aligned_cols=41 Identities=17% Similarity=0.436 Sum_probs=27.9
Q ss_pred cceeeCCCCCCccceee-------cCCCCCCC-CCCcccceEEEEcCccc
Q psy10712 16 KDKLKCPNCSTNLGAFD-------YVSGHKCP-CKQQCVPFIHLVKSKID 57 (75)
Q Consensus 16 ~GKL~CP~C~aKLGsf~-------wv~G~kCs-CG~~v~Paf~i~kSkVD 57 (75)
-.++.|.+|+... .++ =....+|+ ||..+.|.+-+.-.-++
T Consensus 107 ~~~~~C~~C~~~~-~~~~~~~~~~~~~~p~C~~Cg~~lrP~Vv~fgE~~p 155 (218)
T cd01407 107 LFRVRCTKCGKEY-PRDELQADIDREEVPRCPKCGGLLRPDVVFFGESLP 155 (218)
T ss_pred cCcceeCCCcCCC-cHHHHhHhhccCCCCcCCCCCCccCCCeEECCCCCc
Confidence 4568899998764 111 01346897 99999999987655443
No 133
>PRK07591 threonine synthase; Validated
Probab=27.02 E-value=50 Score=25.81 Aligned_cols=29 Identities=24% Similarity=0.379 Sum_probs=21.5
Q ss_pred eeeCCCCCCccceeecCCCCCCC-CCCcccceE
Q psy10712 18 KLKCPNCSTNLGAFDYVSGHKCP-CKQQCVPFI 49 (75)
Q Consensus 18 KL~CP~C~aKLGsf~wv~G~kCs-CG~~v~Paf 49 (75)
+|.|+.|+.....- . . .+|+ ||..+-..+
T Consensus 18 ~l~C~~Cg~~~~~~-~-~-~~C~~cg~~l~~~y 47 (421)
T PRK07591 18 ALKCRECGAEYPLG-P-I-HVCEECFGPLEVAY 47 (421)
T ss_pred EEEeCCCCCcCCCC-C-C-ccCCCCCCeEEEEe
Confidence 69999999988742 4 3 7895 998775443
No 134
>PF06054 CoiA: Competence protein CoiA-like family; InterPro: IPR010330 Competence is the ability of a cell to take up exogenous DNA from its environment, resulting in transformation. It is widespread among bacteria and is probably an important mechanism for the horizontal transfer of genes. Cells that take up DNA inevitably acquire the nucleotides the DNA consists of, and, because nucleotides are needed for DNA and RNA synthesis and are expensive to synthesise, these may make a significant contribution to the cell's energy budget []. The lateral gene transfer caused by competence also contributes to the genetic diversity that makes evolution possible. DNA usually becomes available by the death and lysis of other cells. Competent bacteria use components of extracellular filaments called type 4 pili to create pores in their membranes and pull DNA through the pores into the cytoplasm. This process, including the development of competence and the expression of the uptake machinery, is regulated in response to cell-cell signalling and/or nutritional conditions []. Many of the members of this family are described as transcription factors. CoiA falls within a competence-specific operon in Streptococcus. CoiA is an uncharacterised protein.
Probab=26.95 E-value=35 Score=26.54 Aligned_cols=13 Identities=38% Similarity=0.907 Sum_probs=11.7
Q ss_pred cceeeCCCCCCcc
Q psy10712 16 KDKLKCPNCSTNL 28 (75)
Q Consensus 16 ~GKL~CP~C~aKL 28 (75)
+++..||.|+.+|
T Consensus 28 ~~~~~CP~C~~~v 40 (375)
T PF06054_consen 28 KGKYFCPGCGEPV 40 (375)
T ss_pred CCcEECCCCCCee
Confidence 7899999999877
No 135
>PRK06386 replication factor A; Reviewed
Probab=26.50 E-value=49 Score=26.13 Aligned_cols=26 Identities=23% Similarity=0.476 Sum_probs=17.9
Q ss_pred eCCCCCCccceeecCCCCCCC-CCCcccceEEEEc
Q psy10712 20 KCPNCSTNLGAFDYVSGHKCP-CKQQCVPFIHLVK 53 (75)
Q Consensus 20 ~CP~C~aKLGsf~wv~G~kCs-CG~~v~Paf~i~k 53 (75)
.||.|+-+|= + .+|+ ||. .|.....+
T Consensus 238 rCP~C~R~l~--~----g~C~~HG~--v~~~~dlr 264 (358)
T PRK06386 238 KCSVCNKIIE--D----GVCKDHPD--APVYLDIF 264 (358)
T ss_pred cCcCCCeEcc--C----CcCCCCCC--CCCeeEEE
Confidence 5999999995 2 3897 997 44444433
No 136
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=26.47 E-value=63 Score=17.72 Aligned_cols=29 Identities=24% Similarity=0.501 Sum_probs=17.5
Q ss_pred cceeeCC--CCCCccceee--cCCCCCC-CCCCc
Q psy10712 16 KDKLKCP--NCSTNLGAFD--YVSGHKC-PCKQQ 44 (75)
Q Consensus 16 ~GKL~CP--~C~aKLGsf~--wv~G~kC-sCG~~ 44 (75)
.....|| +|+.-+-.-+ -....+| .||..
