Query psy15072
Match_columns 97
No_of_seqs 115 out of 228
Neff 3.0
Searched_HMMs 46136
Date Fri Aug 16 19:43:03 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15072.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15072hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF01599 Ribosomal_S27: Riboso 100.0 3.8E-33 8.3E-38 173.5 2.8 47 3-49 1-47 (47)
2 COG1998 RPS31 Ribosomal protei 99.9 4.6E-28 9.9E-33 153.6 3.9 50 1-53 1-50 (51)
3 PRK00432 30S ribosomal protein 99.8 2.1E-19 4.5E-24 111.5 4.0 47 2-52 3-49 (50)
4 KOG0004|consensus 99.7 1.7E-18 3.7E-23 129.4 2.0 53 3-55 101-153 (156)
5 smart00661 RPOL9 RNA polymeras 94.7 0.021 4.7E-07 33.5 1.8 33 21-55 1-35 (52)
6 PF08646 Rep_fac-A_C: Replicat 94.6 0.17 3.8E-06 35.2 6.3 64 14-91 6-75 (146)
7 PHA00626 hypothetical protein 94.5 0.025 5.4E-07 37.2 1.8 31 22-54 2-37 (59)
8 KOG0004|consensus 94.4 0.011 2.4E-07 44.8 -0.1 19 56-74 27-47 (156)
9 PF09855 DUF2082: Nucleic-acid 93.1 0.08 1.7E-06 34.5 2.3 19 40-58 36-54 (64)
10 PF01485 IBR: IBR domain; Int 92.3 0.071 1.5E-06 31.5 1.2 35 19-53 17-53 (64)
11 TIGR01384 TFS_arch transcripti 91.3 0.094 2E-06 34.9 1.0 28 21-52 1-28 (104)
12 smart00647 IBR In Between Ring 91.2 0.19 4.1E-06 29.7 2.1 35 19-53 17-53 (64)
13 PF14803 Nudix_N_2: Nudix N-te 90.6 0.18 4E-06 29.3 1.6 27 21-49 1-31 (34)
14 COG1594 RPB9 DNA-directed RNA 89.4 0.44 9.5E-06 33.5 3.1 47 21-71 3-56 (113)
15 PF13248 zf-ribbon_3: zinc-rib 89.1 0.14 3.1E-06 27.5 0.3 23 21-49 3-25 (26)
16 PF08271 TF_Zn_Ribbon: TFIIB z 88.7 0.54 1.2E-05 27.4 2.7 29 22-52 2-31 (43)
17 PF09297 zf-NADH-PPase: NADH p 88.6 0.28 6E-06 27.2 1.3 30 19-50 2-31 (32)
18 PRK00398 rpoP DNA-directed RNA 87.6 0.75 1.6E-05 27.0 2.8 32 22-55 5-36 (46)
19 COG1645 Uncharacterized Zn-fin 86.8 0.53 1.1E-05 34.8 2.2 39 18-60 26-64 (131)
20 KOG0003|consensus 86.7 0.097 2.1E-06 38.7 -1.7 19 56-74 27-47 (128)
21 PRK00241 nudC NADH pyrophospha 86.4 0.46 9.9E-06 37.0 1.8 38 18-57 97-134 (256)
22 PF08792 A2L_zn_ribbon: A2L zi 85.9 0.82 1.8E-05 26.3 2.3 30 20-51 3-32 (33)
23 cd04476 RPA1_DBD_C RPA1_DBD_C: 85.3 2.9 6.3E-05 29.6 5.4 66 7-91 17-89 (166)
24 TIGR02098 MJ0042_CXXC MJ0042 f 84.8 0.94 2E-05 25.3 2.2 29 21-51 3-36 (38)
25 PF02150 RNA_POL_M_15KD: RNA p 84.6 0.63 1.4E-05 26.8 1.4 31 21-53 2-33 (35)
26 PF09538 FYDLN_acid: Protein o 83.9 0.59 1.3E-05 32.9 1.3 32 19-53 8-39 (108)
27 KOG0005|consensus 83.3 0.23 5.1E-06 33.5 -0.9 19 56-74 29-47 (70)
28 COG1997 RPL43A Ribosomal prote 82.1 0.98 2.1E-05 31.7 1.8 33 17-51 32-64 (89)
29 PRK05978 hypothetical protein; 81.0 0.75 1.6E-05 34.2 1.0 33 19-53 32-65 (148)
30 PF10571 UPF0547: Uncharacteri 80.5 0.65 1.4E-05 25.5 0.4 24 21-50 1-24 (26)
31 smart00659 RPOLCX RNA polymera 80.3 2 4.2E-05 26.0 2.5 14 38-51 17-30 (44)
32 PRK09710 lar restriction allev 80.2 1.5 3.3E-05 29.1 2.1 28 20-49 6-36 (64)
33 COG3478 Predicted nucleic-acid 79.1 1 2.2E-05 30.4 1.0 17 41-57 41-57 (68)
34 COG2051 RPS27A Ribosomal prote 78.3 4.9 0.00011 27.0 4.1 46 6-53 5-51 (67)
35 PF09862 DUF2089: Protein of u 77.4 0.7 1.5E-05 33.2 -0.1 42 23-70 1-42 (113)
36 TIGR00617 rpa1 replication fac 77.4 6.7 0.00015 34.3 5.8 69 6-90 456-530 (608)
37 PF01907 Ribosomal_L37e: Ribos 77.3 1.7 3.6E-05 28.2 1.6 26 19-49 14-39 (55)
38 PF11706 zf-CGNR: CGNR zinc fi 75.1 0.97 2.1E-05 27.5 0.1 26 21-47 3-32 (44)
39 PF01780 Ribosomal_L37ae: Ribo 74.7 2.9 6.2E-05 29.2 2.3 29 21-51 36-64 (90)
40 TIGR00595 priA primosomal prot 74.7 3.4 7.4E-05 35.0 3.2 61 22-93 224-295 (505)
41 PF07282 OrfB_Zn_ribbon: Putat 74.1 2.1 4.6E-05 26.3 1.4 39 7-53 19-59 (69)
42 PF13719 zinc_ribbon_5: zinc-r 74.0 2.5 5.4E-05 24.2 1.6 27 22-50 4-35 (37)
43 COG1096 Predicted RNA-binding 73.6 2.6 5.6E-05 32.9 2.1 31 20-54 149-179 (188)
44 PF12760 Zn_Tnp_IS1595: Transp 73.1 2.7 5.9E-05 24.8 1.7 25 21-48 19-45 (46)
45 COG0675 Transposase and inacti 72.6 2.1 4.5E-05 31.3 1.3 27 21-54 310-336 (364)
46 PHA02942 putative transposase; 72.0 2.3 4.9E-05 35.0 1.5 30 20-53 325-355 (383)
47 PF07754 DUF1610: Domain of un 71.9 2.2 4.7E-05 23.4 1.0 24 23-48 1-24 (24)
48 PF14353 CpXC: CpXC protein 71.3 5.7 0.00012 27.2 3.2 10 40-49 38-47 (128)
49 COG2816 NPY1 NTP pyrophosphohy 71.1 1.7 3.6E-05 35.5 0.5 39 18-58 109-147 (279)
50 PF01783 Ribosomal_L32p: Ribos 70.7 3.8 8.3E-05 25.4 2.0 21 21-48 27-47 (56)
51 TIGR02300 FYDLN_acid conserved 70.0 2.7 5.8E-05 31.2 1.4 32 19-53 8-39 (129)
52 PF03604 DNA_RNApol_7kD: DNA d 67.0 3 6.4E-05 23.9 0.9 21 28-49 6-26 (32)
53 PF14319 Zn_Tnp_IS91: Transpos 66.7 2.8 6.2E-05 29.1 0.9 48 19-71 41-90 (111)
54 PF04828 GFA: Glutathione-depe 66.6 2.1 4.5E-05 26.4 0.2 18 36-53 44-61 (92)
55 PF14347 DUF4399: Domain of un 66.5 6.1 0.00013 26.7 2.5 26 53-78 49-74 (87)
56 PF06677 Auto_anti-p27: Sjogre 66.1 5 0.00011 24.1 1.8 27 18-47 15-41 (41)
57 PF00301 Rubredoxin: Rubredoxi 64.7 4.3 9.4E-05 24.9 1.3 26 40-67 1-26 (47)
58 cd00730 rubredoxin Rubredoxin; 64.6 4.5 9.7E-05 25.1 1.4 27 40-68 1-27 (50)
59 PF12773 DZR: Double zinc ribb 64.5 4.4 9.5E-05 23.5 1.3 28 19-49 11-38 (50)
60 PRK00420 hypothetical protein; 64.3 5.5 0.00012 28.5 2.0 33 19-54 22-54 (112)
61 PRK05580 primosome assembly pr 63.9 9.7 0.00021 33.4 3.8 61 22-93 392-463 (679)
62 PF13717 zinc_ribbon_4: zinc-r 63.1 3.5 7.7E-05 23.6 0.7 11 40-50 25-35 (36)
63 TIGR00280 L37a ribosomal prote 62.9 5.1 0.00011 28.0 1.6 31 19-51 34-64 (91)
64 PRK03976 rpl37ae 50S ribosomal 62.5 5.3 0.00011 27.9 1.6 31 19-51 35-65 (90)
65 PF06827 zf-FPG_IleRS: Zinc fi 62.0 7.1 0.00015 21.0 1.8 25 21-47 2-28 (30)
66 PF11781 RRN7: RNA polymerase 60.6 5.5 0.00012 23.1 1.2 26 21-49 9-34 (36)
67 COG1198 PriA Primosomal protei 60.4 12 0.00026 34.1 3.8 63 21-94 445-518 (730)
68 TIGR03683 A-tRNA_syn_arch alan 60.1 4.5 9.8E-05 37.2 1.2 27 18-47 14-42 (902)
69 PRK01103 formamidopyrimidine/5 59.9 7.1 0.00015 30.4 2.1 27 20-48 245-273 (274)
70 PTZ00255 60S ribosomal protein 59.8 6.2 0.00013 27.5 1.6 32 18-51 34-65 (90)
71 PF09788 Tmemb_55A: Transmembr 59.6 11 0.00025 30.6 3.3 54 15-68 118-185 (256)
72 PF13240 zinc_ribbon_2: zinc-r 59.3 4.6 9.9E-05 21.4 0.7 21 22-48 1-21 (23)
73 PRK14810 formamidopyrimidine-D 58.7 8.2 0.00018 30.2 2.3 27 19-47 243-271 (272)
74 KOG1865|consensus 58.0 6 0.00013 35.2 1.5 36 38-78 284-319 (545)
75 cd01793 Fubi Fubi ubiquitin-li 57.7 3.6 7.7E-05 25.6 0.1 18 56-73 27-44 (74)
76 PRK14811 formamidopyrimidine-D 57.5 8.7 0.00019 30.1 2.3 26 20-47 235-262 (269)
77 PRK13902 alaS alanyl-tRNA synt 57.4 5.8 0.00013 36.5 1.4 30 12-47 14-45 (900)
78 PRK10445 endonuclease VIII; Pr 56.9 9 0.0002 29.8 2.2 26 20-47 235-262 (263)
79 PRK12286 rpmF 50S ribosomal pr 56.6 6.4 0.00014 24.9 1.1 22 20-48 27-48 (57)
80 KOG0006|consensus 56.3 3.2 7E-05 35.8 -0.3 33 21-53 316-349 (446)
81 PRK14714 DNA polymerase II lar 56.3 7.8 0.00017 37.8 2.1 16 16-33 663-678 (1337)
82 COG2888 Predicted Zn-ribbon RN 55.8 6.6 0.00014 26.0 1.1 34 21-56 10-43 (61)
83 PRK14873 primosome assembly pr 55.8 10 0.00022 33.7 2.6 58 22-91 394-462 (665)
84 PF10263 SprT-like: SprT-like 54.9 12 0.00027 25.7 2.5 31 17-51 120-154 (157)
85 COG3677 Transposase and inacti 54.8 10 0.00023 27.1 2.1 39 19-60 29-73 (129)
86 cd01794 DC_UbP_C dendritic cel 54.5 3.2 6.9E-05 26.3 -0.5 17 57-73 28-44 (70)
87 PRK13945 formamidopyrimidine-D 54.3 10 0.00022 29.7 2.2 26 20-47 254-281 (282)
88 COG3809 Uncharacterized protei 54.3 11 0.00023 26.6 2.0 33 21-55 2-36 (88)
89 PF05191 ADK_lid: Adenylate ki 54.2 11 0.00024 21.8 1.8 28 20-50 1-31 (36)
90 PF14949 ARF7EP_C: ARF7 effect 54.1 9.7 0.00021 27.0 1.8 33 9-49 48-83 (103)
91 COG1779 C4-type Zn-finger prot 54.1 8.3 0.00018 30.4 1.6 33 15-50 9-53 (201)
92 COG5349 Uncharacterized protei 53.8 4.9 0.00011 29.8 0.3 34 19-54 20-54 (126)
93 cd00350 rubredoxin_like Rubred 53.6 6.7 0.00015 21.8 0.8 14 40-53 1-14 (33)
94 PF07295 DUF1451: Protein of u 53.3 16 0.00034 27.0 2.9 43 7-54 101-144 (146)
95 COG1545 Predicted nucleic-acid 53.1 14 0.0003 26.5 2.5 37 5-49 16-52 (140)
96 COG0484 DnaJ DnaJ-class molecu 53.0 15 0.00033 31.0 3.1 38 21-66 184-222 (371)
97 TIGR00577 fpg formamidopyrimid 51.6 13 0.00027 29.1 2.3 25 20-46 245-271 (272)
98 PRK12366 replication factor A; 51.6 26 0.00057 30.8 4.4 25 21-49 533-557 (637)
99 PF09151 DUF1936: Domain of un 50.7 7.7 0.00017 23.2 0.7 14 21-36 2-15 (36)
100 KOG0466|consensus 50.0 12 0.00026 32.5 2.1 36 13-49 82-118 (466)
101 PF05129 Elf1: Transcription e 50.0 12 0.00025 25.0 1.6 32 22-55 24-61 (81)
102 cd01796 DDI1_N DNA damage indu 49.5 5.2 0.00011 25.0 -0.1 19 56-74 28-46 (71)
103 PF01396 zf-C4_Topoisom: Topoi 49.1 20 0.00043 20.8 2.3 28 21-52 2-36 (39)
104 TIGR00244 transcriptional regu 48.5 12 0.00026 28.2 1.6 17 12-30 20-36 (147)
105 smart00214 VWC von Willebrand 47.5 26 0.00056 21.2 2.8 32 13-46 26-59 (59)
106 PF01927 Mut7-C: Mut7-C RNAse 47.2 12 0.00025 26.6 1.4 17 39-55 123-139 (147)
107 PRK04351 hypothetical protein; 45.8 21 0.00046 26.2 2.6 32 19-53 111-145 (149)
108 COG1571 Predicted DNA-binding 45.8 14 0.00031 31.8 1.9 49 17-69 347-401 (421)
109 PRK11827 hypothetical protein; 45.0 17 0.00036 23.5 1.7 31 22-54 10-40 (60)
110 PRK14290 chaperone protein Dna 44.8 32 0.00069 27.9 3.7 8 40-47 205-212 (365)
111 PRK12380 hydrogenase nickel in 44.2 17 0.00036 25.3 1.7 27 18-48 68-94 (113)
112 KOG2906|consensus 44.0 28 0.0006 25.2 2.9 32 22-55 3-36 (105)
113 PRK03681 hypA hydrogenase nick 43.6 16 0.00035 25.4 1.6 27 18-48 68-95 (114)
114 PRK00415 rps27e 30S ribosomal 43.5 19 0.00041 23.5 1.8 34 17-52 8-42 (59)
115 PRK14890 putative Zn-ribbon RN 43.3 16 0.00034 23.9 1.4 38 21-60 8-45 (59)
116 PRK00423 tfb transcription ini 43.1 19 0.00041 28.6 2.1 30 21-52 12-42 (310)
117 PF00093 VWC: von Willebrand f 43.0 24 0.00052 21.2 2.1 19 13-31 26-44 (57)
118 TIGR00354 polC DNA polymerase, 42.8 18 0.0004 34.7 2.3 26 15-48 620-645 (1095)
119 COG1996 RPC10 DNA-directed RNA 42.7 20 0.00044 22.5 1.8 28 42-71 8-35 (49)
120 TIGR01031 rpmF_bact ribosomal 42.4 15 0.00033 23.0 1.2 21 21-48 27-47 (55)
121 PRK10996 thioredoxin 2; Provis 41.9 11 0.00024 26.1 0.5 30 21-52 3-34 (139)
122 KOG4684|consensus 41.7 15 0.00033 30.2 1.4 52 15-67 133-196 (275)
123 PF13005 zf-IS66: zinc-finger 41.0 30 0.00065 19.8 2.2 26 42-67 4-30 (47)
124 PRK04179 rpl37e 50S ribosomal 41.0 12 0.00026 24.8 0.6 25 19-48 16-40 (62)
125 PF12322 T4_baseplate: T4 bact 40.9 39 0.00085 25.9 3.5 47 38-87 76-122 (205)
126 cd01799 Hoil1_N Ubiquitin-like 40.0 8.3 0.00018 24.9 -0.3 17 56-73 31-47 (75)
127 PRK12496 hypothetical protein; 40.0 14 0.0003 27.2 0.9 34 15-52 122-155 (164)
128 PRK14282 chaperone protein Dna 39.9 32 0.00069 27.9 3.0 13 22-36 171-184 (369)
129 PRK07220 DNA topoisomerase I; 39.1 32 0.00069 30.8 3.1 38 12-51 627-668 (740)
130 TIGR00100 hypA hydrogenase nic 37.9 25 0.00054 24.4 1.8 27 18-48 68-94 (115)
131 KOG3475|consensus 37.3 6.2 0.00013 27.9 -1.3 29 19-52 15-43 (92)
132 cd01791 Ubl5 UBL5 ubiquitin-li 37.2 11 0.00023 24.2 -0.1 13 61-73 35-47 (73)
133 PRK14298 chaperone protein Dna 36.9 34 0.00073 28.0 2.7 26 40-66 198-223 (377)
134 PF04885 Stig1: Stigma-specifi 36.9 21 0.00045 26.3 1.4 22 28-49 100-121 (136)
135 TIGR02443 conserved hypothetic 36.7 27 0.00059 22.8 1.7 34 21-56 10-47 (59)
136 COG0333 RpmF Ribosomal protein 36.6 20 0.00043 23.1 1.1 21 21-48 28-48 (57)
137 cd01411 SIR2H SIR2H: Uncharact 36.5 31 0.00067 26.1 2.3 37 7-49 109-145 (225)
138 PF12172 DUF35_N: Rubredoxin-l 36.4 24 0.00053 19.6 1.3 26 19-50 10-35 (37)
139 PF07191 zinc-ribbons_6: zinc- 36.3 37 0.0008 22.8 2.4 47 22-79 3-51 (70)
140 cd01807 GDX_N ubiquitin-like d 36.0 10 0.00023 23.4 -0.3 16 58-73 31-46 (74)
141 PF09526 DUF2387: Probable met 35.9 54 0.0012 21.6 3.1 33 21-55 9-45 (71)
142 PRK14892 putative transcriptio 35.8 27 0.00058 24.4 1.7 30 21-53 22-55 (99)
143 cd01806 Nedd8 Nebb8-like ubiq 35.5 16 0.00035 21.9 0.5 18 56-73 29-46 (76)
144 TIGR00310 ZPR1_znf ZPR1 zinc f 35.2 69 0.0015 24.5 4.0 11 40-50 30-40 (192)
145 PF13408 Zn_ribbon_recom: Reco 35.2 25 0.00054 20.3 1.3 10 42-51 7-16 (58)
146 TIGR02349 DnaJ_bact chaperone 35.1 40 0.00087 26.9 2.8 7 41-47 201-207 (354)
147 PRK08173 DNA topoisomerase III 34.3 20 0.00043 32.9 1.1 28 21-52 625-652 (862)
148 PTZ00044 ubiquitin; Provisiona 34.0 12 0.00026 22.9 -0.3 18 56-73 29-46 (76)
149 PRK05452 anaerobic nitric oxid 34.0 24 0.00051 29.8 1.4 30 38-69 423-452 (479)
150 PLN03086 PRLI-interacting fact 33.9 24 0.00052 31.4 1.5 33 18-51 431-464 (567)
151 PF10071 DUF2310: Zn-ribbon-co 33.9 19 0.0004 29.2 0.8 41 7-49 207-250 (258)
152 PRK04023 DNA polymerase II lar 33.5 25 0.00054 33.9 1.6 16 15-32 621-636 (1121)
153 PRK14288 chaperone protein Dna 33.4 50 0.0011 26.9 3.2 10 58-67 209-218 (369)
154 PRK14289 chaperone protein Dna 33.3 36 0.00078 27.7 2.3 7 41-47 212-218 (386)
155 PRK11032 hypothetical protein; 33.1 60 0.0013 24.5 3.3 44 7-55 113-157 (160)
156 COG1405 SUA7 Transcription ini 33.1 37 0.00081 27.4 2.4 33 21-55 2-35 (285)
157 cd01797 NIRF_N amino-terminal 32.9 13 0.00028 23.9 -0.2 15 59-73 34-48 (78)
158 smart00731 SprT SprT homologue 32.9 33 0.00071 24.1 1.8 33 17-51 109-144 (146)
159 TIGR03831 YgiT_finger YgiT-typ 32.6 80 0.0017 17.3 3.1 10 22-33 34-43 (46)
160 PRK08402 replication factor A; 32.3 1E+02 0.0022 25.7 4.8 38 7-48 196-238 (355)
161 COG1327 Predicted transcriptio 32.2 15 0.00032 28.1 -0.0 17 12-30 20-36 (156)
162 PF13453 zf-TFIIB: Transcripti 32.1 51 0.0011 18.8 2.2 10 41-50 20-29 (41)
163 PRK03824 hypA hydrogenase nick 31.8 47 0.001 23.7 2.5 10 19-30 69-78 (135)
164 PRK14296 chaperone protein Dna 31.7 67 0.0015 26.3 3.6 13 21-35 167-180 (372)
165 TIGR02261 benz_CoA_red_D benzo 31.6 27 0.00059 27.9 1.4 31 5-38 109-141 (262)
166 cd01798 parkin_N amino-termina 31.4 14 0.00031 22.5 -0.2 18 56-73 27-44 (70)
167 PF09889 DUF2116: Uncharacteri 31.3 2.8 6.1E-05 27.0 -3.5 31 20-56 3-34 (59)
168 TIGR00155 pqiA_fam integral me 31.0 26 0.00055 29.3 1.2 31 20-55 215-245 (403)
169 PRK14285 chaperone protein Dna 30.9 39 0.00084 27.5 2.1 27 41-68 200-226 (365)
170 PF14205 Cys_rich_KTR: Cystein 30.7 72 0.0016 20.7 3.0 37 22-60 6-48 (55)
171 COG1773 Rubredoxin [Energy pro 30.5 29 0.00064 22.3 1.1 26 40-67 3-28 (55)
172 cd01810 ISG15_repeat2 ISG15 ub 30.1 17 0.00037 22.5 -0.0 15 59-73 30-44 (74)
173 KOG1819|consensus 30.0 18 0.00038 33.4 0.1 9 40-48 917-925 (990)
174 COG0551 TopA Zn-finger domain 29.9 49 0.0011 23.0 2.3 38 14-53 54-98 (140)
175 PF04135 Nop10p: Nucleolar RNA 29.8 1.1E+02 0.0025 19.3 3.7 26 12-40 9-34 (53)
176 PRK14559 putative protein seri 29.5 28 0.0006 31.2 1.2 12 38-49 39-50 (645)
177 cd00729 rubredoxin_SM Rubredox 29.3 34 0.00073 19.3 1.1 12 40-51 2-13 (34)
178 PTZ00073 60S ribosomal protein 29.3 25 0.00055 24.8 0.7 26 19-49 15-40 (91)
179 PF14354 Lar_restr_allev: Rest 29.2 48 0.001 19.8 1.9 27 20-48 3-37 (61)
180 PRK14559 putative protein seri 29.0 29 0.00063 31.1 1.2 22 20-49 15-36 (645)
181 PF13878 zf-C2H2_3: zinc-finge 28.8 28 0.00061 20.4 0.8 16 39-54 12-27 (41)
182 cd01800 SF3a120_C Ubiquitin-li 28.6 17 0.00037 22.8 -0.2 18 57-74 27-44 (76)
183 cd00924 Cyt_c_Oxidase_Vb Cytoc 28.4 83 0.0018 21.8 3.2 25 5-37 69-93 (97)
184 PRK09678 DNA-binding transcrip 28.4 26 0.00057 23.3 0.6 15 16-30 23-37 (72)
185 PLN02294 cytochrome c oxidase 28.0 71 0.0015 24.8 3.0 23 6-36 132-154 (174)
186 PRK14278 chaperone protein Dna 28.0 69 0.0015 26.2 3.1 25 42-67 198-222 (378)
187 PRK14287 chaperone protein Dna 28.0 60 0.0013 26.5 2.8 26 40-66 195-220 (371)
188 PF10262 Rdx: Rdx family; Int 27.9 11 0.00024 23.9 -1.2 42 41-82 6-48 (76)
189 PF11720 Inhibitor_I78: Peptid 27.6 62 0.0013 20.0 2.2 14 7-20 45-58 (60)
190 PF13511 DUF4124: Domain of un 27.0 77 0.0017 18.7 2.5 20 6-25 14-34 (60)
191 PRK00564 hypA hydrogenase nick 26.7 29 0.00062 24.2 0.6 26 19-48 70-96 (117)
192 TIGR03655 anti_R_Lar restricti 26.7 30 0.00066 20.8 0.7 29 21-51 2-37 (53)
193 PRK14973 DNA topoisomerase I; 26.2 39 0.00085 31.5 1.5 40 13-54 628-671 (936)
194 PF10080 DUF2318: Predicted me 25.9 1.5E+02 0.0033 20.7 4.1 46 4-53 6-65 (102)
195 PF10005 DUF2248: Uncharacteri 25.9 52 0.0011 27.8 2.1 28 22-55 1-28 (343)
196 PTZ00037 DnaJ_C chaperone prot 25.9 67 0.0014 27.1 2.7 8 40-47 208-215 (421)
197 PF03833 PolC_DP2: DNA polymer 25.9 23 0.00049 33.5 0.0 32 15-48 650-688 (900)
198 cd01802 AN1_N ubiquitin-like d 25.8 21 0.00045 24.3 -0.2 58 6-73 8-73 (103)
199 cd01815 BMSC_UbP_N Ubiquitin-l 25.4 22 0.00048 23.7 -0.1 13 61-73 36-49 (75)
200 PF10083 DUF2321: Uncharacteri 25.3 19 0.00042 27.5 -0.5 33 21-55 40-83 (158)
201 smart00547 ZnF_RBZ Zinc finger 25.2 34 0.00073 17.4 0.6 22 21-48 3-24 (26)
202 PRK14283 chaperone protein Dna 25.1 77 0.0017 25.8 2.9 7 41-47 204-210 (378)
203 smart00614 ZnF_BED BED zinc fi 25.0 30 0.00065 20.4 0.4 23 3-30 1-26 (50)
204 PRK14294 chaperone protein Dna 24.9 83 0.0018 25.5 3.1 26 41-67 198-223 (366)
205 cd01804 midnolin_N Ubiquitin-l 24.7 27 0.00058 22.2 0.2 14 60-73 34-47 (78)
206 cd01812 BAG1_N Ubiquitin-like 24.5 25 0.00055 20.9 0.0 16 58-73 30-45 (71)
207 COG1326 Uncharacterized archae 24.4 62 0.0013 25.7 2.2 28 19-50 5-40 (201)
208 TIGR02259 benz_CoA_red_A benzo 24.4 40 0.00086 29.4 1.2 31 5-38 279-311 (432)
209 PRK00464 nrdR transcriptional 24.4 43 0.00092 24.9 1.2 14 14-29 22-35 (154)
210 PRK13130 H/ACA RNA-protein com 24.1 49 0.0011 21.1 1.3 6 20-25 17-22 (56)
211 PRK14279 chaperone protein Dna 23.7 77 0.0017 26.1 2.7 7 60-66 245-251 (392)
212 PF06044 DRP: Dam-replacing fa 23.4 26 0.00057 28.6 -0.1 30 21-53 32-66 (254)
213 COG0375 HybF Zn finger protein 23.3 39 0.00084 24.4 0.8 25 20-48 70-94 (115)
214 PF04216 FdhE: Protein involve 23.2 67 0.0014 25.0 2.1 28 20-49 172-206 (290)
215 PF00684 DnaJ_CXXCXGXG: DnaJ c 23.2 45 0.00097 20.7 1.0 15 21-37 16-31 (66)
216 PHA02031 putative DnaG-like pr 23.0 42 0.00091 27.3 1.0 36 14-52 18-55 (266)
217 PRK14280 chaperone protein Dna 22.8 93 0.002 25.4 3.0 6 42-47 202-207 (376)
218 PRK01110 rpmF 50S ribosomal pr 22.7 53 0.0011 20.9 1.2 20 21-48 28-47 (60)
219 PF03119 DNA_ligase_ZBD: NAD-d 22.7 67 0.0014 17.5 1.5 13 22-36 1-13 (28)
220 PF09567 RE_MamI: MamI restric 22.6 34 0.00073 28.7 0.4 29 21-55 83-111 (314)
221 PRK15103 paraquat-inducible me 22.4 45 0.00097 28.1 1.1 30 20-55 221-250 (419)
222 PRK10767 chaperone protein Dna 22.3 93 0.002 25.2 2.9 6 42-47 197-202 (371)
223 PRK14291 chaperone protein Dna 22.2 1E+02 0.0022 25.2 3.1 26 40-66 208-233 (382)
224 cd01809 Scythe_N Ubiquitin-lik 22.1 27 0.00059 20.7 -0.2 15 59-73 32-46 (72)
225 smart00531 TFIIE Transcription 21.5 84 0.0018 22.3 2.2 31 22-54 101-137 (147)
226 PRK14297 chaperone protein Dna 21.3 88 0.0019 25.5 2.6 9 59-67 223-231 (380)
227 PRK14276 chaperone protein Dna 21.3 87 0.0019 25.6 2.5 8 40-47 203-210 (380)
228 PF01632 Ribosomal_L35p: Ribos 21.2 34 0.00074 21.6 0.1 17 4-20 9-25 (61)
229 CHL00103 rpl35 ribosomal prote 20.9 71 0.0015 20.8 1.6 17 4-20 10-26 (65)
230 PF00240 ubiquitin: Ubiquitin 20.8 37 0.0008 20.1 0.2 17 57-73 25-41 (69)
231 PF05280 FlhC: Flagellar trans 20.7 61 0.0013 24.4 1.4 33 20-54 134-168 (175)
232 PRK15103 paraquat-inducible me 20.5 52 0.0011 27.7 1.1 34 21-56 11-46 (419)
233 TIGR01206 lysW lysine biosynth 20.5 1.6E+02 0.0035 18.5 3.1 31 21-53 3-35 (54)
234 PF02593 dTMP_synthase: Thymid 20.3 33 0.00071 26.9 -0.1 25 12-37 140-164 (217)
235 TIGR03830 CxxCG_CxxCG_HTH puta 20.2 50 0.0011 21.8 0.8 10 40-49 31-40 (127)
236 KOG4537|consensus 20.2 17 0.00038 28.3 -1.6 27 19-48 39-65 (178)
237 PF02810 SEC-C: SEC-C motif; 20.1 53 0.0011 17.3 0.7 10 20-32 2-11 (21)
238 COG4640 Predicted membrane pro 20.1 40 0.00087 29.7 0.4 29 21-55 2-30 (465)
239 PF08772 NOB1_Zn_bind: Nin one 20.1 36 0.00078 22.7 0.1 11 38-48 22-32 (73)
240 PRK14284 chaperone protein Dna 20.0 84 0.0018 25.8 2.2 25 41-66 212-236 (391)
No 1
>PF01599 Ribosomal_S27: Ribosomal protein S27a; InterPro: IPR002906 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This family of ribosomal proteins consists mainly of the 40S ribosomal protein S27a which is synthesized as a C-terminal extension of ubiquitin (CEP) (IPR000626 from INTERPRO). The S27a domain compromises the C-terminal half of the protein. The synthesis of ribosomal proteins as extensions of ubiquitin promotes their incorporation into nascent ribosomes by a transient metabolic stabilisation and is required for efficient ribosome biogenesis []. The ribosomal extension protein S27a contains a basic region that is proposed to form a zinc finger; its fusion gene is proposed as a mechanism to maintain a fixed ratio between ubiquitin necessary for degrading proteins and ribosomes a source of proteins [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2K4X_A 3U5C_f 3U5G_f 2XZN_9 2XZM_9.