T Consensus 16 ~~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~ 49 (64)
T smart00647 16 PDLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFS 49 (64)
T ss_pred CCccCCCCCCCcceEEecCCCCCCeeECCCCCCe
Confidence 3455798 7877665542 2245778 67753
No 137
>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=26.32 E-value=30 Score=22.75 Aligned_cols=25 Identities=24% Similarity=0.752 Sum_probs=14.6
Q ss_pred eeCC--CCCCccceeecCCC-CCC-CCCCcc
Q psy10712 19 LKCP--NCSTNLGAFDYVSG-HKC-PCKQQC 45 (75)
Q Consensus 19 L~CP--~C~aKLGsf~wv~G-~kC-sCG~~v 45 (75)
..|| .|+.||=.- = .| ..| +|++-+
T Consensus 19 ~aC~~~~C~kKv~~~-~-~~~y~C~~C~~~~ 47 (146)
T PF08646_consen 19 PACPNEKCNKKVTEN-G-DGSYRCEKCNKTV 47 (146)
T ss_dssp EE-TSTTTS-B-EEE-T-TTEEEETTTTEEE
T ss_pred CCCCCccCCCEeecC-C-CcEEECCCCCCcC
Confidence 5799 999997544 2 22 478 588774
No 138
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=26.11 E-value=33 Score=16.87 Aligned_cols=12 Identities=42% Similarity=0.894 Sum_probs=8.9
Q ss_pred ceeeCCCCCCcc
Q psy10712 17 DKLKCPNCSTNL 28 (75)
Q Consensus 17 GKL~CP~C~aKL 28 (75)
+...||.|+..+
T Consensus 34 ~~~~Cp~C~~~~ 45 (45)
T cd00162 34 GKNTCPLCRTPI 45 (45)
T ss_pred CcCCCCCCCCcC
Confidence 467799998754
No 139
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=25.99 E-value=41 Score=26.56 Aligned_cols=15 Identities=40% Similarity=0.860 Sum_probs=10.1
Q ss_pred cceeeCCCCCCccce
Q psy10712 16 KDKLKCPNCSTNLGA 30 (75)
Q Consensus 16 ~GKL~CP~C~aKLGs 30 (75)
..+-.||.|+++|=+
T Consensus 31 g~~a~CpRCg~~L~~ 45 (403)
T TIGR00155 31 GQKAACPRCGTTLTV 45 (403)
T ss_pred CCeeECCCCCCCCcC
Confidence 345678888888743
No 140
>PRK08402 replication factor A; Reviewed
Probab=25.82 E-value=45 Score=26.13 Aligned_cols=10 Identities=30% Similarity=0.976 Sum_probs=8.9
Q ss_pred eeCCCCCCcc
Q psy10712 19 LKCPNCSTNL 28 (75)
Q Consensus 19 L~CP~C~aKL 28 (75)
-.||+|+-||
T Consensus 213 ~aCp~CnKkv 222 (355)
T PRK08402 213 DACPECRRKV 222 (355)
T ss_pred ecCCCCCeEE
Confidence 4699999999
No 141
>TIGR01374 soxD sarcosine oxidase, delta subunit family, heterotetrameric form. Sarcosine oxidase catalyzes the oxidative demethylation of sarcosine to glycine. The reaction converts tetrahydrofolate to 5,10-methylene-tetrahydrofolate. The enzyme is known in monomeric and heterotetrameric (alpha,beta,gamma,delta) form
Probab=25.78 E-value=32 Score=22.16 Aligned_cols=44 Identities=20% Similarity=0.438 Sum_probs=23.7
Q ss_pred eeCCCCCCc-cceeecCCCCCCCCCCcc-cc---eEEEEcCccceeeccCCCCCC
Q psy10712 19 LKCPNCSTN-LGAFDYVSGHKCPCKQQC-VP---FIHLVKSKIDIQYANRSPENT 68 (75)
Q Consensus 19 L~CP~C~aK-LGsf~wv~G~kCsCG~~v-~P---af~i~kSkVD~~~~~~~~~~t 68 (75)
|.||.|+.| .--|.. .|. .-+ .| +=.=.+.-.|+++++.||.|.
T Consensus 2 I~CP~CG~R~~~EF~y-~G~-----A~~~rP~~~~~~sd~~W~~Ylf~R~Np~G~ 50 (84)
T TIGR01374 2 IPCPYCGPRPEEEFTY-GGD-----AHIVRPADPAAASDEEWEDYLFLRDNPKGL 50 (84)
T ss_pred ccCCCCCCccHhhEec-cce-----ecccCCCCCCcCCHHHHHHhccccCCCCcc
Confidence 789999865 234555 332 111 22 111123446678888888764
No 142
>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=25.76 E-value=66 Score=23.93 Aligned_cols=32 Identities=25% Similarity=0.465 Sum_probs=24.7
Q ss_pred ceeeCCCCCCccceeecCCCCCCCCCCcccceEEEEcCccceee
Q psy10712 17 DKLKCPNCSTNLGAFDYVSGHKCPCKQQCVPFIHLVKSKIDIQY 60 (75)
Q Consensus 17 GKL~CP~C~aKLGsf~wv~G~kCsCG~~v~Paf~i~kSkVD~~~ 60 (75)
..+.|.+|++-||. ..-.-++.|.|..|....