Probab=99.97 E-value=3.8e-33 Score=173.48 Aligned_cols=47 Identities=55% Similarity=0.978 Sum_probs=39.2
Q ss_pred ccceEEEECCCCeEEEecccCCCCcCCceEEeceeCCccccCCceeE
Q psy15072 3 NEWQVCNVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSS 49 (97)
Q Consensus 3 ~~LkyYkVdenGKI~rlrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T 49 (97)
|+|||||||+||||+|+|++||+|+||+|||||+|+||+||||||+|
T Consensus 1 AvlkyYkvd~~Gkv~r~rk~CP~~~CG~GvFMA~H~dR~~CGKCg~T 47 (47)
T PF01599_consen 1 AVLKYYKVDENGKVKRLRKECPSPRCGAGVFMAEHKDRHYCGKCGYT 47 (47)
T ss_dssp S----CEEETTTEEEESSEE-TSTTTTSSSEEEE-SSEEEETTTSS-
T ss_pred CcceEEEECCCCcEEEhhhcCCCcccCCceEeeecCCCccCCCcccC
Confidence 68999999999999999999999999999999999999999999997
No 2
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=99.94 E-value=4.6e-28 Score=153.62 Aligned_cols=50 Identities=34% Similarity=0.524 Sum_probs=46.5
Q ss_pred CCccceEEEECCCCeEEEecccCCCCcCCceEEeceeCCccccCCceeEEEee
Q psy15072 1 MSNEWQVCNVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVE 53 (97)
Q Consensus 1 M~~~LkyYkVdenGKI~rlrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~ 53 (97)
+.++++||+||+ +||+|+++.||+ ||+|||||+|.||++|||||||++++
T Consensus 1 ~~~~~~yY~v~~-~kv~rk~~~CPr--CG~gvfmA~H~dR~~CGkCgyTe~~~ 50 (51)
T COG1998 1 KMAVLKYYEVDD-EKVKRKNRFCPR--CGPGVFMADHKDRWACGKCGYTEFKK 50 (51)
T ss_pred CccceeEEEEcC-CcEEEccccCCC--CCCcchhhhcCceeEeccccceEeec
Confidence 357899999995 679999999999 99999999999999999999999875
No 3
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=99.77 E-value=2.1e-19 Score=111.54 Aligned_cols=47 Identities=34% Similarity=0.557 Sum_probs=43.9
Q ss_pred CccceEEEECCCCeEEEecccCCCCcCCceEEeceeCCccccCCceeEEEe
Q psy15072 2 SNEWQVCNVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSV 52 (97)
Q Consensus 2 ~~~LkyYkVdenGKI~rlrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~ 52 (97)
.++|+||+||+ +||+++++.||+ ||+| |||.|.+|++||+||+|++.
T Consensus 3 ~~~~~~y~v~~-~~v~~~~~fCP~--Cg~~-~m~~~~~r~~C~~Cgyt~~~ 49 (50)
T PRK00432 3 MAKREYYEVDG-GKVKRKNKFCPR--CGSG-FMAEHLDRWHCGKCGYTEFK 49 (50)
T ss_pred cceeeeEEECC-CEEEEccCcCcC--CCcc-hheccCCcEECCCcCCEEec
Confidence 57899999985 699999999999 9999 99999999999999999975
No 4
>KOG0004|consensus
Probab=99.72 E-value=1.7e-18 Score=129.37 Aligned_cols=53 Identities=49% Similarity=0.915 Sum_probs=50.2
Q ss_pred ccceEEEECCCCeEEEecccCCCCcCCceEEeceeCCccccCCceeEEEeecc
Q psy15072 3 NEWQVCNVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELK 55 (97)
Q Consensus 3 ~~LkyYkVdenGKI~rlrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~~~ 55 (97)
++++||+||+||+|++++++||+++||+|||||+|+||+|||||.+|+.+.+.
T Consensus 101 ~~~~y~kvd~ngkiq~l~~~~~~~~~~~~v~~a~~~~r~y~gkc~~~~~~~~~ 153 (156)
T KOG0004|consen 101 AVLKYYKVDENGKVQRLRRECPNPACGAGVFMASHADRHYCGKCLLTYKFKKA 153 (156)
T ss_pred CCccceeeccCcchhhhhhhcCCcccccceecccccccccccccceeehhhhc
Confidence 57899999999999999999999999999999999999999999999987654
No 5
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=94.74 E-value=0.021 Score=33.50 Aligned_cols=33 Identities=21% Similarity=0.326 Sum_probs=22.6
Q ss_pred ccCCCCcCCceEEeceeC--CccccCCceeEEEeecc
Q psy15072 21 RECTSEQCGAGVFMAAMS--DRHYCGNKFSSLSVELK 55 (97)
Q Consensus 21 keCP~~eCGaGVFMA~H~--DR~yCGKCg~T~~~~~~ 55 (97)
+.||. ||.=++.-.-. +|+.|.+||+.+..+..
T Consensus 1 ~FCp~--Cg~~l~~~~~~~~~~~vC~~Cg~~~~~~~~ 35 (52)
T smart00661 1 KFCPK--CGNMLIPKEGKEKRRFVCRKCGYEEPIEQK 35 (52)
T ss_pred CCCCC--CCCccccccCCCCCEEECCcCCCeEECCCc
Confidence 46998 99844443322 38999999998765533
No 6
>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=94.59 E-value=0.17 Score=35.23 Aligned_cols=64 Identities=19% Similarity=0.216 Sum_probs=37.8
Q ss_pred CeEEEecc------cCCCCcCCceEEeceeCCccccCCceeEEEeecccccccccCCCCceEEEEEecceeeeeeeeeEE
Q psy15072 14 GKIHRLRR------ECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELKSARSQVRFPPGANFLTFVLGTASFLVSYPVLL 87 (97)
Q Consensus 14 GKI~rlrk------eCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~~~~a~~q~~~p~~~~~l~~~~~~~~~~~~~~~~~ 87 (97)
|+|..+.. .||++.|+..|-.- -.+.++|.||+.+. +....+.++-+..+-.--+-.+.+
T Consensus 6 a~I~~I~~~~~~Y~aC~~~~C~kKv~~~-~~~~y~C~~C~~~~-------------~~~~~ry~l~~~i~D~tg~~~~~~ 71 (146)
T PF08646_consen 6 ATIVEIKSDNWYYPACPNEKCNKKVTEN-GDGSYRCEKCNKTV-------------ENPKYRYRLSLKISDGTGSIWVTL 71 (146)
T ss_dssp EEEEEEETTTTEEEE-TSTTTS-B-EEE-TTTEEEETTTTEEE-------------SS-EEEEEEEEEEEETTEEEEEEE
T ss_pred EEEEEEECCCcEECCCCCccCCCEeecC-CCcEEECCCCCCcC-------------CCeeEEEEEEEEEEeCCCeEEEEE
Confidence 45555544 59966699865432 24689999999764 233456666665555555666777
Q ss_pred Eecc
Q psy15072 88 FDSD 91 (97)
Q Consensus 88 ~~~~ 91 (97)
||..
T Consensus 72 F~~~ 75 (146)
T PF08646_consen 72 FDEE 75 (146)
T ss_dssp EHHH
T ss_pred EhHH
Confidence 7754
No 7
>PHA00626 hypothetical protein
Probab=94.47 E-value=0.025 Score=37.18 Aligned_cols=31 Identities=26% Similarity=0.419 Sum_probs=24.4
Q ss_pred cCCCCcCCceEEec-----eeCCccccCCceeEEEeec
Q psy15072 22 ECTSEQCGAGVFMA-----AMSDRHYCGNKFSSLSVEL 54 (97)
Q Consensus 22 eCP~~eCGaGVFMA-----~H~DR~yCGKCg~T~~~~~ 54 (97)
.||+ ||.+-.+- .|.+|+-|-+|||.+.++.
T Consensus 2 ~CP~--CGS~~Ivrcg~cr~~snrYkCkdCGY~ft~~~ 37 (59)
T PHA00626 2 SCPK--CGSGNIAKEKTMRGWSDDYVCCDCGYNDSKDA 37 (59)
T ss_pred CCCC--CCCceeeeeceecccCcceEcCCCCCeechhh
Confidence 5998 99963333 6789999999999987654
No 8
>KOG0004|consensus
Probab=94.36 E-value=0.011 Score=44.84 Aligned_cols=19 Identities=32% Similarity=0.403 Sum_probs=16.3
Q ss_pred ccccc--ccCCCCceEEEEEe
Q psy15072 56 SARSQ--VRFPPGANFLTFVL 74 (97)
Q Consensus 56 ~a~~q--~~~p~~~~~l~~~~ 74 (97)
+|++| ++||||||+|||+-
T Consensus 27 Kakiq~~egIp~dqqrlifag 47 (156)
T KOG0004|consen 27 KAKIQDKEGIPPDQQRLIFAG 47 (156)
T ss_pred HHhhhcccCCCchhhhhhhhh
Confidence 66666 99999999999973
No 9
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=93.12 E-value=0.08 Score=34.53 Aligned_cols=19 Identities=16% Similarity=0.022 Sum_probs=15.0
Q ss_pred ccccCCceeEEEeeccccc
Q psy15072 40 RHYCGNKFSSLSVELKSAR 58 (97)
Q Consensus 40 R~yCGKCg~T~~~~~~~a~ 58 (97)
-.+|-+|||||+++.+...
T Consensus 36 ~v~C~~CGYTE~Y~~~~~~ 54 (64)
T PF09855_consen 36 TVSCTNCGYTEFYKAKTSN 54 (64)
T ss_pred EEECCCCCCEEEEeecCcc
Confidence 3489999999999866443
No 10
>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=92.34 E-value=0.071 Score=31.47 Aligned_cols=35 Identities=11% Similarity=0.114 Sum_probs=21.9
Q ss_pred ecccCCCCcCCceEEeceeCCc--cccCCceeEEEee
Q psy15072 19 LRRECTSEQCGAGVFMAAMSDR--HYCGNKFSSLSVE 53 (97)
Q Consensus 19 lrkeCP~~eCGaGVFMA~H~DR--~yCGKCg~T~~~~ 53 (97)
..+.||++.|+.++......+. ..|..|+..+.+.
T Consensus 17 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~ 53 (64)
T PF01485_consen 17 NIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFK 53 (64)
T ss_dssp -CC--TTSST---ECS-SSTTS--CCTTSCCSEECSS
T ss_pred CccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccc
Confidence 3469999999988877777666 7999999876554
No 11
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=91.28 E-value=0.094 Score=34.93 Aligned_cols=28 Identities=18% Similarity=0.343 Sum_probs=23.1
Q ss_pred ccCCCCcCCceEEeceeCCccccCCceeEEEe
Q psy15072 21 RECTSEQCGAGVFMAAMSDRHYCGNKFSSLSV 52 (97)
Q Consensus 21 keCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~ 52 (97)
+.||+ ||. .|....++++|..|++++..
T Consensus 1 ~fC~~--Cg~--~l~~~~~~~~C~~C~~~~~~ 28 (104)
T TIGR01384 1 KFCPK--CGS--LMTPKNGVYVCPSCGYEKEK 28 (104)
T ss_pred CCCcc--cCc--ccccCCCeEECcCCCCcccc
Confidence 36998 987 77777889999999988654
No 12
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=91.23 E-value=0.19 Score=29.74 Aligned_cols=35 Identities=17% Similarity=0.294 Sum_probs=26.3
Q ss_pred ecccCCCCcCCceEEece--eCCccccCCceeEEEee
Q psy15072 19 LRRECTSEQCGAGVFMAA--MSDRHYCGNKFSSLSVE 53 (97)
Q Consensus 19 lrkeCP~~eCGaGVFMA~--H~DR~yCGKCg~T~~~~ 53 (97)
..+.||++.|+..+.... ......|.+||+.+.+.
T Consensus 17 ~~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~ 53 (64)
T smart00647 17 DLKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFR 53 (64)
T ss_pred CccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCC
Confidence 457899888999887753 55677898998776543
No 13
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=90.62 E-value=0.18 Score=29.25 Aligned_cols=27 Identities=19% Similarity=0.262 Sum_probs=15.2
Q ss_pred ccCCCCcCCceEEec----eeCCccccCCceeE
Q psy15072 21 RECTSEQCGAGVFMA----AMSDRHYCGNKFSS 49 (97)
Q Consensus 21 keCP~~eCGaGVFMA----~H~DR~yCGKCg~T 49 (97)
|.||. ||.-+-.+ ++..|+.|..||+.
T Consensus 1 kfC~~--CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 1 KFCPQ--CGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp -B-TT--T--B-EEE--TT-SS-EEEETTTTEE
T ss_pred Ccccc--ccChhhhhcCCCCCccceECCCCCCE
Confidence 46888 99865443 45679999999975
No 14
>COG1594 RPB9 DNA-directed RNA polymerase, subunit M/Transcription elongation factor TFIIS [Transcription]
Probab=89.42 E-value=0.44 Score=33.51 Aligned_cols=47 Identities=13% Similarity=0.191 Sum_probs=31.6
Q ss_pred ccCCCCcCCceEEece----eCCccccCCceeEEEeecc---cccccccCCCCceEEE
Q psy15072 21 RECTSEQCGAGVFMAA----MSDRHYCGNKFSSLSVELK---SARSQVRFPPGANFLT 71 (97)
Q Consensus 21 keCP~~eCGaGVFMA~----H~DR~yCGKCg~T~~~~~~---~a~~q~~~p~~~~~l~ 71 (97)
+.||. ||+ .|=. =..+..|.||||.+-...+ .-......|+.+....
T Consensus 3 ~FCp~--Cgs--ll~p~~~~~~~~l~C~kCgye~~~~~~~~~~~~~~~~~~~~~~~~~ 56 (113)
T COG1594 3 RFCPK--CGS--LLYPKKDDEGGKLVCRKCGYEEEASNKKVYRYSVKEAVEKKKEVVL 56 (113)
T ss_pred cccCC--ccC--eeEEeEcCCCcEEECCCCCcchhccccceeEEEEeeccCCcceeee
Confidence 67998 997 5544 2458899999999877753 2223366666665443
No 15
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=89.07 E-value=0.14 Score=27.48 Aligned_cols=23 Identities=30% Similarity=0.579 Sum_probs=17.1
Q ss_pred ccCCCCcCCceEEeceeCCccccCCceeE
Q psy15072 21 RECTSEQCGAGVFMAAMSDRHYCGNKFSS 49 (97)
Q Consensus 21 keCP~~eCGaGVFMA~H~DR~yCGKCg~T 49 (97)
+.||+ ||+. ...+-.+|.+||..
T Consensus 3 ~~Cp~--Cg~~----~~~~~~fC~~CG~~ 25 (26)
T PF13248_consen 3 MFCPN--CGAE----IDPDAKFCPNCGAK 25 (26)
T ss_pred CCCcc--cCCc----CCcccccChhhCCC
Confidence 57998 9982 24567789999963
No 16
>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=88.75 E-value=0.54 Score=27.37 Aligned_cols=29 Identities=21% Similarity=0.347 Sum_probs=19.5
Q ss_pred cCCCCcCCceEEeceeC-CccccCCceeEEEe
Q psy15072 22 ECTSEQCGAGVFMAAMS-DRHYCGNKFSSLSV 52 (97)
Q Consensus 22 eCP~~eCGaGVFMA~H~-DR~yCGKCg~T~~~ 52 (97)
.||. ||+..+.-++. .-..|..||...-.
T Consensus 2 ~Cp~--Cg~~~~~~D~~~g~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 2 KCPN--CGSKEIVFDPERGELVCPNCGLVLEE 31 (43)
T ss_dssp SBTT--TSSSEEEEETTTTEEEETTT-BBEE-
T ss_pred CCcC--CcCCceEEcCCCCeEECCCCCCEeec
Confidence 5998 99977555544 34599999976543
No 17
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=88.59 E-value=0.28 Score=27.19 Aligned_cols=30 Identities=23% Similarity=0.172 Sum_probs=17.2
Q ss_pred ecccCCCCcCCceEEeceeCCccccCCceeEE
Q psy15072 19 LRRECTSEQCGAGVFMAAMSDRHYCGNKFSSL 50 (97)
Q Consensus 19 lrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~ 50 (97)
..+.||+ ||+-...+.-.-...|..||..+
T Consensus 2 ~~rfC~~--CG~~t~~~~~g~~r~C~~Cg~~~ 31 (32)
T PF09297_consen 2 NHRFCGR--CGAPTKPAPGGWARRCPSCGHEH 31 (32)
T ss_dssp TTSB-TT--T--BEEE-SSSS-EEESSSS-EE
T ss_pred CCcccCc--CCccccCCCCcCEeECCCCcCEe
Confidence 3578998 99877766555556788888764
No 18
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=87.59 E-value=0.75 Score=27.05 Aligned_cols=32 Identities=16% Similarity=0.288 Sum_probs=22.3
Q ss_pred cCCCCcCCceEEeceeCCccccCCceeEEEeecc
Q psy15072 22 ECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELK 55 (97)
Q Consensus 22 eCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~~~ 55 (97)
.||+ ||+-+-.-....-..|..||........
T Consensus 5 ~C~~--CG~~~~~~~~~~~~~Cp~CG~~~~~~~~ 36 (46)
T PRK00398 5 KCAR--CGREVELDEYGTGVRCPYCGYRILFKER 36 (46)
T ss_pred ECCC--CCCEEEECCCCCceECCCCCCeEEEccC
Confidence 5888 9985544444446789999987776544
No 19
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=86.78 E-value=0.53 Score=34.76 Aligned_cols=39 Identities=18% Similarity=0.322 Sum_probs=31.7
Q ss_pred EecccCCCCcCCceEEeceeCCccccCCceeEEEeeccccccc
Q psy15072 18 RLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELKSARSQ 60 (97)
Q Consensus 18 rlrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~~~~a~~q 60 (97)
.+...||. ||.=-| .|..+.+|.-||++.......++++
T Consensus 26 ML~~hCp~--Cg~PLF--~KdG~v~CPvC~~~~~~v~~e~~~~ 64 (131)
T COG1645 26 MLAKHCPK--CGTPLF--RKDGEVFCPVCGYREVVVEEEEEEV 64 (131)
T ss_pred HHHhhCcc--cCCcce--eeCCeEECCCCCceEEEeecccccc
Confidence 46678999 998777 5888999999999888877765555
No 20
>KOG0003|consensus
Probab=86.65 E-value=0.097 Score=38.66 Aligned_cols=19 Identities=32% Similarity=0.403 Sum_probs=16.2
Q ss_pred ccccc--ccCCCCceEEEEEe
Q psy15072 56 SARSQ--VRFPPGANFLTFVL 74 (97)
Q Consensus 56 ~a~~q--~~~p~~~~~l~~~~ 74 (97)
+|+.| +++||++++|+|+-
T Consensus 27 KA~i~~~~Gi~~~~~~L~~~~ 47 (128)
T KOG0003|consen 27 KAKIQDKEGIPPDQQRLIFAG 47 (128)
T ss_pred HHHhccccCCCHHHHHHHhcc
Confidence 66666 99999999999974
No 21
>PRK00241 nudC NADH pyrophosphatase; Reviewed
Probab=86.41 E-value=0.46 Score=36.98 Aligned_cols=38 Identities=16% Similarity=0.226 Sum_probs=27.2
Q ss_pred EecccCCCCcCCceEEeceeCCccccCCceeEEEeecccc
Q psy15072 18 RLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELKSA 57 (97)
Q Consensus 18 rlrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~~~~a 57 (97)
+..+.||+ ||.=.......-+..|++|+..++.+...+
T Consensus 97 ~~~~fC~~--CG~~~~~~~~~~~~~C~~c~~~~yp~~~pa 134 (256)
T PRK00241 97 RSHRFCGY--CGHPMHPSKTEWAMLCPHCRERYYPRIAPC 134 (256)
T ss_pred hcCccccc--cCCCCeecCCceeEECCCCCCEECCCCCCE
Confidence 34688999 998655555556779999998776654433
No 22
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=85.91 E-value=0.82 Score=26.25 Aligned_cols=30 Identities=23% Similarity=0.399 Sum_probs=22.7
Q ss_pred cccCCCCcCCceEEeceeCCccccCCceeEEE
Q psy15072 20 RRECTSEQCGAGVFMAAMSDRHYCGNKFSSLS 51 (97)
Q Consensus 20 rkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~ 51 (97)
.+.|+. ||....+-.-.|...|..||.++.
T Consensus 3 ~~~C~~--C~~~~i~~~~~~~~~C~~Cg~~~~ 32 (33)
T PF08792_consen 3 LKKCSK--CGGNGIVNKEDDYEVCIFCGSSFP 32 (33)
T ss_pred ceEcCC--CCCCeEEEecCCeEEcccCCcEee
Confidence 367888 987666645577888999998864
No 23
>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=85.29 E-value=2.9 Score=29.57 Aligned_cols=66 Identities=20% Similarity=0.236 Sum_probs=39.8
Q ss_pred EEEECCCCeEEEecc------cCCCCcCCceEEeceeC-CccccCCceeEEEeecccccccccCCCCceEEEEEecceee
Q psy15072 7 VCNVDENGKIHRLRR------ECTSEQCGAGVFMAAMS-DRHYCGNKFSSLSVELKSARSQVRFPPGANFLTFVLGTASF 79 (97)
Q Consensus 7 yYkVdenGKI~rlrk------eCP~~eCGaGVFMA~H~-DR~yCGKCg~T~~~~~~~a~~q~~~p~~~~~l~~~~~~~~~ 79 (97)
+|.|. |+|..... .||. |..-|. ... ++++|.||+.+. +....+..+-+..+-.
T Consensus 17 ~~~v~--a~I~~I~~~~~~Y~aC~~--C~kkv~--~~~~~~~~C~~C~~~~-------------~~~~~ry~l~~~i~D~ 77 (166)
T cd04476 17 YFTVK--ATIVFIKPDNWWYPACPG--CNKKVV--EEGNGTYRCEKCNKSV-------------PNPEYRYILSLNVADH 77 (166)
T ss_pred EEEEE--EEEEEEcCCCeEEccccc--cCcccE--eCCCCcEECCCCCCcC-------------CCccEEEEEEEEEEeC
Confidence 44443 45555544 4997 987543 334 799999998653 3344555555544444
Q ss_pred eeeeeeEEEecc
Q psy15072 80 LVSYPVLLFDSD 91 (97)
Q Consensus 80 ~~~~~~~~~~~~ 91 (97)
--+..+.+||..
T Consensus 78 Tg~~~~~~F~~~ 89 (166)
T cd04476 78 TGEAWLTLFDEV 89 (166)
T ss_pred CCCEEEEEehHH
Confidence 455667777753
No 24
>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=84.79 E-value=0.94 Score=25.34 Aligned_cols=29 Identities=14% Similarity=0.298 Sum_probs=18.2
Q ss_pred ccCCCCcCCceEEece-----eCCccccCCceeEEE
Q psy15072 21 RECTSEQCGAGVFMAA-----MSDRHYCGNKFSSLS 51 (97)
Q Consensus 21 keCP~~eCGaGVFMA~-----H~DR~yCGKCg~T~~ 51 (97)
-+||+ ||+=..+.. ...+..|++||.++.
T Consensus 3 ~~CP~--C~~~~~v~~~~~~~~~~~v~C~~C~~~~~ 36 (38)
T TIGR02098 3 IQCPN--CKTSFRVVDSQLGANGGKVRCGKCGHVWY 36 (38)
T ss_pred EECCC--CCCEEEeCHHHcCCCCCEEECCCCCCEEE
Confidence 46888 987444432 122468999987653
No 25
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=84.58 E-value=0.63 Score=26.77 Aligned_cols=31 Identities=19% Similarity=0.352 Sum_probs=18.2
Q ss_pred ccCCCCcCCceEEeceeCC-ccccCCceeEEEee
Q psy15072 21 RECTSEQCGAGVFMAAMSD-RHYCGNKFSSLSVE 53 (97)
Q Consensus 21 keCP~~eCGaGVFMA~H~D-R~yCGKCg~T~~~~ 53 (97)
+-||. ||.=-.-.+... +..|-+|+|.+-.+
T Consensus 2 ~FCp~--C~nlL~p~~~~~~~~~C~~C~Y~~~~~ 33 (35)
T PF02150_consen 2 RFCPE--CGNLLYPKEDKEKRVACRTCGYEEPIS 33 (35)
T ss_dssp -BETT--TTSBEEEEEETTTTEEESSSS-EEE-S
T ss_pred eeCCC--CCccceEcCCCccCcCCCCCCCccCCC
Confidence 46887 998444444332 22599999987543
No 26
>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=83.93 E-value=0.59 Score=32.94 Aligned_cols=32 Identities=31% Similarity=0.537 Sum_probs=22.3
Q ss_pred ecccCCCCcCCceEEeceeCCccccCCceeEEEee
Q psy15072 19 LRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVE 53 (97)
Q Consensus 19 lrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~ 53 (97)
.+|.||+ ||+= |---.++--.|-|||.++...
T Consensus 8 tKR~Cp~--CG~k-FYDLnk~PivCP~CG~~~~~~ 39 (108)
T PF09538_consen 8 TKRTCPS--CGAK-FYDLNKDPIVCPKCGTEFPPE 39 (108)
T ss_pred CcccCCC--Ccch-hccCCCCCccCCCCCCccCcc
Confidence 4689998 9983 322223555799999887666
No 27
>KOG0005|consensus
Probab=83.34 E-value=0.23 Score=33.47 Aligned_cols=19 Identities=16% Similarity=0.279 Sum_probs=15.4
Q ss_pred cccccccCCCCceEEEEEe
Q psy15072 56 SARSQVRFPPGANFLTFVL 74 (97)
Q Consensus 56 ~a~~q~~~p~~~~~l~~~~ 74 (97)
..++.++|||-+|+|+|+-
T Consensus 29 rvEEkeGIPp~qqrli~~g 47 (70)
T KOG0005|consen 29 RVEEKEGIPPQQQRLIYAG 47 (70)
T ss_pred HhhhhcCCCchhhhhhhcc
Confidence 3455599999999999973
No 28
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=82.06 E-value=0.98 Score=31.73 Aligned_cols=33 Identities=15% Similarity=0.323 Sum_probs=22.0
Q ss_pred EEecccCCCCcCCceEEeceeCCccccCCceeEEE
Q psy15072 17 HRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLS 51 (97)
Q Consensus 17 ~rlrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~ 51 (97)
.+..-.||. ||.=..=-.-..-|.|.|||+++-
T Consensus 32 ~~~~~~Cp~--C~~~~VkR~a~GIW~C~kCg~~fA 64 (89)
T COG1997 32 QRAKHVCPF--CGRTTVKRIATGIWKCRKCGAKFA 64 (89)
T ss_pred HhcCCcCCC--CCCcceeeeccCeEEcCCCCCeec
Confidence 345567998 987422222235789999999863
No 29
>PRK05978 hypothetical protein; Provisional
Probab=81.02 E-value=0.75 Score=34.22 Aligned_cols=33 Identities=21% Similarity=0.513 Sum_probs=24.6
Q ss_pred ecccCCCCcCCceEEecee-CCccccCCceeEEEee
Q psy15072 19 LRRECTSEQCGAGVFMAAM-SDRHYCGNKFSSLSVE 53 (97)
Q Consensus 19 lrkeCP~~eCGaGVFMA~H-~DR~yCGKCg~T~~~~ 53 (97)
++..||+ ||.|=.+..- +-+..|-.||..+...
T Consensus 32 l~grCP~--CG~G~LF~g~Lkv~~~C~~CG~~~~~~ 65 (148)
T PRK05978 32 FRGRCPA--CGEGKLFRAFLKPVDHCAACGEDFTHH 65 (148)
T ss_pred HcCcCCC--CCCCcccccccccCCCccccCCccccC
Confidence 4667999 9998765543 3477999999877443
No 30
>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=80.46 E-value=0.65 Score=25.49 Aligned_cols=24 Identities=25% Similarity=0.578 Sum_probs=16.8
Q ss_pred ccCCCCcCCceEEeceeCCccccCCceeEE
Q psy15072 21 RECTSEQCGAGVFMAAMSDRHYCGNKFSSL 50 (97)
Q Consensus 21 keCP~~eCGaGVFMA~H~DR~yCGKCg~T~ 50 (97)
|.||. |++-|=.+ -..|-.||+.+
T Consensus 1 K~CP~--C~~~V~~~----~~~Cp~CG~~F 24 (26)
T PF10571_consen 1 KTCPE--CGAEVPES----AKFCPHCGYDF 24 (26)
T ss_pred CcCCC--CcCCchhh----cCcCCCCCCCC
Confidence 57888 99866333 45688888754
No 31
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=80.28 E-value=2 Score=25.96 Aligned_cols=14 Identities=14% Similarity=0.026 Sum_probs=6.4
Q ss_pred CCccccCCceeEEE
Q psy15072 38 SDRHYCGNKFSSLS 51 (97)
Q Consensus 38 ~DR~yCGKCg~T~~ 51 (97)
.|-..|-.||+-..
T Consensus 17 ~~~irC~~CG~rIl 30 (44)
T smart00659 17 KDVVRCRECGYRIL 30 (44)
T ss_pred CCceECCCCCceEE
Confidence 34444555554443
No 32
>PRK09710 lar restriction alleviation and modification protein; Reviewed
Probab=80.15 E-value=1.5 Score=29.09 Aligned_cols=28 Identities=21% Similarity=0.411 Sum_probs=23.8
Q ss_pred cccCCCCcCCceEEeceeCCccc---cCCceeE
Q psy15072 20 RRECTSEQCGAGVFMAAMSDRHY---CGNKFSS 49 (97)
Q Consensus 20 rkeCP~~eCGaGVFMA~H~DR~y---CGKCg~T 49 (97)
-|-||- ||--+....|.++++ |.+|+-.
T Consensus 6 lKPCPF--CG~~~~~v~~~~g~~~v~C~~CgA~ 36 (64)
T PRK09710 6 VKPCPF--CGCPSVTVKAISGYYRAKCNGCESR 36 (64)
T ss_pred ccCCCC--CCCceeEEEecCceEEEEcCCCCcC
Confidence 478999 999999999998776 9999864
No 33
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=79.11 E-value=1 Score=30.40 Aligned_cols=17 Identities=18% Similarity=-0.066 Sum_probs=14.2
Q ss_pred cccCCceeEEEeecccc
Q psy15072 41 HYCGNKFSSLSVELKSA 57 (97)
Q Consensus 41 ~yCGKCg~T~~~~~~~a 57 (97)
.+|-+||||++++++..
T Consensus 41 itCk~CgYtEfY~a~~s 57 (68)
T COG3478 41 ITCKNCGYTEFYSAKIS 57 (68)
T ss_pred EEeccCCchhheecccc
Confidence 48999999999987644
No 34
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=78.32 E-value=4.9 Score=26.97 Aligned_cols=46 Identities=15% Similarity=0.246 Sum_probs=34.5
Q ss_pred eEEEECCCCeEEEecccCCCCcCCceEEeceeC-CccccCCceeEEEee
Q psy15072 6 QVCNVDENGKIHRLRRECTSEQCGAGVFMAAMS-DRHYCGNKFSSLSVE 53 (97)
Q Consensus 6 kyYkVdenGKI~rlrkeCP~~eCGaGVFMA~H~-DR~yCGKCg~T~~~~ 53 (97)
.-|+++.+.+-..++-.||. ||.--..=.|. .+-.|.-||.|+..-
T Consensus 5 ~k~~~p~~p~s~Fl~VkCpd--C~N~q~vFshast~V~C~~CG~~l~~P 51 (67)
T COG2051 5 RKVKIPKEPRSRFLRVKCPD--CGNEQVVFSHASTVVTCLICGTTLAEP 51 (67)
T ss_pred ceeeecCCCCceEEEEECCC--CCCEEEEeccCceEEEecccccEEEec
Confidence 34566545666888999998 99865555676 577999999998654
No 35
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=77.43 E-value=0.7 Score=33.18 Aligned_cols=42 Identities=19% Similarity=0.370 Sum_probs=26.5
Q ss_pred CCCCcCCceEEeceeCCccccCCceeEEEeecccccccccCCCCceEE
Q psy15072 23 CTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELKSARSQVRFPPGANFL 70 (97)
Q Consensus 23 CP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~~~~a~~q~~~p~~~~~l 70 (97)
||. ||.-.-.. |..|..|+.+.--+=..-+-.-+.|++++|+
T Consensus 1 CPv--Cg~~l~vt----~l~C~~C~t~i~G~F~l~~~~~L~~E~~~Fi 42 (113)
T PF09862_consen 1 CPV--CGGELVVT----RLKCPSCGTEIEGEFELPWFARLSPEQLEFI 42 (113)
T ss_pred CCC--CCCceEEE----EEEcCCCCCEEEeeeccchhhcCCHHHHHHH
Confidence 898 99755444 8999999976544333333334555555543
No 36
>TIGR00617 rpa1 replication factor-a protein 1 (rpa1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=77.41 E-value=6.7 Score=34.28 Aligned_cols=69 Identities=17% Similarity=0.202 Sum_probs=42.9
Q ss_pred eEEEECCCCeEEEecc------cCCCCcCCceEEeceeCCccccCCceeEEEeecccccccccCCCCceEEEEEecceee
Q psy15072 6 QVCNVDENGKIHRLRR------ECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELKSARSQVRFPPGANFLTFVLGTASF 79 (97)
Q Consensus 6 kyYkVdenGKI~rlrk------eCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~~~~a~~q~~~p~~~~~l~~~~~~~~~ 79 (97)
.||.|- +.|...+. .||++.|.--|. .+..++|.|-||+.+ +|....+.++-+-..=.
T Consensus 456 ~~f~v~--atI~~Ik~d~~~Y~ACp~~~CnKKV~-~~~~g~~~CekC~~~-------------~~~~~~RYil~~~i~D~ 519 (608)
T TIGR00617 456 DYFSVK--ATISYLKPDNALYRACPSEDCNKKVV-DQGDGTYRCEKCNKN-------------FAEFKYRYILQISISDE 519 (608)
T ss_pred cEEEEE--EEEEEEecCCeEeccCChhhCCCccc-cCCCCCEECCCCCCC-------------CCCccEEEEEEEEEEeC
Confidence 466664 67777664 499877987653 234578999999864 36666676655543333
Q ss_pred eeeeeeEEEec
Q psy15072 80 LVSYPVLLFDS 90 (97)
Q Consensus 80 ~~~~~~~~~~~ 90 (97)
--+.-+.+||.
T Consensus 520 Tg~~~~t~F~~ 530 (608)
T TIGR00617 520 TGQLWVTAFND 530 (608)
T ss_pred CCCEEEEEEhH
Confidence 33344455654
No 37
>PF01907 Ribosomal_L37e: Ribosomal protein L37e; InterPro: IPR001569 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families consists of proteins of 56 to 96 amino-acid residues that share a highly conserved region located in the N-terminal part.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A19_A 4A1D_A 4A18_A 4A1B_A 1S1I_Y 3O5H_d 3IZS_l 3O58_d 2ZKR_2 3IZR_l ....
Probab=77.32 E-value=1.7 Score=28.17 Aligned_cols=26 Identities=15% Similarity=0.318 Sum_probs=19.6
Q ss_pred ecccCCCCcCCceEEeceeCCccccCCceeE
Q psy15072 19 LRRECTSEQCGAGVFMAAMSDRHYCGNKFSS 49 (97)
Q Consensus 19 lrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T 49 (97)
.+-.|.+ ||. .|-|.-..+|++|||.
T Consensus 14 tH~~CrR--CG~---~syH~qK~~CasCGyp 39 (55)
T PF01907_consen 14 THTLCRR--CGR---RSYHIQKKTCASCGYP 39 (55)
T ss_dssp SEEE-TT--TSS---EEEETTTTEETTTBTT
T ss_pred cEeeecc--cCC---eeeecCCCcccccCCC
Confidence 3456888 997 4568889999999974
No 38
>PF11706 zf-CGNR: CGNR zinc finger; InterPro: IPR021005 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 C-terminal zinc finger domain. It seems likely to be DNA-binding given the conservation of many positively charged residues. The domain is named after a highly conserved motif found in many members of the family. ; PDB: 3H0N_A.
Probab=75.15 E-value=0.97 Score=27.52 Aligned_cols=26 Identities=27% Similarity=0.644 Sum_probs=12.6
Q ss_pred ccCCCCcCCceEEe--ceeCCccccC--Cce
Q psy15072 21 RECTSEQCGAGVFM--AAMSDRHYCG--NKF 47 (97)
Q Consensus 21 keCP~~eCGaGVFM--A~H~DR~yCG--KCg 47 (97)
+.|.++.|+ .+|+ +.+..|.+|. .||
T Consensus 3 r~C~~~~C~-~~F~D~sr~~~RrwCsm~~Cg 32 (44)
T PF11706_consen 3 RRCANPDCR-WVFLDTSRNGRRRWCSMERCG 32 (44)
T ss_dssp EE--STT----EEE--SSS-----SS-HHHH
T ss_pred cccCCCCCc-eEEEeCCCCCCceecCccccc
Confidence 679888898 6898 6777888898 676
No 39
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=74.69 E-value=2.9 Score=29.19 Aligned_cols=29 Identities=14% Similarity=0.264 Sum_probs=20.7
Q ss_pred ccCCCCcCCceEEeceeCCccccCCceeEEE
Q psy15072 21 RECTSEQCGAGVFMAAMSDRHYCGNKFSSLS 51 (97)
Q Consensus 21 keCP~~eCGaGVFMA~H~DR~yCGKCg~T~~ 51 (97)
-.||. ||.-.+=-.-..=|.|.+|++++.
T Consensus 36 y~Cp~--Cgk~~vkR~a~GIW~C~~C~~~~A 64 (90)
T PF01780_consen 36 YTCPF--CGKTSVKRVATGIWKCKKCGKKFA 64 (90)
T ss_dssp BEESS--SSSSEEEEEETTEEEETTTTEEEE
T ss_pred CcCCC--CCCceeEEeeeEEeecCCCCCEEe
Confidence 45998 998653333345699999998863
No 40
>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=74.66 E-value=3.4 Score=34.96 Aligned_cols=61 Identities=16% Similarity=0.110 Sum_probs=37.7
Q ss_pred cCCCCcCCceEEeceeC--CccccCCceeEEEeecccccccccCCCCceEE--EEEecce-------eeeeeeeeEEEec
Q psy15072 22 ECTSEQCGAGVFMAAMS--DRHYCGNKFSSLSVELKSARSQVRFPPGANFL--TFVLGTA-------SFLVSYPVLLFDS 90 (97)
Q Consensus 22 eCP~~eCGaGVFMA~H~--DR~yCGKCg~T~~~~~~~a~~q~~~p~~~~~l--~~~~~~~-------~~~~~~~~~~~~~ 90 (97)
.||+ |+. -|..|+ ++..|..||++. +....=|.|...- .+..||- ..+-..||+.+|+
T Consensus 224 ~C~~--C~~--~l~~h~~~~~l~Ch~Cg~~~-------~~~~~Cp~C~s~~l~~~g~Gte~~~e~l~~~fp~~~v~~~d~ 292 (505)
T TIGR00595 224 CCPN--CDV--SLTYHKKEGKLRCHYCGYQE-------PIPKTCPQCGSEDLVYKGYGTEQVEEELAKLFPGARIARIDS 292 (505)
T ss_pred CCCC--CCC--ceEEecCCCeEEcCCCcCcC-------CCCCCCCCCCCCeeEeecccHHHHHHHHHhhCCCCcEEEEec
Confidence 3998 976 788885 577899999864 2234556665532 2333332 1223568888888
Q ss_pred cee
Q psy15072 91 DFT 93 (97)
Q Consensus 91 ~~~ 93 (97)
|-+
T Consensus 293 d~~ 295 (505)
T TIGR00595 293 DTT 295 (505)
T ss_pred ccc
Confidence 854
No 41
>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=74.09 E-value=2.1 Score=26.35 Aligned_cols=39 Identities=23% Similarity=0.308 Sum_probs=25.7
Q ss_pred EEEECCCCeEEEecccCCCCcCCceEEece--eCCccccCCceeEEEee
Q psy15072 7 VCNVDENGKIHRLRRECTSEQCGAGVFMAA--MSDRHYCGNKFSSLSVE 53 (97)
Q Consensus 7 yYkVdenGKI~rlrkeCP~~eCGaGVFMA~--H~DR~yCGKCg~T~~~~ 53 (97)
+-+|++.. .-+.||. ||. .+.. ....+.|-.||++...+
T Consensus 19 v~~v~~~~----TSq~C~~--CG~--~~~~~~~~r~~~C~~Cg~~~~rD 59 (69)
T PF07282_consen 19 VVEVDEAY----TSQTCPR--CGH--RNKKRRSGRVFTCPNCGFEMDRD 59 (69)
T ss_pred EEEECCCC----CccCccC--ccc--ccccccccceEEcCCCCCEECcH
Confidence 34566533 4578998 987 4444 44567999999986443
No 42
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=74.04 E-value=2.5 Score=24.25 Aligned_cols=27 Identities=11% Similarity=0.255 Sum_probs=15.8
Q ss_pred cCCCCcCCceEEecee-----CCccccCCceeEE
Q psy15072 22 ECTSEQCGAGVFMAAM-----SDRHYCGNKFSSL 50 (97)
Q Consensus 22 eCP~~eCGaGVFMA~H-----~DR~yCGKCg~T~ 50 (97)
.||+ |+.-.-..+- .-+..|++|+.++
T Consensus 4 ~CP~--C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPN--CQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred ECCC--CCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 5777 7764444332 2355788887654
No 43
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=73.63 E-value=2.6 Score=32.88 Aligned_cols=31 Identities=16% Similarity=0.274 Sum_probs=23.0
Q ss_pred cccCCCCcCCceEEeceeCCccccCCceeEEEeec
Q psy15072 20 RRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVEL 54 (97)
Q Consensus 20 rkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~~ 54 (97)
.-.|++ ||. .|=.-.+-++|-+||.|+..+-
T Consensus 149 ~A~Csr--C~~--~L~~~~~~l~Cp~Cg~tEkRKi 179 (188)
T COG1096 149 YARCSR--CRA--PLVKKGNMLKCPNCGNTEKRKI 179 (188)
T ss_pred EEEccC--CCc--ceEEcCcEEECCCCCCEEeeee
Confidence 356999 998 4445556779999999986543
No 44
>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=73.14 E-value=2.7 Score=24.77 Aligned_cols=25 Identities=20% Similarity=0.369 Sum_probs=17.4
Q ss_pred ccCCCCcCCc--eEEeceeCCccccCCcee
Q psy15072 21 RECTSEQCGA--GVFMAAMSDRHYCGNKFS 48 (97)
Q Consensus 21 keCP~~eCGa--GVFMA~H~DR~yCGKCg~ 48 (97)
-.||. ||. -..++. ..++.|.+|++
T Consensus 19 ~~CP~--Cg~~~~~~~~~-~~~~~C~~C~~ 45 (46)
T PF12760_consen 19 FVCPH--CGSTKHYRLKT-RGRYRCKACRK 45 (46)
T ss_pred CCCCC--CCCeeeEEeCC-CCeEECCCCCC
Confidence 45999 996 233332 57889999975
No 45
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=72.55 E-value=2.1 Score=31.29 Aligned_cols=27 Identities=15% Similarity=0.300 Sum_probs=20.0
Q ss_pred ccCCCCcCCceEEeceeCCccccCCceeEEEeec
Q psy15072 21 RECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVEL 54 (97)
Q Consensus 21 keCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~~ 54 (97)
+.||. ||. .+...+.|..||++...+.
T Consensus 310 ~~C~~--cg~-----~~~r~~~C~~cg~~~~rD~ 336 (364)
T COG0675 310 KTCPC--CGH-----LSGRLFKCPRCGFVHDRDV 336 (364)
T ss_pred ccccc--cCC-----ccceeEECCCCCCeehhhH
Confidence 77998 997 3344579999998864443
No 46
>PHA02942 putative transposase; Provisional
Probab=72.03 E-value=2.3 Score=35.04 Aligned_cols=30 Identities=20% Similarity=0.377 Sum_probs=21.0
Q ss_pred cccCCCCcCCceEEeceeCCc-cccCCceeEEEee
Q psy15072 20 RRECTSEQCGAGVFMAAMSDR-HYCGNKFSSLSVE 53 (97)
Q Consensus 20 rkeCP~~eCGaGVFMA~H~DR-~yCGKCg~T~~~~ 53 (97)
-+.||. ||. .+....+| +.|..||++...+
T Consensus 325 Sq~Cs~--CG~--~~~~l~~r~f~C~~CG~~~drD 355 (383)
T PHA02942 325 SVSCPK--CGH--KMVEIAHRYFHCPSCGYENDRD 355 (383)
T ss_pred CccCCC--CCC--ccCcCCCCEEECCCCCCEeCcH
Confidence 477998 997 33333445 7899999987444
No 47
>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=71.89 E-value=2.2 Score=23.42 Aligned_cols=24 Identities=29% Similarity=0.361 Sum_probs=15.5
Q ss_pred CCCCcCCceEEeceeCCccccCCcee
Q psy15072 23 CTSEQCGAGVFMAAMSDRHYCGNKFS 48 (97)
Q Consensus 23 CP~~eCGaGVFMA~H~DR~yCGKCg~ 48 (97)
|.+ ||..+-=.++..++.|-+||.
T Consensus 1 C~s--C~~~i~~r~~~v~f~CPnCG~ 24 (24)
T PF07754_consen 1 CTS--CGRPIAPREQAVPFPCPNCGF 24 (24)
T ss_pred Ccc--CCCcccCcccCceEeCCCCCC
Confidence 444 776444344567888988873
No 48
>PF14353 CpXC: CpXC protein
Probab=71.27 E-value=5.7 Score=27.17 Aligned_cols=10 Identities=10% Similarity=0.019 Sum_probs=5.7
Q ss_pred ccccCCceeE
Q psy15072 40 RHYCGNKFSS 49 (97)
Q Consensus 40 R~yCGKCg~T 49 (97)
++.|.+||.+
T Consensus 38 ~~~CP~Cg~~ 47 (128)
T PF14353_consen 38 SFTCPSCGHK 47 (128)
T ss_pred EEECCCCCCc
Confidence 4556666654
No 49
>COG2816 NPY1 NTP pyrophosphohydrolases containing a Zn-finger, probably nucleic-acid-binding [DNA replication, recombination, and repair]
Probab=71.09 E-value=1.7 Score=35.52 Aligned_cols=39 Identities=15% Similarity=0.201 Sum_probs=32.7
Q ss_pred EecccCCCCcCCceEEeceeCCccccCCceeEEEeeccccc
Q psy15072 18 RLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELKSAR 58 (97)
Q Consensus 18 rlrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~~~~a~ 58 (97)
+.+|-||+ ||.=..+..|.....|-+||...+-....+.
T Consensus 109 ~~~RFCg~--CG~~~~~~~~g~~~~C~~cg~~~fPR~dP~v 147 (279)
T COG2816 109 RSHRFCGR--CGTKTYPREGGWARVCPKCGHEHFPRIDPCV 147 (279)
T ss_pred hhCcCCCC--CCCcCccccCceeeeCCCCCCccCCCCCCeE
Confidence 46789999 9999999999999999999988776655443
No 50
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=70.74 E-value=3.8 Score=25.43 Aligned_cols=21 Identities=19% Similarity=0.428 Sum_probs=15.6
Q ss_pred ccCCCCcCCceEEeceeCCccccCCcee
Q psy15072 21 RECTSEQCGAGVFMAAMSDRHYCGNKFS 48 (97)
Q Consensus 21 keCP~~eCGaGVFMA~H~DR~yCGKCg~ 48 (97)
-.||. ||. .+...+.|..||+
T Consensus 27 ~~c~~--cg~-----~~~~H~vc~~cG~ 47 (56)
T PF01783_consen 27 VKCPN--CGE-----PKLPHRVCPSCGY 47 (56)
T ss_dssp EESSS--SSS-----EESTTSBCTTTBB
T ss_pred eeecc--CCC-----EecccEeeCCCCe
Confidence 56998 996 4455678999983
No 51
>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=69.96 E-value=2.7 Score=31.22 Aligned_cols=32 Identities=13% Similarity=0.177 Sum_probs=22.3
Q ss_pred ecccCCCCcCCceEEeceeCCccccCCceeEEEee
Q psy15072 19 LRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVE 53 (97)
Q Consensus 19 lrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~ 53 (97)
.+|.||+ ||.=.+ ---++--.|-|||.++...
T Consensus 8 tKr~Cp~--cg~kFY-DLnk~p~vcP~cg~~~~~~ 39 (129)
T TIGR02300 8 TKRICPN--TGSKFY-DLNRRPAVSPYTGEQFPPE 39 (129)
T ss_pred ccccCCC--cCcccc-ccCCCCccCCCcCCccCcc
Confidence 4689999 998433 2224667899999886444
No 52
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=67.00 E-value=3 Score=23.91 Aligned_cols=21 Identities=29% Similarity=0.347 Sum_probs=8.0
Q ss_pred CCceEEeceeCCccccCCceeE
Q psy15072 28 CGAGVFMAAMSDRHYCGNKFSS 49 (97)
Q Consensus 28 CGaGVFMA~H~DR~yCGKCg~T 49 (97)
||+-+-+. ..|-..|-.||+-
T Consensus 6 Cg~~~~~~-~~~~irC~~CG~R 26 (32)
T PF03604_consen 6 CGAEVELK-PGDPIRCPECGHR 26 (32)
T ss_dssp SSSSE-BS-TSSTSSBSSSS-S
T ss_pred CCCeeEcC-CCCcEECCcCCCe
Confidence 44444322 2334445555543
No 53
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=66.68 E-value=2.8 Score=29.08 Aligned_cols=48 Identities=17% Similarity=0.300 Sum_probs=32.6
Q ss_pred ecccCCCCcCCceEEecee--CCccccCCceeEEEeecccccccccCCCCceEEE
Q psy15072 19 LRRECTSEQCGAGVFMAAM--SDRHYCGNKFSSLSVELKSARSQVRFPPGANFLT 71 (97)
Q Consensus 19 lrkeCP~~eCGaGVFMA~H--~DR~yCGKCg~T~~~~~~~a~~q~~~p~~~~~l~ 71 (97)
.+-.|++ ||.--+.. | ++| .|.+||..+..+......+..+| ..++.+
T Consensus 41 ~~~~C~~--Cg~~~~~~-~SCk~R-~CP~C~~~~~~~W~~~~~~~ll~-~~y~Hv 90 (111)
T PF14319_consen 41 HRYRCED--CGHEKIVY-NSCKNR-HCPSCQAKATEQWIEKQREDLLP-VPYFHV 90 (111)
T ss_pred ceeecCC--CCceEEec-CcccCc-CCCCCCChHHHHHHHHHHhhCCC-CCeEEE
Confidence 4467998 99855443 4 367 89999987766666655556655 766654
No 54
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=66.56 E-value=2.1 Score=26.38 Aligned_cols=18 Identities=28% Similarity=0.265 Sum_probs=12.0
Q ss_pred eeCCccccCCceeEEEee
Q psy15072 36 AMSDRHYCGNKFSSLSVE 53 (97)
Q Consensus 36 ~H~DR~yCGKCg~T~~~~ 53 (97)
.+..|+.|++||-+.+..
T Consensus 44 ~~~~r~FC~~CGs~l~~~ 61 (92)
T PF04828_consen 44 KGVERYFCPTCGSPLFSE 61 (92)
T ss_dssp SSCEEEEETTT--EEEEE
T ss_pred CcCcCcccCCCCCeeecc
Confidence 445688999999887754
No 55
>PF14347 DUF4399: Domain of unknown function (DUF4399)
Probab=66.50 E-value=6.1 Score=26.74 Aligned_cols=26 Identities=27% Similarity=0.517 Sum_probs=21.4
Q ss_pred ecccccccccCCCCceEEEEEeccee
Q psy15072 53 ELKSARSQVRFPPGANFLTFVLGTAS 78 (97)
Q Consensus 53 ~~~~a~~q~~~p~~~~~l~~~~~~~~ 78 (97)
++..++.++..|||+|+|+..+|-+.
T Consensus 49 ~~Gqte~~I~L~PG~htLtl~~~d~~ 74 (87)
T PF14347_consen 49 GKGQTELNIELPPGKHTLTLQLGDGD 74 (87)
T ss_pred CCCEEEEEEEeCCCCEEEEEEeCCCC
Confidence 56677788999999999999887543
No 56
>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=66.12 E-value=5 Score=24.10 Aligned_cols=27 Identities=26% Similarity=0.545 Sum_probs=20.2
Q ss_pred EecccCCCCcCCceEEeceeCCccccCCce
Q psy15072 18 RLRRECTSEQCGAGVFMAAMSDRHYCGNKF 47 (97)
Q Consensus 18 rlrkeCP~~eCGaGVFMA~H~DR~yCGKCg 47 (97)
-+...||. || ...|-++..+.+|-.|+
T Consensus 15 ML~~~Cp~--C~-~PL~~~k~g~~~Cv~C~ 41 (41)
T PF06677_consen 15 MLDEHCPD--CG-TPLMRDKDGKIYCVSCG 41 (41)
T ss_pred HhcCccCC--CC-CeeEEecCCCEECCCCC
Confidence 35678997 97 46666677788998884
No 57
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=64.67 E-value=4.3 Score=24.91 Aligned_cols=26 Identities=19% Similarity=0.208 Sum_probs=16.8
Q ss_pred ccccCCceeEEEeecccccccccCCCCc
Q psy15072 40 RHYCGNKFSSLSVELKSARSQVRFPPGA 67 (97)
Q Consensus 40 R~yCGKCg~T~~~~~~~a~~q~~~p~~~ 67 (97)
|+.|..||+.|..+....+ .+||||.
T Consensus 1 ky~C~~CgyvYd~~~Gd~~--~~i~pGt 26 (47)
T PF00301_consen 1 KYQCPVCGYVYDPEKGDPE--NGIPPGT 26 (47)
T ss_dssp EEEETTTSBEEETTTBBGG--GTB-TT-
T ss_pred CcCCCCCCEEEcCCcCCcc--cCcCCCC
Confidence 6789999988866655443 4556653
No 58
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=64.63 E-value=4.5 Score=25.09 Aligned_cols=27 Identities=15% Similarity=0.124 Sum_probs=18.0
Q ss_pred ccccCCceeEEEeecccccccccCCCCce
Q psy15072 40 RHYCGNKFSSLSVELKSARSQVRFPPGAN 68 (97)
Q Consensus 40 R~yCGKCg~T~~~~~~~a~~q~~~p~~~~ 68 (97)
|+.|.-|||.|..++... ..++|||..
T Consensus 1 ~y~C~~CgyiYd~~~Gd~--~~~i~pGt~ 27 (50)
T cd00730 1 KYECRICGYIYDPAEGDP--DEGIPPGTP 27 (50)
T ss_pred CcCCCCCCeEECCCCCCc--ccCcCCCCC
Confidence 578999998886555443 345666654
No 59
>PF12773 DZR: Double zinc ribbon
Probab=64.54 E-value=4.4 Score=23.54 Aligned_cols=28 Identities=18% Similarity=0.342 Sum_probs=17.0
Q ss_pred ecccCCCCcCCceEEeceeCCccccCCceeE
Q psy15072 19 LRRECTSEQCGAGVFMAAMSDRHYCGNKFSS 49 (97)
Q Consensus 19 lrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T 49 (97)
..+.||. ||.-+. .......+|.+||..
T Consensus 11 ~~~fC~~--CG~~l~-~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 11 DAKFCPH--CGTPLP-PPDQSKKICPNCGAE 38 (50)
T ss_pred cccCChh--hcCChh-hccCCCCCCcCCcCC
Confidence 3567877 876433 233445678888764
No 60
>PRK00420 hypothetical protein; Validated
Probab=64.28 E-value=5.5 Score=28.52 Aligned_cols=33 Identities=18% Similarity=0.349 Sum_probs=24.4
Q ss_pred ecccCCCCcCCceEEeceeCCccccCCceeEEEeec
Q psy15072 19 LRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVEL 54 (97)
Q Consensus 19 lrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~~ 54 (97)
+...||. ||. -++.......+|-.||..+....
T Consensus 22 l~~~CP~--Cg~-pLf~lk~g~~~Cp~Cg~~~~v~~ 54 (112)
T PRK00420 22 LSKHCPV--CGL-PLFELKDGEVVCPVHGKVYIVKS 54 (112)
T ss_pred ccCCCCC--CCC-cceecCCCceECCCCCCeeeecc
Confidence 5678999 996 44444677889999998666543
No 61
>PRK05580 primosome assembly protein PriA; Validated
Probab=63.91 E-value=9.7 Score=33.39 Aligned_cols=61 Identities=20% Similarity=0.220 Sum_probs=35.2
Q ss_pred cCCCCcCCceEEeceeCC--ccccCCceeEEEeecccccccccCCCCceEEEEEeccee---------eeeeeeeEEEec
Q psy15072 22 ECTSEQCGAGVFMAAMSD--RHYCGNKFSSLSVELKSARSQVRFPPGANFLTFVLGTAS---------FLVSYPVLLFDS 90 (97)
Q Consensus 22 eCP~~eCGaGVFMA~H~D--R~yCGKCg~T~~~~~~~a~~q~~~p~~~~~l~~~~~~~~---------~~~~~~~~~~~~ 90 (97)
.||+ |+. -|..|++ +..|-.||+++. ....=|.|...-+...|... .+-.++|+.+|+
T Consensus 392 ~C~~--C~~--~l~~h~~~~~l~Ch~Cg~~~~-------~~~~Cp~Cg~~~l~~~g~G~e~~~e~l~~~fp~~~v~~~~~ 460 (679)
T PRK05580 392 ECPH--CDA--SLTLHRFQRRLRCHHCGYQEP-------IPKACPECGSTDLVPVGPGTERLEEELAELFPEARILRIDR 460 (679)
T ss_pred CCCC--CCC--ceeEECCCCeEECCCCcCCCC-------CCCCCCCCcCCeeEEeeccHHHHHHHHHHhCCCCcEEEEec
Confidence 5888 876 7788864 456888887642 22345666444333332211 122467778887
Q ss_pred cee
Q psy15072 91 DFT 93 (97)
Q Consensus 91 ~~~ 93 (97)
|-+
T Consensus 461 d~~ 463 (679)
T PRK05580 461 DTT 463 (679)
T ss_pred ccc
Confidence 753
No 62
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=63.15 E-value=3.5 Score=23.65 Aligned_cols=11 Identities=9% Similarity=0.135 Sum_probs=6.7
Q ss_pred ccccCCceeEE
Q psy15072 40 RHYCGNKFSSL 50 (97)
Q Consensus 40 R~yCGKCg~T~ 50 (97)
+..|++|+.++
T Consensus 25 ~v~C~~C~~~f 35 (36)
T PF13717_consen 25 KVRCSKCGHVF 35 (36)
T ss_pred EEECCCCCCEe
Confidence 35677776553
No 63
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=62.91 E-value=5.1 Score=28.02 Aligned_cols=31 Identities=13% Similarity=0.265 Sum_probs=20.7
Q ss_pred ecccCCCCcCCceEEeceeCCccccCCceeEEE
Q psy15072 19 LRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLS 51 (97)
Q Consensus 19 lrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~ 51 (97)
..-.||. ||..-+=-.-..=|.|.+|++++.
T Consensus 34 a~y~Cpf--Cgk~~vkR~a~GIW~C~~C~~~~A 64 (91)
T TIGR00280 34 AKYVCPF--CGKKTVKRGSTGIWTCRKCGAKFA 64 (91)
T ss_pred cCccCCC--CCCCceEEEeeEEEEcCCCCCEEe
Confidence 4456998 986433333334589999999863
No 64
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=62.54 E-value=5.3 Score=27.86 Aligned_cols=31 Identities=13% Similarity=0.249 Sum_probs=21.1
Q ss_pred ecccCCCCcCCceEEeceeCCccccCCceeEEE
Q psy15072 19 LRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLS 51 (97)
Q Consensus 19 lrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~ 51 (97)
..-.||. ||..-+=-.-..=|.|.+|++++.
T Consensus 35 a~y~Cpf--Cgk~~vkR~a~GIW~C~~C~~~~A 65 (90)
T PRK03976 35 AKHVCPV--CGRPKVKRVGTGIWECRKCGAKFA 65 (90)
T ss_pred cCccCCC--CCCCceEEEEEEEEEcCCCCCEEe
Confidence 3456998 976444333345589999999863
No 65
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=62.00 E-value=7.1 Score=20.99 Aligned_cols=25 Identities=16% Similarity=0.333 Sum_probs=13.2
Q ss_pred ccCCCCcCCceEEeceeCCcc--ccCCce
Q psy15072 21 RECTSEQCGAGVFMAAMSDRH--YCGNKF 47 (97)
Q Consensus 21 keCP~~eCGaGVFMA~H~DR~--yCGKCg 47 (97)
+.||+ |+.=+-...+..|+ +|.+|-
T Consensus 2 ~~C~r--C~~~~~~~~~~~r~~~~C~rCq 28 (30)
T PF06827_consen 2 EKCPR--CWNYIEDIGINGRSTYLCPRCQ 28 (30)
T ss_dssp SB-TT--T--BBEEEEETTEEEEE-TTTC
T ss_pred CcCcc--CCCcceEeEecCCCCeECcCCc
Confidence 46888 88755555555554 787773
No 66
>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=60.56 E-value=5.5 Score=23.09 Aligned_cols=26 Identities=19% Similarity=0.471 Sum_probs=19.9
Q ss_pred ccCCCCcCCceEEeceeCCccccCCceeE
Q psy15072 21 RECTSEQCGAGVFMAAMSDRHYCGNKFSS 49 (97)
Q Consensus 21 keCP~~eCGaGVFMA~H~DR~yCGKCg~T 49 (97)
..|+. ||+= +...-..++||-+||..
T Consensus 9 ~~C~~--C~~~-~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 9 EPCPV--CGSR-WFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred CcCCC--CCCe-EeEccCCEEEhhhCceE
Confidence 45998 9975 66666679999999953
No 67
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=60.44 E-value=12 Score=34.09 Aligned_cols=63 Identities=17% Similarity=0.155 Sum_probs=42.0
Q ss_pred ccCCCCcCCceEEeceeCCc--cccCCceeEEEeecccccccccCCCCceE--EEEEecc-------eeeeeeeeeEEEe
Q psy15072 21 RECTSEQCGAGVFMAAMSDR--HYCGNKFSSLSVELKSARSQVRFPPGANF--LTFVLGT-------ASFLVSYPVLLFD 89 (97)
Q Consensus 21 keCP~~eCGaGVFMA~H~DR--~yCGKCg~T~~~~~~~a~~q~~~p~~~~~--l~~~~~~-------~~~~~~~~~~~~~ 89 (97)
-+||+ |.. -|.-|+++ ..|--||+.+ +.-..=|.|... -.+..|| ..++=.+||+-||
T Consensus 445 ~~Cp~--Cd~--~lt~H~~~~~L~CH~Cg~~~-------~~p~~Cp~Cgs~~L~~~G~GterieeeL~~~FP~~rv~r~d 513 (730)
T COG1198 445 AECPN--CDS--PLTLHKATGQLRCHYCGYQE-------PIPQSCPECGSEHLRAVGPGTERIEEELKRLFPGARIIRID 513 (730)
T ss_pred ccCCC--CCc--ceEEecCCCeeEeCCCCCCC-------CCCCCCCCCCCCeeEEecccHHHHHHHHHHHCCCCcEEEEc
Confidence 35888 876 78888754 4788888742 223445666554 3444554 3567789999999
Q ss_pred cceee
Q psy15072 90 SDFTF 94 (97)
Q Consensus 90 ~~~~~ 94 (97)
+|-|-
T Consensus 514 ~Dtt~ 518 (730)
T COG1198 514 SDTTR 518 (730)
T ss_pred ccccc
Confidence 99763
No 68
>TIGR03683 A-tRNA_syn_arch alanyl-tRNA synthetase. This family of alanyl-tRNA synthetases is limited to the archaea, and is a subset of those sequences identified by the model pfam07973 covering the second additional domain (SAD) of alanyl and threonyl tRNA synthetases.
Probab=60.13 E-value=4.5 Score=37.20 Aligned_cols=27 Identities=30% Similarity=0.680 Sum_probs=22.6
Q ss_pred EecccCCCCcCCceEEeceeCCccccCC--ce
Q psy15072 18 RLRRECTSEQCGAGVFMAAMSDRHYCGN--KF 47 (97)
Q Consensus 18 rlrkeCP~~eCGaGVFMA~H~DR~yCGK--Cg 47 (97)
-.|+.||. ||.. |-..+.+|.+||- |-
T Consensus 14 ~~r~~c~~--c~~~-fwt~~~~r~~cgd~~c~ 42 (902)
T TIGR03683 14 FVRKQCQV--CGSY-FWTLDPERETCGDAPCD 42 (902)
T ss_pred ceEeECcc--cCCc-cccCCCCcCCCCCCCCc
Confidence 45799999 9974 8888889999997 65
No 69
>PRK01103 formamidopyrimidine/5-formyluracil/ 5-hydroxymethyluracil DNA glycosylase; Validated
Probab=59.94 E-value=7.1 Score=30.37 Aligned_cols=27 Identities=19% Similarity=0.468 Sum_probs=20.5
Q ss_pred cccCCCCcCCceEEeceeCCc--cccCCcee
Q psy15072 20 RRECTSEQCGAGVFMAAMSDR--HYCGNKFS 48 (97)
Q Consensus 20 rkeCP~~eCGaGVFMA~H~DR--~yCGKCg~ 48 (97)
.+.||+ ||.-+-.....+| +||.+|..
T Consensus 245 g~pC~~--Cg~~I~~~~~~gR~t~~CP~CQ~ 273 (274)
T PRK01103 245 GEPCRR--CGTPIEKIKQGGRSTFFCPRCQK 273 (274)
T ss_pred CCCCCC--CCCeeEEEEECCCCcEECcCCCC
Confidence 467998 9988877777766 58988853
No 70
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=59.75 E-value=6.2 Score=27.51 Aligned_cols=32 Identities=13% Similarity=0.232 Sum_probs=20.7
Q ss_pred EecccCCCCcCCceEEeceeCCccccCCceeEEE
Q psy15072 18 RLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLS 51 (97)
Q Consensus 18 rlrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~ 51 (97)
+..-.||. ||..-+=-.-..=|.|.+|++++.