T Consensus 192 ~~v~C~~C~~~LG~------------~~~~~~~rL~K~~l~~~~ 223 (354)
T PF09814_consen 192 RIVRCKRCSSQLGE------------KFSDNTVRLYKWALSLQP 223 (354)
T ss_pred cEEEeCCCCceeCC------------CccCCeEEEEeeeEEEec
Confidence 57999999999998 222457888888887654
No 143
>PRK08197 threonine synthase; Validated
Probab=25.31 E-value=49 Score=25.43 Aligned_cols=26 Identities=23% Similarity=0.608 Sum_probs=18.7
Q ss_pred eeeCCCCCCccceeecCCCCCCCCCCcc
Q psy10712 18 KLKCPNCSTNLGAFDYVSGHKCPCKQQC 45 (75)
Q Consensus 18 KL~CP~C~aKLGsf~wv~G~kCsCG~~v 45 (75)
+|.|++|+.....-.+ -..|.||..+
T Consensus 7 ~~~C~~Cg~~~~~~~~--~~~C~cg~~l 32 (394)
T PRK08197 7 HLECSKCGETYDADQV--HNLCKCGKPL 32 (394)
T ss_pred EEEECCCCCCCCCCCc--ceecCCCCee
Confidence 5999999988764333 2568998654
No 144
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=25.23 E-value=39 Score=20.78 Aligned_cols=11 Identities=45% Similarity=1.053 Sum_probs=8.7
Q ss_pred ccceeeCCCCC
Q psy10712 15 LKDKLKCPNCS 25 (75)
Q Consensus 15 ~~GKL~CP~C~ 25 (75)
.--+..||||+
T Consensus 24 ~~v~F~CPnCG 34 (61)
T COG2888 24 TAVKFPCPNCG 34 (61)
T ss_pred ceeEeeCCCCC
Confidence 34578899999
No 145
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=25.21 E-value=36 Score=18.37 Aligned_cols=11 Identities=27% Similarity=0.827 Sum_probs=6.6
Q ss_pred eeeCCCCCCcc
Q psy10712 18 KLKCPNCSTNL 28 (75)
Q Consensus 18 KL~CP~C~aKL 28 (75)
-+.|++|+-++
T Consensus 21 ~isC~~CGPr~ 31 (35)
T PF07503_consen 21 FISCTNCGPRY 31 (35)
T ss_dssp T--BTTCC-SC
T ss_pred CccCCCCCCCE
Confidence 47899999876
No 146
>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=25.17 E-value=36 Score=20.38 Aligned_cols=12 Identities=33% Similarity=0.930 Sum_probs=6.7
Q ss_pred eeeCCCCCCccc
Q psy10712 18 KLKCPNCSTNLG 29 (75)
Q Consensus 18 KL~CP~C~aKLG 29 (75)
++.||.|+..+-
T Consensus 2 ~v~CP~C~k~~~ 13 (57)
T PF03884_consen 2 TVKCPICGKPVE 13 (57)
T ss_dssp EEE-TTT--EEE
T ss_pred cccCCCCCCeec
Confidence 578999998763
No 147
>COG1066 Sms Predicted ATP-dependent serine protease [Posttranslational modification, protein turnover, chaperones]
Probab=25.04 E-value=55 Score=27.03 Aligned_cols=25 Identities=24% Similarity=0.670 Sum_probs=19.1
Q ss_pred ceeeCCCCCCccceeecCCCCCCC-CCCcc
Q psy10712 17 DKLKCPNCSTNLGAFDYVSGHKCP-CKQQC 45 (75)
Q Consensus 17 GKL~CP~C~aKLGsf~wv~G~kCs-CG~~v 45 (75)
-...|-+|+.. +=.|. -||+ ||.|=
T Consensus 6 t~f~C~~CG~~--s~KW~--GkCp~Cg~Wn 31 (456)
T COG1066 6 TAFVCQECGYV--SPKWL--GKCPACGAWN 31 (456)
T ss_pred cEEEcccCCCC--Ccccc--ccCCCCCCcc
Confidence 45789999987 56683 5786 99995
No 148
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=24.97 E-value=35 Score=20.77 Aligned_cols=10 Identities=50% Similarity=1.082 Sum_probs=7.5
Q ss_pred eeCCCCCCcc
Q psy10712 19 LKCPNCSTNL 28 (75)
Q Consensus 19 L~CP~C~aKL 28 (75)
-.||||+.-|
T Consensus 42 ~~CPNCgGel 51 (57)
T PF06906_consen 42 GVCPNCGGEL 51 (57)
T ss_pred CcCcCCCCcc
Confidence 4699998654
No 149
>PF15616 TerY-C: TerY-C metal binding domain
Probab=24.79 E-value=26 Score=24.14 Aligned_cols=16 Identities=25% Similarity=0.588 Sum_probs=12.1
Q ss_pred cccceeeCCCCCCccc
Q psy10712 14 FLKDKLKCPNCSTNLG 29 (75)
Q Consensus 14 ~~~GKL~CP~C~aKLG 29 (75)
.+.|.--||.|++..+
T Consensus 73 eL~g~PgCP~CGn~~~ 88 (131)
T PF15616_consen 73 ELIGAPGCPHCGNQYA 88 (131)
T ss_pred HhcCCCCCCCCcChhc
Confidence 3567788999999753
No 150
>PHA02942 putative transposase; Provisional
Probab=24.79 E-value=36 Score=26.61 Aligned_cols=25 Identities=20% Similarity=0.677 Sum_probs=15.6
Q ss_pred eeCCCCCCccceeecCCCCCC-CCCCc
Q psy10712 19 LKCPNCSTNLGAFDYVSGHKC-PCKQQ 44 (75)
Q Consensus 19 L~CP~C~aKLGsf~wv~G~kC-sCG~~ 44 (75)
-.||.|+.+....+= .-..| +||..