T Consensus 34 ~a~y~Cpf--Cgk~~vkR~a~GIW~C~~C~~~~A 65 (90)
T PTZ00255 34 HAKYFCPF--CGKHAVKRQAVGIWRCKGCKKTVA 65 (90)
T ss_pred hCCccCCC--CCCCceeeeeeEEEEcCCCCCEEe
Confidence 34456998 986333222234589999999863
No 71
>PF09788 Tmemb_55A: Transmembrane protein 55A; InterPro: IPR019178 Members of this family catalyse the hydrolysis of the 4-position phosphate of phosphatidylinositol 4,5-bisphosphate, in the reaction: 1-phosphatidyl-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 5-phosphate + phosphate.
Probab=59.56 E-value=11 Score=30.60 Aligned_cols=54 Identities=19% Similarity=0.291 Sum_probs=36.5
Q ss_pred eEEEecccCCCCcCCceEEecee--------------CCccccCCceeEEEeecccccccccCCCCce
Q psy15072 15 KIHRLRRECTSEQCGAGVFMAAM--------------SDRHYCGNKFSSLSVELKSARSQVRFPPGAN 68 (97)
Q Consensus 15 KI~rlrkeCP~~eCGaGVFMA~H--------------~DR~yCGKCg~T~~~~~~~a~~q~~~p~~~~ 68 (97)
|++-.|-.|||+.|..=+-++.- .-|..||.|..|+.++.-...+--+=|-|+.
T Consensus 118 k~sS~rIaCPRp~CkRiI~L~~~~~~p~~~~~~~~p~~~rv~CghC~~~Fl~~~~~~~tlARCPHCrK 185 (256)
T PF09788_consen 118 KSSSQRIACPRPNCKRIINLGPSHQGPVTPPVPTQPGSCRVICGHCSNTFLFNTLTSNTLARCPHCRK 185 (256)
T ss_pred ecccccccCCCCCCcceEEeCCccCCCCCCCCCCCCCceeEECCCCCCcEeccCCCCCccccCCCCce
Confidence 44567888999999653333221 2588999999999988655344456666653
No 72
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=59.33 E-value=4.6 Score=21.37 Aligned_cols=21 Identities=33% Similarity=0.795 Sum_probs=13.6
Q ss_pred cCCCCcCCceEEeceeCCccccCCcee
Q psy15072 22 ECTSEQCGAGVFMAAMSDRHYCGNKFS 48 (97)
Q Consensus 22 eCP~~eCGaGVFMA~H~DR~yCGKCg~ 48 (97)
.||+ ||+.+ . .+-..|.+||.
T Consensus 1 ~Cp~--CG~~~--~--~~~~fC~~CG~ 21 (23)
T PF13240_consen 1 YCPN--CGAEI--E--DDAKFCPNCGT 21 (23)
T ss_pred CCcc--cCCCC--C--CcCcchhhhCC
Confidence 4787 88744 1 34556888875
No 73
>PRK14810 formamidopyrimidine-DNA glycosylase; Provisional
Probab=58.66 E-value=8.2 Score=30.20 Aligned_cols=27 Identities=22% Similarity=0.538 Sum_probs=20.7
Q ss_pred ecccCCCCcCCceEEeceeCCc--cccCCce
Q psy15072 19 LRRECTSEQCGAGVFMAAMSDR--HYCGNKF 47 (97)
Q Consensus 19 lrkeCP~~eCGaGVFMA~H~DR--~yCGKCg 47 (97)
..+.||+ ||.-+-.....+| +||.+|.
T Consensus 243 ~g~pCpr--CG~~I~~~~~~gR~t~~CP~CQ 271 (272)
T PRK14810 243 TGEPCLN--CKTPIRRVVVAGRSSHYCPHCQ 271 (272)
T ss_pred CCCcCCC--CCCeeEEEEECCCccEECcCCc
Confidence 3468999 9988877777766 5899984
No 74
>KOG1865|consensus
Probab=58.01 E-value=6 Score=35.21 Aligned_cols=36 Identities=25% Similarity=0.255 Sum_probs=28.5
Q ss_pred CCccccCCceeEEEeecccccccccCCCCceEEEEEeccee
Q psy15072 38 SDRHYCGNKFSSLSVELKSARSQVRFPPGANFLTFVLGTAS 78 (97)
Q Consensus 38 ~DR~yCGKCg~T~~~~~~~a~~q~~~p~~~~~l~~~~~~~~ 78 (97)
.|.+.|+||- ++.+|+-|..|-...|+||++|==.+
T Consensus 284 en~Y~C~~Ck-----~~v~A~K~lti~raPnVLTi~LKRF~ 319 (545)
T KOG1865|consen 284 ENAYHCGRCK-----QKVPASKQLTIHRAPNVLTLHLKRFS 319 (545)
T ss_pred ccccccchhh-----hhCcccceeeeecCCceEEEeeehhc
Confidence 4789999994 45588888888888899999984433
No 75
>cd01793 Fubi Fubi ubiquitin-like protein. Fubi is a ubiquitin-like protein encoded by the fau gene which has an N-terminal ubiquitin-like domain (also referred to as FUBI) fused to the ribosomal protein S30. Fubi is thought to be a tumor suppressor protein and the FUBI domain may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8.
Probab=57.73 E-value=3.6 Score=25.63 Aligned_cols=18 Identities=6% Similarity=-0.031 Sum_probs=14.2
Q ss_pred cccccccCCCCceEEEEE
Q psy15072 56 SARSQVRFPPGANFLTFV 73 (97)
Q Consensus 56 ~a~~q~~~p~~~~~l~~~ 73 (97)
+..++.++|+++|+|+|.
T Consensus 27 ~i~~~~gip~~~q~Li~~ 44 (74)
T cd01793 27 HVAGLEGIDVEDQVLLLA 44 (74)
T ss_pred HHHhhhCCCHHHEEEEEC
Confidence 334447899999999986
No 76
>PRK14811 formamidopyrimidine-DNA glycosylase; Provisional
Probab=57.54 E-value=8.7 Score=30.06 Aligned_cols=26 Identities=23% Similarity=0.625 Sum_probs=21.0
Q ss_pred cccCCCCcCCceEEeceeCCc--cccCCce
Q psy15072 20 RRECTSEQCGAGVFMAAMSDR--HYCGNKF 47 (97)
Q Consensus 20 rkeCP~~eCGaGVFMA~H~DR--~yCGKCg 47 (97)
.+.||+ ||.-+-.....+| +||-+|.
T Consensus 235 g~pC~~--Cg~~I~~~~~~gR~ty~Cp~CQ 262 (269)
T PRK14811 235 GQPCPR--CGTPIEKIVVGGRGTHFCPQCQ 262 (269)
T ss_pred cCCCCc--CCCeeEEEEECCCCcEECCCCc
Confidence 467999 9998888877766 5899995
No 77
>PRK13902 alaS alanyl-tRNA synthetase; Provisional
Probab=57.35 E-value=5.8 Score=36.50 Aligned_cols=30 Identities=40% Similarity=0.784 Sum_probs=24.0
Q ss_pred CCCeEEEecccCCCCcCCceEEeceeCCccccCC--ce
Q psy15072 12 ENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGN--KF 47 (97)
Q Consensus 12 enGKI~rlrkeCP~~eCGaGVFMA~H~DR~yCGK--Cg 47 (97)
++| -.|+.||. ||. -|-..+.+|-+||- |-
T Consensus 14 ~~g---~~r~~c~~--cg~-~fwt~~~~r~~cgd~pc~ 45 (900)
T PRK13902 14 ENG---FERKQCKK--CGS-YFWTLDPDRETCGDAPCD 45 (900)
T ss_pred hCC---ceEeECCc--cCC-ceecCCCCcCCCCCCCCc
Confidence 455 45799999 996 57788899999997 65
No 78
>PRK10445 endonuclease VIII; Provisional
Probab=56.93 E-value=9 Score=29.82 Aligned_cols=26 Identities=23% Similarity=0.523 Sum_probs=19.4
Q ss_pred cccCCCCcCCceEEeceeCCc--cccCCce
Q psy15072 20 RRECTSEQCGAGVFMAAMSDR--HYCGNKF 47 (97)
Q Consensus 20 rkeCP~~eCGaGVFMA~H~DR--~yCGKCg 47 (97)
.+.||+ ||.-+-.....+| ++|-+|.
T Consensus 235 g~~Cp~--Cg~~I~~~~~~gR~t~~CP~CQ 262 (263)
T PRK10445 235 GEACER--CGGIIEKTTLSSRPFYWCPGCQ 262 (263)
T ss_pred CCCCCC--CCCEeEEEEECCCCcEECCCCc
Confidence 467888 9887777777765 4788884
No 79
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=56.60 E-value=6.4 Score=24.93 Aligned_cols=22 Identities=23% Similarity=0.350 Sum_probs=14.7
Q ss_pred cccCCCCcCCceEEeceeCCccccCCcee
Q psy15072 20 RRECTSEQCGAGVFMAAMSDRHYCGNKFS 48 (97)
Q Consensus 20 rkeCP~~eCGaGVFMA~H~DR~yCGKCg~ 48 (97)
--.||. ||. + +..-+.|..||+
T Consensus 27 l~~C~~--CG~--~---~~~H~vC~~CG~ 48 (57)
T PRK12286 27 LVECPN--CGE--P---KLPHRVCPSCGY 48 (57)
T ss_pred ceECCC--CCC--c---cCCeEECCCCCc
Confidence 356998 997 2 333457888884
No 80
>KOG0006|consensus
Probab=56.33 E-value=3.2 Score=35.77 Aligned_cols=33 Identities=21% Similarity=0.352 Sum_probs=24.9
Q ss_pred ccCCCCcCCceEEeceeCCccccCC-ceeEEEee
Q psy15072 21 RECTSEQCGAGVFMAAMSDRHYCGN-KFSSLSVE 53 (97)
Q Consensus 21 keCP~~eCGaGVFMA~H~DR~yCGK-Cg~T~~~~ 53 (97)
--||++.||+|.+--.-.-+.+|-. ||+.+..+
T Consensus 316 VlCP~pgCG~gll~EPD~rkvtC~~gCgf~FCR~ 349 (446)
T KOG0006|consen 316 VLCPRPGCGAGLLPEPDQRKVTCEGGCGFAFCRE 349 (446)
T ss_pred EecCCCCCCcccccCCCCCcccCCCCchhHhHHH
Confidence 4699999999988776555668866 88766544
No 81
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=56.30 E-value=7.8 Score=37.76 Aligned_cols=16 Identities=38% Similarity=0.910 Sum_probs=12.1
Q ss_pred EEEecccCCCCcCCceEE
Q psy15072 16 IHRLRRECTSEQCGAGVF 33 (97)
Q Consensus 16 I~rlrkeCP~~eCGaGVF 33 (97)
|+.-++.||+ ||.-++
T Consensus 663 VEV~~rkCPk--CG~~t~ 678 (1337)
T PRK14714 663 VEVGRRRCPS--CGTETY 678 (1337)
T ss_pred EEEEEEECCC--CCCccc
Confidence 5667889998 997543
No 82
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=55.79 E-value=6.6 Score=26.00 Aligned_cols=34 Identities=21% Similarity=0.236 Sum_probs=19.5
Q ss_pred ccCCCCcCCceEEeceeCCccccCCceeEEEeeccc
Q psy15072 21 RECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELKS 56 (97)
Q Consensus 21 keCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~~~~ 56 (97)
..|.+ ||.++--.++.-.+.|-+||.++...-++
T Consensus 10 ~~CtS--Cg~~i~p~e~~v~F~CPnCGe~~I~Rc~~ 43 (61)
T COG2888 10 PVCTS--CGREIAPGETAVKFPCPNCGEVEIYRCAK 43 (61)
T ss_pred ceecc--CCCEeccCCceeEeeCCCCCceeeehhhh
Confidence 45666 66655555566666666666555444333
No 83
>PRK14873 primosome assembly protein PriA; Provisional
Probab=55.77 E-value=10 Score=33.68 Aligned_cols=58 Identities=19% Similarity=0.275 Sum_probs=33.3
Q ss_pred cCCCCcCCceEEeceeCC--ccccCCceeEEEeecccccccccCCCCce--EEEEEecce-------eeeeeeeeEEEec
Q psy15072 22 ECTSEQCGAGVFMAAMSD--RHYCGNKFSSLSVELKSARSQVRFPPGAN--FLTFVLGTA-------SFLVSYPVLLFDS 90 (97)
Q Consensus 22 eCP~~eCGaGVFMA~H~D--R~yCGKCg~T~~~~~~~a~~q~~~p~~~~--~l~~~~~~~-------~~~~~~~~~~~~~ 90 (97)
.||+ |+. -|.-|++ +..|-.||++. ....=|.|.. +..+..||- ..+-..||+.+|+
T Consensus 394 ~C~~--C~~--~L~~h~~~~~l~Ch~CG~~~--------~p~~Cp~Cgs~~l~~~g~Gter~eeeL~~~FP~~~V~r~d~ 461 (665)
T PRK14873 394 RCRH--CTG--PLGLPSAGGTPRCRWCGRAA--------PDWRCPRCGSDRLRAVVVGARRTAEELGRAFPGVPVVTSGG 461 (665)
T ss_pred ECCC--CCC--ceeEecCCCeeECCCCcCCC--------cCccCCCCcCCcceeeeccHHHHHHHHHHHCCCCCEEEECh
Confidence 4888 865 7888864 56888888742 1234566654 333344431 1222456666666
Q ss_pred c
Q psy15072 91 D 91 (97)
Q Consensus 91 ~ 91 (97)
|
T Consensus 462 d 462 (665)
T PRK14873 462 D 462 (665)
T ss_pred H
Confidence 6
No 84
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=54.93 E-value=12 Score=25.66 Aligned_cols=31 Identities=26% Similarity=0.455 Sum_probs=20.6
Q ss_pred EEecccCCCCcCCceEEeceeC----CccccCCceeEEE
Q psy15072 17 HRLRRECTSEQCGAGVFMAAMS----DRHYCGNKFSSLS 51 (97)
Q Consensus 17 ~rlrkeCP~~eCGaGVFMA~H~----DR~yCGKCg~T~~ 51 (97)
.+-.-.|+. ||..+ ..|. .++.||+|+-.+.
T Consensus 120 ~~~~~~C~~--C~~~~--~r~~~~~~~~~~C~~C~~~l~ 154 (157)
T PF10263_consen 120 KKYVYRCPS--CGREY--KRHRRSKRKRYRCGRCGGPLV 154 (157)
T ss_pred cceEEEcCC--CCCEe--eeecccchhhEECCCCCCEEE
Confidence 456778987 98644 2333 3668999996654
No 85
>COG3677 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=54.77 E-value=10 Score=27.08 Aligned_cols=39 Identities=23% Similarity=0.350 Sum_probs=27.2
Q ss_pred ecccCCCCcCCceE------EeceeCCccccCCceeEEEeeccccccc
Q psy15072 19 LRRECTSEQCGAGV------FMAAMSDRHYCGNKFSSLSVELKSARSQ 60 (97)
Q Consensus 19 lrkeCP~~eCGaGV------FMA~H~DR~yCGKCg~T~~~~~~~a~~q 60 (97)
....||. |++.- +++. .-|+.|-.|+.|+..+-....++
T Consensus 29 ~~~~cP~--C~s~~~~k~g~~~~~-~qRyrC~~C~~tf~~~~~~~~~~ 73 (129)
T COG3677 29 TKVNCPR--CKSSNVVKIGGIRRG-HQRYKCKSCGSTFTVETGSPLSK 73 (129)
T ss_pred ccCcCCC--CCccceeeECCcccc-ccccccCCcCcceeeeccCcccc
Confidence 4567999 98732 2222 46999999999988776655554
No 86
>cd01794 DC_UbP_C dendritic cell derived ubiquitin-like protein. DC_UbP (dendritic cell derived ubiquitin-like protein) is a ubiquitin-like protein from human dendritic cells that is expressed in the mitochondrion. The ubiquitin-like domain of this protein is found at the C-terminus and lacks the canonical gly-gly motif of ubiquitin required for ubiquitinization. DC_UbP is expressed in tumor cells but not in normal human adult tissue suggesting a role for DC_UbP in tumorogenesis.
Probab=54.54 E-value=3.2 Score=26.26 Aligned_cols=17 Identities=12% Similarity=0.089 Sum_probs=13.8
Q ss_pred ccccccCCCCceEEEEE
Q psy15072 57 ARSQVRFPPGANFLTFV 73 (97)
Q Consensus 57 a~~q~~~p~~~~~l~~~ 73 (97)
..+++++|+.+|+|+|+
T Consensus 28 I~~~~gi~~~~q~Li~~ 44 (70)
T cd01794 28 LQAAEGVDPCCQRWFFS 44 (70)
T ss_pred HHHHhCCCHHHeEEEEC
Confidence 33457899999999986
No 87
>PRK13945 formamidopyrimidine-DNA glycosylase; Provisional
Probab=54.26 E-value=10 Score=29.71 Aligned_cols=26 Identities=27% Similarity=0.681 Sum_probs=20.2
Q ss_pred cccCCCCcCCceEEeceeCCc--cccCCce
Q psy15072 20 RRECTSEQCGAGVFMAAMSDR--HYCGNKF 47 (97)
Q Consensus 20 rkeCP~~eCGaGVFMA~H~DR--~yCGKCg 47 (97)
.+.||+ ||.-+-......| +||.+|.
T Consensus 254 g~pC~~--Cg~~I~~~~~~gR~t~~CP~CQ 281 (282)
T PRK13945 254 GKPCRK--CGTPIERIKLAGRSTHWCPNCQ 281 (282)
T ss_pred cCCCCc--CCCeeEEEEECCCccEECCCCc
Confidence 467998 9988877777766 4888884
No 88
>COG3809 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=54.26 E-value=11 Score=26.59 Aligned_cols=33 Identities=21% Similarity=0.316 Sum_probs=24.8
Q ss_pred ccCCCCcCCceEEeceeCC--ccccCCceeEEEeecc
Q psy15072 21 RECTSEQCGAGVFMAAMSD--RHYCGNKFSSLSVELK 55 (97)
Q Consensus 21 keCP~~eCGaGVFMA~H~D--R~yCGKCg~T~~~~~~ 55 (97)
..||. ||+...|..-.+ --||.+|.=...-.++
T Consensus 2 llCP~--C~v~l~~~~rs~vEiD~CPrCrGVWLDrGE 36 (88)
T COG3809 2 LLCPI--CGVELVMSVRSGVEIDYCPRCRGVWLDRGE 36 (88)
T ss_pred cccCc--CCceeeeeeecCceeeeCCccccEeecchh
Confidence 36999 999999998775 3499999866544443
No 89
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=54.21 E-value=11 Score=21.79 Aligned_cols=28 Identities=29% Similarity=0.604 Sum_probs=14.7
Q ss_pred cccCCCCcCCceEEecee---CCccccCCceeEE
Q psy15072 20 RRECTSEQCGAGVFMAAM---SDRHYCGNKFSSL 50 (97)
Q Consensus 20 rkeCP~~eCGaGVFMA~H---~DR~yCGKCg~T~ 50 (97)
|+.||+ ||. +|=-.. +.-..|-+||-.+
T Consensus 1 Rr~C~~--Cg~-~Yh~~~~pP~~~~~Cd~cg~~L 31 (36)
T PF05191_consen 1 RRICPK--CGR-IYHIEFNPPKVEGVCDNCGGEL 31 (36)
T ss_dssp EEEETT--TTE-EEETTTB--SSTTBCTTTTEBE
T ss_pred CcCcCC--CCC-ccccccCCCCCCCccCCCCCee
Confidence 567777 775 321111 1345677777543
No 90
>PF14949 ARF7EP_C: ARF7 effector protein C-terminus
Probab=54.07 E-value=9.7 Score=26.99 Aligned_cols=33 Identities=27% Similarity=0.592 Sum_probs=22.3
Q ss_pred EECCCCeEEEeccc---CCCCcCCceEEeceeCCccccCCceeE
Q psy15072 9 NVDENGKIHRLRRE---CTSEQCGAGVFMAAMSDRHYCGNKFSS 49 (97)
Q Consensus 9 kVdenGKI~rlrke---CP~~eCGaGVFMA~H~DR~yCGKCg~T 49 (97)
.-|++|.+...... |-+++| +|+|.. |.|||.+
T Consensus 48 ~YD~~G~l~~~~~DlCDCL~~~C-~GC~~P-------C~~C~S~ 83 (103)
T PF14949_consen 48 HYDEKGRLISNGKDLCDCLDEDC-PGCHYP-------CPKCGSR 83 (103)
T ss_pred cccCCceEeeCCCccccccCCCC-CCcccc-------CCCCCCC
Confidence 34778877766654 667666 488765 7777754
No 91
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=54.06 E-value=8.3 Score=30.44 Aligned_cols=33 Identities=21% Similarity=0.334 Sum_probs=24.1
Q ss_pred eEEEecccCCCCcCCceEEeceeC------------CccccCCceeEE
Q psy15072 15 KIHRLRRECTSEQCGAGVFMAAMS------------DRHYCGNKFSSL 50 (97)
Q Consensus 15 KI~rlrkeCP~~eCGaGVFMA~H~------------DR~yCGKCg~T~ 50 (97)
.+.-.+-+||. ||. .+++... --+.|-+|||..
T Consensus 9 ~~~~~~~~CPv--Cg~-~l~~~~~~~~IPyFG~V~i~t~~C~~CgYR~ 53 (201)
T COG1779 9 EEFETRIDCPV--CGG-TLKAHMYLYDIPYFGEVLISTGVCERCGYRS 53 (201)
T ss_pred eeeeeeecCCc--ccc-eeeEEEeeecCCccceEEEEEEEccccCCcc
Confidence 45567789999 997 7776542 246899999864
No 92
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=53.78 E-value=4.9 Score=29.84 Aligned_cols=34 Identities=21% Similarity=0.322 Sum_probs=24.7
Q ss_pred ecccCCCCcCCceEE-eceeCCccccCCceeEEEeec
Q psy15072 19 LRRECTSEQCGAGVF-MAAMSDRHYCGNKFSSLSVEL 54 (97)
Q Consensus 19 lrkeCP~~eCGaGVF-MA~H~DR~yCGKCg~T~~~~~ 54 (97)
++-.||+ ||.|=. =+--+-+-.|.-||+.|-+..
T Consensus 20 l~grCP~--CGeGrLF~gFLK~~p~C~aCG~dyg~~~ 54 (126)
T COG5349 20 LRGRCPR--CGEGRLFRGFLKVVPACEACGLDYGFAD 54 (126)
T ss_pred hcCCCCC--CCCchhhhhhcccCchhhhccccccCCc
Confidence 5677999 999853 233356778999998876543
No 93
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=53.58 E-value=6.7 Score=21.84 Aligned_cols=14 Identities=14% Similarity=-0.088 Sum_probs=11.0
Q ss_pred ccccCCceeEEEee
Q psy15072 40 RHYCGNKFSSLSVE 53 (97)
Q Consensus 40 R~yCGKCg~T~~~~ 53 (97)
+|.|..||+++.-.
T Consensus 1 ~~~C~~CGy~y~~~ 14 (33)
T cd00350 1 KYVCPVCGYIYDGE 14 (33)
T ss_pred CEECCCCCCEECCC
Confidence 57899999998543
No 94
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=53.33 E-value=16 Score=26.96 Aligned_cols=43 Identities=19% Similarity=0.216 Sum_probs=28.4
Q ss_pred EEEECCCCeEEEecccCCCCcCCceEEeceeCCcc-ccCCceeEEEeec
Q psy15072 7 VCNVDENGKIHRLRRECTSEQCGAGVFMAAMSDRH-YCGNKFSSLSVEL 54 (97)
Q Consensus 7 yYkVdenGKI~rlrkeCP~~eCGaGVFMA~H~DR~-yCGKCg~T~~~~~ 54 (97)
.|+..| +|..-.-.|-+ ||.-+-+- |.++. -|-+||.++|...
T Consensus 101 ~Y~sGE--~~g~G~l~C~~--Cg~~~~~~-~~~~l~~Cp~C~~~~F~R~ 144 (146)
T PF07295_consen 101 VYHSGE--VVGPGTLVCEN--CGHEVELT-HPERLPPCPKCGHTEFTRQ 144 (146)
T ss_pred CeecCc--EecCceEeccc--CCCEEEec-CCCcCCCCCCCCCCeeeeC
Confidence 354443 44455556887 98877664 56655 7999998887654
No 95
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=53.12 E-value=14 Score=26.55 Aligned_cols=37 Identities=27% Similarity=0.472 Sum_probs=24.9
Q ss_pred ceEEEECCCCeEEEecccCCCCcCCceEEeceeCCccccCCceeE
Q psy15072 5 WQVCNVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSS 49 (97)
Q Consensus 5 LkyYkVdenGKI~rlrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T 49 (97)
.++|+--+.||+. ...|++ ||. + .|-.|.+|-+|+..
T Consensus 16 ~~f~~~l~~~kl~--g~kC~~--CG~-v---~~PPr~~Cp~C~~~ 52 (140)
T COG1545 16 SKFFKGLKEGKLL--GTKCKK--CGR-V---YFPPRAYCPKCGSE 52 (140)
T ss_pred hHHhhhhhhCcEE--EEEcCC--CCe-E---EcCCcccCCCCCCC
Confidence 4455433346654 478998 997 3 24569999999865
No 96
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=53.01 E-value=15 Score=31.03 Aligned_cols=38 Identities=26% Similarity=0.585 Sum_probs=17.9
Q ss_pred ccCCCCcC-CceEEeceeCCccccCCceeEEEeecccccccccCCCC
Q psy15072 21 RECTSEQC-GAGVFMAAMSDRHYCGNKFSSLSVELKSARSQVRFPPG 66 (97)
Q Consensus 21 keCP~~eC-GaGVFMA~H~DR~yCGKCg~T~~~~~~~a~~q~~~p~~ 66 (97)
..||. | |.|... ...|.+|+=.-. ..+....++.||++
T Consensus 184 ~~C~~--C~G~G~~i-----~~pC~~C~G~G~-v~~~~~i~V~IPaG 222 (371)
T COG0484 184 QTCPT--CNGTGKII-----KDPCGKCKGKGR-VKKKKSISVNIPAG 222 (371)
T ss_pred EECCC--CccceeEC-----CCCCCCCCCCCe-EeeeeEEEEECCCC
Confidence 45665 6 444433 445666653322 11222334666664
No 97
>TIGR00577 fpg formamidopyrimidine-DNA glycosylase (fpg). All proteins in the FPG family with known functions are FAPY-DNA glycosylases that function in base excision repair. Homologous to endonuclease VIII (nei). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=51.64 E-value=13 Score=29.09 Aligned_cols=25 Identities=24% Similarity=0.659 Sum_probs=19.7
Q ss_pred cccCCCCcCCceEEeceeCCc--cccCCc
Q psy15072 20 RRECTSEQCGAGVFMAAMSDR--HYCGNK 46 (97)
Q Consensus 20 rkeCP~~eCGaGVFMA~H~DR--~yCGKC 46 (97)
.+.||+ ||.-+-.....+| +||.+|
T Consensus 245 g~pC~~--Cg~~I~~~~~~gR~t~~CP~C 271 (272)
T TIGR00577 245 GEPCRR--CGTPIEKIKVGGRGTHFCPQC 271 (272)
T ss_pred CCCCCC--CCCeeEEEEECCCCCEECCCC
Confidence 457998 9988887777766 488888
No 98
>PRK12366 replication factor A; Reviewed
Probab=51.58 E-value=26 Score=30.81 Aligned_cols=25 Identities=12% Similarity=0.230 Sum_probs=19.3
Q ss_pred ccCCCCcCCceEEeceeCCccccCCceeE
Q psy15072 21 RECTSEQCGAGVFMAAMSDRHYCGNKFSS 49 (97)
Q Consensus 21 keCP~~eCGaGVFMA~H~DR~yCGKCg~T 49 (97)
..||. |.-= |.+..+.|+|-+|+.+
T Consensus 533 ~aCp~--CnkK--v~~~~g~~~C~~c~~~ 557 (637)
T PRK12366 533 YLCPN--CRKR--VEEVDGEYICEFCGEV 557 (637)
T ss_pred ecccc--cCeE--eEcCCCcEECCCCCCC
Confidence 45997 9884 4456788999999964
No 99
>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=50.69 E-value=7.7 Score=23.22 Aligned_cols=14 Identities=36% Similarity=0.907 Sum_probs=9.4
Q ss_pred ccCCCCcCCceEEece
Q psy15072 21 RECTSEQCGAGVFMAA 36 (97)
Q Consensus 21 keCP~~eCGaGVFMA~ 36 (97)
.-||. ||.||...-
T Consensus 2 hlcpk--cgvgvl~pv 15 (36)
T PF09151_consen 2 HLCPK--CGVGVLEPV 15 (36)
T ss_dssp -B-TT--TSSSBEEEE
T ss_pred ccCCc--cCceEEEEe
Confidence 35998 999997653
No 100
>KOG0466|consensus
Probab=50.04 E-value=12 Score=32.54 Aligned_cols=36 Identities=25% Similarity=0.394 Sum_probs=25.0
Q ss_pred CCeEEEec-ccCCCCcCCceEEeceeCCccccCCceeE
Q psy15072 13 NGKIHRLR-RECTSEQCGAGVFMAAMSDRHYCGNKFSS 49 (97)
Q Consensus 13 nGKI~rlr-keCP~~eCGaGVFMA~H~DR~yCGKCg~T 49 (97)
|-||-+.. .+||+|.|-. -|=..-.||..|-+||.+
T Consensus 82 NAKIYkc~~~kCprP~cy~-s~gS~k~d~~~c~~~g~~ 118 (466)
T KOG0466|consen 82 NAKIYKCDDPKCPRPGCYR-SFGSSKEDRPPCDRPGCE 118 (466)
T ss_pred cceEEecCCCCCCCcchhh-ccCCCCCCCCCcccCCCC
Confidence 44554433 4899999854 244466799999999965
No 101
>PF05129 Elf1: Transcription elongation factor Elf1 like; InterPro: IPR007808 This family of uncharacterised, mostly short, proteins contain a putative zinc binding domain with four conserved cysteines.; PDB: 1WII_A.
Probab=49.95 E-value=12 Score=25.01 Aligned_cols=32 Identities=16% Similarity=0.274 Sum_probs=15.8
Q ss_pred cCCCCcCC----ceEEecee--CCccccCCceeEEEeecc
Q psy15072 22 ECTSEQCG----AGVFMAAM--SDRHYCGNKFSSLSVELK 55 (97)
Q Consensus 22 eCP~~eCG----aGVFMA~H--~DR~yCGKCg~T~~~~~~ 55 (97)
.||. || ..|=|-.- .-...|+.||+.+..+..
T Consensus 24 ~CPf--C~~~~sV~v~idkk~~~~~~~C~~Cg~~~~~~i~ 61 (81)
T PF05129_consen 24 DCPF--CNHEKSVSVKIDKKEGIGILSCRVCGESFQTKIN 61 (81)
T ss_dssp --TT--T--SS-EEEEEETTTTEEEEEESSS--EEEEE--
T ss_pred cCCc--CCCCCeEEEEEEccCCEEEEEecCCCCeEEEccC
Confidence 5999 99 34544211 135689999998866543
No 102
>cd01796 DDI1_N DNA damage inducible protein 1 ubiquitin-like domain. DDI1_N DDI1 (DNA damage inducible protein 1) has an amino-terminal ubiquitin-like domain, an retroviral protease-like (RVP-like) domain, and a UBA (ubiquitin-associated) domain. This CD represents the amino-terminal ubiquitin-like domain of DDI1.
Probab=49.51 E-value=5.2 Score=24.99 Aligned_cols=19 Identities=11% Similarity=0.155 Sum_probs=14.6
Q ss_pred cccccccCCCCceEEEEEe
Q psy15072 56 SARSQVRFPPGANFLTFVL 74 (97)
Q Consensus 56 ~a~~q~~~p~~~~~l~~~~ 74 (97)
...++.++|+++|+|+|.-
T Consensus 28 ~I~~~~gip~~~q~Li~~G 46 (71)
T cd01796 28 LCEAESGIPASQQQLIYNG 46 (71)
T ss_pred HHHHHhCCCHHHeEEEECC
Confidence 3334478999999999973
No 103
>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=49.08 E-value=20 Score=20.79 Aligned_cols=28 Identities=18% Similarity=0.428 Sum_probs=15.3
Q ss_pred ccCCCCcCCceEEeceeCCcc----ccCC---ceeEEEe
Q psy15072 21 RECTSEQCGAGVFMAAMSDRH----YCGN---KFSSLSV 52 (97)
Q Consensus 21 keCP~~eCGaGVFMA~H~DR~----yCGK---Cg~T~~~ 52 (97)
+.||. ||. .|-.-..|. .|-. |.+|+..