T Consensus 326 q~Cs~CG~~~~~l~~-r~f~C~~CG~~ 351 (383)
T PHA02942 326 VSCPKCGHKMVEIAH-RYFHCPSCGYE 351 (383)
T ss_pred ccCCCCCCccCcCCC-CEEECCCCCCE
Confidence 459999988653221 12478 58874
No 151
>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=24.79 E-value=34 Score=20.83 Aligned_cols=9 Identities=44% Similarity=1.143 Sum_probs=6.9
Q ss_pred eeCCCCCCc
Q psy10712 19 LKCPNCSTN 27 (75)
Q Consensus 19 L~CP~C~aK 27 (75)
-.||+|++-
T Consensus 10 A~CP~C~~~ 18 (59)
T TIGR02443 10 AVCPACSAQ 18 (59)
T ss_pred ccCCCCcCc
Confidence 369999874
No 152
>KOG2807|consensus
Probab=24.73 E-value=27 Score=28.13 Aligned_cols=36 Identities=28% Similarity=0.617 Sum_probs=27.6
Q ss_pred cceeeCCCCCCccceeecCCCCCCC-CCCcccceEEEEcCc
Q psy10712 16 KDKLKCPNCSTNLGAFDYVSGHKCP-CKQQCVPFIHLVKSK 55 (75)
Q Consensus 16 ~GKL~CP~C~aKLGsf~wv~G~kCs-CG~~v~Paf~i~kSk 55 (75)
-|-..||.|+||+=+. ...|+ |+.-++-+-||.||-
T Consensus 274 ~~Gy~CP~CkakvCsL----P~eCpiC~ltLVss~hLARSy 310 (378)
T KOG2807|consen 274 GGGYFCPQCKAKVCSL----PIECPICSLTLVSSPHLARSY 310 (378)
T ss_pred cCceeCCcccCeeecC----CccCCccceeEecchHHHHHH
Confidence 3557899999999765 46786 888887777777664
No 153
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=24.58 E-value=38 Score=24.87 Aligned_cols=25 Identities=28% Similarity=0.632 Sum_probs=18.5
Q ss_pred eeCCCCCCccceeecCCCCCCC-CCCcc
Q psy10712 19 LKCPNCSTNLGAFDYVSGHKCP-CKQQC 45 (75)
Q Consensus 19 L~CP~C~aKLGsf~wv~G~kCs-CG~~v 45 (75)
-.|++|.+-|=. .| .-++|+ ||.--
T Consensus 150 A~CsrC~~~L~~-~~-~~l~Cp~Cg~tE 175 (188)
T COG1096 150 ARCSRCRAPLVK-KG-NMLKCPNCGNTE 175 (188)
T ss_pred EEccCCCcceEE-cC-cEEECCCCCCEE
Confidence 358888888854 88 688886 88643
No 154
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=24.32 E-value=39 Score=18.35 Aligned_cols=24 Identities=25% Similarity=0.515 Sum_probs=14.4
Q ss_pred eCCCCCCccceeecCC--CCCCC-CCC
Q psy10712 20 KCPNCSTNLGAFDYVS--GHKCP-CKQ 43 (75)
Q Consensus 20 ~CP~C~aKLGsf~wv~--G~kCs-CG~ 43 (75)
.||+|+.-|=.=.+-. -..|+ ||.
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~ 28 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGY 28 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCC
Confidence 5999998773322311 14586 885
No 155
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=24.29 E-value=41 Score=23.40 Aligned_cols=27 Identities=30% Similarity=0.597 Sum_probs=21.1
Q ss_pred ceee--CCCCCCccceeecCCCCCCC-CCCc
Q psy10712 17 DKLK--CPNCSTNLGAFDYVSGHKCP-CKQQ 44 (75)
Q Consensus 17 GKL~--CP~C~aKLGsf~wv~G~kCs-CG~~ 44 (75)
|+|. |++|+..+=-.+| +.++|. ||..
T Consensus 146 Gvv~a~~~~~g~~~~~~~~-~~~~c~~~~~~ 175 (189)
T PRK09521 146 GVIYAMCSRCRTPLVKKGE-NELKCPNCGNI 175 (189)
T ss_pred eEEEEEccccCCceEECCC-CEEECCCCCCE
Confidence 4443 7889998888888 889996 8863
No 156
>COG1867 TRM1 N2,N2-dimethylguanosine tRNA methyltransferase [Translation, ribosomal structure and biogenesis]
Probab=24.25 E-value=52 Score=26.53 Aligned_cols=26 Identities=31% Similarity=0.844 Sum_probs=21.3
Q ss_pred eeeCCCCCCccceeecCCCCCCC-CCCc
Q psy10712 18 KLKCPNCSTNLGAFDYVSGHKCP-CKQQ 44 (75)
Q Consensus 18 KL~CP~C~aKLGsf~wv~G~kCs-CG~~ 44 (75)
-++|+.|+..+++|.= --.+|+ ||..
T Consensus 240 ~~~c~~cg~~~~~~~~-~~~~c~~Cg~~ 266 (380)
T COG1867 240 IYHCSRCGEIVGSFRE-VDEKCPHCGGK 266 (380)
T ss_pred EEEcccccceeccccc-ccccCCccccc
Confidence 4789999988888888 488997 8863
No 157
>KOG0801|consensus
Probab=24.22 E-value=42 Score=24.81 Aligned_cols=16 Identities=44% Similarity=0.928 Sum_probs=12.3
Q ss_pred eecCCCCCCC-CCCcccc
Q psy10712 31 FDYVSGHKCP-CKQQCVP 47 (75)
Q Consensus 31 f~wv~G~kCs-CG~~v~P 47 (75)
+++ +|+||+ |.+.|.|
T Consensus 134 ~~~-~g~KCPvC~K~V~s 150 (205)
T KOG0801|consen 134 MDH-SGMKCPVCHKVVPS 150 (205)
T ss_pred ecc-CCccCCccccccCC
Confidence 344 799998 9888866
No 158
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=24.04 E-value=45 Score=27.80 Aligned_cols=26 Identities=27% Similarity=0.678 Sum_probs=17.3
Q ss_pred eeCCCCCCccceeecCCCCCC-CCCCcccceE
Q psy10712 19 LKCPNCSTNLGAFDYVSGHKC-PCKQQCVPFI 49 (75)
Q Consensus 19 L~CP~C~aKLGsf~wv~G~kC-sCG~~v~Paf 49 (75)
-.||+|+..-. .|-|| .||.-..|.=
T Consensus 143 g~cp~cg~~~a-----rGD~Ce~Cg~~~~P~~ 169 (558)
T COG0143 143 GTCPKCGGEDA-----RGDQCENCGRTLDPTE 169 (558)
T ss_pred ccCCCcCcccc-----CcchhhhccCcCCchh
Confidence 34666664432 48889 4999888854
No 159
>COG2956 Predicted N-acetylglucosaminyl transferase [Carbohydrate transport and metabolism]
Probab=23.99 E-value=46 Score=26.97 Aligned_cols=26 Identities=23% Similarity=0.709 Sum_probs=21.8
Q ss_pred cceeeCCCCCCccceeecCCCCCC-CCCCcc
Q psy10712 16 KDKLKCPNCSTNLGAFDYVSGHKC-PCKQQC 45 (75)
Q Consensus 16 ~GKL~CP~C~aKLGsf~wv~G~kC-sCG~~v 45 (75)
+-.--|-||+-+-=+|-| +| ||..|-
T Consensus 352 ~~~YRC~~CGF~a~~l~W----~CPsC~~W~ 378 (389)
T COG2956 352 KPRYRCQNCGFTAHTLYW----HCPSCRAWE 378 (389)
T ss_pred cCCceecccCCcceeeee----eCCCccccc
Confidence 455679999999999999 68 499986
No 160
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=23.72 E-value=32 Score=20.86 Aligned_cols=22 Identities=27% Similarity=0.871 Sum_probs=13.7
Q ss_pred hhhhHHHhcCccccceeeCCCCCCcc
Q psy10712 3 DWMRTAVEEGNFLKDKLKCPNCSTNL 28 (75)
Q Consensus 3 ~WM~~~i~~~~~~~GKL~CP~C~aKL 28 (75)
-||...+. .+..-.||-|++..
T Consensus 28 gWmR~nFs----~~~~p~CPlC~s~M 49 (59)
T PF14169_consen 28 GWMRDNFS----FEEEPVCPLCKSPM 49 (59)
T ss_pred cccccccc----cCCCccCCCcCCcc
Confidence 37876443 24446788888754
No 161
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=23.63 E-value=37 Score=21.11 Aligned_cols=10 Identities=30% Similarity=0.952 Sum_probs=7.9
Q ss_pred eeCCCCCCcc
Q psy10712 19 LKCPNCSTNL 28 (75)
Q Consensus 19 L~CP~C~aKL 28 (75)
+.||.|+++-
T Consensus 2 m~CP~Cg~~a 11 (72)
T PRK09678 2 FHCPLCQHAA 11 (72)
T ss_pred ccCCCCCCcc
Confidence 5799998765
No 162
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=23.51 E-value=39 Score=20.32 Aligned_cols=10 Identities=30% Similarity=0.992 Sum_probs=7.8
Q ss_pred eCCCCCCccc
Q psy10712 20 KCPNCSTNLG 29 (75)
Q Consensus 20 ~CP~C~aKLG 29 (75)
+||+|+..+-
T Consensus 5 HC~~CG~~Ip 14 (59)
T PF09889_consen 5 HCPVCGKPIP 14 (59)
T ss_pred cCCcCCCcCC
Confidence 6888887765
No 163
>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=23.42 E-value=41 Score=19.01 Aligned_cols=26 Identities=19% Similarity=0.446 Sum_probs=15.2
Q ss_pred eCCCCCCccceee----cCC---CCCCC-CCCcc
Q psy10712 20 KCPNCSTNLGAFD----YVS---GHKCP-CKQQC 45 (75)
Q Consensus 20 ~CP~C~aKLGsf~----wv~---G~kCs-CG~~v 45 (75)
-||.|+.+-=.|. ... ...|+ ||.-.