T Consensus 2 ~~CP~--Cg~--~lv~r~~k~g~F~~Cs~yP~C~~~~~~ 36 (39)
T PF01396_consen 2 EKCPK--CGG--PLVLRRGKKGKFLGCSNYPECKYTEPL 36 (39)
T ss_pred cCCCC--CCc--eeEEEECCCCCEEECCCCCCcCCeEeC
Confidence 56887 884 444433332 4544 6666544
No 104
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=48.45 E-value=12 Score=28.17 Aligned_cols=17 Identities=47% Similarity=0.900 Sum_probs=14.4
Q ss_pred CCCeEEEecccCCCCcCCc
Q psy15072 12 ENGKIHRLRRECTSEQCGA 30 (97)
Q Consensus 12 enGKI~rlrkeCP~~eCGa 30 (97)
++|...|-||+|++ ||.
T Consensus 20 ~dg~~IRRRReC~~--C~~ 36 (147)
T TIGR00244 20 EDGQSIRRRRECLE--CHE 36 (147)
T ss_pred CCCCeeeecccCCc--cCC
Confidence 47888888999998 885
No 105
>smart00214 VWC von Willebrand factor (vWF) type C domain.
Probab=47.52 E-value=26 Score=21.15 Aligned_cols=32 Identities=16% Similarity=0.269 Sum_probs=21.7
Q ss_pred CCe-EEEecccCCCC-cCCceEEeceeCCccccCCc
Q psy15072 13 NGK-IHRLRRECTSE-QCGAGVFMAAMSDRHYCGNK 46 (97)
Q Consensus 13 nGK-I~rlrkeCP~~-eCGaGVFMA~H~DR~yCGKC 46 (97)
+|+ |.-.+..||.. .|..++. ...+..=|.+|
T Consensus 26 ~g~~v~C~~~~Cp~~~~C~~~~~--~~~~g~CCp~C 59 (59)
T smart00214 26 DGETVLCDPVECPPPPDCPNPER--VKPPGECCPRC 59 (59)
T ss_pred CCCEEEeeeecCCCCCCCCCCcc--cCCCCCcCCCC
Confidence 577 99999999885 7988776 23334444443
No 106
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=47.22 E-value=12 Score=26.63 Aligned_cols=17 Identities=6% Similarity=-0.193 Sum_probs=13.5
Q ss_pred CccccCCceeEEEeecc
Q psy15072 39 DRHYCGNKFSSLSVELK 55 (97)
Q Consensus 39 DR~yCGKCg~T~~~~~~ 55 (97)
.-+.|.+||..|+....
T Consensus 123 ~f~~C~~C~kiyW~GsH 139 (147)
T PF01927_consen 123 EFWRCPGCGKIYWEGSH 139 (147)
T ss_pred eEEECCCCCCEeccccc
Confidence 36789999999987644
No 107
>PRK04351 hypothetical protein; Provisional
Probab=45.82 E-value=21 Score=26.17 Aligned_cols=32 Identities=28% Similarity=0.614 Sum_probs=20.4
Q ss_pred ecccCCCCcCCceEEece--e-CCccccCCceeEEEee
Q psy15072 19 LRRECTSEQCGAGVFMAA--M-SDRHYCGNKFSSLSVE 53 (97)
Q Consensus 19 lrkeCP~~eCGaGVFMA~--H-~DR~yCGKCg~T~~~~ 53 (97)
-.-.|.+ ||.- +... | ..|+.||+|+-.+...
T Consensus 111 y~Y~C~~--Cg~~-~~r~Rr~n~~~yrCg~C~g~L~~~ 145 (149)
T PRK04351 111 YLYECQS--CGQQ-YLRKRRINTKRYRCGKCRGKLKLI 145 (149)
T ss_pred EEEECCC--CCCE-eeeeeecCCCcEEeCCCCcEeeec
Confidence 3456877 9863 3221 1 2679999999766543
No 108
>COG1571 Predicted DNA-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=45.82 E-value=14 Score=31.83 Aligned_cols=49 Identities=22% Similarity=0.367 Sum_probs=30.2
Q ss_pred EEecccCCCCcCCceEEeceeC-CccccCCceeEEEeecccccc---c--ccCCCCceE
Q psy15072 17 HRLRRECTSEQCGAGVFMAAMS-DRHYCGNKFSSLSVELKSARS---Q--VRFPPGANF 69 (97)
Q Consensus 17 ~rlrkeCP~~eCGaGVFMA~H~-DR~yCGKCg~T~~~~~~~a~~---q--~~~p~~~~~ 69 (97)
++.+-.||+ ||. -|-+-. +-+-|-|||+++-........ | +-.||++.+
T Consensus 347 ~~~~p~Cp~--Cg~--~m~S~G~~g~rC~kCg~~~~~~~~~~v~r~l~~g~evp~~arR 401 (421)
T COG1571 347 ERVNPVCPR--CGG--RMKSAGRNGFRCKKCGTRARETLIKEVPRDLEPGVEVPPVARR 401 (421)
T ss_pred EEcCCCCCc--cCC--chhhcCCCCcccccccccCCcccccccccccCCCCcCCchhhh
Confidence 445567999 986 454433 378999999987655443111 1 235776654
No 109
>PRK11827 hypothetical protein; Provisional
Probab=44.98 E-value=17 Score=23.55 Aligned_cols=31 Identities=10% Similarity=0.300 Sum_probs=22.1
Q ss_pred cCCCCcCCceEEeceeCCccccCCceeEEEeec
Q psy15072 22 ECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVEL 54 (97)
Q Consensus 22 eCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~~ 54 (97)
.||. |..-...-...+...|..|++.|-...
T Consensus 10 aCP~--ckg~L~~~~~~~~Lic~~~~laYPI~d 40 (60)
T PRK11827 10 ACPV--CNGKLWYNQEKQELICKLDNLAFPLRD 40 (60)
T ss_pred ECCC--CCCcCeEcCCCCeEECCccCeeccccC
Confidence 4998 875555444456789999999886544
No 110
>PRK14290 chaperone protein DnaJ; Provisional
Probab=44.84 E-value=32 Score=27.87 Aligned_cols=8 Identities=13% Similarity=0.127 Sum_probs=4.7
Q ss_pred ccccCCce
Q psy15072 40 RHYCGNKF 47 (97)
Q Consensus 40 R~yCGKCg 47 (97)
+..|.+|+
T Consensus 205 ~~~C~~C~ 212 (365)
T PRK14290 205 EEKCPRCN 212 (365)
T ss_pred cCCCCCCC
Confidence 44566665
No 111
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=44.20 E-value=17 Score=25.28 Aligned_cols=27 Identities=11% Similarity=0.257 Sum_probs=17.3
Q ss_pred EecccCCCCcCCceEEeceeCCccccCCcee
Q psy15072 18 RLRRECTSEQCGAGVFMAAMSDRHYCGNKFS 48 (97)
Q Consensus 18 rlrkeCP~~eCGaGVFMA~H~DR~yCGKCg~ 48 (97)
..+-.|++ ||. ..+....++.|.+||.
T Consensus 68 p~~~~C~~--Cg~--~~~~~~~~~~CP~Cgs 94 (113)
T PRK12380 68 PAQAWCWD--CSQ--VVEIHQHDAQCPHCHG 94 (113)
T ss_pred CcEEEccc--CCC--EEecCCcCccCcCCCC
Confidence 34567988 985 3333334556999994
No 112
>KOG2906|consensus
Probab=43.96 E-value=28 Score=25.23 Aligned_cols=32 Identities=16% Similarity=0.384 Sum_probs=24.9
Q ss_pred cCCCCcCCceEEeceeC--CccccCCceeEEEeecc
Q psy15072 22 ECTSEQCGAGVFMAAMS--DRHYCGNKFSSLSVELK 55 (97)
Q Consensus 22 eCP~~eCGaGVFMA~H~--DR~yCGKCg~T~~~~~~ 55 (97)
-||. ||.......-. +|..|.-|.|.+-+..+
T Consensus 3 FCP~--Cgn~Live~g~~~~rf~C~tCpY~~~I~~e 36 (105)
T KOG2906|consen 3 FCPT--CGNMLIVESGESCNRFSCRTCPYVFPISRE 36 (105)
T ss_pred ccCC--CCCEEEEecCCeEeeEEcCCCCceeeEeee
Confidence 5998 99977776554 68999999998766643
No 113
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=43.62 E-value=16 Score=25.38 Aligned_cols=27 Identities=15% Similarity=0.485 Sum_probs=17.0
Q ss_pred EecccCCCCcCCceEEeceeCCc-cccCCcee
Q psy15072 18 RLRRECTSEQCGAGVFMAAMSDR-HYCGNKFS 48 (97)
Q Consensus 18 rlrkeCP~~eCGaGVFMA~H~DR-~yCGKCg~ 48 (97)
..+-.|++ ||. +......+ ..|.+||.
T Consensus 68 p~~~~C~~--Cg~--~~~~~~~~~~~CP~Cgs 95 (114)
T PRK03681 68 EAECWCET--CQQ--YVTLLTQRVRRCPQCHG 95 (114)
T ss_pred CcEEEccc--CCC--eeecCCccCCcCcCcCC
Confidence 34567988 986 43333333 55999984
No 114
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=43.51 E-value=19 Score=23.48 Aligned_cols=34 Identities=18% Similarity=0.290 Sum_probs=26.0
Q ss_pred EEecccCCCCcCCceEEeceeCCc-cccCCceeEEEe
Q psy15072 17 HRLRRECTSEQCGAGVFMAAMSDR-HYCGNKFSSLSV 52 (97)
Q Consensus 17 ~rlrkeCP~~eCGaGVFMA~H~DR-~yCGKCg~T~~~ 52 (97)
..++-.||. |+.-...=+|... -.|..||.++..
T Consensus 8 ~F~~VkCp~--C~n~q~vFsha~t~V~C~~Cg~~L~~ 42 (59)
T PRK00415 8 RFLKVKCPD--CGNEQVVFSHASTVVRCLVCGKTLAE 42 (59)
T ss_pred eEEEEECCC--CCCeEEEEecCCcEEECcccCCCccc
Confidence 445678998 9987766688764 599999988753
No 115
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=43.30 E-value=16 Score=23.94 Aligned_cols=38 Identities=24% Similarity=0.380 Sum_probs=21.0
Q ss_pred ccCCCCcCCceEEeceeCCccccCCceeEEEeeccccccc
Q psy15072 21 RECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELKSARSQ 60 (97)
Q Consensus 21 keCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~~~~a~~q 60 (97)
..|.+ ||..+---+|.-++.|-.||.++...=++-+.|
T Consensus 8 ~~CtS--Cg~~i~~~~~~~~F~CPnCG~~~I~RC~~CRk~ 45 (59)
T PRK14890 8 PKCTS--CGIEIAPREKAVKFLCPNCGEVIIYRCEKCRKQ 45 (59)
T ss_pred ccccC--CCCcccCCCccCEeeCCCCCCeeEeechhHHhc
Confidence 45666 766443335566777777776644444433333
No 116
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=43.10 E-value=19 Score=28.59 Aligned_cols=30 Identities=13% Similarity=0.320 Sum_probs=21.2
Q ss_pred ccCCCCcCCceEEeceeC-CccccCCceeEEEe
Q psy15072 21 RECTSEQCGAGVFMAAMS-DRHYCGNKFSSLSV 52 (97)
Q Consensus 21 keCP~~eCGaGVFMA~H~-DR~yCGKCg~T~~~ 52 (97)
..||. ||..-+.-++. .-..|+.||+....
T Consensus 12 ~~Cp~--Cg~~~iv~d~~~Ge~vC~~CG~Vl~e 42 (310)
T PRK00423 12 LVCPE--CGSDKLIYDYERGEIVCADCGLVIEE 42 (310)
T ss_pred CcCcC--CCCCCeeEECCCCeEeecccCCcccc
Confidence 57997 99755555553 45689999986543
No 117
>PF00093 VWC: von Willebrand factor type C domain; InterPro: IPR001007 The vWF domain is found in various plasma proteins: complement factors B, C2, CR3 and CR4; the integrins (I-domains); collagen types VI, VII, XII and XIV; and other extracellular proteins [, , ]. Although the majority of VWA-containing proteins are extracellular, the most ancient ones present in all eukaryotes are all intracellular proteins involved in functions such as transcription, DNA repair, ribosomal and membrane transport and the proteasome. A common feature appears to be involvement in multiprotein complexes. Proteins that incorporate vWF domains participate in numerous biological events (e.g. cell adhesion, migration, homing, pattern formation, and signal transduction), involving interaction with a large array of ligands []. A number of human diseases arise from mutations in VWA domains. Secondary structure prediction from 75 aligned vWF sequences has revealed a largely alternating sequence of alpha-helices and beta-strands []. The domain is named after the von Willebrand factor (VWF) type C repeat which is found in multidomain protein/multifunctional proteins involved in maintaining homeostasis [, ]. For the von Willebrand factor the duplicated VWFC domain is thought to participate in oligomerization, but not in the initial dimerization step []. The presence of this region in a number of other complex-forming proteins points to the possible involvment of the VWFC domain in complex formation.; GO: 0005515 protein binding; PDB: 1U5M_A.
Probab=42.95 E-value=24 Score=21.22 Aligned_cols=19 Identities=21% Similarity=0.564 Sum_probs=11.0
Q ss_pred CCeEEEecccCCCCcCCce
Q psy15072 13 NGKIHRLRRECTSEQCGAG 31 (97)
Q Consensus 13 nGKI~rlrkeCP~~eCGaG 31 (97)
+|+|.-.+..||..+|..+
T Consensus 26 ~G~v~C~~~~Cp~~~C~~~ 44 (57)
T PF00093_consen 26 DGEVQCSRIQCPPLDCPNP 44 (57)
T ss_dssp TTEEEEEE---S-SS-S--
T ss_pred CCEEEEcCCCCcCCCCCCC
Confidence 6999999999998889987
No 118
>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=42.85 E-value=18 Score=34.70 Aligned_cols=26 Identities=23% Similarity=0.432 Sum_probs=21.0
Q ss_pred eEEEecccCCCCcCCceEEeceeCCccccCCcee
Q psy15072 15 KIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFS 48 (97)
Q Consensus 15 KI~rlrkeCP~~eCGaGVFMA~H~DR~yCGKCg~ 48 (97)
+|+.-++.||+ ||.=.| ...|-+||-
T Consensus 620 ~vev~~RKCPk--CG~yTl------k~rCP~CG~ 645 (1095)
T TIGR00354 620 EVEIAIRKCPQ--CGKESF------WLKCPVCGE 645 (1095)
T ss_pred EEEEEEEECCC--CCcccc------cccCCCCCC
Confidence 67888999998 997444 667999993
No 119
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=42.71 E-value=20 Score=22.49 Aligned_cols=28 Identities=18% Similarity=0.241 Sum_probs=11.6
Q ss_pred ccCCceeEEEeecccccccccCCCCceEEE
Q psy15072 42 YCGNKFSSLSVELKSARSQVRFPPGANFLT 71 (97)
Q Consensus 42 yCGKCg~T~~~~~~~a~~q~~~p~~~~~l~ 71 (97)
-|.+||... +..+....++=|-|.++++
T Consensus 8 ~C~~Cg~~~--~~~~~~~~irCp~Cg~rIl 35 (49)
T COG1996 8 KCARCGREV--ELDQETRGIRCPYCGSRIL 35 (49)
T ss_pred EhhhcCCee--ehhhccCceeCCCCCcEEE
Confidence 355555433 2222333344454444443
No 120
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=42.44 E-value=15 Score=22.96 Aligned_cols=21 Identities=24% Similarity=0.515 Sum_probs=13.6
Q ss_pred ccCCCCcCCceEEeceeCCccccCCcee
Q psy15072 21 RECTSEQCGAGVFMAAMSDRHYCGNKFS 48 (97)
Q Consensus 21 keCP~~eCGaGVFMA~H~DR~yCGKCg~ 48 (97)
-.||. ||. ++-. -+.|..||+
T Consensus 27 ~~C~~--cG~--~~~~---H~vc~~cG~ 47 (55)
T TIGR01031 27 VVCPN--CGE--FKLP---HRVCPSCGY 47 (55)
T ss_pred eECCC--CCC--cccC---eeECCccCe
Confidence 45998 997 3333 356888873
No 121
>PRK10996 thioredoxin 2; Provisional
Probab=41.93 E-value=11 Score=26.06 Aligned_cols=30 Identities=30% Similarity=0.362 Sum_probs=21.0
Q ss_pred ccCCCCcCCceEEec--eeCCccccCCceeEEEe
Q psy15072 21 RECTSEQCGAGVFMA--AMSDRHYCGNKFSSLSV 52 (97)
Q Consensus 21 keCP~~eCGaGVFMA--~H~DR~yCGKCg~T~~~ 52 (97)
..||+ |.+---++ .|.+|-.||.|+-.++.
T Consensus 3 ~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~ 34 (139)
T PRK10996 3 TVCTS--CQAINRLPDERIEDAAKCGRCGHDLFD 34 (139)
T ss_pred EECCC--CCCcCCCCCccccCCCcCCCCCCccCC
Confidence 46887 76543333 47789999999987764
No 122
>KOG4684|consensus
Probab=41.70 E-value=15 Score=30.16 Aligned_cols=52 Identities=19% Similarity=0.259 Sum_probs=34.3
Q ss_pred eEEEecccCCCCcCCceEE------------eceeCCccccCCceeEEEeecccccccccCCCCc
Q psy15072 15 KIHRLRRECTSEQCGAGVF------------MAAMSDRHYCGNKFSSLSVELKSARSQVRFPPGA 67 (97)
Q Consensus 15 KI~rlrkeCP~~eCGaGVF------------MA~H~DR~yCGKCg~T~~~~~~~a~~q~~~p~~~ 67 (97)
|++-.|-.|||+.|--=+= ||...-|..||.|..|+.++.-.- +--+-|-|.
T Consensus 133 K~sSqRIACPRpnCkRiInL~p~~~~p~~P~~~P~gcRV~CgHC~~tFLfnt~tn-aLArCPHCr 196 (275)
T KOG4684|consen 133 KASSQRIACPRPNCKRIINLDPLIEKPRDPGTAPTGCRVKCGHCNETFLFNTLTN-ALARCPHCR 196 (275)
T ss_pred ecccceeccCCCCcceeeecCCCCCCCCCCCCCCcceEEEecCccceeehhhHHH-HHhcCCccc
Confidence 4566788899999954222 344457999999999988875432 333444443
No 123
>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=41.03 E-value=30 Score=19.76 Aligned_cols=26 Identities=19% Similarity=0.275 Sum_probs=15.3
Q ss_pred ccCCceeEEEeeccc-ccccccCCCCc
Q psy15072 42 YCGNKFSSLSVELKS-ARSQVRFPPGA 67 (97)
Q Consensus 42 yCGKCg~T~~~~~~~-a~~q~~~p~~~ 67 (97)
+|..||..+..-... ...++.+||-+
T Consensus 4 ~C~~Cg~~l~~ig~~~~~q~l~~~p~~ 30 (47)
T PF13005_consen 4 ACPDCGGELKEIGEEKVRQVLDLPPAK 30 (47)
T ss_pred cCCCCCceeeECCceeeEEEEeecccc
Confidence 577777666543444 44457777743
No 124
>PRK04179 rpl37e 50S ribosomal protein L37e; Reviewed
Probab=41.01 E-value=12 Score=24.81 Aligned_cols=25 Identities=20% Similarity=0.428 Sum_probs=20.4
Q ss_pred ecccCCCCcCCceEEeceeCCccccCCcee
Q psy15072 19 LRRECTSEQCGAGVFMAAMSDRHYCGNKFS 48 (97)
Q Consensus 19 lrkeCP~~eCGaGVFMA~H~DR~yCGKCg~ 48 (97)
.+-.|.+ ||. .+-|.-..+|..||+
T Consensus 16 tHt~CrR--CG~---~syh~qK~~CasCGy 40 (62)
T PRK04179 16 THIRCRR--CGR---HSYNVRKKYCAACGF 40 (62)
T ss_pred ccchhcc--cCc---ccccccccchhhcCC
Confidence 3457999 997 466888999999998
No 125
>PF12322 T4_baseplate: T4 bacteriophage base plate protein; InterPro: IPR024364 Proteins in this family are found in T4-like viruses. They have a single completely conserved residue S that may be functionally important. The family includes the two base plate proteins from bacteriophage T4: Gp51 and Gp26, encoded by late genes []. Gp26 is a structural component of central hub of the baseplate. It associates with Gp25 (tail lysozyme) in the assembly process. Gp51 is essential for the formation of the central hub of the phage baseplate, playing a catalytic role for the central hub formation. It may be also a structural component of the hub.
Probab=40.94 E-value=39 Score=25.92 Aligned_cols=47 Identities=13% Similarity=0.164 Sum_probs=33.8
Q ss_pred CCccccCCceeEEEeecccccccccCCCCceEEEEEecceeeeeeeeeEE
Q psy15072 38 SDRHYCGNKFSSLSVELKSARSQVRFPPGANFLTFVLGTASFLVSYPVLL 87 (97)
Q Consensus 38 ~DR~yCGKCg~T~~~~~~~a~~q~~~p~~~~~l~~~~~~~~~~~~~~~~~ 87 (97)
.-++.|.+||.+....-.-...|+ |.+ .-.+...+-...-.-||-+-
T Consensus 76 ~~~~~C~~cg~~~~~~i~l~~~~l--~~~-~~~~~~~~~i~i~~ryP~~~ 122 (205)
T PF12322_consen 76 PVNYTCPDCGEEVKVPINLDQIKL--TDG-KNEIKLSDGIKIKMRYPSLF 122 (205)
T ss_pred eEEEECCCCCcEEEEEecchhccc--CCC-CcceEecCCEEEEEeCCccc
Confidence 347788889886666655555566 666 66666778888999999854
No 126
>cd01799 Hoil1_N Ubiquitin-like domain of HOIL1. HOIL1_N HOIL-1 (heme-oxidized IRP2 ubiquitin ligase-1) is an E3 ubiquitin-protein ligase that recognizes heme-oxidized IRP2 (iron regulatory protein2) and is thought to affect the turnover of oxidatively damaged proteins. Hoil-1 has an amino-terminal ubiquitin-like domain as well as an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain.
Probab=40.03 E-value=8.3 Score=24.85 Aligned_cols=17 Identities=18% Similarity=0.325 Sum_probs=13.2
Q ss_pred cccccccCCCCceEEEEE
Q psy15072 56 SARSQVRFPPGANFLTFV 73 (97)
Q Consensus 56 ~a~~q~~~p~~~~~l~~~ 73 (97)
+..++.++||.+|+| |.
T Consensus 31 kI~~~~gip~~~QrL-~~ 47 (75)
T cd01799 31 KVFLDYGFPPAVQRW-VI 47 (75)
T ss_pred HHHHHHCcCHHHEEE-Ec
Confidence 344448999999999 75
No 127
>PRK12496 hypothetical protein; Provisional
Probab=40.01 E-value=14 Score=27.20 Aligned_cols=34 Identities=18% Similarity=0.300 Sum_probs=22.4
Q ss_pred eEEEecccCCCCcCCceEEeceeCCccccCCceeEEEe
Q psy15072 15 KIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSV 52 (97)
Q Consensus 15 KI~rlrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~ 52 (97)
++.+.+..|+. ||. .|- ....+..|-.||.....
T Consensus 122 ~~~~w~~~C~g--C~~-~~~-~~~~~~~C~~CG~~~~r 155 (164)
T PRK12496 122 KVIKWRKVCKG--CKK-KYP-EDYPDDVCEICGSPVKR 155 (164)
T ss_pred hheeeeEECCC--CCc-ccc-CCCCCCcCCCCCChhhh
Confidence 55666788998 996 221 12355679999976543
No 128
>PRK14282 chaperone protein DnaJ; Provisional
Probab=39.93 E-value=32 Score=27.93 Aligned_cols=13 Identities=31% Similarity=0.877 Sum_probs=6.4
Q ss_pred cCCCCcC-CceEEece
Q psy15072 22 ECTSEQC-GAGVFMAA 36 (97)
Q Consensus 22 eCP~~eC-GaGVFMA~ 36 (97)
.||. | |.|..+..
T Consensus 171 ~C~~--C~G~G~~~~~ 184 (369)
T PRK14282 171 TCPK--CHGTGRIREE 184 (369)
T ss_pred CCCC--CCCcCEEEEE
Confidence 3555 5 45555443
No 129
>PRK07220 DNA topoisomerase I; Validated
Probab=39.09 E-value=32 Score=30.79 Aligned_cols=38 Identities=13% Similarity=0.099 Sum_probs=24.3
Q ss_pred CCCeEEEecccCCCCcCCceEEeceeCCc----cccCCceeEEE
Q psy15072 12 ENGKIHRLRRECTSEQCGAGVFMAAMSDR----HYCGNKFSSLS 51 (97)
Q Consensus 12 enGKI~rlrkeCP~~eCGaGVFMA~H~DR----~yCGKCg~T~~ 51 (97)
.+|+++.+...||. ||.+.+--.-..+ +-|-.|.++..
T Consensus 627 ~~g~~~~~~~~Cp~--Cg~~~~k~~~~g~~~~~~~Cp~C~~~~~ 668 (740)
T PRK07220 627 KSGQIIVTDKVCEA--HGLNHIRIINGGKRPWDLGCPQCNFIEW 668 (740)
T ss_pred CCCccccCCCCCCC--CCCceEEEEecCCccceeeCCCCCCccc
Confidence 35777778888998 9876543222232 36888887653
No 130
>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=37.92 E-value=25 Score=24.38 Aligned_cols=27 Identities=19% Similarity=0.353 Sum_probs=16.2
Q ss_pred EecccCCCCcCCceEEeceeCCccccCCcee
Q psy15072 18 RLRRECTSEQCGAGVFMAAMSDRHYCGNKFS 48 (97)
Q Consensus 18 rlrkeCP~~eCGaGVFMA~H~DR~yCGKCg~ 48 (97)
..+-.|++ ||. ..+.......|.+||.
T Consensus 68 p~~~~C~~--Cg~--~~~~~~~~~~CP~Cgs 94 (115)
T TIGR00100 68 PVECECED--CSE--EVSPEIDLYRCPKCHG 94 (115)
T ss_pred CcEEEccc--CCC--EEecCCcCccCcCCcC
Confidence 34567888 885 3232223456989984
No 131
>KOG3475|consensus
Probab=37.32 E-value=6.2 Score=27.95 Aligned_cols=29 Identities=14% Similarity=0.229 Sum_probs=22.1
Q ss_pred ecccCCCCcCCceEEeceeCCccccCCceeEEEe
Q psy15072 19 LRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSV 52 (97)
Q Consensus 19 lrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~ 52 (97)
....|-+ ||.-. .|.....|++|||.--+
T Consensus 15 shtlC~R--CG~~s---yH~QKstC~~CGYpaak 43 (92)
T KOG3475|consen 15 SHTLCRR--CGRRS---YHIQKSTCSSCGYPAAK 43 (92)
T ss_pred chHHHHH--hCchh---hhhhcccccccCCcchh
Confidence 3456888 99754 58889999999997543
No 132
>cd01791 Ubl5 UBL5 ubiquitin-like modifier. UBL5 (also known as HUB1) is a ubiquitin-like modifier that is both widely expressed and highly phylogenetically conserved. At the C-terminal end of the ubiquitin-like fold of UBL5 is a di-tyrosine motif followed by a single variable residue instead of the characteristic di-glycine found in all other ubiquitin-like modifiers. ULB5 interacts with a cyclin-like kinase called CLK4 but not with other cyclin-like kinase family members.
Probab=37.24 E-value=11 Score=24.20 Aligned_cols=13 Identities=15% Similarity=-0.054 Sum_probs=12.0
Q ss_pred ccCCCCceEEEEE
Q psy15072 61 VRFPPGANFLTFV 73 (97)
Q Consensus 61 ~~~p~~~~~l~~~ 73 (97)
.++|+.+|+|+|.
T Consensus 35 ~~~~~~~qrLi~~ 47 (73)
T cd01791 35 TGTRPEKIVLKKW 47 (73)
T ss_pred hCCChHHEEEEeC
Confidence 5899999999997
No 133
>PRK14298 chaperone protein DnaJ; Provisional
Probab=36.87 E-value=34 Score=28.03 Aligned_cols=26 Identities=23% Similarity=0.308 Sum_probs=12.2
Q ss_pred ccccCCceeEEEeecccccccccCCCC
Q psy15072 40 RHYCGNKFSSLSVELKSARSQVRFPPG 66 (97)
Q Consensus 40 R~yCGKCg~T~~~~~~~a~~q~~~p~~ 66 (97)
+..|.+|.=.-... +....++.+|||
T Consensus 198 ~~~C~~C~G~g~v~-~~~~l~V~IppG 223 (377)
T PRK14298 198 ESPCPVCSGTGKVR-KTRKITVNVPAG 223 (377)
T ss_pred CCCCCCCCCccEEE-EEEEEEecCCCC
Confidence 34577776322222 122334666664
No 134
>PF04885 Stig1: Stigma-specific protein, Stig1; InterPro: IPR006969 This family represents the Stig1 cysteine rich plant protein.The tobacco stigma-specific gene, STIG1 is developmentally regulated and expressed specifically in the stigmatic secretory zone. Pistils of transgenic STIG1-barnase tobacco plants undergo normal development, but lack the stigmatic secretory zone and are female sterile. Pollen grains are unable to penetrate the surface of the ablated pistils. Application of stigmatic exudate from wild-type pistils to the ablated surface increases the efficiency of pollen tube germination and growth and restores the capacity of pollen tubes to penetrate the style []. The function of STIG1 is unknown.
Probab=36.85 E-value=21 Score=26.26 Aligned_cols=22 Identities=27% Similarity=0.416 Sum_probs=15.3
Q ss_pred CCceEEeceeCCccccCCceeE
Q psy15072 28 CGAGVFMAAMSDRHYCGNKFSS 49 (97)
Q Consensus 28 CGaGVFMA~H~DR~yCGKCg~T 49 (97)
|-.|.=.--+.|+.+||+||..
T Consensus 100 cC~G~Cvd~~~d~~~CG~Cg~~ 121 (136)
T PF04885_consen 100 CCGGQCVDLNSDPRHCGACGNK 121 (136)
T ss_pred ecCCEeECCCCCccccCCCCCc
Confidence 3345555566799999999863
No 135
>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=36.68 E-value=27 Score=22.82 Aligned_cols=34 Identities=18% Similarity=0.113 Sum_probs=20.3
Q ss_pred ccCCCCcCCc--eEEec--eeCCccccCCceeEEEeeccc
Q psy15072 21 RECTSEQCGA--GVFMA--AMSDRHYCGNKFSSLSVELKS 56 (97)
Q Consensus 21 keCP~~eCGa--GVFMA--~H~DR~yCGKCg~T~~~~~~~ 56 (97)
-.||+ |++ -+-|- +-.+-.-|-+|||+.....+.
T Consensus 10 A~CP~--C~~~Dtl~~~~e~~~e~vECv~Cg~~~~~~~~~ 47 (59)
T TIGR02443 10 AVCPA--CSAQDTLAMWKENNIELVECVECGYQEQQKDQS 47 (59)
T ss_pred ccCCC--CcCccEEEEEEeCCceEEEeccCCCccccCCcc
Confidence 46998 986 12121 112345799999998554443
No 136
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=36.59 E-value=20 Score=23.10 Aligned_cols=21 Identities=19% Similarity=0.403 Sum_probs=14.7
Q ss_pred ccCCCCcCCceEEeceeCCccccCCcee
Q psy15072 21 RECTSEQCGAGVFMAAMSDRHYCGNKFS 48 (97)
Q Consensus 21 keCP~~eCGaGVFMA~H~DR~yCGKCg~ 48 (97)
.+||+ ||. ..|+ -+.|.+||+
T Consensus 28 ~~c~~--cG~-~~l~----Hrvc~~cg~ 48 (57)
T COG0333 28 SVCPN--CGE-YKLP----HRVCLKCGY 48 (57)
T ss_pred eeccC--CCC-cccC----ceEcCCCCC
Confidence 57998 996 4444 456888885
No 137
>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=36.45 E-value=31 Score=26.08 Aligned_cols=37 Identities=24% Similarity=0.319 Sum_probs=19.7
Q ss_pred EEEECCCCeEEEecccCCCCcCCceEEeceeCCccccCCceeE
Q psy15072 7 VCNVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSS 49 (97)
Q Consensus 7 yYkVdenGKI~rlrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T 49 (97)
.+++. |.+.+ -.|.. |+.-.-.......-.|.+||-.