T Consensus 3 PCPfCGg~~~~~~~~~~~~~~~~~~~C~~Cga~~ 36 (53)
T TIGR03655 3 PCPFCGGADVYLRRGFDPLDLSHYFECSTCGASG 36 (53)
T ss_pred CCCCCCCcceeeEeccCCCCCEEEEECCCCCCCc
Confidence 5999998765442 211 22576 77753
No 164
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=23.39 E-value=34 Score=20.00 Aligned_cols=10 Identities=30% Similarity=1.188 Sum_probs=6.3
Q ss_pred eeCCCCCCcc
Q psy10712 19 LKCPNCSTNL 28 (75)
Q Consensus 19 L~CP~C~aKL 28 (75)
+.||.|+..+
T Consensus 1 i~CPyCge~~ 10 (52)
T PF14255_consen 1 IQCPYCGEPI 10 (52)
T ss_pred CCCCCCCCee
Confidence 3577777654
No 165
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=23.38 E-value=34 Score=18.01 Aligned_cols=26 Identities=27% Similarity=0.727 Sum_probs=19.0
Q ss_pred eeCCCCCCccceeecCCCCCCC-CCCcc
Q psy10712 19 LKCPNCSTNLGAFDYVSGHKCP-CKQQC 45 (75)
Q Consensus 19 L~CP~C~aKLGsf~wv~G~kCs-CG~~v 45 (75)
..|--|+..|...-- +|.+|+ |+.-+
T Consensus 12 ~~C~~C~~~i~~~~~-~~~~C~~C~~~~ 38 (50)
T cd00029 12 TFCDVCRKSIWGLFK-QGLRCSWCKVKC 38 (50)
T ss_pred CChhhcchhhhcccc-ceeEcCCCCCch
Confidence 457779999877633 789997 76554
No 166
>cd00246 RabGEF Nucleotide exchange factor for Rab-like small GTPases (RabGEF), Mss4 type; RabGEF positely regulates the function of Rab GTPase by promoting exchange of GDP for GTP; members of the Rab subfamily of Ras GTPases are important in vesicular transport;
Probab=23.32 E-value=43 Score=22.44 Aligned_cols=11 Identities=18% Similarity=0.800 Sum_probs=8.3
Q ss_pred eeeCCCCCCcc
Q psy10712 18 KLKCPNCSTNL 28 (75)
Q Consensus 18 KL~CP~C~aKL 28 (75)
++.||.|++++
T Consensus 2 ~v~C~~C~S~V 12 (103)
T cd00246 2 AVLCQRCGSRV 12 (103)
T ss_pred ceECCCCCCEE
Confidence 47788888776
No 167
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=23.23 E-value=43 Score=18.46 Aligned_cols=9 Identities=33% Similarity=1.043 Sum_probs=4.8
Q ss_pred eeCCCCCCc
Q psy10712 19 LKCPNCSTN 27 (75)
Q Consensus 19 L~CP~C~aK 27 (75)
-.||+|+.-
T Consensus 2 hlcpkcgvg 10 (36)
T PF09151_consen 2 HLCPKCGVG 10 (36)
T ss_dssp -B-TTTSSS
T ss_pred ccCCccCce
Confidence 358888753
No 168
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=23.17 E-value=50 Score=23.71 Aligned_cols=13 Identities=46% Similarity=0.892 Sum_probs=10.1
Q ss_pred eeCCCCCCcccee
Q psy10712 19 LKCPNCSTNLGAF 31 (75)
Q Consensus 19 L~CP~C~aKLGsf 31 (75)
..||+|++.+...
T Consensus 40 ~~Cp~C~~~IrG~ 52 (158)
T PF10083_consen 40 TSCPNCSTPIRGD 52 (158)
T ss_pred HHCcCCCCCCCCc
Confidence 5699999998543
No 169
>PRK12366 replication factor A; Reviewed
Probab=23.16 E-value=52 Score=27.47 Aligned_cols=29 Identities=24% Similarity=0.456 Sum_probs=18.0
Q ss_pred eeCCCCCCccceeecCCCCCCC-CCCcccceEE
Q psy10712 19 LKCPNCSTNLGAFDYVSGHKCP-CKQQCVPFIH 50 (75)
Q Consensus 19 L~CP~C~aKLGsf~wv~G~kCs-CG~~v~Paf~ 50 (75)
-.||.|+-|| .-.= ....|. ||+- .|-..
T Consensus 533 ~aCp~CnkKv-~~~~-g~~~C~~c~~~-~p~~~ 562 (637)
T PRK12366 533 YLCPNCRKRV-EEVD-GEYICEFCGEV-EPNEL 562 (637)
T ss_pred ecccccCeEe-EcCC-CcEECCCCCCC-CCcEE
Confidence 3599999999 2211 123685 8887 55443
No 170
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=23.13 E-value=41 Score=17.89 Aligned_cols=10 Identities=30% Similarity=1.036 Sum_probs=7.3
Q ss_pred eeCCCCCCcc
Q psy10712 19 LKCPNCSTNL 28 (75)
Q Consensus 19 L~CP~C~aKL 28 (75)
..||.|++.-
T Consensus 3 ~~Cp~Cg~~~ 12 (47)
T PF14690_consen 3 PRCPHCGSPS 12 (47)
T ss_pred ccCCCcCCCc
Confidence 4689998664
No 171
>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=22.86 E-value=39 Score=20.87 Aligned_cols=27 Identities=22% Similarity=0.448 Sum_probs=14.6
Q ss_pred eeCCCCCCcc--cee--ecCCCCCC-CCCCcc
Q psy10712 19 LKCPNCSTNL--GAF--DYVSGHKC-PCKQQC 45 (75)
Q Consensus 19 L~CP~C~aKL--Gsf--~wv~G~kC-sCG~~v 45 (75)
-.||+|++-= =-| |=+.=..| +||..-
T Consensus 9 a~CP~C~~~D~i~~~~e~~ve~vECV~CGy~e 40 (71)
T PF09526_consen 9 AVCPKCQAMDTIMMWRENGVEYVECVECGYTE 40 (71)
T ss_pred ccCCCCcCccEEEEEEeCCceEEEecCCCCee
Confidence 3599999742 212 11122567 588754
No 172
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=22.66 E-value=52 Score=23.37 Aligned_cols=24 Identities=25% Similarity=0.588 Sum_probs=19.7
Q ss_pred ccceeecCCCCCC--CCCCcccceEEEEc
Q psy10712 27 NLGAFDYVSGHKC--PCKQQCVPFIHLVK 53 (75)
Q Consensus 27 KLGsf~wv~G~kC--sCG~~v~Paf~i~k 53 (75)
.=|.|+| .+..| .|+. .|.++|+.
T Consensus 113 ~DG~ftl-~~v~ClGaC~~--AP~vmind 138 (160)
T COG1905 113 ADGKFTL-EPVECLGACGQ--APVVMIND 138 (160)
T ss_pred CCCeEEE-eeeeeeccccc--CCEEEECC
Confidence 3468999 79999 5988 89999875
No 173
>PF12387 Peptidase_C74: Pestivirus NS2 peptidase; InterPro: IPR022120 The pestivirus NS2 peptidase is responsible for single cleavage between NS2 and NS3 of the Bovine viral diarrhea virus 1 polyprotein, a cleavage that is correlated with cytopathogenicity []. The peptidase is activated by its interaction with 'J-domain protein interacting with viral protein' - Jiv. ; GO: 0003968 RNA-directed RNA polymerase activity, 0004197 cysteine-type endopeptidase activity, 0004252 serine-type endopeptidase activity, 0016817 hydrolase activity, acting on acid anhydrides, 0017111 nucleoside-triphosphatase activity, 0070008 serine-type exopeptidase activity
Probab=22.46 E-value=54 Score=24.30 Aligned_cols=28 Identities=29% Similarity=0.818 Sum_probs=21.3
Q ss_pred ccceeeCCCCCCccceeecCCCCCCC-CCCcccc
Q psy10712 15 LKDKLKCPNCSTNLGAFDYVSGHKCP-CKQQCVP 47 (75)
Q Consensus 15 ~~GKL~CP~C~aKLGsf~wv~G~kCs-CG~~v~P 47 (75)
...-+.|--|..| +| .|..|+ ||..=.|
T Consensus 159 ~~hcilCtvCe~r----~w-~g~~CPKCGr~G~p 187 (200)
T PF12387_consen 159 SKHCILCTVCEGR----EW-KGGNCPKCGRHGKP 187 (200)
T ss_pred CCceEEEeeeecC----cc-CCCCCCcccCCCCC
Confidence 4566888889887 58 899998 8887444
No 174
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.29 E-value=37 Score=22.88 Aligned_cols=32 Identities=25% Similarity=0.674 Sum_probs=22.4
Q ss_pred cccceeeCCCCCC----ccceeec-CCCCCCC-CCCcc
Q psy10712 14 FLKDKLKCPNCST----NLGAFDY-VSGHKCP-CKQQC 45 (75)
Q Consensus 14 ~~~GKL~CP~C~a----KLGsf~w-v~G~kCs-CG~~v 45 (75)
+..++++||-|.+ |+|.+.= .+..+|. |+.-.
T Consensus 26 ~~~~~~~cP~C~s~~~~k~g~~~~~~qRyrC~~C~~tf 63 (129)
T COG3677 26 MQITKVNCPRCKSSNVVKIGGIRRGHQRYKCKSCGSTF 63 (129)
T ss_pred hhcccCcCCCCCccceeeECCccccccccccCCcCcce
Confidence 4689999999986 4454433 4778885 88743
No 175
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=22.13 E-value=41 Score=23.58 Aligned_cols=31 Identities=23% Similarity=0.590 Sum_probs=18.4
Q ss_pred eeeCCCCCCccceeecCCCCCCC-CCCc----ccceEEEEc
Q psy10712 18 KLKCPNCSTNLGAFDYVSGHKCP-CKQQ----CVPFIHLVK 53 (75)
Q Consensus 18 KL~CP~C~aKLGsf~wv~G~kCs-CG~~----v~Paf~i~k 53 (75)
.-.||.|+. +.- .-..|+ ||.- +.-|+-|.+
T Consensus 309 S~~C~~cg~----~~~-r~~~C~~cg~~~~rD~naa~Ni~~ 344 (364)
T COG0675 309 SKTCPCCGH----LSG-RLFKCPRCGFVHDRDVNAALNIAR 344 (364)
T ss_pred cccccccCC----ccc-eeEECCCCCCeehhhHHHHHHHHH
Confidence 356999998 332 335787 8853 444444443
No 176
>PRK14701 reverse gyrase; Provisional
Probab=21.50 E-value=39 Score=31.54 Aligned_cols=24 Identities=25% Similarity=0.631 Sum_probs=20.5
Q ss_pred eeCCCCCCccceeecCCCCCCC-CC
Q psy10712 19 LKCPNCSTNLGAFDYVSGHKCP-CK 42 (75)
Q Consensus 19 L~CP~C~aKLGsf~wv~G~kCs-CG 42 (75)
-.||||+..+-+..-..|.-|. |=
T Consensus 7 ~~cpnc~g~~~~~rl~~g~~c~~cl 31 (1638)
T PRK14701 7 EMCPNCGGDITDERLAEKGVCEKCL 31 (1638)
T ss_pred ccCCCCCCccchhHHhcCCCchhhc
Confidence 4699999999999887889886 74
No 177
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=21.39 E-value=57 Score=17.71 Aligned_cols=12 Identities=33% Similarity=1.035 Sum_probs=8.2
Q ss_pred eCCCCCCcccee
Q psy10712 20 KCPNCSTNLGAF 31 (75)
Q Consensus 20 ~CP~C~aKLGsf 31 (75)
.||+|+.+--.|
T Consensus 2 ~Cp~C~~~~a~~ 13 (40)
T smart00440 2 PCPKCGNREATF 13 (40)
T ss_pred cCCCCCCCeEEE
Confidence 588888665554
No 178
>PF06170 DUF983: Protein of unknown function (DUF983); InterPro: IPR009325 This family consists of several bacterial proteins of unknown function.