T Consensus 109 v~elH--G~~~~--~~C~~--C~~~~~~~~~~~~p~C~~Cgg~ 145 (225)
T cd01411 109 VVEFH--GSLYR--IYCTV--CGKTVDWEEYLKSPYHAKCGGV 145 (225)
T ss_pred EEEeC--CCcCe--eEeCC--CCCccchhhcCCCCCCCCCCCE
Confidence 44454 44444 35886 8753322222233579999853
No 138
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=36.39 E-value=24 Score=19.59 Aligned_cols=26 Identities=27% Similarity=0.482 Sum_probs=13.3
Q ss_pred ecccCCCCcCCceEEeceeCCccccCCceeEE
Q psy15072 19 LRRECTSEQCGAGVFMAAMSDRHYCGNKFSSL 50 (97)
Q Consensus 19 lrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~ 50 (97)
+-..|++ ||.= .|..|..|.+||-+.
T Consensus 10 ~~~rC~~--Cg~~----~~pPr~~Cp~C~s~~ 35 (37)
T PF12172_consen 10 LGQRCRD--CGRV----QFPPRPVCPHCGSDE 35 (37)
T ss_dssp EEEE-TT--T--E----EES--SEETTTT---
T ss_pred EEEEcCC--CCCE----ecCCCcCCCCcCccc
Confidence 3477988 9972 345699999998553
No 139
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=36.33 E-value=37 Score=22.76 Aligned_cols=47 Identities=13% Similarity=0.285 Sum_probs=28.3
Q ss_pred cCCCCcCCceEEeceeCCccccCCceeEEEeecccccccccCCCCceEEEE--Eecceee
Q psy15072 22 ECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELKSARSQVRFPPGANFLTF--VLGTASF 79 (97)
Q Consensus 22 eCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~~~~a~~q~~~p~~~~~l~~--~~~~~~~ 79 (97)
.||. |..- |..-.++++|..|...+ +-+-.=|++.+-|.. |-|+++|
T Consensus 3 ~CP~--C~~~--L~~~~~~~~C~~C~~~~-------~~~a~CPdC~~~Le~LkACGAvdY 51 (70)
T PF07191_consen 3 TCPK--CQQE--LEWQGGHYHCEACQKDY-------KKEAFCPDCGQPLEVLKACGAVDY 51 (70)
T ss_dssp B-SS--S-SB--EEEETTEEEETTT--EE-------EEEEE-TTT-SB-EEEEETTEEEE
T ss_pred cCCC--CCCc--cEEeCCEEECccccccc-------eecccCCCcccHHHHHHHhcccce
Confidence 5888 9884 77777899999998765 234567888887765 3455555
No 140
>cd01807 GDX_N ubiquitin-like domain of GDX. GDX contains an N-terminal ubiquitin-like domain as well as an uncharacterized c-terminal domain. The function of GDX is unknown.
Probab=36.02 E-value=10 Score=23.41 Aligned_cols=16 Identities=19% Similarity=0.314 Sum_probs=13.0
Q ss_pred cccccCCCCceEEEEE
Q psy15072 58 RSQVRFPPGANFLTFV 73 (97)
Q Consensus 58 ~~q~~~p~~~~~l~~~ 73 (97)
.+..++|+++|+|+|.
T Consensus 31 ~~~~gi~~~~q~L~~~ 46 (74)
T cd01807 31 SEHLNVPEEQQRLLFK 46 (74)
T ss_pred HHHHCCCHHHeEEEEC
Confidence 3347899999999986
No 141
>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=35.91 E-value=54 Score=21.58 Aligned_cols=33 Identities=15% Similarity=0.052 Sum_probs=20.9
Q ss_pred ccCCCCcCCce-EEe-c--eeCCccccCCceeEEEeecc
Q psy15072 21 RECTSEQCGAG-VFM-A--AMSDRHYCGNKFSSLSVELK 55 (97)
Q Consensus 21 keCP~~eCGaG-VFM-A--~H~DR~yCGKCg~T~~~~~~ 55 (97)
-.||+ |++= ..| - +..+-.-|-+|||+..-..+
T Consensus 9 a~CP~--C~~~D~i~~~~e~~ve~vECV~CGy~e~~~~~ 45 (71)
T PF09526_consen 9 AVCPK--CQAMDTIMMWRENGVEYVECVECGYTERQPDQ 45 (71)
T ss_pred ccCCC--CcCccEEEEEEeCCceEEEecCCCCeeccCCc
Confidence 46998 9761 222 1 22345579999999866555
No 142
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=35.80 E-value=27 Score=24.43 Aligned_cols=30 Identities=27% Similarity=0.316 Sum_probs=18.3
Q ss_pred ccCCCCcCCceEEec----eeCCccccCCceeEEEee
Q psy15072 21 RECTSEQCGAGVFMA----AMSDRHYCGNKFSSLSVE 53 (97)
Q Consensus 21 keCP~~eCGaGVFMA----~H~DR~yCGKCg~T~~~~ 53 (97)
-.||+ ||.- -+. ...-...|.+||+-+-.+
T Consensus 22 f~CP~--Cge~-~v~v~~~k~~~h~~C~~CG~y~~~~ 55 (99)
T PRK14892 22 FECPR--CGKV-SISVKIKKNIAIITCGNCGLYTEFE 55 (99)
T ss_pred eECCC--CCCe-EeeeecCCCcceEECCCCCCccCEE
Confidence 35999 9952 221 122356899999755443
No 143
>cd01806 Nedd8 Nebb8-like ubiquitin protein. Nedd8 (also known as Rub1) has a single conserved ubiquitin-like domain that is part of a protein modification pathway similar to that of ubiquitin. Nedd8 modifies a family of molecular scaffold proteins called cullins that are responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis.
Probab=35.54 E-value=16 Score=21.93 Aligned_cols=18 Identities=17% Similarity=0.355 Sum_probs=13.8
Q ss_pred cccccccCCCCceEEEEE
Q psy15072 56 SARSQVRFPPGANFLTFV 73 (97)
Q Consensus 56 ~a~~q~~~p~~~~~l~~~ 73 (97)
...++.++|+..++|+|.
T Consensus 29 ~i~~~~g~~~~~qrL~~~ 46 (76)
T cd01806 29 RVEEKEGIPPQQQRLIYS 46 (76)
T ss_pred HHhHhhCCChhhEEEEEC
Confidence 333447899999999975
No 144
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=35.18 E-value=69 Score=24.48 Aligned_cols=11 Identities=9% Similarity=-0.043 Sum_probs=7.7
Q ss_pred ccccCCceeEE
Q psy15072 40 RHYCGNKFSSL 50 (97)
Q Consensus 40 R~yCGKCg~T~ 50 (97)
...|..|||..
T Consensus 30 sf~C~~CGyr~ 40 (192)
T TIGR00310 30 STICEHCGYRS 40 (192)
T ss_pred EEECCCCCCcc
Confidence 56788888754
No 145
>PF13408 Zn_ribbon_recom: Recombinase zinc beta ribbon domain
Probab=35.17 E-value=25 Score=20.26 Aligned_cols=10 Identities=30% Similarity=0.537 Sum_probs=4.1
Q ss_pred ccCCceeEEE
Q psy15072 42 YCGNKFSSLS 51 (97)
Q Consensus 42 yCGKCg~T~~ 51 (97)
+||.||.++.
T Consensus 7 ~C~~CG~~m~ 16 (58)
T PF13408_consen 7 RCGHCGSKMT 16 (58)
T ss_pred EcccCCcEeE
Confidence 3444444333
No 146
>TIGR02349 DnaJ_bact chaperone protein DnaJ. This model represents bacterial forms of DnaJ, part of the DnaK-DnaJ-GrpE chaperone system. The three components typically are encoded by consecutive genes. DnaJ homologs occur in many genomes, typically not near DnaK and GrpE-like genes; most such genes are not included by this family. Eukaryotic (mitochondrial and chloroplast) forms are not included in the scope of this family.
Probab=35.09 E-value=40 Score=26.93 Aligned_cols=7 Identities=14% Similarity=0.173 Sum_probs=4.5
Q ss_pred cccCCce
Q psy15072 41 HYCGNKF 47 (97)
Q Consensus 41 ~yCGKCg 47 (97)
..|-+|.
T Consensus 201 ~~C~~C~ 207 (354)
T TIGR02349 201 EPCSTCK 207 (354)
T ss_pred CCCCCCC
Confidence 3477776
No 147
>PRK08173 DNA topoisomerase III; Validated
Probab=34.30 E-value=20 Score=32.88 Aligned_cols=28 Identities=29% Similarity=0.414 Sum_probs=21.2
Q ss_pred ccCCCCcCCceEEeceeCCccccCCceeEEEe
Q psy15072 21 RECTSEQCGAGVFMAAMSDRHYCGNKFSSLSV 52 (97)
Q Consensus 21 keCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~ 52 (97)
..||. ||.++ -....++.|..|+.+.+.
T Consensus 625 ~~CP~--Cg~~~--~~~~~~~~Cs~C~f~~~~ 652 (862)
T PRK08173 625 TPCPN--CGGVV--KENYRRFACTKCDFSISK 652 (862)
T ss_pred ccCCc--ccccc--cccCceeEcCCCCcccch
Confidence 57998 99876 334556999999988764
No 148
>PTZ00044 ubiquitin; Provisional
Probab=34.03 E-value=12 Score=22.91 Aligned_cols=18 Identities=6% Similarity=-0.018 Sum_probs=13.9
Q ss_pred cccccccCCCCceEEEEE
Q psy15072 56 SARSQVRFPPGANFLTFV 73 (97)
Q Consensus 56 ~a~~q~~~p~~~~~l~~~ 73 (97)
...+..++|+.+++|+|.
T Consensus 29 ~i~~~~gi~~~~q~L~~~ 46 (76)
T PTZ00044 29 ALQEKEGIDVKQIRLIYS 46 (76)
T ss_pred HHHHHHCCCHHHeEEEEC
Confidence 334448899999999985
No 149
>PRK05452 anaerobic nitric oxide reductase flavorubredoxin; Provisional
Probab=34.01 E-value=24 Score=29.78 Aligned_cols=30 Identities=13% Similarity=0.124 Sum_probs=20.7
Q ss_pred CCccccCCceeEEEeecccccccccCCCCceE
Q psy15072 38 SDRHYCGNKFSSLSVELKSARSQVRFPPGANF 69 (97)
Q Consensus 38 ~DR~yCGKCg~T~~~~~~~a~~q~~~p~~~~~ 69 (97)
..+|.|.-|||.|.-.....+ .++|||..+
T Consensus 423 ~~~~~c~~c~~~yd~~~g~~~--~~~~~gt~~ 452 (479)
T PRK05452 423 GPRMQCSVCQWIYDPAKGEPM--QDVAPGTPW 452 (479)
T ss_pred CCeEEECCCCeEECCCCCCcc--cCCCCCCCh
Confidence 468899999988866555443 457777543
No 150
>PLN03086 PRLI-interacting factor K; Provisional
Probab=33.93 E-value=24 Score=31.41 Aligned_cols=33 Identities=18% Similarity=0.366 Sum_probs=21.8
Q ss_pred EecccCCCCcCCceEEeceeCCc-cccCCceeEEE
Q psy15072 18 RLRRECTSEQCGAGVFMAAMSDR-HYCGNKFSSLS 51 (97)
Q Consensus 18 rlrkeCP~~eCGaGVFMA~H~DR-~yCGKCg~T~~ 51 (97)
|....||+..||. +|+-...++ ++|-.|+..+.
T Consensus 431 r~~V~Cp~~~Cg~-v~~r~el~~H~~C~~Cgk~f~ 464 (567)
T PLN03086 431 RHNVVCPHDGCGI-VLRVEEAKNHVHCEKCGQAFQ 464 (567)
T ss_pred CcceeCCcccccc-eeeccccccCccCCCCCCccc
Confidence 4455688666886 666655544 47888887653
No 151
>PF10071 DUF2310: Zn-ribbon-containing, possibly nucleic-acid-binding protein (DUF2310); InterPro: IPR016908 This group represents uncharacterised conserved proteins.
Probab=33.92 E-value=19 Score=29.21 Aligned_cols=41 Identities=17% Similarity=0.212 Sum_probs=29.7
Q ss_pred EEEECCCCeEEEecccCCCCcCCceEEeceeC---CccccCCceeE
Q psy15072 7 VCNVDENGKIHRLRRECTSEQCGAGVFMAAMS---DRHYCGNKFSS 49 (97)
Q Consensus 7 yYkVdenGKI~rlrkeCP~~eCGaGVFMA~H~---DR~yCGKCg~T 49 (97)
.|+|.++.+..-..|.||+ ||.--.+++=. --+.|-+|-+.
T Consensus 207 Lyrv~g~~~~~e~~r~CP~--Cg~~W~L~~plh~iFdFKCD~CRLV 250 (258)
T PF10071_consen 207 LYRVGGESLASEQARKCPS--CGGDWRLKEPLHDIFDFKCDPCRLV 250 (258)
T ss_pred EEEccCcchHHhhCCCCCC--CCCccccCCchhhceeccCCcceee
Confidence 4688766778888999999 99876666421 23579999754
No 152
>PRK04023 DNA polymerase II large subunit; Validated
Probab=33.51 E-value=25 Score=33.94 Aligned_cols=16 Identities=38% Similarity=0.816 Sum_probs=11.8
Q ss_pred eEEEecccCCCCcCCceE
Q psy15072 15 KIHRLRRECTSEQCGAGV 32 (97)
Q Consensus 15 KI~rlrkeCP~~eCGaGV 32 (97)
+|+.-++.||+ ||...
T Consensus 621 eVEVg~RfCps--CG~~t 636 (1121)
T PRK04023 621 EVEIGRRKCPS--CGKET 636 (1121)
T ss_pred eecccCccCCC--CCCcC
Confidence 45667788998 88753
No 153
>PRK14288 chaperone protein DnaJ; Provisional
Probab=33.36 E-value=50 Score=26.90 Aligned_cols=10 Identities=20% Similarity=0.371 Sum_probs=5.5
Q ss_pred cccccCCCCc
Q psy15072 58 RSQVRFPPGA 67 (97)
Q Consensus 58 ~~q~~~p~~~ 67 (97)
..+|.+||+.
T Consensus 209 ~l~V~IP~G~ 218 (369)
T PRK14288 209 EIDAIIPEGI 218 (369)
T ss_pred EEEEecCCCC
Confidence 3346666654
No 154
>PRK14289 chaperone protein DnaJ; Provisional
Probab=33.25 E-value=36 Score=27.70 Aligned_cols=7 Identities=14% Similarity=0.083 Sum_probs=4.7
Q ss_pred cccCCce
Q psy15072 41 HYCGNKF 47 (97)
Q Consensus 41 ~yCGKCg 47 (97)
..|..|+
T Consensus 212 ~~C~~C~ 218 (386)
T PRK14289 212 KKCKKCG 218 (386)
T ss_pred cCCCCCC
Confidence 4577776
No 155
>PRK11032 hypothetical protein; Provisional
Probab=33.13 E-value=60 Score=24.47 Aligned_cols=44 Identities=11% Similarity=0.063 Sum_probs=28.2
Q ss_pred EEEECCCCeEEEecccCCCCcCCceEEeceeCCcc-ccCCceeEEEeecc
Q psy15072 7 VCNVDENGKIHRLRRECTSEQCGAGVFMAAMSDRH-YCGNKFSSLSVELK 55 (97)
Q Consensus 7 yYkVdenGKI~rlrkeCP~~eCGaGVFMA~H~DR~-yCGKCg~T~~~~~~ 55 (97)
.|...| -|..-.-.|-+ ||--.-+ .|.++. -|-|||.++|....
T Consensus 113 ~Y~sGE--vvg~G~LvC~~--Cg~~~~~-~~p~~i~pCp~C~~~~F~R~~ 157 (160)
T PRK11032 113 VYHSGE--VVGLGNLVCEK--CHHHLAF-YTPEVLPLCPKCGHDQFQRRP 157 (160)
T ss_pred eeecce--eeecceEEecC--CCCEEEe-cCCCcCCCCCCCCCCeeeeCC
Confidence 565443 23333456887 9985544 455554 79999999987654
No 156
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=33.08 E-value=37 Score=27.39 Aligned_cols=33 Identities=18% Similarity=0.342 Sum_probs=22.8
Q ss_pred ccCCCCcCCceEEeceeC-CccccCCceeEEEeecc
Q psy15072 21 RECTSEQCGAGVFMAAMS-DRHYCGNKFSSLSVELK 55 (97)
Q Consensus 21 keCP~~eCGaGVFMA~H~-DR~yCGKCg~T~~~~~~ 55 (97)
..||. ||.=.+--++. ..+.|+.||.....+.-
T Consensus 2 ~~Cpe--Cg~~~~~~d~~~ge~VC~~CG~Vi~~~~i 35 (285)
T COG1405 2 MSCPE--CGSTNIITDYERGEIVCADCGLVLEDSLI 35 (285)
T ss_pred CCCCC--CCCccceeeccCCeEEeccCCEEeccccc
Confidence 46997 99765555543 57899999987654433
No 157
>cd01797 NIRF_N amino-terminal ubiquitin-like domain of Np95 and NIRF. NIRF_N This CD represents the amino-terminal ubiquitin-like domain of a family of nuclear proteins that includes Np95 and NIRF (Np95/ICBP90-like RING finger) protein. Both Np95 and NIRF have a domain architecture consisting of a ubiquitin-like domain, a PHD finger, a YDG/SRA domain, Rb-binding motifs and a RING finger domain. Both Np95 and NIRF are ubiquitin ligases that ubiquitinate PCNP (PEST-containing nuclear proteins). While Np95 is capable of binding histones, NIRF is involved in cell cycle regulation.
Probab=32.90 E-value=13 Score=23.91 Aligned_cols=15 Identities=13% Similarity=0.186 Sum_probs=12.6
Q ss_pred ccccCCCCceEEEEE
Q psy15072 59 SQVRFPPGANFLTFV 73 (97)
Q Consensus 59 ~q~~~p~~~~~l~~~ 73 (97)
+..++|+++|+|+|.
T Consensus 34 ~~~gi~~~~QrLi~~ 48 (78)
T cd01797 34 ELFNVEPECQRLFYR 48 (78)
T ss_pred HHhCCCHHHeEEEeC
Confidence 337899999999985
No 158
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=32.86 E-value=33 Score=24.13 Aligned_cols=33 Identities=24% Similarity=0.451 Sum_probs=21.3
Q ss_pred EEecccCCCCcCCceEEe-ceeC--CccccCCceeEEE
Q psy15072 17 HRLRRECTSEQCGAGVFM-AAMS--DRHYCGNKFSSLS 51 (97)
Q Consensus 17 ~rlrkeCP~~eCGaGVFM-A~H~--DR~yCGKCg~T~~ 51 (97)
.+-.-.|.. ||....- -.|. .|+.||+|+-.+.
T Consensus 109 ~~~~y~C~~--C~~~~~~~rr~~~~~~y~C~~C~g~l~ 144 (146)
T smart00731 109 KKYPYRCTG--CGQRYLRVRRSNNVSRYRCGKCGGKLI 144 (146)
T ss_pred ceEEEECCC--CCCCCceEccccCcceEEcCCCCCEEE
Confidence 345677876 9876541 1222 4689999997654
No 159
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=32.61 E-value=80 Score=17.34 Aligned_cols=10 Identities=30% Similarity=0.936 Sum_probs=5.6
Q ss_pred cCCCCcCCceEE
Q psy15072 22 ECTSEQCGAGVF 33 (97)
Q Consensus 22 eCP~~eCGaGVF 33 (97)
.||. ||-++|
T Consensus 34 ~C~~--CGE~~~ 43 (46)
T TIGR03831 34 VCPQ--CGEEYL 43 (46)
T ss_pred cccc--CCCEee
Confidence 4665 665544
No 160
>PRK08402 replication factor A; Reviewed
Probab=32.33 E-value=1e+02 Score=25.69 Aligned_cols=38 Identities=24% Similarity=0.447 Sum_probs=25.5
Q ss_pred EEEECCCCeEEEecc-----cCCCCcCCceEEeceeCCccccCCcee
Q psy15072 7 VCNVDENGKIHRLRR-----ECTSEQCGAGVFMAAMSDRHYCGNKFS 48 (97)
Q Consensus 7 yYkVdenGKI~rlrk-----eCP~~eCGaGVFMA~H~DR~yCGKCg~ 48 (97)
|++|. |.|...++ -||. |.--|-.-.+.+.|.|..|+.
T Consensus 196 ~v~v~--g~Iv~i~~~~~y~aCp~--CnKkv~~~~~~~~~~Ce~~~~ 238 (355)
T PRK08402 196 FVEVR--GTIAKVYRVLVYDACPE--CRRKVDYDPATDTWICPEHGE 238 (355)
T ss_pred EEEEE--EEEEEEecCeeEecCCC--CCeEEEEecCCCCEeCCCCCC
Confidence 44554 56666664 6998 988554345567899998873
No 161
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=32.21 E-value=15 Score=28.11 Aligned_cols=17 Identities=53% Similarity=1.036 Sum_probs=13.9
Q ss_pred CCCeEEEecccCCCCcCCc
Q psy15072 12 ENGKIHRLRRECTSEQCGA 30 (97)
Q Consensus 12 enGKI~rlrkeCP~~eCGa 30 (97)
++|.-.|-||+||+ ||-
T Consensus 20 edg~aIRRRReC~~--C~~ 36 (156)
T COG1327 20 EEGNAIRRRRECLE--CGE 36 (156)
T ss_pred cccchhhhhhcccc--ccc
Confidence 46877888999998 984
No 162
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=32.10 E-value=51 Score=18.78 Aligned_cols=10 Identities=10% Similarity=0.003 Sum_probs=5.8
Q ss_pred cccCCceeEE
Q psy15072 41 HYCGNKFSSL 50 (97)
Q Consensus 41 ~yCGKCg~T~ 50 (97)
.+|.+||=..
T Consensus 20 d~C~~C~G~W 29 (41)
T PF13453_consen 20 DVCPSCGGIW 29 (41)
T ss_pred EECCCCCeEE
Confidence 3577776544
No 163
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=31.80 E-value=47 Score=23.70 Aligned_cols=10 Identities=30% Similarity=0.860 Sum_probs=7.6
Q ss_pred ecccCCCCcCCc
Q psy15072 19 LRRECTSEQCGA 30 (97)
Q Consensus 19 lrkeCP~~eCGa 30 (97)
.+-.|++ ||.
T Consensus 69 ~~~~C~~--CG~ 78 (135)
T PRK03824 69 AVLKCRN--CGN 78 (135)
T ss_pred eEEECCC--CCC
Confidence 5677988 985
No 164
>PRK14296 chaperone protein DnaJ; Provisional
Probab=31.68 E-value=67 Score=26.27 Aligned_cols=13 Identities=31% Similarity=0.953 Sum_probs=6.7
Q ss_pred ccCCCCcC-CceEEec
Q psy15072 21 RECTSEQC-GAGVFMA 35 (97)
Q Consensus 21 keCP~~eC-GaGVFMA 35 (97)
+.||. | |.|+.+.
T Consensus 167 ~~C~~--C~G~G~~~~ 180 (372)
T PRK14296 167 HICNN--CHGTGEVLV 180 (372)
T ss_pred ccCCC--CCCCceEEE
Confidence 44665 6 4555443
No 165
>TIGR02261 benz_CoA_red_D benzoyl-CoA reductase, bcr type, subunit D. This model describes the D subunit of benzoyl-CoA reductase, a 4-subunit enzyme. Many aromatic compounds are metabolized by way of benzoyl-CoA. This family shows sequence similarity to the A subunit (TIGR02259) and to the 2-hydroxyglutaryl-CoA dehydratase alpha chain.
Probab=31.56 E-value=27 Score=27.92 Aligned_cols=31 Identities=29% Similarity=0.724 Sum_probs=23.2
Q ss_pred ceEEEECCCCeEE--EecccCCCCcCCceEEeceeC
Q psy15072 5 WQVCNVDENGKIH--RLRRECTSEQCGAGVFMAAMS 38 (97)
Q Consensus 5 LkyYkVdenGKI~--rlrkeCP~~eCGaGVFMA~H~ 38 (97)
-|+.++|+||+|. +.+..|-. |.|-|+-...
T Consensus 109 ~K~I~~~~~G~v~~f~MNdkCAA---GTG~FLe~~A 141 (262)
T TIGR02261 109 GRAIRMDERGKVEAYKMTSQCAS---GSGQFLENIA 141 (262)
T ss_pred eEEEEEcCCCcEeeEEecCcccc---cccHHHHHHH
Confidence 4788999999998 56677876 7777875543
No 166
>cd01798 parkin_N amino-terminal ubiquitin-like of parkin protein. parkin_N parkin protein is a RING-type E3 ubiquitin ligase with an amino-terminal ubiquitin-like (Ubl) domain and an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Naturally occurring mutations in parkin are thought to cause the disease AR_JP (autosomal-recessive juvenile parkinsonism). Parkin binds the Rpn10 subunit of 26S proteasomes through its Ubl domain.
Probab=31.44 E-value=14 Score=22.49 Aligned_cols=18 Identities=17% Similarity=0.278 Sum_probs=13.9
Q ss_pred cccccccCCCCceEEEEE
Q psy15072 56 SARSQVRFPPGANFLTFV 73 (97)
Q Consensus 56 ~a~~q~~~p~~~~~l~~~ 73 (97)
...++.++|+.+++|+|.
T Consensus 27 ~i~~~~gi~~~~q~Li~~ 44 (70)
T cd01798 27 VVAKRQGVPPDQLRVIFA 44 (70)
T ss_pred HHHHHHCCCHHHeEEEEC
Confidence 334447899999999986
No 167
>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=31.25 E-value=2.8 Score=27.04 Aligned_cols=31 Identities=19% Similarity=0.507 Sum_probs=22.3
Q ss_pred cccCCCCcCCceEEeceeCCccccC-CceeEEEeeccc
Q psy15072 20 RRECTSEQCGAGVFMAAMSDRHYCG-NKFSSLSVELKS 56 (97)
Q Consensus 20 rkeCP~~eCGaGVFMA~H~DR~yCG-KCg~T~~~~~~~ 56 (97)
+|.||. ||.-+= .|+.+|. +|...+..+.++
T Consensus 3 HkHC~~--CG~~Ip----~~~~fCS~~C~~~~~k~qk~ 34 (59)
T PF09889_consen 3 HKHCPV--CGKPIP----PDESFCSPKCREEYRKRQKR 34 (59)
T ss_pred CCcCCc--CCCcCC----cchhhhCHHHHHHHHHHHHH
Confidence 688999 998653 3688995 898766555443
No 168
>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=31.03 E-value=26 Score=29.27 Aligned_cols=31 Identities=19% Similarity=0.402 Sum_probs=22.1
Q ss_pred cccCCCCcCCceEEeceeCCccccCCceeEEEeecc
Q psy15072 20 RRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELK 55 (97)
Q Consensus 20 rkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~~~ 55 (97)
...||. |+. -+ .+..+.+|.+||.+....+.
T Consensus 215 ~~~C~~--Cd~--~~-~~~~~a~CpRC~~~L~~~~~ 245 (403)
T TIGR00155 215 LRSCSA--CHT--TI-LPAQEPVCPRCSTPLYVRRR 245 (403)
T ss_pred CCcCCC--CCC--cc-CCCCCcCCcCCCCcccCCCC
Confidence 445998 997 22 45667899999988755544
No 169
>PRK14285 chaperone protein DnaJ; Provisional
Probab=30.91 E-value=39 Score=27.51 Aligned_cols=27 Identities=19% Similarity=0.319 Sum_probs=12.2
Q ss_pred cccCCceeEEEeecccccccccCCCCce
Q psy15072 41 HYCGNKFSSLSVELKSARSQVRFPPGAN 68 (97)
Q Consensus 41 ~yCGKCg~T~~~~~~~a~~q~~~p~~~~ 68 (97)
..|.+|+-.-.. .+....++.+||+.+
T Consensus 200 ~~C~~C~G~g~v-~~~~~~~V~Ip~G~~ 226 (365)
T PRK14285 200 NPCKSCKGKGSL-KKKETIELKIPAGID 226 (365)
T ss_pred CCCCCCCCCCEE-eccEEEEEEECCCCC
Confidence 346666522111 122334466666543
No 170
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=30.67 E-value=72 Score=20.69 Aligned_cols=37 Identities=19% Similarity=0.385 Sum_probs=22.5
Q ss_pred cCCCCcCCceEEeceeCC------ccccCCceeEEEeeccccccc
Q psy15072 22 ECTSEQCGAGVFMAAMSD------RHYCGNKFSSLSVELKSARSQ 60 (97)
Q Consensus 22 eCP~~eCGaGVFMA~H~D------R~yCGKCg~T~~~~~~~a~~q 60 (97)
.||. ||.=.-.---.| -.||.||-..-..+.+.-+..
T Consensus 6 ~CP~--CgnKTR~kir~DT~LkNfPlyCpKCK~EtlI~v~~~~i~ 48 (55)
T PF14205_consen 6 LCPI--CGNKTRLKIREDTVLKNFPLYCPKCKQETLIDVKQLKIT 48 (55)
T ss_pred ECCC--CCCccceeeecCceeccccccCCCCCceEEEEeeccEEE
Confidence 4888 986443322222 469999987666665544443
No 171
>COG1773 Rubredoxin [Energy production and conversion]
Probab=30.51 E-value=29 Score=22.29 Aligned_cols=26 Identities=23% Similarity=0.267 Sum_probs=17.6
Q ss_pred ccccCCceeEEEeecccccccccCCCCc
Q psy15072 40 RHYCGNKFSSLSVELKSARSQVRFPPGA 67 (97)
Q Consensus 40 R~yCGKCg~T~~~~~~~a~~q~~~p~~~ 67 (97)
|+.|.-||+.|.-++...+. ++||+.
T Consensus 3 ~~~C~~CG~vYd~e~Gdp~~--gi~pgT 28 (55)
T COG1773 3 RWRCSVCGYVYDPEKGDPRC--GIAPGT 28 (55)
T ss_pred ceEecCCceEeccccCCccC--CCCCCC
Confidence 88999999988666554443 444443
No 172
>cd01810 ISG15_repeat2 ISG15 ubiquitin-like protein, second repeat of 2. ISG15 is a ubiquitin-like protein containing two ubiquitin homology domains and becomes conjugated to a variety of proteins when cells are treated with type I interferon or lipopolysaccharide. Although ISG15 has properties similar to those of other ubiquitin-like molecules, it is a unique member of the ubiquitin-like superfamily, whose expression and conjugation to target proteins are tightly regulated by specific signaling pathways, indicating it may have specialized functions in the immune system.
Probab=30.14 E-value=17 Score=22.53 Aligned_cols=15 Identities=20% Similarity=0.350 Sum_probs=12.4
Q ss_pred ccccCCCCceEEEEE
Q psy15072 59 SQVRFPPGANFLTFV 73 (97)
Q Consensus 59 ~q~~~p~~~~~l~~~ 73 (97)
+..++|+.+|+|+|.
T Consensus 30 ~~~gi~~~~q~L~~~ 44 (74)
T cd01810 30 QRERVQADQFWLSFE 44 (74)
T ss_pred HHhCCCHHHeEEEEC
Confidence 337899999999985
No 173
>KOG1819|consensus
Probab=29.97 E-value=18 Score=33.42 Aligned_cols=9 Identities=44% Similarity=0.564 Sum_probs=3.8
Q ss_pred ccccCCcee
Q psy15072 40 RHYCGNKFS 48 (97)
Q Consensus 40 R~yCGKCg~ 48 (97)
||+|-.||-
T Consensus 917 rhhcrncgg 925 (990)
T KOG1819|consen 917 RHHCRNCGG 925 (990)
T ss_pred hhhhcccCc
Confidence 444444443
No 174
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=29.88 E-value=49 Score=22.99 Aligned_cols=38 Identities=8% Similarity=0.073 Sum_probs=24.6
Q ss_pred CeEEEecccCCCCcCC-ceEEeceeC------CccccCCceeEEEee
Q psy15072 14 GKIHRLRRECTSEQCG-AGVFMAAMS------DRHYCGNKFSSLSVE 53 (97)
Q Consensus 14 GKI~rlrkeCP~~eCG-aGVFMA~H~------DR~yCGKCg~T~~~~ 53 (97)
+.+.-....||. || ..+.|..+. ....+.+|.+|+...
T Consensus 54 ~~~~~~~~~Cp~--C~~~~~~~k~~~~~~~f~~~~~~Pkc~~~~~~~ 98 (140)
T COG0551 54 AIAEKTGVKCPK--CGKGLLVLKKGRFGKNFLGCSNYPKCRFTEKPK 98 (140)
T ss_pred cccccCceeCCC--CCCCceEEEeccCCceEEeecCCCcCceeecCC
Confidence 344556688998 99 566666653 234677888776443
No 175
>PF04135 Nop10p: Nucleolar RNA-binding protein, Nop10p family; InterPro: IPR007264 H/ACA ribonucleoprotein particles (RNPs) are a family of RNA pseudouridine synthases that specify modification sites through guide RNAs. More than 100 mammalian H/ACA RNAs form an equal number of ribonucleoproteins (RNPs) by associating with the same four core proteins: Cbf5, Gar1, Nhp2 and Nop10. The function of these H/ACA RNPs is essential for biogenesis of the ribosome, splicing of precursor mRNAs (pre-mRNAs), maintenance of telomeres and probably for additional cellular processes []. Recent crystal structures of archaeal H/ACA protein complexes show how the same four proteins accommodate >100 distinct but related H/ACA RNAs []. The complex contains a stable core composed of Cbf5 and Nop10, to which Gar1 and Nhp2 subsequently bind, the complex interacts with snoRNAs []. In eukaryotes Nop10 is a nucleolar protein that is specifically associated with H/ACA snoRNAs. It is essential for normal 18S rRNA production and rRNA pseudouridylation by the ribonucleoprotein particles containing H/ACA snoRNAs (H/ACA snoRNPs). Nop10 is probably necessary for the stability of these RNPs [].; PDB: 2RFK_B 3LWR_B 2HVY_C 3HAX_C 3MQK_B 3LWO_B 3LWV_B 3HAY_C 3HJY_B 2EY4_E ....