Probab=21.19 E-value=41 Score=21.32 Aligned_cols=19 Identities=26% Similarity=0.565 Sum_probs=14.1
Q ss_pred ccceeeCCCCCCccceeec
Q psy10712 15 LKDKLKCPNCSTNLGAFDY 33 (75)
Q Consensus 15 ~~GKL~CP~C~aKLGsf~w 33 (75)
.+=+-.|++|+..++..+=
T Consensus 5 Lk~~~~C~~CG~d~~~~~a 23 (86)
T PF06170_consen 5 LKVAPRCPHCGLDYSHARA 23 (86)
T ss_pred ccCCCcccccCCccccCCc
Confidence 3445579999999987764
No 179
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=21.03 E-value=51 Score=19.65 Aligned_cols=12 Identities=33% Similarity=0.598 Sum_probs=8.5
Q ss_pred ceeeCCCCCCcc
Q psy10712 17 DKLKCPNCSTNL 28 (75)
Q Consensus 17 GKL~CP~C~aKL 28 (75)
=|..||.|++.+
T Consensus 16 Lk~~CP~CG~~t 27 (56)
T PRK13130 16 LKEICPVCGGKT 27 (56)
T ss_pred ccccCcCCCCCC
Confidence 367788888764
No 180
>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=21.00 E-value=44 Score=22.96 Aligned_cols=8 Identities=38% Similarity=1.015 Sum_probs=4.2
Q ss_pred CCCCCCcc
Q psy10712 21 CPNCSTNL 28 (75)
Q Consensus 21 CP~C~aKL 28 (75)
||+|+.|.
T Consensus 112 Cp~c~~r~ 119 (158)
T TIGR00373 112 CPNMCVRF 119 (158)
T ss_pred CCCCCcEe
Confidence 55555544
No 181
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=20.92 E-value=46 Score=16.35 Aligned_cols=11 Identities=27% Similarity=0.981 Sum_probs=7.9
Q ss_pred eeCCCCCCccc
Q psy10712 19 LKCPNCSTNLG 29 (75)
Q Consensus 19 L~CP~C~aKLG 29 (75)
+.||.|+-+.+
T Consensus 3 ~~C~~CgR~F~ 13 (25)
T PF13913_consen 3 VPCPICGRKFN 13 (25)
T ss_pred CcCCCCCCEEC
Confidence 46888887654
No 182
>PF04475 DUF555: Protein of unknown function (DUF555); InterPro: IPR007564 This is a family of uncharacterised, hypothetical archaeal proteins.
Probab=20.56 E-value=50 Score=22.17 Aligned_cols=13 Identities=31% Similarity=0.823 Sum_probs=9.0
Q ss_pred cceeeCCCCCCcc
Q psy10712 16 KDKLKCPNCSTNL 28 (75)
Q Consensus 16 ~GKL~CP~C~aKL 28 (75)
-|-..||+|+..|
T Consensus 45 vG~~~cP~Cge~~ 57 (102)
T PF04475_consen 45 VGDTICPKCGEEL 57 (102)
T ss_pred cCcccCCCCCCcc
Confidence 3667788887665
No 183
>PRK12496 hypothetical protein; Provisional
Probab=20.50 E-value=45 Score=23.18 Aligned_cols=10 Identities=20% Similarity=0.657 Sum_probs=7.5
Q ss_pred eCCCCCCccc
Q psy10712 20 KCPNCSTNLG 29 (75)
Q Consensus 20 ~CP~C~aKLG 29 (75)
.||.|+++|=
T Consensus 145 ~C~~CG~~~~ 154 (164)
T PRK12496 145 VCEICGSPVK 154 (164)
T ss_pred cCCCCCChhh
Confidence 4888888763
No 184
>TIGR01054 rgy reverse gyrase. Generally, these gyrases are encoded as a single polypeptide. An exception was found in Methanopyrus kandleri, where enzyme is split within the topoisomerase domain, yielding a heterodimer of gene products designated RgyB and RgyA.
Probab=20.49 E-value=47 Score=29.83 Aligned_cols=25 Identities=28% Similarity=0.705 Sum_probs=20.7
Q ss_pred eeCCCCCCccceeecCCCCCCC-CCC
Q psy10712 19 LKCPNCSTNLGAFDYVSGHKCP-CKQ 43 (75)
Q Consensus 19 L~CP~C~aKLGsf~wv~G~kCs-CG~ 43 (75)
-.||||+..+-++.-..|.-|. |-.
T Consensus 8 ~~CPnCgg~i~~~rl~~~~~c~~Clp 33 (1171)
T TIGR01054 8 NLCPNCGGEISSERLEKGLPCARCLP 33 (1171)
T ss_pred CCCCCCCCccchhHhhcCCCccccCc
Confidence 4699999999998887788886 754
No 185
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=20.45 E-value=87 Score=22.56 Aligned_cols=27 Identities=30% Similarity=0.774 Sum_probs=18.7
Q ss_pred cceeeCCCCCCccceeecCCCCCCC-CCCccc
Q psy10712 16 KDKLKCPNCSTNLGAFDYVSGHKCP-CKQQCV 46 (75)
Q Consensus 16 ~GKL~CP~C~aKLGsf~wv~G~kCs-CG~~v~ 46 (75)
+-.-.|.+|+..-=.|-| .|+ ||+|=|
T Consensus 352 ~p~~~c~~cg~~~~~~~~----~c~~c~~~~~ 379 (389)
T PRK11788 352 KPRYRCRNCGFTARTLYW----HCPSCKAWET 379 (389)
T ss_pred CCCEECCCCCCCCcccee----ECcCCCCccC
Confidence 334569889887666666 575 888853
No 186
>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=20.19 E-value=41 Score=17.74 Aligned_cols=13 Identities=38% Similarity=0.820 Sum_probs=10.1
Q ss_pred eeCCCCCCcccee
Q psy10712 19 LKCPNCSTNLGAF 31 (75)
Q Consensus 19 L~CP~C~aKLGsf 31 (75)
-.||.|++.-..|
T Consensus 19 ~~CP~Cg~~~~~F 31 (34)
T cd00729 19 EKCPICGAPKEKF 31 (34)
T ss_pred CcCcCCCCchHHc
Confidence 3799999976655
Done!