Probab=29.80 E-value=1.1e+02 Score=19.30 Aligned_cols=26 Identities=23% Similarity=0.494 Sum_probs=15.6
Q ss_pred CCCeEEEecccCCCCcCCceEEeceeCCc
Q psy15072 12 ENGKIHRLRRECTSEQCGAGVFMAAMSDR 40 (97)
Q Consensus 12 enGKI~rlrkeCP~~eCGaGVFMA~H~DR 40 (97)
++.++=.|+..||. ||.-..-| |--|
T Consensus 9 ~~~~~YTLk~~cp~--cG~~T~~a-hPaR 34 (53)
T PF04135_consen 9 PGCRVYTLKDKCPP--CGGPTESA-HPAR 34 (53)
T ss_dssp TTTCEEESSSBBTT--TSSBSEES-SSSS
T ss_pred CCCCcEeCCCccCC--CCCCCcCC-cCCC
Confidence 34456666668887 88654443 5444
No 176
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=29.54 E-value=28 Score=31.18 Aligned_cols=12 Identities=25% Similarity=0.227 Sum_probs=6.8
Q ss_pred CCccccCCceeE
Q psy15072 38 SDRHYCGNKFSS 49 (97)
Q Consensus 38 ~DR~yCGKCg~T 49 (97)
.+-.+|++||..
T Consensus 39 ~~~~fC~~CG~~ 50 (645)
T PRK14559 39 VDEAHCPNCGAE 50 (645)
T ss_pred cccccccccCCc
Confidence 344566666643
No 177
>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=29.35 E-value=34 Score=19.32 Aligned_cols=12 Identities=8% Similarity=-0.263 Sum_probs=7.4
Q ss_pred ccccCCceeEEE
Q psy15072 40 RHYCGNKFSSLS 51 (97)
Q Consensus 40 R~yCGKCg~T~~ 51 (97)
.|-|..||+++.
T Consensus 2 ~~~C~~CG~i~~ 13 (34)
T cd00729 2 VWVCPVCGYIHE 13 (34)
T ss_pred eEECCCCCCEeE
Confidence 356777776653
No 178
>PTZ00073 60S ribosomal protein L37; Provisional
Probab=29.31 E-value=25 Score=24.80 Aligned_cols=26 Identities=15% Similarity=0.340 Sum_probs=20.3
Q ss_pred ecccCCCCcCCceEEeceeCCccccCCceeE
Q psy15072 19 LRRECTSEQCGAGVFMAAMSDRHYCGNKFSS 49 (97)
Q Consensus 19 lrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T 49 (97)
.+-.|.+ ||.- +.|.-..+|+.|||.
T Consensus 15 tHtlCrR--CG~~---syH~qK~~CasCGyp 40 (91)
T PTZ00073 15 THTLCRR--CGKR---SFHVQKKRCASCGYP 40 (91)
T ss_pred Ccchhcc--cCcc---ccccccccchhcCCc
Confidence 4456999 9974 458888899999983
No 179
>PF14354 Lar_restr_allev: Restriction alleviation protein Lar
Probab=29.23 E-value=48 Score=19.78 Aligned_cols=27 Identities=15% Similarity=0.353 Sum_probs=17.4
Q ss_pred cccCCCCcCCceEEeceeCC--------ccccCCcee
Q psy15072 20 RRECTSEQCGAGVFMAAMSD--------RHYCGNKFS 48 (97)
Q Consensus 20 rkeCP~~eCGaGVFMA~H~D--------R~yCGKCg~ 48 (97)
.+-||= ||.....-.... .-+|..||-
T Consensus 3 LkPCPF--CG~~~~~~~~~~~~~~~~~~~V~C~~Cga 37 (61)
T PF14354_consen 3 LKPCPF--CGSADVLIRQDEGFDYGMYYYVECTDCGA 37 (61)
T ss_pred CcCCCC--CCCcceEeecccCCCCCCEEEEEcCCCCC
Confidence 367998 986555544332 235999986
No 180
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=29.03 E-value=29 Score=31.06 Aligned_cols=22 Identities=23% Similarity=0.555 Sum_probs=12.7
Q ss_pred cccCCCCcCCceEEeceeCCccccCCceeE
Q psy15072 20 RRECTSEQCGAGVFMAAMSDRHYCGNKFSS 49 (97)
Q Consensus 20 rkeCP~~eCGaGVFMA~H~DR~yCGKCg~T 49 (97)
.|.||+ ||+.. . ...|.+||..
T Consensus 15 akFC~~--CG~~l--~----~~~Cp~CG~~ 36 (645)
T PRK14559 15 NRFCQK--CGTSL--T----HKPCPQCGTE 36 (645)
T ss_pred Cccccc--cCCCC--C----CCcCCCCCCC
Confidence 456776 76633 1 1357777765
No 181
>PF13878 zf-C2H2_3: zinc-finger of acetyl-transferase ESCO
Probab=28.76 E-value=28 Score=20.38 Aligned_cols=16 Identities=13% Similarity=-0.128 Sum_probs=11.3
Q ss_pred CccccCCceeEEEeec
Q psy15072 39 DRHYCGNKFSSLSVEL 54 (97)
Q Consensus 39 DR~yCGKCg~T~~~~~ 54 (97)
.+..|.+||.+|....
T Consensus 12 ~~~~C~~CgM~Y~~~~ 27 (41)
T PF13878_consen 12 GATTCPTCGMLYSPGS 27 (41)
T ss_pred CCcCCCCCCCEECCCC
Confidence 3567888888886553
No 182
>cd01800 SF3a120_C Ubiquitin-like domain of Mammalian splicing factor SF3a_120. SF3a120_C Mammalian splicing factor SF3a consists of three subunits of 60, 66, and 120 kDa and functions early during pre-mRNA splicing by converting the U2 snRNP to its active form. The 120kDa subunit (SF3a120) has a carboxy-terminal ubiquitin-like domain and two SWAP (suppressor-of-white-apricot) domains, referred to collectively as the SURP module, at its amino-terminus.
Probab=28.57 E-value=17 Score=22.76 Aligned_cols=18 Identities=17% Similarity=0.309 Sum_probs=14.1
Q ss_pred ccccccCCCCceEEEEEe
Q psy15072 57 ARSQVRFPPGANFLTFVL 74 (97)
Q Consensus 57 a~~q~~~p~~~~~l~~~~ 74 (97)
..++.++|+.+|.|+|.-
T Consensus 27 i~~~~gip~~~q~L~~~G 44 (76)
T cd01800 27 IHEETGMPAGKQKLQYEG 44 (76)
T ss_pred HHHHHCCCHHHEEEEECC
Confidence 334488999999999863
No 183
>cd00924 Cyt_c_Oxidase_Vb Cytochrome c oxidase subunit Vb. Cytochrome c oxidase (CcO), the terminal oxidase in the respiratory chains of eukaryotes and most bacteria, is a multi-chain transmembrane protein located in the inner membrane of mitochondria and the cell membrane of prokaryotes. It catalyzes the reduction of O2 and simultaneously pumps protons across the membrane. The number of subunits varies from three to five in bacteria and up to 13 in mammalian mitochondria. Subunits I, II, and III of mammalian CcO are encoded within the mitochondrial genome and the remaining 10 subunits are encoded within the nuclear genome. Found only in eukaryotes, subunit Vb is one of three mammalian subunits that lacks a transmembrane region. Subunit Vb is located on the matrix side of the membrane and binds the regulatory subunit of protein kinase A. The abnormally extended conformation is stable only in the CcO assembly.
Probab=28.41 E-value=83 Score=21.85 Aligned_cols=25 Identities=28% Similarity=0.513 Sum_probs=13.9
Q ss_pred ceEEEECCCCeEEEecccCCCCcCCceEEecee
Q psy15072 5 WQVCNVDENGKIHRLRRECTSEQCGAGVFMAAM 37 (97)
Q Consensus 5 LkyYkVdenGKI~rlrkeCP~~eCGaGVFMA~H 37 (97)
..++.+.+ |+. +.||. ||. +|+..|
T Consensus 69 v~W~~l~~-g~~----~rC~e--CG~-~fkL~~ 93 (97)
T cd00924 69 VIWMWLEK-GKP----KRCPE--CGH-VFKLVD 93 (97)
T ss_pred EEEEEEeC-CCc----eeCCC--CCc-EEEEEE
Confidence 35566664 443 34765 774 666554
No 184
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=28.36 E-value=26 Score=23.28 Aligned_cols=15 Identities=20% Similarity=0.538 Sum_probs=12.6
Q ss_pred EEEecccCCCCcCCc
Q psy15072 16 IHRLRRECTSEQCGA 30 (97)
Q Consensus 16 I~rlrkeCP~~eCGa 30 (97)
+.+++.+|.+.+||.
T Consensus 23 ~~~~Y~qC~N~eCg~ 37 (72)
T PRK09678 23 TKERYHQCQNVNCSA 37 (72)
T ss_pred hheeeeecCCCCCCC
Confidence 677888999888886
No 185
>PLN02294 cytochrome c oxidase subunit Vb
Probab=28.05 E-value=71 Score=24.84 Aligned_cols=23 Identities=22% Similarity=0.421 Sum_probs=12.2
Q ss_pred eEEEECCCCeEEEecccCCCCcCCceEEece
Q psy15072 6 QVCNVDENGKIHRLRRECTSEQCGAGVFMAA 36 (97)
Q Consensus 6 kyYkVdenGKI~rlrkeCP~~eCGaGVFMA~ 36 (97)
.++.+.+ ||..| ||. ||. +|+.+
T Consensus 132 ~Wf~L~k-Gkp~R----Cpe--CG~-~fkL~ 154 (174)
T PLN02294 132 VWFWLEK-GKSFE----CPV--CTQ-YFELE 154 (174)
T ss_pred EEEEecC-CCcee----CCC--CCC-EEEEE
Confidence 4555554 44332 665 664 66554
No 186
>PRK14278 chaperone protein DnaJ; Provisional
Probab=27.98 E-value=69 Score=26.21 Aligned_cols=25 Identities=20% Similarity=0.260 Sum_probs=11.4
Q ss_pred ccCCceeEEEeecccccccccCCCCc
Q psy15072 42 YCGNKFSSLSVELKSARSQVRFPPGA 67 (97)
Q Consensus 42 yCGKCg~T~~~~~~~a~~q~~~p~~~ 67 (97)
.|.+|.=.-.. .+....+|.+||+.
T Consensus 198 ~C~~C~G~g~v-~~~~~~~V~Ip~G~ 222 (378)
T PRK14278 198 PCHECAGDGRV-RARREITVKIPAGV 222 (378)
T ss_pred CCCCCCCceeE-ecceEEEEEECCCC
Confidence 47777632211 11223346666653
No 187
>PRK14287 chaperone protein DnaJ; Provisional
Probab=27.96 E-value=60 Score=26.46 Aligned_cols=26 Identities=23% Similarity=0.401 Sum_probs=12.8
Q ss_pred ccccCCceeEEEeecccccccccCCCC
Q psy15072 40 RHYCGNKFSSLSVELKSARSQVRFPPG 66 (97)
Q Consensus 40 R~yCGKCg~T~~~~~~~a~~q~~~p~~ 66 (97)
+..|..|+-.-... .....++.+||+
T Consensus 195 ~~~C~~C~G~g~v~-~~~~l~V~Ip~G 220 (371)
T PRK14287 195 KQKCATCGGKGKVR-KRKKINVKVPAG 220 (371)
T ss_pred cccCCCCCCeeEEe-eeEEEEEEECCc
Confidence 44577777433332 223334555654
No 188
>PF10262 Rdx: Rdx family; InterPro: IPR011893 This entry represents the Rdx family of selenoproteins, which includes mammalian selenoproteins SelW, SelV, SelT and SelH, bacterial SelW-like proteins and cysteine-containing proteins of unknown function in all three domains of life. Mammalian Rdx12 and its fish selenoprotein orthologues are also members of this family []. These proteins possess a thioredoxin-like fold and a conserved CXXC or CxxU (U is selenocysteine) motif near the N terminus, suggesting a redox function. Rdx proteins can use catalytic cysteine (or selenocysteine) to form transient mixed disulphides with substrate proteins. Selenium (Se) plays an essential role in cell survival and most of the effects of Se are probably mediated by selenoproteins. Selenoprotein W (SelW) plays an important role in protection of neurons from oxidative stress during neuronal development [], []. Selenoprotein T (SelT) is conserved from plants to humans. SelT is localized to the endoplasmic reticulum through a hydrophobic domain. The protein binds to UDP-glucose:glycoprotein glucosyltransferase (UGTR), the endoplasmic reticulum (ER)-resident protein, which is known to be involved in the quality control of protein folding [, ]. The function of SelT is unknown, although it may have a role in PACAP signaling during PC12 cell differentiation [, ]. Selenoprotein H (SelH) protects neurons against UVB-induced damage by inhibiting apoptotic cell death pathways, by preventing mitochondrial depolarization, and by promoting cell survival pathways [].; GO: 0008430 selenium binding, 0045454 cell redox homeostasis; PDB: 2OJL_B 2FA8_A 2P0G_C 2NPB_A 3DEX_C 2OKA_A 2OBK_G.
Probab=27.91 E-value=11 Score=23.94 Aligned_cols=42 Identities=17% Similarity=0.072 Sum_probs=23.1
Q ss_pred cccCCceeEEEeecccccccccCCCCc-eEEEEEecceeeeee
Q psy15072 41 HYCGNKFSSLSVELKSARSQVRFPPGA-NFLTFVLGTASFLVS 82 (97)
Q Consensus 41 ~yCGKCg~T~~~~~~~a~~q~~~p~~~-~~l~~~~~~~~~~~~ 82 (97)
.||+.|++.-....-....+..+|..- .+-.-...+.+|=|+
T Consensus 6 eYC~~C~~~~~a~~l~~~l~~~fp~~~~~v~~~~~~~G~FEV~ 48 (76)
T PF10262_consen 6 EYCTSCGYRPRALELAQELLQTFPDRIAEVELSPGSTGAFEVT 48 (76)
T ss_dssp EEETTTTCHHHHHHHHHHHHHHSTTTCSEEEEEEESTT-EEEE
T ss_pred EECCCCCCHHHHHHHHHHHHHHCCCcceEEEEEeccCCEEEEE
Confidence 589999976555444555557777732 222222345556554
No 189
>PF11720 Inhibitor_I78: Peptidase inhibitor I78 family; InterPro: IPR021719 This family includes Aspergillus elastase inhibitor and belongs to MEROPS peptidase inhibitor family I78.
Probab=27.55 E-value=62 Score=20.04 Aligned_cols=14 Identities=43% Similarity=0.750 Sum_probs=10.9
Q ss_pred EEEECCCCeEEEec
Q psy15072 7 VCNVDENGKIHRLR 20 (97)
Q Consensus 7 yYkVdenGKI~rlr 20 (97)
+..||++|+|++.+
T Consensus 45 nv~~D~~g~I~~v~ 58 (60)
T PF11720_consen 45 NVEVDDDGVITRVR 58 (60)
T ss_pred EEEECCCCcEEEEe
Confidence 45789999998854
No 190
>PF13511 DUF4124: Domain of unknown function (DUF4124)
Probab=27.01 E-value=77 Score=18.72 Aligned_cols=20 Identities=35% Similarity=0.459 Sum_probs=16.4
Q ss_pred eEEE-ECCCCeEEEecccCCC
Q psy15072 6 QVCN-VDENGKIHRLRRECTS 25 (97)
Q Consensus 6 kyYk-VdenGKI~rlrkeCP~ 25 (97)
+.|| +|+||+|+...+-|+.
T Consensus 14 ~vYk~~D~~G~v~ysd~P~~~ 34 (60)
T PF13511_consen 14 EVYKWVDENGVVHYSDTPPPD 34 (60)
T ss_pred cEEEEECCCCCEEECccCCCC
Confidence 5666 5789999999998875
No 191
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=26.74 E-value=29 Score=24.22 Aligned_cols=26 Identities=19% Similarity=0.392 Sum_probs=15.0
Q ss_pred ecccCCCCcCCceEEeceeCCcc-ccCCcee
Q psy15072 19 LRRECTSEQCGAGVFMAAMSDRH-YCGNKFS 48 (97)
Q Consensus 19 lrkeCP~~eCGaGVFMA~H~DR~-yCGKCg~ 48 (97)
.+-.|++ ||. .......++ .|.+||.
T Consensus 70 ~~~~C~~--Cg~--~~~~~~~~~~~CP~Cgs 96 (117)
T PRK00564 70 VELECKD--CSH--VFKPNALDYGVCEKCHS 96 (117)
T ss_pred CEEEhhh--CCC--ccccCCccCCcCcCCCC
Confidence 3456888 985 222222233 3999985
No 192
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=26.73 E-value=30 Score=20.78 Aligned_cols=29 Identities=17% Similarity=0.254 Sum_probs=16.5
Q ss_pred ccCCCCcCCceEEece--eC---Cc-c-ccCCceeEEE
Q psy15072 21 RECTSEQCGAGVFMAA--MS---DR-H-YCGNKFSSLS 51 (97)
Q Consensus 21 keCP~~eCGaGVFMA~--H~---DR-~-yCGKCg~T~~ 51 (97)
+.||- ||.-..+-. +. ++ + .|.+||.+--
T Consensus 2 kPCPf--CGg~~~~~~~~~~~~~~~~~~~C~~Cga~~~ 37 (53)
T TIGR03655 2 KPCPF--CGGADVYLRRGFDPLDLSHYFECSTCGASGP 37 (53)
T ss_pred CCCCC--CCCcceeeEeccCCCCCEEEEECCCCCCCcc
Confidence 56888 886444221 22 22 2 4999986643
No 193
>PRK14973 DNA topoisomerase I; Provisional
Probab=26.16 E-value=39 Score=31.49 Aligned_cols=40 Identities=13% Similarity=-0.129 Sum_probs=27.1
Q ss_pred CCeEEEecccCCCCcCCceEEeceeCCc----cccCCceeEEEeec
Q psy15072 13 NGKIHRLRRECTSEQCGAGVFMAAMSDR----HYCGNKFSSLSVEL 54 (97)
Q Consensus 13 nGKI~rlrkeCP~~eCGaGVFMA~H~DR----~yCGKCg~T~~~~~ 54 (97)
.|++......||. ||..+.|--...| .-|-+|.++....+
T Consensus 628 ~g~~~~~~~~Cp~--CG~p~~~~~r~Gr~g~fl~CP~C~~~~~~~~ 671 (936)
T PRK14973 628 WGWAIRTDEVCPI--HHLNHVRLIRKGARPWDIGCPLCSHIESNTE 671 (936)
T ss_pred cccCCCCCCCCCC--CCCCceEEeecCCCcccccCccccchhhccc
Confidence 3555444567998 9987677655556 25999988876443
No 194
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=25.93 E-value=1.5e+02 Score=20.69 Aligned_cols=46 Identities=22% Similarity=0.437 Sum_probs=32.0
Q ss_pred cceEEEECCCCeEEEe-------------cccCCCCcCCc-eEEeceeCCccccCCceeEEEee
Q psy15072 4 EWQVCNVDENGKIHRL-------------RRECTSEQCGA-GVFMAAMSDRHYCGNKFSSLSVE 53 (97)
Q Consensus 4 ~LkyYkVdenGKI~rl-------------rkeCP~~eCGa-GVFMA~H~DR~yCGKCg~T~~~~ 53 (97)
.|.||.+.++||-.|. --.|-- ||. |.+ +-.|..-|..|+.+...+
T Consensus 6 klh~y~y~~~G~~vrff~i~~~dg~~~va~daCei--C~~~GY~--q~g~~lvC~~C~~~~~~~ 65 (102)
T PF10080_consen 6 KLHRYAYTDDGKEVRFFAIKKPDGSYRVAFDACEI--CGPKGYY--QEGDQLVCKNCGVRFNLP 65 (102)
T ss_pred cEEEEEEcCCCEEEEEEEEECCCCCEEEEEEeccc--cCCCceE--EECCEEEEecCCCEEehh
Confidence 5778888777765543 234766 865 555 667999999999887544
No 195
>PF10005 DUF2248: Uncharacterized protein conserved in bacteria (DUF2248); InterPro: IPR011201 This is a family of uncharacterised bacterial proteins.
Probab=25.93 E-value=52 Score=27.80 Aligned_cols=28 Identities=29% Similarity=0.571 Sum_probs=21.3
Q ss_pred cCCCCcCCceEEeceeCCccccCCceeEEEeecc
Q psy15072 22 ECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELK 55 (97)
Q Consensus 22 eCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~~~ 55 (97)
.||+ ||.=||.- -..|.+||...-+...
T Consensus 1 ~C~~--Cg~~v~Fe----Nt~C~~Cg~~LGf~p~ 28 (343)
T PF10005_consen 1 SCPN--CGQPVFFE----NTRCLSCGSALGFDPD 28 (343)
T ss_pred CCCC--CCCcceeC----CCccccCCccccCCCC
Confidence 5988 99988765 4679999987755543
No 196
>PTZ00037 DnaJ_C chaperone protein; Provisional
Probab=25.89 E-value=67 Score=27.06 Aligned_cols=8 Identities=25% Similarity=0.289 Sum_probs=4.8
Q ss_pred ccccCCce
Q psy15072 40 RHYCGNKF 47 (97)
Q Consensus 40 R~yCGKCg 47 (97)
+..|.+|+
T Consensus 208 ~~~C~~C~ 215 (421)
T PTZ00037 208 SKKCKNCS 215 (421)
T ss_pred cccCCcCC
Confidence 34566665
No 197
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=25.86 E-value=23 Score=33.46 Aligned_cols=32 Identities=22% Similarity=0.404 Sum_probs=0.0
Q ss_pred eEEEecccCCCCcCCceEEece------eC-CccccCCcee
Q psy15072 15 KIHRLRRECTSEQCGAGVFMAA------MS-DRHYCGNKFS 48 (97)
Q Consensus 15 KI~rlrkeCP~~eCGaGVFMA~------H~-DR~yCGKCg~ 48 (97)
+|+.-++.||+ ||.-.|... |. -.++|.+|+.
T Consensus 650 ~vei~~r~Cp~--Cg~~t~~~~Cp~CG~~T~~~~~Cp~C~~ 688 (900)
T PF03833_consen 650 EVEIGRRRCPK--CGKETFYNRCPECGSHTEPVYVCPDCGI 688 (900)
T ss_dssp -----------------------------------------
T ss_pred EEeeecccCcc--cCCcchhhcCcccCCccccceecccccc
Confidence 46677889988 987666432 22 2445666654
No 198
>cd01802 AN1_N ubiquitin-like domain of AN1. AN1 (also known as ANUBL1 and RSD-7) is ubiquitin-like protein with a testis-specific expression in rats that has an N-terminal ubiquitin-like domain and a C-terminal zinc-binding domain. Unlike ubiquitin polyproteins and most ubiquitin fusion proteins, the N-terminal ubiquitin-like domain of An1 does not undergo proteolytic processing. The function of AN1 is unknown.
Probab=25.81 E-value=21 Score=24.35 Aligned_cols=58 Identities=19% Similarity=0.227 Sum_probs=32.9
Q ss_pred eEEEECCCCeEEEecccCCCCcCCceEEeceeCCccccCCceeEEEeecc--------cccccccCCCCceEEEEE
Q psy15072 6 QVCNVDENGKIHRLRRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELK--------SARSQVRFPPGANFLTFV 73 (97)
Q Consensus 6 kyYkVdenGKI~rlrkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~~~--------~a~~q~~~p~~~~~l~~~ 73 (97)
-+|..|.-++.....+ +++ +-=+|. |..-|+.. ++..+.. +..+.+++|+++|+|+|.
T Consensus 8 ~~~~~~~~~~~~~~~~--~~~--~M~I~V-----k~l~G~~~-~leV~~~~TV~~lK~kI~~~~gip~~~QrLi~~ 73 (103)
T cd01802 8 PFFNEDNMGPFHYKLP--FYD--TMELFI-----ETLTGTCF-ELRVSPFETVISVKAKIQRLEGIPVAQQHLIWN 73 (103)
T ss_pred CccccCCcceeEEeec--cCC--CEEEEE-----EcCCCCEE-EEEeCCCCcHHHHHHHHHHHhCCChHHEEEEEC
Confidence 4788887787777554 331 233333 33445542 2222222 222237899999999986
No 199
>cd01815 BMSC_UbP_N Ubiquitin-like domain of BMSC-UbP. BMSC_UbP (bone marrow stromal cell-derived ubiquitin-like protein) has an N-terminal ubiquitin-like (UBQ) domain and a C-terminal ubiquitin-associated (UBA) domain, a domain architecture similar to those of the UBIN, Chap1, and ubiquilin proteins. This CD represents the N-terminal ubiquitin-like domain.
Probab=25.43 E-value=22 Score=23.70 Aligned_cols=13 Identities=23% Similarity=0.209 Sum_probs=10.4
Q ss_pred ccCC-CCceEEEEE
Q psy15072 61 VRFP-PGANFLTFV 73 (97)
Q Consensus 61 ~~~p-~~~~~l~~~ 73 (97)
+++| +++|+|||.
T Consensus 36 egi~~~dqQrLIy~ 49 (75)
T cd01815 36 DSLPDPELIDLIHC 49 (75)
T ss_pred cCCCChHHeEEEeC
Confidence 4565 999999986
No 200
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=25.29 E-value=19 Score=27.52 Aligned_cols=33 Identities=24% Similarity=0.436 Sum_probs=22.1
Q ss_pred ccCCCCcCCc---------eEEec-eeC-CccccCCceeEEEeecc
Q psy15072 21 RECTSEQCGA---------GVFMA-AMS-DRHYCGNKFSSLSVELK 55 (97)
Q Consensus 21 keCP~~eCGa---------GVFMA-~H~-DR~yCGKCg~T~~~~~~ 55 (97)
..||+ |++ |||-- .|. --.||-+||..|-+-+.
T Consensus 40 ~~Cp~--C~~~IrG~y~v~gv~~~g~~~~~PsYC~~CGkpyPWt~~ 83 (158)
T PF10083_consen 40 TSCPN--CSTPIRGDYHVEGVFGLGGHYEAPSYCHNCGKPYPWTEN 83 (158)
T ss_pred HHCcC--CCCCCCCceecCCeeeeCCCCCCChhHHhCCCCCchHHH
Confidence 46888 875 44432 333 35699999999876655
No 201
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=25.18 E-value=34 Score=17.44 Aligned_cols=22 Identities=23% Similarity=0.454 Sum_probs=16.0
Q ss_pred ccCCCCcCCceEEeceeCCccccCCcee
Q psy15072 21 RECTSEQCGAGVFMAAMSDRHYCGNKFS 48 (97)
Q Consensus 21 keCP~~eCGaGVFMA~H~DR~yCGKCg~ 48 (97)
.+|+. |+ ..++..|..|-+|+.
T Consensus 3 W~C~~--C~----~~N~~~~~~C~~C~~ 24 (26)
T smart00547 3 WECPA--CT----FLNFASRSKCFACGA 24 (26)
T ss_pred ccCCC--CC----CcChhhhccccccCC
Confidence 56777 76 346777888988874
No 202
>PRK14283 chaperone protein DnaJ; Provisional
Probab=25.10 E-value=77 Score=25.82 Aligned_cols=7 Identities=29% Similarity=0.491 Sum_probs=4.2
Q ss_pred cccCCce
Q psy15072 41 HYCGNKF 47 (97)
Q Consensus 41 ~yCGKCg 47 (97)
..|.+|+
T Consensus 204 ~~C~~C~ 210 (378)
T PRK14283 204 KPCSNCH 210 (378)
T ss_pred CCCCCCC
Confidence 4466665
No 203
>smart00614 ZnF_BED BED zinc finger. DNA-binding domain in chromatin-boundary-element-binding proteins and transposases
Probab=25.04 E-value=30 Score=20.38 Aligned_cols=23 Identities=35% Similarity=0.898 Sum_probs=13.5
Q ss_pred ccceEEEE---CCCCeEEEecccCCCCcCCc
Q psy15072 3 NEWQVCNV---DENGKIHRLRRECTSEQCGA 30 (97)
Q Consensus 3 ~~LkyYkV---denGKI~rlrkeCP~~eCGa 30 (97)
.+|++|.. ++||+ .+-.|-- |+.
T Consensus 1 ~vW~~F~~i~~~~~g~---~~a~C~~--C~~ 26 (50)
T smart00614 1 KVWKHFTLILEKDNGK---QRAKCKY--CGK 26 (50)
T ss_pred CcCccceEEEEcCCCC---eEEEecC--CCC
Confidence 36888874 45666 3455554 554
No 204
>PRK14294 chaperone protein DnaJ; Provisional
Probab=24.90 E-value=83 Score=25.50 Aligned_cols=26 Identities=27% Similarity=0.358 Sum_probs=11.2
Q ss_pred cccCCceeEEEeecccccccccCCCCc
Q psy15072 41 HYCGNKFSSLSVELKSARSQVRFPPGA 67 (97)
Q Consensus 41 ~yCGKCg~T~~~~~~~a~~q~~~p~~~ 67 (97)
..|-+|.-.-... +....++.+||+.
T Consensus 198 ~~C~~C~G~g~v~-~~~~l~V~Ip~G~ 223 (366)
T PRK14294 198 SPCKTCHGQGRVR-VSKTVQVKIPAGV 223 (366)
T ss_pred cCCCCCCCceEee-cceeEEEecCCCC
Confidence 3477776222111 1223345566654
No 205
>cd01804 midnolin_N Ubiquitin-like domain of midnolin. midnolin_N Midnolin (midbrain nucleolar protein) is expressed in the nucleolus and is thought to regulate genes involved in neurogenesis. Midnolin contains an amino-terminal ubiquitin-like domain.
Probab=24.73 E-value=27 Score=22.18 Aligned_cols=14 Identities=14% Similarity=0.168 Sum_probs=12.2
Q ss_pred cccCCCCceEEEEE
Q psy15072 60 QVRFPPGANFLTFV 73 (97)
Q Consensus 60 q~~~p~~~~~l~~~ 73 (97)
+.++|+.+|+|+|.
T Consensus 34 ~~~~~~~~qrL~~~ 47 (78)
T cd01804 34 RLKVPKERLALLHR 47 (78)
T ss_pred HhCCChHHEEEEEC
Confidence 36799999999987
No 206
>cd01812 BAG1_N Ubiquitin-like domain of BAG1. BAG1_N N-terminal ubiquitin-like (Ubl) domain of the BAG1 protein. This domain occurs together with the BAG domain and is closely related to the Ubl domain of a family of deubiquitinases that includes Rpn11, UBP6 (USP14), USP7 (HAUSP).
Probab=24.49 E-value=25 Score=20.92 Aligned_cols=16 Identities=19% Similarity=0.196 Sum_probs=13.0
Q ss_pred cccccCCCCceEEEEE
Q psy15072 58 RSQVRFPPGANFLTFV 73 (97)
Q Consensus 58 ~~q~~~p~~~~~l~~~ 73 (97)
.++.++|+..|+|+|.
T Consensus 30 ~~~~gi~~~~q~L~~~ 45 (71)
T cd01812 30 APVTGVEPRDQKLIFK 45 (71)
T ss_pred HHhhCCChHHeEEeeC
Confidence 3447899999999986
No 207
>COG1326 Uncharacterized archaeal Zn-finger protein [General function prediction only]
Probab=24.44 E-value=62 Score=25.72 Aligned_cols=28 Identities=21% Similarity=0.345 Sum_probs=17.7
Q ss_pred ecccCCCCcCCceEEeceeC-----C---ccccCCceeEE
Q psy15072 19 LRRECTSEQCGAGVFMAAMS-----D---RHYCGNKFSSL 50 (97)
Q Consensus 19 lrkeCP~~eCGaGVFMA~H~-----D---R~yCGKCg~T~ 50 (97)
..-+||+ ||.+=+ .|. . -..|+.||+..
T Consensus 5 iy~~Cp~--Cg~eev--~hEVik~~g~~~lvrC~eCG~V~ 40 (201)
T COG1326 5 IYIECPS--CGSEEV--SHEVIKERGREPLVRCEECGTVH 40 (201)
T ss_pred EEEECCC--CCcchh--hHHHHHhcCCceEEEccCCCcEe
Confidence 3457998 995433 231 1 34699999766
No 208
>TIGR02259 benz_CoA_red_A benzoyl-CoA reductase, bcr type, subunit A. This model describes A, or gamma, subunit of the bcr type of benzoyl-CoA reductase, a 4-subunit enzyme. Many aromatic compounds are metabolized by way of benzoyl-CoA. This family shows strong sequence similarity to the 2-hydroxyglutaryl-CoA dehydratase alpha chain and to subunits of different types of benzoyl-CoA reductase (such as the bzd type).
Probab=24.44 E-value=40 Score=29.43 Aligned_cols=31 Identities=16% Similarity=0.575 Sum_probs=24.3
Q ss_pred ceEEEECCCCeEE--EecccCCCCcCCceEEeceeC
Q psy15072 5 WQVCNVDENGKIH--RLRRECTSEQCGAGVFMAAMS 38 (97)
Q Consensus 5 LkyYkVdenGKI~--rlrkeCP~~eCGaGVFMA~H~ 38 (97)
-|..++|++|+|. +.+..|-. |.|-|+-...
T Consensus 279 sK~I~ld~~G~V~dF~MNDKCAA---GTGrFLE~mA 311 (432)
T TIGR02259 279 TKGIQIDDHGIVENFQMNDRCAA---GCGRYLGYIA 311 (432)
T ss_pred eEEEEEcCCCcEeeeeecCcccc---cchHHHHHHH
Confidence 4788999999998 77788887 7787875554
No 209
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=24.37 E-value=43 Score=24.89 Aligned_cols=14 Identities=57% Similarity=1.172 Sum_probs=8.7
Q ss_pred CeEEEecccCCCCcCC
Q psy15072 14 GKIHRLRRECTSEQCG 29 (97)
Q Consensus 14 GKI~rlrkeCP~~eCG 29 (97)
|...+-+++||+ ||
T Consensus 22 ~~~~~~~~~c~~--c~ 35 (154)
T PRK00464 22 GNAIRRRRECLA--CG 35 (154)
T ss_pred CCceeeeeeccc--cC
Confidence 544444488886 76
No 210
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=24.13 E-value=49 Score=21.10 Aligned_cols=6 Identities=17% Similarity=0.612 Sum_probs=2.8
Q ss_pred cccCCC
Q psy15072 20 RRECTS 25 (97)
Q Consensus 20 rkeCP~ 25 (97)
+..||.
T Consensus 17 k~~CP~ 22 (56)
T PRK13130 17 KEICPV 22 (56)
T ss_pred cccCcC
Confidence 444444
No 211
>PRK14279 chaperone protein DnaJ; Provisional
Probab=23.65 E-value=77 Score=26.11 Aligned_cols=7 Identities=71% Similarity=1.502 Sum_probs=3.8
Q ss_pred cccCCCC
Q psy15072 60 QVRFPPG 66 (97)
Q Consensus 60 q~~~p~~ 66 (97)
++.+||+
T Consensus 245 ~V~Ip~G 251 (392)
T PRK14279 245 NVRIPPG 251 (392)
T ss_pred EEEeCCC
Confidence 3555654
No 212
>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=23.39 E-value=26 Score=28.64 Aligned_cols=30 Identities=20% Similarity=0.564 Sum_probs=11.6
Q ss_pred ccCCCCcCCceEEeceeCC-----ccccCCceeEEEee
Q psy15072 21 RECTSEQCGAGVFMAAMSD-----RHYCGNKFSSLSVE 53 (97)
Q Consensus 21 keCP~~eCGaGVFMA~H~D-----R~yCGKCg~T~~~~ 53 (97)
-.||+ ||..- +..+.+ -.+|..|+.-|-..
T Consensus 32 ~yCP~--Cg~~~-L~~f~NN~PVaDF~C~~C~eeyELK 66 (254)
T PF06044_consen 32 MYCPN--CGSKP-LSKFENNRPVADFYCPNCNEEYELK 66 (254)
T ss_dssp ---TT--T--SS--EE--------EEE-TTT--EEEEE
T ss_pred CcCCC--CCChh-HhhccCCCccceeECCCCchHHhhh
Confidence 35999 99842 333332 36899999665433
No 213
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=23.26 E-value=39 Score=24.42 Aligned_cols=25 Identities=20% Similarity=0.186 Sum_probs=16.7
Q ss_pred cccCCCCcCCceEEeceeCCccccCCcee
Q psy15072 20 RRECTSEQCGAGVFMAAMSDRHYCGNKFS 48 (97)
Q Consensus 20 rkeCP~~eCGaGVFMA~H~DR~yCGKCg~ 48 (97)
--.|.. |+. +......+++|.+||.
T Consensus 70 ~~~C~~--C~~--~~~~e~~~~~CP~C~s 94 (115)
T COG0375 70 ECWCLD--CGQ--EVELEELDYRCPKCGS 94 (115)
T ss_pred EEEecc--CCC--eecchhheeECCCCCC
Confidence 345776 865 4445566777999993
No 214
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=23.23 E-value=67 Score=25.02 Aligned_cols=28 Identities=21% Similarity=0.447 Sum_probs=10.2
Q ss_pred cccCCCCcCCceEEeceeC------Ccc-ccCCceeE
Q psy15072 20 RRECTSEQCGAGVFMAAMS------DRH-YCGNKFSS 49 (97)
Q Consensus 20 rkeCP~~eCGaGVFMA~H~------DR~-yCGKCg~T 49 (97)
+..||- ||+--.|+.=. .|+ +|+-|+..
T Consensus 172 ~g~CPv--CGs~P~~s~l~~~~~~G~R~L~Cs~C~t~ 206 (290)
T PF04216_consen 172 RGYCPV--CGSPPVLSVLRGGEREGKRYLHCSLCGTE 206 (290)
T ss_dssp -SS-TT--T---EEEEEEE------EEEEEETTT--E
T ss_pred CCcCCC--CCCcCceEEEecCCCCccEEEEcCCCCCe
Confidence 456777 77643443221 133 66666543
No 215
>PF00684 DnaJ_CXXCXGXG: DnaJ central domain; InterPro: IPR001305 The hsp70 chaperone machine performs many diverse roles in the cell, including folding of nascent proteins, translocation of polypeptides across organelle membranes, coordinating responses to stress, and targeting selected proteins for degradation. DnaJ is a member of the hsp40 family of molecular chaperones, which is also called the J-protein family, the members of which regulate the activity of hsp70s. DnaJ (hsp40) binds to DnaK (hsp70) and stimulates its ATPase activity, generating the ADP-bound state of DnaK, which interacts stably with the polypeptide substrate []. Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation []. DnaJ consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acid residues, a glycine and phenylalanine-rich domain ('G/F' domain), a central cysteine rich domain (CR-type zinc finger) containing four repeats of a CXXCXGXG motif which can coordinate two zinc atom and a C-terminal domain (CTD) []. This entry represents the central cysteine-rich (CR) domain of DnaJ proteins. This central cysteine rich domain (CR-type zinc finger) has an overall V-shaped extended beta-hairpin topology and contains four repeats of the motif CXXCXGXG where X is any amino acid. The isolated cysteine rich domain folds in zinc dependent fashion. Each set of two repeats binds one unit of zinc. Although this domain has been implicated in substrate binding, no evidence of specific interaction between the isolated DnaJ cysteine rich domain and various hydrophobic peptides has been found [].; GO: 0031072 heat shock protein binding, 0051082 unfolded protein binding; PDB: 1NLT_A 2CTT_A 1EXK_A.
Probab=23.20 E-value=45 Score=20.71 Aligned_cols=15 Identities=27% Similarity=0.800 Sum_probs=7.2
Q ss_pred ccCCCCcC-CceEEecee
Q psy15072 21 RECTSEQC-GAGVFMAAM 37 (97)
Q Consensus 21 keCP~~eC-GaGVFMA~H 37 (97)
+.||. | |.|..+..+
T Consensus 16 ~~C~~--C~G~G~~~~~~ 31 (66)
T PF00684_consen 16 KTCPQ--CNGSGQVTRRQ 31 (66)
T ss_dssp EE-TT--SSSSSEEEEEE
T ss_pred cCCcC--CCCeeEEEEEE
Confidence 34555 5 555555444
No 216
>PHA02031 putative DnaG-like primase
Probab=22.97 E-value=42 Score=27.34 Aligned_cols=36 Identities=31% Similarity=0.474 Sum_probs=21.2
Q ss_pred CeEEEecccCCCCcCCceEEeceeCCcc--ccCCceeEEEe
Q psy15072 14 GKIHRLRRECTSEQCGAGVFMAAMSDRH--YCGNKFSSLSV 52 (97)
Q Consensus 14 GKI~rlrkeCP~~eCGaGVFMA~H~DR~--yCGKCg~T~~~ 52 (97)
|...|.+..|-+ |+--.+++-.||| ||-+|+.--..
T Consensus 18 g~~~r~~~~~~~---~~~~~~~~~~~~w~ayc~rc~~~~~~ 55 (266)
T PHA02031 18 GQTGRFRHCCGG---GAAMTLYNNPDRWVAYCYRCKEGGKV 55 (266)
T ss_pred cccceeeeccCC---CceeEEecCcchHHHHHHhhcccchh
Confidence 444555533332 3334556667887 99999964433
No 217
>PRK14280 chaperone protein DnaJ; Provisional
Probab=22.81 E-value=93 Score=25.37 Aligned_cols=6 Identities=17% Similarity=0.301 Sum_probs=3.6
Q ss_pred ccCCce
Q psy15072 42 YCGNKF 47 (97)
Q Consensus 42 yCGKCg 47 (97)
.|.+|+
T Consensus 202 ~C~~C~ 207 (376)
T PRK14280 202 KCPTCH 207 (376)
T ss_pred CCCCCC
Confidence 466665
No 218
>PRK01110 rpmF 50S ribosomal protein L32; Validated
Probab=22.74 E-value=53 Score=20.89 Aligned_cols=20 Identities=15% Similarity=0.075 Sum_probs=12.5
Q ss_pred ccCCCCcCCceEEeceeCCccccCCcee
Q psy15072 21 RECTSEQCGAGVFMAAMSDRHYCGNKFS 48 (97)
Q Consensus 21 keCP~~eCGaGVFMA~H~DR~yCGKCg~ 48 (97)
.+||+ ||. ..+. .+.|- ||+
T Consensus 28 ~~c~~--cg~-~~~p----H~vc~-cG~ 47 (60)
T PRK01110 28 SVDKT--TGE-YHLP----HHVSP-KGY 47 (60)
T ss_pred eEcCC--CCc-eecc----ceecC-Ccc
Confidence 56987 986 3333 34577 773
No 219
>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=22.70 E-value=67 Score=17.53 Aligned_cols=13 Identities=23% Similarity=0.739 Sum_probs=5.3
Q ss_pred cCCCCcCCceEEece
Q psy15072 22 ECTSEQCGAGVFMAA 36 (97)
Q Consensus 22 eCP~~eCGaGVFMA~ 36 (97)
.||+ ||+-+....
T Consensus 1 ~CP~--C~s~l~~~~ 13 (28)
T PF03119_consen 1 TCPV--CGSKLVREE 13 (28)
T ss_dssp B-TT--T--BEEE-C
T ss_pred CcCC--CCCEeEcCC
Confidence 4777 877665433
No 220
>PF09567 RE_MamI: MamI restriction endonuclease; InterPro: IPR019067 There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements [, ], as summarised below: Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA. Type II restriction endonucleases (3.1.21.4 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. These site-specific deoxyribonucleases catalyse the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. Of the 3000 restriction endonucleases that have been characterised, most are homodimeric or tetrameric enzymes that cleave target DNA at sequence-specific sites close to the recognition site. For homodimeric enzymes, the recognition site is usually a palindromic sequence 4-8 bp in length. Most enzymes require magnesium ions as a cofactor for catalysis. Although they can vary in their mode of recognition, many restriction endonucleases share a similar structural core comprising four beta-strands and one alpha-helix, as well as a similar mechanism of cleavage, suggesting a common ancestral origin []. However, there is still considerable diversity amongst restriction endonucleases [, ]. The target site recognition process triggers large conformational changes of the enzyme and the target DNA, leading to the activation of the catalytic centres. Like other DNA binding proteins, restriction enzymes are capable of non-specific DNA binding as well, which is the prerequisite for efficient target site location by facilitated diffusion. Non-specific binding usually does not involve interactions with the bases but only with the DNA backbone []. This entry includes the MamI restriction endonuclease which recognises and cleaves GATNN^NNATC. ; GO: 0003677 DNA binding, 0009036 Type II site-specific deoxyribonuclease activity, 0009307 DNA restriction-modification system
Probab=22.64 E-value=34 Score=28.71 Aligned_cols=29 Identities=28% Similarity=0.373 Sum_probs=17.9
Q ss_pred ccCCCCcCCceEEeceeCCccccCCceeEEEeecc
Q psy15072 21 RECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELK 55 (97)
Q Consensus 21 keCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~~~ 55 (97)
+.|-+ ||++|-.= ...|..|+.|-...+.
T Consensus 83 ~~C~~--CGa~V~~~----e~~Cp~C~StnI~r~D 111 (314)
T PF09567_consen 83 GKCNN--CGANVSRL----EESCPNCGSTNIKRKD 111 (314)
T ss_pred hhhcc--ccceeeeh----hhcCCCCCcccccccC
Confidence 45776 88776422 3467778777655544
No 221
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=22.36 E-value=45 Score=28.06 Aligned_cols=30 Identities=23% Similarity=0.467 Sum_probs=20.7
Q ss_pred cccCCCCcCCceEEeceeCCccccCCceeEEEeecc
Q psy15072 20 RRECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELK 55 (97)
Q Consensus 20 rkeCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~~~ 55 (97)
...||. |+. .. ..++..|.+||.+......
T Consensus 221 l~~C~~--Cd~--l~--~~~~a~CpRC~~~L~~~~~ 250 (419)
T PRK15103 221 LRSCSC--CTA--IL--PADQPVCPRCHTKGYVRRR 250 (419)
T ss_pred CCcCCC--CCC--CC--CCCCCCCCCCCCcCcCCCC
Confidence 445998 997 22 3456689999988754443
No 222
>PRK10767 chaperone protein DnaJ; Provisional
Probab=22.31 E-value=93 Score=25.16 Aligned_cols=6 Identities=17% Similarity=0.290 Sum_probs=3.6
Q ss_pred ccCCce
Q psy15072 42 YCGNKF 47 (97)
Q Consensus 42 yCGKCg 47 (97)
.|-+|+
T Consensus 197 ~C~~C~ 202 (371)
T PRK10767 197 PCKKCH 202 (371)
T ss_pred CCCCCC
Confidence 466665
No 223
>PRK14291 chaperone protein DnaJ; Provisional
Probab=22.17 E-value=1e+02 Score=25.25 Aligned_cols=26 Identities=35% Similarity=0.474 Sum_probs=11.2
Q ss_pred ccccCCceeEEEeecccccccccCCCC
Q psy15072 40 RHYCGNKFSSLSVELKSARSQVRFPPG 66 (97)
Q Consensus 40 R~yCGKCg~T~~~~~~~a~~q~~~p~~ 66 (97)
+..|.+|+=.-... +....+|.+||+
T Consensus 208 ~~~C~~C~G~g~v~-~~~~l~V~Ip~G 233 (382)
T PRK14291 208 REPCSKCNGRGLVI-KKETIKVRIPPG 233 (382)
T ss_pred ccCCCCCCCCceEE-eeeEEEEEeCCC
Confidence 34577765211111 122334666665
No 224
>cd01809 Scythe_N Ubiquitin-like domain of Scythe protein. Scythe protein (also known as Bat3) is an apoptotic regulator that is highly conserved in eukaryotes and contains a ubiquitin-like domain near its N-terminus. Scythe binds reaper, a potent apoptotic inducer, and Scythe/Reaper are thought to signal apoptosis, in part through regulating the folding and activity of apoptotic signaling molecules.
Probab=22.11 E-value=27 Score=20.67 Aligned_cols=15 Identities=20% Similarity=0.337 Sum_probs=12.4
Q ss_pred ccccCCCCceEEEEE
Q psy15072 59 SQVRFPPGANFLTFV 73 (97)
Q Consensus 59 ~q~~~p~~~~~l~~~ 73 (97)
++.++|++.++|+|.
T Consensus 32 ~~~gi~~~~q~L~~~ 46 (72)
T cd01809 32 EEVGIPVEQQRLIYS 46 (72)
T ss_pred HHHCcCHHHeEEEEC
Confidence 346899999999984
No 225
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=21.53 E-value=84 Score=22.31 Aligned_cols=31 Identities=16% Similarity=0.236 Sum_probs=18.1
Q ss_pred cCCCCcCCceEEec-----eeCC-ccccCCceeEEEeec
Q psy15072 22 ECTSEQCGAGVFMA-----AMSD-RHYCGNKFSSLSVEL 54 (97)
Q Consensus 22 eCP~~eCGaGVFMA-----~H~D-R~yCGKCg~T~~~~~ 54 (97)
.||+ ||.-.-.- .+.+ ...|..||.......
T Consensus 101 ~Cp~--C~~~y~~~ea~~~~d~~~~f~Cp~Cg~~l~~~d 137 (147)
T smart00531 101 KCPN--CQSKYTFLEANQLLDMDGTFTCPRCGEELEEDD 137 (147)
T ss_pred ECcC--CCCEeeHHHHHHhcCCCCcEECCCCCCEEEEcC
Confidence 4988 98633210 0123 378999997765443
No 226
>PRK14297 chaperone protein DnaJ; Provisional
Probab=21.30 E-value=88 Score=25.48 Aligned_cols=9 Identities=33% Similarity=0.671 Sum_probs=4.9
Q ss_pred ccccCCCCc
Q psy15072 59 SQVRFPPGA 67 (97)
Q Consensus 59 ~q~~~p~~~ 67 (97)
.+|.+||+.
T Consensus 223 i~V~Ip~G~ 231 (380)
T PRK14297 223 IKVNVPAGV 231 (380)
T ss_pred EEEEeCCCC
Confidence 345666654
No 227
>PRK14276 chaperone protein DnaJ; Provisional
Probab=21.26 E-value=87 Score=25.59 Aligned_cols=8 Identities=13% Similarity=0.339 Sum_probs=5.1
Q ss_pred ccccCCce
Q psy15072 40 RHYCGNKF 47 (97)
Q Consensus 40 R~yCGKCg 47 (97)
+..|.+|+
T Consensus 203 ~~~C~~C~ 210 (380)
T PRK14276 203 KEPCQTCH 210 (380)
T ss_pred cCCCCCCC
Confidence 34577776
No 228
>PF01632 Ribosomal_L35p: Ribosomal protein L35; InterPro: IPR021137 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. L35 is a basic protein of 60 to 70 amino-acid residues from the large subunit []. Like many basic polypeptides, L35 completely inhibits ornithine decarboxylase when present unbound in the cell, but the inhibitory function is abolished upon its incorporation into ribosomes []. It belongs to a family of ribosomal proteins, including L35 from bacteria, plant chloroplast, red algae chloroplasts and cyanelles. In plants it is a nuclear encoded gene product, which suggests a chloroplast-to-nucleus relocation during the evolution of higher plants [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2QBE_3 2QBG_3 3SGF_7 2QOV_3 3J0Y_6 3I22_3 3E1D_W 1VS6_3 2VHN_3 1VS8_3 ....
Probab=21.20 E-value=34 Score=21.57 Aligned_cols=17 Identities=35% Similarity=0.415 Sum_probs=12.9
Q ss_pred cceEEEECCCCeEEEec
Q psy15072 4 EWQVCNVDENGKIHRLR 20 (97)
Q Consensus 4 ~LkyYkVdenGKI~rlr 20 (97)
+.+-|+|..+|||.+.+
T Consensus 9 a~KRFk~t~sGkikr~~ 25 (61)
T PF01632_consen 9 AAKRFKVTGSGKIKRKR 25 (61)
T ss_dssp HHTTEEEESSSEEEEE-
T ss_pred hHhheeEcCCCeEEecc
Confidence 34678999999998854
No 229
>CHL00103 rpl35 ribosomal protein L35
Probab=20.86 E-value=71 Score=20.78 Aligned_cols=17 Identities=24% Similarity=0.229 Sum_probs=13.7
Q ss_pred cceEEEECCCCeEEEec
Q psy15072 4 EWQVCNVDENGKIHRLR 20 (97)
Q Consensus 4 ~LkyYkVdenGKI~rlr 20 (97)
.-|-|+|+.+|||.+.+
T Consensus 10 a~KRFKvT~sGKvkr~~ 26 (65)
T CHL00103 10 AAKRYKKTGNGKFLRRK 26 (65)
T ss_pred hhheeEecCCCCEEecc
Confidence 35789999999998743
No 230
>PF00240 ubiquitin: Ubiquitin family; InterPro: IPR000626 Ubiquitinylation is an ATP-dependent process that involves the action of at least three enzymes: a ubiquitin-activating enzyme (E1, IPR000011 from INTERPRO), a ubiquitin-conjugating enzyme (E2, IPR000608 from INTERPRO), and a ubiquitin ligase (E3, IPR000569 from INTERPRO, IPR003613 from INTERPRO), which work sequentially in a cascade. There are many different E3 ligases, which are responsible for the type of ubiquitin chain formed, the specificity of the target protein, and the regulation of the ubiquitinylation process []. Ubiquitinylation is an important regulatory tool that controls the concentration of key signalling proteins, such as those involved in cell cycle control, as well as removing misfolded, damaged or mutant proteins that could be harmful to the cell. Several ubiquitin-like molecules have been discovered, such as Ufm1 (IPR005375 from INTERPRO), SUMO1 (IPR003653 from INTERPRO), NEDD8, Rad23 (IPR004806 from INTERPRO), Elongin B and Parkin (IPR003977 from INTERPRO), the latter being involved in Parkinson's disease []. Ubiquitin is a protein of 76 amino acid residues, found in all eukaryotic cells and whose sequence is extremely well conserved from protozoan to vertebrates. Ubiquitin acts through its post-translational attachment (ubiquitinylation) to other proteins, where these modifications alter the function, location or trafficking of the protein, or targets it for destruction by the 26S proteasome []. The terminal glycine in the C-terminal 4-residue tail of ubiquitin can form an isopeptide bond with a lysine residue in the target protein, or with a lysine in another ubiquitin molecule to form a ubiquitin chain that attaches itself to a target protein. Ubiquitin has seven lysine residues, any one of which can be used to link ubiquitin molecules together, resulting in different structures that alter the target protein in different ways. It appears that Lys(11)-, Lys(29) and Lys(48)-linked poly-ubiquitin chains target the protein to the proteasome for degradation, while mono-ubiquitinylated and Lys(6)- or Lys(63)-linked poly-ubiquitin chains signal reversible modifications in protein activity, location or trafficking []. For example, Lys(63)-linked poly-ubiquitinylation is known to be involved in DNA damage tolerance, inflammatory response, protein trafficking and signal transduction through kinase activation []. In addition, the length of the ubiquitin chain alters the fate of the target protein. Regulatory proteins such as transcription factors and histones are frequent targets of ubquitinylation [].; GO: 0005515 protein binding; PDB: 2DZI_A 2XEW_E 3NOB_E 2KWU_B 2Y5B_F 3PHD_G 2KWV_B 2KOX_A 2XK5_B 3NHE_B ....
Probab=20.84 E-value=37 Score=20.15 Aligned_cols=17 Identities=18% Similarity=0.364 Sum_probs=13.1
Q ss_pred ccccccCCCCceEEEEE
Q psy15072 57 ARSQVRFPPGANFLTFV 73 (97)
Q Consensus 57 a~~q~~~p~~~~~l~~~ 73 (97)
..++..+|+..++|+|-
T Consensus 25 i~~~~~~~~~~~~L~~~ 41 (69)
T PF00240_consen 25 IAEETGIPPEQQRLIYN 41 (69)
T ss_dssp HHHHHTSTGGGEEEEET
T ss_pred cccccccccccceeeee
Confidence 33447899999999983
No 231
>PF05280 FlhC: Flagellar transcriptional activator (FlhC); InterPro: IPR007944 This family consists of several bacterial flagellar transcriptional activator (FlhC) proteins. FlhC combines with FlhD to form a regulatory complex in Escherichia coli, this complex has been shown to be a global regulator involved in many cellular processes as well as a flagellar transcriptional activator [].; GO: 0003677 DNA binding, 0030092 regulation of flagellum assembly, 0045893 positive regulation of transcription, DNA-dependent; PDB: 2AVU_E.
Probab=20.73 E-value=61 Score=24.45 Aligned_cols=33 Identities=15% Similarity=0.219 Sum_probs=10.1
Q ss_pred cccCCCCcCCceEEeceeC--CccccCCceeEEEeec
Q psy15072 20 RRECTSEQCGAGVFMAAMS--DRHYCGNKFSSLSVEL 54 (97)
Q Consensus 20 rkeCP~~eCGaGVFMA~H~--DR~yCGKCg~T~~~~~ 54 (97)
-..|++ ||...+-..|. ....|+=|.....-.+
T Consensus 134 l~~C~~--C~~~fv~~~~~~~~~~~Cp~C~~psRagk 168 (175)
T PF05280_consen 134 LAPCRR--CGGHFVTHAHDPRHSFVCPFCQPPSRAGK 168 (175)
T ss_dssp EEE-TT--T--EEEEESS--SS----TT---------
T ss_pred ccCCCC--CCCCeECcCCCCCcCcCCCCCCCccccCc
Confidence 467998 98554443454 3568999986544333
No 232
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=20.53 E-value=52 Score=27.66 Aligned_cols=34 Identities=18% Similarity=0.310 Sum_probs=21.2
Q ss_pred ccCCCCcCCceEEec--eeCCccccCCceeEEEeeccc
Q psy15072 21 RECTSEQCGAGVFMA--AMSDRHYCGNKFSSLSVELKS 56 (97)
Q Consensus 21 keCP~~eCGaGVFMA--~H~DR~yCGKCg~T~~~~~~~ 56 (97)
..||. ||.=+-.. ++..|-+|.+||.........
T Consensus 11 ~~C~~--Cd~l~~~~~l~~g~~a~CpRCg~~L~~~~~~ 46 (419)
T PRK15103 11 ILCPQ--CDMLVALPRLEHGQKAACPRCGTTLTVRWDE 46 (419)
T ss_pred ccCCC--CCceeecCCCCCCCeeECCCCCCCCcCCCCC
Confidence 45998 99721111 234577899999887554443
No 233
>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=20.51 E-value=1.6e+02 Score=18.51 Aligned_cols=31 Identities=26% Similarity=0.444 Sum_probs=19.9
Q ss_pred ccCCCCcCCceEEecee--CCccccCCceeEEEee
Q psy15072 21 RECTSEQCGAGVFMAAM--SDRHYCGNKFSSLSVE 53 (97)
Q Consensus 21 keCP~~eCGaGVFMA~H--~DR~yCGKCg~T~~~~ 53 (97)
-+||. ||+-+=+..= ..-..|.-||..+-..
T Consensus 3 ~~CP~--CG~~iev~~~~~GeiV~Cp~CGaeleVv 35 (54)
T TIGR01206 3 FECPD--CGAEIELENPELGELVICDECGAELEVV 35 (54)
T ss_pred cCCCC--CCCEEecCCCccCCEEeCCCCCCEEEEE
Confidence 37988 9986654321 2355789998766543
No 234
>PF02593 dTMP_synthase: Thymidylate synthase; InterPro: IPR003745 This entry describes proteins of unknown function.
Probab=20.30 E-value=33 Score=26.90 Aligned_cols=25 Identities=36% Similarity=0.607 Sum_probs=18.6
Q ss_pred CCCeEEEecccCCCCcCCceEEecee
Q psy15072 12 ENGKIHRLRRECTSEQCGAGVFMAAM 37 (97)
Q Consensus 12 enGKI~rlrkeCP~~eCGaGVFMA~H 37 (97)
+||||+..+-...+| ||+--|||..
T Consensus 140 ~~~~I~~V~VlR~aP-CGsT~~vAk~ 164 (217)
T PF02593_consen 140 ENGKIKDVKVLRSAP-CGSTWFVAKR 164 (217)
T ss_pred cCCcEEEEEEEecCC-CccHHHHHHH
Confidence 478887766555544 9999999975
No 235
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=20.23 E-value=50 Score=21.77 Aligned_cols=10 Identities=20% Similarity=0.268 Sum_probs=4.6
Q ss_pred ccccCCceeE
Q psy15072 40 RHYCGNKFSS 49 (97)
Q Consensus 40 R~yCGKCg~T 49 (97)
-++|..||-.
T Consensus 31 ~~~C~~CGe~ 40 (127)
T TIGR03830 31 GWYCPACGEE 40 (127)
T ss_pred eeECCCCCCE
Confidence 3445555443
No 236
>KOG4537|consensus
Probab=20.19 E-value=17 Score=28.29 Aligned_cols=27 Identities=19% Similarity=0.535 Sum_probs=21.8
Q ss_pred ecccCCCCcCCceEEeceeCCccccCCcee
Q psy15072 19 LRRECTSEQCGAGVFMAAMSDRHYCGNKFS 48 (97)
Q Consensus 19 lrkeCP~~eCGaGVFMA~H~DR~yCGKCg~ 48 (97)
+...||. || |+.|-...+-.+|--|-.
T Consensus 39 Lde~Cp~--C~-~Ilm~dr~~~~~CVsC~~ 65 (178)
T KOG4537|consen 39 LDEICPK--CE-KILMRDRDNPMFCVSCIN 65 (178)
T ss_pred hhhhcch--HH-HHHHhhccCceEEEeeec
Confidence 4567998 98 788888777889999953
No 237
>PF02810 SEC-C: SEC-C motif; InterPro: IPR004027 The SEC-C motif found in the C terminus of the SecA protein, in the middle of some SWI2 ATPases and also solo in several proteins. The motif is predicted to chelate zinc with the CXC and C[HC] pairs that constitute the most conserved feature of the motif. It is predicted to be a potential nucleic acid binding domain.; PDB: 1OZB_J 1TM6_A 2I9W_A 2JQ5_A.
Probab=20.15 E-value=53 Score=17.25 Aligned_cols=10 Identities=40% Similarity=1.172 Sum_probs=7.0
Q ss_pred cccCCCCcCCceE
Q psy15072 20 RRECTSEQCGAGV 32 (97)
Q Consensus 20 rkeCP~~eCGaGV 32 (97)
+..|| ||+|-
T Consensus 2 n~~Cp---CgSg~ 11 (21)
T PF02810_consen 2 NDPCP---CGSGK 11 (21)
T ss_dssp TSBTT---TSCSS
T ss_pred CCcCc---CCCCc
Confidence 35688 88864
No 238
>COG4640 Predicted membrane protein [Function unknown]
Probab=20.12 E-value=40 Score=29.68 Aligned_cols=29 Identities=17% Similarity=0.361 Sum_probs=19.4
Q ss_pred ccCCCCcCCceEEeceeCCccccCCceeEEEeecc
Q psy15072 21 RECTSEQCGAGVFMAAMSDRHYCGNKFSSLSVELK 55 (97)
Q Consensus 21 keCP~~eCGaGVFMA~H~DR~yCGKCg~T~~~~~~ 55 (97)
+.||. ||. - +-.|-..|-+||....-.++
T Consensus 2 ~fC~k--cG~--q--k~Ed~~qC~qCG~~~t~~~s 30 (465)
T COG4640 2 KFCPK--CGS--Q--KAEDDVQCTQCGHKFTSRQS 30 (465)
T ss_pred Ccccc--ccc--c--cccccccccccCCcCCchhh
Confidence 57998 994 0 23466669999976544444
No 239
>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=20.08 E-value=36 Score=22.67 Aligned_cols=11 Identities=9% Similarity=0.341 Sum_probs=4.7
Q ss_pred CCccccCCcee
Q psy15072 38 SDRHYCGNKFS 48 (97)
Q Consensus 38 ~DR~yCGKCg~ 48 (97)
.+|..|.|||.
T Consensus 22 ~~k~FCp~CGn 32 (73)
T PF08772_consen 22 MTKQFCPKCGN 32 (73)
T ss_dssp SS--S-SSS--
T ss_pred CCceeCcccCC
Confidence 46888999984
No 240
>PRK14284 chaperone protein DnaJ; Provisional
Probab=20.01 E-value=84 Score=25.77 Aligned_cols=25 Identities=16% Similarity=0.235 Sum_probs=10.8
Q ss_pred cccCCceeEEEeecccccccccCCCC
Q psy15072 41 HYCGNKFSSLSVELKSARSQVRFPPG 66 (97)
Q Consensus 41 ~yCGKCg~T~~~~~~~a~~q~~~p~~ 66 (97)
..|.+|+-.-.. .+....+|.||||
T Consensus 212 ~~C~~C~G~g~v-~~~~~l~V~Ip~G 236 (391)
T PRK14284 212 DPCSVCRGQGRI-KDKRSVHVHIPAG 236 (391)
T ss_pred CcCCCCCCccee-cceEEEEEEECCC
Confidence 346666522111 1122334666665
Done!